Ann Gauger's latest salvo against Dennis Venema's arguments against an original pair of human beings

[T_aquaticus]

Good question. I don’t actually look to this paper concerning bottlenecks. The main things that caught my attention were:

1. The decrease in number of founding alleles and 2. The ages of those founding alleles. Ayala had been trumpeted as disproving the possibility of a founding pair based on his count of alleles at our split from apes. Later data showed him to be wrong.

Which papers do you look to in order to support a severe bottleneck in the human lineage to around the time of early H. erectus?

[agauger]

Sy Garte:

There have been some suggestions made that if Adam and Eve were in fact miraculously created, then perhaps other miraculous events might also explain modern human genetic diversity (this is similar to the AiG idea that pre flood lifeforms were full of “genetic diversity” allowing for very rapid evolution to modern forms by loss of "genetic information), or that Adam and Eve didnt live 6000 ya, but were actually members of an earlier species in the human family line.

I didn’t get my ideas on created genetic diversity from AIG, though I have since found out some of them are similar. They came from staring at a phylogenetic tree with 4 alleles and very long branch lengths, followed by sudden diversification of lineages. This is not in Science and Human Genomes.

If we want to assume a historical Adam and Eve, with theological and biological connections to all of us, there is no reason to reject those parts of Genesis 1 and 2 that clearly indicate Adam was not the first or only man on Earth (in contrast to YEC’s very troubling interpretations).

What troubling implications? I don’t follow AIG much. As for the comment about rejecting other men on earth, here we get into the prospect of interbreeding, which has its own difficulties. I don’t have all the answers.

I truly do not understand these desperate appeals to magic to try to insist that Adam and Eve were the first and only (or only surviving) humans, when the Bible says nothing of the sort.

I am struggling with making sense of the science and the scriptures (I assume you, or some of you, are also). I am trying to frame my solutions from a science-evidentiary based system. If our model doesn’t work, I will change my view. I am not AIG.

[agauger]

OK, sorry. I stand corrected. I am open to hearing what his view is, without commentary on mine. But several people here have assumed they know my view. It leads to misunderstandings.

[agauger]

Which papers do you look to in order to support a severe bottleneck in the human lineage to around the time of early H. erectus?

One was the Von Salome paper. The 4 branches go back for 25-30 million years, followed by explosive diversification at about 450,000 years ago. This was suggestive, not probative, of a stable 4 allele grouping.Then it struck me that the reason for the long age estimates had to do with the diversity between lineages. That rather than having long ages, we could have 4 initial lineages that were genetically diverse from the start. The severity of the bottleneck is not established by this, we’ll need our model to see if it is feasible. The timing is based on fossil evidence: the sudden appearance of Homo erectus with most modern features. My colleagues disagree with me here.

[Sy_Garte]

What troubling implications? I don’t follow AIG much. As for the comment about rejecting other men on earth, here we get into the prospect of interbreeding, which has its own difficulties. I don’t have all the answers.

Ann,

The AiG view has to assume some form of incest to explain Cain’s wife and so on. I find that troubling, and their explanation on Answers in Genesis not very helpful. I am a bit confused by your comment about “interbreeding.” That would suggest (as far as I know) that Adamites (like Cain) and other humans (like his wife) were members of different populations, which I have never heard anyone suggest. Maybe I am not understanding you.

I would certainly echo your remark about not having all the answers. I think none of us do, and I agree that we share a mutual struggle to make sense of the science and scriptures, I also appreciate your remarks about framing solutions in a science based system. And, again like you, I (and many others here) are willing to change our minds, taking into account new scientific or theological information. As an example, after hearing Joshua Swamidass present his novel idea about genealogical modeling being applicable to Adam and Eve, I first scoffed at it (he might remember my question at his talk) and then came to accept it, only three months ago.

I also find the sudden appearance of new alleles in the evolutionary record fascinating, and have been very impressed with the recent work of Andreas Wagner, who has some interesting ideas about biological innovation. I know you are quite familiar with the EES, and some of its impact on modern evolutionary theory, which also include the issue of innovative saltations.

[agauger]

[quote=“Jonathan_Burke, post:74, topic:36790”]

Are you arguing that Adam and Eve were not the first humans on the planet, but in fact were the human descendants of a previous population of at least 10,000 people?

No, I am not arguing that.

[agauger]

Sy Garte

The AiG view has to assume some form of incest to explain Cain’s wife and so on. I find that troubling, and their explanation on Answers in Genesis not very helpful. I am a bit confused by your comment about “interbreeding.” That would suggest (as far as I know) that Adamites (like Cain) and other humans (like his wife) were members of different populations, which I have never heard anyone suggest. Maybe I am not understanding you.

Thanks for your comments. I am glad to admit ignorance in this field. It would be a mistake to dogmatically declare anything. By interbreeding, I mean the Adamite lineage breeding with the pre-Adamite lineage.

[DarrelFalk]

@Sy_Garte (not Ann as indicated by the arrow above–sorry, Ann)

Sy, (with warm personal regards, BTW)

I would like to add that when I first read Joshua Swamidass’s novel idea, I, like you, initially had some pretty significant concerns about its scientific plausibility despite my enormous respect for his scientific work and his Christ-centered witness. I was especially concerned about the likelihood of fitting Adam and Eve into the genealogies of indigenous populations of the Americas as well as individuals in the genealogical far reaches of the African jungles within the last 10,000 years. However, after looking over his references, I now realize it is nowhere near as unlikely as I would have thought. This will impact how I talk (and think) about this in the future. @Swamidass (if you see this) what I think your work makes clear is that questions about the historicity of Adam and Eve as the genealogical ancestors of all of us is a theological matter—science is silent on the issue.

I will always appreciate Dennis and Scot’s book (which I have read—twice) and hope we all take their work very seriously and with much appreciation. But there is something many of us missed and Joshua has laid it out very clearly in a way that I think must also be greatly appreciated.

[littledoweknow]

Dr. Venema: Looking forward to reading your response to Ann Gauger!

Dr. Venema asked Dr. Gauger: “Wouldn’t it be nice if I (and others) could comment on ENV like you are welcome to do here?”

I think that would indeed be very nice if ENV allowed comments. But I think a main reason that ENV doesn’t do comments is because they’d have to spend all their time fending off misplaced+false objections against ID. This is well-illustrated by the reception that IDer Ann Gauger has received here, i.e.:

• Assumptions/accusations that ID proponents are young earth creationists (e.g., “I just don’t see how you can go from 4 alleles to 4,000 alleles in just 6,000 years, and have those alleles spread so evenly across the globe.”)

• Fallacious attacks on the credibility of ID journals and the quality of their peer-review, falsely attempting to undercut the ability of people to cite ID research (e.g., “BIO-Complexity is not considered a peer reviewed journal in the scientific community. It is an echo-chamber.”)

• Constant attacks on competency and credibility of ID proponents (e.g., “are you an expert?”)

• Misplaced attempts to paint ID proponents as the “pouncing” aggressors when they just observe the fact that Venema was the one who compared those believe in a traditional Adam and Eve to those who doubt heliocentrism. (Quote will be provided below.)

• Attempts to paint those who disagree with the evolutionary consensus on human origins as geocentrists–here’s what Dr. Venema writes on page 55 of Adam and the Genome:

“The sun is at the center of our solar system, humans evolved, and we evolved as a population. Put most simply, DNA evidence indicates that humans descend from a large population because we, asa species, are so genetically diverse in the present day that a large ancestral population is needed to transmit that diversity to us. To date, every genetic analysis estimating ancestral population sizes has agreed that we descend from a population of thousands, not a single ancestral couple.”

• Or accusations about the competency of the entire ID and creationist communities, like this accusation from Adam and the Genome, talking about the supposed incompetence of the ID and creationist to simply understand the evidence:

“Meyer’s confident assertions aside, antievolutionary scholars have not yet mounted a convincing response to population genetics evidence, nor is it clear that they will be able to do so, since there does not appear to be anyone in the antievolutionary camp at present with the necessary training to properly understand the evidence, much less offer a compelling case against it.” (Adam and the Genome, page 65)

• Here’s another attack upon the competency of ID proponents: “My overall impression of [Steve] Meyer’s grasp of molecular/cell biology after reading Signature is that he has an approximately introductorycollege- level understanding of the field.” (Dennis Venema, http://www.asa3.org/ASA/PSCF/2010/PSCF12-10Venema.pdf)

I think comments on this thread from ID-critics, as well as from the tone and style of leading ID-critics (in this case, in the form of BioLogos writers), provide good reasons to understand why it would be unfruitful to allow comments on ENV.

As Ann Gauger says…walk a day in the shoes of an ID proponent and you’ll understand.

So Dr. Venema, I agree with you that it would be very nice if ENV could allow comments, but unfortunately I think ENV’s decision is more a reflection of the tone and quality of counter-arguments than it is of a lack of desire to engage. (As Ann Gauger noted, their facebook page allows comments.)

As a last observation, sometimes ENV does allow comments, and Dr. Venema, you were invited once to comment directly at ENV in a post that gave you a respectful invitation:

“We extend this respectful invitation to Dr. Venema to read what Casey Luskin has to say and give us his response. We don’t routinely open the comments feature at ENV because of the staffing requirement that comes into play when we do, cleaning up after Darwinists who don’t know how to have a discussion on science without descending to the gutter. But on Casey Luskin’s reply to Venema regarding LTEE, E. coli, and the results reported by Richard Lenski, the gates to all commenters are now thrown wide open. RSVP.” (https://evolutionnews.org/2011/09/a_cordial_invitation_to_dr_den/)

Dr. Venema: Did you accept the offer to post comments there?

[cwhenderson]

I am in complete agreement that there should be more gracious dialogue between those that hold differing viewpoints, especially if we are addressing fellow brothers and sisters in Christ. But surely, you must be able to see the irony here:

“We extend this respectful invitation to Dr. Venema to read what Casey Luskin has to say and give us his response. We don’t routinely open the comments feature at ENV because of the staffing requirement that comes into play when we do, cleaning up after Darwinists who don’t know how to have a discussion on science without descending to the gutter. But on Casey Luskin’s reply to Venema regarding LTEE, E. coli, and the results reported by Richard Lenski, the gates to all commenters are now thrown wide open. RSVP.”

Calling it a “cordial invitation” does not make it one.

[agauger]

Curtis,

There is a reason I haven’t complained about many of the disses @littledoweknow pointed out. It’s because I am aware that ID people can be nasty too. I probably have let slip a few bon mots myself, especially when provoked. I am always up for gracious dialog, time permitting.

Ann

[cwhenderson]

I probably have let slip a few bon mots myself, especially when provoked.

I cannot claim innocence, myself, but I usually try to moderate my inner smart-alec!

[RHernandez]

[quote=“agauger, post:59, topic:36790”]
My title, which I think is what you are angry about, is Does Science Rule Out a First Human Pair?[/quote]
It is misleading because the argument Buggs makes doesn’t take in all of science.

Buggs explicitly argues that a single breeding pair can retain most of its heterozygosity as long as the population it founded expands rapidly. In other words a first pair is possible.

A far more accurate title would be, Does Heterozygosity Rule Out a First Human Pair?

[quote=“agauger, post:59, topic:36790”]By ‘first human pair’ I meant the first pair to be fully human, coming from a bottleneck of two, which is what Buggs said could not be ruled out.
[/quote]Cannot be ruled out by heterozygosity. Venema’s argument was much broader than that, no?

[Jonathan_Burke]

I truly do not understand these desperate appeals to magic to try to insist that Adam and Eve were the first and only (or only surviving) humans, when the Bible says nothing of the sort. The AiG interpretation of Genesis 1 and 2 and of Romans, is the problem here, not the science.

I agree.

If we want to assume a historical Adam and Eve, with theological and biological connections to all of us, there is no reason to reject those parts of Genesis 1 and 2 that clearly indicate Adam was not the first or only man on Earth (in contrast to YEC’s very troubling interpretations).

Exactly.

Because it’s not true.

What isn’t true?

Being the descendants of pre-human ancestors does not rule out God’s involvement.

I agree.

You are operating from a strictly materialist worldview, where evolution is sufficient explanation for everything, and evolution means a strictly material process.

Did you just try to read my mind or my motivations, based on what you think you know? You know nothing about my thought processes. I’m an evolutionary creationist.

[gbrooks9]

Being the descendants of pre-human ancestors does not rule out God’s involvement. You are operating from a strictly materialist worldview, where evolution is sufficient explanation for everything, and evolution means a strictly material process.

@agauger

You have @Jonathan_Burke completely wrong (as confirmed by @BradKramer).

So I can only assume that you must be misunderstanding lots of other things as well.

[pevaquark]

I was getting caught up on everything, i.e. not only this thread and the original article, but also on the Biologic Institute and BIO-Complexity (and yes, I had to read about the green screen incident).

It seems that how most groups (who disagree) are approaching the main consensus of science when it comes to original population sizes of our species (though not as if there was even some magical time when all of a sudden all the babies were homo sapien sapiens)… is tentatively.

I.e. the main argument is… hold on here science, your claims go a little too far too soon. We need more evidence before we rule out that one piece of evidence that trumps all others…
a) The one piece of evidence, which we hold over the heads of science in this case, is our interpretation of a text that was compiled at least 2300 years ago

My perspective in all of this… this is exactly like the Copernicus problem.

a) At first, Copernicus’ model actually was no better at predicting the motion of planets than Ptolemy’s model
b) And then, Kepler’s laws changed everything and he was the first astronomer to predict a transit of Venus based upon his modification of Copernicus’ model
c) Of course we know the rest of the story with Galileo where when discussing scientific ideas… the standard interpretation of Scripture was given equal footing in scientific explanations and used to triumph any other form of knowledge
d) We learned something important here… our interpretation of Scripture shall never again dictate what we find or don’t find about the natural world–but yet here we are doing the same thing 400ish years later

[Christy]

Did you just try to read my mind or my motivations, based on what you think you know? You know nothing about my thought processes. I’m an evolutionary creationist.

You have @Jonathan_Burke completely wrong (as confirmed by @BradKramer).

So I can only assume that you must be misunderstanding lots of other things as well.

She already apologized (Post 83).

Enough of the ruffled feathers already.

[T_aquaticus]

Fallacious attacks on the credibility of ID journals and the quality of their peer-review, falsely attempting to undercut the ability of people to cite ID research (e.g., “BIO-Complexity is not considered a peer reviewed journal in the scientific community. It is an echo-chamber.”)

They are hardly fallacious. For example, in this article they made such fundamental errors in modeling evolution that no peer reviewer in any respectable journal would have recommended the paper for publication. They claimed that one species evolved from another existing species, which is wrong. Modern species share a common ancestor. If they wanted to truly model the evolution of the protein then they should have constructed a consensus sequence using a phylogeny of many related species, and then mutated that consensus sequence. They didn’t. This is such a basic mistake that it could only pass peer review in an echo chamber.

As to ENV as a whole, they have articles that are seriously misleading and outright lies. For example, in this article the author claims that humans and chimps only share a few dozen orthologous ERV’s:

Out of tens of thousands of ERV elements in the human genome, roughly how many are known to occupy the same sites in humans and chimpanzees? According to this Talk-Origins article, at least seven. Let’s call it less than a dozen. Given the sheer number of these retroviruses in our genome (literally tens of thousands), and accounting for the evidence of integration preferences and site biases which I have documented above, what are the odds of finding a handful of ERV elements which have independently inserted themselves into the same locus?

This article was written well after the chimp genome paper was published in 2005, and after the human genome paper was published in 2001. There is absolutely no excuse for such a claim. Of the more than 200,000 ERVs in the human genome (from the 2001 human genome paper) less than 100 are not found at an orthologous position in the chimp genome (2005 chimp genome paper). It isn’t a few dozen. It is more than 99% of the 200,000 ERVs found in the human genome. I see this article used by creationists all of the time, and the mistruths in that article continue to spread without correction. Allowing comments would surely correct this problem.

[Christy]

All valid points to consider, but please, let’s not turn this thread into another “all the things that are wrong about ID” thread. I know many of you have your lists ready to whip out, but we have been down that road many times before on other threads. Let’s stick to the topic.

[agauger]

T_aquaticus,

They are hardly fallacious. For example, in this article they made such fundamental errors in modeling evolution that no peer reviewer in any respectable journal would have recommended the paper for publication. They claimed that one species evolved from another existing species, which is wrong. Modern species share a common ancestor. If they wanted to truly model the evolution of the protein then they should have constructed a consensus sequence using a phylogeny of many related species, and then mutated that consensus sequence. They didn’t. This is such a basic mistake that it could only pass peer review in an echo chamber.

The paper you reference there is mine. I am familiar with the most common objection to this paper, that we did not do ancestral reconstruction, a la Joe Thornton. There are two comments I can make in response to this criticism.

1. Our proteins are ancient, going back to the time of the first cellular metabolisms in bacteria_. They are only 33% identical. What is very similar are their folds. Reconstruction of an ancestral form is unlikely to work at such a distance. Thornton’s first work was on steroid hormones that diverged about the time vertebrates first appeared, according to Thornton himself. The likelihood of success of any reconstruction for our proteins is poor.
2. More importantly, and this is the heart of the problem, ancestral reconstruction or retracing evolutionary history was not our goal. We wanted to determine whether it was possible to interconvert one related protein into another, starting with extant protein. Such interconversions must have happened in the beginning. The question we are asking is whether such interconversion between modern proteins is possible. Back when all these new proteins were first appearing, they managed to do it somehow.

Here is how we stated it in the paper:

A reasonable assumption, consistent with methods
used for reconstructing evolutionary histories, is that enzyme
pairs with high structural similarity should be most amenable
to functional conversion. Whether or not a particular conversion
> ever occurred as a paralogous innovation (or the direction
> in which it occurred if it did) is not the point of interest here.
Rather, the point is to identify the kind of functional innovation
> that ought to be among the most feasible within this
> superfamily and then to assess how feasible this innovation is.

Ancestral reconstruction and its success suggests that there are very few possible evolutionary paths between proteins A and B, in particular the one that was demonstrated to work in the lab. Even then, though, just one amino acid change could block the way forward, or the pathway may work only in one direction and not the other. That would seem to restrict protein evolution to a very narrowly defined set of pathways fine-tuned for the production of proteins we see now. How did that happen?

I know that everyone is always saying that there are many ways things could have happened (this is merely an expression of faith in the evolutionary process and a not demonstrated fact), that many paths forward are available. Ancestral reconstruction would seem to argue no, that there are in fact very few ways to transition from one enzyme activity to another, or one binding protein to another. That would argue for a high degree of fine-tuning for starting points, and a predictive design sophistication beyond mortal abilities.

For evolution to be true, though, in case you are not comfortable with the above, it must have been possible to get new proteins from old, by many pathways. It must be possible to convert closely related structures to each other’s function; isn’t that the assumption of gene duplication and recruitment, of cooption? Otherwise how could it happen? So what we demonstrated is that cooption, the reconfiguring on one protein to a new function, within the limits of a neo-Darwinian search, is beyond reach, at least in the case we tested. We actually did a follow-on paper where we expanded the search. You might want to take a look.

Besides what I have already said, this criticism you voiced was in its facts. You said “They claimed that one species evolved from another existing species, which is wrong. Modern species share a common ancestor.” That is wrong. We did all our work in E coli, using E coli enzymes, and we weren’t modifying species, we were modifying proteins. I invite you to go back and read the paper.

What I hear from you are repetitions of things that people said on anti-ID “echo chambers”.

As to ENV as a whole, they have articles that are seriously misleading and outright lies.

As for the other criticisms, errors are possible. Please comment to the editor so we can correct them. Calling them lies is, however, immoderate in the extreme, and offensive. You accuse the writers of deliberate deceit, the attempt to deceive. It is this kind of attitude that keeps people like me away from BioLogos. Why fight against such bias? I thought I had made some progress, especially with you. It seems I was wrong.