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

Joao’s comments are dead on, and his antagonism may be explained by his annoyance at the gross mischaracterisation of the history of scientific consideration of non-coding DNA. I too am annoyed by this, but have come to expect it from creationists attacking science, so I tend to take a more philosophical approach. (By this I mean that I just sigh and remind myself that creationism almost never deals straight with science.)

The excerpt you posted was typical in its errors. It is easy enough to find accurate information about how geneticists and molecular biologists have thought about non-coding DNA. (Google Ryan Gregory to start.) The constant repetition of inaccurate accounts of this history is an important glimpse into the intellectual and psychological anatomy of anti-evolution apologetics.

Joao is right about junk DNA and about creationism’s failures. It’s your turn to look up a “history of genetics.” It’s rather different from the fables woven by apologists.

David, of course creationists never deal straight with science. They are creationists after all, right? But evolutionists always deal straight with science, right? They must, because they are evolutionists, they really have no choice, right?

But you have not been specific in your reply. Are you saying that Francis Crick never said what “Scientific American” claims he said? Are you claiming that Ewan Birney is a creationist? Are you saying that “news-medical” is a creationist site?

I’m not sure if Joao’s comments are “dead-on”, deadly, or dead in the water, but I’m quite sure he can explain his own motivations.

Dear johnz,

Your bitter and harsh words, inexcusably twisting (if not deliberately altering) what I wrote, do not mask the inaccuracy of the accounts of genetic history that you seem to prefer. And they are rather obviously inconsistent with the explicit standards for discourse in this forum.

You don’t seem interested in understanding genetics or geneticists. That’s your choice. But those (like me and perhaps several others on this forum) who do understand genetics will always find it difficult to sit quietly while inaccurate (and sometimes deliberately dishonest) fables are cited in lieu of substantive discussion of science and history.

I am truly sorry that you find my criticisms of your sources to be so deeply offensive. I am not at all sure that this is my problem.

I do not find criticisms offensive, David. Criticisms are necessary. But criticisms ought to be specific, dealing with the issue, not with the person. General comments about “someone’s naive ramblings” does not meet this standard. Nor does “creationism almost never deals straight with science” meet this standard. I posted two excerpts: one from news-medical, and the other from scientific american. I’m sorry I did not realize that these were creationist sources.

Since they are not creationist sources, and since the public accepts these sources as valid information, and since the quotes are relatively recent, then they are reasonable quotes in this instance.

Dear John,

I provided a specific source for you to examine (re the history of “junk DNA”) in light of your various claims on this thread, many from apologetic sources with no credibility. The two most recent sources you cite are “news medical” and wikipedia. The “news medical” site contains very basic errors and is unsuitable for serious discussion. A glance at the site should be enough to tell that it is not a serious source of biomedical review or analysis.

I don’t think you’re very curious about the history of “junk DNA” wrt consideration by actual biologists. If you are, read Gregory. Maybe we can get a discussion going after that.

That is not true. If you really believe that is true, why don’t you show me a geneticist who says that?

Do you notice that nothing you post here is based on evidence, John? Why is it all hearsay? Why in the next quote do you resort to hearsay about hearsay?

Here’s a geneticist’s guide to your false equivocation:

Again, not true in two ways. The small pieces of DNA that coded for proteins were always known to be associated with highly functional, noncoding sequences. This was understood in 1968. The second falsehood is that exons do not equal coding sequences. There are literally thousands of exons that are noncoding!

Here are just two examples:

All the results since confirm that. As “junk” is a negative classification, we expect some reclassification from junk to functional.

It’s your claim that “Originally, it was assumed that all non-coding dna was “junk” or pseudogenes.” Quoting a couple of nonscientists does nothing to support it.

They are not expert sources, and hearsay (especially double hearsay) is not evidence.

Nor do unsupported comments about “… it was assumed that all non-coding dna was “junk” or pseudogenes.” You have yet to show that any knowledgeable person did so.

Two specific criticisms:

  1. The vast majority of the genome has no known function and the available evidence is consistent with it having no function. That remains the case. More of the junk will be found to be functional, but the functional fraction of the human genome will remain tiny. (Why is the functional fraction of the fugu genome so much larger?)
  2. You conflate noncoding with junk categories. They have never been and never will be equivalent. This is a matter of evidence, not of hearsay as you are trying to portray it.

Question for you to think about, John: what type of evolution predicts the existence of junk DNA–Darwinian or non-Darwinian? This doesn’t require you to accept either one, but it does require that you understand them.

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David, thanks for your comment. However, it was news-medical and “Scientific American” that I quoted, not wikipedia this time. Are you saying that Francis Crick never said what “Scientific American” claims he said? Are you claiming that Ewan Birney is a creationist? Are you claiming he is unqualified? or simply made a mistake? Are you saying that “news-medical” is a creationist site?

I do not think “junk DNA” is even a scientific term. It is merely an interpretation or description of the characteristics of dna which does not seem to have a function, and which is a useless mutation, or a remnant of some misbegotten process in the past. So whether it is conflated or not with non-coding is not the point. Although you have not yet directly responded to whether the statement by Francis Crick was actually made, or not. re: In the same issue of Nature (284:604), Leslie Orgel and Francis Crick wrote that “much DNA in higher organisms is little better than junk,” and its accumulation in the course of evolution “can be compared to the spread of a not-too-harmful parasite within its host.” Since it is unlikely that such DNA has a function, Orgel and Crick concluded, “it would be folly in such cases to hunt obsessively for one.” evolutionnews.org …also, " …in 1972 Susumu Ohno and David Comings independently used the term “junk” to refer to non-protein-coding DNA (though neither man excluded the possibility that some of it might turn out to be functional)." … and as Dawkins says, “Dawkins continued to rely on junk DNA in his 2009 book The Greatest Show on Earth: The Evidence for Evolution. “It is a remarkable fact,” he wrote, “that the greater part (95 per cent in the case of humans) of the genome might as well not be there, for all the difference it makes.” In particular, pseudogenes "are genes that once did something useful but have now been sidelined and are never transcribed or translated.

Obviously, some geneticists disagreed with the presumption that all non-protein coding genes are non-functional. The Encode project postulated that 80% was functional, and others have indicated that at least 12-15% is functional. This changes the 98% non-functional category to about 85% non-functional. Still a large number. Of course, it depends on the definition of functional, as well as how it is determined and measured that something is functional. My perspective is that everything that affects the activation or deactivation of the genes is functional. It also makes sense to me that genes that are transcribed so faithfully and continuously, are likely to be functional in some way… but of course this is not proof until actually demonstrated. While seeing a function proves a function exists, not seeing a function does not prove a function does not exist… it may be that we simply have not seen it yet.

I am curious, David. Are you recommending that I not take Scientific American or Nature magazine as credible sources?

  1. The vast majority of the genome has no known function and the available evidence is consistent with it having no function. That remains the case. More of the junk will be found to be functional, but the functional fraction of the human genome will remain tiny. (Why is the functional fraction of the fugu genome so much larger?)
  2. You conflate noncoding with junk categories. They have never been and never will be equivalent. This is a matter of evidence, not of hearsay as you are trying to portray it.

Joao, you may be right. It is interesting, and it is okay, that you are not giving numbers as you have so often hammered me for, about how more of the junk will be found to be functional, while the functional fraction will remain tiny. How do you know this? What assumptions are you using to base this on?

It is not me that conflates noncoding with junk. I do not create my own definitions (at least I hope not). Originally non-coding was thought to be junk, and later junk merely referred to non-functional. But as I said to David, I don’t think “junk” is a scientific term anyway.

The real point is how much is assumed to be useless DNA, and how those assumptions play into discovering things about the non-coding portions.

I don’t have the time now to get into Darwinian, non-darwinian, or neo-darwinian evolution. I do recognize that it is not fun for neo or nondarwinian evolutionists to get accused of things they do not believe. On the other hand, it is likely that the theory will change in the future, so that present assumptions will also not be valid anymore.

Dear John,

You write, “I am curious, David.” I am unpersuaded that this is true. You have repeatedly ignored my invitation to read reputable and informed experts on the topic of discussion. In place of the discussion that I invited you to have, you offer a sarcastic taunt in the form of a question. Joao gave you a somewhat similar response, and you ignored that one too.

Here is my open invitation to you: read Ryan Gregory on the history of scientific engagement with junk DNA, and tell me what you think. Until then, I must assume that you are not curious about the subject. And that’s a pity, because the story is rather interesting.

I do not expect a response, and will not offer one of my own if you choose to return for a third time to bluster about your sources.

David, I simply do not have time to read everything. I have not ignored, but postponed. Hopefully one day I will have time to follow up on Ryan Gregory, and also on Joao’s link. I have followed up on several other suggested links. I remember once following up, reading an article while in a discussion about ideology related to similarities and differences in primate genomes, and one of the first things I saw was an ideological statement about finding genome similarity for apes/chimps and humans as motivation for the research (because it would make people protect chimps and apes more). I dont mind reading but I wonder if those who suggest it, have themselves read the piece critically, for example not to have seen something so obvious.

While I would read Ryan Gregory just for you, I already know there are varying opinions on the nomenclature and categorizations of junk. And I have said that it is not a scientific term. It probably makes more sense to have it refer to non-functional, rather than to non-coding. Do I still have to read Ryans paper to come up with a new perspectiveÉ

I see you have still found a way to avoid answering a simple question about Scientific American and Nature magazines. I am going to assume you are uncomfortable with answering it. Perhaps you think you are in a no-win situation in this case… I assume you think they are trustworthy, and donèt know what to do with the fact that they reported these statements.

No, not “some,” ALL. You are pounding on a straw man.

[quote=“johnZ, post:32, topic:574”]
How do you know this? What assumptions are you using to base this on? [/quote]
I’m basing it on evidence, not assumptions nor hearsay.

The people you’re accusing of conflating noncoding with junk have never done so.

Nope, they were never conflated by those doing the work.

No, it never changed. BTW, junk refers to “no known function.” It’s a negative classification.

The real point is that you are falsely accusing people of making false assumptions.

Too bad. You might learn something.

So maybe you should stop doing it. If you think that I am accusing you unjustly, offer evidence of the assumptions you are claiming people have before accusing them of assuming something.

[quote]On the other hand, it is likely that the theory will change in the future, so that present assumptions will also not be valid anymore.
[/quote]Or more importantly, that what you call assumptions aren’t assumptions and never were assumptions. Stop accusing people based on hearsay. Go with evidence.

Poythress is indeed a brilliant man. I have had him as my professor at WTS several times. It troubles me to hear his motives and morality questioned as they have been by some of the posts here. Dennis Venema has made a very generous response; we should do the same.

One thing that seems a problem with scientists and theologians talking together is that their work is done so differently. A scientist finds a problem, does some research, does experiments perhaps, and reports his findings. The report is peer-reviewed before publishing for proper technique and reasoning. The research will be repeated and the same or other findings will be reported in the same way. When it comes to theology, the practitioner reads the text very carefully and prayerfully, reads what others have written on this topic or passage, and then comes up with an insight within his own mind that he finds useful. He then publishes this insight with an argument for why it is a correct reading of Scripture. There is a technique for interpreting Scripture, but there is no commonly known for coming up with an insight into how that technique should be used in a particular case. If the theologian’s insight has raised enough interest, others will engage, perhaps by writing another book, and over time, a satisfying picture of the topic or text will develop. There is a lot of parallel to what goes on in science, but still, the idea of Poythress submitting his paper to peer review, as someone suggested, just seemed very foreign to the world of theology. It isn’t done that way. Theologians, and those who read them, suspect that scientists take a wide leeway with facts, dividing up into groups supporting one view or another, and thus conspire to deliberately make religious ideas look silly, as happens with some preachers and would be theologians. There is much searching by creationists for “true” scientists who won’t do this, but who will use the facts to support creationism of a particular kind, since they believe this to be the truth.

I think we need to teach each other how we think in our own profession. When people like Dennis Venema take the time to carefully explain how science looks at a particular question, this is very helpful. I know that scientists who know the topic so well, must feel that it is beneath them to explain things that are so well known (to them), but it really does help–at least for those of us who are really trying to figure this thing out.
Thanks

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