Hi,
This post is about 2 questions I originally asked on the forum : askabiologist dot org dot uk. The good thing about that forum is that only scientist answer the questions, the bad thing is that they ban you and delete your post if you ask something inconvenient. This happened to my already, but I hope this time they will give a decent answer. Anyhow this is my post (if you are interested in the full story type in precoded equlibrium to google):
Dear Biologists,
Please forgive me for my lengthy introduction, but in order to convey the importance of my question I have to share the thought process that it is based on.
My initial intention was to examine the claim, that the results of DNA studies confirm Darwinian evolution. I think there is no point in discussing the overwhelming evidence for an universal common ancestor (LUA). The issue I would like to address is the actual characterization of the LUA, which was revealed by quite recent discoveries in genetics.
Contrary to earlier expectations the distribution of genes amongst genomes does not point to a genetically simple universal ancestor, but to a very complex one. This is a well known phenomenon termed: The Genome of Eden by Prof. W. Ford Doolittle.1 He suggests that we should avert such complex LUA, but even the best efforts (HGT) in doing so generate more problems than solutions.
From what I gathered it seems traces of the Genome of Eden (GOE for short) are inescapably present on every level of biology. It is a general, overarching pattern in the living world, that wont go away. However, if we stop trying to avert or explaining away this pattern, a radically different view of biology emerges. If the GOE is real, then it is possible that the first cells were not genetically simple organisms like bacteria, but primeval stem cells in which the course of evolution was encoded, just like the process of ontogenesis is determined in a fertilized ovum. To back up this radical conclusion, let's see some of the evidence which I've found compelling.
1. Ernst Walter Mayr's prediction
In 1963 Ernst Mayr described precisely what we should find through DNA sequencing if the universal common ancestor had a simple, bacterial genetic tool-kit, and all the further information accumulated over time.
Much that has been learned about gene physiology makes it evident that the search for homologous genes is quite futile except in very close relatives. If there is only one efficient solution for a certain functional demand, very different gene complexes will come up with the same solution, no matter how different the pathway by which it is achieved. The saying "Many roads lead to Rome" is as true in evolution as in daily affairs2
As it turned out, his prediction failed in every level. What actual DNA sequencing results demonstrate is exactly what we would expect to find if the GOE was real. There are remarkable similarities between most remote species. In hindsight it's easy to come up with excuses about this prediction, but when the scientific method evaluates models and theories, it is the confirmed or falsified predictions that really matter, not the ad hoc interpretations presented after the data arrives. However, one way to interpret this failure supposed to be, that these similarities reflect housekeeping genes. This interpretation is unsustainable in the light of the more recent findings.
Richard Dawkins in his book The Blind Watchmaker demonstrates the power of evolution by examining the echo-location capabilities of bats. As it turned out, probably this trait has nothing to do with bat evolution. The gene complexes responsible for echo-location might have existed before bats and cetaceans diverged: whales and dolphins use the same gene-complexes as bats.3 This should not be the case according to Mayr's prediction, and these genes are not even amongst the housekeeping ones. This makes absolutely no sense in the Darwinian framework, but it makes perfect sense in a GOE based model. (By this I mean, the data does not confirm or fulfil the expectations of a Darwinian world-view, but special, sometimes ad hoc interpretations are required. In a GOE based model complex systems like echo-location were precoded in the LUA.)
In the official view, these genes are produced independently by parallel mutations. Interestingly in the case of the broken vitamin-C gene, the homologous flaw was a proof of the common ancestry of men and chimps, but in this case, the homologous gene-complexes are results of multitudes of parallel mutations. This is the textbook example of an ad hoc interpretation.
Ernst Mayr wasn't wrong because he didn't understand evolution or genetics, by all the discoveries of genetics in the past decades it could still be the case that homologous traits are produced by completely different gene-complexes. Most likely, and this is my point, his prediction failed because in his premise he assumed a simple LUA with a minimally sufficient, bacterium-like genome, and that all the additional genetic information accumulated over time. Darwinian predictions and expectations about common ancestry and change over time are usually confirmed, but expectations and predictions based on a simple LUA and the gradual accumulation of genetic complexity always fail. This is a tendency I'm going to underline by to following points and examples.
2. C-value paradox
If LUA had a simple genome (like a simple bacterium) and genetic complexity and all the additional information accumulated over the course of evolution, we should be able to trace this accumulation by examining the genomes of different organisms on different levels of complexity. This is a reasonable expectation. (If we wouldn't know about the c-value paradox or about the recent results of actual DNA sequences, one should reasonably expect to see this accumulation, given the Darwinian framework. ) A compelling starting point could be the genome of a sponge. This creature is one of the most simple multicellular organisms. However, the content of the genome of Amphimedon queenslandica - a marine sponge - literally shocked the scientific community.4 This simple creature has a remarkably complex genome with more individual genes than an average bird, but the most stunning part is that they posses genes that shouldn't be in their genome. Sponges don't have a nervous system, yet they have many of the genes which required for building synapses (sodium channels). Again, this makes absolutely no sense in the Darwinian framework, but it makes perfect sense if the GOE is real. Dr Kenneth S. Kosik the leader of the sea-sponge genome project puts it in this way:
What are the genes even doing there if they don't have neurons or synapses? We still don't know the answer to that question.
In 2013 there is still no answer for this question. Once again there is no sign of the gradual accumulation of genetic complexity. There is no evidence that a gradual accumulation of so many genes ever happened or if its even possible through natural selection:
In most observed cases organisms tend to get rid of some genes for better fitness or to safe energy. Why would it have been different in the past? If losing genes is way more frequent than gaining them, how had tens of thousands of genes accumulated which were already present in the first multicellular creatures (sponges) more than 700 million years ago? Their genome is in the same range with mammalian ones, sponges share 70% of their genes with us. If the GOE existed, a darwinian, gradual accumulation of genes have never had to happen.
The c-value paradox has another significant aspect: less complex, smaller organisms don't have smaller or less complex genomes, so it is physically possible that the first cells carried enough information for the entire evolution.
3. Results of Evo-Devo
The results of Evolution of Development undeniably support the existence of primeval stem cells. According to Sean B. Carroll:
The Surprising message from Evo Devo is that all of the genes for building large, complex animal bodies long predated the appearance of those bodies in the Cambrian Explosion. The genetic potential was in place for at least 50 million years, and probably a fair bit longer, before large, complex forms emerged
Dr Carroll is a bit sugar-coating the facts by using the phrase potential, when it is really about actual genetic information, genes. The results from various DNA studies suggests that these genes were not evolving together with the structure they control, but preceded them by hundreds of millions of years. This makes no sense in a Darwinian world-view. For example: eyes supposedly evolved multiple times independently, but DNA sequencing revealed that the genes that control the development of these structures are the same in every case (PAX6)5. This is not what someone would expect to find, given the Darwinian framework.
4. The Genome of Eden
The distribution of genes amongst genomes points to a very complex LUA, this is the reality (recognized mostly on the microbe level). W. Ford Doolittle suggests that we should interpret the data in a way that averts the Genome of Eden. The trivial solution involves the adjustment of the assumed rate of horizontal gene transfer to the data (another ad hoc adjustment), but though a very frequent HGT is probable amongst microbes, one must extend it to complex eukaryotes to explain away the genome of eden, and then it is much less probable. Interestingly it seems Prof Doolittle and most of the other biologists who worked on this issue are bothered only about microbes and fail to recognize how big this problem really is.
Many genes required for photosynthesis have been found in the genome of a sea-snail (Elysia chlorotica)6, this represents the same problem and it makes no sense unless we extend HGT to complex eukaryotes. The first difficulty with this move is, that if genes can be transferred between any two species and the recipient can harness the benefits of the transferred genes so easily, we should find a completely different living world in which taxonomy and classification would be impossible. There we would expect to find a chaotic mess of traits, not order and structure. The second problem is that asexual reproduction combined with frequent and effective HGT makes sexual reproduction superfluous. I call this problem the catch 22 of Darwinism.
5. Sexual reproduction and the Catch 22 of Darwinism
The supposed function of sexual reproduction is to provide variation for natural selection. Sarah P. Otto in her paper (Sexual Reproduction and the Evolution of Sex)7 firmly demonstrates that sexual reproduction very often actually hinders natural selection. If a very complex and intricate system in operation fails to sufficiently serve an assumed function, it may be the case that the assumed function is not the actual function. At the same time, the disadvantages of the this system are obvious and sometimes fatal. Sex makes reproduction more circumstantial, dangerous, more time and resource dependant. An ordinary sexually reproducing organism has to find a fertile individual from the opposite gender to reproduce. This condition has led to the extinction of many species, that otherwise should not have gone extinct.
For decades the redeeming evolutionary excuse for sexual reproduction was that it is the source of new gene combinations. However, if in order to avert the GOE we assume a very frequent and effective HGT that includes complex eukaryotes, the existence of Sex is completely unjustified and its privileged status as the source of new gene combinations is over. This is the problem I call Catch 22 of Darwinism. Asexual reproduction combined with frequent HGT is in every way superior, HGT has way more evolutionary potential, if anything then it should have been evolved even further. Why and how did a much more complex reproduction system evolve, which has disadvantageous, sometimes fatal consequences and can't even serve its function effectively? It makes no sense on a standard evolutionary view.
If the LUA was a primeval stem cell as I suggest, then the purpose of sex is to provide viable offspring and at the same time to preserve genetic information, quality as well as possible. In every aspect of sexual reproduction we can find this intention.
[part cut out to save characters]
The purpose of genders is a bit more theoretical issue. Genetic recombination does not justify the existence of genders, it can work without them. To demonstrate the concept, let me use an analogy:
Let's say we have a book and then 10000 monks copy it, one after another. The end result will certainly lack a considerable amount of information that was present in the original version, therefore it probably lose quality, coherence and integrity (for the sake of the analogy put aside creativity and intelligence during the copying process). But let's say we introduce a basic restriction: in order to make a copy one must find two independent but compatible sources. Now even after 10000 copies the final copy will more likely to preserve quality and information.
Conclusion
There is much more to be said about the genetic background of GOE, but I think what I have offered so far is sufficient to make the case.
In conclusion, the results of DNA sequencing and discoveries of genetics do not confirm the Darwinian theory: ad hoc, unjustified assumptions are required to interpret the data (like HGT amongst complex, multicellular eukaryotes or that genes that precedes the structure they control today had some different function in the past or that sponges degenerated from more complex organisms or assuming multitudes of parallel mutations, etc.). These ad hoc hypotheses are needed to explain away the GOE, because on the darwinian view it is not possible that a LUA carried genetic information specific for complex multicellular life.
The results inescapably point to the Genome of Eden, its traces can be found everywhere in biology: in some places it is attributed to horizontal gene transfer (microbes, Elysia chlorotica) in other cases to convergent/parallel evolution and parallel mutations (whale-bat sonar) and in another cases it is attributed to co-optation (PAX6). We must recognize that these examples are parts of the same, one, overarching pattern.
On what scientific basis do you have to exclude the Genome of Eden from possible explanations?
Why must we avert it? If there is no knock down counter evidence of some sort, that prohibits the existence of the GOE or at least makes it highly improbable, I'm rationally and scientifically justified in rejecting the neo-darwinian synthesis and embracing a GOE based model in the light of the evidence.
I hope you are willing to answer my questions in the name of science, in the name of education.
Best regards:
VK
This post is about 2 questions I originally asked on the forum : askabiologist dot org dot uk. The good thing about that forum is that only scientist answer the questions, the bad thing is that they ban you and delete your post if you ask something inconvenient. This happened to my already, but I hope this time they will give a decent answer. Anyhow this is my post (if you are interested in the full story type in precoded equlibrium to google):
Dear Biologists,
Please forgive me for my lengthy introduction, but in order to convey the importance of my question I have to share the thought process that it is based on.
My initial intention was to examine the claim, that the results of DNA studies confirm Darwinian evolution. I think there is no point in discussing the overwhelming evidence for an universal common ancestor (LUA). The issue I would like to address is the actual characterization of the LUA, which was revealed by quite recent discoveries in genetics.
Contrary to earlier expectations the distribution of genes amongst genomes does not point to a genetically simple universal ancestor, but to a very complex one. This is a well known phenomenon termed: The Genome of Eden by Prof. W. Ford Doolittle.1 He suggests that we should avert such complex LUA, but even the best efforts (HGT) in doing so generate more problems than solutions.
From what I gathered it seems traces of the Genome of Eden (GOE for short) are inescapably present on every level of biology. It is a general, overarching pattern in the living world, that wont go away. However, if we stop trying to avert or explaining away this pattern, a radically different view of biology emerges. If the GOE is real, then it is possible that the first cells were not genetically simple organisms like bacteria, but primeval stem cells in which the course of evolution was encoded, just like the process of ontogenesis is determined in a fertilized ovum. To back up this radical conclusion, let's see some of the evidence which I've found compelling.
1. Ernst Walter Mayr's prediction
In 1963 Ernst Mayr described precisely what we should find through DNA sequencing if the universal common ancestor had a simple, bacterial genetic tool-kit, and all the further information accumulated over time.
Much that has been learned about gene physiology makes it evident that the search for homologous genes is quite futile except in very close relatives. If there is only one efficient solution for a certain functional demand, very different gene complexes will come up with the same solution, no matter how different the pathway by which it is achieved. The saying "Many roads lead to Rome" is as true in evolution as in daily affairs2
As it turned out, his prediction failed in every level. What actual DNA sequencing results demonstrate is exactly what we would expect to find if the GOE was real. There are remarkable similarities between most remote species. In hindsight it's easy to come up with excuses about this prediction, but when the scientific method evaluates models and theories, it is the confirmed or falsified predictions that really matter, not the ad hoc interpretations presented after the data arrives. However, one way to interpret this failure supposed to be, that these similarities reflect housekeeping genes. This interpretation is unsustainable in the light of the more recent findings.
Richard Dawkins in his book The Blind Watchmaker demonstrates the power of evolution by examining the echo-location capabilities of bats. As it turned out, probably this trait has nothing to do with bat evolution. The gene complexes responsible for echo-location might have existed before bats and cetaceans diverged: whales and dolphins use the same gene-complexes as bats.3 This should not be the case according to Mayr's prediction, and these genes are not even amongst the housekeeping ones. This makes absolutely no sense in the Darwinian framework, but it makes perfect sense in a GOE based model. (By this I mean, the data does not confirm or fulfil the expectations of a Darwinian world-view, but special, sometimes ad hoc interpretations are required. In a GOE based model complex systems like echo-location were precoded in the LUA.)
In the official view, these genes are produced independently by parallel mutations. Interestingly in the case of the broken vitamin-C gene, the homologous flaw was a proof of the common ancestry of men and chimps, but in this case, the homologous gene-complexes are results of multitudes of parallel mutations. This is the textbook example of an ad hoc interpretation.
Ernst Mayr wasn't wrong because he didn't understand evolution or genetics, by all the discoveries of genetics in the past decades it could still be the case that homologous traits are produced by completely different gene-complexes. Most likely, and this is my point, his prediction failed because in his premise he assumed a simple LUA with a minimally sufficient, bacterium-like genome, and that all the additional genetic information accumulated over time. Darwinian predictions and expectations about common ancestry and change over time are usually confirmed, but expectations and predictions based on a simple LUA and the gradual accumulation of genetic complexity always fail. This is a tendency I'm going to underline by to following points and examples.
2. C-value paradox
If LUA had a simple genome (like a simple bacterium) and genetic complexity and all the additional information accumulated over the course of evolution, we should be able to trace this accumulation by examining the genomes of different organisms on different levels of complexity. This is a reasonable expectation. (If we wouldn't know about the c-value paradox or about the recent results of actual DNA sequences, one should reasonably expect to see this accumulation, given the Darwinian framework. ) A compelling starting point could be the genome of a sponge. This creature is one of the most simple multicellular organisms. However, the content of the genome of Amphimedon queenslandica - a marine sponge - literally shocked the scientific community.4 This simple creature has a remarkably complex genome with more individual genes than an average bird, but the most stunning part is that they posses genes that shouldn't be in their genome. Sponges don't have a nervous system, yet they have many of the genes which required for building synapses (sodium channels). Again, this makes absolutely no sense in the Darwinian framework, but it makes perfect sense if the GOE is real. Dr Kenneth S. Kosik the leader of the sea-sponge genome project puts it in this way:
What are the genes even doing there if they don't have neurons or synapses? We still don't know the answer to that question.
In 2013 there is still no answer for this question. Once again there is no sign of the gradual accumulation of genetic complexity. There is no evidence that a gradual accumulation of so many genes ever happened or if its even possible through natural selection:
In most observed cases organisms tend to get rid of some genes for better fitness or to safe energy. Why would it have been different in the past? If losing genes is way more frequent than gaining them, how had tens of thousands of genes accumulated which were already present in the first multicellular creatures (sponges) more than 700 million years ago? Their genome is in the same range with mammalian ones, sponges share 70% of their genes with us. If the GOE existed, a darwinian, gradual accumulation of genes have never had to happen.
The c-value paradox has another significant aspect: less complex, smaller organisms don't have smaller or less complex genomes, so it is physically possible that the first cells carried enough information for the entire evolution.
3. Results of Evo-Devo
The results of Evolution of Development undeniably support the existence of primeval stem cells. According to Sean B. Carroll:
The Surprising message from Evo Devo is that all of the genes for building large, complex animal bodies long predated the appearance of those bodies in the Cambrian Explosion. The genetic potential was in place for at least 50 million years, and probably a fair bit longer, before large, complex forms emerged
Dr Carroll is a bit sugar-coating the facts by using the phrase potential, when it is really about actual genetic information, genes. The results from various DNA studies suggests that these genes were not evolving together with the structure they control, but preceded them by hundreds of millions of years. This makes no sense in a Darwinian world-view. For example: eyes supposedly evolved multiple times independently, but DNA sequencing revealed that the genes that control the development of these structures are the same in every case (PAX6)5. This is not what someone would expect to find, given the Darwinian framework.
4. The Genome of Eden
The distribution of genes amongst genomes points to a very complex LUA, this is the reality (recognized mostly on the microbe level). W. Ford Doolittle suggests that we should interpret the data in a way that averts the Genome of Eden. The trivial solution involves the adjustment of the assumed rate of horizontal gene transfer to the data (another ad hoc adjustment), but though a very frequent HGT is probable amongst microbes, one must extend it to complex eukaryotes to explain away the genome of eden, and then it is much less probable. Interestingly it seems Prof Doolittle and most of the other biologists who worked on this issue are bothered only about microbes and fail to recognize how big this problem really is.
Many genes required for photosynthesis have been found in the genome of a sea-snail (Elysia chlorotica)6, this represents the same problem and it makes no sense unless we extend HGT to complex eukaryotes. The first difficulty with this move is, that if genes can be transferred between any two species and the recipient can harness the benefits of the transferred genes so easily, we should find a completely different living world in which taxonomy and classification would be impossible. There we would expect to find a chaotic mess of traits, not order and structure. The second problem is that asexual reproduction combined with frequent and effective HGT makes sexual reproduction superfluous. I call this problem the catch 22 of Darwinism.
5. Sexual reproduction and the Catch 22 of Darwinism
The supposed function of sexual reproduction is to provide variation for natural selection. Sarah P. Otto in her paper (Sexual Reproduction and the Evolution of Sex)7 firmly demonstrates that sexual reproduction very often actually hinders natural selection. If a very complex and intricate system in operation fails to sufficiently serve an assumed function, it may be the case that the assumed function is not the actual function. At the same time, the disadvantages of the this system are obvious and sometimes fatal. Sex makes reproduction more circumstantial, dangerous, more time and resource dependant. An ordinary sexually reproducing organism has to find a fertile individual from the opposite gender to reproduce. This condition has led to the extinction of many species, that otherwise should not have gone extinct.
For decades the redeeming evolutionary excuse for sexual reproduction was that it is the source of new gene combinations. However, if in order to avert the GOE we assume a very frequent and effective HGT that includes complex eukaryotes, the existence of Sex is completely unjustified and its privileged status as the source of new gene combinations is over. This is the problem I call Catch 22 of Darwinism. Asexual reproduction combined with frequent HGT is in every way superior, HGT has way more evolutionary potential, if anything then it should have been evolved even further. Why and how did a much more complex reproduction system evolve, which has disadvantageous, sometimes fatal consequences and can't even serve its function effectively? It makes no sense on a standard evolutionary view.
If the LUA was a primeval stem cell as I suggest, then the purpose of sex is to provide viable offspring and at the same time to preserve genetic information, quality as well as possible. In every aspect of sexual reproduction we can find this intention.
[part cut out to save characters]
The purpose of genders is a bit more theoretical issue. Genetic recombination does not justify the existence of genders, it can work without them. To demonstrate the concept, let me use an analogy:
Let's say we have a book and then 10000 monks copy it, one after another. The end result will certainly lack a considerable amount of information that was present in the original version, therefore it probably lose quality, coherence and integrity (for the sake of the analogy put aside creativity and intelligence during the copying process). But let's say we introduce a basic restriction: in order to make a copy one must find two independent but compatible sources. Now even after 10000 copies the final copy will more likely to preserve quality and information.
Conclusion
There is much more to be said about the genetic background of GOE, but I think what I have offered so far is sufficient to make the case.
In conclusion, the results of DNA sequencing and discoveries of genetics do not confirm the Darwinian theory: ad hoc, unjustified assumptions are required to interpret the data (like HGT amongst complex, multicellular eukaryotes or that genes that precedes the structure they control today had some different function in the past or that sponges degenerated from more complex organisms or assuming multitudes of parallel mutations, etc.). These ad hoc hypotheses are needed to explain away the GOE, because on the darwinian view it is not possible that a LUA carried genetic information specific for complex multicellular life.
The results inescapably point to the Genome of Eden, its traces can be found everywhere in biology: in some places it is attributed to horizontal gene transfer (microbes, Elysia chlorotica) in other cases to convergent/parallel evolution and parallel mutations (whale-bat sonar) and in another cases it is attributed to co-optation (PAX6). We must recognize that these examples are parts of the same, one, overarching pattern.
On what scientific basis do you have to exclude the Genome of Eden from possible explanations?
Why must we avert it? If there is no knock down counter evidence of some sort, that prohibits the existence of the GOE or at least makes it highly improbable, I'm rationally and scientifically justified in rejecting the neo-darwinian synthesis and embracing a GOE based model in the light of the evidence.
I hope you are willing to answer my questions in the name of science, in the name of education.
Best regards:
VK
