Do scientists associated with Christian organizations have a point?

This this is very very common. If you look at the work on phylogenomics literature, you will a very large number of examples of:

  1. Very similar proteins with different functions.
  2. Very different proteins with the same function.
  3. 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?)


So you pique my curiosity and don’t give me any hints where to find? :wink:

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 :stuck_out_tongue:

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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:confused:
… 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?

Behe, Axe, and Meyer contend that new functionality/proteins cannot emerge by evolution from older functionality/proteins because the gaps are too large to cross. They state that you cannot get from A to B, much less to Z. Joshua @Swamidass seems to be making the point that you don’t have to go from A to On-Beyond-Zebra in one humongous step. Instead, evolutionary mechanisms permit interesting new protein functions to emerge incrementally. You can get from A to B, then from B to C, and so on. So yes, after billions of steps over a billion years or more we have many protein functions that are vastly different from those found in prokaryotes. But few (perhaps none) of the individual steps along the way represented radically new functionality.

Hope that clarifies the matter. Also, I would welcome any feedback from Joshua, who knows the subject far, far better than this amateur!

[quote=“Daniel_Fisher, post:52, topic:36163”]
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.[/quote]
As an example, are the crystallins in the lenses of your eyes categorically different from all amoeba proteins?

[quote]This seems so self-evident that I think we must be misunderstanding each other somewhere?
[/quote]Things that seem self-evident are often found to be false by following the scientific method.

Are you willing to test your hypothesis?

Curtis, there’s a major elision on Axe’s part here. Axe’s straw man is that one enzyme evolved into the other. Evolutionary theory, supported by evidence, is about both evolving from a common ancestor; it may have had both activities, only one, or a third activity. This is another way in which he sets up his experiment only to find what he wants to see.

Proteins vary because of mutation. They evolve by Darwinian (selection) and non-Darwinian (drift) mechanism. Because non-Darwinian evolution is very important in this case, the use of a polemic adjective like “darwinistic” is an impediment to understanding.

[quote=“benkirk, post:54, topic:36163, full:true”]

:confused:

No, I’m not willing to personally test this “hypothesis”, I have a full-time job that is not involved in biological sciences. But I trust that plenty of people here that know the science far better than I will happily correct me if I am in fact mistaken.

I fear you may have misunderstood: I of course recognize a core similarity in all proteins throughout all forms of life (using same 20 amino acids, etc.), and in fact that we in fact share many of our proteins functions (cell structure, digestion & various catalytic functions, etc.) with those of amoebae - and prokaryotic cells for that matter.

But that was not my point - let me emphasize again I am speaking about protein functions, and observed that if ALL human protein functions were essentially the same as our ancient ancestors, then no matter how complex our mammalian systems, they would possess no unique abilities that were not shared, in at least some nascent manner, with amoebae. If in fact ALL of our proteins have no unique functions that stand apart from those of amoebae or bacteria, I am most willing to stand corrected.

I assume they are not, or you probably wouldn’t have asked. I could add to that various digestive enzymes and those that help replicate DNA, which I assume are not categorically different even in function.

But permit me to ask you a question in return, as this may clarify my point under consideration:


Are the functions of, say, hemoglobin, rhodopsin, and/or the Na+/K+ pump essentially the same, or categorically different, than the functions of proteins found in amoebae?

Chris, I very much appreciate the thought - I recognize all of that in theory, but my observation is simply that, at some point, some proteins had to mutate to take on a categorically new function that was not itself facilitated by a step-by-step incremental process. The protein that transports oxygen, for instance, either does or doesn’t bond/adhere to the oxygen molecule. It can grow better or worse at doing so, but at some point it either has that function or it doesn’t. And unless that function existed in the earliest ancestor to all life on earth (and my understanding is that it did not), then at some point that “leap” had to be made.

Now, I recognize that this leap may have happened 1) because some protein, doing another function, started doing double-duty by mutating, still accomplishing its original function, and coincidentally it happened to be able to bond oxygen as well. The argument from the ID folks, (I am guessing, I don’t recall reading this specifically) would be that the design/structural specifications requirements to hold an O2 molecule are so specific that it is unlkely that anything that could do so could really be very functional at anything else (someone correct me if I am mistaken).

or 2) the other alternative (as Curtis recently educated me about above) is that the gene for a protein was erroneously copied in the code, but was not being transcribed, and therefore over generations was susceptible to all manner of random mutations - thus the intermediate forms did not require any functionality. Then, fortuitously, at some point, the exact code was stumbled upon that would allow O2 transport, and, fortuitously, that part of the code was then activated (allowing transcription).

Now, I am trying to study and understand this better, so please, someone who knows better than I, please let me know if I have mischaracterized anything above.

But all that being said, the pure mathematics of it boggle my mind. In my limited understanding, the requirement of designing an amino acid chain, both the sequence and the folding, that will function to hold even a single O2 molecule are so remarkably specific that the idea of a pseudogene just popping one out after various generations of random mutation seem utterly crazy.

But alternatively, if there is no selective pressure (i.e., benefit to the organism) pushing an active protein to take on oxygen transport function, I cannot imagine all the mutations necessary to allow it to take on that function leaving the original function of the protein intact. So many changes would have to occur before said molecule could begin to carry the O2 molecule that it would almost certainly destroy whatever the original function was before it could take up the new one, no?

Hence, at core, one of my many reasons I remain so skeptical of random mutation working alongside the various natural forces to accomplish these things. But I am always open to being corrected if I have missed, misunderstood, or misconstrued anything above.

Good point, and one I should have included. I got wrapped up in other details that I found wrong about Axe’s portrayal of his work!

Let me make one minor correction, then carry on. Gene duplication and divergence often maintains expression (both transcription and translation) of the duplicate copy. Pseudogenes develop when the reduction in constraint of mutation results in a loss – possibly in protein function, or transcription of the original gene, or some other mechanism.

Now on to hemoglobin! I know this is just a single example, but it is likely you would find a similar story for many other proteins that seem to have a unique, highly-specific function. There is indeed a hemoglobin “family” of genes, not one unique gene encoding an oxygen-transport protein. A good example of the broader family in humans is the myoglobin gene, with a protein product involved in oxygen storage primarily in skeletal muscle fibers. There are also flavohemoglobins present in protists and even bacteria. These related proteins are primarily responsible for a different function - conversion of nitric oxide into usable nitrates. Here is an article with a little more info on the family.

I understand your point - it is incredible to assume that the highly specialized metabolic activities we observe in our own bodies could have possibly have ancestry back to single-celled organisms. I agree, it is incredible! Yet time and again, scientists are able to follow patterns of ancestry in examples just like this. To me, these consistent observations do not detract from the power of our Creator, but emphasize His supremacy and creativity to set such a beautiful system in place.

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Curtis, you have been kind to conitnue to educate me on many things. i stand corrected - I recall (from study decades ago) that there was no oxygen transport system in those cells, I had assumed there was no such similar protein.

(this is why I love discussing these things - I invariably learn something and better understand all the issues involved - you got me curious if you happen to know - is the bacterial hemoglobin similar enough in sequence to any animal O2 transports (hemo, myo, etc.,) that we can surmise that it is in fact ancestral?

So then, I am still curious - are ALL basic functions in our proteins traceable to bacteria? As I mentioned above, rhodopsin and the Na+/K+ pump come to mind, but I am prepared to be corrected if prokaryotes have proteins with similar functions.

Now, all that being said - I fear this simply moves my problem, rather than solving it (like those that think that panspermia “solves” the problem of how life began)… My basic question in response to Chris’ observation still stands, even if your insight moves the timeframe of the event. That is,

At some point in the evolution of prokaryotes, :wink:
a protein evolved to take on a previously nonexistent function, namely, the binding of oxygen. The conceptual problems I have with this activity remain: either a duplicated, divergent protein had to randomly, with no selective pressure, completely randomly stumble upon a sequence to bind oxygen, or an active protein with a prior function is effectively destroyed and loses said function long before enough mutations happen to start allowing O2 capture.

Would very much appreciate any continued thoughts (and corrections) you might offer!

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Intetesting stuff, I wound up reading the Wiki article on hemoglobin a bit. I thought this was interesting:

Hemoglobin and hemoglobin-like molecules are also found in many invertebrates, fungi, and plants.[12] In these organisms, hemoglobins may carry oxygen, or they may act to transport and regulate other small molecules and ions such as carbon dioxide, nitric oxide, hydrogen sulfide and sulfide.

That makes it easier for me to imagine pathways by which oxygen-bearing functions could develop. In my (highly limited) understanding, the presence of an iron molecule is the key to these abilities. It seems that iron has a wide range of functions in proteins and enzymes:

http://flipper.diff.org/app/pathways/info/1670

Interestingly, I also found out that only one vertebrate lacks hemoglobin, a family of fish which have apparently adapted in this way to their cold environment:

Channichthyidae are the only known vertebrates to lack hemoglobin as adults. Although they do not manufacture hemoglobin, remnants of hemoglobin genes can be found in their genome.