Punctuated Equilibria theories

[Buffy]

Originally Posted by Biochemist

I am disappointed and giving up.

<crowd>Awwwww....</crowd>

Originally Posted by Biochemist

1) I have listed a number of demonstrated biochemical mechanisms that are elements in expanding or modifying the genome. The evidence for their mutagenicity is absent.

Yes, and they are mostly things we agree on, but the issue of mutation is the one you're hung up on, and if you feel I'm being unfair to you, you dismiss my discussion of how mutation can indeed work out of hand without responding to it, and indeed, not even indicating that you feel its worth bothering to read or understand at all. I could take that badly too!

Originally Posted by Biochemist

2) I have refrenced the undisputed incongruity in the fossil record, a long list of issues that is widely recognized; Most importantly a sudden occurrence of all major phyhla and even all animal orders; Also the lack of taxonomic parent for any initial anuimal phylum or order representative

I agree with all this evidence. I agree with PE. I simply say that there are viable mechanisms that do not require massive front-loading. Evidence of PE is not proof that mutation has no effect. This argument is unconvincing. (And is used by the way, yes, pretty much exclusively from the creationist/ID crowd, which is why it came up, see below).

Originally Posted by Biochemist

3) I have raised legitimate questions about the likelihood of mutations ever creating positive outcomes, given the current state of biochemical knowledge

And I think your conclusion is premature. At the same time that you're haughtily and dismissively saying that I'm out to lunch because I haven't shown proof of speciation that involves mutation, you have shown no proof that it does not, in spite of the fact that you admit that mutation does cause changes. I personally do not find this logical, and I've been asking why you believe this.

Originally Posted by Biochemist

4) You have acknowledged the majority of my argument, in that you agree there are intracellular biochemical tools that "assist" in steering speciation, even in the absence of any expression of phenotype

Yep! The only issue is the front-loading of all information versus mutation assisting evolutionary development. So this issue is not a problem!

Originally Posted by Biochemist

5) You have offered no justification for including mutation in your schema, as it is not even necessary in your model

Well, actually I just did in the previous post above since I bothered to look. But your statement that it is "not even necessary in your model" indicates that you have not really been reading or understanding my discussion of neural networks: to avoid front loading, experimentation via mutation is an *essential* element. It is *not* the only element. It works in conjunction with the existing rules and data to form new rules and new data, but you can't do it without the mutation/flipping of a coin/whatever you want to choose as a random element. I can prove to you if you wish that programmatic random numbers are wholly inadequate for performing this step, so if you're arguing that your pre-programming does this (and you have not yet), then I can prove that it won't work numerically. It would be horridly off topic though!

Originally Posted by Biochemist

6) I have requested affirmative evidence for mutation in speciation (of coure, there is none)

As I just said, I just did. It was not hard to find, but again, since speciation and phylla changes are rare events, and we're just scratching the surface of analysis of the mechanism (as you point out yourself!) its not surprising that there's not a mountain of proof yet, but there is some and it seems to be growing from what I see....

Originally Posted by Biochemist

If you solution is to label me a "creationist", have at it. I did not see any reference to that in my posts.

No, you've studiously avoided the term, but your arguments seem to exactly parallel the creationist/ID arguments in the ways that I have explicitly described and you have not refuted, however I apologize for calling a spade a shovel.

You shouldn't give up while you're ahead of course! It gives people the incorrect impression that you're wrong and you're not willing to admit it! We know you're right, we just want an explanation! (no smilies!) Honest, given that I'm a programmer and Linda is a determinist and Bumab and I both agree on the gal-who-pushed-the-button, we'd all *love* for this to be true! But your arguments have not held up in my book, and Bumab has been complaining too. That should tell you something other than "we hate you because you're beautiful." Puuuleeeze!

Cheers,
Buffy

[Biochemist]

Originally Posted by Buffy

...Now it took me all of 5 minutes to find this explanation: http://www.ncbi.nlm.nih.gov/books/bv...a.section.1242 which you will claim is inadequate because it does not show absolute proof, but it does explain a mechanism from an expert (rather than amateur lil' ol' me!). This same NIH database had a good 100 papers on the topic including this one (which is a bit harder to read than that other link): Quantum speciation in Aegilops: molecular cytogenetic evidence from rDNA cluster variability in natural populations. which says tantalizingly...

I read your first link in its entirety, and just your excerpt from your second. I admit I am at a little bit of a loss to see your point. I would suggest that you go back and re-read your first link and imagine all of the very same evidence under a presumption that speciation is programmed versus a series of accidental events. There is nothing in the treatise that argues for mutation, other than the explicit assumptions of mutation as stated by the author. It would be easier to suggest that the dramatic flexibility of Drosophilia is engineered rather than random benefit. Ditto for the higher phyla.

[Biochemist]

Originally Posted by Buffy

...You're simply not reading what I wrote: YES feedback into the *rules themselves* is *essential* to make these things move forward! They most certainly can affect all kinds of things in the system, although some of you examples here are exactly the kinds of things that the rules would proscribe, whether it was a neural net or a strand of DNA. You don't understand how these neural nets work, so be careful about dismissing them. You are continuing to see mutation as this awful demon, when in fact it can work what appears to be magic, *IF* it is applied by a *system.* I know this is inconvenient for your theory, but you can't simply dismiss it. We do know these systems work, and they are in fact based on the same model as evolution....

I am pretty sure that you skipped over what I wrote. I was (of course) not talking about feedback into the rule set. I was talking about constraining the "mutations" to a very narrow domain. You did not let the "mutations" change anyting but the rule set. No change to operating environment (hardware, OS, language, verb structure, etc) AND YOU GAVE THE SYSTEM A TARGET.

You really think this is applicable to speciation by mutation? Where do you suppose chordates got their target?

[Biochemist]

Originally Posted by Buffy

... your arguments seem to exactly parallel the creationist/ID arguments in the ways that I have explicitly described and you have not refuted...

It is not really my problem that you maintain a bias (clearly) that avoids any curcumstance that seems to advantage folks with a theistic worldview. I was talking biochemistry in this discussion. I think my hypothesis fits empirical facts better than a mutation based approach. Your main complaints were:

1) I have not proved mutations DO NOT cause speciation (which would, I think, be impossible under the scientific method) and

2) You preceive some risk that my hypothesis makes abiogenesis look more like a theistic solution.

Neither of those are valid scientific arguments. They just reflect your bias.

[paultrr]

There are two types of Speciation. Speciation occurs when two subsets of a formerly interbreeding population become reproductively isolated and it occurs in what's termed sympatric speciation when two lineages of a formerly interbreeding population diverge to the point of reproductive isolation while still residing in the same locale. This was first demonstrated to occur by Guy Bush working on the Apple maggot fly Rhagoletis pomenella.

For past evidence one must look for both. And it might be mentioned that the above case shows it can happen even today. The theoretically preeminent species definition has been the biological species concept (BSC). This concept defines a species as a reproductive community. In the above case, and several others one has two distinct species drived out of a common background. Du Rietz in 1930 first defined this as:

"... the smallest natural populations permanently separated from each other by a distinct discontinuity in the series of biotypes."

Barriers to interbreeding are implicit in this definition and generally depend upon the idea of no interbreading being possible.

Chromosomes 1, 4, 5, 9,12, 15, 16, 17 and 18 in humans have inversions of major tracts of code compared with homologous chromosomes in chimpanzees, and human chromosome 2 results from the end to end fusion of two acrocentric chromosomes that remain separate in all the other great apes. Chromosomal rearrangements occur when substantial tracts of DNA are inverted or repositioned on the chromosome. This generally results itself in interbreading being impossible or not leading to offspring that can bread. But it is also only part of the picture that has tended to evolve when it comes to human's diverging from out of the ape line. In short there are other factors involved.

[paultrr]

Originally Posted by Biochemist

2) You preceive some risk that my hypothesis makes abiogenesis look more like a theistic solution.

The motivation is well proven behind that in the origins of that type of alternative. Which does tend to make us suspecious. However, I'd also say that not everyone out there that holds to such a view also holds to the idea of a real devine being in the classical definition of such.

The problem is generally most of those who first proposed this alternative held to some theistic worldview. It arose as an alternative in light of there being no evidence for the young earth alternative at all. Those of the theistic views where faced with a crisis who's only solution was to adapt or perish. The adapation chosen was the alternative that somehow God, using a long timeline, partial evolution within a species, and other factors had managed to create a world that by left behind evidence appears as if natural process developed everything we have, yet, had those large gaps in the evidence that argues for a creative process simular to Genesis where each species had a distinct special origin. In some ways this whole line is very much akin to the older God of the Gaps theistic evolution approach where you have species divergence as the result of devine intervention. Problem is that approach lacks as much evidence as they tend to claim we lack. If anything it overlooks a lot of modern findings and totally ignors some modern examples of natural occuring seperation into distinct species.

What almost to a tee believers want is a direct evidence of something that's say half ape and half man or rather half dog and half cat. On the first by genetic/historical evidence we do have some examples. On the second, to my knowledge there is none. The problem is there are aspects of our origin we still do not fully understand. Some of these aspects are conditions in the local area we first evolved in, what produced the genetic inversions in our genes, etc, etc. However, the other side on this cannot supply decent answers to all this either, except perhaps invoking the God of the Gaps as a solution. Sorry to term it that way. But that's the origin of the idea you tend to hold to. That's why you find that preceived idea in the first place. You also might say that those who are religious tend to distrust us evolutionists because we totally discount the theistic idea. Yet, all these general arguments here rather point to the fact that such is not always the case across the board.

[paultrr]

One thing you have to consider is how can you present you're ideas devoid of the theistic aspect in the first place if you want to avoid this.

[bumab]

Originally Posted by Buffy

......and Bumab and I both agree on the gal-who-pushed-the-button, we'd all *love* for this to be true!

Well, I don't know about that , but as far as this goes, sure.

Ya go away for a couple days, and miss miles of posts...

[bumab]

Originally Posted by Biochemist

It is not really my problem that you maintain a bias (clearly) that avoids any curcumstance that seems to advantage folks with a theistic worldview.

Good Lord, everybodies gettin' hot under the collar.

Personally, I don't see any theistic bent to Bio's points. Sure, they are mirrored by Behe and many ID folk who clearly have a bias, but guilt by association has never been fair. I think your theory, Bio, is consistent with the facts and possible. It's no harder to believe then all the stuff about the origins of the universe, inflation, etc etc. that has been theorized to agree with the known facts.

My problem with your theory (again) is it's proposing an entirely new mechanism (which you have not supplied) to take care of a "problem" (rapid speciation) that can be taken care of through traditional means (mutation). Rapid speciation (over 10 million years or so) of many phyla would automatically create gaps in the fossil record, since such a short time span could easy skip around in the record. It's just not very long. So right off the bat, the time frame precludes (most likely) a good transitional fossil. Thus, it's not a gap in the theory at all, and you can't use it as such.

Secondly, you've not presented any evidence for your idea. None- it's all problems with the old idea. If you could present some data about the possible future forms of shrimp based on their DNA, great. If we could find dino DNA and look for bird genes, great. But nothings been found yet.

Third, there are other theories. A genetic predisposition to rapid genetic change (good and bad) to increase the palatte on which natural selection can act after a major enivironmental change is certainly more believable then a super-prokaryote, and the mechanism is known and has been described.

I'm still interested in your ideas, Bio, but you've not addressed the main concerns yet- evidence and mechanism.

[TeleMad]

Originally Posted by bumab

Personally, I don't see any theistic bent to Bio's points.

I haven't read through the posts in this thread, but Bio sure presents a 'theistic bent' in many of his posts in other threads. Like when he states it takes as much faith to believe in evolution as in a supernatural God.