Category Archives: Basic Biology

Protein Synthesis: Transcription and Translation

Protein Synthesis: Transcription and TranslationHere is the third BIO101 lecture (from May 08, 2006). Again, I’d appreciate comments on the correctness as well as suggestions for improvement.

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Cell Structure

Cell StructureSecond lecture notes from my BIO101 class (originally from May 08, 2006). As always, in this post and the others in the series, I need comments – is everything kosher? Any suggestions for improvement?

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Underfunded? Or Unpopular?

This week’s question in the Ask a ScienceBlogger series is:

What’s the most underfunded scientific field that shouldn’t be underfunded?

The first and obvious answer is, of course, “my field“, whatever it is.
But then….

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Biology and the Scientific Method

Biology and the Scientific Method
I am currently teaching only the lab portion of BIO101 and will not teach the lecture again until January, but this is as good time as ever to start reposting my lecture notes here, starting with the very first one (originally posted on May 07, 2006) and continuing every Thursday over the next several weeks.
Although this is old, I’d love to get more comments on each of those lecture notes. Did I get any facts wrong? Is the material inappropriate for the level I am teaching? Is there a bette rway to do it? Are there online resources I can tap into?

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Animals with cool names

Animals with cool names (binomial, but cool).
More animals with cool names: Tort and Retort
Even more animals with cool names: That Cyprus mouse is not as unique a find as it was touted in press releases. I was not aware that Balkans were such a hot spot for new species discovery. I thought Josif Pancic got them all!

Teaching Biology 101 (to adults)

Teaching Biology 101I just got the teaching schedule for Spring, so I decided to follow up on last week’s post by putting, under the fold, a series of short posts I wrote when I taught the last time, musing about teaching in general and teaching biology to adults in particular. These are really a running commentary on the course. The actual lecture notes are here:
Biology and the Scientific Method
Lab 1
Cell Structure
Protein Synthesis: Transcription and Translation
Cell-Cell Interactions
Cell Division and DNA Replication
Lab 2
From Two Cells To Many: Cell Differentiation and Embryonic Development
From Genes To Traits: How Genotype Affects Phenotype
From Genes To Species: A Primer on Evolution
What Creatures Do: Animal Behavior
Organisms In Time and Space: Ecology
Lab 3
Origin of Biological Diversity
Evolution of Biological Diversity
Current Biological Diversity
Lab 4
Introduction to Anatomy and Physiology
Physiology: Regulation and Control
Physiology: Coordinated Response

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Evolution Project And A Truly Fair And Balanced Fox

Evolution Project And A Truly Fair And Balanced FoxMeandering Musings on evolutionary psychology and many other things (from February 15, 2005)…

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Biology In Science Fiction

I just discovered (on my Sitemeter referrals list!) a cool new blog – Biology In Science Fiction. Several good posts so far. Go check it out!

Antioxidants

I missed answering AskTheScienceBlogger question for a few weeks now, so let me take a quick stab at the latest one:
What’s an antioxidant, and why are they healthful? I thought oxygen was supposed to be good for you!

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Perhaps on another planet, it really is like that….

In the light of this years’ Nobel Prizes in Physiology and Chemistry (all RNA all the time), it would be interesting to think how would transcription, translation, gene regulation and replication work if DNA has evolved to be like this!?

It’s Getting Warm

In these days of global warming it is important to realize how important temperature is in regulation of a variety of biological processes. Here is today’s sampler of examples:
Why Do Cold Animals Make Bigger Babies?:

Reproduction involves a critical decision: Should an organism invest energy in a few large offspring or many small ones? In a new study from the American Naturalist, biologists used a new statistical approach that can test multiple theories at the same time, an approach they hope will shed light on many evolutionary problems. They used data from many populations of Eastern Fence Lizards (Sceloporus undulatus), which revealed that the lizards in colder environments produce larger offspring than lizards in warmer environments.

Chilly Bugs’ Unique Gene Regulation Gives Them Survival Advantage At Bottom Of The World:

The larvae of Antarctic midges never stop producing special proteins that minimize environmental stress, allowing them to withstand a range of intense environmental conditions in one of the world’s harshest environments. Scientists found that adult midges (Belgica antarctica) lose their ability to continually express these protective heat-shock proteins.

New Study Explains Why Hotter Is Better For Insects:

Organisms have been able to adapt to environments ranging from cold polar oceans to hot thermal vents. However, University of Washington researchers have discovered a limit to the powerful forces of natural selection, at least when it comes to the adaptation of insects to cold temperatures.

Nobel Prize for Medicine/Physiology

As you have probably heard already, Andrew Fire and Craig Mello have won the Nobel Prize in Medicine for the discovery of RNA interference.
Jake Young explains what RNAi are and what they do and why is this so revolutionary. Then he explains why those two people got the Nobel for this work instead of some others.
Alex Palazzo (also here), Abel PharmBoy, Carl Zimmer, Nick Anthis and PZ Myers have more and explain it much better than I could ever do. The last time the Nobel was given for work I really understand and like was in 1973 – ah, the good old days when the Nobel did not require molecular biology!
Anyway, this is the first time a Nobel was given for something that was discovered at the time when I was already in the lab and I remember the rumors about it around the molecular labs in the Department. Usually it takes decades for the finding to get a Nobel (and in my field, all the “founders” are dead by now), so this was really fast – indicating how important it is.

Pilobolus Rules!

You know there is a special place in my heart for Pilobolus.
Now, Jenna took some great pictures of it in her mycology class yesterday. She promises to post the micrographs soon.

The design of everything that flows and moves

The design of everything that flows and movesAn interesting paper came out about nine months ago about a proposed new universal law of biology, so I blogged about it on January 17, 2006 and updated on February 20, 2006.

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Genocentrism aids Anti-Abortion Arguments

Genocentrism aids Anti-Abortion ArgumentsFrom October 09, 2004. I’d write it differently today, but the main point still stands.

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Paramecium is such a cool organism to work with!

Paramecia Adapt Their Swimming To Changing Gravitational Force:

The researchers placed a vial with pond water and live paramecia inside a high-powered electromagnet at the National High Magnetic Field Laboratory in Tallahassee, Fla. The organisms are less susceptible to a magnetic field than plain water is, so the magnetic field generated inside the vial “pulls” harder on the water than on the cells. If the field is pulling down, the cells float. If it’s pulling up, they sink.
Using water alone, Valles and Guevorkian were able to increase the effect of gravity by about 50 percent. To increase the effect even further, they added a compound called Gd-DTPA* to the water. Gd-DPTA is highly susceptible to induced magnetic fields such as those generated in electromagnets. This allowed the researchers to make the water much “heavier” or “lighter,” relative to the paramecia, achieving an effect up to 10 times that of normal gravity. The magnetic field is continuously adjustable, so Valles and Guevorkian were also able to create conditions simulating zero-gravity and inverse-gravity.
By dialing the magnetic field up or down, the researchers could change the swimming behavior of the paramecia dramatically. In high gravity, the organisms swam upward mightily to maintain their place in the water column. In zero gravity, they swam up and down equally. And in reverse gravity, they dove for where the sediments ought to be.
“If you want to make something float more,” said Valles, “you put it in a fluid and you pull the fluid down harder than you pull the thing down. And that’s what we basically do with the magnet. That causes the cell to float more – and that turns gravity upside down for the cell.”
Cranking the field intensity even higher, Valles and Guevorkian could test the limits of protozoan endurance. At about eight times normal gravity, the little swimmers stalled, swimming upward, but making no progress. At this break-even point, the physicists could measure the force needed to counter the gravitational effect: 0.7 nano-Newtons. For comparison, the force required to press a key on a computer keyboard is about 22 Newtons or more than 3 billion times as strong.

The Homunculus

Amanda makes a correct connection between preformationism of old and the anti-abortion ideology of today. The only thing missing is the connection of both to Dawkinsian genocentrism which is just preformationism with modern rhetoric of DNA and genes and “blueprints of life”. The history of the war between epigenetics and preformationism and, within preformationism, between spermists and ovists is masterfully covered in Clara Pinto-Corriea’s book Ovary of Eve.

March Of The Penguins, again

Hungry Hyena has an interesting critique of the movie.

Fossils are, by definition, dead

The phrase “Living Fossil” is second to only “Missing Link” on my list of irks-me-to-no-end abuses of English language. Darren Naish now explains exactly what is wrong with the term, using as the case study the recent rediscovery of the Sumatran rhino. This is your Most Obligatory reading of the day!

Nice essay by Simon A. Levin in the latest PLoS – Biology

Fundamental Questions in Biology. Here is a quote from the end:

The questions that biologists from diverse subdisciplines are asking have commonalities that make clear the continued existence of fundamental challenges that unify biology and that should form the core of much research in the decades to come. Some of these questions are as follows: What features convey robustness to systems? How different should we expect the robustness of different systems to be, depending on whether selection is operating primarily on the whole system or on its parts? How does robustness trade off against adaptability? How does natural selection deal with environmental noise and the consequent uncertainty at diverse scales? When does synchrony emerge, and what are its implications for robustness? When and how does cooperative behavior emerge, and can we derive lessons from evolutionary history to foster cooperation in a global commons?

Now go and read it from the beginning.

ERVs in sheep, though essential, do not make them smart

Remember this post from a couple of weeks ago? It was quite popular on tagging sites like Digg, Reddit and Stumbleupon. It was about endogenous retroviruses and their role in the evolution of placenta (which made the evolution of other mammalian traits possible).
Now, there is a new study in sheep, on this same topic, and it looks very good at first glance:
Researchers Discover That Sheep Need Retroviruses For Reproduction:

A team of scientists from Texas A&M University and The University of Glasgow Veterinary School in Scotland has discovered that naturally occurring endogenous retroviruses are required for pregnancy in sheep.
In particular, a class of endogenous retroviruses, known as endogenous retroviruses related to Jaagsiekte sheep retrovirus or enJSRVs, are critical during the early phase of pregnancy when the placenta begins to develop.
—————snip—————-
The idea that endogenous retroviruses are important for reproduction in mammals has been around for about 30 years, Spencer said. Studies in cultured cells have shown that a protein of a human endogenous retrovirus might have a role in development of the human placenta.
The team blocked expression of the envelope of the enJSRVs using morpholino antisense oligonucleotides, which inhibit translation of specific messenger RNA. When production of the envelope protein was blocked in the early placenta, the growth of the placenta was reduced and a certain cell type, termed giant binucleate cells, did not develop.
The result was that embryos could not implant and the sheep miscarried, Spencer said.

Books: “Coming To Life” by Christiane Nusslein-Volhard

Several ScienceBloggers are reviewing Coming To Life today (see reviews by Janet, Shelley, RPM, Nick and PZ Edit: Razib has also posted his take), each one of us from a different perspective and looking from a different angle, so go read them to get the full scoop.
PZ Myers reviewed the book a few weeks ago. Someting that struck me was that PZ said that the book :

“….assumes nothing more than that the reader is intelligent and curious. Seriously, you don’t need a biology degree to read it!”

…while a reviewer, Edward F. Strasser (a math PhD whose hobby is reviewing books from this angle – how readable they are for laypeople) on Amazon.com states the opposite:

“I don’t think that a person who has never seen this material before is ready for this book, but I think that many people who need it for review will be OK.”

So, when I started reading the book I decided to try to empty my mind of all the knowledge I have and to read it like a complete lay-person. I wanted to see who is right – PZ or Strasser – and try to determine who is the real audience for the book.
First, I have to tell you that I absolutely LOVED the book. And that may be its biggest problem. The book will be appreciated the best by people like me – biologists with expertise in another field who want to brush up on their evo-devo (and just devo) and have an easy reference on the bookshelf. The book does absolutely great for people like that.
But, will it do the same for others? Developmental biologists do not have a need for it because they already know everything in it and 100 times more. But how about complete laymen, people with minimal formal science education but a keen interest in science, people who read popular science magazines, watch Discovery channel and read ScienceBlogs?
I’d say Yes, but very cautiously. In a way, the book is deceptive. Its small size and pretty cover art suggest a breezy read. But it is not. It is a textbook disguised as a non-fiction bestseller. The tone is a matter-of-fact, unexcited monotone. Trying to speed though it will be a disaster. Why?
A textbook on developmental biology would be an expensive, 1000-page, lushly illustrated avalanche of nitty-gritty details. Making the book small by eliminating a lot of that detail means that what remains is highly concentrated. Every sentence matters. Every sentence is a summary of a thousand papers.
There is no “filler” material, e.g., anecdotes and personal stories or interesting examples of, for instance, exceptions to the the rules in a strange species, or philosophical musings, kind of stuff that will let your focus wane every now and then without serious consequences to understanding. Only occasionally she slides in a little bit of history which is always a welcome change of pace on top of being very informative and placing the material in a historical context.
You need to slow down and read every sentence with concentration. Perhaps stop and think what it means every now and then. Sometimes you wish she has NOT omitted some of the details which may serve as a useful illustration of a big principle she is describing in that sentence or paragraph.
Several times I caught her using a technical word without explaining (or at least defining) it first. If you did not have Intro Bio recently, or are not generally well informed on basic genetics and molecular biology, that would throw you off, and make you rush to the back of the book to check the Glossary – something that breaks the flow of reading any book.
So, the book is great for people who have some biology background (at any level) but not much knowledge of developmental biology – people like sophomore biology majors. But how do you get them to slow down and read the book carefully? Well, use it as a textbook! For an Introduction to Development course. I am serious! It’s that good.
The instructor could spend time in class explaining the principles described in the book – a process which slows down the reading of the book. Then, each instructor is free to add as much or as little detail in lectures as the level of the course requires, plus cool examples, flashy images and videos, etc, and add a couple of more readings, e.g., scientific papers and reviews.
Heck, it could be used even for a General Biology class for science majors (e.g., a summer speed class). Genetics, development and evolution are the core of biology, so adding a couple of lectures (with additional notes or a similar book) on physiology, behavior and ecology at the end (and those can be built upon the edifice of genetics, development and evolution covered before), would work just fine in some contexts, eliminating the need for students (like mine, the adults) to buy huge expensive textbooks that only intimidate them with the wealth of detail. It would give the instructor more freedom to design a course well.
Why do I think that this book is better as a potential textbook than the usual texts? Apart from size, price, friendliness and giving the instructor greater freedom, I really like the way the material is explained.
From the very first sentence, and reinforced throughout the book, the message is that the cell is the smallest unit of life. Not genes. Cells. While most textbooks fall into the philosophically untenable habit-of-mind that “genes use cells to make more genes” or “cells are places where genes perform the work of life”, Nusslein-Volhard constantly explains stuff within the proper way of thinking – “genes are tools that cells use to change, to do their job within the organism, and to make more cells”. The shift is subtle. She rarely states it this directly and openly, but if you are reading the book specifically looking for it (as I did), you notice that the word-choice and the way of explainig things is always within this mode of thought. She also, whenever that is appropriate, never forgets to mention important influences of the internal and/or external environment on cells and tfe developing organisms.
The book also makes a gradual progression over levels. After basic introductions to evolution, heredity and molecular biology, she starts with the cell and how it uses genes to change its own and neighboring cells’ properties. As the chapters move on, there is less and less talk of genes and more and more talk of cells, tissues organs and whole organisms, ending with the return to evolution in an excellent chapter on Body Plans.
Understanding that most of the readers will be anthropocentric, she then devotes a chapter to the development and reproduction in those lousy lab animal models – humans.
The final chapter on controversial aspects of developmental biology and its practice – covering stuff like cloning, stem-cell research etc., is as calm and even-tempered (almost dry) as the rest of the book. More importantly, the conclusions given there are derived directly from the science described in the rest of the book, with no Culture-Wars code-words that can trigger automatical resentment on the part of readers that are involved in Culture Wars on one side or the other. Again, it provides the neccessary background that can be useful for a class discussion. And its dry, science-y tone is exactly what is needed for such a discussion.
So, if you are a biologist and you want to refresh and update your knowledge of development really fast and easy – get this book, it is better than any other in this respect.
If you are not a biologist, but have a keen interest and some background, get the book but do not expect to breeze through it in two hours. Do not be deceived by the small size and pretty illustrations Dr.Volhart drew herself. Give yourself a week to read this book, then read it slowly and with full concentration. Read that way, it is worth its weight in gold.
And if you are more interested in the “evo” side of evo-devo and a more future-oriented book (Coming To Life summarizes current knowledge with no speculations about the future), read “Biased Embryos and Evolution” (see my review) – the two books nicely complement each other.
My question to Dr.Nusslein-Volhard: Is it possible to turn Developmental Systems Theory into a useful experimental program and, if so, will that provide discoveries and insights that are lacking within the current paradigm?

Should we rewrite the textbook chapters on voltage-gated potassium channels?

Correct me if I am wrong, but I think this is really ground-breaking:
Study Finds Brain Cell Regulator Is Volume Control, Not On/off Switch:

He and his colleagues studied an ion channel that controls neuronal activity called Kv2.1, a type of voltage-gated potassium channel that is found in every neuron of the nervous system.
“Our work showed that this channel can exist in millions of different functional states, giving the cell the ability to dial its activity up or down depending on the what’s going on in the external environment,” said Trimmer. This regulatory phenomenon is called ‘homeostatic plasticity’ and it refers, in this case, to the channel protein’s ability to change its function in order to maintain optimal electrical activity in the neuron in the face of large changes within the brain or the animal’s environment. “It’s an elegant feedback system,” he added.
——-snip——–
Using this technique, postdoctoral fellow Kang-Sik Park revealed 16 sites where the protein is modified by the cell by via addition of a phosphate group. Further study–in which each of the sites is removed to reveal its role in modulation– followed by careful biophysical analyses of channel function by postdoctoral fellow Durga Mohapatra, revealed that seven of these sites were involved in the regulation of neuronal activity. Since each site can be regulated independently on the four channel subunits, the neuron can generate a huge (>1018) number of possible forms of the channel.
Using this mechanism, Kv2.1 channels are quickly modified, even mimicking the activity of other potassium ion channels. “The beauty of doing it with a single protein is that it is already there and can change in a matter of minutes. It would take hours for the cell to produce an entirely different potassium channel,” Trimmer explained.
Based on these results, Trimmer and his colleagues hypothesize that parts of the Kv2.1 channel protein interact in ways that make it either easier or harder for it to change from closed to open. The protein, they believe, can exist in either loose states that require low amounts of energy, or voltage, to change from one state to another or a locked-down state that requires lots of energy (high voltage) to open or close. The number and position of phosphate molecules are what determine the amount of voltage required to open the channel.

It just makes intuitive sense. It appeals to my aesthetic sense as well. And it is a great example of the power of evolution.
Potassium-Channel-2-2004.JPG

So, elephants actually run (leave the ground with all four feet at the same time)

Have You Ever Seen An Elephant … Run?:

Dr John Hutchinson, a research leader at the UK’s Royal Veterinary College (RVC), has already shown that, contrary to previous studies and most popular opinion, elephants moving at speed appear to be running. Now with funding from the Biotechnology and Biological Sciences Research Council (BBSRC) his team is using Hollywood-style motion capture cameras combined with MRI and CT scans of elephants to build 3D computer models of elephant locomotion to show the forces and stresses at work on muscles, tendons and bones.
The research team has been working with elephants at UK wildlife and safari parks and will shortly travel to Africa and Thailand to study wild animals. Fifteen temporary markers are placed on the elephants’ joints and the animals then move past a motion capture camera, recording at 240 frames per second, at varying speeds. Back in the lab the researchers can then use the footage to reconstruct the rotations of the elephants’ joints on a computer, creating a 3D stick model of the animal.
The computer models are being used to establish how limb structure relates to elephant locomotion and to determine finally if elephants really can run – or in scientific terms, at some point do they have all their feet off the ground at the same time? Dr Hutchinson said: “We are particularly interested how elephants coordinate their limbs and working out which joints contribute most to the length and frequency of their steps. In examining whether elephants truly run or not we need to understand what limits their top speed. Is it the tendons and muscles having to withstand the impact of 7 tonnes of elephant or is it something else?”

Read the whole thing. I love this kind of stuff! I remember when, back in the late 1980s, I first saw a study (from Bulgaria, I believe) done like this – of a horse jumping over a fence. Way cool!
Next step – how do elephants fly! Certainly you’ve heard the old true-life anecdote:
Two elephants are sitting on a tree. A third elephant flies by. The first elephant turns to the second elephant and says: “Hmmm, I bet her nest is close by”
0610_elephant.jpg

Teaching Biology Lab – Week 4

Teaching Biology Lab - Week 4 While I am teaching the biology lab, I set this post to show up automatically at the same time. It describes what we do today, the same stuff we did back on April 02, 2006:

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Teaching Biology Lab – Week 3

Teaching Biology Lab - Week 3 While I am teaching the biology lab, I set this post to show up automatically at the same time. It describes what we do today, the same stuff we did back on March 26, 2006:

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Kevin In China, part 11 – How to avoid getting married in China, or, women are more complex organisms than venomous snakes.

Kevin is popular with the ladies….too popular…

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Friday Weird Sex Blogging – Deepest Lovin’

According to the referrers pages of my Sitemeter, a lot of you are excited by strange penises, strange penises, strange penises and strange penises (or something like it). So, today we have to move to a different topic, traffic-be-damned, for those without phallic fixations. So, read on….

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Hot Peppers – Why Are They Hot?

Blogging on Peer-Reviewed Research

Some plants do not want to get eaten. They may grow in places difficult to approach, they may look unappetizing, or they may evolve vile smells. Some have a fuzzy, hairy or sticky surface, others evolve thorns. Animals need to eat those plants to survive and plants need not be eaten by animals to survive, so a co-evolutionary arms-race leads to ever more bizzare adaptations by plants to deter the animals and ever more ingenious adaptations by animals to get around the deterrents.
One of the most efficient ways for a plant to deter a herbivore is to divert one of its existing biochemical pathways to synthetise a novel chemical – something that will give the plant bad taste, induce vomiting or even pain or may be toxic enough to kill the animal.
But there are other kinds of co-evolution between plants and herbivores. Some plants need to have a part eaten – usually the seed – so they can propagate themselves. So, they evolved fruits. The seeds are enveloped in meaty, juicy, tasty packages of pure energy. Those fruits often evolve a sweet smell that can be detected from a distance. And the fruits are often advertised with bright colors – red, orange, yellow, green or purple: “Here I am! Here I am! Please eat me!”
hot_pepper_fresno.jpg
So, the hot peppers are a real evolutionary conundrum. On one hand, they are boldly colored and sweet-smelling fruits – obvious sign of advertising to herbivores. On the other hand, once bitten into, they are far too hot and spicy to be a pleasant experience to the animal. So, what gives?
Back in 1960s, Dan Johnson had an interesting proposal he dubbed “directed deterrence” which suggested that some plants may make choices as to exactly which herbivores to attract and which to deter. Hot peppers are prime candidates for such a phenomenon. What is hot in peppers is capsaicin, a chemical that elicits a sensation of pain when it bind the vanilloid receptors in the nerve endings (usually inside the mouth) of the trigeminal nerve. As it happens, all mammals have capsaicin receptors, but it was found, relatively recently, that birds do not.
To test that hypothesis, Josh Tewksbury used two variants of hot peppers – one very hot (Capsicum annuum) and the other with a mutation that made it not hot at all (Capsicum chacoense) – and offered both as meals to rodents (packrats and cactus mice) and to birds (curve-billed thrashers).
All species ate the sweet kind about equally. When Josh offered them identically prepared meals made out of the hot stuff, the two rodents refused to eat it while the birds happily munched on it.
hot%20peppers%20graph.JPG
The study appeared in 2001 in Nature (pdf) and I saw Josh give a talk about it at that time as he was joining our department to postdoc with Dr.Nick Haddad. While my lab-buddy Chris and I gave him a lot of grief in the Q&A session on his lenient criteria of what constitutes a “hungry animal” (he needed them to be hungry for the feeding tests), still the main conclusions of the study are OK.
More importantly, it really happens in nature. Mammals avoid hot peppers out in Arizona where Josh studied them (and made videos of their behavior), but the birds gorged on peppers. When he analyzed the droppings of rodents and birds fed peppers, he saw that seeds that passed through avian intestinal tracts were fully fertile, while seeds eaten by mammals were chewed, crushed, broken or semi-digested and not fertile at all.
Additionally, the thrashers tend to spend a lot of time on fruiting shrubs of different kinds. While there, they poop. The hot pepper seeds in the droppings germinate right there and this is an ideal shady spot for them to grow.
What a great example of (co)evolutionary adaptations. Next time on this blog, the second Big Question: Why do we like to eat hot peppers?
Related: Hot Peppers

Obligatory Readings of the Day – Tetrapod Zoology

Do you read Darren Naish’s blog Tetrapod Zoology? If not, you should start now. Just check out some of the most recent posts, for example this two-parter on sea snakes: ‘A miniature plesiosaur without flippers’: surreal morphologies and surprising behaviours in sea snakes and Sea kraits: radical intraspecific diversity, reproductive isolation, and site fidelity.
Or, this two-part post about the importance of the shape of the birds’ bills: The war on parasites: a pigeon’s eye view and The war on parasites: an oviraptorosaur’s eye view.
Or an amazing four-part story about Angloposeidon, a dinosaur from the Isle Of Wight: ‘Angloposeidon’, the unreported story, part I, ‘Angloposeidon’, the unreported story, part II, ‘Angloposeidon’, the unreported story, part III and ‘Angloposeidon’, the unreported story, part IV.
Enjoy and have a good weekend!

Teaching Biology Lab – Week 1

Teaching Biology Lab - Week 1I am teaching the Intro Bio lab right now and thought it would be appropriate to schedule this post to appear at the same time. I wrote it last time I taught this, but today’s lab will be pretty much the same. Being second summer session, the class will probably be really small, which will make the lab go even faster and easier.

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Friday Weird Sex Blogging – Corkscrewing

You really think I am going to put this above the fold? No way – you have to click:

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Cloning – what’s the big deal?

First, there were The Boys From Brazil
cloned%20Hitler%20boysfromBrazil.jpg
not to mention a lof of other science fiction:
cloned%20babies.jpg
like, for example, the cloned dinosaurs of the Jurassic Park:
cloned%20dinoasurs%20-%20jurassic%20park.jpg
Then came Dolly, the cloned sheep:
clone_dolly.jpg
Then came the AskThe ScienceBlogger weekly question: On July 5, 1996, Dolly the sheep became the first successfully cloned mammal. Ten years on, has cloning developed the way you expected it to?…

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Why fish in the Arctic seas do not freeze?

Here is a wonderful new study that demonstrates that the antifreeze substances in notothenioid fish are not produced by the liver as was believed for decades and taught in Comparative Physiology courses. Instead, it is produced in two places: most of it in the exocrine pancreas, and somewhat less in a portion of the stomach at the entry of the esophagus:

…..AFGPs are secreted into the intestinal lumen where they protect the intestinal fluid from being frozen by ice crystals that come in with seawater and food. Internal fluids in notothenioids are about one-half as salty as seawater. While seawater reaches its freezing point at -1.91 degrees Celsius, fish fluids freeze at about -1 degree Celsius. These species dwell in water that rarely rises above the freezing point and is regularly filled with ice crystals.
From the intestine, the AFGPs are, apparently, absorbed into the blood. This hypothesis is based on the near-identical composition and abundance of AFGPs found in the fish serum.

They also looked at other groups of Arctic fish, in some of which liver does produce antifreeze susbtances. In those species, the antifreeze was now also found to be secreted by the stomach and pancreas as well.

Spiders and Bycicles

From The Archives
Since everyone is posting about spiders this week, I though I’d republish a sweet old post of mine, which ran on April 19, 2006 under the title “Happy Bicycle Day!” I hope you like this little post as much as I enjoyed writing it:

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Kevin in China, part 4 – Snakebites as a Daily Hobby

Here is the fourth part of Kevin’s journey. I have just realized that I posted the previous two in the wrong order, thus post #2 should be third and post #3 should be second. I was going by the order in which I received them instead of dates in the journal. And I am doing these things late at night (having them automatically published at a preset time – noon), doing all the HTML for italicising the species names, running the spellcheck, expanding IM-style contractions into full-length words, breaking long paragraphs into multiples of shorter ones for ease of reading on a computer screen, fighting with images, etc. Sorry about that. Also, the series will continue as soon as I get the next report from Kevin….

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Kevin in China, part 3 – The First Westerner in Town

Below the fold is the third report from Kevin. This time it really gets interesting, even fascinating! Hunting snakes, rural China, the people….Kevin has interesting observations about everything.
Since the way Kevin embeds pictures in MSWord makes it very tricky to extract them and still have them look decent, I urge you to go check out the photos he managed to upload onto Photobucket. Enjoy:

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Kevin in China, part 2: Three Kinds of Natural Beauty in Jiuchong

Here is the first of Kevin’s e-mailed reports from China, dated June 1-3, 2006. In it, you will be able to see pictures of some natural beauty he saw in China, then another kind of natural beauty he saw in China, then yet another kind of natural beauty he saw in China….
I love the way he writes – he should (will?) be a great blogger. What a combination of a travelogue, a personal diary, and lab notes of a research scientist – all in one, the three aspects of it connected seamlessly into a single narrative. I hope you enjoy it as much as I do. So, without further ado, here is Kevin:

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Snakes On The Plain: Kevin in China

Let’s see how many people incapable of spelling ‘plane’ arrive here by the way of Google. But I am talking about a real ‘plain’ – a big one, in China, and about some very real live snakes as well!
A good friend (and ex-neighbor) of mine, Kevin Messenger, is in China right now, surveying herpetofauna (that is – reptiles and amphibians, for the non-biologists here) in a remote area of central China, rarely visited by Weesterners, and never before surveyed by scientists.
He is one of those natural-born herpetologists – he lives, breathes and dreams snakes. When I lived in Raleigh I would often see him pull up with his truck next door. He would holler “Hey, Bora! Come see what I got today!”. I’d walk over there and watch the bags in his truck wriggle. He would open one bag at a time, with a gleam in his eyes, showing me “the biggest rattler I ever caught!” and “hey, this one is so rare around here” and “isn’t this one pretty?” His house was full of animals, mostly herps (his veterinarian sister has her own menagerie – but her animals mostly had eyelids), and he always had great stories to tell from his surveys in the Sandhills.
He gave a talk about his research at the meeting of the Society for Herpetology when he was still in high school! He published his first paper when he was a freshman. I will, at some point in the future, write about his excellent paper on the effects of moonlight on snake activity in the Sandhills. The research in China is going to be his MS work, although he just graduated college and has yet to start grad school. Still, since the first day at NCSU he knew he was going to do graduate work with Hal Heathwole, and Hal knew it, too.
As he is sleeping in a tent somewhere in China right now, you can imagine how hard it is for him to get online. He was thinking about recording his trip and his work on a blog, but had to give that idea up – it is just impossible in his situation. Still, every now and then he goes to visit the civilization and manages to send an e-mail or two. He asked me to post his essays here, on my blog. Once he comes back home in Fall, he may republish them elsewhere on the Web, either on a static page, or on a blog that he may wish to continue to write afterwards.
Kevin has sent me a few installments already – they ar fascinating, believe me – which I will post over the next several days. He even managed to send me some pictures of the animals he saw there and I will post those as well. As the new stories and pics come in, I will post them here as well.
Today, I will start with Kevin’s introductory autobiography and description of his researh – under the fold:

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ClockTutorial #1 – What Is Chronobiology

ClockWeb%20logo2.JPG This is the first in a series of posts from Circadiana designed as ClockTutorials, covering the basics of the field of Chronobiology. It was first written on January 12, 2005:

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BIO101 – Lecture 7 – Physiology: Coordinated Response

Last week we looked at the organ systems involved in regulation and control of body functions: the nervous, sensory, endocrine and circadian systems. This week, we will cover the organ systems that are regulated and controlled. Again, we will use the zebra-and-lion example to emphasize the way all organ systems work in concert to maintain the optimal internal conditions of the body:

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The wee, tiny, little ones….

Animalcules 1.9, the carnival of microscopic life, is up on Aetiology. This is the first time I don’t have anything there – just too swamped with everything. I promise I’ll be good next time.

BIO101 – Lecture 6 – Physiology: Regulation and Control

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:

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Teaching Update

This Monday night I taught lecture #7 of the 8-week Intro Biology course (adult education at a community college). First, I gave them their Exam #2 (on Diversity, see my lecture notes on those topics here, here and here). The flat distribution of the first exam has now turned bimodal: some students are making big improvements and I will probably end with a nice cluster of As and Bs, while other students are falling and may end up with a few Ds and Fs, with nobody left in-between.
Then, I continued with the physiology topics. The week before, I covered nervous, sensory, endocrine and circadian systems. This week, I covered the muscular, circulatory, respiratory, excretory and reproductive systems. How does one teach all of those systems in such short time? By sticking to the basics of the basics, of course, skipping a lot of stuff that textbook deems important. I am late at writing and posting here my lecture notes for those two lectures, but once I do, you’ll see the strategy I took, putting emphasis on how all those systems are intertwined and work together in solving challenges posed by the environment.
Next week is the final exam on anatomy and physiology. The students will then give oral presentations on an organ system each. Unlike me, they will keep the systems separate from each other, and focus entirely on the human body. One student will do the immune system which I did not have time to cover at all. This will be an opposrtunity for me to add teh information that I could not sqeeze into my formal lecture before.
Last week, they also gave short presentations on diseases. I have to say that I learned a lot about Shingles, Grave’s disease, Herpes Simplex, Osteoporosis, etc. They did a great job, all of them. Finally, they will do the evaluations and the class will be over. Later this summer I will teach the lab only, then in Fall it’s back to both the lecture and the lab again.
Technorati Tag: teaching-carnival

Transgenic Chicken

SEED Magazine has an interesting article on the advances in avian transgenics….

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Sexual Selection is not dead yet!

A few months ago I reviewed Joan Roughgarden’s book “Evolutions Rainbow”. Now that SEED magazine has published an interview with her, I thought about writing about it again (or just republishing the old one), but now I see that I do not have to, because PZ Myers did a much better job at it than I could ever dream of doing, so go and read it.
The only sentence I did not like was: “There are objections that this requires group selection, which always puts an idea on shaky ground….” As someone who has studied group selection (both biological and philosophical literature) intensely over the past few years, I do not think it is on a shaky ground at all, though some people (mostly those who believe in mathematical models more than real data) may tell you so.

BIO101 – Lecture 5: Introduction to Anatomy and Physiology

After three lectures on the basics, a long lecture on diversity, and a hard first exam, it is time to turn our attention to anatomy and physiology for the rest of the course:

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