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Author
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Topic: Is the DNA code universality strong evidence for evolution?
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Cornelius G. Hunter
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Member # 81
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posted 12. March 2003 20:47
Folks:
Evolutionists say their theory is a fact. If true, or if there is good reason to think this, then IMO ID is quite weak at best, superfluous at worst. OTH, if evolution is clearly not a fact, then ID is strengthened. Hence, the claim that evolution is a fact is very relevant to ID. I'm intrigued by, what I see as, the great weakness of the claim that evolution is a fact. I contend that the data, evidences and arguments do not establish this and that the typical pattern is that evidences which are rather ambiguous at best are elevated to being compelling arguments for evolution.
It would be too ambitious to tackle the subject of all evidences in one topic thread. What I'd like to explore is a typical example: the universality of the DNA code. Evolutionists claim the universality of the code is compelling evidence for evolution (for a typical example see: Johannes Schul, Slide 19, http://www.biology.missouri.edu/courses/Bio302_Schul/Evidence.htm, where Schul claims that the universality of the code is " Best evidence that all life shares a common ancestor!").
I contend the evidence is weak and therefore there is a disparity between the evidence itself and the evolutionist's claims about the evidence. Either I'm misinterpreting the evidence, or there is something amiss in the evolutionist's claims.
I would prefer to avoid getting into discussions about whether the DNA code really is universal or not. It seems to me that we can safely assume that it is, albeit with minor deviations. At this point I do not see the deviations as detracting from the evolutionist's argument, nor do I see the deviations reinforcing their argument. Certainly, the evolutionist's high evidential claims vis-à-vis the universality of the code are exclusive of any deviations.
I would also prefer to avoid getting into discussions about evolutionary speculations or hypotheses of how the code may have evolved. My reasoning here is that such hypotheses certainly exist, but they are not part of the evolutionist's high evidential claims. IOW, evolutionists are not saying they have an explanation that is so absolutely compelling, and that the explanation mandates universality, that therefore the universality is compelling evidence. In fact, this would be a fallacy anyway (affirming the consequent).
Evolution envisions the code arising from simpler codes (IOW, the code did not pop into existence out of nowhere). Therefore, according to evolution the code can evolve and so evolution does not require the code to be universal. Furthermore, multiple codes could have arisen via multiple biogenesis events. In addition to not requiring the universality of the code, the evolution of the code and associated machinery would not be trivial.
This is attested to in the many different hypotheses there are for how it could have evolved. For example, perhaps the genetic code arose as a result of interactions with clay minerals, perhaps as a result of non enzymatic chemical reactions, perhaps due to stereochemical effects, perhaps it arrived on earth from outer space, either on meteors, comets, spores driven by radiation pressure or even deliberately planted by extraterrestrial beings. Perhaps it evolved from simpler codes where fewer amino acids were originally coded for, or perhaps the code distinguished between classes of amino acids, rather than specific amino acids. Perhaps the alphabet was originally binary, or perhaps the words were only two letters long. Perhaps the original machinery was imprecise so that a given gene did not always code for the same protein. All good ideas but clearly, evolutionists agree, there is uncertainty*. It is not as though there is a clear and compelling explanation for how the code could have evolved.
The situation is that evolution speculates about how the code could have evolved, and evolution does not require the code to be universal. Yet evolutionists claim the universality of the code as compelling evidence. So, what I'd like to explore in this thread is this claim. Is the claim sound and valid or is there something wrong with evolutionist's reasoning?
--Cornelius
*See for example, Leslie E. Orgel, “The Origin of Life—How Long Did it Take?,” Origins of Life and Evolution of the Biosphere, pp. 91-96, Vol. 28, 1998; Mitchell K. Hobish, “Studies on Order in Prebiological Systems at the Laboratory of Chemical Evolution,” Origins of Life and Evolution of the Biosphere, pp. 124, Vol. 28, 1998; Jacques Ninio, Molecular Approaches to Evolution, p. 89, Princeton University Press, 1983.
[ 12. March 2003, 21:47: Message edited by: Cornelius G. Hunter ]
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yersinia
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posted 12. March 2003 20:56
Isn't the key difference here between the following statements:
1) Life originated via evolution
...and...
2) All (known, extant) life shares a common ancestor* that had the standard genetic code.
An essentially universal code (known deviant codes are all phylogenetically derived) would be evidence for #2 but not #1.
* or ancestral gene pool of gene-trading protocells/bacteria
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Argon
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posted 12. March 2003 22:17
I like to think in small baby steps and then work my way backward...
Is the universality of the genetic code compelling evidence that humans share a common ancestor? In other words, given what we know of protein translation, is it perfectly reasonable, nee expected that humans would share a common genetic code if they were related? If we found a group of humans (perhaps in Cincinnati) that used a set of coding sequences that were completely different from the rest of humanity and the rest of the planet, would we suspect that we weren't actually related? I think so.
A step further back...
What about the idea of sharing a code with apes?
With mammals? Should we expect to see a great divergence of the triplet code among mammals? I don't think it is surprising to see such similarities, given 10-100 million years of divergence.
Another step:
Reptiles? This includes mammals too.
Another...
Vertebrates? Metazoans? All Eukaryotes?
With each step further back into an evolutionary tree and covering a wider range or species, my expectation would be that more variation could be possible.
Does the general universality of the code prove that everything shared a common ancestor? Hmm... that's harder to determine. Clearly the stronger case can be made for organisms thought to have diverged more recently. But given what we know of biochemistry, the connection between common descent and a common code doesn't sound too far fetched.
Cornelius, you say the argument for common descent based on a common code is "circular". I don't think it necessarily is, although I'll conceded that very old events are tougher to evaluate. I guess what I'd like to know is your opinion of how far back in the past the connection between common descent and a common code becomes suspect. For example most would agree that if foxes and dogs shared a common ancestor, we would expect them to have the same genetic code. The same would probably apply to apes and similarly, the rest of the mammals. Where would you draw the line at the point where organisms that shared a common ancestor would be unlikely to share a similar genetic code? How many millions of years since divergence would that be, or which taxonomic groups would you think this applies to?
[ 12. March 2003, 22:21: Message edited by: Argon ]
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Cornelius G. Hunter
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posted 12. March 2003 22:34
Good point Yersinia. The high claims vis-à-vis the universality of the DNA code have to do with common descent, not the origin of life (OOL) problem. The universality of the code and associated machinery is taken to be essentially proof of common descent. For example: "The fundamental unity of this great diversity of life lies in the fact that virtually all organisms carry their genetic information in the DNA molecule, within the cell. The only reasonable explanation of this fact is that all organisms are related by descent." [Berra, *Evolution and the Myth of Creationism,* Stanford Press, 1990, p. 19]. Mark Ridley makes essentially the same claim in Ch. 3 of his *Evolution* text, though his point is in direct reference to the universality of the code.
The problem, as I see it, is that common descent doesn't predict a single code since the code is acknowledged to be evolvable. You seem to deny this, saying that the universality of the code is "evidence" for common descent. How strong did you intend this claim? Are you saying that under common descent the code is more likely to be universal, but perhaps could not be, or are you saying it *must* be universal, and therefore common descent would be falsified if it weren't universal?
To forestall the obvious, let me go further. If your claim is in the weak sense, then you are on safer ground but fail to make your point that the universality is strong evidence. If your claim is in the strong sense, then you have quite a burden of proof. Given the fact that a highly sophisticated code with sophisticated molecular machinery is acknowledged to be evolvable*, I don't know how you would support your claim that common descent would be falsified if the code weren't universal.
Furthermore, as noted in the IP, even if you did make the strong claim, and you were able to defend it, you would still be committing the fallacy of affirming the consequent if you made the high claim, for example, that Berra does above.
--Cornelius
*I'm referring to the next to the last version of the universal code just before "codification" in the last common ancestor, which is supposed to have evolved into the final form; as well as to the minor deviations we now see which must have evolved since the LCA if evolution is true.
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Moderator
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posted 12. March 2003 22:34
Cornelius,
We prefer that Brainstorms threads start off with positive hypotheses rather than critiques. It is a great deal easier to offer up a slew of critiques. It is far more difficult to develop creative hypotheses. We are trying to nurture the latter while utilizing critiques as constructive tools for helping ideas along. The board does not exist to make sweeping metaphysical statements.
Please take a look at the posts by Mike Gene for a good example of what we're about at Brainstorms. Metaphysical and philosophical critiques are more appropriate elsewhere: www.arn.org
BTW, what do you mean by evolutionists? This is a broad and vague term that probably includes everyone participating at this board. When defining theoretical positions it is best to be as specific as possible so as not to confuse the already noisy art of communication.
[ 12. March 2003, 22:39: Message edited by: Moderator ]
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Cornelius G. Hunter
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posted 12. March 2003 22:47
Argon:
You make a big leap when you go from humans having a common ancestor to humans and apes because we know humans *do* share common ancestors (empirically) whereas we have never observed the kind of evolutionary change needed to change an ape into a human. We’re getting into the problem of evaluating the theory of evolution itself, which this thread is not big enough to do.
Take a look simply at the evidential claim being made. Evolutionists routinely claim that the universality of the code essentially *proves* common descent. How could this be given what I laid out in the IP?
What you seem to be saying in your post is, "hmmm, there seems to be some logic behind the idea that a common code is evidence for common descent." I agree. You ask: "I guess what I'd like to know is your opinion of how far back in the past the connection between common descent and a common code becomes suspect?" I'm not saying it is suspect at all. The idea that common descent could produce a universal code seems quite reasonable to me. What seems suspect is the high evidential claim by evolutionists that this proves evolution.
Do you see the difference? There is a big difference between saying, "yeah, our theory can accommodate that finding, maybe it even prefers that finding," to saying, "this is highly compelling evidence, essentially proof, of our theory." The point is crucial, because this happens over and over in evolutionary arguments dealing with a wide range of evidences and data.
--Cornelius
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Cornelius G. Hunter
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posted 12. March 2003 22:59
Moderator:
I didn't intend to make a "sweeping metaphysical statement." (what was it?). In any case, it sounds like we ought to drop this thread; I thank you for the corrective.
--Cornelius
ps—you asked about my definition of "evolutionist." My sense is there is a pretty clear delineation between those who see evolution as the dominant process of how the species got here and those who do not. The former, whether theistic, materialistic, or somewhere in between tend to use much the same arguments for the veracity of evolution and differ mainly on OOL and metaphysical issues. The latter would see evolution acting only in a limited sense, such as one type of gull giving rise to a highly-related, but non interbreeding cousin.
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yersinia
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posted 13. March 2003 04:34
Cornelius,
OK, so we're talking about common descent, that clears it up considerably.
Here's a way to think about it. Let's say we found life on Mars. One of the first questions we'd ask, naturally, is whether it originated independently on Mars or whether it is related to us (e.g. via impact transplantation).
Let's say we found any of the following in Martian microbes:
- made of right-handed amino acids
- used a different nucleic acid than DNA as the hereditary material
- didn't use nucleic acids at all as the hereditary material
...etc.
In these cases I think we would have no difficulty in concluding independent origins.
Similarly, there are a large number of conceivable genetic codes. I know there is much debate about code optimality but the highest optimality estimate I can recall is about "1 in a million" (i.e., you would have to randomly sample a million codes to get another one as good) but as there are something like 2.3e69 possible codes (*with the current distribution of codons per aa and 20 aa plus a stop codon*; without these restrictions there are many, many more possibilities)...therefore, there are a very large number of "about as good" ways to build the code even if this "good" class is a small proportion of all possible codes.
So, the argument goes, as we have no particular reason to expect that whatever process that resulted in the standard code would have a reason to generate the same code twice, then we need an explanation for the shared code, and "one ancestor got it and passed it on to all its descendants" seems like a pretty good one in accord with lots of data from other sources.
I think the reason the standard code is considered so compelling are the absolute abyssmal odds of a randomly generated code, even one with similar optimality features etc., duplicating the same code twice. Left-vs-right-handed amino acids is a 50-50 kind of thing on the other hand.
Similar things could be said for numerous other parts of universal biology, e.g. highly conserved and universal rRNA sequences, etc.
nic
PS: Keep in mind that common descent is a hypothesis about a group of organisms. Would discovery of independent-origin of life on Mars "falsify" evolution/common descent?
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Cornelius G. Hunter
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posted 13. March 2003 12:43
Nic:
I'm not sure what the status of this thread is. The moderator has said it is not positive enough, but I'm still waiting on what my "metaphysical statement" was so I don't repeat it. In any case, I will respond to your post, understanding that we may be instructed to terminate this thread.
***********************
In an earlier post you pointed out that the universality of the code is best viewed as compelling evidence for common descent, not "Life originated via evolution." OK, so we're talking about common descent, not the OOL problem. But, I pointed out, this doesn't help because common descent doesn't predict a universal code. So now in your most recent post, you reintroduce OOL.
Your argument is that "we have no particular reason to expect that whatever process that resulted in the standard code would have a reason to generate the same code twice." So now, it seems that this compelling evidence for common descent, in fact, is rooted in OOL. If I have this right, then we must bring back the other problem I pointed out, that evolution doesn't have an explanation, beyond a series of speculations, about how the code could have evolved.
So the situation is, common descent doesn't predict a universal code, nor is it clear how the code itself could/would have evolved. Yet it proves common descent because the OOL process would not have generated the same code twice. Your argument is valid, but is it sound? That is, is your premise correct that : "we have no particular reason to expect that whatever process that resulted in the standard code would have a reason to generate the same code twice" ?
For example, are you restricting your claim to naturalistic processes? I see nothing wrong with this; however, you cannot then conclude that common descent must be true (you may only claim that common descent is true *if* life arose via naturalistic processes). As I pointed out, the evidential claim being made is not so restricted. You seem to be agreeing with and defending the claim. As such, you must not be restricting your premise to naturalistic processes. In that case, I think your logic holds; however, your premise entails metaphysical assumptions about the Designer/Creator. Make sense?
--Cornelius
PS: You asked: "PS: Keep in mind that common descent is a hypothesis about a group of organisms. Would discovery of independent-origin of life on Mars "falsify" evolution/common descent?" No, I don't think so. What't the point?
[ 13. March 2003, 14:11: Message edited by: Cornelius G. Hunter ]
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Noel Rude
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posted 13. March 2003 15:21
This thread, I believe, has potential. I'm by no means a philosophical or methodological materialist, yet just by casual observation of our living environment I am driven to suspect some kind of common descent. And I think Yersina rightly points out that this planet's DNA coding mechanism certainly at some level suggests a common origin. Thus for me the question is whether common descent, to the degree it is valid, is best accounted for by a materialist theory or by ID.
It may be that common descent is not predicted by our theological tradition, but I think it must be admitted that any theory of ID based upon what we know of human creativity -- meaning human technology -- would predict some kind of common descent.
Therefore a profitable direction for this thread might be to speculate to what degree both Darwin and ID predict common descent, to what degree it can be confirmed, and which theory -- Darwin or ID -- comes the closest to predicting the kind of common descent we observe.
Even if the fossil record contained every conceivable transitional form (and microbiology seemed to confirm the same), it would still be a valid question as to whether chance and necessity really could account for the increase in specified complexity (from nonlife to you sitting there) or whether ID must be implicated. Narrowing it down we could simply stick to the DNA code -- both the system and whatever codal variation there is.
[ 13. March 2003, 15:27: Message edited by: Noel Rude ]
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Moderator
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posted 13. March 2003 15:36
I'm going to let this thread continue, but seriously, there are several things that will cause me to shut the thread down immediately:
1. If it becomes a theological discussion
2. If it becomes a "world-view"/metaphysics discussion
3. If it rehashes this thread
4. If it degenerates into a naive dualist "us vs. them" discussion
5. If stereotypes are propagated
6. Etc.
Got the point? If the discussion stays civil and progresses as a consideration of what conclusions we are able to draw from the universality of DNA, then I will let it go (though I still think it only falls on the very periphery of acceptable Brainstorms topics).
A better thread topic would have been to develop a conversation along the lines of "what we might expect to find in the future given the universality of DNA" - That might not be the most promising route, but you get the idea -> something positive -> the development of new ideas.
[ 13. March 2003, 15:36: Message edited by: Moderator ]
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yersinia
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posted 13. March 2003 16:23
Cornelius,
I'm not sure what you're arguing in this thread, but I will persist a bit longer:
Note that I didn't have to go into any specifics on how the code originated. The argument is based on the possible combinatorials of genetic codes.
So here is the premise:
1) There are an immense number of possible codes, and a smaller but still immense number of codes with the same degree of optimality as the standard code.
Here is the argument:
2) A simple explanation for all known, extant life sharing the standard code (instead of the nearly infinite array of other possibilities) is that they all got it from a common ancestor with the code.
My point with the Mars life thing is that if we did find Mars life with e.g. a radically different code (or even different biochemistry) there would be no difficulty in concluding independent origins. And technically, this would "falsify" common descent as we would (finally) have a good example of life unrelated to previously known life. Of course, it wouldn't acheive what you seem to want, which is independent origins of various earth lifeforms (at some unspecified taxonomic level), but it does show that common descent is easily testable.
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Cornelius G. Hunter
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posted 13. March 2003 16:47
Folks:
There seems to be a general misunderstanding of what is intended in this thread. Just about everyone has commented that common descent is a good explanation for the universality of the DNA code. Yes, agreed. I don't think anyone would doubt that. Nic, in your latest post you seem to be reiterating this :
Nic wrote: "Here is the argument:
2) A simple explanation for all known, extant life sharing the standard code (instead of the nearly infinite array of other possibilities) is that they all got it from a common ancestor with the code. "
Again, no disagreement. I thought I made it clear in the IP that the universality of the code is assumed to present us with compelling evidence and proof for common descent, a major pillar of evolution. So what I wanted to resolve is the question: "why is the universality of the code taken to be proof of common descent?" not "is common descent a reasonable explanation for common descent?" Do you see there is a big difference between the two statements? I see this question as not only interesting but also important in terms of theory / evidence evaluation and how we understand evolution and ID.
Nic, about your Mars example. I'm not sure how life on another planet would falsify our current theory of common descent of *life on earth* (which is what you seem to be saying). I have hard time understanding why we should drop common descent of earth life if a different sort of life on another planet were discovered. Can you elaborate? You say: "there would be no difficulty in concluding independent origins." Yes, but was this ever in doubt? IOW, separate biogenesis events on earth could account for different earth life forms (say with different DNA codes), but this wouldn't falsify common descent. It would merely mean there are multiple common descent trees acting in parallel. In any case, this is an aside as the question of falsification of common descent is not germane to this thread.
--Cornelius
[ 13. March 2003, 16:54: Message edited by: Cornelius G. Hunter ]
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yersinia
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posted 13. March 2003 17:45
Cornelius,
To clarify, I have not been saying that the universal (standard) genetic code is either "proof" or merely "can be explained". You are dichotimizing things too much.
It is just one good piece of evidence among many good pieces of evidence supporting the notion that all known life shares a common ancestor.
You seem to agree, as you acknowledge that e.g. if earth had three radically different genetic codes we would have good evidence for common descent within each of the three codes but not between them. But of course we only have one known standard code so scientists treat this as a piece of evidence supporting the common descent of known life. We could discover radically different codes in some new biochemical study of an obscure organism tomorrow, but until then the code is a strong point in favor of common descent of known life.
So what are we talking about? You seem to have some discontent with using the code as evidence for common descent but I can't figure out what it is.
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Cornelius G. Hunter
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posted 13. March 2003 20:39
Nic:
You wrote: "You seem to agree, as you acknowledge that e.g. if earth had three radically different genetic codes we would have good evidence for common descent within each of the three codes but not between them." No, I didn't mean to say that. My point was that three radically different genetic codes would not *falsify* common descent; not that they would serve as good evidence within their respective clades for common descent.
You wrote: "So what are we talking about? You seem to have some discontent with using the code as evidence for common descent but I can't figure out what it is." My discontentment lies in the fact that common descent doesn't require a single code, so therefore the universality of the code is not evidence for common descent (again, please note folks, I am *not* saying common descent doesn't explain the universality of the code; that is not the point). Yet the universality of the code is routinely claimed as compelling evidence that ~proves common descent. Clearly, this does not follow. So I am asking, what is behind this claim? How are we to understand it?
And furthermore, as I've pointed out, even when Theory X does predict Observable A, the finding of A does not prove X. This is affirming the consequent. This isn't that mysterious, it is all spelled out in the IP.
--Cornelius
[ 13. March 2003, 20:40: Message edited by: Cornelius G. Hunter ]
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