DNA Information Evolution and ID

[SailingCyclops]

In a Random Ramblings discussion dadman asserted:

.. since all code derives from an intelligent source . . .
[...]
I do believe the subject is not so much evolution . . . but intelligence . . .
do you know anything about this "evolution coder/de-coder" ??

ref:This post

The assertion is made that since DNA is a code, there must be a coder. Presumably, some intelligent entity.

Questions for debate:

Is the coding, and information transfer we observe in DNA a product of evolution by natural selection? Or does DNA information and it's transfer demand an intelligence?

Does all code derive from an intelligent source?

Bob

[Starboard Tack]

If the process is natural, then you should have an explanation for where the DNA came from in the first place.

I though we had some pretty good ideas already?

What would be your favorite for the origin of the universal DNA code? RNA world? Thioester World?

If you don't have that explanation, but believe that it's only because we haven't studied the problem enough, you're not up to date on origins research, where the bottom up approach has all but been abandoned, with teams like Venters throwing in the towel on where life came from and have turned instead to doing remarkable science using the building blocks whose origins are inexplicable.

A quick scopus search showed me around 60 papers on abiogenesis within the past 5 years.

60 papers in 5 years. Perhaps do a quick count on how many papers have been published on say, mettallurgy, or oncology and see what you come up with.

By positioning that all of this is "natural" like an earthquake, avalanche or oxidation is tap dancing away from the problem, but I suppose is a necessary part of the philosophical requirements for hard core methodological naturalism.

We try to reason out the problem using the knowledge we have. We dont give up and resort to "god did it". If we had all the answers, we would have no need to continue searching. Just because the problem is hard, doesnt mean that "god" is the answer

Completely agree. However, if the knowledge is not advancing under the current paradigm of thought, perhaps it is time to change?

Back to Iris Fry, she wrote something pretty interesting. She is so contemptuous of anyone who would be dumb enough to believe in God that she sometimes doesn't seem to realize what her statements actually say about the basis of her position, (nevermind that of many on this thread). She wrote on page 213 of "The Emergence of Life on Earth": "Thus the theory of evolution is indeed based on a naturalistic wordview that entails a metaphysical commitment...." She goes onto to say that her metaphysics are fine what with being based on science and all. Couldn't have said it better myself. Evolution = metaphysics. So I suppose to her as well, the existence of the DNA code is just something "natural."

Im not sure you are quoting her properly because in the preceeding pages she seems to say something different.

The quote is verbatim. On page 211, she writes: "My claim is that origin of life scientists, purposefully or inadvertently, implicitly or explicitly, by the very act of conducting their research are making a philosophical decision and taking a metaphysical stand." Seems like she is saying that naturalism is a metaphysical and philosophical position. She feels it is the only sane position, of course, but it is interesting that she acknowledges what so many atheists get all fluttery over when you point it out to them.

[nygreenguy]

What would be your favorite for the origin of the universal DNA code? RNA world? Thioester World?

Currently, I like the RNA world hypothesis

60 papers in 5 years. Perhaps do a quick count on how many papers have been published on say, mettallurgy, or oncology and see what you come up with.

Thats just using one database and one term, which is not used as much as you would think. Many papers are just titled "origins of life" research, so it was a brief examination but it shows that there is still research being done.

By positioning that all of this is "natural" like an earthquake, avalanche or oxidation is tap dancing away from the problem, but I suppose is a necessary part of the philosophical requirements for hard core methodological naturalism.

We try to reason out the problem using the knowledge we have. We dont give up and resort to "god did it". If we had all the answers, we would have no need to continue searching. Just because the problem is hard, doesnt mean that "god" is the answer

Completely agree. However, if the knowledge is not advancing under the current paradigm of thought, perhaps it is time to change?

Well I see it as advancing.

Back to Iris Fry, she wrote something pretty interesting. She is so contemptuous of anyone who would be dumb enough to believe in God that she sometimes doesn't seem to realize what her statements actually say about the basis of her position, (nevermind that of many on this thread). She wrote on page 213 of "The Emergence of Life on Earth": "Thus the theory of evolution is indeed based on a naturalistic wordview that entails a metaphysical commitment...." She goes onto to say that her metaphysics are fine what with being based on science and all. Couldn't have said it better myself. Evolution = metaphysics. So I suppose to her as well, the existence of the DNA code is just something "natural."

Im not sure you are quoting her properly because in the preceeding pages she seems to say something different.

The quote is verbatim. On page 211, she writes: "My claim is that origin of life scientists, purposefully or inadvertently, implicitly or explicitly, by the very act of conducting their research are making a philosophical decision and taking a metaphysical stand." Seems like she is saying that naturalism is a metaphysical and philosophical position. She feels it is the only sane position, of course, but it is interesting that she acknowledges what so many atheists get all fluttery over when you point it out to them.

It appears to me you misinterpret what she is saying. Perhaps I can explain further tomorrow, Ive got to get to bed. Killer headache all day....ugh....

[Starboard Tack]

What would be your favorite for the origin of the universal DNA code? RNA world? Thioester World?

Currently, I like the RNA world hypothesis

Leslie Orgel, one of the originators of that approach, acknowledged towards the end of his life that "it would have taken a miracle for a single strand of RNA to ever appear on the early earth." This was stated at the 2002 ISOOL meeting in his presentation. The problems with the model are significant, and my impression is that most researchers are now looking for a 'pre-RNA' world approach that might bring RNA into existence since it certainly doesn't look like it can manifest itself on its own. There was a lot of excitement about clay substrates as possible catalysts, but those don't seem to work since once you get a polymer over about 50 long you can't get the molecule unstuck. That plus you have to introduce stringent laboratory conditions to get anywhere, and presumably there was a shortage of laboratories on early earth. Read some of Robert Shapiro's thoughts on this. He's a naturalist, but is ruthless in pointing out how impossible the RNA scenario is.

60 papers in 5 years. Perhaps do a quick count on how many papers have been published on say, mettallurgy, or oncology and see what you come up with.

Thats just using one database and one term, which is not used as much as you would think. Many papers are just titled "origins of life" research, so it was a brief examination but it shows that there is still research being done.

Yes, I understand. You're at NYU, correct? I believe Shapiro is there as well, or he was. Take him to lunch and find out what he thinks about the current state of OOL research.

By positioning that all of this is "natural" like an earthquake, avalanche or oxidation is tap dancing away from the problem, but I suppose is a necessary part of the philosophical requirements for hard core methodological naturalism.

We try to reason out the problem using the knowledge we have. We dont give up and resort to "god did it". If we had all the answers, we would have no need to continue searching. Just because the problem is hard, doesnt mean that "god" is the answer

Completely agree. However, if the knowledge is not advancing under the current paradigm of thought, perhaps it is time to change?

Well I see it as advancing.

Look closer. Talk to Shapiro.

Back to Iris Fry, she wrote something pretty interesting. She is so contemptuous of anyone who would be dumb enough to believe in God that she sometimes doesn't seem to realize what her statements actually say about the basis of her position, (nevermind that of many on this thread). She wrote on page 213 of "The Emergence of Life on Earth": "Thus the theory of evolution is indeed based on a naturalistic wordview that entails a metaphysical commitment...." She goes onto to say that her metaphysics are fine what with being based on science and all. Couldn't have said it better myself. Evolution = metaphysics. So I suppose to her as well, the existence of the DNA code is just something "natural."

Im not sure you are quoting her properly because in the preceeding pages she seems to say something different.

The quote is verbatim. On page 211, she writes: "My claim is that origin of life scientists, purposefully or inadvertently, implicitly or explicitly, by the very act of conducting their research are making a philosophical decision and taking a metaphysical stand." Seems like she is saying that naturalism is a metaphysical and philosophical position. She feels it is the only sane position, of course, but it is interesting that she acknowledges what so many atheists get all fluttery over when you point it out to them.

It appears to me you misinterpret what she is saying. Perhaps I can explain further tomorrow, Ive got to get to bed. Killer headache all day....ugh....

[nursebenjamin]

60 papers in 5 years. Perhaps do a quick count on how many papers have been published on say, mettallurgy, or oncology and see what you come up with.

Thats just using one database and one term, which is not used as much as you would think. Many papers are just titled "origins of life" research, so it was a brief examination but it shows that there is still research being done.

Yes, I understand. You're at NYU, correct? I believe Shapiro is there as well, or he was. Take him to lunch and find out what he thinks about the current state of OOL research.

Robert Shapiro is dead, so no one will be inviting him to lunch. Shapiro did argue against a sudden and spontaneous emergence of RNA. He proposed an energy-driven networks of small molecules model of abiogenesis.[1] Robert Shapiros model in no way supports your argument that bottom-up research on abiogenesis has all but been abandoned. Nor does it support your claim that the science of abiogenesis is not advancing.

Examining the various proposed models of abiogenesis is interesting stuff, but likely beyond the scope of this forum. Theres almost certainly a natural process by which the first replicating molecules appeared on earth. Perhaps we shouldnt get too bogged down over which hypothesis currently has more support?

[nursebenjamin]

I'm tired of revolving around the same old mulberry bush. Here is a reference that introduces the possibility that mutations may not be spontaneous and random. In fact they may be controlled by the environement. Epigenetic?
http://www.sciencedaily.com/releases/20 ... 145519.htm

Weve discussed the research from your link in another thread. The article mentions mutations, but the article is really about natural selection on an existing mutation and population-specific allele frequency changes.

<<<Here is a reference that introduces the possibility that mutations may not be spontaneous and random. In fact they may be controlled by the environement.>>>
What is meant by spontaneous and random? Weve talked about this before.

Clearly, the environment can induce some mutations: radiation, UV light, chemicals, and some viruses can all affect the rate of mutation.

Also, genomes are said to have hot spots and cold spots with regards to mutation rates. Some genes are more prone to mutation, and others, such as those that code for histones have been highly conserved across species.

Some bacteria have a pathway or mechanism that can regulates the rate of mutations. In a stressful environment, the mechanism triggers an SOS response that increases the rate of mutations. It would do this by making DNA replication more prone to mutations or by disabling the machinery that repairs mutations. This is SOS response is also known as adaptive mutations or Directed mutagenesis.

What random means is they have no definite aim or purpose; not guided towards a particular direction. Even if the rate of mutation increases, they are still basically random with regards to where they occur in the genome.[3] There is no guiding cause to mutations. Even if organisms have an SOS response, the mechanism is still complex organic chemistry, not the bacteria making a conscious decision to mutation in a certain way.

... The introduction clause of the article said:

For more than a decade, Dr. Susan Rosenberg, professor of molecular and human genetics at Baylor College of Medicine, has solidified her premise that when cells are under stress, the rate of gene changes called mutations goes up
Source: redOrbit (http://s.tt/13Ysv)

Emphasis added.

That quote is not in the article that you linked.

... The mundane and hardly proven premise that all mutations are errors has always seemed peculiar to me.

Mutations are, by definition, errors in the DNA sequence. Not all of the errors in the DNA base sequence occurred during replication. Radiation, UV light, chemicals, and viruses cause some mutations. As for your question of why the process of DNA replication isnt perfect, I cant answer. Perhaps its just a crappy design? DNA replication is simply an imprecise process[4]. Some mutations are simply spontaneous in nature because DNA replication and repair is not 100%.

I think that your argument is that epigenetics (though you are now talking about plain old gene regulation, not epigenetics) could be responsible for some mutations, ie. the SOS response. Is this correct? This particular argument for adaptive mutagenesis is all well and good, and theres evidence to support adaptive mutations. However, again, this in no way counters the Modern Evolutionary Synthesis.

[Starboard Tack]

60 papers in 5 years. Perhaps do a quick count on how many papers have been published on say, mettallurgy, or oncology and see what you come up with.

Thats just using one database and one term, which is not used as much as you would think. Many papers are just titled "origins of life" research, so it was a brief examination but it shows that there is still research being done.

Yes, I understand. You're at NYU, correct? I believe Shapiro is there as well, or he was. Take him to lunch and find out what he thinks about the current state of OOL research.

Robert Shapiro is dead, so no one will be inviting him to lunch. Shapiro did argue against a sudden and spontaneous emergence of RNA. He proposed an energy-driven networks of small molecules model of abiogenesis.[1]

Robert Shapiros model in no way supports your argument that bottom-up research on abiogenesis has all but been abandoned. Nor does it support your claim that the science of abiogenesis is not advancing.

Ah, I see he died in June. Sad. I listened to an interview with him earlier this year and he was an outstanding scientist.

I don't belief I said that Shapiro's work disproved a bottom up approach to OOL research. In fact, his work was directed at the only alternative to replication first for an origin - metabolism first - which is another bottom up proposal dependent on chemical evolution. As I believe William Schopf stated, if replication first can't work, and metabolism first can't work, then you're stuck with Intelligent Design (horror of horrors.) Unfortunately, neither proposal seems to be able to be made to work, although perhaps we will one day discover the chemical process that can't be made to happen under controlled conditions in the lab supervised by brilliant minds that can occur in a mud puddle. Can't wait.

Incidentally, if you look into Dr. Shapiro's work, you'll find it dependent on the existence of a cell membrane. Just as we know that the cell is no simple blob of protoplasm, we now know this simple entity doesn't look so simple anymore, and figuring out how it could come into existence on primordial earth so the rest of a metabolism first model can work is looking less likely the more we learn about how such membranes are sturtured and function.

Examining the various proposed models of abiogenesis is interesting stuff, but likely beyond the scope of this forum. Theres almost certainly a natural process by which the first replicating molecules appeared on earth. Perhaps we shouldnt get too bogged down over which hypothesis currently has more support?

That would be a metaphysical, not a scientific statement, equivalent to my saying "there's almost certainly no natural process by which the first replicating molecule appeared on earth." The difference would be that my metaphysical statement would have scientific backing, while yours appears to be wishful thinking, given the state of OOL research.

[nygreenguy]

Ah, I see he died in June. Sad. I listened to an interview with him earlier this year and he was an outstanding scientist.

I was going to say I would get weird looks going to lunch with a corpse.

As I believe William Schopf stated, if replication first can't work, and metabolism first can't work, then you're stuck with Intelligent Design (horror of horrors.)

Which is just a false dilemma.

Incidentally, if you look into Dr. Shapiro's work, you'll find it dependent on the existence of a cell membrane. Just as we know that the cell is no simple blob of protoplasm, we now know this simple entity doesn't look so simple anymore, and figuring out how it could come into existence on primordial earth so the rest of a metabolism first model can work is looking less likely the more we learn about how such membranes are sturtured and function.

The first membrane would be quite simple. If you want to see how membranes work, put a drop of oil in water. The only thing that makes membranes different is they have a hydrophobic AND a hydrophillic end.

[nygreenguy]

The article said:

"We made a list of the genes that changed the most," Nielsen said, "and what was fascinating was that, bing!, at the top of that list was a gene that had changed very strongly, and it was related to the response to oxygen."
The SNP with the most dramatic change in frequency, from 9 percent in Han Chinese to 87 percent in Tibetans, was associated with lower red blood cell count and lower hemoglobin levels in Tibetans. That variation occurred near a gene called EPAS1, which earlier studies suggest is involved in regulating hemoglobin in the blood as a response to oxygen levels. The mutation may be in a transcription factor that regulates the activity of EPAS1.
Tibetans carrying only one allele with this mutation had about the same hemoglobin concentration as Han Chinese, but those with two mutated alleles had significantly lower hemoglobin concentration. However, they all have about the same oxygen concentration in the blood. For some reason, individuals with two copies of the mutation function well in high altitude with relatively low hemoglobin concentration in their blood. The mutation seems to provide an alternative inborn mechanism for dealing with the low oxygen levels, Nielsen said.

Where does the article suggest the mutations were not "spontaneous" or "random"?

Cherry picking, always cherry picking. The introduction clause of the article said:

For more than a decade, Dr. Susan Rosenberg, professor of molecular and human genetics at Baylor College of Medicine, has solidified her premise that when cells are under stress, the rate of gene changes called mutations goes up
Source: redOrbit (http://s.tt/13Ysv)

Emphasis added.

and:

This time, she used bacteria that had a defective gene for resistance to an antibiotic called tetracycline. If the gene had worked, the cells would be resistant to the antibiotic. Instead, these cells were susceptible. Again, she starved the cells. In response to the starvation, the cells increased their rate of mutation including mutation of the defective gene.
Source: redOrbit (http://s.tt/13Ysv)

and:

In another set of experiments, she and her colleagues attempted to find out how much stress-induced mutagenesis contributed to spontaneous mutation. To do this, they studied starved cells that were not being stimulated with a second stressor, a DNA break.

One by one, they eliminated the stress-response pathways within the cells that they knew contributed to stress-induced mutagenesis.

"When we did that, half of the mutagenesis went away," said Rosenberg. "That means we can say half of spontaneous mutation is stress-inducible.

Source: redOrbit (http://s.tt/13Ysv)

Mutations are still random. Do you understand the underlying genetics on WHY there was increased mutation (or how we get mutations at all)? Stress tends to create more mutations because the cells are working faster. We are getting more activity within the genome increasing the rate of mutations.

If they have a lottery drawing 5 times a day instead of once, the results are still just as random, they just happen more frequently.

The main premise of epigenetic changes is they are environment driven. Obviously, what she has found here is that the rate of mutations is also environmentally driven. Coincidence?

Yes. Can you show otherwise how the two are in any way causally correlated?

The mundane and hardly proven premise that all mutations are errors has always seemed peculiar to me.

A mutation is, by definition, an error.

First a mistake has to be made. Considering millions of individual base pair copies are made why do a few get copied wrong.

Because it is imperfect.

Then there is the proof reading mechanism that corrects the errors.

Which is also imperfect.

It seems strange and highly improbable that this mechanism would fail to correct some of the same errors made previously.

Do you understand the mechanism, the protein complexes involved and how they interact? Once an error gets past the first proofreading, it will not ever be switched back to the "original" because of the nature of the mechanism. The mechanism has no knowledge of what the sequence should be, it only checks for errors through chemical physical incompatibility.

It would seem far more probable that the proof reading mechanism would miss correct some base pairs.

Most of the time, the proofing mechanism and the DNA replicator are the same protein (DNA ploymerase) although there are other enzymes involved.

The question needs to be asked why is the proof reading mechanism 100% efficient on millions of base pairs and then goof on the very few miss copied base pairs.

This statement doesnt make sense. It is like me looking at a test where I got 2 problems wrong and saying "I got a 100% expect for these 2 problems!"

Of course I am looking at all this from a purely logical standpoint, but it seems to me that scientists are blindly accepting a premise just as they blindly accepted "junk DNA."

Instead of criticizing the people who spend their lives doing this, and doing this pretty effectively, have you considered the fact you may be wrong?

Also, you cant do science by logic alone. All logic does is analyze statements. If you dont have the scientific background to make, understand, or interpret the facts and concepts, logic is useless.

[nygreenguy]

I don't belief I said that Shapiro's work disproved a bottom up approach to OOL research. In fact, his work was directed at the only alternative to replication first for an origin - metabolism first - which is another bottom up proposal dependent on chemical evolution. As I believe William Schopf stated, if replication first can't work, and metabolism first can't work, then you're stuck with Intelligent Design (horror of horrors.) Unfortunately, neither proposal seems to be able to be made to work, although perhaps we will one day discover the chemical process that can't be made to happen under controlled conditions in the lab supervised by brilliant minds that can occur in a mud puddle. Can't wait.

Incidentally, if you look into Dr. Shapiro's work, you'll find it dependent on the existence of a cell membrane. Just as we know that the cell is no simple blob of protoplasm, we now know this simple entity doesn't look so simple anymore, and figuring out how it could come into existence on primordial earth so the rest of a metabolism first model can work is looking less likely the more we learn about how such membranes are sturtured and function.

Examining the various proposed models of abiogenesis is interesting stuff, but likely beyond the scope of this forum. Theres almost certainly a natural process by which the first replicating molecules appeared on earth. Perhaps we shouldnt get too bogged down over which hypothesis currently has more support?

That would be a metaphysical, not a scientific statement, equivalent to my saying "there's almost certainly no natural process by which the first replicating molecule appeared on earth." The difference would be that my metaphysical statement would have scientific backing, while yours appears to be wishful thinking, given the state of OOL research.

And remember the Crick paper? Here are some more which support exactly what I was saying.

http://www.ncbi.nlm.nih.gov/pubmed/15764708
J Theor Biol. 2005 Apr 21;233(4):527-32. Epub 2004 Dec 29.
The triplet genetic code had a doublet predecessor.
Patel A.
Source
Centre for High Energy Physics and Supercomputer Education and Research Centre, Indian Institute of Science, Bangalore 560012, India. adpatelcts.iisc.ernet.in
Abstract
Information theoretic analysis of genetic languages indicates that the naturally occurring 20 amino acids and the triplet genetic code arose by duplication of 10 amino acids of class-II and a doublet genetic code having codons NNY and anticodons GNN. Evidence for this scenario is presented based on the properties of aminoacyl-tRNA synthetases, amino acids and nucleotide bases.


www.ncbi.nlm.nih.gov/pubmed/16059752?or ... rom=pubmed
Evolution of the genetic triplet code via two types of doublet codons.
Wu HL, Bagby S, van den Elsen JM.
Source
Department of Biology and Biochemistry, University of Bath, 4 South, Claverton Down, Bath BA2 7AY, UK.
Erratum in
J Mol Evol. 2006 Sep;63(3):426.
Abstract
Explaining the apparent non-random codon distribution and the nature and number of amino acids in the 'standard' genetic code remains a challenge, despite the various hypotheses so far proposed. In this paper we propose a simple new hypothesis for code evolution involving a progression from singlet to doublet to triplet codons with a reading mechanism that moves three bases each step. We suggest that triplet codons gradually evolved from two types of ambiguous doublet codons, those in which the first two bases of each three-base window were read ('prefix' codons) and those in which the last two bases of each window were read ('suffix' codons). This hypothesis explains multiple features of the genetic code such as the origin of the pattern of four-fold degenerate and two-fold degenerate triplet codons, the origin of its error minimising properties, and why there are only 20 amino acids.



www.ncbi.nlm.nih.gov/pubmed/15748913?or ... logdbfrom=
Proc Natl Acad Sci U S A. 2005 Mar 22;102(12):4442-7. Epub 2005 Mar 11.
A mechanism for the association of amino acids with their codons and the origin of the genetic code.
Copley SD, Smith E, Morowitz HJ.
Source
Cooperative Institute for Research in Environmental Sciences, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA. shelleycires.colorado.au
Abstract
The genetic code has certain regularities that have resisted mechanistic interpretation. These include strong correlations between the first base of codons and the precursor from which the encoded amino acid is synthesized and between the second base of codons and the hydrophobicity of the encoded amino acid. These regularities are even more striking in a projection of the modern code onto a simpler code consisting of doublet codons encoding a set of simple amino acids. These regularities can be explained if, before the emergence of macromolecules, simple amino acids were synthesized in covalent complexes of dinucleotides with alpha-keto acids originating from the reductive tricarboxylic acid cycle or reductive acetate pathway. The bases and phosphates of the dinucleotide are proposed to have enhanced the rates of synthetic reactions leading to amino acids in a small-molecule reaction network that preceded the RNA translation apparatus but created an association between amino acids and the first two bases of their codons that was retained when translation emerged later in evolution.


http://nar.oxfordjournals.org/cgi/conte ... 27/17/3389
Did DNA replication evolve twice independently?
Detlef D. Leipe, L. Aravind1 and Eugene V. Koonin
DNA replication is central to all extant cellular organisms. There are substantial functional similarities between the bacterial and the archaeal/eukaryotic replication machineries, including but not limited to defined origins, replication bidirectionality, RNA primers and leading and lagging strand synthesis. However, several core components of the bacterial replication machinery are unrelated or only distantly related to the functionally equivalent components of the archaeal/eukaryotic replication apparatus. This is in sharp contrast to the principal proteins involved in transcription and translation, which are highly conserved in all divisions of life. We performed detailed sequence comparisons of the proteins that fulfill indispensable functions in DNA replication and classified them into four main categories with respect to the conservation in bacteria and archaea/eukaryotes: (i) non-homologous, such as replicative polymerases and primases; (ii) containing homologous domains but apparently non-orthologous and conceivably independently recruited to function in replication, such as the principal replicative helicases or proofreading exonucleases; (iii) apparently orthologous but poorly conserved, such as the sliding clamp proteins or DNA ligases; (iv) orthologous and highly conserved, such as clamp-loader ATPases or 35 exonucleases (FLAP nucleases). The universal conservation of some components of the DNA replication machinery and enzymes for DNA precursor biosynthesis but not the principal DNA polymerases suggests that the last common ancestor (LCA) of all modern cellular life forms possessed DNA but did not replicate it the way extant cells do. We propose that the LCA had a genetic system that contained both RNA and DNA, with the latter being produced by reverse transcription. Consequently, the modern-type system for double-stranded DNA replication likely evolved independently in the bacterial and archaeal/eukaryotic lineages.

[Starboard Tack]

Ah, I see he died in June. Sad. I listened to an interview with him earlier this year and he was an outstanding scientist.

I was going to say I would get weird looks going to lunch with a corpse.

As I believe William Schopf stated, if replication first can't work, and metabolism first can't work, then you're stuck with Intelligent Design (horror of horrors.)

Which is just a false dilemma.

It's only a false dilemma if it is untrue. Beyond life beginning with replication or with metabolism, what do you propose as the third naturalistic option?

Incidentally, if you look into Dr. Shapiro's work, you'll find it dependent on the existence of a cell membrane. Just as we know that the cell is no simple blob of protoplasm, we now know this simple entity doesn't look so simple anymore, and figuring out how it could come into existence on primordial earth so the rest of a metabolism first model can work is looking less likely the more we learn about how such membranes are sturtured and function.

The first membrane would be quite simple. If you want to see how membranes work, put a drop of oil in water. The only thing that makes membranes different is they have a hydrophobic AND a hydrophillic end.

I suppose the first membrane could be simple. But if simple, shouldn't we be able to make one that functions? Intelligence plus money plus equipment can't, but you would propose that chemicals in a warm pond could? By the way, stating that a cell membrane is only more complicated than a drop of oil on the basis of its bilayer structure is real thigh slapper. That and the ability to encapsulate metabolic chemical processes, transport molecular compounds to sustain the metabolic processes, and spontaneously grow and divide. But other than that, just like a drop of oil.