Last year I blogged about Robert Shapiro’s excellent article in Scientific American that gave cogent critiques of many standard models of the chemical origin of life. Shapiro critiqued the view that a primordial soup existed on the early earth that ultimately gave birth to a self-replicating molecule, which eventually evolved into RNA and then DNA. After critiquing this standard model, Shapiro gave his alternative explanation, proposing that life evolved from metabolic pathways that naturally occurred on the early earth. As I wrote at that time, Shapiro “gives scant explanation for how these life-like metabolic networks can come into existence naturally, and he gives no details as to how these thermodynamic states produce real life–life as we know it today.”
Now Leslie Orgel, the eminent and late origin of life chemist has published (posthumously) a direct critique of Shapiro-like hypotheses which claim that life arose through metabolic pathways.
Orgel is no proponent of intelligent design. In fact, the purpose of his paper is to offer sage advice to those seeking to explain the origin of life via evolving metabolic pathways. As this 2-part blog series will show, Orgel clearly states that many new breakthroughs must be necessary before such origin of life theories are to be plausible.
Orgel recounts many obstacles to the spontaneous formation of metabolic pathways (also called “cycles”) on the early earth. He observes that such cycles “must be evaluated in terms of the efficiencies and specificities that would be required of its hypothetical catalysts in order for the cycle to persist.” In other words, Orgel inherently assumes there are irreducible thresholds of reactivity and numbers of catalysts that must be crossed in order for these metabolic pathways to exist.
But even according to Orgel, simply having such metabolic pathways is not enough, for “the identification of a cycle of plausible prebiotic reactions is a necessary but not a sufficient step toward the formulation of a plausible self-organizing prebiotic cycle. The next, and more difficult step, is justifying the exclusion of side reactions that would disrupt the cycle.” Again, Orgel essentially assumes that cyclic metabolic pathways are irreducibly complex systems that require a large number of parts in order to function–including parts that allow them to avoid many side pathways that will disrupt the cycle. In Orgel’s view, it is not plausible to contend that such complex systems, with all of their numerous required components, would simultaneously come into existence:
At the very least, six different catalytic activities would have been needed to complete the reverse citric acid cycle. It could be argued, but with questionable plausibility, that different sites on the primitive Earth offered an enormous combinatorial library of mineral assemblies, and that among them a collection of the six or more required catalysts could have coexisted.
(Leslie E. Orgel, “The Implausibility of Metabolic Cycles on the Prebiotic Earth,” PLOS Biology (January 2008, Volume 6(1):e18).)
Finally, Orgel observes that catalysts often react with more than one substrate, and that these enzymes would require sufficient specificity to be able to discriminate between different substrates so as not to react with the wrong component of the cycle. Orgel writes that such specificity is not produced naturally, and normally requires “a skilled synthetic chemist”:
It is likely that such catalysts could be constructed by a skilled synthetic chemist, but questionable that they could be found among naturally occurring minerals or prebiotic organic molecules. … It is not completely impossible that sufficiently specific mineral catalysts exist for each of the reactions of the reverse citric acid cycle, but the chance of a full set of such catalysts occurring at a single locality on the primitive Earth in the absence of catalysts for disruptive side reactions seems remote in the extreme. Lack of specificity rather than inadequate efficiency may be the predominant barrier to the existence of complex autocatalytic cycles of almost any kind.
So what is going on here? The multiple specificities required could be constructed by “a skilled synthetic chemist” but are highly unlikely to exist in nature. Just like the case of the ribosome, the evidence shows that the complexity of life requires an intelligent cause.
Here are the facts of this situation:
(1) On Feb. 3, I posted this blog post. A co-worker had recommended that I include a graphic that said this was discussing peer-reviewed research. At the time, I had not seen ResearchBlogging.org and I was unaware of the fact that they requested registration in order to use their graphic. Important note: It should be clear that when I first posted my post, I had not yet seen ResearchBlogging.org and was unaware of how it worked.
(2) On Feb. 4, I became aware of the fact that ResearchBlogging.org requested registration to use their graphic, and I immediately attempted to register with ResearchBlogging.org so that I would not be in violation of their rules. In fact, I tried to register twice because when I submitted the registration request, I was directed to a page that looked something like garbled code. I tried a second time, and the same thing happened. So it wasn’t clear to me if the registration process was working properly. I then submitted an inquiry to ResearchBlogging.org wondering if they could correct the problem. I asked them for guidance, requesting direction for how I should proceed in this situation.
(3) On Feb. 5, I received a response from Dave Munger from ResearchBlogging.org, and his response, among other things, directed me to this discussion page which stated that the graphic I originally used was copyrighted by them. At the time that I posted my post, I was not aware that the graphic I had used was owned by ResearchBlogging.org. Mr. Munger in fact never requested that I remove their graphic, and in fact I believe the rules are ambiguous, making it seem that it is possible that the graphic I used may be used while one is seeking an application with Researchblogging.org. Nevertheless, I never had any intention of violating anyone’s copyright, and so I as soon as I saw this thread, I removed their graphic from this page and the EvolutionNews.org server at my own choice.
(4) In the response from ResearchBlogging.org, Mr. Munger also told me that, (a) they did indeed receive my registration requests, (b) registration requests were granted at their discretion, and (c) a discussion thread was taking place about whether I should be granted registration. I was told that, “At present, after 26 comments, the consensus appears to be that your post is in violation of our guidelines. If you believe your post does meet our guidelines, I would encourage you to post your explanation in the discussion there.” The conclusion was therefore: “We can’t approve your registration at this time because your post does not appear to follow our guidelines, but if you can show us either that your post does now follow the guidelines, or if you can append the post itself so that it follows the guidelines, then we’ll proceed with approving your registration.”
(5) On Feb. 5th, after receiving Mr. Munger’s e-mail, I replied back to Mr. Munger cordially and told him that “I will post one comment at ResearchBlogging.org to clarify the facts of this situation, and state my position.” Also on Feb 5th, I posted the following comment at ResearchBlogging.org to state my position on this matter:
Thank you for the opportunity to comment. Let me say that this website–which I just discovered yesterday–is both fascinating and useful. A wide variety of scientific topics are apparently discussed, ranging from science of the mind to cancer and disease research, to geology to evolution. I will most certainly revisit this site in the future, if for no other reason than the fact that it’s a great way to stay informed about new scientific developments.
Second, I want to state upfront that I have no ill will towards anyone on this thread. But it saddens me that from the very first post on this thread and others, people were directing users to pages that made unjustified personal attacks against me (there are various examples on this thread, but here are two: “Casey Lying For Christ” and another user even linked a URL where people can talk about “about how terrible Luskin is”). People commonly make unjustified personal attacks against me, and my response is not to get mad or even get upset. Rather, my response is that it is to feel that this kind of behavior is saddening because it does damage to what might otherwise be a fruitful, friendly, and objective scientific debate. Regardless, I absolutely refuse to respond in kind as I do not make personal attacks against other people. That is my personal ethic, and though I am not perfect, I try to live up to it.
I am thus faced with two conflicting desires here: I have no desire to involve myself in a discussion that allows personal attacks, even allowing further personal attacks after warnings from the moderator, who is apparently permitting such personal attacks to stand. Nonetheless, I do desire to honor Mr. Munger’s invitation to make a comment here and his attempt to keep the conversation focused away from personal attacks. My compromise is that I will make one, and only one comment. If people want to continue to make personal attacks, cite irrelevant issues like the Wedge Document, etc., so be it. I’m not here to engage in personal attacks.
I frequently discuss peer-reviewed research related to evolution at www.evolutionnews.org. In fact, when I posted my post at EvolutionNews, that’s all I thought I was doing–I had no idea that rules, including copyright issues, existed for using the graphic nor did I have any idea that by using the graphic, I would be accused of breaking rules. Given my ignorance prior to using the graphic, I would not necessarily expect my post to conform to rules that I wasn’t even aware of when I posted my post. Nonetheless, I believe that my post does not break any of the 9 rules. Here’s why:
It satisfies Rules #1 and #2: Dr. Orgel’s paper was clearly a respectable “armchair theorizing” paper by an eminent chemist in a mainstream biology journal that represented his views after a lifetime of prestigiously-funded research. It was reviewed and edited by another eminent chemist from the same field, Gerald Joyce. Thus, the paper states: “This manuscript was completed by the author in September 2007. Gerald Joyce provided comments to the author on earlier versions of the manuscript and edited the final version, which was submitted posthumously. The author received longtime research support from the NASA Exobiology Program and benefited from many helpful discussions with Albert Eschenmoser.”
It satisfies Rules #3, #6, and #7: My post provided the complete formal citation in my post, and I also linked back to the original source. The post also contained original material that I wrote. These are black-and-white questions. Some people concede that I satisfied these. But the fact that some people have claimed that I did not satisfy a single rule makes me wonder about the fairness of some of the analyses presented here.
It does not break Rules #8 or #9: There is also the issue of my using the ResearchBlogging.org graphic. As I mentioned earlier, not having visited ResearchBlogging.org at the time I posted my post, at that time I was unaware that there was anything wrong with my using the graphic. However, I now have learned that ResearchBlogging.org has certain rules for using the graphic. Apart from using the graphic before registering (something I did not know I was supposed to do when I posted my post, but I tried to register as soon as I learned of the rules), I do not believe I have violated any of the rules: Even though Dave Munger never asked me to do so, I’ve removed the graphic from my post. Moreover, rule #9 indicates that a single instance of breaking a rule (in my case, unknowingly) does not warrant expulsion from ResearchBlogging.org. (Rule #8 is simply a rule stating that users may report abuses, and is not violable.)
It satisfies Rules #4 and #5: Many people on this thread have said that these rules represent the key issues. One would expect that therefore this would be the focus of the discussion. But it wasn’t. Only 3 of the 30 posts here actually quoted my article, or discussed it in any meaningful way, to allege, using direct evidence, that I made any errors or misunderstood anything. Here are those posts with my response:
Post # 9: Claims I was wrong to state, “Again, Orgel essentially assumes that cyclic metabolic pathways are irreducibly complex systems that require a large number of parts in order to function”
My response: My comment is not mistaken. For example, Orgel states, “At the very least, six different catalytic activities would have been needed to complete the reverse citric acid cycle. It could be argued, but with questionable plausibility, that different sites on the primitive Earth offered an enormous combinatorial library of mineral assemblies, and that among them a collection of the six or more required catalysts could have coexisted.” That seems to meet the definition of irreducible complexity.
Post # 11: “Just like the case of the ribosome, the evidence shows that the complexity of life requires an intelligent cause.”
My response: This was my personal commentary on the data (which is permitted by the rules), and was not intended to represent Dr. Orgel’s viewpoint. In fact I never claimed Orgel supported ID. In fact, I explicitly stated precisely the opposite, stating that “Orgel is no proponent of intelligent design. In fact, the purpose of his paper is to offer sage advice to those seeking to explain the origin of life via evolving metabolic pathways.” In his e-mail back to me, Dave Munger stated: “We welcome a variety of divergent opinions at ResearchBlogging.org, as long as posts follow our guidelines, designed to encourage reasoned and thoughtful discussion of peer-reviewed research.” So there is no violation here, unless the pro-ID opinion is fundamentally disbarred from participation. In fact some users may seem to desire censorship of the pro-ID viewpoint, as one person wrote, “This is blatant abuse of the program to lend an air of credibility and should be stopped.” In short, they just don’t want my application approved because it might “lend an air of credibility” to my views.
Post # 12: “Again, Orgel essentially assumes that cyclic metabolic pathways are irreducibly complex systems that require a large number of parts in order to function–including many side pathways that can remove products that will disrupt the cycle. Saying that cycles need side pathways is the exact opposite of what Orgel said in the original – cycles need to avoid side pathways to maintain themselves.”
My response: In fact I quoted Orgel accurately, including the portion where he explicitly said that side-pathways must be avoided or they will disrupt the cycle. My comment, “including many side pathways that can remove products that will disrupt the cycle,” was intended to show that there must be other parts present to avoid allow the cycle to avoid these side-reactions. But I can see how my statement is unclear and does not communicate that very well. In his e-mail back to me, Mr. Munger stated that I may amend my post if I feel it is necessary. In this regard, I’ve amended my post to fix this unintended unclear statement as follows: “Again, Orgel essentially assumes that cyclic metabolic pathways are irreducibly complex systems that require a large number of parts in order to function–including parts that allow them to avoid many side pathways that will disrupt the cycle.”
I read and understood the article. I studied origin of life research in both my undergraduate and graduate studies at UC San Diego studying earth sciences, and taking courses and seminars learning from people like Jeffrey Bada, Stanley Miller, and others. I also conferred with a biochemist friend about the paper.
I won’t enter a philosophical discussion about how “understanding” or “accuracy” might be a function of whether people agree with my commentary, which is obviously pro-ID. I’ll just say that I am not so presumptuous to assume that if someone comes to a different conclusion than I do, that they therefore do not understand the topic, or were therefore necessarily inaccurate.
Regarding rules #4 and #5, I see no evidence that I have broken rules #4 or #5 here. Given that these were the only complaints, I can only conclude that in fact my discussion was actually quite accurate.
My final conclusion:
In conclusion, these are your rules. I didn’t know about them when I posted my post, but I think I nonetheless have not violated any of them. I’ll respect Mr. Munger’s decision, whatever it is, and whatever its stated or unstated justification is.
If you decide to allow my registration–superb! I’m not doing this to get “credibility” but because like all of you, I too love science and I’d like to think that this is a website worth contributing to. If my registration is permitted, I’ll gladly contribute to what I hope this website is all about.
But if you don’t want to follow your own rules, that is saddening, and it would not be the first time that a different set of rules has been applied to ID proponents vs. other scientists. Indeed, I find it most likely that one user admitted the most forceful reason why my registration would be denied: “This is blatant abuse of the program to lend an air of credibility and should be stopped.”
But I’ll respect Mr. Munger’s decision, whatever it is, and the stated and unstated reasons are. I just hope that this does not become another example where, as in many corners of academia, “We welcome a variety of divergent opinions,” as long as those opinions do not support intelligent design.
But I won’t presume that Mr. Munger will make such an inappropriate decision, and I’ll respect whatever he decides in the future. If anyone would like to contact me personally, please feel free to do so at firstname.lastname@example.org.
Sincerely in good will and friendship,