Kinds and diversification through microevolution and hybridization

Yes, I like the new thread, too.Please go here, TB:http://www2.norwich.edu/spage/alignmentgam.htmand, using this objective data, tell us how we are to determine where 'microevolution within kinds' ends.Thanks.Oh - also, some evidence that introns were created by God, as per the other thread.Thanks.

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Originally posted by Tranquility Base:
SLPx

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In general:

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We believe that seqeunces were created (in each kind) and have since drifted by microevoltuion.

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You BELIEVE that, sure. There are folks that believe that if you go to the south pole you will fall off the earth, too.

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Almost any sequence alignment will have clusters of more closely realted sequences and we could identify those as kinds perhpas. But, now that we have genomes, it is far more enlightening to identify kinds based on presence/absence of protein families! There is much less noise in doing this.

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Good thing that the 'protein families' - which are of course encoded by gene families - show good support for evolutionary hypotheses.[/quote]There is no agenda here, it is simply a matter of what is easier to reconstruct. If there are underlying kinds then genomes are far more informative than homologous sequences.[/quote]Funny, too, that the homologous sequences - which are, amazingly, found within the 'underlying genome' - are so clearly pattern-containing.

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Your sequecne alignment?

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Why don't you first tell us what organisms these sequences are from? I seem to recall they are primate seqeunces(?). We aren't all primate experts - especially biophysicists.

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[This message has been edited by Tranquility Base, 09-16-2002]

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What difference does that make? One need not be an expert on anything to see the distinct patterns of shared mutation.But I forgot about that ever-prsent "tack on criteria" schtick from the creationist crowd...

TB:{quoteSLPx
OK, can you explain what the precise significance of those sequences is again in your opinion (for poor old TB) - and what organisms they came from, and what they code for and . . . ?[/quote]Primates, from several families, both Old and New world Primates. The loci are both coding and noncoding/nonregulatory (as I already explained).The precise significance, as per this discussion, is that it is quite easy to see the patterns of shared synapomorphy, in both coding and noncoding regions. There is no big 'jump' in the amount of change between families (calling into question the creationist claims that "kind" is roughly equivalent to 'family'), indeed, the patterns are relatively 'smooth' across taxa.

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Synapomorphic seqeunces?

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No, sequences that contain synapomorphies.

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Sure, but let's clearly define what we are trying to achieve. Are we trying to figure out what are the key differences between significantly different taxa? Or what? What are you trying to achieve?

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I thought you knew all about this stuff such that you can say your preferred criteria are more meritous? Guess not...We are looking at the patterns of shared mutation among taxa, and since we know that 1.mutations occur, and 2.they can be passed on, the logical deduction is that the obsevred patterns are the result of descent.
The goal of phylogenetics is not, nor do I think it has ever been, to 'discover' the molecular mechanisms of speciation and such, rather, it is to provide an objective mechanism for determining biological relationships between taxa. While it is true that such knowledge (mechanisms of speciation) can in principle be examined using phylogentic methods, again, it is not a goal of the field to do so.

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I am trying to find out what the key differences are between taxa. To a large extent I see hemoglobin in man and rat as being almost exactly the same thing. I want to see what really new things came up.

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Good for you. So basically, you are willing to thumb your nose at tested methodologies because it isn't exactly what you are interested in...

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Originally posted by Tranquility Base:
SLPx

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The point is that although your molecular phylogeny work very clearly deomnstrates the plausibility of common descent it does not prove it.

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Can you please tell me what you consider to have been proved scientifically. Havew you proved anything in your field, or know of any concept in your field that has been?

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Mol-phylo is completely compatible with creaiton of kinds and diversification via mutations and natural selection. If all you want to do is demonstrate which species are more closely related then what you are doing is fine.

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You missed the point. As I mentioned, that one alignment alone contains taxa from several different Families.
If the creation postulate is that the "kind" is about the same as the Familt, then there should be some huge discrepency between the different families - something very distinct and obvious. That is not what is seen.So, you don't have a probelm with the demonstraton that humans are quite closely related to other primates?

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For some reason you simply do not allow the possibility that God could have sat there and chosen initial seqeunces for each organism.

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Anything is possible. It is possible that the winged monkeys that live in my colon could have done the same.
Plausability and logic play a role here. Other than saying that your postulate is 'possible', do you know of any way to logically infer that? Scientifically?

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The more physiologically similar the more similar the sequences.

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Oh, my... TB, what will I do with you? That is Ken Ham stuff. That is Karl Crawford stuff.
You are constraining your Universal Creator with such a limited repertoire of abilities, I have to wonder why one would believe Him so great....

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Becasue sequences can drift so far without changing function I do not expect to see the kind conept from homolgous sequences. But I do expect to see the kind concept from the complement of genes in the genome.

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Of course you do....

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The true quesitons of what genes originated when can be studied via comparative genomics where we find out what new genes are responsible for what new physiological features. And of course the new genes at each stage of complexity are a complete mystery.

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Are they really? To whom? Of course, not too lonmg ago, the cell itself was a "complete mystery", bandied about by creationists as being 'proof' of Creation. DNA - same thing. Creeationism has a pretty shopworn track record on such things...

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You are locked in a faith trap just as we are. The part of evolution which generates real novelty, that we say never happened naturalistically, is the part you have no evidence for. So you believe it happened.

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I accept that it happened via inferrence from what we do know. That is not the Faith of the creationist, that is the 'faith' of the realist. Why abandon reason just because we do not have all the answers right this minute? The Faithful, in this debate, have relied upon ignorance as their 'proof' all along. And as we have seen, once one question is answered naturalistically, the creationist just asks another, and another.
It takes no Faith to accept that someday, there will probably be an answer to these questions. It takes a slim knowledge of history.

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Originally posted by Tranquility Base:
SLPx

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You asked about 'anything in my field proven'?

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* Protein folding is dictated by sequence. Chaperones did not change this.
* Certain amino-acids have certain preferences for particular secondary structure
* The ribosome makes proteins from an RNA template
* Phe is more hydrophobic than Ser

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Is it possible to falsify the above statements? If so, then they are not proven.

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You said "If the creation postulate is that the "kind" is about the same as the Family, then there should be some huge discrepency between the different families". But I already explained that due to sequence drift this may not be evident.

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You must be an old, old, old earth creationist then.
Do you not think it odd then, the patterns that are seen? Are you suggesting that drift obscures 'true' differnces while at the same time producing what appear to be pattenrs of descent??
Where are the probability mongers when you need them!

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If there were 5 created amino-acid diffs between man and pig hemolglobin what's the chances that bias is still visible? The phylogentic trend will still be there (as it is) but the distinctness will be washed out. That's why looking at distinct protein families is, depending on what one is trying to achieve, better for both evolutionists and creationists.

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But the real question is Why would there have been 5 aa diffs between the same proteins in the first place? Why woiuld pigs and humans both even need the same proteins? Is the Cosmic Designer so unoriginal and constrained that It could nbot really dazzle us with some innovation?
You are simply favoring this protein family schtick because you think you can find 'evidence' for creation in it. We've been down that road before.

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And, correct, I have no problem with sapiens being very similar to other primates. Anyone can see that at a zoo.

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That is not what I asked. I asked if you accept that Homo and Pan are related via descent, as the evidence indicates.

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You can't compare 'winged monkeys in colons' with the simple possibility that we were created. (Well maybe you can).

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Why not? There is as much evidence for winged colon monkeys as there is for some anthropomorphic superbeing creating humans from the dust of the ground.

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See above post for evidence of creation. I am not constraining my creator. But if he created he already constrained himself.

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Well, isn't that convenient.Creation evidence (note - not proof, just evidence): the distinctness of protein families, distinctness of Linnean families, irreducible complexity of cellular systems (as well as the unlikelihood of abiogenesisHave you considered the fact that evolution can actually explain these things?See, TB, when I read things like this, I see shades of Michael Denton. You know about him, right? He wrote in his first book that cldograms based on amino acid sequences show not descent, but types (kinds - he didn't want to be called a creationist either).
Problem was, it was quite clear that he had his head up his arse when it came to interpreting the cladograms and understanding what goes into their construction. He claimed that the 'gaps' between extant organisms - the distinctness of the Linnaean groups, if you will - were due to creation (he didn't call it that, but that is what he meant).
But, there is a little thing called extinction that he failed to take into account. That and common sense and an understanding of evolution.
A hypersimplified analogy as to why there are 'gaps':I stand in a field with two baseballs. I turn to the east and throw one as far as I can. I turn west and throw the other. They are now maybe a couple hundred yards apart (hey, I can throw, baby!). Yet they originated from the same spot, they just went in other directions...If thats the best you've got, well, I think my materialist dogma is safe for now

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Yes the mystery of the origin of life could be creation or macroevolution.

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You 'accept that it [evolution] happened via inferrence from what we do know'. But you ignore the possibility that God created kinds which have since diverged.

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NO, I don't. I have contemplated it and found that the evidence does not provide for this.

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They are both possible.

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Yes, as is my monkey scenario. But plausability is not equal among the contestants.

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It's not necessarily a reason or ignorance issue - it could be a common sense and conscience issue too. '

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What does conscience have to do with how one interprets evidence? I have my understanding, of course, but what is yours?

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It does take faith to 'accept that someday, there will probably be an answer to these questions'. Maybe God created and you are wrong.

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Yes, that is a possibility.But is it probable?

Agreed.

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Originally posted by Tranquility Base:
Peter

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It is an issue of extent. I think our bodies, our eyesight, our consciousness is incrdible evidence that God created. How the sun works? You're right we understand that now - but I still think how we got here is qualitatively differnet.

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Oh brother...Life is soooo incredible, that it MUSTA been done by the God of the bible...Sorry TB, 'awe' and personal incredulity does not count as evidence of anything other than a lack of actuqal proof for one's position.Such appeals work on school children and the mentally challenged, but using it with educated adults is just insulting.