Jeffrey Tomkins is up to his old dishonest tricks again

Tomkins is a creationist with a little bit of technical knowledge, and his usual game is to focus on one tiny detail of a story to claim an incompatibility with evolution, while ignoring the majority of the information, which is simply screaming in contradiction with him. I’ve dealt with his nonsense before, specifically his claim that human chromosome 2 can’t be the product of a chromosome fusion event because he can’t find perfectly intact telomeres or a complete second centromere in the chromosome. I tried pointing out that we wouldn’t expect an intact fossilized centromere, and that the real evidence lies in the synteny, or the concordant array of genes between chimpanzee and human chromosomes. He’s never acknowledged this. Instead, he just moves on to some other detail.

Larry Moran nails him on a bad pseudoscientific paper about the beta-globin pseudogene, which Tomkins claims is not a pseudogene, because it is functional (not true). It’s a very confused paper, which is typical for Tomkins, and the only place it could have been published is in one of those hothouse fake creationist journals.

Then Moran slams him again for claiming that the GULO pseudogene was independently disabled in multiple primate lineages. It’s got to get tiresome. This is what Tomkins and most creationists do — ignore the consilience of the whole data set to zero in on some tiny, irrelevant point that is incompletely explained. It’s the neglect of the big picture that is so annoying.

Before addressing the specific criticisms in this article it’s important to not lose sight of the bigger issue. Creationists tend to focus on particular examples while ignoring the big picture. In this case, there is abundant evidence of gene duplicationS in all species and there’s abundant evidence that the fate of one duplicated copy of a gene is often to become inactivated rendering it a pseudogene. This has given rise to a robust explanation of multigene families referred to as Birth-and-Death Evolution [The Evolution of Gene Families] [On the evolution of duplicated genes: subfunctionalization vs neofunctionalization]. In order for Young Earth Creationists to mount a serious challenge to evolution they need to provide a better explanation for all this data and they need to provide solid evidence that the Earth is less than 10,000 years old.

I think Larry has him pegged.

Shameful pseudo-scientists

Dan Phelps sent me a link to a terrible, awful video of the Answers in Genesis astronomers babbling about how the JWST proves the universe is young. I know, that’s just nuts, but what else can you expect from AiG?

Fortunately, Dan provides a description, so I don’t have to watch it. You don’t have to either.

Young Earth Creationist Astronomers Declare Victory for Creationism Because of the Findings of the James Webb Space Telescope

Our favorite Young Earth Creationist (YEC) astronomers have finally discussed the James Webb Space Telescope (JWST) at length. On Wednesday 9/14/22 on Facebook Dr. Danny Faulkner and Rob Webb of AiG, and Dr. Jason Lisle (formerly of AiG, now at the Biblical Science Institute) discuss the early findings of the JWST for a full excruciating hour. See: https://fb.watch/fymizG2T2H/ .

Faulkner and Lisle have PhDs in astronomy. Rob Webb, recently was hired by AiG as a preacher/scientist and has experience in aerospace engineering, helping design several different spacecraft (hence his AiG nickname “Rocket Rob”). Their “discussion” consists mostly of self-congratulation and sundry claims that every new finding supports Young Earth Creationism including having light from galaxies billions of light years away getting to Earth in 6,000 years (a miracle!). Their self congratulations are based on the fact that astronomers are revising their ideas about how quickly galaxies and heavy elements formed in the early universe because of new data from JWST findings. This motley crew seem to be gloating that other astronomers are, gasp!, doing science. Much of the rest is preaching/scripture quoting and, at about 23 minutes in, claiming a nefarious conspiracy of morally questionable “secular astronomers” based on their “worldview.” Most astronomers I know are rather upright citizens. The exceptions know who they are ;-).

About 32 minutes in Drs. Lisle and Faulkner joke about dead Democrats voting in Chicago, and Dr. Lisle claims “dead people vote Left.”

In Dr. Faulkner’s esteemed scientific opinion God only created life on earth, not elsewhere (~36 minutes in). However, he intones, this only includes “physical life like us; I’m not talking about spirit beings like angels and demons, and so forth.” (Is this video from the 13th century?). Then, after a discussion of exoplanets, Dr. Faulkner also tells us that God will destroy stars and galaxies when he creates a “new heavens and a new Earth” (~39 minutes). Golly wow! Thankfully, Dr. Faulkner goes on to rebuff an online questioner who asks about the Flat Earth, giving Biblical and scientific reasons the ancient Bible-based cosmology is wrong. Dr. Faulkner has even written a thick tome about the subject (for sale at the Creation Museum and Ark Park, as well as online). The three gentlemen then discuss Flat Earth Theory and the psychology of the cultish behavior behind it for a bit. They appear oblivious to the irony, that, in spite of their education, promoting a 6,000 year old universe and Earth. When they agreed that it is a “psychological issue,” I stopped the video for a few minutes out of necessity. I couldn’t decide to laugh or cry, so I took a bathroom break.

Near the end (~53 minutes) Dr. Lisle bemoans that mainstream science is ignoring his claim that he predicted the findings of the JWST. He goes on to claim that science itself wouldn’t be possible if the Bible weren’t true. Lisle then posts the inane cartoon below (my screenshot) insulting scientists and intelligent people as well as confusing evolution and cosmology/cosmogony.

The video ends with mentions of books they have for sale and the Creation Museum planetarium.

But, you ask, what about the biologists? We have to turn to the Institute for Creationist Research, which employs the most appallingly awful guy with some credentials in biology, Jeffery Tomkins. I’ve discussed Tomkins several times before, and I’m tired of. He’s incredibly dishonest fellow whose entire expertise is about distorting the scientific evidence in ways that anyone who knows the field sees is wrong, but he throws around technical terms that make lay people think he’s smart. It’s a classic pseudoscientific move.

I am spared the pain of working through Tomkins’ lies by Dan Cardinale, who explains how his arguments about junk DNA are totally bogus.

It just goes round and round and round

I joined the Great Debate Community last night to talk about this chromosome 2 fusion thing again. One of the topics was about why we have to keep hammering away at the obvious beyond the point where any rational human being would have to accept the facts. Another question was why Jeffrey Tomkins is so committed to promoting a counterfactual that is neither supported by the evidence nor is required by the doctrines of his religion.

If you have an explanation, tell me. Or just watch the video.

Would you like to play a game?

Later today, I’m going to chat with some folks about the creationist claim that human chromosome 2 is not the product of a fusion of chromosomes 2A and 2B in a primate ancestor. I’ve mentioned this guy before, Jeffrey Tomkins, and I’ve criticized the silliness of his approach, which involves staring fixedly at the putative fusion site and ignoring everything else and pompously declaring that he doesn’t see what he expects to see. My response is always “LOOK AT THE SYNTENY OF THE WHOLE CHROMOSOME, YOU ADDLED DOOFUS!”

Synteny is the conservation of blocks of order within two sets of chromosomes that are being compared with each other. That is, stop looking at one tiny little spot and look at the whole chromosome, and ask if there are similar genes in a similar order between human chromosome 2 and chimpanzee chromosomes 2A and 2B. That’s the evidence.

And then I realized that most people don’t know how to look at the genomic data and do these kinds of comparisons. So in this post I’m going to tell you how to do that. It’s fun! It’s easy! It’s like a little game!

First step: go to ensembl.org. Here’s what you’ll see:

browse

We’re going to select “human”. GRCh38.p7 is just the latest, most up-to-date, complete assembly. You can come back later if you want to play with all that data from other species.

viewkaryo

Oh, look. You could suck in the whole human genome sequence to your computer, but then you’d be wondering how to read it and what you can do with it, and might turn into a bioinformatician. Play it safe and easy for now and click on “view karyotype”.

karyotype

There you are, all 23 human chromosomes and the mitochondrial genome! For now, just click on chromosome 2. From the popup menu, choose “view summary”.

chromsummary

That’s a tempting summary map of what is on chromosome 2, but ignore it for now. Look at top left menu.

summarymenu

Select “Synteny” from the “Comparative Genomics” section.

It’s going to default to showing you how regions with similar sequences line up with human chromosome 2. That’s interesting — you can see that human chromosome 2 is made up of chunks of DNA from mouse chromosomes 12, 17, 6, 1, 19, 16, 5, 11, 2, 10, and 18, but use “Change Species” to switch to “Chimpanzee”. It’s simpler, because we are more closely related to chimps than to mice. Shocking, I know.

chimphumansynteny

Are we done now?

Now if you’d like, you can play with looking at other chromosomes. Or if you’re really clever, you’ll just browse the zebrafish genome.

Creationist myopia

Tomkins is at it again. He’s a creationist who, for some reason, detests the idea that human chromosome 2 is the production of a fusion of a pair of ancestral ape chromosomes. I don’t understand why; all he’s got to do is invoke The Fall and claim it’s an error of Biblical origin, it’s not as if the Bible has anything at all to say about chromosomes. But he does like to go on and on about searching for evidence of a fusion at the fusion site, like he’s expecting an intact centromere and telomere to be right there, fossilized in the sequence. He’s written another article for Answers in Genesis that is an amazing welter of obfuscation.

In 2013, it was shown that the alleged interstitial telomeric repeat site of the human chromosome 2 fusion corresponding to chimpanzee chromosomes 2A and 2B of a hypothetical common ancestor was actually a second promoter in the DDX11L2 long noncoding RNA gene. Additional ENCODE related data are provided in this report that not only debunk evolutionary criticism and obfuscation in response to this discovery, but solidify the original finding. New data come from epigenetic-modifications, transcription factor binding, and transcription start site information. It is also shown that the alleged cryptic centromere site, which is very short in length compared to a normal centromere, is completely situated inside the actively expressed protein coding gene ANKRD30BL—encoding both exon and intron regions. Other factors refuting this region as a cryptic centromere are also discussed. Taken together, genomic data for both the alleged fusion and cryptic centromere sites refute the concept of fusion in a human-chimpanzee common ancestor.

This is remarkable. His entire ‘evidence’ consists of looking in a region of poorly conserved, non-functional DNA, and failing to find a conserved sequence, as if that’s what is expected. It’s the wrong approach. He has to ignore all the other cytological and sequence data that show that chromosome 2 is similar in structure to two chimpanzee chromosomes. This makes no sense. I explained all this before.

…what they do is focus on just the region of the fusion, and complain that it is a tangled mess and hard to interpret — that it is a degenerate telomeric region, rather than a complete and intact telomere, which is what they demand be present. This is an unrealistic expectation, given that every paper on the structure of the fusion region makes the point that it is degenerate.

An analogy: imagine a red Ford Mustang and a blue BMW X6 are in a head-on collision, and both have totally wrecked front ends, with bumpers and radiators and headlights interlocked and everything about their grilles in tangled confusion, and with bits and pieces torn loose and flung about. You’d be able to look at the crash and still tell by everything in and behind the engine compartment that Car #1 was a Mustang and Car #2 was an X6.

Bergman and Tomkins are the bewildered and incompetent investigators who ignore every other factor in the crash, look at a few particularly mangled bits of the wreckage, and declare that they can’t identify it, therefore…the two vehicles were assembled at the factory in this particular configuration, and no crash occurred. But they use lots of sciencey language to explain this at tendentious length, which is sufficient to convince non-scientists that the interpretation of an obvious historical event has been refuted. And that’s all they need to do to accomplish their goals: fling about unfounded fear, uncertainty, and doubt to win over the ignorant.

Tomkins has done it again. He stares fixedly at the debris and fails to pay any attention at all to the intact, functional regions of the human chromosome and ape chromosomes, which are all you need to tell the tale.

Do the creationist shuffle and twist!

Don’t you hate it when you get up in the morning and the first thing you read on the internet is the news that your entire career has been a waste of time, your whole field of study has collapsed, and you’re going to have to rethink your entire future? Happens to me all the time. But then, I read the creationist news, so I’ve become desensitized to the whole idea of intellectual catastrophes.

Today’s fresh demolition of the whole of evolutionary theory comes via Christian News, which reports on a paper in the journal Molecular Biology and Evolution which challenges the ape to human evolutionary theory. Wait, that’s a journal I read regularly. What did I miss?

[Read more…]

Creationist FUD refuted

If you’re looking for a meaty weekend read, look no further than Paul McBride’s thorough dismantling of Science and Human Origins, the new bad book from the Discovery Institute, by Gauger, Axe, and Luskin. It’s in 6 parts, taking on each chapter one by one: Part 1, Part 2, Part 3, a prediction about what will be in chapter 4 before reading it, Part 4 (prediction confirmed!), and Part 5.

The creationists are howling. McBride’s evisceration, with Carl Zimmer’s detailed description of the evidence for chromosome fusion, all discrediting what they thought would be a hot new text on the scientific evidence for creation, has made them so furious that they’re even lashing out at me in email — I just linked to the evidence, so I imagine Zimmer and McBride must be seeing some entertaining spectacles in their inboxes. I do so love to see the creationists dancing in the flames of their own immolation.

I will say this, though: I did get one very polite email from a creationist, who told me that he was not a scientist, but that he’d read a couple of articles that sounded impressively sciencey to him, and asked if they didn’t represent a legitimate criticism of the chromosome fusion idea? And he very nicely sent along the two papers for me to read. Here they are:

Bergman J, Tomkins J (2011) The chromosome 2 fusion model of human evolution—part 1: re-evaluating the evidence. Journal of Creation 25(2):106-110.

Tomkins J, Bergman J (2011) The chromosome 2 fusion model of human evolution—part 1: re-evaluating the evidence. Journal of Creation 25(2):111-117.

Two things jumped out at me: it’s by batty Jerry Bergman, no credible source at all, and it’s published in the inbred in-house journal of the Institute for Creation Research. These are not legitimate science papers, although they do throw around enough science terms and techniques, and follow the form of a real science paper, to generate confusion in the mind of the naive reader. They’re beautiful examples of cargo cult science by creationists. Would you like to read them, or use them as bad examples? Here you go, download it for entertainment purposes only.

I read them anyway. I’m not going to bother with a detailed refutation, but I’ll give you the gist. The fundamental confusion in both papers is the nature of the evidence for an ancestral chromosome fusion, and a focus on irrelevant details that are not central to the argument.

The story is this. At some time after the separation of the human and chimpanzee lineages, two ancestral chromosomes, #12 and #13 in the chimpanzee, fused end-to-end to form a single chromosome, #2, in humans. Chimpanzee chromosome 13 forms the short arm (2p) and part of the long arm (2q) of human chromosome 2, while chimpanzee chromosome 12 forms most of the long arm (2q) of chromosome 2.

The primary evidence for this fusion is the comparative genetic content of these chromosomes. That is, most of the genes in chimpanzee chromosome 13 are found in human 2p, and most of the genes in chimpanzee chromosome 12 are in human 2q. The chromatin binding patterns line up, the sequence analysis confirms, and there have been some lovely FISH studies that show the correspondence.

What has since been done is that a prediction was made that there ought to be fragments of telomeres (the end caps of chromosomes) in the middle of chromosome 2, at the fusion site. Which has been examined. And the prediction has been confirmed.

Bergman and Tomkins ignore every single bit of that. Instead, what they do is focus on just the region of the fusion, and complain that it is a tangled mess and hard to interpret — that it is a degenerate telomeric region, rather than a complete and intact telomere, which is what they demand be present. This is an unrealistic expectation, given that every paper on the structure of the fusion region makes the point that it is degenerate.

An analogy: imagine a red Ford Mustang and a blue BMW X6 are in a head-on collision, and both have totally wrecked front ends, with bumpers and radiators and headlights interlocked and everything about their grilles in tangled confusion, and with bits and pieces torn loose and flung about. You’d be able to look at the crash and still tell by everything in and behind the engine compartment that Car #1 was a Mustang and Car #2 was an X6.

Bergman and Tomkins are the bewildered and incompetent investigators who ignore every other factor in the crash, look at a few particularly mangled bits of the wreckage, and declare that they can’t identify it, therefore…the two vehicles were assembled at the factory in this particular configuration, and no crash occurred. But they use lots of sciencey language to explain this at tendentious length, which is sufficient to convince non-scientists that the interpretation of an obvious historical event has been refuted. And that’s all they need to do to accomplish their goals: fling about unfounded fear, uncertainty, and doubt to win over the ignorant.