I agree.
Exactly.
What isn’t true?
I agree.
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.
Ann Gauger's latest salvo against Dennis Venema's arguments against an original pair of human beings
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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.
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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
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She already apologized (Post 83).
Enough of the ruffled feathers already. 
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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.
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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.
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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.
- 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.
- 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.
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Andreas Wagner, in many papers on enzyme function, gene networks, and metabolic pathways, has found that there are many pathways leading to the same very robust features. His book Arrival of the Fittest summarizes many of these findings. His results are consistent with the known fact that many deletion mutants have no phenotype, and with the preponderance of degenerate pathways in cell physiology. So I don’t think the idea of “many ways things can happen” is a faith statement. I think it is rapidly becoming an important part of evolutionary theory. I am not disputing your results on ancestral reconstruction, but pointing out that other approaches give very different answers to the issue of robustness in biology.
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Thanks for your comment. I have been intending to read that book for some time but Doug Axe “borrowed” it. I will try to make it a priority. But I am not sure how data about the robustness of pathways to gene deletion addresses the problem of getting new enzymes.
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Dr. Gauger,
You seem to be assuming that the pathway from A to B was the only way forward for evolution. Since that pathway was so improbable from a statistical viewpoint, according to your reasoning, traversing the path must have required intervention (i.e., intelligent design) from outside the system under consideration.
What I want to know is: what is the foundation for your assumption that the only evolutionary path available from A was to B? Is it possible that pathways were also available to M, Q, W, and on beyond Zebra, even if they were not taken?
Thanks,
Chris Falter
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D[quote=“Chris_Falter, post:108, topic:36790”]
You seem to be assuming that the pathway from A to B was the only way forward for evolution. Since that pathway was so improbable from a statistical viewpoint, according to your reasoning, traversing the path must have required intervention (i.e., intelligent design) from outside the system under consideration.
[/quote]
What you ask is at the heart of the problem. And we don’t know how flexible evolution is or how many palthways are available as a solution. I see your idea used in many answers to questions and challenges, but I haven’t seen any justification for it . Perhaps Andrea Wagner’s book will provide that.
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I very much appreciate your response about the protein fold paper. As the moderator stated earlier, it is a rabbit trail that would pull the thread off topic so I will gladly let you have the last word.
Your email would hold way more weight than mine would, so if you find the time I would really appreciate it if you would bring it to their attention. All one has to do is look at the number of ERVs in the human genome paper and the lineage specific ERVs in the chimp genome paper to get accurate numbers. Also, there were no PtERV1 insertions that violated a nested hierarchy in the Yohn et al. (2005) paper, even though the author of the ENV article claims there were. I would also suggest that you read the Yohn paper and the ENV article and decide for yourself if an honest person would portray the Yohn paper in that manner.
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I take it from your post that you would like Science to have the preferred place, the authority to judge in all matters. Unfortunately, due to human nature, this is not always wise. And especially in regard sacred texts that have been held for thousands of years, as you say, we should be reluctant to jettison them until we are sure Science is right. That means that Science has to be scrutinized very carefully by people who oppose its position on that particular point. That’s what we’re doing.
I know this is mainly an evangelical group, but I’m going to add in some words of Pope John Paul II. In his speech to the Pontifical Academy of Sciences he said that evolution was more than a hypothesis, meaning that evolution as a theory should be taken seriously. But he went on to say that qualified people including scientists philosophers and theologians should sit down together and discuss this matter, because it was of prime importance. He did not say let the scientists decide.
But is he really saying that science should have the authority to judge in all matters? [quote=“agauger, post:111, topic:36790”]
And especially in regard sacred texts that have been held for thousands of years, as you say, we should be reluctant to jettison them until we are sure Science is right.
[/quote]
And who is saying we should jettison sacred texts?
Hi Dr. Gauger,
I am not a professional biologist, but as a reader of biology papers and blog posts, I have come across many examples of flexible pathways. Here are a few examples:
- Adult lactase persistence has arisen along at least 6 different pathways .
- There is also the possibility that a single precursor (call it C) takes 2 different pathways in different lineages to A and B. In other words, C can take paths to multiple destinations (to A and B, at a minimum). Weng, et al., identified 3 specific examples of these “promiscuous” precursors.
- Amitai, et al., discovered that half of the 300 neutral variants from the enzyme PON1 possessed adaptive potential for phenotypic changes.
- Directed evolution studies have shown that while the sequence space has a “low overall density of functional sequences: the vast majority do not code for any functional protein, much less the desired protein,” the functional sequences tend to cluster, allowing transitions between different functionalities in spite of the overall low density of functional sequences.
- Weinrich, et al. identified 18 plausible pathways to a new sequence that increased antibiotic resistance by 100,000-fold in a beta-lactamase allele.
Food for thought.
Grace and peace,
Chris Falter
I think a much more profound question is -
“If Science ruled out God, would it make a difference?”
They should be grateful God doesn’t rule out science.
What say you?
How would scientists – that are confined to God’s laws – ever use those laws to “rule out” something transcendent to them?
Who is “they”? Why would God, who created humanity in His image, require that His image-bearers stop studying His creative work?
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So, let’s assume that we were even willing to " let the Theologians decide." Is there some position that Evangelical theologians have not yet accepted that you wish they would accept?
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I remember that Karl Giberson, a Christian and a scientist (and a past contributor to BioLogos) said that only nature gets to vote!
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The pope did not say let the theologians decide either; he said that men of learning should talk to one another.
He also said that when our scriptural hermeneutics were properly understood, as well as our scientific results, the problem would resolve. It is in the free dialogue of members of all academies, that the truth will be discerned. And we have neither perfect understanding of Scripture or evolutionary science .
It is my firm belief that there is truth to be discerned concerning our origins that will be reconciling both science and theology and scripture. We just aren’t there yet.
With a little humility on both sides perhaps we can come to understand that we don’t yet have the truth and we can agree that there is more to be done.
Nature it doesn’t Vote. It is the people who interpret what they see that vote, and interpretations can be in error.
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