A Minimal Genome
by BradfordStephen Jones of CreationEvolutionDesign has posted on 'Smallest genome clocks in at 182 genes' Some of his comments appear below in bold print. The context can be seen in the entire post which appears at the link.
"It's rather as if a computer can be put together from just a handful of transistors."
This is not a good example for a Darwinist to use. The problem with "a computer" is that, in its basic form, i.e. one that "can be put together from just a handful of transistors", it would be irreducibly complex in that it would not work half as well with the first half of the transistors-it would not work at all (as a computer-it would work as a door stop!) until all the transistors were assembled in the right order!
"Like any engineering project, this requires detailed blueprints, raw synthetic capabilities and an overall diagnostic and debugging strategy" (again, how would a `blind watchmaker' comprised of non-living chemicals - by definition for the origin of the first living cell-come up with the equivalent of an "engineering project" which "requires detailed blueprints" and "an overall diagnostic and debugging strategy"):
"Theoretical and experimental studies have attempted to establish a minimal set of genes needed for a self-replicating system in a cushy constant environment of unlimited, small molecule nutrients" (so how did a `blind watchmaker' do it on the early Earth where there was no artificial, air-conditioned lab, with a "cushy constant environment of unlimited, small molecule nutrients"):
Good question Stephen! Why assume the watchmaker was blind and without purpose?
October 24th, 2006 at 3:01 am
Stephen Jones is indeed correct when he says that 182 protein-coding genes is not small. Clearly, such an organism may be simple compared to others but in no way it could have been assembled spontaneously. But who would make such a claim anyway? Even if there is a long way to create such a simple yet complex organism out of amino acids, it hardly demonstrates darwinian evolution to be wrong.
What a sloppy logic! Computers can indeed be assembled from just a handful of transistors. Eniac, the world first super computer, was ridiculously more simple than even the simplest computer one can find in his or her cellphone. Anyway, the important point is that Stephen Jones is trying to show that this bacteria cannot be made any simpler, in other word, it is irreducibly complex. I keep encountering this logic amongst advocates of ID. Claiming that something is true does not make it true. Claiming that something is irreducibly complex does not make it irreducibly complex either. I invite Stephen Jones to try removing any of the parts of that bacteria to verify that indeed it cannot function anymore. That would certainly be a lot tougher to explain for evolution advocates.
Although I do not doubt the conclusion that the bacteria cannot be grown on its own, it does not follow that it must have been the case for its ancestors. After all, there are many examples of living organisms that depend on other organisms although their ancestry did not depend on any other organism. A great example is lichen.
Indeed, building a bacterium from scratch requires enormous amount of intelligence, there is no denying it. But nobody claims that a bacterium was the originator of all life on earth.
Researchers have attempted to recreate the conditions that prevailed several billion years ago before life as we know it appeared. In no way, these lab experiences represent a cushy environment. They demonstrated the seemingly spontaneous creation of amino acids, the creation of cells that could be used as a skin. Much progress has been made on the origin of life in the past few years. I find this pretty amazing given the short time span and infinitely smaller scale these experiences are take place. As a matter of fact, I would not be surprised to hear an ID advocate claim these experiences confirm the presence of inteligent design.
In conclusion, Stephen Jones demonstrated one thing extremely well and that is his logic is extremly sloppy.
Comment by StephInSD — October 24, 2006 @ 3:01 am
October 24th, 2006 at 6:53 am
Anyway, the important point is that Stephen Jones is trying to show that this bacteria cannot be made any simpler, in other word, it is irreducibly complex. I keep encountering this logic amongst advocates of ID. Claiming that something is true does not make it true.
Agreed. But that cuts both ways. Counter claims are not true because of the vigor of the claim.
Claiming that something is irreducibly complex does not make it irreducibly complex either. I invite Stephen Jones to try removing any of the parts of that bacteria to verify that indeed it cannot function anymore. That would certainly be a lot tougher to explain for evolution advocates.
A minimal genome concept is linked to function. It should be a matter for testing; not claims and counter claims.
Comment by Bradford — October 24, 2006 @ 6:53 am
October 24th, 2006 at 1:24 pm
StepheninSD
Perhaps you are unaware of previous knock-out gene studies on simple parasite bacteria. Those experiments have set the number of essential genes at about 300, 184 is well below that. Given that the previous minimum was approximately 300 genes, how many of the 184 genes do you expect can be deleted and still have a viable organism? It is very likely that this organism is already at the bare minimum or extremely close to it.
What? No. That is not what happens. You are watching too much PBS.
No it hasn't. The idea of life from nonlife is further away from reality than ever. The more we learn about life the less probable the spontaneous generation myth becomes. Even an organism that accurately replicates a single protein exceeds the potential of being created by random chance, yet a non-parasite bacteria requires at least 1500 genes. At this time, there is not even a viable working hypothesis about how life could have evolved from nonlife.
Sorry, but if you believe that life can occur from nonlife by random chance, you are living in the world of fantasy not science. Spontaneous generation was disproven by Louis Pasteur in the 19th century.
Comment by Jehu — October 24, 2006 @ 1:24 pm
October 24th, 2006 at 2:15 pm
Bradford:
"Good question Stephen! Why assume the watchmaker was blind and without purpose?"
Bradford, read this carefully: the blind watchmaker is a metaphor, not a hypothesis. Can you wrap your mind around the significant difference between the two?
Also, do you find it amusing that you, who clearly didn't understand the most basic aspect of the RNA World hypothesis before denigrating it, are approvingly quoting someone who completely rejects it by pretending that the first life was bacterial, and that it necessarily must have had proteins and DNA?
"A minimal genome concept is linked to function."
Yes, but your statement is totally vacuous. Since bacteria have been evolving for just as long as we have, the minimal bacterial genome does nothing to further your argument.
Jehu wrote:
"No it hasn't."
Yes, it has. There has been enormous progress in testing predictions of the RNA World hypothesis, for example. If you disagree, would you please review the hundreds of relevant papers and explain why their data are meaningless?
"Even an organism that accurately replicates a single protein exceeds the potential of being created by random chance,…"
So what, Jehu? Why do you keep misrepresenting variation plus selection as "random chance"
"… yet a non-parasite bacteria requires at least 1500 genes. At this time, there is not even a viable working hypothesis about how life could have evolved from nonlife."
Has the RNA World hypothesis not shown its viability? Why is the enzymatic core of a ribosome RNA and not protein?
"Sorry, but if you believe that life can occur from nonlife by random chance, you are living in the world of fantasy not science."
If you believe that portraying MET as mere random chance is honest, given that selection is clearly nonrandom, you are living in a fantasy world.
Comment by Smokey — October 24, 2006 @ 2:15 pm
October 24th, 2006 at 2:35 pm
Bradford, read this carefully: the blind watchmaker is a metaphor, not a hypothesis. Can you wrap your mind around the significant difference between the two?
Smoke, read this carefully. The blind watchmaker is a metaphor. Jones used the phrase blind watchmaker and I never claimed it was anything other than a metaphor. Can you wrap your mind around that?
"A minimal genome concept is linked to function."
Yes, but your statement is totally vacuous. Since bacteria have been evolving for just as long as we have, the minimal bacterial genome does nothing to further your argument.
Your comments are vacuous. Bacteria do not evolve without a functional genome. Assessing minimal genomic function is irrelevant to changes occuring after genomes are in place.
Comment by Bradford — October 24, 2006 @ 2:35 pm
October 24th, 2006 at 4:22 pm
Bradford:
"Smoke, read this carefully. The blind watchmaker is a metaphor. Jones used the phrase blind watchmaker…"
And you used it too. Did you forget already?
"… and I never claimed it was anything other than a metaphor. Can you wrap your mind around that?"
Claimed? I didn't claim that you claimed it. I pointed out that you did not use the term metaphorically.
"Your comments are vacuous."
Snappy comeback! Original, too.
"Bacteria do not evolve without a functional genome."
True, but irrelevant. The life from which bacteria evolved had a functional genome, but it wasn't a bacterial one. This is why the minimal *bacterial* genome isn't relevant to your argument. Get it yet?
"Assessing minimal genomic function is irrelevant to changes occuring after genomes are in place."
Huh? No one is "assessing minimal genomic function" here. The papers are about identifying the existing bacterium with the smallest known genome.
If you find it so convincing, why did you link to an incoherent blog post instead of to the papers containing the actual data?
Comment by Smokey — October 24, 2006 @ 4:22 pm
October 24th, 2006 at 4:59 pm
Smokey
Typical literature bluff. The RNA world hypothesis is a joke. The "RNA world" is nothing more than an idea, there is no evidence that any "RNA world" ever existed and therefore there is no "RNA world data." Even if the mythological RNA world ever existed, it wouldn't create life anymore than cow farts create rocket ships. Setting aside the fact that the nitrogenous base cytosine needed to form RNA does not exist outside of being created by living cells and that nucleotides do not form themselves into chains of RNA withyout enzymes, little bits of RNA do not suddenly or even gradually become life.
It is not a misrepresentation. While selection is not random, everything that happens before the selection is random, and that is the difficult part. Furthermore, selection does not work until there is life. Just to create one gene with one protein you are left with pure random chance and even that is impossible much less the necessary 1500 some odd genes needed for a non-parasite life form.
That is totally irrelevant and an example of chasing ghosts. I am not aware of a ribozyme than can catalyze anything without enzymes present. Are you?
I will try to make this simple. Selection of a trait is nonrandom, arrival of the trait is random. It is the arrival of a trait that is difficult, not the selection of the trait. Even selection only occurs after life exists, so you are left with a purely random event that is clearly not possible without a miracle.
Comment by Jehu — October 24, 2006 @ 4:59 pm
October 24th, 2006 at 6:18 pm
Jehu wrote:
"Typical literature bluff."
The only one bluffing is you.
"The RNA world hypothesis is a joke. The "RNA world" is nothing more than an idea, there is no evidence that any "RNA world" ever existed and therefore there is no "RNA world data.""
You're bluffing. You haven't even looked.
"Even if the mythological RNA world ever existed, it wouldn't create life anymore than cow farts create rocket ships."
Since you deny below that RNA can have enzymatic activity without proteins, your analogy is colorful, but based on ignorance.
"Setting aside the fact that the nitrogenous base cytosine needed to form RNA does not exist outside of being created by living cells…"
Dead wrong:
http://www.nature.com/nature/j...
"… and that nucleotides do not form themselves into chains of RNA withyout enzymes, little bits of RNA do not suddenly or even gradually become life."
Since most of your premises are false, your conclusion is weak. But don't let that stop you from proclaiming that you can prove a negative!
"It is not a misrepresentation."
It is a deliberate, dishonest misrepresentation.
"While selection is not random, everything that happens before the selection is random, and that is the difficult part."
Not really. Even if it were, it would not justify your claim that a process with random and nonrandom components is simply random.
"That is totally irrelevant and an example of chasing ghosts. I am not aware of a ribozyme than can catalyze anything without enzymes present. Are you?"
Absolutely. Maybe you should read that literature instead of bluffing!
"I will try to make this simple. Selection of a trait is nonrandom, arrival of the trait is random. It is the arrival of a trait that is difficult, not the selection of the trait."
Doesn't matter. It's still dishonest and deliberately deceptive to describe this process as only random chance.
Comment by Smokey — October 24, 2006 @ 6:18 pm
October 24th, 2006 at 6:47 pm
Smokey
I am very familiar with the exceedingly lame RNA world myth. If evidence exists that an RNA world actually existed, kindly post it.
If you are aware of a ribozyme that can catalize a reaction without enzymes, post a link.
Yes, I was aware of that experiment that requires high concentrations of urea. The problem is that the cytosine is consumed by deanimation. http://www.pnas.org/cgi/conten...
Now tell me, where in nature do we find cytosine other than living cells? In pools of highly concentrated urea just sitting around?
Is that it? Your defense of the RNA world fantasy is that disproving it is an attempt to prove a negative? That is science?
It is clearly a random process. One nonrandom step at the very end of a long chain of random events does not make the whole process nonrandom. In regards to abiogenises, you don't even have natural selection to help you, just randomness.
Then why don't you post a link?
Comment by Jehu — October 24, 2006 @ 6:47 pm
October 24th, 2006 at 6:55 pm
"Bacteria do not evolve without a functional genome."
True, but irrelevant. The life from which bacteria evolved had a functional genome, but it wasn't a bacterial one.
Thanks for treating us to the usual stories.
This is why the minimal *bacterial* genome isn't relevant to your argument.
Let me know when you observe a non-bacterial genome evolving to become a bacterial genome.
Comment by Bradford — October 24, 2006 @ 6:55 pm
October 24th, 2006 at 7:04 pm
If you are aware of a ribozyme that can catalize a reaction without enzymes, post a link.
Instead why not point to an instance where a ribozyme itself arises. That includes the component nucleotides. No reliance on intelligent sources. Just a series of reactions leading to nucleotides and then ribozymes.
Comment by Bradford — October 24, 2006 @ 7:04 pm
October 24th, 2006 at 7:15 pm
Jehu wrote:
"If you are aware of a ribozyme that can catalize a reaction without enzymes, post a link."
Why just one? Do you realize how spectacularly ignorant your claim was, especially your claim that I was bluffing?
"Setting aside the fact that the nitrogenous base cytosine needed to form RNA does not exist outside of being created by living cells"¦"
"Yes, I was aware of that experiment that requires high concentrations of urea. The problem is that the cytosine is consumed by deanimation."
Whether there's a problem with degradation or not, you were lying when you claimed that cytosine "does not exist outside of being created by living cells." You knew it was false, but you wrote it anyway. Why?
"It is clearly a random process. One nonrandom step at the very end of a long chain of random events does not make the whole process nonrandom."
ANY nonrandom steps means that your characterization of the whole process as "random chance" is dishonest.
"Then why don't you post a link?"
Just one? How many papers did you read before you decided that you were sure that catalytic RNAs lacking protein components did not exist?
Comment by Smokey — October 24, 2006 @ 7:15 pm
October 24th, 2006 at 7:34 pm
"Yes, I was aware of that experiment that requires high concentrations of urea. The problem is that the cytosine is consumed by deanimation."
Whether there's a problem with degradation or not, you were lying when you claimed that cytosine "does not exist outside of being created by living cells." You knew it was false, but you wrote it anyway. Why?
Where does cytosine become part of reactions leading to nucleotides in extra-cellular envirnoments? Where are the formations of extra-cellular ribozymes?
"It is clearly a random process. One nonrandom step at the very end of a long chain of random events does not make the whole process nonrandom."
ANY nonrandom steps means that your characterization of the whole process as "random chance" is dishonest.
Smokey, I'm tiring of your constant personal attacks. Dishonesty implies intent which you are in a poor position to judge. If you can't focus on the topic without the superfluous insults then get off the thread.
Comment by Bradford — October 24, 2006 @ 7:34 pm
October 24th, 2006 at 7:37 pm
Smokey,
You are attempting to avoid the issue by parsing words. The fact is you need cytosine to get RNA. Cytosine is not found in nature except living cells. The urea experiment you point to produces cytosine that is consumed by deanimation and so doesn't solve your problem.
That is patently false. A single nonrandom event does not render the whole process nonrandom.
What you are doing is "seed picking." The whole argument for an RNA world is so speculative that you attack syntax and definition instead of trying to make an actual point.
Tell me, how does natural selection work before you have life? Without natural selection what part of the process is not purely chance?
Comment by Jehu — October 24, 2006 @ 7:37 pm
October 24th, 2006 at 8:32 pm
Hi Jehu,
You wrote…
Last week, Bradford started an excellent thread on the RNA World. Unfortunately, it looks like attention got distracted just as we were discussing the meat of the book, Chapter 3? From that chapter…
This provided for a compare and contrast set of questions I posed to Bradford and Smokey (they generally have opposing positions).
Bradford didn't respond (I suspect he had real world priorities to attend to)
Smokey answered with…
"1) I'm familiar with it.
2) Not necessarily. It clearly would be tough to replace if it failed to be supported by the data.
3) Probably, at least in the short term.
4) The data are cited in the chapter."
I pressed Smokey for more specifics on which of the 114 citations he was referring to. He directed my to the following
In anticipation that you will find this insufficient, what scientific OOL hypothesis would you forward that you think is better supported by the evidence?
Comment by Thought Provoker — October 24, 2006 @ 8:32 pm
October 24th, 2006 at 8:33 pm
What you are doing is "seed picking." The whole argument for an RNA world is so speculative that you attack syntax and definition instead of trying to make an actual point.
You've nailed it.
Tell me, how does natural selection work before you have life? Without natural selection what part of the process is not purely chance?
And if the process is not stochastic then how is the process chemically described?
Comment by Bradford — October 24, 2006 @ 8:33 pm
October 24th, 2006 at 9:28 pm
Apparently, antievolutionists do not believe in proteases and nucleases, as well as their prebiotic predecessors. Not surprising - the teleological approach to life pretty much ignores them as well, even though they sit right next to the RNA World at the center of life.
Natural selection preceded life- which is why it's no surprise that Darwinian processes are so completely interwoven with life at every level.
As far as cytosine in the the prebiotic world, it would be a change of pace if the antievolutionists here displayed even a modicum of comprehension of simple chemical kinetics. The objections raised in this thread are only valid of one ignores the basics (something I'm sure is expected in the PostWedge World, but still something most of the rest of us have a hard time adjusting to).
In case I'm being too cryptic - think, carefully and kinetically, about the sort of reaction that cytosine breakdown is. 0 order, first order, second order, etc. Put another way - is the rapidity of breakdown dependent on the concentration of cytosine? Then ask what happens when you put together even a large first order degradation rate constant with a slow but steady rate of synthesis? What does the steady-state look like? Surely those math-savvy ID types can figger this one out. Once you ponder things a bit, then the antievolutionist objection vanishes into thin air. (Rock can chime in about how this very simple demonstration of robustness is so, um, …, well, whatever…)
One more thing that bears repeating - it's interesting that antievolutionists so reflexively deny the very core of all life. It's not easy taking some of the ranting seriously, when the denial is so vigorous.
Comment by Art — October 24, 2006 @ 9:28 pm
October 24th, 2006 at 9:43 pm
Speaking of the RNA World and its importance throughout the history of life, the report describing another very small bacterial genome, that of the organism Buchnera aphidicola BCc, is most tantalizing. Along with Figure S2, there is this remark (from Science. 2006 Oct 13;314(5797):312-3. A small microbial genome: the end of a long symbiotic relationship? Perez-Brocal V, Gil R, Ramos S, Lamelas A, Postigo M, Michelena JM, Silva FJ, Moya A, Latorre A.):
Moreover, nucleases are part of the "irreducible" repertoire. As are proteases. There's no escaping the garbage disposal and its importance to life (it's almost as important as the RNA World, and probably more ancient). No matter what teleologists would say.
Comment by Art — October 24, 2006 @ 9:43 pm
October 24th, 2006 at 9:45 pm
One more comment - any bets as to how long its may take for Kwang Jeon's evolving endosymbionts to approach the stage of reduction seen in Carsonella ruddii?
Comment by Art — October 24, 2006 @ 9:45 pm
October 24th, 2006 at 10:06 pm
Apparently, antievolutionists do not believe in proteases and nucleases, as well as their prebiotic predecessors. Not surprising - the teleological approach to life pretty much ignores them as well, even though they sit right next to the RNA World at the center of life.
This is a typical non-answer. Instead of citing proteases and nucleases why not give a causal explanation as to how a functional genome enabling their synthesis came about or acknowledge the inadaquacy of the model.
Natural selection preceded life- which is why it's no surprise that Darwinian processes are so completely interwoven with life at every level.
This is more argument by assertion. Declare that NS preceeded life while ignoring questions as to what was selected and how you know it.
Comment by Bradford — October 24, 2006 @ 10:06 pm
October 24th, 2006 at 10:17 pm
Moreover, nucleases are part of the "irreducible" repertoire. As are proteases. There's no escaping the garbage disposal and its importance to life (it's almost as important as the RNA World, and probably more ancient). No matter what teleologists would say.
Who is denying their importance? Denied was the adaquacy of explanations as to how an initial genome was generated.
Comment by Bradford — October 24, 2006 @ 10:17 pm
October 24th, 2006 at 11:00 pm
Bradford:
Denied is a good choice of words, Bradford. Here, and in other threads, you respond to bona-fide positive experimental support for specific hypotheses regarding the OOL with denial that is unaccompanied by any sort of positive experimental support.
The "head-in-the-sand" approach is in vogue in the Post Wedge World, to be sure. I'm afraid it hasn't yet reached my neck of the woods.
Comment by Art — October 24, 2006 @ 11:00 pm
October 24th, 2006 at 11:02 pm
This actually shows that genes for RNA metabolism are highly specified, reducing the probability that such a sequence would arise by random chance. It does not show that there ever was an RNA world.
Comment by Jehu — October 24, 2006 @ 11:02 pm
October 24th, 2006 at 11:20 pm
Denied is a good choice of words, Bradford. Here, and in other threads, you respond to bona-fide positive experimental support for specific hypotheses regarding the OOL with denial that is unaccompanied by any sort of positive experimental support.
Experimental results do not support broader OOL arguments that you and others have advanced.
Comment by Bradford — October 24, 2006 @ 11:20 pm
October 24th, 2006 at 11:43 pm
Jehu:
Unsupported assertion. In fact, the claim about probabilities is refuted by direct experimental measurement (not that a little thing like data is going to come between an antievolutionist and his/her creed).
Bradford:
Actually, they do exactly that.
I recommend that you review what it means for a hypothesis to be supported in experimental terms. And then, if you still wish to cling to the "deny at all costs" approach, try to re-word your groundless assertion.
Comment by Art — October 24, 2006 @ 11:43 pm
October 24th, 2006 at 11:56 pm
Art
Maybe you don't understand why it is a gene is highly conserved. A gene is highly conserved when it cannot tolerate mutation and/or variation. If the gene sequence is highly specified then it reduces the number of nucleotide sequences that can provide a functional substitute, making the chance formation of a sequence, or a sequence of equal function less probable.
As for your so-called experimental data, I do not believe that expiremental data showing the probabilities of forming by chance the genes that regulate RNA metabolism exists. If such data exists, why don't you post a link instead of wasting everybody's time?
Comment by Jehu — October 24, 2006 @ 11:56 pm
October 25th, 2006 at 12:33 am
Jehu, you are hopelessly confused. The conservation of genes involved in RNA metabolism that is mentioned in the paper I referred to relates to genes as units, and not to conservation of nucleotide sequence. Fact is, many or most of the genes of interest here are not any more "highly conserved" than other genes at the nucleotide sequence level. Another fact is that totally unrelated sequences can and do substitute for many of the relevant proteins. (Review the literature on ribosomal proteins sometime.) Yet another fact is that the enzymatic activities that are central to RNA metabolism are RNA-based and, in the vernacular, completely lacking in CSI. We know this because analogous functions occur with relatively high frequencies in populations of random oligomers.
Zero CSI is more than an exhortation for the kids to turn off the TV. It's a fact of life. Get used to it.
Comment by Art — October 25, 2006 @ 12:33 am
October 25th, 2006 at 1:16 am
Experimental results do not support broader OOL arguments that you and others have advanced.
Actually, they do exactly that.
I recommend that you review what it means for a hypothesis to be supported in experimental terms. And then, if you still wish to cling to the "deny at all costs" approach, try to re-word your groundless assertion.
The broader argument relates to the origin of cells; something your references fall far short of documenting.
Comment by Bradford — October 25, 2006 @ 1:16 am
October 25th, 2006 at 1:54 pm
I know I'm going out on a limb here with a radical hypothesis I'm going to call the "DNA-World Hypothesis."
Due to the intrinsic functional advantage of DNA over RNA and proteins, all extant biology is evolved from the "DNA-World," in which all biological functions (catalysis, kinesis, editing, information storage, etc.) were performed by ssDNA polymers. Extant biology is due to the co-option of DNAptazyme and deoxyribozyme functionalities by RNA and protein to the specific functionalities to which they now seem best suited (short-term memory, amplification, reconfiguration, reutilization, graceful degradation, etc.).
I realize that my "DNA-World Hypothesis" is contrary to the current Hollywood-style hype of RNA, but I'm pretty confident that the competing "RNA-World Hypothesis" fad will pass. Once any kind of reasonable and empirically-grounded alternative is proffered. (Which hasn't yet occurred. Biologists are so fickle after all, and I'm making an explicit appeal to that fickleness"”just like your average Hollywood hooker.)
I will admit that there is one problem with the "DNA-World Hypothesis." Even though it leaves a trace far stronger than the "RNA-World Hypothesis," as anyone can confirm by consulting a basic biology textbook, I can't connect it to the OOL.
I can't make statements such as: "A key event in the origin of life on this planet has been formation of self-replicating RNA-type molecules, which were complex enough to undergo a Darwinian-type evolution (origin of the "RNA world")." But I do have the advantage of not immediately qualifying any such statement by saying: "However, so far there has been no explanation of how the first RNA-like biopolymers could originate and survive on the primordial Earth."
I freely admit that me talking about the primordial "DNA-World" is like talking about the primordial "Planet Krypton."
(You may have heard about Krypton. It's in all the comic books.)
(I intentionally left the quotations anonymous. Not to protect the innocent. But to protect the guilty. I guess that makes me a liberal! Is that the same thing as being a "Darwinist")
Comment by Rock — October 25, 2006 @ 1:54 pm
October 25th, 2006 at 1:54 pm
Art: Yet another fact is that the enzymatic activities that are central to RNA metabolism are RNA-based and, in the vernacular, completely lacking in CSI. We know this because analogous functions occur with relatively high frequencies in populations of random oligomers.
Specified complexity consists of two important components, both of which are essential for making reliable design inferences. The first component is the criterion of complexity or improbability. In order for an event to meet the standards of Dembski's theoretical notion of specified complexity, the probability of its happening must be lower than the Universal Probability Bound which Dembski sets at one chance in 10^150 possibilities.
The second component in the notion of specified complexity is the criterion of specificity. The idea behind specificity is that not only must an event be unlikely (complex), it must also conform to an independently given, detachable pattern. Specification is like drawing a target on a wall and then shooting the arrow. Without the specification criterion, we'd be shooting the arrow and then drawing the target around it after the fact.
Art, CSI is found in nucleic acids, not activities. What detachable pattern are you referencing?
Comment by Bradford — October 25, 2006 @ 1:54 pm
October 25th, 2006 at 2:01 pm
Jehu wrote:
"Maybe you don't understand why it is a gene is highly conserved. A gene is highly conserved when it cannot tolerate mutation and/or variation."
Great! Let's see if you have the courage to make a prediction from this assertion that Bradford lacks.
"If the gene sequence is highly specified then it reduces the number of nucleotide sequences that can provide a functional substitute…"
So, if I change a
1) highly conserved residue (in ALL members of the family in "higher" eukaryotes)
2) in the active site
3) that is in contact with the substrate
4) in a member of a huge protein family
5) to a residue NOT found in ANY member of the family
6) and the substitution is the most radical size change possible,
what do you predict will happen, Jehu?
A) Will the mutant protein still recognize the original substrate?
B) Will the mutant protein acquire a new function without losing the old?
C) Will a mammal homozygous for this radical substitution have any detectable phenotype?
Bradford runs away. Will you?
Comment by Smokey — October 25, 2006 @ 2:01 pm
October 25th, 2006 at 3:15 pm
It has nothing to do with the "minimal genome," but Who cares?! Right?
It is just my "teleological" perspective talking. DNA is the master catalyst of life. Therefore there exists a specifically identifiable design rationale for the utilization of DNA in that capacity. There is therefore no other class of molecules, extant in life forms that quite serves the same purpose. It's not such a reach to say that the OOL, as used to be said, is coincident with the origin of DNA.
The whole "RNA-World" thing is a recent enchantment with (what had not been previously thoroughly investigated) the catalytic capabilities of short RNA molecules (or short subsequences of RNA molecules–
Comment by Rock — October 25, 2006 @ 3:15 pm
October 25th, 2006 at 3:17 pm
That should be: "(or short subsequences of RNA molecules–
Comment by Rock — October 25, 2006 @ 3:17 pm
October 25th, 2006 at 5:04 pm
Minimally-specified Organisms…
(H/T Telic Thoughts)
At CreationEvolutionDesign, there is interaction from the author with current news about the genetically smallest organism yet found….
Trackback by Exiled from GROGGS — October 25, 2006 @ 5:04 pm
October 25th, 2006 at 6:14 pm
Bradford wrote:
"Smokey, I'm tiring of your constant personal attacks."
Pointing out that premises are false is not a personal attack.
"Dishonesty implies intent which you are in a poor position to judge."
If one makes contradictory statements without acknowledging that one of them is false, intent to decieve is the only rational conclusion.
—————-
Jehu wrote:
"Setting aside the fact that the nitrogenous base cytosine needed to form RNA does not exist outside of being created by living cells"¦"
"Yes, I was aware of that experiment that requires high concentrations of urea. The problem is that the cytosine is consumed by deanimation."
"You are attempting to avoid the issue by parsing words."
Most people call this reading and noting that you contradicted yourself by claiming that cytosine does not exist outside of being created by living cells, despite knowing that it has been created without the help of living cells.
"The fact is you need cytosine to get RNA."
Dead wrong again! You're on a streak here. The fact is that a number of different combinations of bases stack and pair like the four we have now.
"Cytosine is not found in nature except living cells."
So you've moved the goalposts. Why did you stake out an initial position that you already knew was false? It would seem that if you were arguing from a robust position/hypothesis, you would acknowledge assumptions up front instead of exaggerating your premises.
Jehu: "It is clearly a random process. One nonrandom step at the very end of a long chain of random events does not make the whole process nonrandom."
Smokey: ANY nonrandom steps means that your characterization of the whole process as "random chance" is dishonest.
"That is patently false. A single nonrandom event does not render the whole process nonrandom."
Your first sentence is false, and your second true. I'm pointing out that the process has BOTH RANDOM AND NONRANDOM COMPONENTS, so your characterization of the whole process as "random chance" is dishonest. I'm not claiming that the whole process is nonrandom, so your attempt to misrepresent my position speaks volumes about your intent.
Moreover, you don't seem to understand mutational mechanisms, because there's only one aspect of mutation that is quasi-random, while most aspects are nonrandom. For example, in the following sequence:
…cgatcatcgatAcgatgctactacta…
if we limit the discussion to substitutions, is the upper-case A equally likely to mutate to G,C, or T, or is one substitution much more likely than the others?
Rock wrote:
"DNA is the master catalyst of life. Therefore there exists a specifically identifiable design rationale for the utilization of DNA in that capacity."
Then why don't we have ribosomal DNA and transfer DNA?
Comment by Smokey — October 25, 2006 @ 6:14 pm
October 25th, 2006 at 7:35 pm
It is just my "teleological" perspective talking. DNA is the master catalyst of life. Therefore there exists a specifically identifiable design rationale for the utilization of DNA in that capacity. There is therefore no other class of molecules, extant in life forms that quite serves the same purpose. It's not such a reach to say that the OOL, as used to be said, is coincident with the origin of DNA.
Rock, if you are emphasizing the suitability of DNA for its function then you get no argument but this begs the question of DNA's origin.
Comment by Bradford — October 25, 2006 @ 7:35 pm
October 25th, 2006 at 8:20 pm
Art,
And yet, you go on and try to correct him. I don't know if that is touchingly admirable, or indicative of some sort of teaching obsession.
(Note to Jehu: I'm not saying you are confused - I don't know if you are or not.)
Comment by Douglas — October 25, 2006 @ 8:20 pm
October 25th, 2006 at 8:22 pm
Bradford,
Because we can't see Him, and aren't smart enough to figure out His intent?
Comment by Douglas — October 25, 2006 @ 8:22 pm
October 25th, 2006 at 8:44 pm
Bradford:
The points I've been making here and in other threads are pertinent to the origins of cells (as we are probably speaking of). They are bona fide positive experimental evidence that supports hypotheses that relate exactly to the origin of cells.
The fact that that no lab has yet recapitulated eons of prebiotic evolution in a few weeks in a test tube, that no single experimental demonstration of an origination of E. coli from the vacuum of deep space is forthcoming (which, in a nutshell, seems to be the only thing you are interested in), does not mean that the approaches being taken by scientists are not useful, or informative, or steps along the way to a clearer understanding of the OOL. It only means that you have your head buried pretty firmly in the sand, and that no matter of evidence, or even discourse, is ever going to interest you.
Douglas:
That's some Freudian slip there, Douglas.
Rock, "Life Without 2' Hydroxyls" sounds like a new virtual reality attraction at Epcot. I'm not sure the paying public is quite ready for it, though.
Comment by Art — October 25, 2006 @ 8:44 pm
October 25th, 2006 at 8:52 pm
Bradford said:
As I've been saying, nothing in life even comes close to satisfying this aspect of Dembski's formulation.
Bradford, in the last sentence there, you've described quite nicely what IDists do when they "calculate" the CSI in living things.
Bradford, you're the one who seems to be supporting the notion that there is CSI in nucleic acids. You tell me - what is the detachable pattern that goes with your claim? Be specific, if you would. And remember the above quote, about painting targets around arrows. Prove to us that your description of a detachable pattern is not what you describe as being inappropriate.
Comment by Art — October 25, 2006 @ 8:52 pm
October 25th, 2006 at 9:43 pm
Bradford, you're the one who seems to be supporting the notion that there is CSI in nucleic acids. You tell me - what is the detachable pattern that goes with your claim? Be specific, if you would. And remember the above quote, about painting targets around arrows. Prove to us that your description of a detachable pattern is not what you describe as being inappropriate.
The detachable pattern is the genome. I have two questions for you. Is there CSI in this message? What represents the wall with respect to this message and a genome?
Comment by Bradford — October 25, 2006 @ 9:43 pm
October 25th, 2006 at 10:59 pm
Bradford, about the detachable pattern in nucleic acids:The detachable pattern is the genome.
You have painted a target around the arrow.
Try again.
Who knows. Tell me how to measure the complexity of the message.
Huh?
Genomes are not typed messages. If you wish to argue that some symbolic mapping or representation of the chemistry that underlies the workings of genomes is specified information of any sort, then once again you are guilty of painting a target around an arrow.
Comment by Art — October 25, 2006 @ 10:59 pm
October 25th, 2006 at 11:39 pm
Bradford, about the detachable pattern in nucleic acids: The detachable pattern is the genome.
You have painted a target around the arrow.
Try again.
On a planet where no genomes exist, a genome is the target and the wall is the range of possible sequences.
Is there CSI in this message?
Who knows. Tell me how to measure the complexity of the message.
Words like of, cat and dog are specified without being complex. A long succession of random letters is complex without being specified. An article is both complex and specified.
Genomes are not typed messages. If you wish to argue that some symbolic mapping or representation of the chemistry that underlies the workings of genomes is specified information of any sort, then once again you are guilty of painting a target around an arrow.
There could be no genetic code if the order of nucleotides were chemically determined. The order is determined by the selective value of proteins.
Comment by Bradford — October 25, 2006 @ 11:39 pm
October 25th, 2006 at 11:56 pm
Bradford:
A genome without a context is an utterly meaningless concept. Are you saying that a specification is meaningless? Isn't this turning the concept on its head?
The nucleotide sequence of a genome is not its specification - rather, it's a fabrication, a target painted around an arrow that some IDist shot into a wall.
The independent "pattern", the unconnected concept that permits one to speak about specified information in genomes, is not sequence but function. Esterase, to pull an easy-to-spell example out of my hat, is a concept that exists entirely apart from any notion of genome or sequence. That is what a specification must be, and that is how one "specifies" the information in a genome.
Sorry if this sounds harsh, but if you cannot understand this, then you are as deficient in ID theory as you are in biology. I'm glad to help you sort things out, but I'm not going to argue about something (like this) that is so obvious.
Comment by Art — October 25, 2006 @ 11:56 pm
October 26th, 2006 at 12:47 am
A genome without a context is an utterly meaningless concept. Are you saying that a specification is meaningless? Isn't this turning the concept on its head?
At what point in your conception of an OOL model is a genome generated and how is context acquired?
The nucleotide sequence of a genome is not its specification - rather, it's a fabrication, a target painted around an arrow that some IDist shot into a wall.
The sequencing demands an explanation identifying why a process generated specificity rather than random nonsense. If this target was painted around then specify the actual target.
The independent "pattern", the unconnected concept that permits one to speak about specified information in genomes, is not sequence but function. Esterase, to pull an easy-to-spell example out of my hat, is a concept that exists entirely apart from any notion of genome or sequence. That is what a specification must be, and that is how one "specifies" the information in a genome.
What did you think I was alluding to when I wrote:
There could be no genetic code if the order of nucleotides were chemically determined. The order is determined by the selective value of proteins.
Nucleotide order, representing genomic information, is function dependent. Acknowledging that does not explain the origin of the information.
Comment by Bradford — October 26, 2006 @ 12:47 am
October 26th, 2006 at 7:09 am
Bradford, most recently:
From a few posts ago (also Bradford speaking):
Yer trying some of that Post Wegde World doublespeak on me.
Which is it, Bradford?
Also:
There's no CSI in life to explain. I don't understand why you are so fixated on a concept that has no relevance to life or its origins.
Comment by Art — October 26, 2006 @ 7:09 am
October 26th, 2006 at 7:13 am
Bradford:
We've been thru this. The "context" is established by RNA-amino acid interactions. You've seen positive experimental evidence for the idea, and you choose to pretend that is is not relevant or does not exist.
Comment by Art — October 26, 2006 @ 7:13 am
October 26th, 2006 at 11:08 am
Nucleotide order, representing genomic information, is function dependent.
Art, CSI is found in nucleic acids, not activities. What detachable pattern are you referencing?
Yer trying some of that Post Wegde World doublespeak on me.
Which is it, Bradford?
Information is expressed by nucleotide sequences whose selective value is determined by protein function. What's the problem?
We've been thru this. The "context" is established by RNA-amino acid interactions. You've seen positive experimental evidence for the idea, and you choose to pretend that is is not relevant or does not exist.
RNA-amino acid interactions are as close as the tRNA in your cells. The unanswered question is why such interactions, outside a cellular environment, would lead to the generation of a cell.
Comment by Bradford — October 26, 2006 @ 11:08 am
October 26th, 2006 at 1:20 pm
Bradford, when you bring up the compartmentalization into cells in the context of trying to smack down the RNA World hypothesis, you are:
1) Conceding that you have no evidence to contradict the hypothesis,
and/or
2) not cognizant of the fact that the RNA World hypothesis isn't about cells–it's a hypothesis about the ancestry of enzymes and replication of genetic material. Compartmentalization into cells could have occurred before, after, or during the RNA World. It simply has no bearing on the subject.
Comment by Smokey — October 26, 2006 @ 1:20 pm
October 26th, 2006 at 3:06 pm
Smokey,
In the prebiotic scenario what causes the nucleotides to start linking via phosphodiester bonds? How does the phosphate group become activated? The oxygens in the phosphate molecule don't make the problem any easier. You have a molecule that is very polar. The disparity in electronegativity values between the oxygen and the phosphorus (3.5 for O compared to 2.1 for P), along with the formal charges on 3 of the 4 oxygens, compounded with the oxygen atoms having electron lone pairs makes this molecule pretty reactive. Left on its own, with all of the other molecules that could have undergone an additive chemical reaction with the phosphate molecule, it seems very unlikely that a polymer of nucleotides would randomly form. A nucleophilic molecule like the oxygen on the phosphate group will form a covalent bond with close to all of the hypothesized prebiotic molecules in that scenario.
The rule in that scenario would be more biological deadends.
Comment by Doug — October 26, 2006 @ 3:06 pm
October 26th, 2006 at 3:22 pm
Then why don't we have ribosomal DNA and transfer DNA?"”Smokey
I already answered that. But let me clarify (like spoon-feeding pabulum to a baby): There exists a specifically identifiable design rationale for the utilization of RNA in that capacity. There is therefore no other class of molecules, extant in life forms that quite serves the same purpose.
(You coulda figured that out by yourself. C'mon.)
Rock, if you are emphasizing the suitability of DNA for its function then you get no argument but this begs the question of DNA's origin."”Bradford
I addressed that too. But I do know something quite specific about the origin of DNA-aptamers and deoxyribozymes. I know exactly when, where, and why they were created and even better, I know who created them!
"Life Without 2' Hydroxyls" sounds like a new virtual reality attraction at Epcot. I'm not sure the paying public is quite ready for it, though.–Art
It's called capitalism, Art. Academics should learn to embrace it. Now the "paying public" can be parted from their $$$ by a carnival ride right down the block.
If evolutionary scientists wore buckled shoes and flounce collars would IDers expend all their efforts criticizing fashion? Yes!
Here's a suggestion: Try to have an original idea. One you can make your own. Gimme something to work with here–like the "DNA-World Hypothesis."
LOL
Comment by Rock — October 26, 2006 @ 3:22 pm
October 26th, 2006 at 3:39 pm
Excellent design-theoretic study related to the DNA-World Hypothesis:
http://www.science.mcmaster.ca...
Comment by Rock — October 26, 2006 @ 3:39 pm
October 26th, 2006 at 7:24 pm
Doug wrote:
"In the prebiotic scenario what causes the nucleotides to start linking via phosphodiester bonds?"
I don't know. Probably reactions similar to the ones Sigma-Genosys uses when they make my oligos.
"…Left on its own, with all of the other molecules that could have undergone an additive chemical reaction with the phosphate molecule, it seems very unlikely that a polymer of nucleotides would randomly form."
I agree. However, "unlikely" isn't a problem.
"The rule in that scenario would be more biological deadends."
Absolutely (pun intended), but all we need is one exception. For that matter, the rule in biology is biological deadends.:grin:
Rock wrote:
"I already answered that. But let me clarify (like spoon-feeding pabulum to a baby): There exists a specifically identifiable design rationale for the utilization of RNA in that capacity. There is therefore no other class of molecules, extant in life forms that quite serves the same purpose."
But I disagree. I presume that the "purpose" to which you refer is a genome, and RNA can and does do that, even today. What's the design rationale for the RNA genome and massive amounts of defective interfering particles made by rabies and related viruses?
Comment by Smokey — October 26, 2006 @ 7:24 pm
October 26th, 2006 at 9:59 pm
Bradford:
Better still - they reflect the genesis of tRNAs.
Smokey has commented on this, but I'll repeat the statement with a twist - the matter of the generation of cells in the prebiotic world is really a trivial one. Fox showed (decades ago, mind you) that a very simple mixture of amino acids could give rise to cells that grow, divide, metabolize, and respond to stimuli. Whether Fox's mixture, or other recipes that include lipids and other prebiotic molecules, are more pertinent to the origins of LAWKI is still a subject of debate. But the origins of cells are not a particularly great problem for OOL theorists.
Growth, division, metabolism, responses - all zero-CSI propositions. I really don't get the fascination IDists have with the concept.
Comment by Art — October 26, 2006 @ 9:59 pm
October 27th, 2006 at 9:13 am
I see what you're saying. But it's not just a matter of 2 linking (or 3, 4, 5, 6…..). The problem is both quantitative (how many nucleotides linking) and qualitative (an arrangment that confers some enzymatic function for that molecule).
The organic chemistry is just glossed over. Heat of the reaction is ignored (enthalpy) as is the fact that there is a positive Gibbs free energy value for the product of each link in the polymer chain. For some reason when it comes to pre-biotic pathways to biological life the rule of thumb "all systems seek to achieve the lowest free energy configuration" is tossed aside.
It seems to be the case because only mechanistic, reductionistic means are allowed.
Comment by Doug — October 27, 2006 @ 9:13 am
October 27th, 2006 at 10:07 am
I dropped into this interesting discussion, and saw the following from Smokey:
Do you agree, Art?
Comment by Paul Nelson — October 27, 2006 @ 10:07 am
October 27th, 2006 at 4:52 pm
Doug wrote:
"I see what you're saying. But it's not just a matter of 2 linking (or 3, 4, 5, 6"¦..). The problem is both quantitative (how many nucleotides linking) and qualitative (an arrangment that confers some enzymatic function for that molecule)."
Yes, but we know that the qualitative part is not insurmountable, as selection can easily coax enzymatic function out of random RNA sequences.
"The organic chemistry is just glossed over."
I'd say it's more that it is premature–scientists are working backwards in time. The data point to an RNA world, but the presence of other subunits has not been excluded. Assuming that progress leads to better support of RNA-only hypotheses and exclusion of RNA/protein hybrids, etc., I think you'll see loads of organic chemists flocking to take center stage.
"Heat of the reaction is ignored (enthalpy) as is the fact that there is a positive Gibbs free energy value for the product of each link in the polymer chain."
For polymerization from triphosphates?
Comment by Smokey — October 27, 2006 @ 4:52 pm
October 27th, 2006 at 5:03 pm
I'm talking about the advent of the 1st RNA molecule that acts as a template and can perform the enzymatic activities to replicate itself. Because isn't that what you need? The 1st one can't just be a template it also needs to be able to catalyze the reproduction of itself. The advent of the 1st self-replicating RNA molecule wouldn't be culled by natural selection if it is the 1st. If it can't catalyze its own synthesis it's no good. NS would only be a factor once the process is already underway: a template that has catalytic ability to duplicate itself.
Comment by Doug — October 27, 2006 @ 5:03 pm
October 27th, 2006 at 10:49 pm
Art:
Actually, this is all a matter of perspective ("looks like," if you like). For example, Art's "simple mixture of amino acids" is actually a specified recipe. More fundamentally, let's not make the mistake of interpreting "grow, divide, metabolize, and respond to stimuli" in a biological sense when speaking of Fox's work. All living cells are homeostatic entities, so much so that I suppose I can supplement Art's RNA World and Rock's DNA World with the Homeostatic World "“ the universal core of Life. In living things, growth, division, metabolism, responsiveness are integrated into a homeostatic whole. That's what makes it living. They are not isolated, simple shadows.
Comment by MikeGene — October 27, 2006 @ 10:49 pm
October 28th, 2006 at 5:24 am
Art:
The amino acids used in Fox experiment were derived from living cells. The starting mixture was not a very simple but a refined mixture of 20 AA's found in living cells. The question is how natural process (or a miller-urey type experiment) could lead to such a pure and highly concentarted mixture (not to mention the right and left chirality problem). The other problem is that Fox used a highly specialized process; Take mixture X, heat it, combine it with mixture Y, cool it, add mixture Z, refine it, cool it again, and chemical W, refine it, heat it and so on. I'm not sure in which way nature could follow such a process spontaneously. Moreover, the Fox's so-called protocells were not living cells or self-replicating machines.
MikeGene:
Yes, using the terms "grow, divide and metabolize", while referring to Fox's protocells, can be very misleading.
Comment by Farshad — October 28, 2006 @ 5:24 am
October 28th, 2006 at 9:04 am
Hi Paul,
You asked:
Well, since I've speculated along somewhat different lines, I'd tentatively say no. At least with respect to the compartmentalization of an RNA genome. I'm tentative because I would not insist that protocell formation and the catalytic activities of thermal proteins need go hand-in-hand. Thus, for example, it's not clear that Ikehara's preparations form the same sorts of protocells as did Fox's. But they are still pertinent to the subject.
(Lateral thinking exercise for the week - track down any recent review by Paul Ahlquist, ponder the relationships and roles of membranes, and try to replace the various RNA viruses he speaks of with entities from the early history of life.)
MikeGene, Bradford was referring to the formation of cells. Your own quirky definition of life is really irrelevant here.
Farshad, Fox's studies involved many different conditions and mixtures of amino acids, including those that are found in urey-Miller type experiments. Also, it's a stretch to claim that a simple evaporation-rewetting cycle never could have occurred on the early earth, especially since it's not hard to find places where it happens regularly on the modern one.
One more thing - the issue here is Bradford's claims regarding the origins of cells. Denying that Fox's protocells were cells or cell-like, which is the relevant matter in these comments, is taking the typical ID/teleological/antievolution denial game to a pretty absurd end. IMO at least.
Comment by Art — October 28, 2006 @ 9:04 am
October 28th, 2006 at 9:38 am
Art:
I suppose my view of life would look quirky to a non-teleologist who is guided by the perspective of reductionism. As for it being irrelevant, if so, it is because you inserted certain abilities of this cell-like entity - grow, divide, metabolize, and respond to stimuli. If it was simply about ways to sequester chemistry into a microenvironment, why bring up these biological properties? If my definition was irrelevant, it is because your assertion was an irrelevancy dressed up to look like it mattered.
Comment by MikeGene — October 28, 2006 @ 9:38 am
October 28th, 2006 at 10:04 am
Art:
Actually, this is pretty typical of Art. He introduces "cell-like" entities and endows them with properties that look biological: " Fox showed (decades ago, mind you) that a very simple mixture of amino acids could give rise to cells that grow, divide, metabolize, and respond to stimuli." When someone questions the way he portrays these entities, he lashes out and labels us as playing an "antievolution game." In other words, he blames, ands then labels, others for his own mistakes.
Comment by MikeGene — October 28, 2006 @ 10:04 am
October 28th, 2006 at 11:20 am
In my conversations with origin-of-life researchers — e.g., in discussions with David Deamer last fall at UC-Santa Cruz — they wave off the relevance of Fox's experiments. Deamer explains why:
(D. Deamer, "The First Living Systems: A Bioenergetic Perspective," Microbiology & Molecular Biology Reviews 61 [1997]:239-261; p. 245; footnote numbers omitted.)
Fox's "protocells" were "cell-like" only to the superficial extent that they were spherical, etc. In every other respect, they had nothing to do with the problem of the origin of the first cells. To say that is hardly to take a "typical ID attitude," Art, because nearly all abiogenesis researchers, most of whom loathe ID, agree.
Fox's work has not led to an ongoing research program, following up the approach he tried, for reasons having everything to do with the implausibility and biological irrelevance of his results. One needn't be a crazy ID theorist to see this. Deamer himself, for instance, thinks ID is dead wrong. He also thinks Fox got it wrong.
Back to my original question. The reason I asked you about the necessity of immediate encapsulation of catalytic RNAs had to do with (1) error catatrophe problems for copying ribozymes, and (2) the relative fragility of RNA molecules on the early Earth. Most of those workers whose ideas I follow — e.g., Jack Szostak or Pier Luisi — stress that immediate isolation of any active RNAs within a "cell" would be essential for any ongoing evolution.
Comment by Paul Nelson — October 28, 2006 @ 11:20 am
October 28th, 2006 at 1:43 pm
A few comments before I hit the road fer a day:
1. First and foremost, the statement "Fox's protocells were cell-like entities capapble of growing, dividing, metabolism, and responses to external stimuli" is nothing but a bare-bones, simple, straightforward statement of fact. Teleologists don't like it, but that's just too bad. If a simple statement of fact is going to put bad ideas (like the possibility that the OOL is not the completely black room that light-hating IDists have gravitated to) in the heads of TTers, commenters, and lurkers, so much the better.
2. Certainly, knowing that my factual and honest description of Fox's protocells would get a rise out of MikeGene was part of the reason I made the comment I did. That it has drawn Paul into the discussion is an added and unanticipated benefit. (File that button somewhere.) But the main point can be seen in context - such as the statement I made after describing protocells:
Bradford is fixated on CSI, and I thought it would be good to point out that Fox's work (among others) shows CSI to be irrelevant when it comes to several basic properties of living things.
3. Paul, weve been over much of this before, and the ARN thread I pointed to discusses ways in which I disagree with many OOL researchers, and hypotheses that address the conceptual problems you fixate on. That having been said, I would point out that the claim that "…for the most part this approach has been abandoned" is not quite accurate (of course, we could quibble about what "for the most part" means). I've provided some pointers and will leave things at that.
4. As for the fragility of RNA, again the conceptual and physical link of RNA with thermal proteins would overcome many of the problems you claim to be in force. (The mention of Ahlquist is intended to spur others to think along these lines, in a round-about fashion.) But you seem to have missed the bigger picture. Of course RNA is fragile (although not nearly as fragile as you think), and in fact some of the primordial catalytic activities were likely to be nucleases. This is the stuff of which a Darwinian scenario is born.
For all RNAs are not created equal - some are much more resistant to chemical and enzymatic breakdown than others. I've mentioned to examples before - viroids and TMV. These examples inform us as to the selective forces that one would expect to be in play at the outset of the RNA World, and how selection shaped this World.
More connections to play with: think about how viroids replicate (specifically, what enzyme copies them, and how might it work), think about how this might be an analogy (or metaphor) for the world Ikehara hypothesizes, and think about the lessons viroids provide when it comes to understanding really stable RNAs. Briefly, Paul, none of your objections provide an airtight case, and in fact they only direct us along the "true" path to the RNA World (and beyond!).
Comment by Art — October 28, 2006 @ 1:43 pm
October 28th, 2006 at 1:48 pm
One aside - how come I can pique Paul's interest as I have, but he won't join in and discuss the difficulties in reconciling his ideas regarding ORFans with the front-loading ideas that pop up from time to time here? What's with that anyways?
Someone's liable to get a complex (or a big head, or both :razz:).
Comment by Art — October 28, 2006 @ 1:48 pm
October 28th, 2006 at 2:53 pm
Art,
Posting here is an indulgence I rarely allow myself, because I have SO MANY INCOMPLETE PROJECTS IT'S GENUINELY TERRIFYING.
But I love how you provoke my thinking, so I do indulge from time to time. Only one or two chocolates, however. To gorge on the whole box — e.g., the ORFans vs front-loading problem, which I agree is significant — would be wrong. Not because the problems aren't worthy of attention, but because I need to complete what I've already started elsewhere.
I recently met Krauze in person for the first time, and we talked for a while about my skepticism concerning front-loading. He explained to me why he has adopted the position provisionally, and his explanation made perfect sense. I'm still a skeptic, but I'm eager to see what he might find (in fact I just sent Krauze and Mike Gene a paper I found by some Hindu scientists, on front-loading, which I may write up for IDTF).
Art, did you see the new paper about ORFans in mimivirus? Fascinating.
Thanks for the leads re Ikehara, etc. I'll follow those up.
Comment by Paul Nelson — October 28, 2006 @ 2:53 pm
October 28th, 2006 at 3:10 pm
Hi Art,
You write: First and foremost, the statement "Fox's protocells were cell-like entities capapble of growing, dividing, metabolism, and responses to external stimuli" is nothing but a bare-bones, simple, straightforward statement of fact.
You still don't seem to get it. This is a perfect example where you conflate your own perspective on reality with "fact." It is simply false that you offered "nothing but a bare-bones, simple, straightforward statement of fact." You specifically chose words with strong biological connotations to embellish those facts for effect. Either that, or the needs of you mindset chose them for you. For example, consider what Deamer said: