Probabilities and the Genesis of Life

_{Gil Dodgen

December 13, 2009

Intelligent Design}

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The important thing to keep in mind concerning probabilities and the origin of life is that proteins, and everything else in a living cell, are manufactured by machinery which is controlled by an abstract-representation digital coding system. Proteins not only don’t self-assemble, they cannot self-assemble, because basic chemistry drives the process in the opposite direction.

Once this is taken into consideration all arguments that assert, “But it could have happened by chance,” are rendered ludicrous on their face.

By way of analogy, the basic Darwinian argument for the origin of life goes something like this:

1) Clay occurs naturally.
2) Bricks are made of clay.
3) Therefore, there is some (given enough time) probability that houses made of clay bricks came about by stochastic processes and the chemistry of clay.

This is the way I see it, and so do most people with common sense. Apparently, one needs a Ph.D. in Darwinian Speculation (or sufficient indoctrination in this academic, “scientific” specialty) not to recognize the obvious.

Comments

… and how would you test that proposal?
Mung: 1a.) Evaluate the results of guided abiogenesis experiments. 1b.) Evaluate the results of unguided abiogenesis experiements.
Could you possibly be more vague?Zachriel_{December 16, 2009
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vjtorley: What this exchange of views tells me (and it’s obvious in retrospect) is that any realistic probability assessment for a model of how life could have originated naturally, is incomplete without a computation of the probability of the prebiotic conditions invoked by the model.
The authors cite studies concerning the prebiotic Earth.
vjtorley: However, the wording in chemstandup’s post suggests that several parameters in their experiment (pH, temperature, reaction medium, reaction mixture, contact time, and energy input) were tightly controlled. That suggests to me that the results they achieved would have been highly improbable on the early Earth.
Because the primordial Earth didn't have pH, temperature, energy or time?
vjtorley: Abiogenesis fans are crowing about the highly artificial synthesis of a molecule which is one million times smaller than the simplest bacterium.
RNA World hypotheses predict a natural pathway to the synthesis of nucleotides. This experiment provides evidence of such a pathway. It doesn't purport to provide a complete history of abiogenesis. - We apologize for the long, and heretofore unexplained moderation delay.Zachriel_{December 16, 2009
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#111 After all, it took several billion years for multicellular life to evolve after the first microbes arrived on the scene. That’s longer than the evolution of life itself. Apparently, that major transition is not highly probable to occur. That is a good point that is easily overlooked. Any theory that suggests that multicellular or eukaryotic life could arise easily from prokaryotic life is implausible. It has to be a very infrequent series of events. If life was designed then you have to wonder why the designer waited so long to implement this important stage. But then we again run up against the problem that it is impossible to critique a design hypothesis without saying something about the designer's motives and powers. Maybe it wanted to delay for reasons unfathomable.Mark Frank_{December 16, 2009
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vjtorley:
What I think more likely, though, is that the universe itself might have been extraordinarily fine-tuned, both in its carbon chemistry and in its initial conditions, such that the emergence of life through natural processes was inevitable.
You may be right, but it contradicts your earlier claim that natural emerge of life is astronomically improbable.
But I would call that evidence for directed evolution. Wouldn’t you?
No, I wouldn't. I would call it directed setup of initial conditions. The subsequent evolution of life by natural processes would be undirected, and it's a big question to what extent the detailed properties of such life are predictable (Gould's famous tape being played twice). After all, it took several billion years for multicellular life to evolve after the first microbes arrived on the scene. That's longer than the evolution of life itself. Apparently, that major transition is not highly probable to occur.IrynaB_{December 16, 2009
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lryna,
you could have repeated their answer. Instead, you are silent.
The direct answers to the questions given by two profs of chemistry were just a few inches away based on my 21” monitor. I hardly think I needed to re-copy their words – did you not see them? In any case, suggesting silence is a wee bit petty, since it was one of my posts (containing the words from one of the quoted profs) to which you responded.
Maybe you friends don’t know the answer either.
When the chemistry professor emeritus of NYU says “the chances that blind, undirected, inanimate chemistry would go out of its way in multiple steps and use of reagents in just the right sequence to form RNA is highly unlikely then I think he is meaning to say that the chances that blind, undirected, inanimate chemistry would go out of its way in multiple steps and use of reagents in just the right sequence to form RNA is highly unlikely. His opinion seems to dovetail perfectly with the opinions of others whom are well-credentialed in the field. It was pointed out that the researchers used “the best reagents and lab equipment, supervised by intelligent chemists. They use pure components, separate and purify products using the most up to date methods. They control the pH, temperature, reaction medium, reaction mixture, contact time, and energy input of each stage. They isolate their reactions in nice clean compartments. None of these conditions pertain to the prebiotic earth.”. I don’t think the professors are saying that demonstrating a pathway is impossible, but they question the pathway being demonstrated. If you are suggesting that if any pathway is demonstrated, it therefore cannot be challenged, then please just say so. If that is not your position, then the alternative position is that the pathway can indeed be questioned, and that the objections of the many biologists, chemists, physicists (and others) who question it may be accepted for their content. Indeed, they may even be viewed for the level of consistency among their objections.
Since you seem to rule out unguided abiogenesis, how do you propose that life got started, and how would you test that proposal?
First it’s fair to remember we are talking about a momentous event (regardless of your perspective) that took place billions of years ago in an environment that we can only speculate about. I am not certain anything can be “tested” in the sense of certainty, if that is the point of your question. However, it is a question I have some familiarity with. I asked the same of Cornell Prof Allen MacNeil regarding the testability of assuming purely unguided processes in nature, and he did a series of fanciful pirouettes just in order to exit stage left. You may be able to shed some light on it if you wish – how would you test the assumption of purely unguided processes in the existence of life on this planet? To answer your question: In place of certainty, we have the evidence of life as we know it. We may investigate that by appropriate reasoning.
Let me ask you this then: do you or do you not agree that experiments performed by intelligent scientists could indicate plausible unguided pathways to life? Yes or no?
I believe I have answered this. Do I think it is conceptually possible that scientists could demonstrate a plausible pathway to abiogenesis by purely unguided processes (yes or no)? Yes. But that is not the question. In fact, that is not even a question; it’s a rather junior debating point. The question is – did life result from purely unguided processes? If those processes will allow life to organize without agency input, then logically, scientists should be able to demonstrate it. If those processes will not allow life to organize without agency input, then scientists will not be able to demonstrate it can. Given the testability issues either way, this is where priori assumptions come into the picture. Science has operated with the assumption that purely unguided processes led to life for well over 100 years. It is the central theme in every textbook and is spoken to the public (to which science has a responsibility) on a daily basis, ranging from unabashed proclamations made on television and in newspapers, to popular books written by scientists using their status as a means to further the assumption. Do you think that science has provided the evidence that life came about by purely unguided processes? “Yes or no?”Upright BiPed_{December 16, 2009
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I need to correct the above. Not only did the irradiation step generate ctosine and uracil, it also converted some of the ribocytidine (the "C" letter" to ribouridine, (the "U" letter"). So the pathway described by the authors is capable of producing one-half of the types of ribonucleotides needed to synthesize RNA.Dave Wisker_{December 16, 2009
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vjtorley,
Just to set the achievements of Sutherland et al. in perspective: The longest of the various chemical pathways leading to ribo-cytidine phosphate, the molecule they synthesized, has only four steps, as readers can verify from this linkto an article in The New York Times (May 13, 2009) by Nicolas Wade, entitled “Reconstructing the Master Molecules of Life.” The synthetic M. genitalium I mentioned above has a molecular weight of 360,110 kilodaltons (kDa), or 360,110,000 daltons. Printed in 10 point font, the letters of the M. genitalium JCVI-1.0 genome span 147 pages. By contrast, the RNA nucleotide which Sutherland et al. manufactured (ribo-cytidine phosphate) has a molecular weight of less than 360 daltons: less than a millionth that of the simplest bacterium.
Methinks you are making an inappropriate comparison. The number of steps in the chemical pathway may only be four, but that doesn't mean that pathway only resulted in one single molecule. It produced many ribo-cytidine phosphate molecules. That is, it produced one of the four basic types of ribonucleotides:, those with the base cytosine (the letter “C” in the RNA sequence), and lots of them.. In other words, it generated lots of “C’s”. However, one key finding of the paper was that the irradiation step, which generated the cytosine needed for steps further down the path also generated uracil, (found in the ribonucleotide for the letter “U”). This is probably because uracil and cytosine are similar chemically (they are in the class of molecules known as pyrimidines). The authors used cytosine for the rest of the work, but there is no reason to think the path would be much different for uracil because of the similar chemistry of the two. So in reality, the authors found a simple path that can generate one, and most likely two of the four different ribonucleotides found in RNA. Now, when you talk about the number of letters in an organism's genome, you are actually counting the physical number of nucleotides, the building blocks of DNA . But you have to keep in mind in any genome there are only four different types of nucleotides in DNA and ribonucleotides in RNA, only four different “letters”. In DNA, those letters are “A”, “T”, “C” and “G”, and in RNA, “A”, U”, C” and “G”. So, to put the paper in perspective, it describes a simple 4-step pathway capable of generating at least one quarter and likely one-half of the kinds of ribonucleotides necessary to build an RNA genome.Dave Wisker_{December 15, 2009
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Mr. Nakashima & IrynaB: Mr. Nakashima, you wrote:
How about we circle back to the improbability concerns raised earlier.
An excellent idea. I shall spend my Christmas / New Year vacation boning up on biochemistry. I have taken your "Gambatte" (Go for it!) to heart.
To someone flogging those as an impossiblity proof, even one counter-example is significant.
Quite so. However, I never said that abiogenesis was impossible. All I ever said was that it was astronomically improbable, through undirected natural processes. By all means let's make the probability estimates more precise. IrynaB, you asked:
What kind of experiment would it take to convince you of the plausibility of “unguided” abiogenesis?
Speaking for myself: a computer simulation, starting with plausible prebiotic conditions and simple organic molecules and ending with a self-replicating life-form. Of course, I'd have to see the program code to make sure it wasn't rigged. And of course, you'd need a very, very fast computer to perform such a simulation of the early Earth. Maybe the advent of quantum computing will make it possible to perform these calculations some day. In the meantime, origin-of-life research could still make some very interesting discoveries in the lab (see below). You also asked:
Do you or do you not agree that experiments performed by intelligent scientists could indicate plausible unguided pathways to life? Yes or no? Please explain your answer.
Realistically, I don't think it at all likely that experiments will reveal an unguided mechanism, although theoretically speaking, they could surprise us all. What I think more likely, though, is that the universe itself might have been extraordinarily fine-tuned, both in its carbon chemistry and in its initial conditions, such that the emergence of life through natural processes was inevitable. Professor Michael Behe entertains this hypothesis in The Edge of Evolution when he discusses the possibility that an uberphysicist may have set up the universe so as to ensure the emergence of life, in the beginning. For those who dislike acts of Divine intervention, that's a possibility to be considered. The late astronomer Sir Fred Hoyle once predicted that predicted that the carbon-12 nucleus would have a certain energy level (or resonance) to enable helium to undergo fusion. Likewise, scientists, using a process of reverse engineering, may one day discover that carbon compounds have certain surprisingly fine-tuned chemical properties which would have favored the emergence of life, and that these properties, in conjunction with a very specific set of initial conditions, could explain the origin of life. That kind of research I would encourage. But I would call that evidence for directed evolution. Wouldn't you?vjtorley_{December 15, 2009
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Mr Vjtorley, How about we circle back to the improbability concerns raised earlier. To someone flogging those as an impossiblity proof, even one counter-example is significant. That is the relevance of very small first steps.Nakashima_{December 15, 2009
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Hi everyone, It's interesting to compare the responses of various contributors to the experiments reported by Sutherland et al.: "Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions", Nature, 459:239-242 (2009) chemstandup (#86)
It's nice chemistry, carried out with the best reagents and lab equipment, supervised by intelligent chemists. They use pure components, separate and purify products using the most up to date methods. They control the pH, temperature, reaction medium, reaction mixture, contact time, and energy input. Although they claim their route is plausible under prebiotic conditions, nothing in their paper makes this believable.
Dave Wisker (#90)
He [Professor Walton - VJT] fails to address their incorporation of UV light, nor the simulation of periodic light/day via sublimation. Or having phosphate present from the beginning. How exactly, are these features of the work so unbelievable?
What this exchange of views tells me (and it's obvious in retrospect) is that any realistic probability assessment for a model of how life could have originated naturally, is incomplete without a computation of the probability of the prebiotic conditions invoked by the model. Sutherland et al. are to be commended for including UV light and phosphates, and for simulating light and day. However, the wording in chemstandup's post suggests that several parameters in their experiment (pH, temperature, reaction medium, reaction mixture, contact time, and energy input) were tightly controlled. That suggests to me that the results they achieved would have been highly improbable on the early Earth. Mr. Nakashima (#98) estimates that between 1 and 10 million sequential steps would have been required to get from simple organic chemicals to the simplest bacterium, M. genitalium, the synthetic version of which has 582,970 base pairs, according to this press release by the J. Craig Venter Institute. If many of these 1 million-plus steps were highly improbable steps, then the likelihood is abiogenesis is rendered extremely remote: it dies the death of a million cuts. Just to set the achievements of Sutherland et al. in perspective: The longest of the various chemical pathways leading to ribo-cytidine phosphate, the molecule they synthesized, has only four steps, as readers can verify from this linkto an article in The New York Times (May 13, 2009) by Nicolas Wade, entitled "Reconstructing the Master Molecules of Life." The synthetic M. genitalium I mentioned above has a molecular weight of 360,110 kilodaltons (kDa), or 360,110,000 daltons. Printed in 10 point font, the letters of the M. genitalium JCVI-1.0 genome span 147 pages. By contrast, the RNA nucleotide which Sutherland et al. manufactured (ribo-cytidine phosphate) has a molecular weight of less than 360 daltons: less than a millionth that of the simplest bacterium. Four steps versus 1 million plus steps. That's something like the distance from New York to Atlanta, if you want a visual metaphor. Some progress! Abiogenesis fans are crowing about the highly artificial synthesis of a molecule which is one million times smaller than the simplest bacterium. May I respectfully suggest that their excitement is a little premature?vjtorley_{December 15, 2009
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Since you seem to rule out unguided abiogenesis, how do you propose that life got started, and how would you test that proposal?
1.) Guided abiogenesis. 2.) Life never had a start. Life has always existed.
... and how would you test that proposal?
1a.) Evaluate the results of guided abiogenesis experiments. 1b.) Evaluate the results of unguided abiogenesis experiements. 2.) Evaluate attempts to show that life can be produced from non-life, guided or not.Mung_{December 15, 2009
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IrynaB, one of the interesting things about these kinds of discussions is that people forget that there are two propositions and that disproving one does not prove the other. It is the scientists' burden to prove that their theories are correct and it is beneficial to be skeptical and critical in order to find the truth. But if you are saying that Upright Bipedal does not have a very good alternative in OOL, you are right. Nevertheless, that does not do anything for the weakness in mainstream OOL. I'm beginning to believe that all scientific endeavor is faith-based. That's not bad! But just because you've made discoveries before does not mean that you will tomorrow. Yet you keep searching, hoping that you will find more knowledge. It is a noble endeavor, but let's get real. It's based on faith and hope and that's just fine.Collin_{December 15, 2009
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Upright BiPed:
I think your question to me has already been on the table for those who are in a much better position to answer it.
Then you could have repeated their answer. Instead, you are silent. Maybe you friends don't know the answer either. Here, let me repeat one of my questions: Since you seem to rule out unguided abiogenesis, how do you propose that life got started, and how would you test that proposal?
If you look at the reasoned objections of trained chemists over the measure of investigator input in reaching a result, and then feel the need to throw up your arms and say “then we can never prove our case”. Then perhaps the problem is the case you are trying to prove.
The case is that unguided chemical evolution led to life. Let me ask you this then: do you or do you not agree that experiments performed by intelligent scientists could indicate plausible unguided pathways to life? Yes or no? Please explain your answer.IrynaB_{December 15, 2009
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Nakashima, Your comparison of Columbus, Lewis and Clark with scientific research is apt. They had to have had a high amount of confidence and maybe even some arrogance to accomplish what they did. They didn't know what was out there, but they had faith in their idea and were able to discover, not what they sought, but something far better. But it may be that our modern biological explorers will end up finding a whole new world that they never expected to find. Here's an interesting quote from Columbus' diary: "It was the Lord who put it into my mind ... the fact that it would be possible to sail from here to the Indies." His deity seemed to give him promise of something that would never happen, yet it led to something far more important than spice trading. Maybe that is analogous to what we will find with OOL. See http://endtimepilgrim.org/columbus.htm for columbus diary quote.Collin_{December 15, 2009
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????, The burden to demonstrate the power of chance is on the "chance worshippers"---those indoctrinated in materialism. But mainly---way off topic here---I just wanted to see if a non-Latin script comes through. I see it now---will I in a moment?Rude_{December 15, 2009
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lryna, I think your question to me has already been on the table for those who are in a much better position to answer it. I am not limited in my ability to see rational significance in the variance of degree. You should try it. If you look at the reasoned objections of trained chemists over the measure of investigator input in reaching a result, and then feel the need to throw up your arms and say "then we can never prove our case". Then perhaps the problem is the case you are trying to prove.Upright BiPed_{December 15, 2009
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Mr Vjtorley, My reply, all together again! I hope writing it twice made it better. I would like to ask you a simple question: are you a chemist of some sort? No, but I know how to find the work of respected chemists on the Internet! ;) I respect people’s right to privacy, and I’m not asking you to reveal your identity. But the fact is that you have made several posts in this thread, attempting to rebut assertions by researchers – including chemistry professors such as Dr. Walton – that the origin of life through undirected processes is massively improbable, and that the RNA world scenario is simply not feasible. The question I have to ask myself is: should I believe you, and if so, why? I'd say you have to ask yourself the same question about Dr Walton. A Ph.D in Chemistry doesn't make him an expert in OOL. His letter does not quote any substantive or relevant work of his own, it just puts forward a talking point you could have heard from Casey Luskin just as easily. You may respond that you shouldn’t have to identify yourself; your arguments stand or fall on their own merits. That would be fair enough, except for one small problem: I simply don’t understand your arguments. To me, they read like so much gobbledygook, because of the technical jargon they employ. That is a problem. Since you began participating in this thread, you've made several references to your own lack of understanding of the subject you chose to talk about. I've gone back and forth on whether you are actually expressing ignorance or are displaying a rhetorical stance. Because I respect your integrity, I will take your words at face value. Although I have studied a little chemistry at university level (two years of undergraduate chemistry, WAY back in 1979-80, and it was mostly inorganic chemistry at that), I am NOT a chemist. My background is in philosophy. So when I come across an argument which I cannot fully understand, in which you contradict a chemistry professor, I’m inclined to believe the professor. As someone trained in philosophy, I'm surprised your approach is not more nuanced. I have a citation, he has an assertion. Credential fail. To overcome this natural bias in my belief-forming system, you’ll have to either raise your credibility (e.g. “I am a senior chemist with 20 years’ research experience,” or “I’m not a chemist, but a chemist who is a friend of mine, Dr. X, has vetted my post and vouches for its accuracy”) OR make your arguments a lot clearer. I am abashed, and will try harder. Thank you for sticking with me. Take this statement of yours, attacking Dr. Stephen Meyer’s probability calculations for the origin of life: Of the original 10^-164, 45 orders of magnitude was from producing only peptide bonds, and templating on RNA supports that. Another 74 orders of magnitude was functional specificity, and the RNA was functionally specific for arginine-arginine sequences while the polypeptide showed enzymatic activity for the associated RNA. (The remaining 45 orders of magnitude were chirality, which this experiment does not address.) With regard to “templating on RNA,” I have to say that your statement sounds rather vague. (The link you provided to an article entitled Direct templating of amino acids on RNA wasn’t much clearer, either: it spoke of a “simple model system,” based on “the observation that several RNAs modestly accelerated the chemical ligation of the two basic peptides.” The rest went over my head.) I wouldn't conflate my vagueness with the article's technicality. I know you've followed cosmology for a long time, and even though you are not a cosmologist, feel confident assessing arguments in that area. I'm sure you are capable of doing the same in chemistry. Gambatte! The direct templating idea is simply that nucleotide sequences (RNA) has a surface whose physical contour and arrangement of electric charges allows some amino acids to attach directly. A made up example: triplet GAC will let AA1 attach for 1 second, AA2 attach for 2 seconds, ... , AA20 attach for 0.005 seconds. The preferences are not perfect. Why triplets? I don't know, maybe they are the same basic size as amino acids. A further development has been the discovery that if two amino acids attach, the alignment brought about makes it easy for their peptides to connect (ligate, in chemical jargon, but if you know Latin that is obvious). Are you asserting that the peptide problem has been solved, and we can all go home now? If not, how much work remains to be done? Could we have a progress metric, please? Yes, basically. Not that 'the peptide problem' has been a great concern. I've never seen it raised in OOL discussions outside of Dr Meyer's improbability argument. The same goes for your remarks on functional specificity. Functional specificity, as Meyer uses the term, is something you can quantify. Can you quantify the degree of specificity found for arginine-arginine sequences and compare it with that required for the synthesis of RNA? In other words, how far along the road are we? We can also reference Szostak for a definition of functional specificity, and many ID friendly people are happy to do so. If some RNA strand prefers to ligate Arg-Arg, and Arg-Arg enhances ribozyme activity, that is functional specificity. Yes, it can be measured and quantified. It is true that in modern biology, enzymes are large proteins with highly functional, highly specific attributes. It would be a mistake to assume the same had to be true in the distant past. Functional specificity is a metric that can be applied to a broad hill as well as a narrow peak. When you say, 'compared to the synthesis of RNA', it isn't clear to me that that is a valid comparison to ask for. The abiotic environment is going to continue making RNA, nucleotide by nucleotide until something changes. I would put the burden on proteins to push the synthesis of nucleotides until much further in the development of early life. Yes, you can talk of progress, but one step on a thousand mile journey would hardly count as significant progress. That is equivocating on the meaning of significant. The Wright Flyer and Neil Armstrong hopping off the ladder onto the Moon were single steps, and yet they were significant. We choose to celebrate our first or last steps on a journey, yet each has significance in the sense that you would not arrive without them!. And what if the journey I thought was a thousand miles long suddenly turned out to be two thousand miles, due to an unexpected roadblock? What of it? The world is joyously more complicated than we have ever expected. I’d like to return to the journey metaphor. When people embark on a journey, they usually have a good idea where they want to go, how far they will have to travel, and how long it will take them to get there. If they’ll be stopping at a couple of places along the way, they also know the relative distances between these places – i.e. which leg of the trip will be the longest, and which will be the shortest. Yes, most trips over known territory are like that. Journeys of exploration, such as Columbus or Lewis and Clark, are not. This is the limit of your analogy. All right. Let’s go with that. At the moment, the most promising naturalistic model for the origin of life is something like this: simple organic chemicals (e.g. amino acids) => RNA => (DNA and protein) => first cell. Sorry for skipping over so many vital steps, but I can only keep a limited number of things in my head at once (four’s about the limit, I’m afraid), and those are the key steps. I’ve identified three steps: (1) amino acids to RNA, (2) RNA to DNA and proteins, and (3) DNA & proteins to first cell. What I want to know is this: Let's stop here and rewrite the steps in slightly more realistic and well agreed form. 1 - the abiotic synthesis of amino acids, nucleotides, and lipid membranes, faster than these structures can degrade in the environment 2 - the confinement of these components in close physical proximity and concentration (at this point, molecular evolution starts working) 3 - the elaboration of metabolism in the confined environment 4 - the replacement of confinement with containment by lipid vesicles 5 - the ability of these protocells to reproduce themselves to an agreed level of fidelity to allow natural selection at the cellular level (biology per se begins) We have no idea when DNA entered the picture, and it is unecessary to get to 5. (1) Which of the three steps is the most difficult to achieve, and which is the least, in a given time period, under plausible prebiotic conditions? This is a qualitative statement. If you cannot even answer this question, then how can I possibly trust your quantitative assertions, in which you critique Dr. Meyer’s probability estimates? To answer the last first, I don't see the force of your question. If we read over this reasoning into the field of cosmology, would you agree with it? If someone refused to listen to your interpretation of COBE data because you hadn't explained how to tie QM and GR together, or whether the curvature of the universe is positive, negative or 0, would that be an appropriate response? No. To return to the first question, of the items in 1, nucleotides have been the hardest to synthesize. 2 is easy to acheive in the lab, and pumice, sand, ice, mud and other similar confining physical compartments are expected to have been available on the early Earth. I think 3 is the area where the least experimental work has been done, even though we have Kaufman's autocatalytic networks and Eigen's hypercycles as guidance. Dr Meyer in Signaure in the Cell correctly identifies hypercycles as an explanation of development, not origination of early life. (2) At the present time, can scientists quantify the relative probabilities of the steps involved (e.g. step 2 is 1,000,000 times harder to achieve, over a given time period, than step 1)? For chemists, nucleotides have been hard, much harder than amino acids (which you can find if you crack open a meteorite!). Step 3, I have no data on. (3) At the present time, can scientists quantify the probabilities of any of the key steps in absolute terms, given plausible assumptions about the prebiotic Earth and the amount of time over which they took place (say, 500 million years)? 1a and 1c are pretty certain - probability approaching 1. (4) Breaking it down into small steps, suppose we follow the long path from amino acid to first cell, focusing on the largest chemical molecule at each stage along the way, and tracking its growth as it gets bigger and more complex. For simplicity’s sake, we’ll ignore all the other molecules that it must have reacted with. We’re just looking at the most direct chemical pathway from amino acids to the first cell. Using this metric, how many chemical steps were there from amino acid to first cell, to the nearest order of magnitude? 10,000? 1,000,000? 1,000,000,000? More? I'd guess between 1 and 10 million. We know that bacteria such as M. genitalium have very small genomes and protein sets. So you are asking how many steps to build a 600,000 base pair genome. There are slightly less than 300,000 different RNA sequences that are only 9 bases long. So you could easily generate many copies of every possible sequence and confine these in a small space. The research I cited shows that there is some functional specificity even for such short sequences and the proteins that can template directly on them. So the most direct route that you are asking for is going to be some sequence of combining small sequences like this. Starting from this collection of random snippets, by the most direct route you will need 599,999 events to connect them into the genome of M. gen, so guessing 10 million allows a fair bit of backing and filling in the estimate. So if we could get just one of those events to happen every thousand years or so, we'd be happy. (5) Typically, journeys have a known distance. The relevant analogue to distance here might be the estimated probability of getting from amino acid to first cell, or the number of steps that must have been traversed. Newspapers always report breakthroughs in origin-of-life research, but they never reported unexpected roadblocks: that doesn’t sell with the reading public, who only want to hear about progress. So I would like to ask: has the estimated probability of life arising by undirected natural processes risen or fallen over the past 15 years? Again, exploratory journeys do not have a known distance. Lewis and Clark did not know that hundreds of miles of mountainous terrain lay on the other side of the Continental Divide. Columbus did not know the width of the Atlantic Ocean. Having said that, I would say the circle of our ignorance is shrinking, and therefore that the probability is rising over the last 15 years. Ditto for the number of steps required. Now that would be a valid measure of whether abiogenesis is more difficult to achieve than scientists had first anticipated, or whether it is easier than they first thought. Or a measure of analogical failure, as the case might be. Now, I respect honest ignorance, and it may be that no-one in the world knows the answers to any of these questions (although I very much doubt it). In that case, proponents of aabiogenesis should have the intellectual honesty to admit their ignorance, and then maybe we can all return to this discussion in 20 years’ time. But if that’s the case, then it would not be fair of you to criticize researchers who identify problems in abiogenesis, by downplaying the improbabilities involved. Instead, a more appropriate response would sinply be: we don’t know. Again, I'm happy to share an admission of ignorance, but arguments from implausibility aren't admissions of ignorance. They are claims to sufficient knowledge to make the calculation. If those that make a calculation have such knowledge they should share it, or stop making claims (of improbability) based on ignorance. Which brings me to question (6): If we don’t know, then when will we? And if we don’t know that, then we really are up salt creek without a paddle. If our ignorance is that severe, then scientists are in no position to affirm that abiogenesis is scientifically possible. A non-quantifiable possibility is mere hand-waving. Heavier-than-air powered flight may be an interesting analogy here. During the late 19th century, there were people who argued that it was impossible for humans to construct such devices. However, those working on the problem had the feeling of a race to solve the problem, that the solution was imminent. Even as they solved the puzzle step by step, I'm not sure that the Wright Brothers would have been able to offer you the estimate you are asking for. Yet the Wright Brothers knew birds could fly, and birds were heavier than air. They knew the goal was acheivable. Similarly, we know living cells exist. But suppose you have some answers to my first five questions, and suppose that your answers are significantly at variance with Dr. Meyer’s. Here’s my suggestion. Let’s have an online debate – or series of debates – between opposing teams of biochemists. I for one would like to get to the bottom of this. This is a geat idea, and I've picked out a name for this grand debate: PubMed. After all, the question of whether life on Earth could have arisen by undirected natural processes during the time available is an important one. It’s a question with philosophical and theological implications, and it affects how we live our lives. It does, and it is the grand intellectual challenge of the age. Over to you, Mr. Nakashima. And return!Nakashima_{December 15, 2009
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Upright BiPed, Correct me if I am wrong, but it seems that according to your reasoning it is impossible that intelligent scientists ever demonstrate experimentally plausible chemical pathways of abiogenesis. After all, experiments are always designed by intelligent humans. What kind of experiment would it take to convince you of the plausibility of "unguided" abiogenesis? Since you seem to rule out unguided abiogenesis, how do you propose that life got started, and how would you test that proposal?IrynaB_{December 15, 2009
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Behe tried it, Walton tried it, and Sharpiro apparently tried it too. What is the it? Perhaps it is the professional discipline to not trample the evidence.Upright BiPed_{December 15, 2009
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And, to be quite honest, if you want to talk about proper definitions, we don’t have a proper definition of natural or non-natural. This is where the real problem lies.
Indeed. What is a natural thing? That which is not a supernatural thing. What is a supernatural thing? Why, it is that which is not a natural thing. If you ask me, everything that exists has a "nature" or "essence" and anything which does have a "nature" or "essence" is therefore, by definition, natural. Take a being who by it's very nature cannot not exist. Why, such a being would be the most natural thing possible. So here's my attempt at a definition of natural. A natural thing is a thing which is contingent. It can exist or not exist, come into being and cease to exist. Now, this obviously excludes God as conceived above, but does it also give away the store? The natural world, in order to be natural, must be contingent.Mung_{December 15, 2009
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The following sequence by Zachriel seems to be a complaint, followed by a refutation of the complaint, followed by an excuse.

Walton doesn’t bother to explain why it’s not plausible, ignoring the supporting cites.
Walton: "They haven’t solved the stereoselectivity problem. They haven’t solved the problems of chemoselectivity in assembly of the pyrimidine ribonucleotides and they don’t address the problem of the information needed to assemble the nucledotides in the right order."
The study doesn’t intend to address anything more than the narrow issue of the plausible synthesis of ribonucleotides.
And then, Dave Whisker chimes in. He seemingly misses the point that one of the central reasons the synthesis is not considered plausible is because of the intense investigator manipulation to control the unfolding of a planned chemical event. Not seeing the forest for the trees, Dave states:
He fails to address their incorporation of UV light, nor the simulation of periodic light/day via sublimation. Or having phosphate present from the beginning. How exactly, are these features of the work so unbelieveable?
Again, investigator input is simply ignored for the obvious reasons of design. In Dave's case, he goes further and takes the opportunity to have a couple cheap shots at one of the chief villains in his play, Michael Behe. This reaction can virtually always be counted on when the design argument hits its target. In any case, Prof Walton's critique of Sutherland's work is in good company. "Although as an exercise in chemistry this represents some very elegant work, this has nothing to do with the origin of life on Earth whatsoever" ... "the chances that blind, undirected, inanimate chemistry would go out of its way in multiple steps and use of reagents in just the right sequence to form RNA is highly unlikely" - Robert Shapiro, Prof Emeritus NYUUpright BiPed_{December 15, 2009
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Clive, Thank you for knowing what begging the question means. It does not mean implying a question like so many others think.Collin_{December 15, 2009
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lastyearon,
Given that you believe the universe-and life-had a beginning, then at some point, wether here on earth, or somewhere else, non-life became life. Some scientists are doing good work trying to figure out how that happened. They don’t know, probably aren’t close to knowing, and may not ever know. But that doesn’t change the fact that abiogenesis isn’t just likely, it is certain to have happened. Life exists.
But that begs the question doesn't it, for that is the question at hand, and asserting it as the answer is begging the question.Clive Hayden_{December 15, 2009
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lastyearon,
However, that statement is not only not reasonable, it is non sensical. A “process” is by definition natural. If you are going to argue that life could have happened non-naturally, then you are going to have to come up with some alternative language so as to allow it to make sense.
A process only means a sequence of events, whether they be physical or metaphysical. The word "process" does not necessitate "natural process". And, to be quite honest, if you want to talk about proper definitions, we don't have a proper definition of natural or non-natural. This is where the real problem lies. One must take it for granted that they "understand" the "natural" world, when in reality they don't, for through science we can get descriptions of nature, but not explanations of why nature is the way it is, nor can we get an explanation of why it couldn't have been otherwise. Therefore, we cannot use descriptions as normative explanations against anything non-natural, because descriptions are not explanations. You have to have an explanation before you can explain why it's counterpart is ruled out. You cannot judge that which is non-natural until you can explain (not just describe) that which is natural. The truth is that nature is just as baffling and wanting of an explanation as is anything non-natural. We don't understand the basis of nature, and cannot rule-out non-natural by comparison. If anything "non-natural," to you, is crazy, I think you've forgotten just how crazy "natural" things are. They are equally baffling concerning an explanation. All we could hope to do by comparison of the two would be to compare both of their descriptions. But descriptions (which is all we can ever have in science and the study of nature) are not an argument against proscriptions.Clive Hayden_{December 15, 2009
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vjtorely, Frankly, I was disappointed in Professor Walton's response. Perhaps it was too much to expect specific objections to the paper, or the work it cited from him, other than they carefully controlled certain parameters of the work, which he uses, oh-so-cleverly, as an excuse to dredge up the old, tired ID bromide of "they used a laboratory and test tubes and stuff, therefore it was all Intelligent Design!" He fails to address their incorporation of UV light, nor the simulation of periodic light/day via sublimation. Or having phosphate present from the beginning. How exactly, are these features of the work so unbelieveable? Walton doesn't even attempt to address them. His reaction, I'm afraid, is much like Michael Behe's reaction to the immune system literature at the Dover trial: non-specific dismissal. Do you really find this kind of response useful?Dave Wisker_{December 15, 2009
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Mr Vjtorley, Dr Walton's views are in consonance with those already expressed in much the same terms via ID-friendly outlets such as ENV. As with the improbability argument and the Dobzhansky quote, he isn't bringing his own qualifications as a chemist to bear on the issues. As such, I would be careful of a credentials based preference for his opinion. This is a small part of the larger response I was trying to give to a previous post of yours. I fear it will have to come in disjoint segments. My apologies.Nakashima_{December 15, 2009
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Vjtorley, Sorry, I thought the comma was a decimal point.Collin_{December 15, 2009
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vjtorley: Recently, I emailed Professor John Walton and asked him for his comments about the paper by Powner MW, BG Gerland & JD Sutherland (2009), entitled “Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions” in Nature 459:239-242.

Walton: Although they claim their route is plausible under prebiotic conditions, nothing in their paper makes this believable.
Walton doesn't bother to explain why it's not plausible, ignoring the supporting cites.
Walton: They haven’t solved the stereoselectivity problem. They haven’t solved the problems of chemoselectivity in assembly of the pyrimidine ribonucleotides and they don’t address the problem of the information needed to assemble the nucledotides in the right order.
The study doesn't intend to address anything more than the narrow issue of the plausible synthesis of ribonucleotides.Zachriel_{December 15, 2009
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Dave Whisker: You suggested the paper by Sutherland and co-workers: “Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions”, Nature, 459:239-242 (2009) as a refutation of my statement that: “Intense laboratory research has failed to produce even one nucleotide (RNA component) under geologically plausible conditions.” Professor Sutherland and his group certainly deserve full credit for designing a viable route through the maze from some possible prebiotic precursors to pyrimidine ribonucleotides. They can also be congratulated for their literary acumen in crafting a title likely to persuade the editor of the journal Nature to publish their article, and to bring the naturalist claque on to their side. Theirs is nice chemistry, carried out with the best reagents and lab equipment, supervised by intelligent chemists. They use pure components, separate and purify products using the most up to date methods. They control the pH, temperature, reaction medium, reaction mixture, contact time, and energy input of each stage. They isolate their reactions in nice clean compartments. None of these conditions pertain to the prebiotic earth. Although they claim their route is plausible under prebiological conditions, nothing in their paper makes this believable. Their claim will remain wildly optimistic until they demonstrate their preparative sequence taking place, on its own, in some unsupervised corner of mother nature. (It is of course debatable if “mother” is an appropriate descriptor for prebiological nature!) They haven't solved the stereoselectivity problem. They haven't solved the problems of chemoselectivity in assembly of the ribonucleotides and they don't address the problem of the information needed to assemble the nucledotides in the right order. What their work actually shows is that with intelligent chemists supervising each step of the process, nucleotides can be accessed from some simple molecules. Their paper, and others like it, provide good examples of intelligent design at work.chemstandup_{December 15, 2009
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To those who may be interested (Mr. Nakashima and Dave Wisker, I presume): Recently, I emailed Professor John Walton and asked him for his comments about the paper by Powner MW, BG Gerland & JD Sutherland (2009), entitled "Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions" in Nature 459:239-242. Professor Walton was courteous enough to reply. I hope he won't mind if I quote an extract from his response:
I have seen previous papers by Sutherland and co-workers on supposed prebiotically plausible syntheses. The Nature paper you mention is of much the same kind. It's nice chemistry, carried out with the best reagents and lab equipment, supervised by intelligent chemists. They use pure components, separate and purify products using the most up to date methods. They control the pH, temperature, reaction medium, reaction mixture, contact time, and energy input. Although they claim their route is plausible under prebiotic conditions, nothing in their paper makes this believable. They haven't solved the stereoselectivity problem. They haven't solved the problems of chemoselectivity in assembly of the pyrimidine ribonucleotides and they don't address the problem of the information needed to assemble the nucledotides in the right order. What they show is that with intelligent chemists supervising each step of the process, nucleotides can be accessed from some simple molecules. It is good evidence of intelligent design at work.
I especially like that last sentence.vjtorley_{December 15, 2009
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