Texas, again

That place is just a magnet for nuts. There is going to be a review of the science curriculum next month, and the creationists on the state board of education are gearing up by appointing more creationists to staff the panels. Furthermore, they’re gathering specific curriculum materials, and skewing them towards lunacy.

One submission has come from a company called International Databases, LLC. It’s a one-man operation run by Stephen Sample, who says he has a degree in evolutionary biology and taught at the high school and junior college levels for 15 years.

The material he submitted consists of eight modules dealing with current issues in biology and ecology. Most are well within the mainstream scientific consensus. But there are two that deal with the origin of life. Those sections say the “null hypothesis” is that there had to be some intelligent agency behind the appearance of living things. It is up to the scientists proposing a naturalistic explanation to prove their case.

International Databases, LLC is a grand name for a shell — all it is is those eight modules. There are collections of pdf files there that you can download, but don’t bother — they’re all password protected, so you won’t be able to read them. So all I have to go on is the summaries.

But that’s quite enough. The null hypothesis is that there is a super-intelligent, all powerful being manipulating the universe? Madness. How does one test against a hypothesis that is ill-defined, shifts constantly, and makes no specific predictions? “My null hypothesis is that god will or won’t affect the results of my experiment, depending on his mood, which I can’t measure.”

It’s just more stealth creationism, gussied up to look sciencey with a few abused science terms.

Kentucky pays off Ken Ham

Today was the day: Kentucky officially approved giving Ken Ham $43 million in tax breaks plus $11 million in road improvements. That’s a nice number; it’s about twice what Answers in Genesis sunk into their Creation “Museum” in total. Now they get double that back from the state, and they can use it to build their grandiose Ark Park.

There was only one surprise. Answers in Genesis brought up an alternative scenario, where they would build a slightly less flamingly insane version of the park. It doesn’t seem to have mattered, because the state seems to have stumbled all over themselves rushing to give the Hamites a big bucket of money, with no reservations.

Hunden divided his study under two scenarios for Ark Encounter. Under “Scenario A”, Ark Encounter would take a “mainstream approach”, where it “does not promote a creationist view of Biblical events that may turn off a portion of the potential market”. Under “Scenario B”, Ark Encounter would be full on Flintstone Truth, where kids are taught that a 600-year old herded T-Rexes onto a giant boat a few thousand years ago.

Now I know what you must be saying: “there’s no way that Ken Ham and Answers in Genesis would agree to Scenario A, as they make their living off of vilifying Christians who don’t take a 100% literal interpretation of the Bible and Young Earth Creationism”. First of all, you’re right. But when I questioned Hunden after the meeting about this, he said that AiG/AE assured them that they would consider doing this. In other words, Ken Ham has (as the title of his latest book is called and is about) Already Compromised. Yes, he agreed to abandon the core beliefs of everything he’s done throughout his entire career in order to not potential damage his ability to milk $43 million in tax breaks, plus the $11 million in state money for infrastructure at his park. Truly amazing that he would (1) agree to this, doubting the inerrant Word of God, and (2) that people would actually believe that they really considered this.

But back to the study. In the completely unrealistic fantasy of Scenario A, Hunden claimed that Ark Encounter would create 3,000 new full-time jobs over the next 10 years, 600-700 expected to be onsite. It would have a total fiscal impact of $103.4 million over 10 years and a yearly attendance of 1.24 million a year, in this fantasy world. But the numbers for Scenario B seem to be just as much a fantasy. Under Scenario B it would have a $53 million impact, and create 400-500 fewer jobs, and have a yearly attendance of 871,000.

Well, wait…it’s not just the unlikeliness of Ham actually compromising on his fanatically rigid views, but how do you take a park with a gigantic centerpiece of a life-size version of Noah’s Ark and make it any less of a Flintstone Truth? Its fundamental premises are all based on biblical literalism!

Evolution is a Jewish conspiracy

The essay starts off stupidly enough.

In 1867 Karl Marx dedicated DasKapital to Charles Darwin.

Actually, no, he didn’t. It’s a fairly common lie in creationist circles, though, just like the others sprinkled throughout the story.

Modern creation science is led by an array of top-flight Ph.D. scientists, including biochemists, paleontologists, astronomers and geologists. It presents a formidable battery of evidence now knocking hundreds of holes in traditional evolutionary arguments. As never before, scientific creationism debunks the contrived “evidence” that evolutionary theory has fed on since Darwin.

No, it isn’t. Creation science is led by a gang of ignorant clods who can’t read a paper without mangling it.

But OK, so far this is just your standard modus operandi for creationists. The really weird stuff is shouted out in the title: JEWISH SUPREMACISTS USE EVOLUTION TO CORRUPT MANKIND. Did you know that evolution is a Jewish conspiracy to corrupt Western civilization?

Why doesn’t the scientific community abandon Darwin’s failed hypotheses? Simple: The Jewish-dominated media and educational establishment are determined that, like unconditional support of Israel, Holocaust mythology, hate laws, and “civil rights” favoritism, there will be no end to the relentless force-feeding of evolution. Belief in evolution is a prerequisite for Jewish supremacism’s new-world order.

Yet anti-Zionist leadership on the right remains oblivious to the fact that evolution is the largest, ugliest, most aggressive tentacle of the Jewish revolutionary octopus. Anti-Zionists are often evolutionists, claiming that Jews evolved in a way that makes them inherently degenerate, subversive, and corruptive. They make the most Luciferian, dehumanizing fable ever invented by pseudo-science into a pillar of their thinking!

The Reverend Ted Pike is kind of obsessed with Jews. They’re behind everything.

You see, the degenerate Jews promote evolution, which led the Nazis to kill Jews, and we must organize resistance to the Jewish agenda and the Judaic threat, and we absolutely must support Israel without question. Every paragraph drips with anti-semitic bigotry, but at the same time he rants against the wicked anti-Zionists.

I’ve seen this often in fundamentalist Christians. Jews aren’t really people; they’re just props in the script of their eschatology. We have to keep them around because the True Final Solution is for Jesus to exterminate most of them and convert the survivors, and if we jump the gun and kill them all now, why, that would invalidate the Bible, which would be wicked.

The problem we face today originates in Jewish rebellion to Christ. It is primarily a moral issue which cannot be addressed by dehumanizing Jews or violence. It must be met with reason and persuasion, even love. The Bible presents Jewish apostasy as part of a long-range scenario that will ultimately result in anti-Christ world rule but also redemption of a remnant of Jews out of great tribulation at Christ’s second coming. The problem of Jewish supremacism ultimately is Christ’s problem, to be resolved by Him, not military or persecutive measures.

This is why Adolf Hitler and the Nazis must be damned. Not because they killed people, but because they lead us into “anti-biblical, evolutionary, racist errors”. We must support Israel because it’s a kind of holding pen for the Jews, where they will be annihilated in Armageddon, and you’re a bad, bad person if you begin the slaughter prematurely.

Despite the fact that I don’t have any evidence of any Jewish background in my lineage, I do have to cop to being an ugly evolutionary tentacle, and there are most certainly Jews in my readership. Does it make you feel all warm and happy and safe to peek into the minds of some of the most ardent Christian supporters of Israel?

Synthese scandal makes the New York Times

You may recall the furious debate among philosophers about a philosophy journal, Synthese, that made a tacit rebuke of critics of Intelligent Design creationism in an editorial added after acceptance of a number of papers on ID; it’s not just that they caved to creationist pressure, but that the editors-in-chief went over the heads of the working editors who assembled that issue of the journal to criticize excellent work by rational philosophers like Barbara Forrest. There has been a boycott of the journal; links to various commentaries on the issue can be found on a status page.

Well now the furor has hit the big time, with a summary article in the New York Times.

It’s clear from that article what the problem is: Francis Beckwith, weasely creationist apologist, got his butt hurt by a discussion of his role as a public enabler of bad science. I have long rolled my eyes at every mention of Beckwith — he’s a disingenuous creationist who struggles mightily to pretend that he’s a serious scholar arriving at serious conclusions, despite the fact that his conclusions always agree with those of professional liars and academic frauds. Did Barbara Forrest call him out on his history of baloney? Yes, she did. Is this a problem in an academic journal? I should hope not.

Reactions from Kamloops

The Kamloops News has obligingly published a couple of reactions to my appearance in their fair city. There is a very abbreviated summary of what I discussed on Friday: Prof shoots holes in creationism. Yes, that’s about right. I specifically addressed the fallacies of Intelligent Design creationism.

Now, though, the editor of the newspaper, Mel Rothenburger, has responded: Name callers are just stupid. He begins with this:

I didn’t take in the presentation by American associate professor Paul “PZ” Myers, and I’m glad.

Gosh, I’m chastened already. He objects to the fact that I said creationists were “ignorant and stupid and don’t know anything about history,” facts which I backed up in the talk. Also, facts which were then confirmed in his very own paper, by publishing a letter from David Buckna, the same ignorant, ahistorical creationist I mentioned in a previous post. He showed up with a double-sided list in small print of his objections to evolution; his letter is titled Some questions for Prof. Myers, and it is nothing but the first couple of points from his list.

On May 6 professor of biology P.Z. Myers (University of Minnesota Morris) gave a public lecture (Evolution is True; Intelligent Design Isn’t) in Kamloops.

Questions for Prof. Myers:

Edward Blyth, English chemist/zoologist (and creationist), wrote his first of three major articles on natural selection in The Magazine of Natural History, 24 years before Darwin’s “Origin of Species” was published. Why then, do evolutionists think of natural selection as Darwin’s idea?

Why do textbooks claim the 1953 Miller-Urey experiment shows how the cell’s building blocks may have formed on the early Earth, when repeated experimentation has never demonstrated this claim? Efforts to replicate the supposed origin-of-life events have produced embarrassingly small amounts of cell building blocks (eg. trace amounts of amino acids, sugars) with the majority of the mixture being a toxic tar.

On page one of Richard Dawkins’ 1986 book, The Blind Watchmaker, he writes: “Biology is the study of complicated things that give the appearance of having been designed for a purpose.” If living things look designed, then how do evolutionists know they weren’t designed? What is the criterion for “apparent” design?

How does geology explain dinosaur bones with soft tissue, supposedly dated at “80 million years”? (Schweitzer et al, Science 324:626). Bones with red blood cells, including hemoglobin, and blood vessels, which are still elastic.

Most geologists believe diamonds formed deep below the earth’s surface, one to three billion years ago. How do these geologists explain the presence of carbon-14 in a number of diamond samples?

How does evolution explain non-winged pterosaurs gradually developing fully functional wings, with its long bony fourth finger?

These are the very same questions I answered to his face in a two-hour session after my talk. The Schweitzer reference is the same one he has been haranguing me about in email ever since. I already answered him, and here he is simply disingenously repeating the same questions as if I’d never heard of them before. He’s dishonest and contemptible; he’s fairly typical of creationists.

There are answers to his questions in the comments in the paper. I’m not going to bother, since Buckna has amply demonstrated that he’s not going to accept any answer, but will continue to parrot the same oft-answered objections over and over again.

The saga of Junk DNA

So you’re tantalized by this strange obsession creationists have with junk DNA. It offends them mightily, I think because they find comfort in the idea that everything in the universe must have a purpose, because if it doesn’t, maybe that means they are nothing more than spots of dandruff on a dead rock hurtling blindly through space, and we can’t have that then.

It’s true that the odious Jonathan Wells has written a whole book declaring that everything in the genome has a glorious function implicitly designed by his god, the Rev. Sun Myung Moon. Larry Moran has begun the process of dismantling Wells, with, so far, three posts critiquing his claims, all well worth reading.

Osama bin Laden disproves Darwin!

Oh, yeah…didn’t you know it was a crack team of Darwinist commandos who took out bin Laden, all to protect our secrets? David Klinghoffer doesn’t go quite that far, but he does demonstrate just how insane the gang at the Discovery Institute have gotten. After all, he does claim that Obama delayed the raid on Osama in order to promote creationism.

President Obama is said to have known the whereabouts of Osama bin Laden since September but chose to wait until May to authorize action against him. Why the delay? Could it perhaps have been to provide a super-timely news hook for the rollout of Jonathan Wells’ new book, The Myth of Junk DNA? If so, an additional note of congratulation is owed to Mr. Obama.

How do you think OBL’s body was identified? By a comparison with his sister’s DNA, evidently those non-coding regions singled out by Darwin defenders, among the pantheon of other mythological evolutionary icons, as functionless “junk.” Indeed, the myth has featured in news coverage of Osama’s death. Reports the website of business magazine Fast Company:

Because your parents give you some of their DNA, they also give your siblings some of the same genetic code — which is why sibling DNA tests work. They sometimes concentrate on areas of the genome called “junk DNA” which serves no biological function but still gets passed along to offspring. By testing for repeat strands of DNA code in these areas, it’s possible to work out if two individuals are related as siblings.

Uh, what? Wells is quite possibly the worst and most dishonest “scholars” employed by the Discovery Institute; I’ve been thinking of picking up a copy of his book simply because it will be hilariously bad. He won’t have shown the utility of junk DNA, but I’m pretty sure he will have do a silly dance while trying to justify his claims…rather like Klinghoffer here.

The reason junk DNA is useful for identification purposes is that it varies so much — it is subject to random change at a higher rate than coding DNA, because it is not subject to functional constraints. It’s been called a genetic fingerprint, and that’s a useful comparison. Think about your fingerprints: you can make a general argument that a pattern of ridges creates a texture useful for gripping, but it’s not important that there be a particular whorl or loop at a specific place. Junk DNA also lacks any specific function, but the analogy only breaks down because it also doesn’t seem to have much of a general function, given that some species like Fugu have lost significant quantities of it. The one purpose I find plausible is that, since cell growth is regulated by the ratio of cytoplasm to nuclear volume, adding junk can lead to an overall increase in cell size.

Somehow, the creationist incomprehension of the basic science is used to argue that evolution didn’t happen.

If Darwin is right, there ought to be huge swaths of ancestral garbage cluttering the genome, serving no purpose other than to identify otherwise unidentified forensic remains. So if those huge swaths turn out after all to be vitally important to the functioning organism, what does that say about Darwin’s theory? Ah, that’s exactly the question addressed in Jonathan Wells’ book.

Hang on. Darwin had no molecular biology and no genetics, knew nothing about DNA, and didn’t even know that chromosomes carried genetic information … he postulated the existence of migratory particles called gemmules that were the units of heredity (he was completely wrong, by the way). His claim to fame is discovering and documenting a mechanism that shapes adaptive heritability, and if anything, he thought selection ought to hone the heritable factors, whatever they were, to a high degree of optimality.

And now the creationists want to argue that junk DNA is a Darwinian prediction? They’ve totally lost the plot.

Explain this to me. Darwin, in their confused minds, claims that there ought to be lots of junk having no purpose other than to identify dead bodies. Junk DNA is used to identify a specific dead body, bin Laden’s. Therefore, Darwin is wrong. Even if I grant them their premise (which I won’t, because it is stupid), this doesn’t work.

Let’s see how many Darwin lobbyists have the guts and honesty to acknowledge that another icon has fallen. They have not, on the whole, left themselves a lot of room for deniability on this.

Gibbering lunatics like Klinghoffer and Wells are actually rather easy to deny.

A nefarious plan

Another tawdry semi-biblical cesspit has opened, the Creation Museum of the Ozarks. Of course it gets horrible reviews.

Then I looked it up. It’s located in Strafford, Missouri, which is a town 20 minutes away from Springfield.

Springfield. What do we think of when we hear Springfield, Missouri? No, not the Assemblies of God. We think…Skepticon. Hey, you know what that means…

ROAD TRIP. Make it so, Skepticon organizers. Set aside some time for a godless invasion of your local creation “museum”.

The true story of the Archaean genetic expansion

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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.

One of the creationist summaries is by an intelligent design creationist. He looks at the paper and claims it supports this silly idea called front-loading: the Designer seeded the Earth with creatures that carried a teleological evolutionary program, loading them up with genes at the beginning that would only find utility later. The unsurprising fact that many gene families are of ancient origin seems to him to confirm his weird idea of a designed source, when of course it does nothing of the kind, and fits quite well in an evolutionary history with no supernatural interventions at all.

The other creationist summary is from an old earth biblical creationist who tries to claim that “explosive increase in biochemical capabilities happened in anticipation of changes that were to take place in the environment”, a conclusion completely unsupportable from the paper, and also tries to telescope a long series of changes documented in the data into a single ancient event so that they can claim that the rate of innovation was so rapid that it contradicts the “evolutionary paradigm”.

So lets take a look at the actual paper. Does it defy evolutionary theory in any way? Does it actually make predictions that fit creationist models? The answer to both is a loud “NO”: it is a paper using methods of genomic analysis that produce evolutionary histories, it describes long periods of gradual modification of genomes, and it correlates genomic innovations with changes in the ancient environment. It is freakin’ bizarre that anyone can look at this work and think it supports creationism, but there you are, standard operating procedure in the fantasy world of the creationist mind.

Here’s the abstract, so you can get an idea of the conclusions the authors draw from the work.

The natural history of Precambrian life is still unknown because of the rarity of microbial fossils and biomarkers. However, the composition of modern-day genomes may bear imprints of ancient biogeochemical events. Here we use an explicit model of macro- evolution including gene birth, transfer, duplication and loss events to map the evolutionary history of 3,983 gene families across the three domains of life onto a geological timeline. Surprisingly, we find that a brief period of genetic innovation during the Archaean eon, which coincides with a rapid diversification of bacterial lineages, gave rise to 27% of major modern gene families. A functional analysis of genes born during this Archaean expan- sion reveals that they are likely to be involved in electron-transport and respiratory pathways. Genes arising after this expansion show increasing use of molecular oxygen (P=3.4 x 10-8) and redox- sensitive transition metals and compounds, which is consistent with an increasingly oxygenating biosphere.

This work is an analysis of the distribution of gene families in modern species. Gene families, if you’re unfamiliar with the term, are collections of genes that have similar sequences and usually similar functions that clearly arose by gene duplications. A classic example of a gene family are the globin genes, an array of very similar genes that produce proteins that are all involved in the transport of oxygen; they vary by, for instance, their affinity for oxygen, so there is a fetal hemoglobin which binds oxygen more avidly than adult hemoglobin, necessary so the fetus can extract oxygen from the mother’s circulatory system.

So, in this paper, David and Alm are just looking at genes that have multiple members that arose by gene duplication and divergence. They explicitly state that they excluded singleton genes, things called ORFans, which are unique genes within a lineage. That does mean that their results underestimate the production of novel genes in history, but it’s a small loss and one the authors are aware of.

If we were looking for evidence for evolution, we might as well stop here. The existence of gene families, for cryin’ out loud, is evidence for evolution. This paper is far beyond arguing about the truth of evolution — that’s taken for granted as the simple life’s breath of biology — but instead asks a more specific question: when did all of these genes arise? And they have a general method for estimating that.

Here’s how it works. If, for example, we have a gene family that is only found in animals, but not in fungi or plants or protists or bacteria, we can estimate the date of its appearance to a time shortly after the divergence of the animal clade from all those groups. If a gene family is found in plants and fungi and animals, but not in bacteria, we know it arose farther back in the past than the animal-only gene families, but not so far back as a time significantly predating the evolution of multicellularity.

Similarly, we can also look at gene losses. If a gene family or member of a gene family is present in the bacteria, and also found in animals, we can assume it is ancient in origin and common; but if that same family is missing in plants, we can detect a gene loss. Also, if the size of the gene family changes in different lineages, we can estimate rates of gene loss and gene duplication events.

I’ve given greatly simplified examples, but really, this is a non-trivial exercise, requiring comparisons of large quantities of data and also analysis from the perspective of the topologies of trees derived from that data. The end result is that each gene family can be assigned an estimated date of origin, and that further, we can estimate how rapidly new genes were evolving over time, and put it into a rather spectacular graph.


(Click for larger image)
Rates of macroevolutionary events over time. Average rates of gene birth (red), duplication (blue), HGT (green), and loss (yellow) per lineage (events per 10 Myr per lineage) are shown. Events that increase gene count are plotted to the right, and gene loss events are shown to the left. Genes already present at the Last Universal Common Ancestor are not included in the analysis of birth rates because the time over which those genes formed is not known. The Archaean Expansion (AE) was also detected when 30 alternative chronograms were considered. The inset shows metabolites or classes of metabolites ordered according to the number of gene families that use them that were born during the Archaean Expansion compared with the number born before the expansion, plotted on a log2 scale. Metabolites whose enrichments are statistically significant at a false discovery rate of less than 10% or less than 5% (Fisher’s Exact Test) are identified with one or two asterisks, respectively. Bars are coloured by functional annotation or compound type (functional annotations were assigned manually). Metabolites were obtained from the KEGG database release 51.0 and associated with clusters of orthologous groups of proteins (COGs) using the MicrobesOnline September 2008 database28. Metabolites associated with fewer than 20 COGs or sharing more than two- thirds of gene families with other included metabolites are omitted.

Look first at just the red areas. That’s a measure of the rate of novel gene formation, and it shows a distinct peak early in the history of life, around 3 billion years ago. 27% of our genes are very, very old, arising in this first early flowering. Similarly, there’s a slightly later peak of gene loss, the orange area. This represents a period of early exploration and experimentation, when the first crude versions of the genes we use now were formed, tested, discarded if inefficient, and honed if advantageous.

But then the generation of completely novel genes drops off to a low to nonexistent rate (but remember, this is an underestimate because ORFans aren’t counted). If you draw any conclusions from the graph, it’s that life on earth was essentially done generating new genes about one billion years ago…but we know that all the multicellular diversity visible to our eyes arose after that period. What gives?

That’s what the blue and green areas tell us. We live in a world now rich in genetic diversity, most of it in the bacterial genomes, and our morphological diversity isn’t a product so much of creating completely new genes, but of taking existing, well-tested and functional genes and duplicating them (blue) or shuffling them around to new lineages via horizontal gene transfer (green). This makes evolutionary sense. What will produce a quicker response to changing conditions, taking an existing circuit module off the shelf and repurposing it, or shaping a whole new module from scratch through random change and selection?

This diagram gives no comfort to creationists. Look at the scale; each of the squares in the chart represents a half billion years of time. The period of rapid bacterial cladogenesis that produced the early spike is between 3.3 and 2.9 billion years ago — this isn’t some brief, abrupt creation event, but a period of genetic tinkering sprawling over a period of time nearly equal to the entirety of the vertebrate fossil record of which we are so proud. And it’s ongoing! The big red spike only shows the initial period of recruitment of certain genetic sequences to fill specific biochemical roles — everything that follows testifies to 3 billion years of refinement and variation.

The paper takes another step. Which genes are most ancient, which are most recent? Can we correlate the appearance of genetic functions to known changes in the ancient environment?

the metabolites specific to the Archaean Expansion (positive bars in Fig. 2 inset) include most of the compounds annotated as redox/e– transfer (blue bars), with Fe-S-binding, Fe-binding and O2-binding gene families showing the most significant enrichment (false discovery rate<5%, Fisher’s exact test). Gene families that use ubiquinone and FAD (key metabolites in respiration pathways) are also enriched, albeit at slightly lower significance levels (false discovery rate<10%). The ubiquitous NADH and NADPH are a notable exception to this trend and seem to have had a function early in life history. By contrast, enzymes linked to nucleotides (green bars) showed strong enrichment in genes of more ancient origin than the expansion.

The observed bias in metabolite use suggests that the Archaean Expansion was associated with an expansion in microbial respiratory and electron transport capabilities.

So there is a coherent pattern: genes involved in DNA/RNA are even older than the spike (vestiges of the RNA world, perhaps?), and most of the genes associated with the Archaean expansion are associated with cellular metabolism, that core of essential functions all extant living creatures share.

Were we done then, as the creationists would like to imply? No. The next major event in the planet’s history is called the Great Oxygenation Event, in which the fluorishing bacterial populations gradually changed the atmosphere, excreting more and more of that toxic gas, oxygen.

What happened next was a shift in the kinds of novel genes that appeared: these newer genes were involved in oxygen metabolism and taking advantage of the changing chemical constituents of the ocean.

Our metabolic analysis supports an increasingly oxygenated biosphere after the Archaean Expansion, because the fraction of proteins using oxygen gradually increased from the expansion to the present day. Further indirect evidence of increasing oxygen levels comes from compounds whose availability is sensitive to global redox potential. We observe significant increases over time in the use of the transition metals copper and molybdenum, which is in agreement with geochemical models of these metals’ solubility in increasingly oxidizing oceans and with molybdenum enrichments from black shales suggesting that molybdenum began accumulating in the oceans only after the Archaean eon16. Our prediction of a significant increase in nickel utilization accords with geochemical models that predict a tenfold increase in the concentration of dissolved nickel between the Proterozoic eon and the present day but conflicts with a recent analysis of banded iron formations that inferred monotonically decreasing maximum concentrations of dissolved nickel from the Archaean onwards. The abundance of enzymes using oxidized forms of nitrogen (N2O and NO3) also grows significantly over time, with one-third of nitrate-binding gene families appearing at the beginning of the expansion and three-quarters of nitrous-oxide-binding gene families appearing by the end of the expansion. The timing of these gene-family births provides phylogenomic evidence for an aerobic nitrogen cycle by the Late Archaean.

So I don’t get it. I don’t see how anyone can look at that diagram, with its record of truly ancient genomic changes and its evidence of the steady acquisition of new abilities correlated with changes in the environment of the planet, and declare that it supports a creation event or front-loading of biological potential in ancestral populations. That makes no sense. This is work that shouts “evolution” at every instant, yet some people want to pretend it’s an endorsement of theological hocus-pocus? Madness.

Scientists, you need to be aware of this. The David and Alm paper is an unambiguously evolutionary paper, using genomic data to describe evolutionary events via evolutionary mechanisms, and the creationists still appropriate and abuse it. If you publish anything about evolution, be sure to google your paper periodically — you may find that you’ve been unwittingly roped into endorsing creationism.

David LA, Alm EJ (2011) Rapid evolutionary innovation during an Archaean genetic expansion. Nature 469(7328):93-6.