Category Archives: Mind & Brain

Sound and Music at ScienceOnline2012

Text, image, video…what about sounds? Sounds of human voice, sounds of nature, sounds of science in action, sounds of music…all of those have strong emotional impact on the listeners, but it takes some skill to make it work, to get listeners to pay attention and learn. We have lined up some amazing people to help us learn how to do exactly that:

Podcasting for Beginners (hands-on workshop) – Ginger Campbell and Alok Jha

Experienced podcasters Ginger Campbell (the Brain Science Podcast) and Alok Jha (Science Weekly) will lead this session for everyone who is interested in creating audio content with a focus on podcasting. This is a practical “nuts and bolts” session aimed at beginners, but it is also an opportunity for all podcasters to share questions, tips, and advice.

Science Podcasting: Pros and Cons (discussion) – Julia Galef and Desiree Schell

Desiree Schell (host of Skeptically Speaking) and Julia Galef (co-host of Rationally Speaking) both host successful podcasts that inform and entertain the science-loving public. They’ll lead a discussion on the creative ways that science communicators of all types can get their message out via podcast. Topics include: finding your voice, reaching your audience, involving bloggers and non-blogging scientists, and helping experts make the topics accessible and engaging to laypeople.

The Sound of Science (discussion) – Rose Eveleth

Science is most often communicated visually. We all remember the flow charts, there are beautiful field guide illustrations, and sometimes you just need a good diagram. But look over there in the corner, where poor little sound is sitting, just waiting for you to recognize its potential. This session would explain why, and how, you should use sound to explain science. We’d look at ways in which sound can enhance your story. Whether it’s the voice of the researcher, or just the sound that the stuff you’re talking about makes, there’s something to be said for hearing a story. And this doesn’t require Radiolab-style production (we can’t all be MacArthur geniuses after all). A simple sound, embedded into your story, can turn things up to 11. The session will explore what kinds of stories are worth “soundifying”, look at some good examples of sounds within stories, and talk about how to embed sound into your work in an easy, sensical way.

The Music of Science: An Effective Tool for Science Communication? (discussion) – Princess Ojiaku and Adrian J. Ebsary

A review of what’s currently happening in the music and science worlds and how it influences the public perception of science. From Symphony of Science to Bjork’s new album, Biophilia, in what way do people making science musical inspire themselves and others? We’ll present examples from scientists and science communicators who make educational music about science to musicians who use science as a vehicle for personal expression. We’ll take examples from the big names and the smaller names and analyze their reach and effectiveness. We’ll also discuss how to get involved in the conversation by presenting platforms for scientist-musician collaborations across distances.

The late-night Open Mike, a big hit last year as so many of our attendees are talented musicians, may still happen this time around – stay tuned.

Learn more:

Planning Wiki
Draft Program
See who’s registered
Waitlist sign-up
Facebook page
FriendFeed group
Tumblr coverage blog
Google Plus official page
Google Plus circle of participants
Twitter account
#scio12 hashtag
Twitter repository
Twitter list of participants
Previous conferences
Nice things people said about ScienceOnline2010
ScienceOnline2011 on YouTube
ScienceOnline2011 on Flickr
ScienceOnline2011 official recordings

Previously in this series:

What is: ScienceOnline2012 – and it’s coming soon!
ScienceOnline participants’ interviews
Some updates on #scio12, #NYCscitweetup, Story Collider and more.
Updates: ScienceOnline2012, Science blogging, Open Laboratory, and #NYCSciTweetup
ScienceOnline2012 – we have the Keynote Speaker!
Mathematics – Algebra and Statistics and more – at ScienceOnline2012
Information, data and technology at ScienceOnline2012
Health and Medicine at ScienceOnline2012
Education at ScienceOnline2012
Movies and Video at ScienceOnline2011


Upcoming North Carolina Science Conference
Obsessively early planning for science online 2012
ScienceOnline2012 – only two registration slots to go
ScienceOnline 2012
Understanding Audiences at Science Online 2012
Math at Science Online 2012 ???
Sixth time around – ScienceOnline2012 coming soon
Let’s Talk About ScienceOnline2012

BIO101 – Physiology: Regulation and Control

In this lecture, as well as in the previous one and the next one, I tackle areas of Biology where I am really weak: origin of life, diversity of life, and taxonomy/systematics. These are also areas where there has been a lot of change recently (often not yet incorporated into textbooks), and I am unlikely to be up-to-date, so please help me bring these lectures up to standards…. This post was originally written in 2006 and re-posted a few times, including in 2010.

As you may know, I have been teaching BIO101 (and also the BIO102 Lab) to non-traditional students in an adult education program for about twelve years now. Every now and then I muse about it publicly on the blog (see this, this, this, this, this, this and this for a few short posts about various aspects of it – from the use of videos, to the use of a classroom blog, to the importance of Open Access so students can read primary literature). The quality of students in this program has steadily risen over the years, but I am still highly constrained with time: I have eight 4-hour meetings with the students over eight weeks. In this period I have to teach them all of biology they need for their non-science majors, plus leave enough time for each student to give a presentation (on the science of their favourite plant and animal) and for two exams. Thus I have to strip the lectures to the bare bones, and hope that those bare bones are what non-science majors really need to know: concepts rather than factoids, relationship with the rest of their lives rather than relationship with the other sciences. Thus I follow my lectures with videos and classroom discussions, and their homework consists of finding cool biology videos or articles and posting the links on the classroom blog for all to see. A couple of times I used malaria as a thread that connected all the topics – from cell biology to ecology to physiology to evolution. I think that worked well but it is hard to do. They also write a final paper on some aspect of physiology.

Another new development is that the administration has realized that most of the faculty have been with the school for many years. We are experienced, and apparently we know what we are doing. Thus they recently gave us much more freedom to design our own syllabus instead of following a pre-defined one, as long as the ultimate goals of the class remain the same. I am not exactly sure when am I teaching the BIO101 lectures again (late Fall, Spring?) but I want to start rethinking my class early. I am also worried that, since I am not actively doing research in the lab and thus not following the literature as closely, that some of the things I teach are now out-dated. Not that anyone can possibly keep up with all the advances in all the areas of Biology which is so huge, but at least big updates that affect teaching of introductory courses are stuff I need to know.

I need to catch up and upgrade my lecture notes. And what better way than crowdsource! So, over the new few weeks, I will re-post my old lecture notes (note that they are just intros – discussions and videos etc. follow them in the classroom) and will ask you to fact-check me. If I got something wrong or something is out of date, let me know (but don’t push just your own preferred hypothesis if a question is not yet settled – give me the entire controversy explanation instead). If something is glaringly missing, let me know. If something can be said in a nicer language – edit my sentences. If you are aware of cool images, articles, blog-posts, videos, podcasts, visualizations, animations, games, etc. that can be used to explain these basic concepts, let me know. And at the end, once we do this with all the lectures, let’s discuss the overall syllabus – is there a better way to organize all this material for such a fast-paced class.

These posts are very old, and were initially on a private-set classroom blog, not public. I have no idea where the images come from any more, though many are likely from the textbook I was using at the time. Please let me know if an image is yours, needs to be attributed or removed. Thank you.


It is impossible to cover all organ systems in detail over the course of just two lectures. Thus, we will stick only to the basics. Still, I want to emphasize how much organ systems work together, in concert, to maintain the homeostasis (and rheostasis) of the body. I’d also like to emphasize how fuzzy are the boundaries between organ systems – many organs are, both anatomically and functionally, simultaneously parts of two or more organ systems. So, I will use an example you are familiar with from our study of animal behavior – stress response – to illustrate the unity of the well-coordinated response of all organ systems when faced with a challenge. We will use our old zebra-and-lion example as a roadmap in our exploration of (human, and generally mammalian) physiology:

So, you are a zebra, happily grazing out on the savannah. Suddenly you hear some rustling in the grass. How did you hear it?

The movement of a lion produced oscillations of air. Those oscillations exerted pressure onto the tympanic membrane in your ears. The vibrations of the membrane induced vibrations in three little bones inside the middle ear, which, in turn, induced vibrations of the cochlea in the inner ear.

Cochlea is a long tube wrapped in a spiral. If the pitch of the sound is high (high frequency of oscillations), only the first portion of the cochlea vibrates. With the lowest frequences, even the tip of the cochlea starts vibrating. Cochlea is filled with fluid. Withing this fluid there is a thin membrane transecting the cochlea along its length. When the cochlea vibrates, this membrane also vibrates and those vibrations move the hair-like protrusions on the surface of sensory cells in the cochlea. Those cells send electrical impulses to the brain, where the sound is processed and becomes a conscious sensation – you have heard the lion move.

The perception of the sound makes you look – yes, there is a lion stalking you, about to leap! How do you see the lion? The waves of light reflected from the surface of the lion travel to your eyes, enter through the pupil, pass through the lens and hit the retina in the back of the eye.

Photoreceptors in the eye (rods and cones) contain a pigment – a colored molecule – that changes its 3D structure when hit by light. In the rods, this pigment is called rhodopsin and is used for black-and-white vision. In the rods, there are similar pigments – opsins – which are most sensitive to particular wavelengths of light (colors) and are used to detect color. The change in 3D structure of the pigment starts a cascade of biochemical reactions resulting in the changes in the electrical potential of the cell – this information is then transferred to the next cell, the next cell, and so on, until it reaches the brain, where the information about the shape, color and movement of the objects (lion and the surrounding grass) is processed and made conscious.

The ear and the eye are examples of the organs of the sensory system. Hearing is one of many mechanical senses – others include touch, pain, balance, stretch receptors in the muscles and tendons, etc. Many animals are capable of hearing sounds that we cannot detect. For instance, bats and some of their insect prey detect the high-pitched ultrasound (a case of a co-evolutionary arms-race). Likewise for dolphins and some of their fish prey. Dogs do, too – that is why we cannot hear the dog whistle. On the other hand, many large animals, e.g., whales, elephants, giraffes, rhinos, crocodiles and perhaps even cows and horses, can detect the deep rumble of the infrasound.

Vision is a sense that detects radiation in the visible specter. Many animals are capable of seeing light outside of our visible specter. For instance, many insects and birds and some small mammals can see ultraviolet light, while some snakes (e.g., pit vipers like rattlesnakes and boids like pythons) and some insects (e.g., Melanophila beetle and some wasps) can perceive infrared light.

Another type of sense is thermoreception – detection of hot and cold. Chemical senses are attuned to particular molecules. Olfaction (smell) and gustation (taste) are the best known chemical senses. Chemical senses also exist inside of our bodes – they are capable of detecting blood pH, blood levels of oxygen, carbon dioxide, calcium, glucose etc. Finally, some animals are capable of detecting other physical properties of the environment., e.g., the electrical and magnetic fields.

All senses work along the same principles: a stimulus from the external or internal environment is detected by a specialized type of cell. Inside the cell a chemical cascade begins – that is transduction. This changes the properties of the cell – usually its cell membrane potential – which is transmitted from the sensory cell to the neighboring nerve cell, to the next cell, next cell and so on, until it ends in the appropriate area of the nervous system, usually the brain. There, the sum of all stimuli from all the cells of the sensory organ are interpreted (integrated and processed over time) and the neccessary action is triggered. This action can be behavioral (movement), or it can be physiological: maintanance of homeostasis.

The sensory information is processed by the Central Nervous System (CNS): the brain and the spinal cord.

All the nerve cells that take information from the periphery to the CNS are sensory nerves. All the nerves that take the decisions made by the CNS to the effectors – muscles or glands – are motor nerves. The sensory and motor pathways together make Peripheral Nervous System.

The motor pathways are further divided into two domains: somatic nervous system is under voluntary control, while autonomic (vegetative) nervous system is involuntary. Autonomic nervous system has two divisions: sympathetic and parasymphatetic. Symphatetic nervous system is active during stress – it acts on many other organ systems, releasing the energy stores, stimulating organs needed for the response and inhibiting organs of no immediate importance.

Thus, a zebra about to be attacked by a lion is exhibiting stress response. Sympathetic nervous system works to release glucose (energy) stores from the liver, stimulates the organs necessary for the fast escape – muscles – and all the other systems that are needed for providing the muscles with energy – the circulatory and respiratory systems. At the same time, digestion, immunity, excretion and reproduction are inhibited. Once the zebra successfully evades the lion, sympathetic system gets inhibited and the parasympathetic system is stimulated – it reverses all the effects. The two systems work antagonistically to each other: they always have opposite effects.

But, how does the nervous system work? Let’s look at the nerve cell – the neuron:

A typical neuron has a cell body (soma) which contains the nucleus and other organelles. It has many thin, short processes – dendrites – that bring information from other neighboring cells into the nerve cell, and one large, long process that takes information away from the cell to another cell – the axon.

There is an electrical potential of the cell membrane – the voltage on the inside and the outside of the cell is different. The inside of the neuron is usually around 70mV more negative (-70mV) compared to the outside. This polarization is accomplished by the specialized proetins in the cell membrane – ion channels and ion transporters. Using energy from ATP, they transport sodium out of the cell and potassium into the cell (also chlorine into the cell). As ions can leak through the membrane to some extent, the cell has to constantly use energy to maintain the resting membrane potential.

An electrical impulse coming from another cell will change the membrane potential of a dendrite. This change is usually not sufficiently large to induce the neuron to respond. However, if many such stimuli occur simultaneously they are additive – the neuron sums up all the stimulatory and inhibitory impulses it gets at any given time. If the sum of impulses is large, the change of membrane potential will still be large when it travels across the soma and onto the very beginning of the axon – axon hillock. If the change of the membrane potential at the axon hillock crosses a threshold (around -40mV or so), this induces sodium channels at the axon hillock to open. Sodium rushes in down its concentration gradient. This results in further depolarization of the membrane, which in turn results in opening even more sodium channels which depolarizes the membrane even more – this is a positive feedback loop – until all of the Na-channels are open and the membrane potential is now positive. Reaching this voltage induces the opening of the potassium channels. Potassium rushes out along its concentration gradient. This results in repolarization of the membrane. The whole process – from initial small depolarization, through the fast Na-driven depolarization, subsequent K-driven repolarization resulting in a small overshoot and the return to the normal resting potential – is called an Action Potential which can be graphed like this:

An action potential generated at the axon hillock results in the changes of membrane potential in the neighboring membrane just down the axon where a new action potential is generated which, in turn, results in a depolarization of the membrane further on down the axon, and so on until the electrical impulse reaches the end of the axon. In vertebrates, special cells called Schwann cells wrap around the axons and serve as isolating tape of sorts. Thus, the action potential instead of spreading gradually down the axon, proceeds in jumps – this makes electrical transmission much faster – something necessary if the axon is three meters long as in the nerves of the hind leg of a giraffe.

What happens at the end of the axon? There, the change of membrane polarity results in the opening of the calcium channels and calcium rushes in (that is why calcium homeostasis is so important). The end of the axon contains many small packets filled with a neurotransmitter. Infusion of calcium stimulates these packets to fuse with the cell membrane and release the neurotransmitter out of the cell. The chemical ends up in a very small space between the axon ending and the membrane of another cell (e.g., a dendrite of another neuron). The membrane of that other cell has membrane receptors that respond to this neurotransmitter. The activation of the receptors results in the local change of membrane potential. Stimulatory neurotransmitters depolarize the membrane (make it more positive), while inhibitory neurotransmitters hyperpolarize the membrane – make it more negative, thus harder to produce an action potential.

The target of a nerve cell can be another neuron, a muscle cell or a gland. Many glands are endocrine glands – they release their chemical products, hormones, into the bloodstream. Hormones act on distant targets via receptors. While transmission of information in the nervous system is very fast – miliseconds, in the endocrine system it takes seconds, minutes, hours, days, months (pregnancy), even years (puberty) to induce the effect in the target. While transmission within the nervous system is local (cell-to-cell) and over very short distances – the gap within a synapse is measured in Angstroms – the transmission within the endocrine system is over long distances and global – it affects every cell that possesses the right kind of receptors.

Many endocrine glands are regulated during the stress response, and many of them participate in the stress response. The thyroid gland releases thyroxine – a hormone that acts via nuclear receptors. Thyroxine has many fuctions in the body and several of those are involved in the energetics of the body – release of energy from the stores and production of heat in the mitochondria. It also produces calcitonin which is one of the regulators of calcium levels in the blood.

Parathyroid gland is, in humans, embedded inside the thyroid gland. Its hormone, parathormone is the key hormone of calcium homeostasis. Calcitonin and parathormone are antagonists: the former lowers and the latter raises blood calcium. Together, they can fine-tune the calcium levels available to neurons, muscles and heart-cells for their normal function.

Pancreas secretes insulin and glucagon. Insulin removes glucose from blood and stores it in muscle and liver cells. Glucagon has the opposite effect – it releases glucose from its stores and makes it available to cells that are in need of energy, e.g., the muscle cells of a running zebra. Together, these two hormones fine-tune the glucose homeostasis of the body.

Adrenal gland has two layers. In the center is the adrenal medulla. It is a part of the nervous system and it releases epineprhine and norepinephrine (also known as adrenaline and noradrenaline). These are the key hormones of the stress response. They have all the same effects as the sympathetic nervous system, which is not surprising as norepinephrine is the neurotransmitter used by the neurons of the sympathetic system (parasympathetic system uses acetylcholine as a transmitter).

The outside layer is the adrenal cortex. It secretes a lot of hormones. The most important are aldosterone (involved in salt and water balance) and cortisol which is another important stress hormone – it mobilizes glucose from its stores and makes it available for the organs that need it. Sex steroid hormones are also produced in the adrenal cortex. Oversecretion of testosterone may lead to development of some male features in women, e.g., growing a beard.

Ovary and testis secrete sex steroid hormones. Testis secretes testosterone, while ovaries secrete estradiol (an estrogen) and progesterone. Progesterone stimulates the growth of mammary glands and prepares the uterus for pregnancy. Estradiol stimulates the development of female secondary sexual characteristics (e.g., general body shape, patterns of fat deposition and hair growth, growth of breasts) and is involved in monthly preparation for pregnancy.

Testosterone is very important in the development of a male embryo. Our default condition is female. Lack of sex steroids during development results in the development of a girl (even if the child is genetically male). Secretion of testosterone at a particular moment during development turns female genitals into male genitals and primes many organs, including the brain, to be responsive to the second big surge of testosterone which happens at the onset of puberty. At that time, primed tissues develop in a male-specific way, developing male secondary sexual characteristics (e.g., deep voice, beard, larger muscle mass, growth of genitalia, male-typical behaviors, etc.).

Many other organs also secrete hormones along with their other functions. The heart, kidney, lung, intestine and skin are all also members of the endocrine system. Thymus is an endocrine gland that is involved in the development of the immune system – once the immune system is mature, thymus shrinks and dissappears.

Many of the endocrine glands are themselves controlled by other hormones secreted by the pituitary gland – the Master Gland of the endocrine system. For instance, the anterior portion of the pituitary gland secretes hormones that stimulate the release of thyroxine from the thyroid gland, cortisol from the adrenal cortex, and sex steroids form the gonads. Other hormones secreted by the anterior pituitary are prolactin (stimulates production of milk, amog else) and growth hormone (which stimulates cells to produce autocrine and paracrine hormones which stimulate cell-division). The posterior portion of the pituitary is actually part of the brain – it secretes two hormones: antidiuretic hormone (control of water balance) and oxytocin (stimulates milk let-down and uterine contractions, among other functions).

All these pituitary hormones are, in turn, controlled (either stimulated or inhibited) by hormones/factors secreted by the hypothalamus which is a part of the brain, which makes the brain the biggest and most important endocrine gland of all.

Pineal organ is a part of the brain (thus central nervous system). In all vertebrates, except mammals and snakes, it is also a sensory organ – it perceieves light (which easily passes through scales/feathers, skin and skull). In seasonally breeding mammals, it is considered to be a part of the reproductive system. In all vertebrates, it is also an endocrine organ – it secretes a hormone melatonin. In all vertebrates, the pineal organ is an important part of the circadian system – a system that is involved in daily timing of all physiological and behavioral functions in the body. In many species of vertebrates, except mammals, the pineal organ is the Master Clock of the circadian system. In mammals, the master clock is located in the hypothalamus of the brain, in a structure known as the suprachiasmatic nucleus (SCN).

Retina is part of the eye (sensory system), it is part of the brain (nervous system), it also secretes melatonin (endocrine system) and contains a circadian clock (circadian system) in all vertebrates. In some species of birds, the master clock is located in the retina of the eye. The day-night differences in light intensity entrain (synchronize) the circadian system with the cycles in the environment. Those differences in light intensity are perceived by the retina, but not by photoreceptor cells (rods and cones). Instead, a small subset of retinal ganglion cells (proper nerve cells) contains a photopigment melanopsin which changes its 3D structure when exposed to light and sends its signals to the SCN in the brain.

Wherever the master clock may be located (SCN, pineal or retina) in any particular species, its main function is to coordinate the timing of peripheral circadian clocks which are found in every single cell in the body. Genes that code for proteins that are important for the function of a particular tissue (e.g., liver enzymes in liver cells, neurotransmitters in nerve cells, etc.) show a daily rhythm in gene expression. As a result, all biochemical, physiological and behavioral functions exhibit daily (circadian) rhythms, e.g., body temperature, blood pressure, sleep, cognitive abilities, etc. Notable exceptions are functions that have to be kept within a very narrow range of values, e.g., blood pH and blood concentration of calcium.

So, nervous, endocrine, sensory and circadian systems are all involved in control and regulation of other functions in the body. We will see what happens to all those other functions in the stressed, running zebra next week.

Previously in this series:

BIO101 – Biology and the Scientific Method
BIO101 – Cell Structure
BIO101 – Protein Synthesis: Transcription and Translation
BIO101: Cell-Cell Interactions
BIO101 – From One Cell To Two: Cell Division and DNA Replication
BIO101 – From Two Cells To Many: Cell Differentiation and Embryonic Development
BIO101 – From Genes To Traits: How Genotype Affects Phenotype
BIO101 – From Genes To Species: A Primer on Evolution
BIO101 – What Creatures Do: Animal Behavior
BIO101 – Organisms In Time and Space: Ecology
BIO101 – Origin of Biological Diversity
BIO101 – Evolution of Biological Diversity
BIO101 – Current Biological Diversity
BIO101 – Introduction to Anatomy and Physiology

BIO101 – Introduction to Anatomy and Physiology

In this lecture, as well as in the previous one and the next one, I tackle areas of Biology where I am really weak: origin of life, diversity of life, and taxonomy/systematics. These are also areas where there has been a lot of change recently (often not yet incorporated into textbooks), and I am unlikely to be up-to-date, so please help me bring these lectures up to standards…. This post was originally written in 2006 and re-posted a few times, including in 2010.

As you may know, I have been teaching BIO101 (and also the BIO102 Lab) to non-traditional students in an adult education program for about twelve years now. Every now and then I muse about it publicly on the blog (see this, this, this, this, this, this and this for a few short posts about various aspects of it – from the use of videos, to the use of a classroom blog, to the importance of Open Access so students can read primary literature). The quality of students in this program has steadily risen over the years, but I am still highly constrained with time: I have eight 4-hour meetings with the students over eight weeks. In this period I have to teach them all of biology they need for their non-science majors, plus leave enough time for each student to give a presentation (on the science of their favourite plant and animal) and for two exams. Thus I have to strip the lectures to the bare bones, and hope that those bare bones are what non-science majors really need to know: concepts rather than factoids, relationship with the rest of their lives rather than relationship with the other sciences. Thus I follow my lectures with videos and classroom discussions, and their homework consists of finding cool biology videos or articles and posting the links on the classroom blog for all to see. A couple of times I used malaria as a thread that connected all the topics – from cell biology to ecology to physiology to evolution. I think that worked well but it is hard to do. They also write a final paper on some aspect of physiology.

Another new development is that the administration has realized that most of the faculty have been with the school for many years. We are experienced, and apparently we know what we are doing. Thus they recently gave us much more freedom to design our own syllabus instead of following a pre-defined one, as long as the ultimate goals of the class remain the same. I am not exactly sure when am I teaching the BIO101 lectures again (late Fall, Spring?) but I want to start rethinking my class early. I am also worried that, since I am not actively doing research in the lab and thus not following the literature as closely, that some of the things I teach are now out-dated. Not that anyone can possibly keep up with all the advances in all the areas of Biology which is so huge, but at least big updates that affect teaching of introductory courses are stuff I need to know.

I need to catch up and upgrade my lecture notes. And what better way than crowdsource! So, over the new few weeks, I will re-post my old lecture notes (note that they are just intros – discussions and videos etc. follow them in the classroom) and will ask you to fact-check me. If I got something wrong or something is out of date, let me know (but don’t push just your own preferred hypothesis if a question is not yet settled – give me the entire controversy explanation instead). If something is glaringly missing, let me know. If something can be said in a nicer language – edit my sentences. If you are aware of cool images, articles, blog-posts, videos, podcasts, visualizations, animations, games, etc. that can be used to explain these basic concepts, let me know. And at the end, once we do this with all the lectures, let’s discuss the overall syllabus – is there a better way to organize all this material for such a fast-paced class.


Anatomy is the sub-discipline of biology that studies the structure of the body. It describes (and labels in Latin) the morphology of the body: shape, size, color and position of various body parts, with particular attention to the internal organs, as visible by the naked eye. Histology is a subset of anatomy that describes what can be seen only under the microscope: how cells are organized into tissues and tissues into organs. (Classical) embryology describes the way tissues and organs change their shape, size, color and position during development.

Anatomy provides the map and the tools for the study of the function of organs in the body. It describes (but does not explain) the structure of the body. Physiology further describes how the body functions, while evolutionary biology provides the explanation of the structure and the function.

While details of human anatomy are essential in the education of physicians and nurses (and animal anatomy for veterinarians), we do not have time, nor do we need to pay too much attention to fine anatomical detail. We will pick up on relevant anatomy as we discuss the function of organs: physiology.

There are traditionally two ways to study (and teach) physiology. The first approach is medical/biochemical. The body is subdivided into organ systems (e.g., respiratory, digestive, circulatory, etc.) and each system is studied separately, starting with the physiology of the whole organism and gradually going down to the level of organs, tissues, cells and molecules, ending with the biochemistry of the physiological function. Only the human body is studied. Often, pathologies and disorders are used to illustrate how organs work – just like fixing a car engine by replacing a broken part helps us understand how the engine normally works, so studying diseases helps us understand how the healthy human body works.

The other approach is ecological/energetic. The physiological functions are divided not by organ system, but by the problem – imposed by the environment – that the body needs to solve in order to survive and reproduce, e.g., the problem of thermoregulation (body temperature), osmoregulation (salt/water balance), locomotion (movement), stress response, etc., each problem utilizing multiple organ systems. Important aspect of this approach is the study of the way the body utilizes energy: is the solution energetically optimal? Individuals that have solved a problem with a more energy-efficient physiological mechanism will be favored by natural selection – thus this approach is also deeply rooted in an evolutionary context. Finally, this approach is very comparative – study of animals that live in particularly unusual or harsh environments helps us understand the origin and evolution of physiological mechanisms both in humans and in other animals.

The textbook is unusually good (for an Introductory Biology textbook) in trying to bridge and combine both approaches. Unfortunately, we do not have enough time to cover all of the systems and all of the problems in detail, so we will stick to the first, medical approach and cover just a few of the systems of the human body, but I urge you to read the relevant textbook chapters in order to understand the ecological and evolutionary aspects of physiology as well (not to mention some really cool examples of problem-solving by animal bodies). Hint: use the “Self Test” questions at the end of each chapter and if you answer them correctly, you are ready for the exam.

Let’s start out by looking at a couple of important basic principles that pertain to all of physiology. One such principle is that of scaling, for which you should read the handout that we will discuss in class next time. The second important principle in physiology is the phenomenon of feedback loops: both negative and positive feedback loops.

Negative feedback loop works in a way very similar to the graph we drew when we discussed behavior. The body has a Sensor that monitors the state of the body – the internal environment (as opposed to external environment we talked about when discussing behavior), e.g,. the blood levels of oxygen and carbon dioxide, blood pressure, tension in the muscles, etc. If something in the internal environment changes from the normal, optimal values, the sensor informs the Integrator (usually the nervous system) which initiates action (via an Effector) to bring back the body back to its normal state.

Thus, an event A leads to response B which leads to the countering and elimination of the event A. Almost every function in the body operates like a negative feedback loop. For instance, if a hormone is secreted, along with the functional effect of that hormone, there will also be a trigger of a negative feedback loop that will stop the further secretion of that hormone.

There are very few functions in the body that follow a different pattern – the positive feedback loop. There, an event A leads to response B which leads to re-initiation and intensification of the event A which leads to a stronger response B…and so on, until a threshold is reached or the final goal is accomplished, when everything goes abruptly back to normal.

We will take a look at an example of the positive feedback loop that happens in the nervous system next week. For now, let’s list some other notable positive feedback loops in humans.

First, the blood clotting mechanism is a cascade of biochemical reactions that operates according to this principle. An injury stimulates production of a molecule that triggers production of another molecule which triggers production of another molecule as well as production of more of the first molecule, and so on, until the injury has completely closed.

Childbirth is another example of the positive feedback loop. When the baby is ready to go out (and there’s no stopping it at this point!), it releases a hormone that triggers the first contraction of the uterus. The contraction of the uterus pushes the baby out a little. That movement of the baby stretches the wall of the uterus. The wall of the uterus contains stretch receptors which send signals to the brain. In response to the signal, the brain (actually the posterior portion of the pituitary gland, which is an outgrowth of the brain) releases hormone oxytocin. Oxytocin gets into the bloodstream and reaches the uterus triggering the next contraction which, in turn, moves the baby which further stretches the wall of the uterus, which results in more release of oxytocin…and so on, until the baby is expelled, when everything returns to normal.

Next example of the positive feedback loop is also related to babies – nursing. When the infant is hungry, mother brings its mouth to the nipple of the breast. When the baby latches onto the nipple and tries to suck, this stimulates the receptors in the nipple which notify the brain. The brain releases hormone oxytocin from the posterior pituitary gland. Oxytocin gets into the bloodstream and stimulates the mammary gland to release milk (not to synthesize milk – it is already stored in the breasts). Release of milk at the nipple stimulates the baby to start suckling vigorously, which stimulates the receptors in the nipple even more, so there is even more oxytocin released from the pituitary and even more milk is released by the mammary gland, and so on, until the baby is satiated and unlatches from the breast, when everything goes back to normal.

Next example of the positive feedback loop is also related to babies, but nine months earlier. Copulation – yes, having sex – is an example of a positive feedback loop, both in females and in males. Initial stimulation of the genitals stimulates the touch receptors which notify the brain which, in turn, stimulates continuation (and gradual speeding up) of movement, which provides further tactile stimulation, and so on, until the orgasm, after which everything goes back to normal (afterglow notwithstanding).

The last example also applies to the nether regions of the body. Micturition (urination) is also a positive feedback loop. The wall of the urinary bladder is built in such a way that there are several layers of cells. As the bladder fills up, the wall stretches and these cells move around until the wall is only a single cell thick. At this point, urination is inevitable (cannot be stopped by voluntary control). Beginning of the urination starts the movement of the cells back from single-layer state to multi-layer state. This contracts the bladder further which forces urine out even more which contracts the wall of the bladder even more, and so on until the bladder is completely empty again and everything goes back to normal.

The concept of feedback loops is essential for the understanding of the principle of homeostasis. Homeostatic mechanisms ensure that the internal environment remains constant and all the parameters are kept at their optimal levels (e.g,. temperature, pH, salt/water balance, etc) over time. If a change in the environment (e.g., exposure to heat or cold) results in the change of internal body temperature, this is sensed by thermoreceptors in the body. This triggers corrective mechanisms: if the body is overheated, the capillaries in the skin expand and radiate heat and the sweat gland release sweat; if the body is too cold, the capillaries in the skin contract, the muscles start shivering, the hairs stand up (goosebumps), and the thyroid hormones are released, resulting in opening of pores in the membranes of mitochondria in the muscles, thus reducing the efficiency of the break-down of glucose to water and carbon-dioxide, thus producing excess heat. Either way, the body temperature will be returned to its optimal level (around 37 degrees Celsius), which is called the set-point for body temperature. Each aspect of the internal environment has its own set-point which is defended by homeostatic mechanisms.

While essentially correct, there is a problem with the concept of homeostasis. One of the problems with the term “homeostasis” is linguistic: the very term homeostasis is misleading. “Homeo” means ‘similar, same’ and “stasis” means ‘stability’. Thus, the word homeostasis (coined by Walter Cannon in the early 20th century) suggests strong and absolute constancy. Imagine that you were told to draw a graphical representation of the concept of homeostasis in 10 seconds. Without sufficient time to think, you would probably draw something like this:

The main characteristic of this graph is that the set-point is constant over time. But that is not how it works in the real world. The graph above is correct only if the time-scale (on the X-axis) spans only seconds to minutes. If it is expanded to hours, days or years, the graph would be erroneous – the line would not be straight and horizontal any more. The set point changes in a predictable and well-controlled manner. For instance, the set-point for testosterone levels in the blood in human males over the course of a lifetime may look like this:

That would be an example of developmental control of a set-point. At each point in time, that set-point is defended by homeostatic mechanisms, but the set-point value is itself controlled by other physiological processes. Another example of controlled change of a set-point may look like this:

This would be an example of an oscillatory control of a set-point. In the early 1980s, Nicholas Mrosovsky coined a new term to replace ‘homeostasis’ and specifically to denote controlled changes in set-points of all biochemical, physiological and behavioral values – rheostasis.

Almost every aspect of physiology (and behavior) exhibits rheostasis, both developmental and oscillatory (daily and/or yearly rhythms). Some notable exceptions are blood pH (which has to be kept within very narrow range 7.35-7.45) and blood levels of Calcium. If pH or Calcium levels move too far away from the optimal value, cells in the body (most notably nerve cells, muscles and heart cells) cannot function properly and the body is in danger of immediate death.

Additional Readings:

‘Medicine Needs Evolution’ by Nesse, Stearns and Omenn

Previously in this series:

BIO101 – Biology and the Scientific Method
BIO101 – Cell Structure
BIO101 – Protein Synthesis: Transcription and Translation
BIO101: Cell-Cell Interactions
BIO101 – From One Cell To Two: Cell Division and DNA Replication
BIO101 – From Two Cells To Many: Cell Differentiation and Embryonic Development
BIO101 – From Genes To Traits: How Genotype Affects Phenotype
BIO101 – From Genes To Species: A Primer on Evolution
BIO101 – What Creatures Do: Animal Behavior
BIO101 – Organisms In Time and Space: Ecology
BIO101 – Origin of Biological Diversity
BIO101 – Evolution of Biological Diversity
BIO101 – Current Biological Diversity

Spring Forward, Fall Back – should you watch out tomorrow morning?

I originally published this on November 2, 2008. You really need to reed the comments there, at the original post, as well as the “related” posts at the bottom of this post, as this story had some legs – a lot of discussion ensued.

If you live in (most places in) the United States as well as many other countries, you have reset your clocks back by one hour last night (or last week). How will that affect you and other people?

One possibility is that you are less likely to suffer a heart attack tomorrow morning than on any other Monday of the year. Why? Let me try to explain in as simple way as possible (hoping that oversimplification will not lead to intolerable degrees of inaccuracy).

Almost all biochemical, physiological and behavioral parameters in almost all (at least multicellular) organisms display diurnal (daily) rhythms and most of those are directly driven by the circadian clock (or, more properly, by the circadian system). Here is an old and famous chart displaying some of the peaks (acrophases) of various physiological functions in the human:

It may be a little fuzzy, but you can see that most of the peaks associated with the cardiovascular function are located in the afternoon. The acrophases you see late at night are for things like “duration of systole” and “duration of diastole” which means that the Heart Rate is slow during the night. Likewise, blood pressure is low during the night while we are asleep.

Around dawn, heart rate and blood pressure gradually rise. This is a direct result of the circadian clock driving the gradual rise in plasma epinephrine and cortisol. All four of those parameters (HR, BP, Epinephrine and Cortisol) rise roughly simultaneously at dawn and reach a mini-peak in the morning, at the time when we spontaneously wake up:

This rise prepares the body for awakening. After waking up, the heart parameters level off somewhat and then very slowly rise throughout the day until reaching their peak in the late afternoon.

Since the four curves tend to be similar and simultaneous in most cases in healthy humans, let’s make it easier and clearer to observe changes by focusing only on the Cortisol curve in the morning, with the understanding that the heart will respond to this with the simultaneous rise in heart rate and blood pressure. . This is how it looks on a day when we allow ourselves to wake up spontaneously:

But many of us do not have the luxury of waking up spontaneously every day. We use alarm clocks instead. If we set the alarm clock every day to exactly the same time (even on weekends), our circadian system will, in most cases (more likely in urban than rural areas, though), entrain to the daily Zeitgeber – the ring of the alarm-clock – with a particular phase-relationship. This usually means that the rise in cardiovascular parameters will start before the alarm, but will not quite yet reach the peak as in spontaneous awakening:

The problem is, many of us do not set the alarm clocks during the weekend. We let ourselves awake spontaneously on Saturday and Sunday, which allows our circadian clock to start drifting – slowly phase-delaying (because for most of us the freerunning period is somewhat longer than 24 hours). Thus, on Monday, when the alarm clock rings, the gradual rise of cortisol, heart rate and blood pressure will not yet be as far along as the previous week. The ring of the alarm clock will start the process of resetting of the circadian clock – but that is the long-term effect (may take a couple of days to complete, or longer.).

The short term effect is more dramatic – the ring of the alarm clock is an environmental stressor. As a result, epinephrine and cortisol (the two stress hormones) will immediately and dramatically shoot up, resulting in an instantaneous sharp rise in blood pressure and heart rate. And this sharp rise in cardiovascular parameters, if the heart is already damaged, can lead to a heart attack. This explains two facts: 1) that heart attacks happen more often on Mondays than other days of the week, and 2) that heart attacks happen more often in the morning, at the time of waking up, than at other times of day:

Now let’s see what happens tomorrow, the day after the time-change. Over the weekend, while you were sleeping in, your circadian system drifted a little, phase delaying by about 20 minutes on average (keep in mind that this is an average – there is a vast variation in the numerical value of the human freerunning circadian period). Thus, your cardiovascular parameters start rising about 20 minutes later tomorrow morning than last week. But, your alarm clock will ring an entire hour later than last week – giving you an average of a 40-minute advantage. Your heart will be better prepared for the stress of hearing the ringing than on any other Monday during the year:

Now let’s fast-forward another six month to the Spring Forward weekend some time in March or April of next year. Your circadian system delays about 20 minutes during the weekend. On top of that, your alarm clock will ring an hour earlier on that Monday than the week before. Thus, your cardiovascular system is even further behind (80 minutes) than usual. The effect of the stress of the alarm will be thus greater – the rise in BP and HR will be even faster and larger than usual. Thus, if your heart is already damaged in some way, your chances of suffering an infarct are greater on that Monday than on any other day of the year:

This is what circadian theory suggests – the greater number of heart attacks on Mondays than other days of the week (lowest during the weekend), the greatest number of heart attacks on the Monday following the Spring Forward time-change compared to other Mondays, and the lowest incidence of heart attacks on the Monday following the Fall Back time-change compared to other Mondays.

A couple of days ago, a short paper appeared that tested that theoretical prediction and found it exactly correct (Imre Janszky and Rickard Ljung, October 30, 2008, Shifts to and from Daylight Saving Time and Incidence of Myocardial Infarction, The New England Journal of Medicine, Volume 359:1966-1968, Number 18.). The authors looked at a large dataset of heart attacks in Sweden over a large period of time and saw that (if you look at the numbers) the greatest number of heart attacks happens on Mondays compared to other days of the week (and yes, the numbers are lowest during the weekend), the greatest number of heart attacks occur on the Monday following the Spring Forward time-change compared to Mondays two weeks before and after, and the lowest incidence of heart attacks happens on the Monday following the Fall Back time-change compared to Mondays two weeks before and after:

Thus, the predictions from the circadian theory were completely and clearly correct. But I was jarred by the conclusions that the authors drew from the data. They write:

The most plausible explanation for our findings is the adverse effect of sleep deprivation on cardiovascular health. According to experimental studies, this adverse effect includes the predominance of sympathetic activity and an increase in proinflammatory cytokine levels.3,4 Our data suggest that vulnerable people might benefit from avoiding sudden changes in their biologic rhythms.

It has been postulated that people in Western societies are chronically sleep deprived, since the average sleep duration decreased from 9.0 to 7.5 hours during the 20th century.4 Therefore, it is important to examine whether we can achieve beneficial effects with prolonged sleep. The finding that the possibility of additional sleep seems to be protective on the first workday after the autumn shift is intriguing. Monday is the day of the week associated with the highest risk of acute myocardial infarction, with the mental stress of starting a new workweek and the increase in activity suggested as an explanation.5 Our results raise the possibility that there is another, sleep-related component in the excess incidence of acute myocardial infarction on Monday. Sleep-diary studies suggest that bedtimes and wake-up times are usually later on weekend days than on weekdays; the earlier wake-up times on the first workday of the week and the consequent minor sleep deprivation can be hypothesized to have an adverse cardiovascular effect in some people. This effect would be less pronounced with the transition out of daylight saving time, since it allows for additional sleep. Studies are warranted to examine the possibility that a more stable weekly pattern of waking up in the morning and going to sleep at night or a somewhat later wake-up time on Monday might prevent some acute myocardial infarctions.

And in the quotes in the press release they say the same thing, so it is not a coincidence:

“It’s always been thought that it’s mainly due to an increase in stress ahead of the new working week,” says Dr Janszky. “But perhaps it’s also got something to do with the sleep disruption caused by the change in diurnal rhythm at the weekend.”

Dr.Isis has already noted this and drew the correct conclusion. She then goes on to say something that is right on the mark:

And, of course, my first thought is, what about all the other times we are sleep deprived by, you know, one hour. Is waking up in the middle of the night to feed Baby Isis potentially going to cause Dr. Isis to meet her maker early? In that case Baby Isis can freakin’ starve. But, this is the New England Journal of Medicine and Dr. Isis appreciates the innate need that authors who publish here have to include some clinical applicability in their work.

The authors responded to Dr.Isis in the comments on her blog and said, among else:

We wonder whether you have ever tried to publish a research letter somewhere. The number of citations (maximum 5!) and the number of words are strictly limited. Of course we are familiar with studies on circadian rhythms and cardiovascular physiology. There was simply no space to talk more about biological rhythms than we actually did.

But what they wrote betrays that even if they are familiar with the circadian literature, they do not really understand it. Nobody with any circadian background ever speculates about people’s conscious expectations of a stressful week as a cause of heart attacks on Monday mornings. Let me try to explain why I disagree with them on two points they raise (one of which I disagree with more strongly than the other).

1) Sleep Deprivation. It is important to clearly distinguish between the acute and the chronic sleep deprivation. Sleepiness at any given time of day is determined by two processes: a homeostatic drive that depends on the amount of sleep one had over a previous time period, and a circadian gating of sleepiness, i.e., at which time of day is one most likely to fall asleep. Sleep deprivation affects only the homeostatic drive and has nothing to do with circadian timing.

Humans, like most other animals, are tremendously flexible and resilient concerning acute sleep deprivation. Most of us had done all-nighters studying for exams, or partying all night with non ill effects – you just sleep off the sleep debt the next day or the next weekend and you are fine. Dr.Isis is not going to die because her baby wakes her up several times during the night. This is all part of a normal human ecology, and human physiology had adapted to such day-to-day variations in opportunities for sleep.

The Chronic sleep deprivation is a different animal altogether. This means that you are getting less sleep than you need day after day, week after week, month after month, year after year, with rarely or never sleeping off your sleep debt (“catching up on sleep”). As a result, your cognitive functions suffer. If you are a student, you will have difficulties understanding and retaining the material. If you are a part of the “creative class”, you will be less creative. If you are a scientist, you may be less able to clearly think through all your experiments, your data, and your conclusions. No matter what job you do, you will make more errors. You may suffer microsleep episodes while driving and die in a car wreck. Your immune system will be compromised so you will constantly have sniffles and colds, and may be more susceptible to other diseases.

And yes, a long term chronic sleep deprivation may eventually damage your heart to the extent that you are more susceptible to a heart attack. This means that you are more likely to suffer a heart attack, but has no influence on the timing of the heart attack – it is the misalignment between the natural circadian rhythms of your body and the social rhythms imposed via a very harsh stressor – the alarm clock – that determines the timing. Being sleep deprived over many years means you are more likely to have a heart attack, but cannot determine when. Losing just one hour of sleep will certainly have no effect at all.

Thus, the data presented in the paper have nothing to say about sleep deprivation.

2) Cytokines. These are small molecules involved in intercellular signaling in the immune system. Like everything else, they are synthesized in a diurnal manner. But they act slowly. Maybe they play some small part in the gradual damage of the heart in certain conditions (prolonged inflammation, for instance), thus they may, perhaps, have a role in increasing risk of a heart attack. But they play no role in timing of it. Thus they cannot be a causal factor in the data presented in the paper which are ONLY about timing, not the underlying causes. The data say nothing as to who will suffer a heart attack and why, only when you will suffer one if you do.

If I was commissioned to write a comprehensive review of sleep deprivation, I may have to force myself to wade through the frustratingly complicated and ambiguous literature on cytokines in order to write a short paragraphs under a subheading somewhere on the 27th page of the review.

If I had a severe word-limit and needed to present the data they showed in this paper, I would not waste the space by mentioning the word “cytokine” at all (frankly, that would not even cross my mind to do) as it is way down the list of potential causes of heart attack in general and has nothing to do with the timing of heart attacks at all, thus irrelevant to this paper.

So, it is nice they did the study. It confirms and puts clear numbers on what “everybody already knew for decades” in the circadian community. But their interpretation of the data was incorrect. This was a purely chronobiological study, yet they chose to present it as a part of their own pet project instead and tried mightily to make some kind of a connection to their favourite molecules, the cytokines, although nothing warranted that connection. Nails: meet hammer.

The fake-insulted, haughty and inappropriate way/tone they responded to Dr.Isis is something that is important to me professionally, as is there misunderstanding of both the role and the tone of science blogs, so I will revisit that issue in a separate post later. I promise. It is important.

But back to Daylight Saving Time. First, let me ask you (again) to see Larry’s post from last year, where you will find a lot of useful information and links about it. What is important to keep in mind is that DST itself is not the problem – it is the time-changes twice a year that are really troubling.

Another important thing to keep in mind is that DST was instituted in the past at the time when the world looked very different. At the time when a tiny sliver of the population is still involved in (quite automated and mechanized) agriculture, when electricity is used much more for other things than illumination (not to mention that even the simple incandescent light bulbs today are much more energy efficient than they used to be in the past, not to mention all the newfangled super-efficient light-bulbs available today), when many more people are working second and third shifts than before, when many more people work according to their own schedules – the whole idea of DST makes no sense any more.

Even if initially DST saved the economy some energy (and that is questionable), it certainly does not do so any more. And the social cost of traffic accidents and heart attacks is now much greater than any energy savings that theoretically we may save.

Furthermore, it now seems that circadian clocks are harder to shift than we thought in the past. Even that one-hour change may take some weeks to adjust to, as it is not just a singular clock but a system – the main pacemaker in the SCN may shift in a couple of days, but the entire system will be un-synchronized for some time as it may take several weeks for the peripheral clocks in the liver and intestine to catch up – leading to greater potential for other disorders, e.g., stomach ulcers.

The social clues (including the alarm clocks) may not be as good entraining agents as we thought before either, especially in rural areas where the natural lighting still has a profound effect.

Finally, the two time-change days of the year hit especially hard people with Bipolar Disorder and with Seasonal Affective Disorder – not such a small minority put together, and certainly not worth whatever positives one may find in the concept of DST. We should pick one time and stick with it. It is the shifts that cost the society much more than any potential benefits of DST.

Related reading:

Roosevelts on Toilets
The Shock Value of Science Blogs
Add yet another factor to the circadian hypothesis of morning heart-attacks
Daylight Saving Time
Daylight Savings Time worse than previously thought
Sun Time is the Real Time
Lesson of the Day: Circadian Clocks are HARD to shift!
Everything You Always Wanted To Know About Sleep (But Were Too Afraid To Ask)
Seasonal Affective Disorder – The Basics
Circadian clock without DNA–History and the power of metaphor
Lithium, Circadian Clocks and Bipolar Disorder
Are Zombies nocturnal?
Diversity of insect circadian clocks – the story of the Monarch butterfly
Me and the copperheads–or why we still don’t know if snakes secrete melatonin at night
The Mighty Ant-Lion
City Of Light: Insomniac Urban Animals

Sun Time is the Real Time

I originally published this on January 31, 2007.

If you really read this blog “for the articles”, especially the chronobiology articles, you are aware that the light-dark cycle is the most powerful environmental cue entraining circadian clocks. But it is not the only one. Clocks can also be entrained by a host of other (“non-photic”) cues, e.g., scheduled meals, scheduled exercise, daily dose of melatonin, etc.

Clocks in heterothermic (“cold-blooded”) animals can also entrain to temperature cycles. Lizards can entrain to temperature cycles (pdf) in which the difference between nightime low and daytime high temperatures is as small as 2 degrees Celsius. When taken out of a warm-blooded animal, the SCN clock can also be entrained (if you are a regular here, you recognize the name, don’t you) by temperature cycles (presumably a nice feedback loop that stabilizes the mammalian rhythms: the clock entrains body temperature cycles and body temperature cycles entrain the clock).

Some rodents can phase-shift (and thus presumably entrain if presented daily) their clocks under the influence of conspecifics odors or pheromones. In an old study (which was not very good, but enough can be concluded from the data), rats held in groups in constant conditions entrained their rhythms to each other (while the quail did not), suggesting some kind of social entrainment, perhaps mediated by smell.

Social animals are supposed to be sensitive to social cues and it is presumed that their clocks can be entrained by social cues as well. It is also widely believed that no other animal’s clock is as sensitive to social cues as the human’s.

Everyone who’s been in this field has heard the anecdotes about the experiments conducted by Jurgen Asschoff and others at Andechs, Germany in the 1950s and 60s, in which human volunteers were kept in constant light conditions for prolonged periods of time in old underground bunkers (I think Asschoff’s bunkers are now preserved as monuments to science, just like the Knut Schmidt-Nielsen’s camel chamber is preserved over at Duke University with a nice brass plaque). According to the lore of the field (were those things ever published?), social cues like newspapers, or physical appearance of technicians called in to bring in the food (e.g., sleepy look, or the 5-o-clock stubble) were sufficient cues to entrain human subjects.

It is always difficult to directly test the relative importance of different environmental cues. Sure, one can put them in direct competition by having, for instance, a light-dark cycle and a temperature cycle being 180 degrees out of phase and see to which one of those animals actually entrain (such a study in Neurospora was published a few years back). But, how do you know that the intensities are equivalent? What is the equivalent of 1000 lux in degrees Celsius? Ten, twenty, a hundred?

So, perhaps one should look at the ecologicaly relevant levels of intensity of environmental cues. But how does one dissociate two synchronous cues out in nature in order to do the experiment? Well, of course, use humans for this experiment as the society has already made sure some cues get dissociated! And that is exactly what Till Roenneberg, C. Jairaj Kumar and Martha Merrow did in a new paper in Current Biology: The human circadian clock entrains to sun time (Volume 17, Issue 2 , 23 January 2007, Pages R44-R45)

What they did is take advantage of the fact that time zones are very broad – about 15 angle degrees each. This means that the official (social) midnight and the real (geophysical) midnight coincide only in a very narrow strip running smack through the middle of the time zone. Most of Europe is one time zone. If it is officially midnight in Europe, i.e., the clock strikes 12, it is really midnight (as in “Mid-Night”) in a place like Munich, but it is already something like an hour later in Bucharest, and still something like an hour to wait for it in Lisbon.

So, in this paper, they looked at actual entrainment patterns of more than 21000 Germans to see if they entrain to the real midnight – suggesting that light cues are stronger, or to official midnight, suggesting that social cues are stronger. They controlled for age, sex, chronotype (owls/larks) and general culture (former East and West Germanies) and what they found was very interesting: in small cities, towns and villages, people entrain to the light-dark cycles and mostly ignore the official time. However, bigger the city, more independent the entrainment was from the real light-dark cycle. The phase was delayed and more in sync with the official time.

It is hard to interpret the findings, really. Do people in big cities entrain to official time due to stronger social cues (the busy big-city life and social scene) or because they are better sheltered from the natural light-dark cycle and, due to all the light pollution and technology, better able to impose on their clocks an artificial light-dark cycle. I am assuming that untangling this question is going to be their next project.

But, one thing this study did was make us take a more skeptical look at all those Andech bunkers anecdotes. Sure, social cues may work in the absence of all other cues, but they are not THAT powerful and do not seem to be able to overcome the effects of natural light cycles in places in which people are able to perceive a natural light cycle. I guess one can view the life in a big city (“black box”) as being in a laboratory experiment in which the society acts as an experimenter, imposing the light-dark cycle on people, while the life out in the country is more like a field experiment in which the human subjects are exposed to the natural environmental cues.



Sun Time is the Real Time
Lesson of the Day: Circadian Clocks are HARD to shift!
Everything You Always Wanted To Know About Sleep (But Were Too Afraid To Ask)
Seasonal Affective Disorder – The Basics
Circadian clock without DNA–History and the power of metaphor
Are Zombies nocturnal?
Diversity of insect circadian clocks – the story of the Monarch butterfly
Me and the copperheads–or why we still don’t know if snakes secrete melatonin at night
The Mighty Ant-Lion
City Of Light: Insomniac Urban Animals

Lesson of the Day: Circadian Clocks are HARD to shift!

I originally published this on February 28, 2007.

This is a story about two mindsets – one scientific, one not – both concerned with the same idea but doing something very different with it. Interestingly, both arrived in my e-mail inbox on the same day, but this post had to wait until I got out of bed and started feeling a little bit better.

First, just a little bit of background:

Circadian oscillations are incredibly robust, i.e., resistant to perturbations and random noise from the environment. Ricardo Azevedo has described one model that accounts for such robustness in his two-part post here and here and others have used other methods.

Circadian clock can be re-set only by a very limited set of environmental cues. For each cue, there is a dedicated, evolved pathway by which such cue resets the clock. Light is one such cue – the one we understand the best, down to each molecule. Temperature is another one (in warmblooded animals, the clock is exposed to a constant temperature of the body, but taken out into a dish, it does entrain to temperature cycles). In some animals, olfactory cues (smell) can affect the clock. Scheduled feeding and bouts of exercise can also reset the clock. In each case we have a decent idea which part of the brain is responsible for feeding this information to the clock and by which neurotransmitters or hormones.

For a long time it was thought that humans are especially sensitive to social cues, but perhaps this conclusion is erroneous as, at the time, it was thought that very dim light cannot shift human clocks so many exchanges between subjects and staff occurred in dim light. We now know that dim light resets the human clock.

Clock regulates timing of thousands of body functions, sleep being only one of them. Most of the functions timed by the clock cannot themselves feed back on the clock. Of the hormones whose release is timed by the clock, melatonin is the only hormone that can phase-shift and entrain the rhythms, while in some organisms, sex steroids can also have a slower, long-term effect on the period and phase.

So, can the act of sleeping reset the clock?

This is not a bad question as there is nothing theoretically against such a notion. The question was asked by sleep and clock researchers in the past and, them being scientists, they tested it in several different ways. Every time the answer came out the same: No, timing of sleep cannot affect the working of the clock. Falling asleep and waking up at unusual times does not reset the clock. Naps do not reset the clock.

This is now a well-known fact in chronobiology which was creatively used in the experimental design of the study reported here and here. The question they asked was if the circadian time affects athletic ability in competitive swimmers.

But, how can they eliminate all the other potentially confounding factors, e.g., time since waking-up, time since last meal, etc.? It is impossible to control for all those other factors. So, they did the opposite, they made sure that every confounding factor is present at every time of day and every swimming test. They did it by utilizing the knowledge that naps do not reset the clock. All the swimmers were made to sleep for an hour and be awake for two hours and over and over agaian, for a very long period of time (about 55 hours). They swam 200m during every bout of wakefulness.

What they found was that the time of day made a big difference – as much as 5 seconds (remember that 5 hundredths of the second can make a difference between Olympic Gold and no medal at all!). Afternoon times were better than morning times. Period between 2am and 8am was awful! The 11pm time was the best.

What is also important is that the findings from this study are very similar to findings of previous studies which in no way attempted to control for confounding factors. This suggests that, coaches’ beliefs notwithstanding, all those other factors have little or no effect on swimming performance compared to the effects of the circadian time.

Anyway, that was a good scientific study utilizing the knowledge that repeated naps do not reset the biological clock.

Now, to the second story.

How about a story about a guy who wakes up one morning with a brilliant idea – if something could reset the clock a little bit, perhaps something like a massage, doing a series of those while on an intercontinental flight could potentially beat jet-lag!

Now, someone with a scientific mindset would get on Google and, in two-to-five minutes of searching discover those few cues that actually do reset clocks. No massage there. Back to the drawing board. This idea has no legs. It’s over. One of those many brilliant ideas to discard before breakfast.

But if you do not have a scientific mindset but a predatory business mindset? What then? Then, of course, your next question is not going to be if your idea is valid, but how to turn your idea into dollars. So, you build a website, give it a catchy name of Jet Lag Passport and sell a PDF explaining to the unitiated how to get rid of jet-lag for $19.95. Which doesn’t work.

But, sounding all scientific only brings in some potential customers. How can one bring in some others, for more money? Well, that’s easy. Pepper your idea with additional woo. How about some New-Agey mind-body woo plus some Oriental “medicine”? Sure, why not? People seem to fall for that kind of stuff. You just need to press some acupressure points every two hours and that will help reset your clock (I am wondering how molecular transcription factors in the SCN respond to pressing your nose?!). Oh, and don’t forget to say some magic words as you do this (“Even though I have this jet lag, I deeply and completely accept myself, and I choose to feel good now and when I arrive in (your destination). “) because self-persuasion must really be effective! Oh, drink enough fluids as dehydration prevents this method from working!

Frankly, reading through the PDF (provided to me for free by the author who, for some unexplained reason, thought I’d like it! Sometimes one wonders if the quacks are really aware how bad their stuff is! Or is it the huge ego?). I did not know where to start. Nothing in it makes any sense. This is just NOT the way a human body works. Not even close. Molecules in our cells could not care less what we say and what we want and what parts of the skin we touch. I could not deceive my body that I was feeling fine last week – I had to take antibiotics instead. Likewise, chanting and acupressure and self-suggestion will not in any way change the rate of transcription of clock genes in your SCN or the rate of degradation of the clock proteins. And that is just SCN. Jet-lag is not a symptom of resetting of the SCN clock but the result of internal desynchronization between myriads of clocks in all our organs. Drinking water will not help, sorry.

Remember the beginning of this post? How difficult it is to shift the clock? How robust it is? How useful this fact was for the swimming study? Only people’s gullibility can match its robustness!

But then I looked around the website and realized that this is no naive amateur writing this. This is a subset of the notorious Emotional Freedom Technique (EFT) which is a variant of the Thought Field Therapy (TFT). See the first link for a who’s-who in medical woo on the sidebar (starting with Deepak Chopra of course) and check the second link for a beautiful fisking of another EFT-related quackery by Orac. There is an ocean of woo there – far too much for just one person – little me – to debunk on one’s own. So, let’s just remain on the topic of jet-lag.

If anyone offers to sell you a cure for jet-lag that does not combine, in some way, use of bright lights, melatonin pills and strict scheduling of meals and exercise upon reaching the destination, do not buy it – it will not and cannot work. There are just no physiological explanations even how it might work – it is so New-Agey and gooey and mystical it is not even approaching a form of a testable hypothesis and thus does not warrant any time wasted by scientific researchers on it. Go read something else….The correct information about alleviating jet-lag is available online for FREE!

Are Zombies nocturnal?

For Halloween, I thought I’d republish this old post of mine from July 1, 2010.

Blame ‘Night of the Living Dead’ for this, but many people mistakenly think that zombies are nocturnal, going around their business of walking around town with stilted gaits, looking for people whose brains they can eat, only at night.

You think you are safe during the day? You are dangerously wrong!

Zombies are on the prowl at all times of day and night! They are not nocturnal, they are arrhythmic! And insomniac. They never sleep!

Remember how one becomes a zombie in the first place? Through death, or Intercision, or, since this is a science blog and we need to explain this scientifically, through the effects of tetrodotoxin. In any case, the process incurs some permanent brain damage.

One of the brain centers that is thus permanently damaged is the circadian clock. But importantly, it is not just not ticking any more, it is in a permanent “day” state. What does that mean practically?

When the clock is in its “day” phase, it is very difficult to fall asleep. Thus insomnia.

When the clock is in its “day” phase, metabolism is high (higher than at night), thus zombies require a lot of energy all the time and quickly burn through all of it. Thus constant hunger for high-calory foods, like brains.

Insomnia, in turn, affects some hormones, like ghrelin and leptin, which control appetite. If you have a sleepless night or chronic insomnia, you also tend to eat more at night.

But at night the digestive function is high. As zombies’ clock is in the day state, their digestion is not as efficient. They have huge appetite, they eat a lot, but they do not digest it well, and what they digest they immediately burn. Which explains why they tend not to get fat, while living humans with insomnia do.

Finally, they have problems with wounds, you may have noticed. Healing of wounds requires growth hormone. But growth hormone is secreted only during sleep (actually, during slow sleep phases) and is likewise affected by ghrelin.

In short, a lot of the zombies’ physiology and behavior can be traced back to their loss of circadian function and having their clock being in a permanent “day” state.

But the real take-home message of this is…. don’t let your guard down during the day!

Picture of me as a Zombie drawn by Joseph Hewitt of Ataraxia Theatre whose latest project, GearHead RPG, is a sci-fi rogue-like game with giant robots and a random story generator – check it out.

Revenge of the Zombifying Wasp

As it is Halloween, I am republishing my old post (from February 04, 2006, reposted on July 1, 2010):

Ampulex compressa

I was quite surprised that Carl Zimmer, in research for his book Parasite Rex, did not encounter the fascinating case of the Ampulex compressa (Emerald Cockroach Wasp) and its prey/host the American Cockroach (Periplaneta americana, see also comments on Aetiology and Ocellated).

In 1999, I went to Oxford, UK, to the inaugural Gordon Conference in Neuroethology and one of the many exciting speakers I was looking forward to seeing was Fred Libersat. The talk was half-hot half-cold. To be precise, the first half was hot and the second half was not.

In the first half, he not just introduced the whole behavior, he also showed us a longish movie, showing in high magnification and high resolution all steps of this complex behavior (you can see a cool picture of the wasp’s head here).

How the wasp injects the cockroach

First, the wasp gives the roach a quick hit-and-run stab with its stinger into the body (thorax) and flies away. After a while, the roach starts grooming itself furiously for some time, followed by complete stillness. Once the roach becomes still, the wasp comes back, positions itself quite carefully on top of the raoch and injects its venom very precisely into the subesophageal ganglion in the head of the roach. The venom is a cocktail of dopamine and protein toxins so the effect is behavioral modification instead of paralysis.

Apparently, the wasp’s stinger has receptors that guide it to its precise target:

“To investigate what guides the sting, Ram Gal and Frederic Libersat of Ben-Gurion University in Beer-Sheva, Israel, first introduced the wasp to roaches whose brains had been removed. Normally, it takes about a minute for the wasp to find its target, sting, and fly off. But in the brainless roaches, the wasps searched the empty head cavity for an average of 10 minutes. A radioactive tracer injected into the wasps revealed that when they finally did sting, they used about 1/6 the usual amount of venom. The wasps knew something was amiss.”

The wasp then saws off the tips of the roach’s antennae and drinks the haemolymph from them. It builds a nest – just a little funnel made of soil and pebbles and leads the roach, by pulling at its antenna as if it was a dog-leash, into the funnel. It then lays an egg onto the leg of the roach, closes off the entrance to the funnel with a rock and leaves. The roach remains alive, but completely still in the nest for quite some time (around five weeks). The venom, apart from eliminating all defense behaviors of the roach, also slows the metabolism of the cockroach, allowing it to live longer without food and water. After a while, the wasp egg hatches, eats its way into the body of the roach, eats the internal organs of the roach, then pupates and hatches. What comes out of the (now dead) cockroach is not a larva (as usually happens with insect parasitoids) but an adult wasp, ready to mate and deposit eggs on new cockroaches.

Why was the second half of the talk a disappointment? I know for a fact I was not the only one there who expected a deeper look into evolutionary aspects of this highly complex set of behaviors. However, the talk went into a different direction – interesting in itself, for sure, but not as much as an evolutionary story would have been. Libersat described in nitty-gritty detail experiments that uncovered, one by one, secrets of the neuroanatomy, neurophysiology and neurochemistry of the cockroach escape behavior – the one suppressed by toxin – as well as the chemistry of the toxin cocktail. Ganglion after ganglion, neuron after neuron, neurotransmitter after neurotransmitter, the whole behavior was charted for us on the screen. An impressive feat, but disappointing when we were all salivating at a prospect of a cool evolutionary story.

He did not say, for instance, what is the geographic overlap between the two species. I had to look it up myself afterwards. American cockroach can be found pretty much everywhere in the world. The wasp also has a broad geographical range from Africa to New Caledonia (located almost directly between Australia and Fiji) and, since 1941, Hawaii (another example of a non-native species wreaking havoc on the islands), but not everywhere in the world, especially not outside the tropics – there are most definitely parts of the planet where there are roaches but no Ampulex compressa.

In most cases in which one species is susceptible to the venom or toxin of another species, the populations which share the geography are also engaged in an evolutionary arms-race. The victim of the venom evolves both behavioral defenses against the attack of the other species and biochemical resistance to the venom. In turn, the venom evolves to be more and more potent and the animal more and more sneaky or camouflaged or fast in order to bypass behavioral defenses.

There are many examples of such evolutionary arms-races in which one of the species is venomous/toxic and the other one evolves resistance. For instance, garter snakes on the West Coast like to eat rough-side newts. But these newts secrete tetrodotoxin in their skins. The predator is not venomous, but it has to deal with dangerous prey. Thus, in sympatry (in places where the two species co-exist) snakes have evolved a different version of a sodium channel. This version makes the channel less susceptible to tetrodotoxin, but there is a downside – the snake is slower and more lethargic overall. In the same region, the salamanders appear to be evolving ever more potent skin toxin cocktails.

Similar examples are those of desert ground squirrels and rattlesnakes (both behavioral and biochemical innovations in squirrels), desert mice (Southwest USA) and scorpions (again it is the prey which is venomous), and honeybees and Death’s-Head sphinx-moths (moths come into the hives and steal honey and get stung by bees after a while).

But Libersat never wondered if cockroaches in sympatry with Emerald wasps evolved any type of resistance, either behavioral or physiological. Perhaps the overwhelming number of roaches in comparison with the wasps makes any selective pressure too weak for evolution of defenses. But that needs to be tested. He also never stated if the attack by the wasp happens during the day or during the night. Roaches are nocturnal and shy away from light. The movie he showed was from the lab under full illumination. Is it more difficult for the wasp to find and attack the roach at night? Is it more difficult for the roach to run away or defend itself during the day? Those questions need to be asked.

Another piece of information that is missing is a survey of parasitizing behaviors of species of wasps most closely related to Ampulex compressa. Can we identify, or at least speculate about, the steps in the evolution of this complex set of behaviors (and the venom itself)? What is the precursor of this behavior: laying eggs on found roach carcasses, killing roaches before laying eggs on their carcasses, laying eggs on other hosts? We do not know. I hope someone is working on those questions as we speak and will soon surprise us with a publication.

But let me finish with a witty comment on Zimmer’s blog, by a commenter who, for this occasion, identified as “Kafka”:

“I had a dream that I was a cockroach, and that wasp Ann Coulter stuck me with her stinger, zombified my brain, led me by pulling my antenna into her nest at Fox News, and laid her Neocon eggs on me. Soon a fresh baby College Republican hatched out, burrowed into my body, and devoured me from the inside. Ann Coulter’s designs may be intelligent, but she’s one cruel god.”

That post on The Loom attracted tons of comments. Unfortunately, most of them had nothing to do with the cockroaches and wasps – Carl’s blog, naturally, attracts a lot of Creationists so much of the thread is a debate over IDC. However, Carl is happy to report that a grad student who actually worked on this wasp/cockroach pair, appeared in the thread and left a comment that, among else, answers several of the behavioral and evolutionary questions that I asked in this post.

You can watch some movies linked here and here.

Cicadas, or how I Am Such A Scientist, or a demonstration of good editing

Originally published on May 16th, 2011 at my old blog.

Charles Q. Choi runs a bi-weekly series on the Guest Blog over at Scientific American – Too Hard for Science? In these posts, he asks scientists about experiments that cannot be or should not be done, for a variety of reasons, though it would be fun and informative it such experiments could get done.

For one of his posts, he interviewed me. What I came up with, inspired by the emergence of periodic cicadas in my neighborhood, was a traditional circadian experiment applied to a much longer cycle of 13 or 17 years.

Fortunately for me, Charles is a good editor. He took my long rant and turned it into a really nice blog post. Read his elegant version here – Too Hard for Science? Bora Zivkovic–Centuries to Solve the Secrets of Cicadas.

Now compare that to the original text I sent him, posted right here:

The scientist: Bora Zivkovic, Blog Editor at Scientific American and a chronobiologist.

The idea: Everything in living organisms cycles. Some processes repeat in miliseconds, others in seconds, minutes or hours, yet others in days, months or years. Biological cycles that are most studied and best understood by science are those that repeat approximately once a day – circadian rhythms.

One of the reasons why daily rhythms are best understood is that pioneers of the field came up with a metaphor of the ‘biological clock‘ which, in turn, prompted them to adapt oscillator theory (the stuff you learned in school about the pendulum) from physics to biology.

And while the clock metaphor sometimes breaks down, it has been a surprisingly useful and powerful idea in this line of research. Circadian researchers came up with all sorts of experimental protocols to study how daily rhythms get entrained (synchronized) to the environmental cycles (usually light-dark cycles of day and night), and how organisms use their internal clocks to measure other relevant environmental parameters, especially the changes in daylength (photoperiod) – information they use to precisely measure the time of year and thus migrate, molt or mate during an appropriate season.

These kinds of experiments – for example building Phase-Response Curves to a variety of environmental cues, or a variety of tests for photoperiodism (night-break protocol, skeleton photoperiods, resonance cycles, T-cycles, Nanda-Hamner protocol etc.) – take a long time to perform.

Each data point requires several weeks: measuring period and phase of the oscillation before and after the pulse (or a series of pulses) of an environmental cue in order to see how application of that cue at a particular phase of the cycle affects the biological rhythm (or the outcome of measuring daylength, e.g., reproductive response). It requires many data points, gathered from many individual organisms.

And all along the organisms need to be kept in constant conditions: not even the slightest fluctuations in light (usually constant darkness), temperature, air pressure, etc. are allowed.

It is not surprising that these kinds of experiments, though sometimes applied to shorter cycles (e.g., miliseconds-long brain cycles), are rarely applied to biological rhythms that are longer than a day, e.g., rhythms that evolved as adaptations to tidal, lunar and annual environmental cycles. It would take longer to do than a usual, five-year period of a grant, and some experiments may last an entire researcher’s career. Which is one of the reasons we know so little about these biological rhythms.


Living out in the country, in the South, just outside Chapel Hill, NC, every day I open the door I hear the deafening and ominous-sounding noise (often described as “horror movie soundtrack) coming from the woods surrounding the neighborhood. The cicadas have emerged! The 13-year periodic cicadas, that is. Brood XIX.

I was not paying attention ahead of time, so I did not know they were slated to appear this year in my neck of the woods. One morning last week, I saw a cicada on the back porch and noticed red eyes! A rule of thumb that is easy to remember: green eyes = annual cicadas, red eyes = periodic cicadas. I got excited! I was waiting for this all my life!

Fortunately, once they emerge, cicadas are out for a few weeks, so my busy travel schedule did not prevent me from going to find them (just follow the sound) to take a few pictures and short videos.

There are three species of periodic cicadas that emerge every 17 years – Magicicada septendecim, Magicicada cassini and Magicicada septendecula. Each of these species has a ‘sister species’ that emerges every 13 years: M.tredecim, M. tredecassini and M.tredecula. A newer species split produced another 13-year species: Magicicada neotredecim. The species differ in morphology and color, while the 13 and 17-year pairs of sister species are essentially indistinguishable from each other. M.tredecim and M.neotredecim, since they appear at the same time and place, differ in the pitch of their songs: M.neotredecim sings a higher tone.

So, how do they count to 13 or 17?

While under ground, they undergo metamorphosis four times and thus go through five larval instars. The 13 and 17-year cicadas only differ in the duration of the fifth instar. They emerge simultaneously, live as adults for a few weeks, climb up the trees, sing, mate, lay eggs and die.

When the eggs hatch, the newly emerged larvae fall from the trees to the ground, dig themselves deeper down, latch onto the tree roots to feed on the sap, and wait another 13 or 17 years to emerge again.

There are a number of hypotheses (and speculations) why periodic cicadas emerge every 13 or 17 years, including some that home in on the fact that these two numbers are prime numbers (pdf).

Perhaps that is a way to fool predators which cannot evolve the same periodicity (but predators are there anyway, and will gladly gorge on these defenseless insects when they appear, whenever that is, even though it may not be so good for them). Perhaps this is a speciation mechanism, lowering the risk of hybridization between recently split sister species?

Or perhaps that is all just crude adaptationist thinking and the strangeness of the prime-number cycles is in the eye of the beholder – the humans! After all, if an insect shows up every year, it is not very exciting. Numerous species of annual cicadas do that every year and it seems to be a perfectly adaptive strategy for them. But if an insect, especially one that is so large, noisy and numerous, shows up very rarely, this is an event that will get your attention.

Perhaps our fascination with them is due to their geographic distribution. Annual cicadas may also have very long developmental times, but all of their broods are in one place, thus the insects show up every year. In periodic cicadas, different broods appear in different parts of the country, which makes their appearance rare and unusual in each geographic spot.

In any case, I am more interested in the precision of their timing than in potential adaptive explanations for it. How do they get to be so exact? Is this just a by-product of their developmental biology? Is 13 or 17 years just a simple addition of the duration of five larval stages?

Or should we consider this cycle to be an output of a “clock” (or “calendar”) of sorts? Or perhaps a result of interactions between two or more biological timepieces, similarly to photoperiodism? In which case, we should use the experimental protocols from circadian research and apply them to cicada cycles.

Finally, it is possible that a ling developmental cycle is driven by one timing mechanism, but the synchronization of emergence in the last year is driven by another, perhaps some kind of clock that may be sensitive to sound made by other insects of the same species as they start digging their way up to the surface.
The problem: In order to apply the standard experiments (like construction of a Phase-Response Curve, or T-cycles), we need to bring the cicadas into the lab. And that is really difficult to do. Husbandry has been a big problem for research on these insect, which is why almost all of it was done out in the field.

When kept in the lab, the only way to feed them is to provide them with the trees so they can drink the sap from the roots. This makes it impossible to keep them in constant conditions – trees require light and will have their own rhythms that the cicadas can potentially pick up, as timing cues, from the sap. So, the first thing we need to do is figure out a way to feed them artificially, without reliance on living trees for food.

Also, we do not know which environmental cues are relevant. Is it light cycle? Photoperiod? Or something cycling in the tree-sap? Or temperature cycles? What are the roles of developmental hormones like Juvenile Hormone or Ecdysone? We would have to test all of them simultaneously, hoping that at least one of them turns out to be the correct one.

Second, more obvious problem, is time. These experiments would last hundreds of years, perhaps thousands! Some experiments rely on outcomes of previous experiments for the proper design. Who would do them? What funding agency would finance them? Why would anyone start such experiments while knowing full well that the results would not be known within one’s lifetime? Isn’t this too tantalizing for a scientist’s curiosity?

The solution? One obvious solution is to figure out ways to get to the same answers in shorter time-frames. Perhaps by sequencing the genome and figuring out what each gene does (perhaps by looking at equivalents in other species, like fruitflies, or inserting them into Drosophila and observing their effects), hoping to find out the way timing is regulated. This will probably not answer all our questions, but may be good enough.

Another way is to set aside space and funding for such experiments and place them into an unusual administrative framework – a longitudinal study guided by an organization, not a single researcher getting a grant to do this in his or her lab. This way the work will probably get done, and the papers will get published somewhere around 2835 A.D.


See? How long and complex my text is? Now go back to the post by Charles to see again how nicely he edited the story.

Diversity of insect circadian clocks – the story of the Monarch butterfly

As the Monarch butterflies are passing through New York right now, I thought this would be a good time to republish my old January 2006 post about this butterfly (see also 2008 version):

There are pros and cons to the prevalent use of just a dozen or so species as standard laboratory models. On one hand, when a large chunk of the scientific community focuses its energies on a single animal, techniques get standardized, suppliers produce affordable equipment and reagents, experiments are more likely to get replicated by other labs, it is much easier to get funding, and the result is speedy increase in knowledge.

On the other hand, there are drawbacks. One is the narrow focus which can breed arrogance. The worst offenders are people who work with rats. They rarely put the word “rat” in the title of the paper, and often it is not even found in the abstract, introduction and discussion of the paper. One has to dig through the materials and methods to find out, although if you know about this little secret, the very fact that the species is not noted in the title is a dead giveaway that it is a paper about rats. Some of the papers dealing with humans also make the same mistake of not pointing out the species in the title.

One of the most important animal laboratory models for the study of genetics and molecular biology is the wine-fly Drosophila melanogaster. For a century now, almost all advances in knowledge in these areas came from fly research first, then this knowledge got applied to other species, e.g., mice and humans.

Last month (December 2005), a paper came out that highlights both the pros and the cons of the “model” approach. On one hand, all the techniques used in the work were developed by fruitfly researchers and are now standard methods, easily replicable between labs.

On the other hand, it shows how important it is to sometimes move away from the models and take a reality check: is the mechanism described in the model animal generalizable to other animals or is it idiosyncratic to the model. The papers dealing with models, including wine-flies (and of course rats!), often make the implicit claim for generalizibility (helps funding!) without data to support this claim.

The model of the molecular mechanism of the circadian clock has been initially developed in Drosophila melanogaster and massive research is still going on in this animal. It is regarded as a reference model in a way – models developed later in mice, bread-mold, Arabidopsis plant, Synechococcus bacterium, etc, are always compared to the fruitfly model to look for similarities and differences. In a sense, it is the ‘deafult’ model in chronobiology.

This paper took a look at a non-model animal and found out that the fruitfly mechanism does not appear to be even typical of other insects. Steven Reppert and colleages at the University of Massachusets Medical School are studying circadian system in Monarch butterflies (mainly in order to better understand migratory orientation).

In this paper they discover that the Monarch, unlike the fruitfly, has two copies of a clock gene called Cryptochrome (cry). One copy (cry1) is very similar to that of Drosophila. The other copy (cry2), however, is much more similar to the mouse version of the gene.

In the brain pacemakers of fruitflies, cry is not the core component of the clock but is a blue-light photoreceptor. In the peripheral tissues, the same gene may be a component of the clock (it represses expression of some other clock genes).

In mammals, cry is not directly photosensitive, but is a core clock gene and a strong repressor of expression of other clock genes.

In Monarchs, as they show in this paper, cry1 is responsive to light, just like the cry of fruitflies. The cry2, though, does not respond to light, but represses expression of other genes, just like the mouse cry.

The best thing about this paper, though, is that the authors then went on and looked into genebanks of several other insect species and, lo and behold, discovered cry2 in a few more insects, including moths, honeybees, mosquitoes and flour beetles. Actually, the honeybees and flour beetles appear to have ONLY the mammalian-like version of the gene.

They also plotted the phylogeny of the cry gene, showing the genealogical relationship between the fruitfly-like and mouse-like versions of cry, both versions presumably resulting from a gene duplication some time in the past (the apparent precursor, bacterial photolyase, appears as only one copy in E.coli and its function is in DNA repair).

The PERIOD protein does not enter the nucleus in the Chinese silkmoth and the Monarch butterfly. Thus, at least in these two insects, the molecular mechanism of the circadian clock must be different from that of the fruitfly. Presence of the mammalian-like version of the cry gene, a potent gene repressor, suggests that it may be fulfilling the function of Per in these species. Thus, there appears to be more than one way to run a clock in an insect and the fruitfly mechanism is not as ‘standard’ at previously thought.

And working with Monarch butterflies must be great fun!


Haisun Zhu,1 Quan Yuan,1 Oren Froy, Amy Casselman, and Steven M. Reppert, 2005, The two CRYs of the butterfly.Current Biology, Vol 15, R953-R954, 6 December 2005.


What does it mean that a nation is ‘Unscientific’?

I first wrote and published this blog post on December 22, 2009. I thought I’d re-publish it here, on the new blog, in light of the recent discussion on the network about scientists communicating to the public (see Social Media for Scientists Part 1: It’s Our Job, Social Media for Scientists Part 2: You Do Have Time., Science communication? I wish it were that easy…, On Naïveté Among Scientists Who Wish to Communicate and Social Media for Scientists Part 2.5: Breaking Stereotypes). It’s long, so take your time, perhaps print it out or save on Instapaper if you have difficulty reading it all on screen.

If a publisher offered me a contract to write a book under a title that would be something like “Unscientific America”, how would I go about it?

I would definitely be SUCH a scientist! But, being such a scientist does not mean indulging in Sesquipedalian Obscurantism.

Being such a scientist means being dilligent, thorough and systematic in one’s reasearch. And then being excited about presenting the findings, while being honest about the degree of confidence one can have in each piece of information.

I was not offered a book contract, and I do not have the resources and nine or twelve months to write such a book. But in the next couple of hours days I will write a blog post (this one, I am just starting) thinking through the methodology I would use for such a project, musing about difficulties, jotting down notes and – this being a blog – asking readers for links to information that can either reinforce or challenge my hypotheses. So please follow me under the fold…..

Reasons and Goals and Target Audience

Why write such a book? What is the reason a publisher would want to invest in it? What’s the point?

I assume that the motivation comes from seeing a distressing world in which Global Warming Denialists, anti-vaccination mobs, Creationists, Animal Rights activists, opponents of genetically-modified food, and other anti-science forces are having far too much effect – most definitely a negative, potentially disastrous effect – on local, national and international policies. The book should be an exploration for the causes of such a situation and then should derive the possible remedies from the identified causes.

The authors of Unscientific America, Am I Making Myself Clear? and Don’t Be Such a Scientist are pretty explicit about the target audience for their books being scientists.

This implies (and the content of all three books supports this implication) that reaching the goal is in the hands of scientists ONLY (and implicitly out of jurisdiction of anyone else). But this implication should not be a starting point of the book. It is one of the several possible alternative hypotheses that the books should be testing, and the results of the investigation may or may not lead to accepting this result. Work needs to be done first.

Thus I would do the research first and only in the end, once I come to some conclusions, would I decide who is the most appropriate target audience, i.e., which groups of people have potentially the greatest power to effect change in a positive direction. Then I’d write a book specifically for them.

Definitions of Terms

For a longer piece of writing, like a book, it is essential to precisely define the key terms in the beginning and then to stick to those definitions throughout. Doing this prevents one from falling into a trap of shifting one’s working definitions from chapter to chapter because it’s easier (e.g., there is more information out there to discuss).

The key term for this project is the word “unscientific” (and its opposite “scientific”). How would I define it in the light of the Reasons And Goals I outlined above?

There are several candidate definitions that people explicitly or implicitly use in books, papers or blog posts on the topic. Let’s take a look.

1) An unscientific nation is one in which most citizens do not do well on tests of scientific facts.
2) An unscientific nation is one in which most citizens do not understand the Scientific Method and the way scientists really work.
3) An unscientific nation is one in which most citizens do not have trust in scientists, physicians and scientific institutions.

All three of these definitions are important and potentially useful for different projects. But are they useful for this particular project?

I’d say No. Why? Because the Reasons And Goals of the project are to figure out why some nations do not base policy on science. These three definitions focus on, I think, the wrong population: all citizens. And thus they are likely to come up with wrong solutions (better science education, better science popularization/communication, etc.). But it is not all citizens who enact policies. It is their governments who do so. So, for the purposes of my project, I would use a definition somewhat like this:

4) An unscientific nation is one in which the government is not Reality Based.

While it is unfortunate that countries are decision-makers on global policies, that is the reality right now and we need to work within a reality framework. There are also many other science-related policies that are not necessarily global but affect the lives, health and productivity of the citizens of an individual country, so the nation (aka it’s government) is, for now, the appropriate place to focus on.

And the project should also study the way the definitions 1 through 3 relate to Definition 4. And thus explore how other sub-populations outside the government (including, among others, working scientists), can influence the governmental policies.

Once decided on the working definition, I’d write it on a Post-It note and stick it on my monitor, always being reminded of it, not allowing myself to switch to any seductive alternatives.


Governments are groups of people. Writing laws and enacting policies (and all the politicking and decision-making and horse-trading that goes into it) are behaviors of people. Thus I would study the behavior of governments using the demonstrably best framework for the study of any behavior – Niko Tinbergen’s Four Questions (PDF).

To refresh your memory, Tinbergen’s four questions are:

1) Mechanism:
– defining the behavior
– describing the behavior
– describing the underlying mechanisms of behavior at all levels of organization from molecules to neurons to organ systems to organisms to populations.

2) Ontogeny
– development of the behavior
– timing (during one’s lifetime or daily/seasonal) of behavior
– is the behavior instinctive or due to learning

3) History
– how and from what precursors did the behavior evolve
– was the behavior directly selected for or a by-product of selection for something else or a more-or-less random effect of genetic drift
– what kinds of environments have, in the past, resulted in the appearance of the behavior

4) Function
– is the behavior adaptive, maladaptive or neutral
– are there situations in which an adaptive behavior becomes maladaptive

Behavior of policy-making governments is a little bit different from the behavior of seagulls and sicklebacks, so I would have to rephrase some of these ideas somewhat, while keeping true to the spirit of the Four Questions.

The first two (mechanism and ontogeny) are also known as Proximate Causes, asking the How questions. The latter two (History and Function) are known as Ultimate Causes, asking the Why questions. Those who have studied the history of Behavioral Biology know that research projects based on Tinbergen’s framework are necessarily Integrative (asking the question from many angles at many levels of organization) and Comparative (asking the question from many related species).

Making an exciting finding in Drosophila melanogaster is not an answer to a basic biological question – it is a hypothesis that can only be tested by doing the same research in a bunch of other species. This can tell us if the finding is generalizable (thus fundamental) or is it just a quirk of Drosophila melanogaster.

Likewise, study of only one nation, e.g., United States, is not sufficient. Only a comparison with other nations can tell us if the analysis of the American situation is insightful for studying the question of “national unscientificness” or if it is just a unique quirk of this country alone.


Let’s start with the definition again: “An unscientific nation is one in which the government is not Reality Based.”

What does that mean? How does such a government operate?

An unscientific government is one that does not tackle the world as it is, but through wishful thinking and ideology. It is impervious to logic, uninterested in data and does not keep empirical knowledge in any regard. It prefers decisions made “from the gut” to those made by studying the world with one’s brain and devising realistic policies meant to fix real problems. It is essentially posturing (to voters, for example, as needed for re-election, or to political opponents, or to leaders of other countries) coupled with treating one’s own emotional problems (often related to power and a hierarchical view of the world). It usually but not always operates independently of any outside influences (voters, academics, media, etc.) because it can.

The flip side is a Scientific government. It is not necessarily scientistic or technocratic, just Reality Based. It attempts to figure out as best it can how the world really works, what is the real source of the problem, and what policy is most likely to fix the problem. Often this process entails getting information from experts on the way the world really works, which are often scientists. They will get the most reliable information, build the most realistic models, and figure out actions that are most likely to result in the solution to the problem. Such a government would not always follow exactly what scientists suggest – they are elected to their best in governing a country, so they will have to take into account other considerations, e.g., political consideration (can we sell this to voters), economic consideration (can we afford to do this) and foreign policy consideration (will we make some countries enemies if we do this). Thus art of the compromise comes in, but it is based on reality – it is not an ideological compromise.

And such a government does not just consult science, but acts like a scientist in a sense. A new law or regulation is not writ in stone, but is regarded as an experiment. Once enacted, the new policy is continuously monitored and measured for effectiveness and if necessary modified, replaced or removed.


Let’s start with the definition again: “An unscientific nation is one in which the government is not Reality Based.”

How does a country get a government like this? How does a country get any kind of government? It can happen slowly (election, of succession of royalty), or abruptly (a coup or revolution or outside invasion).

Or, to be more precise, how does a country get its policies made?

What is really essential to bear in mind is the level of independence of the government – how much are they forced to listen to the voice of the people. An Emperor or King or Generalissimus does not need to listen to the people. He can make any laws or policies he wants. Some such dictators make it very clear that the punishment for even the mildest dissent will be painful (see Ceausescu for a historical example). Others are much better at using the power of the state, including the schools and the media, to get the population to love them and thus willingly support everything they do (see Tito for a historical example).

On the other extreme of the spectrum are countries in which elections are frequent and the voters have the power to remove one from the government pretty swiftly – the countries with perpetual ‘campaign mode’ in politics.

And there is an entire continuum in-between.

So we have two main players here: the government and the population it governs.

We have four possible combinations of ‘scientificness’ of the two players: scientific government + unscientific voters, scientific government + scientific voters, unscientific government + unscientific voters and unscientific government + scientific voters. In which ‘scientificness’ is used in the sense of “Reality-Based” for the government and in the sense of Definition 3 (trust in scientists and scientific institutions) for the voters.

And then we have the long spectrum of the influence of the population on the government ranging from zero to all.

If both the government and the voters are scientific, it does not matter how much the government has to listen to the voters – it will do the right thing.

If both the government and the voters are unscientific, it also does not matter how much the government has to listen to the voters – it will do the wrong thing anyway.

But if the government is scientific and voters are not, then it takes an independent, courageouos or strong government to do the right thing despite the will of the people.

And if the government is unscientific but voters are scientific, it takes a tentative, voter-dependent government in perpetual ‘campaign mode’ to be persuaded to do the right thing despite their own instincts and beliefs.

OK, this is a simple, two-element model. It is a scaffolding on which to build more complex yet more realistic models. Of course there are other players involved, those who can push either the government or the people in the direction of greater or lesser ‘scientificness’:

Industry – often new scientific data suggest that the industry needs to change the way it does its business, e.g., to reduce negative environmental impact, or to reduce negative health effects on their employees or customers. In a country in which the economic and financial systems are set up in a way that rewards only short-term profits (or worse, rely on bad proxy numbers like the value of stocks in the stock market which is, remember, the market of second-hand stocks traded by others, not by companies themselves), then the industry will have to resist Reality-Based solutions and will try to affect the governmental policies in that direction.

They can do that via lobbyists in some countries, or more directly (during a golf game with their buddies in the government) in other places. Or they can try indirectly – trying to persuade the people (if the people are deemed influential in that country) directly or via influence on the media (during a golf-game with the star TV pundit, or by building a PR machine – read that link!!!).

In other countries, though, the particular industry may be government-run, or may be persuadable by people or the media to quickly adopt science-based solutions without risking much in the market-place. It all depends on the way the economy is set up.

National Academy of Sciences and other scientific institutions (or even individual scientists) will have a much greater voice in the the policy-making process in some countries than in others. Where not having direct influence on the government, they may try to work indirectly, persuading the people via media or other venues.

Media is another important player here. It has the power to influence the voters, and also has the power to influence the industry leaders and the governments. How? The government thinks that the media presents the view of the people. The people think that the media presents the view of the government. The latter are, in many countries (most notably in the USA) correct. The media writes what it thinks the government thinks. And government reads the media to find out what the people think yet only finds the reflection of itself and is satisfied to find the will of the people so wonderfully aligned with their own. Add some PR machinery or direct money from the industry to the leaders of the media, and their interests miraculously become the “voice of the people” that the government will be happy to go along with. This is a short and condensed version of an important argument, to which I will return a little later (if you have the patience to read this post to the very end).

Religious organizations are a very powerful lobby in some countries, often, but not always, on the anti-science side of things.

So, it is a model with a number of players and in each country the power-dynamics between them are different: who can persuade whom, the final executor of the resulting decision of all these players being the national government which then, in cases like Climate Change or global pandemics, has to enter a higher-level field, negotiating with other governments which all have different kinds and intensities of fire aimed at their toes at home.

To summarize: the development and enactment (“ontogeny”) of policy decisions depends on relative power of various players, the key player being the government. The ‘relative power’, or ‘independence’ means ability to influence or overpower other players while at the same time being immune to the influence by the other players.


Let’s start with the definition again: “An unscientific nation is one in which the government is not Reality Based.”

So, if the ontogeny of each policy decision is dependent on the relative power and relative ‘scientificness’ of all the involved players, how does such a system, with those particular power-relations evolve, i.e., come to be over time? What kinds of events, or actions (by whom?), produce change in the system?

Who gets to be in the government? Who gets to be an industry leader? Who gets to be a talking head on TV? What are their backgrounds? Ideologies? Do they get better science education than the rest of the population or is the educational system equal for everyone?

Education – not just science education, but more importantly education that fosters critical thinking and openness to new ideas, is an important factor in developing ‘scientificness’ (in the sense of being Reality Based) in different segments of the society. Is there such an educational system in a particular nation? For all or just for the the chosen few (rich and powerful)?

Education is important, but not a be-all and end-all of it. After all, people have received PhDs in geology or evolutionary biology and still remained Creationists.

Ideological and religious background can trump all education, through mental filters of various kinds.

Does knowing scientific facts make one more likely to be Reality Based? Perhaps a little, but is it enough to spread through the population and lead to a strong pro-science voice?

Does understanding the Scientific Method make one Reality Based? Perhaps a little, but is it enough to spread through the population and lead to a strong pro-science voice?

Can the school have any effect on the level of trust one has in scientists and scientific institutions? Probably very little….

How much critical-thinking and scientific education of the population actually translates into reality-based policies enacted by their government is something that needs to be studied. I expect that this will differ between countries and will, in the end, not make much of a difference.

After all, tests of scientific trivia across many countries do not show great differences between countries (the results are pretty bad everywhere), yet the scientificness of their governments’ policies vary hugely.

Keep reading, I’ll explain why I think that a little later….

It is in the answering the History question (of the Tinbergen’s four questions) that the Comparative Method really comes to the fore. By studying a behavior across many species one can figure out if the behavior, wherever it occurs, is the result of evolutionary history going back deep in time, tracing back to some ancient ancestor of all the studied species. That behavior is than retained in all extanct species because it either remains adaptive or because, even though not very useful any more, it is not maladaptive enough to be selected against. And if it does disappear from some lineages, we can ask what environmental forces led to their disapperance (selection against it or random event). On the other hand, we can figure out if the behavior emerges independently, over and over again, in every species that finds itself in a particular environment – that tells us something not just about history but also about Function of that behavior.

So, focusing here only on the ‘scientificness’ of the United States is blind. One has to analyze a number of other countries, their current policies, their histories and how they got to where they are now. This is a big project, but I am sure that researchers in other nations have done studies of their own homelands and published their findings.

It’s just that we here in the US tend not to pay attention to those.

I do not assert that I have any expertise on the matter, but I can provide anecdotally a view from one other country as an illustration, and perhaps as a motivation to others to conduct relevant studies in various countries and then do head-to-head comparisons.

I grew up in Yugoslavia. It is several countries now, but culturally they are all similar so for the sake of this argument, I can pretty much use Yugoslavia and Serbia interchangeably in this example.

It was a country where garbage was on the streets. Black smoke was proudly emanating from the factory smoke-stacks. The patriarchal machismo saw Nature as something to be exploited and conquered.

I went to Serbia a few months ago. Belgrade is spotlessly clean and beautiful. What happened in the elapsed time?

First, there was a switch from socialism (though a strange, market-based socialism) to capitalism. Brand-new, still unregulated capitalism to which people are not used to (and don’t yet know how to play the game, or feel that it is not even ethical to try playing that game) breeds insecurity, which inflames nationalism and empowers religion.

Second, there was a decade of wars, and sanctions, and anti-government demonstrations not noticed by the West, and being a pariah, and being presented as criminals in the international press, and being a bargaining tool between the superpowers. And then getting bombed at the end of it all. And then the internal political fights and sending Milosevic to The Hague. With all that pounding over so many years, all the machismo is gone.

Look at these two guys:

They live in Eastern Serbia. The first thing they asked me when I got off the bus in their town (Milosevic’s hometown) was “are you one of those communists?”. I had to think fast: what communists – 19th century Marxists, Tito-era communists, Milosevic-style communists, current powerless/marginalized Communist party? Then I smiled – I realized they used the word “communist” as a synonym for “government”. I could say I was not and be true to it. They are anti-government royalists! They support the church not because they are very religious, but because it is the only institution that really cares about national pride of Serbs. They want a King not because they love the guy so much but because they cannot stomach the insecurity that comes with frequent changes in the government that naturally flow from having regular democratic elections. They crave stability (who could blame them after the crazy 1990s!), hopefully headed by an iron-fisted ruler who will sit in his palace, looking beautiful in his kingly dress, for decades without change.

If they lived in the USA they would be extreme Right, perhaps teabaggers. And totally anti-science on every issue from Climate Change to Creationism. A perfect example, seen in every country in the world, of the tension between city and country (that leads to so many wars!).

Yet, they are actually scientists. Furthermore, they are die-hard environmentalists. They do research on how to recycle some nasty industrial byproducts. And they made it their lives’ main goal to teach kids to think like environmentalists, with several projects involving local schools. For them, being an environmentalist and making and keeping Serbia clean and not contributing to global warming is a matter of national pride.

I am still kicking myself in the butt for forgetting my camera one day in Belgrade when I encountered a garbage can that had an inscription, in black marker (obviously written by a neighbor) appealing to national pride. It said something along the lines of “If you are a true Serb, you will not put recyclables in this trash can – the recycling container is in the back yard”.

Edit, October 6th, 2011: Bothered by this omission, when I visited Belgrade again two years later, and almost two years since I wrote this post, I made a point of going again to that part of town, walking up that street, finding that house, entering the hallway and taking the pictures – it says “Brothers Serbs!!!, do not throw trash bags and bottles into this can”:

Somebody, at some point over the past decade, had a great idea to harness national pride in the pursuit of environmental goals, devised a PR campaign towards that goal – and succeeded. I will have to figure out how that exactly happened. If I figure it out, I promise to blog about it.

Nikola Tesla being a Serb is a matter of national pride. The results of scientific research from nuclear physics to maize genetics are a matter of national pride. Petnica is a matter of national pride (which explained why the defunding of it was vigorously and successfully fought by the people). Being an intellectual, a prolific reader, and someone who can discuss Selfish Gene at the bar are matters of national pride. Serbs are supposed to be smart and educated. None of that anti-intellectualism stuff – we are Europeans with a long intellectual and scientific tradition.

Does it mean people are actually well educated in science? I am not sure what is the state of science education right now, but when I was in school there was TONS of science in the classroom – but taught as factoids. By the time I graduated high school I had behind me eight years of physics, eight years of chemistry, eight years of biology (also a year each of ecology, microbiology, molecular biology, botany and zoology due to my occupational tracking), eight years of geography (including basics of cosmology, geology, meteorology and oceanography), and twelve years of math. But we barely had any labs. And we never really tackled Scientific Method much. And we did not have it presented in any kind of historical or philosophical context. We did learn detailed biographies of Darwin and Tesla and Pupin and Milankovich and Pancich, but in a hero-mode of history. So, yes, we learned a lot of facts, and we learned to admire a few scientific geniuses (especially if they were from our homeland), but we did not really learn any critical thinking skills from it.

Thus, Serbs can talk at length about science, yet not always be critical about it. They fall oh-so-easily for scientific-sounding gibberish, from astrology to medical quackery, despite having a huge repository of science-trivia knowledge typical of Eastern European educational systems. They reject Creationism because Darwin is a hero and believing in evolution is a mark of an educated European (likewise for Climate Change – it is what educated people are supposed to understand and support, not fight against like the Troglodytes do), but they are not really able (like citizens of any country, really) to be fully skeptical of pseudoscientific ideas that sound scientific on the surface.

There are currently strong voices against getting vaccinated for swine flu. But the reasons are different than in the USA. The typical Jenny McCarthy autism-vaccine quasi-connection is not strong there. They reject the vaccine because it comes from the West. And West is always suspect. What is the Western interest in selling us the vaccines? Are they trying to poison us? Is it warfare? The scars are too fresh.

But then Dr.Kon comes on TV and tells them to get vaccinated and why they should do so. And they believe him (well, he is on TV all the time!). He is a premier authority on epidemiology there. And scientists there have authority. And they are trusted. Thus when the government wants to enact policies that are Reality Based and require the people to change their habits (as in many environmental issues), the government invites academics to speak and uses those academics as authorities they rely on for enacting such policies.

Last time I was there, I watched a long (2 hours long) show on TV that everyone was glued to. About swine flu and vaccines. Who was in the studio? Dr.Kon. And a few other physicians. And a bunch of medical students. The only person in the studio who was obviously uneducated and dumb was the moderator from the TV station (I later heard, from one of the participants, that she was even drinking during the breaks). No politicians. No representatives of politically-motivated nay-saying groups. Facts only wanted, thus experts only. And it was still a contentious and occasionally downright aggressive debate – experts debating fine points of timing of vaccines, how many, which kind of vaccine, who should get it first, etc.

And that kind of show is not unique there. Scientists, physicians, academics are often in the media, revered and trusted as relevant sources of expertise on the information how the world really works and what are the most likely actions that can potentially solve a problem. There have always been science and nature shows on TV and nobody ever thought that watering down the language was needed – the audience understood, or understood enough. And was fascinated. And believed it all. And loved it. And kept the love and reverence for science for the rest of their lives.

In a nation in which it is perfectly normal that the local drunk sitting at the bar is reading Feynman while drowning sorrow in slivovitz, where bookstores are full of books about science and nature (and philosophy! – it’s big there), where the media is full of science and reveres scientists (while the anti-science cranks are mostly ignored, never invited, or laughed at), where the government takes the academics’ word as law – is it surprising that people trust scientists and encourage the government to enact science-based solutions to problems even if they don’t truly understand them?

Both this year and last year when I visited Belgrade I gave multiple radio interviews (a few of those were hour-long) and a brief TV interview (where I met ubiqutous Dr.Kon who was also on the same show right after me). Thus I had a chance to chat with a lot of media people there and discuss the state of the media and journalism in today’s world.

Of course, as people everywhere are wont to do, they complained about the state of Serbian media. Did they forget the state it was in during Milosevic era? I tried to tell them how for me, looking from the outside, it looked perfectly good. I watched the TV there and noticed that TV anchors called a spade a spade and were very well informed about the issues they were talking about.

For example, back in 2008 there were many TV debates ahead of the elections. The anchor would not ask “Can you explain your economic plan?” in an open-ended manner, let the candidate trot our talking points and then, like Wolf Blitzer, say Let’s leave it there. They would say something like this “When one runs the math on your economic proposal, one finds out that it would lead to X number of jobs lost, X billion in lost revenue, X billion in budget deficit, and X percent of inflation. How can you propose such a destructive plan?”. When the candidate tries to weasel out, the anchor turnes to the opposing candidate and says “What do you think?” and gives him 30 minutes to actually DO the math on air, totally destroying the bad proposal, leaving the opponent to fume and the audience to laugh. Then she turns to that other candidate and does the same grill on him. One with a more reasonable plan that survives the math and on-air dissection wins. And probably wins the election. How it should be done. And – even when it comes to economics – Reality rules the day. Facts. Numbers. Logic.

So I would tell my media friends about it and say that is so much better than the US media. To which they laughed – “What US media? US does not have media!”. And then they would explain to me how in the US there may be something that superficially looks like media because it uses the same technological channels – the technology of TV, radio and newspapers. But that what goes through those channels has no resemblance to journalism. It is a combination of entertainment (bread and circuses for the masses) and propaganda for whichever President’s strings are currently being pulled by the military-industrial complex.


I guess looking from the outside, one is able to see more clearly….

From their point of view, US foreign policy is what matters. From that point of view there is not much difference between Republicans and Democrats – they are both involved in the American imperialist project (oops, “American interests abroad”). Remember that Bush Sr. screwed up the region at the time when it could still be saved, and that then Clintonistas came in, ignorant of the local history, geography and politics and did every single thing wrong there, prolonging the war by years resulting in many more dead, wounded and displaced, and ending up bombing Belgrade, while at the same time frustrating the opposition that was trying to get rid of Milosevic and could have done so years earlier if the Democratic U.S. president did not keep interfering. So, differences in domestic policy do not really matter for foreign observers. I guess Serbs were still hopeful, until this week, that at least Obama would be more reliable on Global Warming. Eh. But from their point of view, and rightly so, there is no real media in the US, at least not media that is visible by many Americans and potentially visible to foreigners if one searches really hard.

To summarize, Serbia has a population that possesses a lot of knowledge of science trivia, an honest interest in science, has no idea how science works, has no skeptical skills, yet reveres science and trusts scientists. It is a matter of national pride. And is not aligned with any particular ideology or political party. And it is something that is mirrored by and perpetuated, however imperfectly, by schools, media and government. Thus, despite the population being either scientific or unscientific, depending on which definition one uses (yes on being scientific if using definition #1, no if #2, yes if #3), the country as an entity that really matters here (definition #4) is a Reality-Based one and can easily be so as it is in sync with the voters and the media on this account. And can be so no matter which party is in power there. Most of the parties there (at least serious ones that have a chance of getting elected to govern) are Reality Based enough at least to know they cannot ignore science and reality with impunity.

I am sure my American readers have already done the comparative study in their minds while reading the case of Serbia above. And probably readers from other countries as well. Put your thoughts in the comments, please, so we can all learn more.


Let’s start with the definition again: “An unscientific nation is one in which the government is not Reality Based.”

First question here is: is having a Reality Based government adaptive for the country? Does it do better than if it was not Reality Based?

Ahm. Look at the USA. Reagan years (trickle-down economics), plus Bush Sr. years (voodoo economics), plus Clintonite conservative triangulation followed by devastatingly dangerous Contract On America, and the final nail in the coffin in 2000-2008 with recklessly ideological bullying by the Bush Republicans. It is a testament to natural wealth and the robustness of the US economy that the country still exists and that we are not all literally starving in the streets. Any other country would not be able to survive 30 years of Fairy-Tales-based policy-making and would have been annihilated from within. Yet even America is hurting. Badly. Ask the Afghans and Iraqis.

Ask the tens of millions of poor, unemployed/underemployed and uninsured Americans. Look at the economic numbers. See the environmental devastation we produced.

Policy based on ideology and wishful thinking and “from the gut” is disastrous.

But, just because having a Reality Based government is adaptive does not mean it is a “natural state of things”, thus….

The second question: is the Reality-Based or Unscientific the default state for a nation?

That’s a question that can be thought of in terms of entropy (which of the two extreme states is lower energy, thus easy to attain, while the opposite state requires input of energy) or in terms of an adaptive landscape (which of the two extreme states is on the adaptive peak that requires climbing onto, and which one is in the valley).

In other words, is it natural for a country to be Unscientific and work needs to be done to make it Scientific? Or is it a natural state for a country to be Scientific and work needs to be done to make it Unscientific? This absolutely requires comparative study and a historical study.

If ancient state was Unscientific because there was no science and thus all the nations were originally Unscientific, did some nations become Scientific easily (it’s all downhill so just let it slide) or did it always require a lot of effort? What explains why some nations are still Unscientific, including the USA?

I do not have the answer to that question – it would be a part of the project of book-writing to study the issue and try to come up with an answer. But it is a neccessary question for this project. No prescription can be made without getting an answer to it first.

So, let’s for the sake of the argument assume that the “natural”, low-energy state is somewhere in-between the extreme states. As science progresses and governments want to generally do the best they can for their people, they more and more consult the “experts on reality” i.e., scientists and come up with more and more reality-based solutions.

There will be forces that try to speed up the process. And there will be forces that try to slow down the process. The rate of change will be a resulting vector or the sum of those forces. In each country those forces will have different indentities, strengths and directions, so the rate of movement and the trajectory of movement will be different.

What are some of the likely forces and their relative effectiveness? What factors will influence their effectiveness?

I already talked about Industry above so there’s not much new to say here. If, due to the economic and financial system, they have to pay attention primarily to short-term profits, they will be a force that slows down the process and will use direct line to politicians, or lobbyists, or PR machinery, or will try to
influence the media, whatever it takes to have their way.

Education is an important factor here. How much science is taught? How is it taught? Is the curriculum updated frequently to keep up with the advances of science? Does it teach trivia/facts, or scientific method, or critical thinking, or reverence for hero-scientists? Or does it consist of memorizing some ancient religious book? Who determines the curriculum – a national organization of educational experts, or a locally elected school board composed of who knows who?

While education in itself is no panacea, the populace that is well educated in science will be more receptive to scientific ideas in the media, will not need watering down of language when the science is presented in the media and, indirectly, may be more likely to support governmental initiatives that are demonstrably based on the best current scientific understanding of the world.

Organized Anti-Science Movements are usually allies of, or funded by, political or religious organizations. Thus, they should be treated as such, on a case-by-case basis.

The pseudoscience associated with the political Left is usually fragmented – each with its own organization – and has no influence on the Democratic Party in the USA or on much of public discourse. Chopra-style purveyors of NewAge spiritual woo don’t have any common interests with Animal Rights activists. On the other hand, anti-science movements of the Right are all parts of the same movement, coordinated with each other, and heavily funded by the same conservative network of rich organizations.

Creationists ARE Global Warming Denialists ARE opponents of stem cell research ARE Republican activists and elected officials. Their goal is not just blocking one particular area of science, but a much broader cultural rewinding of the clock. They are the key elements of the Republican party (what is left of it today), not just having an outside influence on it.

Religion tends to be, in most places, a force trying to slow down the progress. But we have to think about this smartly. It is not religion per se, it is religion used as a scaffolding for ideology, an excuse for ideology, and a symbol for rallying the ideological brethren.

Ideology is quite dependent on geography. Liberal ideology tends to thrive in big cities, where diversity of people and their beliefs breeds tolerance, where higher education is abundantly available, and where traveling is something that is done on a regular basis – seeing the world is a great liberalizer. On the other hand, small rural communities tend to be conservative because they are racially, culturally, ideologically and religiously homogeneous. The group cohesion is necessary for daily survival.

Outsiders are potentially disruptive and viewed with suspicion. They are The Other. To be scorned.

So, the more people move from country to city (as industrial revolution engendered) more they become liberalized and more they are likely to embrace reality. Those who stay in the country are more likely to stick to tradition (organized by the local religious institution) and resist disruptive change. If the rural folks perceive a science-based change in policy to be disruptive of their tradition, they will resist it (or, like my Serbian friends above, will embrace it for their own reasons, e.g., national pride).

So the city/country ratio of the country is an important determinant of the potential for a change towards scientificness of the government. Also, the relative voice that city and country have will be a factor. In countries, like USA, in which rural states and counties have disproportionately large representation in Congress, their negative influence on the movement towards Reality Based governance will be greater. In other countries, the intelligentsia that lives in the capital drives the policy and the rural areas are ignored.

Another problem with hiding an ideological resistance to change behind the skirt of religion is that in many places religion is a taboo topic for conversation, including in the media. Thus religion cannot be analyzed, questioned and criticized in public without a huge backlash. Any talk of it makes even some of the liberal seculars nervous who then try to advise the critics to abide by the tradition of silence and keep it quiet – a strategy that historically never worked and only emboldens the regressives to try harder to take control of the government and turn the country into a theocracy. Sunshine is the best disinfectant and cockroaches scurry off when you shine a light on them. Likewise, a silence about religion, and undue “respect” for religion just gives the cowards boldness to try harder to proselytize. Remember they are essentially cowards – afraid of everything new and unfamiliar. Cowards understand the language of force. They can recognize who has the balls and will run away if threatened (oh, sure, they will be yelling loudly while running away, but that can be ignored).

Even the most dry and technical analysis of religion tends to receive a very aggressive counter-response. Is it due to calculated resistance to criticisms that are seen as challenges to tradition, or an incredibly thin skin of the religious, or such a tight identification of the believers with their belief that they are incapable of seeing critiques of ideas as anything but personal attacks – I don’t know.

But as a strong factor slowing down progress towards a Scientific Nation, religion has to be openly analyzed and criticized. The topic must be made palatable to the media.

And even those liberal atheists who are uneasy, due to cozy yet traditional upbringing, with discussions of religion will have to get used to the fact that regressive, conservative religion has to be challenged in public. The faked “hurt feelings” of the religious should not be a consideration here – they need to hear the criticism (many will be responsive – they just never thought about it before, took it for granted because of the silence) and grow up to withstand it, or cower in the corner if they don’t like it, or break the shackles themselves. The super-religious will not be moved one way or another. Liberal believers have to be challenged: whose side they are on – reality or their regressive religious brethren? But fence-sitters are more likely (though they will take time, nothing instantly) to move away from religion if exposed to criticisms, despite the initial recoiling and distaste, than become more religious just because “those atheists are so uncivil”. It is ugly, and slow, but the net result is positive.

The Overton Window (illustrated) is an important concept to think about when discussing the struggle against conservatism dressed up as religion. And it is important to understand how it fits within the project of communicating science (important link) to the public. It is also related to the way we can work on changing what is acceptable to say in the media.

The struggle against religious digging-in-the-heels is a two-tiered project that requires two sets of people using two different strategies. One group uses gentle hand-holding tactics to help individuals cross over. The other group moves the Overton Window of what is acceptable to say by being very public and even harsh in their criticisms. The two groups cannot work without each other. The first group cannot start moving people over if there is no acceptable discussion of religion in the public and the media.

The latter cannot be successful if there are no troups in the trenches to hold the hands of individuals and bring them into the public square they prepared. And even the shouting matches between the two groups – the former trying to silence the latter – are actually good: the noise is also part of the moving of the Overton Window and making criticism of religion acceptable topic in the mainstream society.

In any country in which religion is a powerful force slowing down (or even reversing) the movement towards a Reality Based government, one has to have a counter-force: either a a well-organized or a loose secular/atheist coalition that has the courage to speak up and make possible the environment in which discussion of religion is deemed normal and respectable. I understand not everyone has the guts for this (how many death threats has PZ Myers received in his life?), but those who do should be applauded, not silenced. They are making a real and positive difference.

Scientists tend to be a force that helps usher a government toward becoming more Reality Based. The average density of scientific researchers per million of population is around 1000 (Source PDF). The highest is in Japan (a little over 5000 per million) and USA (a little below 5000 per million). That is a very small number. Consider also that only a very small proportion of researchers are in academia. In all countries most of the researchers are employed by the government, the military or the industry.

Only a sliver works in universities or in basic-science Centers or Institutes (where the currency are publications, not patents). And many have leaked out of the tenure-track rat-race and work as teachers, journalists, writers, press information officers, journal editors, museum curators, etc.

Thus the voice of the scientists themselves will always be small, even if all scientists get up in arms and organize and get really loud in demanding something. Some scientists are interested in doing their work and have no interest in any kind of activism or popularization or education. Others are interested in making sure funding keeps flowing. Others are interested in making sure that the published research findings are freely available to all. Only a small number of scientists are primarily interested in seeing research findings applied to policy, be it public health, or local environmental problems, or global problems like Climate Change.

So, scientists will always be viewed by the government as an interest group, a small and feeble one at that. Which is why the ScienceDebate2008 action was safely ignored, though it did have some small effects around the edges, probably not sufficient to affect election, though. And the group can certainly keep working on having the voice of scientists, unified, heard in the halls of power.

While scientists can be leaders, they cannot accomplish anything in politics on their own. They have to recruit millions of non-scientists to their cause if they are to be effective. To do so, they have to be trusted. In order to get trust, they have to defeat the forces that paint them in negative light – otherwise, the general population is quite inclined to view scientists with reverence for their intellect. The industry lobbyists and PR agencies have brought in (in the USA) the negative stereotypes of scientists as pointy-headed intellectuals whose only interest is personal wealth and destruction of free market. That’s BS and you know where that came from (tobacco lobby until defeated, then later the same PR henchmen now working for the oil/coal lobby), and you know it is not the case in most other countries. Re-read Chris Mooney’s Republican War On Science for a detailed history and analysis of the sources of anti-intellectualism and anti-science sentiment in America.

In a country with a decent general education, which includes some decent science education, there is no need to water down science for the audience. Serbs have no problem with scientific terminology on TV or in books. Those scientists who are not good at communicating tend to retreat into their labs and not attempt to communicate. Which is just fine. But many, perhaps most scientists are excellent communicators – they speak with passion and clarity and need no special ‘communications’ classes to get any more effective than they already are.

I organize ScienceOnline conferences every year. Scientists, either currently active in research or not any more, keep contacting me directly (or I hear about them from others who suggest I take a look at their work), asking to do a demo of their popularization activities. You have no idea how many scientists tweet and blog and make podcasts and produce videos, and do museum demonstrations, and do Science Cafes, and run local radio shows, and give public lectures, etc, etc. Thousands! And most of the stuff they produce is excellent! There are tons of scientists who are very active in popularization of science and are very good at it. And very effective for their audiences. We don’t need more of them. We don’t need them to learn how to become better communicators. What we need is to push their existing work onto unsuspecting audience that does not already flock to them. The “push” strategy in place of the “pull” strategy. Talking to the people who don’t even know they would be excited by a scientific topic, not just to those who actively search for them.

Saying that it is up to scientists to turn their government into a Reality Based one, that it is scientists who are inactive at communication who are responsible for the government being Unscientific, suggesting that all can change if only more scientists learned how to communicate better and then do it, in short the theses of Unscientific America, Am I Making Myself Clear? and Don’t Be Such a Scientist, are misguided at best. The scientists are doing their best already, a fantastic job actually, but their efforts are just a subset of a subset of a subset of a sliver of a side-show of a tangent of the solution to the problem. They are the only ones really on board in the USA right now and giving their maximum. How do we get others on board, too?

The very few scientists who are charged with actually lobbying the government in some way should get special training in how to do it. This has nothing to do with ‘science communication’ or learning how to become more exciting speakers. The chapter in Unscientific America about talking to politicians is the best chapter in the book. It explains what mistakes untrained scientists make when trying to persuade a politician. A very useful lesson. But it has nothing to do with having more scientists become better communicators. It’s a specialized task that requires specialized training for a very small number of specially chosen scientists. Perhaps the organization that got built around ScienceDebate can set up a training camp for those rare scientists who will be talking to politicians, whoever they are and whenever that happens. That can ve very useful.

Entertainment Industry is a special case. Back in Yugoslavia I had the pleasure of working with several film crews, some local, some international, as they paid to use our horses as props (or sometimes us as riders of those horses in action scenes). I have never met, in my life before or after, such an unbelievable collection of arrogant, ignorant Narcissists as the film crews, especially the directors (or other people supposed to be creative – folks in charge of technical or managerial aspects, e.g., the sound or lighting techs or the cameramen and even most actors tended to be quite normal). I was flabbergasted at the mere existence of such completely self-loving idiots, whose self-importance and over-inflated egos were based on nothing but hot air and some New-Age woo. But they certainly held themselves in high regard. They knew everything about everything and were never wrong about anything and got all pouty if contradicted (especially with facts). It was a nightmare working with such blowhards.

I was lucky never to work on a film in the USA, but from what I can see and read (and the results they put on screen), it does not seem like Hollywood is any better, perhaps worse. Sure, there are a few humble and educated exceptions, here as well as there, but they are rare – and they are too far up in the hierarchy for me, a mere mortal, to ever meet them and thus evaluate them in person. Don’t believe me? Just read this, this, this, this, this and this for the latest illustration of how they think and operate (lots of informative stuff in the comments as well). Gah! They don’t even know how idiotic they are.

Yet, the entertainment industry has a large effect on the perception of science and scientists by the public. And while they have their own mores and traditions that drive most of what they do, they are also a reflection of what the general society thinks. It is a two-way street, which gives one hope that even they can be reformed, with a lot of effort and time.

Remember that many scripts are proposed. Only a few are actually turned into movies. The decision as to what will get filmed rests on the movie moguls – heads of big studios. The smaller fish watch what the big fish do and try to emulate it next year. Thus our targets need to be the Big Producers and Big Directors, people who actually have influence on the movie industry as a whole.

How do we change the culture of Hollywood? There are many scientists who drop out of science careers. Some may be interested in a career in the movie industry.


The thing is, don’t be such a Randy Olson. When you go to Hollywood, don’t leave all your critical faculties behind. Do not accept the Hollywood voodoo. They have no idea, no matter how loudly they yell, about what they are doing. Really. They have no idea what really makes a good movie. Multi-million dollar projects were flops.

Tiny-budget independent movies became big hits. They are all winging it. There is no real system to their madness. Don’t believe it when they tell you otherwise.

The idea is not to infiltrate them in order to become yet another hyper Hollywood idiot. The idea is to remain who you are, unimpressed by the glitz, and change their culture from within. Use your science – do research on what works on audiences. Demonstrate how much more exciting is a story that stays true to reality than the one that just stays with old worn-out movie-making tropes. Challenge the old wrong ideas they have about “what works”.

And above else, keep your cool. The Hollywood crowd loves Randy Olson because he is such a stereotypical scientist. Unfortunately, he is uncomfortable in that role and eager to try to blend in with them and be deemed “cool” (which is the currency of Hollywood) instead of capitalizing on what he is – the brainiac at the table, the one they should all look up to for realistic, grounded advice. He is playing right into their stereotypes instead of busting them.

Now, I have never met Randy [edit: I have, briefly, since this post was first published], but he admits he is stiff and that he had to work hard on becoming a good communicator (and then through the camera lens, not talking). But he is an exception to the rule. I dare you to put me on stage or in front of a microphone – we’ll all have a lot of fun. I also don’t know why are Randy’s experiences with other scientists so bad.

Yes, I have seen some dreary science talks, but they were a minority. Most talks were fun, engaging, humorous, crystal-clear on the substance and joy to listen to. Perhaps my experience is unusual? Perhaps chronobiologists are somehow better speakers than other scientists (no, there are a couple of famously bad ones there)? Perhaps NCSU is a place where the art of giving oral presentation is much more strongly fostered than elsewhere (after all, an NCSU professor wrote the best book on the subject)?

Perhaps I saw all the best speakers in departmental seminars (and I saw 3-4 per week in 3-4 departments over ten years – that’s a lot of talks, but I guess I am one of those few irresistibly curious scientists) because we have a special culture of it? Or because I was on the departmental seminar committee for two years and myself picked the best? I doubt it. I think Randy just had bad luck. Or selective memory. Most scientific talks, no matter if the audience is the inner-most circle of the discipline or lay audience at a museum, are a blast.

So, scientists can be and usually are interesting and animated. What leads to the horrendous movies in the end is that it does not really matter what scientists say. Matt Weddell was quote-mined. It happens to everyone (not just scientists) when interviewed for a movie. The entertainment guy comes to you with a pre-set story, uninterested at all in changing it, and is fishing for quotes that are usable. If you say that something he wants to show is not true, he will edit the “not” out of your sentence and have you say it’s true. Too arrogant to even know they are being dishonest. This is the world they operate in. Better become media-savvy or refuse interviews. Being media-savvy, not falling into traps that the entertainments sets, is a completely different skill from ‘becoming a better communicator’. Scientists in general can talk great, but some how-to-deal-with-inherently-dishonest-media training is in order if one is to be interviewed for a documentary.

We as scientists will never be able to get millions of people to refuse to go see a movie just because we say it’s misrepresenting science. But we can start affecting the big studio moguls by working for them, or, like Jennifer and others are doing, giving them structured, correct and respectful advice. It will be a long uphill slog. But it can be done as a part of changing the broader culture. With little help from us, movie world will gladly follow the changes in the broader society if that means ticket sales.

But in the end, the entertainment industry is not a major source of pro- or anti-intellectual sentiment, or of scientific information. When you watch a movie you know it’s fantasy. Do you know how much people learn from a science documentary? Almost zero. You all remember Ida (Darwinius massilae), don’t you? When the paper came out I bought a shirt with a picture of Ida. I wore it around a lot. Many people I met in the street knew what it was….a fossil. At best a primate fossil. Seen “on TV the other night”. When asked to say more – nobody could. Nobody uttered the phrases “human ancestor” or “missing link” let alone any Latin. All they knew there was this fossil discovered and that it was beautiful and cool. Actually – a win for the science. They found something scientific to be cool. They were never going to or meant to learn any more than that. The documentary did its job: showed that science is cool. No more, and one should not expect any more. And if it was not “pushed” on the general audience everywhere (instead of just the History Channel which is “pull” method), nobody would have ever heard of it. From our perspective, it was a media circus (perhaps because we are not used to it). From the perspective of general audience, it was a small blip on the radar, but something that showed that science is cool.

So, I think that the entertainment industry tends to reflect the society. In the big scheme of things, they tend to be followers, not leaders. I’d rather focus energies on changing the society (and let the movies follow) than try the difficult struggle to change the movie industry first. It’s more cost-effective that way.

Corporate Media also differs from country to country.

In some places, the press is officially or unofficially owned, run and controled by the government. The ‘Government Knows Best’ press. It serves as a progaganda organ for the government, telling citizens (and other countries, which is usually more important) what the government thinks and does. That way people know what NOT to say in public if they want to avoid imprisonment. In this kind of country, the government is independent (belligerently so) and does whatever it wants. It can choose to be Reality Based or not while being completely impervious to criticism and uninterested in popular opinion. And people are unlikely to rise just because their opinions are ignored – they need to really hurt in order to revolt. And this may take decades of suffering.

On the other extreme are countries in which the independent press acts as an unofficial political opposition. It is the ‘Government is Always Wrong’ press. It does not represent the thinking of the government, but also does not represent the views of the broader population either, rather it represents a particular political view of the group (perhaps a political party) that de facto runs the press. This is a rare situation and does not last long – either the government goes down, or the press gets shut down and replaced by something more to the liking of the government. This is a theoretical case – anyone know of a real-world example of this?

In between the two extremes, there are media with various degrees of independence and various degrees of influence.

My constant criticisms of the press are really focused on the US situation only. This is because the US press is in a league of its own. It is not government-owned but acts as one and, more insidiously, pretends to be independent and “watchdog” while not being so. Worse, many people buy into that lie. How does that work?

The local and metro journalists take their cues from the D.C. press, the so-called Village. They trust the Villagers because they are “at the source”. Villagers rub shoulders with the politicians every day, get ‘insider’ information (often planted to them on purpose, but they are too giddy to notice) and act very wise in the matters of politics. This is what Jay Rosen calls the Church of the Savvy. They are buddies with the Democrats and the Republicans, consider both to be their friends and hear from both what their stands are on various topics. Thus they decide that whatever these guys say is within the realm of realistic. Everything else is not.

Even if they venture outside of the capital, when they hear people saying things that are not in their realm of possible, they dismiss it as ‘naive’ or ‘extreme’.

They are the keepers of the Overton Window, working hard on preventing anyone from moving it in any direction. They are comfortable in the status quo and hate change so they work hard on preventing change from happening. That way they keep all their politician friends.

They do not see themselves as judges of the veracity of claims – they make reality. They are just scribes – they transcribe what someone from the Left says, then what someone from the Right says, then stake their reasonable and realistic position smack in the middle (do they use the ruler and compass to determine exactly where the mid-point is?). Everyone outside of that middle is an extremist. And every idea outside that narrow domain is unworthy of mention. Like single-payer healthcare system – not savvy, not realistic (or so they determined in advance, thus not worth a mention, which then makes it unrealistic). Or WMDs being a lie.

Sorry, but the mid-point between a truth and a lie is still a lie.

Sometimes they encounter difficulties when trying their best to do the HeSaidSheSaid journalism. One side is so obviously right and the other so obviously wrong. What to do, what to do? Invent a new side, of course! Here is a great recent example: the GW denialists salivating over hacked e-mails were so obviously wrong (and morons) and the other side, the scientists and the Reality-Based community are so obviously right, the journos could not have any of that – that would be equal to conceding defeat. So they dug out from under some rock a completely irrelevant party – the Greens and environmentalists. Yeah, cool, those wackos can be portrayed as equally nutty as the GW denialists, thus the journos remain firmly in the middle, grinning smugly about their own wisdom. Oh, and the “middle-ground” they thusly discovered? It is suspiciously palatable to the anti-scientific forces of the oil/coal industry and their Republican marionettes. The savvy middle, yeah right.

Then the next morning, Washington politicians wake up and open their Washington Post, New York Times and Wall Street Journal to see what is the pulse of the nation.

They see that only the stances they are happy with are reported as being the discourse of the people. They go happily with their day. No challenge permitted.

In short, the US press acts as a barrier between the people and their government. They report to the people what the politicians deem reasonable (which would never change if left entirely to them – have you seen the average age of the US Senators?) and they report the same stuff to the politicians as the view of the people. No free exchange of ideas and opinions can pass through that barrier – the Villagers are keeping those gates closed and they decide what is and what is not “realistic”. When change happens, it is always because information bypasses the press. And then they are distressed and surprised. It’s hard work adapting to a new landscape, learning all over again who now supports what and reporting thusly.

Another reason they do this is because they are themselves not Reality Based. Unlike that Serbian anchor I mentioned above, they are incapable of doing the math and analysing a policy proposal themselves. All they are capable of doing is transcribing what various political spokes-persons say with no ability to estimate (let alone actually know) who is based in reality and who is just bullshitting them. Such ignorance is the source of their post-modernism – it’s all opinion to them, because they have no idea how to determine and assign a Truth value to any statement. “We report you decide” also means “we are too ignorant to decide for ourselves”. It also means “Truth is what we say it is, reality be damned”.

By actively preventing any change from occurring, and by staking their position as “realistic” although it is a mid-point between reality and batshit insane (thus keeping the batshit-insane ideas legitimized), the Villagers (and their followers in the provinces) keep the country from moving in the direction from Unscientific to Scientific. Always halfway to Reality-Based, never really getting there. The press is working mightily to make sure that never happens.


Let’s start with the definition again: “An unscientific nation is one in which the government is not Reality Based.”

Focus back on the Government. It appears that, due to the Media, the US government is geometrically precisely mid-way between Reality-Based and Anti-Reality Based points. That is a pretty abysmal place to be, when you think about it. Far too far away from Reality-Based.

There are strong anti-Reality forces in the country: the Industry (because the economic system rewards only short-terms thinking), the Educational system (being determined on the local level), Electoral system (disproportionately rewarding the rural areas), Religion (unchallenged in its privileged position of being unquestioned), Entertainment Industry (which is just dumb), Republican Party (what is left of it now that the teabaggers aka birthers aka Palin-drones aka 26%-ers have purged it from the last human with a brain, but still not laughed out of court by the press), and the Media (which actively legitimizes insane views and prevents change).

The pro-Reality forces are much smaller, much less organized, much less funded, and all outside of the power establishment: scientists, good science teachers, good science writers/journalists, and vocal atheists. So how can such a small bunch break the gates and effect change? By recruiting more people and then making the government know what the will of the people really is. This means bypassing the media and, in the process, opposing all the other powerful players. It’s a dangerous game!

So how does one build a coalition, oppose the negative forces, bypass the media and talk directly to the government? In other words, how does one make it obvious to the government that their only option is to become Reality Based if they wish to get re-elected and remain in power?

First, one should identify the forces that are either purposefully trying to slow down or reverse the movement towards a Reality Based nation, or inadvertently helping such forces. Then do all of these:

1) Organized Action – build coalitions and actively oppose the anti-science activity, policy proposals, anti-science political candidates, etc.
2) Stick and Carrot – praise the people/organizations when they do something right, and slam them when they do something wrong. Make sure they hear it in both cases.
3) Punishment – organize boycotts of products, for example
4) Infiltration – reform the organization from within, making it more pro-Reality
5) Bypassing – build parallel organizations that do the job better, then put efforts into marginalizing the older, traditional organizations you are replacing

By using all of these approaches simultaneously, one can potentially win. How does one do all of that? It’s all about communication.

New Media

The ultimate target of communication is the government. One can get to it directly or indirectly.

You can go to or or contact your representatives. Many are now on Facebook and Twitter – follow them and reply. Some employee there is probably tasked with reporting to the boss what the people are saying. Or go to OSTP blog – they are listening. Or to ExpertLabs (Anil Dash will be at ScienceOnline2010, specifically to get your feedback as to how to build and run that site to make it useful for the administration to get input from the experts).

Or you can go indirectly. Remember that the politicians, geriatric patients for the most part, get their ‘pulse of the nation’ by reading traditional media. If the message of

Reality is not fairly represented in the media, see the above five tactics. Praise the journos who do it right (directly or in various online venues). Slam the journos who do it wrong (they’ll burn, they’ll squeal, but most will learn their lesson). Infiltrate – become a journalist and do a better job. Bypass – build new online communications and media powerhouses. Those tactics are not mutually exclusive, they are complementary.

Sure, the governments (as well as other anti-Reality forces) are also aware of the new media channels and will try to use them for their own purposes. But there’s more of us. And we last longer – we don’t get elected for a few years, we breed. In the end, we’ll win.

Bad Guys TM also can use the Web for organizing, sure. But who has the advantage? The side that has a numerical advantage online. Remember that 26% of Americans are fundamentally anti-science. That means that 74% are reality-based, or at least amenable to intelligent persuasion. That is already a numerical advantage. Also remember that most of the anti-science forces are in the hinterland, where there is much less likelihood one can get online access (no cable, wifi or internet cafes out in the country), or have a computer or iPhone, or be mentally eager to start using such tools – a much more traditional society. That is also an advantage (for now, that will get erased pretty fast).

Getting a link from a Creationist site brings a few hits, an almost undiscoverably small number. Getting a link, even if just in a comment thread, from Pharyngula or Panda’s Thumb or sends a humongous avalanche of traffic. While the Creationists may be having their own echo-chambers, our echo-chamber is much bigger, by being realistic it is much more likely to grow (and not be limited to the 26%) through new recruits, and will thus be potentially much louder and much effective in the long run.

How did those online communities (to take atheists as an example here) get to be so big? Before the Web, most atheists in the States thought they were alone, or in a tiny minority. Usenet newsgroups, forums, blogs, social networks revealed they count in millions – many, often pseudonymously at first, revealed online what they never told anyone before. This recognition engendered boldness. More people came out of the closet and told census workers and pollsters they are atheists. More became open about it in RL. Suddenly atheism is the fastest-growing religious self-identification in the country.

When media started discussing atheism as an emerging phenomenon by having two religious leaders discussing it in the studio (CNN), they got slammed so hard, they had to do another show and invite an actual atheist to it. The proliferation of books and blogs by vocal atheists made the topic acceptable in the public sphere. Media was forced to change to reflect this. Overton Window has moved. While Bush Sr. could say with impunity that atheists are not real Americans, his son, who is himself much more of a fundamentalist Christian, could not say that (or was prevented by advisors to say that). Vocal atheists, who found each other and organized online, engendered a large cultural shift.

The same can be done with a shift towards becoming a more Reality Based nation. It was especially disappointing to see that authors of the three books about science communication I linked to above, although three of them are bloggers, do not understand the power of the Web. You don’t need to have diligently read blogs, articles and books by Clay Shirky, danah boyd, Kevin Kelly, Jeff Jarvis, Eszter Hargittai, Dan Gilmor, Dave Winer, Theresa Nielsen Hayden, Jay Rosen and Scott Rosenberg to grok it.

Being a blogger for a few years and witnessing (and even participating in) numerous instances of the online community getting organized and effecting change (resignation or firing of officials, media mea culpas, passage or defeat of legislation, GOTW efforts, electoral results, etc.) should be sufficient.

When people formerly known as audience have communicaton tools at their disposal, they can communicate with each other (thus discover each other, agree on the goals, and organize action) and to those in power. When those in power become more afraid of us than of the CEOs or TV pundits, they’ll do their job for which we hired them.

Are we there yet? No, but we are getting there fast. In 2004, the existing handful of bloggers could not affect the results of the Presidential election. Already in 2006, they affected some mid-term elections. In 2008, online organizing was one important element of the Obama strategy to win. Locally, it can be even stronger. If you are running for office here in Chapel Hill, you better show up at Orange Politics. If you don’t (or worse, show up and be belligerent), your candidacy (and probably all future candidacies) is doomed.

Don’t judge a new communications ecosystem by its first unsteady steps. It will get there…. And sooner the worst of the traditional media goes under, sooner we can build a more modern media system in which it is much more likely that the participation of many people will ensure that the best expertise gets transmitted the broadest (techies are frantically working on better filtering tools, combining algorithms with human-curated recommendation systems) and that the best available information, as well as the will of the people, gets to its intended target, which is the government.

So, grooming a few more scientists to become a little better at talking about their research is a drop in the bucket of the solution. They are already excellent communicators and doing their maximum. It is a smart use of the new communication tools to find and organize non-scientists interested in a Reality Based government that will do the trick. Smart use of the new communication tools is necessary because the traditional communication tools – the media – keep the people away as passive observers. It is merely a method for people already in power – politicians, D.C. pundits, lobbyists, industry leaders, religious leaders, etc. – to send signals to each other.

Which is why the media in the USA is as it is – designed to exclude the people.

It will be a hard, uphill battle against very rich and powerful interests, but it can be done – there’s more of us, and we now have a way to communicate with each other and to those in power. Let’s use that new ability to make a Reality Based government here. And in other countries citizens will do the same as well.

BIO101 – What Creatures Do: Animal Behavior

This post was originally written in 2006 and re-posted a few times, including in 2010.

As you may know, I have been teaching BIO101 (and also the BIO102 Lab) to non-traditional students in an adult education program for about twelve years now. Every now and then I muse about it publicly on the blog (see this, this, this, this, this, this and this for a few short posts about various aspects of it – from the use of videos, to the use of a classroom blog, to the importance of Open Access so students can read primary literature). The quality of students in this program has steadily risen over the years, but I am still highly constrained with time: I have eight 4-hour meetings with the students over eight weeks. In this period I have to teach them all of biology they need for their non-science majors, plus leave enough time for each student to give a presentation (on the science of their favourite plant and animal) and for two exams. Thus I have to strip the lectures to the bare bones, and hope that those bare bones are what non-science majors really need to know: concepts rather than factoids, relationship with the rest of their lives rather than relationship with the other sciences. Thus I follow my lectures with videos and classroom discussions, and their homework consists of finding cool biology videos or articles and posting the links on the classroom blog for all to see. A couple of times I used malaria as a thread that connected all the topics – from cell biology to ecology to physiology to evolution. I think that worked well but it is hard to do. They also write a final paper on some aspect of physiology.

Another new development is that the administration has realized that most of the faculty have been with the school for many years. We are experienced, and apparently we know what we are doing. Thus they recently gave us much more freedom to design our own syllabus instead of following a pre-defined one, as long as the ultimate goals of the class remain the same. I am not exactly sure when am I teaching the BIO101 lectures again (late Fall, Spring?) but I want to start rethinking my class early. I am also worried that, since I am not actively doing research in the lab and thus not following the literature as closely, that some of the things I teach are now out-dated. Not that anyone can possibly keep up with all the advances in all the areas of Biology which is so huge, but at least big updates that affect teaching of introductory courses are stuff I need to know.

I need to catch up and upgrade my lecture notes. And what better way than crowdsource! So, over the new few weeks, I will re-post my old lecture notes (note that they are just intros – discussions and videos etc. follow them in the classroom) and will ask you to fact-check me. If I got something wrong or something is out of date, let me know (but don’t push just your own preferred hypothesis if a question is not yet settled – give me the entire controversy explanation instead). If something is glaringly missing, let me know. If something can be said in a nicer language – edit my sentences. If you are aware of cool images, articles, blog-posts, videos, podcasts, visualizations, animations, games, etc. that can be used to explain these basic concepts, let me know. And at the end, once we do this with all the lectures, let’s discuss the overall syllabus – is there a better way to organize all this material for such a fast-paced class.


Today, we discuss animal behavior. Note that I tend to do a lot of drawing on the whiteboard in this lecture, which is not seen in these notes. I also show a lot of short YouTube videos that show examples of strange animal behaviors.


Imagine that you are a zebra, grazing in the savanna. Suddenly, you smell a lion. A moment later, you hear a lion approaching and, out of the corner of your eye, you see the lion running towards you.

What happens next? You start running away, of course. How does that happen? Your brain received information from your sensory organs, processed that information and made a decision to pursue a particular action. That decision is relayed to the muscles that do the actual running.
In short, that is behavior and it can be schematically depicted like this:

Environment———> Sensor ———-> Integrator———> Effector

Here, the change in the environment (appearance of a lion) is perceived by the sensors (eyes, nose, ears), processed by the integrator (the brain) and results in the activity of the effectors (muscles).

But, it is usually not that simple. The flow chart, as depicted, may be accurate when describing behavior of a bacterium, a protist, a fungus or a plant. A molecule in the cell membrane of a bacterium may sense nutrients, toxins or light. This information is processed by the cell as a whole, and as a result, the cilia or flagella move the bacterium in an appropriate direction.

Specialized cells in the shoot-tips or root-tips may detect up and down, or the position of the Sun, and guide growth in an appropriate direction (shoots up, roots down). Sunflowers and some other plants track the position of the Sun throughout the day. Many plants open and close their flowers or leaves at particular times of day. Some flowers, e.g, Venus flytrap and some orchids, can move even faster in order to capture insects.

Pilobolus, a fungus (seen as fine white fuzz on manure), shoots its spores towards the Sun at a particular angle at a particular time of day. Those are all simple behaviors involving a single sensor, a single integrator and a single effector in a simple unidirectional flow of information.

Once we get to animals with central nervous systems, things get a little bit more complicated. There are often multiple sensors. In the zebra example, the changes in environment are detected by three separate sensors: for vision, audition and olfaction. Effectors are many muscles, working in a highly coordinated manner.

Sensors located in the muscles feed the information about their activity back to the integrator. Integrator feeds back to the sensors as well – raising the sensitivity of the sensory organs, including vision, hearing, smell and the tactile sense (touch), while reducing the sensitivity of other sensors, e.g., for pain. The subjective perception of the rate of passage of time slows down, allowing for more fine-grained sensation and faster decision-making by the integrator.

Furthermore, the integrator will stimulate secretion of the hormones which, in turn, may increase the ability of effectors (muscles) to do their work. Integrator will also raise the activity of other organ systems that are important in allowing muscles to perform at their maximal level, e.g., circulatory and respiratory systems that bring oxygen and energy to the muscles.

At the same time, the brain temporarily shuts down the activity of organ systems not necessary for short-term survival, but which may take the valuable energy away from the muscles. Thus, the digestive, immune, excretory and reproductive systems are inhibited.

As the zebra runs away, the act of running results in subsequent changes in the environment, which are again detected by the sensors. The integrator makes decisions to suddenly swerve if the lion gets closer, or to buck and kick if the lion gets very close, or to stop and find the safest route back to the herd if the lion has abandoned the chase.

All the changes described in the zebra example above are elements of the stress response, which is an excellent example of a complex behavior. There are multiple sensors, multiple effectors, various modifications of the body’s physiology, and several kinds of information feedbacks involved. Behavioral biology studies all aspects of it.
In addition, it is not just the activity itself, but also the propensity for such activity that is studied by behavioral biology. Probability of a behavior happening depends on the motivation, or the state of the effector. The state can be modified by hormones, hunger, tiredness, libido, general energy levels, etc. The effector (e.g, the brain) also possesses timing mechanism (clocks and calendars) which make some behaviors much more likely during the day or during the night, some more likely during spring or summer, others more likely during fall or winter.

What Is Behavior?

It is difficult to define behavior without resorting to just listing examples of various kinds of behaviors, but let’s try to define it anyway: Behavior is a change in body’s position, shape or color, or a change in potential for such change, in response to changes in the external or internal environment. Behavior is endogenously generated (i.e., if I move your arm – that is not your behavior, it’s mine), purposive (meant to achieve a goal), and is an evolved adaptation that contributes to survival or reproduction, thus increases one’s fitness (which is obvious in the case of the fleeing zebra).

How to study behavior?

The most informative and profitable way to study behavior is an integrative approach. This means that the behavior under study is approached at all levels of organization (from molecules to ecosystems) and from four different angles. The first angle is Mechanism, which denotes study of the physiology underlying behavior. Most of the analysis of the zebra’s behavior described above focused on this aspect – the physiology of the sensory, neural, muscular and other systems and the way they work together to produce the behavior.

The second one is Ontogeny, the study of embryonic and post-embryonic development of the behavior – how does an individual acquire the behavior, how much is the behavior inherited vs. learned, at what time in one’s life cycle can the behavior be learned or expressed, at what times of day or year are the behaviors most likely to be expressed, etc.

These first two angles – mechanism and ontogeny – are sometimes called Proximate Causes of behavior and are designed to ask and answer the “How” questions of behavior (how does it work, how does it develop). The next two are called Ultimate Causes of behavior and are designed to ask and answer the “Why” questions (why behave in such way).

History is the third approach. It studies the evolutionary history of a behavioral trait, usually by employing the comparative method, i.e., comparison of a number of related species, trying to discover if the behavior is common in all of them, in which case it is present due to the deep phylogenetic history, or of it most reliably varies with the type of environment the species lives in, suggesting that the behavior is a recent adaptation for a particular way of life.

Finally, the fourth approach is Function. It tests the hypothesis that the behavior in question increases the animal’s fitness, aids in survival and/or reproduction, and has evolved for that function – is it an adaptation.

Recently a fifth question has been added to this list. Animal cognition asks “Can animals think?” Here, careful use of some unusual (and quite controversial) methods, including anecdotes, introspection and anthropomorphism, aids in the development of testable hypotheses about the inner worlds of animals.

No other area of biology is as integrative as behavioral biology. It is possible for a biochemist to ignore ecology or for an ecologist to ignore biochemistry (though at the risk of performing irrelevant research), but a behavioral biologist cannot ignore any aspect of the biology of the species under study. This makes the study of behavior the glue that holds all of biology together. This makes behavioral biology difficult to do, as one needs to have strong background in many areas of biology, technical expertise in a broad range of laboratory and field techniques, and lots of time to follow up on the literature in a number of related fields.

Only a few – the best – behavioral biologists are capable of exploring every aspect of a behavior at all levels. Mostly, the problem is divided among a number of laboratories around the world, each researcher using a slightly different approach and different techniques. The laboratories then communicate with each other via formal channels – the publications in scientific journals – and via informal channels – conferences and personal communication (and more recently, on the Web). Thus, a big picture is slowly being built out of its smaller parts, each piece of research being informed by all other pieces of research.

Types of behaviors

Foraging behavior involves finding, catching, handling and ingesting food. It includes the formation and use of feeding territories, learning the hunting techniques, the physiology of hunger, as well as behavioral strategies for avoiding becoming prey.

Animal movement includes, most prominently, long-distance migration including the neural mechanisms of spatial orientation and navigation.

Communication is the ability of animals to communicate information to each other (within and between species) via several sensory channels (or modalities). Those modalities include vision (including infrared, ultraviolet and polarized light, as well as thermoreception), sound (including ultrasound, infrasound and substrate vibrations), chemical signals (smells, pheromones, taste), touch and electrical signals (as in electrical fish).

Reproductive behaviors encompass a broad range of behaviors. Mate-finding, male-male competition, mate-choice and courtship are behaviors involved in securing a mate. Mating behavior ensures fertilization. Nesting and parenting behaviors are meant to ensure the survival of the offspring.

Reproductive behaviors are important elements of evolutionary change. Many phenotypic traits are a result not of natural selection, but of sexual selection, where a trait is selected not by the physical environment but by potential mates. Traits favored by the individuals of the opposite sex tend to be more likely to be passed on to the next generation in that population. This leads to the evolution of exaggerated traits (e.g., the peacock’s tail) and to differences between sexes (e.g., in many bird species the male is brightly colored while the female looks drab).

Mate choice can, potentially, be involved in sympatric speciation, if different individuals in the population favor different traits in their mates, so the gene flow between the two groups gets progressively smaller with each generation. This kind of mating is called assortative mating (as opposed to random mating, where each individual is equally likely to mate with each individual of the opposite sex).

The most common types of mating systems are monogamy, polygyny, and polyandry. A good example of polygyny is the elephant seal in which only one male (after defeating all the other males in one-on-one fights) mates with all the females in his territory.

Polyandry is found only a little less often – one female mates with multiple males over the course of a breeding season, resulting in her offspring being of mixed paternity (i.e., different eggs were fertilized by different males). This has been studied mostly in frogs.

Monogamy is the rarest form of mating strategy in the animal kingdom. A distinction is made between social monogamy and sexual monogamy. Many animals that form breeding pairs, including most species of birds, are engaged in social monogamy – the male and the female build the nest together, mate and raise the chicks together. However, DNA fingerprinting has shown that a small proportion of the eggs is invariably fertilized by a different male – a fleshy neighbor who may not be a good “husband” and “father”, but whose size, bright colors or powerful song indicate other genetic qualities. Thus, some of the progeny of the same female will be fleshy sons, some will be “good husband” sons and some will be daughters – the female is hedging her bets about the production of grandoffspring.

Humans are not officially classified as monogamous animals – though human polygamy (both polygyny and polyandry) tends to be in the form of serial monogamy, i.e., sticking monogamously with one partner for a particular length of time, then changing the partner. Social norms have strongly opposed, but did not eradicate human non-monogamy. Increased life-span, invention of reliable contraception, and economic independence of women are making it more and more difficult to suppress the non-monogamous tendencies in humans, as seen from statistics for divorce (around 50%), re-marrying, and cheating (around 60% of both men and women) that have held quite steady over the past 50 years or so.

Social behaviors involve relationships between individuals of the same species. Some animals tend to live alone, each individual defending a territory, and a male and a female meeting only briefly during the mating season. Other animals tend to live in smaller or larger groups. Some animals change their social structure seasonally – for instance, European quail live in coveys (10-12 birds) during the winter), in huge flocks during spring and fall migrations, and in breeding pairs during summer.

Within groups, there is often a hierarchy of individuals – the so-called “pecking order”. The social hirearchy is established through aggression, often in form of ritualized displays. In many species, the ritualized aggressive behaviors are so-called “fixed-action patterns“, i.e., a strongly heritable order of particular movements. Mating behaviors are also often fixed-action patterns.

In some species, the mating fixed-action patterns are also used for aggressive encounters. In some cases, when a male mounts another male utilizing a typical mating pattern, this is actually a display of social dominance. However, in other species, a male mounting a male is actually homosexual behavior, evolved not to determine social hierarchy, but quite the opposite, to increase social coherence within the group (“making friends”). In pygmy chimps (bonobos), everyone in a troop mates with everyone else in the troop, regardless of gender. This makes the troop socially cohesive (which helps in group’s defense if attacked by another troop, predators or other enemies).

Previously in this series:

Biology and the Scientific Method
BIO101 – Cell Structure
BIO101 – Protein Synthesis: Transcription and Translation
BIO101: Cell-Cell Interactions
BIO101 – From One Cell To Two: Cell Division and DNA Replication
BIO101 – From Two Cells To Many: Cell Differentiation and Embryonic Development
BIO101 – From Genes To Traits: How Genotype Affects Phenotype
BIO101 – From Genes To Species: A Primer on Evolution

Seasonal Affective Disorder – The Basics

First published on February 05, 2006.

So, why do I say that it is not surprising the exposure to bright light alleviates both seasonal depression and other kinds of depression, and that different mechanisms may be involved?

In mammals, apart from visual photoreception (that is, image formation), there is also non-visual photoreception. The receptors of the former are the rods and cones that you all learned about in middle school. The receptors for the latter are a couple of thousand Retinal Ganglion Cells (RGCs) located in the retina in each eye. Each of these cells expresses a photopigment melanopsin (the cryptochrome challenger apparently lost the contest about a year ago after several years of frantic research by proponents of both hypotheses).

The axons – nerve processes – from these cells go to and make connections in three parts of the brain. One is the brain center that controls pupillary reflex – when the light is bright the pupils constrict, while in the dark the pupils dilate.

The second is the brain center involved in the control of mood. There is still a lot to work out about this center, but that is probably the place where exposure to light helps alleviate regular, i.e., non-seasonal depression.

The third place where these RGCs project is the suprachiasmatic nucleus (SCN) – the main circadian pacemaker in the mammalian circadian system. The first light of dawn perceived by the eyes tells the SCN that it is day. Likewise, at dusk, the gradual decrease in light intensity perceived by these RGCs signals to the SCN that night is about to start.

Much of the work on seasonal depression (SAD) suggests that it appears in response to the changes in daylength – the photoperiod. While other aspects of the weather, e.g., brightness, temperature, etc., may modulate the response, the basic mechanism appears to be the same way other mammals time their seasonal activities, including breeding, migration, molting and hibernation. Recent studies indicate that other mammals also suffer from winter depresssion, which is triggered by long night and short days (that last link is to a really cool study – perhaps I should write a separate post just on that!).

What is important to keep in mind is that total amount of received light, its intensity and quality, do not matter in photoperiodic response in mammals. What matter is the duration of the night AS PERCEIVED BY THE SCN. One can fool the SCN by, for instance mimicking a long summer day with skeleton photoperiods (a light pulse in the morning and a pulse in the afternoon) – the clock perceives only two pulses of light (a total of a couple of hours of illumination), yet interprets is as a long day.

The output of the SCN, among else, is a projection to the superior cervical ganglia (SCG) in the upper neck region, which are part of the sympathetic (autonomic or vegetative) nervous system. The SCGs, in turn, project their axons onto the pineal gland where release of nor-epinephrine controls the synthesis and secretion of the pineal hormone melatonin. So, whenever the SCN ‘thinks’ it is night, the pineal secretes melatonin into the bloodstream.

During the day, the SCN inhibits the secretion of melatonin. The duration of melatonin secretion is the signal for the duration of the night. This signal is then read and interpreted by other parts of the brain that trigger changes in development, morphology, physiology, reproduction and behavior in a seasonally appropriate manner. So, it is the duration of exposure to melatonin, not any direct hormonal activity of melatonin, that is the key to seasonal phenomena.

Here is a schematic of the melatonin profile in the blood of normal people in summer and winter:

Such profiles are very important for fitness (survival and reproduction) in hamsters, sheep, deer and most other mammals. Humans are not so strikingly seasonal – we breed throughout the year – but our distant ancestors certainly were. Some traces of the seasonality of our ancestors can be seen. For instance we crave different foods in different seasons, put on or lose weight seasonally, etc. The best evidence for the human seasonality is the existence of Seasonal Affective Disorder – SAD. Just like other mammals, we get slow, grouchy, and in severe cases, clinically depressed during the winter (yes, I know, there are some rare people who are opposite – depressed in summer, but they are seasonal, too, and their SAD is also due to photoperiodic time measurement).

How does exposure to bright light alleviate SAD? Most humans have an inherent freerunning period (tau) of their circadian clock somewhat longer than 24 hours – around 25, actually. Thus, the two figures I drew above are idealized – very few people have profiles exactly like that. We tend to wake up some hours after dawn. We sleep indoors in relatively dark rooms, perhaps under covers, with our eyes closed. The RGCs do not perceive the first light of dawn at the time of dawn but some time afterwards. Thus, the SCN entrains to the environmental light-dark cycle with a slight delay. Most humans are mild “owls” in this respect. And even when we get up, we expose ourselves only to the relatively weak artificial light, or the dim light of a dark and dreary winter morning.

In the evening, most people do not go to bed at dusk, but switch on the lights (curse you, Edison!) and go to bed much later – often around midnight. We phase-delay our clocks with our daily behaviors. Yet, the artificial light is not sufficiently intense to shut down the secretion of melatonin. What you get is something like this – an artificially lengthened night and even longer duration of the melatonin signal than what the actual duration of night warrants:

By exposure to very bright light (a ‘light-box’ that you can buy online) in the morning, we phase-advance our clocks every morning, just enough to place ourselves into a more normal phase. High intensity is needed as the speed and size of phase resetting is dependent on light intensity. This way, we reduce the perceived duration of the night to what it really is (instead of the artificially lengthened night), thus alleviating some of the mood-related effects of short photoperiods.

“Larks” are people whose clocks run with a period at or shorter than 24 hours and who are, thus, somewhat phase-advanced in relation to the environmental light-dark cycles. The strategy for “larks” is to expose the RGCs to bright light in the evening, thus phase-delaying the clock and, again, reducing the perceived duration of night to the actual duration of night, hopefully eliminating mood-altering effects of long winter nights:

Melatonin supplements are often used in treatment of clock-related disorders. Melatonin has been suggested to treat jet-lag, effects of night-work and shift-work (“shift-lag”) and various clock-related insomnias. But beware – melatonin is also a signal of season.

I have not seen a study of this, but here is something that, in theory, can happen. If you are an extreme night owl, i.e., phase-delayed and try to reset your clock by taking melatonin earlier in the evening than your normal (i.e., very late) bed-time, what is going to happen?

Even if you do this in the middle of summer, the melatonin supplement will prolong the nightly melatonin signal (exogenous melatonin in early night + endogenous melatonin during late night). Your brain will interpret this as an abrupt onset of very long winter nights. If you are susceptible to winter depression (and if I remember some studies correctly, owls are more susceptible to SAD than larks), you will artificially trigger SAD in the middle of the summer. So, beware!

Now, you may understand why are people who live in very high latitudes chronically depressed. After all, they are exposed to a continuous night that lasts for several months! One wonders if the reindeer are depressed, too.

What I outlined here is just the very basic mechanism of SAD – the textbook version. There are, as one should expect, many more details, complications and strange data out there. Those are, frankly, outside my domain of expertise. I am a bird kind of guy, after all. So, if you want more details, or medical advice, you will be better off to ask somebody who does research on (and clinical work with) human subjects, or at least on mammals.

The Mighty Ant-Lion

First written on March 04, 2005 for Science And Politics, then reposted on February 27, 2006 on Circadiana, and re-posted a few more times as I moved my blog around (the latest in 2009) a post about a childrens’ book and what I learned about it since.

When I was a kid I absolutely loved a book called “Il Ciondolino” by Ricardo Vamba – a book in two slim volumes for kids (how times change – try to publish a 200+ page book of dense text for children today!). I later found out that it was translated into English under the title The Prince And His Ants in 1910 (Luigi BERTELLI (M: 1858 or 1860 – 1920) (&ps: VAMBA) The Prince And His Ants [It-?]. Holt.(tr S F WOODRUFF) [1910] * Il Giornalino Di Gran Burrasca [It-?] (tr ?) [?] ) and was even The Nation’s Book of the Week on June 2nd 1910.

[“Vamba” is the pseudonym of Italian fantasist Luigi Bertelli. The Prince and His Ants (1910) tells the tale of a boy who becomes an ant, and a girl who becomes a butterfly. The English translation by one Miss Woodruff was edited by Vernon Kellogg, an insect authority at Stanford University. Ninety interior illustrations are scientifically accurate.]

This book is hard to find – don’t even bother with Amazon – but my brother was persistent and after several weeks of patient searching he got a copy from Alibris and sent it to me. It is a story of a boy who wakes up one morning transformed into an ant. The book describes his travels and adventures in the world of the small. Of course, he meets a bunch of really cool creatures, like various wasps, and bees, and moths, and honey-ants, etc. But the one I remember the most was the ant-lion.

Photo by Jonathan Numer at Wikimedia Commons.

The antlion is actually quite pretty, yet short-lived, as an adult. But it is the larva that is really cool:

It digs a pit in the sand and hides underneath the sand right under the bottom of the pit. When an ant or some other insect comes by, it falls into the pit and has trouble climbing out of its steep walls again. The ant-lion lunges out of the sand (like a scene from “Tremors”) and eats the poor bug:

Now the really cool part: the volume of the pit is bigger when the antlion is hungrier (or so they say at this marvelous website that I highly recommend you browse around). But, hungry or not, the ant-lion digs a bigger pit when the moon is full. Nobody has any idea why that would be so. Here is a photograph (from the site I linked in the previous sentence) of a colony of ant-lions, each with its own little pit:

But here is the coolest part of all. If you take ant-lions out of the field and put them in little sandboxes in the laboratory and isolate them from any cues about the outside world they will still dig bigger pits roughly every four weeks – they have an internal lunar rhythm:

They have, somewhere in their brains, a lunar clock that tells them to dig larger pits whenever the moon is full even if they canot see the moon itself (e.g., on a dark cloudy night). If and when somebody figures out how this little brain works, I’ll be sure to tell you, but you may have to wait years for it – I don’t think anybody is even thinking about studying it right now.


G.J. Youthed, V.C. Moran, The lunar-day activity rhythm of myrmeleontid larvae, Journal of Insect Physiology,Volume 15, Issue 7, July 1969, Pages 1259-1271

Inon Scharf, Aziz Subach, Ofer Ovadia, Foraging behaviour and habitat selection in pit-building antlion larvae in constant light or dark conditions, Animal Behaviour, Volume 76, Issue 6, December 2008, Pages 2049-2057 (PDF)


Everything You Always Wanted To Know About Sleep (But Were Too Afraid To Ask)

This post is by far, my most popular ever. Sick and tired of politics after the 2004 election I decided to start a science-only blog – Circadiana. After a couple of days of fiddling with the template, I posted the very first post, this one, on January 8th, 2005 at 2:53 AM and went to bed. When I woke up I was astonished as the Sitemeter was going wild (getting a couple of thousand hits was a big deal back then, but within a few days, this post got to about 60,000 visits)! This post was linked by BoingBoing and later that day, by Andrew Sullivan. It has been linked by people ever since, rediscovered over and over again, although the post is six and a half years old.
I decided to move the post from the old archives here without any editing. I hope my writing has improved since then. And beware that it is more than six years out of date. It is here, really, to show my first real scienceblogging post, the one that convinced me, due to positive response, to switch from political to science blogging. A piece of personal history, if you wish.

What are you doing up so late, staring at the computer screen reading this? For that matter, what am I doing up late writing this at 11pm? Are we all nuts?

Until not long ago, just about until electricity became ubiquitous, humans used to have a sleep pattern quite different from what we consider “normal” today. At dusk you go to sleep, at some point in the middle of the night you wake up for an hour or two, then fall asleep again until dawn. Thus there are two events of falling asleep and two events of waking up every night (plus, perhaps, a short nap in the afternoon). As indigenous people today, as well as people in non-electrified rural areas of the world, still follow this pattern, it is likely that our ancestors did, too.The bimodal sleep pattern was first seen in laboratory animals (various birds, lizards and mammals) in the 1950s, 60s and 70s, i.e, before everyone moved their research to mice and rats who have erratic (un-consolidated) sleep patterns. The research on humans kept in constant conditions, as well as field work in primitive communities (including non-electrified rural places in what is otherwise considered the First World) confirmed the bimodality of sleep in humans, particularly in winter.

Larks and Owls
There is a continuum of individual sleep patterns ranging from extreme “larks” who fall asleep at the first inkling of dusk but wake up before dawn, all the way to the extreme “owls” who stay up quite late and wake up once the day is in full swing, and of course everything in between. No matter where you are on this continuum, you tend to sleep more during the winter long nights than during the short summer nights.

The genetic basis of extreme “larkiness” has been elucidated. It is a mutation in a phosphorilation site on the protein product of the core-clock gene period (per). A phosphorilation site on a protein is a place where another protein may add a phosphate group. Phosphate groups are ubiquitous sources of energy in biology (remember ATP from high-school biology? That’s it!). Thus, an addition of the phophate may make it easier for the protein to react with another molecule. That other molecule may give it stability, or destroy it, or allow it to move to another part of the cell. In the case of period, it appears that lack of the phosphate group allows the protein to move into the nucleus sooner than normal where it blocks transcription of its own gene.

Of course, we are talking statistics here: hundreds or thousands of period proteins per cell, several thousand pacemaker clock-cells in the suprachiasmatic nuclei, plus trillions of peripheral clock-cells all over the body: each of these molecules has a statistical chance of moving back into the nucleus sooner than in a person without a mutation. Moving sooner into the nucleus means that the inherent (“freerunning”) period of the clock is shorter. In most people it is about 24-25 hours long (when measured in completely constant environmental conditions, i.e., no light-dark, temperature, sound, or social cycles). The “owls” have longer periods and “larks” have shorter periods. Period determines phase relationship between the internal clock and the environmental synchronizing cue (e.g., the light-dark cycle), thus longer the period of the clock, later the clock will trigger waking up in the morning or feeling sleepy in the evening, and vice versa. People like me go to bed at 4am and wake up at noon. People with the extreme lark mutation wake up at about 4am, but are real party poopers, snoozing at 7pm or so. The whole continuum is believed to be determined by similar small mutations in which just a single DNA base-pair is replaced in one of the clock genes (12 such clock-genes are known so far to operate in mammals).

During a normal night’s sleep, REM occurs every 90 minutes or so. As the night progresses, the REM episodes get longer and the non-Rem periods in-between become shorter (thus still adding up to 90 minutes) as well as shallower. Thus, the really deep sleep (e.g, Stage 3) occurs only during first 1-2 cycles early in the night. Lack of Deep Sleep results in tiredness. Usually adults wake up from REM (children do not), unless waking is forced (e.g., alarm clock). Research on relative roles of REM and NREM in consolidation of memory is very controversial (look for Jerome Siegel on Google Scholar). Growth Hormone surges during episodes of Deep Sleep, and falls during REM, and is almost undetectable during wakefulness.

In the morning, our body prepares us for waking by increasing blood levels of ACTH and cortisol (leading to preponderance of heart attacks at waking time). Our body temperature is the lowest just an hour or two before waking and highest an hour or two before falling asleep. If you feel a chill sometimes when you are up at strange times, it is because your clock is at a pre-waking (late-night) phase.

Melatonin is secreted only at night (circadian clock time) and is not dependent on sleep. However, bright light tends to reduce melatonin levels. In summer, nights are short, thus the duration of the melatonin “signal” is short. In winter, nights are long, thus the duration of the melatonin “signal” is long. The duration of the melatonin signal is the cue that the circadian clock (this is in mammals only) uses to detect season, i.e., the changes in photoperiod (daylength) – information important for timing of seasonal events, e.g., molting, migration, hibernation, reproduction. Humans are only mildly seasonal – our ancestors about 70 million years ago were living in little holes in the ground, were tiny, were nocturnal, were seasonal breeders, and were hibernators. Some traces of our ability to measure photoperiod are retained in “winter blues”, or Seasonal Affective Disorder (SAD). It is almost a form of hibernation.

Phase-disorders of the circadian clock (i.e., extreme larks or owls) can have a similar effect by tricking the melatonin signal (or the reading of the signal by the clock) into believing it is always winter, thus time to be depressed. Lithium treats depression by affecting the period (thus indirectly phase) of the circadian clock (both in vivo and in vitro). In bipolar disorder, manic episodes are characterized by phase-delays and depressive episodes by phase-advances of the diurnal sleep-wake and activity patterns. In a way, phase-delayed people are constantly in the depressive phase of the bipolar disorder.

Treating Extreme Larks and Owls

Trying to regulate sleep-time with melatonin supplements can be tricky. If you are phase-delayed, thus producing melatonin in summer from 2am until 10am, if you take a melatonin pill at 10pm in order to go to sleep earlier, your clock will see a winter-like melatonin signal of 12 hours duration (10pm-10am) and will make you depressed within a couple of days.

The best way to shift a clock is by using bright light. Instead of buying a $500 light-box, you can, for much less money, build your own for a fraction of that money. You need a piece of board, 3-4 strong neon lightbulbs, balasts, a switch, a plug, and some wires. An hour of fun, and you have an apparatus that is just as good and effective as the hifallutin corporate gizmo. Use the light box at appropriate times (dawn for owls, dusk for larks). If you are an extreme owl, when you first get up in the morning, immediately go out in the sunlight (that is thousands of lux of light energy, compared to hundreds from a lightbox) for a jog with your dog. If you do not have a dog, buy one – that will force you to go for a walk early in the morning. Well-scheduled meals also help.

Do not take anti-depressants. They tend to not work for circadian-based depression and may just mask the symptoms (i.e., you “feel” good while your body is falling apart). Do not use melatonin supplements. Do not use alcohol – it may make you fall asleep fast, but the sleep will be shallow and erratic and you will wake up feeling lousy instead of rested. Caffeinated drinks are fine, except during the last 2-3 hours before your intended bedtime, at which time a warm glass of milk may be better.

Make a routine in the evening. The last 2-3 hours before bedtime stay out of the bedroom (bedroom is only for sleep and sex), and switch off all the screens: no TV, no computer, no gameboy. Reading a book while sitting in an armchair in the living room is fine. Just sitting on the porch and thinking will help you wind down. As the evening progresses gradually turn down the lights. Once the bedtime arrives, go to the bedroom, go to bed, switch off the light (pitch darkness) and go to sleep if you can. If you cannot, get up for a few minutes, but keep your lights dim, still no screens, no caffein, no food.

Of course, all of the above are the strategies to shift your clock to a “socially accepted” phase. But you are not crazy or sick. It is the societal pressure to get up at a certain time that is making you sick. Try to get a job that fits your natural schedule. Work at night, sleep during the day (in a pitch-dark, light-tight, sound-proof room) and enjoy life in all its quirkiness.

If you need to go to the bathroom in the evening or during the night, do not turn on the light. Can’t you find your vital organs in the dark? If neccessary, a very dim nightlight (or indirect light from the hall) is OK. If you wake up in the middle of the night, do not get up or switch on the light. Have sex instead. Hopefully your partner will enjoy being woken up by your kinky activities. You will both crash into pleasant deep sleep afterwards. If you do not have a partner, just do it yourself without switching on the lights (as I said, you can find your vital organs in the dark). Jocelyn Elders was onto something….

Why We Sleep Like This?
A classical sociobiological just-so story posits that this kind of individual variation on the lark/owl continuum had an adaptive function, namely to ensure that at every time of night at least one member of the tribe was awake. Thus some stood guard early in the night, others late in the night, listening to the sounds of the jungle (or savannah, or whatever) while the midnight break is thought to have been used for copulating with whomever also happens to be awake at the time – this was before the social invention of sexual monogamy.

Why did cave-men live in caves? Caves are rare and expensive pieces of real estate. If you find one, it is likely to be already inhabited, thus you need to kick out the old tenants (bears?) in order to move in. Then you have to defend it from others who also want this nice piece of property. And it is difficult to defend a cave – it has one entrance – the rest is a trap. If the intruder is really dangerous you have two options: to go out and be killed outside, or remain inside and get killed in the cave. What is so important about the cave that warrants such a risk? Is it that a possible attack can come only from one side, thus requiring only one guard at a time? Is it that newly naked human animals needed shelter from bad weather that they did not need while they were still furry? Is it to protect the newly acquired fire from being extinguished by rain? Does it make easier the task of keeping the herd of not-yet-that-well domesticated animals all together and preventing it from running away? Possibly all of it – we’ll never know – it’s a “just-so” story. But do not forget one very important property of the cave: it is dark inside. It is easy to sleep in the dark. Most animals find shelter or burrow when they want to sleep – this is not just to hide from the enemies and weather, but also to hide from the sunlight.

Sleep is one of the strongest human needs. If you have read the last part of my four-part series featured on the previous Tangled Bank, you have read my ideas why we still don’t know what sleep is for (though see the current state of knowledge in, e.g., this paper: Origin and evolution of sleep: roles of vision and endothermy (pdf)). While I am not advocating ditching modernity, cutting off electricity and going back to the old sleep pattern, we still do not know enough about sleep in order to make the 24-hour society work for us without too much in the way of health consequences.

Hey, teacher, leave us kids alone (to sleep late)

It has been known for a while that adolescents are quite extreme “owls” no matter what their chronotype may be earlier and later in life (and fortunately, school districts are starting to recognize this). This has been attributed to the surge of sex hormones in early adolescence. Responsiveness of the circadian clock to sex hormones has not been studied much (virtually not at all, though I should be able to publish my data within a year or so, sorry for not being able to divulge more detailed information yet), yet most people in the field believe this to be the case, even if no details are available yet.

Now a new paper suggests that the end of adolescence should be defined as a time when the circadian clock goes back to its “normal” state. But, wait a minute, the hormones do not disappear at that time. Thus, if the clock is responding to the hormones at the onset of the adolescence, does this mean that the end of adolescence should be defined as the time when the clock becomes UNRESPONSIVE to the hormones? How does that happen and how is that triggered?

Anyway, I still have to look at the study itself (this is just a press release). I want to see if females both become “owls” AND quit being “owls” earlier than males [OK, I took a peek at the paper and yes, they do]. Also, in women, hormones (mostly estrogen and progesterone) surge in monthly cycles that end abruptly at menopause, while in men testosterone (mainly) is pretty high (with a small circadian variation) continuously and only gradually declines in old age. The lifelong sex difference they found in the study is quite interesting in this light.

Also, I like the way they tried to tease away social influences from pure biology, though they are correct to warn they do not know in which direction causation flows: do the teenagers sleep late because they party, or do they party because they are wide awake…..and now a closet sociobiologist is waking up somewhere in my head trying to explain why would it be adaptive for teens to stay up late and play, including perhaps experimentation with sex while elders are asleep (squash, bad sociobiologist…go back to sleep…there, good boy)….

Wake Me When It’s Over

“Societies define adulthood in different ways, from entering puberty to entering the workforce. But circadian clock researchers now suggest that adolescence ends when we stop sleeping in.Teenagers are more likely to have trouble getting out of bed in the morning than are young children or adults–a finding many studies attribute to a chronic lack of sleep. But researchers at the University of Munich wondered if a more fundamental biological factor played a role.Using a brief questionnaire distributed in clinics, universities and online, Till Roenneberg and colleagues collected data on sleeping patterns from more than 25,000 people in Germany and Switzerland. As part of their analysis, the researchers determined each person’s “chronotype” by calculating the mid-point of their sleep–halfway between going to bed and waking up–on days when the subjects slept as late as they wanted.A surprising pattern emerged. Average chronotypes drift later and laterduring the teen years, but then begin to move steadily earlier after the age of 20, the researchers report in the 28 December issue of Current Biology. It still isn’t clear why, says Roenneberg.

Teenagers may sleep late because they’ve been out partying or they may go out because they’re wide awake at 11 pm. However, he says, the team also saw a similar pattern in teenagers in rural valleys in South Tyrol–where nightclubs are relatively scarce. There, the average chronotype wasabout an hour earlier, but the overall age pattern was the same. The researchers also saw differences between the sexes, with females having an earlier average chronotype than males until around age 50–consistent with menopause–when the correlation between age and chronotype seems to break down. This suggests, Roenneberg says, that biological factors such as hormones have an important influence on the tendency to sleep late.Sleep researcher Mary Carskadon of Brown University in Providence, Rhode Island, says that both social and biological factors are likely involved. Finding the biological trigger–if any–could lead to a better understanding of what drives circadian rhythms, she says.”

Of course, the study was done on Germans. Even in disco-less South Tyrol there is electricity and modernity. It would be cool to see a similar study performed in a culture where sleep is divided in two parts (late-night sleep and afternoon Siesta), like in Mediterranean and Latin American countries, as well as in a real primitive society in which sleep is divided into two parts (early-night sleep and late-night sleep with a break for sex around midnight).

Societal Constraints

One thing we know is that darkness is an important aspect of the environment conducive to sleep. Silence is another. And we do not need science to tell us this – it’s been known forever. I remember, as a kid, learning the “sleep manners”, along with learning how to say “please” and “thank you”, how not to interrupt adults when they were on the phone, and other early lessons of life. By “sleep manners” I mean behavior when there is someone asleep in the house: one is not to enter the room with the sleeping person, not to switch on the lights, not to switch on the noisy appliances (TV, vacuum cleaner, hair dryer or wash machine), not to talk at all if possible, or reduce it to the briefest quietest whisper if absolutely neccessary. One is to walk around on tiptoes, although the best idea is just to leave the house for a while. There was also a ban on telephone use between 10pm and 8am and again between 2pm and 5pm (so-called “house order”). Sleep was treated as something sacred. Be it at night, or the afternoon siesta, only a life-or-death emergency situation warranted waking someone up.

As Robert Anston Heinlein said:

Waking a person unnecessarily should not be considered a capital crime. For a first offense, that is.

One thing I noticed upon arriving to the States is that nobody here seems to have any notion of “sleep manners”. I have seen (and experienced) many times people barging into the room containing a sleeping person, switching on the lights and TV, talking, even talking to the sleeping person, all the while not being even aware that this is a Big No-No, very inconsiderate, and extremely rude. When confronted, the response is usually very defensive, stressing the person’s individual right to do whatever he/she wants and not bother about being considerate about some lazy bum who is sleeping at an inappropriate time. Whoa! Stop right there!

First, individual rights are assumed to mean that you can do whatever you want as long as that does not hurt another person in some way. Waking someone up is harassment – of course it hurts someone. Second, there is no such thing as inappropriate time. If you can, you sleep whenever you can. There is no appropriate or inappropriate time. What do you do if someone is working the night-shift (like my wife often does, and I sometimes do, too)? That person will sleep during the day, so you better shut up. Third, what is this about sleeping being a sign of laziness. The “owls” are constantly being treated as lazy, though they are more likely to be sleep-deprived (cannot fall asleep until the wee hours, then being rudely awoken by the alarm clock after just a couple of hours) and spend more hours awake (and presumably productive) than “larks” do. If you are asleep, this means you need it. If you are rested enough you cannot physically remain asleep or go back to sleep again. You are wide awake. Thus, when you see someone asleep, it is because that person needs sleep right there and then. Sleep is not laziness. Laziness is “lots of front-porch picking”.

Pretending that sleep-need does not exist is also institutionalized. I am not talking just about night-shifts and rotating shifts (those will kill you), night flights, being available for communication 24/7, stores open 24/7, etc – those are part of a modern society, will not go away, and we just need to learn how to adjust. I am talking about the building standards. With a huge proportion of the population working at night, why do windows have no blinds? Some old manors do, but new buildings do not. Never. Some have fake blinds, just for show, screwed into the outside walls on the sides of windows, yet cannot be closed. There are no built-in black curtains, or roll-down wooden blinds. It is difficult to find such curtains in stores if one wants to install one. What is going on? I have never seen, heard, read about, or experienced another country in the world in which sleep is not sacred, and blinds are not an essential part of a house.

I see some striking parallels between the way this society treats sleep and the way it treats sex. Both are sinful activities, associated with one of the Seven Deadly Sins (Sloth and Lust). Both are associated with the most powerful biological needs. Both are supposed to be a taboo topic. Both are supposed to be done in private, at night, with a pretense that it is never actually happening. Education in sleep hygiene and sex hygiene are both slighted, one way or another (the former passively, the latter actively opposed). Both are thought to interfere with one’s productivity – ah, the good old Protestant work ethic! Why are Avarice and Greed not treated the same way? Raking in money by selling mega-burgers is just fine, and a decent topic of conversation, even a point of pride. Why are we still allowing Puritan Calvinist way of thinking, coupled with capitalist creed, to still guide the way we live our lives, or even think about life. Sleeping, whether with someone or alone, is a basic human need, thus a basic human right. Neither really detracts from the workplace productivity – au contraire: well rested and well satisfied people are happy, energetic, enthusiastic and productive. It is sleep repressed people, along with the dour sex repressed people, who are the problem, making everyone nervous. How much longer are we going to hide under the covers?

Perhaps not that long. It appears that we are slowly waking up to sleep problems (pun intended). More and more companies are allowing naps, and even providing nap-rooms. More and more school districts are moving high-school morning schedules later, as during teenage years, under effects of sex hormones, the circadian clocks are all temporarily “owlish”. Adolescents are not crazy and lazy – they physically cannot fall asleep at a normal bed time, and physically cannot awake and feel rested early in the morning (elementary and middle school kids can, as their hormones have not surged yet).

It seems political advisors have caught on, too. During the presidential debates I blogged about the likely tacks used by the handlers to get their candidates to be at their peak performance levels in early evening – something apparently more difficult for Bush than Kerry ( see this and this). Battle for More Free Time, including its subset: the Battle for Sleep, is re-entering the political domain again. Check the links to the websites commenting on this newly-brewing movement. And of course, the art of matchmaking is starting to include the lark/owl questionnaire, assuming that people of the same chronotype are a perfect match (I saw this in a magazine in a waiting room, but if anyone knows if online dating services are doing this, please let me know).

Popping melatonin pills is one of the latest crazes. Melatonin failed as a sleeping pill and its uses as a scavenger of free radicals are dubious at best. It can shift one’s clock, though. However, it cannot help against jet-lag or effects of shift-work (shift-lag) as melatonin is likely to shift only the main brain pacemaker in the suprachiasmatic nuclei. The problem with jet-lag and shift-lag is dissociation of rhythms between cells in different tissues, i.e., your brain clock may resynchornize to the new time-zone/schedule in a couple of days, the clocks in your heart and lungs in a week, and in your stomach and liver in a month. In the meantime, everything in your body is desynchronized and you feel really bad. If you keep changing your work shift over and over again, you never get to achieve complete synchronization, leading to long-term effects on health, including significant rise in heart attacks, stomach ulcers, and breast cancer.

Well, intercontinental flight is here to stay, and some shift-work is neccessary for the modern society to survive. It is now understood that some people (chronotypes) adjust to night-shifts and even properly executed (non-rapid, phase-delaying) rotating shifts, better than others. People have always tried to self-select for various schedules, yet it has recently started to enter the corporate consciousness that forcing employees into unwanted shifts has negative effects on productivity and safety, thus bottom line. See Chernobyl, Bhopal, Exxon Valdese and Three Mile Island accidents – all caused by sober but sleepy people at about 3am, just like thousands of traffic accidents every year.

So how does the future look like? As usual, don’t ask scientists, especially members of the Academy. If you want answers to scientific questions about the future, you have to read science-fiction – this is a sacred duty of all scientists. Cory Doctorow who blogs on the group blog Boing Boing, has written a novel “Eastern Standard Tribe” (you can buy it, or download for free here) that answers just such questions. In the future not so far, people form communities not according to geography, or hobbies, or ideology, but their time zone. Everyone, no matter where on the planet, awake and at the computer at the same time, belongs to a particular Time Zone Tribe. Thus an owl from one country, an average from another and a lark from another will all be typing and reading at the same time, thus will meet in cyberspace and forge alliances against other time-zone communities. Inter-time-zone wars ensue, intrigue and treason happen, boy meets girl…the story is wonderful and will make you think about sleep, and about circadian rhythms, about Internet, and about being human, all in ways you never thought before. Enjoy.

City Of Light: Insomniac Urban Animals

The Cities are the topic of the month here at Scientific American (and at least this week on the blogs), so I should chime in on an aspect of urban ecology that I am comfortable discussing – the effects of increased light at night on animals.

Not all species of animals are negatively affected by the urban environments. Even humans are not driven to insanity by the urban jungle. Some species are really thriving – rats, mice, squirrels, bats, alligators in sewers, sparrows, pigeons, starlings, crows, house flies, mosquitoes and cockroaches come to mind. Many birds have evolved (or invented) quite nifty adaptations to urban life. Of course, animals we domesticated and keep as pets, like cats and dogs, don’t really care about the city vs. country, as long as they are with us and we take good care of them.

But there are definitely negative effects as well. After all, just counts and surveys of species make it obvious that many species are not thriving in dense urban ecosystems. Not all cities are the same either. A large, dense city is likely to be much less hospitable to many species than urban sprawl where much greenery and the original natural habitat are still preserved between the cul-de-sacs. Just watch the wilderness appearing on my back porch: skinks, tree frogs, Luna moths, white-tailed deer, rabbits, opossums, racoons, cicadas, endless species of birds…and I am in the middle of the Triangle, NC.

Large animals, in general, will not do well in cities, and not just because direct encounters with humans can often be deadly (imagine what would happen to a herd of bison if it tried to trek through streets of Manhattan?). Herbivores will be starved due to lack of plants, and carnivores will starve due to lack of herbivores. Thus many ecological factors affect the ability of species to adapt to the City – food, predators, shelter, and, importantly, noise.

But I will focus only on light today. Light pollution is often discussed in the context of impossibility to see the wonderful starry night, but effect of night light on wildlife is a problem beyond human esthetics – it has real-world consequences for the health of ecosystems. And the effect of light almost always involves, in some way, the circadian clock.

Circadian clock – a very, very quick primer

There is quite a lot of biological complexity in the circadian clock, but let’s just remember the few key, basic points.

Circadian clock is a structure (in animals it is in the brain) that governs the daily rhythms of biochemistry, physiology and behavior.

All organisms living on or near the surface of the Earth have a circadian clock. Those that now live deep down inside the soil or rocks or caves, or on the bottom of the ocean, may have secondarily lost the clock that their ancestors once had [1,2].

Having a circadian clock is an adaptation to the cycles of day and night in the environment. Where such cycles are altered, e.g., near the poles, the animals have evolved the ability to turn their daily clocks on or off as appropriate.

Circadian clock keeps ticking in constant darkness, or constant dim light. But in many species, constant intense light disrupts the rhythm.

The clock is reset (entrained, synchronized) each day by the alternation of light and darkness. Species differ as to the intensity of light needed for this resetting to take place. While physiological laboratory experiments usually test the light intensity against the background of complete darkness (in which the sensory systems can get adapted to the dark and become more sensitive to light), it is the difference in light intensity between day and night that is of ecological relevance.

Clock is not a dictator

As much as the circadian clock is “hard-wired” in the brain and determined by the clock-work of genes turning each other on and off, there is still quite a lot of plasticity of behavior – animals can act against the signals from the clock and do stuff at odd times if needed.

For example, when hungry, nocturnal animals will hunt during the day, e.g., man-eating lions hunting at dusk and early night on moon-less night, have to hunt during the day when the moon is full.

Also, these days bats in Austin, TX are flying out earlier at dusk due to prolonged dry weather conditions decimating their food.

Two species of golden spiny mice in Israel live in the same spot – one of them is more aggressive, so the other one has evolved adaptations (including even changes in the eyes) to forage during the day instead of night. Yet, when placed in isolation in the lab, both species are strictly nocturnal, active only at night, which shows that day-time foraging goes against the clock, i.e., is not the adaptation of the clock itself [3].

Finally, when population of rats in a city gets too big, some individuals are displaced. They are displaced in space – foraging on the surface instead of underground – and they are displaced in time – foraging during the day instead of during the night. If you see a rat digging through the garbage bags on the street in the middle of the day, you know that the total population of rats under ground is absolutely enormous! If you are interested in learning more about the fascinating ecology of urban rats, read the wonderful book ‘Rats‘ by Robert Sullivan.

Light at night, clocks and the outside world – behavior

One of the adaptive functions of having a clock is to synchronize one’s activities to that of other players in the ecosystem [4]. You want to go out hunting at the time when your prey is out and about and easy to catch. You want to hide (and sleep) while your predators and enemies are out on the prowl.

But what happens when the difference in the intensity of light is not very different between day and night, as in well illuminated cities? Some species will remain nicely entrained to the cycle, but others will not. Some individuals will be better entrained than others. Some will have their clocks reset over and over again and they will behave at different odd times each day, while in others all rhythms will get lost and they will be out and about all the time.

Thus, many individuals will be going about their lives at inappropriate times, perhaps when the predators are around (and predators are doing the same – one or another will be hunting at any time of day or night), or when the prey is hiding (so too much energy is wasted in looking for elusive food). As a result, many individuals will starve, or get eaten, or miss reproductive opportunities (hey, where are all the potential mates – why are they all hiding and sleeping at the time I am looking for them everywhere?).

Living in an environment in which is is hard to tell if it is day or night is similar to living without having a circadian clock at all. A couple of studies out in the field [5,6,7], with a couple of different species of rodents in which the clocks have been surgically removed from their brains, showed that such animals wonder around at unusual times and are significantly more prone to predation (this is a scientific way of saying: “they got slaughtered by wild cats within hours”).

Light at night, clock and the inside world – physiology

Another adaptive function of the clock is to synchronize events happening inside the bodies, both with each other and with the outside environment. It saves energy if two compatible functions in the body happen simultaneously, while incompatible events are happening at different times. By tuning into the outside cycles of light and dark, the body allocates different biochemical and physiological functions to different times of day, thus saving energy for the animal overall.

And energy is the key. At the time when food is around, it pays to invest energy in finding it. At times when food is hard to find, it is a good idea to use less energy, to stop, hide and sleep. The rate of energy production and use by the body – the metabolism – can be measured in warm-blooded animals (the ‘euthermic’ animals like birds and mammals) by measuring their core body temperature. Higher the metabolism, higher the temperature.

Normally, body temperature cycles throughout the day. Circadian clock drives this cycle so, for example, our bodies are coldest at dawn, and warmest in late afternoon. In birds the difference between the low and high point during the day is routinely a whole degree Celsius. And some small birds, like swifts and hummingbirds, let their temperature drop much, much more during the night (this is called “daily torpor”).

Having or not having food affects how much the body temperature will drop during the night. A hungry animal will save energy by dropping body temperature at night much more than a satiated animal [8]. Yet, temperature will rise to its normal levels the next day in order to give the animal sufficient energy (and speed of reaction) to successfully forage again.

Body temperature drops at night when there is no food, and it also drops during the day if there is no light-dark difference - Ref.8


Light affects this: if there is no difference in light intensity between day and night, e.g., in the laboratory in constant darkness, both daytime and nighttime temperatures will fall in hungry animals [8] – they would become too slow and feeble to forage effectively if out in the field. But constant light has the opposite effect – keeping the body temperature artificially high at all times, i.e., not allowing the hungry animal to save energy by dropping its body temperature. The energy balance, especially in a small animal, can quickly become negative, leading to death of starvation.

Reduced perception of day-night changes in light reduces the amount of change and slows down the change in body temperature (top - normal vision, middle - eyeless, bottom - obstructed vision) - Ref.9


Light at night, clock and reproduction

In many birds, length of day affects egg-laying in a way that helps the animal determine the total size of the clutch of eggs: how many she lays in one breeding attempt (usually one per year). Data from the laboratory (in chicken, quail and turkeys) [9,10] and from the field (bluebirds [11], also swallows and owls – unpublished data) suggests that this is a widespread mechanism in a variety of bird species.

In early spring, a bird may lay a lot of eggs in a clutch - Ref.10

In late summer, the bird may lay a smaller clutch - Ref.10

If the difference between light intensities at day and night is too small for the bird’s brain to integrate, the bird may be making too much of a breeding effort – laying too many eggs over a period of too many days, perhaps even throughout the year, thus exhausting her internal energy resources, while bringing too many hatchlings to life while unable to feed them all…a disaster all around.

Light at night, clock and calendar

There is a reason for the season. Many organisms do certain things at particular times of the year; breeding, molting, migration and more. The internal “calendar” they use to time such changes in behavior is dependent on the circadian clock which measures the gradually changing length of day throughout the year. The precision of such a measurement can be quite astonishing (see swallows of San Capistrano) [12].

So, what happens if there is not much of a difference between daytime and nighttime illumination? The clock interprets this as constant light, which is the ultimate “long day”, so the animal will constantly be in the “summer mode”, e.g.,. constantly breeding, or constantly trying to migrate or constantly molting its feathers or hair. All of this is energetically costly, and thus maladaptive, and will lead to exhaustion and eventual death of the animal (that is on top of not being in synchrony with other individuals of its species, see above).

Light at night, clock and orientation

When a moth wakes up in the evening and starts flying to find food, it orients by the Moon. It assumes a constant angle to the Moon and keeping that angle allows it to fly in a straight line. After all, the Moon is high and very far away, so flying along does not change the Moon’s relative position in the sky. This is called “transverse” or “Y-axis” orientation.

But the Moon moves across the sky during the night. If a moth is flying for a longer time, it will use its internal clock to compensate for this movement by gradually changing the angle.

What if, instead of the Moon, the moth sees another bright light, perhaps the one on your porch? It starts using it for orientation. At first, it will fly in the straight line. But as it comes closer to the light, the angle changes – the light “moves” in relation to the moth. So the moth compensates by turning in order to keep the constant angle. And then it turns again, and again, and again, spiraling in until it hits the light itself. By that time the light is so close and so bright it looks more like the Sun than the Moon. Its clock gets reset to “day”. So the nocturnal moth alights nearby and, instead of foraging for food, falls asleep. In a wrong place, where it is an easy pick for predators – bats at night, birds at dawn [13,14,15,16].

Birds also orient by celestial bodies. During the day, they orient by the Sun. Again, they use their internal clocks to compensate for the Sun’s movement across the sky. At night, they may use the Moon for orienting, but they certainly use the stars [17]. All the artificial lights become stars. Birds get disoriented, fly in all the wrong directions, and hit the windows and die.

What to do?

This post is really NOT about the solutions, but rather about the underlying science of light effects on animal behavior, physiology and health. I will leave the solutions to others who are experts on engineering or urban policy, who may use the science described above to get informed as to what kinds of solutions may work best.

From what I know, many cities are now starting to tackle the problem of light pollution. Sky lights are banned in some places or at some times of the year (e.g., times of big bird migrations). Many tall corporate buildings now instruct their tenants to turn off the lights at night. There are new designs of street lights that point down – the street below is illuminated even better, much much less light (and diffused, not pointed) goes up to the sky wasting energy and confusing the critters flying by. I am sure there are other things that people do, or things that can be done to reduce the amount of light, or at least the appearance of light sources as “points”, that can be adopted by cities worldwide.

We will never make the cities completely dark at night. And that is OK. After all, the Moon and the stars make nights quite bright out in the wilderness as well. All we need is to make sure that the difference in light intensity between day and night is sufficient for animals to entrain their clocks properly to the daily cycle of bright-light and not-as-bright-light, and they should be fine.


[1] Lee, D.S. (1969). Possible circadian rhythm in the cave salamander Haideotriton wallacei. Bull.Maryland Herp.Soc. 5:85-88.

[2] Trajano, E. and Menna-Barreto, L. (2000). Locomotor activity rhythms in cave catfishes, genus Taunayia, from Eastern Brazil (Teleostei: Siluriformes: Heptapterinae). Biol.Rhythm Res. 31:469-480.

[3] Kronfeld-Schor, N., Dayan, T., Elvert, R., Haim, A., Zisapel, N. and Heldmaier, G. (2001). On the use of time axis for ecological separation: Diel rhythms as an evolutionary constraint. Amer.Nat.158:451-457.

[4] Fleury, F., Allemand, R., Vavre, F., Fouillet, P. and Bouletrau, M. (2000). Adaptive significance of a circadian clock: temporal segregation of activities reduces intrinsic competitive inferiority in Drosophila parasitoids. Proc.R.Soc.Lond.B 267:1005-1010.

[5] DeCoursey, P.J., Krulas, J.R., Mele, G. and Holley, D.C. (1997). Circadian performance of Suprachiasmatic nuclei (SCN)-lesioned antelope ground squirrels in a desert enclosure. Physiol.&Behav. 62:1099-1108.

[6] DeCoursey, P.J. and Krulas J.R. (1998). Behavior of SCN-lesioned chipmunks in natural habitat: a pilot study. J.Biol.Rhythms 13:229-244.

[7] DeCoursey, P.J., Walker, J.K. and Smith, S.A. (2000). A circadian pacemaker in free-living chipmunks: essential for survival? J.Comp.Physiol.A 186:169-180.

[8] Herbert Underwood, Christopher T. Steele and Bora Zivkovic, Effects of Fasting on the Circadian Body Temperature Rhythm of Japanese Quail, Physiology & Behavior, Vol. 66, No. 1, pp. 137-143, 1999

[9] Zivkovic BD, Underwood H, Siopes T., Circadian ovulatory rhythms in Japanese quail: role of ocular and extraocular pacemakers, J Biol Rhythms. 2000 Apr;15(2):172-83.

[10] Zivkovic, B.D., C.T.Steele, H.Underwood and T.Siopes. Critical Photoperiod and Reproduction in Female Japanese Quail: Role of Eyes and Pineal. American Zoologist 2000, 40(6):1273 (abstract).

[11] Caren B. Cooper, Margaret A. Voss, and Bora Zivkovic, Extended Laying Interval of Ultimate Eggs of the Eastern Bluebird, The Condor Nov 2009: Vol. 111, Issue 4, pg(s) 752-755 doi: 10.1525/cond.2009.090061

[12] BD Zivkovic, H Underwood, CT Steele, K Edmonds, Formal Properties of the Circadian and Photoperiodic Systems of Japanese Quail: Phase Response Curve and Effects of T-Cycles, Journal of Biological Rhythms, Vol. 14, No. 5, 378-390 (1999)

[13] Kenneth D. Frank, Impact of Outdoor Lighting on Moths: An Assessment, Journal of the Lepidopterists’ Society 42 (no. 2, 1988): 63-93.

[14] Sotthibandhu, S. & Baker, R.R. (1979). Celestial orientation by the Large Yellow Underwing Moth, Noctua pronuba L. Anim. Behav., 27, 786-800.

[15] Baker, R.R. (1979). Celestial and light trap orientation of moths. Antenna, 3, 44-45.

[16] Baker, R.R. & Sadovy, Y.J. (1978). The distance and nature of the light-trap response of moths. Nature, Lond., 276, 818-821.

[17] Sauer, E.G.F. and E.M.Sauer, 1960. Star Navigation of Nocturnal Migrating Birds. In Cold Spring Harbor Symposia on Quantitative Biology, Vol. 25. pp.463-473.

Images: U.S. light pollution map: NOAA; San Francisco at night, by Thomas Hawk on Flickr (part of the Ligh pollution Flickr collection); Moth attracted by porchlight from Wikimedia Commons. The rest of the images are drawn by me, including from my papers (the original raw files, not copied from final PDFs).

The Science Of Driving And Traffic – the importance of breaking the rules

I wrote this post back in December of 2006 (yes, I think my writing has improved since then) and not much has changed except that the roundabout on Hillsborough Street in Raleigh has been in place for a while now, I drove it several times, and it seems to be fine (though they had to add signs ahead of it to teach the drivers how to use a roundabout) and is certainly successful in eliminating congestion.


Let me state up front that this is not a topic I know anything about, but I have always had a curiosity for it, so let me just throw some thoughts out into the Internets and see if commenters or other bloggers can enlighten me or point me to the most informative sources on the topic. This is really a smorgasbord of seemingly disparate topics that I always felt had more in common with each other than just the fact that they have something or other to do with traffic. I am trying to put those things together and I hope you can help me.

1. Models of Traffic Flow

There are two kinds of people modelling traffic: traffic engineers and physicists. The former use traditional modelling techniques, while the latter indulge themselves in using more esoteric methods, e.g., cellular automata, etc. The traffic engineers, apparently, are not too fond of the models developed by physicists, and I always wondered what the reason for this was and tended to dismiss it as mere professional jealousy and turf-protection. But now I think there is a deeper reason – the two groups do their modelling with two different motivations.

The physicists are testing the math and playing with the computers. Their models are applicable not just to traffic but also to other types of flow, e.g., blood flow. Their main goal is to figure out the conditions that determine when the flow will be smooth, when there will be stop-and-go traffic, and when the whole thing will be ground to a stop.

The traffic engineers, on the other hand, have two goals: smooth traffic flow is one of them, but the other one is to ensure the maximal safety of every individual participant in traffic, something that physics models are barely starting to address. The engineers’ goals are practical – how to build roads in a way that maximizes flow AND maximizes safety. For that, their models have to incorporate not just the behavior of the entire system, but also the behaviors of each individual driver based on the real-life behavior of people operating motor vehicles (as well as cyclists and pedestrians). The physics models have only recently made some baby steps into incorporating realistic human behavior into their models. After all, humans beings behave differently in traffic than red blood cells in blood circulation.

I could not find a study that I remember from a few years back that shows that the “jerks”, those people we hate because they speed and weave in-and-out of lanes, actually contribute to smooth flow – without them, the traffic would be more likely to get congested. Although the speeders only shave off a couple of minutes of their own traveling time, their behavior prevents the blockage of traffic and thus also shortens the travelling time for everyone else.

For (I think) excellent summaries of the current state of traffic modelling I recommend these two articles: Stop-and-Go Science and The Computer Minds the Commuter. Is there anything better or more recent I should read?

2. City Traffic

Most of the traffic flow models I read about deal with the flow and congestion on highways. I could not find that much on modelling traffic of city streets. Such models must exist, though, as someone must have made some calculations when suggesting roundabouts on Hillsborough Street in Raleigh (the street that serves as a northern border of the North Carolina State University campus). For the heated debate about this, check out this excellent blog post and comments and this commentary, just to quickly get up to speed. This discussion has been going on for quite some time now, with quite strong feelings exhibited by the two sides of the issue – the pro and con groups. I have nothing empirical to base my feelings on, but I instinctively aligned myself with the pro-roundabout side. It just felt right. Am I wrong? Why or why not?

3. Car Safety

About a year ago, I have read (in ‘Discover’ magazine, I believe), several people’s essays on the “Future of the Car”. Most wrote about new gizmos and gadgets, more entertainment, and more automation. But one was thinking completely out of the box and I loved it! How to improve safety of the cars, he asked? Not by building bigger, harder and stronger cars with more and more nifty safety features – that is just a never-ending arms-race. Instead, take a lesson from the inflatable gas bags – what makes it useful is its softness, not hardness! So, the author argues, why not make the OUTSIDE of the car as soft as a marshmallow? People would still not want to bump into each other because it affects their own speed and direction, but if such a contact occurs, nobody gets hurt! Brilliant!

4. Geography of Driving Philosophy

I learned to drive back in Belgrade when I was about 18 (min. driving age there), but never bought a car so I did not drive there very much. Still, the driver ed there is a long grueling process, about 40 lessons stretching over several months. During the course, I drove on the highway and in miniscule city streets. I climbed a mountain (and drove back down again on a very narrow twisty road). I drove out in the woods outside the city in freshly fallen deep snow (and my instructor and I helped a couple of other people get their cars out of the ditches). When the city streets were covered with ice one day, my instructor made me go to the hilliest part of town and taught me how to negotiate very steep uphills and downhills on ice.

But, although the driving school was just a couple of blocks away, I had to wait until almost the end of the course until I was allowed (Allowed? Forced – I was terrified!) to try to negotiate Slavija (see picture) – a huge roundabout in the very center of Belgrade where there are absolutely no traffic signs! There are some simple basic rules of traffic applicable to the situation, but most of the rules were actually unwritten rules and all the traffic around it was based on driver-driver negotiation. The way people drive there, everywhere in the country but nowhere felt as palpably as on Slavija, is by such driver-driver negotiations: one part applied psychology, one part hand-and-eye signals.

When I arrived in the United States I had to start driving because there is no other way to get from A to B. And that is when I realized that the driving philosophy is different here – it is not based on negotiations, but rather on strict obedience to much better defined nitty-gritty rules. There are exceptions – driving in Manhattan is more Europen-style in this matter and there may be some other geographical differences within the USA. See this and this for examples.

There is something about this that makes me uneasy. I have a feeling that many people here drive on ‘automatic pilot’, lulled into complacence by a naive expectation that strict following of rules will automatically make them safe. I see it in myself. When I have a sense of flow and a full awareness of my surroundings I drive much safer but that also means that I often buck the rules. After all, the rules are just suggestions, the scaffolding on which we build our driving behavior using our knowledge and experience.

When we drive we make decisions every moment. Most of the time, the decisions we make will be within the rules and laws of traffic. But sometimes, the best decision is to not follow the rules. Safety is the primary concern. When it is satisfied, efficiency comes in as a second concern, followed by wish to minimize wear-and-tear of the car, greater comfort for the driver and passengers, and the fuel efficiency. Blind obedience to rules often does not satisfy either one of these, and when safety is challenged, bucking the rule is the best thing to do.

But, I got a couple of tickets the other year for “rolling through a stop sign” so now I obediently stop. And I discovered that this gives me a false sense of security – I do not pay as much attention to what is really happening in traffic around me. That is unsafe!

What I think is happening is that these stop signs are unnecessary – they should not be there – and when I drive well, somewhere deep inside my mind there is a decision to ignore the sign because it is an obstruction in the way of safe driving. They are inside Southern Village – a little urban village that looks like a toy-set for kids. The fact that the streets are paved at all is kinda nice, and that streets have names is probably useful for the mailman, but traffic signs are totally useless and counterproductive because everyone here drives within the “negotiation paradigm” of driving. Unfortunately, there is a police station in the Village and some cops find it easy to hide in the narrow curvy streets (especially the corner or Parkside and Meeting streets) and quickly gather a bunch of tickets from me and my neighbors without having to go too far [Note; I have moved out about a year ago]. And who is going to argue cognitive science and the physics models of traffic flow with a guy who so clearly enjoys the power of his badge and his gun (and his BLACK uniform – I thought that no police or military force in the world, after the WWII, would be so stupid to use black uniforms of the SS again – as a son of a Holocaust survivor, my first visceral reaction to a black uniform is distrust and fear, not something that makes the cop’s job easier to do)?

So, I was really happy to find that I am not the only one who thinks that most traffic signs are unnecessary or even potentially dangerous. Garry Peterson wrote a great post about this very topic, in which, among else, he quotes from this excellent Wired article:

Hans Monderman is a traffic engineer who hates traffic signs. Oh, he can put up with the well-placed speed limit placard or a dangerous curve warning on a major highway, but Monderman considers most signs to be not only annoying but downright dangerous. To him, they are an admission of failure, a sign – literally – that a road designer somewhere hasn’t done his job. “The trouble with traffic engineers is that when there’s a problem with a road, they always try to add something,” Monderman says. “To my mind, it’s much better to remove things.”

Riding in his green Saab, we glide into Drachten, a 17th-century village that has grown into a bustling town of more than 40,000. We pass by the performing arts center, and suddenly, there it is: the Intersection. It’s the confluence of two busy two-lane roads that handle 20,000 cars a day, plus thousands of bicyclists and pedestrians. Several years ago, Monderman ripped out all the traditional instruments used by traffic engineers to influence driver behavior – traffic lights, road markings, and some pedestrian crossings – and in their place created a roundabout, or traffic circle. The circle is remarkable for what it doesn’t contain: signs or signals telling drivers how fast to go, who has the right-of-way, or how to behave. There are no lane markers or curbs separating street and sidewalk, so it’s unclear exactly where the car zone ends and the pedestrian zone begins. To an approaching driver, the intersection is utterly ambiguous – and that’s the point.

Monderman and I stand in silence by the side of the road a few minutes, watching the stream of motorists, cyclists, and pedestrians make their way through the circle, a giant concrete mixing bowl of transport. Somehow it all works. The drivers slow to gauge the intentions of crossing bicyclists and walkers. Negotiations over right-of-way are made through fleeting eye contact. Remarkably, traffic moves smoothly around the circle with hardly a brake screeching, horn honking, or obscene gesture. “I love it!” Monderman says at last. “Pedestrians and cyclists used to avoid this place, but now, as you see, the cars look out for the cyclists, the cyclists look out for the pedestrians, and everyone looks out for each other. You can’t expect traffic signs and street markings to encourage that sort of behavior. You have to build it into the design of the road.”

Definitely read Distracting Miss Daisy, On “Distracting Miss Daisy” and WHERE THE SIDEWALK ENDS for more thoughts about the idea that too much regulation, and too many signs, are actually making us less safe in traffic:

Do you love or hate Cilantro?

This post, originally published on April 25, 2009, although relatively short (for me, at least) and relatively devoid of new information, was a huge hit. It got lots of traffic, many comments, many incoming links, and the discussion spread around online social networks and lasted for quite a while. All it shows, really, is how passionate people are about their food….


If you think that political or religious debates can get nasty, you haven’t seen anything until you go online and see how much hate exists between people who love cilantro and those who hate cilantro. What horrible words they use to describe each other!!!!

Last weekend, I asked why is this and searched Twitter and FriendFeed for discussions, as well Wikipedia and Google Scholar for information about it.

First – cilantro is the US name for the plant that is called coriander in the rest of the world. In the USA, only the seed is called coriander, and the rest of the plant is cilantro.

Second – there are definitely two populations of people: one (larger) group thinks that it is the best taste ever, while the other group thinks it is awful. The latter group is not simply incapable of tasting cilantro – they can taste it in minuscule quantities hidden in food and describe it as “dirty dish-soap water taste”. People who cannot stand cilantro leaf are perfectly OK with eating the coriander seed.

So, it is something in the leaf that makes the difference.

Third – anecdotal information from scouring the Web suggests (“me and my Dad hate it…”) that the type of response to cilantro is inherited. It is also not experiental (those who hate it, hated it when they were kids, those who love it sometimes first tried it when they were already old and loved it at first try, and the response does not change with age, amount, kind of food preparation, etc).

Fourth – there is no scientific literature that I could find on the genetics of this. Is the difference at the level of the gustatory (or olfactory) receptors, or at higher-level processing centers in the brain?

Fifth – there is one paper that shows that the type of response to cilantro taste has nothing to do with the individual being a supertaster or not.

Sixth – There are a few older papers that identified chemical compounds in the leaves of cilantro, and a few about the allergy to cilantro, but no final identification of the compound that makes the difference in taste to the two groups.

So, does anyone else know more about this? Let us know in the comments.

In the meantime, be nice to people who are not your cilantro-type – they cannot help it.

Image: Wikimedia Commons

Blogs: face the conversation

The 20th century was highly unusual when it comes to the media and to the way people receive and exchange information. Telephone, telegraph, telegram, telex and telefax changed the way we communicated with each other. Inventions of radio and television, in addition to the final maturation of newspapers and magazines, changed the way people got informed (and subsequently educated after graduation).

Taking a long historical view, the 20th century was an exception, an anomaly.

But several generations grew up during that anomaly. And while the return to the older communication modes ushered and modernized by the Web, presumably more “natural” to us, may make it more pleasant to receive and exchange information today than it was in the last century, for most people there is also a sense of un-ease. There are habits that need to be broken. There are conventions that need to be re-standardized. There are mental abilities that need to be re-learned.

I have touched on some of these before. For example, in this older post I argued that abilities to assign trust to sources and to employ critical thinking need to be re-learned after a century on “automatic pilot”. I am not saying that our ancestors over the millennia were perfect, but at least they tried – these abilities were part of one’s everyday mental tool-kit.

In a more recent post, I argued that people will need to re-learn to discriminate between purely information-imparting texts from narrative and explanatory texts (and non-textual media) at a glance, without making automatic assumptions like they could do in the last century, i.e., just based on the “vessel’ in which the articles were held.

Now I am going to turn to yet another change in a habit of mind that has the 20th century media as a source and that Web is trying to revert: the continuity of the story.

And for that, the best approach, I think, is to start by looking at blogs and how they are changing the type of discourse on the Web. So, what is a blog?

Blog is software

Blog is primarily a platform. It is a piece of software that makes publishing cheap, fast and easy.

What one does with that platform is up to each individual person or organization.

Some media organizations publish their daily fare – the usual stuff you expect, e.g., news articles – on a blogging platform.

Others use it for PR and marketing. Or corporate news and announcements.

Some use it to engender political action, while others use it as a personal diary. Some use it to share kids’ photos with extended family, while some use it to post travelogues.

Remember that the first blogs were collections of links, without much additional input or commentary from the blogger. The tradition continues, and many bloggers still use their platform to filter the online content, to reach out to and support each other via links, or entire linkfests and blog carnivals. Other bloggers have moved that kind of community building efforts to social networks, like Twitter, FriendFeed, Facebook and Google Plus.

Some use blogs to post images, be it original art, or photography, or photoshopped humor and satire, or LOLcats. Though many have since moved to image-specific online communities and platforms, like Flickr, Picassa, DeviantArt and even Tumblr (the latter still has not fixed the problem of losing proper credit and attribution to the original artist, often leading to breach of copyright or loss of livelihood to the artists, but I will let my colleagues discuss that on appropriate blogs on the network, e.g., Symbiartic and Compound Eye.)

Some use it to document their day-to-day scientific research, in what is now known as Open Notebook Science (see Rosie Redfield for an example, though many practitioners have moved to wikis as more suitable platforms for this).

Some use it as a classroom tool (either as a place for students to easily access the lecture notes, like I do with my BIO101 adult students, or as a place where students are supposed to publish their own work, e.g., see archives of Extreme Biology).

Some scientists use blogs to talk to each other. The level of detail is so great that nobody but experts in their field can understand (e.g., some math and chemistry blogs) or with the level of expertise that lay audience does not have but can understand and appreciate anyway (e.g., some paleontology blogs, like Sauropod Vertebra Picture of the Week). But that is OK – we are not the target audience, their peers are.

Others science bloggers write for educated lay audiences interested in science, including scientists in other fields. Yet others are trying to reach out to completely broad and lay audiences, including children, and including audiences that do not even know yet that science is cool.

Some science bloggers focus on the latest research (the Maestro of this form is Ed Yong of Not Exactly Rocket Science blog, but many others do this and their posts are aggregated at

Others avoid discussing latest research and rather try to organize and systematically explain decades of research on a particular topic (see Tetrapod Zoology for a good example).

And yet others combine the two – using a recent paper to write “explainers” that provide historical context for it (I sometimes like to do that, e.g., see this post for an example).

I am sure I forgot another million ways blogging software can be used, and is used by other people. But these examples are illustrative – one can do whatever one wants with this software (see a good presentation about science blogs here).

Just here, at the Scientific American blog network, we have the “official” blog for corporate news and updates (@ScientificAmerican), a blog for editors to write in a standard journalistic form (Observations), a blog that is all about linking and filtering and networking and community building (The SA Incubator), a blog that combines updates/announcements with linking and community building (The Network Central), several blogs that are personal writings by our editors (though they are aware that they are always going to be seen as public faces of the organization), blogs by our network bloggers who write in various styles on a variety of topics at a broad range of “reading levels”, including those who focus on art, photography, video or music, and blogs where people outside of our organization can get published, though their work is chosen and approved by us, and lightly edited (The Guest Blog and Expeditions).

So even on a single blogging network, you can see a whole plethora of ways that the blogging platform can be used. You can find many more examples if you explore and Blog. It’s just a piece of software.

Does it mean that the medium does not affect the message? Of course not…

Blog is writing with a voice

Let’s for now ignore organizational and corporate blogs and focus only on the blogs written by individuals as themselves and for themselves.

As many have written about before (including myself, focusing on the ‘phatic’ language usually missing from 20th century-style media), individuals’ blogs are inbued with personality. This does not mean they need to reveal anything about their personal life, not even who they are, what they do, and where they live. But their personality shines from each sentence. It seeps in-between the lines. You quickly get to know “where they are coming from”.

Here you are reading a person, not a conglomerate. And our brains are attuned to listening to other people, and to evaluate how trustworthy they are by listening to their voice, their personality. The 20th century media style forces the writers to assume the impersonal form, which in the age of the Web is disconcerting – where is the voice, where is the personality, how can I possibly trust the writing of a person I cannot quite figure out? So in such cases we have to fall back on trusting the brand, the banner up on top.

Personality breeds trust (yes – honesty, transparency, generosity with links, willingness to admit errors and other signs of humanness also contribute to trust, and they are also a part of the blogger’s personality – those things tell you something important about the person). And the personality makes you come back for more, over and over again, every day, or every time your RSS feed reader tells you there is a new post. You get to know the blogger over time, and with time your trust grows (or is diminished, in which case you abandon reading it and move on). And your repeated return to the same blog over time is an important aspect of what I am talking about – the importance of understanding the continuity of conversation online.

Blogging is writing without a safety net

This is the formulation that came from Dave Winer, one of the first bloggers. The earliest mention of the phrase I could find is here.

What does that mean: Blogging is writing without a safety net?

This means that you are on your own. Your work is all yours, and it rises or falls on its own merits. Nobody is fact-checking you before you hit “Publish” (though many commenters will afterwards), and nobody is having your back after your publish – you are alone to defend your work against the critics. If you are good and trusted, you may have a community of bloggers or commenters who will support you, but there is no guarantee.

You can see, from the above paragraph, that there are two senses of “blogging is writing without a safety net”. One concerns pre-publication – there is no editor to check your work. The other concerns post-publication – nobody protects you.

How does it work on our network?

Since I got this job, I try to come up to the office once a month to participate in the editorial meetings. I find the process fascinating! It takes months for an article to go from the initial idea to proposal through several drafts to the final product that gets published in our magazine in print, on the Web, or both. Every word is parsed, every fact checked – the pre-publication safety net is big and strong.

And once the article is published, the safety net is there as well – we stand by our articles, and will defend and support the authors. They have our institutional backing (I am not sure about all the legalese and details for extreme cases, so treat this as a general statement). If an error squeezes through, we try to be honest and transparent, correct the errors, publish Letters to the Editor about it, let someone write a rebuttal on the Guest Blog, etc.

How about our blogs?

Blogging is much faster. Things get written and immediatelly posted. This is part of the definition of a blog: “software that allows frequent, fast and easy updates”. Posts written by our editors and writers on the Observations blog (as well as on their personal blogs) may get a quick check by another editor, and by copy-editor. We trust each other we’ll get stuff right. And, if there is an error, we trust each other to correct errors with transparency. Very little pre-publication safety net, but the post-publication safety net is all there, in full force.

Guest Blog and Explorations have a little bit more of a pre-publication safety net. We actively ask for submissions, and we often get proposals. Thus, we have the ability to choose whose work goes there. Quackery, pseudo-scientific rants, or angry personal attacks will not show up there (or anywhere else on our site, for that matter). Some posts get more scrutiny than others (and on a rare occasion I may ask our copy-editors to proofread a post, or even send one out for “peer review” if it is outside of my area of expertise), but there is generally not much time for fact-checking and proof-reading – most of the posts get published in more or less the same form as they arrive. The editorial decision really comes in the choice of the authors – who we trust to write a good article. Then we let them do it. If an error sneaks in – the same principle applies as always: a transparent correction, offer of a rebuttal by a decent critic, etc., but we stand by our authors and will not pull down posts just because someone says so.

How about the bloggers on our network? Again, the editorial decision was primarily mine: who to choose. Once chosen (out of thousands of possibilities – see the bottom part, the very end of my introductory post for how I made choices), the bloggers are trusted to do their best and are left on their own. Nobody tells them what to write about and how to write it (this is the #1 Rule Of Blogging: never tell a blogger what to write about and how to do it).

There is zero pre-publication safety net: nobody ever sees their posts to edit, fact-check or proofread before they post (though they have the open option to ask us to do it if they want – the network is young, three weeks only, so we don’t yet know how often that will happen). But, just as if they were our own editors, we stand by them. It is up to them to correct errors if needed, etc., but we will not ask them to take posts down or exert any strong editorial influence on them (unless it is as bad as a Kanazawa-size blunder, but I don’t think I hired an equivalent of Kanazawa). That is how blogging works.

What is interesting to watch are comments and letters we sometimes get. Some people, arriving to our site via links from who knows where, do not yet have the developed ability to instantly distinguish between heavily edited finalized articles, editorial blogs posts, guest posts and posts by our network bloggers. Their expectations are often different from what they see. And they are not yet able to quickly figure it out (which is one of the reasons for writing this post you are reading right now, and why we take care to clearly label everything on the site, e.g., look up: it says “Blog” there).

Especially if they are unhappy with an article, they may use their misunderstanding of the form as an excuse for angry calls for lynching (or deletion of the article). If they are activists for something, they do not appreciate the very existence of articles that do not 100% toe their line. So they often misread the form on purpose, as they think they can intimidate us that way.

So, yes, our network bloggers are SciAm bloggers. And yes, their posts are SciAm publications (yes, “real” publications: they can put those posts in their portfolios, or use them as ‘clips’ when applying for jobs or memberships in journalistic organizations). But saying “I can’t believe SciAm would publish this” or “How can SciAm possibly let this author publish this”, shows basic misunderstanding of how the modern media works and what the media blogs are – we don’t “let” them publish. They are free to do so on their own. And we back them up afterwards. No pre-publication safety net. Full post-publication safety net.

Critics are free to post comments (and bloggers are free to moderate their comments – those are their personal spaces after all), free to write their own posts on their own blogs, and if a rebuttal article is offered we will carefully vet it before publishing (we are not a priori going to refuse any offer for a rebuttal – we actually like vigorous debate, but all actors in it have to stick to the highest scientific and journalistic standards if they expect their work to appear on our site).

And of course, there is an old truism: a commenter complaining about a typo is, in reality, unhappy about the content and the complaint is there as a way to derail the real conversation. This is a typical opening gambit in the comments by various denialists (we tend to get swarms of Global Warming denialists who are well organized and some of them paid to post comments, but other kinds occasionally show up as well).

Finally, one of the frequent complaints is “why did you write about A when I really want you to write about B”. Apart from breaking the #1 Rule Of Blogging (see above), this also comes from another misunderstanding – that blog posts are NOT meant to be a final word on anything.

For examples of all such types of comments (and you can use Google Blogsearch to find blog posts written in the same vein), just wade through the comment section of this blog post by Christie Wilcox, already one of the biggest hits (at least as measured by traffic, incoming links and comments) on the new network. And read the comments while keeping this post in mind. See?

Which brings us to an essential aspect of blogging…and I would argue of all of media as it slowly grapples with the Web and the realities of the 21st century.

Blog is conversation

Many people linked to and discussed this excellent article by Paul Ford last week. It is about what he calls The Epiphanator. It is about the way the traditional media ends its articles (or radio/TV segments) with a big, black period. Full stop. Resolution.

Contrasted to that are online social networks, where everything is in constant flow, there are no sharp endings, no resolutions.

Blogs are both.

A blog post is supposed to cover a topic reasonably well. Some blog posts – the best (and usually the longest) ones, may even put a big, black period at the end. Such posts may not get much in the way of comments (there is not much to add – it is all in the post already), but are likely to have a lot of traffic, especially accumulated over time, as such posts are viewed as useful resources. They are “Explainers” of sorts.

But good bloggers know that, if they want to get comments and a vigorous discussion, they need to have some I’s undotted and some T’s uncrossed. They purposefully leave openings, leave stuff unfinished, some lines uncolored, there for the commenters to fill in with their own crayons.

Moreover, one does not need to be an experienced blogger who does this purposefully for this effect to happen all the time anyway. It is in the nature of blogging to take only small chunks at the time. One writes on the fly. Jotting down one’s thought at the moment. A typical blog post does not even try to cover every angle of a bigger issue. Other angles of the same issue are covered elsewhere – in other posts by the same blogger, or in posts by others.

Very few bloggers focus narrowly on a single topic and beat it to death day in and day out. Those are usually activist bloggers of some sort, paying attention to – and responding to – every little bit of the mention of their topic in the media or other blogs, fighting a good fight for their cause.

This narrow focus works for such rare bloggers, but the idea that this is the best way to blog well (and I see that advice given all the time to novice bloggers – to focus, focus, focus) is misplaced.

Most people are not so narrowly focused in their own day-to-day lives. Most people have multiple interests, and even multiple areas of expertise. It is natural, if they are active online, that they cover a plethora of topics in their postings on their blogs or on social networks. Which is perfectly fine – their readers get an even fuller picture of the person, the personality, which helps them decide if they like and trust that person.

It is also natural to comment on stuff one has no expertise on. Out of curiosity. Using a blog as a tool for exploration. Using a blog as a writing laboratory.

A journalist may have to cover many topics – whatever the editor assigns. A journalist on a science beat may have to cover topics ranging from astronomy to zoology and everything in-between.

A blogger has the luxury of picking and choosing topics of one’s own interest of the day. And science bloggers are usually reluctant to go far and wide from their own area of expertise. Biology bloggers are unlikely to write about physics and vice versa. But that does not mean they will stick to a very narrow topic, just the narrow research line they are involved with (or used to be involved with) in the laboratory.

It is natural to be interested in other topics, and to explore them by writing about them: using the blogs as a way to study, to learn, to get feedback from experts in the comments, and to get entertained in the process. Blogging, after all, is supposed to be fun (or otherwise we’d all quit after a week of doing it). One may go through ‘phases’, focusing on a single topic for a while, covering everything one can about it, then, when the topic is exhausted, moving on to something else.

Thus, many a blog post starts with a link or two that connect it to something previously written by the same blogger (see the first three links in this post, for example) or by other bloggers, or occasionally by the mainstream media. These links provide continuity – the blog post is not supposed to be a finished product that can stand on its own. It is dependent on what was said before, and it connects to all sorts of supporting information, opposing opinion, tangential information, and more. It is a part of a conversation. It is one link in a chain. It is one segment of a long series.

I link to you, responding to or following up on or adding to what you wrote. Then you (or someone third) does the same by linking back to me. Conversation keeps going.

Now think about Christie Wilcox’s post in this context. Check out the rest of her blog (both the posts she wrote so far on this network, and the archives of her old blog). How many, out of hundreds of her posts, are about agriculture? One. This one. What are the other posts about? All sorts of other biology, environment, conservation, ecology, genetics, being a scientist and more. Whatever struck her fancy on any given day, within a range of topics on which she feels at least some confidence that she can cover it well.

So, her focus on the myths about organic farming are a one-off intellectual foray into a new topic. Will she return to it one day? I don’t know. Perhaps. Perhaps not. We don’t ever tell bloggers what to write about.

Does she have a right to write about it? Of course, everyone can. If nobody else is writing about your favorite topic to your liking, you have a right to start your own blog.

Does she have to also write about myths about industrial agriculture, for “balance”? No. That is up to her. But why? There is TONS of that stuff out there already. Lots has been written about industrial agriculture, nobody really likes the way it is done in the USA, and there is no need for yet another blog post about it. Her post was a part of a much broader conversation – why would anyone expect her to cover the whole issue in a complete manner? That would take a few books, not a one short blog post.

Christie, in her analysis of myths of organic agriculture, never defended the industrial kind. But for the activists, every critical look at organic is automatically a defense of industrial. Very black and white. So they demand she covers “the other side” (“I want you to write about A and not about B”), they insist she must be paid by Monsanto (heh, it would be nice if they paid for the study of genetics of lionfish), they call her names, and yes, they demand that SciAm removes her post. Sorry, but we do not tell our bloggers what to blog about and how.

When seen as a part of a broader conversation about food, and when seen in the context of what she normally blogs about and her blogging style, there is absolutely nothing she needs to change, or do different, or do in addition (there are no factual errors in her post, the quibbles by activists are mostly about her framing not being 100% pro-organic or anti-GMO). Her audience were regular folks who do not know anything about agriculture and may actually believe, as many do, the myths she was pointing out; her audience were not the activists. She had her say in the conversation. She was impartial, detailed and diligent in her research and writing. You want her to shut up? How undemocratic! And how blind about what blogging is all about.

But this also illustrates something else. Her post can be seen as an Explainer. With a big, fat period at the end. But, because it was an explainer on a very limited topic, it is also a part of River Of News – the constant stream of updates. It can stand alone for a narrow topic. But it is also a part of a bigger conversation on a broader topic. It serves both functions, depending on scale.

And it certainly did not end the conversation with a big, fat period. Several blog posts have appeared in response to hers, some praising her, some attacking her, some dissecting it to death, and some being just plain insulting (I linked to a few of them above). And most do not understand how media and blogs work in the 21st century.

Furthermore, the conversation is not over even on our own site. We will publish a response to her post on our site, probably next week. She may, if she wants to, respond to the response. And I also asked several other people to contribute their angles for the Guest Blog. So the conversation will continue. This is the 21st century and this is how it’s done. And hopefully people will, sooner or later, regain their mental abilities to distinguish, at a glance, between ‘finished’, stand-alone stories and stories that are parts of a larger conversation. And then respond to it accordingly and appropriatelly.

Image source

Welcome to A Blog Around The Clock – Next Generation.

The day has finally arrived – the new Scientific American blog network is live! And, after almost a year of relative rest, my blog is about to get active again, with substantive posts coming up on a regular basis.

For my old readers who followed me here – you may not be as interested in my introduction below, as it is a partial rewrite and re-edit from several of my old posts, so just pick up the new feed and go check out all the other bloggers on the new network.

But before you leave, you may also be curious to know who made the delightful new banner? It is the artistic creation of Claire Fahrbach, a young artist, illustrator and designer from North Carolina who recently moved to San Francisco in search of a job and a career. See the banner big (and click to see even bigger):

Now for the new readers…a little bit about myself and about this blog. I don’t often write about myself, but every blog needs to have something biographical so readers can figure out where the author is coming from, what to expect, how to connect.

I was born in Belgrade, Yugoslavia (now Serbia). I always loved animals and planned to do something with them, perhaps become a biologist or a veterinarian (or join a circus, or work at a zoo). I grew up in a family that valued language, art, theater, literature and scholarship, so I grew up to be quite a bookworm.

In school, being a brainy math geek and science nerd did not make me ostracized – it made me popular. It was a different time in a different place. It was a different culture. Ever since, I have been trying to re-create that kind of culture around me – make it possible again for a science geek to be seen as cool (for example, getting a picture of myself taken, right, with an inflatable toy sauropod on my shoulder – click to see big).

I was in vet school at the University of Belgrade when the war broke out in 1991. I escaped the country a week before, on one of the last trains out before the borders closed, sanctions were imposed, and the country descended into a decade of chaos. Several flights later, I found myself in North Carolina and, after a couple of years of getting my bearings, decided not to pursue veterinary medicine any more, but to go back to basic science – biology at North Carolina State University.

I did research on circadian (daily) and photoperiodic (seasonal) rhythms in a bird, Japanese quail. I wanted to understand how a brain measures and perceives such long periods of time, and especially how sex hormones affect this timing, which is relevant for understanding why human adolescents cannot fall asleep at night and then wake up in the morning, as well the subtle differences between the sexes (you can click on the image, left, to see large so you can see the quail – orange breasted one is a male, mottled gray-white is a female).

After ten years of grad school, I realized that things I was good at – thinking, connecting ideas from disparate research traditions, designing clever experiments, observing animal behavior, animal surgery, discussing, teaching, placing my work in historical and philosophical context – were going out of fashion. Instead, biology was becoming more and more an exercise in things I was bad at – pipetting all day and running gels, following recipes, doing what I am told to, working at the bench in complete silence for 13 hours a day seven days a week, getting all secretive and competitive.

So I bailed out. While I was still finishing up my last experiments, I started blogging about politics. When the 2004 election was over, I switched to blogging about science and science education. Then I fused those three interests into a single blog. The rest is history.

Now you probably understand the name of the blog and the banner better. The quail on the banner is my old laboratory model animal (Coturnix japonica – I am also known online as ‘Coturnix’). The clock, on the banner and in the title, symbolizes the Biological Clock, the subject of my research. The Web is, of course, the World Wide Web that connects us all. And the blog name as a whole, apart from alluding to my scientific interest, also dates me back to the 1960s (when The Beatles rocked around the clock, with their version of the Bill Haley song), and refers to the question I often get: “Do you ever sleep? You seem to be online around the clock!”.

While much of what I do these days has something to do with writing and publishing and the media, I still find it strange to think of myself as a science journalist. While I still sometimes blog about science, I more often write about meta-stuff, e.g., about science communication, science blogging, science journalism, science publishing, science education, media in general etc. I have not published any articles printed on paper in legacy media and while I am open to that possibility, I am not actively doing anything to make that happen – I feel at home on the Web. I am active on Twitter, Facebook, Tumblr, Posterous and numerous other online spaces. My blogging has brought a number of jobs, gigs and other opportunities.

Together with my friend Anton Zuiker, I organize an annual conference on the intersection between science and the Web – ScienceOnline. The fifth one was a few months ago, and the sixth one will be in January. Every year I also conduct blog interviews with some of the participants of the conference.

Anton and I also teamed up with some friends and built two aggregators you may be interested in – (organized by networks) and (organized by topics). Both are, we think, useful starting points for exploring and keeping up with the science blogosphere and news.

I also edit an annual anthology of the best writing on science blogs, The Open Laboratory. The next, sixth edition of the book will be published by FSJ/Scientific American.

More recently, I got interested in promoting young and new science writers, and thus in the way science programs work in schools of journalism. I am currently on the advisory board of the Medical and Science Journalism program at UNC, and, starting in September, will be a Visiting Scholar in the Science, Health and Environmental Reporting Program at NYU.

To get a sense of kinds of topics I like to cover, here are some of my most recent posts:

Circadian clock without DNA–History and the power of metaphor

The line between science and journalism is getting blurry….again

Me and the copperheads–or why we still don’t know if snakes secrete melatonin at night

Web breaks echo-chambers, or, ‘Echo-chamber’ is just a derogatory term for ‘community’ – my remarks at #AAASmtg

Cicadas, or how I Am Such A Scientist, or a demonstration of good editing

Giant Dino exhibit at the American Museum of Natural History, or why I should not be a photojournalist

A “sixth sense” for earthquake prediction? Give me a break!

Book review: Pink Boots and the Machete by Mireya Mayor

And if you want more, I have compiled some selections of my best old posts about the media and posts about biology.