Digital Genetics and Evolution Theory

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sciborg

Registered Member
There is a new book on evolution theory: The Evolution of Aging (2nd ed), ISBN 0978870905, by Theodore Goldsmith that discusses digital information aspects of inheritance and their implications for evolution theory.

Darwin tells us that selective breeding and the corresponding evolutionary mechanism of natural selection both depend on the natural variation of characteristics between different individuals. Variation creates differences for selection to select.

According to the book, natural variation in more complex species is not actually "natural" in the sense of being a fundamental characteristic of all living things. Instead, because of the digital nature of the genetic code, the "natural" intrinsic situation is that members of a species should nominally tend toward being genetically identical. "Natural" variation in complex organisms is actually created and maintained primarily by the action of a long list of complex evolved mechanisms that process mutations including sexual reproduction, genetic recombination, certain behaviors, etc. The degree of variation produced by these mechanisms is described to be much greater than that produced by the occasional propagatable mutation.

This brings up the issue of how all these variation-producing traits evolved. It seems to be a somewhat circular situation: organisms are evolving the means for evolving.

Further, variation considered as an evolved design feature is itself incompatible with Darwinian evolution as generally understood. If organisms are striving to propagate their personal designs, then variation is adverse because it acts to reduce the ability of an organism to do that. A Darwinian organism would rather clone itself and therefore propagate ALL of its design characteristics than dilute its design via sexual reproduction and other evolved variation-producing characteristics. Cloning is the "natural", easier, route given digital genetics.

So how did these characteristics evolve? Wouldn't an organism that had the variation-producing characteristics be at a disadvantage relative to one that did not (such as one that reproduced by cloning) and therefore "select out?" An organism that happened to possess an advantageous design would certainly seem to be less able to propagate that design. Its descendents would likely be less able to survive, breed, etc. than would a clone. Somehow variation-producing characteristics were able to evolve despite fitness disadvantage, apparently because they convey an evolutionary advantage, an improvement in the capacity for evolution.

The question: Is this a plausible idea? If not, where is the fatal logical flaw?

If you accept these arguments, Goldsmith then goes on to suggest that aging, seen as a design feature that deliberately limits life span, also enhances the evolution process in several different ways. If variation can evolve, then aging can evolve even though both are fitness-adverse. This is counter to traditional theories of aging that say that aging is an adverse "side effect" linked to some beneficial and therefore evolvable trait such that there is a net Darwinian benefit. ("Beneficial" means a trait that helps in survival or reproduction as in "survival of the fittest.")

I realize these concepts might seem radical, but they are nonetheless interesting.
 
his brings up the issue of how all these variation-producing traits evolved. It seems to be a somewhat circular situation: organisms are evolving the means for evolving.

Further, variation considered as an evolved design feature is itself incompatible with Darwinian evolution as generally understood. If organisms are striving to propagate their personal designs, then variation is adverse because it acts to reduce the ability of an organism to do that. A Darwinian organism would rather clone itself and therefore propagate ALL of its design characteristics than dilute its design via sexual reproduction and other evolved variation-producing characteristics. Cloning is the "natural", easier, route given digital genetics.
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I see at least two flaws here. The first is the assumption that the means for genetic variability had to be evolved. The introduction of mutation is inherent in the way DNA is duplicated. Even proof reading polymerases introduce errors every now and then. Moreover many mutations are introduced by mutagens, some of witch are produced by the cells themselves during normal metabolism.

Other than that, a lot of organisms clone themselves (e.g. prokaryotes and haploids). Yet apparently a kind of genetic shuffle appears to be beneficial given the fact that a lot of organisms developed polyploidy. And this is the second flaw. Evolutionary theories do not work on individuals. As such it is not necessarily beneficial to pour all of ones genes into the next generation. It is better to maximize the genes that are being retained in following generations. And the ability to shuffle genes might increases the overall fitness of the following generations to allow them to be better adapted and thus creating even more offspring.

However these arguments are not necessary perequisites to accept that aging might have positive effects on evolution. In fact he points several out in his papers...
 
Yes, but the book describes all the mechanisms in genetics that accomplish the variation in complex organisms including multiple chromosomes, unequal crossover during meiosis, sexual reproduction, digital issues, even behaviors. These things are different in more complex organisms, have short-term disadvantages, and certainly seem too complicated to have occurred by accident so therefore have apparently evolved. The issue is not that mutations occur but what happens to them after they occur and how complicated and long-term this process is.

I think classical "Darwin" evolution theory leads to the idea that individuals are key. Individuals have those elusive beneficial mutations. This leads to a short-term view of the evolution process.

Current thinking seems to be that evolution is somewhat longer-term and population oriented as you suggest. The selfish gene theory is an example. The book is taking an even longer-term view such that any feature that improves an organism's ability to evolve might itself evolve. This evolvability argument agrees with your comment below. Most of the arguments that aging is an evolved design feature as opposed to a defect seem to be based on long-term evolvability benefits.

And the ability to shuffle genes might increases the overall fitness of the following generations to allow them to be better adapted and thus creating even more offspring.
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sciborg said:
These things are different in more complex organisms, have short-term disadvantages, and certainly seem too complicated to have occurred by accident so therefore have apparently evolved.
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Don't fall into this trap. Just because you don't understand it doesn't mean it has to due to a reason. It's very complicated. that could be due to a driving force, or due to secondary effects of other driving forces. Or (though unlikely) a reall accident.. Most likely, it's a mixture of all three.

sciborg said:
So how did these characteristics evolve? Wouldn't an organism that had the variation-producing characteristics be at a disadvantage relative to one that did not (such as one that reproduced by cloning) and therefore "select out?"
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No; the logic here is too short sighted. If an individual has a trait that is positive such that it has a .05% higher chance of reproducing than others that don't, but at the same time, the speed of successful* genetic variation allowed for by sexual reproduction is such that offspring gain a 1% chance of reproducing successfully**, then the individual's trait may be subsumed by the population's drive toward sexual reproduction.

*successful here meaning a trait with a net positive effect on survival and reproduction
**successful here meaning a trait with a net positive effect on survival and reproduction of the overall population for the next few generations


amazon link (I've added this book to my wishlist, thanks for the tip!):
http://www.amazon.com/Evolution-Agi...9848834?ie=UTF8&s=books&qid=1173211939&sr=8-1

And a link to my personal theory on why we die:
http://episteme.arstechnica.com/eve...95/m/400001223831?r=219008823831#219008823831
I think aging follows: it forces the parent out of the way in a gradual fashion; perfect in particular for social species like ours, where the old have a time where they *have* to teach the young, because they can no longer do things themselves.
 
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River-Wind: It seems to me again that all the theories mainly hinge on whether evolution is a short-term or long-term process. Aging as part of a design has no intrinsic short-term benefit but does have several plausible longer-term benefits. You seem to have a "medium-term" view, similar to selfish gene theory or kin selection. Strict Darwinists have a short-term view. The book is advancing a long-term view and is essentially a compilation of evidence and arguments supporting that view.

The main way for determining which "term" is most plausible appears to be to look for characteristics that appear to be design characteristics (as opposed to accidental or side-effects) and assess if they could be the result of a short-term or long-term process. The book also describes long-term processes involved in inheritance that seem to directly suggest a long-term evolutionary process. Empirical proof appears to be impossible.
 
Sciborg I found your post very interesting. Goldsmitth's take on aging seems a new one, but his suggestion that natural selection is somewhat unnatural is not a new one. I believe Gould, in his classic The Structure of Evolutionary Thoery talks at length about the evolution of evolution.
There are still many biologists who resist the notion of evolution working on anything above the level of the species. This is short sighted and, as you suggest, short term. I suspect when biologists review Darwin's theory on the second centennial of its publication they will find precious little of the original concept left. That will not mean science does not owe Darwin a huge debt, but by then the debt will have been fully paid off. We shall have a much clearer perception of the complexity, elegance and mechanisms of the evolutionary process. Goldsmith's work is a step towards that point.
 
I'd agree that I'm medium-term; both the short-term (local population level) and long-term (trends in life-forms on a longer scale) seem to place a role, and balance off of each other.

Of particular interest to me at the moment is the evolution of society; as a species moves toward becoming a social species, what behaviors become standardized through instinct to that end? As time moves one, at what point (if ever), does society become more that those innate behaviors defined by bio-chemical drives; when does it take on a life of it's own and start forming rules and accepted behaviors that are not strictly driven by instinct, but must be taught to each new generation.



Back to the OP; how would you describe the term "digital genetics"? I'm having a hard time applying the word digital to the jobs that DNA plays in the cell.
 
river-wind said:
Back to the OP; how would you describe the term "digital genetics"? I'm having a hard time applying the word digital to the jobs that DNA plays in the cell.
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A digital information scheme is one in which information is carried in a sequence of symbols as opposed to one in which information is represented by the magnitude of something (analog scheme). In the digital scheme known as English, "cat" is different from "tac" and different from "cot." Watson and Crick discovered that information defining the design of an organism is handled by a digital scheme in which the sequence of the symbols A, G, C, and T in the DNA molecule carries the information. As with English, CAT is not the same as TAC. The genetic scheme therefore shares a long list of properties that are common to any digital information scheme. This turns out to have some fairly profound impact for evolution theory.

Further, since Watson and Crick we have developed a great deal of detail as to the exact nature of the genetic digital scheme including data on how the digital data varies between individuals and between closely related species. This also has implications for evolution theory. See Chapter 5 in the book (ISBN: 0978870905) for a detailed treatment of these issues.

Ophiolite: Yes, I think evolvability (the "evolution of evolution" or the evolution of the capacity for evolution) is a major key. All of the apparent discrepancies between empirical evidence and classical evolution theory seem to have evolvability explanations.
 
Further, variation considered as an evolved design feature is itself incompatible with Darwinian evolution as generally understood. If organisms are striving to propagate their personal designs, then variation is adverse because it acts to reduce the ability of an organism to do that. A Darwinian organism would rather clone itself and therefore propagate ALL of its design characteristics than dilute its design via sexual reproduction and other evolved variation-producing characteristics. Cloning is the "natural", easier, route given digital genetics.
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Most of this apparent difficulty disappears once the the unit of actual survival is identified as a stretch of DNA. Or the "Selfish Gene".

A stretch of DNA might find much better odds of survival acquiring new (properly screened) neighbors on the genome occasionally - variability in entire genomes within the "gene pool" might easily act to secure the fortunes of each of the various shuffled genes individually. And so forth.

Organisms do not evolve.They live and die. They are not necessarily striving to propagate their personal designs, unless that is what would be best for the genetics that have organized them.
 
sciborg said:
Watson and Crick discovered that information defining the design of an organism is handled by a digital scheme in which the sequence of the symbols A, G, C, and T in the DNA molecule carries the information....Further, since Watson and Crick we have developed a great deal of detail as to the exact nature of the genetic digital scheme including data on how the digital data varies between individuals and between closely related species.
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Umm, no. You’re ascribing discoveries to W&C that were achieved by others. IIRC, the polymer nature of nucleic acid (ribose-phosphate backbone with nitrogenous bases) was discovered prior to W&C. The triplet codon, semi-conservative replication and sequence similarity between organisms was discovered after W&C.
 
Hercules: OK I stand corrected re historical background.

Iceaura: I think a lot of people share my difficulty with Dawkins' selfish gene theory. It makes sense that it would be that way and genes are conserved between species which suggests that it is that way but when you get down to the nitty gritty of A begat B who begat C it still is not clear to me how an individually adverse design property can propagate. Genes don't reproduce themselves, organisms reproduce themselves.

Evolvability seems to me to have two advantages over selfish gene: It explains aging and biological suicide as a selected design characteristic and I think also explains some other observed characteristics that are not explained by standard Darwinism or selfish gene. And evolvability (to me) seems to have fewer problems regarding propagation.
 
sciborg said:
but when you get down to the nitty gritty of A begat B who begat C it still is not clear to me how an individually adverse design property can propagate. Genes don't reproduce themselves, organisms reproduce themselves.
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Few multicellular organisms reproduce themselves by preference or under normal circumstances, and the closer they get to doing that the more problems with the approach show up - Google "inbreeding depression".

All kinds of individually adverse properties have been shown to be theoretically immediate consequences of frequency boosting in the relevant genes - consider the social insects, as obvious examples. Worker bees don't reproduce themselves, by genetically coded prohibition, driven by their nature to work themselves to death instead, yet their genes do, on average - just using them and discarding them, in the process.
 
sciborg said:
Genes don't reproduce themselves, organisms reproduce themselves.
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Yes, but it’s the action of genes that creates an organism’s reproductive drive in the first place! To a very large extent (if not to a complete extent for a large proportion of organisms on Earth), "selfish genes" dictate the behaviour of an organism – behaviour that enables the selfish genes to reproduce themselves. The idea of the "selfish gene", as far as I understand it, is that they are in control by acting through the organism.
 
I always thought that evolution allowed aging because evolution does not care if you live past reproduction, any trait that is a detriment only after you reproduce cannot be removed by evolution.
 
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