Adaptations only occur from *sets* of genetic information, not from individual mutes

[sfs]

I can support my idea and still not be able to teach it in a forum.

" Our observations suggest that the mutation rate has been evolutionarily optimized to reduce the risk of deleterious mutations. "
http://www.nature.com/nature/journal/v485/n7396/full/nature10995.html?WT.ec_id=NATURE-20120503

By the way, I forgot to mention: thanks for providing support for your position. Too often people just post stuff and evaporate when challenged.

 

[SkyWriting]

Not support for your statement, I'm afraid. You said that there were programmed mutations, which yield useful variation in a population, and also non-programmed mutation that leads to bad stuff. That breakdown is simply not consistent with what is known about genetics. What the (rather out of date) book you cited is talking about is an increase in all kinds of mutations, good and bad, when bacteria are placed under stress....What you're talking about would be news indeed but is not, alas, true.

I'd be happy to find better quality news for you then.





"This work demonstrates evidence for a universal, persistent and iterative feedback mechanism between the environment and heredity, whereby acquired variation between cell divisions can outweigh inherited variation."
]

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"Although mutation is still often casually described as a ‘random process’ [Gerrish, 2002; Ayala, 2007; Kondrashov and Kondrashov, 2010], there is now abundant evidence that the process of mutation is far from random. Indeed, over the last 20 years, it has become ever clearer that human gene mutation is frequently a highly sequence-specific process, irrespective of the type of lesion involved. Further, we have come to understand that certain DNA sequences are inherently mutation-prone by virtue of their base composition, sequence repetitivity, epigenetic modification, and/or characteristic secondary structures, and hence have a tendency to mutate in very specific ways."

-----------------------------------------------------------------------

"Normal genetic variation of the human foot: A revised populationist approach is proposed and supported by paleoanthropologic evidence that reflects a picture of emerging suitability for bipedalism that is driven by natural genetic divergence."

 

[SkyWriting]

By the way, I forgot to mention: thanks for providing support for your position. Too often people just post stuff and evaporate when challenged.

A few of the people I reply to as well.

 

[SkyWriting]

This is more relevant than your other citation but it still doesn't support your claim. This paper describes evidence that mutation rates are lower in critical genes, reducing the rate of deleterious mutations. It's quite interesting, but not really all that surprising -- there is broader evidence for evolution of mutation rates, and the structure of the genetic code itself is well known to make deleterious mutations less likely.

What the paper doesn't do is make your claim, which is that some mutations are programmed because they are potentially useful and that deleterious mutations are not programmed. Rather, they find that rates of all mutations, good and bad, are higher in some regions and lower in others. In fact, it specifically rejects the possibility that mutation rates are higher where new variation would be useful, noting that antigen-producing genes (where variation is very useful for evading host immune systems) do not have elevated mutation rates. Instead, what seems to be happening is that there is strong selection against having mutations in certain genes, since they're almost always deleterious, and that mechanisms have therefore evolved to keep mutation rates unusually low there.

That supports my position perfectly. Except I claim the process is brilliantly masterminded, and you prefer the dumb-as-a-rock explanation for the same results. I get that.

 

[SkyWriting]

Based on your complete failure to support your claim about mutations, is it fair to conclude that you had no idea what you were talking about?

Or I work full time and have a full class load as well.
One can never accurately assume anything.

 

[sfs]

I'll take these in separate posts.

"This work demonstrates evidence for a universal, persistent and iterative feedback mechanism between the environment and heredity, whereby acquired variation between cell divisions can outweigh inherited variation."

This paper is mildly interesting, but it suggests wildly inflated conclusions that are not sustained by their results -- explaining perhaps why it was published in PLoS One, not exactly a journal where one puts path-breaking research. Have you read the paper? Where did you get the citation?

I'm afraid this paper also does not support your claim. The authors present evidence that mutation rates are higher in genes that are expressed during parts of the metabolic cycle that make the cell a more chemically reactive environment. This is sort of interesting, as a detailed look at details of the mechanisms of mutation, but does nothing to suggest that some mutations are programmed and that bad mutations are not. Contrary to the authors' suggestions, there is nothing remotely novel about a mechanism for mutations occurring between cell divisions, or about the environment influencing mutations. It's well known that transcription is mutagenic, and this process is simply an embellishment of that fact.

 

[sfs]

"Although mutation is still often casually described as a ‘random process’ [Gerrish, 2002; Ayala, 2007; Kondrashov and Kondrashov, 2010], there is now abundant evidence that the process of mutation is far from random. Indeed, over the last 20 years, it has become ever clearer that human gene mutation is frequently a highly sequence-specific process, irrespective of the type of lesion involved. Further, we have come to understand that certain DNA sequences are inherently mutation-prone by virtue of their base composition, sequence repetitivity, epigenetic modification, and/or characteristic secondary structures, and hence have a tendency to mutate in very specific ways."

All true and quite standard. Remember, though, that your claim was that good, variation-producing mutations were programmed, while bad mutations where outside the programming. Now take a look at what you're actually citing here; the paper is "On the Sequence-Directed Nature of Human Gene Mutation: The Role of Genomic Architecture and the Local DNA Sequence Environment in Mediating Gene Mutations Underlying Human Inherited Disease". These sequence-directed mutations, the ones that you're claiming are programmed, are identified in the title as being disease-causing; in fact, they cause a wide range of horrific diseases. How exactly does this support your claim?

 

[sfs]

"Normal genetic variation of the human foot: A revised populationist approach is proposed and supported by paleoanthropologic evidence that reflects a picture of emerging suitability for bipedalism that is driven by natural genetic divergence."

?? I don't have access to this paper, but what makes you think it says anything in support of your statement? (And what makes you think that the Journal of the American Podiatric Medical Association is a reliable source for information about evolution?)

 

[sfs]

That supports my position perfectly. Except I claim the process is brilliantly masterminded, and you prefer the dumb-as-a-rock explanation for the same results. I get that.

I'm sorry, but what I'm saying and what you claimed are quite different. You said that some mutations were programmed (to provide variation) and that really bad mutations were outside that programming. That claim is not true, based on what I know about genetics and mutation, and these kinds of distinctions are important in science.

It is true that there are factors that reduce the rate of deleterious mutations, and there are factors that make useful variation more likely (although I don't think you've mentioned any of the latter). An example of the first is that the genetic code is arranged in such a way that the most common mutations, chemically speaking, tend not to change the amino acid that a gene codes for. An example of the second is the subtelomeric placement of var genes in malaria, which makes their duplication (quite useful for evading the human immune system) more likely; another is mutator strains of bacteria that mutate faster, and thus can adapt to novel and difficult environments.

In all the cases I know of, however, you can't get the good without the bad. The genetic code arrangement also reduces mutations that woud provide useful variation; var genes are more likely to be duplicated, but also more likely to be lost (a deleterious mutation); mutator strains also acquire deleterious mutations more rapidly than normal strains.

This isn't a matter of design vs. darwinism; it's a matter of getting the facts right.

 

[SkyWriting]

I'm sorry, but what I'm saying and what you claimed are quite different. You said that some mutations were programmed (to provide variation) and that really bad mutations were outside that programming. That claim is not true, based on what I know about genetics and mutation, and these kinds of distinctions are important in science.

It is true that there are factors that reduce the rate of deleterious mutations, and there are factors that make useful variation more likely (although I don't think you've mentioned any of the latter). An example of the first is that the genetic code is arranged in such a way that the most common mutations, chemically speaking, tend not to change the amino acid that a gene codes for. An example of the second is the subtelomeric placement of var genes in malaria, which makes their duplication (quite useful for evading the human immune system) more likely; another is mutator strains of bacteria that mutate faster, and thus can adapt to novel and difficult environments.

In all the cases I know of, however, you can't get the good without the bad. The genetic code arrangement also reduces mutations that woud provide useful variation; var genes are more likely to be duplicated, but also more likely to be lost (a deleterious mutation); mutator strains also acquire deleterious mutations more rapidly than normal strains.

This isn't a matter of design vs. darwinism; it's a matter of getting the facts right.

We agree perfectly then.

 

[SkyWriting]

?? I don't have access to this paper, but what makes you think it says anything in support of your statement? (And what makes you think that the Journal of the American Podiatric Medical Association is a reliable source for information about evolution?)

I assume that evolution (CHANGE) can be addressed from any perspective. If it's correct, I mean.

 

[SkyWriting]

All true and quite standard. Remember, though, that your claim was that good, variation-producing mutations were programmed, while bad mutations where outside the programming. Now take a look at what you're actually citing here; the paper is "On the Sequence-Directed Nature of Human Gene Mutation: The Role of Genomic Architecture and the Local DNA Sequence Environment in Mediating Gene Mutations Underlying Human Inherited Disease". These sequence-directed mutations, the ones that you're claiming are programmed, are identified in the title as being disease-causing; in fact, they cause a wide range of horrific diseases. How exactly does this support your claim?

"...Architecture.. Mediating...Mutations.."
Design.

 

[SkyWriting]

I'll take these in separate posts.

This paper is mildly interesting, but it suggests wildly inflated conclusions that are not sustained by their results -- explaining perhaps why it was published in PLoS One, not exactly a journal where one puts path-breaking research. Have you read the paper? Where did you get the citation?

I'm afraid this paper also does not support your claim....

I never expect agreement. I just present my case as I see it. That is my only calling.

 

[SkyWriting]

?? I don't have access to this paper, but what makes you think it says anything in support of your statement? (And what makes you think that the Journal of the American Podiatric Medical Association is a reliable source for information about evolution?)

I try to stick to open sources. Sorry.

 

[sfs]

We agree perfectly then.

If by "agree" you mean "disagree", then yes . . . I agree.

 

[sfs]

I try to stick to open sources. Sorry.

I have no problem with most non-open journals -- I access journals through Harvard, and they have as good a library system as anyone in the world, especially for biomedical stuff. If they don't carry a journal, well, it's probably not a cutting edge paper you were looking for anyway.

 

[sfs]

"...Architecture.. Mediating...Mutations.."
Design.

No defense of the claim you made, then. (Also, both here and in reading the New Testament, you might want to learn to recognize non-literal language better.)

 

[sfs]

I assume that evolution (CHANGE) can be addressed from any perspective. If it's correct, I mean.

Sorry, that still doesn't mean you should be looking for information about mutational processes from podiatrists. (Nor does it explain what this paper has to do with supporting your claim.)

 

[sfs]

I try to stick to open sources. Sorry.

I'd still like to know where you got these citations and whether you've read the papers or not.

 

[SkyWriting]

I'd still like to know where you got these citations and whether you've read the papers or not.

I believe I did read each one. Though on occasion, I feel an abstract alone covers the topic well enough.

One person challenged that there were no peer reviewed articles on the "Garden of Eden" and I countered with 10 - 20 abstracts on the topic. On that occasion I didn't read any of them.

I try to stick to Pubmed central because of the available free text.

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