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Does Genomics Need Darwin?

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Are cracks appearing in the Darwinian facade? There appears to be increasing recognition in at least some genomic centres that Darwin needs to be laid quietly to rest as scientific discoveries progress. Professor John Dupre of Egenis for instance writes in the Genomics Network Newsletter – April 2009 – Does Genomics Need Darwin? (p.23)

“Whereas until recently it was thought that the vast majority of the genome (>98%) not directly involved in coding for proteins was ‘junk’, perhaps selfish DNA involved in its own project of colonizing the genome, this view is now widely discredited. At least 70% of the genome appears to be transcribed, and it is increasingly suspected that much of this is involved in regulation of genome expression. Especially prominent among these regulatory elements are the small RNA molecules that are now known to be a major feature of all cellular environments, and that have been divided into a rapidly diversifying taxonomy of kinds. Exploration of the functions of these systems of molecules is one of the most exciting areas of contemporary biology.”

Comments
Here's an article about guppy "evolution". Is it really proper to talk about "evolution" here? Isn't this really adaptation? And, isn't this adaptive behavior tied into epigenetics, given that it is maternal and rapid (directly from one generation to another)? Most of what passes for "evolution" is, IMO, nothing more than "adaptation", whose genetic basis we're only now beginning to discover. There is an article somewhere---I can't remember where now!---that talks about L1 retrotransposons and how the reverse transcriptase works at 4-8 cell embryonic stage; that is, the DNA that is 'read back' into the genome happens outside of the germline. This is rather novel, and the implications compelling.PaV
June 14, 2009
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Alan Fox,
What, pray, is an “evolutionary astronomer”?
In addition to what Joseph already said, I would add the assumption of a 4.6 billion year old solar system. BTW, I'm aware the Hydroplate Theory is relatively young and will likely have to be tweaked as new evidence comes in, but so far it at least passes the beverage through the nose test, unlike the mainstream theories.herb
June 14, 2009
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Mr Sibley, Alan - my rejection of Darwinism is mainly based on the fact that I consider the concept of an undirected evolutionary progression to be an oxymoron. Basically it is a claim for ‘undirected direction.’ You are reading into evolution a teleogical position that is not there. Drop the 'progression' and 'direction' ideas in favor of 'history' and you are good to go! Of course, if the issue is really a prior theological commitment to progress (Adam to Jesus) please be clearer next time.Nakashima
June 14, 2009
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Andrew:
Alan - my rejection of Darwinism is mainly based on the fact that I consider the concept of an undirected evolutionary progression to be an oxymoron. Basically it is a claim for ‘undirected direction.’
Zachriel elsewhere observes: "Just like a river has a direction towards the sea, but is considered undirected. It's a conflation of different senses of the word direction."Diffaxial
June 14, 2009
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What, pray, is an “evolutionary astronomer”?
An astronomer who accepts the theory of evolution and translates that to his/ her own venue. IOW an astronomer who thinks that atomic accidents and cosmic cokkisions are all that is required to explain the cosmos.Joseph
June 14, 2009
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I was under the impression that the mountains and the ocean basins were created during the Flood episode- which was much more than just a flood. Alan Fox:
If it wasn’t you writing it, Joe, I’d be intrigued by “…more than just a flood”.
Just by reading the Bible it is clear that it was more than just a flood. Herb has provided a reference- you should read it.Joseph
June 14, 2009
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It even accounts for the origin of the asteroid belts, which has long baffled evolutionary astronomers.
What, pray, is an "evolutionary astronomer"?Alan Fox
June 14, 2009
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Mr Sibley, For your benefit epigenetics was recently discussed here. I did read the newsletter. That is how I noticed all the positive comments on Darwin and evolution, and the mention of Uncommon Descent on the previous pages. As a comment directly to your post - there is nothing in the section you quote or in the newletter as a whole to justify your opening paragraph. If you see a crack, quote the source directly. If you see a scientist arguing to lay aside evolution, quote her. The significance of the article you have quoted is that whatever the mechanism, heritable variation is an evolutionary process. (I now return you to the discussion of Flood geology. ;) )Nakashima
June 14, 2009
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Mr. Sibley,
Where did all the water come from and where did it go? This question isn’t related to ID, but you don’t have to be a maths genius to work out that 70% of the earth is covered by ocean water to a depth of 3km. There is more than enough water to cover the land to a depth of 2km if you allow for isostatic changes and thermal expansion of the sea due to something like Baumgardner’s catastrophic plate tectonics.
Dr. Walt Brown's Hydroplate Theory is one of the more refined "flood" theories out there, in my view. It even accounts for the origin of the asteroid belts, which has long baffled evolutionary astronomers.herb
June 14, 2009
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So, prior to the flood, there were no mountains and ocean basins? So, where was the water?Alan Fox
June 14, 2009
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I was under the impression that the mountains and the ocean basins were created during the Flood episode- which was much more than just a flood.
If it wasn't you writing it, Joe, I'd be intrigued by "...more than just a flood".Alan Fox
June 14, 2009
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Alan Fox:
Mount Ararat is not at sea level.
Did Mount Ararat always exist? I was under the impression that the mountains and the ocean basins were created during the Flood episode- which was much more than just a flood.Joseph
June 14, 2009
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Andrew Mount Ararat is not at sea level.Alan Fox
June 14, 2009
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It's obvious that the theory of evolution does not rely on genomics. There isn't any genetic data which demonstrates that single-celled orhanisms can evolve into anything but single-celled organisms. The best we have are colonies but no evolution. Then there is the fact that we don't even know what genes/ DNA sequence(s) are responsible for our eyes and vision system. Unguided processes cannot answer the question of how regulatory sequences arose...Joseph
June 14, 2009
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Alan - my rejection of Darwinism is mainly based on the fact that I consider the concept of an undirected evolutionary progression to be an oxymoron. Basically it is a claim for 'undirected direction.' Where did all the water come from and where did it go? This question isn't related to ID, but you don't have to be a maths genius to work out that 70% of the earth is covered by ocean water to a depth of 3km. There is more than enough water to cover the land to a depth of 2km if you allow for isostatic changes and thermal expansion of the sea due to something like Baumgardner's catastrophic plate tectonics.Andrew Sibley
June 14, 2009
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...takes a keen interest in science and environmental issues, and also aspects of Flood geology...
It just occurs to me that Flood with a capital "F" refers to the creationist idea of a global flood with Noah's ark etc. I have often wondered, having read various debates about the evidence (thanks AFDave!), where all the water came from and where it is now? I don't know if you have any thoughts about this.Alan Fox
June 14, 2009
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Mr Sibley, I see from following your link that you are a creationist. Do your theological beliefs drive your assessment of Darwin? I get that impression from the tone of news articles, for instance on "Ida" and "Tiktaalik" at your site. I haven't seen you presenting the weather recently on BBC TV. Have you retired from meteorology?Alan Fox
June 14, 2009
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Mapau quotes this from the news letter "DNA carries with it signals from our evolutionary past which are wholly unaccountable for by theories of special creation." In response, if the work of the genomics network and Egenis (as discussed in the newsletter) is to show that lateral gene transfer calls into question the Tree of Life, then surely so called 'signals from our evolutionary past' in the genes cannot be used as evidence for common descent. If genetic information can be transferred laterally, then that does not necessarily call into question special creation, but provides a possible explanation within such a framework. As for Nakashima's comments. I merely posted the item to allow discussion and did not feel the need to spoon-feed the content to all and sundry - please read it for yourself and add some comments. And if there is another discussion then please link to it.Andrew Sibley
June 14, 2009
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Mr Sibley, It is a pity you wrote this without seeing the extensive discussion here on UD about this exact issue of the relevance of epigenetics and "Lamarckism" to evolution, whether considered historically as Darwin saw it or as we understand it today. Even more incredible is that you pass over the mention of Uncommon Descent itself on page 20!!Nakashima
June 13, 2009
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Genomics does not need Darwin. Nothing practical needs Darwin as least with regard to his views on history of species development.tribune7
June 13, 2009
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Nice article and interesting link. Here's a quote from the link that caught my attention. Dr Staffan Müller-Wille writes on page 22:
On the other hand it remains questionable if we could fully decipher the meaning of the multitude of patterns discernible in human DNA without having some grounding in Darwinian evolutionary theory. DNA carries with it signals from our evolutionary past which are wholly unaccountable for by theories of special creation. Thus Collins is more than happy to concede that “a common ancestor for humans and mice is virtually inescapable”.
This may be a refutation of special all-at-once creation (I knows many would disagree) but I don't see how it refutes intelligent design. If an intelligent designer chooses a set of building blocks (nucleotides) to create an initial design and continually modifies and improces on the design over the years to come up with a huge number of later more complex variations, I would call it evolution by design and not Darwinian evolution. My point is that I don't understand why Dr Staffan Müller-Wille and others insist that common descent can only be explained by assuming Darwinian evolution.Mapou
June 13, 2009
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Khan:
First, the question itself shows great confusion because there is no fundamental discord between Lamarckian modes of inheritance and evolution.
I don't get this. If evolution turns out to be controlled by a Lamarckian evolutionary mechanism (synonymous with front loading, IMO), this means that the genome has the ability to anticipate future environmental conditions and adjust the expression of its genes accordingly. How is this compatible with Darwinian evolution since DE is based on natural selection and mutations over millions of years? Why would evolution evolve a new anticipatory evolutionary mechanism if the non-anticipatory one was working perfectly? I say this because any evolutionary system that can design (oops!) a subsystem that can predict the future is extremely effective and there is no pressure to replace it. Now, I have heard some evolutionists reason that all the genes required for Lamarckian evolution arose over millions of years and were recorded in the genetic memory of the species. My question is, assuming a Lamarckian anticipatory system both evolved and is necessary for the survival of a species, how did the species do without this mechanism at a time when environmental upheaval on the planet was the norm rather than the exception?Mapou
June 13, 2009
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Andrew, THis quotation was taken from an answer to the question "What light do new developments in molecular biology shed on the importance of Darwin's natural selection compared to, say, Lamarckian modes of inheritance?" First, the question itself shows great confusion because there is no fundamental discord between Lamarckian modes of inheritance and evolution. Second, taken in context, Dupre was referring not to evolution but to the central dogma of molecular biology- that information from DNA flows outward only, and is not affected by environment. Dupre is saying that the environment of the cell, perhaps affected by transcripts of junk DNA, can affect gene expression, contrary to the dogma. thus, it would be more accurate to say that "the fundamental dogma of molecular biology needs to be laid quietly to rest as scientific discoveries progress."Khan
June 13, 2009
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