2 + 2 = 17, for certain values of 2

A while back, I responded to Behe/Luskin’s claim that his model proving the impossibility of evolution of chloroquinone resistance was vindicated. I pointed out (as did Ken Miller) that showing that a particular trait required multiple point mutations did not affect the probability in the naive way that Behe and Luskin calculated — in particular, it did not require that the mutations be simultaneous. We’re familiar with a great many known mutations that involve multiple sequential hits to have their effect. I mentioned the work on steroid receptor evolution, and how cancer is an amazing example of the power of the accumulation of sequential variants.

Behe fired back, issuing a challenge to ‘show my numbers’. If he could have said anything to confirm that he was obliviously ignoring my point, that was it, and so I blew him a raspberry and ignored his challenge. I wasn’t arguing with his numbers, and we could even use his very own set of numbers — my point was in the operation he was doing with those numbers. His assumption is that you must have two mutations occur simultaneously, in the same individual, so that you simplistically multiply the probabilities together to get an improbably low frequency. I’m saying that’s invalid: these mutations can happen independently, they can accumulate to some frequency in the population, and then a second mutation can occur.

Now Larry Moran has carried through on the calculations. Using the known data on mutation rates, and throwing away Behe’s bogus demand that everything occur in the very same instant, he shows that the evolution of chloroquinone resistance ought to be rare, but not at all impossible, and with frequencies that are in the ballpark of what is observed.

Furthermore, Moran describes a paper that quantifies the presence of malaria strains in the population that contain pieces of the resistant combinations and that further describe the sequential series of mutational events that led to the most resistant strains.

All of the strains (except D17) are found in naturally occurring Plasmodium populations and the probable pathways to each of the major chloroquine resistant strains are shown. It takes at least four sequential steps with one mutation becoming established in the population before another one occurs.

None of the mutations occurred simultaneously as Behe claimed in his book.

The intelligent design creationists are somehow still crowing victory. I don’t quite understand how — their premises have been demolished, they’ve been cut off at the knees, but I guess their followers are easily bamboozled if they shout “math!” loud enough. Even if the math is wrong.

There’s a secular argument for wearing underpants on your head. So?

Sarah Moglia points out that David Silverman has been saying some weird things recently.

Yesterday, an article was published about atheists at CPAC (Conservative Political Action Conference). Featured prominently in the article was Dave Silverman, president of American Atheists. In it, Dave was quoted as saying, “I will admit there is a secular argument against abortion. You can’t deny that it’s there, and it’s maybe not as clean cut as school prayer, right to die, and gay marriage.” Is that so?

I’m trying to figure out what this ‘secular argument’ actually is; he didn’t say. I have encountered anti-choice people tabling at an atheist convention, and they couldn’t say either — I got the impression these were actually religious people trying to evangelize to the atheists with a pretense, and they stood out oddly from the rest of the crowd…rather like an atheist shilling at CPAC. So speak up, Dave, tell us what these secular arguments are.

I’m also wary because in my business we’ve run into folks peddling religious bullshit under the guise of being secular before: we call them intelligent design creationists. No one is fooled. Similarly, the anti-choicers who claim to be making a rational secular argument are easy to see through, since they ultimately always rely on some magical perspective on the embryo.

But here’s the bottom line: it is not enough to make a purely secular argument. It has to also be a good argument, unless atheism is to become a smokescreen for nonsense, to be accepted purely because of its godless label. And then atheism might as well just be another religion.

Magic RNA editing!

One of those wacky Intelligent Design creationists (Jonathan McLatchie, an arrogant ignoramus I’ve actually met in Scotland) has a theory, which is his, to get around that obnoxious problem of pseudogenes. Pseudogenes are relics, broken copies of genes that litter the genome, and when you’ve got a gang of ideologues who are morally committed to the idea that every scrap of the genome is designed and functional, they put an obvious crimp in their claims.

So here’s this shattered gene littered with stop codons and with whole exons deleted and gone; how are you gonna call that “functional”, creationist? McLatchie’s solution: declare that it must still be functional, it’s just edited back into functionality. He uses the example of GULOP, a gene responsible for vitamin C synthesis, which is pretty much wrecked in us. Nonfunctional. Missing big bits. Scrambled. With missing regulatory elements, so it isn’t even transcribed. No problem: it’s just edited.

As I mentioned previously, the GULO gene in humans is rendered inactive by multiple stop codons and indel mutations. These prevent the mRNA transcript of the gene from being translated into a functional protein. If the GULO gene really is functional in utero, therefore, presumably it would require that the gene’s mRNA transcript undergo editing so that it can produce a functional protein. It’s not at all difficult to understand how this could occur.

Yes, RNA editing is a real thing. RNA does get processed before it’s translated into protein. McLatchie has a teeny-tiny bit of knowledge and is abusing it flagrantly.

I’ve hammered out dents in a car, and I’ve touched up rust spots with a little steel wool and a can of spray paint. My father was also an auto mechanic and could do wonders with a wrench. Auto repair exists, therefore…


…patching up that vehicle should be no problem at all, right? I expect to see it cruisin’ down the highway any time now.

Maybe two cans of spray paint this time…?

Historical and observational science

Dealing with various creationists, you quickly begin to recognize the different popular flavors out there.

The Intelligent Design creationists believe in argument from pseudoscientific assertion; “No natural process can produce complex specified information, other than Design,” they will thunder at you, and point to books by people with Ph.D.s and try to tell you they are scientific. They aren’t. Their central premise is false, and trivially so.

Followers of Eric Hovind I find are the most repellently ignorant of the bunch. They love that presuppositional apologetics wankery: presuppose god exists, therefore god exists. It’s like debating a particularly smug solipsist — don’t bother.

The most popular approach I’ve found, though, is the one that Ken Ham pushes. It’s got that delightful combination of arrogant pretense in which the Bible-walloper gets to pretend he understands science better than scientists, and simultaneously allows them to deny every scientific observation, ever. This is the argument where they declare what kinds of science there are, and evolutionary biologists are using the weak kind, historical science, while creationists are only using the strong kind, observational science. They use the distinction wrongly and without any understanding of how science works, and they inappropriately claim that they’re doing any kind of science at all.

A recent example of this behavior comes from Whirled Nut Daily, where I’m getting double-teamed by Ray Comfort and Ken Ham (don’t worry, I’m undaunted by the prospect of being ganged up on by clowns.)

According to Ken Ham’s blog at Answers in Genesis, Minnesota professor PZ Myers, who was interviewed by Comfort, said: “Lie harder, little man … Ray Comfort is pushing his new creationist movie with a lie. … What actually happened is that I briefly discussed the evidence for evolution – genetics and molecular biology of fish, transitional fossils, known phylogenies relating extant groups, and experimental work on bacterial evolution in the lab, and Ray comfort simply denied it all – the bacteria were still bacteria, the fish were still fish.”

But Ham explained that Comfort “asks a question something like this: ‘Is there scientific evidence – observable evidence – to support evolution?’ Well, none of them could provide anything remotely scientific. Oh, they give the usual examples about changes in bacteria, different species of fish (like stickleback fish) and, as to be expected, Darwin’s finches. But as Ray points out over and over again in ‘Evolution vs. God,’ the bacteria are still bacteria, the fish are still fish, and the finches are still finches!”

Isn’t that what I said? I gave him evidence, which he denied by falling back on a typological fallacy: the bacteria are still bacteria. What he refuses to recognize is that they were quantitatively different bacteria, physiologically and genetically. To say that something is still X, where X is an incredibly large and diverse group like fish and bacteria, is to deny variation and diversity, observable properties of the natural world which are the fundamental bedrock of evolutionary theory.

But the giveaway is that brief phrase “scientific evidence — observational evidence”. That’s where the real sleight of hand occurs: both Comfort and Ham try to claim that that all the evidence for evolution doesn’t count, because it’s not “observational”. “Were you there?” they ask, meaning that the only evidence they’ll accept is one where an eyewitness sees a complete transformation of one species to another. That is, they want the least reliable kind of evidence, for phenomena that are not visual. They’re freakin’ lying fools.

All scientific evidence is observational, but not in the naive sense that all that counts is what you see with your eyes. There is a sense in which some science is regarded as historical, but it’s not used in the way creationists do; it does not refer to science that describes events in the past.

Maybe some examples will make that clearer.

We can reconstruct the evolutionary history of fruit flies. We do this by observation. That does not mean we watch different species of fruit flies speciate before our eyes (although it has been found to occur in reasonable spans of time in the lab and the wild), it means we extract and analyze information from extant species — we take invisible genetic properties of the flies’ genomes and turn them into tables of data and strings of publishable code. We observe patterns in their genetics that allow us to determine patterns of historical change. Observation and history are intertwined. To deny the history is to deny the observations.

Paleontology is often labeled a historical science, but it doesn’t have the pejorative sense in which creationists use it, and it is definitely founded in observation. For instance, plesiosaurs: do you think scientists just invented them? No. We found their bones — we observed their remains imbedded in rock — and further, we found evidence of a long history of variation and diversity. The sense in which the study of plesiosaurs is historical is that they’re all extinct, so there are no extant forms to examine, but it is still soundly based on observation. Paleontology may be largely historical, but it is still a legitimate science built on observation, measurement, and even prediction, and it also relies heavily on analysis of extant processes in geology, physics, and biology.

The reliance on falsehoods like this bizarre distinction between observational and historical science that the Hamites and Comfortians constantly make is one of the reasons you all ought to appreciate my saintly forebearance, because every time I hear them make it, I feel a most uncivilized urge to strangle someone. I suppress it every time, though: I just tell myself it’s not their fault their brains were poisoned by Jesus.

The last intelligent creationist


Earlier today, Maggie Koerth-Baker posted this tweet:

I dig this graph, but I think it misses an outreach opportunity by ascribing common misconceptions to creationists only bouncingdodecahedrons.tumblr.com/post/17808416988

It links to a diagram showing evolution as a linear path rather than a branching tree, and it got me thinking about terribly popular misconceptions about evolution that were started by smart people, and a doozy came to mind. A whole collection of doozies, actually, from one single terribly clever person.

You’ve all heard the stupid creationist objection to evolution — “if evolution is true, how come there are still monkeys?” — but have you ever wondered who the first person to come up with that criticism was? You might be surprised.

The first instance I’ve been able to find was by Richard Owen, head of the British Museum and one of the premiere scientists of his day, and it was said in a rather notorious review of Darwin’s Origin, published in the Edinburgh Review in 1860. So not a stupid fellow, but one with an axe to grind, and also a creationist…but then, just about everyone was a creationist in 1860. Still, it’s a remarkable document.

Some background you need to know, though. This review was authored by Owen. When it needs to cite a scientist for its claims, it cites…Professor Richard Owen. It does so 11 times. Reading it with knowledge of its authorship really diminishes its authority to an amazing degree, and greatly inflates Owen’s appearance of pomposity.

It’s also an agonizing read. Darwin sometimes sounds a bit quaint and wordy nowadays, but at least he’s lucid and logical, and his writing flows well: I found Owen’s review to be a rough read, turgid and inelegant. I know I’ve got a bit of a bias which colors my opinion, but seriously, when you read the excerpt below, you’ll see what I mean.

On the other hand, if you read the whole thing, you’ll be struck by how it uses a whole collection of arguments that sound little different than what creationists say now, but that it is considerably more erudite. I hate to give them advice, but if creationists tossed out the trash written by Gish and Ham and any of the hacks at the Discovery Institute, and just regurgitated Owen’s words, there is a great deal that most of the warriors for evolution would have a tough time rebutting. Owen knew a lot of zoology, and he deploys it effectively to buttress some fundamentally flawed arguments.

Like this one. He doesn’t literally say “if evolution is true, how come there are still monkeys?” — he uses much more obscure examples and far more convoluted language, but it’s the same sentiment.

But has the free-swimming medusa, which bursts its way out of the ovicapsule of a campanularia, been developed out of inorganic particles? Or have certain elemental atoms suddenly flashed up into acalephal form? Has the polype-parent of the acalephe necessarily become extinct by virtue of such anomalous birth? May it not, and does it not proceed to propagate its own lower species in regard to form and organisation, notwithstanding its occasional production of another very different and higher kind. Is the fact of one animal giving birth to another not merely specifically, but generically and ordinally, distinct, a solitary one? Has not Cuvier, in a score or more of instances, placed the parent in one class, and the fruitful offspring in another class, of animals? Are the entire series of parthenogenetic phenomena to be of no account in the consideration of the supreme problem of the introduction of fresh specific forms into this planet? Are the transmutationists to monopolise the privilege of conceiving the possibility of the occurrence of unknown phenomena, to be the exclusive propounders of beliefs and surmises, to cry down every kindred barren speculation, and to allow no indulgence in any mere hypothesis save their own? Is it to be endured that every observer who points out a case to which transmutation, under whatever term disguised, is inapplicable, is to be set down by the refuted theorist as a believer in a mode of manufacturing a species which he never did believe in, and which may be inconceivable?

Doesn’t it sound so much more intelligent to ask, if evolution is true, why haven’t inorganic particles evolved into free-swimming medusae, and hey, why are there still polype-parents of the acalephe? Why aren’t we observing new forms bursting up out of the inanimate world in the same way they must have in Darwin’s version of the past?

The intelligent design creationists are also missing an opportunity. This is one of my favorite parts: Owen is snidely berating Darwin for thinking up this cunning new mechanism and then discarding the other ‘scientific’ mode of biological change…that is, divine creation. Transmutationists, as he calls evolutionists, are unable to see other ways that creation might work. “You can’t handle the truth!” is what he’s saying here.

Here it is assumed, as by Mr. Darwin, that no other mode of operation of a secondary law in the foundation of a form with distinct specific characters, can have been adopted by the Author of all creative laws that the one which the transmutationists have imagined. Any physiologist who may find the Lamarckian, or the more diffused and attenuated Darwinian, exposition of the law inapplicable to a species, such as the gorilla, considered as a step in the transmutative production of man, is forthwith clamoured against as one who swallows up every fact and every phenomenon regarding the origin and continuance of species ‘in the gigantic conception of a power intermittently exercised in the development, out of inorganic elements, of organisms the most bulky and complex, as well as the most minute and simple.’ Significantly characteristic of the partial view of organic phenomena taken by the transmutationists, and of their inadequacy to grapple with the working out and discovery of a great natural law, is their incompetency to discern the indications of any other origin of one specific form out of another preceding it, save by their way of gradual change through a series of varieties assumed to have become extinct.

Similarly, Owen siezes on Darwin’s remark that all life descended from one primordial form “into which life was first breathed” to chastise him for limiting god:

By the latter scriptural phrase, it may be inferred that Mr. Darwin formally recognises, in the so-limited beginning, a direct creative act, something like that supernatural or miraculous one which, in the preceding page, he defines, as ‘certain elemental atoms which have been commanded suddenly to flash into living tissues.’ He has, doubtless, framed in his imagination some idea of the common organic prototype; but he refrains from submitting it to criticism. He leaves us to imagine our globe, void, but so advanced as to be under the conditions which render life possible; and he then restricts the Divine power of breathing life into organic form to its minimum of direct operation.

I have some sympathy for this argument, and I think Darwin himself regretted making that one concession, because as we can see, creationists will sieze any excuse to invoke their personal god.

There’s also a section where he chides Darwin for not giving enough credit to Lamarck, and another where he favorably cites Buffon for his idea that species are mutable to a limited degree (Owen himself accepted some range of change over time), and calculated that all mammals could be reduced to 15 basic stocks. Creationists calculating storage space on the ark, take notice.

So yes, a lot of creationist arguments have their source not in really stupid people, but in some very intelligent and scientifically conservative people in the past. The problem is that modern creationists are clinging to rotten antique ideas that have long been dismantled. I’d also point out that creationist arguments have decayed: Owen’s writing, opaque and pretentious as it is, is far more challenging than anything I’ve seen from his degraded intellectual descendants.

I think if I were teaching a course in anti-creationism, I’d give this essay to my students and we’d spend about a week taking it apart — it would be a good exercise for them. And oh, they would hate me for it.

The Genetic Code is not a synonym for the Bible Code

Oh, boy. The Intelligent Design creationists are all excited about a new paper that purports to have identified an intelligent signal in the genetic code.

Here’s a new paper that can be added to the growing stack of intelligent-design articles in peer-reviewed journals. Even though the authors do not use the phrase “intelligent design,” their reasoning centers on the detection of an intelligent signal embedded in the genetic code — a mathematical and semantic message that cannot be accounted for by a natural cause, “be it Darwinian, Lamarckian,” chemical affinities or energetics, or any other.

I’ve read the paper by ShCherbak and Makukov, and by golly, the Discovery Institute flack really has accurately summarized the paper: it does explicitly and clearly claim to have identified evidence of design in the genetic code! That’s newsworthy in itself, that the creationists can accurately summarize a scientific paper…as long as the results conform to their ideological expectations.

Unfortunately, what they’ve so honestly described is good old honest garbage.

Here’s the short summary of what they do: they jigger the identities of the amino acids coded for by each codon into a number, a nucleon sum. What is that, you might ask? It’s determined by adding up the number of protons and neutrons in the amino acid, which is simply the mass number of the compound. Further, you can distinguish the amino acid into it’s R group, and the atoms that make up the peptide chain proper, which he calls the B group, for standard block. The mass number of the B group is always 74, except for proline, so he transfers a hydrogen from the R group to the proline B group to bring it up to 74, and by the way, did you notice that 74 is two times 37, which is a prime number? Now if you take all the three-digit decimals with identical digits (111, 222, 333…999), and sum their digits (111=3, 222=6, 333=9, etc.) you get the quotient of the number divided by…37!!!1!!

Are you impressed yet? This is simply numerology, juggling highly derived quantities that have little to do with functional properties of the molecules to come up with arbitrary numerical relationships, and then claiming that they’re somehow significant. They also play games with the sums of the mass numbers of just the R groups for certain codons, adding or subtracting the B number, finagling things until they get numbers that are evenly divisible by their magic prime number of 37, etc. It’s pure nonsense through and through.

But every once in a while, something sensible emerges out of the murk. Here’s the logic of their argument:

To be considered unambiguously as an intelligent signal, any patterns in the code must satisfy the following two criteria: (1) they must be highly significant statistically and (2) not only must they possess intelligent-like features, but they should be inconsistent in principle with any natural process, be it Darwinian or Lamarckian evolution, driven by amino acid biosynthesis, genomic changes, affinities between (anti)codons and amino acids, selection for the increased diversity of proteins, energetics of codon-anticodon interactions, or various pre-translational mechanisms.

(1) is simply saying that there must be a pattern of some sort — if the code were purely random assignment of arbitrary nucleotides to each amino acid, it wouldn’t be much of a sign — it would suggest that the sequence is noise, not signal. (2) is the really hard part, the one where you’d have to do a lot of work: you’d have to show that natural processes did not contribute to the pattern. They do not do that. They can’t do that. They take a different and curious tack.

They literally argue that because organizing the code by their nucleon sums makes no sense and has no reasonable functional consequences…therefore it must be an artificial and intentional feature. I’ve heard this argument before. It’s called the Chewbacca defense. Ladies and gentlemen, think about it: that does not make sense! If nucleon numbers show a mathematical pattern of any kind in their relationship to codons, you must accept the existence of a designer.

However, if we can show a natural property that leads to the organization of the genetic code, then I’m afraid their argument evaporates. Even more so than building an argument on the Chewbacca defense, that is.

There’s a very good discussion of the genetic code in Nick Lane’s book, Life Ascending: The Ten Great Inventions of Evolution, and I’ll briefly summarize it.

First, there is a pattern to the genetic code! No one has ever denied that; it’s obviously not the case that amino acids are randomly assigned to trios of nucleotides. Here’s the code:


Let’s look at one amino acid, glycine (Gly), down in the bottom right corner. The genetic code is degenerate: that means that most amino acids have multiple combinations of nucleotides that can specify them. Glycine’s codes are GGU, GGC, GGA, and GGG. Do you see a pattern? The code is actually GG_, where the third position has a lot of slack or wobble, and any nucleotide will do. We see similar cases where just the first two nucleotides are sufficient to specify leucine, valine, serine, proline, threonine, alanine, and arginine. Even with the other amino acids, there are some constraints; CA_ can identify histidine or glutamine, but if the third letter is a pyrimidine (U or C), you get histidine, while if it’s a purine (A or G), you get glutamine. There are patterns all over the place here! So of course ShCherbak and Makukov could find evidence of significant organization.

But there’s more. There are other rules associated with this pattern.

In the synthesis of these amino acids, biochemistry typically modifies a raw starting material. The first letter of the codon says something about the biosynthesis of the associated amino acid.

If the first letter is:
• C, then the amino acid is derived from alpha-ketoglutarate.
• A, then the amino acid is derived from oxaloacetate.
• T, then the amino acid is derived from pyruvate.
• G, then the amino acid is derived in a single step from simple precursors.

The second letter of the codon is correlated with chemical properties of the amino acid.

If the second letter is:
• A, then the amino acid is hydrophilic.
• T, then the amino acid is hydrophobic.
• G or C, the amino acid has an intermediate hydrophobicity.

Wait…so there’s a pattern to the genetic code, and that pattern is associated with the physical properties of the amino acids? Why, that makes sense. Chewbacca is routed! The most likely origin of the code lies in likely catalytic properties of dinucleotides; pairs of nucleotides in ancient organisms were initially functioning as proto-enzymes before they were incorporated into strings of coding information. At least that provides a historical physico-chemical route to the particular code we now have that does not require weird numerological masturbation.

It’s rather pathetic that the Discovery Institute thinks this is a beautiful piece of science. It’s not. It’s nonsense. But look how the DI spins this story:

How will evolutionists respond to this paper? It’s hard to see how they could dismiss it. Maybe they will try to mock it as old Arabian numerology, or religiously inspired (since Kazakhstan, which funded the study, is 70% Muslim). Those would be unfair criticisms. The authors have Russian names, certified doctorates, and wrote in collaboration with leading lights in the West. Or perhaps critics could argue that the authors hail from a foreign country whose name has too many adjacent consonants in it to take them seriously.

No, it appears the only way out for Darwinists would be the “Dawkins Dodge.” You may remember that one from the documentary Expelled, where Dawkins admits the possibility of panspermia for Earth, so long as the designers themselves evolved by a Darwinian process.

What’s most notable about this paper is the similarity in design reasoning between the authors and the more familiar advocates of intelligent design theory. No appeals to religion or religious texts; no identifying the designer; just logical reasoning from effect to sufficient cause. The authors even applied the “design filter” by considering chance and natural law, including natural selection, before inferring design.

If Darwinists want to go on equating intelligent design with creationism, they will now have to take on the very secular journal Icarus.

I didn’t even consider the religious or ethnic basis of this study; it didn’t come to mind at all. It is clearly simple stupid numerology, though. Look at the rationale given for all of the conclusions, which consist entirely of mathematical manipulations of arbitrary derived properties of the molecules, to arrive at a claim of prime number significance.

We certainly don’t need to invoke panspermia. Nothing in the genetic code requires design. and the authors haven’t demonstrated otherwise.

I am most amused by the cute parallelism of claiming surprise that the authors of this paper use “design reasoning” similar to that used by American Intelligent Design creationists. They’ve been slinging this slop for decades; why be impressed that another set of Intelligent Design creationists in Kazakhstan are using the same tired tropes?

I’m also not impressed with the failure of implementation of their logic. OK, they have a ‘design filter’ that they apply, but so what? Their methods failed to recognize a well-known functional association in the genetic code; they did not rule out the operation of natural law before rushing to falsely infer design.

And that last bit…I don’t care what journal it was published in. The prestige of a journal does not confer infallibility, and even the best of journals will occasionally publish crap. They will be especially likely to publish garbage when they stretch beyond the expertise of their reviewers. Icarus is a journal of planetary science that publishes primarily on astronomy and geology. This particular paper conveniently falls between the cracks — it’s a weird paper full of trivial arithmetical manipulations for arcane purposes with no scientific justification for any of its procedures. I don’t know how it got accepted for publication, other than by boring the reviewers with its incomprehensible digit fiddling.

One last thing: don’t rush to claim a secular purpose behind this work. It’s already been appropriated by freaky strange religious fanatics and lovers of the bible codes. You can’t blame shCherbak directly for this weirdo’s interpretations, but certainly he isn’t far from his temperament.

The facts presented on this site, when combined with those now revealed to us by shCherbak, constitute invincible evidence of the truth of the Judeo-Christian Scriptures, and of the Being and Sovereignty of their Divine Author.

Yeah, numerology. Nothing but wanking over tables.

Larry Moran has more — it turns out that Uncommon Descent and Cornelius Hunter also liked this paper. Flies are drawn to shit, I guess.

ENCODE gets a public reaming

I rarely laugh out loud when reading science papers, but sometimes one comes along that triggers the response automatically. Although, in this case, it wasn’t so much a belly laugh as an evil chortle, and an occasional grim snicker. Dan Graur and his colleagues have written a rebuttal to the claims of the ENCODE research consortium — the group that claimed to have identified function in 80% of the genome, but actually discovered that a formula of 80% hype gets you the attention of the world press. It was a sad event: a huge amount of work on analyzing the genome by hundreds of labs got sidetracked by a few clueless statements made up front in the primary paper, making it look like they were led by ignoramuses who had no conception of the biology behind their project.

Now Graur and friends haven’t just poked a hole in the balloon, they’ve set it on fire (the humanity!), pissed on the ashes, and dumped them in a cesspit. At times it feels a bit…excessive, you know, but still, they make some very strong arguments. And look, you can read the whole article, On the immortality of television sets: “function” in the human genome according to the evolution-free gospel of ENCODE, for free — it’s open source. So I’ll just mention a few of the highlights.

I’d originally criticized it because the ENCODE argument was patently ridiculous. Their claim to have assigned ‘function’ to 80% (and Ewan Birney even expected it to converge on 100%) of the genome boiled down to this:

The vast majority (80.4%) of the human genome participates in at least one biochemical RNA- and/or chromatin-associated event in at least one cell type.

So if ever a transcription factor ever, in any cell, bound however briefly to a stretch of DNA, they declared it to be functional. That’s nonsense. The activity of the cell is biochemical: it’s stochastic. Individual proteins will adhere to any isolated stretch of DNA that might have a sequence that matches a binding pocket, but that doesn’t necessarily mean that the constellation of enhancers and promoters are present and that the whole weight of the transcriptional machinery will regularly operate there. This is a noisy system.

The Graur paper rips into the ENCODE interpretations on many other grounds, however. Here’s the abstract to give you a summary of the violations of logic and evidence that ENCODE made, and also to give you a taste of the snark level in the rest of the paper.

A recent slew of ENCODE Consortium publications, specifically the article signed by all Consortium members, put forward the idea that more than 80% of the human genome is functional. This claim flies in the face of current estimates according to which the fraction of the genome that is evolutionarily conserved through purifying selection is under 10%. Thus, according to the ENCODE Consortium, a biological function can be maintained indefinitely without selection, which implies that at least 80 − 10 = 70% of the genome is perfectly invulnerable to deleterious mutations, either because no mutation can ever occur in these “functional” regions, or because no mutation in these regions can ever be deleterious. This absurd conclusion was reached through various means, chiefly (1) by employing the seldom used “causal role” definition of biological function and then applying it inconsistently to different biochemical properties, (2) by committing a logical fallacy known as “affirming the consequent,” (3) by failing to appreciate the crucial difference between “junk DNA” and “garbage DNA,” (4) by using analytical methods that yield biased errors and inflate estimates of functionality, (5) by favoring statistical sensitivity over specificity, and (6) by emphasizing statistical significance rather than the magnitude of the effect. Here, we detail the many logical and methodological transgressions involved in assigning functionality to almost every nucleotide in the human genome. The ENCODE results were predicted by one of its authors to necessitate the rewriting of textbooks. We agree, many textbooks dealing with marketing, mass-media hype, and public relations may well have to be rewritten.

You may be wondering about the curious title of the paper and its reference to immortal televisions. That comes from (1): that function has to be defined in a context, and that the only reasonable context for a gene sequence is to identify its contribution to evolutionary fitness.

The causal role concept of function can lead to bizarre outcomes in the biological sciences. For example, while the selected effect function of the heart can be stated unambiguously to be the pumping of blood, the heart may be assigned many additional causal role functions, such as adding 300 grams to body weight, producing sounds, and preventing the pericardium from deflating onto itself. As a result, most biologists use the selected effect concept of function, following the Dobzhanskyan dictum according to which biological sense can only be derived from evolutionary context.

The ENCODE group could only declare function for a sequence by ignoring all other context than the local and immediate effect of a chemical interaction — it was the work of short-sighted chemists who grind the organism into slime, or worse yet, only see it as a set of bits in a highly reduced form in a computer database.

From an evolutionary viewpoint, a function can be assigned to a DNA sequence if and only if it is possible to destroy it. All functional entities in the universe can be rendered nonfunctional by the ravages of time, entropy, mutation, and what have you. Unless a genomic functionality is actively protected by selection, it will accumulate deleterious mutations and will cease to be functional. The absurd alternative, which unfortunately was adopted by ENCODE, is to assume that no deleterious mutations can ever occur in the regions they have deemed to be functional. Such an assumption is akin to claiming that a television set left on and unattended will still be in working condition after a million years because no natural events, such as rust, erosion, static electricity, and earthquakes can affect it. The convoluted rationale for the decision to discard evolutionary conservation and constraint as the arbiters of functionality put forward by a lead ENCODE author (Stamatoyannopoulos 2012) is groundless and self-serving.

There is a lot of very useful material in the rest of the paper — in particular, if you’re not familiar with this stuff, it’s a very good primer in elementary genomics. The subtext here is that there are some dunces at ENCODE who need to be sat down and taught the basics of their field. I am not by any means a genomics expert, but I know enough to be embarrassed (and cruelly amused) at the dressing down being given.

One thing in particular leapt out at me is particularly fundamental and insightful, though. A common theme in these kinds of studies is the compromise between sensitivity and selectivity, between false positives and false negatives, between Type II and Type I errors. This isn’t just a failure to understand basic biology and biochemistry, but incomprehension about basic statistics.

At this point, we must ask ourselves, what is the aim of ENCODE: Is it to identify every possible functional element at the expense of increasing the number of elements that are falsely identified as functional? Or is it to create a list of functional elements that is as free of false positives as possible. If the former, then sensitivity should be favored over selectivity; if the latter then selectivity should be favored over sensitivity. ENCODE chose to bias its results by excessively favoring sensitivity over specificity. In fact, they could have saved millions of dollars and many thousands of research hours by ignoring selectivity altogether, and proclaiming a priori that 100% of the genome is functional. Not one functional element would have been missed by using this procedure.

This is a huge problem in ENCODE’s work. Reading Birney’s commentary on the process, you get a clear impression that they regarded it as a triumph every time they got even the slightest hint that a stretch of DNA might be bound by some protein — they were terribly uncritical and grasped at the feeblest straws to rationalize ‘function’ everywhere they looked. They wanted everything to be functional, and rather than taking the critical scientific view of trying to disprove their own claims, they went wild and accepted every feeble excuse to justify them.

The Intelligent Design creationists get a shout-out — they’ll be pleased and claim it confirms the validity of their contributions to real science. Unfortunately for the IDiots, it is not a kind mention, but a flat rejection.

We urge biologists not be afraid of junk DNA. The only people that should be afraid are those claiming that natural processes are insufficient to explain life and that evolutionary theory should be supplemented or supplanted by an intelligent designer (e.g., Dembski 1998; Wells 2004). ENCODE’s take-home message that everything has a function implies purpose, and purpose is the only thing that evolution cannot provide. Needless to say, in light of our investigation of the ENCODE publication, it is safe to state that the news concerning the death of “junk DNA” have been greatly exaggerated.

Another interesting point is the contrast between big science and small science. As a microscopically tiny science guy, getting by on a shoestring budget and undergraduate assistance, I like this summary.

The Editor-in-Chief of Science, Bruce Alberts, has recently expressed concern about the future of “small science,” given that ENCODE-style Big Science grabs the headlines that decision makers so dearly love (Alberts 2012). Actually, the main function of Big Science is to generate massive amounts of reliable and easily accessible data. The road from data to wisdom is quite long and convoluted (Royar 1994). Insight, understanding, and scientific progress are generally achieved by “small science.” The Human Genome Project is a marvelous example of “big science,” as are the Sloan Digital Sky Survey (Abazajian et al. 2009) and the Tree of Life Web Project (Maddison et al. 2007).

Probably the most controversial part of the paper, though, is that the authors conclude that ENCODE fails as a provider of Big Science.

Unfortunately, the ENCODE data are neither easily accessible nor very useful—without ENCODE, researchers would have had to examine 3.5 billion nucleotides in search of function, with ENCODE, they would have to sift through 2.7 billion nucleotides. ENCODE’s biggest scientific sin was not being satisfied with its role as data provider; it assumed the small-science role of interpreter of the data, thereby performing a kind of textual hermeneutics on a 3.5-billion-long DNA text. Unfortunately, ENCODE disregarded the rules of scientific interpretation and adopted a position common to many types of theological hermeneutics, whereby every letter in a text is assumed a priori to have a meaning.

Ouch. Did he just compare ENCODE to theology? Yes, he did. Which also explains why the Intelligent Design creationists are so happy with its bogus conclusions.

The Gumby Gambit

Tom Bethell is a fellow traveller with the Intelligent Design creationists of the Discovery Institute; he often publishes on their website, and he’s the author of quite a few books questioning the dogma of science. He also thinks he’s a polymath: he wrote Questioning Einstein: Is Relativity Necessary?, which claims that Einstein was wrong, and he also wrote The Politically Incorrect Guide to Science, which claims that radiation is good for you, there is no global climate change going on, Shakespeare didn’t write those plays, and evolution is bunk, among many other remarkable assertions.

He’s a gumbyesque crackpot, in other words.

His latest effort is a rant on l’affaire greenscreen in which he explains natural selection to us. Read on; you will be in awe as Mr Gumby bellows out his definitions and explanations. He gets everything absolutely backwards.

An analogous situation arises with varieties of bacteria that are immune to antibiotics. The immune varieties are suddenly “fit” and so they survive. But the word “adaptation” is misleading because the immune varieties have to appear first. They don’t “adapt,” or reshape themselves in recognition of the suddenly hostile environment. They are not like people who “adapt” to cold weather by putting on overcoats. They are like people who accidentally had overcoats on before the cold snap came.

NS is not supposed to be an explanation of how we get more of something; a dark moth, for example. It’s supposed to show how the moth itself arose. And that is what the Darwinists have never been able to demonstrate; not just with moths but with anything else. That’s why I hesitate to call NS “real.” Well, I guess it is, as long as it’s defined narrowly enough.

Read that last paragraph again. It’s a marvel. Tom Bethell doesn’t have even a basic understanding of the principle of natural selection; he doesn’t even understand it as well as Darwin, who wrote it up in 1859.

Natural selection is an explanation of how we get more (or less) of something; it describes one mode of change in the frequency of a trait in a population over multiple generations. It is not about physiological adaptation, but about changes in allele frequency. That’s all biologists have claimed for the concept, ever; it’s one of the things population geneticists have lots of math to describe.

Natural selection is not an explanation for how evolutionary novelties arise in the first place. For that, we have to look at mutations and subtler enabling changes that facilitate the emergence of new phenotypes, like recombination and genetic accommodation. The idea that variation in the environment can induce appropriate changes in heritable traits of organisms is the discarded notion of Lamarckian inheritance — we don’t see evidence of that.

He gets it all completely wrong. Even more remarkably, he gets it wrong after giving a useful analogy with his overcoat example.

Yes, natural selection works exactly like “people who accidentally had overcoats on before the cold snap came.” That’s Darwin’s key insight and Bethell’s key failure: natural selection isn’t about how individuals adapt, it’s about how populations adapt by winnowing out less fit individuals (those who don’t have an overcoat) and promoting the more fit individuals (those who happened to have an overcoat, and will pass it on to their children).

I really don’t understand how someone could write a whole book with chapters about evolution and not grasp that beautiful, simple, elegant idea. I suppose it’s the same way someone with no understanding of physics could write a whole book with no math in it disproving Einstein.

Isn’t it revealing, though, how the Discovery Institute promotes people like Bethell and Gauger who have no understanding of the field they aim to disprove? It’s as if the only people they can find who share their goals are all incompetents with delusions of understanding the science about as well as a reasonable high school student.

αEP: Complexity is not usually the product of selection

This is another addition to my αEP series about evolutionary psychology. Here’s the first, and unfortunately there are several more to come.

By the way, people are wondering about the α in the title. Don’t you people do any immunology? α is standard shorthand for “anti”.

I mentioned in the last one this annoying tendency of too many pro-evolution people to cite “complexity” as a factor that supports the assertion of selection for a trait. Strangely, the intelligent design creationists also yell “Complexity!” at the drop of a hat, only it’s to prove that evolution can’t work.

They’re both wrong.

I ran across a prime example of this recently in a post by John Wilkins (It’s pick-on-John-Wilkins day! Hooray!)

[Read more...]

Sunday Sacrilege: Sacking the City of God

(This is the text of the talk I’m giving at the Global Atheist Convention; I also thought it would make a good Sunday Sacrilege, so here you go.)

I must apologize for some topic drift — I came up with a title for this talk some months ago, but the as I was working on it, it…evolved. So what I’m actually going to talk about today is my plan to assault heaven and kill God. You don’t mind, do you?

A little background, first. You may have heard this common phrase.

In the beginning was the Word.

But, wait, no…that’s not true. In the beginning of human society, there was the Blood. The marker of our identity was the family, the tribe, the clan. What united us into functioning social units was our pedigree: the web of familial ties that knit us together. Unfortunately, that union was limited to a fairly small group of people, and could only be expanded by the commitment of marriage and birth. It limited us.

So next was the Word, right?

No, next was the King. The king was a proxy for the Blood: you declared allegiance to the big man, the chief, the royal family. Maybe you werenÕt directly linked by familial relationship, but the King or Pharaoh represented you–he was a symbol of your identity. The size of the social unit grew.

Now we come to the Word?

No, next was the City. In the ancient world, the large social unit was the city: Babylon. Athens. Rome. Kings come and go, but Rome was eternal. People didn’t say they were Greek; there was an awareness of a similarity of language and history, but when you asked who they were, they thumped their chests and said, “I am an Athenian!” or “I am a Spartan!” Rome built a whole empire with an arrogance of pride in that special Roman citizenship, so it was even an identity that could be expanded to a remarkable degree; people standing on Hadrian’s Wall in farthest Britain or on the frontiers of Syria would find honor in calling themselves Roman.

So now we come to the Word.

There’s a problem with basing your identity on a city. Cities fall. When Alaric the Goth sacked Rome in AD410, St Augustine could sit back in the relative safety of his home in North Africa and note the event with both horror and triumph: the Fall of Rome was an immense cataclysm that shook the ancient world, shattering that sense of identity and constancy, but was also an opportunity for an alternative way of thinking about ourselves to come to ascendancy: the way of the Word, the People of the Book.

Augustine didn’t think of it. It had been tried for a long time. The most notable people of the book are the Jews; they attached their sense of identity to a collection of laws and stories and commentaries and books, part of which is the Christian Old Testament. They acquired a persistence that cities couldn’t have. When Jerusalem fell, the Jewish people were not destroyed; the event became a chapter in their books, a remembered part of their history. It strengthened their identity. A Roman couldn’t be landless, cityless, countryless, but a Jew could: you could take everything away from the Jewish people, you could make them homeless and scattered, and still they knew who they were.

The most brilliant thing Christianity ever did was to take that idea of the Word, that concept of identity wrapped up in an abstract set of ideas and stories, and to open it up to everyone. Aww, Rome fell? YouÕre all alone? Here, we can help you find yourself, we can give a new meaning to your life, we have a standard that you can hold high and find unity with a greater people. It’s called the Bible.

I repeat, absolutely brilliant. It made Christianity bulletproof.

Cities fall. Kings die. Bloodlines fade. But ideas can go on and on and on. Now, a 21st century person can feel continuity with a 5th century priest; an American can share a central element of their self with someone in South Africa, with someone in China, with someone in Australia; heck, with someone on the space station, or walking on the moon. We can have the concept of an ecumene; people tied together by a common belief that crosses borders. It’s a powerful tool. It’s widely used, too; what is a United States citizen but someone bound by a set of documents, the Constitution?

There’s also the power that comes from an unkillable idea. You’ll find a version of this in V for Vendetta, Alan Moore’s graphic novel or the movie, which is precisely what the story is all about. Here’s what Evie had to say:

“We are told to remember the idea, not the man, because a man can fail. He can be caught. He can be killed and forgotten. But four hundred years later an idea can still change the world. I’ve witnessed firsthand the power of ideas. I’ve seen people kill in the name of them; and die defending them. But you cannot kill an idea, cannot touch it or hold it. Ideas do not bleed, it cannot feel pain, and it does not love.”

You were probably dubious and wondering what the heck I was doing saying the Bible was powerful and important, but maybe now that I’ve cited nerd god Alan Moore for the concept you’ll accept what I’m saying.

You can kill a man, you can sack a city, but Alan Moore says you cannot kill an idea. And ideas can change the world.

Ideas can change the world.

Say it again: Ideas can change the world.

Live it: Ideas can change the world.

This is something atheists share in common with Christians; you’ll get no argument from the believers in any religion that ideas can change the world. It’s what they’ve been doing for thousands of years, usually for the worse.

But I have to disagree with Alan Moore on one thing. You can kill an idea. This is also something that the people of faith are all aware of — perhaps unconsciously, perhaps not in any intellectual sense. But they know, and they are afraid. History is littered with dead ideas. Christians struggled hard to kill some of them, and succeeded in some cases, failed in others. They know it’s hard, but they also know from experience that it can be done.

Read the pronouncements of popes and archbishops, read the newspapers and web columns, look to the priests in their pulpits, and you’ll see something wonderful: they are reacting to the rise of the New Atheists in the same way the Roman establishment reacted to the Visigoths appearing on the horizon. I cannot blame them for being fearful; we are galloping towards the central ideas of their identity, and we aim to tear down their walls and replace their obsolete myths with change and something more vital.

Deep in their heart of hearts, they fear that a sequel to St Augustine’s City of God is in the works, and it’s going to be written by an atheist…and it will speak of a brand new world and new opportunities, it will create a new ecumene of people united under something other than the folly of faith.

So how do you kill an idea? How will we sack the city of faith?

By coming up with a better, more powerful idea. That’s the only way we can win.

Now I’m not so arrogant that I’d come in front of you all to tell you that I’ve come up with the grand idea that will be a religion-killer. This isn’t the kind of thing that pops into existence out of one guy’s mind — it takes refinement over time, lots of smart people hammering it out, just like those holy books weren’t magicked into existence in an instant. Fortunately, our idea has been incubating for a few centuries, and has involved multitudes of our civilization’s greatest minds.

It’s called science.

Science is our weapon, our god-killer. It’s the greatest tool humanity has ever invented — it’s taken us from a hodge-podge of bickering near-savages living in the mud and dying young of disease and childbirth and starvation and sword-pokes to a hodge-podge of bickering near-savages who sometimes walk on the moon, who sometimes cure diseases, who live twice as long as our predecessors, who can look deep into cells or far out to distant galaxies. It has given us great power to accomplish marvelous things or to screw up the whole planet.

Science also has the power to transform our sense of identity. Some of us are no longer People of the Word, members of a special tribe bound together by the narratives and rules in quaint old books. We are instead the People of Reality: we are united by common knowledge, by a sense of universality, by our commitment to evidence. Personally, I find no sense of myself in the Judeo-Christian fairy tales I was brought up with–they are too narrow, too bigoted, too false. The words of my people are written in the strands of DNA I find in every cell of my body, and the story they tell is clear and inspiring. We are all products of the natural world; stars died to create the elements we are made of, and 4 billion years of churning life struggled and was born and died to shape us. We are close kin to every single human being on the planet, without exception — there is no tribe that is outside our family. And even deeper, we are related to every living thing on earth. You simply cannot get any more universal than the scientific story of life.

I take far greater pride in the accomplishments of science than I do of my ethnic group, or my place in Western culture, or my particular ruling form of government, or least of all, the church I was brought up in. Science bridges differences: I can find common ground with American scientists, Canadian scientists, Mexican scientists, Chinese scientists, Iranian scientists, Australian scientists. Maybe you aren’t a scientist, strictly speaking, but you’ve read the latest book by Dawkins or Hawking, or you love David Attenborough’s TV shows, or you’re a bird watcher or like weekend hiking in the Mountains. You are my people! We are one, united in an appreciation of the natural world!

There’s another reason I can take pride in science. Science has real power. Science actually works. But maybe I should actually take a moment to define what science is.

Science is the process that does its damnedest to figure out how stuff actually works, rather than how we wished it worked.

You know, I kinda wish peach pits actually cured cancer, but I think it’s more important to do the experiments and measure the results and see if they really do…because if they don’t, I think it would be a good idea for people to move on to more effective treatments.

You know, when I’m shopping for a used car, I kinda wish that cherry shiny sports car that I look so good in and that the seller is dumping for cheap also had a smoothly functioning engine and a trouble-free transmission, but I’ll still take it for a test drive and bring it to a mechanic for inspection.

You know, my ancestors probably wished the shaman’s magic talisman kept tigers away, but he probably trusted more in a fire and palisades and a spear close to hand.

The real power of science comes beyond that immediate effect, though. It turns out that if you’re disciplined and careful, if you reject ideas based on superstition, revelation, and tradition and actually require confirmable evidence for any suppositions about even mundane things, you find yourself on good stable ground, and are able to ask even deeper questions, and get answers. And before you know it, you find yourself in possession of a strong chain of evidence that leads you to answers about the fundamental nature of the universe. That’s real power.

When theologians argue, they try to resolve differences by turning to murky sources remote from anything fundamental: they open their holy texts, they cite fellow theologians, they try to reinterpret words that have been reinterpreted many times before. Have you ever heard scientists argue, though? They do all the time. But they don’t resolve issues by appealing to higher authorities: they don’t usually argue that because Richard Dawkins said it, it’s settled. They don’t argue that we have to parse Charles Darwin’s words a little more finely to arrive at the truth.

No, they say, “I’m going into the lab and do an experiment to test that proposition.”

They say, “I’m going to build a new instrument to measure that and see who’s right.” Our only authority is reality, and that’s what we test all of our inferences against. When you’re studying the world, your source of information is the world.

I’ll have more respect for theologians, whose object of study is god, when they actually start querying their subject directly. OK, they can start small and begin by pinning down ghosts or angels and asking them the tough questions that will eventually lead to collaring the deity, but you know, it’s just absurd that people who make so many assertions about the supernatural never seem to actually study supernatural sources of information.

It’s almost as if they don’t exist.

Now I’m sniping a bit at religion, and there’s a reason for that. Science and religion are in opposition. Faith is the atheist’s enemy. Remember, science is a process for figuring out how the world actually works. If you short-circuit the process and declare that you already have the answer, you just have to believe, then you are an enemy of science. If you simply assert your desired conclusion, and ignore the fact that reality is rarely about the answer you want, you’re an enemy of science. Truth is often uncomfortable, you have to value it because it is true, not because it makes you feel good.

The clearest examples of the dangers of religious thinking can be found in issues of science policy. Questions about the environment, for instance, ought to be resolved by careful examination of the evidence and by weighing the costs and benefits of proposed solutions, right? That’s what you and I would do. That’s how reasonable people operate.

Not George Pell, as you Australians know lives in a state of denial. Not James Inhofe. Not John Shimkus. These are our American representatives, who have influence on energy and environmental policy, who endorse the “Green Dragon” philosophy and actively deny the evidence of the world around us. What is the green dragon, you might ask? Here’s a statement from one of its proponents. The green dragon is environmentalism.

“Around the world, environmentalism has become an unbalanced, radical movement. Something we call “The Green Dragon.” And it is deadly, deadly to human prosperity, deadly to human life, deadly to human freedom and deadly to the gospel of Jesus Christ. Make no mistake about it, environmentalism is no longer your friend. It is your enemy. And the battle is not primarily political or material, it is spiritual. As Christians, we must actively trust God and obey His word. So when it comes to environmental stewardship, we must reject the false world view, the faulty science and the counterfeit gospel that threatens to corrupt society and the church.”

So in addressing the problems of the world, they deny evidence of the world to favor of mysticism and dogma. Both Inhofe and Shimkus have come out with unbelievably clear statements: we don’t have to worry about climate change, global warming, and CO2. Why? Because, in the bible, God said we don’t have to worry about a flood anymore, he promised it wouldn’t happen. And besides, god is also going to end the world soon, so it’s out of our hands.

Oh, yeah, it’s the End Times, don’t you know. Would you believe that, according to a recent Pew survey, 40% of Americans believe that Jesus is finally going to get around to fulfilling that promise he made 2000 years ago of global death and judgment, and it’s going to happen in our lifetimes? Aren’t we lucky? And here’s the creepy thing: those affirmative respondents all think that yes, we are lucky. Hooray for Armageddon and Apocalypse! Bring on famine, war, plague, and death! The demented ghouls of the end times are actually a significant political lobby, fighting to support Israel, no matter what. Why? Because they have a prophecy in Revelation that the Jewish state must be restored, in order that it be destroyed in a nuclear holocaust, after which the surviving Jews will convert en masse to Christianity. Go on, read the Left Behind books, which spell it all out, so it must be true.

If a scientist saw a cataclysm coming, say a meteor on collision course for earth in 2050, we wouldn’t be saying, “Hallelujah, physics is true, bring it on! Our faith in mathematics is strengthened!” We’d be trying to stop it. Which makes the Christian reaction puzzling. If I actually believed Jesus was coming to end the world, I’d be preparing by stocking up on timber and nails. They were pretty effective last time.

Now wait, there might be some people saying (not anyone here, of course) that that’s no fair. Maybe you’re a liberal Christian, and I’m picking on the extremists (although, when we’re talking about roughly half the United States being evolution-denying, drill-baby-drill, apocalypse-loving christians, it’s more accurate to say I’m describing a representative sample). Perhaps you’re a moderate, you support good science, education, and the environment, you just love Jesus or Mohammed, too.

I’m sorry, but I don’t like you. I’ll concede that you are doing less direct harm, and I will thank you for your support of shared causes, and I’ll also happily work alongside you in those causes, but I also think you are still doing indirect harm to foundational principles of a rational society. You believe in some outrageous bullshit; the christian myths of a virgin giving birth to a god who dies are illogical lunacy, and the Christian doctrines of original sin and redemption through blood sacrifice by proxy are crippling psychopathological abominations. You promote unreason by telling people that it is OK to believe in some things without evidence, and even in contradiction to evidence and reason. You are cafeteria realists, and you undermine the essential goal of bringing the whole of humanity out of the darkness of ignorance and into the light of the real world.

I tell such people that the universe is clearly lacking in gods and supernatural forces, so grow up and set all that nonsense aside. Join us and become a good atheist — you’ll be much happier and will waste less time in pointless just-pretend foolishness.

So, what does it mean to be a good atheist in the 21st century? How do you live as a good atheist? What should our values be?

We’re a diverse group, and we never agree on everything, so I’ll give you just a few: truth, autonomy, community.


This one is so fundamental that it’s hard to say much about it. If you aren’t dedicated to learning and discovery, to finding out the factual truth of matters, then you can’t be a good atheist. Goodbye.

You might be saying to yourself, but this isn’t a very good criterion, because doesn’t everyone seek the truth? Don’t Christians say they value truth, too?

Unfortunately, they say it, but they don’t practice it. If that were true, all the major Christian denominations wouldn’t have denial of the mechanisms of evolution as core parts of their doctrine. Now I know right away that many of you will be protesting that the Catholic church nominally accepts that humans evolved over time; so does the church of latter day saints and many other denominations. But note that I said the mechanisms of evolution; we have a battery of well-supported, unambiguously factual mechanisms driving evolutionary change, and none of them involve fairies, aliens, angels or gods. The only process of evolution endorsed by any of these religious institutions is of god-guided, directed, teleological change, a mechanism completely unsupported by any evidence, in direct contradiction to known processes, and propped up only by an irrational need to make their holy dogma relevant to human origins.

They’re all intelligent design creationists, in other words, and they’re all wrong.

I left my liberal Lutheran church when I was 13 years old and learned that I was expected to believe in a lot of false ideas to be a member. This has been a lifelong value for me; how much of the facts and data and evidence are you willing to compromise? My answer was zero.


For many years, atheists have been in the minority; I have talked with so many people who thought for so long that they were the only one, the only person in their community who saw through the godawful babble of the church. (of course, now that we have the internet, those same people are discovering that they are part of a global movement). What that means, though, is that many atheists are nonconformists, boat-rockers, weirdos, and outcasts.

And we like it that way.

We are not sheep. We love people who stand up for themselves, we detest people who try to impose rules on us — I have to be very careful to keep my description of values general, and be clear that I’m not dictating them to you, but describing what I see emerging as a consensus, because otherwise I’ll be pilloried by my own kind. We’re a pitiless bunch.

But what it means is that we find common cause with the people who have also been oppressed by this racist patriarchal culture we live in. People should be free to be who they are…and more, they should be free to stand up loud and proud and be that person with impunity. We will not live in a monoculture. We’re going to find strength in diversity.

I can think of no clearer example than a struggle that has riven the online atheist community for the last year or two, the effort to acknowledge the role of women in atheism. For years, the face of atheism has been white, male, and middle-aged, and a certain complacency had settled in — women by default had their role, as wives or organizers, and we had adopted a casually masculine expectation that all of our intellectual leaders would look like, well, me. Atheist meetings looked a lot like meetings of the Mormon leadership.

That’s changing. We’re telling people to come out, join us, be free of the straitjacket of convention, and what’s happening is the discovery that women have even more reason to be pissed off at religion than men, and they are a fast-growing segment of our community. Some people resent that — I cannot and will not argue that being an atheist makes you free of irrationality — but I can say for myself and the majority of atheists that we are all overjoyed. Our ranks are swelling with fierce independent women who are changing us, making us stronger and louder, and standing up for their causes and making all of us fight for women’s rights, reproductive freedom, and equality of opportunity. This is atheism, too.

Are you LGBT, wanting equality and social justice? You are atheism.

Are you a member of a minority, seeking recognition for your rights as a human being and respect in a society you helped shape? You are atheism.

If you are a human being with real world concerns, who wants to change the world, who wants to contribute in a unique way that encourages those diverse views, then you should be one of us.

The club is only closed to people who fuss about an imaginary afterlife, getting right with an imaginary god, conforming to an arbitrary dogma, and who think the most useless act of all, prayer, is a contribution you deserve thanks for.


There is a tired stereotype of atheists current in conservative circles. We are all cranky curmudgeons, grim nihilists and loners. Not a word of it is true. When you’re a social pariah, as so many atheists have been, is it any wonder that some of us might be a bit lonely and bitter? As my colleague on freethoughtblogs, Greta Christina, has been arguing, we also have good reason to be angry with a discriminatory society that does stupid things in the name of the Lord.

But atheism is blossoming. Atheists are coming out everywhere, speaking up on the Internet and public spaces, gathering together in meetings and discovering that we are not alone, and yes, it is good. We like each other. We work together. We’re happy together.

Three weeks ago, we had a wonderful meeting in Washington DC,the Reason Rally. 20,000 people gathered together in utterly miserable weather — it was cold, and it rained all day. I walked around in the crowds, and you know what? Everyone was smiling. Nobody was complaining (except for the cranky protesters on the fringe). The policemen monitoring the crowd were smiling. Goddamn, if I were the Grinch my heart would have grown three sizes that day.

I was also privileged to be backstage with all the speakers and celebrities and leaders of atheist organizations, and they were all jubilant, too. We were all damp and soggy — I remember watching Tim Minchin doing his set, barefoot on a stage puddled with water and strung with cables to Bad Religion’s amps and speakers, and thinking one good short and the atheist movement could be decapitated today — and every one of us had big goofy smiles on our faces.

And now this weekend we meet 4000 strong in Melbourne–and what an amazing crowd this is.

This is not surprising. We are a social species, and we thrive in communities, it’s how we have survived and grown so far. And atheists, contrary to some of our critics, are fully human, not aliens at all.

This willing cooperativity is something we have to value. Not only is it who we are, but it’s how the good atheists of the 21st century will win in the end.

We humans are different from other species in this regard. I have a favorite story from the primatologist Robert Sapolski to highlight this human attribute. We are not baboons.

“When baboons hunt together they’d love to get as much meat as possible, but they’re not very good at it. The baboon is a much more successful hunter when he hunts by himself than when he hunts in a group because they screw up every time they’re in a group. Say three of them are running as fast as possible after a gazelle, and they’re gaining on it, and they’re deadly. But something goes on in one of their minds — I’m anthropomorphizing here — and he says to himself, “What am I doing here?I have no idea whatsoever, but I’m running as fast as possible, and this guy is running as fast as possible right behind me, and we had one hell of a fight about three months ago. I don’t know why we’re running so fast right now, but I’d better just stop and slash him in the face before he gets me. ” the baboon suddenly stops and turns around, and they go rolling over each other like Keystone cops and the gazelle is long gone because the baboons just become disinhibited. ÊThey get crazed around each other at every juncture.”

I think that’s cool. That’s not us, we aren’t baboon-like at all. Even though baboons are really scary animals — they’re stronger than us, individually fiercer, and they have those savage huge fangs — they have this weakness, and we have this strength. We work together.

You know that in the childhood of our species, we were prey to the predators of the African continent. Alone, we were soft, weak, and tasty, and I’m sure the lions and leopards enjoyed a hominid snack. But together…I’m sure that when some ferocious big cat came upon a tribe of humans, together, and when they all turned 10 or 15 pairs of eyes on the predator and reached for stones and sharpened sticks, that cat felt fear and slunk away. Those eyes, those hunter’s eyes on the front of the face…when a group of us turn those eyes in cold calculation on any problem, when our hands work together, we are the most powerful force on the planet.

Yesterday I was listening to our Christian protesters outside, and I thought, “Huh. So that’s what you get when you give a sheep a microphone, amplified bleating.” There they were, calling on everyone to deny the richness of human experience and join the flock in the narrow boring confines of the sheep pen, so mindless they didn’t even realize they were calling to the wolves.

I have a different metaphor for us, my brothers and sisters in atheism. We are not sheep; there are no shepherds here. I look out from this stage and I see 4000 pairs of hunter’s eyes, 4000 hunter’s minds, 4000 pairs of hunter’s hands. I see the primeval primate hunting band grown large and strong. I see us so confident in our strength that we laugh at our enemies. I see a people thinking and planning, fierce and focused, learning and building new tools to conquer new worlds.

You are not sheep. You, my brothers and sisters in atheism, are a fierce, coordinated hunting pack — men and women working together, and those other bastards have cause to fear us. So let’s do it: make them tremble as we demolish the city of god.