There are papers that test ID hypothesis. There is a whole field of study that does this and finds that similarity is not best explained by common function (this falsifies a classic ID hypothesis).
the question isn’t whether or not one does or doesn’t accept “science”, …it is the interpretation of the scientific facts that are themselves not in dispute, and making conclusions about things that everyone agrees are not immediately demonstrable.
So, for instance, here are some basic scientific facts that no one (to my knowledge) disputes:
— life (as we know it) requires an intricate interaction between a complex, replicatable encoded database, a decoding / manufacturing system that creates detailed, terribly complex, molecular machines as directed by the encoded instructions, and a reliable data transfer system between those two.
— the specific arrangement of data in this system, and the complex interaction between them, rules out any possibility that it developed spontaneously.
— there are no experiments that even remotely demonstrate any means for this system to have arisen naturally. There are nothing but speculations, and hypotheses upon hypotheses. At best, some experiments have produced results that are at least consistent with some limited elements of various hypotheses (the RNA hypothesis, for instance.
These facts are not in dispute, to my knowledge. The question is what one does with this scientific data. The observation of the difficulty of abiogenesis is such that some otherwise credible scientists have capitulated to such bizarre hypotheses as panspermia, and some otherwise credible scientists (such as Francis Collins) are even open to considering other such bizarre hypotheses as special creation.
‘Why the mouthful of “any research that supports intelligent design,” instead of “research in which an ID hypothesis is empirically tested”?’
Simply, because I would not dispute that plenty of papers are welcome for publication in which an ID hypothesis is empirically tested so long as its conclusions are presented as being in conflict with the ID hypothesis.
4 posts were split to a new topic: Does a commitment to methodological naturalism mean you have to ignore evidence of special creation
This doesn’t seem very relevant to a BioLogos audience… it seems to be a topic to discuss with an Atheist.
We here already acknowledge God the creator…
All things are possible with God … with His miracles… and with natural processes that God turns to as well.
That’s why Old Earther Creationism seems more like an oddity… rather than an internally consistent position.
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I was probably not as objective as I should have been in my previous post, so I might as well go ahead and “show my cards.” In both of his talks that I attended, he used some of his own research as an example to refute the concept of evolution.
He shows the audience ribbon models of two different proteins that look remarkably similar. He then explains that if evolution were true, then mutations could allow one protein to carry out the function of the other – they are remarkably similar, right? He goes on to state that he has not been able to successfully mutate one enzyme to assume that activity of the other. Clearly, evolution on the most basic of molecular scales is false, how could any of the rest of it possibly be true?
What he does not tell his audience is that the two enzymes have only 34% amino acid identity. Now, this level of similarity is definitely significant (as Axe defended to me in personal communication), but the problem is apparent. How could one logically conclude that changing a handful (29, to be precise) of amino acids out of 250 dissimilar amino acids should allow the mutated enzyme to functionally replace another? But he presents it as “these two remarkably similar proteins (see my model and be amazed with their similarity!) cannot functionally substitute for one another, even after we change the amino acids!! Clearly, evolution falls flat on its face.”
In addition, the 3D structures of these enzymes has not been determined by x-ray crystallography, so the model he uses to show their similarity is only hypothetical. To be forthright, I am basing this on my inability to find the structure and the lack of any reference to the x-ray structure in his paper.
Overall, his claims of similarity are overstated to a lay audience, and pertinent information like amino acid dissimilarity is withheld. I’m sure he could justify it by stating that the scientific explanation would be inappropriate for his audience, but it seems rather sketchy to me.
Although this does damage his credibility in my book, this is not what really “gets my goat”. In his second talk I attended, he had the audacity to claim that the average child had more insight into God’s creation than PhD scientists who support evolution (knowing he would be having lunch with science faculty afterward). I suppose I should “give him props” for saying exactly what he thought, but it certainly was insulting.
Sorry, Daniel, that’s probably more than you wanted to know!
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Thanks for the elucidation. By chance, were you able to gather why he chose those particular 2 proteins for his illustration (or for his experimentation?). Are they the closest to each other that exist in nature that yet have different functions?
Doug Axe and his colleague, Ann Gauger, used two members of the PLP-dependent transferase enzyme superfamily, 2-amino-3-ketobutyrate CoA ligase (Kbl2) and 8-amino-7-oxononanoate synthase (BioF2). I suspect they used these two because they are clearly different in function despite their structural and mechanistic similarity.
They focused on changing amino acids in the active site, but I would expect a majority of my undergraduate students to understand a major flaw in this approach. Protein structure is highly intricate – an amino acid substitution in a residue seemingly far away from an active site can have profound effects on the overall structure of the enzyme including the active site itself. Non-competitive inhibitors work by binding to an allosteric site (that is completely separate from an active site) and causing a conformational change that disrupts normal interactions between substrate and enzyme. Focusing attention on the active site is an exceedingly narrow approach to draw the conclusions they have made.
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Sir, thank you again for your insight. Please let me see if i follow:
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a key requirement for darwinistic theory to be viable is that proteins can evolve (through genetic mutation) and take on new functions, which also implies some functionality/viability of the intermediate forms.
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if I understand you rightly, the two chosen to be “coaxed” to mutate by Dr. Axe were not good choices since they were already so disparate, and for various biochemical properties, would never have worked in any case… especially as their mutation was limited to the active site and did not explore all the effects of substitutions all along the entire protein chain.
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now, please forgive my ignorance: are there any two proteins, that have clearly different functions, that do, in fact, share more than 34% similarity in their amino acid sequence? That information would be important for me to in order to determine how skeptical to be of Axe’s work.
One of the key concepts to evolutionary theory is duplication and divergence. DNA sequences periodically undergo duplications due to a variety of different causes (Gene duplication - Wikipedia). These duplications often occur non-specifically, but they can include genes, so a duplicaiton will lead to an extra copy. The “extra” gene would then be able to diverge from the original sequence without the selection pressure (and without a functional/viable intermediate form) that would be enforced on a single, necessary gene. Scientists believe that this divergence allows for the development of an array of results – from nonfunctional “pseudogenes” to new versions of previous genes with slightly different activity. It is thought that duplication and divergence is a common mechanism for the generation of “gene families” like the PLP-dependent transferase family that DI was/is working on. (Side note - BioLogos’s Dr. Dennis Venema writes about pseudogenes quite a bit - see here to read more)
Shorter response here - bingo, you got it!
Nothing to forgive here, I’m pretty ignorant of these kinds of specific details of protein biochemistry, too!. Maybe @Swamidass, @glipsnort, or @Argon could share some of their professional experience to address this question. I did find a somewhat technical article from 2007 that addresses unexpected structural dissimilarity when compared to sequence similarity (Sequence-similar, structure-dissimilar protein pairs in the PDB - PMC). Here is a quote from the paper that might be relevant:
We find numerous protein pairs, of 50–100% sequence identity, that have dissimilar structures, as measured by RMSDs greater than 3 Å or 6 Å. A database of structure-dissimilar pairs is available online at http://luna.bioc.columbia.edu/rachel/seqsimstrdiff.htm. Our results suggest that when creating non-redundant subsets of the PDB or when selecting templates for homology modeling, two proteins or domains in the PDB should be judged as redundant only if both their sequences and structures are similar.
(Firefox was extremely alarmed when I tried to follow that link, by the way…)
If I qualify up-front that I am NOT a professional biochemist, I can offer at least a conjecture. I don’t think it is very rare for different members of the same protein family to share similarities along the same scale while having significantly different functions, particularly for some of the larger protein families.
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This this is very very common. If you look at the work on phylogenomics literature, you will a very large number of examples of:
- Very similar proteins with different functions.
- Very different proteins with the same function.
- Proteins with multiple functions (how this even possible if function is so difficult to produce?)
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Sir, thanks. I guess I wonder, methodologically, why Dr. Axe would not have proceeded with experimenting on two of the most similar proteins one could find in our databases that nonetheless had different functions in order to either confirm or deny his working hypothesis.
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It might very well be unfair, but the skeptic in me would guess that such a study would not support the narrative he wants to present. I saw a couple of articles earlier today that may be worth reading and reporting on in this vein. I just didn’t have the time to get to them today.
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I would fear that as well. But out of curiosity, have the counter-claims been tested? I mean by anyone? Is it documented that any proteins can be coaxed to mutate to take on entirely new functions?
(I’m aware of slightly different functions, like digestive enzymes adapting to consume a slightly different diet… but I mean the categorically different functions that the evolutionary process would require?)
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So you pique my curiosity and don’t give me any hints where to find? 
What makes you think evolution needs categorically different functions? I’m not sure I believe that.
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Good morning, Daniel.
Yeah, sorry about that… I check my phone one last time before going to bed last night. As engaging as this dialogue has been, I wasn’t about to get back up and find them 
I did a little more research this morning, and although it’s a far cry from “exhaustive”, I can at least report back a little on what I found. Joseph W. Thornton has been working on similar experiments to Axe’s for about a decade now. His particular subject of study is a pair of closely-related hormone receptors – the mineralocorticoid receptor (MR) and the glucocorticoid receptor (GR). The hypothesis is that these two genes originated by the “Duplication and Divergence” model I mentioned yesterday. Sequence analysis of these two genes suggests that the MR sequence is much closer to the original and the GR did a little more of the diverging. In a very interesting approach, Thornton generated a protein he believed to be the most likely sequence of the ancestral protein, then carried out site-directed mutagenesis and x-ray crystallography to track the effects of the mutations. Regardless of how much credence you place on his ability to generate the ancestral sequence, the fact is that he has been able to mutate an enzyme with MR function into one with GR function.
There is a LOT of interesting stuff packed into his research and it has apparently caught the eye of the DI crew. Michael Behe has posted on Thornton’s work here, here, and here. There are probably comments from Axe and Gauger on the DI site, as well, but I haven’t searched extensively for them. I also found a Discover magazine (haha, lots of “Discovery” going on!) article that contains correspondence from Thornton to Behe’s criticism. Check that out here.
I’m a little curious about what Thornton has done in these last few years, but I haven’t yet had the time to investigate any further. Bottom line, Daniel, is that this work has been done by others, but there is a lot of work yet to be performed in this area. You could also do an internet search on “directed evolution” if you want to check out other work in the area.
Have a great Sunday!
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There’s also work on random evolution of proteins and RNAs; it shows that mutation can easily lead to new function. Two examples:
The first paper describes an experiment in which an enzyme was randomly mutated and the mutated versions were tested for activity on five substrates. The parental version had little or no activity on any of the five. Screening 16,000 mutant-substrate pairs, they found 17 that showed new or improved activity on one of the 5 substrates. Presumably if they had looked at a wider range of alternative substrates, they would have found many more cases of increased activity.
In the second paper the authors describe randomly mutating an enzyme that has a well-defined function, but that is also active on a wide range of other substrates. They kept only mutants that preserved the original function, and observed large changes to the activity on other substrates.
These kinds of study are more relevant to real evolution, in which change can occur in any of a large number of directions. The important question is whether a mutated gene can do something interesting, not whether it can mutate to perform a specific function.
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What work? Meyer is all rhetoric.
Correct. The context, which I should have reiterated, was ID proponents. Thus, I should have written:
Why isn’t there any research from ID proponents in which an ID hypothesis is tested?
I’ve done far more than Doug Axe has to test Doug Axe’s hypothesis, just in the process of doing something else!
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… because if no protein functions were categorically different that those that existed in, say, the proposed common ancestor to all life, then we wouldn’t exist as we do? If all protein functions were essentiallly the same as that of our ancient ancestors, then we would not have the protein functions that are categorically different than amoebae, giving us no ability to see, think, etc., etc.
This seems so self-evident that I think we must be misunderstanding each other somewhere?