Common ancestry passes another test. News at 11.

Most excellent.Thanks for the write-up Nick.

The paper itself (like the commentary) is paywalled, so all I have to go on here is Todd Charles Wood's commentary. And I think he makes a couple of valid points. Here's my version, which may not be Wood's:

1. Theobald is really, apparently, testing whether the sequences are significantly similar, i.e. more so than can be explained by chance resemblance. If they are, the single-tree model explains the data best. If they aren't, a multiple-tree model is at least as good. But he began by choosing proteins that were similar enough for homology to be clear. Is that a bias? Well, I'm pretty sure that level of similarity can't be explained by chance even if we correct for the sequences having been chosen from a universe of many more sequences. But it's something to think about. The creation model assumed here -- randomized sequences -- is falsified if we find any proteins at all with detectable homology.

2. It's not explicitly claimed to be a test of separate creation, but everyone is going to take it that way. Given that, what's the proper model for separate creation? We don't know. It could be that a rational creator would have originally made "kinds" using conserved (in the creation model, that equals "under strong purifying selection") proteins that were initially identical. Why not? (Then again, why? That's a problem with creation models.) And that's the same as having a common ancestor on a star tree. This is actually a test of significant similarity, and a creator could have made proteins with any degree of similarity from complete to none. The only creation model falsified here is one in which each "conserved" protein in each kind is randomly chosen from among all possible sequences that would perform the same function. And even then we would have to know how many such sequences there are, and know their range of similarity; this model seems to assume that sequences are effectively unconstrained.

Dr. Theobald is rather busy at the moment with the end of the semester and media inquiries. He has promised me that he will write something up about this research for us later this week.

So THIS explains the Tea Party!

This is actually a test of significant similarity, and a creator could have made proteins with any degree of similarity from complete to none. The only creation model falsified here is one in which each “conserved” protein in each kind is randomly chosen from among all possible sequences that would perform the same function. And even then we would have to know how many such sequences there are, and know their range of similarity; this model seems to assume that sequences are effectively unconstrained.

I see a problem here. A randomized protein, even with preserved amino acid frequencies, is a major assumption. If we suppose that god wanted the protein to function, and to have the same function (more or less) in the different organisms, that's not a good model. Presumably a small proportion of the randomized sequences would have the appropriate function. What constraints are imposed by functional necessity? We don't know, and would have to take that into account in any model of separate creation. I strongly suspect that constraints aren't enough to account for the observed data, but the present study doesn't show that.

It seems to me there are two more or less reasonable (scare quotes may be appropriate there) creation models: one in which god chooses random sequences from the set of all possible functional sequences, and one in which he chooses identical sequences. The first case emphasizes his infinite creativity, while the second emphasizes his (I guess) efficiency. Either seems equally likely considering his claimed attributes. Again, I haven't see the paper, but as described by Wood neither model is tested. A randomized model would inflate the likelihood difference compared to that first, functionally constrained model. And the second model would produce (after some considerable evolution, though potentially within separate kinds, as in a lawn) a correlation structure just like real common descent: instead of an ancestor there's a single identical part common to a variety of models. Like I said, that would be a star tree, so if Theobald also tests and rejects a star tree, he has dealt with that model. Does he?

The latter idea is particularly strange: did anyone ever think that the “common ancestor” of e.g. humans and chimps was a single individual? I think not; it was always an ancestral population.

Mike Haubrich, don't get hung up on the 'definition' red herring. Whole civilizations preceded the definition concept. This has nothing to do with what Nick said; it is immaterial whether some would say "X is life" or "X is not quite life" at some early stage. Don't think of the first life as a cell as we know them either.

I'm glad Nick made this 'starter' post on the paper. This will help everyone next week when Doug gets deeper into it. Stay tuned!

Pete Dunkelberg said: I'm glad Nick made this 'starter' post on the paper. This will help everyone next week when Doug gets deeper into it. Stay tuned!

did anyone ever think that the “common ancestor” of e.g. humans and chimps was a single individual?

I don't think Mike was disagreeing with me, just applying the same logic further back. And he's right, it's probably populations all the way back to chemicals. Especially if you take the direction of recent OOL work which suggests self-replicating RNA-like molecules might be more likely to emerge from a collection of short sequences than from a single sequence...

Scott -- interesting points. The molecular Adam/Eve stuff was based specifically on mitochondria DNA (passed only through the mother) and Y-chromosome (passed only through the father, most of it doesn't recombine with the X). Each non-recombining marker does indeed trace back to a single individual -- this is called "coalescence". But the single individuals lived tens of thousands of years apart from each other, and each was living in a population at the time. And the thousands of recombining regions in the rest of the genome (the autosomes) each have their own histories, with few/none of them the same as the mtDNA or Y-DNA.

I see a problem here. A randomized protein, even with preserved amino acid frequencies, is a major assumption. If we suppose that god wanted the protein to function, and to have the same function (more or less) in the different organisms, that’s not a good model. Presumably a small proportion of the randomized sequences would have the appropriate function.

Scott said:

did anyone ever think that the “common ancestor” of e.g. humans and chimps was a single individual?

I think that would in fact be the general belief even now. That's where the notion of a "missing link" came from: that one individual who bridges the entire current gap between current species.

Creationists have, for quite a while, been saying that similarity between living things is an indication of a common designer. As if the pattern of similarities and differences reflected in taxonomy could be reduced to "all living things are similar".

As a practical matter, I think that if one could convince creationists of common ancestry just within the order Primates over a few tens of millions of years, that would be the end of creationism. There would be a few holdouts for separate creation/design of larger taxa, or about supernatural intervention hundreds of millions or billions of years ago, but there would be no general public interest in that.

TomS said: As a practical matter, I think that if one could convince creationists of common ancestry just within the order Primates over a few tens of millions of years, that would be the end of creationism.

I have a question on the Zuckerandl and Pauling quote, and I'm not sure whether it bears on the paper or not (I don't have a subscription to Nature, so I'm going on what's written here). I was under the impression that modern 'organismal biology' phylogenetic trees incorporated genetic data - i.e. are sometimes corrected based on the genetic data - so the two tree types are no longer independent but rather dependent factors. This would greatly increase the probability of the two matching regardless of whether the model is correct. Is this a relevant issue? If so, how was it addressed?

Joe Felsenstein said:

Scott said:

did anyone ever think that the “common ancestor” of e.g. humans and chimps was a single individual?

I think that would in fact be the general belief even now. That's where the notion of a "missing link" came from: that one individual who bridges the entire current gap between current species.

That isn't where the idea of "the missing link" came from. In Darwin's day a criticism of him was that there was no fossil connecting humans with apes (or as we would now say, other apes). This missing link was filled in 1891 when Dubois found what we now call Homo erectus, and also in 1924 when Dart found Australopithecus. There was never any assumption that this was a single individual, what was missing was a species. The phrase "missing link" is well known, but people don't remember what it was, and, alas, are unsure whether it is still missing -- and that's why the disgraceful publicity around the fossil "Ida" (Darwinius masillae) was able to blatantly misuse the phrase "The Link".

Scott said:

did anyone ever think that the “common ancestor” of e.g. humans and chimps was a single individual?

I think that would in fact be the general belief even now. That's where the notion of a "missing link" came from: that one individual who bridges the entire current gap between current species.

TomS wrote:

"Creationists have, for quite a while, been saying that similarity between living things is an indication of a common designer. As if the pattern of similarities and differences reflected in taxonomy could be reduced to “all living things are similar”."

Exactly. That is why it is so important to point out that not only are thing "similar" but they are similar in a very specific way. That is that they are similar in exactly the way predicted by descent with modification. Many of these similarities do not make any sense whatsoever from a design perspective. The precise types of similarities and the precise pattern of similarities are what is important, not some nebulous "god could have done it that way so common design" similarity.

I've been convinced for some time of a single common ancestor for all living things. This raises some interesting speculation. If the conditions were right for the origin of the common ancestor, perhaps the conditions were right for origin or other potential common ancestors. Was it a matter that they were out competed by the common ancestor? Or were conditions for the origin of the common ancestor so rare and unusual that no competitors originated? This has some connection to speculation about origin of life elsewhere in the universe. If it is difficult and unusual, there may not be much life off earth, If it is common and easy, there may be living things all around.

So perhaps creationism wasn’t the main target of Doug’s paper?

"I’ve been convinced for some time of a single common ancestor for all living things. This raises some interesting speculation. If the conditions were right for the origin of the common ancestor, perhaps the conditions were right for origin or other potential common ancestors. Was it a matter that they were out competed by the common ancestor? Or were conditions for the origin of the common ancestor so rare and unusual that no competitors originated?"

Like I said, it could be populations all the way down. It is important to realize that even without competition/selection, in any replicating population, one replicator will eventually take over the entire population. Google "coalescence". Throw in selection and you get even more of this. This kind of selective sweep probably happened umpteen times in the gradual origin of replicating sequences and then cells and then the LUCA. The only significance of the LUCA is that it represents just the *last* time this happened on a global scale. (but different genes, etc., might have done it differently, producing different trees, but nevertheless there is good evidence that a bunch of genes did this, as Theobald shows)

stevaroni said: I think the big issue is that fossils usually come in units of one individual, so when an important transition is found it's easy to point to the head on the table and say "We've found the link. There he is." rather than the far more accurate "Here's an individual from the transitional population".

John Harshman said: It's not explicitly claimed to be a test of separate creation, but everyone is going to take it that way. Given that, what's the proper model for separate creation?

Jim Thomerson said: I've been convinced for some time of a single common ancestor for all living things. This raises some interesting speculation. If the conditions were right for the origin of the common ancestor, perhaps the conditions were right for origin or other potential common ancestors. Was it a matter that they were out competed by the common ancestor? Or were conditions for the origin of the common ancestor so rare and unusual that no competitors originated? This has some connection to speculation about origin of life elsewhere in the universe. If it is difficult and unusual, there may not be much life off earth, If it is common and easy, there may be living things all around.

Scott said:

did anyone ever think that the “common ancestor” of e.g. humans and chimps was a single individual?

I think that would in fact be the general belief even now. That's where the notion of a "missing link" came from: that one individual who bridges the entire current gap between current species. It's that misguided creationist belief that evolution means you have the birth of the "first" man who then has to wait for the birth of the "first" woman so that they can start the human race. Or something like that. Even recently, wasn't there a study looking for and finding a probably genetic "Eve" and a genetic "Adam" for the human race? If I recall, they were separated by several tens of thousands of years, which seemed kind of odd. I consider myself to be fairly well educated (for someone without a PhD), but up until a few years ago (think Dover) if you had asked I might have said there was a single individual common ancestor. Once you all have pointed out why this isn't the case, it becomes "obvious" you need an evolving population, but that doesn't appear to be the "common" understanding.

eric said: My two cents on the whole missing link verbiage is that calling a single fossil a missing link was not inaccurate when we didn't know much, but now its just confusing. Lucy was a missing link because it was the first scientific discovery of an ancient hominid. More hominids help us understand how hominids evolved but that they evolved has already been established.

I think I talked with this man on the Dawkins forums.
two points.
First biogeography is a friend to YEC. The migrations from the ark filling the earth all work fine.
In fact otherwise it seems to be a chaos of migration.
Its creationist doctrine that all life comes from a common blueprint.
Even kinds are just a twist on the blueprint. Everything has eyes, ears, legs, head.
It seems clear that there is a thinking being behind such organization and it seems that if evolution was true diversity and great happanchance would make creatures so wildly different looking.
The sameness of creatures inside and out and like sameness with all biology suggests simple plans that lead to logical diversity.
The sameness and fewness of creatures shows a poverty of evolution but fits limited kinds coming from simple, relative, basic plans from a general blueprint.
Perhaps models on what the biology should look like from billions of years and millions etc of selections should be made. The world today and in fossil seems rather bare and simple from what otherwise evolution would predict.

Leave it. You couldn't ask for better.

"Leave it. You couldn’t ask for better."

Yes, Byers at his ignorant best.

Robert Byers said: I think I talked with this man on the Dawkins forums. two points. First biogeography is a friend to YEC. The migrations from the ark filling the earth all work fine. In fact otherwise it seems to be a chaos of migration. Its creationist doctrine that all life comes from a common blueprint. Even kinds are just a twist on the blueprint. Everything has eyes, ears, legs, head. It seems clear that there is a thinking being behind such organization and it seems that if evolution was true diversity and great happanchance would make creatures so wildly different looking. The sameness of creatures inside and out and like sameness with all biology suggests simple plans that lead to logical diversity. The sameness and fewness of creatures shows a poverty of evolution but fits limited kinds coming from simple, relative, basic plans from a general blueprint. Perhaps models on what the biology should look like from billions of years and millions etc of selections should be made. The world today and in fossil seems rather bare and simple from what otherwise evolution would predict.

I can’t wait to read creationist/ID reaction to this paper. They will likely do what they always do, which is make up something ad hoc on the spot, like, “Oh, God would have done it [i.e. produced the observed sequence patterns] that way when he miraculously created species.” Until they produce a quantifiable model to compare to the common ancestry one via a likelihood ratio test (LRT) or Akaike Information Criterion (AIC), such verbiage is pretty much pointless. Either that, or there will just be confused bickering based on misunderstandings of likelihood, probability, statistics, etc. It should be great sport.

— Nick Matzke

peter said: "Leave it. You couldn’t ask for better." Yes, Byers at his ignorant best.

TomS said: Creationists have, for quite a while, been saying that similarity between living things is an indication of a common designer. As if the pattern of similarities and differences reflected in taxonomy could be reduced to "all living things are similar". As a practical matter, I think that if one could convince creationists of common ancestry just within the order Primates over a few tens of millions of years, that would be the end of creationism. There would be a few holdouts for separate creation/design of larger taxa, or about supernatural intervention hundreds of millions or billions of years ago, but there would be no general public interest in that.

I can’t wait to read creationist/ID reaction to this paper. They will likely do what they always do, which is make up something ad hoc on the spot, like, “Oh, God would have done it [i.e. produced the observed sequence patterns] that way when he miraculously created species.” Until they produce a quantifiable model to compare to the common ancestry one via a likelihood ratio test (LRT) or Akaike Information Criterion (AIC), such verbiage is pretty much pointless. Either that, or there will just be confused bickering based on misunderstandings of likelihood, probability, statistics, etc. It should be great sport.

In a comment to the AtBC thread, "Uncommonly Dense Thread 3," REC pointed out that creationist dipstick Cornelius Hunter had blagged on Doug's article.

Having screwed himself, Cornhole retraced his blog after Doug tried to gently point out the many errors- but ol' Corney still calls Doug a liar.

One problem with your approach, Steve P., is that creationists and Intelligent Design proponents refuse to explain how to divine the goals of the "Intelligent Designer" in the first place. Another problems is that creationists and Intelligent Design proponents refuse to explain how the "Intelligent Designer" tinkers with life in the first place.

And then there is the tremendous problem of how creationists and Intelligent Design proponents refuse to explain how saying GODDESIGNERDIDIT is relevant to science to begin with (many at the Discovery Institute have even confessed the opposite).

So, Steve P., before you continue whining about current scientific theories and procedures, it would be best if you explained to us exactly how and why saying GODDESIGNERDIDIT will benefit researchers.

(cue Steve P. making a moronic and childish taunt as a reply)

Gary Hurd said: In a comment to the AtBC thread, "Uncommonly Dense Thread 3," REC pointed out that creationist dipstick Cornelius Hunter had blagged on Doug's article. Having screwed himself, Cornhole retraced his blog after Doug tried to gently point out the many errors- but ol' Corney still calls Doug a liar.

Everyone knows that I would never stoop so low as to respond to Byers. However, interestingly enough, I already addressed exactly these points in my post above, so fortunately I don't have to. Except to point out, as so many others already have also, that his migration routine is also completely bogus as well. I guess this guy never heard of continental drift.

Funny how he somehow addressed completely new research without ever reading it, or explaining it, or even referring to it. Just the same old lies and distortions. Doesn't this guy ever come up with anything new? Oh well, at least he admitted that the supposed "blueprint" was actually "simple" and "basic". Doesn't seem to be much of a barrier to evolution then I guess. And of course if you are completely ignorant of all evolutionary theory it is easy to claim that it doesn't fit the data. More is the pity.

Dave Luckett said: Leave it. You couldn't ask for better.

Steve P; has indeed spouted all of this nonsense long ago. The thing is that he refuses to even read the literature that proves him wrong. You can't argue with that kind of closed mindedness, so I won't even try. I will simply point out once again that Steve is deliberately ignoring almost all of the research in modern genetics and it is all completely consistent with the modern theory of evolution. The supposed gap is found only between his ears.

6.66

Includes points for two word sentence without capitalization and has religious implications.

Just Bob said: Suggestion for all future Byers posts: Just give them a rating, like Olympic figure skating judges. 0 would be perfectly rational. 10 would be absolute batshit, fundie, made-up-on-the-spot, out-of-touch-with-reality, straight-from-a-sunday-school-bible-stories-book (with technical points for unreadability).

For myself, I don’t see any illogic in taking the alternate approach of assuming a teleological insertion of a natural but as yet undefined element being responsible for the complexification of life and seeking that element just as diligently as an evolutionist would pursue confirmation (through reverse engineering) that replication error is at the core of complexity.

peter said: "Leave it. You couldn’t ask for better." Yes, Byers at his ignorant best.

DS--

Minor point that drives me crazy. "Continental drift" was rejected by geologists because it makes no sense. Granite plowing through basalt? Never happened. Plate tectonics, on the other hand, not only explains the pattern of fossil distribution perfectly, but also has all kinds of evidence, like sea floor spreading, to back it up. Writing continental drift when you mean plate tectonics may sound less like techno-jargon, but they really aren't the same thing.

Plus, you're setting up a situation where creationists can correctly "disprove" continental drift-- without mentioning the fact that geologists have already done so. Of course, the geologists who replaced continental drift with plate techtonics actually strengthened the evidence for ancient dispersions and subsequent evolutionary radiations. But the creationists won't mention that, will they?

here’s a reaction from a creationist layman. The issue is not about the validity of common ancestry, but method.

— Steve P.

Like Mike Elzinga said in another thread about his years of experience dealing with creationist literature, should we not consider the assumptions being made before delving into the merits of an argument?

hoary puccoon said: DS-- Minor point that drives me crazy. "Continental drift" was rejected by geologists because it makes no sense. Granite plowing through basalt? Never happened. Plate tectonics, on the other hand, not only explains the pattern of fossil distribution perfectly, but also has all kinds of evidence, like sea floor spreading, to back it up. Writing continental drift when you mean plate tectonics may sound less like techno-jargon, but they really aren't the same thing.

I'm enjoying this conversation immensely. I can't even hope to get this much from reading the paper--stats, ugh! So thanks to all of you who can put it into easier concepts.

I have a comment on the semantics of the term common ancestor. I suppose that as a layperson I have always thought of this meaning a single organism--until I really think about it anyway. When Dawkins talks about going back to that ancestor and making the turn through the lineage of another organism, I don't recall him saying "ancestors".

The answer to this confusion would not be to use the plural*, but perhaps some term like ancestor species would work better. Perhaps it's a bit cumbersome, but I'm going to try to start using the term.

Just like using the terms continental drift or global warming opens a conversation up for debate (among laymen), so can common ancestor.

What do you think? Is there a better term.

*the plural would not work because it implies the entire lineage, which is likely why we don't use it now.

Steve P. said: here's a reaction from a creationist layman. The issue is not about the validity of common ancestry, but method. It seems, from an evolutionary perspective, that life at its core is ultimately the result of replication error ( use the word error as modification seems too teleological a description). Like Mike Elzinga said in another thread about his years of experience dealing with creationist literature, should we not consider the assumptions being made before delving into the merits of an argument? If in fact life got its' start and then developed as a result of replication error, then mustn't we support that assumption in a rigorous manner in advance?

OK, now I've actually read the paper, thanks to Doug Theobald. I have quite a few questions, but I guess I'll wait until he's free.

I think most of us think of common ancestor as being a species. The process for forming lineages from a common ancestor is speciation. Cladistic speciation is the splitting up of an ancestral species. So, perhaps, we have not really thought much about the nature of the common ancestor. A bacteriologist might see speciation differently, perhaps.

I wrote a blog article about this yesterday if anyone wants another non-paywall coverage of this:

http://sciblogs.co.nz/code-for-life/2010/05/14/testing-common-ancestry-to-all-modern-day-life/

Stanton said: (cue Steve P. making a moronic and childish taunt as a reply)

Steve P. said: Stanton, It is sometimes tempting to fight fire with fire in these debates, but I'll pass. Thanks for the comment, anyway.

Stanton said: (cue Steve P. making a moronic and childish taunt as a reply)

Sylvilagus said:

Steve P. said: Stanton, It is sometimes tempting to fight fire with fire in these debates, but I'll pass. Thanks for the comment, anyway.

Stanton said: (cue Steve P. making a moronic and childish taunt as a reply)

Care to reply to my comment? No taunting, nothing moronic, just layman to layman on the science.

Robert Byers said: I think I talked with this man on the Dawkins forums. two points. First biogeography is a friend to YEC. The migrations from the ark filling the earth all work fine.

In fact otherwise it seems to be a chaos of migration. Its creationist doctrine that all life comes from a common blueprint. Even kinds are just a twist on the blueprint. Everything has eyes, ears, legs, head. It seems clear that there is a thinking being behind such organization and it seems that if evolution was true diversity and great happanchance would make creatures so wildly different looking. The sameness of creatures inside and out and like sameness with all biology suggests simple plans that lead to logical diversity. The sameness and fewness of creatures shows a poverty of evolution but fits limited kinds coming from simple, relative, basic plans from a general blueprint. Perhaps models on what the biology should look like from billions of years and millions etc of selections should be made. The world today and in fossil seems rather bare and simple from what otherwise evolution would predict.

Dale Husband said: Maybe the reason Byers believes in an idiotic God is because he has created God in his own image.

Grant said: I wrote a blog article about this yesterday if anyone wants another non-paywall coverage of this: http://sciblogs.co.nz/code-for-life/2010/05/14/testing-common-ancestry-to-all-modern-day-life/

Frank J said:

here’s a reaction from a creationist layman. The issue is not about the validity of common ancestry, but method.

— Steve P.

Funny that you call yourself a "creationist" after clearly stating (some months ago in another thread) that you accept common ancestry. While IDers who either vaguely reject common ancestry or at least refuse to take a position insist that they are not creationists. But given their "big tent" strategy they'll surely forgive your "error," while pouncing on any "Darwinist" for the same "error." Unfortunately for you, common ancestry, and specifically human common ancestry with other species, is the most important question, to most fans of creationism/ID. You can play word games all you want with "errors," "chance of the gaps," etc., but the bottom line is that, whatever the ultimate or proximate cause(s) of species change - and please don't bait-and-switch that with abiogenesis - common ancestry has no promising alternative. Even some "creationists" like you have admitted that.

Frank J said:

here’s a reaction from a creationist layman. The issue is not about the validity of common ancestry, but method.

— Steve P.

Funny that you call yourself a "creationist" after clearly stating (some months ago in another thread) that you accept common ancestry. While IDers who either vaguely reject common ancestry or at least refuse to take a position insist that they are not creationists. But given their "big tent" strategy they'll surely forgive your "error," while pouncing on any "Darwinist" for the same "error." Unfortunately for you, common ancestry, and specifically human common ancestry with other species, is the most important question, to most fans of creationism/ID. You can play word games all you want with "errors," "chance of the gaps," etc., but the bottom line is that, whatever the ultimate or proximate cause(s) of species change - and please don't bait-and-switch that with abiogenesis - common ancestry has no promising alternative. Even some "creationists" like you have admitted that.

Mike Elzinga said:

Like Mike Elzinga said in another thread about his years of experience dealing with creationist literature, should we not consider the assumptions being made before delving into the merits of an argument?

This is the usual quote-mining and misrepresentation by a creationist. They simply cannot help themselves. It is the creationists who make the argument of “same data, different perspective.” And that claim is pure crap. None, I repeat, none of the ID/creationist “interpretations” of nature work in the laboratory or in real field research. They simply cannot use their notions of thermodynamics, entropy, and the 2nd law to design and build equipment that works in the lab. They cannot calibrate thermometry and measure temperatures, they cannot design adiabatic cooling and heating methods, they cannot design cryostats. They cannot take data. They cannot write working computer programs that encode the rules of nature into working algorithms that replicate what nature does. And they certainly cannot understand the results of working programs written by people who do understand. They wreck everything they get their hands on. They cannot go out into the field and collect data while preserving the relevant information needed to place the data in context. In short, every damned ID/creationist I have ever encountered over the years was a total incompetent at research, teaching, design and construction of lab equipment, interpreting data, preserving data, cross-checking data, doing controls, checking for systematic effects and confounding factors, and everything else that real scientists have learned to do routinely. So when a creationist tells you that it is a matter of interpretation, that claim is total bullshit. Nature knows, and nature tells. And real scientists listen.

Steve P. said: Got it!

A tiny crack of light opens into SteveP's ideas. He has been very averse about specifying them so far. Steve appears to be conceding an ancient Earth, ancient life, and common ancestry of all life (and hence, slow change in allele over generational time).

It's the mechanism he balks at. Mutation, natural selection and genetic drift, he thinks, are insufficient to explain the origin of species, notwithstanding ample evidence that they operate to change allele over generational time, and that it has been demonstrated that they are sufficient in all known cases of change in allele.

Although he has produced no evidence for it, Steve thinks an invisible hand is guiding change in allele in a given direction. He hasn't the faintest idea whose this hand might be, nor how it operates, nor what it does, nor can he give any specific instance of its operations, nor can he cast any light on the direction of its intervention, which can only be seen in retrospect.

That is, his conjecture has no structure, no specific proposal, no testable implication, and no evidence whatsoever. His entire argument consists only of the repeated assertion that there must be such a cause, and that the observed natural causes are insufficient to explain the origin of species and the variety of life.

This is nothing more than the arguments from incredulity and ignorance in fancier dress than usual. Steve is saying no more than "I don't know how it happens, but I can't believe it happens this way, so it doesn't happen this way."

The most hilarious aspect of this is that the violence Steve has done to his own rationality is irrelevant. He has gouged out his own reasoning faculties for nothing. Denying the operant end of the theory of evolution means nothing to the dominionists and reconstructionists and the marching morons who support them. If they ever achieved their goals, they would as cheerfully immolate Steve as anyone else here.

Hence, his extreme reluctance to specify his own ideas. He knows, I think, that he has no allies at all. Hardly anyone occupies his contorted position: accepting common ancestry, but denying that speciation is explained by natural causes.

It's odd that a person as alive to his strategic position could be so obtuse in the matter he argues.

TomS said:

peter said: "Leave it. You couldn’t ask for better." Yes, Byers at his ignorant best.

He strikes at our weakness. Who can resist the temptation to say something about all of God's creatures having eyes? Flatworms have eyes, potatoes have eyes, hurricanes have eyes, needles (well, they are intelligently designed) ...

Dale Husband said:

Robert Byers said: I think I talked with this man on the Dawkins forums. two points. First biogeography is a friend to YEC. The migrations from the ark filling the earth all work fine.

That's a flat out lie if there ever was one, of course.

In fact otherwise it seems to be a chaos of migration. Its creationist doctrine that all life comes from a common blueprint. Even kinds are just a twist on the blueprint. Everything has eyes, ears, legs, head. It seems clear that there is a thinking being behind such organization and it seems that if evolution was true diversity and great happanchance would make creatures so wildly different looking. The sameness of creatures inside and out and like sameness with all biology suggests simple plans that lead to logical diversity. The sameness and fewness of creatures shows a poverty of evolution but fits limited kinds coming from simple, relative, basic plans from a general blueprint. Perhaps models on what the biology should look like from billions of years and millions etc of selections should be made. The world today and in fossil seems rather bare and simple from what otherwise evolution would predict.

And this is why I consider Creationism to be worthless, because it implies that the Creator is incompetent and limited in his abilities. Human imagination easily comes up with animals like Pegasus, Centaurs, and other creatures that have more than four limbs, yet all real vertebrates have no more than four. Maybe the reason Byers believes in an idiotic God is because he has created God in his own image.

Maybe a 6. Only marginally incoherent. A point extra for the supreme vapidity of "Its more math theory then chaos theory". Perhaps half one more for the way he destroys his own thesis in the last sentence.

Funny how Steve conveniently mentions only "replication error" and forgets all about selection. Oh well, what can you expect from a guy who doesn't even believe in competition?

As for Byers, yea, no one ever bothered to think about how a blind process would look different from one guided by an intelligence before. how novel.

It seems that the only argument that creationists have is to project their own ignorance onto everyone else. That should fool everybody.

Steve P. said: Frank J., How is common ancestry inconsistent with a theistic perspective on biological activity? Let me know what your specific definition of creationism is before I concede the point. Common ancestry is much easier to explain (a general claim)than common descent via replication error(a specific claim). It is the latter that is being hotly contested since it is speculative in nature and has not been empirically validated.

How is common ancestry inconsistent with a theistic perspective on biological activity? Let me know what your specific definition of creationism is before I concede the point. BTW, the bait and switch is not coming from me. Rather, it seems some of you on this board want to conflate common ancestry with common descent via replication error.

— Steve P.

I never said that common ancestry is “inconsistent with a theistic perspective on biological activity.” It is, however, inconsistent with what most self-described creationists believe.

— I

I endorse completely your latest comments in rebuttal to Steve P. You didn't need to clarify yourself in your second comment, but I concur with your assessment.

Behe loves to play word games so much that I think he should have earned his Ph. D. in that. However, that's a mere aside.

More importantly, of course, is asking oneself whether an Intelligent Designer would be so "inefficient" to allow, over the course of the Phanerozoic Eon (approximately the last 540 million years of Earth's history, from the Cambrian Period to the present) at least seven, maybe eight, mass extinctions which completely "reshuffled the deck" with respect to biological diversity. Why go through the trouble of exterminating Burgess Shale type faunas, conodonts, graptolites, trilobites, nautiloid and ammonoid cephalopods, early mammal-like reptiles, all dinosaurs except for the sole avian lineage, and countless others, if all these meant "unsuccessful Designs" for an Intelligent Designer - I must presume Klingon scientists - to weed out. Doesn't strike me as a rational course of action for any Intelligent Designer to take.

John Kwok said: More importantly, of course, is asking oneself whether an Intelligent Designer would be so "inefficient" to allow, over the course of the Phanerozoic Eon (approximately the last 540 million years of Earth's history, from the Cambrian Period to the present) at least seven, maybe eight, mass extinctions which completely "reshuffled the deck" with respect to biological diversity. Why go through the trouble of exterminating Burgess Shale type faunas, conodonts, graptolites, trilobites, nautiloid and ammonoid cephalopods, early mammal-like reptiles, all dinosaurs except for the sole avian lineage, and countless others, if all these meant "unsuccessful Designs" for an Intelligent Designer - I must presume Klingon scientists - to weed out. Doesn't strike me as a rational course of action for any Intelligent Designer to take.

Steve P. said: So Mr. Elzinga, You can reject Dembski's paper out of hand because you disagree with his fundamental assumption of information as a real and separate entity

but we are not allowed to question replication error as the root cause of biological complexity.

Got it! I see now that Behe, Minnock, Marks, Sternberg, and a host of other scientists that just happen to reject replication error as the root of biological complexity are all just simply incompetent. Why didn't I see that before. Sheesh.

Lie? About what?

Anyways. The creator is not incompetent for using a same equation in nature for conclusions. A blueprint that insists on equations is very likely from a thinking being. Not wild fancys. Nature looks just like a guy with a computer program. I do not see the chaos one would expect if evolution by billions of selections on trillions of mutations was a actual process. Nature would not be so orderly and consistent in conclusions. Its more math theory then chaos theory. Origin thinkers need to carefully think about how a blind process would look different that a process with a watching eye.

Robert Byers said: These are not living creatures. Biology is all about brilliant equations. More then the stuff about gravity and orbits etc. Its a great rule in nature of creatures that they have eye(s). In fact most just two (well insects etc). It surely shows a common idea is all that is needed. A creatore. In fact evolution must say there is something right about so many unrelated creatures coming ending up with two eyes. Like its a very good idea. I still say if evolution was true 3/4 of mammals , for example, would have any number of eyes or vestigals (sp) of eyes formerly used. Nope. just a simple basic but brilliant common conclusion from a common blueprint. Its more reasonable.

Did nobody else react to Byers's statement, "....evolution must say there is something right about so many unrelated creatures coming ending [sic] up with two eyes...."

Unrelated creatures? The entire basis of evolution is that all these two-eyed critters are related creatures. It's under the doctrine of separate creation that our boring binocularity makes no sense. (Haven't we all wished at times for eyes in the back of our heads?)

Nor do we know what it is that they did - nor what they didn’t (wouldn’t, couldn’t, won’t) do. Nor do we know how many of them there were - or even whether there are any still around. Nor do the advocates of strict ID show any interest in any of these questions. Which makes any talk about “intelligent design” about as vacuous as human ingenuity is capable.

— TomS

hoary puccoon said: Did nobody else react to Byers's statement....

SteveP,

You've used the term 'replication error' many times in this thread. I assume by that term you mean 'mutation', if so why not just use the term commonly used in discussions of evolution?

I only ask because I suspect you have a possibly amusing reason for using the non-standard term.

RWard said: SteveP, You've used the term 'replication error' many times in this thread. I assume by that term you mean 'mutation', if so why not just use the term commonly used in discussions of evolution? I only ask because I suspect you have a possibly amusing reason for using the non-standard term.

stevaroni said:

hoary puccoon said: Did nobody else react to Byers's statement....

React? Hell, I don't even read Byer's statements anymore.

Oh, lack of reply on here doesn't equate to lack of reaction - there may be other reactions than simply posting a response on this blog. Of course, we're talking about somebody who doesn't seem to realize that "common conclusion from a common blueprint" is what evolution says.

I find the idea of common descent to be a bit paradoxical depending on how it is defined. It is usually defined as the idea that all life has descended from a single self-replicating entity that somehow came into existence in the distant past. But if one self-replicating entity came into existence, why not two? And if two, why not 3? It seems to me that the idea of common descent is a basic admittance to the staggeringly low likelihood of the appearance of life. Could it be that the formation of life was a very likely event in the primeval world? If so, the lifeforms we know today might not all trace back to one single common ancestor.

It seems to me that the idea of common descent is a basic admittance to the staggeringly low likelihood of the appearance of life.

Yes, it could be that the formation of life was a very unlikely event. I know this goes against intuition, but "very unlikely" is nothing like the same as "impossible". What we are considering is every successive chemical environment on the planet, over a period of a billion and a half years. When dealing with such enormous numbers, anything that can happen, did happen. And life, manifestly, can happen.

It simply does not follow that because life is unlikely, it must have arisen several or many times. In fact the converse is true. Life, once it occurred, changed its environment by being part of it, and this may explain the fact that other types of life, were they possible at all, did not arise.

Oh, good. Mr. Fibonacci. Here we go again.

Sylvilagus said:

Steve P. said: Stanton, It is sometimes tempting to fight fire with fire in these debates, but I'll pass. Thanks for the comment, anyway.

Stanton said: (cue Steve P. making a moronic and childish taunt as a reply)

Care to reply to my comment? No taunting, nothing moronic, just layman to layman on the science.

Steve P. said: Sylvilagus, I think shuang would beg to differ with your use of the molecular clock as evidence to support your position.

Sylvilagus said:

Steve P. said: Stanton, It is sometimes tempting to fight fire with fire in these debates, but I'll pass. Thanks for the comment, anyway.

Stanton said: (cue Steve P. making a moronic and childish taunt as a reply)

Care to reply to my comment? No taunting, nothing moronic, just layman to layman on the science.

According to a standard objective Bayesian interpretation of the model selection criteria, the scores are the log odds of the hypotheses. Therefore, UCA is at least 10^(2,860) times more probable than the closest competing hypothesis. Notably, UCA is the most accurate and the most parsimonious hypothesis.

Steve P. said: Sylvilagus, I think shuang would beg to differ with your use of the molecular clock as evidence to support your position.

As a layman, like you, I know better than to rely on fringe voices with no expertise in the area they claim to be debunking.

— Silvilagus

Robert Byers said: These are not living creatures. Biology is all about brilliant equations. More then the stuff about gravity and orbits etc. Its a great rule in nature of creatures that they have eye(s). In fact most just two (well insects etc). It surely shows a common idea is all that is needed. A creatore. In fact evolution must say there is something right about so many unrelated creatures coming ending up with two eyes. Like its a very good idea. I still say if evolution was true 3/4 of mammals , for example, would have any number of eyes or vestigals (sp) of eyes formerly used. Nope. just a simple basic but brilliant common conclusion from a common blueprint. Its more reasonable.

Robert Byers said: Lie? About what? Anyways. The creator is not incompetent for using a same equation in nature for conclusions. A blueprint that insists on equations is very likely from a thinking being. Not wild fancys. Nature looks just like a guy with a computer program. I do not see the chaos one would expect if evolution by billions of selections on trillions of mutations was a actual process. Nature would not be so orderly and consistent in conclusions. Its more math theory then chaos theory. Origin thinkers need to carefully think about how a blind process would look different that a process with a watching eye.

Robert Byers said: Origin thinkers need to carefully think about how a blind process would look different that a process with a watching eye.

TomS said:

Robert Byers said: Origin thinkers need to carefully think about how a blind process would look different that a process with a watching eye.

Indeed. How does a "blind process look different than a process with a watching eye"? We do have a reasonably detailed description of what common descent with modification looks like. Unfortunately, nobody seems interested in giving even the barest fragment of a description of what creationism/intelligent design would look like, how an "alternative" to evolution would "look different". What we do have, from the Young Earth Creationists, is that something-or-other happened about 6000 years ago, while Old Earth Creationists say something-or-other happened much earlier, and Intelligent Design advocates decline to say "when". But none of them tells us what "something-or-other" looks like.

Dave Luckett said: It simply does not follow that because life is unlikely, it must have arisen several or many times. In fact the converse is true. Life, once it occurred, changed its environment by being part of it, and this may explain the fact that other types of life, were they possible at all, did not arise.

Above, Henry J believes that if there were separate instances of life formation they would have differences at the basic level.

Dale Husband said: Robert Byers said:

Lie? About what?

About the distrubution of animals around the world being compatible with the Biblical flood mythology. Only profound ignorance and/or dishonesty allows for such nonsense.

Anyways. The creator is not incompetent for using a same equation in nature for conclusions. A blueprint that insists on equations is very likely from a thinking being. Not wild fancys. Nature looks just like a guy with a computer program. I do not see the chaos one would expect if evolution by billions of selections on trillions of mutations was a actual process. Nature would not be so orderly and consistent in conclusions. Its more math theory then chaos theory. Origin thinkers need to carefully think about how a blind process would look different that a process with a watching eye.

What part of "Human imagination easily comes up with animals like Pegasus, Centaurs, and other creatures that have more than four limbs, yet all real vertebrates have no more than four." did you not notice? If an Intelligent Designer made all life on Earth, he is in fact an idiot. Sorry, I will not worship an idiot. Look, we know already what a fraud or an moron you are. You don't need to keep confirming it with every comment you make here.

Disappointing. 3. Apart from the confession of near-idiotic ignorance, is actually coherent. Must Do Better, Byers.

Dale Husband said:

Robert Byers said: These are not living creatures. Biology is all about brilliant equations. More then the stuff about gravity and orbits etc. Its a great rule in nature of creatures that they have eye(s). In fact most just two (well insects etc). It surely shows a common idea is all that is needed. A creatore. In fact evolution must say there is something right about so many unrelated creatures coming ending up with two eyes. Like its a very good idea. I still say if evolution was true 3/4 of mammals , for example, would have any number of eyes or vestigals (sp) of eyes formerly used. Nope. just a simple basic but brilliant common conclusion from a common blueprint. Its more reasonable.

No, it is NOT more reasonable. If I were an Intelligent Designer of vertebrates, I would have given most of them four eyes to enable them to see in all directions, to see both out of water and underwater at the same time, and/or to add additional redundancy in case one or more eyes is lost or damaged. It seems only an accident that primitive fish started out with two eyes and got stuck that way, because the right mutations to add additional eyes never arose. People often think of evolution as "survival of the fittest", but in fact it is the "reproduction of the fit enough". Two eyes is indeed enough for most vertebrates to live long enough to reproduce, but it is hardly ideal for them.

Robert Byers said:

Dale Husband said:

Robert Byers said: These are not living creatures. Biology is all about brilliant equations. More then the stuff about gravity and orbits etc. Its a great rule in nature of creatures that they have eye(s). In fact most just two (well insects etc). It surely shows a common idea is all that is needed. A creatore. In fact evolution must say there is something right about so many unrelated creatures coming ending up with two eyes. Like its a very good idea. I still say if evolution was true 3/4 of mammals , for example, would have any number of eyes or vestigals (sp) of eyes formerly used. Nope. just a simple basic but brilliant common conclusion from a common blueprint. Its more reasonable.

No, it is NOT more reasonable. If I were an Intelligent Designer of vertebrates, I would have given most of them four eyes to enable them to see in all directions, to see both out of water and underwater at the same time, and/or to add additional redundancy in case one or more eyes is lost or damaged. It seems only an accident that primitive fish started out with two eyes and got stuck that way, because the right mutations to add additional eyes never arose. People often think of evolution as "survival of the fittest", but in fact it is the "reproduction of the fit enough". Two eyes is indeed enough for most vertebrates to live long enough to reproduce, but it is hardly ideal for them.

Lets think about this. I say two eyes is the best idea. It has worked fine. Or if evolution is true then evolution has concluded , consistently, that two eyes is best. It seldom has selected for more eyes despite mutations must of been making more constantly as evolution teaches. Evolution never saw a need for eyes above/below the waterline. Surely in all the great diversity and potential of selection, with its claims for creating everything, it would of often had picked four eyes as usefull. There must be something about two eyes lasting two billions as a general rule. And so on. Nope. The eyes, ears, arms, legs, mouth all show a common conclusion as one would expect from a simple computer program from a thinking being. A important problem with evolution is not just explaining diversity but explaining why such a lack of in biology! It should be chaos in looks and form. Instead its common, almost boring, patterns . Everybody almost looks inside and out the same. With a wee bit of twists. Surely this suggests thinking design and suggests against blind happenchance.

hoary puccoon said: Did nobody else react to Byers's statement, "....evolution must say there is something right about so many unrelated creatures coming ending [sic] up with two eyes...." Unrelated creatures? The entire basis of evolution is that all these two-eyed critters are related creatures. It's under the doctrine of separate creation that our boring binocularity makes no sense. (Haven't we all wished at times for eyes in the back of our heads?)

Robert Byers said: Lets think about this. I say two eyes is the best idea. It has worked fine.

Or if evolution is true then evolution has concluded , consistently, that two eyes is best. It seldom has selected for more eyes despite mutations must of been making more constantly as evolution teaches.

Evolution never saw a need for eyes above/below the waterline. Surely in all the great diversity and potential of selection, with its claims for creating everything, it would of often had picked four eyes as usefull. There must be something about two eyes lasting two billions as a general rule. And so on.

Nope. The eyes, ears, arms, legs, mouth all show a common conclusion as one would expect from a simple computer program from a thinking being. A important problem with evolution is not just explaining diversity but explaining why such a lack of in biology! It should be chaos in looks and form. Instead its common, almost boring, patterns . Everybody almost looks inside and out the same. With a wee bit of twists. Surely this suggests thinking design and suggests against blind happenchance.

Robert Byers said:

Dale Husband said:

Robert Byers said: These are not living creatures. Biology is all about brilliant equations. More then the stuff about gravity and orbits etc. Its a great rule in nature of creatures that they have eye(s). In fact most just two (well insects etc). It surely shows a common idea is all that is needed. A creatore. In fact evolution must say there is something right about so many unrelated creatures coming ending up with two eyes. Like its a very good idea. I still say if evolution was true 3/4 of mammals , for example, would have any number of eyes or vestigals (sp) of eyes formerly used. Nope. just a simple basic but brilliant common conclusion from a common blueprint. Its more reasonable.

No, it is NOT more reasonable. If I were an Intelligent Designer of vertebrates, I would have given most of them four eyes to enable them to see in all directions, to see both out of water and underwater at the same time, and/or to add additional redundancy in case one or more eyes is lost or damaged. It seems only an accident that primitive fish started out with two eyes and got stuck that way, because the right mutations to add additional eyes never arose. People often think of evolution as "survival of the fittest", but in fact it is the "reproduction of the fit enough". Two eyes is indeed enough for most vertebrates to live long enough to reproduce, but it is hardly ideal for them.

Lets think about this. I say two eyes is the best idea. It has worked fine. Or if evolution is true then evolution has concluded , consistently, that two eyes is best. It seldom has selected for more eyes despite mutations must of been making more constantly as evolution teaches. Evolution never saw a need for eyes above/below the waterline. Surely in all the great diversity and potential of selection, with its claims for creating everything, it would of often had picked four eyes as usefull. There must be something about two eyes lasting two billions as a general rule. And so on. Nope. The eyes, ears, arms, legs, mouth all show a common conclusion as one would expect from a simple computer program from a thinking being. A important problem with evolution is not just explaining diversity but explaining why such a lack of in biology! It should be chaos in looks and form. Instead its common, almost boring, patterns . Everybody almost looks inside and out the same. With a wee bit of twists. Surely this suggests thinking design and suggests against blind happenchance.

http://en.wikipedia.org/wiki/Four-eyed_fish

Robert Byers said: I never understand why ________

Robert Byers said:

Dale Husband said: Robert Byers said:

Lie? About what?

About the distrubution of animals around the world being compatible with the Biblical flood mythology. Only profound ignorance and/or dishonesty allows for such nonsense.

Anyways. The creator is not incompetent for using a same equation in nature for conclusions. A blueprint that insists on equations is very likely from a thinking being. Not wild fancys. Nature looks just like a guy with a computer program. I do not see the chaos one would expect if evolution by billions of selections on trillions of mutations was a actual process. Nature would not be so orderly and consistent in conclusions. Its more math theory then chaos theory. Origin thinkers need to carefully think about how a blind process would look different that a process with a watching eye.

What part of "Human imagination easily comes up with animals like Pegasus, Centaurs, and other creatures that have more than four limbs, yet all real vertebrates have no more than four." did you not notice? If an Intelligent Designer made all life on Earth, he is in fact an idiot. Sorry, I will not worship an idiot. Look, we know already what a fraud or an moron you are. You don't need to keep confirming it with every comment you make here.

Fauna/flora distribution from YEC concepts is in NO way bothered by present/fossil evidence. Name your top three problems! Everything shows that walking etc from a Ark origin can fill the earth as now. I never understand why biogeography is in any way , AT ALL, helpful to evolution claims. Really!!

Robert Byers said: Fauna/flora distribution from YEC concepts is in NO way bothered by present/fossil evidence. Name your top three problems! Everything shows that walking etc from a Ark origin can fill the earth as now. I never understand why biogeography is in any way , AT ALL, helpful to evolution claims. Really!!

Robert Byers said: Fauna/flora distribution from YEC concepts is in NO way bothered by present/fossil evidence.

Robert Byers said: Lets think about this. I say two eyes is the best idea. It has worked fine. Or if evolution is true then evolution has concluded , consistently, that two eyes is best. It seldom has selected for more eyes despite mutations must of been making more constantly as evolution teaches. Evolution never saw a need for eyes above/below the waterline. Surely in all the great diversity and potential of selection, with its claims for creating everything, it would of often had picked four eyes as usefull. There must be something about two eyes lasting two billions as a general rule. And so on. Nope. The eyes, ears, arms, legs, mouth all show a common conclusion as one would expect from a simple computer program from a thinking being. A important problem with evolution is not just explaining diversity but explaining why such a lack of in biology! It should be chaos in looks and form. Instead its common, almost boring, patterns . Everybody almost looks inside and out the same. With a wee bit of twists. Surely this suggests thinking design and suggests against blind happenchance.

Robert Byers said: YEC concepts ... NO way bothered by ... evidence.

Robert Byers said: They are unrelated at early levels and more unrelated at levels not much removed from leaving the seas for land(as reported). I'm saying that evolution has little blobs turning into so many creatures and so long and mnuch evolution and yet the two eyes etc ends up natures choice for most. This is a better clue of a common design then what one would think a blind but powerful mechanism would achieve. Biology , relatively, is based on very few concepts and results. Like a programe for a computer and not the dice of wonderous mutations.

MrG said: Hmm, you could even strip it down a bit for generality:

Robert Byers said: YEC concepts ... NO way bothered by ... evidence.

I suppose this might be considered quote mining, but in this case the quote mine is less misleading than the cited text.

Stanton said: .... or how i'iwis and flightless ducks made it to Hawaii from Mount Ararat?

2.666

Just the same crap over and over again. As has already been pointed out, most species do not have two eyes so Byers has not even got his facts straight. big surprise.

As for the ark nonsense, yea a single origin of all living things four thousand years ago is certainly the best explanation for the current distribution of organisms on the surface of the earth. That's what all of the experts have concluded. That;'s what it says in all the textbooks. Right?

Henry J said:

Above, Henry J believes that if there were separate instances of life formation they would have differences at the basic level.

That's not so much a belief as an inference. Traits constrained by the laws of chemistry may well be shared by species having totally separate origin events. Traits not so constrained would vary, and species from one such group would not fit in a nested hierarchy constructed for the other group of species. Henry J

0112358 said:

Henry J said:

Above, Henry J believes that if there were separate instances of life formation they would have differences at the basic level.

That's not so much a belief as an inference. Traits constrained by the laws of chemistry may well be shared by species having totally separate origin events. Traits not so constrained would vary, and species from one such group would not fit in a nested hierarchy constructed for the other group of species. Henry J

So, if I understand correctly, what you are saying is that you believe that the nested hierarchy that we observe among species at the DNA level has been sufficiently worked out so that we can infer that there was a single common ancestor? If there was an environment in the distant past where the appearance of self-replicating organisms was not an unusual event it is likely that any formation would be both conditioned and constrained by that environment. If so, it would not be surprising to see some similarities at the DNA level among descendants with disparate original ancestors.

stevaroni said: And platypus (er, platapusses? um, platapi?) which walked, or swam, or crawled or...

It depends on whether you regard "platypus" as a Greek word, or an English word. I take it to be an English word, made up from Greek roots by a classicist, no doubt, but an English word nonetheless. If it is an English word, it should be pluralised by English conventions. Therefore the plural is "platypusses".

"Octopus", on the other hand, is a genuine Greek word. It would then depend on whether you think it has become an English word. I think it has, so the plural is "octopusses". If you differ, it's "octopodes".

English is a whore of a language that mixes and matches. Platypi sounds better and it's in the tradition of mixing things that don't match.

Along the lines of the old weak gag about the fellow trying to order ... mongooses? ... mongeese? ... mongi?

"Dear Sir: Please send me a mongoose. And while you're at it, please send me another one."

Robert Byers said: Fauna/flora distribution from YEC concepts is in NO way bothered by present/fossil evidence. Name your top three problems! Everything shows that walking etc from a Ark origin can fill the earth as now. I never understand why biogeography is in any way , AT ALL, helpful to evolution claims. Really!!

Robert Byers said: Lets think about this. I say two eyes is the best idea. It has worked fine. Or if evolution is true then evolution has concluded , consistently, that two eyes is best. It seldom has selected for more eyes despite mutations must of been making more constantly as evolution teaches. Evolution never saw a need for eyes above/below the waterline. Surely in all the great diversity and potential of selection, with its claims for creating everything, it would of often had picked four eyes as usefull. There must be something about two eyes lasting two billions as a general rule. And so on. Nope. The eyes, ears, arms, legs, mouth all show a common conclusion as one would expect from a simple computer program from a thinking being. A important problem with evolution is not just explaining diversity but explaining why such a lack of in biology! It should be chaos in looks and form. Instead its common, almost boring, patterns . Everybody almost looks inside and out the same. With a wee bit of twists. Surely this suggests thinking design and suggests against blind happenchance.

As much as I enjoy debates in the internet, I have noticed that certain people tend to engage in tactics that cause the debates to degenerate into slugfests instead of allowing them to end on a civil note. Here are some examples of what they do: 1.Lie constantly. It does not matter if what you say has no basis in fact whatsoever. As long as you can make a counter to any statement of fact or logical argument that someone makes, you will appear to be on an equal level with your opponent. 2.Never bother to provide a basis for your assertions by linking to a credible source of information or providing a reference regarding a matter that is not common knowledge. Of course, if you are already doing No. 1, then No. 2 comes naturally. 3.Engage in the practice of what I call “parroting and nitpicking” constantly: Making an exact copy of your opponent’s arguments and answering them point by point exactly instead of stating a new point of your own to move the debate forward. This has two effects: It makes you appear equal to your opponent, no matter how dumb your statements turn out to be, and it encourages your opponent to respond to you in the same way, taking the debate into an endless circle. 4.When you are accused of lying, just call your opponent a liar as well. 5.Engage in frequent sarcastic insults to annoy your opponent. 6.When your opponent complains that your tactics are unfair or dishonorable, accuse him of not really wanting a debate. 7.If you know your opponent has a short temper, wait until his patience has run out and he has gotten angry and then take advantage of the situation to torture your opponent still more! 8.Never admit you are wrong about anything. Always accuse your opponents of not thinking or of being stupid, brainwashed, ignorant, mindless, etc. 9.Use religion as a excuse to justify your extreme position. If your opponent is not of the same religion, use that fact against him. 10.Keep the debate going as long as possible until your opponent gives up in frustration, allowing you to claim “victory” later. 11.Last. but not least, CREATE NEW PROFILES TO INFILTRATE AND THEN DISRUPT GROUPS YOU WERE PREVIOUSLY BLOCKED FROM, THUS VIOLATING THE GROUP OWNER’S PROPERTY RIGHTS! If you use these tactics repeatedly, you may appear very successful in debates. But you will also gain the contempt of most people who have a sense of honor and ethics. And that contempt for you personally may also lead to a rejection of your position as well, even if the position has some truth in it.

Here are some tips on how to promote Creationism: 1.Align yourself with a religion accepted by most of the population you are trying to reach. If in the United States, that would be Christianity. In Turkey, that would be Islam. 2.Be willing to lie outright about the evidence for evolution. For example, since it is common knowledge that certain fossils like Archaeopteryx are recognized as transitional, deny that there are any transitional forms and that the fossil record actually does not support evolution. Some among your audience will be so desprate to cling to their delusions that they will blindly believe you and pay for your nonsense to be fed to them. 3.Run for school boards as a “pro-family” advocate, but keep your Creationist beliefs hidden until you are elected. 4.Slander your evolutionist opponents by painting them all as atheists or promoting “anti-religious bigotry”. 5.Say you are trying to “teach the controversy”. Appeal to principles of freedom of speech. Never mind that fraud is actually illegal. 6.In debates with evolutionists, states many, many claims in rapid sucessions without stopping to clarify anything. Your opponent won’t be able to keep up, because it takes time to rebut a prejudicial but appealing claim with facts that debunk them.

John Kwok said: Which is exactly what Douglas Theobald did in his paper published last week in the journal Nature . . .:

0112358 said:

John Kwok said: Which is exactly what Douglas Theobald did in his paper published last week in the journal Nature . . .:

As in all models, Theobald made a number of assumptions. In the last paragraph of the main section he tells us why the universal common ancestry model gave the best fit. If I read him correctly he says that it was due to the homology that exists across organisms. Without that homology he says that multi-origin models would fit better. There is no question that homology exists. It seems to me the real question is whether the homology that exists is a result of UCA or something else.

0112358 said:

John Kwok said: Which is exactly what Douglas Theobald did in his paper published last week in the journal Nature . . .:

As in all models, Theobald made a number of assumptions. In the last paragraph of the main section he tells us why the universal common ancestry model gave the best fit. If I read him correctly he says that it was due to the homology that exists across organisms. Without that homology he says that multi-origin models would fit better. There is no question that homology exists. It seems to me the real question is whether the homology that exists is a result of UCA or something else.

0112358 said:

John Kwok said: Which is exactly what Douglas Theobald did in his paper published last week in the journal Nature . . .:

As in all models, Theobald made a number of assumptions. In the last paragraph of the main section he tells us why the universal common ancestry model gave the best fit. If I read him correctly he says that it was due to the homology that exists across organisms. Without that homology he says that multi-origin models would fit better. There is no question that homology exists. It seems to me the real question is whether the homology that exists is a result of UCA or something else.

Dale Husband said:

Robert Byers said: Fauna/flora distribution from YEC concepts is in NO way bothered by present/fossil evidence. Name your top three problems! Everything shows that walking etc from a Ark origin can fill the earth as now. I never understand why biogeography is in any way , AT ALL, helpful to evolution claims. Really!!

Yeah, there is a lot of things you never understand. Or tell the truth about. Indeed, you just outright lied again. And I don't need three problems, just one: Why would God create marsupials and put most of them in Australia?

Robert Byers said: Lets think about this. I say two eyes is the best idea. It has worked fine. Or if evolution is true then evolution has concluded , consistently, that two eyes is best. It seldom has selected for more eyes despite mutations must of been making more constantly as evolution teaches. Evolution never saw a need for eyes above/below the waterline. Surely in all the great diversity and potential of selection, with its claims for creating everything, it would of often had picked four eyes as usefull. There must be something about two eyes lasting two billions as a general rule. And so on. Nope. The eyes, ears, arms, legs, mouth all show a common conclusion as one would expect from a simple computer program from a thinking being. A important problem with evolution is not just explaining diversity but explaining why such a lack of in biology! It should be chaos in looks and form. Instead its common, almost boring, patterns . Everybody almost looks inside and out the same. With a wee bit of twists. Surely this suggests thinking design and suggests against blind happenchance.

I have written about people like you: http://circleh.wordpress.com/2007/07/21/how-to-make-enemies-and-irritate-people/

As much as I enjoy debates in the internet, I have noticed that certain people tend to engage in tactics that cause the debates to degenerate into slugfests instead of allowing them to end on a civil note. Here are some examples of what they do: 1.Lie constantly. It does not matter if what you say has no basis in fact whatsoever. As long as you can make a counter to any statement of fact or logical argument that someone makes, you will appear to be on an equal level with your opponent. 2.Never bother to provide a basis for your assertions by linking to a credible source of information or providing a reference regarding a matter that is not common knowledge. Of course, if you are already doing No. 1, then No. 2 comes naturally. 3.Engage in the practice of what I call “parroting and nitpicking” constantly: Making an exact copy of your opponent’s arguments and answering them point by point exactly instead of stating a new point of your own to move the debate forward. This has two effects: It makes you appear equal to your opponent, no matter how dumb your statements turn out to be, and it encourages your opponent to respond to you in the same way, taking the debate into an endless circle. 4.When you are accused of lying, just call your opponent a liar as well. 5.Engage in frequent sarcastic insults to annoy your opponent. 6.When your opponent complains that your tactics are unfair or dishonorable, accuse him of not really wanting a debate. 7.If you know your opponent has a short temper, wait until his patience has run out and he has gotten angry and then take advantage of the situation to torture your opponent still more! 8.Never admit you are wrong about anything. Always accuse your opponents of not thinking or of being stupid, brainwashed, ignorant, mindless, etc. 9.Use religion as a excuse to justify your extreme position. If your opponent is not of the same religion, use that fact against him. 10.Keep the debate going as long as possible until your opponent gives up in frustration, allowing you to claim “victory” later. 11.Last. but not least, CREATE NEW PROFILES TO INFILTRATE AND THEN DISRUPT GROUPS YOU WERE PREVIOUSLY BLOCKED FROM, THUS VIOLATING THE GROUP OWNER’S PROPERTY RIGHTS! If you use these tactics repeatedly, you may appear very successful in debates. But you will also gain the contempt of most people who have a sense of honor and ethics. And that contempt for you personally may also lead to a rejection of your position as well, even if the position has some truth in it.

http://circleh.wordpress.com/2010/05/18/how-to-be-a-good-creationist/

Here are some tips on how to promote Creationism: 1.Align yourself with a religion accepted by most of the population you are trying to reach. If in the United States, that would be Christianity. In Turkey, that would be Islam. 2.Be willing to lie outright about the evidence for evolution. For example, since it is common knowledge that certain fossils like Archaeopteryx are recognized as transitional, deny that there are any transitional forms and that the fossil record actually does not support evolution. Some among your audience will be so desprate to cling to their delusions that they will blindly believe you and pay for your nonsense to be fed to them. 3.Run for school boards as a “pro-family” advocate, but keep your Creationist beliefs hidden until you are elected. 4.Slander your evolutionist opponents by painting them all as atheists or promoting “anti-religious bigotry”. 5.Say you are trying to “teach the controversy”. Appeal to principles of freedom of speech. Never mind that fraud is actually illegal. 6.In debates with evolutionists, states many, many claims in rapid sucessions without stopping to clarify anything. Your opponent won’t be able to keep up, because it takes time to rebut a prejudicial but appealing claim with facts that debunk them.

Quite simply, Byers, you don't get to promote outright fraud and/or bigotry around here and not get smacked down for it. That's what Creationism is and always has been since Darwin's time.

Lynn Wilhelm said: Robert,

Robert Byers said:

Dale Husband said:

Robert Byers said: These are not living creatures. Biology is all about brilliant equations. More then the stuff about gravity and orbits etc. Its a great rule in nature of creatures that they have eye(s). In fact most just two (well insects etc). It surely shows a common idea is all that is needed. A creatore. In fact evolution must say there is something right about so many unrelated creatures coming ending up with two eyes. Like its a very good idea. I still say if evolution was true 3/4 of mammals , for example, would have any number of eyes or vestigals (sp) of eyes formerly used. Nope. just a simple basic but brilliant common conclusion from a common blueprint. Its more reasonable.

No, it is NOT more reasonable. If I were an Intelligent Designer of vertebrates, I would have given most of them four eyes to enable them to see in all directions, to see both out of water and underwater at the same time, and/or to add additional redundancy in case one or more eyes is lost or damaged. It seems only an accident that primitive fish started out with two eyes and got stuck that way, because the right mutations to add additional eyes never arose. People often think of evolution as "survival of the fittest", but in fact it is the "reproduction of the fit enough". Two eyes is indeed enough for most vertebrates to live long enough to reproduce, but it is hardly ideal for them.

Lets think about this. I say two eyes is the best idea. It has worked fine. Or if evolution is true then evolution has concluded , consistently, that two eyes is best. It seldom has selected for more eyes despite mutations must of been making more constantly as evolution teaches. Evolution never saw a need for eyes above/below the waterline. Surely in all the great diversity and potential of selection, with its claims for creating everything, it would of often had picked four eyes as usefull. There must be something about two eyes lasting two billions as a general rule. And so on. Nope. The eyes, ears, arms, legs, mouth all show a common conclusion as one would expect from a simple computer program from a thinking being. A important problem with evolution is not just explaining diversity but explaining why such a lack of in biology! It should be chaos in looks and form. Instead its common, almost boring, patterns . Everybody almost looks inside and out the same. With a wee bit of twists. Surely this suggests thinking design and suggests against blind happenchance.

As Jesse says, keep paying attention here. I think you've almost got it. Once you give up the idea that god had to do it, you'll advance quickly. I think the seat of your confusion is that you think evolution would "choose" something (like a creator would). The process of evolution only has so much to work on. Once 2 eyes developed in a common ancestor species that's what evolution had to act on.* As long as those two eyes didn't keep organisms from reproducing, the trait was likely to continue. Yes, eyes above and below the water would be great for aquatic species, and just because such a thing does not seem to exist doesn't mean evolution didn't think it was necessary or advantageous. Evolution doesn't think. Maybe that's one of the big problems with people who don't understand. They assume that any force able to evolve/create such a creature as us, must be able to think. After all, humans created the creator in our image--a thinking being that can design and make decisions. At least you seem to starting to think--keep it up. * don't forget most of the organisms in the world have more than 2 eyes--Insecta

Alas, only a 2. While the ideation is risible, the actual expression is actually coherent. "Not to see same shaped creatures as the same creatures" is worth a couple of points, I suppose, for sheer, overwhelming stupidity and the pride of ignorance, but this is not the Byers word-salad we've come to know.

Say, Byers, here's an idea. Why don't you submit your ground-breaking research on the commonality of marsupials and other animals shaped like them to “The Proceedings of the Natural History Society of South Burlington (Vermont)"? The editor tells us that he would welcome such, and you would both no doubt amuse each other endlessly.

Robert Byers insults our intelligence again: Since you brought it up. There is a excellent essay on the internet called "Post Flood Marsupial Migration Explained" by Robert Byers. Just google. In it it explains how marsupials are not a segregated order etc of creatures related to each other but rather simply the same creatures as elsewhere who adapted to a marsupial mode of reproduction. Another creationist independently suggested this too. The essay expands on the theme to show its been a common classification error to not see same shaped creatures as the same creatures. Again there is no and less problems with biogeography from a YEC stance.

Robert Byers then says stupidly: Lets keep thinking here. To say that all creatures with two eyes come from a single original creature and so evolution never on its way to great diversity saw a chance or need for more eyes is a great saying. You have evolution doing everything else about changing this into that but the eyes stay put. Truly a living fossil. Saying evolution only had so much to work with and yet claiming evolution as the origin for biological diversity is defeating itself as a saying. In everything else its work is fantastic and yet with eyes (and a lot more) there is this ceiling. Surely in the long march there must of been need or advantage for more eyes by many! Then from that result more addition or subtraction. With vestigal remnants observable.! Yet there isn’t. Two eyes is the great conclusion of evolution for billions of years of cells to cows. Naw. Its a much more reasonable and loud conclusion to see here in nature a law. A created law, like any other, that has fixed principals on how biology should be. Eyes, ears, mouth, legs, arms, butt, nose, etc all show a common idea for common needs. Not a chaotic world of chance and advantages with dizzying conclusions. Biology like cosmology seems greatly ordered and logical with simple variation. Like somebody made a program that allowed diversity within boundaries.

Robert Byers said: Lets keep thinking here. To say that all creatures with two eyes come from a single original creature and so evolution never on its way to great diversity saw a chance or need for more eyes is a great saying. You have evolution doing everything else about changing this into that but the eyes stay put. Truly a living fossil. Saying evolution only had so much to work with and yet claiming evolution as the origin for biological diversity is defeating itself as a saying. In everything else its work is fantastic and yet with eyes (and a lot more) there is this ceiling. Surely in the long march there must of been need or advantage for more eyes by many! Then from that result more addition or subtraction. With vestigal remnants observable.! Yet there isn't. Two eyes is the great conclusion of evolution for billions of years of cells to cows. Naw. Its a much more reasonable and loud conclusion to see here in nature a law. A created law, like any other, that has fixed principals on how biology should be. Eyes, ears, mouth, legs, arms, butt, nose, etc all show a common idea for common needs. Not a chaotic world of chance and advantages with dizzying conclusions. Biology like cosmology seems greatly ordered and logical with simple variation. Like somebody made a program that allowed diversity within boundaries.

Which such bizarre "logic" as yours, I am reasonably certain that the Canadian Navy would never leave its home ports of Halifax and Victoria afloat. Moreover, as a Canadian civil servant, aren't you ashamed to be writing such drivel as this? Based on prior scores, I would assign a grade of one for your latest instance of breathtakingly inane lunacy:

"Lets keep thinking here. To say that all creatures with two eyes come from a single original creature and so evolution never on its way to great diversity saw a chance or need for more eyes is a great saying. You have evolution doing everything else about changing this into that but the eyes stay put. Truly a living fossil. Saying evolution only had so much to work with and yet claiming evolution as the origin for biological diversity is defeating itself as a saying."

As for the rest of your absurdity, it's mere verbal diarrhea emanating from you.

Dale Husband said: Why don't you START thinking, Byers?

Stanton said:

0112358 said:

John Kwok said: Which is exactly what Douglas Theobald did in his paper published last week in the journal Nature . . .:

As in all models, Theobald made a number of assumptions. In the last paragraph of the main section he tells us why the universal common ancestry model gave the best fit. If I read him correctly he says that it was due to the homology that exists across organisms. Without that homology he says that multi-origin models would fit better. There is no question that homology exists. It seems to me the real question is whether the homology that exists is a result of UCA or something else.

So tell us why do you think that homology supports a "multi-origin" model?

Robert Byers said: Since you brought it up. There is a excellent essay on the internet called "Post Flood Marsupial Migration Explained" by Robert Byers. Just google. In it it explains how marsupials are not a segregated order etc of creatures related to each other but rather simply the same creatures as elsewhere who adapted to a marsupial mode of reproduction. Another creationist independently suggested this too. The essay expands on the theme to show its been a common classification error to not see same shaped creatures as the same creatures. Again there is no and less problems with biogeography from a YEC stance.

Jesse said: Creationists should really come up with a commonly accepted definition of "kind" so that they can compare it against physical evidence.

Theobald acknowledges that if you shuffle the columns in a given clad so that the correlations between that clad and the rest of the tree are eliminated then the multiple ancestry models fit better.

this assumption best fits the independent data we do have, so...

sure you could randomly reassemble the tree, but would it make sense?

nope.

In short his research shows that a single tree structure is the best way to model correlations among a subset of proteins that are shared by the 3 domains of life.

frankly, that's still quite a strong statement, and the only one so far that statistically is based on the data we actually can use to model with.

Creationists should really come up with a commonly accepted definition of “kind” so that they can compare it against physical evidence.

I believe their current attempts to do so revolve around the "field" (if one could actually call it that without laughing) of "baraminology":

http://baraminology.blogspot.com/

so far, what I see is that slowly but surely, as they better define their terms and then try to actually apply them to the data at hand, they themselves are coming to the same conclusion post-hoc as evolutionary biologists did ages ago.

they won't admit this, of course, but it sure looks that way to anyone who cares to look at the state of their current "research".

The definition that seems to come closest to the usage of "kind" is simply "clade" - the basic meaning of both is that descendants of members are still part of that grouping.

Henry

Henry J said: The definition that seems to come closest to the usage of "kind" is simply "clade" - the basic meaning of both is that descendants of members are still part of that grouping. Henry But can you imagine a "scientific creationist" ever trying to do bona fide phylogenetic systematics (cladistics)? Hennig forbid!!!

Henry J said: The definition that seems to come closest to the usage of "kind" is simply "clade" - the basic meaning of both is that descendants of members are still part of that grouping.

Oh. Then a "kind" can contain several clades, since evolution within a "kind" is kind of allowed (depending on who you're talking to at the moment).

(How come "clade" isn't in the spell checker?)

Henry J said: Oh. Then a "kind" can contain several clades, since evolution within a "kind" is kind of allowed (depending on who you're talking to at the moment).

Dale Husband said:

Robert Byers insults our intelligence again: Since you brought it up. There is a excellent essay on the internet called "Post Flood Marsupial Migration Explained" by Robert Byers. Just google. In it it explains how marsupials are not a segregated order etc of creatures related to each other but rather simply the same creatures as elsewhere who adapted to a marsupial mode of reproduction. Another creationist independently suggested this too. The essay expands on the theme to show its been a common classification error to not see same shaped creatures as the same creatures. Again there is no and less problems with biogeography from a YEC stance.

I read your essay. It's total rubbish, but I wouldn't expect a delusional, arrogant loon like you to openly admit it in public. I know if I were a creator of life forms on Earth, I would never bother with marsupials. Placental reproduction is far more efficient, which is why placentals have displaced marsupials almost everywhere except Austrialia, where placentals couldn't reach until the age of man. The molecular evidence shows that marsupials are all more closely related to each other than to any placental mammals, so your claim was debunked already.

Robert Byers then says stupidly: Lets keep thinking here. To say that all creatures with two eyes come from a single original creature and so evolution never on its way to great diversity saw a chance or need for more eyes is a great saying. You have evolution doing everything else about changing this into that but the eyes stay put. Truly a living fossil. Saying evolution only had so much to work with and yet claiming evolution as the origin for biological diversity is defeating itself as a saying. In everything else its work is fantastic and yet with eyes (and a lot more) there is this ceiling. Surely in the long march there must of been need or advantage for more eyes by many! Then from that result more addition or subtraction. With vestigal remnants observable.! Yet there isn’t. Two eyes is the great conclusion of evolution for billions of years of cells to cows. Naw. Its a much more reasonable and loud conclusion to see here in nature a law. A created law, like any other, that has fixed principals on how biology should be. Eyes, ears, mouth, legs, arms, butt, nose, etc all show a common idea for common needs. Not a chaotic world of chance and advantages with dizzying conclusions. Biology like cosmology seems greatly ordered and logical with simple variation. Like somebody made a program that allowed diversity within boundaries.

Must I repeat the obvious? OK. Natural selection only operates on those traits that arise by accident via mutation. Vertbrates appearantly never got a mutation for more than two eyes. Are you aware that most spiders have eight eyes? They got a mutation for that many and it proved better for them than having just two eyes. Do you seriously think the Creator likes spiders better than vertbrates, including human beings?! Why don't you START thinking, Byers?

Better. 6.5. The first para is up to the old standard, about equal parts ignorance, idiocy and incoherence, the three I's of a classic Byers. (Three, Byers, not two. Here's one place where a vertebrate has three I's. Always assuming that you're a vertebrate.)

Stanton said:

Henry J said: Oh. Then a "kind" can contain several clades, since evolution within a "kind" is kind of allowed (depending on who you're talking to at the moment).

Depending on who you ask, either evolution doesn't count because it occurs only within clades, or what we assume is evolution actually isn't evolution because it's actually just "variation" within the clade.

If this thread isn't dead yet (though it was coughin' up blood last night) I would like to return to the topic with a few questions.

It's pretty clear how a scrambled sequence order can produce a data set that prefers separate trees to a single one, since that would eliminate an effectively infinitely long branch. But I don't understand how the unscrambled data set prefers a single tree to separate ones. How can a part of the tree, and two trees are just a single tree minus one branch, have a lower likelihood than the whole tree? I can see how a model selection critierion like AIC might prefer the single tree, given the extra free parameters in the separate trees, but I don't see how the raw likelihood scores can come out better for the single tree.

Second quetion: I don't understand how a single sequence (H, for example) can have a likelihood score.

Is anyone still reading?

Apparently not.

John Harshman said: If this thread isn't dead yet (though it was coughin' up blood last night) I would like to return to the topic with a few questions. It's pretty clear how a scrambled sequence order can produce a data set that prefers separate trees to a single one, since that would eliminate an effectively infinitely long branch. But I don't understand how the unscrambled data set prefers a single tree to separate ones. How can a part of the tree, and two trees are just a single tree minus one branch, have a lower likelihood than the whole tree? I can see how a model selection critierion like AIC might prefer the single tree, given the extra free parameters in the separate trees, but I don't see how the raw likelihood scores can come out better for the single tree. Second quetion: I don't understand how a single sequence (H, for example) can have a likelihood score. Is anyone still reading?

0112358 said: Proteins highly conserved across the three domains of life were chosen for the study. My understanding is that when the tree is broken into discrete units the correlations that previously existed between separated units were lost. This caused the UCA model to fit the data better than the multi-ancestry models.

John Harshman said: Thanks, but I still don't understand why this should be so. You don't seem to have addressed my questions. The two separate trees should be merely subtrees of the combined tree, and it seems to me that a subtree of the full tree, even a disjunct one, should actually have a higher likelihood than the combined tree, just becuase in the former case there's a branch you don't have to include transformations for, and all the other branches should be the same. Or so it seems to me.

You are merely repeating your previous statement. And I don't see how that affects the likelihood calculation for a tree. The likelihood is the product of a great many probabilities of state transformations between nodes. Separate trees have all the same nodes as a single tree, minus two. The probabilities for the shared internodes should be the same in both cases. A combined tree would divide two internodes and add another. Adding an internode should reduce the likelihood, since its transition probablities are additional multipliers.

Can you explain this?

One potential explanation is that the two broken internodes (that is, the two branches by which the separate trees are attached) have significantly higher transition probabilities when broken than when unbroken. Is that it, perhaps?

John Harshman said: One potential explanation is that the two broken internodes (that is, the two branches by which the separate trees are attached) have significantly higher transition probabilities when broken than when unbroken. Is that it, perhaps?

I think what Cornelius Hunter fails to understand is that, for the cases where Doug Theobald is evaluating sets of models which are disjoint and complete, his numbers are not just relative likeliness but absolute likeliness. The argument that they are only relative requires the existence of unaccounted-for alternatives.

For example, when testing "humans share ancestry with the rest of life" versus "humans have separate ancestry from the rest of life", there is no other possibility. The absolute likelihoods of the two models must sum to 1. Now, it is certainly possible that some other model could be better - for example, it could theoretically have been the case that the model "humans and other primates have separate ancestry from the rest of the tree of life" was more likely than either of the above - but in that case the complementary model would be "humans and other primates share ancestry with the rest of life".

The key thing here is that adding constraints to a model can only lower its likelihood. So, once you have established that "humans have separate ancestry from the rest of life" has likelihood no greater than 10^-3000 with no additional constraints, you have also shown that ALL models which include that as one constraint (and have other constraints as well) have likelihoods which are no greater. Thus, NO creationist model which includes the idea that humans were created separately can be any better than that.

Howard A. Landman said: I think what Cornelius Hunter fails to understand is that, for the cases where Doug Theobald is evaluating sets of models which are disjoint and complete, his numbers are not just relative likeliness but absolute likeliness. The argument that they are only relative requires the existence of unaccounted-for alternatives. For example, when testing "humans share ancestry with the rest of life" versus "humans have separate ancestry from the rest of life", there is no other possibility. The absolute likelihoods of the two models must sum to 1.

John, I'd like to hear Doug's view on that. It seems to me that Bayes' Rule is sufficient to transform what was said in the paper into something very close to what I said.

Specifically, consider two complementary hypotheses like (A) "Humans had no common ancestor with any of the 11 other species considered in the paper" and (B) "Humans had a common ancestor with at least one of the 11 other species considered in the paper", and let D stand for the data. We obviously must have P(A) + P(B) = 1 and P(A|D) + P(B|D) = 1, and also by Bayes Rule P(A|D) = P(D|A)P(A)/P(D) and P(B|D) = P(D|B)P(B)/P(D).

What Doug gives us is essentially P(D|A) and P(D|B). And yes, those don't add up to 1, nor did I ever say they did. But if you make the maximum entropy assumption that the a priori probabilities of A and B (ignoring the data) are equal, then we have P(A) = P(B) = 0.5. Given that, then P(A|D)/P(B|D) = P(D|A)/P(D|B), and hence P(A|D) = P(D|A)/(P(D|A) + P(D|B)) and P(B|D) = P(D|B)/(P(D|A) + P(D|B)) by simple normalization.

That was my claim: that you can calculate the absolute probabilities of the hypotheses corresponding to the models from what's given in the paper with only a few, reasonable, assumptions. You still see something wrong there?

Howard A. Landman said: Specifically, consider two complementary hypotheses like (A) "Humans had no common ancestor with any of the 11 other species considered in the paper" and (B) "Humans had a common ancestor with at least one of the 11 other species considered in the paper", and let D stand for the data. We obviously must have P(A) + P(B) = 1 and P(A|D) + P(B|D) = 1, and also by Bayes Rule P(A|D) = P(D|A)P(A)/P(D) and P(B|D) = P(D|B)P(B)/P(D). What Doug gives us is essentially P(D|A) and P(D|B).

And yes, those don't add up to 1, nor did I ever say they did. But if you make the maximum entropy assumption that the a priori probabilities of A and B (ignoring the data) are equal, then we have P(A) = P(B) = 0.5.

That was my claim: that you can calculate the absolute probabilities of the hypotheses corresponding to the models from what's given in the paper with only a few, reasonable, assumptions. You still see something wrong there?

I agree that the paleontological and other data should give common ancestry a very much better than 50% a priori likelihood. I was trying to be (perhaps unfairly) fair to the creationists. When you have a 3000 orders of magnitude advantage, you can afford to be generous.

It is true that the a priori probabilities P(A) and P(B) directly affect the final probabilities. But it doesn't seem to matter much whether we start believing that common ancestry is 99.99999999% likely or 0.00000001% likely; the end result after applying 10^3000 from the protein evidence is that we either think UCA is 10^3010 times more likely, or that it's 10^2990 times more likely. Either one is completely overwhelming odds.

I see your point about a single tree not covering all possibilities. However, the two trees Doug compares are (usually) identical except for a single disconnection in one. Thus it seems to me that the relative likelihoods mostly give information about that particular connection or disconnection, and not much about the rest of the tree (which should apply roughly equally to both models, and hence cancel out). I would expect, for example, that if you rearranged a few other branches of the tree the same way in both models, without anything jumping from one subtree to the other, then the relative likelihood would be nearly unchanged. This is easily testable, and if true would mean that the "sum over all trees that fit your requirements" would just give roughly the same answer we already got from the first tree, regardless of what relative weighting we gave those trees in the sum.

The presence or absence of a single edge on the graph corresponds pretty directly to the kind of complementary hypotheses I proposed. So, while I acknowledge that there are some gaps in my chain of reasoning that are not (yet) completely rigorous, it still seems unlikely to me that any of these would throw off the conclusion by very much.

I think you are straying quite far from your original claim here. Would you agree? In fact you have gone from "absolute probability" to "relative probability", though you think the relative probabilities could be used to estimate absolute probabilities. That may be true, but each new assumption (and you have at least two rounds of them so far in response to my objections) adds another layer of uncertainty. You also fail to consider other alternative trees that divide the taxa into two or more groups.

Also, where are you getting this figure of 10^2990? According to the supplementary information, the log likelihood of ABE is -126,299 while the log likelihood of ABE(-H) + H is -140,339, which would mean that the difference in log likelihoods is nearly 14,000, or a factor of 10^6000. I will note that the log likelihood of ABE(-H) is -121,200, while H is -19,139. So just about the whole difference here lies with H. How does anyone come up with a likelihood for H? That's one thing I can't figure out.