On the Origin of Species by Means of Natural Selection
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The remarkable fact about Darwin's classic is that it covers every topic under the sun except for the title problem: the mechanics of creativity in Nature and, in particular, "the origin of species." There has been progress with the first part of the unaddressed mystery (what drives speciation in the world that has already been populated by species). There has been almost no progress on the origin of the Darwinian Threshold. Why are there species to begin with?
The question has never been convincingly answered or even intelligently asked. It is worse than that. It is unclear where to begin looking for the answer. Actually, it is worse still. It is not clear that the answer might exist, if you discount "it just so happened" as the answer. Yet I'll try to answer this question to the best of my ability. Of course, it will be pure speculation. Maybe someone will offer a better answer. I do not want to sweep it under the carpet.
Only the eukaryotes have species, and the alternative is before our very eyes: the prokaryotes. Bacteria and archae do not have species, the ecotypes freely swap their genes given the opportunity. There is common gene pool from which one can borrow and to which one can contribute. It obviously works, and it works extremely well: they rule this planet; everything else is marginalia. The eukaryotes do not swap with this pool, though. Each species is a genetic universe upon itself. Surely, the eukaryotes are much more complex than the bacteria, but this, in itself, does not explain speciation. There is no reason to believe that the complexity excludes free swapping of one's genes. After all, we do have sex, right? Why can't we have sex with any other species? The "answer" is that the other species had so much diverged from our own that it is no longer possible for us two to have viable progeny. But that's circuitous logic: the species have diverged precisely for the lack of this cross-breeding ability. It is speciation itself (the creation of artificial barriers to breeding) that enforces the species, and this order of things exists only in the Eukarya. Isn't it strange? Maybe it is just the complexity? Here is Woese:
were [cellular] organization simple and modular enough, all of the componentry of a cell could potentially be horizontally displaceable. Suppose that the primitive ancestors of modern cells were of this nature. That would mean that at its beginning, cellular evolution would have been driven in the main by gene transfers. In its subsequent evolution a primitive cell of this type would become ever more complex, idiosyncratically connected, and thereby increasingly refractory to horizontal gene acquisition, especially the more spectacular forms of it. In other words, there would come a stage in the evolution of cellular organization where the organismal genealogical trace (recorded in common histories of the genes of an organism) goes from being completely ephemeral to being increasingly permanent. This point in evolution, this transition, is appropriately call the “Darwinian Threshold.” On the far side of that Threshold “species” as we know them cannot exist. Once it is crossed, however, speciation becomes possible. The Darwinian Threshold truly represents the Origin of Species, in that it represents the origin of speciation as we know it. It could represent a point in cellular evolution where something drastic occurs. I posit the latter. The cell is a complex dynamic system. As its connectedness increases such a system can reach a critical point, where a phase change occurs, where a new, higher level organization of the whole emerges. That, I suggest, is what the Darwinian Threshold represents, a hitherto unrecognized phase change in the organization of the evolving cell. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC124369/
So we are dealing with one of the most momentous transformations, and no one has any idea what this "something drastic" could have been. The latent potential for speciation might have existed well before it occurred, but decoupling from the common genetic pool would be expected to decrease(!) fitness. If the goal of evolution is producing increasingly fit organisms, the speciation should never had occurred in the first place.
The usual take on eukarogenesis is symbiogenesis. The protoeukaryon archae found an ingenious solution to the inherent limitations of all bacteria: as they store energy as a chemical gradient across their membranes, they have to be small. The host had internalized a bacterium and started using many of such endosymbionts to produce a lot of energy by respiration. Because the latter produces radicals that can easily kill the host cell, the operation of mitochondria had to be tightly regulated and controlled, and their genes passed to the host's nucleus. This increased the demands on the fidelity and the amount of replicating DNA. The host had the machinery for this feat, and the mitochondria provided the energy needed by this costly machinery. For the first time ever, vast amounts of DNA could had been copied with high fidelity. The bacteria need to replicate very rapidly, and they keep their genomes as lean as possible, shedding the DNA that is not neeeded, hoping that another bacteria would pick it up. The protoeukaryon did not need to shed anything. It was accumulating the goodies. Its dramatically increased capacity to copy DNA was immediately exploited by viruses and selfish genetic elements that overrun the genome, but the eukaryon was able to tolerate even this abuse, thanks to its unconstrained energy source. It pursued the classical K-strategy: slow replication, high quality vs. r-strategy: rapid replication, low quality. However, having the potential ability to speciate does not explain speciation. There were still the distinct advantages to swapping genes. Then it all stopped. One idea I've heard is that such potentiality is binding: if there is a physical barrier, the differences between subpopulations would grow so great over time that the gene-swapping protocols would become different and the speciation will occur. I think this is wrong. Such speciation has never happened in the Prokarya, despite very formidable barriers, and the molecular machinery of sex is similar for all protists. The breeding barrier was not spontaneous; it was erected. So the question is, to what purpose? This purpose was not selfishness of the individual, as there was no "individual" at that point. So it was for the greater good of all. But how speciation can be this common good?
It was the logical conclusion of the eukaryogenesis itself. Bacteria do not parasitize on bacteria, as they are too small for such invasions (there are rare exceptions). However, the sheer size of the protoeukaryon made such infections possible. Furthermore, as the latter internalized its bacterial food, the bugs were invited to take advantage of their predator. "The Struggle for Life" has finally began, and it began on unfavorable terms for the Eukarya. The bacteria can live on uranium ore, gasoline, and even crystalline penicillin; living off the eukarya was unproblematic. The only consideration for letting the host to stay alive was (and still is) having someone to feed you. Now, imagine the world with bacterial infections, but no speciation. We get the Red Queen problem.
The bacterial virulence is adjusted to its host and other parasitic bacteria living in the host, but new strains appear constantly. Some of these strains will try to take the undue advantage over other bacterial strains possibly killing the host in the process. The very logic of the parasitism and evolution makes this situation inevitable: bacteria can adjust their virulence only through trial and error. If there are no barriers to eukaryote interbreeding, the killer infection will spread accross the entire population and kill everyone. This is the situation in which speciation is rewarded. Erecting artificial barriers helps to curb such pandemics, as the accumulated differences in the cellular machinery make this bacterial spread limited. The interspecies jumps are devastating but relatively rare which improves the chances for all parties involved. Divided, we stand: speciation IS a communal advantage for the eukaryotes.
One can ask, why does not this logic does apply to bacteria and their phages: why wouldn't bacteria speciate? I think that the reason is that the phages are not free living: they are produced by the bacteria themselves. Furthermore, the bacteria can outpace the phages, but the slowly replicating eukaryons cannot outpace their bacterial parasites. Finally, the bacteria use heritable immunity that relies on high variability and imprecise copying. Again, the eukaryons can't quite do that. The K-strategy limits the choices and makes certain outcomes foreordained. I think that speciation was one of such outcomes. The host-parasite dynamics involving r- and K-strategists inevitably leads to it. The eukaryotes have to be divided into species separated by barriers they themselves erect and maintain, as otherwise the first nasty bacterial infection will do them all in before the bacteria readjust their virulence. For the bacteria, this is business as usual, but for the Eukarya it would be the end of the road. They cannot afford not being species.
In short, I suggest that the speciation was a communitarian means of giving everyone a sporting chance through building robust diversity hampering bacterial parasitism. It was one of the first attempts at making this place a better world, and it ended like other such attempts. It assumed the logic of its own, producing the world as we know it, where a species is against a species, and an individual is against an individual.
Why are there species?
лет немалое число
по бокам возникнут ушки
вспухнет мозга вещество
http://aptsvet.livejournal.com/585550.html
The remarkable fact about Darwin's classic is that it covers every topic under the sun except for the title problem: the mechanics of creativity in Nature and, in particular, "the origin of species." There has been progress with the first part of the unaddressed mystery (what drives speciation in the world that has already been populated by species). There has been almost no progress on the origin of the Darwinian Threshold. Why are there species to begin with?
The question has never been convincingly answered or even intelligently asked. It is worse than that. It is unclear where to begin looking for the answer. Actually, it is worse still. It is not clear that the answer might exist, if you discount "it just so happened" as the answer. Yet I'll try to answer this question to the best of my ability. Of course, it will be pure speculation. Maybe someone will offer a better answer. I do not want to sweep it under the carpet.
Only the eukaryotes have species, and the alternative is before our very eyes: the prokaryotes. Bacteria and archae do not have species, the ecotypes freely swap their genes given the opportunity. There is common gene pool from which one can borrow and to which one can contribute. It obviously works, and it works extremely well: they rule this planet; everything else is marginalia. The eukaryotes do not swap with this pool, though. Each species is a genetic universe upon itself. Surely, the eukaryotes are much more complex than the bacteria, but this, in itself, does not explain speciation. There is no reason to believe that the complexity excludes free swapping of one's genes. After all, we do have sex, right? Why can't we have sex with any other species? The "answer" is that the other species had so much diverged from our own that it is no longer possible for us two to have viable progeny. But that's circuitous logic: the species have diverged precisely for the lack of this cross-breeding ability. It is speciation itself (the creation of artificial barriers to breeding) that enforces the species, and this order of things exists only in the Eukarya. Isn't it strange? Maybe it is just the complexity? Here is Woese:
were [cellular] organization simple and modular enough, all of the componentry of a cell could potentially be horizontally displaceable. Suppose that the primitive ancestors of modern cells were of this nature. That would mean that at its beginning, cellular evolution would have been driven in the main by gene transfers. In its subsequent evolution a primitive cell of this type would become ever more complex, idiosyncratically connected, and thereby increasingly refractory to horizontal gene acquisition, especially the more spectacular forms of it. In other words, there would come a stage in the evolution of cellular organization where the organismal genealogical trace (recorded in common histories of the genes of an organism) goes from being completely ephemeral to being increasingly permanent. This point in evolution, this transition, is appropriately call the “Darwinian Threshold.” On the far side of that Threshold “species” as we know them cannot exist. Once it is crossed, however, speciation becomes possible. The Darwinian Threshold truly represents the Origin of Species, in that it represents the origin of speciation as we know it. It could represent a point in cellular evolution where something drastic occurs. I posit the latter. The cell is a complex dynamic system. As its connectedness increases such a system can reach a critical point, where a phase change occurs, where a new, higher level organization of the whole emerges. That, I suggest, is what the Darwinian Threshold represents, a hitherto unrecognized phase change in the organization of the evolving cell. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC124369/
So we are dealing with one of the most momentous transformations, and no one has any idea what this "something drastic" could have been. The latent potential for speciation might have existed well before it occurred, but decoupling from the common genetic pool would be expected to decrease(!) fitness. If the goal of evolution is producing increasingly fit organisms, the speciation should never had occurred in the first place.
The usual take on eukarogenesis is symbiogenesis. The protoeukaryon archae found an ingenious solution to the inherent limitations of all bacteria: as they store energy as a chemical gradient across their membranes, they have to be small. The host had internalized a bacterium and started using many of such endosymbionts to produce a lot of energy by respiration. Because the latter produces radicals that can easily kill the host cell, the operation of mitochondria had to be tightly regulated and controlled, and their genes passed to the host's nucleus. This increased the demands on the fidelity and the amount of replicating DNA. The host had the machinery for this feat, and the mitochondria provided the energy needed by this costly machinery. For the first time ever, vast amounts of DNA could had been copied with high fidelity. The bacteria need to replicate very rapidly, and they keep their genomes as lean as possible, shedding the DNA that is not neeeded, hoping that another bacteria would pick it up. The protoeukaryon did not need to shed anything. It was accumulating the goodies. Its dramatically increased capacity to copy DNA was immediately exploited by viruses and selfish genetic elements that overrun the genome, but the eukaryon was able to tolerate even this abuse, thanks to its unconstrained energy source. It pursued the classical K-strategy: slow replication, high quality vs. r-strategy: rapid replication, low quality. However, having the potential ability to speciate does not explain speciation. There were still the distinct advantages to swapping genes. Then it all stopped. One idea I've heard is that such potentiality is binding: if there is a physical barrier, the differences between subpopulations would grow so great over time that the gene-swapping protocols would become different and the speciation will occur. I think this is wrong. Such speciation has never happened in the Prokarya, despite very formidable barriers, and the molecular machinery of sex is similar for all protists. The breeding barrier was not spontaneous; it was erected. So the question is, to what purpose? This purpose was not selfishness of the individual, as there was no "individual" at that point. So it was for the greater good of all. But how speciation can be this common good?
It was the logical conclusion of the eukaryogenesis itself. Bacteria do not parasitize on bacteria, as they are too small for such invasions (there are rare exceptions). However, the sheer size of the protoeukaryon made such infections possible. Furthermore, as the latter internalized its bacterial food, the bugs were invited to take advantage of their predator. "The Struggle for Life" has finally began, and it began on unfavorable terms for the Eukarya. The bacteria can live on uranium ore, gasoline, and even crystalline penicillin; living off the eukarya was unproblematic. The only consideration for letting the host to stay alive was (and still is) having someone to feed you. Now, imagine the world with bacterial infections, but no speciation. We get the Red Queen problem.
The bacterial virulence is adjusted to its host and other parasitic bacteria living in the host, but new strains appear constantly. Some of these strains will try to take the undue advantage over other bacterial strains possibly killing the host in the process. The very logic of the parasitism and evolution makes this situation inevitable: bacteria can adjust their virulence only through trial and error. If there are no barriers to eukaryote interbreeding, the killer infection will spread accross the entire population and kill everyone. This is the situation in which speciation is rewarded. Erecting artificial barriers helps to curb such pandemics, as the accumulated differences in the cellular machinery make this bacterial spread limited. The interspecies jumps are devastating but relatively rare which improves the chances for all parties involved. Divided, we stand: speciation IS a communal advantage for the eukaryotes.
One can ask, why does not this logic does apply to bacteria and their phages: why wouldn't bacteria speciate? I think that the reason is that the phages are not free living: they are produced by the bacteria themselves. Furthermore, the bacteria can outpace the phages, but the slowly replicating eukaryons cannot outpace their bacterial parasites. Finally, the bacteria use heritable immunity that relies on high variability and imprecise copying. Again, the eukaryons can't quite do that. The K-strategy limits the choices and makes certain outcomes foreordained. I think that speciation was one of such outcomes. The host-parasite dynamics involving r- and K-strategists inevitably leads to it. The eukaryotes have to be divided into species separated by barriers they themselves erect and maintain, as otherwise the first nasty bacterial infection will do them all in before the bacteria readjust their virulence. For the bacteria, this is business as usual, but for the Eukarya it would be the end of the road. They cannot afford not being species.
In short, I suggest that the speciation was a communitarian means of giving everyone a sporting chance through building robust diversity hampering bacterial parasitism. It was one of the first attempts at making this place a better world, and it ended like other such attempts. It assumed the logic of its own, producing the world as we know it, where a species is against a species, and an individual is against an individual.
Why are there species?