Punctuated Equilibria theories

[Fishteacher73]

Originally Posted by gubba

I'd love some info on species irreversibility. Is it possible for less complex organisms to follow from highly specialised precedents? I doubt it and hope not for things a quite complicated enough as it is.

There is some evidence of this occuring in some marine inverts. There are a few corals that seem to have reverted back to a filter-feeding form w/o any zooanthelae from their photosynthetic pre-cursors.
Dendronepthya species, also known as carnation corals are purely filter feeders that are not photosynthetic. The precursors are the nepthia or tree corals, that are photosynthetic.

[Biochemist]

Thanks for the post, Gub-

Originally Posted by gubba

...I'm not too fussed about punctuated equilibria for, unless there have been major finds recently, the evidence for any theory simply is NOT YET IN.

I admit that I was relying on the assessments of Gould and Eldridge from the 1970's with respect to the overall assertion that the paleontological evidence is generally not supportive of gradualism.

which prokaryote? The one 4 (or is it 5?) billion years ago at the beginnings of organic life, or the latecomer..

I think it would have to be the first (oldest) one for my hypothesis to hold any water.

I'd love some info on species irreversibility. Is it possible for less complex organisms to follow from highly specialised precedents?

Good question, Gub. I do not know the asnwer, other than the behvior of cancer cells when they dedifferentiate when they adopt cancerous behavior. They do not, however, step back on the evolutionary sequence. They do back up in the embryonic sequence.

[Buffy]

Originally Posted by Biochemist

I never heard this from the ID camp. They typically discuss irreducible complexity. I am try to address the PE problem.

No seriously, check out James Putnam's threads here on Hypography. He concentrates on cosmology and physics, but he's got a similar macro idea, which is that "intelligence" was programmed in before the Big Bang (the *really* big original one, not yours). I use a broader definition of ID, which refers to any theory in which "intelligence" is pre-existing with no explainable mechanism for its existence. As Bumab and Fish have both aluded to above, the kind of "loading" you're talking about goes *way* beyond the handful of fundamental parameters of our universe, and there are a number of theories from the dissatisfying anthropic to the more intreguing but still naturalistic multiverse theories that explain them rather easily.

Since you are insisting that in order to deal with PE, that no changes or alterations do anything except express or inhibit genes, or if they are meta-genes "uncompress" them selves into the relevant genes, this means that *all* of the details necessary to describe all of the features of every being that not only ever has existed but ever *will* exist was in that first prokaryote. Whoa! What you are describing here is a computer program that is far more complex than anything yet written by man, that just *appeared*. Poof! And it begs the question, is there *any* naturalistic process at all that could even be imagined that would cause that big bang to happen? I don't see one, which is why I call it ID...As usual, you don't really need to explain it if you don't want to, but at this point you've described a Star Trek episode. If it were true, I guess it would be a good explanation of PE, but It also seems, um, awfully overcomplicated: it kinda fails Occam's Razor....

Originally Posted by Biochemist

...this does nothing to address the primary punctuated equilibrium problem: How did so many species arrive so quickly? I am suggesting that there are a small number of (relatively) likely morphological changes that are precoded in the parent species DNA....There is a significant body of paleontological evidence that suggests the sudden arrival of phyla.

I don't see the problem here at all. The really hard to explain explosions are all proving to be post-major-cataclysm (gotta love those asteroids!), but that just provides lots of environmental pressure and lots of niches to fill. My sense is that we agree on the effect of these, but what I don't see is why your extremist "gotta all be preprogrammed" is *necessary* to explain PE. An explanation based on mutations accumulating, being tested, selected re-expressed, etc, provides the same end result without demanding that no additional information was added along the way.

Originally Posted by Biochemist

There are known progeny of lower species that are morphologically different in a single generation.

That's actually not a necessary conclusion, since as referenced in some of the links provided above, even Darwin pointed out that its not that one species turns into another, but that the new species splits *off* and both can exist, possibly separately or even together. And as Bumab points out, single gene changes can result in major changes. It seems to me that the evidence that mutations are cancelled is something you are carrying to an illogical extreme. Just because there are mechanisms that reverse out mutations--arguably a *very*useful evolutionary mechanism that avoids many truly debilitating mutations--does *not* mean that *all* mutations are reversed out. I think that one would be a great experiment that would not involve any measures of complexity or parallelism between highly dissimilar DNA, trying to prove that certain meta-genes in lower forms map exactly onto expanded genes in higher form, when there's no Rosetta Stone to go by: simply find gene sequences in all their various forms for say, eyes, and if there are simple variations that cannot be shown to exist in other places, you may have proof of an included mutation. All you'd need is one to invalidate your theory.

Its definitely true that there could be programming in all that "junk DNA"--which is quite obviously *not* all junk--but to load all that information in it, not only for now but forever into the future for every species that will ever be decended from us is really getting out there on the edge. But you do remind me of Zaphod Beeblebrox: "We're not just gonna be amazing! We're gonna be *amazingly* amazing!"

Cheers,
Buffy

[bumab]

Originally Posted by Fishteacher73

There is some evidence of this occuring in some marine inverts. There are a few corals that seem to have reverted back to a filter-feeding form w/o any zooanthelae from their photosynthetic pre-cursors.
Dendronepthya species, also known as carnation corals are purely filter feeders that are not photosynthetic. The precursors are the nepthia or tree corals, that are photosynthetic.

But they aren't neccessarily less complicated, just less specialized. I think Bio would take this as possible support. The genes for all those structures (except the chloroplasts, which are another thing entirely) would still be present, just no longer used.

[Biochemist]

Originally Posted by Buffy

...I use a broader definition of ID, which refers to any theory in which "intelligence" is pre-existing with no explainable mechanism for its existence.

This is interesting. By your definition, all of empirical experience is included in ID, since we have not established initial casuality for anything. I am not sure your definition is useful but feel free to use it. Just keep in mind that I am going to label you an ID proponent in any post where do do not establish initial causality. That would be all of your posts, I think. This will make the ID folks happy, because it means that folks like Lindagarette and Freethinker are ID proponents.

...and there are a number of theories from the dissatisfying anthropic to the more intreguing but still naturalistic multiverse theories that explain them rather easily.

Explains what easily? First cause? These theories say nothing about initial causality. They just kick the problem back further in history. That is all I did too.

..What you are describing here is a computer program that is far more complex than anything yet written by man

Intrigueing. I don't believe you meant to say this. The trivial parts of DNA behavior that we understand currently are already orders of magnitude more complex than any program written by man. Surely you don't think otherwise. DNA code is:
1) extraordinarily tight, in that a very small body of code handles a massive amount of processing
2) extraordinarily flexible, in that the number of services delivered and conditions covered is unbelieveably large
3) extraordinarily reslilient, even to the point of being self healing
4) extraordinarily well integrated, in that a common storage and processing architecture is used for all main programs and subroutines,
5) extraordinarily simple, in that all processes are founded on permutations of 4 machine-level instructions, with the "higher" level language being only 20 instructions.
6) Even the subroutines are tight, averaging 200-600 "lines" of code (i.e., residues in a typical protein)

Do keep in mind that the description above would apply to any single life form. The very same processing architecture applies to all life forms, which raises the sophistication of the architecture up several orders of magnitude further. Comparing the sophistication of DNA to anything done by man is laughable. Are you going to compare DNA coding to SAP? Powerpoint? The PacBell billing system? Those are pinpoints in complexity compared to the DNA architecture in the simplest bacterium.

My main point is that DNA in any one species is so complex already that assembling the coding for all species into a single life form does not really increase the complexity very much. What are there? A billion species? This would probably not raise complexity by 10^9, given the processing overlap.

...that just *appeared*...

Everything just "appeared". So what?

... is there *any* naturalistic process at all that could even be imagined that would cause that big bang to happen...

There is not a "naturalistic" process for the genesis (no pun intended) of either big bang.

...I guess it would be a good explanation of PE, but It also seems, um, awfully overcomplicated:

Maybe, but 1) every time we learn more about the fundamentals of DNA it gets orders-of-magnitude more complex, 2) there really is no other explanation for PE. It is ludicrous (probabilisitically) to assume that rapid "mutatations" happen under cataclysmic stress, unless there is some intrinsic propensity for life forms to act that way. I just bit the bullet and described the intrinsic propensity. The notion that the majority of biological coding existed at the first life form is a byproduct of trying to explain the empirical data.

...it kinda fails Occam's Razor....

That would be true if we had a simpler explanation that was consistent with observed facts. I don't think we do. I think this is the simplest explanation.

...The really hard to explain explosions are all proving to be post-major-cataclysm (gotta love those asteroids!), but that just provides lots of environmental pressure and lots of niches to fill.

Again, the triumph of hope over experience. This does not provide a mechanism for the adaptation post cataclysm. This is a data point, not a mechanism. By all "rules" of natural selection, cataclysms should eradicate species, not generate new phyla. By any measure, a cataclysm should decrease the number of individuals available for mutation. A cataclysm provides more niche space, but less genetic capacity to respond to the niche space. That is the essence of the problem that is not reasonably addressed by the mutation model.

...I don't see is why your extremist "gotta all be preprogrammed" is *necessary* to explain PE....

All of this is to provide a mechanism to explain PE adaptive speed. The notion of genetic loading at a Biological Big Bang is an unnecessary extrapolation, but a logical one.

An explanation based on mutations accumulating, being tested, selected re-expressed, etc, provides the same end result without demanding that no additional information was added along the way.

Except that this mechanism is at odds with the well structured tendency for cells to repair their own mutations, reject foreign proteins, and adapt rapidly. This model fails logically. You could argue it is simpler, but is is at odds with experimental evidence. Newton was pretty close (and simpler), but not corrrect: data overturned Newtonian mechanics. The data is overturning mutative adaptation.

... even Darwin pointed out that its not that one species turns into another, but that the new species splits *off* and both can exist, possibly separately or even together.

Sorry, but Darwin's opinion is hardly relevant. He was before the discovery of DNA, and your point is not related anyway. Nothing in my model requires species to go extinct or precludes branching. I just suggested a mechanism for rapid speciation. We don't use Newton's views to critique Feynman. Feynman had a lot more data than Newton had.

And as Bumab points out, single gene changes can result in major changes.

Again, this supports my case. If a single gene change produces a massive morphological change, it shows exactly how complex a single gene change is.

...Just because there are mechanisms that reverse out mutations...does *not* mean that *all* mutations are reversed out. ...

Buff- I don't know why you are stuck on this. I never said all mutations are revered out- you keep repeating that. I said that mutations have almost nothing to do with speciation. The accumulation of serial positive mutations concurrent with the (obligatory) destruction of serial nonfunctional mutations is so unlikely as to be untenable. No one has ever done the math on this to make it remotely feasible. There are a number of simplistic computer models (like the one that TeleMad referenced about eye development) that are easily refuted since they ignore major obstacles and complexities. Even though Gould did not say it, I think that Gradualism, as a mechanism for speciation, is not supported any any data set: Paleontological or biochemical.

...trying to prove that certain meta-genes in lower forms map exactly onto expanded genes in higher form ...

This is probably not true. The lower genes are probably swap-permutations of higher genes. This would be similar to attempting to show that if you twist a Rubik's cube 50 times, you can show the connection to the 50-generation-earlier parent configuration. Except we are turning thousands/millions of Rubik's cubes concurrently (to make the analogy the correct order of magnitude), and the cubes are about a micron across. This is a tall order....

...simply find gene sequences in all their various forms for say, eyes, and if there are simple variations that cannot be shown to exist in other places, you may have proof of an included mutation. All you'd need is one to invalidate your theory.

This is not rational, Buff. There might be a gene (or a gene shred) that carries through multiple species generation. This is consistent with the BBB hypothesis. It certainly does not refute it. But most base sequences probably did NOT preexist, but the Rubik's cube swapping that generates new genes is PART OF THE CODE, not an accident. The problematic issue for Gradualism is the speed of production of new, fully functional genes. And there are millions (literally) of these. If a higher function gene shred was maintained in earlier life forms where there was no selective reason for the previous life form to maintain the shred, it would support BBB, not Gradualism. And if a new functional gene shows up quickly via a rubik's-cube-like swapping mechanism, it supports BBB, not Gradualism.

There is almost no data to support Gradualism. And there is a mass of data to obviate it.

[Buffy]

Originally Posted by Biochemist

This is interesting. By your definition, all of empirical experience is included in ID, since we have not established initial casuality for anything.

No, you just conveniently turned what I said on its head, silly! You dyslexic? I said "intelligence" which you just ignored... As you skipped over, I say there are naturalistic explanations for the universe's parameters. The rest of us think intelligence and DNA evolved. You're saying here that they did not!

Originally Posted by Biochemist

Explains what easily? First cause? These theories say nothing about initial causality. They just kick the problem back further in history. That is all I did too.

Again, "huh?" Explains the handful of initial parameters G, c, e, h, etc. hit go button. You're insisting that "explainable mechanism" is the same as causality, and while thats a neat rhetorical device, its disingenuous. I'm not asking at all for causality, I'm asking for a mechanism that could create it, and that's a *very* different thing. You are trying to hide a very big elephant behind the curtain, and its showing!

Originally Posted by Biochemist

Intrigueing. I don't believe you meant to say this. The trivial parts of DNA behavior that we understand currently are already orders of magnitude more complex than any program written by man.

Dyslexia: read it over again: I *am* saying that DNA is more complex than any computer program...

Originally Posted by Biochemist

Do keep in mind that the description above would apply to any single life form. The very same processing architecture applies to all life forms, which raises the sophistication of the architecture up several orders of magnitude further....My main point is that DNA in any one species is so complex already that assembling the coding for all species into a single life form does not really increase the complexity very much.

So what? Yeah, DNA is pretty incredible. Alot of those basic mechanisms evolved over 3 BILLION years and we've got no record of them cuz like bananas, they have no bones. But I still say you're 1) incredibly trivializing the differences we do see in both the dna and the morphology of still existing species with no justification other than repeating "theres no proof of gradualism". That statement is nice, some of us agree with it partially, but it sure doesn't look like dna is a completely static thing that has not changed in 4 billion years. That's a real stretch...

Originally Posted by Biochemist

Maybe, but 1) every time we learn more about the fundamentals of DNA it gets orders-of-magnitude more complex, 2) there really is no other explanation for PE. It is ludicrous (probabilisitically) to assume that rapid "mutatations" happen under cataclysmic stress, unless there is some intrinsic propensity for life forms to act that way.

You've really not been reading my posts then. I am NOT saying that "a whole bunch of mutations happen instantly under stress". I'm saying that pre-existing mutations *express* themselves under stress, which is almost *exactly* the same mechanism you're describing, except in my case, I'm saying that the these parts of the DNA came from accumulated mutations where you're insisting that all of them were in the first prokaryote.

Let me repeat this, because you're obviously ignoring it and I hate being misquoted:

I am NOT saying that "a whole bunch of mutations happen instantly under stress". I'm saying that pre-existing mutations *express* themselves under stress, which is almost *exactly* the same mechanism you're describing, except in my case, I'm saying that the these parts of the DNA came from accumulated mutations where you're insisting that all of them were in the first prokaryote.

Secondly, yes, DNA is pretty amazing. You know what though? The programming properties you listed end up being the *simple* parts! We've got lots of research on self replication and repair, but most of it is done in hardware, and the software folks are too lazy to incorporate it (I know, I've had to fire a lot of them!)! I'm in awe of DNA's complexity, but the properties you've described are a useful base to start everything else that's happened since. There's still no excuse in my book to put anything other than self-replication, input-driven modification, and self-repair in the first prokaryotes and hit the go button. Why does that prokaryote need to have instructions for a human brain, let alone what we may become? Moreover, according to your model, we just need to turn a few bits of the sequences on and we'll turn into a dinosaur or back into a prokaryote, right?

Originally Posted by Biochemist

Newton was pretty close (and simpler), but not corrrect: data overturned Newtonian mechanics. The data is overturning mutative adaptation.

No, Newton was *modified*. Newton did not propose a cause, he did propose a mechanism that mass has an intrinsic quality of attraction which obeys the equations he provided describing the mechanism. Einstein modified it by describing another layer in which the conveyance of the mechanism was descibed as warping of spacetime. I know you want to portray Gradualism and PE as mutually exclusive, but as others have posted, thats really not necessary at all, unless you really do believe that "mutation has absolutely no effect and is always cancelled out" and I don't see anything in the literature that agrees with that point of view.

Originally Posted by Biochemist

Again, this supports my case. If a single gene change produces a massive morphological change, it shows exactly how complex a single gene change is.

Well, it also argues against your position as well, because if a mutation does occur in a single gene, then it can produce a large morphological change. Again, you have done nothing to show that *all* such changes are eliminated and return to the "original prokaryote programming."

Originally Posted by Biochemist

Buff- I don't know why you are stuck on this. I never said all mutations are revered out- you keep repeating that. I said that mutations have almost nothing to do with speciation. The accumulation of serial positive mutations concurrent with the (obligatory) destruction of serial nonfunctional mutations is so unlikely as to be untenable.

This makes no sense at all. I grant you said earlier that you agree mutations occur. You also have said they have no effect on speciation. You also say that they can be reversed, which we both agree on. But if they are *are not* reversed out, how can you argue with a straight face that over time they continue to have *no effect* on permanent morphological changes?

I guess even if I grant you that one, the whole concept that no matter how many mutations there are, the system always reverts to the "original prokaryote programming" indicates that the mechanism predicted every possible environmental pressure as well as the programming necessary to decide how to do it, since you have also indicated you don't believe selection has anything to do with it either. Like I say, a pretty amazing program you're describing.

Originally Posted by Biochemist

There are a number of simplistic computer models (like the one that TeleMad referenced about eye development) that are easily refuted since they ignore major obstacles and complexities.

That's an opinion, and it is based on the view that there can be no effect from accumulated mutations, so the rest of us are free to disagree on this point.

Originally Posted by Biochemist

Even though Gould did not say it, I think that Gradualism, as a mechanism for speciation, is not supported any any data set: Paleontological or biochemical.

I think its very significant that he did *not* say that. In fact everything that I read by him indicates that the notion of Gradualism that he disagreed with was indeed directly related to rates of change and mechanisms for accumulation and expression of mutations. If you've got some quote from him somewhere that indicates he believed in your concept that mutation has no effect at all, I'd love to see it.

Originally Posted by Biochemist

... the Rubik's cube swapping that generates new genes is PART OF THE CODE, not an accident. The problematic issue for Gradualism is the speed of production of new, fully functional genes.

Again, if you keep refering to Gradualism as "the instantaneous mutation of genes resulting in immediate morphological changes showing constant gradual change in morphology over time," which is quite frankly the same as the rest of us, you can't turn around and say that anything that involves a mutation process is Gradualism, therefore it must be false. This is completely illogical. None of us here are defending the traditional, strict definition of Gradualism, we're describing mechanisms that include mutation model that like I say, has an expression mechanism that's not too different from yours. The only thing that's really puzzling is your abhorence of mutation in any form. Its fine to say that the pure Gradualist view is not proven, we agree with that, but to say that because of that, any mechanism associated with Gradualism needs to be discarded makes no sense whatsoever.

Cheers,
Buffy

[Biochemist]

Originally Posted by Buffy

No, you just conveniently turned what I said on its head, silly! You dyslexic? I said "intelligence" which you just ignored...

It seems this discussion is now completely wrapped around the axel on at least 4 separate topics. I will need to recompose a straight thesis again when I get an hour.

[bumab]

Oy!

A plethora of confusion.

The positions (correct me if I'm wrong):

Bio: Mutation cannot explain morphological changes because DNA itself is programed to resist mutations. Thus, mutations cannot provide any viable changes in the species, since they are inherently selected against by the DNA itself. Therefore, the information for those changes must already be present, like an insider, or a spy, and only gets expressed when some stress comes along.

Buff: Mutations accumulate gradually, according to the traditional model, and are only expressed when an environmental stress allows those mutations to be expressed in beneficial ways. Traditional PE.

Me: A mutation causing gene, or some structure that causes rapid mutation, could be activated after an environmental stress, thus providing for the rapid speciation we see after an extinction event. This would be selected for because any organism with it would pass it along quite successfully, even though the offspring would be very divergent. It's a selfish gene argument.

I think only Buffy is standing on established ground, but I share Bio's adversion towards acceptance, based on the difficulty of randomly aquiring successful, useful, and viable protiens that wouldn't be attacked like all other new protiens AHEAD OF TIME. The mutations required to create the vast morphological changes would have to, according to gradualism and traditional PE, be already present (built up) in the introns and other non-coding regions of the DNA. This would require them to already be functional, which is a stretch.

Neither gradulaism nor PE has a satisfactory explanation for the fossil record, as I see it. The jumps around the mass extinction events are simply too rapid for gradualism to explain, and PE has no real mechanism.

Bio solves this conundrum by saying it's all pre-programmed, everything was set up already in the beginning. It really is pushing the problem back further in time, but it's also turning that problem into a 200 pound gorilla.

I solve the problem by saying there could be a yet undiscovered mechanism (most likely genetic) that creates mutations INTENTIONALLY after an environmental stress of a magnitude to open up many niches. This would solve the problem by creating rapid change in genetic structure, but, not mutagen gene has been discovered. Heck, I doubt people are looking. Perhaps something to do with cancer...

Buffy says there is no real problem.

Sufficient summary?

[Buffy]

Man Bumab, you're good! I'd say that I agree with how you've summarized my position. I guess I have more "faith" in what can happen over time. I really think the junk dna has an important role in building up new steps, and while there's proven mechanisms for undoing bad mutations, I've done enough neural network coding (aka "viral coding" for you kiddies), to know that time does have a huge impact: the "mutation police" have rules, but unless they pass *some* of the mutations through, the system (in my experience, the neural net) has to tolerate some changes. So what you see is the cop going "nope, nope, nope, nope, nope, okay, nope, nope, nope, nope, nope, nope, nope, nope, nope, nope, nope, nope, okay..." etc. so you get enough time, and you've got some useful stuff sitting there in the middle of an already useful gene that is currently "off". Then you go through a stress, it gets turned on, if it helps the organism survive the stress, the newly activated gene survives. Note also the lather-rinse-repeat notion going on here: that gene could get turned on, prove to be deleterious as is, but its still sitting there in the original species turned off, it gets mutated again, turned on again and this time it works, so the if-at-first-you-don't-succeed rule of learning works quite effectively, because the branching ensures that both the orignal configuration (off) AND the new configuration (turned on) survive to "test" the proposed mutated gene.

Okay, I'm no biologist, I'm an amateur, but I have made things like this work with silicon and code, and to me its amazing how *well* they work even with hardly any time spent "learning"...seeing it happen can be very convincing, so forgive me for thinking this model is "obvious."

Cheers,
Buffy

[Biochemist]

This is a great summary, Bumab, particularly because you got Buff to agree with your digestion of her position. Let me add a couple of comments:

Originally Posted by bumab

Bio: Mutation cannot explain morphological changes because DNA itself is programed to resist mutations. Thus, mutations cannot provide any viable changes in the species, since they are inherently selected against by the DNA itself. Therefore, the information for those changes must already be present, like an insider, or a spy, and only gets expressed when some stress comes along.

I actually have no problem with mutation driving morphological change occasionally. I just suspect that it never launched a new phylum. Further, the main problem (actually, the only problem) I was trying to address is the mechanism for PE. My suggestion is that the only credible mechanism for a rapid transition (e.g., a couple of hundred thousand years) to a new phylum is for the parent species to have a codified transition to the daughter species. The corollary to this notion (which need not be accepted) is that if all daugher species are codified by their parent species, then all species came from one parent. This is not neccessary to accept to understand the proposed PE mechanism. It is just a logical corollary.

Buff: Mutations accumulate gradually, according to the traditional model, and are only expressed when an environmental stress allows those mutations to be expressed in beneficial ways. Traditional PE.

And my contention is that this does nothing to address PE. There is (almost) nothing in the Gradualism model that suggests an acceleration of acceptance of mutation after cataclysms. The increase in newly noncompetitive niches should be more than offset by the aggregate loss of genetic source material to mutate. I do not think this is a viable PE mechanism.

Me: A mutation causing gene, or some structure that causes rapid mutation, could be activated after an environmental stress, thus providing for the rapid speciation we see after an extinction event. This would be selected for because any organism with it would pass it along quite successfully, even though the offspring would be very divergent. It's a selfish gene argument.

Bumab- I think your position and mine are not differentiable. If a gene causes a "mutation", it is not a mutation. It is a predefined genetic expression. I am suggesting (as you are, I think) that there is more to the genetic code than the primary codon sequence. I am suggesting that the likely alterations to the code (which I described above as "rubik's cube swapping" ) are part of the code as well. Otherwise, the incidence of material, viable mutation in higher life forms would be nearly zero. Since they do exist and not just occur, but recur with some regularity, they are not accidents. They are part of the "code". The "code", in this context is not just the extant codon sequence. It includes the likely new sequences that will occur after the likely code swaps.

I think only Buffy is standing on established ground,

Yes, it looks like she can't take the heat of heresy.

... but I share Bio's adversion towards acceptance, based on the difficulty of randomly aquiring successful, useful, and viable protiens that wouldn't be attacked like all other new protiens AHEAD OF TIME. ...Neither gradulaism nor PE has a satisfactory explanation for the fossil record, as I see it.

Agreed. Although I don't think that Gould attempted to identify a mechanism when he identified the PE issue. He just named the problem.

Bio solves this conundrum by saying it's all pre-programmed, everything was set up already in the beginning. It really is pushing the problem back further in time, but it's also turning that problem into a 200 pound gorilla.

True. But that problem is not (currently) out of synch with observed data. Gradualism is out of synch with observed data.

I solve the problem by saying there could be a yet undiscovered mechanism (most likely genetic) that creates mutations INTENTIONALLY after an environmental stress of a magnitude to open up many niches. This would solve the problem by creating rapid change in genetic structure...

Bumab- If you just delete the notion of "mutation" from your text you have exactly my solution. You ALSO have the problem that the INTENTIONAL changes exist in all parent species, and hence roll back to the source of all parent species. You have the 200 pound gorilla too.

One more note: Buff- You mentioned that the mutations "had" to roll back to get back onto the coded "'track". That would not really be necessary. Any successful, beneficial mutation would then exist as a species until it "mutated" again, existed in stasis, or died out. It would not affect the "coded" evolutionary track which would exist in parallel.

I just suspect it never happened this way.