[Buffy]

Originally Posted by bumab

I am just speculating, of course, but I am not completely satisfied (like Bio) that mutation rates alone can explain punctuated eq., since in most organisms mutatitve propensities are selected against- witness the sharks, a constant evironment has made them very resistant to mutations.

I agree with that, I just keep getting the impression that Bio is saying 1) mutations do occur, but 2) they are always cancelled out and have *no* effect on speciation at all: that some other action causes genes to spontaneously rearrange themselves *only* when envronmental stresses occur. I think I'm arguing more along the same lines you are that there's mutations and they only express themselves under stress, probably due to other parts of the equation like proteins and hormones which do pretty bizarre things... Bio, you want to correct my impressions?

Cheers,
Buffy

[Biochemist]

Originally Posted by Buffy

I agree with that, I just keep getting the impression that Bio is saying 1) mutations do occur, but 2) they are always cancelled out and have *no* effect on speciation at all: that some other action causes genes to spontaneously rearrange themselves *only* when envronmental stresses occur....

This is close. I suggest the following:

1) Mutations do occur, but they are not a significant driver of speciation. They are essentially unrelated to the discussion. Their relationship to speciation is not established in the fossil record, and that vast, vast, vast majority of viable "incremental" mutations would have been suppressed. The higher the life form, the more successful the suppression.
2) Sudden arrival of a new species (or phylum) cannot be via mutation in the sense that we usually use it. If a parent species is able to generate a daughter species that is both viable and yet different enough to preclude interbreeding in a small number of generations, it is probably because the DNA of the parent species provided for the DNA of the daughter species. DNA is remarkably stable over time (consider mitochondrial DNA). Dramatic changes in morphology are not accidental: they are part of the information load of the parent.
3) The probability of a life form producing a viable daughter species with significant morphological change is vanishingly small. This would include the examples (yours, Bumab?) about insects or frog progeny with additional legs. I contend this is not a mutation. It is an adaptive feature of the source DNA.
4) The implications are that the aggregate complexity of higher species (e.g., humans) is not a lot higher than the aggregate complexity of prokaryotes because the majority of the predispostiion for generation of higher life forms was already in the prokaryote.
5) This would turn the customary interpretation of natural selection a little bit sideways. It would suggest not that life forms adapt as environments change to enable survival. Rather, life forms are structured for adaptation, and environmental changes let the existing information features express themselves.
6) This is testable. There are many extant examples of viable offspring after dramatic morphological changes. Frogs with five legs. Insects with additional legs. If we check to see how many new functional genes there are after a single generation, it would be highly suggestive. If a single generation can produce even ten new funcitonal genes, it would be ludicrous to suggest that it was a random occurence in the progeny. The probabilistic numbers are easily less than 1 in 10^100. It would have to be intrinsic in the information load of the parent.
7) The examples in number 6 (above) are only noticed because the progeny look like the parents. If a single generation alteration can produce 10 functional genes, why not 100? Why not 1000? Within reason, the probability is essentially the same, as long as the feature was part of the parental information load.
8) If the number of new genes is high, the new species would not have to resemble the parent species. If it did not, we would not be able to find the link to the parent. Sound familiar?
9) This implies that a species could arrive without a morphologically similar precursor. Ergo, the links are missing in the fossil record because they are not there. Species arrive quickly because they are supposed to.

Have I seduced anyone toward the idea yet? If so, consider how complex that first prokayote really was. If it sounds ludicrous to put all that information load back on the prokaryote, consider the odds that the very,very first, most "simple" life form would use the very same nucliec acids and the very same amino acids as humans. There are an infinite number of possibilities (truly infinite) for amino acids but the same 20 lasted 4 billion years? Seem strange to anyone?

Strikes me as one of those things that makes you go "Hmmmmm".

[bumab]

Hmmmmm......

Originally Posted by Biochemist

1) Mutations do occur, but they are not a significant driver of speciation. They are essentially unrelated to the discussion. Their relationship to speciation is not established in the fossil record, and that vast, vast, vast majority of viable "incremental" mutations would have been suppressed. The higher the life form, the more successful the suppression.

True, as far as the fossil record shows. I'd agree.

Originally Posted by Biochemist

2) Sudden arrival of a new species (or phylum) cannot be via mutation in the sense that we usually use it. If a parent species is able to generate a daughter species that is both viable and yet different enough to preclude interbreeding in a small number of generations, it is probably because the DNA of the parent species provided for the DNA of the daughter species. DNA is remarkably stable over time (consider mitochondrial DNA). Dramatic changes in morphology are not accidental: they are part of the information load of the parent.

A logical step.

Originally Posted by Biochemist

3) The probability of a life form producing a viable daughter species with significant morphological change is vanishingly small. This would include the examples (yours, Bumab?) about insects or frog progeny with additional legs. I contend this is not a mutation. It is an adaptive feature of the source DNA.

"Adaptive feature" sounds like my idea of a "mutative gene." DNA is not a mind, it can't "decide" to mutate. It's simply an information processing device. Input in, various protiens out. Something would need to be present to respond to the environmental change. You information load would simply be in the form of many genes, and then something to control them, right?

Originally Posted by Biochemist

4) The implications are that the aggregate complexity of higher species (e.g., humans) is not a lot higher than the aggregate complexity of prokaryotes because the majority of the predispostiion for generation of higher life forms was already in the prokaryote.
5) This would turn the customary interpretation of natural selection a little bit sideways. It would suggest not that life forms adapt as environments change to enable survival. Rather, life forms are structured for adaptation, and environmental changes let the existing information features express themselves.

Life forms are structured for adaptation, you just don't think the existing theories account for the speed of adaptation accounted for in the fossil record. I certainly agree.

Originally Posted by Biochemist

6) This is testable. There are many extant examples of viable offspring after dramatic morphological changes. Frogs with five legs. Insects with additional legs. If we check to see how many new functional genes there are after a single generation, it would be highly suggestive.

The extra legs are a single gene which doesn't get turned off in growth, so that's one strike. I'm not sure about the frogs, I'll look when I get home. Regardless, genetic mapping is coming up with a lot of dramatic morphological changes that can result from single gene mutations.

Originally Posted by Biochemist

If a single generation can produce even ten new funcitonal genes, it would be ludicrous to suggest that it was a random occurence in the progeny. The probabilistic numbers are easily less than 1 in 10^100. It would have to be intrinsic in the information load of the parent.

Originally Posted by Biochemist

8) If the number of new genes is high, the new species would not have to resemble the parent species. If it did not, we would not be able to find the link to the parent. Sound familiar?
9) This implies that a species could arrive without a morphologically similar precursor. Ergo, the links are missing in the fossil record because they are not there. Species arrive quickly because they are supposed to.

Possible, although that would make a lot of species where the parents are raising strange, strange offspring. I don't know how many animals will raise offspring that look nothing like them. But perhaps. Still- what turns this on? If the information load is present (which I'll grant could be, we've got all sorts of wierd genes in us), how does it become expressed?

Originally Posted by Biochemist

There are an infinite number of possibilities (truly infinite) for amino acids but the same 20 lasted 4 billion years? Seem strange to anyone?

Yes and no- could be that any (ANY) change to the amino acid structure proved deleterious, because the whole DNA would need to change AT THE SAME TIME in order for all the genes and protiens to be expressed in any consistent way. That's a pretty big roadblock of amino acids changing over time.


Interesting ideas!

[Biochemist]

Originally Posted by Biochemist

...If it sounds ludicrous to put all that information load back on the prokaryote, consider the odds that the very,very first, most "simple" life form would use the very same nucliec acids and the very same amino acids as humans. There are an infinite number of possibilities (truly infinite) for amino acids but the same 20 lasted 4 billion years? Seem strange to anyone?....

I cannot think of any way to calculate the probability of the above this state of nature without the answer coming out essentially zero, unless you assume that the entire information load for development of life was already in the prokaryote.

An interesting probklem.

[Biochemist]

Originally Posted by bumab

"Adaptive feature" sounds like my idea of a "mutative gene." DNA is not a mind, it can't "decide" to mutate. It's simply an information processing device. Input in, various protiens out. Something would need to be present to respond to the environmental change. You information load would simply be in the form of many genes, and then something to control them, right?

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. It suggests that many as-yet-unexpressed permutations of the extant genes are already in the information load. Imagine a 100 number combination lock that requires 5 dials for the combination. There are 100^5 "dialable" combinations, but you could design the lock with 50 valid unlock combinations. I am suggesting that the adaptive combinations of "new" genes are already present in the parent species, like one of the 50 valid combinations. This is not random, so it is not a mutation.

The extra legs are a single gene which doesn't get turned off in growth, so that's one strike. I'm not sure about the frogs, I'll look when I get home. Regardless, genetic mapping is coming up with a lot of dramatic morphological changes that can result from single gene mutations.

I would argue that a sigificant morphological change pursuant to a singe gene change supports my case.

...that would make a lot of species where the parents are raising strange, strange offspring. I don't know how many animals will raise offspring that look nothing like them.

This assumes the offspring need raising, but this is a good point.

... what turns this on? If the information load is present (which I'll grant could be, we've got all sorts of wierd genes in us), how does it become expressed?

Well, since I am hypothesizing an inexplicable quantity of information load into the prokaryote, it isn't a much larger step to hypothesize that the trigger recognition is there as well. What the heck.

... could be that any (ANY) change to the amino acid structure proved deleterious, because the whole DNA would need to change AT THE SAME TIME in order for all the genes and protiens to be expressed in any consistent way....

Sure. But doesn't that support the case that the probability of the first prokaryote was even smaller than one might have imagined previously? Exactly one set of 20 amino acids out of an infinite set of possibilities???

[bumab]

Originally Posted by Biochemist

I am suggesting that the source DNA already had the "pre-genes" (if you will) to allow for significant rapid adaptation.

Sounds good, I was just looking for clarification.

Originally Posted by Biochemist

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. It suggests that many as-yet-unexpressed permutations of the extant genes are already in the information load.

Seems that emerging molecular biology more then supports that idea. Our understanding of just how many protiens can come from a single gene through alternate splicing and other methods is continually growing.

Originally Posted by Biochemist

But doesn't that support the case that the probability of the first prokaryote was even smaller than one might have imagined previously? Exactly one set of 20 amino acids out of an infinite set of possibilities???

Well, perhaps there were many possible sets of amino acids taht would work, however those 20 were simply the chosen one. Once that is established, however, it would be nearly set in stone. During the establishment period, however, your point is valid. Why aren't there seperate lines of organisms with seperate amino acid sequences? Possible fitness variances, or interbreeding, or whatever...

[Biochemist]

Originally Posted by bumab

Well, perhaps there were many possible sets of amino acids taht would work, however those 20 were simply the chosen one. Once that is established, however, it would be nearly set in stone. During the establishment period, however, your point is valid. Why aren't there seperate lines of organisms with seperate amino acid sequences? Possible fitness variances, or interbreeding, or whatever...

Good points, both.

[Buffy]

Originally Posted by Biochemist

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]

Originally Posted by Buffy

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]

Originally Posted by Biochemist

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! ) 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