Adam, Eve and human population genetics, Part 12: addressing critics - Poythress, population genomics, and locating the historical Adam | The BioLogos Forum


(system) #1

Note: In this series, we explore the genetic evidence that indicates humans became a separate species as a substantial population, rather than descending uniquely from an ancestral pair.

In the last two posts in this series (here and here), we have been exploring the anti-evolutionary arguments of Dr. Vern Poythress in his brief book Did Adam Exist? – specifically, his arguments alleging that that the human and chimpanzee genomes are only 70% identical. As we have seen, this line of argumentation is intended to call human – chimpanzee common ancestry into question, in part because shared ancestry is used in some methods of estimating the ancestral population size of our lineage. Since Poythress intends to argue that human ancestral population genetics cannot establish that humans descend from a population, rather than a pair, attempting to undermine confidence in common ancestry is part of the overall thrust of the book.


#3

Another great post Dennis!

It baffles me how somebody who doesn’t understand the science can think they are qualified to explain it to others in a book.

If Poythress’ goal was to report the truth, he would surely have checked his claims over with experts first? The fact that he didn’t do this tells me that he was less interested in the truth and more interested in shoring up peoples faith with contrived facts.

I find it truly disappointing when Christians engage in this sort of dishonest behaviour but it happens all the time. We see it in books like this (Creation vs. Evolution - Ralph O Muncaster) or this (Doctrine: What Christians should believe - Mark Driscoll).

Poythress’s book is just another among many that will deceive Christians because his agenda outweighs his commitment to the truth.


(Dcscccc) #4

from the article:

" we see mutations in genes that form nested hierarchies in the human, chimpanzee, gorilla, and orangutan genomes."-

and we also find mutations that doesnt form nested hierarchies. so according to this logic- does it disprove commondescent?

"By far and away the simplest reason for this pattern is common ancestry, "-

we also find nested hierarchies in cars .doest it prove that cars share common ancestry?

“We also see the remains of a gene in the human genome devoted to large-scale egg yolk production”-

not realy. the viteliogenin is a multi functional protein. so the claim that human have a pseudo-gene for egg yolk function isnt true:

http://www.sciencedaily.com/releases/2011/11/111129092428.htm


#6

An ortholog of this gene does serve a purpose in insects but this is irrelevant because it has no function in non-oviparous mammals. We know this because in mammals it is a highly fragmented pseudogene. The fact that only egg laying mammals have a working ortholog of this gene should serve as a clue for you (it’s for egg yolk in vertebrates which is why there isn’t a single non-egg laying mammal that has a working copy of it).

There are literally 3 - 4 tiny fragments of this gene that are found in apes (representing a mere 5% of the original gene). It is only these fragments which link us back to our egg laying ancestors. What is left of this pseudogene is so far removed from a working gene that it is laughable when creationists suggest that this was once a working gene in humans.

Here I’ve taken VTG1 in chickens and aligned it to the fragments that remain in various mammals.

Here is the neighbourhood for VTG1 in chickens (Note the neighbouring genes)

And here is where these fragments of VTG1 are found in apes. I’ve labelled the three remaining fragments that match the working gene: S1, S3, S4 (These codes correlate to the aligned portions in my original diagram)

Even though a mere 5% of this gene remains, the same 5% is found in all the apes. The fragments are found in the same correct order in all the apes (ELTD1 -> S1 -> S3 -> S4 -> PTGFR). The fragments are found in identical locations (the same gene neighbourhood) in all the apes.

Regarding your critique about nested hierarchies, you say the same thing in every article and this has been explained to you on multiple occasions.


(David Hume (nom de plume)) #7

Aceofspades nicely expresses how I see this series on Prof Poythress’ incompetence. As I’ve written on other threads, I think the most important question for evangelicals is: why are you so prone to believing uninformed commentators who write tosh? Why is it even reasonable for a Christian geneticist to respond at great length, in multiple blog posts, to a person with no qualifications or scientific credibility at all, when that person puts easily-refuted scientific claims into a non-peer-reviewed religious publication? Friends, in what world is this anything other than madness? Have you noticed that this happens all the time?

Prof Poythress deserves censure, but the bigger question is why evangelicalism has created such a welcoming environment for scholars and pseudoscholars alike to splatter the world with intellectual garbage. I have my theories.


#8

A response by Pierre Jerlstrom of creation.com: :kissing:

A closer look at the pseudogene DNA sequence data that supposedly supports the primate evolutionary tree reveals some major inconsistencies:

A large fraction of most pseudogenes differ considerably from their alleged parent genes which makes the interpretation of the data questionable.
Although some pseudogenes such as LINEs and Alus appear to be hierarchically shared between primates, others clearly are not. An example of such a discordancy is the sharing of SINE elements between evolutionarily more-distant organisms to the exclusion of animals of intermediate evolutionary derivation, despite the presence of intact homologous genetic loci in the latter.
Pseudogene sequences are frequently exchanged. This complicates any interpretation of phylogeny.
One evolutionary tenet is that pseudogenes such as SINEs and LINEs insert randomly. The independent insertion of such sequences in the genomes of two clearly unrelated animals should therefore be virtually impossible. So the presence of identical sequences at homologous sites in the genomes of two organisms unquestionably indicates common ancestry. However, the independent acquisition of both LINE and SINE elements at the exact site in different animals has now been demonstrated. Moreover, it has now been shown that these elements have insertion hotspots at specific DNA sequences, and at chromosomal cleavage/break sites in bent or coiled DNA.

It would also not seem impossible to me that truncated sequences might in some cases actually have a purpose and a function. Too often junk dna has been found to have a useful purpose, just like vestigial organs have been found not to be vestigial, but to have a useful purpose. So this should make one cautious about expressing a uselessness for sequences for which one does not know the purpose at the present time.

Pointedly, ratios of synonymous/non-synonymous substitution are largely, if not completely, inapplicable to some pseudogenes with known or potential functions. The Makorin1-p1 murine pseudogene10 performs a function completely different from that of its peptide-encoding paralogous (counterpart) gene, and it is very doubtful if any analysis of the KA/KS of the Makorin1-p1 pseudogene would cause the analyst to realize that this ‘severely crippled’ pseudogene is actually functional. Two snail pseudogenes are each functional in spite of being unable to code for even a full-length protein, or for any peptide at all,11 let alone for peptides that are, relative to those synthesized by their gene paralogs, conserved at synonymous sites! In addition, it has been shown that pseudogenes, despite being incapable of encoding peptides of appreciable length, can nevertheless encode very short peptide segments (8–11 amino acids length, with only a modest degree of sequence conservation over even this 8–11 amino acid span) that can at least potentially serve an immunobiological function.12 Clearly, the potential or actual function of a pseudogene can only be determined by direct experiment, and it is high time that evolutionists abandoned KA/KS as a ground for the a priori discounting of pseudogene function. (John Woodmorappe, Dec. 2004)


(Dennis Venema) #9

Ace & David,

I too share your bafflement about Poythress’ confidence in expounding what he does not understand - but I don’t think he’s doing this with an intent to deceive. I suspect he feels he does understand the material.

One also wonders who peer-reviewed the paper / book. Poythress is the editor of the journal his paper appears in (before it was adapted into the short / popular book) - so he would have had complete control of who peer reviewed it. It does not seem to have been reviewed by anyone with expertise in genetics. Todd Wood would have been a good choice if Poythress did not want an “evolutionist” to review it.

I too wonder why evangelicals are so very prone to accept “science” that supports their views when they are so reluctant to accept genuine science that does not (seem to) square with their prior convictions. It shows that their disposition to science is not scientific - the mark of a genuine researcher is that they are equally skeptical of material that seems to support or oppose prior views, and equally willing to follow the evidence where it leads in either case.


#10

Too often? Not too often for me; in fact, it’s about what I would expect. Precisely how often is too often, John?

More specifically, how much of the human genome that was categorised as “junk” (no known function) has been found to be functional? Please give real numbers, based on evidence, either as a ratio or in bp.

P.S. Merely being transcribed does not imply function.


(Dcscccc) #11

ace. 3 questions before we will continue:

1)how do you know that this is a real pseudogene?(see john coment about pseudognes)
2)if it only remains 5% from the original gene, how you can even know it was a gene?
3)what about convergent loss of those genes? we know about a lots of examples that genes loss convergently (like the igw gene for example).


#12

Joao, how often would you expect junk dna to have a useful purpose, some type of function?

(By “too often”, I meant so often that it seems rather inappropriate to even call junk dna, junk. Rather, it might be better to assume that it actually does have a purpose, even when we don’t know what the purpose is. This would change the thinking approach to pseudogenes or junk dna.)

I agree that merely being transcribed does not imply function.


#13

John, your inability to provide even a single number says it all.

Numbers, man. You don’t have them! Words won’t do.


#14

Numbers are important. I see you did not provide any either.


#15

Yes, numbers are important. So when you make quantitative claims like “Too often junk dna has been found to have a useful purpose,” you should be familiar with the quantitative evidence.

You aren’t. So why make quantitative claims when you haven’t examined any quantitative evidence, John?

You show me your numbers and I’ll point you to the actual evidence that you’re avoiding in favor of pure hearsay.


#16

And numerically, how often is that?


(David Hume (nom de plume)) #17

Prof Venema,

I too share your bafflement about Poythress’ confidence in expounding what he does not understand - but I don’t think he’s doing this with an intent to deceive. I suspect he feels he does understand the material.

Just my opinion, but I think evangelicalism looks far worse when behaviour like Poythress’ is described as anything other than deception (to some degree). If he’s just another propagandist, then his conduct can be dismissed as ‘sin’ or dysfunction. But, as we all seem to agree on, Poythress’ tosh is probably not merely the product of a less-than-completely forthright person. That means it is the product of something(s) other than plain old moral weakness. Leaving aside the question of whether such lapses of integrity are more common among certain kinds of believers, I would repeat what I think is the bigger question for evangelicals:

Why is this so common in your religion? Why does this thread itself include easily-discredited claims from pseudoscholars, quoted approvingly by believers? Friends, those questions are a lot more interesting than questions about the mixed motivations of scholars whose livelihood depends on their profession of belief in anachronistic readings of weird ancient writings.

If you want to attempt to think clearly about all this, I suggest you begin with some recent experimental psychology examining the moral competence of people in a societal sector unrelated to religion. Extremely interesting stuff, of evident relevance to any consideration of why Poythress or thousands/millions like him become unreliable, perhaps even dishonest, in certain circumstances.


(Ray Calvert) #18

I will need to read what Dr. Ploythress has written to know exactly what his argument actually is. If what is reported here is correct I might point out that while Dr. Polythress teaches New Testament at Westminster TS he has a Ph.D. in Mathematics from Harvard and has taught college level math at Fresno State. I had Dr. Polythress as an instructor many years ago. He is a brilliant individual. As I read what has been written here I suspect the argument he is making is coming from the world of probability. I would not be so fast to dismiss his argument as the naive rambling of someone who does not understand science.


(David Hume (nom de plume)) #19

Ray, once you have read the series of posts by Prof Venema, you will know that Prof Poythress’ intelligence is not even a peripheral topic.

Poythress’ writings on this topic are indeed naive ramblings of someone who does not understand population genetics. Of course, no one said that this means that Poythress “does not understand science.” It does mean that he engaged in scholarly incompetence worthy of censure.


#20

In 2012, the ENCODE project, a research program supported by the National Human Genome Research Institute, reported that 76% of the human genome’s noncoding DNA sequences were transcribed and that nearly half of the genome was in some way accessible to genetic regulatory proteins such as transcription factors.[6] However, the suggestion by ENCODE that over 80% of the human genome is biochemically functional has been sharply criticized by other scientists,[7] who argue that neither accessibility of segments of the genome to transcription factors nor their transcription guarantees that those segments have biochemical function and that their transcription is selectively advantageous.[8][34][40][41] In a 2014 paper the leaders of the ENCODE project tried to address “the question of whether nonconserved but biochemically active regions are truly functional”. They acknowledged that “the larger proportion of genome with reproducible but low biochemical signal strength and less evolutionary conservation [e.g. 70% of the documented transcribed coverage] is challenging to parse between specific functions and biological noise”, that the essay resolution often is much broader than the underlying functional sites, and that therefore some of the reproducibly “biochemically active but selectively neutral” sequences are unlikely to serve critical functions. On the other hand, they argued that the 12–15% fraction of human DNA under functional constraint, as estimated by a variety of extrapolative methods, may still be an underestimate (Wiki)

Originally, it was assumed that all non-coding dna was “junk” or pseudogenes. Again, this is led by the tendency of some scientists to assume that if they don’t know what it is good for, it is probably no good. (My opinion is that this is an outgrowth of evolutionary theory. Your opinion may differ. ) The treatment of so-called vestigial organs is similar (IMO). So now, instead of 98% non-functional, there is estimated to be at least 12-15% functional in some way. While this is obviously less than 50%, it is also not proven that the rest or a substantial part of the rest is not functional in some way. The geneticists are still discussing this issue, and will continue to investigate it in the years and decades to come.


#21

Why aren’t the creationists investigating, John? Why don’t they produce new evidence?

And don’t you see that you’ve contradicted your claim of “it was assumed,” because anyone simply assuming that would never have been looking for function. Or are you implying a distinction between geneticists and “evolutionists”? If so, what would that be?

Questions for you:

  1. Are introns coding or noncoding? Are they functional?
  2. Are promoters coding or noncoding? Are they functional?
  3. Are enhancers coding or noncoding? Are they functional?
  4. Are telomeres coding or noncoding? Are they functional?
  5. Are replication origins coding or noncoding? Are they functional?

When were each of these sequence features discovered, John? To what specific time period does your vague “it was assumed” refer?


#22

Joao, you will have to take up your argument with the many others who disagree with you on this. Eg.

"www.news-medical.net/health/What-is-Junk-DNA.aspx
Nov 17, 2014 - In genetics, the term junk DNA refers to regions of DNA that are noncoding. DNA contains instructions (coding) that are used to create proteins in the cell. However, the amount of DNA contained inside each cell is vast and not all of the genetic sequences present within a DNA molecule actually code for a protein."
What was once known as junk DNA turns out to hold hidden treasures, says computational biologist Ewan Birney > By Stephen S. Hall | Sep 18, 2012 In the 1970s, when biologists first glimpsed the landscape of human genes, they saw that the small pieces of DNA that coded for proteins (known as exons) seemed to float like bits of wood in a sea of genetic gibberish. What on earth were those billions of other letters of DNA there for? No less a molecular luminary than Francis Crick, co-discoverer of DNA’s double-helical structure, suspected it was “little better than junk.”
The phrase “junk DNA” has haunted human genetics ever since. In 2000, when scientists of the Human Genome Project presented the first rough draft of the sequence of bases, or code letters, in human DNA, the initial results appeared to confirm that the vast majority of the sequence—perhaps 97 percent of its 3.2 billion bases—had no apparent function. The “Book of Life,” in other words, looked like a heavily padded text. (scientificamerican.com)