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:

geneticcode

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.

I’m sure you’ve all been wondering what Answers in Genesis thinks of feminism

Haven’t you? Or perhaps you’ve all assumed the answer is obvious.

Sadly, I don’t have any surprises to spring — the answer is actually rather predictable. They’re agin’ it. They do concede that suffrage was OK, and they think it’s acceptable for women to vote — how liberal of them, and it only took them a century to come around — but all that 2nd and 3rd wave feminism destroyed the family!

So what’s the problem here?

Does history hold a bias against women? Members of the radical feminist movement seem to think so. Radical feminism has had incredibly destructive effects on marriage and the family—and its influence has also been felt on the church. Evangelical feminism teaches an egalitarian view of marriage and roles in the church, to the point where passages that clearly teach male headship are reinterpreted, explained away, or ignored altogether. As a result, many men are abdicating or being forced out of their God-given roles as heads of their households and as leaders in the church. The negative effects of this kind of postmodern thinking have led to serious attacks on the authority of God’s Word.

They don’t really address the issues they bring up…anti-feminism is more or less a fait accompli. As you can see hinted above, they deny any real oppression of women — ladies, your role as a helpmeet is valuable and just perfect for you! The real problem is that feminism erodes male authority. And if you weaken male authority, you weaken the authority of scripture, which says that males are the authority and therefore you weaken male authority, which weakens scripture…hey! Extinction vortex! Goodbye, fundamentalists!

I wish.

Now why would feminists want to diminish godly authority? Easy. They hate men.

Most evangelical feminists would profess to believe in the authority and inerrancy of Scripture, setting them apart from many other forms of feminism. However, their method of interpreting and applying Scripture leaves something to be desired. What is at the heart of a reluctance or even outright refusal to refer to God as “he” and “father”? What drives the redefinition and dismissal of passages of Scripture that promote male headship in marriage and leadership in the church? Grudem concludes, “At the foundation of egalitarianism is a dislike and a rejection of anything uniquely masculine.”

When it comes right down to it, creationist and atheist MRAs are all kind of similarly stupefied and bovine when it comes to recognizing the legitimacy of women’s right to autonomy. Why aren’t they helping me stand at the head of the church, the godly men are wondering, and why aren’t they making me a sammich, the godless ones marvel. Women are so good at performing those subservient tasks, why don’t they appreciate the opportunities to do more and more and more?

Nature made them that way. Or god did. Follow your natural/divine purpose, as revealed to me.

New pope, same as the old pope

It’s Bergoglio, an Argentinian Jesuit that the Rationalist Association had as a 33:1 longshot.

Rumor has it that he’s conservative, hates that contraception and gay marriage crap, believes he has a magic spiritual hotline to the lord of the universe who is named Jesus, and is not — I repeat, is not — scientifically minded or an atheist. He also engages in magical rituals several times a week, and does not encourage women to touch his penis. At least, not openly.

He’s also old.

There. Now you know everything you need to know about the new head of one of the world’s oldest criminal organizations. You can turn off your TVs now.

Good report on Federal wildlife torture from a surprising source

Sometimes, even Fox News gets one right [trigger warnings, as you might expect from the post title]:

The brutal approach by Wildlife Services is part of a culture of animal cruelty that has long persisted within an agency that uses taxpayer money to wage an unnecessary war on wildlife, according to two U.S. congressmen who have repeatedly called for a thorough investigation.

“This agency has become an outlet for people to abuse animals for no particular reason,” Rep. John Campbell, R-Calif., told FoxNews.com.

“It is completely out of control,” he said. “They need to be brought into the 21st century.”

The story covers an investigation that was spurred, in part, by revelations that USDA “Wildlife Services” employee Jamie P. Olson had posted photos of his dogs tearing trapped coyotes to pieces on Facebook. (Previously, on Pharyngula.) The issue’s been kept on the front burner by my colleague Camilla Fox at Project Coyote; she and her organization deserve your attention and support.

Prediction: Some of you will read this and grab a roll of tape

“Ratters”. Ick.

These are pathetic people who use a canned remote administration tool (RAT) to seize control of other people’s computers…especially to activate their laptop cameras so they can spy on them (which is why I predict some of you will want to tape over your camera). Ars Technica has a whole article on these deeply creepy human beings.

Not all human beings, obviously. Unfortunately, most of them seem to be feeble little child-men.

By finding their way to forums filled with other ratters, these men—and they appear to be almost exclusively men—gain community validation for their actions. “lol I have some good news for u guys we will all die sometime, really glad to know that there are other people like me who do this shit,” one poster wrote. “Always thought it was some kind of wierd sick fetish because i enjoy messing with my girl slaves.”

Please, guys, could you stop making me ashamed of my sex? What the fuck is the matter with you?

Hamza Tzortzis’s reputation goes before him

Ophelia is hosting a wonderfully entertaining guest post on Hamza Tzortzis and the UCL segregation debacle. I know that guy; Tzortzis seems to show up somewhere every time I’m in Europe to peddle his peculiar brand of ignorance, and he’s invited me to debate him a couple of times now. The article will make clear why I’ve turned him down every time, even though it would have gotten me an expenses-paid trip to London. There are some things I just won’t do.

Sadly, it’s International Women’s Day

It’s that day when we’re supposed to celebrate the accomplishment’s of women. I say “sadly,” because unfortunately there are way too many people out there who would rather sneer at and diminish women’s status in the world.

Case in point: on twitter, I ran across this lovely tweet from one of those repugnant slymepitters.

On #IWD remembered the nearly 0 wimmin – Nobels in science, highbrow art, chess GMs, great standups, but 100s of pop-culture hos #ftbullies

`

Yes. Let’s remember those women.

Let’s remember Lise Meitner, Hilde Mangold, Chien-Shiung Wu, Rosalind Franklin, and Jocelyn Bell — who were all well-qualified (men won the prizes for work equivalent to what they did, instead) to win a Nobel but didn’t get one.

Rather than 0 women, perhaps we should remember Marie Curie and Maria Goeppert Mayer, who won Nobels in physics; Irène Joliot-Curie, Dorothy Crowfoot Hodgkin, and Ada E. Yonath in chemistry; Barbara McClintock, Carol W. Greider, Christiane Nüsslein-Volhard, Elizabeth H. Blackburn, Françoise Barré-Sinoussi, Gertrude B. Elion, Gerty Cori, Linda B. Buck, Rita Levi-Montalcini, and Rosalyn Yalow, in physiology or medicine. Clearly women are not intrinsically incapable of scientific work at the highest levels. Of those whose work I’m familiar with in detail, I have to tell you that McClintock blows me away with the stunning brilliance of her abstract reasoning — I know of no other male scientist whose work is at all comparable (that of course is a matter of taste!)

The relatively lower frequency of women recieving Nobels is not something any man should take pride in; what it really indicates is that we’ve been shortchanging half the human population, depriving them of opportunities to excel. Wait — we’ve been doing worse than shortchanging women; we’ve been depriving all of humanity of the potential in those minds. This pattern of discrimination against women has hurt us all.

Let’s not forget also all the people, men and women alike, deprived of opportunities because of their race or class — deprived by the kind of endemic bigotry that would, for instance, denigrate an entire group of people as “pop-culture hos”. And it’s not just science — it was good of our petty MRA to remind us that we’ve also lost their contributions to art and theater and games.

That’s what I think of everytime some bigot crows about the absence of some group of people from some field of endeavor — it’s a reminder of all that we’ve lost to selfish stupidity.

Bora 1, Climate Denialist Kooks 0

This is really a thing of beauty: climate pseudoscientist Willis Eschenbach whines at the inadvertent comedy blog Watt’s Up With That that Bora Zivkovic has been moderating comments on his SciAm blog.

Eschenbach, who’s also a Mass Extinction denialist, objects to Bora’s having instituted some basic anti-troll measures at A Blog Around The Clock that relegate comments with certain field marks of the climate denialist loon to the spam bin. Says Bora, in a passage that apparently made Eschenbach’s cranial temperature spike like a Warmist hockey-stick graph:

If I write about a wonderful weekend mountain trek, and note I saw some flowers blooming earlier than they used to bloom years ago, then a comment denying climate change is trolling. I am a biologist, so I don’t write specifically about climate science as I do not feel I am expert enough for that. So, I am gradually teaching my spam filter to automatically send to spam any and every comment that contains the words “warmist”, “alarmist”, “Al Gore” or a link to Watts. A comment that contains any of those is, by definition, not posted in good faith. By definition, it does not provide additional information relevant to the post. By definition, it is off-topic. By definition, it contains erroneous information. By definition, it is ideologically motivated, thus not scientific. By definition, it is polarizing to the silent audience. It will go to spam as fast I can make it happen.

What Eschenbach doesn’t mention, and a basic point of Bora’s post on how trolls derail substantive conversation, is that climate denialism is just the most pernicious and prevalent of a number of kinds of pseudoscience that have afflicted some of the sites on SciAm of late:

I know that I used the example of Global Warming Denialism here the most – mainly because it is currently the most acute problem on our site – but the same goes for people harboring other anti-scientific ideas: creationists, anti-vaxxers, knee-jerk anti-GMO activists, and others.

This post is not about climate denial, it is about commenting and comment moderation. It is about the fact that eliminating trolls opens the commenting threads to more reasonable people who can actually provide constructive comments, thus starting the build-up of your own vigorous commenting community.

There are seven billion people on the planet, many of them potentially useful commenters on your site. Don’t scare them away by keeping a dozen trolls around – you can live without those, they are replaceable.

Eschenbach’s month-late response to Bora’s post is as pure and canonical a paean to the hallowed practice of JAQing off as I have seen. A sample:

I can only bow my head in awe. I mean, what better way is there to keep you from answering people from WUWT and other sites who might want answers to actual scientific questions, than not allowing them to speak at all?… See, Bora, the beauty of your plan is, you don’t even have to think about censorship once you do that. The computer does the hard work for you, rooting out and destroying evil thoughtcrimes coming from … from … well, from anyone associated with Watts Up With That, or with Steven McIntyre’s blog Climate Audit, or anyone that you might disagree with, or who is concerned about “alarmists”, you just put them on the list and Presto!

No more inconvenient questions!

I probably ought to feel sorry for Eschenbach: anyone who would proudly link to a piece like this alleged debunking of extinctions — as opposed to deleting it, salting the earth of the server on which it once resided, and denying under oath that you’d ever heard of the thing — is definitely more properly pitied than mocked. “No continental forest bird or mammal is recorded as having gone extinct from any cause,” Eschenbach says. That’s some Time-Cube-level obliviousness.

But I can’t help snickering, and feeling slyly jealous that Bora was able to elicit a response like that just by mentioning idly that he’s keeping his own comment threads on topic despite a massive campaign by a few fanciers of metallic haberdashery to disrupt them. Well done, my friend. Well done.

Christian hypocrisy…no surprise at all

Here’s a sign of women’s progress: you can’t get fired by a Christian school for getting pregnant anymore. That’s against the law. Unfortunately, you can still be fired for fornicating, along with a few other things.

The way that Christian organizations try to get around the Pregnancy Discrimination Act of 1978, which bars firing women for pregnancy, is to claim they’re not firing them for the pregnancy, but for the fornicating. San Diego Christian College went another step by making employees sign a pledge requiring employees to abstain from "abusive anger, malice, jealousy, lust, sexually immoral behavior including premarital sex, adultery, pornography and homosexuality, evil desires and prejudice based on race, sex or socioeconomic status." Also, drinking, which means that Jesus would not be able to teach at this college established in his name.

Which does make me wonder how the school would respond if some woman got pregnant via artificial insemination or worse, in vitro fertilization. Test case, anyone?

That doesn’t help Teri James, though. She got fired from SDCC for getting pregnant the old-fashioned way, via <gasp> fornicating with a man. Escape clause met! College has an out and can get rid of the wicked woman!

Except…in a fit of the stupids to which adherents of ridiculous religions are prone, the college turned around and offered the job to a man. The man who fathered Teri James child. Who is, presumably by the symmetry of the act, a fornicator himself.

Unless this is one of those things where it’s IOKIYAM — it’s OK if you are male.

Ha ha, Harvard!

This year, UMM will have Al Franken as our commencement speaker. Guess who Harvard gets?

nelson-ha-ha

A comment on the Crimson story got me poking around (I am not a big Oprah watcher) and now I wonder: Did anyone on the Harvard honorary degrees committee consider the fact that Oprah is a major purveyor of pseudoscience? Four years ago Newsweek did an extensive debunking of pseudo-medicine pandered on her show. She was #1 on Brian Dunning’s list of the top 10 purveyors of pseudoscience, citing her as follows: “she promotes the paranormal, psychic powers, new age spiritualism, conspiracy theories, quack celebrity diets, past life regression, angels, ghosts, alternative therapies like acupuncture and homeopathy, anti-vaccination, detoxification, vitamin megadosing, and virtually everything that will distract a human being from making useful progress and informed decisions in life.” Or read Martin Gardner’s take on Oprah — and her frequent guest, Harvard’s own Dr. Oz.

Score: UMM 1, Harvard -1,000,000.