OOL Researchers: No Soup for You!!

_{Barry Arrington

February 6, 2010

Intelligent Design}

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For 80 years it has been accepted that early life began in a ‘primordial soup’ of organic molecules before evolving out of the oceans millions of years later. Today the ‘soup’ theory has been over turned in a pioneering paper in BioEssays which claims it was the Earth’s chemical energy, from hydrothermal vents on the ocean floor, which kick-started early life.

Rest of the story here.

Comments

Dr Giem, An experiment cannot be agnostic as to the source of energy. One has to use electrical discharge, or UV, or some other source, or one will simply not get any significant chemical reactions. Sorry if I was not clear, I meant agnostic as to which source (UV, lightning, radiation, etc.) but assuming there was a source. It appears to me that the Zinc World hypothesis is that the zinc sulfide deposits upon which RNA might form are the direct result of massive vulcanism, such as might also create lightning discharges in the atmosphere. Since these formations are many kilometers across, it could be that amino acids created in on place would be transported to other locations by rain or other water movements. Note also that while this hypothesis restricts where life might have started to some kinds of coastlines, there was a lot more coastline back then! Large continental blocks had not formed yet. I think Adel DiBagno has answered your quote of Shapiro well enough. I will note though, that some scientists are quite wedded to their research agendas and have a hard time backing down from them even when the evidence starts to mount against them. Shapiro himself on metabolism first OOL is an example, as is Rubens on the "birds are not dinosaurs" issue. Personally, I see these more as ego commitments than philosophical commitments.Nakashima_{February 21, 2010
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Dr Giem, To your #45: To my request for a list of theories about intelligently assisted origin of life, you answered,
One general theory is that all it takes to create life from inorganic molecules is ordinary human intelligence and ingenuity, along with the usual laws of nature and chance (whether ordinary human intelligence and ingenuity are outside of nature will be left as an open question). Several research teams are currently working on this theory, the most notable being that headed by Craig Venter. Many are convinced that one or more of these teams will succeed; I am not so sure. But it is an active area of research.
I agree that there is some research along these lines, but I don’t find a “theory” driving such efforts. Looks more like an engineering feat to me, akin to sending humans to Mars. My concept of a theory is like this, quoted from Wikipedia:
A theory, in the scientific sense of the word, is an analytic structure designed to explain a set of empirical observations.
You know the kind of thing I mean: the theory of relativity, the theory of evolution, etc.
Another hypothesis is that it takes superhuman intelligence and/or ingenuity to create life.
Yes. A hypothesis. Not a theory. You continued,
Perhaps you are right that scientific theories about abiogenesis have nothing directly to say about one’s moral behavior. But if one translates those scientific theories into history, which is commonly done, it conflicts with certain other historical statements which tends to undercut the moral authority of certain prescriptive statements coming from the same source(s). Thus one’s behavior might be influenced by a long and complex but nevertheless causal chain starting with (unassisted) abiogenesis or the lack thereof.
I enjoyed this comment, because it illustrates a basic difference between us with respect to educational backgrounds and attitudes about relationships between religion and science. I was raised a Roman Catholic, in an Old World tradition, whereas you, judging from comments you have posted on this site and on your blog, were brought up to be a biblical literalist, and so you remain. (If I have judged incorrectly, I would like to be corrected.) As you know, we Catholics are content to accept the Church’s authority and tradition in theological matters. (We are not dealing with empirical matters here; we are dealing with matters of faith.) So we take Revelation as a grand parable for our edification, not as an infallible history. Nor do we feel a need for Natural Theology to prove the existence of God. We are comfortable with the notion that God ’s creation is perfectly capable of generating life and all of life’s diversity without periodic (miraculous) intervention. Consequently, we do not feel threatened by naturalistic science. On the contrary, we embrace it as a manifestation of God's love for his creatures. I tell you these things just to provide a different perspective, not to start another Thirty Years' War!
And I agree that I am at risk for that, and try to counter it with the requirement that I make unambiguous predictions and rigorously (well, as rigorously as possible) test them. One of those tests is supposedly being completed within the next 2 weeks. If I can, I’ll let you know how it comes out.
Please do so. If you like, you can email me at: adelardinbath@yahoo.comAdel DiBagno_{February 21, 2010
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Adel (#44), Thank you in turn for your thoughtful response. I will try to respond to several of your comments and questions. You said,
If you would care to list various theories of intelligently assisted origin of life and the persons investigating them, I would be interested.
One general theory is that all it takes to create life from inorganic molecules is ordinary human intelligence and ingenuity, along with the usual laws of nature and chance (whether ordinary human intelligence and ingenuity are outside of nature will be left as an open question). Several research teams are currently working on this theory, the most notable being that headed by Craig Venter. Many are convinced that one or more of these teams will succeed; I am not so sure. But it is an active area of research. Another hypothesis is that it takes superhuman intelligence and/or ingenuity to create life. This is difficult to test directly by humans except for falsifiability (which makes it scientific?), but some stories of resurrection could be considered positive evidence for it. You say,
I assume you mean your moral behavior. If so, I think I understand where you’re coming from with regard to the impact of such theories on your moral behavior. But I don’t see how scientific theories about abiogenesis are necessarily relevant to anyone else’s moral behavior, anymore than are scientific theories about astrophysics.
Perhaps you are right that scientific theories about abiogenesis have nothing directly to say about one's moral behavior. But if one translates those scientific theories into history, which is commonly done, it conflicts with certain other historical statements which tends to undercut the moral authority of certain prescriptive statements coming from the same source(s). Thus one's behavior might be influenced by a long and complex but nevertheless causal chain starting with (unassisted) abiogenesis or the lack thereof. You say,
In my experience, what it takes to convince someone that she/he is wrong depends on how important it is to that person to hold on to her/his conviction of being right. I admit to being a victim of that affliction
I agree with you wholeheartedly. I think that the unraveling of the AGW movement provides an apt illustration. And I agree that I am at risk for that, and try to counter it with the requirement that I make unambiguous predictions and rigorously (well, as rigorously as possible) test them. One of those tests is supposedly being completed within the next 2 weeks. If I can, I'll let you know how it comes out.Paul Giem_{February 20, 2010
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Paul Giem @43, Thank you for your thoughtful response. You said:
Right now it looks to me like spontaneous generation is a loser based on the scientific evidence. Therefore it seems reasonable to explore various theories of the intelligently assisted origin of life, and their ramifications for my behavior.
You are entitled to your opinion. If you would care to list various theories of intelligently assisted origin of life and the persons investigating them, I would be interested. I assume you mean your moral behavior. If so, I think I understand where you’re coming from with regard to the impact of such theories on your moral behavior. But I don’t see how scientific theories about abiogenesis are necessarily relevant to anyone else's moral behavior, anymore than are scientific theories about astrophysics.
I could be wrong. But arguing that I could be wrong won’t impress me much. Showing me data that is more compatible with me being wrong than right would impress me far more.
You are entitled to your own judgment on such matters. In my experience, what it takes to convince someone that she/he is wrong depends on how important it is to that person to hold on to her/his conviction of being right. I admit to being a victim of that affliction.Adel DiBagno_{February 20, 2010
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Adel DiBagno (#42), I don't actually have the book. I read it in the library. Your quotation of the next sentence is correct. I am not stating, and do not wish to imply, that Shapiro does, or did, express despair. It is misreading me to state that I proposed or propose that. I am merely pointing out his commitment, which I believe he expressed honestly. Look, none of the conditions he raised are fulfilled. We haven't even explored thoroughly our own little corner of the galaxy, let alone all the galaxies in the universe. It is doubtful we ever will. The origin of life might be narrowed down to a half a billion years by the standard chronology, but it is doubtful that we can do significantly better. And depending on how you determine reasonable and unequivocal, it is doubtful that we will ever run all reasonable experiments, let alone that they will all fail unequivocally. So not only are we not there yet, but we will probably not get there in the reasonably foreseeable future. But I would ask where the weight of evidence is. And I would say that someone with the commitment that Shapiro has expressed might not be the person I would want to make the choice I must, at times, act on at present, regardless of his expertise. I understand all about the foibles of science. In medicine, there are all kinds of controversies about what is the best treatment for congestive heart failure, for example. But sooner or later one has to decide either to prescribe furosemide, or lisinopril, or some other drug, or all three, or not. Life does not always allow us to do some more study. The job of living is the job of deciding, and following the decision with action, based on incomplete and inaccurate information. Right now it looks to me like spontaneous generation is a loser based on the scientific evidence. Therefore it seems reasonable to explore various theories of the intelligently assisted origin of life, and their ramifications for my behavior. I could be wrong. But arguing that I could be wrong won't impress me much. Showing me data that is more compatible with me being wrong than right would impress me far more.Paul Giem_{February 19, 2010
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Paul Giem @41, quoting Shapiro:
Some future day may yet arrive when all reasonable chemical experiments run to discover a probable origin for life have failed unequivocally. Further, new geological evidence may indicate a sudden appearance of life on the earth. Finally, we may have explored the universe and found no trace of life, or processes leading to life, elsewhere. In such a case, some scientists might choose to turn to religion for an answer. Others, however, myself included, would attempt to sort out the surviving less probable scientific explanations in the hope of selecting one that was still more likely than the remainder.
With that attitude, it will never be settled by experiment. Shapiro indicates that there are others like him.
Maybe your edition of Shapiro’s book doesn’t contain the next sentence: “We are far from that state now.” As I read it, Shapiro does not express the attitude of despair that you have proposed. Indeed, some in the scientific community may think we are even farther from that state (“when all reasonable chemical experiments … have failed unequivocally.”) I see no overarching sign of discouragement about pursuing the quest for plausible scenarios for the origins of life forms. Plausible scenarios, entailing experimentally testable hypotheses are all that science can be expected to generate. Nothing has ever been “settled” in science, and the idea that there should be anything “settled” is a misunderstanding of the scientific enterprise.Adel DiBagno_{February 19, 2010
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Nakashima-san, You're probably right regarding Bada (and Miller for that matter); volcanic eruptions, such as those at Mt. St. Helens in the U.S. and Pinatubo in the Philippines can produce their own lightning. Whether it is quantitatively enough to do the work attributed to it is a different question, but it's a start. What I was commenting on was not so much Bada's scenario as the attempt to combine this with the ZnS world. A volcanic spring, such as we have in Yellowstone, appears to be incompatible with an actual volcanic erupttion. If Yellowstone blows, it is pretty certain that Minerva Terrace will be no more. An experiment cannot be agnostic as to the source of energy. One has to use electrical discharge, or UV, or some other source, or one will simply not get any significant chemical reactions. Perhaps your most important statement is that "It will all be settled by experiment, eventually." i wish. Robert Shapiro, one of the leading researchers into the origin of life, wrote a brutally honest book called Origins: A Skeptic's Guide to the Creation of Life on Earth. On p. 130 he wrote,
Some future day may yet arrive when all reasonable chemical experiments run to discover a probable origin for life have failed unequivocally. Further, new geological evidence may indicate a sudden appearance of life on the earth. Finally, we may have explored the universe and found no trace of life, or processes leading to life, elsewhere. In such a case, some scientists might choose to turn to religion for an answer. Others, however, myself included, would attempt to sort out the surviving less probable scientific explanations in the hope of selecting one that was still more likely than the remainder.
With that attitude, it will never be settled by experiment. Shapiro indicates that there are others like him. I like Shapiro, at least what I know from his writing. He is knowledgeable, witty, writes in a clear style, and rarely plays favorites, and when he does, he clearly labels it as such. And I like his honesty as to where he is coming from. But his comment above leads me to believe that this will never be settled by experiment, because the commitment comes before the research. Cornelius Hunter was right.Paul Giem_{February 19, 2010
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Dr Giem, I think your caution is appropriate. The papers proposing the Zinc World are clearly labelled hypothesis. I think Bada's volcano/lightning work was assuming that volcanos create their own lightning, but I'm also under the impression that most Miller-Urey style experiments are relatively agnostic as to the source of the energy. It will all be settled by experiment, eventually.Nakashima_{February 17, 2010
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JPCollado (#37) I agree. You probably noted that I quoted the Pusey passage in Chapter 4, along with a long passage from the other side that said essentially the same thing. A lot of comments that masquerade as science or the results of scholarship are really products of a worldview choice that then worked its way through the data, and the result is not unsurprisingly compatible with the original worldview. I do think that one can do science without worldview considerations swamping the science, just as one can do scholarly Biblical research without worldview considerations swamping the data. But it requires a humility and honesty that aren't instinctive to humankind.Paul Giem_{February 17, 2010
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Nakashima-san (#36) Your extended quote noted that CdS and TiO2 could reduce nitrogen to ammonia, and suggested that ZnS should be able to do so also. If so, formamide might be able to produce the amino acids necessary to produce complicated proteins, as well as RNA and DNA. To me, this should all be labeled speculation; fascinating for those who believe there must be a pathway to life but who don't know what it is. To those of us who need solid evidence for (unguided) abiogenesis before we can believe it, this does not qualify as such evidence. You reference Dr. Bada, who apparently presented a paper that has just recently come out. I'd like to see the paper. However, there is a problem with Bada's scenario helping the ZnS world. The ZnS world is supposed to originate in the lateral expanses of a hot-water spring such as we have in Yellowstone National Park here in the USA. Bada's reactions, assuming that they are as fabulously productive as reported, require some kind of lightning-like discharge. The center of a volcanic spring seems unlikely to sustain lightning strikes often enough that its water would be significantly rich in such things as amino acids. It seems the this would be even less likely to be the case when the ZnS-containing part of the springs is being significantly irradiated by UV light. This method of argument seems to me to be like arguing that since here and there in some woods one can find a flat stone, that one can drive an automobile through the woods on a pavement of flat stone. The conclusion requires more faith than I have.Paul Giem_{February 17, 2010
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Paul Giem: "Statements like this persuade me that Cornelius Hunter is right; the choice to disregard Behe is being made for metaphysical reasons, not scientific ones." Incidentally, I’ve encountered the same insidious attitude early on in my studies wrt book of Daniel (again) where there is much common ground shared with the debate over origins. Hunter’s sentiments find excellent expression in the great 19th century scholar, Edward B. Pusey, when he wrote, whilst contending against the then prevailing rationalism of the day, that:
They overlooked the historical point that the disbelief had been the antecedent to the criticism. Disbelief had been the parent, not the offspring of their criticism; their starting point, not the winning-post of their course. (Preface to Lectures on Daniel the Prophet (1864), p.vi.)
In the end, it is really all a matter over metaphysic and not so much about the finer details.JPCollado_{February 14, 2010
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Dr Giem, I agree that the use of the term irreducible complexity in that place was ironic, note the scare quotes. However, Mulkidjanian immediately above that spot makes reference to papers by Trevors and Abel in completely serious consideration of their ideas. You quote from the beginning of the section to which I wished to draw your attention. Here is a quote from the end of that section. Besides reducing organic compounds and catalysing condensation reactions, semiconductors can drive the photoreduction of dinitrogen to ammonium. This reaction has been demonstrated with preparations of CdS [280] and TiO2 [281-284]. The photoreducing capacity of ZnS is higher than that of CdS and TiO2 [154,190], and therefore one would expect that primordial ZnS systems were capable of reducing dinitrogen to ammonium as well, thus complementing the ammonium content of hydrothermal fluids. The interaction of formate, produced upon CO2 reduction, with ammonium could yield formamide, which could serve as a universal building block for the (photocatalyzed) synthesis of both nucleobases and amino acids [285]. Ref 285 is to Saladino R, Crestini C, Ciciriello F, Costanzo G, Di Mauro E: Formamide chemistry and the origin of informational polymers. Chem Biodivers 2007, 4(4):694-720 It seems that Miller-Urey type experiments have been re-run under atmospheres similar to those considered in the Zinc World papers. I haven't been able to find an online reference, but here is an extract from the Scientific American reporting: Miller, along with his colleague Harold Urey, used a sparking device to mimic a lightning storm on early Earth. Their experiment produced a brown broth rich in amino acids, the building blocks of proteins. The disclosure made the pages of national magazines and showed that theories about the origin of life could actually be tested in the laboratory. But the Miller-Urey results were later questioned: It turns out that the gases he used (a reactive mixture of methane and ammonia) did not exist in large amounts on early Earth. Scientists now believe the primeval atmosphere contained an inert mix of carbon dioxide and nitrogen—a change that made a world of difference. When Miller repeated the experiment using the correct combo in 1983, the brown broth failed to materialize. Instead, the mix created a colorless brew, containing few amino acids. It seemed to refute a long-cherished icon of evolution—and creationists quickly seized on it as supposed evidence of evolution's wobbly foundations. But Bada's repeat of the experiment—armed with a new insight—seems likely to turn the tables once again. Bada discovered that the reactions were producing chemicals called nitrites, which destroy amino acids as quickly as they form. They were also turning the water acidic—which prevents amino acids from forming. Yet primitive Earth would have contained iron and carbonate minerals that neutralized nitrites and acids. So Bada added chemicals to the experiment to duplicate these functions. When he reran it, he still got the same watery liquid as Miller did in 1983, but this time it was chock-full of amino acids. Bada presented his results this week at the American Chemical Society annual meeting in Chicago. So it would seem that while the Zinc Wolrd hypothesis is more interested in establishing the prerequisites for RNA and the general RNA World scenario, these Miller-Urey results support the idea that when the RNA becomes available abiotically, the amino acids will be there to interact with them.Nakashima_{February 13, 2010
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Nakashima-san, P. S. If you look at the orchestra members for the Tokyo Phil, you might be able to guess the (well, at least a major) reason for my recommendation.Paul Giem_{February 13, 2010
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JPCollado (#30), You're welcome.Paul Giem_{February 13, 2010
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Nakashima-san, I have now read the other article. Part of it describes a computer model where UV light breaks down competing polymers leading to an excess of RNA and/or DNA. I would be more impressed with actual experiments showing this. They shouldn't be too hard, or otherwise we can't obtain large amounts of RNA to fuel an RNA world. You are right that this article details some reactions. Near as I can tell, this pretty much sums it up:
Besides the reduction of CO2 to formate (see Fig. 1 for a scheme), the photosynthesis of dicarbonic, tricarbonic, and tetracarbonic acids has also been shown [146,155]. Yanagida and co-workers have reported the photoreduction of diverse acyclic and cyclic ketones to the corresponding alcohols [274,275] and the ZnS mediated formation of diethylamine from ethylamine [192].
That's not much, and it particularly not much when one compares it to Miller-Urey apparati. This seems to be one step forward and two steps back to me. You write about this being a hypothetical paper, and that there is a lot of "connecting the dots" to be done. I agree that much of what the paper presents can be fairly characterized as "hopeful noises". One remark struck me as interesting:
In summary, we have an example of a Darwinian function co-option [404]: the "irreducible complexity" of the first replicators can still be reduced by suggesting that their simpler "ancestors" underwent selection for a different, less structurally demanding aptitude (namely for their ability to survive in a UV-irradiated environment).
Reference 404 is The Origin of Species by C. Darwin. I find it fascinating that Behe is obviously being quoted ("Irreducible complexity") but is not referenced. It's great that there is this much message control. But in addition, I am fascinated that irreducible complexity can be refuted simply by suggesting that there was a simpler function for which the assembly in question was selected. No need to prove the simpler function, or even show experimental evidence that the function actually can be selected for. The mere suggestion is enough. Statements like this persuade me that Cornelius Hunter is right; the choice to disregard Behe is being made for metaphysical reasons, not scientific ones.Paul Giem_{February 13, 2010
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Zeroseven: "It refers to the origin of species from a common ancestor. You need the ancestor. Your criticism is somewhat ironic given ID’s professed lack of interest in the identity of the designer" I know what it says, but it still lacks substance and a basis in reality. If it says "the Origin of Species from a common ancestor" it still begs the question - the ancestor needs an origin. If the original ancestor cannot be explained through a natural process (which I don't believe it can), I can't really assume that it is necessary for the entire process of evolution from a common ancestor to be naturalistic. It doesn't mean that it isn't, it just means that I can't start with that assumption. I must start with something else - perhaps not making any assumptions either way would be a better place to begin. It seems that Darwinian ToE starts from the top and works backwards, which works in the here and now I suppose, but it may not work for it in considering OOL issues. It lacks substance because of the naturalistic assumptions. You are correct that ID as a science is not interested in the identity of the designer. However, this is not to say that ID advocates are not interested, but they use other means apart from scientific rational to determine that identity. It's a poor comparison. The identity of the designer is not the same as the origin of the first life. We have evidence that points to design, but not to the designer. Even staunch Darwinists admit that there is at least an appearance of design, yet deny the designer. So they still make an inference to design, while denying that there is a designer. Why is that? It seems that design inferences, and design language in science is natural. We naturally make the assumption that biological systems are purposeful. Yet such assumptions do not lead all scientists to determine the identity of the designer - most, in-fact, deny that any designer exists. Yet it is entirely reasonable (and natural) to infer design without identifying a designer. It is not entirely reasonable to infer natural causes acting without purpose upon systems for which one would naturally make a design inference. Hence, it is more reasonable and parsimonious to infer design than it is to infer naturalism alone as the cause of complex biological systems. Darwin's theory went against the natural inclination of scientists before him to infer design because biology appears designed. It seems this point needs to continually be explained on this forum.CannuckianYankee_{February 11, 2010
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Dr Giem, Thank you for the follow up. The other article does have a slightly larger discussion of the formation of the requisite monomers, but the focus is on the formation of pi-systems in general. The energetic argument is that UV and ZnS are going to help generate ring shaped molecules that can survive UV quite well. and that stacked rings survive even better. That is not specific to any particular ring shaped molecule. The paper references the creation of formate, makes an argument for the formation of ammonium by ZnS, and then makes hopeful noises that formate and ammonium will combine to foramide, and then a diverse assortment of important molecules will result. I think there is still a lot of 'connecting the dots' to be done - that is why it is a hypothesis paper.Nakashima_{February 11, 2010
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off-topic - Dr. Giem, just offering my thanks for making your online book Scientific Theology freely available. More specifically, the material in chapter 4 has been quite useful in my ongoing research and studies concerning the authenticity of the book of Daniel.JPCollado_{February 10, 2010
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Nakashima-san, Thanks for your reply. I read the abstract of the article you referenced in #24. It states that formic acid, and to a lesser extent acetic and propionic acids, can be made by irradiating carbon dioxide, water, and zinc sulfide. The maximal yield of formate is 10%. The yield of acetic and propionic acids is presumably much less. The abstract makes no mention of other byproducts. The body of the article seems to be behind a paywall. Assuming that the abstract is accurate, this would seem to be a poor substitute for a Miller-Urey apparatus. I fail to see how this has solved the problem of obtaining amino acids and or nucleosides from an atmosphere dominated by carbon dioxide. I have now read one of the articles ( http://www.biology-direct.com/content/4/1/27 ), and it contains a critique of the proposal of Russell et al, that started this thread:
In the most recent of the scenarios put forward by Russell and co-workers, hydrogen and hydrocarbons were produced below the sea floor in the complex "serpentinization" reactions and then brought to the surface by hydrothermal fluids (see [71] and references therein). Considering the primeval polymerization reactions inside the porous, compartmentalized bodies of hydrothermal vents, these authors suggested that the pH gradient across the inorganic membranes of these compartments, between the alkaline hydrothermal fluids and the more acidic primordial ocean, could have served as the energy source for primeval syntheses [70,71], by analogy with the transmembrane proton gradients on the membranes of modern bacterial cells. However, coupling of the transmembrane proton gradient to synthetic reactions – even in most primitive bacteria – is performed by a sophisticated enzyme machinery which seems to be evolutionarily recent [73]. Therefore it remains unclear whether and how such coupling could have occurred in the inorganic systems.
This seems to me to be a pretty devastating critique. The article seems to argue for the ZnS proposal in every way except the most important one; answering positively the question, can ZnS produce the necessary building blocks for life in an atmosphere dominated by carbon dioxide? Formate is just not adequate for life. For all we know, zinc fingers, and the zinc they require, are necessary for specific kinds of protein/DNA or protein/RNA interactions. At least it appears that certain (humanly) engineered proteins that bind to specific DNA sequences contain zinc fingers (see Wikipedia on zinc fingers). The article does offer critiques of competitors:
Other hypotheses on the origin of life either do not consider the energetics of abiogenesis explicitly (heterotrophic origin of life/RNA World) or, as the above discussed concepts of Wächtershäuser [56-61] and of Russell and co-workers [62-71], suggest mechanisms that do not seem to be plausible from the physical or (bio)chemical viewpoints (see [72] and the Background section above).
What it fails to recognize is that it is subject to a similar critique. Apparently zinc leads to the breakdown of DNA and especially RNA (see the third reviewer's second comment). This is briefly mentioned in the article, but seems to be an important obstacle in the development of life in a Zn++- rich environment. The methodology is not actually Popperian, to its detriment.
In addition, following the Popper's principles, we have tested the Zn world concept by considering the ability of this concept to provide explanations for obscure facts that other theories either ignore or cannot explain. The fact that the Zn world concept has successfully passed all these tests makes it a serious contender for the title of a syncretic concept of the origin of life.
The method, as described, is actually more like that of Lakatos, with its dependence upon what could be termed novel facts. In some ways this is a superior method, but it does miss an important point. Falsification, although now recognized to be a relative test, is still an important one. It does not matter how many disparate observations can be explained by a hypothesis; if the mechanism is frankly inadequate or fatally flawed, the hypothesis should be rejected. Thus the present inadequacy of ZnS-mediated photosynthesis to produce significant amounts of the requisite biologically significant monomers, let alone polymers, is at present a fatal flaw. Further research should be aimed primarily at fixing this flaw, or it will remain fatal. Furthermore, quantification of the Zn++- mediated lysis of DNA and RNA should establish that the Zn world will not destroy life before it can get started. The situation is analogous to blaming 9/11 on G. W. Bush's Iraq war. One can make all kinds of connections, for example, Al Quaida disliked the war and blamed all kinds of other actions on the Iraq war. One might even find notes by 9/11 participants stating that they were flying their airplanes into the towers because of "Bush's war against Iraq". But until the time problem is solved, the hypothesis is a failed one. Just so, until ZnS-mediated photosynthesis can produce a varied and rich enough "soup", it remains a failed, or at least significantly unsupported, hypothesis. Here, I believe skepticism is warranted. I'll look at the other article later.Paul Giem_{February 10, 2010
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contra zeroeleven, who has been trying hard to cancel the chance vs. intention duality by introducing a third variable, we find this statement made by materialist Albert Lehninge (as quoted in The Mystery of Life’s Origin, p.145):
We now come to the critical moment in evolution in which the first semblance of "life" appeared, through the chance association of a number of abiotically formed macromolecular components, to yield a unique system of greatly enhanced survival value.'
(emphasis mine) There is no three ways of cutting it. As long as chance is conjured up in the reckoning of life’s origin (or any other event dealing with probability for that matter), its polar opposite will be the default logical derivation, so that the negation of one continues to be the affirmation of the other.JPCollado_{February 10, 2010
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zeroseven: "But the question is what caused the earthquake. It wasn’t chance" Using natural disasters as an analogy to illustrate the dualistic relationship between chance and intention is rather vacuous and ill-conceived, for if (i) neither are implicit in the equation of earthquakes (as is the case you are trying to make with the point above), then the whole thing is a moot point as far as the illustration goes, and (ii) the very word 'disaster' carries with it a counter-intuitive meaning that is itself ‘destructive’ to the sense you are attempting to impute to the argument of self-organization, self-assembly, etc. ...and I don't know about you, but I never heard of earthquakes creating something of the magnitude of cars, cells, or even the simplest of biological nano-machines necessary for life, which is the whole gist of the discussion.JPCollado_{February 10, 2010
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zeroseven: "An earthquake caused a beautiful harbour in my home town." And I’m sure it has the order and symmetrical beauty we find with technological creations such as cars, right? Those Haitians will probably agree with you.JPCollado_{February 10, 2010
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zeroseven: “No, it’s not a valid logical conclusion.” JPCollado: “Fine, Mr. zeroseven. What is the opposite of something occuring by chance.” zeroseven: “I don’t know.” Mr. zeroseven, if you don’t know how are you so sure it is not a valid conclusion?JPCollado_{February 10, 2010
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Dr Giem, My sincerest apologies for not using your correct title. I will try to remember it for the future. I agree that the way the article flows is not particularly clear. Mulkidjanian is presenting the use of zinc in our current biochemistry as hint to the correctness of the overall hypothesis of the "Zinc World", but the ability of ZnS to use UV to break down CO2 is well documented, as in this article which is one of several referenced by Mulkidjanian. In general, the two papers by Mulkidjanian are well written and bring together a wealth of research. In making a detailed and testable hypothesis, and reviewing the relevant literature (semiconductor chemistry, OOL hypotheses, geochemistry of the early earth) I think they are substantial and would reward your attention. I agree with your point that we can understand the function of hemoglobin without knowing its history. However, Mulkidjanian was speaking of the more broad term 'properties' in the quote you criticize. Answering a 'how' question might not need history, but answering a 'why' question might. Why does hemoglobin use a specific metal ion? Why does chlorophyll use another specific ion? To what degree are these and many other uses of trace metals a necessity vs a choice dependent on historical contingency? Thank you for your recommendation of the Tokyo Philharmonic. I'm not in Tokyo as much these days as I used to be, haven't been there since October.Nakashima_{February 10, 2010
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Nakashima-san, I appreciate your polite approach. Culture is interesting, as in some circles calling me "Mr Giem" is an insult, because I have a doctorate in medicine. The proper title is "Dr. Giem". But I'm sure you didn't mean it that way. You said,
There are other proposals for abiogenesis at the surface that treat the energy from UV as a net positive. The page that Mr Arrington links to has a link to another article on the “Zinc world” hypothesis published last year.
I assume by this that you felt the proposal at the linked page was worthy of consideration. So let's look at it. To summarize the article, the Miller-Urey experiment used the wrong atmosphere; not wrong for forming amino acids, but wrong in the sense that it was not the original atmosphere. As they quote Mulkidjian approvingly (and I agree),
“After it became clear that the origin of the atmosphere was made of carbon dioxide,” says Mulkidjanian, “there was no physically or chemically plausible hypothesis of the origin of life.”
They go on to say,
Living organisms can exist only if there is some form of energy flow—solar radiation or chemical reactions, for example. “If you have an atmosphere of carbon dioxide, you need, in addition, a source of electrons to reduce carbon dioxide if you want to make complex compounds,” Mulkidjanian explains.
So the whole point is find some way to reduce carbon dioxide. At this juncture they point out that zinc sulfide can store light energy. Now one is tempted to think that they will present evidence that light and ZnS can reduce carbon dioxide (and water) to ribose, or glyceraldehyde, or formate, or perhaps with ammonia to amino acids, bases, or nucleosides. The article even says,
Mulkidjanian explains that, once illuminated by UV light, zinc sulfide can efficiently reduce carbon dioxide, just as plants do.
And now, the evidence:
To test the hypothesis, Mulkidjanian and Galperin analyzed the metal content of modern cells and found “surprisingly high levels of zinc,” particularly in the complexes of proteins with DNA and RNA molecules. “We have found that proteins that are considered ‘evolutionarily old’ and particularly those related to handling of RNA specifically contain large amounts of zinc,” Mulkidjanian says.
What!? The evidence of ZnS reducing carbon dioxide in abiotic environments is that it is used in enzymes in modern life? The words non sequitur come to mind. To quote two paragraphs or parts thereof,
But as the authors indicate in their paper, acceptance of a new hypothesis for the origin of life will likely require more work, particularly to further describe the nature of life and the chemical reactions in these zinc-rich communities. . . . “If this hypothesis is adopted in the origins of life community, it would represent a real conceptual shift, and so it would be significant,” says NASA astrobiologist Max Bernstein. “Whether it will be adopted or not eventually I cannot say, but I expect that many will want to see experimental evidence of the viability of reactions consistent with the hypothesized scheme under prebiotic conditions.”
I'll say it requires more work, and that we will want to see the experimental evidence of the viability of reactions under prebiotic conditions. Cornelius Hunter is right; this kind of speculation can only pass muster in an environment that categorically rejects the concept of intelligent intervention, for non-scientific reasons. One last rather blatant error is present in the article:
“We cannot explain fully the properties of modern organisms unless we understand how life has originated,” says Mulkidjanian.
How something operates in the present does not depend on how it was made. We may understand how hemoglobin binds oxygen in the lungs and releases it in the tissues, without the foggiest notion of the causal history of hemoglobin. If life is completely reducible to such mechanisms, it is perfectly understandable without any known causal history whatever. Try making that argument with a computer. The article cites two papers. I have not read them yet, and will do so as I get time. However, given the summary, there doesn't seem to be much substance to them. PS If you have the chance, go see the Tokyo Philharmonic Orchestra.Paul Giem_{February 9, 2010
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Heinrich: “'yes' or 'no'? ....did they provide the new perspective?" Yes. They dealt with all possible scenarios throughout the whole book, especially chapter 8 (Thermodynamics and the Origin of Life), where, most pertinently, they discussed:
the arduous task of using simple biomonomers to construct complex polymers such as DNA and protein by means of thermal, electrical, chemical, or solar energy. We will first specify the nature and magnitude of the "work” to be done in building DNA and enzymes. (p.129)
...but I agree with the more realistic prespective provided on page 5: “the mystery behind life's origin continues in spite of the undaunted confidence of some that a solution is near.”JPCollado_{February 9, 2010
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JPCollado @ 12, I don't know. Do you think its possible to cause something to happen unintentionally? @14, An earthquake caused a beautiful harbour in my home town. But the question is what caused the earthquake. It wasn't chance, but neither did anyone direct it to happen. CannuckianYankee, It refers to the origin of species from a common ancestor. You need the ancestor. Your criticism is somewhat ironic given ID's professed lack of interest in the identity of the designerzeroseven_{February 9, 2010
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Heinrich, Thaxton et.al only argued the inadequacy of the pre-biotic soup hypothesis. They did not (to my knowledge) have anything to do with the vent hypothesis.CannuckianYankee_{February 9, 2010
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mikev6:
ID, on the other hand, doesn’t seem to change much at all – “X is too improbable to happen by chance; ergo, design”.
Not quite. If there isn't any evidence that X can arise via chance and necessity AND it has some specification (even if that is nothing more than it looks designed) then and only then do we INFER design. As for possible mechansims available to the designer- Start with the experiments by Sutherland et al- purifying chemicals to get the proper molecules- then use some sort of targeted search to get those molecules to configure properly.Joseph_{February 9, 2010
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J.P. Collado - Is your answer "yes" or "no"? Fair enough that Thaxton et al gave some reasons why an old view might not work, but did they provide the new perspective?Heinrich_{February 9, 2010
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