I have interacted with Doug Axe a bit. I think I can safely say he is NOT drawing different conclusions from the same evidence that a more typical scientist would. His current work is poor science, at best. I have heard him speak twice and both times he presented a very skewed and even misleading (possibly intentionally so) case to a primarily lay audience. My follow up conversations with him suggest that his over-reaching claims are not simply out of ignorance.
I realize that Dr. Axe is not the entirety of DI, let alone all ID, But he is definitely a poor representative.
I couldn’t speak to axe’s work in terms of peer-reviewed submissions and its quality. Like I said, I’m only a casual observer and have only read his recent book (and was not overly impressed myself), but that work was more polemic in nature.
But you piqued my curiosity… could you detail which parts of his presentation or description of the science involved you found skewed and/or misleading?
Stephen Meyer’s work, both his books and the articles (professional journal style) that I’ve read through are more impressive to me. I’d be interested in your impression of any of these, if you happen to have familiarity with such.
Is it mere ideas, or is it evidence? What is “ID-supporting research” anyway? If one reads DI news and views, they claim that a lot of “ID-supporting research” is being published, just that the authors aren’t smart enough to see it.
I would agree that public proponents of Intelligent Design and YEC creationism are intentionally excluded from mainstream scientific publications, scientific institutions, and scientific jobs. That appears to be essentially accurate. I am not sure who would dispute this.
The real question is why they are excluded and if this reason is unfair.
In specific the case of the Grand Canyon access, it is possible that the exclusion was not justified or fair. At the same time, there is a perceived history of misrepresentation of science by these groups, so some might argue that excluding those with this track record is justified. I am sympathetic to both sides, because I think individual scientists should be assessed separately for their honesty and compliance with the ground rules of science in their scientific work.
We already know that he is not doing science under the rules of the rest of us. He has signed the AIG belief statement, in which he promises to ignore any evidence that points to an old earth. That is not “science” as we understand it. Even AIG agrees that they do science in a different way than the rest of us.
I’m not exaggerating the AIG belief statement’s requirement:
By definition, no apparent, perceived or claimed evidence in any field, including history and chronology, can be valid if it contradicts the scriptural record
This means he has promised to declare “invalid” any apparent or perceived evidence that supports an old earth. There is also great examples of this happening among AIG scientists. If I was in charge of this process, I would ask him to specify how he would report evidence for an old earth that he discovers. If he could not give an honest answer, I would reject the application because it is by definition not a scientific inquiry into the age of the earth if only one answer is acceptable. This would not be based on prejudice, but the public belief statement of his organization.
I agree that good science can, in principle, be published outside peer review. I also agree that because it is clear they are excluded now on principle, it is not fair to level this as an unqualified critique. Once again, it is important to ask if is fair exclude them.
The bigger problem is that their arguments are not good science, and the mathematical arguments often have large errors. I have not had good experiences in my attempts to directly approach ID proponents with informal “peer-review” of their work. I cannot think of a single case where an error has been retracted or fixed. That is concerning, and does not foster trust.
Related, there is a journal that accepts ID submissions (BIO-Complexity). Ignoring the scientific quality in these articles (which sometimes have important content), look at the number per year. It is pitifully low. About two articles per year, many of which are not actually original research. For comparative reference, I am submitting two peer review articles this week alone to journals from a small scientific group with just 3 graduate students. ID appears to have hit a major dead end in terms of coming up with new ideas.
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.
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!
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.
Sir, thank you again for your insight. Please let me see if i follow:
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.
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.
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.
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.
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.
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?)
…
So you pique my curiosity and don’t give me any hints where to find?
