DaveRAFinn
Posts: 15
Joined: April 2005
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Further answers to commentators.
C.J.O'Brien
Information on bacterial genes in the human genome can be found simply by using the two phrases "human genome" and "bacterial gene" in a search. It is a relatively recent outcome of the human genome project and is surprisingly underreported, I found it only because I was specifically looking for it. The other area of interest is the way in which the bacterial genes are identified as such. Documents in the area make it clear that recent bacterial genes are a normal feature of the genomes of "higher" forms of life.
Henry J
The situation of the HGT genes showing up is arguably true. It is certainly true that there are inheritance trees that simply cannot be made to function because of the conflicting information available from adjacent related trees. The human genome cannot be resolved into the gene patterns resolve into a simple structure based on geographical separation and race. Because the writers on the subject are operating within an environment where assumption of neo-Darwinism is mandatory, if you wish to keep your job, they do not report on whether or not the observed pattern can be simply resolved on the assumption of HGT. My suspicion is that it can be, but I do not have the time, resources or energy to undertake the research myself.
Your calculation on rate of gene change is unfortunate. (I took first humanoid rather than preceding ape for the time interval, it is of little import, the answer comes out the same for one million or ten million years). Your calculation implicitly assumes that the modern human genome was present and could be used to determine which of the base pairs should change and in which way that should change. The whole point of natural evolution is that the future genomes are not pre-determined. There has to be sufficient genetic change to account for not only the actual change which did occur but also all the equally probable changes which did not occur. Unless you can think of some good reason why only the changes which did occur should occur you need to include other possible changes in your calculation and then the rate is (spectacularly) too low.
Swoosh
HGT is very different its operation from "traditional" genetic change. It is therefore essential that in discussing it you avoid taking assumptions from "traditional" theory without checking first that they apply in the HGT case. A surprising number do not, mostly because the "resource" for genetic change is an external pool and not the internal genome. For example you assume that the rate of HGT would depend on the number of places to mutate, because this is the case for neo-Darwianian mutation. A moments thought will convince you that for HGT the number of places to mutate in the recipient species can have no effect on mutation in the donor species and the number of changes involved in HGT is one, the insertion of a gene, so that the presence of 10, 100, 1000 or 10,000 possible insertion points will have no effect whatever on the rate of HGT, this is determined by the content of the pool of available genes and the rate at which the genes find their way through the various barriers that normally keep then out of the genome. This, incidentally, provides a check which you might care to make on my claims. For neo-Darwinian evolution the rate should depend on the length of the chromosomes, as you indicate and therefore the proportion of new species arising from neo-Darwinism vs HGT can be estimated by looking at species with particularly long or short DNA and comparing the extent to which they are associated with fast or slow evolution of species. Be my guest and try it, I would be interested to see what you come up with.
The point about the abandon ship analogy is not the matter of choice. The point is that in that situation, as in many others, the probabilities are different from "normal" and therefore the optimal strategies are different. Doing nothing is normally an option with considerable survival value. In the case of extinction this is not true. This is what I mean by the normal rules being different. Your statement that rates of mutation are basically constant is an oversimplification. For most forms of mutation this is essentially true, as long as a reasonable time frame is used. However HGT differs from most forms of mutation in being mediated. The incoming gene has to be passed through the outer cell wall, the nucleus wall and then be incorporated into the chromosomes. There is a lot of cell chemistry involved and this can be affected by temperature, acidity, salinity, magnetic or electric fields etc etc. The assumption of a uniform rate cannot be made in this case. The point of the argument is that if, as a result of some random mutation, an organism ends up with some coupling between some feature of the environment that correlates with extinction and the operation of the mechanisms involved in HGT which has the overall effect that the rate of HGT increases under extinction then this mutation will be selected for under normal rules of evolution. It is a way of being "fitter", it increases the probable number of descendants. This peculiar characteristic is naturally selected for the reasons I have given. This being so one may expect that an increasing proportion of new species will have inherited this characteristic. The process is similar to arguing that it is useful for a member of a species to be able to locate other members of its species and that therefore you would expect a substantial proportion of species to emit a chemical, audible or visible sign which other members of the species were equipped to detect and use to find each other. Those species with this characteristic can survive with more sparse populations than those that cannot therefore the mechanism is selected. The characteristic can be analysed in terms of its probable success as a strategy without any suggestion that there was any though that went into its adoption. Genetically encoded strategies are a legitimate form of inheritable characteristic, this is, after all, why evolution tends toward greater complexity. There is no suggestion that species are choosing to increase the rate of mutation in any stronger sense that one might say a seed chose to germinate. Simply that the mechanism is present purely because any organism with it will tend to leave more descendants than one without. I left neutral mutations out because they do not significantly affect the argument, and they are, in the case of the massive injection of genetic information in HGT, considerably rarer than for single changes with DNA normally discussed.
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