Punctuated Equilibria theories

[Buffy]

At the risk of raising semantic arguments, folks that discuss "mutation" usually are presuming that some random occurence resulted in a morphological change. I am suggesting that the source DNA already had the "pre-genes" (if you will) to allow for significant rapid adaptation. This does NOT mean that the "new" genes were preexisting and already functional. It suggests that there is MUCH more information in the nucleic acid sequence than the genes that are expressed.

Then it is semantics mostly. I've been arguing something similar, which is that they might be "recessive" which isn't the right word either I know (you and Bumab are the pros here, I'm just an amateur!). I think I'm more aligned with Bumab's description than yours, in that these genes are there and get expressed, but they're all just sitting there waiting to be turned on, rather than environmental effects actually doing some complex shuffling of genes. I share Bumab's point that single gene expression is actually proving quite common, as far as I've been able to see. Your "pre-gene" notion sounds like its headed our way though! Bottom line is that all that "junk" in DNA is proving more and more not to be junk at all, just "ignored at the moment" and thats where mutations can pile up with no expression for long periods of time and then under environmental stress, have one last mutation turn them on...I still don't buy the notion of gene mutation as being "not important."

 

Cheers,

Buffy

[Biochemist]

Then it is semantics mostly. I've been arguing something similar, which is that they might be "recessive" which isn't the right word either I know (you and Bumab are the pros here, I'm just an amateur!). I think I'm more aligned with Bumab's description than yours, in that these genes are there and get expressed, but they're all just sitting there waiting to be turned on, rather than environmental effects actually doing some complex shuffling of genes. ...

I don't think I have gotten the core point through to you yet, Buff, but I am not sure. Because the core issue is certainly not semantic.

 

I am suggesting that the functional genes in any life form are a tiny subset of the VALID information in their DNA. That is, there is other unexpressed information that is not even yet genes, and it is most certainly NOT junk. The triggers that invoke adaptation are probably mostly environment, given the paleontological data. But it is NOT fundamentally true that a new environment fosters selection of features that occur out of a large number of random mutations. There are a small number of precoded likely morphological changes that express themselves. Some are substantially advantaged by environmental change.

 

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.

 

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.

 

Hence the process is:

 

1) Species exist in stasis for extended periods.

2) The likely next species (or set of species) is always precoded in any parent species.

3) The complex change that results in the next species is biochemically identical to what happens in natural selection, but the process is truly neither "natural" nor "selected". It is a precoded feature waiting for a specific opportunity for expression.

4) Most species act this way. Perhaps all.

5) Cataclysms affect many species at once, each responding to their respective environmental triggers with ther precoded adaptive features.

6) Daughter species may be morphologically very dissimilar from their parents.

 

And the key contrasts with the prevailing view are:

 

1) All species were precoded in their parent species genes.

2) Rapid morphological change in not only possible, but likely.

3) There is really no "randomness" in it, although one could characterise the cataclysms as "random".

4) The acceptance of predefined parent-species-to-daughter-species sequences inevitably leads to the notion of a common historical DNA code base that substantially predefined all species.

 

Does this sound like semantics? Do you understand why I labeled it the Biological Big Bang?

 

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

[Buffy]

I don't think I have gotten the core point through to you yet, Buff, but I am not sure. Because the core issue is certainly not semantic.

Now its clear. You sound like James Putnam! This is definitely an ID argument because it basically says that everything including what we're going to be is already in there. Yes, imagine the information load. 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. Otherwise you have to explain why they changed over time. 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.

 

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. There's no real reason this junk could be turned on and off. Note here I'm using the term junk in the genomic sense: geneticists call anything that does not have immediate expression--dominant or recessive--as junk, but there's lots of research starting to show that that junk isn't junk and is used in some of the ways we're discussing here.

 

Bottom line, 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, in fact there's no way for it to have happened at all witout an intelligent creator. To the extent that I've said I may think that the Creator "pushed the button", yes BBB is a good name for it in my book (note I've never said she set the parameters though! :hihi: ) If that's what you wanna believe, I don't mind, but on the other hand, like I say, that information had to survive lots of transmogrification as evidenced by the broad dissimilarity in DNA across species and the fact that there is increasing size/complexity of DNA correllated with size/complexity of organism. Suffice to say its an interesting idea, but I see too much data that contradicts it, so you haven't convinced me you've got a scientific argument that withstands scrutiny....

 

Cheers,

Buffy

[Fishteacher73]

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]

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]

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.

 

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.

 

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 :hihi:

 

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

 

No kidding.

[bumab]

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]

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]

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]

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.

 

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 :hihi: 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... :hihi:

[Fishteacher73]

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.. :hihi:

[Biochemist]

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.

[Fishteacher73]

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-

...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]

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....

...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.

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]

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.