3/20/2005

Evolution, The Process by Carl Cox

The Fossil Record

As part of Darwin's theory on Origin of Species, he proposed that random, gradual, continuous changes was the mechanism for changing one species to another. But even as he was formulating his theory he had information that showed species remained the same for long periods of time. He explained the lack of fossil that recorded the speciation event to the incompleteness of the fossil record, and persisted in teaching the gradual change as the mechanism for evolution. Biologists for over 100 years have diligently sought for those fossils which would verify that theory, but with extremely limited success.

Geologists, not trained as biologists, did not know they were supposed to find gradually changing fossils, so they identified what they found. They noticed that world wide certain fossils appeared in certain strata of rock, and when they found the means to accurately date the strata/fossils, they used the fossils as markers for dates in their explorations. The fossils they found remained the same for the duration of the time they were found, a time of up to several million years.

As time went on, paleontologists realized the same thing, that the fossil record showed organisms in stasis, or unchanging. Stephen Jay Gould and Niles Eldredge were among the major proponents of this idea, starting about 30 years ago. An article in Models in Paleobiology in 1972 was an early attempt to inform the professionals of what the fossil record showed.

But Darwin's theory still reigns supreme, and in order to explain how speciation could proceed without leaving a fossil record the current theory was proposed. It states that a small group of a larger population found themselves isolated, in a poor environment for their species. The environmental stress made many of the hidden mutations beneficial, so much change occurred in a geologically short while in this small population. The small area and the short time made fossils very difficult to find.

I have many questions about the proposed method of speciation.

The large group of the species had a great body of mutations to draw upon, but we are told that the large group tends to stabilize the population, that changes would die out rather than become fixed. But once the small population became detached, mutations would rapidly proceed to fixing.

I find this reasoning rather strange. I have read in biology texts the formulas for fixing of mutations, which takes into account the added benefit of the mutation and the size of the population. Those formulas are presented as being quite precise, once the additional benefit of the mutation is known. While the time to fixation is longer in a large population, it still seems to proceed to fixing. Recently the idea of neutral mutations has surfaced, and it becomes a random walk to fixation. In larger populations, I assume that the random mutations would not likely be fixed, thus supporting the proposal for speciation. However, beneficial mutations should still be
fixed, and these are the ones most likely to play a part in speciation.

So, according to the theory, a small group would be separated from the main body, and the mutations which were neutral in the main body would become beneficial in the stressed environment. But now you only have a small group to mine mutations from, so the process of speciation could slow way down.

The mutations that would not fix in the large group now fix quickly. This seems to be a contrived explanation, and is difficult to support. The large quantity of mutations available in the large group are no longer available, which makes the speciation process less probable. As soon as the residual mutations are fixed, the speciation process would almost grind to a halt.

Species are different from other species. Each species is different enough that paleontologists can assign markers to identify them from other similar species. But looking at the small group that are proposed to do the speciation. We find that in the best case, they have fixed several beneficial mutations, and are slightly different from the large group, but not yet different enough in the several markers to be considered a new species. Why does speciation not stop there?

To realize the importance of this point some discussion of speciation is needed. As we look at the fossil record, we note that every step in a species history is a discrete step. Tooth shape is one identifier of a species, and as I understand it is a major part of the new species. (I will have more to say about the size of step in speciation later in this paper.)

The small group that is separated from the main body of the species in question is a major player in speciation. However, in many species the small isolated group is the rule rather that the exception. A stressful environment is also common. Over a million year period it is probable that stressful environments will occur many times, so what would trigger a speciation event after such a long period of time with similar stresses and other conditions?

In trying to analyze the detailed process for speciation, it seems the most logical scenario is that mutations would gradually be accumulated in the group, but the mutation that finally made the difference would most probably be in a single individual. Just how a spouse would come by the same mutation is a great problem, but if we assume it could then we have a group that cannot mate with the others left behind. A major problem here is the amount of variation in the species. The evidence I have seen indicates that the new species has the same variation that the previous species had. But a bottleneck of one or two leaves behind most variation. The alternative is for the whole small group to change one mutation at a time, but this
requires much time. It also requires a viable path for each character that is different in the successor species from the equivalent character in the parent species. For the number of DNA bases that must be changed to describe the new species, it is almost impossible. To get an idea of the number of DNA bases that are different between species, it is instructive to follow such examples as Homo and chimp. The DNA clock studies give an estimate of the time when both species had the same ancestor, and the number of speciations since then in both lines can be intelligently guessed at. The number of DNA base differences is also known, so simple divisions gives a ball park number of the number of changes per speciation. The amount of 'junk' DNA is also known, as well as the number of places where 'don't care' mutations can be made. That leaves a guess as to the number of working bases
that change in each speciation. Recent studies have shown that some genes have more changes than has been expected by the current theory.

The above discussion shows that there are problems with the New Synthesis of Darwin's theory, and attempts to come up with answers to the problems sound contrived and not very convincing.

A proposal

What kind of speciation process would answer the fossil record? What predictions could be made from such a process? Here is the answer to both questions.

Speciation in a single generation would fit the fossil record completely. For speciation, only the necessary genes would be changed, and there would be multiple changes in those genes, which would preserve the variation found in the parent species. Now a definition: Speciation has several meanings so I have chosen microevolution and macroevolution to define exactly what changes make speciation.

This definition is based entirely on DNA. Microevolution is made up of random mutations, the source of SNPs.(Single Nucleotide Polymorphisms) It can also include any of the mistakes made in division of the germ cells, improper division and recombination of the chromosomes, or the transfer of parts of chromosomes (DNA material) by bacteria or by other methods that science has found. Variation in species is made up by microevolution. The finches that spread around a lake in Russia, and have gone so far that the furthest around the lake cannot breed with those near the start, even though each adjacent variation can interbreed, another example of microevolution.

Species that spread over a countryside with gradual changes in coloration or habits are also microevolution.

Macroevolution is multiple DNA base changes within a single gene. This could be read as multiple microevolution, but the rate of the DNA clock is known within some rather broad error band and macroevolution would far exceed that known rate. Also, the multiple changes are only in a few genes, while microevolution is in most genes.

In the fossil record, one species disappears and another may appear in it's place. Thus macroevolution completely fits the fossil record.

Predictions

About 5 years ago I predicted that studies of developing embryos would identify the genes that determined such things as the shape of the tooth, and at that time comparison of those genes in closely related organisms would show that multiple bases have been changed between the two. Last year, sequencing of the chimp/Homo 20/21 genes proved that prediction. The researchers, according to news reports, discovered some genes that have more changes than were expected between the two. I have not been able to get details, but this is exactly what I predicted, and what Darwin cannot
explain.

How much change for speciation - is there any guidelines? I say, yes. According to the proposal, these changes take place in a single generation, so the new embryo is a different species from the mother. The change in a successor species is the maximum that can be made, considering these constraints:
1. The new species cannot disrupt the parents immune system, and vice versa.
2. The new species cannot be too big for the parent to bear, if a mammal or
egg laying animal.
3. Habits of the new species must be compatible with the parents, as they
must teach them while young. (For species that rear their young.)
4. Appearance of the new species must be compatible with expectation of the
parents. They cannot look like some foreign species.

While we do not know all about the habits and environment of each step of all organisms, we can make good guesses enough to see that the species in the fossil record would generally follow the above guidelines.

There are many other examples in the fossil record that give great problems for Darwin, but fit in easily to this proposal. Also, many evolutionary biologists have made statements of problems with Darwin's new synthesis, but this proposal answers those concerns very well.

One remaining problem: I do not have a mechanism for the process of macroevolution. But if the fit with the fossil record and the predictions are acceptable, the good biologists can probably find a mechanism. I note that Einstein's work with the speed of light has no mechanism for the limiting speed, or the properties of matter nearing that speed, and has been that way for most of 100 years, so the mechanism is desirable but not mandatory if everything else fits.

Carl Cox
Mansfield, MO

6 Comments:

You should be honored, you are the first theory that we are even dealing with on this site. I may be jumping the gun a little bit by posting it for you, but I think that group participation is more important than following any kind of "syllabus."

"What needs to be said now, loud and clear, is the truth: that the theory of puctuated equilibrium lies firmly within neo-Darwinian synthesis. It always did. It will take time to undo the damage wrought by the overblown rhetoric, but it will be undone." - Richard Dawkins

We should also distinguish between genotypic change (which is utterly random and gradual) with phenotypic changes (which may not be). This is why genetic provides so much better evidence for evolution, not the fossil record which creationists simply can't let alone.

"Darwinians, with their traditional preferences for gradualism and continuity, might not shout hosannas for large phenotypic shifts induced rapidly by small genetic changes that affect early development; but nothing in Darwinian theory precludes such events, for the underlying continuity of small genetic changes remains." - Gould

"One may be excused for retorting: 'so what else it new?' Has any biologist ever denied it? But... progress in science often demands the recovery of ancient truths and their rendering in novel ways." - Gould

We should also mention a few more things:
1) Not all species reproduce sexually. But once they do, they are usually "intelligent" enough to recognize other members of the same species. This brings about

2) The Baldwin effect. "What Baldwin discovered whas that creatures capable of 'reinforcement learning' not only do better individually than creatures that are entirely 'hard-wired'; their species will evolve faster because of its greater capacity to discover design improvements in the neighborhood." - Dennett

When a particular organism stumbles on a Good Trick, genotypically speaking, neighboring members of the same species will attempt to phenotypically imitate this mutation. Thus, those organisms whose future genotypic mutations are closer to the original Good Trick, will be better suited for acquiring and taking advantage of the Good Trick. Thus, genetic evolution will tend in the direction of the Good Trick faster than it would otherwise.

Do not be confused, this is not Lamarckianism where in phenotypic redesign produces genotypic redesign. It is the favoring of certain genotypic mutations which still must come gradually and randomly.

That all said, I don't see how this attempt at reconciliation, if that's what it is, reconciles anything. It just seems to be an attempt to say that God took some part, but this is hardly the biggest issue regarding evolution. Perhaps you could elaborate on how this view might help in some of the points mentioned by Mc Conkie in the first post.

3/21/2005 12:56:00 AM  

Carl,

Can you provide more information about the research you say supports your prediction? A link to the new article would be fine. I want to see if I can get the article so I can better understand your argument.

3/21/2005 09:31:00 AM  

Jared asked for more information.

Gould, in his big book, went into much more detail about the stasis found in the fossil record. Also I have a quote from another paleontologist in The Book of Life, edited by Gould, p100 that says the fossil record does not show the gradualism that Darwin predicted. You will also note that the post, Evolution, the Process, takes to task the hypotheses used by Gould to explain the absense of fossils for the rapid speciation he proposed. I believe that proposal is on very shaky ground.

I think Jared was asking for more information on my predictions. There are no other references I know of for those predictions. They have been developed entirely by me. I have been unable to find any professional evolutionary biologist that I could discuss these ideas with.

Jeff commented on phenotype vs. genotype. I am convinced that the only type of change that can be inherited is genetic, so I focus on that. It is the details of genetic change that I have been pondering, which has led me to the proposal you have seen.

Carl

3/21/2005 07:41:00 PM  

Carl,

Actually I was interested in the paper you cited that supports your predictions. You said,

"Last year, sequencing of the chimp/Homo 20/21 genes proved that prediction. The researchers, according to news reports, discovered some genes that have more changes than were expected between the two. I have not been able to get details, but this is exactly what I predicted, and what Darwin cannot
explain."

If I can, I'd like to track the paper down. Do you have any more clues that would help me?

3/21/2005 08:45:00 PM  

Unfortunately I did not write down the source, but about all the reference I saw said was that there were more changes than expected, or similar statement, in a few of the genes. Google should find some reference. I don't remember if chromosome 21 was the chimp or homo, but the other one was 20. I never saw the original paper, which I would have liked very much to see.

Carl

3/22/2005 08:30:00 PM  

I found the reference to the comparison of the chimp chromosome 21 to human 20, but it was in Japanese language and I couldn't find any English version. However, chimp 22 and human 21 were compared, with almost the same result. It was reported in Nature 429, p382-88 (and a letter earlier in that issue) 27 May 2004.

Here is one quote of interest:
We found large human insertion/chimp deletion in the first introns of NCAM2 (~10 KB) and GRIK1 (~4 KB) genes, which are both related to neural functions.

IMO this fits the prediction of more changes in a few genes than can be explained by Darwin's gradualism. It would be enough change to be noted as not expected by the researchers.

Carl

3/24/2005 08:50:00 PM  

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