PZ Myers Archives

Good news! The gorilla genome sequence was published in Nature last week, and adds to our body of knowledge about primate evolution. Here's the abstract:

Gorillas are humans' closest living relatives after chimpanzees, and are of comparable importance for the study of human origins and evolution. Here we present the assembly and analysis of a genome sequence for the western lowland gorilla, and compare the whole genomes of all extant great ape genera. We propose a synthesis of genetic and fossil evidence consistent with placing the human-chimpanzee and human-chimpanzee-gorilla speciation events at approximately 6 and 10 million years ago. In 30% of the genome, gorilla is closer to human or chimpanzee than the latter are to each other; this is rarer around coding genes, indicating pervasive selection throughout great ape evolution, and has functional consequences in gene expression. A comparison of protein coding genes reveals approximately 500 genes showing accelerated evolution on each of the gorilla, human and chimpanzee lineages, and evidence for parallel acceleration, particularly of genes involved in hearing. We also compare the western and eastern gorilla species, estimating an average sequence divergence time 1.75 million years ago, but with evidence for more recent genetic exchange and a population bottleneck in the eastern species. The use of the genome sequence in these and future analyses will promote a deeper understanding of great ape biology and evolution.

I've highlighted one phrase in that abstract because, surprise surprise, creationists read the paper and that was the only thing they saw, and in either dumb incomprehension or malicious distortion, took an article titled "Insights into hominid evolution from the gorilla genome sequence" and twisted it into a bumbling mess of lies titled "Gorilla Genome Is Bad News for Evolution". They treat a phenomenon called Incomplete Lineage Sorting (ILS) as an obstacle to evolution rather than an expected outcome.

Last week, I gave a talk at UNLV titled "A counter-revolutionary history of evo devo", and I'm afraid I was a little bit heretical. I criticized my favorite discipline. I felt guilty the whole time, but I think it's a good idea to occasionally step back and think about where we're going and where we should be going. It's also part of some rethinking I've been doing lately about a more appropriate kind of research I could be doing at my institution, and what I want to be doing in the next ten years. And yes, I want to be doing evo devo, so even though I'm bringing up what I see as shortcomings I still see it as an important field.

I think of myself as primarily a developmental biologist, someone who focuses on processes in embryos and is most interested molecular mechanisms that generate form and physiology. But I'm also into evolution, obviously, and recently have been trying to educate myself on ecology. And this is where the conflicts arise. Historically, there has been a little disaffection between evolution and development, and we can trace it right back to Richard Goldschmidt and the neo-Darwinian synthesis.

I've been guilty of teaching bean-bag genetics this semester. Bean-bag genetics treats individuals as a bag of irrelevant shape containing a collection of alleles (the "beans") that are sorted and disseminated by the rules of Mendel, and at its worst, assigns one trait to one allele; it's highly unrealistic. In my defense, it was necessary — first-year students struggle enough with the basic logic of elementary transmission genetics without adding great complications — and of course, in some contexts, such as population genetics, it is a useful simplification. It's just anathema to anyone more interested in the physiological and developmental side of genetics.

The heart of the problem is that it ignores the issue of translating genotype into phenotype. If you've ever had a basic genetics course, it's quite common to have been taught only one concept about the phenotype problem: that an allele is either dominant, in which case it is expressed as the phenotype, or it's recessive, in which case it is completely ignored unless it's the only allele present. This idea is so 19th century — it's an approximation made in the complete absence of any knowledge of the nature of genes.

I have read the entirety of Hamza Andreas Tzortzis' paper, Embryology in the Qur'an: A scientific-linguistic analysis of chapter 23: With responses to historical, scientific & popular contentions, all 58 pages of it (although, admittedly, it does use very large print). It is quite possibly the most overwrought, absurdly contrived, pretentious expansion of feeble post hoc rationalizations I've ever read. As an exercise in agonizing data fitting, it's a masterpiece.

Here, let me give you the short version…and I do mean short. This is a paper that focuses with obsessive detail on all of two verses from the Quran. You heard me right: the entirety of the embryology in that book, the subject of this lengthy paper, is two goddamned sentences, once translated into English.

We created man from an essence of clay, then We placed him as a drop of fluid in a safe place. Then We made that drop of fluid into a clinging form, and then We made that form into a lump of flesh, and We made that lump into bones, and We clothed those bones with flesh, and later We made him into other forms. Glory be to God the best of creators.

Seriously, that's it. You have just mastered all of developmental biology, as taught by Mohammed.

In my previous post, I described the misguided approach Gauger and Axe have taken to criticizing evolution, and one of the peculiarities of their criticism is that they cited another paper by a paper by Carroll, Ortlund, and Thornton which traced (successfully) the evolutionary history of a class of proteins. Big mistake. As I pointed out, one of the failings of the Gauger/Axe approach is that they're asking how one protein evolved into a cousin protein, without considering the ancestral history …they make the error of trying to argue that an extant protein couldn't have directly evolved into another extant protein, when no one argues that they did.

The tactical error is that right there in the very first paragraph of their paper, Carroll, Ortlund, and Thornton point out the fallacy of what the creationists were doing.

Direct comparisons among present-day proteins can sometime yield insights into the sequence and structural mechanisms that underlie functional differences. Such "horizontal" comparisons, however, cannot determine which protein features are ancestral and which are derived, so they are not suited to reconstructing the events that produced functional diversity.

They don't mention Gauger and Axe, of course — this paper was written before the creationists wrote theirs — but a methodological flaw is still spelled out plainly, the creationists reference it so I presume they read it, and they still charged ahead and did their flawed study, and then had the gall to claim their work was superior.

The Discovery Institute has me on a mailing list for their newsletter, Nota Bene. That's probably unwise: usually I just glance at it, see another ignorant bit of fluff from Luskin or Nelson or one of the other usual suspects, and I snigger and hit 'delete', but sometimes they brag about how they're really doing science, and I look a little closer. And then I might feel motivated to take a slap at them.

The latest issue contains an article by Ann Gauger, babbling about her recent publication disproving Darwinism, written with her colleague Douglas Axe, published in their tame 'science' journal, Bio-complexity, and edited by Michael Behe. It's not work that could survive in a real journal, I'm afraid.

This is one beautiful plesiosaur, Polycotylus latippinus.

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(A) Photograph and (B) interpretive drawing of LACM 129639, as mounted. Adult elements are light brown, embryonic material is dark brown, and reconstructed bones are white. lc indicates left coracoid; lf, left femur; lh, left humerus; li, left ischium; lp, left pubis; rc, right coracoid; rf, right femur; rh, right humerus; ri, right ischium; and rp, right pubis.

A lovely new dinosaur fossil from China is described in Nature today: it's named Xiaotingia zhengi, and it was a small chicken-sized, feathered, Archaeopteryx-like beast that lived about 155 million years ago. It shares some features with Archaeopteryx, and also with some other feathered dinosaurs.

That's not hyperbole. I really mean it. How else could I react when I open up the latest issue of Bioessays, and see this: Cephalopod origin and evolution: A congruent picture emerging from fossils, development and molecules. Just from the title alone, I'm immediately launched into my happy place: sitting on a rocky beach on the Pacific Northwest coast, enjoying the sea breeze while the my wife serves me a big platter of bacon, and the cannula in my hypothalamus slowly drips a potent cocktail of cocain and ecstasy direct into my pleasure centers…and there's pie for dessert. It's like the authors know me and sat down to concoct a title where every word would push my buttons.

The content is pretty good, too. It's not perfect; the development part is a little thin, consisting mainly of basic comparative embryology of body plans, with nothing at all really about deployment of and interactions between significant developmental genes. But that's OK. It's in the nature of the Greatest Science Papers Ever Written that stuff will have to be revised and some will be shown wrong next month, and next year there will be more Greatest Science Papers Ever Written — it's part of the dynamic. But I'll let it be known, now that apparently the scientific community is aware of my obsessions and is pandering to them, that the next instantiation needs more developmental epistasis and some in situs.

This paper, though, is a nice summary of the emerging picture of cephalopod evolution, as determined by the disciplines of paleontology, comparative embryology, and molecular phylogenetics, and that summary is internally consistent and is generating a good rough outline of the story. And here is that story, as determined by a combination of fossils, molecular evidence, and comparative anatomy and embryology.

I found a recent paper in Nature fascinating, but why is hard to describe — you need to understand a fair amount of general molecular biology and development to see what's interesting about it. So those of you who already do may be a little bored with this explanation, because I've got to build it up slowly and hope I don't lose everyone else along the way. Patience! If you're a real smartie-pants, just jump ahead and read the original paper in Nature.

A little general background.

Let's begin with an abstract map of a small piece of a strand of DNA. This is a region of fly DNA that encodes a gene called svb/ovo (I'll explain what that is in a moment). In this map, the transcribed portions of the DNA are shown as gray shaded blocks; what that means is that an enzyme called polymerase will bind to the DNA at the start of those blocks and make a copy in the form of RNA, which will then enter the cytoplasm of the cell and be translated into a protein, which does some work in the activities of that cell. So svb/ovo is a small piece of DNA which, in the normal course of events, will make a protein.

Phil Senter has published the most deviously underhanded, sneaky, subtle undermining of the creationist position I've ever seen, and I applaud him for it. What he did was to take them seriously, something I could never do, and treat their various publications that ape the form of the scientific literature as if they actually were real science papers, and apply their methods consistently to an analysis of taxonomy. So on the one hand, it's bizarre and disturbing to see the like of Ken Ham, Jerry Bergman, and Henry Morris get actual scientific citations, but on the other hand, seeing their claims refuted using their own touted methods is peculiarly satisfying.

Senter has published a paper in the Journal of Evolutionary Biology that takes their claims at face value and analyzes dinosaur morphology using their own methods. 'Baraminologists' have published a set of taxonomic tools that use as input a matrix of morphological characters for an array of animals, and then spits out numbers that tell whether they were similar enough to be related. You can guess what the motivation for that is: they want to claim that Noah didn't have to carry representatives of every dinosaur species on the Ark, but only representatives of each 'kind', which then diversified rapidly after the big boat landed to generate all the different species found in the fossil record.

The problem for them is that Senter found that it works far too well. Using creationist techniques, all of the Dinosauria reduce to…eight kinds. That makes the boat haulage problem relatively even easier.

I got a letter from a creationist today, claiming that "Darwinism is falsified," based on an article in Nature. It's kind of amazing; this article was just published today, and the metaphorical digital ink on it is barely metaphorically dry, and creationists are already busily mangling it.

It's a good article describing some recent fossil discoveries, found in a 515 million year old deposit in South Australia. Matthew Cobb has already summarized the paper, so I'll be brief on the details, but it's very cool. What was found was a collection of arthropod eye impressions, probably from cast-off molts. No sign of the bodies of these animals was found, suggesting that perhaps they were not fully sclerotized, or as the authors suggest, that disarticulated eyes were more prone to rapid phosphatization than eyes attached to a decaying body. There is no evidence of biomineralization, so these were animals with a very light armor of chitin alone.

I've been giving talks at scientific meetings on educational outreach — I've been telling the attendees that they ought to start blogs or in other ways make more of an effort to educate the public. I mentioned one successful result the other day, but we need more.

I give multiple reasons for scientists to do this. One is just general goodness: we need to educate a scientifically illiterate public. Of course, like all altruism, this isn't really recommended out of simple kindness, but because the public ultimately holds the pursestrings, and science needs their understanding and support. Another reason, though, is personal. Scientific results get mangled in press releases and news accounts, so having the ability to directly correct misconceptions about your work ought to be powerfully attractive. Even worse, though, I tell them that creationists are actively distorting their work. This goes beyond simple ignorance and incomprehension into the malign world of actively lying about the science, and it happens more often than most people realize.

I have another painful example of deviousness of creationists. There's a paper I've been meaning to write up for a little while, a Nature paper by David and Alm that reveals an ancient period of rapid gene expansion in the Archaean, approximately 3 billion years ago. Last night I thought I'd just take a quick look to see if anybody had already written it up, so I googled "Archaean genetic expansion," and there it was: a couple of references to the paper itself, a news summary, one nice science summary, and…two creationist distortions of the paper, right there on the first page of google results. I told you! This happens all the time: if there's a paper in one of the big journals that discusses more evidence for evolution, there is a creationist hack somewhere who'll quickly write it up and lie about it. It's a heck of a lot easier to summarize a paper if you don't understand it, you see, so they've got an edge on us.

My direct experience with prokaryotes is sadly limited — while our entire lives and environment are profoundly shaped by the activity of bacteria, we rarely actually see the little guys. The closest I've come was some years ago, when I was doing work on grasshopper embryos, and sterile technique was a pressing concern. The work was done under a hood that we regularly hosed down with 95% alcohol, we'd extract embryos from their eggs, and we'd keep them alive for hours to days in tissue culture medium — a rich soup of nutrients that was also a ripe environment for bacterial growth. I was looking at the development of neurons, so I'd put the embryo under a high-powered lens of a microscope equipped with differential interference contrast optics, and the sheet of grasshopper neurons would look like a giant's causeway, a field of tightly packed rounded boulders. I was watching processes emerging and growing from the cells, so I needed good crisp optics and a specimen that would thrive healthily for a good long period of time.

It was a bad sign when bacteria would begin to grow in the embryo. They were visible like grains of rice among the ripe watermelons of the cells I was interested in, and when I spotted them I knew my viewing time was limited: they didn't obscure much directly, but soon enough the medium would be getting cloudy and worse, grasshopper hemocytes (their immune cells) would emerge and do their amoeboid oozing all over the field, engulfing the nasty bacteria but also obscuring my view.

What was striking, though, was the disparity in size. Prokaryotic bacteria are tiny, so small they nestled in the little nooks between the hopper cells; it was like the opening to Star Wars, with the tiny little rebel corvette dwarfed by the massive eukaryotic embryonic cells that loomed vastly in the microscope, like the imperial star destroyer that just kept coming and totally overbearing the smaller targets. And the totality of the embryo itself — that's no moon. It's a multicellular organism.

Most of you don't understand evolution. I mean this in the most charitable way; there's a common conceptual model of how evolution occurs that I find everywhere, and that I particularly find common among bright young students who are just getting enthusiastic about biology. Let me give you the Standard Story, the one that I get all the time from supporters of biology.

Evolution proceeds by mutation and selection. A novel mutation occurs in a gene that gives the individual inheriting it an advantage, and that person passes it on to their children who also gets the advantage and do better than their peers, and leave more offspring. Given time, the advantageous mutation spreads through the population so the entire species has it.

One example is the human brain. An ape man millions of years ago acquired a mutation that made his or her brain slightly larger, and since those individuals were slightly smarter than other ape men, it spread through the population. Then later, other mutations occured and were selected for and so human brains gradually got larger and larger.

You either know what's wrong here or you're feeling a little uneasy—I gave you enough hints that you know I'm going to complain about that story, but if your knowledge is at the Evolutionary Biology 101 level, you may not be sure what it is.

I'm one of those dreadful animal-centric zoologically inclined biologists. Plants? What are those? Fungi? They're related to metazoans somehow. Lichens? Not even on the radar. The first step in fixing a problem, though, is recognizing that you have one. So I confess to you, O Readers, that my name is PZ, and I am a metazoaphile. But I can get better.

My path to opening up to wider horizons is to focus on what I find most interesting about animals, and that is that they are networks of cells driven by networks of genes that generate patterned responses of expression by cell signaling, or communication. See? I'm already a little weird. Show me a baby bunny, and I don't just see a cute little furry pal with an adorable twitchy nose, I see an organized and coherent array of differentiated tissues that arose by a temporal sequence of cell-cell interactions, and I just wanna open him up and play with his widdle epithelial sheets and dismantle his pwetty ducts and struts and fibers and fluids, oochy coo. And ultimately, I want to take apart each cell and ask why it has its particular assortment of genes switched off and on, and how its state affects its neighbors and the whole of the organism.

Which means, lately, that I've acquired a growing interest in bacteria. If I were 30 years younger, I could probably be seduced into a career in microbiology.

There are a couple of reasons why an animal-centric biologist would be interested in bacteria. One is the principle of it; the mechanisms that animal cells use to build complex arrangements of tissues were all first pioneered in single-celled organisms. We have elaborated and added details to gene- and cell-level phenomena, but it's a collection of significant quantitative differences, with nothing known that is essentially new in metazoan cells. All the cool stuff was worked out by evolution in the 3-4billion years before the Cambrian, a potential that simply blossomed in the past half-billion years into big conglomerations of cells. Understanding how the building blocks of multicellularity work individually ought to be a prerequisite to understanding how the assemblages work.

But there's another reason, too, a difference in perspective. It is our conceit to regard ourselves as individuals of Homo sapiens, a body of cells clonally derived from a single human cell. It's not true. It turns out that each one of us is actually a whole population of species, linked by our evolutionary history and lumbering through the world as a team. Genus Homo is also genera Escherichi and Bacteroidetes and Firmicutes and many others.

This is a sweet little story of evolutionary divergence, and a reunion. Of sorts.

A lot of people have been writing to me about this free webgame, CellCraft. In it, you control a cell and build up all these complex organelles in order to gather resources and fight off viruses; it's cute, it does throw in a lot of useful jargon, but the few minutes I spent trying it were also a bit odd — there was something off about it all.

Jonathan Sarfati, a particularly silly creationist, is quite thrilled — he's crowing about how he has caught Richard Dawkins in a fundamental error. The eye did not evolve, says Sarfati, because it is perfectly designed for its function, and Dawkins' suggestion that there might be something imperfect about it is wrong, wrong, wrong. He quotes Dawkins on the eye.

Well, more like great-great-many-times-great-aunt of all squid, but it's still a spectacular fossil. Behold the Cambrian mollusc, Nectocaris pteryx.

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Reconstruction of Nectocaris pteryx.