Category Archives: Basic Biology

Bone anatomy

Oh, how I wish eSkeletons website existed back at the time I was teaching anatomy! Very, very cool! You can focus on human bones only, look at movement, insertions and origins, etc. Or you can make comparison between bones of several primates. Thanks Anne-Marie.

The Hopeless Monster? Not so fast!

Olivia Judson wrote a blog post on her NYTimes blog that has many people rattled. Why? Because she used the term “Hopeful Monster” and this term makes many biologists go berserk, foaming at the mouth. And they will not, with their eye-sight fogged by rage, notice her disclaimer:

Note, however, that few modern biologists use the term. Instead, most people speak of large morphological changes due to mutations acting on single genes that influence embryonic development.

So, was Olivia Judson right or wrong in her article? Both. Essentially she is correct, but she picked some bad examples, overgeneralized a bit, over-reached a little and she used the dreaded term that was bound to shut down all rational processes occurring in some biologists’ brains. Remember that she wrote to general audience. If she took time and space to explain all the nuances and details she would have lost her audience somewhere in the middle of the second paragraph. I think that her post explains the topic just fine for the intended audience, pointing out that not all evolutionary changes take millions of years of imperceptible change – some do, indeed, happen relatively abruptly (yet it can be explained completely mechanistically, not giving Cdesign Proponentsists any hope). Not every day, but they do.
So, who jumps first into the fray with an angry rebuttal – one of the Usual Suspects: Jerry Coyne in a guest-post on The Loom:

Unfortunately, her piece is inaccurate and irresponsible, especially for a journalist with a strong science background (Judson has a doctorate from Oxford). I’ve admired Judson’s columns and her whimsical and informative book Dr. Tatiana’s Sex Advice to All Creation. But this latest posting is simply silly. As an evolutionary biologist, I’m used to seeing our field twisted out of shape to satisfy the demands of journalists who love sensational new findings–especially if they go against long-held Darwinian beliefs like the primacy of gradual, stepwise evolution. But I’m not used to seeing one of my own colleagues whip up excitement about evolutionary biology by distorting its findings.

Unfortunately, in bashing Judson along with making legitimate points (how many people will ignore this caveat in their responses?), Coyne ends up being more wrong than she is. And his intended audience is, arguably, better scientifically educated than hers – it’s the Scienceblogs.com readers, not NYTimes. While bashing her head into a rock, Jerry makes visible his emotional enmity towards everybody who has a bigger picture of evolution than he has and has at their disposal both a methodological and a conceptual toolkit that Jerry lacks.
Before you jump on me, read the historical reviews of the concept of the Hopeful Monster by Brian and John. Then, read Greg and Razib who are far too lenient on Coyne but add good points of their own. Finally, read PZ Myers and especially Larry Moran for a clear explanation of the entire set of issues – the history, sources of current emotional disputes, and the current science. Reading all of these is essential to understanding the claims in this post as I do not have space/time to repeat all of their claims at length – so click on the links and read first before commenting.
In a back-and-forth with a commenter, Coyne defends himself that he is talking about the changes in genes, not evolution. This just shows his bias – he truly believes that evolution – all of it – can be explained entirely by genetics, particularly population genetics. His preferred definition of evolution is probably the genocentric nonsense like “evolution is a change of gene frequencies in a population over time”. I prefer to think of it as “evolution is change in development due to ecology” (a softening of Van Valen’s overly-strong definition “evolution is control of development by ecology”). Population genetics is based on the Hardy-Weinberg equilibrium – pretty much all of it is a build-on and embellishment of it. Population geneticists tend to forget, once they get into complex derivations of HW, that HW has about a dozen completely unrealistic assumptions underlying it. Now, in a case-to-case basis, some of those assumptions can be safely ignored, some can be mathematically taken care of, but some are outside of the scope of mathematics (or at least the kind of math that can be integrated into the development of HW). Those are ignored or dismissed and, if this is pointed out by those working on evolution from a Bigger Picture perspective, met with anger.
When Goldshmidt’s book The Material Basis of Evolution was reissued, Stephen Jay Gould wrote a lengthy Introduction. About a dozen years ago I checked the book out of the library and skimmed the book itself. I read Gould’s intro very carefully (I wonder if it is available somewhere online for free? Update: Gould’s introduction is available online here, hat-tip to Michael Barton.). It is also worthwhile to read Gould’s 1980 essay The Return of Hopeful Monsters keeping in mind that evo-devo was barely beginning at the time (yes, it is 28 years old, so do not judge it by current knowledge – put a historian’s cap on when reading it).
In his Big Book, Gould wrote:

“By proposing a comprehensive formalist theory in the heyday of developing Darwinian orthodoxy, Richard Goldschmidt became the whipping boy of the Modern Synthesis–and for entirely understandable reasons. Goldschmidt showed his grasp, and his keen ability to utilize, microevolutionary theory by supporting this approach and philosophy in his work on variation and intraspecific evolution within the gypsy moth, Lymantria dispar. But he then expressed his apostasy by advocating discontinuity of causality, and proposing a largely nonselectionist and formalist account for macroevolution from the origin of species to higher levels of phyletic pattern. Goldschmidt integrated both themes of saltation (in his concept of “systemic mutation” based on his increasingly lonely, and ultimately indefensible, battle to deny the corpuscular gene) and channeling (in his more famous, if ridiculed, idea of “hopeful monsters,” or macromutants channeled along viable lines set by internal pathways of ontogeny, sexual differences, etc.). The developmental theme of the “hopeful monster” (despite its inappropriate name, virtually guaranteed to inspire ridicule and opposition), based on the important concept of “rate genes,” came first in Goldschmidt’s thought, and always occupied more of his attention and research. Unfortunately, he bound this interesting challenge from development, a partially valid concept that could have been incorporated into a Darwinian framework as an auxiliary hypothesis (and now has been accepted, to a large extent, if under different names), to his truly oppositional and ultimately incorrect theory of systemic mutation, therefore winning anathema for his entire system. Goldschmidt may have acted as the architect of his own undoing, but much of his work should evoke sympathetic attention today.”

So, Coyne’s Gould-bashing, as Larry Moran demonstrated, is just petty and baseless sniping by one scientist of limited scope at another who actually “got it”.
I thought the discussion so far has been far too tame. So, here is the red meat! I want to see a real fight – a blogospheric war that brings in some serious traffic, OK?

Life Sciences in North Carolina

OK, this may not be very new, but for all of you taking a look at science in North Carolina next week due to the focus on the Science Blogging Conference, The Scientist has published a number of essays looking at every aspect of Life Science in the state – check it out: The State of Life Sciences.
For the latest news on life science in North Carolina, visit the Bioscience Clearinghouse, a very useful website hosted by The North Carolina Association for Biomedical Research.

Pilobolus, Antlion and the Vertebrate Eyes

On Pilobolous:
When I first wrote my post on Pilobolus (here and here) I really wanted to do something extra, which I could not do at the time. If you scroll down that post, you will see I reprinted the Figure 1 from the Uebelmesser paper. What I wanted to do was find (and I asked around for something like that) the exact times of dawn and dusk at the site where Uebelmesser did her work and thus be able to figure out the dates when the tests were done and the exact phase-relationship between the dawn and the time when Pilobolus shoots its spores.
Now, I see that such a chart exists (via) and I can, if I find time and energy, do it one of these days. Then, I can do the same thing for the Chapel Hill coordinates, go out to a nearby farm, and repeat the experiment myself.
On Antlions:
I knew, when I wrote my post on antlions (here and here) that they had endogenous circalunar rhythms. But today, I also learned that:
– antlions secrete a toxin that paralyses their prey
– the antlion toxin is produced by its bacterial endosymbiont Enterobacter aerogenes
– the normal function of that toxin in the bacterial cell is as a chaperonin, i.e., a protein that makes sure that other proteins are folded correctly into their normal 3D shapes
– the Enterobacter aerogenes toxin is very similar to a protein made by Escherichia coli
– the Enterobacter aerogenes toxin is 1000 times more toxic to cockroaches than the E.coli one
– neither of the proteins is toxic to mice (and presumably to us).
One learns something new and cool every day.
On Vertebrate Eyes:
Eye is a very important organ in my own specialty, so I was surprised to see how much new I learned by reading this eye-opening post by PZ. Bookmarked for future use in teaching….

It’s In Your DNA!

That is one of the phrases that has been getting on my nerves for years now. So, I chuckled when I saw Keith Robison explain why that is not such a good corporate slogan.
I’ll add another one to his funny list:
– Most of our organization sits there inert and dead while all of the work is performed by janitors, cooks, chauffeurs and outside contractors.

Has the word “gene” outlived its usefulness?

Blogging on Peer-Reviewed Research

When Wilhelm Johannsen coined the word “gene” back in 1909 (hmmm, less than two years until the Centennial), the word was quite unambiguous – it meant “a unit of heredity”. Its material basis, while widely speculated on, was immaterial for its usefulness as a concept. It could have been tiny little Martians inside the cells, it would have been OK, as they could have been plugged into the growing body of mathematics describing the changes and properties of genes in populations. In other words, gene referred to a concept that can be mathematically and experimentally studied without a reference to any molecules or intracellular processes.
Fast-forward half a century to the discovery of DNA and subsequent discoveries of the genetic code, transcription, translation, various types of gene regulation, etc. Everyone was happy – finally, we had a material gene. We had a molecule of inheritance that we could study. And an army of thousands started studying it, announcing breakthroughs at a breath-taking pace.
The confusion about the use of the term ‘gene’, as everyone used it differently, grew over the years. The use of terminology from information theory (e.g., program, transcription, translation, algorithm) affected the way researchers thought and designed experiments, limiting for a long time all discourse on inheritance to just DNA and worse, just to the DNA sequence.
But research went on, hit the walls, and smart people found the ways around the conundrum. What the research uncovered undermined the “gene” as a unit of inheritance, and for that matter undermined DNA as the molecule of inheritance. What we have learned is that:
– there is a difference between what an organism gets from parents (a static concept of the gene) and what it does with it to properly develop, function and behave in a species-specific way (a dynamic concept of the gene)
– the DNA sequence is just one of many properties of DNA that is important for proper development, function and behavior of an organism – there are other properties of DNA, as well as other non-DNA factors that are equally important.
– a sequence of nucleotides that gets transcribed is a very poor definition of a gene, as so much happens between transcription and the generation of the final protein shape, not to mention the complexity of the question how a single protein contributes to the appearance of a phenotypic trait.
– DNA is not the only “thing” that an organism gets from the parents. There is also a DNA methylation pattern, the transcription/translation machinery of the egg cell, various molecules (RNA, proteins, steroid hormones, etc.) present in the egg cell or introduced by the sperm cell, the environment inside the egg or womb, and the external environment into which the parents deposit the progeny (including the special case of teaching/learning).
I have thought about this quite a lot over the years (see, for instance this, this, this, this and this) and more I thought about it, more I liked the ideas that Developmental Systems Theory had to offer. Last ten years of published research changed the way we think about this and changed my mind in many ways. In a way, I was right all along – it’s not just DNA that confers heredity (static concept of the gene). In other cases, I was wrong: it turned out that it is, in fact, DNA, just not its sequence, that does this or that job in running the organism (the dynamic concept of the gene).
Two of the books I have read over the years that tackled the problem in a very good way (though sometimes not going far enough for my own tastes) are Refiguring Life and The Century of the Gene by Evelyn Fox Keller, one of the most prominent thinkers about the problem right now.
Thus, I got really excited when I heard that Chris Surridge, editor of PLoS ONE, after mulling over it for a long time (philosophy of science is not supposed to be one of the topics ONE publishes papers on, at least officially and at least until now), decided to go with the reviewers’ recommendations and publish a paper by Evelyn Fox Keller and David Harel – Beyond the Gene – in which the concept of the gene is discussed. What the paper does, on top of coming up with concepts that clearly differentiate between the static and the dynamic meanings and incorporate the current understanding of the complexity of both, is propose new names for those concepts. Read it carefully – it is quite thought-provoking.
Proposing new terminology is easy. Having it accepted and used by others is far more difficult. Especially when the terms are picked very cleverly to pick up on particular mental associations, while at the same time being (probably intentionally) catchy and funny (if you read them out loud they sound like deans, beans and janitors). The straight-laced researchers will probably balk at the new words. The folks that give funny names to Drosophila genes (e.g., Sonic hedgehog or fruity…er, fruitless) will probably grok why these new proposed terms are potentially useful.
Just like their conception of gene in everyday work differs, I expect that the response to this article’s proposal will differ between a biochemist, a bioinformatics scientist, a biological anthropologist, a medical researcher and a developmental biologist, between someone who works on microbial genomes, or mammalian genetics, or compares all genomes or looks at the way viral and mammalian genomes interract, or someone who looks at evolution of genes, or population genetics, history of biology or philosophy of biology. I hope they and others chime in.

Happy birthday “Origin of Species”

Or, Happy Evolution Day! It’s time for a party!
It is easy to look up blog coverage – if you search for “Origin of Species” you mostly get good stuff, if you search for “Origin of the Species” you get creationist clap-trap as they cannot even copy and paste correctly (hence they are better known these days as cdesign proponentsists).
Pondering Pikaia and The Beagle Project Blog were first out of the gate this morning with wonderful posts.
Here is a recent book review of the Origin by someone who knows some biology and another one by someone who does not – both are quite nice and eye-opening.
Corpus Callosum, John Wilkins, Shalini, Paul Erland also mark the date.
The first printing of 1250 copies did not fly off the shelves, because they were all already sold to subscribers – yes, amazon.com did not invent pre-ordering of books. The second printing was then rushed immediatelly for public sales in actual physical bookstores.
Upon first reading The Origin, Thomas Henry Huxley famously exclaimed: “How extremely stupid not to have thought of that!”
I first read The Origin (4th edition) when I was about 13 or 14. That was the third serious book I have ever read in English (the first two were Jonathan Livingston Seagull and a biography of Bruce Lee) and it was heavy slogging. I do not remember if I actually finished it (probably not) and mostly remembered the pigeons. Too young.
I read The Origin again (the 1st edition), the whole thing, while taking a “History of Life Science” course with Will Kimler some ten years ago, and then again next semester for his “Darwin In Science And Society” course. As well as a bunch of secondary literature, autobiography, a couple of biographies, some papers…Then the following year, Will and Roger Powell co-taught a graduate seminar “Darwin (Re)visited” where we actually read the entire Origin, entire Voyage of the Beagle, huge chunks of Descent of Man (I read the whole thing), the whole The Expression of the Emotions in Man and Animals, some letters, excerpts from the Orchid book, etc. I also read pieces from the Power Of Movement in Plants and the Earthworm book. I need to re-read all that stuff again (one should, every ten years or so). And you should, too.
More from Dispersal of Darwin, Laelaps, Sandwalk, Afarensis and Yikes!

UNC researcher wins a Nobel for the Knock-Out Mouse

Dr. Oliver Smithies, the Excellence Professor of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, NC, USA, together with Mario R. Capecchi and Martin J. Evans, won this year’s Nobel Prize in Physiology and Medicine:

This year’s Nobel Laureates have made a series of ground-breaking discoveries concerning embryonic stem cells and DNA recombination in mammals. Their discoveries led to the creation of an immensely powerful technology referred to as gene targeting in mice. It is now being applied to virtually all areas of biomedicine – from basic research to the development of new therapies.
Gene targeting is often used to inactivate single genes. Such gene “knockout” experiments have elucidated the roles of numerous genes in embryonic development, adult physiology, aging and disease. To date, more than ten thousand mouse genes (approximately half of the genes in the mammalian genome) have been knocked out. Ongoing international efforts will make “knockout mice” for all genes available within the near future.

Update: Here is the UNC press release.
[Hat-tip to Abel]

Oxytocin and Childbirth. Or not.

Blogging on Peer-Reviewed Research

When teaching human or animal physiology, it is very easy to come up with examples of ubiqutous negative feedback loops. On the other hand, there are very few physiological processes that can serve as examples of positive feedback. These include opening of the ion channels during the action potential, the blood clotting cascade, emptying of the urinary bladder, copulation, breastfeeding and childbirth. The last two (and perhaps the last three!) involve the hormone oxytocin. The childbirth, at least in humans, is a canonical example and the standard story goes roughly like this:

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.

As usual, introductory textbook material lags by a few years (or decades) behind the current state of scientific understanding. And a brand new paper just added a new monkeywrench into the story. Oxytocin in the Circadian Timing of Birth by Jeffrey Roizen, Christina E. Luedke, Erik D. Herzog and Louis J. Muglia was published last Tuesday night and I have been poring over it since then. It is a very short paper, yet there is so much there to think about! Oh, and of course I was going to comment on a paper by Erik Herzog – you knew that was coming! Not just that he is my friend, but he also tends to ask all the questions I consider interesting in my field, including questions I wanted to answer myself while I was still in the lab (so I live vicariously though his papers and blog about every one of them).
Unfortunately, I have not found time yet to write a Clock Tutorial on the fascinating topic of embryonic development of the circadian system in mammals and the transfer of circadian time from mother to fetus – a link to it would have worked wonderfully here – so I’ll have to make shortcuts, but I hope that the gist of the paper will be clear anyway.

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Who is Eva Vertes?

I have linked to and posted pictures of Eva Vertes from SciFoo before and you may ask: “Who is she? Why was she invited there?” The Wikipedia page I linked to earlier is a short stub and full of errors. So, to make it clear, see this page as well as comments on this talk she gave two years ago when she was 17:

More science of Harry Potter

I can’t stay away (a charming spell?) from the series that Anne-Marie is churning out at a supernatural rate (what kind of magic?). Here are the latest three installments, totally enchanting:
Conservation Biology
The Botany of Wands
Kin selection

Friday Weird Sex Blogging – The Birds Do It….

Friday Weird Sex Blogging - The Birds Do It....You should check out all of my SiBlings’ Friday Blogging practices, then come back here for a new edition of Friday Weird Sex Blogging. Last week you saw an example of a corkscrew penis. But that is not the only one of a kind. See more under the fold (first posted on July 14, 2006)…

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Friday Weird Sex Blogging – Corkscrewing

Friday Weird Sex Blogging - CorkscrewingYou really think I am going to put this above the fold? No way – you have to click (First posted on July 7, 2006):

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Everything You Always Wanted to Know About Pennicillin (and more)

Here is an example of perfect science blogging. It starts seemingly innocuously, with a quiz: Monday’s Molecule #30, where you are supposed to figure out what the compound is.
Then, after a couple of days, there is a post that you may not even realize at first is related to the first one: Bacteria Have Cell Walls
Another day or two, and A and B get connected: How Penicillin Works to Kill Bacteria
But how do we know this? Well, some people figured it out: Nobel Laureates: Sir Alexander Fleming, Ernst Boris Chain, Sir Howard Walter Florey – and now you know how we know.
Finally, putting everything in context of science, society, medicine and history, a two-parter: Penicillin Resistance in Bacteria: Before 1960 and Penecillin Resistance in Bacteria: After 1960
A tour-de-force of science blogging. I wish I could do something like that.

Garden-Variety Experiment

Literally. If you want to know how to figure out what your slug has eaten today, just ask Aydin.

Teaching tonight

Physiology: Coordinated Response
Blogging resumes later tonight….

Teaching tonight

Introduction to Anatomy and Physiology
Physiology: Regulation and Control

Obligatory Reading of the Day

Evolution of direct development in echinoderms
It’s been several years since I last heard Rudolf Raff talk about his work and apparently he’s been busy in the meantime. The new stuff is exciting, and PZ knows how to explain it really well.

Why Are There No Unicorns?

Is natural selection omnipotent or are there developmental constraints to what is possible and it is only from a limited range of possibilities that natural selection has to choose? The tension betwen two schools of thought (sometimes thought of in terms of pro-Gould and anti-Gould, as he has written much about developmental constraints and against vulgar adaptationism) is still alive and well. It is nice to see someone actually do an experimental test of the thesis:
Why Are There No Unicorns?:

Why are there no unicorns? Perhaps horses develop in a way that cannot be easily modified to produce a unicorn, so such creatures have never arisen. Or maybe unicorn-like animals have been born in the past but because there is no advantage for a horse to have a horn, such creatures did not thrive and were weeded out by natural selection.
The problem highlights a general issue in evolutionary biology of what determines the range of plants and animals we see compared to those that might have evolved theoretically. To what extent does observed biodiversity reflect the rules of development or the action of Darwinian selection?
To address this problem, Enrico Coen at the John Innes Centre and Dr. Przemyslaw Prusinkiewicz and colleagues at the University of Calgary analysed not Unicorns, but a more tractable system, the evolution of flower branching displays, or inflorescences. Flowering plants have three basic types of inflorescence – racemes, cymes and panicles.
Theoretically there are many other possible branching arrangements so why has nature chosen only these three? The researchers showed how the three types arise quite naturally from a simple mathematical model for how growing tips switch to make flowers. The model was supported by experimental studies on genes in the garden weed Arabidopsis.

That was the basic theoretical background. Now, what did they actually do?
Nature Surrenders Her Flowery Secrets:

The poet Dylan Thomas wrote, “The force that through the green fuse drives the flower drives my green age.” Now, a team of international scientists has unlocked some of the secrets of that force: it has described the rules that govern how plants arrange flowers into branching structures, known in technical terms as ‘inflorescences.’ Nature has literally thousands of examples of inflorescences, which include the flower clusters of Mountain Ash, the tiny filigreed blossoms on Lilac and the stalkier inflorescences in Fireweed.
————snip————
Dr. Lawrence Harder, a University of Calgary biologist and co-author of the paper, says one of their model’s key features is that it is able to anticipate regional variations in inflorescence structures and recognizes that some developmental patterns are impossible.

Nice. I guess Gould was right after all. He would be pleased with this study, I bet. I am.

Diversity Tonight

No more blogging until late tonight or tomorrow morning as it is a Monday and on Monday evenings I teach. Today’s topic is Biological Diversity, from its origins through its evolution to its current state. Fun!

The Encyclopedia of Life

Everybody is talking about Encyclopedia of Life these days. It is alll still very Beta – we’ll wait and see how it turns out in the end. Many are enthusiastic, some are skeptical. But, what happened to the Tree of Life? Remember it from 1995 and after? I found it useful during the last decade for teaching and finding info. Why build a whole new thing when the old one could be updated and modernized instead – it is already chockful of information.

Looking for good educational biology movies

I am teaching my BIO101 again starting this Monday. The class is very small, so the discussions and student presentations will not last very long. Thus, I will have extra time at the end of each lecture. This can be a good time to show some videos. So, if you know of good movies available online or that can be ordered as CDs or VHS tapes, let me know in the comments (check the link for the topics I need to cover). I have a couple of ancient tapes whcih will do in a jiffy, but I am looking for more recent and better stuff. Keep in mind that this is VERY basic biology. Thus, the cool Harvard movie of the inside of the cell won’t work – too many molecules I do not cover and nothing is labelled anyway.

I can feel it in my bones….

Sperm Cells Created From Human Bone Marrow:

Human bone marrow has been used to create early-stage sperm cells for the first time, a scientific step forward that will help researchers understand more about how sperm cells are created.

Gives a new meaning to the word “boner”, doesn’t it? OK, too late at night – I am losing all sense of what is appropriate on a science blog. Actually, the study is interesting besides its potential for humor.

In Memoriam: Knut Schmidt-Nielsen (September 24, 1915-January 25, 2007)

How did I miss this!?
Knut Schmidt-Nielsen, one of my personal scientific idols, died on January 25th, 2007at the age of 92.
KSN%201.jpgHe has re-invented, or perhaps better to say invented, the field of comparative physiology (now often refered to as ‘evolutionary physiology’). He wrote the standard textbook in the field – Animal Physiology: Adaptation and Environment, that he updated through several editions, from which generations of biologists (including myself) learned to think of physiological mechanisms as adaptations.
He wrote a definitive book on Scaling, as well as a wonderful autobiography – The Camel’s Nose: Memoirs Of A Curious Scientist.
KSN%202.jpgI had a good fortune to meet him a couple of times. He was a Guest Speaker at an NCSU Physiology Graduate Student Research Symposium several years ago where he gave an unusual but fascinating talk. I was his host for the day so I got to spend a lot of time with him one-on-one and try to osmotically draw in some of his genius.
A couple of years later, when his memoir came out, I persuaded Nansy Olson to have a public reading at Quail Ridge Books, which was well attanded and quite fascinating. The very last question from the audience was “Did any of your findings find a practical application?” to which he proudly responded “No!”. The old-style scientist. In it for the curiosity and nothing else.
While Schmidt-Nielsen did research on myriads of different animal species, he will forever be remembered as the Camel Guy. When he arrived at Duke University as a young new professor, he persuaded the Department to let him build an isolation chamber where he could measure the metabolic rate of a camel. They let him do it. He brought in the camel. Fascinating research resulted. He also built an identical, but much smaller, chamber into the wall right next to the camel chamber for the equivalent research in desert mice.
KSN%203.jpgWhen he retired, his position was filled by Steve Nowicki, a birdsong researcher. Duke offered to demolish the camel chamber and turn it into a lab. Steve declined in horror. Instead, he made sure that a plaque was installed at the door (“…this is the camel chamber in which…”) as well as on the little wall-chamber next to it. He turned the inside of the chamber into a grad student office (now, who can beat that – having the office in the ‘camel chamber’?!).
A few years later, Duke University built a monument to Knut Schmidt-Nielsen – a lifesize sculpture of the man and his camel – right outside the Biology building.
For many years after his retirement, Knut Schmidt-Nielsen kept a small office in the Department and came “to work” almost every day. He read the literature, including popular science magazines, and clipped the interesting papers/articles out of them to place in his colleagues’ mailboxes according to their interests. If there was Internet 50 years ago, Knut Schmidt-Nielsen would have been a science blogger for sure!
Always curious, always humble, always learning, always reading, always teaching, always popularizing science, every day of his long life. And that is on top of being truly one of the giants of science of all times.

Bodies

The Bodies Exhibition is coming to The Streets at Southpoint in Durham.
My wife saw it last year in NYC. My daughter will probably be too squeamish for it, but I’ll try to get my son to come with me.
Once I go….well, it is certainly a bloggable event.

Evo-Devo: what new animal models should we pick?

A review of evo-devo (Jenner, R.A., Wills, M.A. (2007) The choice of model organisms in evo-devo. Nat Rev Genet. 8:311-314. Epub 2007 Mar 6.) is starting to make rounds on the blogs. I cannot access the paper (I’d like to have it if someone wants to e-mail me the PDF), but the press release (also found here) is very vague, so I had to wait for some blogger to at least post a summary.
This is what the press release says (there is more so click on the link):

The subject of evo-devo, which became established almost a decade ago, is particularly dependent on the six main model organisms that have been inherited from developmental biology (fruit fly, nematode worm, frog, zebrafish, chick and mouse).
To help understand how developmental change underpins evolution, evo-devo researchers have, over recent years, selected dozens of new model organisms, ranging from sea anemones to dung beetles, to study.
One of the selection criteria deemed most crucial is the phylogenetic position of prospective model organisms, which reflects their evolutionary relationships.
Phylogenetic position is employed in two common, but problematic, ways, either as a guide to plug holes in unexplored regions of the phylogenetic tree, or as a pointer to species with presumed primitive (ancestral) characteristics.
Drs Ronald Jenner and Matthew Wills from the Department of Biology & Biochemistry at the University of Bath (UK), call for a more judicious approach to selecting organisms, based on the evo-devo themes that the organism can shed light on.

Larry Moran and PZ Myers went into a completely different direction which I find quite uninteresting: evo-devo was and currently is a study of animals and if people who study other organisms want to make their own equivalents, good for them, more the merrier, hi-ho-hi-ho, etc.
I have no problem with the idea that Earth is a planet dominated by bacteria and that the animals are a recent afterthought. I sympathize with those who lament the lack of interest, funding and teaching in the ares of plant, protist and fungal biology. But evo-devo is currently an area of Zoology, so the search for new animal models, as opposed to plant models, is a perfectly appropriate question. We want to know how animals develop and evolve and evo-devo tries to put those two questions together. I am sure botanists, mycologists, microbiologists are working on their own version within their own domains – and hopefully the groups will read each other and learn – but that is outside the realm of this particular review paper.
What bothers me about the press release is its vagueness. Different people have different definitions of the terms “development”, “evolution” and “evo-devo”. Different people have different evo-devo questions they deem important and the review appears to reflect the biases of the authors (and so do posts by Larry and PZ).
Development
Some people focus on the early embryos and things like pattern formation, determination of dorso-ventral axis, or limb development. Others consider the entire life-cycle, including growth, maturation and senescence, to be parts of development. Some focus on patterns of expression of developmental genes. Others are more interested in phenotypes. Some focus entirely on the development of anatomical structures, while others are more interested in the development of biochemical, physiological and behavioral traits and how they evolved. Obviously, people with different focus in development will ask evo-devo to pursue different questions.
Evolution
Again, some people are interested in genotypic evolution. They use the population-genetic definition of evolution as “change in frequency of alleles in a population over time”. Their models can detect some things (e.g, type, strength and direction of selection), but not others (levels/units of selection, effects of population structure, etc.), so they focus on the former and the latter is ignored, or given lip-service, or even deemed unimportant (or even non-existent!).
Others are interested in phenotypic evolution. After all, genes are invisible to selection – it is organisms that get selected and the changes in gene frequences are a downstream result of that process. They have different aims and goals for evo-devo as a discipline.
Using the broadest definitions of both development and evolution, the classical studies of imprinting, developmental ‘windows’ for learning birdsong, and organizing vs. activating effects of hormones are smack in the middle of evo-devo research – the mainstream onto which some genetic stuff has been added lately.
Evo-devo
Evo-devo is short for “evolution of development”. But, it actually asks three distinct questions:
How animal development evolved
Trying to trace and document how various developmental mechanisms evolved over time, in essence building a phylogenetic tree of developmental changes in animals on this here planet Earth since the apperance of first animals until today.
How animal development evolves
Figuring out generalizations, hopefully rules, and perhaps even laws, about the ways different evolutionary mechanisms affect different developmental mechanisms.
How animal development affects animal evolution
Figuring out the way different developmental mechanisms affect the way evolution can proceed, i.e., developmental constraints in the positive sense of ‘funneling’ evolutionary direction by making some directions more likely than others. From the very inception of the field, fueled by the publication of Stephen Jay Gould’s “Ontogeny and Phylogeny” (his by far the most influential book, though ALL the others are more popular), the focus has been on things like allometry, heterochrony, heterotopy, etc. This paper appears to be focused on this goal as all the suggestions appear to have such processes in mind:

Developmental programming. Allometry of horns in the beetle Onthophagus nigriventris.
Developmental bias. Variation in body size in C. elegans.
Developmental constraint. Shell morphology in the gastropod Cerion.
Redundancy. Anterior-posterior axis development in Drosophila melanogaster.
Modularity. Sense organs in the cavefish Astyanax mexicanus.
Evolvability. In silico cell-lineage evolution.
Origin of evolutionary novelties. The sea anemone Nematostella vectensis (bilateral symmetry, triploblasty).
Relationship between micro- and macroevolution. The three-spined stickleback and Heliconius butterfly wing patterns.
Canalization and cryptic genetic variation. D. melanogaster phenotypic variation increase during HSP90 impairment.
Developmental and phenotypic plasticity, polyphenism. Ant caste polyphenism and caste determination by primordial germ cells in the parastic wasp Copidosoma floridanum.

Frankly, ALL of these topics I find immensely exciting and, sure, I’d love to see these ideas implemented and these models adopted, and this research done. But what bothers me is that this list just enlarges the Big Six list into a Big Many list. It does not do what it is purported to do – move from separate studies of devo and evo to an evo-devo research program.
You can study development in an organism, but to study evolution of development you HAVE to do comparative work. This means that choices of single species miss the mark completely. If I have written this paper I would have suggested pairs and groups of species, not single species.
For some questions, one wants to compare closely related species, perhaps all in the same genus, e.g., Drosophila (D. melanogaster, D. pseudoobscura, D. yakuba, etc.). Rudolf Raff made great strides early on in the field of evo-devo by comparative studies of two closely related species of sea-urchins, one of which undergoes metamorphosis (i.e., goes through a larval stage) and the other one skips it and develops directly from an egg to an adult.
For other questions, one may want to look at somewhat less related species that cover a greater spread of evolutionary relationships. Perhaps a bunch of different insects: fruitlies, house flies, mosquitoes, cockroaches, termites, beetles, butterflies, moths, sandflies, wasps, honeybees, etc. (like this paper does, for instance), or a bunch of different fish, e.g., zebrafish, medaka and fugu, or comparing chicken to quail to turkey to ostrich.
For yet other questions, looking at the philogenetic depth is quite fine. It is exciting what we are learning about the origin, evolution and development from the studies of Cnidaria (see this, this and this for an example), or about the origin of Vertebrates from the comparative studies of echinoderms, hemichordates, urochordates, cephalochordates, agnathans and fish (check out this and this).
So, if you had unlimited space, time, manpower, money and freedom, tell me what pairs or groups of animals you’d choose as new evo-devo models, not individual species, and what would you study with them? What for? Which of the defintions of development and evolution you ascribe to? Which of the three evo-devo questions excite you personally?

Genes, green caterpillars and brown caterpillars

About a year ago, there was a great paper about polyphenism in moth caterpillars.
Now, in the new issue of Seed Magazine, PZ Myers uses that example to teach you all about it. Cool reading on one of my favourite topics (outside clocks, of course).

Physiology: Coordinated Response

Physiology: Coordinated ResponseThis is the last in the 16-post series of BIO101 lecture notes for a speed-course targeted at adults. As always, I welcome corrections and suggestions for improvement (June 17, 2006)…

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Physiology: Regulation and Control

Physiology: Regulation and Control
The penultimate installment of lecture notes in the BIO101 series. Help me make it better – point out errors of fact and suggest improvements:

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More Basic Concepts

Basic Concepts, Ecology: Know Your Biomes I

More Basics….

There are two new additions to the Basic Concepts and Terms in Science list that appeared today:
Voltage Gate: What Is Ecology?
The World Fair: Epistemology (what is a flower?)
Any others?

Basic Terms and Concepts in Math and Science

I don’t know how many of you check out the constantly growing list of links to posts that cover Basic Terms And Concepts in Science, but you should. Our Seed Overlords are cooperating and will soon set up a place where all those posts will be re-posted, commented upon, edited, etc. – a one-stop shopping for all basic stuff useful, for instance, in teaching at all levels from Kindergarden to Postdoc!
Until then, here is my unofficial list – not the one compiled by Wilkins – that also includes some of my own posts, as well as some of the other people’s posts that I found useful in teaching myself.
If you are a science blogger and your area of expertise is not represented – write a post and let us know about it (“us” being pretty much everyone on scienceblogs.com, but John Wilkins is the #1 person to go to). If you are a scientist, but not a blogger, I’m sure many of us will be happy to let you publish a ‘guest-post’ on a missing topic, written in a way that can be understood by lay-people and used in the classroom.
Here is my ‘enhanced’ list, under the fold:

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Oh, how thoughtful of the Intelligent Designer!

A-ha! Finally! Now I understand the connection between Creationism and the overall anti-sex sentiment of the Fundamentalists!
New reseaarch shows that E.coli swim upstream due to the Design of their flagellum! And where do they swim from and swim to? Yes, you guessed it right! And you can also watch the movie.

Introduction to Anatomy and Physiology

BIO101 - Lecture 5: Introduction to Anatomy and PhysiologyNext in the series of BIO101 lecture notes. Chime in to correct errors and make it better (reposted from June 11, 2006):

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Gene?

In the series of “Basic Concept And Terms” (yup, I know, John is well known for misspelling people’s last names, including mine), several people have already chimed in with their own definitions of the “gene”, demonstrating how unclear this concept is and how much disagreement there is among the practitioners depending on the type of research they are doing (e.g, molecular biology, developmental biology, population genetics, evolution, etc.).
See how the term was defined and explained by PZ, Sandra and Greg so far and you’ll see those differences in emphasis.
Now Larry Moran joins the fray with one post on what a gene is not (though many erroneously cling to this definition) and one post on what a gene is, at least from Larry’s perspective. Good reading altogether.

Basics: Biological Clock

Considering I’ve been writing textbook-like tutorials on chronobiology for quite a while now, trying always to write as simply and clearly as possible, and even wrote a Basic Concepts And Terms post, I am surprised that I never actually defined the term “biological clock” itself before, despite using it all the time.
Since the science bloggers started writing the ‘basic concepts and terms’ posts recently, I’ve been thinking about the best way to define ‘biological clock’ and it is not easy! Let me try, under the fold:

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Back to the Classroom

This is what I will be doing tomorrow morning again. I have so much fun!

Question to my readers

My SciBling John Wilkins is regularly updating the list of ‘Basic Terms and Concepts’ posts (which you should check dilligently every day!), at least until a more permanent repository is made.
Today, he included my Lecture #13 on Current Biological Diversity on the list, though my reposting of it was a part of my regular Thursday noon series of educational posts, not intended specifically to be picked up for the ‘Basics’ series (though I believe it belongs there).
On one hand, I feel silly to repost stuff that I just reposted a month or two ago (moving it from the old blogs to the new one). On the other hand, I have written in the past a number of posts I considered “basic” and perhaps they should be brought out to light again (and also relieve me from having to write too much new stuff and spend more time on the Dissertation).
So, should I, for the sake of the “Basics” series, quickly (i.e., over the next week or two) repost everything I think is a “basics” post? If so, which ones truly are ” basic”? Or just forget the whole thing?

Current Biological Diversity

Current Biological Diversity The latest re-post of my BIO101 lecture notes (this one originally from June 05, 2006). I know I will have to rewrite everything about the Three Domain Hypothesis, but you also tell me if I got other stuff wrong or if this can be in some way improved for the classroom use.

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Basic Terms and Concepts

In the wake of the conference, I suspect that my blog is getting checked out today by many a science teacher, so I thought this would be a good time to point out all the posts written so far by my science-blogging friends on ‘Basics Terms and Concepts’ in math and science. Here they are:
Good Math Bad Math:
Normal Distribution
Mean, Median and Mode
Standard Deviation
Margin of Error
Uncertain Principles:
Force
Fields
Pharyngula:
Gene
Discovering Biology in a Digital World:
Gene
How do you sequence a genome?
Sandwalk:
Evolution
The Central Dogma of Molecular Biology
Evolving Thoughts:
Clade
Fitness
Greg Laden:
The Three Necessary and Sufficient Conditions of Natural Selection
The Modes of Natural Selection
I am still thinking what to write myself. Looking back at the stuff I have written in the past, I tend not to focus narrowly on a single term or concept, but prefer to cover a broader area. An exception may be the post in which I explain that a “biological clock” is A Metaphor, for the most part – but not always – a useful and productive metaphor. It is a language concept that helps us understand the phenomenon, not a real thing itself. If you start thinking about a biological clock as a real entity, you may just as well think it was intelligently designed.
For teachers, I think my BIO101 speed-course lecture(and lab) notes may be useful, though almost none of them cover a very narrow term or concept (some come close):
Introduction
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
Going up a level – to senior/grad school material in my own field, I have written about half of my planned series of Clock Tutorials which students taking real-world classes in Biological Clocks have so far found very useful in their studies.
I have also started slowly to cover chronobiology on a taxon-by-taxon basis but did not get too far yet. Only the series on clocks in bacteria is finished (for now, until the next batch of revolutionary studies comes out):
Circadian Clocks in Microorganisms
Clocks in Bacteria I: Synechococcus elongatus
Clocks in Bacteria II: Adaptive Function of Clocks in Cyanobacteria
Clocks in Bacteria III: Evolution of Clocks in Cyanobacteria
Clocks in Bacteria IV: Clocks in other bacteria
Clocks in Bacteria V: How about E.coli?
I just barely started on Protista:
Biological Clocks in Protista
And scratched the surface of Invertebrates:
Do sponges have circadian clocks?
Daily Rhythms in Cnidaria
and scratched the surface of Vertebrates:
Mammals
Non-mammalian vertebrates
Japanese Quail
I need to get some more of that kind of stuff written soon.

Evolution of Biological Diversity

Evolution of Biological DiversityPart 12 of my BIO101 lecture notes. As always, click on the web-spider icon to see the original post (from June 04, 2006). Correct errors and make suggestions to make this better. Perhaps this entire series can be included in the “Basic Concepts” series.

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Origin of Biological Diversity

Origin of Biological DiversityContinuing with the Thursday series of the BIO101 lecture notes. Check for errors of fact. Suggest improvements (June 01, 2006):

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What Creatures Do: Animal Behavior

BIO101: What Creatures Do: Animal BehaviorHere is the next installment of my lecture notes for teh adult education speed-class in biology. As always, I ask for corrections and suggestions for improvement (May 20, 2006):

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From Genes To Species: A Primer on Evolution

From Genes To Species: A Primer on EvolutionThe eighth part of my lecture notes series. As always, please pitch in and make my lectures better by pointing out the factual errors or making suggestions for improvement (originally posted on May 17, 2006):

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So, just inject the humans right away and see what happens?

Just How Useful Are Animal Studies To Human Health?:

Animal studies are of limited usefulness to human health because they are of poor quality and their results often conflict with human trials, argue researchers in a study online in the British Medical Journal.
Before clinical trials are carried out, the safety and effectiveness of new drugs are usually tested in animal models. Some believe, however, that the results from animal trials are not applicable to humans because of biological differences between the species.
So researchers compared treatment effects in animal models with human clinical trials.
They used systematic reviews (impartial summaries of evidence from many different studies) of human and animal trials to analyse the effects of six drugs for conditions such as head injury, stroke and osteoporosis.
Agreement between human and animal studies varied. For example, corticosteroids did not show any benefit for treating head injury in clinical trials but did show a benefit in animal models. Results also differed for the drug tirilazad to treat stroke – data from animal studies suggested a benefit but the clinical trials showed no benefit and possible harm.
Some results did agree. For instance, bisphosphonates increased bone mineral density in both clinical trials and animal studies, while corticosteroids reduced neonatal respiratory distress syndrome in animal studies and in clinical trials, although the data were sparse.
Animal studies are generally of poor quality and lack agreement with clinical trials, which limits their usefulness to human health, say the authors. This discordance may be due to bias, random error, or the failure of animal models to adequately represent clinical disease.
Systematic reviews could help translate research findings from animals to humans. They could also promote closer collaboration between the research communities and encourage an interative approach to improving the relevance of animal models to clinical trial design, they conclude.

First of all, it’s not just efficacy of drugs that is tested in animals but also – and more importantly – safety. If a drug kills all the mice, it will never be tested in humans in the first place.
How about animal studies in the research in basic biology: evolution, ecology, behavior, physiology, cell biology, developmental biology, genetics….? So what if those studies are never even done in humans. We are, after all, just one species out of millions, and a lousy lab animal to boot. Yet, those kinds of animal studies teach us basic biology that subsequently give us ideas for further studies of medical treatments.

From Genes To Traits: How Genotype Affects Phenotype

From Genes To Traits: How Genotype Affects PhenotypeThe seventh part of my lecture notes. Let me know if I made factual errors or if you think this can be improved (from May 15, 2006):

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From Two Cells To Many: Cell Differentiation and Embryonic Development

From Two Cells To Many: Cell Differentiation and Embryonic DevelopmentIt’s Thursday, so it is time for the next portion of my BIO101 lecture notes (May 15, 2006). As alway, I’d appreciate corrections of errors, and suggestions for improvement.

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From One Cell To Two: Cell Division and DNA Replication

From One Cell To Two: Cell Division and DNA ReplicationConitnuing with the Thursday BIO101 lecture notes, here is the fifth part. As always, I ask you to correct my errors and make suggestions to make the lecture better. Keep in mind that this is a VERY basic speed-course and that each of the lecture-notes covers roughly 45 minutes (often having 3-4 of these within the same day). This part was first posted on May 14, 2006.

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Books: “On Becoming a Biologist” by John Janovy

Janovy%20cover.jpgI wish that, many many years ago when I was becoming a biologist, that I could have read this wonderful little book – On Becoming a Biologist by John Janovy! What a little gem!
On the surface, or by looking at the Table of Contents, this slim volume appears to be just yet another in a long line of books giving advice to people who are interested about joining the profession. And sure, it does contain important information about getting accepted into a program, choosing one’s project, teaching, research, publishing, getting funded, giving talks etc. But it is also much more than that. The entire volume is permeated by personal experience and sprinkled with little gems of wisdom. In the end, you realize that biology is not just a profession – it is what you love and, more impportantly who you are, how you define yourself and how you think about the world.
In other words, biology is not what you do but who you are. A biologist is primarily a naturalist, someone who looks at the world and sees the interconnectedness, someone whose primary preoccupations are not politics, economics, entertainment, fashion or money, but the way humans are related to every other living thing on the planet.
Thus, you can earn a living by being a lawyer, clerk or politician, and still call yourself a biologist – never being bored when out in nature, never too engrossed in the business of society to lose sight of the awe and beauty of nature, never too busy chasing money to forget that you and that cockroach you just squashed are distant relatives. It is a worldview more than a profession, being able to see the natural forest for he social trees.
Likewise, you can earn your living doing biology yet not be a biologist. Being good at using a particular technique or solving puzzles makes you a good technician, but without the sense of wonder, without noticing what others do not in nature, you are not really a biologist. If you are more interested in the properties of a protein than in what that protein does in an organism to make it be adapted to its environment, you are a chemist, not a biologist. There is nothing wrong with being a chemist, of course, but this book is about being a biologist. The focus of the biologist’s attention is always the organism. One can study complex ecosystems, or one can study details of molecular biology, but if the organism is not front and center, it is not biology.
A biologist, according to Janovy,

“has, by virtue of his or her interests, the obligation to continually attemp (1) an integration of parts into a whole, and (2) an explanation of the whole in which both the behavior of the whole, and the role of the part, are considered. This manner of thinking is, or at least should be, characteristic of one who considers the function of an organelle relative to the life of a cell, of a cell relative to the life of a tissue, and so forth up to and including the roles of wholeorganisms in the organization of an ecosystem. With this kind of perspective, an average citizen should be able to metaphorically place his or her time on Earth into a context that includes the entire planet and its evolutionary history. A biologist has an obligation to explain, and perhaps promote acceptance of, this metaphor.”

Thus, it is a duty of a biologist to be a public person, a vocal spokesman for the kind of thinking about the world in which the humans are not set apart and valued on their own, but only as one of many parts in a complex system of nature. Part of this loud voice, again according to Jacoby, is the duty of a biologist to strongly and vocally denounce anthropocentric points of view – from Creationism to anti-envrionmental activities – and replace them with a naturalistic worldview in which we play an important part, but are codependent with other organisms in space and time and cannot safely regard ourselves and our societies in isolation from Nature.
This book should be a required reading for every college freshman considering a major in biology. If you have a niece or nephew who appears to ba a “natural” naturalist, this book is a perfect gift for the upcoming holiday season.

Cell-Cell Interactions

Cell-Cell InteractionsContinuing with my BIO101 lecture notes (May 08, 2006). As always, please correct my errors and make suggestions in the comments.

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