Oldest vertebrate fossil found in Australia, scientists say

A question about this 300-gene-difference figure. Is this saying that the human has 300 genes that simply aren't found in the mouse, or that there are, say 120 genes in the mouse that are not found in the human and 180 genes in the human that are not found in the mouse?

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...And we were gettin so damn close. I was holding my breath.

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Rosborne, it was the article's discussion of the cumulative or stochastic nature of evolution and the calculation of the probability of an evolutionary event that I found most interesting. The probability of condition C is calculated not from condition A, but from condition B. This suggests as the article pointed out, that the answer to the question Ican posed, the probability of directionality, is not one big calculation but a myriad of small ones.

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Acquiunk wrote:

Rosborne, it was the article's discussion of the cumulative or stochastic nature of evolution and the calculation of the probability of an evolutionary event that I found most interesting. The probability of condition C is calculated not from condition A, but from condition B. This suggests as the article pointed out, that the answer to the question Ican posed, the probability of directionality, is not one big calculation but a myriad of small ones.

Agreed. I also don't see how natural selection is represented in Ican's equations. That's why I noted the difference between natural *selection* and natural *chance* in the post above. I see how "elimination" is represented, but not "selection".

If the formula isn't representative of the process, then the results are, shall we say... less than compelling. Smile

Thanks,

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Quote:

...And we were gettin so damn close. I was holding my breath.

Well, I have other questions, too -- like just why the gene in question would need to sample 10^100 possible sequences to arrive at one that's useful when genes are not created out of thin air but descend from other genes, especially when the functional differences between different products depends on the identity of only a few amino acids -- but I thought I'd ask one at a time. An exercise in brevity that I could use...

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patiodog wrote:

A question about this 300-gene-difference figure. Is this saying that the human has 300 genes that simply aren't found in the mouse, or that there are, say 120 genes in the mouse that are not found in the human and 180 genes in the human that are not found in the mouse?

"Life Script", Nicholas Wade, Simon and Schuster, 2001, Chapter 3, "The Meaning of the Life Script", page 75, 2nd paragraph:

"The first analyses of the human genome have brought home the long familiar fact that all organisms are intimately related to one another through being twigs on the same tree of life. But even evolutionary biologists may have been surprised by the overwhelming degree of similarity of people to other forms of life at the DNA level. About the only thing people have in common with the mouse is that we are fellow mammals, although separated by 100 million years from our last common ancestor. Yet Venter, having assembled the mouse genome, said that of the 26,000 confirmed human genes he could find only 300 that had no counterpart in the mouse. On this basis he expected the chimpanzee, our closest living relative, to have essentially the same set of genes, with the difference between the two species being caused by variant versions of the same genes."

... Venter, having assembled the mouse genome, said that of the 26,000 confirmed human genes he could find only 300 that had no counterpart in the mouse.

patiodog wrote:

... Is this saying that the human has 300 genes that simply aren't found in the mouse ...

Yes!

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ican711nm wrote:

"Life Script", Nicholas Wade, Simon and Schuster, 2001, Chapter 3, "The Meaning of the Life Script", page 75, 2nd paragraph:

"... caused by variant versions of the same genes."

What does this guy mean when he says "variant versions of the same gene"?

And we already know that genes can affect other genes, activating or suppressing them. Given this, it's possible that even a single gene could cause a cascade which could completely alter an organism, right? Or am I missing something?

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patiodog wrote:

Well, I have other questions, too -- like just why the gene in question would need to sample 10^100 possible sequences to arrive at one that's useful when genes are not created out of thin air but descend from other genes, especially when the functional differences between different products depends on the identity of only a few amino acids -- but I thought I'd ask one at a time. An exercise in brevity that I could use...

First, my Suppose ... was merely my attempt to illustrate why the average number of codons edited in individual events doesn't significantly affect the relevance of the modified lottery model to the standard evolution model.

Second, the total number of possible codon sequences among a sequence of 9000 codons per gene in a sequence of 300 genes is more than 10^4,876,685 which is more than 10^4,876,585 times 10^100.

Third, I wasn't speaking about one gene, I was speaking about a sequence of 300 genes. These genes are not sampling possible sequences. These genes are initially being assembled (e.g., assembled from all or parts of other genes in GL genomes) by editing events of various kinds. Subsequently, these assembled genes are themselves edited to evolve them to something viable and/or more viable.

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Quote:

Second, the total number of possible codon sequences among a sequence of 9000 codons per gene in a sequence of 300 genes is more than 10^4,876,685 which is more than 10^4,876,585 times 10^100.

Sorry if I'm being incredibly obtuse, but why is a gene -- that is, a bit of DNA that is expressed as a biological product -- assumed to average 9000 codons? A very large polypeptide is about 300 amino acids in length.

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rosborne979 wrote:

I also don't see how natural selection is represented in Ican's equations. That's why I noted the difference between natural *selection* and natural *chance* in the post above. I see how "elimination" is represented, but not "selection".

What in fact is natural selection? I claim it is manifest only as that which eliminates. More precisely, it is that which decreases genetic variation.

Please See:

"Mechanisms that Decrease Genetic Variation
Natural Selection"

http://www.talkorigins.org/faqs/faq-intro-to-biology.html

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rosborne979 wrote:

What does this guy mean when he says "variant versions of the same gene"?

J. Craig Ventor sequenced both the mouse and human genome in a tight race with others. Wade was quoting Ventnor. I do not know what Ventnor means by "variant versions of the same gene". Perhaps Ventnor was referring to genetic variation. In that case, he may have been referring to the fact that alleles are different versions of the same gene (please see the same link I gave above)

rosborne979 wrote:

it's possible that even a single gene could cause a cascade which could completely alter an organism, right? Or am I missing something?

I think you are right.

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patiodog wrote:

Sorry if I'm being incredibly obtuse, but why is a gene -- that is, a bit of DNA that is expressed as a biological product -- assumed to average 9000 codons? A very large polypeptide is about 300 amino acids in length.

Not assumed! The average gene of the 300 I've been referring to is observed by Ventnor, et al to average 9000 codons or 27,000 bases. Please see "Life Script ..., 2nd paragraph, page 70.

Genes in general, are found to have lengths much larger and much smaller than that.

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ican711nm wrote:

What in fact is natural selection? I claim it is manifest only as that which eliminates. More precisely, it is that which decreases genetic variation.

Natural selection eliminates selectively, which carries a component value with it. There is a key difference between selective elimination and random elimination. Would you agree?

Evolution is about populations, not individuals.

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But you are assuming that the position of each codon is critical to the function of the gene's product. We do not know this to be the case. Short of an understanding of gene regulation which I do not possess, only a handful of the base pairs need to be in a precise order to result in a functional product. The gene for the beta subunit of hemoglobin, for instance, contains three exons (coding regions) containing a total of 438 base pairs (146 codons) and two introns (noncoding regions) containing a total of 982 base pairs (Nelson and Cox, "Lehninger Principles of Biochemistry," 3rd edition).

And you are supposing that the process is totally random. Here is an example where it isn't.:

Quote:

In vertebrates, at least one set of genes normally undergoes permanent rearrangements of DNA segments. These rearrangements occur in the developing immune system during cell differentiation, the sepcialization in cellular structure and function. Several kinds of genes become rearranged as cells of the immune system differentiate. Let's look at the genes encding antibodies, or immunoglobins...

Immunoglobins are made by cells of the immune system called B lymphocytes... As an unspecialized cell differentiates into a B lymphocyte, functional antibody genes are pieced together using segments from DNA regions that are physically separated in the genome of an emryonic cell.

This is Campbell and Reece, "Biology" (6th ed.) Sorry I haven't had much time to get outside of textbooks the last couple of years. The variable element in immunoglobin formation is the binding site, though there are also a variety of immunoglobins with different functions.

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rosborne979 wrote:

Natural selection eliminates selectively, which carries a component value with it. There is a key difference between selective elimination and random elimination. Would you agree?

Yes! Selective elimination is when organisms or populations of organisms, or species of organisms are not viable or become no longer viable and become extinct. Sometimes this change in viability is traceable to environmental changes. Sometimes it is traceable to self-crippling flaws in the population of organisms. Sometimes it is traceable to some populations eating others.

Random elimination is like being hit with floods or tornadoes, or volcanic erruptions or bolide fallout. Some populations survive and some don't.

From the link I gave above:

"Evolution within a Lineage

In order for continuing evolution there must be mechanisms to increase or create genetic variation and mechanisms to decrease it. The mechanisms of evolution are mutation, natural selection, genetic drift, recombination and gene flow. I have grouped them into two classes -- those that decrease genetic variation and those that increase it.

Mechanisms that Decrease Genetic Variation

Natural Selection

Some types of organisms within a population leave more offspring than others. Over time, the frequency of the more prolific type will increase. The difference in reproductive capability is called natural selection. Natural selection is the only mechanism of adaptive evolution; it is defined as differential reproductive success of pre- existing classes of genetic variants in the gene pool.

The most common action of natural selection is to remove unfit variants as they arise via mutation. [natural selection: differential reproductive success of genotypes] In other words, natural selection usually prevents new alleles from increasing in frequency. This led a famous evolutionist, George Williams, to say "Evolution proceeds in spite of natural selection."

Natural selection can maintain or deplete genetic variation depending on how it acts. When selection acts to weed out deleterious alleles, or causes an allele to sweep to fixation, it depletes genetic variation. When heterozygotes are more fit than either of the homozygotes, however, selection causes genetic variation to be maintained."

This last case makes your point, I think.

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ican711nm wrote:

rosborne979 wrote:
Natural selection eliminates selectively, which carries a component value with it. There is a key difference between selective elimination and random elimination. Would you agree?

Yes! Selective elimination is when organisms or populations of organisms, or species of organisms are not viable or become no longer viable and become extinct.

So my point was that your statement below:

ican711nm wrote:

What in fact is natural selection? I claim it is manifest only as that which eliminates. More precisely, it is that which decreases genetic variation.

Is overly simplistic when defining natural selection. And even more to the point, you must find a way to modify your equations to more accurately reflect natural selection as something more than just elimination. Currently, your equations do not do this.

Note the more detailed definition of natural selection which you extracted from the links you provided:

ican711nm wrote:

"Natural selection is the only mechanism of adaptive evolution; it is defined as differential reproductive success of pre- existing classes of genetic variants in the gene pool.

...

Natural selection can maintain or deplete genetic variation depending on how it acts.

Natural selection is not just elimination, and although it can cause reduction of genetic varieties, it can also allow for the proliferation of others (especially in comparison).

[among other things] In order to account for this, your equations need to be modified to reflect the evolution of populations, not individuals.

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patiodog wrote:

But you are assuming that the position of each codon is critical to the function of the gene's product. We do not know this to be the case.

While there are exceptions I'll not mention now, all my references claim that it is generally true that the chromosome-gene-codon-base sequence determines in germline genome meiosis what shall be procreated. If that is wrong, then the modified lottery model is definitely not applicable to the standard evolution model.

patiodog wrote:

And you are supposing that the process is totally random.

No! Only my modified lottery model assumes that the process of increasing genetic variation is random. I've applied the model to determine the probability that such assumption is true. From the results of that calculation, I infer that assumption is not true and that there is 2ndI (a second influence) in addition to random processes for increasing genetic variation.

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A brief summary of some numbers from the human genome project. http://www.ornl.gov/sci/techresources/Human_Genome/project/journals/insights.html

A couple of things jump out at me:

Quote:

The total number of genes is estimated at 30,000 to 35,000, much lower than previous estimates of 80,000 to 140,000 that had been based on extrapolations from gene-rich areas as opposed to a composite of gene-rich and gene-poor areas.

Wide-ranging estimates, those. Not denying the complete lack of homology between some genes of humans and mice, certainly.

Quote:

Humans share most of the same protein families with worms, flies, and plants, but the number of gene family members has expanded in humans, especially in proteins involved in development and immunity.

Just a reiteration of a point I've been trying to make: genes don't evolve from randomness, but from other genes.

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rosborne979 wrote:

... Is overly simplistic when defining natural selection. And even more to the point, you must find a way to modify your equations to more accurately reflect natural selection as something more than just elimination. Currently, your equations do not do this.

Yes!
Thanks to you, I'm realizing this now for the first time.

"Natural selection can maintain or deplete genetic variation depending on how it acts."

rosborne979 wrote:

Natural selection is not just elimination, and although it can cause reduction of genetic varieties, it can also allow for the proliferation of others (especially in comparison).

You're right. I'll work on it.

rosborne979 wrote:

[among other things] In order to account for this, your equations need to be modified to reflect the evolution of populations, not individuals.

I don't think populations evolve independently of the evolution of their members. I realize that there is much in the literature that says otherwise, but the evidence for such is thin at best.

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patiodog wrote:

Just a reiteration of a point I've been trying to make: genes don't evolve from randomness, but from other genes.

I believe the standard evolution model claim is that generally genes evolve randomly from themselves, other genes, etc. Yes, genes do not evolve from randomness. Yes, genes evolve from genes, etc.

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Oldest vertebrate fossil found in Australia, scientists say

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