Tuesday, September 07, 2004

Hunter in Wonderland, Part 2.5

UPDATE: Sept. 8, 4:20 pm: I corrected some typos and made small changes in the phrasing in certain parts of this entry.


When I began to respond to Cornelius Hunter's thoughts from this thread over at ISCID, I said I would not respond to any further posts he made on this topic. I said that because these sorts of internet debates can easily go on forever, and I wanted to cut-off the discussion at a point where failure to respond would not be interpreted as admission of defeat.

However, Hunter has now responded to my second entry in this series (my essay is available here, Hunter's reply is available here (scroll down to the bottom of the page)). I'm afraid that Hunter's reply is so wide of the mark, that I have to weigh in one more time to try to make my argument clear. But I definitely will not be replying directly to any reply he makes to this post. And this time I really mean it!

One of the main points of contention is whether the universality of the genetic code can be considered strong evidence for evolution. I say it is. He says it isn't.

To be precise, I argued that the complete universality of the cellular machinery used to translate the code across all known species speaks well for common descent, since it would be very difficult to defend common descent in the face of multiple, different sets of cellular machinery. I then argued (basing myself on Miller, who was basing himself on Landweber) that the small variations in the code that are known occur in patterns that also are suggestive of common descent.

Finally, I addressed the question of how many changes from the standard code could be tolerated before we would have to discard the idea of universal common descent. I commented that it would require far more knowledge of evolutionary genetics than I possess to answer that question. It would depend on things like how sensitive an organism is to changes in the code, and what sorts of natural mechanisms could be produced to explain how a codon that originally coded for one amino acid (or a stop) later comes to code for something different.

After providing a brief quote of my thoughts on the matter, Hunter writes this:


Rosenhouse is not alone here, as this is a difficult question. What is clear, however, is that it would be difficult, as I earlier pointed out, to place a tight limit on the evolution of the code without presupposing evolution. Amino acids tyically have multiple codons so single codon reassignment does not mean a complete absence of the corresponding amino acid. Furthermore, many amino acids are similar, so conservative code changes are conceivable. And finally, proteins are quite robust to amino acid substitutions. Perhaps someday we'll find evidence for the code's rigidity, but at this point we have only speculation.

So this invalidates Rosenhouse's claim that the near universality of the code is strong evidence for common descent. Greater differences in the code, at this point anyway, could be explained by evolution and common descent.


Hunter does not address my point that the universality of the cellular apparatus speaks well for common descent. Common descent would be out the window without this universality, and there is no rival theory that also accounts for this universality. Chalk it up to common design if you want to, but then you will have to explain why it amused the designer to make trivial changes in the code in a handful of species.

And while it is true that common descent could account for greater changes than we actually find, it is equally true that there are good reasons to believe that there are limits to how far you can change the code before sacrificing the viablility of the organism. For that reason, the fact that the code varies very little across species speaks well for common descent.

To put it another way, the more universal the genetic code the easier it is to accept common descent. To bring variant codes under the tent of common descent, we need to invoke other mechanisms to explain how the divergence happened. As things stand, geneticists have provided a number of possible mechanisms for how one codon could change what it codes for in a given species, and these mechanisms are adequate to explain the variations we actually encounter. These mechanisms have their limits, however.

But where Hunter really starts to go wrong is in his next paragraph. He says I was too uncritical in my acceptance of Miller's claim that the pattern of divergences from the standard code is itself suggestive of common descent. Hunter writes:


Actually, there is no such evidence. Miller's powerful confirmation is, in reality, scattered across various types of organisms. For example, the UAR codon is observed to switch from &lduqo;stop” to “Gln” in green algae, various ciliates, and some diplomonads. Likewise, the UGA codon is observed to switch from “stop” to “Trp” in other various ciliates and two firmicutes. There is no powerful, unexpected confirmation of evolution here. [1]

Unfortunately Rosenhouse accepts Miller's tale unequivocally, concluding that “the pattern of divergences that are known are also consistent with the idea that they are derived from the standard code via descent with modification.”


The citation at the end of the first paragraph is to the paper “Rewiring the Keyboard: Evolvability of the Genetic Code” by Knight, Freeland, and Landweber (though for some reason Hunter only mentions Knight). Landweber was the senior author on the paper. It appeared in Nature Reviews: Genetics in 2001. This is the same paper Miller was citing in his work.

Miller was basing his statement about the pattern of differences from the standard code on a similar statement made by Dr. Landweber herself. So if Miller is confused on this point, then so is the senior author on the paper in question.

Happily, Miller and Landweber are right, and Hunter is wrong. Landweber et al are quite explicit in the paper that in certain cases, the same codon shift occurred in unrelated species. Nothing Miller wrote (or by extension me in quoting him) contradicts that. That was not the issue. The question is whether the patterns of divergences that we find across species is consistent with common descent. For example, once a shift occurs in some lineage, does the change persist in the evolutionary cousins of that species? Or are the variations from the standard code effectively random with respect to the phylogenies we have inferred from other means? The elaborate diagram reproduced by Miller in his essay shows that these patterns are indeed consistent with common descent.

This is another example of Hunter being too enamored of the idea that convergence is some sort of problem for evolution. He seems to think that the mere fact that same codon shift was converged upon in separate lineages condemns common descent. He consistently fails to consider what sorts of natural mechanisms can account for such convergences.

From here Hunter turns back to fossils. Sadly, he also turns back to some of the truly dopey arguments I criticized so strongly in my initial posting in this discussion (avialable here):


Regarding the fossils, Rosenhouse mistakenly thinks that “The fossil record reveals a history of life that is consistent with evolutionary expectations.” Actually, evolution does not expect for phenomenal complexity to appear abruptly. In fact, it does not expect phenomenal complexity at all. Also, if the earth was full of nothing but bacteria that could just as easily be described as being consistent with evolutionary expectations.


Hunter made a similar remark in responding to criticisms of Richard Wein. After describing the complexity of the echolocation system in bats, he writes:


Evolution does not predict this complexity, nor does it have a scientific explanation for how it arose. Therefore, this is not consistent with evolution and is evidence against it.


Alas, this is total nonsense.

Hunter seems to think that “phenomenal complexity” is some sort of precisely defined technical term. Like maybe evolution could explain mere complexity, or perhaps extreme complexity, but not phenomenal complexity.

What could it possibly mean to say that “evolution does not expect phenomenal complexity”? A process in which random variations are sifted through a non-random selection process can lead to outcomes far more complex than what you started with. That's simply a fact about such processes. On the other hand, since there is also an element of chance involved in the process, there is no guarantee that complexity will increase (Hunter is, at least, right on that point). So complexity by itself is not evidence one way or another for evolution.

Curiously, ID proponents like Michael Behe and William Dembski understand this very well. That is why both of them attempted to identify special kinds of complexity (irreducible complexity in Behe's case, complex specified information in Dembski's) that were outside of what natural selection could produce. As it happens, neither was successful, but we won't rehash that debate here.

To determine if a particular system could have been crafted by natural selection it is not enough to diagnose it as being complex. Furthermore, there is no shortage of complex systems whose origins have been largely revealed. No doubt Hunter would sweep this work under the rug as being unscientific, but he would simply be wrong to do so.

Hunter continues to deteriorate with his next paragraph:


Regarding comparative anatomy, a few posts back Rosenhouse agreed that massive convergence would be a problem for evolution, now he finds it to be vindication:


quote:
--------------------------------------------------------------------------------
But why is convergence a problem for evolution? If the various genetic modifications required to produce saber teeth occur with reasonably high probability, and if there is selection pressure in favor of such teeth, then the convergence of these structures is easy to explain in terms of standard mechanisms. In fact, under such circumstances, a lack of convergence would be puzzling. In this sense, many known convergences can be viewed as vindications for evolutionary theory.
--------------------------------------------------------------------------------

Evolutionists generally do not acknowledge evidential problems. Hence, massive convergence becomes a vindication for evolution. Rosenhouse denies evolution invokes ad hoc explanations, but this is ad hoc.


The interior quote is from me. Hunter begins his reply to this with a slur against the intellectual integrity of evolutionists. He then attributes to me the idea that massive convergence becomes a vindication for evolution, which is not what I said. (And let me also point out that “massive” like “phenomenal” and “striking” is not a technical term). He then says that my brief description of the conditions under which we might expect convergence to happen is ad hoc. It is not. I am simply pointing out that the prolonged action of natural selection can lead to similar solutions to similar problems. Again, that's simply a fact about natural selection. It is not a kluge meant to get around inconvenient data.

Hunter continues:


Although he agreed that massive convergence is a problem for evolution, Rosenhouse now asks why evolution is incapable of explaining convergences. That is a convenient way of framing the problem, but it misses the point. Above, Rosenhouse claimed the pentadactyl pattern strongly suggests common descent. They are obvious similarities right? So they strongly suggest common descent because they must have come from a common ancestor.


Of course, I did not say that massive convergence is a problem for evolution. Here's what I actually said:



Rampant convergent evolution would be a problem if we found several lineages evolving major, complex morphological innovations in parallel.



I thought my point here was obvious, but for Hunter's sake I guess I better spell it out. First, at the risk of being repetitive, we note that “convergent evolution” is not a precisely defined term. Generally we have in mind certain similarities in design that did not arise as a result of common descent. By itself, this is not a problem. The end result of prolonged natural selection is that organisms end up better adapted to their environment than they were at the start. Sometimes that means crafting similar adaptations to solve similar problems. The streamlined shape of fish and dolphins is a good example of this. So there is nothing in the mere fact of convergence that calls evolutionary theory into doubt.

However, though evolution will often craft similar solutions to similar problems, it is asking too much of chance for evolution to produce identical complex systems in unrelated lineages. That's what I was holding out as troubling for common descent.

Hunter's statement that I have framed the problem conveniently is yet another example of his unwillingeness to take seriously just what it is that evolutionists have been saying all these years. The problem isn't that I have framed the problem in some convenient way, it is that Hunter thinks he can make bold assertions about what evolution does and does not predict without fully considering all of the available resources evolution has at its disposal.

The identical forelimb design of humans, cats, whales and bats is an example of having the identical bones in the same relative positions to one another in a situation where there is no functional explanation for the similarity (indeed, the design seems rather ill-suited for many of the purposes it is put to). The level of morphological similarity here is far greater than in any of the examples of convergence Hunter is so fond of. The lack of a functional explanation for the structure makes it hard to view it as the outcome of natural selection crafting similar solutions to similar problems. That all suggests common descent as the most likely explanation. In my opening post of this series, I discussed the various methods scientists use to distinguish homologies from analogies. Hunter asserted that I missed his point (and more on that in part three). But here Hunter plainly needs to give more thought to how homologies and analogies can be distnguished.

Hunter continues:


But now, with similarities that could not conceivably have been inherited from a common ancestor, this too is a vindication because it must have been caused by similar mechanisms responding to similar selective pressures. This is ad hoc. If a similarity can conceivably be ascribed to a common ancestor then it is viewed as a homology and strong evidence. If it cannot be, then it is viewed as an analogy, and again strong evidence.


This is just a repetition of his earlier pargraph, but it does make explicit his refusal to consider the possibility that homologies can be distinguished from analogies. Hunter is plainly descending into cartoon arguments here. As I've already explained, there is nothing ad hoc in explaining convergence as the end result of known evolutionary mechanisms.


The point is that if similar designs are present in distant species, where common descent cannot be used to explain those similarities, then common descent need not be invoked to explain similarities in species that are not so distant. Homologies, such as the pentadactyl pattern, were a key argument for Darwin. He viewed them as a mandate for common descent. But this argument is contradicted by the convergences. It is not scientific to say that the pentadactyl similarity mandates common descent when there are other such similarities that do not mandate common descent. The argument is arbitrary. It is not a question of whether the theory allows for similar adaptations to evolve, it is question of whether or not evolution is supported by the evidence.


But there aren't “other such similarities” that do not mandate common descent. That's the whole point! “Similarity” is not a technical term. The pentadactyl pattern of various mammalian forelimbs shows a fundamentally different sort of similarity from the saber-like teeth of certain marsupial and placental mammals, or the streamlined shape of fish and dolphins. Hunter's failure to recognize this point is fatal is to his argument here.

Hunter concludes his essay with a cartoon discussion of my thoughts about the distinction between origin of life research and evolutionary biology. He writes:


Regarding the question of origin of life (OOL) Rosenhouse continues to maintain that the creation of the DNA code is outside of evolution and an OOL problem. But he avoided answering my question. Does he think the creation of the DNA code is a serious problem for OOL? If not then this is merely a rhetorical dodge since he would believe the code evolved (somehow).


The answer to Hunter's question here will depend on what he means by the phrase “serious problem”. The origin of the DNA code is the central question in OOL research. Currently I agree that there is no really persuasive explanation for how it formed. In that sense, it is a serious problem for OOL research.

There are a lot of possible explanations, however, and that is enough to dismiss any claims that we must resort to the supernatural in explaining its origin. If Hunter means that our failue so far to come up with a fully plausible explanation for the code is good reason to think that the problem is fundamentally insoluble then I would not agree with his description. OOL is an infant science, and it seems to me that progress is being made.

Also, I'm not comfortable with saying that the code evolved. I would say that it formed by some naturalistic process that probably shared certain characteritics with evolution by natural selection.

Hunter continues:


Furthermore, Rosenhouse fails to understand that DNA code evolution falls into the category of Darwinian evolution, even according to his own definition:

quote:
--------------------------------------------------------------------------------
The universal common ancestor possessed a genetic code, and that is the point from which evolution is considered to begin. To even discuss anything like a Darwinian evolutionary process, you need a collection of imperfect replicators competing for resources. The first replicators were likely far simpler than the first thing that was unambiguously alive, but the fact remains that evolutionary theory takes for granted a certain minimal level of complexity. The distinction between the origin of life, and the subsequent development of life once it appeared, is not complicated.
--------------------------------------------------------------------------------

We can agree with all this, and it means the DNA code evolution falls into the Darwinian evolutionary process. The code had to have evolved from simpler codes. How strange that the first cells to appear with the extant code constitute “a collection of imperfect replicators” but in going back just one step in the code's evolution we no longer have “a collection of imperfect replicators.”


Here I thought I was writing in English, but perhaps not. I asserted that anytime you have a collection of imperfect replicators competing for resources, you have something “like a Darwinian evolutionary process”. Indeed. But the fact remains that when we talk about evolutionary biology we are thinking of the development of life from the universal common ancestor onward. Learning what happened before the universal common ancestor is certainly of interest to evolutionary biologists, but studying that question requires different tools and different ideas from those evolutoinary biologists rely on.

Probably the modern code did form through a process that shares certain attributes with natural selection. OOL researchers often use the term “chemical selection” to capture this similarity, while also making it clear that they are talking about something different from natural selection as that term is usually used.

Hunter is eager to lump evolutionary biology together with OOL because the latter is not nearly as well developed a science as the former. He accuses me of resorting to various rhetorical tricks, but here we find him trying to bring down evolution by associating it with a branch of science with some large unresolved questions.

The remaining paragraphs of Hunter's essay contribute nothing new to the discussion. Since I'm sure my regular readers must be getting tired of these very long posts, I will stop here for now. I will write one more long post addressing the third part of Hunter's original essay.

17 Comments:

At 12:03 AM, Anonymous Anonymous said...

"Since I'm sure my regular readers must be getting tired of these very long posts, I will stop here for now."

Not me!

Sincerely,
Regular Reader
(aka RBH)

 
At 4:54 AM, Anonymous Anonymous said...

I appreciate Professor Rosenhouse clarifying his remarks in his previous post. Among other things, he had contended that the deviations from the standard code "are themselves related by common descent" and are "consistent with the idea that they are derived from the standard code via descent with modification."

I responded by pointing out that this, actually, is not the case. For example, the UAR codons are observed to switch from "stop" to "Gln" in green algae, various ciliates, and some diplomonads. Likewise, the UGA codon is observed to switch from "stop" to "Trp" in other various ciliates and two firmicutes.

Likewise, in the mitochondria, the same variants are sprinkled across many different species. For instance, the UGA codon switches from "stop" to "Trp" in a great many species, but in many of those cases there are cousin genera that lack that switch. The phylogenetic structure is weak. If one tried to fit a tree to variants it would look very different from the accepted evolutionary tree of life.

Professor Rosenhouse disagreed. He acknowledged that there are many cases of convergence, but he contended that "The question is whether the patterns of divergences that we find across species is consistent with common descent. For example, once a shift occurs in some lineage, does the change persist in the evolutionary cousins of that species?"

Rosenhouse posed this as a rhetorical question, but actually the answer is "no." In fact, for the data to fit the accepted evolutionary tree, there are likely to be reversals. For example, the AUA switches from Ile to Met in some of the Metazoa, but not all. So the author of the paper hypothesizes that the switch occurred in a distant ancestor, but then was reversed (i.e., Met back to Ile) in more recent ancestors leading up to the Hemichordates, Echinoderms, and Platyhelminthes. So, to answer Professor Rosenhouse's question, no, shifts do not (necessarily) persist.

But Professor Rosenhouse has another argument. Remember, he claimed the code variants are powerful evidence for the common descent because they fall into the right pattern. I showed that they do not fall into such a pattern. Now, Professor Rosenhouse uses a strawman argument. He puts me in the position of claiming the evidence falsifies evolution, and he is merely explaining the data:

"He seems to think that the mere fact that same codon shift was convergence upon condemns common descent. He consistently fails to consider what sorts of natural mechanisms can account for such convergences."

So since we are unable to disprove common descent, and since we certainly can think up all sorts of ways that evolution might have created convergences, then these code variants are, after all, powerful evidence for evolution. Unfortunately, this tactic is not uncommon. It makes meanginful debate difficult though.

--CGH

 
At 4:55 AM, Anonymous Anonymous said...

Testing.

 
At 11:41 AM, Anonymous Anonymous said...

Trying for a second time:

I appreciate Professor Rosenhouse clarifying his remarks in his previous post. Among other things, he had contended that the deviations from the standard code "are themselves related by common descent" and are "consistent with the idea that they are derived from the standard code via descent with modification."

I responded by pointing out that this, actually, is not the case. For example, the UAR codons are observed to switch from "stop" to "Gln" in green algae, various ciliates, and some diplomonads. Likewise, the UGA codon is observed to switch from "stop" to "Trp" in other various ciliates and two firmicutes.

Likewise, in the mitochondria, the same variants are sprinkled across many different species. For instance, the UGA codon switches from "stop" to "Trp" in a great many species, but in many of those cases there are cousin genera that lack that switch. The phylogenetic structure is weak. If one tried to fit a tree to variants it would look very different from the accepted evolutionary tree of life.

The sequence of the release factor eRF1 correlates well with the observed nuclear code variants. One group made a careful phylogenetic reconstruction of the ciliates based on the eRF1 sequence and not surprisingly there was convergence of several code changes across lineages. [Luzopone CA, Knight RD, Landweber LF, "The molecular basis of nuclear genetic code change in ciliates," Curr Biol, 2001.]

Professor Rosenhouse disagreed. He acknowledged that there are many cases of convergence, but he contended that "The question is whether the patterns of divergences that we find across species is consistent with common descent. For example, once a shift occurs in some lineage, does the change persist in the evolutionary cousins of that species?"

Rosenhouse posed this as a rhetorical question, but actually the answer is "no." In fact, for the data to fit the accepted evolutionary tree, there are likely to be reversals. For example, the AUA switches from Ile to Met in some of the Metazoa, but not all. So the author of the paper hypothesizes that the switch occurred in a distant ancestor, but then was reversed (i.e., Met back to Ile) in more recent ancestors leading up to the Hemichordates, Echinoderms, and Platyhelminthes. So, to answer Professor Rosenhouse's question, no, shifts do not (necessarily) persist.

But Professor Rosenhouse has another argument. Remember, he claimed the code variants are powerful evidence for the common descent because they fall into the right pattern. I showed that they do not fall into such a pattern. Now, Professor Rosenhouse uses a strawman argument. He puts me in the position of claiming the evidence falsifies evolution, and he is merely explaining the data:

"He seems to think that the mere fact that same codon shift was convergence upon condemns common descent. He consistently fails to consider what sorts of natural mechanisms can account for such convergences."

So since we are unable to disprove common descent, and since we certainly can think up all sorts of ways that evolution might have created convergences, then these code variants are, after all, powerful evidence for evolution. Unfortunately, this tactic is not uncommon. It makes meanginful debate difficult though.

--CGH

 
At 3:17 PM, Blogger Jason said...

Blogger was having some technical difficulties earlier today, which is why there may have been some difficulties in posting comments.

 
At 3:26 PM, Blogger Jason said...

CGH-

If only all your points were so sensible! You've certainly persuaded me that I need to bone up a bit on my genetics. But the fact remains that the variations from the standard code that we observe seem pretty insignificant compared with the vastly greater domain of agreement.

 
At 5:23 AM, Blogger Richard Wein said...

The error which CGH makes here (and in his responses to me in another thread) is to assume that, for an explanation to explain a pattern, it must predict the _exact_ outcome observed. We can easily see that this is not the case if we look at a simple analogy.

Observation: two students have handed in papers which contain an identical passage.
Explanation: both students based their work on a common source.

The explanation does not predict which passage will be identical in both papers, or even that their will be any identical passage. Nor does it predict what differences there will be between the papers, or even that there will be any differences at all. But it does explain why the two papers are more similar than can reasonably be attributed to chance. Therefore, we say that it explains the observation (even though it doesn't explain every detail of it).

By analogy...
Observation: two taxonomic groups (fungi and green algae) have all but one DNA code assignment in common.
Explanation: both groups have evolved from a common ancestor.

The explanation does not predict which code assignments will be the same in both groups, or even that there will be any shared code assignments. Nor does it predict what differences there will be between the groups, or even that there will be any differences at all. But it does explain why the two codes are more similar than can reasonably be attributed to chance. Therefore, we say that it explains the observation (even though it doesn't explain every detail of it).

Perhaps it would be better if we worded the observations differently...
Observation: two students have handed in papers which are more similar than can reasonably be explained by chance.
Observation: two taxonomic groups (fungi and green algae) have DNA codes which are more similar than can reasonably be attributed to chance.

In saying that common ancestry explains the pattern of DNA codes, we don't mean that it predicts every detail of the codes. We mean that it explains why the pattern is more hierarchical (and consistent with the taxonomic hierarchy from other evidence) than can reasonably be attributed to chance.

 
At 5:39 AM, Blogger Richard Wein said...

Clarification: my analogy above does not show that common ancestry is necessarily the _correct_ explanation, just that it is one potential explanation (just as the students using a common source is one potential explanation of the identical passage in their papers).

 
At 2:30 AM, Anonymous Anonymous said...

I respond to Professor Rosenhouse's first entry at the ISCID Brainstorms here:

http://www.iscid.org/ubbcgi/ultimatebb.cgi?ubb=get_topic&f=6&t=000540&p=3#000041

toward the bottom. This is also relevant to Richard's comments. For instance, he says I "assume that, for an explanation to explain a pattern, it must predict the _exact_ outcome observed." Actually, I never assumed that at all. --CGH

 
At 6:17 AM, Blogger Richard Wein said...

CGH: "This is also relevant to Richard's comments. For instance, he says I 'assume that, for an explanation to explain a pattern, it must predict the _exact_ outcome observed.' Actually, I never assumed that at all."

Well, you keep claiming that various observations (the pattern of DNA codes, the complexity of bat sonar, etc) are not consistent with evolution. What do you mean by this?

Let's go back to my student paper analogy again. It's a a very useful one, and I recommend that you consider it carefully. Is the fact that there are differences between the papers inconsistent with the hypothesis that both students based their work on a common source? If not, then why should divergences from a perfectly hierarchical pattern be considered inconsistent with common ancestry? Evolution theory does not predict a _perfectly_ hierarchical pattern, because evolution is a contingent process, and contingent events can produce variations in the pattern. That's why you were wrong when you wrote:

CGH: "But Professor Rosenhouse has another argument. Remember, he claimed the code variants are powerful evidence for the common descent because they fall into the right pattern. I showed that they do not fall into such a pattern."

But they do fall into such a pattern. It is not a _perfectly_ hierarchical pattern, but it is _overwhelmingly_ hierarchical. That is why it is such powerful evidence for common ancestry.

If you were only claiming that the DNA code is not as strong evidence for common ancestry as it would be if the hierarchy were perfect, then I would agree with that. But you appear to be making a stronger claim than that.

In your latest post to ISCID, you complain that your critics make a strawman of your arguments, casting them as claims that certain observed facts could not have occurred under evolution. I suggest the reason that they have interpreted your arguments this way is because:
(a) you keep writing that these facts are "not consistent with" or "contradict" evolution, or some aspect of it; and
(b) you have not given any other argument as to why these facts should be interpreted as evidence against evolution.

I have repeatedly (in an earlier thread) asked you to give an argument explaining _why_ these facts should be interpreted as evidence against evolution, and you have repeatedly failed to do so.

Perhaps it would help if I outline why I think the DNA code provides such strong evidence for common ancestry. The reason is that the pattern is far too hierarchical to have occurred by chance; it can only be explained by some sort of process of copying with variations. The only hypotheses anyone has come up with to explain how the code got copied from species to species are (a) common ancestry and (b) creation by a designer. Scientists prefer the former explanation because it is far more parsimonious. It requires only the normal processes of reproduction and inheritance. (Note: for the present I am only arguing for common ancestry as the explanation for the hierarchical pattern we observe. I am not saying anything about the origin of the complexity of organisms.) The second hypothesis requires us to assume a designer for whom we have no independent scientific evidence, whose existence and powers are themselves unexplained, and who happens to have chosen to copy species in a hierarchical fashion.

 
At 12:53 PM, Anonymous Anonymous said...

Richard: You wrote: "Perhaps it would help if I outline why I think the DNA code provides such strong evidence for common ancestry. The reason is that the pattern is far too hierarchical to have occurred by chance; it can only be explained by some sort of process of copying with variations."

Really ... Can you elaborate? Any papers on this? Have you done some computations? --CGH

 
At 3:46 AM, Blogger Richard Wein said...

Surely that much is obvious. Think about it. If two students turn in papers with an identical long passage, would you need to do a computation to see that this couldn't plausibly have happened by chance?

Are you going to address my other points, including telling us what you mean by "not consistent"?

 
At 5:00 AM, Blogger Richard Wein said...

Here's a quick computation for you. The triplet code has 64 mappings onto 20 amino acids (plus "stop"). So the number of possible codes is 21^64, which is over 10^84. So the probability of even _two_ species having exactly the same code, if they are completely random, is 1 in 10^84.

Now, it's not really as simple as that, because some possible codes are more efficient than others, and, even if each species had evolved independently, we might expect it to have a relatively efficient code (thanks to natural selection). (Similarly, if each species had been designed independently, we might expect the designer(s) to have used efficient codes in all of them.) In particular, the grouping of amino acids in the code table, so that the the last base is often irrelevant, means that errors in the last base of a triplet will often have no adverse consequence. For example ACU, ACC, ACA and ACG all code for Thr. So let's assume that all the codes necessarily have the same pattern, and just switch around the amino acids. In other words, ACU, ACC, ACA and ACG will always code for the same amino acid, but it won't necessarily be Thr. The number of ways of permuting the 20 amino acids is 20x19x18...x3x2x1 which is more than 10^18. So the probability of even _two_ species having exactly the same permutation is only 1 in 10^18.

In fact, all vertebrates have exactly the same code, or perhaps we should say all vertebrate species tested so far. I don't know how many that is; let's call it N. Then the probability of all those species having exactly the same permutation of amino acids in their code is 1 in (10^18)^(N-1). And that's just the vertebrates. Do similar calculations for the other taxonomic groups having identical codes within the group. Then multiply all those probabilities together. And that's just taking the groups separately. Do another calculation to get the probability of all these _groups_ having such similar codes. (And, since we're only looking at amino acid permutations, and not the full details of the codes, the various groups are even more similar.) And multiply by that. You end up with an incredibly small probability.

 
At 5:29 AM, Blogger Richard Wein said...

Cornelius, I just read you latest post (14 September 2004 04:23) at ISCID. You're still making ambiguous assertions that "evolution cannot explain" such-and-such a fact, in this case the trilobite eye. What do you mean by this?

If you mean that evolutionary theory has no explanation at all, you're wrong. Evolutionary theory has a great deal to say about evolution of structures generally, and eyes in particular, much of which--it's reasonable to assume--applies also to the trilobite eye. Even if there's no literature specific to the evolution of the trilobite eye (have you checked?), it doesn't follow that evolutionary theory has no explanation for it.

If you mean that evolutionary theory does not have a _complete_ explanation, then you're just making the old argument from ignorance or "gaps" argument. As I've already pointed out to you, there are gaps in every area of scientific knowledge. If we used that as an excuse for rejecting theories, we would have to reject many other well-supported theories too.

 
At 5:40 AM, Blogger Richard Wein said...

Cornelius, I think I've wasted enough time on this. Unless you are willing to provide a substantive argument, instead of just making vague and ambiguous assertions (see also our earlier discussion at http://evolutionblog.blogspot.com/2004/09/does-this-guy-have-job.html), I will not respond again.

 
At 3:33 AM, Anonymous Anonymous said...

I respond at the ISCID Brainstorms:

http://www.iscid.org/ubbcgi/ultimatebb.cgi?ubb=get_topic&f=6&t=000540&p=4#000051

 
At 1:21 PM, Blogger jasmine said...

Great job on your talk on dna testing. I have a dna testing secrets blog if you wanna swing by my place!

 

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