[Fishteacher73]

Originally Posted by Buffy

I think I'm getting a good sense of what you're talking about the more you do. I don't get the sense from my reading of Gould that he has in fact done anything to discount mutation as a key factor, although he clearly states that environmental pressures actually cause the spurt in changes, and the data clearly shows that these changes in many cases correspond to catastrophic events. What I don't get the sense of at all from my reading of contemporary evolutionary biology is the sense that mutation plays no significant role at all (not that it doesn't *happen*. I understand you're not saying that...). It seems to me that mutations that survive--and its *clear* that many do not get backed out--can remain dormant *until* stress causes them to express themselves. I don't really understand how changes--that must *eventually* be recorded in changes in DNA--just spontaneously happen, but its clear that mutations that happen all the time can get turned on and off once the they *exist*.

I need to go do some more reading as its been awhile since I've thought about this much. Continue guys!

Cheers,
Buffy

I'm wading in again andits already hip deep....


I think that open niches are the direction that allows speciation to occur. Mutation is one of the driving factors as well as genetic drift. As I stated earlier I think the true mechanism is a mix of PE and gradualism.

[Biochemist]

Originally Posted by Buffy

This is definitely an ID argument...

If that category makes you happy, use it. I never heard this from the ID camp. They typically discuss irreducible complexity. I am try to address the PE problem.

...This would not at all explain why there are any differences at all in the DNA between species. For this to really make sense, prokaryote DNA would have to be the *SAME* as all other species.

Untrue. It just means that there is information in the DNA that is other than the expressed genes. It means that future DNA versions, including additional nonfunctional DNA is precoded in prior versions. This model accounts for that fact that extremely unlikely transitions occur reasonably frequently.

Otherwise you have to explain why they {DNA structures} changed over time.

I did above.

While its true that pig DNA looks "a lot" like human DNA, that is a tremendous oversimplification, and it simply doesn't match at all. Other wise it would be very easy to create hybrids from extremely different species, which obviously we can't.

You are now supporting my argument. I contend that the complexity of DNA is even higher than we have imagined to date. The nonfunctional DNA fragments, in concert with genes already expressed, are predisposed toward a specific set of dramatic morphological changes. That is, the DNA that is superfluous in any particular species is at least partially required for specification of the next dramatic morphological change for the species. Although it may seem that it is tough to make hybrids, in fact it is pretty easy to insert a functiounal foreign gene into an existing DNA host, and yet a dysfunctional gene causes a ruckus or cell death. If our odds of success were the same as the odds of getting past a lysosome, we would probably only be successful every billionth time or so. But foreign functional genes seem to frequently work. Hmmmm. Maybe the lysosomes do not see them as foreign for a reason.

Now there's lots of other stuff here that does make sense, but I wonder why its not enough for you to stop at the notion that junk DNA performs exactly the way you're talking about, but that it does come from random mutations that may have been expressed in the past but were not dicarded.

Because 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. Ergo, subsequent to a trigger cataclysm, they alter core structure (among a very small number of likely possibilities) and subsequently express. The notion that the accumulated precoding carries back to the first prokaryote is (perhaps unfortunately) the only logical conclusion.

....unless we're getting into "programming by God", there's no logical reason to imagine that all that information loading happened in a big bang...

Buff, you are a woman of science. I was not drawing any conclusions about the source of the precoding, any more than Lindagarette does about the source of the Big Bang (the other one). It is not legitimate to disregard a theory because you dislike the implications. The issue is whether evidence points to the model. My suggestion is that there is no proposed mechanism that explains puncuated equilibrium. There is a significant body of paleontological evidence that suggests the sudden arrival of phyla. There are known progeny of lower species that are morphologically different in a single generation. The fact that there is a real (but small) number of viable human dramatic morphological changes, and that they recur with regularity (e.g., trisomy 13), suggests that the incidence of progeny viabiliy after dramatic change is extraordinarily high. The biochemical machinery (e.g., lysosomes) tends to efficiently detect and destroy any superfluous protein that arrives in the cell with remarkable efficiency. The reason that new ones that arrive after a dramatic change are not destroyed is that they are recognized as non superfluous. Furthermore, now the fundamental mechanism that expresses itself in major morphological changes is identical to the mechanism underlying natural selection. It is, in fact, not really either natural or selected, but it is precoded and anticipatory.

Suffice to say its an interesting idea, but I see too much data that contradicts it

I must have missed that part. Which part contradicts it?

[bumab]

Originally Posted by Biochemist

This would also suggest that the species behavior that we call "natural selection" is neither natural nor selected. It suggests they any species has a small number of precoded "next steps" and some of those steps express themselves. Even in Darwin's finch beaks, the birds lose thier adaptation when the environment changes. The same species can then get it back later. This is CERTAINLY NOT a random mutation. It is a precoded adaptive feature.

It's a misconception to label the finch's as "losing" their adaptation. That adaptation (large or small beaks) simply "goes out of style." They, in fact, adapted again, towards a smaller beak size.

Originally Posted by Biochemist

So the big leap I am suggesting (and this ain't semantics) is that the entire sequence of "next steps" in terms of serial precoded adaptive features for all species was encoded in the first prokaryote.

It might sound ludicrous, but as soon as you accept the notion that a single species has precoded its likely daughter species via precoded adaptive features, the next logical assumption is the grandfather-of-all-species DNA code-base.

If that is the case, then there is a truely huge amount of information in that first prokaryote. The first problem I see is that all those adaptations continued to be useful, and viable, 4 billion years after that first little cell. That's another stretch. To accomodate that, you'd have to include tons of other possibilities that could be called forth to any environmental change life could undergo, making the info load powers of 10 times larger.

There is definitly a deficiency with the prevailing view as to explaining rapid changes. A single gene or subset of genes (possibly piggy backing on another coding region) that induced mutations after an environmental stress is more likely then that huge info load.

Originally Posted by Biochemist

Do you understand why I labeled it the Biological Big Bang?

At first I didn't get it, but now it makes perfect sense. Aptly named

Originally Posted by Biochemist

Ergo, all extant, historical and future species were precoded in the first prokaryote. Imagine that information load.

No kidding.

[bumab]

Originally Posted by Biochemist

But foreign functional genes seem to frequently work. Hmmmm. Maybe the lysosomes do not see them as foreign for a reason.... The biochemical machinery (e.g., lysosomes) tends to efficiently detect and destroy any superfluous protein that arrives in the cell with remarkable efficiency. The reasons that new ones that arrive after a dramatic change are not destroyed is that they are recognized as non superfluous.

This is a great point. Certainly something to think about.

[Biochemist]

Originally Posted by bumab

It's a misconception to label the finch's as "losing" their adaptation. That adaptation (large or small beaks) simply "goes out of style." They, in fact, adapted again, towards a smaller beak size.

Your wording is better, Bumab. I can't recall if the finches readapted forward again to the larger beaks, but my point was that they probably would in the face of the same environmental stress because there is a relatively small number of likely outcomes.

If that is the case, then there is a truely huge amount of information in that first prokaryote. The first problem I see is that all those adaptations continued to be useful, and viable, 4 billion years after that first little cell. That's another stretch. To accomodate that, you'd have to include tons of other possibilities that could be called forth to any environmental change life could undergo, making the info load powers of 10 times larger.

yes. Lots of powers of 10.

There is definitly a deficiency with the prevailing view as to explaining rapid changes. A single gene or subset of genes (possibly piggy backing on another coding region) that induced mutations after an environmental stress is more likely then that huge info load.

Sure, but you sort of have to pick your poison. We have to either go with the gradualism model, and then wonder why all of these changes can sit "on hold" successfully through generations of efficient degradation by lysosomes, and subsequently make a large number of extremely unlikely adaptations quickly, or you essentially push the problem back further in time. I pushed it back. I think it matches the biochemical and paleontological data better.

I really don't think this is any more difficult to swallow than quantum mechanics (much less string theory). It just sort of makes you feel small. Like the Big Bang does.

[Fishteacher73]

Originally Posted by Biochemist

Your wording is better, Bumab. I can't recall if the finches readapted forward again to the larger beaks, but my point was that they probably would in the face of the same environmental stress because there is a relatively small number of likely outcomes.

Organisms do not "revert" to old forms. They may re-evolve to forms that are similar to the original, just recall the "panda's thumb".

[bumab]

Originally Posted by Biochemist

Sure, but you sort of have to pick your poison. We have to either go with the gradualism model, and then wonder why all of these changes can sit "on hold" successfully through generations of efficient degradation by lysosomes, and subsequently make a large number of extremely unlikely adaptations quickly, or you essentially push the problem back further in time. I pushed it back. I think it matches the biochemical and paleontological data better.

Well, not neccessarily. Gradualism is not the only alternative to your theory, just the most prevalent one. Like I said before, some mechanism (most likely genetic) that induced mutations, possibly by reducing the efficacy of spell checking protiens, after a catacylsm would certainly fit the data as well- creating lots of new species relativally quickly.

Originally Posted by Biochemist

I really don't think this is any more difficult to swallow than quantum mechanics (much less string theory). It just sort of makes you feel small. Like the Big Bang does.

It's not a bad theory, I'm just testing it The other thing- the information load in the Big Bang was not neccessarily functional. It just was. the information load in the prokaryote you proposed isn't just random information that will interact according to simple rules to create a variety of structures, it's got to be a large information load AND exqusitly organized into functional units. Throwing hydrogen every which way will produce the same stars in different places. Thowing base pairs around is highly likely to produce nothing anywhere.

I'm not downplaying your idea. It's really interesting, and would be as likely a place as any for gene research to go. Can you think of a way to test that out? Induce stress in bacteria and attempt to predict their response?

I would search for a mutagen inducing gene for mine...

[Fishteacher73]

Originally Posted by Bumab

I'm not downplaying your idea. It's really interesting, and would be as likely a place as any for gene research to go. Can you think of a way to test that out? Induce stress in bacteria and attempt to predict their response?

Many bacteria can reproduce sexually by exchanging genetic info, even bacteria of differing species. The gain of genetic material could be explained by a "selfish" bacteria that got "theirs" and rolled over to go to sleep..

[Biochemist]

Originally Posted by bumab

Well, not neccessarily. Gradualism is not the only alternative to your theory, just the most prevalent one. Like I said before, some mechanism (most likely genetic) that induced mutations, possibly by reducing the efficacy of spell checking protiens, after a catacylsm would certainly fit the data as well- creating lots of new species relativally quickly.

This is almost rephrasing what I said, except I elect to not call anything a mutation. I am reserving the use of "mutaion" for unlikely things that express themselves probablistically after a single or series of quasi-random events. If your mechanism includes any specificty in the nature of protection from degradatory pathways (which I think you said above) then we are not that far apart.

... the information load in the Big Bang was not neccessarily functional. It just was. the information load in the prokaryote you proposed isn't just random information that will interact according to simple rules to create a variety of structures, it's got to be a large information load AND exqusitly organized into functional units.

Agreed. I did not mean to take the comparison to the Big Bang too far, other than to suggest that it is not necessary to agree to causality in order to accept the consistency with empirical data.

I'm not downplaying your idea. It's really interesting, and would be as likely a place as any for gene research to go. Can you think of a way to test that out?

Yes, a couple. If we examine the genotypic nature of dramatic morphology changes (like the extra frog leg) and then look at a probabilisitic analysis of this kind of event, you could get some interesting results. If we can't find a way to make the likelihood of a specific, viable dramatic change less than say, 1 in 10^10, that would suggest there is something going on here, particularly if the event recurs. I think outcomes like human trisomy 13 or even Kleinfelter's syndrome are really unlikely. We can look at these examples at non-beneficial genetic outcomes, but that fact that a major alteration in chromosomes can occur at all and retain viability is odd. And we have more than one. And they recur. If the dramatic, positive morphological changes occur at perhaps 1 in 10^5 or 1 in 10^6 factor lower incidence, we might actualy have some of those on the planet now, but we would not recognize it unless it happened to a human. Even that we might miss.

[gubba]

g'day Bio,

My only formal training has been in the historical area with a fair leaning towards archeology and so I'll claim a little expertise re. evaluating the practises of palaeontology and I recommend extreme caution. Quite baldly 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. While far from fully accepting gradualism (again, the evidence is not yet in), I'm strongly attracted to the field of genetics as our most fruitful area for research.

Bio, a simple question, which prokaryote? The one 4 (or is it 5?) billion years ago at the beginnings of organic life, or the latecomer 1 billion years ago which Buffy would claim as her direct Eve? There's some scope there for genetic complexity to develop I hope.

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.

Buffy, you're dead right, love the thread, thanks bumab!

Have no time at moment except to say; look towards systems of competing and interacting genetic tendencies for the development of viable patterns of evolution and don't lose too much sleep searching for unifying answers, cheers gub.