James Tour on Orphan Genes

(Curtis Henderson) #1

A colleague of mine sent me a link yesterday to a rather lengthy essay by James Tour. Much of it is on pre-biotic chemistry, but Tour eventually hits on a few evolution-related topics like the ENCODE project and orphan genes.

https://www.jmtour.com/personal-topics/evolution-creation/

He has this to say about orphan genes:

Then again, other geneticists contest that many biologists have simply ignored a rapidly growing list of thousands of putative orphans in the human genome because they cannot find homologous non-gene sequences in the chimpanzee genome. If it is true that some biologists are ignoring data that does not easily fit with their common descent model, it is disconcerting.

Does anyone know who these geneticists are and where these claims are? A quick Google search brought me to an essay from Uncommon Descent.

The claims there sound a lot like Tour’s claim, but surely this is not where he is getting his information on a serious scientific topic. Right? The UD article is pure propaganda.

P. S. I’m hoping this thread is appropriate for the new venue, but feel free to move it elsewhere, @swamidass

Human and Chimp Similarity (Mind the Controls)
(T J Runyon) #2

“Evolutionary bias” :man_facepalming:t2: If there were an evolutionary bias and they are ignoring orphan genes to ignore problems with common ancestry why would they even announce the discovery of orphan genes? Evolution affirming scientists are the ones who sequence the genomes and do all the work. So if they were into ignoring evidence they wouldn’t even announce their existence.

(Mikkel R.) #3

Well I’d be interested in the claim that there are no homologous non-gene sequences in the chimpanzee genome. I’d like to see some concrete examples. It’s one thing to just SAY this is the case, it’s another to give examples of that. Tour gives zero.

I predict the claim is bullshit. I’ll eat my words should they be proven wrong.

#4

I am with @Rumraket on this one. Nearly every ID/creationist I have read or discussed this topic with has completely confused gene with DNA. What they don’t seem to understand is that all genes are DNA sequences, but not all DNA sequences are genes. When they read a papers saying that humans have genes that chimps do not they automatically assume that they don’t share homologous DNA sequence. In many, many of the cases I have seen there is homologous DNA for human orphan genes. The only difference is that the DNA is transcribed into RNA in the human genome.

@pnelson is currently working on orphan genes, but I suspect it will be a case of ID theorists being hoisted by their own petard. Orphan genes are a perfect example of how a few mutations in seemingly random DNA sequence can produce function. Orphan genes are an absolute gold mine for evidence that supports evolution.

(Mikkel R.) #5

Yep. Ironically because IDcreationists have some sort of a priori conviction that proteins can’t evolve de novo from non coding DNA, they take their very existence as evidence against evolution.

It just keeps being the case that homologous non coding regions exist in closely related species. So they are forced to make these weird probability argument, which essentially rest on their a priori belief that de novo protein evolution should be impossibly rare.

#6

Exactly. ID/creationists are dragging the goal posts all over the field. They always have teleology and front loading to fall back on so that even when we see novel and functional sequence evolve right in the lab they will claim that it was designed to take on that function. That may make their non-scientific audience happy, but it elicits one big eye roll from the scientific community.

Just to head off any misunderstanding, I don’t want to rope EC’s and TE’s into this criticism. ID theorists are claiming that evolution can not produce the features. EC’s and TE’s are not saying this. Rather, EC/TE incorporates God into the evolutionary process, and into nature as a whole (if I understand it correctly).

(S. Joshua Swamidass) #7

If someone writes a clear, evidenced based note to him, I can send it to him. He would likely read it. Work from @roohif might help, he blasted the orphan genes against the human genome: Jeff Tomkins’ Orphan Genes – Mind The Gap! – roohif.

(John Harshman) #8

I’m surprised that the sequences are on average only 95% identical. Is that counting alignment gaps, i.e. indels, as differences?

(S. Joshua Swamidass) #9

That is average for the whole genome if you include gaps and indels.

(John Harshman) #10

Yes. It’s just that it’s a bad idea to measure genetic distance that way. I can think of one valid reason: when estimating heteroduplex melting temperatures. Certainly not in any evolutionary context, though.

(Curtis Henderson) #11

A bit of digging resulted in finding a document written by @pnelson and Richard Buggs.

https://www.researchgate.net/publication/304039133_Next_generation_apomorphy_The_ubiquity_of_taxonomically_restricted_genes

Here is a specific claim made in the article:

The origins of TRGs continue to be a mystery, and their existence seems to be at odds with many of our hypotheses about how evolution works. An hypothesis-driven reaction to this might be to ignore TRGs. For example, two pioneering studies of gene evolution in humans (Wu et al., 2011, Knowles and McLysaght, 2009) excluded over 200 genes that had no detectable orthologs in other primates, on the assumption that their TRG status was simply due to incompleteness of other primate genome drafts. Similarly, in an analysis of gene family evolution across 12 Drosophila genomes, Hahn et al. (2007) “found 23,070 families that consisted of a single gene and that appeared to have evolved on a terminal lineage (i.e., they are found in only a single species). These single-gene families were regarded as artifacts of the annotation process, and were removed from further analysis.”

The assertion is that, according to the work of Wu and Knowles/McLysaght, over 200 genes had no detectable orthologs in other primates. I’ll be working on getting to those article soon.

(S. Joshua Swamidass) #12

Now that we have more complete genomes, though, we can test the two hypotheses here:

  1. @pnelson and Buggs hypothesize that these 200 genes will have no homologous sequences in the new ape genomes.

  2. Wu, Knowles, and McLysate hypothesize that many of them will have will have homologous sequences in the ape genomes, though not necessarily all of them (deletions in the ape lineage would prevent this).

@roohif, @glipsnort, @Troendle, or @evograd, are any of you willing to help us test these two hypotheses? This analysis be a great way to present this to Tour.

(S. Joshua Swamidass) #13

For the record, I am the scientist in that article who led him to write this text:

Some biologists say that “random mutation and natural selection” have long-been recognized by many evolutionists themselves to be insufficient to account for the complexity of life. They cite research from the 1960s and 1970s suggesting that neutral drift is quantitatively more important than natural selection in understanding genetic differences between organisms. Neutral drift (Neutral theory of molecular evolution - Wikipedia) can be considered as small genetic variations that occur from, for example, parent to their offspring, and this occurring for successive generations. Moreover, the mechanisms of evolution and their relative importance are continuously subject to careful scientific examination and revision so “careful examination of the evidence” has not been avoided. Some biologists suggest that the core of evolutionary studies for the last several decades has not centered upon the sufficiency of Darwinian Theory, defined as “random mutation and natural selection.” (So maybe those biologists should join me in signing A Scientific Dissent from Darwinism .) But evolution is both about the mechanism by which change occurs over time, and the theory of universal common descent (Common descent - Wikipedia). This is the idea that all life shares a common ancestor. For those less trained in science, this theory does not propose, for example, that humans evolved or descended from chimpanzees, but that humans and chimpanzees share a common ancestor in the distant past. I can understand why those fluent in the field of genetics would be convinced by that theory; there is an impressive quantity and insightfulness to the work.

(Blogging Graduate Student) #14

Sure, point me to a list of de novo gene sequences and I’ll look for homologous sequences.

#15

Recombination events would also mask detection if they are using BLAST/BLAT. The settings in the BLAST/BLAT searches could also result in false negatives. It might be interesting to look at the actual DNA from that syntenic region for a few of them.

(S. Joshua Swamidass) #16

@pnelson, to maximize the value of this exercise, can you please give us the list of de novo genes you identified in humans?

(Faizal Ali) #17

Good discussion here by Larry Moran of a paper investigating the issue. The paper, BTW, is from 2015.

Take home messages:

  1. There is a high rate of false-positives in initial genome screens for putative orphan genes. The large majority of these turn out not to be genes at all.

  2. There is a high rate of expression of new transcripts from previously unexpressed parts of the genome. This the most likely source of the “orphan genes”, as opposed to their being magically poofed into existence by God.

It’d be interesting to see Tour’s response to this. It’ll give us an idea if he is really open to changing his views when presented with evidence he had overlooked. Hopefully he will. He’d be a formidable person to have on the side of the good guys, given his history.

#18

Those are separate, but still important, issues. Even Larry Moran would agree that there is possible evidence (e.g. sequence conservation) for some orphan genes being functional. I would also agree with Moran that there are many cases where non-functional transcripts are being incorrectly reported as functional orphan genes.

If nothing else, James Tour is asking how the human genome can have stretches of DNA not found in the chimp genome.

(S. Joshua Swamidass) #19

He has legitimate questions. He does not have means to see the data for himself. He has relied on hearsay like that from @pnelson and Buggs. If we can show him the data so he can understand for himself, testing their assessment, he is likely to change his mind.

(Faizal Ali) #20

Point two addresses that: They are found in the chimp genome. They just aren’t genes.

Tour probably doesn’t know the difference.