Welcome to Tangled Bank #63. Probably a pretty good reason to start scienceblogging again. I was going to do a clever little theme, but I’m neither clever nor little. I thought about doing something primate-related. But I’m too obsessed with monkeys as it is; I research them with no funding, no position faculty or student, and no prospects. And then I thought about doing a country music themed edition. But I figured that in these circles, my musical tastes are possibly even more anathema than my political opinions.

So you’re getting a straight up carnival. Deal.

Phil B. presents Phil for Humanity: A Better Purpose for N.A.S.A. posted at Phil for Humanity. He makes the proposition that NASA research is best directed toward developing the technology to maintain longterm space colonies, rather than simple basic science. Personally, I like my weekly NASA wallpaper way too much to support ditching telescopes that can take pretty pictures, but it’s not a bad suggestion.

Wandering Visitor exposes a dirty truth when it comes to ‘ready to eat’ food. Thank god I buy fresh.

Avant News tells us about a study that Finds Human Brain Capable of Finite Number of Thoughts. Well, at least I have an excuse for my performance on last week’s midterms. Seriously though. I guess it turns out there is a limit to what human imagination can do.

…Ok, I guess I wasn’t so serious…but then again neither were they…

Dr. Kavokin continues his series on how pharmaceutical compnies use you as a guinea pig (Part III). Part I and Part II are also worth a read if you’re interested in the history and mechanics of how clinical trials work.

For a change of pace, Dr. David Ng brings us a very different entry titled ‘Be Very Afraid‘. It’s a fun stream of conscious romp through various aspects of science that currently have the public’s attention. Everything from GM foods to alternative energy to eugenics, he hits it all. If it were a book I’d buy it.

You know what pisses me off? The titmouse (Baeolophus spp.). Not because of anything it’s done, but because of its name. Its name is clearly British in origin, because the rather vugar colloquial use of those first three letters didn’t exist back when it was named. But the bird is American. And to make it worse, the bird doesn’t resemble either of its namesakes. Luckily, 10000 birds has come to my rescue. I’m still annoyed, but at least now I know what I’m so pissy about.

Apparently there’s something called plum pox. And at some point in the vague future, it might possibly threaten the plum production capabilities of this great nation. Sound familiar? *cough* Avian Flue *cough*

Anyway, genetically modified foods come to our rescue with the Honeysweet Plum, Guaranteed Pox Resistant ™. Brought to you by Genetics and Health. The story, not the plums. Although they may grow the plums too. They didn’t mention it in the conflict of interest disclosure form though. So let’s assume it’s just the story.

Never trust authority is my motto. In government, in science, and at home (the latter probably explains why my parents kicked me out of their house 3 times before I graduated). And RPM shows us exactly why in ‘On Somatic Variation of the Genome‘. Just because someone is more famous than you does not mean he necessarily knows more. And the founder of Wired magazine shows his ignorance about the nature of the genome writ large for all to see. The sad thing is that because he’s a figure of some influence, he will be taken at face value, setting science back a small, but significant amount. Kudos to an excellent fisking, RPM. I’ll use it if that misconception ever comes up amongst my peers.

Balancing Life brings us a discussion about why a Japanese crab’s carapace would resemble a Samurai mask so strongly, for reasons other than artificial selection. That’s a geographical coincidence if I’ve ever seen one. I mean, North Carolina blue crabs don’t have carapaces that look like samurai masks. Although the Blue Devils are in North Carolina…Now explain that to me.

Flocking behavior. Finally, something I studied in school. CPBVK of Rigor Vitae does an excellent job of bringing what can be a boring subject to life as he explains why selfish animals would group with their competitors. Some of the benefits aren’t necessarly intuitive, which makes them all the more fascinating. And he discusses monkeys. Brownie points.

Tim Abbott of Walking the Berkshires presents Thar She Breaches!, an account of a recent whale watching experience. Good background info and well written. Whale watching is definitely one of those things on my ‘to do’ list. There’s something romantic about mammals who chose to return to the sea of their piscine forefathers. The way they sing to each other across miles of empty ocean only heightens the image.

Libertarians can be green. And one thing that upsets this green libertarian is invasive species. They’re just so destructive and so hard to stop. And in many cases such waste could have easily been avoided. Perhaps the most galling is that I have to accept that humans are the most invasive, most destructive of any of these. Dr. Jenn Orth of the Invasive Species Weblog picked the time I was hosting the Tangled Bank to send an entry in about the controversy surrounding the introduction and control of Buffelgrass in Arizona. She’ll be receiving a bill for my aneurysm repair surgery.

The Hairy Museum of Natural History brings us news that Coelophysis might not be the babykiller we’d all pegged it as. I liked the piece, but I wasn’t even aware that Coelophysis had been pegged as a cannibal. Which is weird because I’m even more obsessive about dinosaurs now than I was at 4, which is really saying something. It does heighten my belief that these days paleontologists of all stripes (human and dinosaur especially) are becoming more and more obsessed with creating controversy. I blame Horner and Bakker. They started it all. And Alvarez too. And, come to think of it Cope and Marsh. And if we mention them we have to mention the real life Indiana Jones Mr. Andrews. Ok, maybe paleontologists have always been obsessed with creating controversy. Nevermind.

Lab Cat discusses the interesting, but difficult process of objectively measuring the color of various foods. If it sounds a bit dull to you, consider her excellent synopsis of its importance:

How many people remember the fuss when blue M&Ms first came out?

Physics nerds beware. This one will grab you.

Ouroboros discusses how the failure of normal cellular turnover (autophagy) may be linked to aging. He seems a little concerned with the ravages of father time as he’s sent me another post, this one dealing with oxidative damage and age-related hearing loss. As a future psychiatrist, I must caution him that such a preoccupation is frequently a marker of deeper insecurities that would be best addressed before they fester like an untended sore.

Dan Rhoads discusses the results from a new paper and compares two possible scenarios detailing how the results of said paper influence the polarity, movement, and cytoskeleton in motile cells. Hypothesizing is the fun part of science. Unfortunately that’s not what you get paid for. Which is why you blog.

Martin of Salto Sobrius takes a look at the unorthodox field of childhood treehouse archaeology. Interesting analogy between the development of one of these ‘archaeological sites’ and the development of the mind.

Diane Kelly of Science Made Cool points out a few good resources for bug identification. If I wasn’t the type to scream like a 6 year old girl and run at the site of a terrestrial arthropod, I might have been willing to try that out. But the saga continues. The caterpillar they identified in the first post spouted parasites! All in all a very clever way to develop your child’s interest in science.

Daniel Collins of Down To Earth discusses what a genetic algorithm is:

Genetic algorithms (GA) are types of computer models that incorporate processes inspired by evolutionary biology such as selection, inheritance, mutation, and recombination…GAs are used to find optimal solutions to complex problems, though in practice you can never be sure they find the absolute optimum instead of just a local optimum (just as in evolution).

and then he discusses how these algorithms can be applied to further our understanding of plant diversity.

Which segues nicely into the final entry of this edition of the Tangled Bank. Mine. Daniel discussed how other disciplines (especially engineering) could benefit by using genetic/evolutionary algorithms. I instead focus on the dire need for a pseudobiological discipline (Medicine) to learn to use an evolutionary perspective.

Well that’s it for this week. I hope my commentary wasn’t too offensive, or tiresome. And at any rate even if I volunteered again, you wouldn’t see me till February. Which gives you a minimum of 4 months to to recover from the psychological trauma.

Tangled Bank 64 will be hosted by the Neurophilosopher’s Blog on October 11. Now if you’ll excuse me, I’m off to bed.

First science post in a long time. Expect more though. Because I feel like I’m in a political rut.

I get more than a little frustrated when doctors and fellow medical students tell me they don’t see how evolution has any bearing on the practice of medicine. Perhaps it’s because they’re taught to think of the body as a machine that on occasion malfunctions and needs to be repaired, and so find themselves inclined to think of Paley’s watch rather than Haeckel’s famous theory. Perhaps it’s because they view biology as a means to an end rather than the end in and of itself. Whatever the reason, Dobzhansky’s most famous utterance is lost upon far too many of them.

Learning
A knowledge of evolution makes understanding several subjects considerably easier. This applies to embryology perhaps more than any other. As a tutor for the dental students at my university, I’ve found phylogenetic comparison an invaluable teaching aid. I’ve also found it immensely frustrating since, being in Oklahoma, I have to preface it with “I don’t know if you’re a creationist or not, but this is an evolutionary example that helps me understand things.” When helping students to understand why the sclerotome of the paraxial mesoderm forms only axial skeletal elements but not appendicular (limb) bones, I invoke the humble lamprey. Possessed of the simplest body plan, the poor creature lacks both limbs and a true jaw. I tell them “The sclerotome is pretty old stuff, it’s only got enough material to produce a lamprey skeleton.” Vertebrae, ribs, and a skull encasing the brain and eyes. That’s about it. Jaws, ‘faces’, and limbs, being newer vertebrate features, have a different embryological derivation. And a lightbulb goes off. “Paraxial=lamprey”. Stupid simple.

Staying with embryology just a few moments longer, the development of the kidney is a rather confusing process. The embryo/fetus actually develops three different excretory systems in succession, the latter two of which are functional at various points of development. First come the cervical nephrotomes, then the mesonephros, then the metanephros. This developmental process is an elegant (and possibly the finest) example of the idea that ontogeny recapitulates phylogeny. And because of this, a sprinkling of evolutionary context can help to make sense of this process well enough for a student to keep things straight.

Perhaps the most fun use of evolutionary perspective comes when learning about physiology. Everything in physiology revolves around homeostasis. Maintaining a constant internal environment. For the most part, complexity of a given taxon is directly proportional to its ability to maintain its internal state at a constant rate. Mammals are perhaps the finest example of this ability, but all, from the simplest ball of Volvox to the lizard basking in the sun show some aptitude for this. And as to the nature of this internal state they’re trying to maintain? Blood bears a remarkable (or perhaps expected) resemblance to seawater in many respects. And this has prompted several of my physiology teachers to describe us as “a collection of cells that figured out how to take the sea with us.” Much like Wernstrom’s goldfish and his reverse scuba suit.

The greatest vindication of the use of evolutionary history as a teaching aid is the fact that although these represent extra–what mainstream physicans would less charitably call extraneous–information, they nevertheless make the testable material easier to understand. In short, the extra learning investment is more than returned.

Looking Forward
Evolutionary thinking also gives us a more stable platform from which to study the human body in sickness and in health. Understanding that the human body is an evolved construct allows us to better understand exactly what ‘normal’ is, and what conditions may bring on disease.

Anatomically and genetically, humans haven’t changed all that much in the past 100,000 years. Yet our environs and our lifestyles have shifted to the point that our current circumstances have no resemblance whatsoever to our past lives. More importantly, as technology, healthcare, and standards of living have improved, we are less and less likely to die before reproducing no matter how feeble or infirm.

What this means is that we have to treat the body as evolutionarily static at least from the birth of modern H. sapiens, and perhaps even as far back as H. heidelbergensis. And although I am somewhat critical of the view of the body as a machine, it remains a useful framework within certain limits. The heating element in your water heater would quickly warp if powered up in open air. And the coil on your stovetop wouldn’t function under water. Their failure under such circumstances is not an indicator that they are defective, but rather that they were forced to operate outside their design parameters.

I hate to use the word ‘design’ in such a context, but preventive medicine hinges upon our ability to ensure that our bodies are not placed in situations they haven’t evolved to cope with. Diet, activity patterns, and exercise are just a few of the areas in which we differ from earlier examples of our species. How does this deviation affect our health? In the realm of genetics, sickle cell anemia is probably one of the most well-known examples of the intersection of evolution and medicine. A potentially beneficial allele in one environmental context becomes nothing but a nuisance at best, lethal at worst in another. Type II diabetes is another example.

My personal agenda revolves around the basic proposition that the brain’s purpose isn’t whatever some psychologist claims it is, but rather that it is wired and coded with software that is designed for a certain environment. It is not a blank slate but an evolved construct optimally suited to certain physical and social contexts. When placed in a different social or learning structure, it can easily go haywire.

The latest area of medicine I’ve seen a place for evolution in is cancer. This might be because we just finished the unit on neoplasia in pathology class and I’d been studying it 24/7 for the past couple weeks. But everything about the pathogenesis of cancer hearkens back to lessons I had in undergrad on selective advantage, differential reproduction, and natural selection. Without getting into too much detail, cancer is essentially a progression of genetic changes, each of which allow these cells to escape the restraints that prevent normal cells from proliferating and spreading unchecked. The neoplastic cells that beget a tumor were often present 10 or 20 years before anything was clinically evident. This is because the immune system ruthlessly destroy those cells that appear genetically different from the host. Like multi-drug resistant bacteria, those neoplastic cells exist in an environment that consistently selects for the ones that evade detection, escape destruction, and reproduce faster than they can be killed. The ability of these tumors to continually reappear despite the immune system’s best efforts, and in many cases from apparently successful chemotherapy should thus come as little surprise when thought of this way. We are in fact selecting for those mutant genes that confer the ability to escape normal therapeutic and preventive methods.

We, our genes, our physiology, and our behavioral patterns evolved in one environment. They are a product of that intimate interaction between the organism and its surroundings. Changing the surroundings not only changes the nature of the interaction, but may substantially affect the fitness of said organism. While nothing so dramatic as the explosion of a polychaete worm when placed in a freshwater aquarium, there can be little doubt that much of the ’cause’ of human illness may not be rooted internally at all. Understanding the difference between our current environment and the one we evolved in will play an ever greater role in the prevention and treatment of disease.

Conclusion
Medicine has much to learn from evolution. It can provide us a foundation from which to better ground ourselves. And a scaffolding from which to reach for the sky. No other facet of the biological disciplines has remained as recalcitrant to simple Darwinian concepts as this field, and perhaps it’s time we were brought kicking and screaming into a mindset most of our colleagues found in the early 1900’s.

I’m not a fan of determinism. Especially when it comes to medicine. Partially this is because I’m just stupid and naive enough to think of medicine as a calling and not just a job. And I, personally, would only be happy if I never had to refill a prescription or even see a given patient ever again after 6 months. Of course, free will is also a crock when it comes to medicine. People are predisposed to certain conditions by dint of genetics, environment, and other factors. But predisposition and cause are two very different things, something many doctors either don’t understand or willfully ignore. Patients like it too. “It’s not my fault I’m diabetic, it’s genetic.” Certainly feels a lot better than “I should’ve paid more attention to lifestyle.

I’m sure most of my readers have heard about Ad36, an adenovirus similar to what causes the common cold. And they’ve heard about how it “makes” you fat. In a small study, they did find that 30% of obese people carried this virus, versus only 10% of others.

One thing I want to mention is that Ad36 causes paradoxical obesity. You’re fat, but you aren’t necessarily an unhealthy fat. You don’t necessarily have the high cholesterol, triglycerides and insulin problems.

But whenever someone throws percentages at me, I know that there’s another way to look at these things that can put it into a better, less alarmist/determinist, perpsective.

What they did was talk about the percentage of people of a given BMI category that are infected. But we could turn it around and look at the percentage of infected people that are obese. Roughly 30% of the country is obese, 70% not. When we compute everything out, we find that roughly 16% of the country is infected with Ad36. Of them, roughly 56% are obese, 44% not. For a virus that ’causes’ obesity, it sure seems to be kind of hit or miss.

I’ve hit this issue before. But it’s in the news again, so I thought I’d return to it. For a little background, you can see a piece I wrote or a highly recommended, if slightly older article written by a real doctor. Sorry for the lack of links. I’ll throw up a link list sometime in the next few days.

When Michael Reagan stood up at his father’s funeral and cried about how Embryonic Stem Cells could have saved the man who ended the cold war, I cried a little myself. I cried because I wish I was old enough to have better memories of a president who was by most accounts an amazing statesman and just a great man all around. I cried because it was wrong for the man’s own flesh and blood to use his father’s death as an excuse for political posturing. But mostly I cried because every time someone stumps for the new panacea, I see development of a real cure farther and farther away.

I’ll start by saying that my political position is that despite being pro-life, I have no moral qualms with harvesting new ESC cultures from cord blood or discarded embryos. In the former case, there is simply no moral quandary; the cells weren’t taken from an embryo/fetus/bay. With regard to the latter case, the operative term here is discarded. Any objections one would have to harvesting stem cells in that case would also apply to organ donation in adults as far as I’m concerned.

My scientific position is that ESC’s make for excellent models but bad therapy. ASC’s on the other hand are the exact opposite. Each have their place in the biomedical sciences and medicine. Embryonic stem cells are comparatively easy to harvest, sustain, and grow in culture. They’re also capable of differentiating into more kinds of tissue than any given adult stem cell. In addition, ESC lineages are standardized (currently 19 of them. Should be more), meaning studies are more repeatable. Adult stem cells, on the other hand are not as amenable to laboratory manipulation. They’re harder to get to (although we’re finding more accessible places where they exist), they’re harder to sustain, and they’re much harder to grow in cell cultures. On the other hand, despite tiny budgets and little attention from funding bodies or the public at large, ASC researchers have had much more success in therapeutic applications in animal models and humans alike. Even at a theoretical, freshman biology level, the advantages of ASCs in therapy are fairly obvious.

Embryonic Stem Cells

A recent issue of Scientific American highlighted the similarities between ESC’s and cancer cells (which is one of the objections to the use of ESC’s as therapy). ESC research may lead to greater understanding of the etiology (development) of various cancers. And more importantly, since when we were embryos our stem cells didn’t go tumor on us, we may be able to reverse engineer the process by which ESC’s are controlled. This could very well lead to better cures and preventive treatments when it comes to cancer. ESC’s are also a good deal more pliable than ASC’s (another problem when it comes to therapy). Which means you can do more with them in a laboratory setting, particularly when it comes to understanding developmental biology. ESC’s give us a convenient model with which to study proliferation, differentiation, and apoptosis. They’d be useful in studying how things go wrong in human embryonic development as well as how things go right. As well as in understanding the nature of the switches that turn these cells on and off and how to operate them. This is stuff we’ve been doing for decades, but thus far only with animal embryos. The moral implications of raising a human embryo for the purpose of experimentation are pretty grim. ESC harvesting methods are much more morally neutral while allowing many of the same benefits.

Of course, what makes ESCs so suited as models is what makes them so poor at therapy. Which is something the ESC researchers conveniently forget to tell the press and the public. After high school, I worked in a cell biology lab with CHO cell cultures. CHO stands for Chinese Hamster Ovary. No ordinary reproductive cells, these are all descended from an unlucky rodent’s bout with cancer. I always found it interesting that what made it such a useful laboratory model is why it killed that poor little pet. Like cancer, ESCs are immortal. Like cancer, a lot of the regular processes that differentiated cells go through are shut down. Like cancer, ESCs love to grow. Getting an ESC to stop growing once it’s in an adult body has proven to be a difficult proposition in animal models. Getting an ESC to turn into the kind of cell you want is also tough. And assuming you’ve got past all those roadblocks, you now have to deal with immunocompatability issues. When you get an organ transplant there is a pretty high risk of rejection, no matter how close a match the new organ is. It isn’t you. Your immune system knows it isn’t you. And it wants to kill it off. The immune system is a marvelous and sophisticated system that was designed for the sole purpose of killing off foreign cells. If you want those donor cells, tissues, or organs to stick around, you have to cage up that immune system, leaving yourself open to the depredation of other foreign cells. In other words, taking immunosuppresants for the rest of your life is not exactly fun. ESC researchers don’t mention to you that these problems apply to ESC therapy as well, do they? The one big success I’ve seen with them is in the nervous system. Which is somewhat expected. The nervous system is one step removed from a lot of other bodily processes, including circulatory and immune processes. Not to mention the fact that glia (support cells in the brain and nerves) secrete a chemical that actively inhibits nerve cell division and proliferation, meaning less likelihood of tumors. The one big benefit to ESCs compared to ASCs is that because they are less constrained, a single ESC culture can be turned into many different types of tissues, whereas any given ASC colony is significantly more limited.

Adult Stem Cells

What about adult stem cells, surely they can’t be any better, right? Not as models, no. ASCs are by their very nature dormant. That’s part of why they’re so hard to find and why people weren’t even sure they existed until recently. They’re hard to culture and hard to ‘turn on’. And because ASCs are at a later stage of differentiation than ESCs, they can turn into fewer types of cells. Meaning that it might take 2 or 3 different ASC colonies taken from different parts of the body to create all the kinds of tissue you can with just one ESC colony. ASCs can also be rather hard to get to: the hollows of your bones, deep in your brain, embedded in your heart muscle. Not a whole lot of people are going to volunteer for major operations just so some guy with no social skills in a white coat can play with test tubes. And, even if you could get people to do that, you’d still have the problem of lack of standardization. A researcher using stem cells he harvested from my bone marrow could do one experiment and get completely different results from another researcher halfway around the country who used your stem cells, not because the experimental process is unpredictable, but simply because you and I are different, and so are our cells.

Again, these weaknesses as a model translate to strengths as therapy. Imagine that you are told you have to hold a gun to the head of your best friend and you have your choice of two trigger types. One gun doesn’t go bang as long as you pull the trigger. Release it and you’ll be covered in brain stew. The other gun is much more conventional. If ESCs are the former, ASC’s are the latter. I’m pretty sure which one I would choose. While ASCs can be hard to get to, more accessible sources (that don’t require surgery) are being found even as we speak. These same studies are also finding that ASCs are easier to culture and are perhaps more flexible than was once imagined. At any rate, a situation in which one person has multiple degenerative disorders each needing a different ASC is bound to be rather rare. And the implications of self-harvesting for therapy are pretty obvious. Unlike ESCs–which are essentially transplants–ASCs are you. They’re your DNA and your tissue. Instead of organ transplantation, the process is more analagous to a scar fading to nothing over time.

Conclusion

Both ESCs and ASCs have much to offer us in understanding and treating disease, and they do so in a complementary, rather than competitive manner. Of course, research is highly competitive, and so whichever works better in a laboratory setting is the more likely to be funded. And it’s true that ESCs have greater potential to increase our understanding of cell biology because of this. But treatment doesn’t necessarily require understanding. When Fleming invented Penicillin he had no idea that the compound contained within put holes in bacteria cell walls, causing them to burst open. He just knew that the stuff killed bacteria. When Edward Jenner invented the smallpox vaccine, he probably had very little idea of how immune systems worked, he just knew that if you gave someone cowpox (which isn’t deadly) they woudln’t get smallpox (which is). Understanding can improve treatment, which is why it’s important. But there’s no harm in getting the ball rolling, which is exactly what we’re refusing to do by focusing on the politically expedient and the glamorous (if laboratory biology can be glamorous).

Adult stem cells offer us the potential to literally heal ourselves. To quote some old dead guy, ’tis a consummation devoutly to be wished’

Radio sucks. Ergo, it got stuck on Tammy Bruce during my iced tea run. She was going on about how the guy who woke up from the coma changes everything about the Schiavo situation. I was going on about how she’s a stupid [censored]. Apparently the conservative world needs a quick lesson in neurobiology. So here we go.

This is a nerve cell (neuron):

(from http://faculty.washington.edu/chudler/color/pic1.html)

Notice that there’s a big fat part at the top. That’s the cell body. That’s where all the machinery that makes the cell do its thing is. That’s where the DNA, the mitochondria, the ribosomes, all of that are. These provide the instruction set, energy, and proteins, respectively.

Now the long part is called the axon. It’s basically a biological combination of an electrical conduit and a subway tunnel. It’s essentially a passive structure. Nothing starts in the axon, merely passes through it.

At the end are the synaptic terminals. This is how the nerve cell sends a message to the next nerve cell in the chain.

Looking back to the top of our picture, the yellow branch-looking thingies are what receive the signals sent by the synaptic terminals.

Ok, now that we know all about that we can discuss how nerves respond to injury. Nerve cells, along with muscle cells, don’t keep proliferating and dividing in adulthood. They’re done. This is why after a heart attack you have reduced heart function. Once those cells die from lack of oxygen, nothing can grow back to replace them. This is also why in stroke patients, even after they recover function, it’s rarely as good or as natural-feeling as it used to be. The injured area doesn’t regenerate, other cells just learn to pick up the load.

But while we can’t make new nerve cells, injured nerve cells can regenerate. This is why finger re-attachments work. They can even take the relatively useless sensory nerves that pass over your collar bone and put them into your face to replace damaged or congenitally absent nerves there.

It’s important to note that a neuron can only regenerate if its body is intact. As I mentioned, all the machinery is in that body. Without that machinery, there’s no way to repair the damage. If it’s the axon though, the nerve cell’s body can repair it, although it may take years.

The difference between a coma and a persistent vegetative state is that in a coma, generally the cells are all there (well most of them anyway), it’s just that the axons are all screwed up. Generally as a result of blunt force trauma. In a PVS on the other hand, the cells themselves are dead. Hence the term braindead (the old non-PC term for PVS).

In a coma there is generally brain activity because the cells themselves are still alive. It’s just scattered and disorganized since the wires are tangled and snapped off. Axon growth is inhibited by several chemicals in the brain (that you don’t see in the peripheral nervous system) which is why regrowth can take months, years, even decades…but at least it can potentially actually happen. In a PVS there is nothing. There are no cells to fire. There are no cells to regenerate themselves. There is no chance of recovery.

Terry Schiavo’s brain was gone. This guy’s wasn’t. I don’t want to get overly philosophical here, but if the brain is the seat of the soul and the brain itself is no longer functioning, I really can’t consider it taking her life. Terry was a vacant body, this guy was not.

until CAID stops sucking and until after the conference. I still haven’t started preparing for that. Because I suck at life. I’ll be doing a piece or two over there, but more aimed at the ID mess than just plain enjoyment of science. This is also why the science stuff has been light for the past week or so. Sorry (for those of you who actually read it).

In a couple weeks I’ll be back up to at least 3 posts a week on science. Until then, I suck.

Introduction
Razib (second contributor at CAID, not to mention the guy who got the buzz going) is up to his usual tricks of making me think.

Anyway, it was a pretty far-ranging post of his, discussing systematics, species concepts, and the difference between micro and macro evolution (none). I’m going to restrict this to a discussion of the latter. Which also happens to be a favorite theme of creationists/IDers since many evolution enthusiasts (and biologists) don’t really understand the concepts. I hope I can shed some enlightenment.

Many contend that micro and macro evolution are really the same biological process, something called Scale Independence of Evolution. The basic gist of this is that no matter what we’re talking about, the mechanism behind it is nothing more than changes in alleles over time and fixation of mutant alleles in the population.

In other words when a creationist says ‘I accept micro-evolution, just not macroevolution’, he doesn’t have a leg to stand on since the only difference between the two is the degree of change in allelic frequency. Up until recently my defense idea has been “look damn you, it’s obvious.” Which is not a good scientific explanation. Even though it is obvious, you have to be able to articulate why without degenerating into screaming fits, broken furniture and insults. This might explain why my publication record is nonexistent, come to think of it.

So without further ado, I give you the simplest explanation I’ve come up with…

The Thought Experiment
Let’s take a population of capuchin monkeys and put sayyy 100 of them on a small island off the coast of India, just because they’re my favorite critter ever and I’m from India. Now, your average creationist has to accept micro-evolution since it can be shown directly in the lab, in the wild, and in humans. Allelic frequency changes are obvious. But mutation fixations have been documented as well. (sorry no links). This is why most of them concede that point to us. So we have a population of animals upon which microevolution is operating.

Now, since this is a thought experiment, we’re just going to take a wall and plunk it down across the middle of the island separating the population into two noncommunicating halves, just like the Berlin wall. We now have two different populations of the same species undergoing microevolution. In subtly different ways. Even if there is no difference in habitat on either side of the wall, the quirks of sexual selection (See marmosets), neutral selection, etc. will result in population level differences in allele frequency between the two. Furthermore, mutations that arise in one population can become fixed in that one, but can’t even get to the other one (no gene flow). Should these mutations affect pre or post zygotic mechanisms, you now have two species who can no longer interbreed and produce fertile offspring.

To complicate matters (and make it more real-worldy), let’s now turn one side of the wall into a marsh, and the other side into a rainforest, complete with a change in flora and fauna. Now selection pressures operating on each population are considerably different. The process will be much more speedy.

All that happened was your basic change in allelic frequency and fixation of mutations. It just happened in a population that was divided into two halves due to external factors.

In other words, the only difference between micro and macro evolution isn’t biological, it’s geographical (biogeographical?). Something in the physical world divides a single population in twain. That’s it.

Species Concepts
This is another problem, one that’s existed since we started classification, and one that I don’t pretend to solve in the following. The idea of pre-zygotic and post-zygotic recognition mechanisms is part of Ernst Mayr’s Biological Species Concept. The basic idea is that if two animals can interbreed and produce fertile offspring, they belong to the same species.

I see a certain problem with this as it completely ignores what to do about ‘incomplete speciation’ and speciation events that are still occurring. Recent research as far as the human-chimp split and the Homo sapiens/Homo neanderthalensis mess reveal that far from being instantaneous, speciation can take a considerably long time.

A couple of examples of the problems the Biological Species Concept has include hybrid zones. There’s a pretty famous picture of the geographical distribution of the 6 (or 8…people argue) species of baboons and they hybrid zones where you get varied degrees of admixture between the two ’species’. You get the same thing with marmosets as well. Are these guys no longer different species despite differences in appearance, behavior, feeding ecology, and the fact that less than 1% of either population mates with the others?

What about tigons and ligers? They can be fertile. And in India, where they have (or once had) adjacent ranges, they’d even be possible, if not a definite occurence on occasion. Do you really mean to tell me that lions and tigers, despite one being a savannah adapted group-living social hunter with more constrained shoulder rotation similar to canids and one being a solitary hunter with an incredible degree of freedom in its joints, not to mention vastly different appearances and builds, are really the same species?

No, the BSC has a problem in that, unlike evolution, it’s ahistoric. It looks at a single point in time. Furthermore, it ignores total amount of genetic variation, as well as differences in phenotype and behavior, restricting itself solely to the reproductive system.

I’m a much bigger fan of chronospecies, the evolutionary species concept, and the ecological species concept. There is very little difference between the three, and for the sake of this discussion it’s safe to say that the main characteristic of all of these is that the process (and thus historicity) of evolution of species is incorporated. They all recognize that a population can change in fundamental characteristics from one generation to the next without a speciation event occuring. Furthermore, the evolutionary species concept in particular allows us to more easily talk about two daughter populations that haven’t completely parted ways according to the BSC, yet have changed in fundamentally different ways relative to each other.

The nice thing about these latter three is that since they’re historical, they can synapse more directly onto the basic idea of how evolutionary change comes about (allelic frequency and fixation).

I’ll update with pics when I get a chance, but right now I’m grabbing my straw hat, my corncob pipe, and going camping.

A lot of my friends smoke. And every so often one of them will say ‘I’m trying to cut back’ or ‘I’m trying to quit’. People tend to see them as similar actions. I don’t think that’s really the case, though. Quitting involves completely severing the chain of nicotine addiction. ‘Cutting Back’ merely means you make the chain a bit longer, but ultimately leaving you just as tethered as before.

Furthermore, someone who’s already cut back will have less reason to quit than someone who’s still got the chain-smoking thing going on. The person with a pack a day habit spends a lot more money, is more short of breath, has uglier teeth and skin, and just in general feels the ill effects more than the guy who grabs 3 or 4 ciggies a day. In other words, the guy with the stronger habit has that much more incentive to quit.

Let’s compare this with the oil situation. Typically, the Evil Party is calling for more restriction and regulation. Taxes, tarrifs, credits, in general more regulation, and, most stupidly, higher CAFE standards. For those of you who don’t know what those are, basically, car companies have to maintain a minimum fleet-wide fuel economy average or be heavily fined. The higher the CAFE standards, the fewer gas guzzlers and the more fuel efficient cars they have to sell.

This in turn means that we get more miles to the gallon and that all else held equal we spend less on gas each year. In turn, gas prices will drop as demand does. We’re ‘cutting back’ on our oil addiction. It’s interesting to note that despite the higher-than-ever gas prices (I’m too young to remember the 70’s/80’s mess), our expenditures on gas relative to the entire household budget are actually lower. Which are why complaints are surprisingly few despite the near-doubling of prices in some areas.

The Evil Party wants us to cut back ever further. This won’t change the fact that our entire infrastructure centers around oil, it’ll merely mean that our infrastructure centers around slightly less oil than before.

And furthermore, just as in smokers, it’ll actually reduce our incentive for moving off oil. The lower prices are, the less likely we are to pursue alternative technologies. Corporations won’t research it, consumers won’t be interested in it. As an example, hybrids from Honda and Toyota had record sales this past month. I’m not a fan of hybrids in general (they don’t work), but it does serve as a perfect illustration. They’re being pursued because they’re thought of as an ‘alternative’ (even though they aren’t). Do you think they’d be snapped up with such fervor if gas prices were half of what they are now?

Technologies like ethanol, biodiesel, and fuel cells will remain under-explored and under-utilized because we’ll ahve no reason to go for it. Promising methods like biomass ethanol production (rather than corn fermenting) won’t be pursued. Ethanol, subsidized or not, would be less competitive with $1.50 gas rather than $3 gas, especially in its infancy as technology, distribution, and other aspects of supply were still maturing.

Believe it or not, short term expensive gas is a good thing. It’ll put the hurt on us. And, like all animals, we’ll attempt to eliminate the source of that hurt. Which’ll mean weaning ourselves off oil.

Crossposted at Homeland Stupidity, where I’ll be publishing more on the theme of libertarian conservation efforts as time goes on. Probably healthcare as well.

Environmental conservation and libertarianism aren’t words frequently heard in the same sentence, unfortunately. Instead when we think conservation, we think hippies. Hippies and annoying rangers and officials telling us we aren’t allowed to play in the park anymore, build a house on our own property, or drive that gas guzzling sports car.

I say this is unfortunate because capitalist ideas, where they’ve been tried, have been more effective than anyone could have dreamed. It’s pretty easy to see why, when you think about it. One method makes the process of conservation antagonistic whereas in the other people actually profit from it. I’ve heard it said that the way to succeed in life is to make everyone think they’ve gained in a deal. That’s the beauty of capitalistic strategies; everyone leaves happy.
To an economist, life can be seen as a series of ‘games’. These are decisions that create winners or losers. Now, there are two kinds of outcomes: Zero-Sum and Non-Zero-Sum games. The difference between the two is that in the former, there is no new wealth created. The winner ‘wins’ because he takes wealth from the loser. In the latter there is new wealth created. So both parties can win, although one might make out on the deal better than the other.

Typical conservation efforts use the zero-sum model. Man against nature. Which is slightly ironic considering our stereotype of your typical environmentalist. It’s easy to see why people will be perpetually unhappy with that:

“You want to take my land to give to that endangered newt?!?!? A newt, who the heck cares about a newt, for crying out loud?”

Conservation programs that have been popular with the locals and haven’t hemorrhaged money on the other hand are based around the non-zero-sum model. I’d like to claim that libertarians were the ones who spearheaded these programs, although largely they weren’t, just conservationists who were willing to give evil capitalism a try. The way these programs work by and large is to tie the identity and the prosperity of a local community into the natural habitat that the overbearing white people are trying to preserve.

For us to turn conservation into something that profits everyone (non-zero-sum), we have to give value to the protected area and animals within. This can be done in two ways: Giving them intrinsic or extrinsic value. Extrinsic value is what the pricetag says. Intrinsic value is why you could never sell it, at any price.

Hippies try to appeal to conservation efforts based on the intrinsic value of the natural world. As a Hindu and an outdoor kinda guy, I wish it could work that way. Hindus and buddhists, and to a lesser degree Tao and Shinto, are the best target population for this kind of entreaty, their religions being based to a large degree on interaction with the natural world. And, well, if you’ve seen the changes that have occurred in India and Southeast Asia in my lifetime alone, you’d understand the futility of that.

No, our best chance is to appeal to the extrinsic value of that which we would protect. Money. I don’t like that it has to be that way, but I’m mature enough to admit it. One of the most spectacular conservation successes has been the Karisoke Wildlife Reserve, a mountain gorilla habitat in Rwanda. This is the camp that Diane Fossey setup, where she went slightly native as she studied and yes, possibly engaged in fornical activities with, gorillas. It wasn’t her efforts, but the work of her successors Bill Weber and Amy Vedder, that I’m going to mention in passing.

(great read, great animals, great people. Their passion is just amazing, I was lucky enough to see a talk they gave over their conservation efforts. Very good stuff.)

The couple decided to try a more local-friendly approach than is traditional (usually the locals are treated like the enemy). They paid the wardens well, hired local trackers, camp workers, and publicizers. They went to the schools in the area to educate kids about the intelligence and beauty of gorillas. And, in a coup-de-grace, they set up a tourist program in which rich Americans and Europeans funnel thousands of dollars per head into the local and national economy just to point and laugh at the gorilla scratching himself funny. The result was that when the Rwanda/Uganda civil war of the 1980s erupted, only 2 gorillas were killed by underfed soldiers turned to poaching…on the Rwanda side anyway. Just across the imaginary line where Karisoke stops and the Ugandan part of the Virunga mountains start, close to 100 times that number exist.

Here, we’re not quite as impoverished as Africa, the same kind of economic incentives don’t necessarily work to the same degree. But we are a nation of hunters. And that’s a vastly under-utilized resource. Sure, there are yahoos out there that will shoot at anything that moves, but most hunters are responsible, ethical, intelligent individuals. As such they understand that if there’s no more pristine habitat, there is no more good hunting. If we better tapped them as a resource, the national park system would be a good deal more robust, and conservatives would be much happier with conservation efforts.

Kim Du Toit brings us an example that has to do with culling an elk population in Rocky Mountain Forest. The government plan will of course cost 18 million dollars and take 20 years…to kill 1500 elk. Which, as Kim points out, is something that hunters pay to do. His modest proposal would resultin a 1.5 million dollar profit based on hunting permits alone. Throw in the money spent on travel, lodging, food, guides, and we’re talking a fair amount of money injected into the economy here.

I guess what I’m trying to say is that with capitalism, not only can we make conservation less painful, we can even make it a substantial new growth sector in the economy. As Weber and Vedder showed us, it’s at least worth a shot.

Interesting

Most people know that the appendix is a vestigial organ, a remnant of an intestinal system that in our ancestors was much, much larger. Plant material, particularly leaves, is hard to digest. Mammals can’t even do it if it weren’t for gut flora (bacteria) that breakdown the cellulose and other fibrous tissue for their own energy needs. Once broken down into smaller, more absorbable and digestible products, we can use it. But even with the aid of the bacteria, it’s still not particularly easy. So animals that rely on high fiber plant diets for their sustenance tend to have long intestines. The length means there’s more bacteria to do the initial breakdown, and more surface area to absorb the remnants. You can contrast this with meat eaters. Meat is much more readiliy broken down and absorbed, which is why carnivore guts are a lot less complex and a lot less large.

Just think of the complexity of the ‘four-stomached’ cow versus the simple, almost straight-line gastrointestinal path of the cat. All primates rely heavily on fruits and leaves in their diet. Humans, believe it or not, aren’t any different in this regard. Most of our calories should come from non-meat sources. But we don’t place anywhere near the emphasis on folivory that say colobines (leaf-eating monkeys) or even other apes do. So we dont’ need that much gut. Unfortunately, because of the way natural selection works, we end up with a useless remnant that only serves to make us sick.

But is it really completely useless? Chris Wanjek points out that it isn’t quite the layabout we’ve made it out to be:

Biologists in the early 20th century surmised that the human body had over 100 useless parts left over from our more ape-like lifestyle a few million years ago. The parathyroid was one such organ, now known to regulate calcium-phosphorous metabolism. The appendix was another…

As quickly as 11 weeks after conception, the appendix starts making endocrine cells for the developing fetus. Endocrine cells secrete useful chemicals, such as hormones, and the appendix endocrine cells secrete amines and peptide hormones that help with biological checks and balances as the fetus grows.

After birth, the appendix mainly helps the body stave off disease by serving as a lymphoid organ. Lymphoid organs, with their lymphoid tissue, make white blood cells and antibodies.

While this is true, the appendix’s endocrine cells don’t secrete any different hormones than the rest of the gut. And while it’s full of lymphoid tissue, so is the rest of the gut as well. I know this because I consistently failed to identify them properly on our histology final. And while it may or may not provide a better ‘training ground due to various aspects of its organization…

The dirty gut is a good training ground for young white blood cells. The appendix, with its sac routinely collecting and expelling foodstuffs, exposes the white blood cells to myriad bacteria, viruses and drugs passing through the gastrointestinal tract. This way, the white blood cells learn to fight potentially deadly bacteria, such as E.coli.

…I’m not sure just how important that really is to overall immune function.

The gut is a highly specialized and complex organ system. It has its own separate nervous system, an amazing range of hormonal functionality, forms an important part of the immune system, and, of course, digests our food. The appendix has lost the latter function, but retained the rest. Which doesn’t necessarily make it an important part of the body, just means that it’s only truly vestigial in one respect.

But he does bring up some interesting uses for the appendix when it comes to reconstructive surgery:

In the not-too-distant past, zealous doctors would remove the appendix during other types of surgery—to get it “out of the way” just in case it would some day become infected. The philosophy was: The appendix is useless; I’m already elbow-deep into this person’s gut; why don’t I just snip the appendix now.

But no more.

Doctors now realize they can use the appendix for reconstructive surgery. In one type of bladder “replacement” surgery, doctors take part of the intestine to form a bladder and use the appendix tissue to recreate a sphincter muscle, which can contract and open the bladder when urinating. Similarly, the appendix is used as a substitute ureter, a tube that carries urine from the kidneys to the bladder.

Good stuff.

This is the second installment of the series on Evolution, Economics, and Political Philosophy, the introduction of which can be found here.

Introduction
Actually, I probably could have titled this ’self-interested nature.’ Self interest doesn’t quite make the world go round, but it certainly makes us go round. Beyond DNA and various parts of our molecular machinery, self interest is the unifying theme of all living organisms. Selfishness is why evolution has produced such myriad forms as the Mantis Shrimp and the Scaly Anteater.

Some have accused me of being a neo-Randian, of worshipping at the altar of selfishness even as they deny its very existence as our primary motivator. The self-interested nature of all living beings is morally neutral. It isn’t something to deify as anarcho-capitalists do, or to vilify and attempt to expunge as collectivists do. It exists, it is the single rule that all life obeys. It is responsible for our greatest masterpieces and our worst catastrophies. Mother Teresa was motivated by self interest as much as any Fortune 500 executive. Self interest just is.

Modeling Behavior: The Assumptions Behind Game Theory
The assumption that individuals will act in a self-interested and rational manner has allowed the study of behavior–both human and animal–to move beyond the nebulous world of thoughts and feelings, archetypes and motivations, to a predictive model of behavior. While not as refined or determinate as physics or chemistry, mathematical models of behavior are capable of astonishing accuracy when it comes to predicting the choices we make both conscious and unconscious. John Nash of Beautiful Mind fame, and sociobiologists John Maynard Smith and Robert Trivers are a few of the great names out there when it comes to the mathematical modelling of behavior.

Any explicative theory or paradigm is built upon certain assumptions. Game theoretics and other mathematical models of behavior are dependent on the following three:

• 1. Individuals will always act to further their own interests

• 2. Individuals will act in a rational manner

• 3. Individuals are party to all necessary information to make an informed decision

To present this from a Platonic point of view, if the model is the perfect form, the real world is the slightly bastardized expression of it. In other words, these conditions don’t always hold true. Humans aren’t completely rational, and natural selection isn’t rational in the least, merely appearing so when looked upon with a teleologic perspective . And we are never possessed of perfect information; at some level, our cost/benefit analysis is never going to be 100% accurate. We can never quite know whether what we think is a winning choice actually is. The idea of imperfect information is a pretty basic one, and needs little further discussion other than to understand that there is always uncertainty in decision-making. Rationality, however, is a topic worthy of further discussion at a later point.

The high fidelity of these models in predicting behavior is what lends credence to the assertion that self interest is ultimately our sole motivation. The only other major paradigm that has been asserted is group selection (in sociobiological literature); its political equivalent–one which it enjoys an incestuous ideological and historical relationship with–is collectivism. For the past 200 years, group selectionists of every stripe–sociobiological, economic, and political–have tried to assert the viability of this selective domain, and have continued to fail in presenting any evidence for its existence.

Given this long history of failure of the group selectionist paradigm and the equally long history of success of that of the individualists, it is probably safe to say that self-interest is our primary motivation. However, another thing one must remember about models is that in addition to the fact that their assumptions aren’t ever completely fulfilled, they are often narrower in scope than the real world. By this I mean self interest is a wide-ranging and broad concept that cannot be reduced simply to maximization of economic wealth or reproductive gains. Mere observation makes it patently obvious that very few individuals’ lives revolve around either of those goals.

Self Interest Defined
The truth is that self interest manifests itself in everything from the food we eat to our education to our work ethic. Major failings of both libertarian and mixed model ideologies is that they over-estimate the importance of economic (material) wealth. Many libertarians believe that ‘the market’ will solve all problems. Many leftists believe that no one would want to stay on welfare, the standard of living (material wealth) being so low. However, few individuals would feel adequately compensated for the loss of a child if they received in return every cent they had spent raising him. And many people don’t believe that leaving welfare and getting an entry-level job in order to increase material wealth only incrementally is worth the 40 hours a week of exertion.

While it would be nigh on impossible to catalog, model, and codify all the various avenues in which self interest expresses itself, understanding the ways in which self interested behavior impacts social and political systems is considerably easier. Although imperfect, a useful classification arises if we define selfish behavior as either acting at an internal or an external level. Internal self-interest is about ‘feeling good’. External self-interest could be conceived of as ‘being superior’. The former, of course is about the position the individual sees himself in, while the latter is about how others perceive the individual in question. The primary internal interest is maximizing comfort. Whereas the primary external interests are power and influence. Wealth actually contributes to all three; serving to grease the wheels as it were.

Comfort is fairly self-explanatory. While many dream of a mansion, a summer home on the spanish riviera, a supercar, and a yacht, most aren’t motivated to turn this dream into reality. People are quite content with reasonably comfortable accomodation, a trip every year or two, and a car that gets the job done. While what they define as adequate may vary, few would need to become highly paid executives, plastic surgeons, or hollywood entertainers to achieve their relatively modest goals. Most people are content not to find themselves wanting for any of life’s basic and not-so-basic necessities.

While obviously wealth is necessary to achieve all of these material goals, after a certain point, such wealth becomes superfluous. At that point, the marginal utility of undertaking extra work, vying for promotion, getting more training, is considerably less. The attendant increase in comfort just isn’t worth the extra work.

Influence–an external interest–is perhaps the most nebulous. The academic who after 10 years of schooling and postdoctoral work is making about as much as an electrician and considerably less than a plumber. Who nevertheless spend 60, 80, even more, hours a week relentlessly pursuing research. Who takes off for the wild jungles of Brazil or Africa to make notes on what a monkey is doing every minute of every day for a year. He’s driven by the desire to be influential, at least in the limited circle of individuals engaged in similar pursuits. George Soros pouring millions and billions into moveon.org and Air America, he too is thirsting after such a title.

Power differs from influence in that power is a more direct attribute. The prince under Machiavelli’s tutelage was a man questing after power. Machiavelli’s primary concern was influence. The man behind the man on the throne. Frederick Delano Roosevelt, though, was a man after nothing more than power. From his assumption of Emergency Powers to his dramatic expansion of the Executive, to the fact that he fully intended to continue being elected president for the remainder of his life, there can be little doubt that no matter what other motivations he had, power was clearly one of them. Some would say the same of George W. Bush’s recent expansion of Executive–indeed all goverment–power.

It would be a fair assumption to say that there are scarcely few elected officials at the national level who aren’t drawn to the position out of some desire for power and influence. The same could be said of those in the upper echelons of civil service as well. Teasing apart influence and power can be a difficult proposition at best, but is more or less unnecessary to the understanding of the operation of political systems. Influence manifests itself through its effects on the projection of power; so one merely needs to look at power and how it is distributed and used to understand the contribution of both. As in comfort, wealth is clearly involved in attaining and maintaing both influence and power. Here, however, the marginal utility of increased wealth is considerably greater, to look at the interplay of wealth and power in the legislature alone.

Conclusion
The distribution and control of wealth is all too often the centerpiece around which political systems are drawn. As I’ve attempted to show in the preceding paragraphs, this view is at once both myopic and overly constrained. Wealth is merely the currency through which one’s aims are realized. It is the motivations of comfort and power that we need to understand. It is these which people thirst for, and which they will attempt to gain, often enough at the expense of others.

In order for a government to be stable, in order for the people under said government to be free of oppression, the political system under which it operates must be constructed to be proof against the depredations of those who would obtain their material wealth from the pocketbooks of others, as well as against those who would use the power of the government to oppress the very people it was meant to keep free.

The next installment will cover cooperation. How self interest is ultimately the motivator behind it, and how group selectionist and collectivist paradigms will always fail to incite cooperation, instead tending toward exploitation of the few against the many.

Yup.  Just ‘Why Fat People’.  Why do they exist?  Why is it so hard for some to lose weight while others have trouble gaining it?  Well, quite frankly it’s because the human body is an evolved construct.  It evolved under certain circumstances and is best adapted to a certain pattern of activity.  It’s been tens of thousands of years since we left that adaptive zone, more or less, but our bodies haven’t changed all that much.  Partly this is because unlike other animals, we left that adaptive zone by way of technology instead of changes in our bodies.  From about 1.8 million years ago with the rise of Homo ergaster through around 60,000 years ago (the Middle-to-Upper Paleolithic), hominid technology; what little there was, was pretty crude.  Instead of taking us beyond the capability of other animals, it merely allowed us to break even with the carnivores.  You see, as monkey playing wolf, we didn’t have sharp teeth and claws.  Our primitive wooden spears, hand axes, and cutters served as prostheses.  But, as Neandertals dwindled and modern humans expanded their range, newer, more advanced tools came to the fore.  These novel tools did take us beyond the capabilities of other omnivorous mammals.  It made hunting, gathering, virtually everything involved in living easier.

That technology is one of the reasons our bodies haven’t had to change that much.  We’re simply less likely to die from things that would kill other animals.  A wolf that can’t run fast won’t eat.  A man that can’t run fast can just hurl a spear.  And, because that technology acts as a prop, it’s allowed us to accrue all sorts of genetic and developmental baggage that makes us in many ways less healthy than we were 40,000 years ago.  From the hafted tools our umpteen-great grandfathers used to the computers many of us spend most of our time on, technology has made us fat.  What follows is partially science, partially scientific-informed speculation.  In other words, while a lot of what I’ll be presenting is fact, a lot is only likely, or merely plausible.

The most important thing to understand about the human body is that it’s an evolved construct.  By this I mean it’s a pretty jury-rigged affair when all is said and done.  A complex and marvelous mechanism, but shoddily put together nonetheless.  Anyone who’s studied Engineering Control Theory would be appalled by the lack of logic of the body’s mechanisms of homeostasis.  What I mean by this is that things that are clearly inter-related from an external perspective aren’t necessarily from an internal perspective.  The relationship between food intake, energy expenditure, and body composition is one of the most counterintuitive, complex, and just plain retarded systems in the human body.  Which might explain why weight control is one of the most difficult things for us to do.

Diet Composition 

It would make sense that we eat more food when we expend more energy, food being the primary source of fuel for us.  And, that’s a relationship that tends to hold true.  The converse would also make sense, that we eat less when we do less.  Unfortunately that isn’t quite the case.  Our hormonal control systems for appetite and activity are separately maintained, with different ’set points’, different degrees of sensitivity, and different timelines of adaptation.  While they do talk to each other, think of them as a long distance relationship rather than a codependent couple.

First, let’s start with food intake.  Clearly, how much you eat is a part of the weight equation, but its role is often far overstated.  There are a lot of fat people who eat too much.  There are also a lot who don’t.  And, we all know the rail thin guy or girl who eats 4000 calories a day and can’t put on a single pound.  Clearly, food isn’t the be all end all.  When I hear about friends who spent weeks, months or even years on one of those super-restrictive 1000-or-fewer calorie diets, I cringe with sympathy.  They were misled.

Diet is extremely important to weight loss and maintenance, but not so much the amount as the composition.  In fact, low-cal diets can make weight loss harder than if one were to go by a regular 2000 calorie daily regimen.  We must ask ourselves what hominids evolved to eat.  They are descended from monkeys, which means largely fruit-eating (and occasionally insect, lizard, and egg eating) mammals.  Other apes and a couple types of monkeys are known to scavenge and hunt occasionally (1-4% of their diet by weight).  So there’s little doubt that hominids were doing at least that.  And, there’s very good evidence that hunting and scavenging became a much more important (some would say dominant) aspect of their lives well over one million years ago.  Hominids in this respect were probably a lot like the wild social canids (wolves, jackals, etc) in their omnivorous nature.  A typical temperate or tropical canid diet can be 40% or more plant product by weight.

And then we can look at intestinal length.  The longer the intestine, the more comes from plants.  Cows have looong intestines.  Monkeys and most apes have shorter ones.  Humans are shorter than other primates.  Canids are shorter than the above.  And cats are shorter than the rest of these guys.  In other words, we’re very much in the middle.  We’re not carnivores, we’re not frugivores.  We’re omnivores.  We need a lot of sugars from fruits and other plant parts.  And we need a fair amount of protein (from meat, generally).

Which brings us back to the importance of diet composition.  Humans are limited not by their fat intake (for the most part), but by their carbohydrate and protein intake.  You need carbohydrates to fuel the body.  They’re what we’re most efficient and fastest at processing.  Fat has more energy per gram, but it’s harder for us to start using it.  Just think about that intestine length.  We need a lot of sugar in our diet.  And we need protein.  Although protein can be metabolized as an energy source, mostly it goes to repair, rebuild, and renovate the body.  Exercise, metabolism, basically everything we do causes our cell machinery to wear down a bit.  That machinery is made up of proteins.  Keeping ourselves in top form requires enough protein building blocks coming through our digestive system to undo that damage and a little extra to build bigger and better machinery.

Just about the only thing muscles and the brain run well on are carbs (other parts of the body, like certain organs, do better with fats).  Starving your body of them will only destroy your body’s ability to do any work at all.  And without protein, you’ll basically find yourself falling apart from the inside out.  Some of the stuff I’ve seen and read about what happens in a vegan’s body is nothing short of shocking.  Same can be said for those who get most of their calories from meat and none from vegetables.

Old-school hunter gatherer hominids probably burned roughly 3000-4000 calories a day of food.  We can estimate that based on what modern hunter gatherers expend.  That’s what the human body expects to come through it.  Any less than that, and you’re operating in fuel starvation mode.  Any more than that and you’re flooding the system with more than it wants.  In starvation mode, your body shuts certain things down to conserve energy, and decreases the ability of other parts to exert themselves.  In other words, it’s not burning as much as it used to, at least partially negating the effects of caloric reduction.

What’s more, because as I said, activity level and diet don’t perfectly correlate, the super-low calorie diets can shut down so much of your body’s machinery that you actually put on fat because the reduction in energy expenditure has dropped more than the reduction in energy intake.  And that’s just talking basal, cell-level, non-activity-dependent expenditure of energy.  Of course, caloric reduction also affects one’s ability to undertake activity and thus expend energy, which brings us to our next major topic.

Activity Levels 

As I said in the introduction, our activity levels and behavioral energy expenditure are considerably lower than they were in the prehistoric days.  I used to get in one to two ‘antisocial’ days when I was in graduate school.  On these days I used to strap on a backpack holding roughtly 60lbs of granite and walk 20-25 miles through the streets of London.  Beyond giving me a much needed chance to unwind and lose myself in physical exertion, it gave me a taste of what daily life would be like for an early hominid.  Based on archaeological remains, we surmise that hominid groups would travel anywhere from 10 to 30 miles in a given period.  Furthermore, these finds lead use to believe that they butchered their prey away from their campsites, meaning that, like little old me, they were toting a load for at least part of the journey.  I was also a pretty good model because at 5′11″ and about 200lbs I was more or less a walking facsimile of Homo heidelbergensis, the first of the hominids with brain sizes about like ours.

These were 4000 calorie days.  But the interesting thing was that not only was I eating a lot on the walking days, I was eating around 3300 on the non-walking days.  And not gaining weight.  Now, leading a much more sedentary lifestyle with little or no exercise (just like I was 5-6 days out of the week in London), I’m down to 2600-2700 calories a day at a steady 210lbs.

Basal Metabolic Rate

Strange you say? Not especially once you think about it.  It all has to do with arousal.  I don’t mean the dirty kind, or mental alertness, but the readiness of your muscles and supporting tissues to leap into action.  Immediately after blasting through a set on the bench at 100% intensity, you’ll probably notice that your muscles are warmer.  Your muscles are metabolizing more sugar, doing more work, and in consequence, releasing more heat as a waste byproduct.  Your ability to do work is dependent on the level of this metabolism.  The more carbohydrates your muscles are turning over, the more you can lift.  Now, getting your muscles primed and ready to do 100% intensity can take a while can’t it?  That’s why we warm up.  We’re increasing the level of metabolism in our muscles before we actually start doing work with them.  But even when we’re just sitting there doing nothing, our muscles and other tissues are metabolizing substrates, burning energy.

This is our basal metabolic rate.  Your BMR depends on a number of factors ranging from genetics to diet composition (more sugar, higher BMR, to a point).  Another factor it depends on is how warmed up you are when you’re doing nothing at all.  You can think of this as priming.  Different people have different levels of priming, some of it genetic, some of it having to do with expectation of activity (not activity level).  I’m naturally pretty well-primed.  My warmup tends to be flexing and shaking a bit and then getting right to it.  Which is why with less than an hour of real exercise a week, I still eat close to 3000 calories a day.  Other people aren’t quite so lucky, but even they can change their level of priming based on the body’s unconscious expectation of activity.  This is the reason I ate more even on my non-walking days back in England than I do now.  My body was under the influence of both my genetic priming, and my activity-based priming.  My body expected to be worked hard and was maintaining a higher level of readiness, which of course burned more energy.  Think standing to attention versus at ease.  Both you’re completely stationary, but one’s much easier to maintain than the other.

Conclusion

I’m going to tie all this together with a car analogy.  Cars have an air/fuel ratio they like to maintain.  For cruising it’s generally about 14.7:1 air/fuel by volume.  Less air and you’re lean, more air and you’re rich.  Both result in loss of power and efficiency.  If we think of dietary composition the same way, too little carbohydrates and too little protein can be just as damaging.  It’s important to maintain a good ratio to keep the car operating at a good level of efficiency.

Now, while all cars do best with a single air fuel ratio, the total rate of flow they do best with can be worlds apart.  The rate of fuel flow my Mustang has the best fuel efficiency at comes at around 77mph.   Whether the rate of fuel flow is higher (faster speed) or lower (slower speed), my Mustang gets worse efficiency.  It’s much the same for people, eating less can be just as bad as eating more; under either condition, our ‘rate of fuel flow’ causes us to be in a suboptimal position.
I don’t know how many of my readers have ever drag raced, but there’s a thing you do called power-braking.  When you’re at the tree (the lights that tell you when to go), you put your left foot on the brake, pressing down harder than you would at idle.  Then with your right you gas it.  Depending on the car, the brakes, the horsepower, and the tire, you try to get to the highest RPM’s without either your tires spinning or your car moving.  You’re not going anywhere, but you’re burning a lot more fuel than you do at idle.  Why?  Because when the green hits on the tree, and you let go of the brake, you’re that much further into the efficiency zone of your engine.  Priming.

Air/fuel ratio.  Fuel flow rate.  Idle RPM’s.  “Work smarter, not harder”, as Uncle Scrooge from Duck Tales was fond of saying.

I call BS. The study does say that they can guage our testosterone levels from our faces. To which I say of course. That’s kind of a ‘duh’. Signalling theory predicts that various aspects of our bodies serve as visual markers of aspects of our internal condition, particularly with regard to reproduction and health. Examples include the link between waist-hip ratio and fertility, and facial symmetry as a signal of health and a bountiful juvenile growth period.

Beyond determination of basic secondary sex characteristics (external genitalia, body hair, fat and muscle distribution, boobies, etc.), estrogens and androgens also affect the degree to which we express those things. “He has chiseled features,” or “she has a jaw like a man,” are cases in point where testosterone is concerned.  Guys with baby faces and girls that don’t have hairy arms are examples of low testosterone.  Or, take a look at the faces of pro wrestlers who aren’t fat like John Cena (i think that’s his name).  Their faces almost look like caricatures of male-ness because nearly everything they do has a stimulatory effect on testosterone release.

But this part:

“Women’s ability to estimate men’s interest in infants from face photographs is perhaps the most novel finding to emerge from the study,” researchers wrote in British journal the Proceedings of the Royal Society B: Biological Sciences.”

This I find a little more sketchy.  Testosterone has little to do with paternal care from my readings (and this is what I research, albeit at the wild animal behavior level).  Instead what matters is prolactin levels.  Obviously from the root stem we get that its a hormone involved in milk production.  But it’s also vital to the initiation, maintenance, and focus on parental care in both males and females.  Good dads in the animal kingdom have high prolactin levels.  And considering that some animals with very high prolactin levels also have high testosterone levels (alpha male capuchins, wolves, and, well, me), I’d think that we can safely say there isn’t that much correlation between the two.  And because prolactin levels only increase when babies are around, there’s little reason to believe that it affects appearance in a way that could be guaged by the study.
This is speculation but what I think we’re seeing is a secondary cultural effect.  Our culture has created an expectation that males with high testosterone are whores with little interest in long term relationships (especially at the college level).  And in consequence, low testosterone males have chosen the alternative mating strategy of appearing to be nurturing and caring.  Having recently left undergraduate study, I can attest that this does indeed seem to be the case.  Not only do males feel like this is the way they should behave, females assume this is how males will behave as well.

Being a big aggressive looking male, most people assumed I was a manwhore, where nothing could be further from the truth.  And to this day, most people laugh or look in disbelief when I tell them with 100% certainty that I want to be a child and adolescent psychiatrist.

Like I said, I see plenty of high testosterone aggressive males all over the animal kingdom who are great fathers.  In fact, low testosterone males in a lot of taxa actually choose the ‘hit it and quit it’ method when it comes to making babies.  An example are orangutans. The big 200lb honkers with the big old fleshy cheekpads are the ones with high testosterone.  While they aren’t particularly good fathers, they do at least stay around the females they mate with.  There are other males, though, who have low testosterone, so low in fact that they pretty much look like females.  They’re the sneaking type, even going so far as to rape the females.

It happens in fish too, who actually can be good fathers.  The big aggressive males make a nest, fight off all comers, and take care of babies.  ‘Sneaker’ males are about the same size as females and don’t fight or defend territory, instead they try to fertilize eggs laid in a big male’s nest before he has a chance to.  Again, they don’t parent.

Where am I going with this?  Nowhere special.  Just making the point that although my dispossesion is a bit like Marv from Sin City, I love kids.

Go. See. Puke.

I know I never shut up about it, but that’s because it’s an important point. Collectivism is based on the false, unproven idea of ‘group selection’. That animals work for the good of their social group or their species, instead of just themselves. There are, however, two situations where you can end up with what looks like a collective:

1) When all the animals in the group are closely related to each other. In this case, what’s good for the group is the same thing as what’s good for you. Because everyone in the group is related to you, by helping them, you’re helping what amounts to a part of yourself. Still not group selection.

2) When an individual needs a group for selfish reasons. Now this is a bit more confusing, but I’ll use one of my infamous hypothetical monkey examples (people who know me in person are running now). So imagine you’re a big strong male monkey. You’d be alpha male if you were in a troop without a problem. What’s going to limit how many babies you have? The number of females in the group. The more females in a group, the more you can impregnate at any one time, the more who will have babies during a given period with you as alpha, etc. In other words, if by your own action you can keep a larger group cohesive, you’ll make a lot more babies. Now, because you’re putting a lot of effort into the maintenance of the group, it can certainly look like you’re doing things for the good of the group. But of course nothing could be further from the truth. You’re doing it for yourself. So you can make babies.

Group selection has never been proven, never been shown to exist. I doubt it ever will. Group selection is prone to all sorts of problems including cheaters, defectors, exploiters, and lazy bastards. Actually the last two aren’t technical terms, they’re terms I use when I talk the politics of the Left and why it will never really work. They’ve been obsessed with group selection, ‘progressivism’, and all those other funny little terms that talk about ‘group consciousness’, or people ‘pulling together’. Unnatural, the lot of it. Many biologists over the years have taken this leftist interest in ‘the collective’ and attempted to search for it in biology, probably most famous among them Teilhard de Chardin. And of course almost every leftist political theorist from Karl Marx onward has attempted to look to nature to justify his belief in people working together ‘for the good of the species’.

This article represents egregious egregiousness on the part of both journalist and study author. An attempt to allow their political ideology to influence their science. In this way it is no different from the transgressions of the Intelligent Design, and indeed the methods both use aren’t too different from the other group.

This next part was probably just a misunderstanding on the part of the journalist:

Writing in the journal Nature today, the team reports that studies of lab-grown yeast populations suggest the benefits of cheating are eventually counterbalanced by the costs. This contradicts classic evolutionary theory, which states that in a competition for common resources the long-term winner will always be the individual acting selfishly rather than the one working as part of a group.

Actually many individuals act in a selfish manner while participating in the maintenance of a group.  If they didn’t, that would mean us sociobiologists have wasted the past 40 or so years.  Which would kinda piss me off.  No, evolutionary theory states that those organisms acting in a self interested manner will leave behind more offspring than those who act solely ‘for the good of the group’ (who will eventually eliminate themselves).  Selfish animals form groups, selfish animals help maintain groups, selfish animals help increase the prosperity of groups.  But they do it because it benefits them to do so.

Now on to study design:

In one corner were the ‘cooperators’, which produce energy efficiently by taking in sugar slowly and fully converting into energy all that they ingest. This method maximises resources available to the group by avoiding any waste.

Against them were the ‘cheaters’, which produce energy rapidly by quickly taking in all the sugar they can and only partially converting it into energy. While this ensures swift energy production for the individual, it is a wasteful method that reduces resources available for the group as a whole.

Before I get any farther I’m going to predict that ‘cooperators’ do better than ‘cheaters’.  And that they’re going to use this as evidence that ‘group selection’ or working for the good of the group or altruism or whatever they want to call it is valid.  They can go screw themselves.

To pre-empt them, I’m going to attempt to discuss the real differences between ‘cooperators’ and ‘cheaters’.  These are single-celled organisms, not exactly the most complex of social creatures.  And as the researchers mention the only thing that was different was how these guys metabolize resources.  The ‘cooperators’ do it nice and slow with a minimum of waste.  The ‘cheaters’ do it pretty dang fast.  Now the difference between these two has nothing to do with group behavior, but the efficiency and amount of waste.    ‘Cooperators’ are more efficient, turning more of the substrate into energy, and producing less waste.  They grow slower, but can grow for a longer period of time.  ‘Cheaters’ can grow faster initially because they metabolize things a lot faster.  But because they are a lot more wasteful, they end up freeing less total energy.  In addition, metabolic waste products are usually poisonous for most organisms.  So ‘cheaters’ are poisoning themselves.

Notice that there was nothing in the above that had anything to do with group living?  It’s simply two alternate feeding strategies, stable slow growth vs. exponential growth followed by a plateau.  What does that have to do with cooperation or cheating?  Nothing.  Bastards.

And he’s about to trot out his little political point:

“This evidence that a cooperative group can resist invasion by exploitative cheats is unexpected and gives us greater insight into how cooperation evolves. This is important because we live in a world in which cooperations exists at every level, from genes working together to build functioning individuals to individuals forming societies.”

The researchers suggest that the ideal organism type would be one that can switch between selfish and efficient metabolism. Dr MacLean adds:

“While microbes are obviously not capable of rational thought, they can change their behaviour rapidly in response to simple environmental cues. The possibility that one type could become both a cheater and a cooperator depending on what’s needed at the time is intriguing. We hope examining social conflict at the level of individual cells will shed more light on this.”

I’m dumbfounded Mr. Teilhard de Chardin, jr.  Dumbfounded.  You’ve tried to define ‘cheater’ as self-interested and ‘cooperator’ as group selectionist, and then tried to prove your point with an irrelevant experiment.  You, sir, I just don’t even know what to say.

So I got this Union of Concerned Scientists email today. The subject was, get this: “Defending Science From Political Interference.” Oh my god, I nearly died. If there is one thing the UCS is, it’s politically biased. They are a bunch of socialists and ‘environmentalists’ (note that that’s different from conservationist) with PhD’s. They then try to imply a correlation between the two.

Why am I on their mailing list? Because they’re a pretty big voice, and occasionally even a blind man can paint a mona lisa. Some of their more conservation-oriented stuff is pretty good. Like their defense of the Endangered Species List as ‘developers’ tried to destroy its intent for financial gain, Bush and the Republican Party of course proving to be all too willing to allow it.

But considering that UCS was, is, and will always be about political interference, by its very nature the UCS is a tainted organization:

UCS was founded in 1969 by faculty members and students at the Massachusetts Institute of Technology who were concerned about the misuse of science and technology in society. Their statement called for the redirection of scientific research to pressing environmental and social problems.

Hard to stay apolitical if we’re talking about ’social problems’. In fact once you use the phrase ’social problem’, no matter what position you take on how to fix it (or whether to ignore it) you’ve made a choice to become politically biased.

Conservation? Ok. Sustainability? I’ll give you that, even if the way they approach it is contradictory (increase population and wealth while decreasing consumption? Something doesn’t add up). But World Peace? Very scientific. Or just look at their mission statement:

Established in 1969, we seek to ensure that all people have clean air, energy and transportation, as well as food that is produced in a safe and sustainable manner. We strive for a future that is free from the threats of global warming and nuclear war, and a planet that supports a rich diversity of life. Sound science guides our efforts to secure changes in government policy, corporate practices and consumer choices that will protect and improve the health of our environment globally, nationally and in communities throughout the United States. In short, UCS seeks a great change in humanity’s stewardship of the earth.

Oh yes, the scientific nature of this organization is practically dripping from these very pages. Spare me. Please. One of my pet peeves is when people in a position of trust or authority misuse it. Whether it’s one of the many ‘Doctors [who are neither scientists nor social engineers] for x’ groups or ‘Mothers [who all need therapy] against y’, it’s wrong.

UCS is as guilty as anyone of this when they pontificate on and on about ‘nuclear war’. Last time I checked, taking a position for or against the existence of nuclear weapons isn’t scientific. Granted I’m not a nuclear physicist, but I do know a couple. I don’t remember them talking about the partial differential equation that could tell you whether it was a good or a bad idea.

Neither do I remember where in my scientific training government regulation of fuel economy was discussed. I certainly don’t remember the part where decreased gasoline prices, and decreased percentage of household income spent on gasoline would somehow increase our incentive to move off oil (yet that’s what UCS supports).

I could keep going on but I think I’ve made my point. Beware of false authority and anyone who claims to be unbiased. And if you excuse me I’m going to have to go puke. The lack of integrity among both scientists and doctors makes me sick.

Linky

Whales, ichthyosaurs, flightless birds, all beg the interesting question of why a taxon would seem to move ‘backward’ evolutionarily? Why would a mammal or reptile leave the land they’d evolved to conquer, only to become ocean-bound like their fishy ancestors once again? Why would a bird forego the use of his wings, choosing to run across the open African plain in a manner not too different from his bipedal dinosaur ancestors? Doesn’t make sense, doesn’t fit in with our idea of ‘progress’, of the evolutionary chain of being, of animals somehow evolving in a certain direction.

This is because evolution doesn’t work that way. Natural selection is by its very nature both directionless and purposeless. When we see trends in evolution, such as the increase in intelligence in primates from prosimians through humans, this is merely because intelligence, up through now, has been selected for. It needn’t be that way, however. Some species of monkey are as smart as any ape, some apes are as dumb as your average monkey. The hominid lineage didn’t have an increase in brain size over other apes for anywhere from 4-6 million years, depending on who you ask.

In other words, mammals were bound to land simply because up through that point, those who’d used that strategy had had left behind offspring. When the whales’ ancestors found an open niche, they lept in feet first and never stopped paddling (with their front limbs anyway).

More than 50 million years ago the ancestors of whales and dolphins were four-footed land animals, not unlike large dogs. They became the sleek swimmers we recognize today during the next 15 million years, losing their hind limbs in a dramatic example of evolutionary change.

“We can see from fossils that whales clearly lived on land - they actually share a common ancestor with hippos, camels and deer,” said team member Martin Cohn, Ph.D., a developmental biologist and associate professor with the UF departments of zoology and anatomy and cell biology and a member of the UF Genetics Institute. “Their transition to an aquatic lifestyle occurred long before they eliminated their hind limbs. During the transition, their limbs became smaller, but they kept the same number and arrangement of hind limb bones as their terrestrial ancestors.”

They weren’t using their back legs, so they lost them. There was no advantage to keeping them, and probably a disadvantage in terms of drag and developmental costs that meant those with smaller hindlimbs did better than those with fullsize ones. It might have been an increase in locomotor efficiency (needing to eat less while moving the same distance), predator avoidance (smaller limbs=faster), or prey acquisition. Whatever it was, small hindlimbs just worked better. Which is exactly what we saw in Ichtyosaurs as well. But as these researchers point out, for the first 15 million years or so it was just that; small but otherwise anatomically generic legs. The interesting part comes in the transition from a ‘full’ mammalian leg to actual reduction in the number of bones that make up the leg itself.

The new research shows that, near the end of 15 million years, with the hind limbs of ancient whales nonfunctional and all but gone, lack of Sonic hedgehog clearly comes into play. While the animals still may have developed embryonic hind limb buds, as happens in today’s spotted dolphins, they didn’t have the Sonic hedgehog required to grow a complete or even partial limb, although it is active elsewhere in the embryo.

The team also showed why Sonic hedgehog became inactive and all traces of hind limbs vanished at the end of this stage of whale evolution, said Cohn. A gene called Hand2, which normally functions as a switch to turn on Sonic hedgehog, was shown to be inactive in the hind limb buds of dolphins. Without it, limb development grinds to a halt.

“By integrating data from fossils with developmental data from embryonic dolphins, we were able to trace these genetic changes to the point in time when they happened,” Thewissen said.

In developmental biology we learn that patterning of the axes, organs, and skeletal structures is dependent on a variety of molecular signals that turn genes on and off, telling them where to do their work and how long to do it. Sometimes they tell something to start growing, sometimes they tell something to keep growing, and sometimes they tell something to stop growing. Sonic hedgehog (Shh) is one of those molecular signals which is expressed all over the place, but in the case of limb development is responsible for keeping a limb bud growing.

Up until the very end of those 15 million years, the whale had a pretty generic developmental expression of Shh, maintaining and allowing all four limb buds to fully mature. Even if the hindlimbs were pretty pathetic, they were the real deal. But at some point, whales’ ability to express Shh in the hindlimb buds was lost. So while the hindlimb buds could start, they couldn’t finish the job. This is why if you look at skeletons of some whales (notably the baleen whales), if you’re lucky you can still see vestigial remnants of hip bones and occasionally even the heads of the femurs. It’s a situation not all that different from that found in snakes, with some still having vestigial hip spurs while others show a complete loss of the pelvis.

I don’t have the patience or the free time to bother trying to convince closed minds about evolution, but obviously the existence of vestigial structures in whales, snakes, humans, and all sorts of other taxa is good evidence for evolution, not to mention providing interesting context as to the complexity and essential randomness of evolutionary process.

Linky

Honestly there ain’t no such thing as excessive biodiversity, like the country song goes “It’s like too much money, theres no such thing/Its like a girl too pretty, with too much class/Being too lucky, a car too fast…” The more biodiversity, the more branches on the cladogram, and the more fun you can have figuring out why things branched when and where they did. And what differences those branches represent. But when you have a surprising amount of species density, even for tropical climes, it’s something that must be explained.

The long separation of Madagascar from Africa and India explains only some aspects of the island’s endemism. Even more intriguing is that many of these plants and animals have very small distributions on the island, something that is called micro-endemism.

For the first time, this new research presents a comprehensive theory explaining how so many animals came to be limited to such small geographic areas across the island, which lies off the eastern coast of Africa. In some lowland areas of the island these animals tended to be isolated by the configuration of certain watersheds, and this isolation led to speciation, the evolution of new species.

Madagascar is I’m told a beautiful place, but there just isn’t much left of it after 20,000 or so years of us playing invasive species to our hearts’ content. It’s a place where you can see lemurs fill all sorts of niches that other prosimians could only dream of. Like being awake during the day. Or in the case of the recently extinct Giant Lemur, living off leaves and reaching a size that most apes rarely do. At close to 6′ and 180 lbs, this guy was bigger than a lot of us.

You can even see the Aye-aye, ‘closely’ related to lemurs (closer than anything else but still at least 10 million years of separation, IIRC):

(from the wiki)

If you look closely at his hand you’ll see a finger that looks like it has a thin pointy spike at the end, compared to the fleshy pads at the tips of his other fingers. That’s not a congenital malformation; he uses the big fleshy finger to tap on the outside surface of hollow logs, listening for insects inside. He’ll then stick the pointy one in there and dig them out. These guys are absolutely captivating to watch in a good zoo habitat.

Enough about my primate obsession. The point is that in the space of one (admittedly big) island, you can see more diversity in primates than you can in India and Southeast Asia. This holds true for lots of other taxa as well.

Recently scientists have made strides in explaining this biodiversity:

Using an analysis of watersheds in the context of paleoclimatic shifts, the authors provide a new mechanistic model to explain the process of explosive speciation on the island. Existing data show that substantial climatic shifts took place during the end of the Tertiary, as well as more recently during the Quaternary. The latter period is also known as “The Age of Man.”

When the climate was dry and cold, considerable portions of the Earth were covered by glaciers. On Madagascar, habitats at higher elevations would have remained more humid, as compared to the drying-out of more lowland areas. Therefore, groups of animals tended to “retreat” to higher elevations along riverine habitat that would have remained relatively humid during these periods of climatic change. The animals that did not “retreat” tended to be left behind in small, limited geographic areas where river sources commenced at relatively low elevations. Since they were isolated, those populations that were able to survive were more likely to develop into new species.

This is a modification to the old ‘Island Forest’ theory that’s been around much longer than I have. The big thing here was that they were able to back this up empirically by reconstructing the process of ‘island formation’ and the fact that they posited that in addition to the highland ‘island forests’ everyone’s known about, they mention that you can get even smaller ‘lowland forests’ as well. Which helps explain the micro-endemism. Basically, when everything is nice and tropical, you get one big forest. But as things got a little colder (and less humid because cold air can hold less water than warm air) the one big forest turns into many little forests with tracts of savannah between them. These ‘little forests’ provided the geographic isolation necessary for allopatric speciation. Then, when it got all pretty outside again, and the little forests grew and grew until they turned into a big forest once again, you had all these separate species where there’d once been one.

This is a particularly powerful theory when it comes to explaining the minimal variation in behavior and functional morphology yet large (almost extreme) variation in appearance between closely related species that now have nearly contiguous distributions. Sexual selection (which tends to be the reason animals get flashy) was responsible instead of natural selection. They kept living the same way, but the females in different areas decided they’d rather see their males have mustaches, or shiny red coats, or maybe white mohawks (all of which you can see in marmosets and tamarins).

Good stuff.

To feed your newfound interest in Madagascar, I’d head here and here. Sorry I can’t help with book recommendations. My interest in madagascar and micro-endemism is pretty new.

Razib had intended to get a rough consensus of the top ten evolutionary biologists of all time based on our comments. I’m honestly surprised he didn’t succeed. I thought 10 was more than enough to get a decent sampling of the geneticists, theoreticians (usually sociobiologists), and paleontologists who’ve been crucial to our field. It wasn’t apparently. Perhaps I thought so because as a (half-trained) bioanthropologist I’m in a theory-impoverished empirical-finding-rich field.

Here’s what he had to say:

On the one hand, the discipline was too broadly construed. Biases creep in. On the other hand, the category was too narrow in that many scientists contributed to evolutionary biology without being evolutionary biologists (most trivally G.H. Hardy). Since many readers of this weblog are highly credentialized in some particular field, I invite all to:

1) State a category where you know your shit (e.g., “evolutionary developmental biology of three-toed sloths”)

2) Your list of “top 10″

1) Tough one. M.Sc Human Evolution and Behavior, University College London. Basically bioanthropology. But my focus is on neotropical primates, which I’m pretty fanatical about. I don’t think there are 10 neotropical primate specialists that have contributed substantially to theory, period. Although they have done fine work in supporting and disproving extant theory, they just haven’t added much to our greater understanding of biology, which I think is crucial to any ‘top ten’. Warren G. Kinzey did some brilliant work on island forests, sexual selection, and allopatric speciation. You probably haven’t heard of him. I only know of him because I do New World Monkeys. If I did Old World Monkeys, Apes, and/or Dead People, I wouldn’t know him either. Plus he died younger than he should have. Bioanthropology on the whole–although there are more great minds to turn to–simply hasn’t contributed enough to theory. Mammalian Sociobiology it is, then.

2) My Top Ten
1. Edward O. Wilson - More a popularizer than anything else, his text is not only a great reference and resource, but got the movement off the ground. Since its birth, the movement has had several names and a few bastard offspring (evolutionary psych for one). But it has continued to heighten our understanding of the complexity of animal behavior. Personally, I also think sociobiological principles can ultimately inform the philosophy and structure of political systems.

2. W.D. Hamilton - The guy who came up with Kin Selection in 1964, thus providing us a mechanism that could help explain everything from the evolution of hive ’superorganisms’ to grandmothers. Kin selection, more than any other principle, is the impetus behind the development of ever more complex social and mating systems.

3. Robert Trivers - Some quibble over the importance of reciprocal altruism. Having watched it firsthand in (unfortunately captive) monkeys, I don’t doubt its existence or its importance to social structure. Razib objected to his inclusion on the grounds that kin selection is ‘more important’ (something like that IIRC). I’ll grant him that. And it’s certainly far and away more important when it comes to understanding the genetic side of evolution. But as a behavioral ecologist, I can tell you for a fact that the range of behaviors and interactions you can see among social mammals would not exist were it not for reciprocal altruism. Beyond that there was his classic on Parental Investment and Sexual Selection. I’m not going to start talking about that because I won’t stop (I’m involved in paternal care stuff). Because, like kin selection, both of these principles are unequivocally crucial to the development and understanding social complexity, I think Trivers not only deserves inclusion but deserves to be very high up on the list.

4. John Maynard Smith - Evolution and the Theory of Games (1982). ‘Nuff Said. For those who aren’t familiar with the work (and I admit I myself have only skimmed it), in it Maynard Smith brings together a culmination of work over the preceding decade in which a way to mathematically model the evolution of behavior is developed. The beautiful thing about the work of Maynard Smith et al. is that they were able to describe behavior in mathematical terms without overly reducing it (as genetics can be prone to do) until the complexity of it is lost.

5. Amotz Zahavi - The Handicap Principle. A signal should be costly to produce, broadcast, and/or maintain. The traditional example are the Birds of Paradise. A male’s long tail makes it difficult for him to start flying. In other words he has a tougher time getting away from a predator. So a male that has a nice long tail and doesn’t get eaten is essentially the same thing as a guy claiming he can tie one hand behind his back and still beat you up…and then goes on to do it. Actually Maynard Smith was involved in this stuff too, come to think of it.

6. Emlen & Oring - Ecology, Sexual Selection, and the Evolution of Mating Systems. Couldn’t and didn’t want to separate these two. I was lucky enough to have Emlen as a professor for a couple of classes in undergrad. But because he did a lot of naked mole rat work, and I found those animals boring, I didn’t take advantage of this fact. I was 17, so give me a break damn you. Little did I know that just a couple years later I’d be knee deep in exactly this all encompassing problem, just with a lot cuter taxon than mole rats. I mean. Come on. Mole rats? Nevertheless, it remains an important work because they didn’t treat mating system as just another heritable phenotypic characteristic. Instead they took an ecological perspective, furthering our understanding of how mating systems are determined by the circumstances surrounding the individuals rather than anything intrinsic. I just presented an extremely oversimplified surface treatment. You do not want me to go on. Trust me.

7. Richard Wrangham. The Evolution of Female-Bonded Primate Groups. Another extremely biased choice here. Wrangham’s a bioanthropologist. He hasn’t always done the most ’scientific’ work (demonic males for instance), but this 1980 paper is famous for bringing the idea of ecological determination of mating system to the fore. It’s not perfect by any means. But it certainly brought primatology out of the dark ages and in line with the rest of evolutionary biology

8. Ernst Mayr. All the traditional stuff. But mainly for keeping the focus at the level of the individual. There are certain things that will probably be never understood even if we completely ‘decode’ the genome. As ‘unscientific’ as it is for me to say so, I firmly believe that there are certain ‘emergent’ properties especially when it comes to intelligent and social animals (birds, cephalopods, mammals, and sometimes I wonder about poison arrow frogs). Too much of what they do and how they act is just too developmentally labile, too context and environment dependent.

9. Theodosius Dobzhanski. I’ve just always respected the fact that fieldwork was so important to this geneticist. People working from various perspectives can lose sight of everything else. When it comes to evolutionary biology, I’m in the ‘forest research’ camp, focusing on the whole individual and its behavior. Geneticists are in the ‘tree research’ camp, choosing to focus on isolated parts of a greater whole. Both camps are necessary to understanding evolution, but sometimes they can fail to communicate and integrate properly. Dhobzanski has always come across as a man who kept his eye on both perspectives. It’s something I hope I’ll do once my research career starts.

10. Garret Hardin. Another highly biased choice. I most admire Mr. Hardin for his many statements that economics is just a subset of ecology. In a simple statement, he showed us how all the work we do in behavioral ecology, all the discussion of modelling, fitness, cheaters, bluebeards, etc can help us understand how to build a more perfect political system. It was basic ecological thinking that he applied to the Tragedy of the Commons paper

It’s important to note that while there’s some overlap with Razib’s general list, I’ve included people on here that I wouldn’t on a general top ten (Wrangham, Zahavi, Emlen/Oring). This is a list of the top ten guys as far as this particular half-trained primate behavioral ecologist is concerned. 6, 7, and 10 could be considered biased choices, even within the subfield of behavioral ecology. But I think they’re fairly valid, nonetheless.

Linky(Coincidence here, I went to UCL for my Master’s. Great environment, great teachers. A year I genuinely treasure.)

Primatologists are supposed to be obsessed with dominance heirarchies, even half-trained ones like me. This particular issue isn’t just about dominance but also about eusociality, which is when most adults in a given group don’t try to reproduce. At its most elaborate level we see this in ants, bees, and wasps (all closely related), but we also see some degree of this among many social mammals, including naked mole rats (the hallmark example), wolves, and marmosets and tamarins (the guys I study). Since the end goal of all organisms is to make babies, one would think that this is a pretty odd arrangement. In certain contexts it can make a lot of sense, though, depending on associated tradeoffs.

In 1964, W.D. Hamilton solved a crucial part of this enigma when he proposed the idea of relative fitness. Traditionally, fitness has been defined as how many babies you make that live to reproductive age. However, Hamilton realized that the only difference between one’s offspring and one’s relatives is the strength of genetic similarity. You share 50% of your genes with each of your parents, your siblings, or your children. 25% with a first cousin. Rather than bore you with the details, lets just leave it with the conceptual framework that the more closely related you are to an individual, the more you gain by helping them out (in other words, playing ‘wingman’ for your brother is as worthy of effort as raising your own children). Although the issue could get a lot thornier (for instance although your parents share the same number of genes with you as your children do, your parents are a lot less likely to have babies, so in theory you should be less likely to help them), we’ll leave it at that for this discussion.

Scientists at UCL (University College London) have discovered that even wasps are driven by their status. The study, published today in Nature, shows that lower-ranked female wasps work harder to help their queen than those higher up the chain because they have less to lose, and consequently are prepared to take more risks and wear themselves out.

Because they’re eusocial, all of the female wasps tend to be sisters or half-sisters (I forget the mechanics of it, which are unimportant for the discussion anyway). So they get quite a bit of benefit from helping the one who actually does the breeding in raising the babies. But here we see the tradeoffs that complicate the issue. The higher up in the heirarchy you are, the more likely it is that you’ll get a turn as the breeding female. Those with a looong succession ahead of them have little or no chance at ever breeding. Too many queens would have to die. Think of the 3rd or 4th son of a king taking a military career where he has a much higher likelihood of dying than his layabout older brothers (who even if they don’t get kingship at least will get a decent parcel of property).

To quote the study’s author, Dr. Jeremy Field:

The wasps in this queue face a fundamental trade-off: by working harder, they help the group as a whole and as a result indirectly benefit themselves, but they simultaneously decrease their own future survival and fecundity because helping is costly. It involves energy-expensive flight to forage for food, and leaving the nest is dangerous. We have found that the brighter the individual wasp’s future, the less likely it is to take risks by leaving the safety of its nest to forage for food.”

In other words we’re seeing what amounts to a cost/benefit analysis in each of these females. The older you are, the more cost there is to helping and the less relative benefit. For an illustration, half of you imagine you’re female. The other half stay as you were. Now imagine you have two sisters, one who’s fertile, and one who’s barren. The fertile one is still searching for a sperm donor, but she’s hot and wears skimpy clothing, so there’s little doubt she’ll find one. Your husband tragically dies during childbirth from blunt force trauma as you knock his head against the wall screaming “WHY DID YOU DO THIS TO ME YOU BASTARD!” And on top of that you just had triplets. Which sister is more likely to help you out? The barren one. If she stays at home Saturday nights, it’s not like she loses any reproductive opportunity. On the other hand, the one with the fully functioning ovaries would lose major mating opportunities if she were to give up her nights and weekends during these, the most fecund and attractive years of her life. The lower-ranking wasp females might as well not have ovipositors, their likelihood of breeding is so low.

Now, because this is so close to a topic I spend inordinate amounts of time on, I’m going to contrast this situation to that which you see in Marmosets and Tamarins. Most monkeys mothers raise the kids on their own while Dad spends all his time eating, scratching himself in less than genteel places, showing off his canines, grunting, beating up every other male that looks at him funny, and trying to copulate with anything that moves and is suitably equipped. When it comes to certain South American monkeys, instead what we see are mothers that are basically walking incubators and milk dispensers. Very similar to queen wasps in that respect except that I don’t think you can milk a wasp (and at around half a pound, it’s pretty hard to milk a marmoset too. Trust me…I’ve tried). This is because they routinely produce twins, which is hard to manage considering monkey infants are already pretty expensive to take care of compared to other mammal babies. Not only does dad help out, but the infant’s older adult siblings stick around and help as well.

With these guys, there are a couple of reasons why they’d do this instead of going off to pitch woo with similarly young and free adult offspring from neighboring troops. First, marmosets need territory (which makes the wooing situation a lot like the Montagues and Capulets). It’s hard to maintain territory when it’s just a male and a female. Not to mention that your population is high enough that you’re completely surrounded by other marmoset groups. So these guys bide their time waiting for an opening. But there’s another aspect as well. Parenting is not necessarily natural for males. But they’re the ones who do most of the behavorial parenting (carrying, provisioning, playing, protecting, watching) as compared to the physiological stuff (pregnancy and lactating). So older sons (and daughters to an extent) can get a signifiant benefit by ‘training’ with a younger sibling. They do better when they finally leave and have higher success rates with their babies. In other words, while a lower ranking wasp is more likely to help out, in marmosets you see the reverse. Because the older you are, the more likely you are to be able to get in on new territory (dominance and preference), have a mating opportunity, and need the ability to parent. The younger you are, the less likely you’ll be making babies any time soon, so the less reason you’d have to learn how to do it (and in the process help out mom and dad).

While not earth-shattering, this is just a cool find in that it continues to expand our knowledge, understanding, and appreciation of how the many factors and variables involved in reproduction and survival play into the choices an animal makes, and in the determination of a given social system. It is something all too easy to miss, whether one is a geneticist blathering on and on about genes being the only unit of selection (some geneticists are pretty cool, though. I’ve been having a lot of fun going back and forth with Gene Expression recently…and his linking me has improved my stats) or one of those silly humanists who can only think of nature as ‘red in tooth and claw’. The ways in which self-interested behavior can result in such complex, cooperative societies is a thing of beauty unparalleled, like a snowflake growing in size and complexity at the behest of ever-so-simple a rule.

Razib over at Gene Expression asks a very interesting question:

Between 3 million & 200,000 years ago the average cranial capacity of this planet’s dominant hominids increased along a upward trendline, in starts and stops. Bipedal apes went from having nearly chimp sized crania to one similar to modern human beings (Neandertals had larger brains that H. sapiens sapiens). Symbolic culture as we know it though seems to really explode (a.k.a. “The Great Leap Forward”) between 50,000 and 30,000 years ago. Nevertheless, what do you think happened??? Was it climate change (I’m skeptical)? Was it some sort of cultural ratchet? Was it God?

First off, here’s a picture from talkorigins.org (beautiful place by the way):

Pretty self-explanatory, but also confusing. Early modern humans have smaller brains than both archaic Homo sapiens (now called Homo heidelbergensis) as well as neandertals. Yet we were the ones who went through the cultural expansion. Which is the crazy strange hard to understand part.

The first thing to note is that although our brain size is similar or even slightly to our congeners’ advantage, brain shape is drastically different. From ergaster and erectus up through heidelbergensis and neandertalensis, a characteristic football shaped skull is seen:

Homo erectus

Homo ergaster

Homo heidelbergensis

Compare those guys to us:

Pretty obvious differences there. We’ve got a much more upright forehead (frontal bone) and the curve is a lot smoother and rounder around the back. What do those differences mean exactly? We barely know enough about the brain in living organisms as it is. Doing it in dead ones is even harder. The only way to study it is by the impresssions the brain leaves on the skull. But we can get an idea of general brain shape and size from the skulls.

Similar size, different shapes. We have a relatively bigger frontal region, they had a bigger temporal (sides around the ears) region. The frontal lobes, as most people know, are the seat of the conscious will. It’s the part of you that does the thinking. The temporal lobes on the other hand are responsible for aspects of hearing, language, and spatial manipulation and object recognition (one should probably focus on the latter when thinking of temporal lobe function). Whether it actually makes a difference between the two in this case, no one really knows.

Besides, the oldest anatomically modern human remains have been dated to 150,000-200,000 years ago. A long time before the cultural explosion Razib was talking about. What about genetics? Perhaps not astonishingly, a few ‘key’ genetic alleles necessary for normal development of the brain and/or language all seem to have arisen at around that point in time. So not much help there either.

Climate change? It’s tempting, but I’m not entirely happy with it. The weirdest and craziest thing about the cultural explosion was that it seemingly happened simultaneously all over the range of human colonization. Beautiful artifacts come from the northernmost reaches of early human settlement. They also come from the tropical parts of Africa. Meh.

Nope, personally I believe we just got really good at being hominids. See the hominid lifestyle is very different from the typical anthropoid lifestyle. As I’ve said before, apes and monkeys are more similar than they are different in behavior. On the other hand, although we retain a lot of anthropoid characteristics, we live a lot more like wolves. It’s a point I’ve made before but really must be made over and over again. Ever since Homo erectus we’ve probably been meat eaters (and not ‘meat eaters’ like chimps with a massive 1.4% of their diet coming from meat), there’s good evidence that our home ranges expanded dramatically around then, and some more circumstantial evidence that we cooperated in the hunt.

This is completely different from how a monkey should behave. It took us a while to adjust. And by the time anatomically modern humans came around, we were getting pretty good. And there’s a thing about energy. Animals try to conserve it. But when they don’t have to, they waste it. They play, they spend less time resting, or more time moving, or more time fornicating. Depends from animal to animal. I’ve been lucky enough to observe full grown male elk ‘playing tag’ in the bounty of summer (no they weren’t fighting). Pretty rare sight, but one that can happen when there’s enough around.

Personally, I think the cultural explosion occurred because we’d gotten good enough at being hominids that we had excess energy to burn. Instead of spending it in play, we spent it in thought. After all, our brains do represent 25% of our metabolic load as it is.

Probably the most fascinating thing that monkeys have taught me is the evolutionary and historical origin of ‘magic’. They’re pretty smart cookies, and they have a sense of what’s called object permanence. This means that if you drop something like a fruit or berry down a raingutter, they’ll expect it to come out down below. They know there was food up top, they know it fell, so it should come out right below. Nevertheless, you can trick them, because their sense isn’t necessarily perfect, just like a baby playing peekaboo. The look on a monkey’s face when your baseball cap suddenly ‘appears out of nowhere’ is an amazing thing. A veritable caricature of a surprised human. And in that look you know the monkey’s thinking “That wasn’t what I expected. Must be magic.” Of course, you know that the monkey simply didn’t understand what was going on…

In the most fluffy class of my entire academic career (intro to cultural anth), I learned about the relationship between religion, magic, and science. The interesting thing about ‘magic’ is that no matter what the society or who the person is, ‘magic’ starts where ’science’ ends. We all have our ‘magic’ point. More often than not, it’s limited by our education. The point is that just because we don’t understand it doesn’t mean it’s not understandable. Religion, which can influence the thoughts we’re allowed to have, may prevent us from even trying to comprehend that which at first we don’t. So when I hear that apparently some biochemist can’t figure out how something could have evolved through natural selection and we therefore must’ve been designed, I have to wonder if he isn’t a bit like one of those monkeys full of round-eyed open-mouthed wonder, the theoretical problem much like my baseball cap.

Linky

There is a push to document the biodiversity of the world within 25 years. However, the magnitude of this challenge is not well known, especially when it comes to vast and often inaccessible marine environments. To date, surveys of species diversity in the world’s oceans have focused on adult organisms, but new research from Boston University has found that studying marine life in its larval phase with DNA barcoding is a valuable way to estimate biodiversity.

And very smart too. Especially with invertebrates, a lot, if not most, oceanic species go through a planktonic (floating near the top) larval stage. Later on they might become nektonic (free swimming in the ‘middle zones’) or benthic (bottom dwelling or deep sea living). By going after larval stages, researchers can concentrate their efforts in the most accessible part of the ocean while having the best chance of catching examples of as many species as possible. Increased efficiency and accuracy. They deserve major props for that.

Using this novel approach, Paul Barber, an assistant professor of biology at BU, discovered that biodiversity is greatly underestimated in the region of the Pacific known as the “Coral Triangle” and in the Red Sea. The study, which focused on coral reef-dwelling mantis shrimp (stomatopods), is the first to compare larval stage organisms to adults.

By using DNA barcoding (basically sophisticated species-level ‘fingerprinting’) they were able to eliminate the problems of attempting to identify immature (and likely identical-looking larvae). In other words, they can approach this with much more confidence than a purely phenotypic researcher could. In the past, when a phenotypic researcher would come in with a 99% similar animal and say “look his spots are a different pattern, new species!” the immediate retort would be “Naw, just a regional variation and/or subspecies. Maybe a naturally-occurring hybrid.” Some of the time the researcher was correct, some of the time his naysayers were. Either way, figuring it out wasn’t fun. This method eliminates a lot of those issues. Either DNA differences represent different species or they don’t.

As Drs. Barker and Boyce relate:

“Our results show that biodiversity in mantis shrimp in these regions is estimated to be at least 50 to 150 percent higher than presently believed,” said Barber. “Given that few groups of marine organisms are as well studied as mantis shrimp, the biodiversity in other groups is likely even more poorly known. What’s unique about this study is that we didn’t just discover new species, we used DNA barcoding to quantify how much biodiversity is out there that we don’t know about.”

Once again, they show impeccable study design in that they picked a heavily researched taxon to study, which gives them a great lowball estimate on how off our ideas of extant biodiversity are. Science loves lowball estimates. They love it when you say “my model provides a worst case 75% predictive ability” (I wish I could say that about the couple I’ve done). They love this because, if that’s the worst it can be, there’s little chance of it being wrong. Think about if medical research operated the same way that insurance ads did: “This drug can save as many as 98% of the people put on it, while side effects could be as low as 7%.” Sounds pretty good don’t it. “…of course, it could save as few as 3% of the people who take, while harming 57%.” Don’t look so hot now.

In addition to an alternative way to explore marine biodiversity, Barber hopes the findings will promote conservation. Despite being considered a “biodiversity hotspot,” the Coral Triangle is one of the most threatened marine environments in the world. Often areas with particularly high rates of biodiversity are targeted for conservation, so the new method could help by highlighting potential regions for protection.

YAY! Conservation rocks. Okay I love you buh-bye (10 points to the person who gets the mid-90’s cartoon series reference).

Linky

Yes, the ’surprise’ was typed sarcastically. The large explosions in diversity that often accompany the origin of major clades are generally either a result of a gene duplication event or the discovery of an entirely new mode of life (HOX genes and the Cambrian Explosion, or the Amphibian colonization of land), so the fact that this was a gene duplication event wasn’t unexpected. In fact, for certain reasons having to do with plant anatomy, it’s completely expected. Still, very cool.

HOX patterning genes show a particularly beautiful pattern when duplication events are mapped against vertebrate evolutionary trees:

This image from PZ’s old site is the best I can do at the moment. But a much better one can be found in Endless Forms Most Beautiful: The New Science of Evo Devo (about evo-devo, an exciting new approach that finally incorporates an evolutionary perspective into the study of embryology and developmental biology).

However while genes and gene clusters have been duplicated many times in vertebrate evolution, whole genome events are pretty rare. The number of copies of the genome present are indicated by the prefix in front of the number n. For instance, eggs and sperm each have a genome count of 1n, whereas the human body has a 2n number. This is why you need both the egg and the sperm to make a baby that can live to adulthood. The 2n rule is pretty constant for eukaryotes (including fungi, animals, and plants), whereas most bacteria only have a 1n count.

Many angiosperms (flowering plants) display a quality referred to as polyploidy which is the presence of more than 2 copies of the genome. Now for the article.

Researchers from the Floral Genome Project at Penn State University, with an international team of collaborators, have proposed an answer to Charles Darwin’s “abominable mystery:” the inexplicably rapid evolution of flowering plants immediately after their first appearance some 140 million years ago. By developing new statistical methods to analyze incomplete DNA sequences from thirteen strategically selected plant species, the researchers uncovered a previously hidden “paleopolyploidy” event, an ancient whole-genome duplication that preceded the appearance of the ancestral flowering plant.

This makes sense, you see a whole-genome duplication event provides that much more genetic material that could develop potentially fitness-conferring mutations. It also means that since the plant has two functional sets of DNA, the functionality of the gene on one copy would change while the other would remain in the ancestral condition. Meaning the plant would have the best of both worlds.

Dr. Claude dePamphilis provides a pithy nugget:

One unexpected observation from the study is the relatively slow accumulation of mutations in primitive flowering plants like the yellow water lily (Nuphar). “We can view these basal angiosperms like the Hubble Space Telescope, which helps us get a deeper look into the early history of the universe–these plants allow us to take a deeper look into genomic history.”

Although his statement isn’t directly relevant to this particular finding, it’s a well-illustrated point that has served evolutionary biologists well since time immemorial. The ‘living fossil’ principle. Basically it means we have less logical gaps to fill. It’s hard to imagine what the first primate was like, but the tree shrew (whose status as a primate is still debated because it’s so ‘primitive’) provides us a living breathing example of an animal that while not exactly identical, was similar enough to serve as a model, thus giving us at least somewhat more context than a bare fossil or a bunch of A’s T’s C’s and G’s.

The new results support the idea that “whole-genome duplications are rare in vertebrates, but common in plants,” according to dePamphilis. Independent whole-genome duplications occurred relatively recently in soy, potato, and tobacco, and longer ago in maize. But the thinking was that human breeders might be artificially selecting for duplication events in crop species by “selecting desirable traits like rapid growth, high yield, and even large stature,” says dePamphilis.

He doesn’t make the inference–in this news release anyway–but dePamphilis provides one of the primary ways in which genome duplication in and of itself can be an advantageous trait: you do everything better than normal individuals. You get bigger, you do it faster, and you make more seeds. And, as I intimated earlier, you have more raw material for the building blocks of evolution to do their thing with.

You know how strawberries are pretty regular in shape, almost conical? But every now and then you get a big old honker. And these huge ones…aren’t very regular. They’re much wider than they are deep, and taller than regular strawberries to boot. Grab the stem, turn it upside down, now count the peaks. There’s not just one, there’ll be at least 2, sometimes as many as 5. Each of these ‘peaks’ represents a 2n count. Those big strawberries had multiple genome copies. Which meant they were making much more mRNA. Which in turn meant more protein. Hence bigger. Although no vertebrate I know of can reach ‘birth’ or its equivalent in the polyploid state, those polyploid feti that are recovered are often much larger than is typical for the given species as well.

Whole-genome duplications have attracted attention as a possible mechanism to drive sudden bursts of evolution, like the one that so vexed Darwin over a century ago. While the vast majority of duplicate genes quickly accumulate mutations and are deleted from the genome, a few mutations will be selected for evolutionarily advantageous function. Rather than gradually collecting genetic novelty by single-gene duplications, simultaneously having a full genome’s worth of raw material to elaborate new genetic function could drive sudden evolution.

And then a lot of stuff about how to figure out something that you can’t directly see by reconstructing ancestral states. I won’t talk about it like the article did because from personal experience there is no way to explain those methods without putting everyone, including yourself, to sleep.

A paleopolyploidy event previously demonstrated by other investigators is associated with a burst of evolution in the economically important grass family. The new results from the Penn State paper confirm a previously-reported paleopolyploidy event in eudicots (a group that includes beans, tomatoes, sunflowers, roses, and apples) associated with their rapid divergence, and demonstrates the first evidence of a paleopolyploidy event associated with the ancient explosion of all angiosperms.

Mere guilt by association? “We can take it farther than just correlation,” asserts dePamphilis. The MADS-box genes, a family of transcription factors that are required for flower development, are known to have undergone an expansion through duplication that was critical to the evolution of angiosperm flowers. A whole-genome duplication explains the sudden emergence of novel traits better than a series of single-gene duplications, explains dePamphilis. “Some of the MADS-box genes and many other genes important in plant development were produced by paleopolyploidy.”

Good times.

Linky

If you couldn’t tell from the italics, this is a pretty big deal. First new African genus named in 83 years. In and of itself, the new genus name is pretty meaningless. Unlike species and subspecies, which can be objectively determined more or less, when it comes to the higher taxonomic levels, although you still use objective traits the decision of how much those traits matter is left up to opinion. Geneticists cause my fists to clench and holes to appear in my walls when they say that humans and chimps belong in the same genus. Nothing against chimps mind you, just that they’re too different from us. I’m a ’splitter’, I think genera should be composed of related species in a similar adaptive zone. Chimps are typical frugivorous (fruit eating) primate. Just smarter. We, on the other hand, are a lot more like wolves in the way we live than we are like monkeys. Chimps and humans live completely differently, ergo, different genus.

Coming partway back to the subject of the article, an illustrative point can be made about the ambiguity of genera. Baboons and Geladas are a group of 5 to 8 species (still debated) that are monophyletic (all derived from the same common ancestor, to the exclusion of non-baboon/geladas), and are broadly similar in anatomy (long dog snouts and terrestrial locomotor adaptations), behavior (they’re roid-raging monkeys, more or less), feeding and mating habits. In other words, they’re very clearly part of the same adaptive zone. Despite this, Geladas are usually not considered ‘true’ baboons. They belong to the genus Theropithecus whereas ‘proper’ baboons are found within the genus Papio.

Olive Baboon (Papio anubis)

Gelada (Theropithecus gelada)

Here’s a taxonomic diagram, the dotted line representing what you could easily argue Papio should be.

Yeah, Geladas are excluded from ‘baboons’, but they’re still much closer to ‘baboons’ than they are to any other kind of monkey. A a similar situation exists in New World Monkeys, and I’ll omit some detail for brevity, but basically there’s two kinds of Saguinus (Tamarin Monkey). There’s ‘big’ Saguinus (which still weighs less than a pound) and ’small’ Saguinus. On a taxonomy like the one above, ’small’ Saguinus occupies the same position as the Gelada. Unlike the situation with the Gelada, there are much bigger differences in feeding, behavior, and anatomy between ’small’ and ‘big’ Saguinus than there are between Gelada and ‘Baboon’s. I’ve read at least the abstract of every paper on New World Monkeys written in the past 40 years (that’s not a brag, but a testament to how OCD I can get when I actually care about something…like my thesis), and I’ve never seen it argued that ’small’ Tamarins be placed in a separate genus.

Compare this to the genus Macaca which includes species from all over Asia and Africa (and Spain if you count the Barbary Macaque which is so different from other monkeys it was once thought to be an ape). Clicking through the links on that wiki page will give you a good look at not only the geographical distribution and diversity in size and appearance, but also how differently they all live from each other. In Southeast Asia alone, one can encounter members of Macaca that look an awful lot like baboons (stumptail macaques) to little 8lb things that you’d swear were wearing a wig (bonnet macaques).

Stumptail Macaque

Bonnet Macaque

Point made? Who’s to say if this new genus, Rungwecebus, is actually deserving of such a high-level name. Maybe it’s really only a species of an extant genus. But the fact that these scientists found it prudent to give it one in the first place shows us that regardless of its to-be-determined taxonomic affinities, it’s a strange bird for a monkey.

We’ll turn to the article for a description:

Kipunji is grayish-brown and has an erect “crown” of hair on its head, long cheek whiskers and a cream-colored belly and tail. The monkey stands about 3 feet tall and makes an unusual, low-pitched call that scientists describe as a “honk-bark.” Kipunji has a thick coat of long fur that comes in handy for living at 8,000 feet above sea level, where temperatures frequently drop below freezing.

An omnivore, Kipunji dines on leaves, shoots, flowers, bark, fruit, lichen, moss and invertebrates. The monkeys appear to be social creatures, living in groups of about 30-36 males and females. Their main predators are crowned eagles and possibly leopards, but they humans also hunt the monkeys for meat.

I keep tabs on all the major Primatological journals anyway so I’ll update with more info when I run across the ‘official’ announcement. Oh and, insert typical Nick rant about the need for conservation (only 500 of these guys left in threatened habitat) and that if we lose our ties with nature, we lose our bridge to what created us; we lose our heritage and our history. Sprinkle liberally with my ‘People are just primates. If we want to know ourselves we have to know our relatives’ spiel.

I’m going to limit my typical tirade against anthropocentrism to three sentences for the sake of brevity and boredom prevention: Human brains did not evolve in a vacuum; as neuroanatomists have noted for close to 200 years, there are scarcely any differences in kind between the monkey brain and the human brain, merely differences in degree. People act surprised at the fact that other animals have emotions and the ability to infer. Which is why psych is such a radioactive pile of cow dung; it has a flawed view of just how deep the roots of our cognitive and emotional attributes go and why they came to be in the first place.

Ok, done. And yeah, I guess I cheated by using semicolons, making it five sentences not 3. But my blog. My bandwidth. Deal.

This is not a problem I have. Luckily for me, I wasn’t raised in an epistemological framework of unjustified humanism (whether religious or atheistic in nature), but rather was taught to appreciate the commonalities of all living things. Especially monkeys. Not only that but I’ve had a lot of face time with them. I’ve been tricked, outsmarted, beaten, berated, bitten, and generally abused by several species of monkeys originating from three different continents. I have no doubts as to their intelligence or as to the fact that they think just like we do, just in a less sophisticated manner.

A new study from Harvard researcher Dr. Marc Hauser highlights the ability of monkeys to make inferences about situations they’ve never encountered before.

Monkeys keep turning out to be smarter than people think they are. Researchers have shown that they can count to four and are aware of differences between languages like Dutch and Japanese, even though they don’t known what is being said. Now, Harvard psychologists find that monkeys can draw correct conclusions about novel situations. For example, shown a white towel that turns blue, a blue knife, and a glass of blue paint, they can figure out that the paint not the knife is responsible for the change in color.

“Our studies reveal a striking continuity between humans and monkeys in their capacity to draw causal inferences without the help of familiarity with the events or situation,” says Marc Hauser, a Harvard professor of psychology. “This ability highlights the richness of the monkey mind in terms of its understanding of the material world.”

Thank you, Dr. Hauser. And I mean that wholeheartedly. Both scientists and the public need to understand that there isn’t very much that makes humans unique, not because I’m one of those ‘human rights for great apes’ freaks, but simply because we can’t develop a conception of who we really are unless we understand just how we’re related to others.

Anyway, moving on to the experiment itself:

Next, they saw the glass of water and two halves of an apple. Following this, a knife was lowered, and two apple halves seemingly became a whole apple.

To a human, even an infant who had never seen such things before, the last two apparent happenings would never really happen. Can monkeys infer the same outcomes? Evidently, the answer is “yes.” They looked longer when a glass of water appeared to cut the apple than when a knife seemed to do the same. The longer look signaled disbelief.

Surprisingly, they didn’t fail. Without ever having seen a glass of water and two apple halves, or a blue knife and blue and white towels, the monkeys inferred that water cannot cut fruit and knives can’t change the color of towels.

And that’s the key here, just by looking at the objects, the monkeys were able to figure out what their actions were. Inference at its finest.

The experiments, then, answer a key question about human versus monkey intelligence. Is the capability for figuring out what is possible and not possible when you see something for the first time uniquely human? For Hauser, Spaulding, and a lot of scientists who read their report in the May 2 issue of the Proceedings of the National Academy of Sciences, the answer is a resounding “No.”

“Humans are not alone in their capacity to draw causal inferences from limited experiences,” the Harvard researchers write. “This capacity is part of the evolved psychology of rhesus monkeys and most likely other animals as well.”

Which really says it all, I’d head to the article itself since it ends with a great David Hume-bashing ending. I’m not much of a fan of philosophers either (although I’m a fan of philosophizing), like the psych establishment, they seem to have an allergy to the real world.

The saddest thing about this whole business is that people like Dr. Hauser have to go out and prove something that should simply be assumed based on parsimony.

I’ll end this by saying that, as I’ve mentioned before in my psych rantings, unless we understand the selective forces that led to the differentiation of the primate brain from those of other mammals, and the forces that led to the gigantic increase in encephalization between hominins and other primates, we won’t really understand what the brain was designed to do. And if we don’t understand that how the hell can we know when something is actually wrong with it?

This group might as well be called Cosmetologists Against Taco Bell. I’ll explain why below.

HT: Orac and Aetiology

Introduction
My first thought when I heard about this group was that it was a good thing someone was going to try to clean up the shoddy logic used in translating basic research findings into concepts of disease and treatment; I’ve heard some absolute horsecrap come out of doctors’ mouths when they’re interpreting medical studies. And then I found out that this is just another one of those organizations posing as ‘a collection of intellectual skeptics’ of Darwinism.

I didn’t even bother to vet their mission statement because there remains no scientific alternative to Darwinism. ID is based on an untestable assumption, therefore it isn’t scientific. A scientific theory must not only be based upon observation, it must be falsifiable. ID has neither, but rather, apparently, a biochemist throwing his hands up in the air and saying ‘I don’t see how this could have evolved’ followed by ‘it must have been designed’. As I discussed above and in my own personal example, ‘I don’t see’ isn’t a valid basis from which to proceed with inductive reasoning (as ID attempts to do), nor does it count as a repeatable observation. And any inference as to a creator is certainly way off limits if as reasonable inference as the one I made turned out to be wrong. [yes that is a canned rant, and if it feels like you've read it before, that's because you probably have, in thousands of iterations across thousands of blogs. ID has no scientific basis, for really ummm basic reasons]

As one of the only people I’ve ever met who’s had at least some graduate training in both evolutionary biology (Master’s) and medicine (finished first year yesterday), I felt obliged to comment.

I’ve got a problem with most of the ‘doctors for [insert cause here]‘ groups. I feel they try to imply the existence of an authority they don’t really have. This is especially true for Doctors For Sensible Gun Laws and Physicians For Social Responsibility (god I feel dirty even linking them). Although I’ve only finished my 1st year, I don’t expect to be taking any classes on criminology, constitutional scholarship, comparative political systems, or political economy. In other words, the fact that they are doctors has no bearing on the opinions they hold; medical training provides no insight into these causes. This is just as true of PSSI as either of the above groups, although the intimations that PSSI makes are far more insidious.

These groups, no matter what their cause is, attempt to trick the public into over-generalization. Doctors are held in high esteem for a lot of reasons, and they should be. A minimum of 11 years of education and training, more in most cases (it’ll be 13 all told for me). They’ve put themselves through the wringer and come out swinging. Not only that but they literally hold our lives in their hands. And don’t forget how oh-so-authoritarian those white coats are. What these groups hope is that by appending the title ‘Doctors’ where ‘Citizens’ would normally go, we’ll make the logical fallacy of assuming their authority in social or scientific matters is just as great as in medical matters. A dirty, manipulative trick which by its dissembling nature tarnishes our reputation as healers and community leaders.

Physicians are not the same thing as biologists. And they have little more in the way of education in evolution than does a high school graduate. Which is something a lot of people don’t realize. Only an introductory class in evolutionary biology is required for most undergraduate biology students whether they’re in the Ivy Leagues or Chico State. Furthermore, this class is more a survey of population genetics rather than a proper introduction to Darwin’s theory. In other words, even a slightly motivated layman often knows more about evolutionary biology than what a doctor is formally taught.

The Difference Between Doctor and Scientist
Now, I’m going to catch a lot of flack for this next statement (mostly from indignant doctors), but I’ll go ahead and say it:

Doctors aren’t scientists. They are engineers. What I mean by this is that like engineers, they take scientific concepts and apply them to practical matters. The engineer sees a chasm that needs to be spanned and builds a bridge. The doctor gives diuretics to a congestive heart failure patient, to reduce the blood volume and thus the amount of pressure the heart must push against each time it beats. This isn’t a jab at the profession, but simply a statement of limitations. You wouldn’t want a primatologist to do your appendectomy, and you wouldn’t want a doctor to comment on the evolution of intelligence in neotropical primates.

The reason for this is simple: Learning what science says is not the same as learning how to do science. Most of us can read and understand Shakespeare, but probably none of us could write like him. Although doing science isn’t quite that difficult, it remains an entirely different proposition from simply knowing science. The scientific method, although simple in appearance, is extremely difficult to operate in reality. The human brain doesn’t like moving that way. It doesn’t like making a hypothesis, testing it, and reaching a conclusion based on the data. It doesn’t like having to go through all the statistics to remove confounding values to prove a relationship it can clearly see anyway. It doesn’t like the fact that it’s not allowed to infer. It doesn’t like the fact that it isn’t allowed to make assumptions (and we all know what happens when you ASS-U-ME). The human brain has evolved to be a supreme pattern generator. But as all those optical illusions tell us, sometimes that very power can get in the way of differentiating between what’s actually there and what we’re expecting. It is that basic fact of our neurobiology that makes the scientific method so necessary, so difficult, and so misunderstood.

I learned the importance of the scientific method while writing my dissertation. I had a trend I knew was right, just by looking at the raw data (as had several people before me). But to prove it I first had to develop an annoyingly complex mathematical model integrating all those numbers so there was something quantifiable. Then I had to run statistics. And then phylogenetic comparative methods. And boy am I glad I did. Oh, the trend turned out even stronger than I suspected after controlling for everything (it was a really obvious trend, I was just the first to do the mathematical modelling to make it ‘official’). But the inference I had made turned out to be total crap, which was surprising considering all the older, wiser heads I’d talked it over with had made the same inference I had. But it’s a perfect illustration of my point. Not only did it make sense to me, it made sense to some of the biggest names in bioanthropology, all of whom expected the assumption to be borne out in the end…yet it wasn’t.

You see, the scientific method is a check against the natural way a human thinks; it’s an attempt to prevent ’scientific illusions’ like the one I suffered from early in my dissertation research. Learning how to do it can be hard, like learning to breathe in when you lift a heavy weight, not hold your breath or breathe out.

Inherent Bias Against Evolution:
The last point I want to mention goes back to the doctors as engineers analogy. Engineers work with ’systems’. So do doctors. The cardiovascular system, the renal system, the gastrointestinal system, the urinary system, the musculoskeletal system. Because of the way doctors have to do their jobs, they think of these as fine-tuned machines. They think of cogwheels carefully intertwined in dynamic balance. They think of control theory and redundancy. They see a finicky 1960’s Jaguar. What they don’t see is a series of parts added together over millions of years to make a jury-rigged barely-functioning system.

As a bioanthropology student, I was shown a picture of a tree shrew, a lemur, a tarsier, a monkey, an orangutan and a human, I was taught what made each of these categories different from the preceding one; what was added, what was lost. Earlier in my education, I learned a bit more about evolution; of our 6 layered cerebral cortex versus the reptile and bird 3-5 layers. I learned how fish left the riverbeds to become amphibians. I learned about the common patterning genes shared by insects and humans that allow us to have such a complex array of orderly structures from head to toe. In short, evolution was told as a story of how a series of additions and deletions lead from god knows what to where we are now.

As a medical student, I learned about the HPA and HPG axes: a series of 3 intimately connected glands that control a variety of metabolic functions. I learned how in response to environmental factors the Hypothalamus (master gland) would release certain hormones, which could activate or inhibit the Pituitary which could in turn activate the Adrenal Cortex and/or Gonads. And I learned how the products of each of these glands could inhibit the glands that controlled them. The glandular system was presented as a complex device.

The glandular system wasn’t presented to us as an evolved mechanism to compensate for changes in environment and internal state. It wasn’t shown how from fish to amphibians to reptiles/birds to mammals you see an increasing degree of complexity in what are termed homeostatic mechanisms (trying to keep the body in the same condition). The most recognizable illustration of this is that we are ‘warm blooded’ while reptiles are ‘cold blooded’ (the Hypothalamus controls body temperature too). If medical education is a repair manual for a Ford Focus, then evolutionary biology presents us with the scientific version of Kipling’s ‘Just So Stories’.

In other words, doctors can see design when they look at the body because they were taught to see Paley’s Watch.

Conclusion:
None of the above is meant as a criticism of medicine. I don’t know that there’s a better way of teaching medicine than what is currently done. A knowledge of evolution can be helpful for the research investigator but I don’t know yet if I’d say there’s value for it in the practitioner. You don’t want a doctor to be a scientist; those inferences he makes can and will save your life; but they’d cost him his career if he was a scientist. He doesn’t need to know the evolutionary history of major organ systems to be an effective clinician. And given how much time they must already put in before they begin to practice, it’s probably best we don’t add to the load. Seriously.

But it is important to recognize why whatever PSSI says is meaningless. As I said earlier, they simply have no background in evolutionary theory. Many doctors have probably never read Origin. Those that have read it have likely not had the benefit of a teacher to guide them. Even if they do know what Darwinian evolution really is, they have no more justification in questioning the scientific merit of the theory than anyone else; they aren’t scientists, so they can’t speak as scientists. And don’t forget the role their educational perspective has played in their ’skepticism’ of evolution. As I’ve tried to show above, they’ve made every mistake that the scientific method was designed to prevent (showing their lack of training both in evolution and doing science).

What really bothers me, more than their anti-evolution stance, or their dissemination when they talk about ‘academic freedom’ and ’scientific alternatives’ is that they are misusing the power of their authority. Physicians hold a place of trust in the community. In a lot of ways we’re held to a higher ethical standard, and it is simply unacceptable for us to attempt to bully and lie to change peoples’ minds when we have neither the knowledge nor the authority to do so.

…Knowing what the position is you’re debating against. And know who it is supporting that position.

The second rule of debate is actually debating the position. It gets real old…it really does…having people argue against a position that you’re not actually supporting. What does that accomplish? Nothing.

The goal of debate is to present reasoned arguments both for and against a certain proposition. There’s a structure, a rhythym to it. One side starts, the other responds. If you’ve ever listened to symphony you might have heard the first violin section play a riff, followed by the second violin section. Or sometimes it’d be the cello against both violins. It’s called point-counterpoint in music. Heck, point-counterpoint is a good enough characterization of what debate is all about.
But these days what I get is:

As you might expect, I’m going to say that I get this from both creationists and leftists. Intellectimpure will likely comment that I’m preferentially excluding people on the right and libertarians. I debate people on the right almost as often as I debate ‘libertarians’ (who are often as childish in their thirst for anarchy as ‘democrat/liberals’ are in their child-like reverence for fairy-tale socialism). I was serious in my post on defending marriage by removing all state sanctions whatsoever, for crying out loud. The people on the right at least pay me the courtesy of actually arguing my point when we disagree, rather than arguing a point that they’ve got a canned and recycled version of someone else’s words for. Anyway, back to my point.

Creationists: Ohhhh, where to start and where to end. I really don’t know. They’ve been beaten to a pulp by anyone who understands and accepts the scientific method. Their only supporters are either those whose beliefs won out agains their scientific education, or those who don’t know how science works in the first place. Now, I’ve actually got nothing against creationists, people can believe what they want to believe. It does pain me, as an evolutionary biologist, to realize how many people accept creationism in designer clothing, but that’s their business, not mine. I’m sure plenty of people are pained by my refusal to bow my head to a Christian God.

I probably wouldn’t have even made a big deal, made a single public statement, or been in the middle of founding a new group if they hadn’t decided to call ID/creationism ’science’. That’s not how science works. You don’t pick a stance and then cherry pick data to fit it. You pick a stance and then challenge it. Anyway, on to their debate tactics:

1) Their favorite, of course is that Evolution is ‘just a theory.’ They try to insinuate that the word ‘theory’ when appended to ‘evolutionary’ puts it on par with unconfirmed speculation like string theory or Descartes’ theory of Mind-Body Dualism. Coming back to the title, you have to know what you’re debating. And if you don’t know how the scientific definition of theory is different from that in other fields, you clearly didn’t do your homework. Some other things that are ‘just theories’ include Einstein’s ‘theory of relativity’ which has been experimentally confirmed in all sorts of ways. Or Newton’s Theory of Universal Gravitation, whose equations are the same ones that scientists use to get rockets into space.

2) Another one, trotted out by the particularly juvenile is the ‘if humans evolved from monkeys, why are there still monkeys around?’ objection. There is probably no more inferior, infuriating argument in the world than this one. Darwinian evolution says nothing about a ‘chain of being’. In fact it explicitly says that natural selection is both directionless and purposeless. We are not the crown jewel of the anthropoid clade, natural selection was not pushing inexorably toward us. We are the result of a series of climate and habitat changes leading to dense forest growth in Africa and Asia that led to first our chimp-like ancestors, followed by a rapid growth in grassland that led to a bunch of chimp-like animals deciding to stand upright for a bit. Anyone who uses this when debating evolution should be dragged out into the street and beaten until they realize that the smartest thing the ignorant can do is keep their mouths shut. People who use this argument don’t even know what Darwinian Evolution is. How can they debate it?

3) Almost as irrelevant to the theory itself as objection 1 is the ‘Evolution can’t explain how the first living cell came to be.’ It doesn’t try to. Evolution is how life changes from ’so simple a beginning into endless forms most beautiful’. It’s about what happened after the first cell. To draw an example, regular old plain Jane physics can explain the current world but it can’t explain what happened during the big bang. But it doesn’t pretend to. It seeks only to explain why things react to each other the way they do in the here and now. Same sorta thing for evolution.

4) This next one requires a misunderstanding of two different theories, making it particularly heinous. Oh yes, the predictable old ‘The Second Law of Thermodynamics says entropy is increasing. So how could more complex forms come into being.’ Yes, the total entropy of a closed system can only stay the same or increase. But note the word closed. The universe is a closed system, a specially prepared device in the lab blocking all measurable outside influences is close to being closed. A living breathing animal, not so closed. You just breathed in air. Not closed. The sun just stimulated the synthesis of Vitamin D in your skin. Not closed. What? You ate? Not closed. Hey what’re you doing in the bathroom for so long? Doesn’t matter, either way, not closed. Do you get it? Huh? Misunderstand evolution because you don’t accept it. Misunderstand thermo because you attempt to use it to support a position when it inadvertently proves the evolutionary biologists’ point. Real smart.

5) ‘Evolutionists refuse to acknowledge the differences between microevolution and macroevolution. Microevolution is the change in alleles and frequency over time. Macroevolution is actual speciation’ This one’s particularly retarded since by accepting microevolution they’ve basically built the trojan horse, filled it with Greeks, and brought it inside their walls themselves. If you accept ‘microevolution’ then you accept that mutations can be incorporated into the genome. All it would take is one mutation, one single mutation, that would make a given male’s sperm incompatible with a given female’s eggs. This could eventually result in what’s called reproductive isolation, which is one of the ways that new species are created. Two groups that used to be part of the population can now no longer interbreed.

Five’s a good number, I’m stopping there and moving on to leftists. Leftists’ favorite tactic is to say that if person A holds position C, and person B holds position C, since person B’s arguments were stupider, if we attack person B, then person A loses. This is what we call a logical fallacy, children. It’s something leftists seem unable to debate without doing.

1) ‘You voted for Bush. How can you claim to be against [any of the 1000's of non-conservative things Bush did]‘ I didn’t vote for Bush. ‘But you didn’t vote for Kerry?’ Do I look like a socialist? ‘But the point remains, if conservatives don’t believe in X, why did Bush do X.’ Or ‘If conservatives are better than democrats in [whatever] then why does Bush suck so bad?’

Bush’s approval ratings are lower than ever. Apparently 45% of conservatives disagree with his handling of, well, everything. Do we stop being conservatives because we disapprove of him? Didn’t think so. Bush does not equal conservatism. Support for a given policy does not equal support for Bush. A senator may support a certain law because of lobbyists. Private individuals may support the law because it’s a good law (as in the protection of lawful commerce in firearms act). Or, to put it more succinctly, as one of my most influential professors once said ‘Argument by analogy is only as strong as the analogy.’ Conservatives and libertarians think in different ways and have different reasons for their positions on certain political issues.

2)’The Founding Fathers were actually quite liberal.’ You’re right, they were. That’s why I don’t use the word ‘liberal’ to describe democrats or socialists of any kind. They’re leftist is what they are. Not liberal. The Founding Fathers had a vision and a definition of freedom. Ever since FDR, the American Left has had a different vision, a different definition of freedom. I’ve talked about this at length in my ‘political philosophy’ category, and will continue to talk about it while there’s breath in my body and fingers on my hands. The founding fathers believed in minimal government intrusion, they believed liberty was about the right to live unaccosted and uninterfered with so long as you did the same to others; they believed that the larger the government, the smaller the amount of liberty. Leftists on the other hand believe that liberty is about ‘the freedom from want and fear’ and that government has an ‘enabling role’ in liberty. So yeah, they were very liberal. Why aren’t you like them? You’re debating a guy who goes back to first principles. You’re not dating some idiot scumbag who thinks definitions change when you want them to.

3) ‘If you care about x, then why don’t you want to spend money on it?’ This is a particularly stupid tactic, especially with me and a few other classical liberals I know. In past years, I’ve averaged literally hundreds of hours volunteering helping out elderly veterans, children, abused and neglected animals, and helping conservation efforts. While that’s not so true anymore (and i feel like a douchebag about it), it’s hard to say I don’t care when I’m the one with the scars and calluses and they’re the ones with mommy’s credit card.

But more importantly, they make the mistake of assuming that non-leftists don’t care about something just because they don’t want the government involved. Seeing as we have a policy of minimal government because we don’t trust it, judging what we care about based on what we want government involved in is a bad idea. You don’t let your kids stay at a known child molester’s house. And you likewise wouldn’t want to give your charity money to a thief who claims he’ll get it to the right place. If the free market and community support can get the job done, the I don’t want a bungling, mildly evil, and mercurious government involved. Government is a last resort and something to use when the old fallbacks don’t work.

That’s enough for today. Back to studying.

Introduction
What a lot of people forget or just don’t understand is that unlike the traditional ‘computer/problem-solver/integrator’ analogy, the brain is highly context-dependent. The way it reacts to the outside world, and in fact the way it perceives it, is highly dependent on both exteroceptive (the world outside) situations and interoceptive(mood, motivation, etc) responses. This is a function of the limbic system. Which is one of the most fascinating parts of the brain.

It’s one of the weaknesses of most facets of psych that they don’t take into account how the wiring and reactions of the limbic system can radically change the way we think, without us even knowing about it. I’m not going to get hugely detailed today because I have a final in four hours, and because that would bore everyone, including me.

Instead, I’ll give a quick and dirty overview and integrate it with a story about my ancient dog that illustrates my main point dramatically.

Neuroanatomy of the Limbic System
First, a few pictures.

(From the wiki page I linked to earlier–Limbic System in red)
This is a real simplistic image, but it allows us to consider the gross brain anatomy and introduce a couple of evolutionary considerations.

The yellow, blue, and green areas collectively make up the brainstem. Each of them has a different function: the yellow and blue areas are called the medulla oblongata and the pons, respectively. The green is called the cerebellum. The yellow and blue areas are arranged basically like the spinal cord on steroids, and handle a lot of the basic aspects of physiological maintenance. They do the breathing and the intestinal movement and the heart and all that. You can actually cut off or destroy most of the brain structures above them and still have a live animal…just one that can’t do anything (essentially a coma). The green area is completely different from these guys. It handles coordination and making sure your movements are smooth, certain, and accurate. People with strokes often have this area affected, which is why they might shake when they move (intention tremor), have trouble walking (ataxia), or be unable to adjust their movements in the middle of an action. The brainstem is about as basic as a brain can get: You can live with it, but not really do much. Some of the non-vertebrate chordates seem to just have a brainstem and nothing above it.

The tan part of the brain that’s surrounded by the red limbic system is what’s called the diencephalon or sometimes the basal ganglia. This area of the brain serves as a relay station between the tan stuff outside (the cortex–stuff that does the ‘thinking’) and the ‘lower stuff’ below. Basically, it filters and gets sensory information to the right place to perceive it; it also modifies the info just a bit. And after the cortex is done sensing, integrating, and responding, it takes the cortex’s signal, processes it again, and sends it to the right places in the brainstem and spinal cord to get the motor response we want.

The basal ganglia are pretty complex and can do a little behaving of their own. ‘Motor programs’ such as throwing a punch or walking are found there. It also helps with keeping your head on straight. Two degenerative diseases that affect the basal ganglia are Huntington’s and Parkinson’s. Huntington’s preferentially attacks a basal ganglia nucleus called the caudate, which is important for cognition. This is why Huntington’s patients develop dementia in addition to the chorea (involuntary movements). Parkinson’s, on the other hand, attacks the Substantia Nigra, which help in the initiation and cessation of movement. This is why Parkinson’s patients shake when they’re still, but have a hard time moving on purpose; it’s like a faintly heard radio station. The static is almost as loud as the signal.

The limbic system is one of the phylogenetically oldest parts of the cerebral cortex; even the way it’s constructed at a cellular level is more primitive than the rest of the cortex (but more complex than lower structures). The oldest part of the limbic system is called paleocortex or archicortex, while the newer parts are called allocortex. All vertebrates have well-developed limbic lobes, but many don’t have much–if any–of the cortex surrounding it (the outer tan stuff). This is why goldfish seem so stupid. And why rats are less complex than cats, which are less complex than monkeys. Less of what’s called neocortex.

Archicortex has 3 layers of neurons that interact with each other in a complex network. Allocortex has 3-5 layers that can be kind of indistinct. And neocortex has 6 well-defined layers. Your emotions start in the paleocortex, move through the allocortex and then on into the neocortex. We’ll look at that in detail after a couple more pictures…

Here’s a schematic of how these structures talk to each other:

(click for larger)

And here are a couple of drawings:

(click for larger)

(click for larger)

This last one is probably the best. It not only shows the structures but how they connect.

(clicky)

Stuff comes from the sensory cortices (the unshaded cortical parts toward the back and sides of the brain) into the Hippocampus (the archicortex) and Amygdala. Sensory information travels to the hippocampus and amygdala through the parahippocampal cortex (allocortex)The hippocampus is the organizer for sensing and remembering details about the outside world (exteroceptive information) while the amygdala handles emotional context (interoceptive information).

Together, they send information to the anterior cingulate gyrus (which is part of the neocortex) through the thalamus which is part of the relay system we talked about earlier. The cingulate gyrus then projects back to the hippocampus and amygdala through the parahippocampal cortex. Making Papez Circuit.

Confusing, but what it all boils down to is that the hippocampus and amygdala are what help us store memory, recognize similar situations, and, in the case of the amygdala, tell the brain how to feel about that. The emotional side of things is what we’re most concerned with today, so we’ll talk about the amygdala a bit more. The anterior cingulate cortex is what turns the amygdala’s emotional response into a guiding behavior for the frontal cortex (the part that does the thinking). The anterior cingulate is important in motivation; lesions to it result in people that understand that something scary is happening, but don’t respond to it. The amygdala also projects to the nucleus accumbens. If you’ve ever read about the neurobiology of addiction you’ve probably heard of this structure. It’s the one that dopamine activates. It’s our ‘reward center’. So together the areas the amygdala projects to provide motivation (anterior cingulate) and reward (nucleus accumbens). One encourages you to do something, the other one congratulates you on achieving it.

These areas in turn project to the frontal cortex, the area we think of as the seat of cognition, personality, and consciousness. In other words, any time you think about anything, your conscious thoughts are being unconsciously modified by the limbic system. This is evolutionarily important because it allows the brain to be efficient and speedy. It makes sure you’re more motivated to do things that’ll help you avoid dying or help you make more babies. It rewards you for doing something that doesn’t get you killed or helps you so you’ll do it next time.

Instead of spending equal time dealing with things in the environment, it lets you ignore crap like dirt and leaves and focus on the jaguar approaching you and the pretty little thing that just smiled at you. But, of course, it does all this without actually letting you know.

The Story
My dog has been going through a rough patch. Breathing heavy, coughing up a little phlegm. Didn’t touch her food all day yesterday. But she ate everything else she was given; fruits, pudding, bread, whatever. Mom was freaking out. Dad was worried. I was at school taking a test and knew nothing of her going off her feed. So I get home, see the full bowl, and then I started freaking out. Called mom. She told me the dog had something to eat.

So I figured she had a viral infection. Would explain the phlegm and the thirstiness and the heavy breathing. And if you’ve ever had a lingering respiratory viral infection (like RSV), you might have noticed a change in your sense of smell, even if your nose wasn’t plugged up (anosmia). We have really bad noses but really good tongues. Dogs are the reverse. Flavor is mainly to do with your nose, believe it or not. So with her nose all blocked up, that food wouldn’t mean much to her.

Little brown pellets are just little brown pellets. They go through the hippocampal (exteroceptive) system but completely fail to activate the amygdala. The amygdala doesn’t tickle the cingulate, so the frontal cortex doesn’t care too much either. So my dog has no interest in a food that to her aging eyes looks just like gravel. That slightly off-putting odor, on the other hand, sends her into a frenzy. She remembers eating it with fondness as the amygdala grabs interoceptive memories of her nucleus accumbens rewarding her for eating. Her cingulate gyrus motivates her to go right after that food. The motivational memory was tied to the smell, and only the smell.

But that doesn’t explain the fact she’d eat her various ‘treats’. Well, actually it does. To a dog, when their master gives them something from his hand, it’s literally a reward. And that nucleus accumbens fires right up. So Shelly has generalized taking food from my hand to mean she’s going to be rewarded when the food hits her taste buds. Her amygdala and hippocampus together recognize me holding something in my hand and holding it out to her as food in my hand. Her amygdala adds the memory of the ‘reward’. It tells the cingulate gyrus which promptly kicks her frontal cortex in the pants, sending her questing after the tidbit. Of course, in her senility, usually she misses and chews on my finger first.

We’d tried everything to get her to eat. Brought the bowl to her, held her upside down and stuck her nose in it, threw it at her. At one point I was considering chewing on it like you do with a baby to convince them that Gerber’s isn’t as nasty as it looks.

I was explaining the reward and motivation thing to my little bro, when he said “Doofus, then hold her dog food in your hand like it’s a treat. She’ll start eating it then and probably keep eating.” Sure enough, it worked. Once I’d gotten her to take the ‘treat’ from my hand, the taste memories kept her motivated.

Final Thoughts
Same object, different responses. Not because my dog’s thoughts changed but because which thoughts she was enabled to perceive were different. The subconscious mind is some powerful stuff, and while we do have some control over it, we only get that way by understanding the way our brains work in the first place. The challenge of psych and mental health research in the coming decades is to understand how to work with these subconscious processes as much as any conscious ones. Cognitive Behavioral Therapy is all fine and good, but if the problem isn’t necessarily cognitive (as limbic system could be argued to be), it won’t have much of an effect.

Linky

Occam’s little blade could have told you that decision-making is an evolved attribute. The assumption of self interest provides the shared underpinning of behavioral ecology and economics. In fact, neither discipline could operate without that assumption. Predictive models show high fidelity, can be interchangeable between the two fields, and in general provide some of the most powerful tools for understanding behavior, human or otherwise.

Of course, what goal self-interest is directed toward can vary. Economics obviously tends to look at money (but behavioral economics is expanding the study to include any desire). Behavioral ecology at its most fundamental level concerns itself with reproductive success and inclusive fitness. But it too can look at more specific aspects. Feeding ecology and the rules of food choice in monkeys is an increasingly growing (and interesting) field.

Garret Hardin, a famous ecologist turned economist/political theorist/conservationist noticed these obvious similarities way back in the 1970’s. He was fond of saying that economics was just a division of ecology. And his magnum opus Tragedy of the Commons represents one of the earliest works seeking to apply ecological principles to political matters (in this case, conservation). Hardin called his way of thinking ecolacy. Hardin was a committed libertarian, believing it to be the only behavioral ecologically valid political system (as I do). Sadly, he passed away two weeks before I began my intensive study of his work. I would loved to have met him.

Back in the summer of 2003, I became infatuated with the confluence of philosophy and biology. This happened courtesy of a random course selection. Seminar in the History of Biology taught by Dr. Allen MacNeill. Scarily enough, I just dropped by his blog so I could link to it. And his most recent post mentions this course being taught again this summer. Coincidences like that scare the crap out of me. The course material, and Allen, quite literally changed my life in the most amazing way. He showed all of us just how deep evolutionary thinking can take us. I can’t thank him enough for that.

Anway, I saw too many problems with western philosophy to count; it was too suffused with the concept of man’s special status as the children of God. So deep is this nature in fact, that Western Atheism, such as the existentialism of Sartre, continues to propound some of the same untenable and unrealistic concepts of theosophy. There was just too much ‘Man apart from Nature’ garbage for me.

Eastern philosophy, on the other hand, I felt was on the right track. Of course, this might be personal bias, as I was born and raised a Hindu. And still technically am, although I might be better described as a buddhist. Eastern philosophy has never denied man as a part of nature. Furthermore, at least in Hinduism, the blatant phylogenetic similarities and mental capacity we share with other animals. The pedestal that western philosophy places us on was reduced to a series of steps, leading from insects up through social mammals, other primates and then us. And, although the chain-of-being model of evolution is exceedingly faulty (and is part of the basis for claims that Marxism is the next step in evolution), it’s a much better place to start than the garbage spewing from west of the Urals. Even the oldest Hindu scriptures discuss at length Man’s intimate connection with nature, and ultimately his inseparability from it. We are a part of the landscape. And from this comes one of the most powerful concepts in Eastern Philosophy: Natural Law.

By that I don’t mean things like the ‘natural rights’ classical liberals like myself often discuss, but quite literally Law from Nature. There are many schools of Hindu thought, but the one that’s had the strongest pull on me is the agnostic tradition, almost the Nietzschean ‘God is dead’ conception. The agnostic Hindus discuss how morality stems from understanding the way nature works, the way animals interact with their environment and each other, and ultimately how we can do as the animals do. But Eastern Philosophy as i’ve said earlier can be pretty vague about such things, preferring to simply say ‘nature’ and then let you do the figuring out. Still, it provides a few useful concepts from which to develop a more concrete theory of knowledge and the way the world works.

Incorporating ecolacy and evolutionary thought into other disciplines is a matter of epistemology. It’s about understanding how things got to be how they are. A large proportion of leftists are atheists. They also claim to believe in evolution. However, in many ways they don’t allow evolution to become a part of the epistemological underpinnings of their political or social beliefs. When they do, they use faulty theoretical concepts, such as the above mentioned chain of being, or even more insidious, Teilhard de Chardin’s Omega Point.

I happen to think this is a problem. If we’re going to be rational about our belief systems (as atheistic and agnostic leftists insist they are), then we need to make rational assumptions. Theories are only as strong as their assumptions, which is why Marxist philosophy is not a good idea in theory. Its assumptions are completely flawed, with little epistemological basis as to the nature of individual human behavior. Although Marx made some interesting observations about the nature of power, his proposed ’solution’ has repeatedly shown itself to be just as bad as the conditions which caused him to propose his unrealistic philosophy.

In the coming weeks and months, I intend to explore the confluence of evolution, philosophy, and politics. Money and baby-making are the most obvious aspects of self-interest worthy of study, but there are three more that have greater implications for political philosophy (and psychology for that matter…another area where ecolacy is under-applied): Comfort, Power, and Status/Influence. Furthermore, we’ll discuss some of the concepts of game theoretic systems (which all regimented social actions–including government–are); the natural tendency for individuals to cheat and/or defect from a system, how to prevent that, and how to construct a system that will not fall (an evolutionarily stable system). It’s scary how much the Founding Fathers were able to understand of all of this, considering neither game theory nor evolution were well understood until the mid-1800’s…and neither in wide application until the mid 1900’s.

Theodosius Dhobzansky, one of the architects of the Modern Synthesis, was fond of saying that ‘Nothing in Biology makes sense, except in the light of Evolution.’ I’ll one up him and say that Nothing in Life makes sense, except in the light of Evolution.

Introduction
Razib of Gene Expression got me thinking about peer review in this post. My short comment was threatening to degenerate into a thousand word exposition on the problems with the current publishing process. So I’ll blog it instead.

He characterizes peer review eloquently with:

There’s a lot of shoddy crap being published in stuff like the Tuvan Journal of Entomology, and always has been, but the big issue is when crap gets into Science and Nature. Ultimately science is a social enterprise based on trust and long term self-correction. There’s a lot of noise in the system, but I don’t see any other alternative out there.

I do not want to hear about problems with peer review right now. As soon as finals are over, I’ll be in the process of distilling my master’s thesis into a couple of publications, and I’m quivering like a virginal bride entering the honeymoon suite, equal parts anticipation and fear and far too much of both.

But my situation is in a lot of ways a perfect illustration of some of the problems surrounding peer review…

Paradoxically, the problems with scientific research and publication stem from the fact that we know so much and that our tools have become so sophisticated. Biology has simply become too expansive a field for a person to become ‘just a biologist.’ You have to become a physiologist, a geneticist, an ecologist, or a primatologist. But it doesn’t end there. Within each discipline people specialize in certain areas; kidney physiologists, HOX gene embryologists, or marmoset specialists. And then you have to choose which aspect of your subject you want to research. Which in turn determines the tools you use and the methods of analysis most pertinent.

And you specialize early. Fresh out of undergrad, I’d not only had to decide which primate taxa I wanted to study, but the specific facet of their behavior as well. It’s no different for any graduate student. This leaves one with only a smattering of very superficial knowledge about other aspects of biology. And even within the discipline at large, the most thorough education leaves you only with the knowledge of what the science says but not how to do the science. Because of my bioanthropology degree, I’ve got a fairly strong background in hominid evolutionary anatomy. But if you handed me a season’s worth of bones from Lake Turkana, I wouldn’t even begin to know how to measure, compare, and analyze the finds. I’d venture most paleoanthropologists would have similar problems when working with data from primatological research.

The Paucity of True Peers
Which is the root of the problem; while all biologists have a decent breadth of education and knowledge, the depth of that knowledge isn’t particularly profound. But more importantly, they’re highly segregated and compartmentalized in terms of what might be called ‘vocational training’.

Your ‘peers’ are thus actually quite few in number. While I might be an extreme case, I can count on the fingers of one hand the number of primatologists who have published papers using similar research methods to my own. The last paper was in 2000, the one before that in 1997. And then a couple in the 1970’s and 1960’s. The only researchers who might still be involved in the field are the ones who published the 1997 paper. And all of the above focused on old world monkeys (African and Asian) whereas my work covers New World Monkeys exclusively.

Finding a ‘true’ peer to review your paper can be a tough task indeed. And in mine, is pretty much impossible.

Cross-Pollinating and Novel Methods
Backtracking a bit to the idea of ‘vocational training’, research tools and methods are often highly individualistic. Many famous researchers have a trademark analytical method that appears in nearly all their papers. Others specialize in using laboratory tools like radioassays or fMRI. Often enough though, most in the field understand the basic concepts behind such tools and methods well enough to review a paper with confidence. The problem comes when, as Razib mentioned, new methods come into vogue. There can be significant pressure to use such methods in one’s work whether they understand them or not.

My personal example is the phylogenetic comparative method. Without going into too much historical detail, the idea was introduced by Felsenstein in 1977(?). The basic idea is that we can’t treat individual species as points on a blank space, but must take into account their phylogenetic relationships when comparing traits. My dissertation advisor is a paleoanthropologist, and the phylogenetic comparative method is quite popular in that field. However, I’ve never seen a primatological paper that used such methods. He encouraged me to use it, and it made my dissertation a stronger work. But its novelty means that many primatologists won’t be familiar with it (as i wouldn’t have been if my advisor had been one).

Another important factor is cross-pollination. Robert Sapolsky was one of the first to study neuroendocrine properties in wild primates. He took techniques from one discipline (neurobiology) and applied it to a different discipline (primatology). Syncretism rocks my world. And the result of hybrid research like his is a deeper understanding in both fields. Like Sapolsky, I’m attempting a bit of syncretism myself. Coelho in 1966(?) was the first to apply physiological methods of estimating energy expenditure to the study of wild primate behavior. It’s in Coelho’s footsteps I’m attempting to follow. But, because I’m not trained as a physiologist, there might be all sorts of problems in both my methodology and results that I’m not aware of. And neither will my reviewer. However, simple psychology makes it likely that a reviewer will give a researcher a ‘pass’ on elements the reviewer lacks expertise in, feeling that they have little right to judge such things. Personally, feeding ecology not being my specialty, if I were asked to review a paper in said discipline, I’d be likely to give the benefit of the doubt to the author even if I felt there might be a problem with their methodology.

The take home point is that the increasing novelty and diversity of research methods mean that both the researcher and the reviewer are often outside their comfort zone. And while just about any reviewer can judge the introduction, background, and discussion sections, they may be unable to properly gauge the quality of the methods and results of a given paper.

Wide Implications of Narrow Research
Discussions are my favorite part of a paper. It’s where the results are integrated with what is known and what is merely postulated. It’s the part that helps us actually further our knowledge. That power comes from the simple fact that a ’small’ result can have wide-ranging implications across a variety of disciplines. A perfect example comes from the FoxP2 paper. Not only does it give us a mechanism by which language may have arisen, it also allows us to date the origin of language. Furthermore, it has interesting neurological implications with regard to language. It even impacts the shape of the skull. All from studying a single gene variant found only in one Pakistani family. Neurobiology, phylogeny, paleoanthropology, functional anatomy, all from a relatively routine research method in a different field.

The problem lies in the fact that it was a genetic research method, performed by geneticists. In their discussion, they commented on most of the aspects mentioned above. A glaring error that a bioanthropologist would sieze upon immediately is that they believed that because the human FoxP2 allele is correlated with a reduction in jaw muscle size and strength, the resultant reduction in strain would have allowed the brain case to grow larger.

Anatomists have long known that the strength of jaw muscles has little correlation with braincase size, but rather with shape (the stronger the jaw muscles the more exaggerated the skull is longitudinally). Furthermore, paleoanthropologists could have told them that hominid brain size has actually been fairly constant, if not decreasing, for the past 500,000 years. So a mutation about 100,000 years ago stimulating an increase in brain size has little corroboration in empirical evidence. Because the peers chosen to review what is essentially a genetics paper would likely be geneticists, we once again run into the problem of biologists being out of their depth.

Conclusion
The almost anarchic and tribal nature of biology is what limits the strength of peer review in our field. It’s like the fission-fusion societies found among spider monkeys. The membership of a group changes so dramatically and frequently that identifying the right peers to actually review a given paper can be nearly impossible.

Is there a solution? Short of making sure a paper is peer reviewed by a committee of every type of biologist that would have something to say, I don’t have one. But I needed a study break, so this is what you get.