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Author Topic:   The "Digital Code" of DNA
Matt P
Member (Idle past 4884 days)
Posts: 106
From: Tampa FL
Joined: 03-18-2005


Message 63 of 143 (409633)
07-10-2007 4:00 PM
Reply to: Message 62 by iceage
07-10-2007 2:36 AM


Dean Kenyon
quote:
Dean Kenyon was the leading evolutionary biologist in 1970s and 1980s, but eventually became a reluctant creationist after being challenged by one of his students to explain protein assembly without original sequence information
Ha! How disingenuous! I've recently read Dean Kenyon's own pre-creationist book "Biochemical Predestination", which is surprisingly good and well-researched for its time (1969). He has a full chapter on prebiotic polymer/protein assembly without genetic information, so I find it quite hard to believe that he would have completely converted with so simple a question.
Also, Kenyon wasn't a leading evolutionary biologist in the 1980s. His last publication was 1976, and most of his work was done in the 1960s on prebiotic chemistry.
Convert first, rethink evolution later...

This message is a reply to:
 Message 62 by iceage, posted 07-10-2007 2:36 AM iceage has not replied

Replies to this message:
 Message 64 by Rob, posted 07-12-2007 2:02 AM Matt P has not replied

  
Matt P
Member (Idle past 4884 days)
Posts: 106
From: Tampa FL
Joined: 03-18-2005


Message 115 of 143 (410165)
07-13-2007 2:57 PM
Reply to: Message 101 by Rob
07-13-2007 2:18 AM


Re: Dean Kenyon
Hi Rob,
Isn't it interesting that he remains silent.
I'm quite busy and tend not to respond instantaneously, what with work, research, homelife, and all. I also don't have sound on this computer, so I can't listen to the video here, though I did listen to the first half of it at home when you posted it. All I can recall is that the first half completely ignored the role of RNA. I will need to listen to fully engage in this discussion.
I stand by my claim of disingenuous, especially with regards to the way the website you linked to that introduced the video. I've investigated a bit further, and Dean Kenyon was never trained as an evolutionary biologist. His training is in prebiotic/organic chemistry. He also was never a "leading" researcher, he has a grand total of two first author publications (journals and major books), of which one was his book "Biochemical Predestination". The way the website presents may be considered grandstanding, but it's grandstanding to a deceptive degree.
Again, I will try to watch your video again once I get more time at home to do so.

This message is a reply to:
 Message 101 by Rob, posted 07-13-2007 2:18 AM Rob has replied

Replies to this message:
 Message 116 by Rob, posted 07-14-2007 2:15 AM Matt P has replied

  
Matt P
Member (Idle past 4884 days)
Posts: 106
From: Tampa FL
Joined: 03-18-2005


Message 119 of 143 (410277)
07-14-2007 5:15 AM
Reply to: Message 116 by Rob
07-14-2007 2:15 AM


Re: Concession + not so fast...
Hi Rob,
Fair enough- I'm basing my assessment of Kenyon solely on what he has published. As far as I can tell, he's never done any biological research, which is the qualifying characteristic of someone labeled a biologist. Still, it's definitely not the point at hand.
I'm glad for your redirect into the field of prebiotic chemistry. You quote Shapiro:
The attractive features of RNA World prompted Gerald Joyce of the Scripps Research Institute and Leslie Orgel of the Salk Institute to picture it as "the molecular biologist's dream" within a volume devoted to that topic. They also used the term "the prebiotic chemist's nightmare" to describe another part of the picture: How did that first self-replicating RNA arise?
Shapiro is the author of "A skeptic's guide to the origin of life", which he wrote in part to combat the irrational exuberance exhibited by many of his contemporaries (including some of what's in "Biochemical Predestination"). A lot of what he discusses includes the random assembly of amino acids to form proteins, or the spontaneous assembly of a strand of RNA. His counter-proposal is that life began with short monomers, wherein proto-metabolic processes eventually led to life (he's termed it "Garbage bag world" if you'd like to look it up- I'm not sure if it's published, this is just what I saw him present at a conference).
I think it's extremely important to raise the points that 1) the weak RNA world is nearly universally accepted by prebiotic chemists, and 2) the strong RNA World is only accepted by about half of prebiotic chemists. Sorry for the confusion, but there are two fundamental tenets of the RNA-World.
The weak RNA world holds that an RNA-based system preceded the DNA/Protein world we have today. This is pretty well evidenced in biochemistry, from RNA fragments dominating metabolic cofactors, to ribozymes playing key roles, and in the fact that ribosomal peptide synthesis is an RNA catalyzed reaction. Cech and others won the Nobel prize for the discovery of the ribozyme, and not even Shapiro doubts that RNA preceded the DNA/protein world of today.
Conceptualize the weak RNA world as follows, with "?" being the gap in our knowledge:
?--> RNA --> DNA/Protein
Shapiro's main beef is with the "strong RNA World", which suggests that the origin of life corresponds to the de novo synthesis of an autocatalytic, self-replicating ribozyme. The strong RNA world provides a very definite view of the origin of life, and frankly, Shapiro is justified in his skepticism. The de novo synthesis of this ultimate ribozyme from random nucleotides is highly unlikely, as is the specific formation of those nucleotides in quantities high enough to proceed. However, it's still a common theme encountered in the prebiotic chemist/origin of life community, mainly due to the strong emphasis of DNA and genetics in biology. It's kind of funny- among prebiotic researchers, pure chemists are the most likely to follow the strong RNA world, whereas geochemists, cosmochemists, and even some physicists don't agree (I'm in this latter camp).
Conceptualize the strong RNA world as follows:
non-life --> RNA --> DNA/Protein
However, this does reveal a counter straw-man: the RNA world (weak version) is extremely well supported, and fairly well fits into the idea that catalysts and replicators can be the same thing. When researchers like Shapiro dismiss the RNA world, they're usually dismissing the "strong" version. The weak version is quite well supported, and be cautious that broad dismissals of the RNA world are usually dismissals of only the strong version, not the whole thing. This also kind of dampens the idea that there's a mystical relationship between DNA and protein (I know you didn't say that, but this is something I got from the title of the video, "Unlocking Life's Mysteries"). However, the RNA world (strong version) is much more difficult to conceptualize, though it's still a fairly active area of research. As much as I doubt the strong version of the RNA world, the spontaneous assembly of nucleotides into RNA is remarkably easy- you can do it on the surface of clays, by drying bubbles, on PAHs, even with a bit of heat. It's not dismissable out of hand (don't dismiss what hasn't been tried yet!). What we don't know with this may still come around to be demonstrable- for example, I think the smallest autocatalytic RNA strand is currently clocked at about 30 nucleic acids, which is starting to get past that "miraculous" and move into the realm of only "difficult".
What Shapiro doesn't like is the strong version of the RNA world. He's fine with the weak version (based on my personal conversations). Many who don't like the strong RNA world suggest instead a metabolic-focused life which would form the chemicals that lead to replicative material through specific chemical reactions. It's easy to do chemistry when something is making the starting materials. This already-developed metabolism assisted with the eventual appearance of RNA, giving it the necessary support for the origin.
So, my main point here is that there are two views of the RNA world- one that is immensely well supported (and which solves the chicken/egg problem of DNA/protein), the other of is still in the realm of "unlikely, but maybe."
Hope this helps!

This message is a reply to:
 Message 116 by Rob, posted 07-14-2007 2:15 AM Rob has replied

Replies to this message:
 Message 120 by Rob, posted 07-14-2007 10:20 AM Matt P has replied

  
Matt P
Member (Idle past 4884 days)
Posts: 106
From: Tampa FL
Joined: 03-18-2005


Message 122 of 143 (410394)
07-14-2007 7:23 PM
Reply to: Message 120 by Rob
07-14-2007 10:20 AM


Re: Concession + not so fast...
Rob- it's a bit difficult to get your objections when you have so much extraneous material in your post. Some of it seems to be random rants and side commentaries. Also, what do you mean by 'theo'? God? Theorizing? Why the disdain for speculation? As scientists, we research these projects because they are fun, and because along the way impressive results can be produced. Two examples off the top of my head are Victor Hruby, who does some origins of life research and who has helped invent a new class of drugs for fighting cancer and diabetes (Page not found | Biochemistry and Molecular & Cellular Biology Graduate Program), and Steve Benner, whose research into alternative nucleobases in the origin of life has also led to a potent new class of drugs (Object not found!). My own research may eventually benefit dentistry and environmental remediation, though it's focused on origins work.
When we do know... then all of this 'theo' may actually be worth something more than the title of science fiction. All of the technical jargon is not useful at all other than for the purpose of intimidation, of which I am not inclined.
You boys speak often of testability (the hallmark of science) yet you are far from it...
Without a doubt, there are gaps in our knowledge. However, in many ways it's because the experiments haven't been done yet. Research in the origin of life is still beginning in some respects, and sticking God in there does a disservice to both God and to research. The amount of extra variables in the experimental setups is huge, and takes time to explore. As a recent example, the Miller-Urey synthesis has been criticized for a lack of production of amino acids under a CO2 atmosphere (as opposed to a CH4 atmosphere). However, the addition of small amounts of ferrous salts increased their production significantly even under these oxidizing conditions. In the case of this experiment, there were untried conditions. All the experiments are testable, and repeatable, so I'm not sure of your objection there.
This smallest autocatalytic strand you talk of, with 30 amino acids... is that a computer generated model? If so, were the computer and the software not designed by intelligent agents for the purpose of creating this cenario? If not, was it found within the confines of an already complete organism?
One might tend to think it was found all alone in some swamp the way you referred to it. As though it were anything more than grand speculation. What do you mean clocked? Do you mean postulated by a computer 'virtual creation' with intelligent agents at the helm who's purpose is to show that we don't need intelligent guidance?
Molbiogirl has directed you to one set of experiments, and there have been more done recently. From Joyce (Science 16 March 2007), citing work done by Robertson and Scott in the same issue:
No known RNA enzyme in biology catalyzes the polymerase-like joining of RNA. However, the powerful methods of in vitro evolution have made it possible to generate such enzymes from scratch, starting from a large population of RNAs with random sequences
These projects weren't done on computer, nor were they based on biology. They were formed by random assembly and selection.
By clocked, I mean the smallest strand. It's a research race to get the smallest molecule amongst RNA workers, and so far its about 30 units long.
Like intelligent agents in a lab coat? You might succeed some day... but don't count your chickens until you first design a fertile egg (and keep it nice and warm in an incubator specifically designed for that egg).
...
Isaac Asimov would be proud of the way you refer to imaginary things as though they are real.
What? You've parsed a single paragraph too much here. I've never presented these as anything beyond speculation.
Speculation may be shown to be correct or incorrect depending on work in the future. Schrodinger speculated on DNA in the 1940s, was DNA imaginary prior to its discover by Watson and Crick? No, DNA is real. Maxwell postulated the existence of an ether, till disproved by Einstein and colleagues. Was the ether imaginary? Yes. But we're not at the proving/disproving point yet with this research, so we can't claim it's imaginary or anything else.
When you say 'immensely well supported' do you mean that it is a very popular 'theo'ry'? Because you almost give the impression that there is actually evidence that self exists out there... like some uncaused, self evident truth (better known as logic).
As molbiogirl says, it's quite well supported by about 25 years of research. We're just starting to use RNA, ribozymes, and such in a variety of medical practices.
The fault with your video is that it suggests only that the following exists:
DNA codes for protein which catalyzes the formation of DNA.
In reality, it's:
DNA codes for RNA which is a potent catalyst itself for many reactions, which can transfer genetic information, bits of which are metabolic coenzymes, and which catalyzes the formation of proteins which catalyze the formation of DNA.
It's no longer a "which came first" problem when an entity can do both things.
Matt, fate takes some strange twists... these arguments they give you are not just exaggerations, but beyond conjecture presented as fact, they are pure deception; clever, pea palming magic. They are miraculous signs and wonders...
...
Gaurd your mind friend. There are wolves who seek to devour you.
The origins field is especially cautious not to let speculation become dogma, like all science should be. In fact, because of the wealth of research opportunities, origins scientists are much more tolerant of unusual ideas. Your accusation of deception is a bit silly too, and I don't understand why you make it. How is speculation deceptive? I for one don't believe the strong RNA world is the answer, but that future work will eventually reveal the answer. If not in my lifetime, then so be it.

This message is a reply to:
 Message 120 by Rob, posted 07-14-2007 10:20 AM Rob has replied

Replies to this message:
 Message 128 by Rob, posted 07-15-2007 1:56 AM Matt P has not replied

  
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