Punctuated Equilibria theories

[TeleMad]

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

 

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

[bumab]

Read this thread. It's very well written. A "theistic bent" has been presented by many people in other philosophy threads, where it belongs (for now). This has been an excellent thread, in my opinion, in keeping to the physical issues.

[TeleMad]

Mutations aren't restricted to just nucleotide substitutions within a gene, they can also involve several forms of chromosome-level rearrangements (as others here have already alluded to). And mutations of this sort have been shown to be capable of creating a new species.

 

"The mechanism of sympatric speciation has been experimentally verified for many plants. One example is a group of species, collectively called hemp nettles, that occurs in temperate parts of Europe and Asia. One hemp nettle, Galeopsis tetrahit (2n = 32), is a naturally occurring allopolyploid thought to have formed by the hybridization of two species, G. pubescens (2n = 16) and G. speciosa (2n = 16). This process occurred in nature but was experimentally reproduced. Galeopsis pubescens and G. speciosa were crossed to produce F1 hybrids, most of which were sterile. Nevertheless, both F2 and F3 generations were produced. The F3 generation included a polyploid plant with 2n = 32 that self-fertilized to yield fertile F4 offspring that could not mate with either of the parental species. These allopolyploid plants had the same appearance and chromosome number as the naturally occurring G. tetrahit. When the experimentally produced plants were crossed with the naturally occurring G. tetrahit, a fertile F1 generation was formed. Thus, the experiment duplicated the speciation process that occurred in nature." (Biology: Fifth Edition, Eldra Pearl Solomon, Linda R. Berg, and Diana W. Martin, Saunders College Publishing, 1999, p411-412)

 

And, key to this thread, the mutations can lead to a new species in just 4 generations.

[Biochemist]

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

I never presented a theistic aspect. It is true that I imputed more information load into the first prokaryotye, but I never drew any conclusions about the solution to that problem. There are several possibilities.

[Biochemist]

Good Lord, everybodies gettin' hot under the collar.

More like grumpy. Sorry all.

... you've not presented any evidence for your idea. None-

My intent was to list some of the existing, demonstrable genetic alteration mechanisms and underline that none of them are necessarily mutative. All of the machanisms I listed have specific excision and insertion mechanisms. They are certainly not random. They all could be specified by the code of the parent species. If we found five or 10 more codified mechanisms, it will just gradually improve the core of the case.

 

The real dramatic point that I would like to emphasize is that I am assuming that daughter species can be morphological dissimilar from the parent species. This seems to be true in the fossil record, and I am not sure (short of gene mapping all phyla and runnign a bunch of really ugly computer algorithms) how we might find connections to a parent species that is phenotypically very different than the daughter species.

 

I think it is time to actively consider that the fossil record is reasonably complete, and that phenotypical expression of at least some parent species may be very different than the phenotypical expression of daughter species. Our taxonomic classification is thus misleading. We have spent a century classifying animals by mophology, and have almost accidently presumed that morphologic similarity correlates with ancestry.

 

But the large number of discontinuities in the fossil record suggests we ought to presume otherwise. This means we should be actively searching for mechanisms that produce a daughter species rapidly without any phenotypical expression required for selection.

 

I will bet a buck this is true. I already have a cup of coffee on the line with FishTeacher on this. Yes, I am a big risk taker.

 

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

I assume you meant the rapid mutation mechanism. I just don't think there is any evidence for that, in spite of the general acceptance. And the math looks so terrible, that I have a hard time fathoming how it could work.

 

We have maybe 250 million years between the advent of chordates and the advent of mammals. Most of those generaations are annual, and the offspring set is small. It is really hard to believe that we can get to mammalian physiology from simple chordates in 250 million generations via mutation.

 

Even if we assume that the parent species genes are only a single amino acid off from the live genes in the daughter species, the odds of a viable new enzyme are no better that 1/20 x1/300=1/6000. If we assume that a typical enzyme sequence is a half doxzen enzymes, we would be at 1/6000^6, or less than 1 in 10^18. That is for one new enzyme system that is a single amino acid (in each enzyme) off from the parent species. Even if we assume a million offspring in each generation, we are still at a likelihood of less than 1 in 10^9 for mutation alone to get a single new "close" enzyme system in mammals from chordates.

 

If we take Buffy's assumption that there are "steering" mechanisms that decrease the odds, why assume there were mutations at all? What did that do for the model?

 

But I do understand your point.

[bumab]

The real dramatic point that I would like to emphasize is that I am assuming that daughter species can be morphological dissimilar from the parent species. This seems to be true in the fossil record, and I am not sure (short of gene mapping all phyla and runnign a bunch of really ugly computer algorithms) how we might find connections to a parent species that is phenotypically very different than the daughter species.

 

This is a great taxonomic point, but really beside the issue.

 

This means we should be actively searching for mechanisms that produce a daughter species rapidly without any phenotypical expression required for selection.

 

This is a point I haven't seen you make before. Perhaps I just missed it (or am dense), but it's a dramatically more significant idea then the majority. It's a good summary point, I'm going to think it over...

[ldsoftwaresteve]

In reading back over this thread and coming at it from a simple minded direction (which is my natural state), if PE is correct then it is probably associated with some kind of catastrophic event. It seems there is agreement on that.

 

it occurs to me that the nature of the events that may cause massive changes to take place may each be different in some significant way.

 

What might be the differences? Radiation, poisons, temperature change, the introduction of massive quantities of water, - help me - my imagination is running thin here.

 

Also, there is a tendency is to assume that the solar system is the same today as it was 500 million years ago. I have read about the possibility that the earths orbit has changed, that some planets are actually quite new, or have had their orbits changed, etc. Nobody really knows, I guess is my point.

 

Also, if there is any doubt about the efficacy of the methods used for dating these events, that doubt should carry down to any conclusions based upon the related measurements.

 

I see the eventual need for some way to connect all prior assumptions to any current conclusions. This is not something that we can allow our memories to handle. We need an automated way to show how strong the branch is that we happen to be hanging on the end of.

 

What I bet would happen is that we'd spend very little time arguing about the color of the leaf at the end of a branch, when the truth value of the branch is only 30%. I think it would tend to push us in the direction of verifying and certifying assumptions which, if I understand the process correctly, is more in line with actual science.

[bumab]

it occurs to me that the nature of the events that may cause massive changes to take place may each be different in some significant way.

 

True, however it's normally assumed that the reason for the adaptive radiation (PE) we see in the fossil record is due to the same fundamental cause- niche's are now open, due to the massive extinctions, regardless of cause.

 

Perhaps the disaster itself plays some role in causing the spike in speciation, however a variety of extinction events would not support this, since all (or most) mass extinctions resulted in dramatic radiation of species. The only common thing the disasters have that we know of is the induced stress on the survivors- lack of food, water, etc. all create a survival stress. We've been argueing about how that stress could be a cause of speciation. The disaster itself is really besides the point.

 

But we all could be wrong, perhaps each extinction event brings some species causing stimuli to the surface, each disaster different. Probably not, however...

[Biochemist]

...What I bet would happen is that we'd spend very little time arguing about the color of the leaf at the end of a branch, when the truth value of the branch is only 30%. I think it would tend to push us in the direction of verifying and certifying assumptions which, if I understand the process correctly, is more in line with actual science.

I think this is a good point.

[bumab]

The real dramatic point that I would like to emphasize is that I am assuming that daughter species can be morphological dissimilar from the parent species. This seems to be true in the fossil record, and I am not sure (short of gene mapping all phyla and runnign a bunch of really ugly computer algorithms) how we might find connections to a parent species that is phenotypically very different than the daughter species.

 

True.

 

I think it is time to actively consider that the fossil record is reasonably complete, and that phenotypical expression of at least some parent species may be very different than the phenotypical expression of daughter species.

 

Over the long term, but I think you are thinking PE happens at a faster rate then has been established. Rats didn't give birth to leopards right away, that's an overly dramatic change. Adaptive radiation events are usually on the scale of 10-30 million years, not 30.

 

This means we should be actively searching for mechanisms that produce a daughter species rapidly without any phenotypical expression required for selection.

 

You are certainly correct that if no phenotypic expression on which selection can act is achieved, we need a new model. But there's still no convincing evidence that new daughter species are being born viably and regularly. A large number of offspring can be born, most won't make it. Most phenotypic expressions are not viable!

 

We have maybe 250 million years between the advent of chordates and the advent of mammals. Most of those generaations are annual, and the offspring set is small. It is really hard to believe that we can get to mammalian physiology from simple chordates in 250 million generations via mutation.

 

In a single line. Now multiply that by the number of individuals in that species, plus whatever factor local disasters play into it (local radiations), times the number of offspring per year, times all the mutations that produced non-viable eggs and thus were never born, times....

 

If we take Buffy's assumption that there are "steering" mechanisms that decrease the odds, why assume there were mutations at all? What did that do for the model?

 

The steering mechanisms somehow encourage advantageous mutations and discourage deleterious ones. That increases the odds of viable daughter species. However, there's scant evidence for this idea other then something else is needed. I share your aversion. But it's simple to think how it arose through selection- those parent species that had it did well (through their daughter species), and those that didn't, didn't.

 

All in all, the main problem with your theory is it's trading difficulty for difficulty, and your theory runs into trouble in areas we know decently well. Traditional theory is lacking a mechanism, your's is lacking a mechanism AND support. If the BBB theory is sound, we should be able to find our genes coded in all other species, since we all decended from the same info laden prokaryote. We should be able to predict the forms E. coli will take when we stress the culture. Etc.

 

Traditional theory can't explain the speed of mutation, that's really it. I agree we need to look for another mechanism, but at least we aren't also looking for another cause.

 

I'm sure you don't agree :hyper:. Let me know how...

[Biochemist]

Over the long term, but I think you are thinking PE happens at a faster rate then has been established. Rats didn't give birth to leopards right away, that's an overly dramatic change. Adaptive radiation events are usually on the scale of 10-30 million years, not 30....

B- I think you know more than I do about adaptive radiation. But as I understand it (please, correct me) this is mostly applicable to radiation/generation of species where the Order already exists. That is, is is mostly in the lower taxonomies: genus and species.

 

The problem I was trying to noodle is the sudden advent of phyla/class/order on the scene. The original new species with new body plans are fundamentally inexplicable, and are not really addressed by adaptive radiation.

 

This is where I am suggesting that we need a more dramatic biological mechanism. Zohar would suggest it is aliens. I am not willing to go that far yet.

[Biochemist]

...In a single line. Now multiply that by the number of individuals in that species, plus whatever factor local disasters play into it (local radiations), times the number of offspring per year, times all the mutations that produced non-viable eggs and thus were never born, times.......

This is the math I did, although I only asumed a million offspring per generation. And for a complex change, it WOULD have to be in a line. You would need serial mutations to get a new enzyme systems (for example). I still think this math is problematic, particular once you get to higher phyla with llonger generation times.

[Biochemist]

...If the BBB theory is sound, we should be able to find our genes coded in all other species, since we all decended from the same info laden prokaryote. We should be able to predict the forms E. coli will take when we stress the culture. Etc.....

Well, ignoring the grandiose implications of BBB, just consider the implications of programmed speciation form the parent to the daughter species.

 

I suspect it would take a pretty rigorous computer algorithm to find the traces of parent species protogenes in the daughter species, unless the entire gene, or a material fractions of it were exactly replicated. I am suggesting that may not be true.

 

TeleMad's example above is illustrative. The genetic transition is pretty dramatic if the changes are at the level of the chromosome. If we were to imagine the notion of a rubik's cube twist of a chromosome that severed and reconnected 8 genes, it might be tough to find the precursor gene fragments. I suspect a computer could do it for one generation back, but it would be very unlikely to predict one generation forward, since the permutaions are in the trillions of trillions of trillions, and we would have to know the exact mechanism to even get that close. I think we ought to be looking for high-level gene-adaptive biochemical processes under an assumption that the processes are NOT mutative, but programmed.

 

I don't know much about botany, but it seems to me that one of the core difference between plants and animals is that plants have very few rejection mechanisms. It is easy to graft plants together and get viable species. I even have quad-grafted apple trees in my yard (i.e., one trunk, four varieties of apples).

 

Mammals reject such a graft without pretty serious immunosuppression. I think we ought to look at the specifics of immunosuppression. When a mutation is NOT suppressed, we ought to ASSUME there is someting odd, because there certainly is, statistically. Acceptance of a gene change should be regarded as an indicator of possible preprogramming in the parent species.

[bumab]

I don't know much about botany, but it seems to me that one of the core difference between plants and animals is that plants have very few rejection mechanisms. It is easy to graft plants together and get viable species. I even have quad-grafted apple trees in my yard (i.e., one trunk, four varieties of apples).

 

It is very different. New species are produced all the time, and as such, plant examples are not super supportive of speciation events.

 

When a mutation is NOT suppressed, we ought to ASSUME there is someting odd, because there certainly is, statistically. Acceptance of a gene change should be regarded as an indicator of possible preprogramming in the parent species.

 

I agree with this, although perhaps the gene itself is not pre-programmed, but rather then acceptance mechanisms of protiens are more complicated. I've only been riding your theory so hard because it is very different, and as such needs some extra scrutiny. :hyper:

 

New protiens that survive the lysosomic gauntlet should be investigated more closely, for reasons why. Are immune responses less dramatic inside the cell? I assumed they were the same inside and out, but perhaps that is not a safe assumption. Perhaps these protiens are not tagged for destruction- as I recall, lysosomic activty responds to a molecular marker, right? You're the biochemist... There are several branches that could come off the BBB without requiring the information load of staggering implications you've brought up before.

[Biochemist]

...New protiens that survive the lysosomic gauntlet should be investigated more closely...

Ooh. Cool phrase: "the lysosome gauntlet". Sounds like a Clint Eastwood movie. I think will borrow that one.

... Are immune responses less dramatic inside the cell? I assumed they were the same inside and out, but perhaps that is not a safe assumption....

Actually, you make a good point. We usually regard immunosuppression as the processes mediated by antibodies and lymphocytes. Technically, the internal cell mechanism is not immunosuppression. But it is self recogniiton (or not) and I was throwing it into that genre. I don't know of a term specific to intracellular self recognition. You?

[Biochemist]

There are several branches that could come off the BBB without requiring the information load of staggering implications you've brought up before.

True. But if we could demonstrate that a significant genetic change was actually pre-recognized by the parent species, imagine the implications.

[bumab]

I don't know of a term specific to intracellular self recognition. You?

 

No, I don't. I would assume it would be along the lines of immunosuppression as well. The major difference (I thought) was new bodies outside the cell were automatically attacked, whereas things in the cell are not degraded unless tagged. I certainly could be wrong about that. So perhaps a place to start looking would be in the selection methods for what gets tagged for degredation (I believe it's a methylation type tagging, but that's really reachin right now...)