Prediction: self-promoting hype meets interdisciplinary ignorance

There is a maddeningly vague press release floating around, and I think everybody has sent me a link to it now. It contains a claim by some chemists that they have discovered a new organizing principle in evolution.

A team of Princeton University scientists has discovered that chains of proteins found in most living organisms act like adaptive machines, possessing the ability to control their own evolution.

The research, which appears to offer evidence of a hidden mechanism guiding the way biological organisms respond to the forces of natural selection, provides a new perspective on evolution, the scientists said.

The researchers — Raj Chakrabarti, Herschel Rabitz, Stacey Springs and George McLendon — made the discovery while carrying out experiments on proteins constituting the electron transport chain (ETC), a biochemical network essential for metabolism. A mathematical analysis of the experiments showed that the proteins themselves acted to correct any imbalance imposed on them through artificial mutations and restored the chain to working order.

If true, this would be an extremely remarkable claim. An amazing claim. Something that would make all biologists sit up and take notice. Unfortunately, the puff piece writer and the scientists involved seem incapable of actually explaining what they found, which makes me extremely suspicious. This is just empty noise:

The research, published in a recent edition of Physical Review Letters, provides corroborating data, Rabitz said, for Wallace’s idea. “What we have found is that certain kinds of biological structures exist that are able to steer the process of evolution toward improved fitness,” said Rabitz, the Charles Phelps Smyth ’16 Professor of Chemistry. “The data just jumps off the page and implies we all have this wonderful piece of machinery inside that’s responding optimally to evolutionary pressure.”

How? What is the mechanism? What kind of data suggests this peculiar notion? I’m unimpressed, so far, and unfortunately, Physical Review Letters hasn’t yet put the paper online. I’ll also point out that the history of statistical claims for exceptional mechanisms that extend evolution is littered with “never mind” moments — some clever dick comes along and points out the ways in which the result is an epiphenomenon, a product of the same old rules all along.

The other problem that often occurs is that one of the investigators opens his mouth and reveals that he is completely out of his depth, and that the team has absolutely no conception of how evolution actually works. This time, there is no exception.

“The discovery answers an age-old question that has puzzled biologists since the time of Darwin: How can organisms be so exquisitely complex, if evolution is completely random, operating like a ‘blind watchmaker’?” said Chakrabarti, an associate research scholar in the Department of Chemistry at Princeton. “Our new theory extends Darwin’s model, demonstrating how organisms can subtly direct aspects of their own evolution to create order out of randomness.”

Dear gob. Is this an indictment of Princeton, of chemists, or is Chakrabarti just a weird, isolated crank? That first sentence is not even wrong. Darwin answered the question of how complexity can arise, so no, we haven’t been puzzled by that general question; evolution is not completely random, so that part is a complete non sequitur; randomness easily generates lots of complexity, so even if we accept his premise, it invalidates his question; and how does he reconcile his assertion of “completely random” with his use of the simple metaphor of the “blind watchmaker”, which implies non-randomness? That’s a sentence that contradicts itself multiple times in paradoxical ways.

Anyway, I’ll be looking for the paper. My bet would be that it says nothing like the claims made for it by the press release, or that it will be an embarrassing error of interpretation by the authors.

Entropy and evolution

Blogging on Peer-Reviewed Research

One of the oldest canards in the creationists’ book is the claim that evolution must be false because it violates the second law of thermodynamics, or the principle that, as they put it, everything must go from order to disorder. One of the more persistent perpetrators of this kind of sloppy thinking is Henry Morris, and few creationists today seem able to get beyond this error.

Remember this tendency from order to disorder applies to all real processes. Real processes include, of course, biological and geological processes, as well as chemical and physical processes. The interesting question is: “How does a real biological process, which goes from order to disorder, result in evolution. which goes from disorder to order?” Perhaps the evolutionist can ultimately find an answer to this question, but he at least should not ignore it, as most evolutionists do.

Especially is such a question vital, when we are thinking of evolution as a growth process on the grand scale from atom to Adam and from particle to people. This represents in absolutely gigantic increase in order and complexity, and is clearly out of place altogether in the context of the Second Law.

As most biologists get a fair amount of training in chemistry, I’m afraid he’s wrong on one bit of slander there: we do not ignore entropy, and are in fact better informed on it than most creationists, as is clearly shown by their continued use of this bad argument. I usually rebut this claim about the second law in a qualitative way, and by example — it’s obvious that the second law does not state that nothing can ever increase in order, but only that an decrease in one part must be accompanied by a greater increase in entropy in another. Two gametes, for instance, can fuse and begin a complicated process in development that represents a long-term local decrease in entropy, but at the same time that embryo is pumping heat out into its environment and increasing the entropy of the surrounding bit of the world.

It’s a very bad argument they are making, but let’s consider just the last sentence of the quote above.

This represents in absolutely gigantic increase in order and complexity, and is clearly out of place altogether in the context of the Second Law.

A “gigantic increase in order and complexity” … how interesting. How much of an increase? Can we get some numbers for that?

Daniel Styer has published an eminently useful article on “Entropy and Evolution” that does exactly that — he makes some quantitative estimates of how much entropy might be decreased by the process of evolution. I knew we kept physicists around for something; they are so useful for filling in the tricky details.

The article nicely summarizes the general problems with the creationist claim. They confuse the metaphor of ‘disorder’ for the actual phenomenon of entropy; they seem to have an absolutist notion that the second law prohibits all decreases in entropy; and they generally lack any quantitative notion of how entropy actually works. The cool part of this particular article, though, is that he makes an estimate of exactly how much entropy is decreased by the process of evolution.

First he estimates, very generously, how much entropy is decreased per individual. If we assume each individual is 1000 times “more improbable” than its ancestor one century ago, that is, that we are specified a thousand times more precisely than our great-grandparents (obviously a ludicrously high over-estimate, but he’s trying to give every advantage to the creationists here), then we can describe the reduction in the number of microstates in the modern organism as:

i-c0218e37d26a7638417f556b4e668d64-microstates.jpg

Now I’m strolling into dangerous ground for us poor biologists, since this is a mathematical argument, but really, this is simple enough for me to understand. We know the statistical definition of entropy:

i-cee140176f0d54e5df841106965edeba-entropy.jpg

In the formula above, kB is the Boltzmann constant. We can just plug in our estimated (grossly overestimated!) value for Ω, have fun with a little algebra, and presto, a measure of the change in entropy per individual per century emerges.

i-fe99f87a61a6afae1fe0d0de2fe265b5-change_in_entropy.jpg

Centuries are awkward units, so Styer converts that to something more conventional: the entropy change per second is -3.02 x 10-30 J/K. There are, of course, a lot of individual organisms on the planet, so that number needs to be multiplied by the total number of evolving organism, which, again, we charitably overestimate at 1032, most of which are prokaryotes, of course. The final result is a number that tells us the total change in entropy of the planet caused by evolution each second:

-302 J/K

What does that number mean? We need a context. Styer also estimates the Earth’s total entropy throughput per second, that is, the total flux involved from absorption of the sun’s energy and re-radiation of heat out into space. It’s a slightly bigger number:

420 x 1012 J/K

To spell it out, there’s about a trillion times more entropy flux available than is required for evolution. The degree by which earth’s entropy is reduced by the action of evolutionary processes is miniscule relative to the amount that the entropy of the cosmic microwave background is increased.

This is very cool and very clear. I’m folding up my copy of Styer’s paper and tucking it into my copy of The Counter-Creationism Handbook, where it will come in handy.

Styer DF (2008) Entropy and evolution. Am J Phys 76(11):1031-1033.

The Mason’s Apprentice

My latest Seed column slipped quietly onto the interwebs last week — it’s an overview of how the glues that hold multicellular organisms together first evolved in single celled creatures, represented today by the choanoflagellates.

Just as a teaser, the next print edition that should be coming out soon will continue the focus on enlightening organisms of remarkable simplicity with a description of the results of the Trichoplax genome. Get it! You will also be rewarded with a great issue focusing on science policy.

The dumbification of Spore

As anyone who has followed computer games at all lately knows, Spore is the recently released computer game from Maxis that was initially touted as a kind of partial simulation of evolution. Unfortunately, It wasn’t a very good simulation of much of anything, and as a game it has only been a partial success, with some parts being quite entertaining and others deserving a resounding “meh”. (Disclaimer: I have the game, but haven’t bothered to install it yet; I’ve let Skatje play it for me, and I’ve read the reviews, and suffered a noticeable loss of enthusiasm from that exposure.)

Now there is a revealing inside view of the Spore development process, with some tantalizing hints of some really great stuff that was implemented in early versions of the game, that never made it to release. Here’s the problem: the developers divided into two competing/complementary teams with radically different goals, a “cute team” and a “science team”. Guess who won?

This was Spore’s central problem: Could the game be both scientifically accurate and fun? The prototyping teams were becoming lost in their scientific interests. Chaim Gingold, a team member who started as an intern and went on to help design the game’s content creation tools, recalls a summer spent playing with pattern language and cellular automata: “It was just about being engaged with the universe as a set of systems, and being able to build toys that manifested our fascination with these systems and our love for them.” But from within this explosion of experimental enthusiasm came an unexpected warning voice. Spore’s resident uber-geek and artificial intelligence expert Chris Hecker was having strong misgivings about how appealing all this hard science would be to the wider world. “I was the founding member of the ‘cute’ team,” he says with pride. “Ocean [Quigley, Spore’s art director] and Will were really the founding members of the ‘science’ team. Ocean would make the cell game look exactly like a petri dish with all these to-scale animals and Will would say, ‘That’s the greatest thing I’ve ever seen!’ and some of us were thinking, ‘I’m not sure about that.'”

(That, by the way, is from the Seed magazine article on the game. You’ve probably already seen it since you all subscribe, right?)

This is the annoying mantra of far too many people, from Barbie to Chris Hecker: “science is hard”. Yes, it is…and that’s what makes it fun! Games are also hard, if they’re any good — you often have to master difficult moves, arcane strategy, work fast or plan far ahead, or solve tricky puzzles, and that’s why we choose to play them, that’s the appeal. What I was looking for in Spore was for someone to take a look with a gamer’s eyes at the process of science and extract from it the puzzle-solving essence and make it approachable and entertaining; instead, they seem to have given up on the science and instead created animated plush dolls for amusement’s sake.

It’s a real shame. There is a little hope in an unlikely suggestion:

I hope that Maxis announces that it intends to rectify this odd deviation from their plan through expansion packs, including a complete overhaul of the Cell Stage and Creature Stage, at minimum. The forced linear progression of the game and forced evolution should also be removed from the Cell and Creature Stages, as it is not faithful to the freedom of the advertised product. (Evolution to a better brain should be optional, at least in the Creature Stage, as it was in the earlier videos.) I do not believe that we have a right to demand it be free, as the development costs of this game are already astronomical. This may have not been as much of a problem if they hadn’t been spending the past few years removing content.

Somebody at Maxis should have encouraged everyone to embrace the science. It could have been great. I don’t know why they didn’t, but I suspect that a bean counter somewhere noted that it never hurts to underestimate the intelligence of the buying public…and decided to embrace the lowest common denominator instead of aspiring to greatness.

Will the availability of C-sections give humans bigger brains?

Blogging on Peer-Reviewed Research

While Steve Jones might think human evolution has stopped, I have to say that that is impossible. If human technology removes a selective constraint, that doesn’t stop evolution — it just opens up a new degree of freedom and allows change to carry us in a novel direction.

One interesting potential example is the availability of relatively safe Cesarean sections. Babies have very big heads that squeeze with only great difficulty through a relatively narrow pelvis, so the relationship in size between head diameter and the diameter of the pelvic opening has been a limitation on human evolution. We know this had to be a factor in our evolution: the average newborn mammal has a cranial capacity that is roughly 50% of the adult size, chimpanzee babies have heads about 40% of the adult size, but human babies have crania that are only 23% of what they will be in adults. While our brains have gotten larger over evolutionary time, they have not gotten proportionally larger in utero, because large-headed babies increase the difficulty of labor and cause increased mortality in childbirth. If childbirth could bypass the pelvic bottleneck, that would allow for fetal heads to grow larger without increasing the risk of killing mother and/or child.

And childbirth is a risky proposition for women; 529,000 die every year from this natural process (although only about 1% of those deaths occur in places where women have access to good, modern medical facilities — hooray for modern medicine). About 8% of those deaths occur from obstructed labor, where the fetus is unable to proceed through the birth canal for various reasons, and these are the kinds of birth problems that can be circumvented by C-sections. In practice, teaching health care workers how to carry out emergency C-sections has been tested in regions in Africa, where it has actually worked well at reducing maternal mortality.

This is the subject of an article by Joseph Walsh in the American Biology Teacher, which suggests that C-sections will have an effect on human evolution.

“Nothing in biology makes sense except in the light of evolution.” This was the title of an essay by geneticist Theodosius Dobzhansky writing in 1973. Many causes have been given for the increased Cesarean section rate in developed countries, but biologic evolution has not been one of them. The C-section rate will continue to rise, because the ability to perform a safe C-section has liberated human childbirth from natural selection directed against too small a maternal pelvis and too large a fetal head. Babies will get bigger and pelves will get smaller because there is nothing to prevent it.

The evidence so far is entirely circumstantial, but Walsh makes an interesting case. There are several correlations that imply an effect, but I can’t help but think there are alternative explanations that may swamp out any heritable, evolutionary effect. The kinds of evidence he describes are:

  • A known trend for increasing birth weight in the US, by about 40 g over 18 years in one study. It’s there, all right, but these studies don’t demonstrate a genetic component to increased size — it could be a consequence of better nutrition and medical care.

  • An increasing frequency of C-sections. Again, this isn’t necessarily genetically based at all, but could be a consequence of fads in medicine, or social factors, such as an increase in the likelihood of medical malpractice suits making doctors more cautious.

  • Walsh describes a couple of studies that seem to show that cephalopelvic disproportion (small pelvis or large babies or both together) does have a genetic component. So at least it is likely that there are heritable variations in these parameters that could influence the likelihood of obstructed labor.

  • There is statistical variation in neo-natal mortality that varies with birth weight in a suggestive way. Low birth weight clearly puts infants at risk, and there is an optimum weight around 3600 grams for newborns that minimizes mortality. Death rates also rise with increasing birth weight above the optimum. There is some data that suggest that availablity of modern medical care and C-sections reduces infant mortality at larger birth weights.

That increasing availability of C-sections might lead to an evolutionary shift towards increasing cranial capacity at birth is a reasonable hypothesis, but I’m not convinced that it has been convincingly demonstrated yet. There are too many variables that effect brain size at birth to make a clean analysis possible; in addition, many of the measures are indirect. Often, we use birth weight as a proxy for cranial capacity, and that means the numbers and correlations are sloppier than they should be. Many of the measurements made are of factors that are readily influenced by the environment, which makes it difficult to imply that these are the product of genetics.

So the idea is weakly supported, but tantalizing. Even as a purely theoretical exercise, though, what it does say is that it is obvious that human culture cannot end human evolution…all it can do is shape the direction in which it can occur.

Walsh J (2008) Evolution & the Cesarean Section Rate. The American Biology Teacher 70(7):401-404.

Old scientists never clean out their refrigerators

Blogging on Peer-Reviewed Research

We all know the story of the Miller-Urey experiment. In 1953, a young graduate student named Stanley Miller ran an off-the-wall experiment: he ran water, methane, ammonia, and hydrogen in a sealed flask with a pair of electrodes to produce a spark, and from those simple building blocks discovered that more complex compounds, such as amino acids, were spontaneously produced. Stanley Miller died in 2007, and in going through his effects, the original apparatus was discovered, and in addition, several small sealed vials containing the sludge produced in the original experiment were also found.

This isn’t too surprising. I’ve gone through a few old scientists’ labs, and you’d be surprised at all the antiquities they preserved, all with notes documenting exactly what they are. It’s habit to keep this stuff.

Now the cool part, though: the scientists who unearthed the old samples ran them through modern analysis techniques, which are a bit more sensitive than the tools they had in the 1950s. In 1953, Miller reported the recovery of five amino acids from his experiment. The reanalysis found twenty two amino acids and five amines in the vials. He was more successful than he knew!

i-fd77777a341fb3ccad00b07dda6d2e80-miller.jpg
Moles (relative to glycine = 1) of the various amino acids
detected in the volcanic apparatus vials. Amino acids underlined have not been previously
reported in spark discharge experiments. Values for amines are minimum values because of loss due to their volatility during workup.

Yes, I know that Miller’s reducing atmosphere is no longer considered to be an accurate representation of the ancient earth’s atmosphere. However, the experiment still supported a key idea: that the synthesis of these organic compounds did not require any kind of guiding hand, but would naturally emerge from unassisted chemical reactions. Furthermore, the authors of this paper argue that while it was not a good model of the global atmosphere, it might still model local conditions in isolated areas.

Geoscientists today doubt that the primitive atmosphere had the highly reducing composition Miller used. However, the volcanic apparatus experiment suggests that, even if the overall atmosphere was not reducing, localized prebiotic synthesis could have been effective. Reduced gases and lightning associated with volcanic eruptions in hot spots or island arc-type systems could have been prevalent on the early Earth before extensive continents formed. In these volcanic plumes, HCN, aldehydes, and ketones may have been produced, which, after washing out of the atmosphere, could have become involved in the synthesis of organic molecules. Amino acids formed in volcanic island systems could have accumulated in tidal areas, where they could be polymerized by carbonyl sulfide, a simple volcanic gas that has been shown to form peptides under mild conditions.

So good work, Dr Miller!

Johnson AP, Cleaves HJ, Dworkin JP, Glavin DP, Lazcano A, Bada JL (2008) The Miller Volcanic Spark Discharge Experiment. Science 322(5900):404.

Why Evolution is True

I hope Jerry Coyne will forgive me that my frequent thought as I was reading his new book, Why Evolution Is True(amzn/b&n/abe/pwll) was, “Wow, this sure is easier to read than that other book.” That other book, of course, is Coyne and Orr’s comprehensive text on Speciation(amzn/b&n/abe/pwll), which is a technical and detailed survey of the subject in the title, and that I wouldn’t necessarily recommend to anyone who wasn’t at least a graduate student in biology. We all have our impressions colored by prior expectations, you know, and Jerry Coyne is that high-powered ecology and evolution guy at the University of Chicago whose papers I’ve read.

The new book is simple to summarize: just read the title. It’s aimed at a lay audience and answers the question of why biologists are so darned confident about the theory of evolution by going through a strong subset of the evidence. It begins with a discussion of what evolution is, then each subsequent chapter is organized around a class of evidence: fossils, embryology and historical accidents, biogeography, natural selection, sexual selection, speciation, and human evolution. If you want a straightforward primer in the experiments and observations that have made evolution the foundational principle of modern biology, this is the book for you.

Why Evolution is True makes an almost entirely positive case for evolution; it has an appropriate perspective on the current American conflict between science and religious fundamentalism that avoids dwelling on creationist nonsense, but still acknowledges where common misconceptions occur and where creationist PR, such as the Intelligent Design creationism fad, has raised stock objections. It’s a good strategy — the structure of this book is not dictated by creationist absurdities, but by good science, and creationism is simply noted where necessary and swatted down efficiently. It’s a more powerful tool for it, too — creationists can lie faster than anyone can rebut them, so the best strategy is to focus on the real evidence and force critics to address it directly.

You all really ought to pick up a copy of this book if you don’t already have a sound understanding of the basic lines of evidence for evolution (or, if you do, you could always get Speciation to get a little more depth). I recommend it unreservedly. Oh, except for one little reservation: it won’t be available until January. Go ahead and put it on your Amazon pre-order list, then.

Very peculiar

I’ve read Steve Jones’ books and enjoyed them — so I’m really baffled by this bizarre report of a talk he gave. It’s either a massive example of misreporting, or Jones has a solid grip on everyone’s ankles and he’s straining to pull our legs right off.

He claims human evolution is over. The reason? Because not enough fathers over 35 are having children. That’s bad because mutations are the source of evolutionary novelty, and older fathers are more likely to have accumulated errors in the replication of sperm, and therefore pass on more mutations.

This is because cell divisions in males increase with age. “Every time there is a cell division, there is a chance of a mistake, a mutation, an error,” he said. “For a 29-year old father [the mean age of reproduction in the West] there are around 300 divisions between the sperm that made him and the one he passes on – each one with an opportunity to make mistakes.

“For a 50-year-old father, the figure is well over a thousand. A drop in the number of older fathers will thus have a major effect on the rate of mutation.”

This is true, but it makes no sense. It’s not as if younger fathers produce no mutations — they generate plenty. It’s a difference in degree, nothing more, so we still have plenty of new mutations percolating into the population. And of course, over most of human history parents have been relatively young, since you couldn’t count on living to the age of 35.

And then there’s this odd argument.

Another factor is the weakening of natural selection. “In ancient times half our children would have died by the age of 20. Now, in the Western world, 98 per cent of them are surviving to 21.”

That makes even less sense. Natural selection is going to eliminate variants; by reducing its effects, we permit more mutations to persist in the population. One moment he’s complaining that fewer mutations are being produced, the next he’s complaining that the mutants are thriving. Which is it?

I’m thinking Jones must be making some colossal joke here, or maybe he’s testing his audience to see how much illogic and absurdity they will accept. That’s the only way I can explain these strange claims.

I see that Larry Moran has just thrown up his hands in exasperation at all the errors.

Watson/Wilson

There is good cause to be aggravated by some of James Watson’s recently expressed views, but he’s still an interesting fellow who made a significant contribution to our understanding of biology; and E.O. Wilson, of course, is always cool. So here they are together in an interview with Charlie Rose, discussing the significance of Charles Darwin:

(It was a little too gushy at the beginning — Darwin certainly did get some things very wrong! — but it’s still the kind of conversation it’s fun to hear.)

Anthropology of war

Last weekend’s bloggingheads was an interesting discussion between John Horgan and Brian Ferguson on the unfortunate misconception many people have about human evolution — the simplistic idea that evolution is always about selection for individuals who are better at killing their competitors. It doesn’t work that way! Ferguson discusses the interesting and obvious idea that the data does not back up the notion that being a great warrior is generally a good strategy, because being a great warrior also greatly increases the likelihood that you’ll end up dead.

Evolution is about whatever works, and often cooperation is a winning tactic.