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Why must we avert the genome of Eden?

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Why must we avert the genome of Eden?

Postby Hunor » Mon Sep 23, 2013 12:08 am

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 scientists 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. In any case, maybe some expert on this forum can also answer these question, and I would really appreciate it.

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 affairs”2


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.

Some weeks ago I posted a question about female ova on this forum: http://www.askabiologist.org.uk/answers … p?id=10184
I was interested in the evolutionary explanation of the fact that unlike sperm cells, ova are produced in advance and are stored in the ovaries for decades. This significant difference begs for a decent explanation. I was very disappointed in the answer I got. John Steemson depicted this difference as a resource management issue, but this certainly doesn’t make any sense. He says:

“It comes down to parental investment. From the perspective of females, each pregnancy is a major investment of resources.”

But it is anything but not economical to produce millions of ova in advance and store them for decades instead of producing only a few when it is necessary.
On a GOE based model, the purpose of this feature is to provide uncorrupted, healthy mitochondrial DNA for the offspring. MtDNA mutates magnitudes faster then nDNA (and MtDNA is responsible for ageing), therefore ova are produced early during the development of the female fetus, then they are kept on a low energy state, preventing any division, mutation or radiation that could distort the information in the mtDNA. The offspring inherits mtDNA purely from the mother, so it makes perfect sense that such precautions exist only in the female body. It makes perfect sense in contrast to the incoherent polemics of the Darwinian approach.
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. This is the purpose of genders, and it makes perfect sense.
On the Darwinian view it is the job of natural selection to preserve quality, so genders are superfluous.

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. These are genotypes that can't be explained by common ancestry unless we assume a very complex very early ancestor: The Genome of Eden. At the same time there is absolutely no evidence for a bacterium-like, simple universal common ancestor.

I am aware that I use the term a bit differently than Prof Doolittle. By Genome of Eden he merely means a LUA with very many genes. I take it a step forward by saying a LUA with very many genes can be interpreted as a primeval stem cell to explain the results of DNA sequencing, and unlike him, I extended the issue to eukaryotes.

Here I might add, that of course I don't think that these stem cells possessed every gene ever existed, but I do think that the major innovations of biology were encoded. The examples I provided are referring to systems of this kind: echo-location, vision, photosynthesis, and nervous system. These are exactly the kind of complex traits where a Darwinian pathway is questionable.
Also I think probably these traits were not coded in the same format as we find them today, it is possible that a protected or even more redundant coding is genetically possible for reducing the loss of information.
The process of evolution could have gone a similar way as embryonic stem cells are differentiated into different cell types, by genetic expressions. The ingenuity of eukaryote genome continuously impresses the scientific community so I don’t think if I attribute anything impossible to this complex code. Having that said, this is my question:

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. Actually I'm working on that model and I call it Precoded Equilibrium (by typing the keywords “precoded equilibrium” my blog can be found for those who are interested). It's easy to see that fossil records and evolution in most individual cases can be much better explained if the LUA was a primeval stem cell. Examining the proposed mechanism of Darwinism (natural selection working on random genetic variation) also reveals major faults that are not present in my model.

There is one reason I cant think of for averting the genome of Eden: science might not be able to explain the origin of such genome. However, this problem is already upon us. There is no convincing explanation of the origin of life. Despite the relentless efforts of biologists during the past 100 years, it has not been demonstrated that natural processes can produce life from non living matter. The huge complexity gap lies between inorganic matter and life, switching to a stem cell is just a nuance in contrast. There is nothing to lose by embracing the Genome of Eden.

I have one more question, but it might be tricky. It seems it is impossible to conceive any DNA content that would shake the confidence in Darwin's theory. Walter Mayr's prediction was referring to a core concept of genetic evolution based on the darwinian framewok, but it was completely wrong. Exactly the opposite is true, but this fact didn't change a thing. If his prognosis had been confirmed that would also mean that DNA supports Darwinism. The data shows that simple organisms don't necessarily have less complex genomes, does that matter? No, but if simple organisms - like sponges - had an appropriate small, simple genome, that would also prove a Darwinian evolution. The distribution of genes points to the Genome of Eden, no problem, it was HGT. Would that be the case, that distribution of genes confirmed a simple LUA, that would also prove the current model. There are genes that precede the structures they control, doesn’t matter at all, they have been co-opted for their new function, so in summary:
Every feature in genetics is a proof of Darwinian evolution – as we have been taught – but the exact opposites of those features would equally prove Darwinian evolution. It is an a priori established principle and it has nothing to do with the actual DNA content. (The evidence for common decent is not at all, at any means, prove the truth of darwinism.)

Is it even possible to conceive any pattern in DNA, distribution of genes or any genetic evidence that would disprove Darwinian evolution?

All the patterns and counter evidences I can think of are already in place, yet biologists perception of DNA as a solid proof of Darwinism hasn't changed a bit. By contrast, a Genome of Eden based model would be impossible without the C-value paradox.
To be clear, I'm not trying to discredit Darwin or evolutionary biology. My point was, that even on the aspect of falsifiability a GOE based model is superior.

I hope you are willing to answer my questions in the name of science, in the name of education, but remember: you have to provide evidence against the Genome of Eden, not against special creation! Evidence for common decent won't do it. Nevertheless, I think this topic definitely worth discussion.


Best regards:

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Postby Cat » Sat Sep 28, 2013 6:09 pm

It is much easier to learn than to unlearn something... From the molecular/genetic standpoint universal ancestor should have had more gene rich genome. However, as I said before, we as species have a superiority complex. We are used to thinking of cave men as our ancestors. Should you find evidence that the said cave man was genetically superior to us, it would be very difficult to comprehend. Also, I would imagine that calling this genome "Genome of Eden" does not help either...
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Re:

Postby wildfunguy » Mon Sep 30, 2013 12:40 am

Cat wrote:From the molecular/genetic standpoint universal ancestor should have had more gene rich genome.

I would criticize your position, but frankly, I'm amazed you read through the entire OP. If I was going to read something of that length, I would read a Nature article.
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Re: Why must we avert the genome of Eden?

Postby biohazard » Tue Oct 01, 2013 1:01 pm

Hunor wrote:...


I am having a hard time figuring out from where did this omnipotent piece of DNA pop up in the first place. Are you saying that out of nothing emerged the genes for an eye and a lung and an antenna and an anus, just like that?

My spider sense is tingling... are you sure this is not just another ID/creationist plot? Well, at least the time frame suggested is more than six thousand years. Other than that this makes little sense.
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Re: Why must we avert the genome of Eden?

Postby wildfunguy » Fri Oct 04, 2013 7:49 pm

Hunor wrote:...

The Mayr quote is nearly 50 years old, and indeed, this article mentions the quote as it explains how the introduction of developmental biology is changing evolutionary theory.
http://www.ncbi.nlm.nih.gov/books/NBK10128/

In your OP, you spend a lot more time explaining the background of your argument rather than the argument itself. You are not a trusted source of information, so nobody wants to sit their reading all of the information you have put forth. It is better to provide background information through trusted articles, for example:
http://www.nri.ucsb.edu/news/2012/clues ... ess-sponge
I always go on MyWot to read the comments about a website before I post its links as sources. Dot edu sources are generally good.
http://www.mywot.com/en/scorecard/ucsb.edu

Hunor wrote: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.

What are you arguing here, that complexity should increase as we look at organisms that are more closely related to us? This would be wrong. Those sponges are distant relatives, but they're still present-day organisms. All present-day organisms should be relatively complex compared to the most ancient organisms, irrespective of their relationship to Homo sapiens.

Hunor wrote: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.

http://www.ncbi.nlm.nih.gov/books/NBK10128/
This article, near the end, apparently gives a developmental-genetics explanation of how the eye evolved, but I don't understand it. Maybe somebody who is systems-biology-literate can explain what this source is saying.

Here is a Nature article explaining the term "modularity".
http://www.nature.com/msb/journal/v4/n1 ... 20083.html


Hunor wrote: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.

You give us two explanations for the observations in Elysia chlorotica, HGT and GOE. Of course, we shouldn't assume that these are the only possible explanations, these are merely the two that are given by your OP. As far as your OP goes, both models seem to fit the observations.
But then, rather than working out your GOE model and its precise implications, you bash the HGT hypothesis. To make it worse, your argument is a slippery slope. Suggesting frequent HGT for Elysia chlorotica doesn't lead to HGT being frequent for all of domain Eukaryota. In fact, this source says that newer data is inconsistent with the HGT hypothesis, suggesting that scientists were testing the HGT hypothesis specifically for Elysia chlorotica.
http://www.ncbi.nlm.nih.gov/pubmed/23645554

... that's enough analysis for this thread.

onto BioHazard's post.

biohazard wrote:I am having a hard time figuring out from where did this omnipotent piece of DNA pop up in the first place. Are you saying that out of nothing emerged the genes for an eye and a lung and an antenna and an anus, just like that?

My spider sense is tingling... are you sure this is not just another ID/creationist plot? Well, at least the time frame suggested is more than six thousand years. Other than that this makes little sense.

I haven't learned about origin of life theories yet, but I think less DNA would be more surpising. If the ancestor had more DNA, that would mean more potential for the appearance of functional genes.

But when I put this quote (given in the OP) into Google, I got a bunch of religious websites.
“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.”
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Re: Re:

Postby Cat » Sat Oct 05, 2013 1:27 pm

wildfunguy wrote:
Cat wrote:From the molecular/genetic standpoint universal ancestor should have had more gene rich genome.

I would criticize your position, but frankly, I'm amazed you read through the entire OP. If I was going to read something of that length, I would read a Nature article.


It seems that you read it too... :)
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Re: Re:

Postby Luxorien » Sat Nov 16, 2013 7:39 pm

wildfunguy wrote:I would criticize your position, but frankly, I'm amazed you read through the entire OP. If I was going to read something of that length, I would read a Nature article.


You, sir, have earned the highest of fives.
If arguing with people on the internet helps me understand science, then I will do it. FOR THE CHILDREN.
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