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.
If two chromosomes underwent a Robertsonian Fusion, so there was now some former terminal repeat stuff located around the point of fusion, wouldn’t we expect that this was no longer functioning the way real terminal sequences do? Then we would not expect it to continue to be conserved. And isn’t that what he is seeing?
Wait a minute – doesn’t the absence of conserved sequence mean that the gene wasn’t intelligently designed but rather evolved instead?
believers have to focus on some tiny detail that they can make no sense out of because the predominance of the evidence always points against their point of view. They seem to have a pathological fear of being wrong and will defend their position far into the absurd.
works the same in politics.
uncle frogy
As a geneticist at an actual university, Tomkins is one of only a few dozen core antievolutionists who make fact claims with technical source documentation (I keep track of the dramatis personae and their output in my #TIP project at http://www.tortucan.wordpress.com). As a result, countering those “heavy guns” is paramount compared to jousting with lower level redactors (however prominent they may be) like a David Klinghoffer (ID) or a Ken Ham (YEC). Denyse O’Leary has recently linked directly to Tomkins work (mispelling his name as “Tompkins”) and not noticing that he’s writing as a doctrinal YECer) so his work has leaked over into the compartmentalized ID land after all. It’s good seeing that counter-punches are getting done on Tomkins, and hope more will be done, especially given the likelihood that antievolution efforts (YEC or ID inspired) will be emboldened by the new Trump administration pushing its thumb down on the pro-Kulturkampf scale.
A study of the King James Bible refutes the concept of a fusion of an alleged Old and New Testament. Close examination of the texts show that they are written in 17th-century English. This contradicts the fact that the alleged Old Testament, being the same as the Jewish Tanakh, is composed in Hebrew and Aramaic, and the New Testament is composed in Greek. When both Testaments are fused, one would expect a bilingual book in the middle, most likely a synthesis of the Book of Malachi and the Gospel of Matthew, in both Hebrew and Greek or perhaps in a combination of the two, referred to as Grebrew.
Another fine case of the creationist ability to focus on little anomalies (or what they imagine to be anomalies) while ignoring completely the bulk of the relevant data. Is that a beam in your eye or are you just glad to see me?
There might be some real question buried in the crap, though. Is the area of fusion more degenerate than would be expected from simple neutral evolution? Could there have been selection to deactivate the centromere? Is there a mechanism involved in altering the ex-telomeres that doesn’t happen in most junk sequences, or are other short repeats different between species by about the same amount? (I have no idea.)
I’m not sure chromosome fusions generally are adaptively driven, just luck of the mutation draw and then selection can play off what remains. I do see one paper that identified regional hotspots in C2 https://www.researchgate.net/profile/Laura_Scheinfeldt/publication/221804042_Clusters_of_Adaptive_Evolution_in_the_Human_Genome/links/0a85e52fe245c61ff6000000/Clusters-of-Adaptive-Evolution-in-the-Human-Genome.pdf
I would have thought it would be hard to argue with whole chromosome painting. I guess that’s why Tomkins doesn’t mention it.
#7. In case that was a reply to me, I’m pretty sure chromosome fusions are not adaptively driven. But I do wonder if, given fusion, deactivation of the extra centromere is adaptive, and thus faster than drift would suggest.
Indeed I was reacting to your point, John. I’m processing the new primary source citations Tomkins’ new paper for my #TIP work http://www.tortucan.wordpress.com as we speak (I strive to track all such comprehensively), but trying to follow up on this interesting issue on the fly, adding the info as relevant so its like lagniappe for me right now. There seems to be some analysis of centromere inactivation in sticklebacks, recently done, https://link.springer.com/article/10.1007/s10577-016-9535-7
…He hasn’t updated his argument in 5 years. How can he have gone that long and still a) not get that we would expect a telomere to be degenerate after being stuck in the center of a chromosome and unable to perform its function, and b) not get that the main reason why the chromosome is identified as a fusion is because the overall sequences of the two halves are homologous to the sequences of the chimp chromosomes? Moreover, in five years, why hasn’t he come up with any new arguments and just stuck with this one? It’s like creationists are static and incapable of changing their ideas or coming up with new ones.
@11/emergence
Because he’s a goddamn liar, that’s why.
Listen, these people are pretending to do science but that’s it. Worse, they’re attempting to turn science, like everything else they touch, into a lurching shit-golem zombie parody of itself to further their agenda. I can’t adequately put words around this; it’s like what a pimp does, almost, one with a sadistic streak and a complete vulgarian outlook, who can’t even appreciate what he’s pimping out.
We can’t keep treating these people like decent functioning human beings. They are every bit as insane as any given suicide bomber with a shirt full of dynamite, just a lot less courageous. Expect them to do this. Don’t give them an inch.
Marissa, I must beg to differ. Tomkins, and most antievolutionists, completely believe every thing they say. And the previous poster has hit on what is going on in Tomkins’ head, how over years he seems unable to see something that should be obvious. And that’s because Tomkins is literally NOT SEEING it. I’ve been studying the methodology of creationism (and its ID spinoff) at depth for 20 years, #TIP “Troubles in Paradise: The Methodology of Creationism” project at http://www.tortucan.wordpress.com, working through the details of thousands of writings and the 2000-odd antievolutionists producing them. These range from silly nutballs like Kent Hovind, to quite bright folk like lawyer Phillip Johnson (who got into Harvard when he was 16), and surveying the mechanics of how they assemble their arguments ultimately offers clues as to what is (and isn’t) going on in their heads.
All antievolutionists share 4 core traits with others who believe things that are really not true, and none of them involve lying (in the sense of genuine mendacity, where the person says something they know isn’t so).
1) a pathological over-reliance on secondary sources, which they don’t fact check. In the antievolution case, as virtually all of them are “Kulturkampf” conservative religious, they are in a sense pre-adapted to accept as non-negotiable secondary sources like the Bible. 95% of the 2000 antievolutionists I’ve been surveying do not draw on primary source work, they simply repeat secondarily things they want to be true, and incorporate those tropes into their reinforcement mechanisms.
2) The 5% of antievolutionists who do generate core claims (and its only about 3 dozen people currently, 2/3 YECers & 1/3 IDers) draw on a very limited data set, roughly 10% of the relevant available technical data stream. I’m measuring this directly, cataloguing bit by bit the full range of their work, involving around 2300 sources so far out of a 20,000+ primary source dataset. Tomkins is one among that small band of core fact claimants.
3) Here’s where Tomkins merges with the non-core majority: the object of any genuine hypothesis is explain the data, say what you think happened. But as the antievo dataset is already trimmed, they’re screwed on that up front. But it’s much worse than that: no antievolutionist actually thinks through what they think happened, even with that limited 10% set. Apart from claiming the centromere bits are functional, we don’t really get a picture of what he thought was going on when God engineered Adam & Eve only 6000 years ago, along with the primates and australopithecines and trilobites and therapsids and dinosaurs, all of which must have been living simulatenously in the pre-Flood world. None of that filtered into his 2017 paper, not by evasion, but because Tomkins literally hasn’t thought through a “Map of Time” in his own head that he could be applying in the way scientists outside of his box would. Tomkins can tunnel vision in on minutia effortlessly, of course, always with the object of verifying what must be so no matter what. Btw I’ve been source cataloguing the citations in the new 2017 paper, and Tomkins added 17 new citations he had not previously drawn on in his earlier work. So its not that he isn’t expanding his citation field, its just that he only allows them to fit into a puzzle that is already done and cannot be changed.
4) which leads to the deep fundamental glitch in antievos’ heads: they literally cannot conceptualize evidence that would prompt them to change their mind. Ken Ham was being revealingly honest when he answered the questioner at the Ham/Nye debate on this point, that NOTHING could persuade him that the Bible argument was wrong. He means it. And even “honest” creationists like Todd Wood, who can readily acknowledge that there is evidence for evolution, has to ignore that consciously in presuming somehow that evidence can’t really mean what it appears to. Yet still he will not lie about it.
The most diagnostic example of this 4th core problem is the inability of antievos to imagine what transitional forms would need to look like for them to accept them as such. NOTHING can qualify for them, and if you ask them you won’t get prevarications, you’ll get “deer in the headlight” not thinking moments.
I’ve tried to sum up the mindset in the general term “Tortucans,” people who live in a mindshell that is impervious to evidence, just bounces off the mindshell. We’ve all met them over the years. https://www.youtube.com/watch?v=QOuCmIDKEkg Tortucans can be brilliant or stupid, well educated or illiterate, politically liberal or conservative. and everything in between. They can be religious, or not (and I have met many a Tortucan atheist over the years).
So lots of fascinating things are going on (and not) in the noggins of people who believe things that are not true. The antievolution case is simply an extremely useful measurement tool, because so many have spilt ink over so long a time that we can see the underlying patterns of behavior. It’s just rarely something so simple as “lying.”
@rjdownard #13:
Bloody hell!
When you publish your thesis (if it passes), can I have a copy, please?
Fascinating stuff. I’ve just got to be careful not to want it to be true ;-)
While I do have a BA in history from Eastern Washington University, my #TIP research has been an applied hobby. The traits I’ve laid out are based on the observed activity of the field (whether any of that could be buffed up into a doctoral thesis I may be too old to find out), but I have been following the relevant technical work to at least feel my way into what brain systems might ultimately be involved in the phenomenon. I’ll quote this section from page 367 of my “Evolution Slam Dunk” work surveying antievolutionist coverage of the reptile-mammal transition case (which I just brought out a few months ago):
The psychological concepts of how minds resolve Cognitive Dissonance or how they can fall into a Confirmation Bias mode have been the subject of much scientific study, such as Louisa Egan et al. (2007), Keise Izuma et al. (2010), Bradley Doll et al. (2011) and Johanna Jarcho et al. (2011). But either attitude might be all too easy for anyone capable of what Bryan showed on the stand in 1925. In honor of him, or rather his Inherit the Wind doppelgänger, I dubbed such a hypothetical cognitive property (the actual ability to not think about things you don’t think about) Matthew Harrison Brady Syndrome, or MHBS for short. I do confess to having liked the serendipitous implication of the “BS” part too.
There appear to be separate brain centers devoted to belief, disbelief and uncertainty, Sam Harris et al. (2008), and I suspect that my hypothetical MHBS component would involve at least the anterior cingulate cortex, a primate-derived social problem-solving system which plays a significant role in human self-deception and conflict resolution, Cameron Carter et al. (1998; 2000), George Bush et al. (2002), Vincent Van Veen & Carter (2002), Kristin Laurens et al. (2003), Phan Luu & Michael Posner (2003), Nobuhito Abe et al. (2006), Peter Rudebeck et al. (2006), Posner et al. (2007), John Anderson et al. (2009), Benjamin Hayden et al. (2009), Thilo Womelsdorf et al. (2010) and Jill O’Reilly et al. (2013).
Whether or not something like MHBS actually exists as a neurobiology component (and only time and neuroscience could settle an issue like that), it was an interesting concept to play around with, and certainly made a lot of sense of what I was seeing in the many antievolutionists I have studied, where not thinking about things was on display for all to see, again and again.
[The sources I cited for this passage were:]
Abe, Nobuhito, Maki Suzuki, Takashi Tsukiura, Etsuro Mori, Keiichiro Yamaguchi, Masatoshi Itoh, & Toshikatsu Fujii. 2006. “Dissociable Roles of Prefrontal and Anterior Cingulate Cortices in Deception.” Cerebral Cortex 16 (February): 192-199.
Anderson, John R., John F. Anderson, Jennifer L. Ferris, Jon M. Fincham, & Kwan-Jin Jung. 2009. “Lateral inferior prefrontal cortex and anterior cingulate cortex are engaged at different stages in the solution of insight problems.” Proceedings of the National Academy of Sciences 106 (30 June): 10799-10804.
Bush, George, Brent A. Vogt, Jennifer Holmes, Anders M. Dale, Douglas Greve, Michael A. Jenike, & Bruce R. Rosen. 2002. “Dorsal anterior cingulate cortex: A role in reward-based decision making.” Proceedings of the National Academy of Sciences 99 (8 January): 523-528.
Carter, Cameron S., Todd S. Braver, Deanna M. Barch, Matthew M. Botvinick, Douglas Noll, & Jonathan D. Cohen. 1998. “Anterior Cingulate Cortex, Error Detection, and the Online Monitoring of Performance.” Science 280 (1 May): 747-749.
Carter, Cameron S., Angus M. Macdonald, Matthew Botvinick, Laura L. Ross, V. Andrew Stenger, Douglas Noll, & Jonathan D. Cohen. 2000. “Parsing executive processes: Strategic vs. evaluative functions of the anterior cingulate cortex.” Proceedings of the National Academy of Sciences 97 (15 February): 1944-1948.
Doll, Bradley B., Kent E. Hutchison, & Michael J. Frank. 2011. “Dopaminergic Genes Predict Individual Differences in Susceptibility to Confirmation Bias.” The Journal of Neuroscience 31 (20 April): 6188-6198.
Egan, Louisa C., Laurie R. Santos, & Paul Bloom. 2007. “The Origins of Cognitive Dissonance: Evidence From Children and Monkeys.” Psychological Science 21 (November): 978-983.
Harris, Sam, Sameer A. Sheth, & Mark S. Cohen. 2008. “Functional Neuroimaging of Belief, Disbelief, and Uncertainty.” Annals of Neurology 63 (February): 141-147.
Hayden, Benjamin Y., John M. Pearson, & Michael L. Platt. 2009. “Fictive Reward Signals in the Anterior Cingulate Cortex.” Science 324 (15 May): 948-950.
Izuma, Keise, Madoka Matsumoto, Kou Murayama, Kazuyuki Samejima, Norihiro Sadato, & Kenji Matsumoto. 2010. “Neural correlates of cognitive dissonance and choice-induced preference change.” Proceedings of the National Academy of Sciences 107 (21 December): 22014-22019.
Jarcho, Johanna M., Elliot T. Berkman, & Matthew D. Lieberman. 2011. “The neural basis of rationalization: cognitive dissonance reduction during decision-making.” Social Cognitive & Affective Neuroscience 6 (September): 460-467.
Laurens, Kristin R., Elton T. C. Ngan, Alan T. Bates, Kent A. Kiehl, & Peter F. Liddle. 2003. “Rostral anterior cingulate cortex dysfunction during error processing in schizophrenia.” Brain 126 (March): 610-622.
Luu, Phan, & Michael I. Posner. 2003. “Anterior cingulate cortex regulation of sympathetic activity.” Brain 126 (October): 2119-2120.
O’Reilly, Jill X., Urs Schüffelgen, Steven F. Cuell, Timothy E. J. Behrens, Rogier B. Mars, & Matthew F. S. Rushworth. 2013. “Dissociable effects of surprise and model update in parietal and anterior cingulate cortex.” Proceedings of the National Academy of Sciences 110 (17 September): E3660-E3669.
Posner, Michael I., Mary K. Rothbart, Brad E. Sheese, & Yiyuan Tang. 2007. “The anterior cingulate gyrus and the mechanism of self-regulation.” Cognitive, Affective, & Behavioral Neuroscience 7 (December): 391-395.
Rudebeck, P. H., M. J. Buckley, M. E. Walton, & M. F. S. Rushworth. 2006. “A Role for the Macaque Anterior Cingulate Gyrus in Social Valuation.” Science 313 (1 September): 1310-1312.
Van Veen, Vincent, & Cameron S. Carter. 2002. “The anterior cingulate as a conflict monitor: fMRI and ERP studies.” Physiology & Behavior 77 (December): 477-482.
Womelsdorf, Thilo, Kevin Johnston, Martin Vinck, & Stefan Everling. 2010. “Theta-activity in anterior cingulate cortex predicts task rules and their adjustments following errors.” Proceedings of the National Academy of Sciences 107 (16 March): 5248-5253.
Meanwhile, I’ll continue plowing away with my #TIP work http://www.tortucan.wordpress.com (with out without a PhD to dangle lol). It’s sometimes been a slow slog for me, but I was gratified to learn just yesterday that Christine Janis had ESD (and had been following my efforts from the UK) and was revising some of her upcoming mammal book to incorporate some of the sources I called attention to in my wee tome. One step at a time gang.
In case anyone wants the link of the human/chimp synteny of chromosome 2, but doesn’t know how to easily find it
http://uswest.ensembl.org/Homo_sapiens/Location/Synteny?db=core&r=2&otherspecies=Pan_troglodytes