Eugene V. Koonin’s Darwin-free book free on Kindle! – No. 1 in Biology

_{Denyse O'Leary

September 6, 2011

Darwinism, Natural selection, Self-Org. Theory}

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Here. (UD News Kindle got the book. A commenter notes below that it also works on the Android App. You can download a free reader for nearly any device.)

The Logic of Chance offers a reappraisal and a new synthesis of theories, concepts, and hypotheses on the key aspects of the evolution of life on earth in light of comparative genomics and systems biology. The author presents many specific examples from systems and comparative genomic analysis to begin to build a new, much more detailed, complex, and realistic picture of evolution. The book examines a broad range of topics in evolutionary biology including the inadequacy of natural selection and adaptation as the only or even the main mode of evolution; the key role of horizontal gene transfer in evolution and the consequent overhaul of the Tree of Life concept; the central, underappreciated evolutionary importance of viruses; the origin of eukaryotes as a result of endosymbiosis; the concomitant origin of cells and viruses on the primordial earth; universal dependences between genomic and molecular-phenomic variables; and the evolving landscape of constraints that shape the evolution of genomes and molecular phenomes.

#1 in Biology in Kindle store, as of noon EST September 6, 2011.

No, it’s not ID, but this guy thinks pretty much what we do about natural selection as a creative force: Pffffttt!!

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Comments

Yes, I too am grateful that science keeps searching and continues in its quest to find answers. However, the fact that someone is still looking for a way out of the conundrum does not mean that the conundrum does not exist. Elizabeth's reasoning is entirely circular on this single (but important) point and needs to be called out. Sure, sure, it is theoretically possible that at some future unknown date we will know more than we do now and may have to change our minds. But based on what is known now, the naturalistic OOL scenario is very clearly not the best explanation. I much prefer to follow the evidence, not sit around on my philosophical hopechest anxiously awaiting some new evidence that will at long last confirm my philosophical position.Eric Anderson_{September 18, 2011
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Pardon me for stating what, I hope, will be obvious to most readers, but that seems pretty circular.
It might be circular if the argument ended there, but the fact is that there are active research programs looking for scenarios that could establish naturalistic pathways to OOL. That's the distinguishing feature of science. Looking for explanations. Koonin notes that the prospects are not promising, but one might have said the same thing about gravity before Newton, or about the ultraviolet catastrophe before quantum theory. That's the distinguishing feature of breakthroughs in science. Often the are unanticipated, and often they explain previously mysterious phenomena.Petrushka_{September 9, 2011
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Elizabeth, I guess the site won't let me reply (the columns become too skinny), so I'm replying here to your comments in #5 above. Thank you for the detailed explanation of your position. In summary, your position is that because we don't know exactly how life arose through purely natural processes (there might always be some possibility we haven't considered), it is meaningless to try to determine the probability of it arising through purely natural processes. And, therefore, it might be that it arose through purely natural processes. Pardon me for stating what, I hope, will be obvious to most readers, but that seems pretty circular. Further, the fact that there is a mere hypothetical, theoretical possibility that something could have occurred, doesn't mean that we should view it as the most likely explanation for the occurrence. It is possible that the sun will cease to shine tomorrow at noon (after all, there might be some natural law or other process we haven't yet ascertained), but no-one in their right mind views it as a live possibility. Sheer logical possibility doesn't mean something should be taken seriously as a live possibility in the real world. However, I do largely agree with your following point: "In other words, all we can say, from a calculation that shows that a certain scenario is extremely improbable given certain assumptions, is that the assumptions are wrong, that the thing didn’t happen that way, or that there have been more opportunities for it to happen than we have assumed." [Note: more opportunities is really just one of the assumptions of the calculation.] I understand you don't disagree with the calculations themselves, and that, based on those assumptions, we are safe to conclude that it didn't happen that way. So, we are left with the assumptions, and how reasonable they might be. And what OOL researchers have been trying to do is give chance the best possible chance it can have. Even with all the odds stacked in its favor, it doesn't look good. Logically, there are a limited number of possible approaches. Either you have an information-first scenario, a metabolism first scenario, etc. So far all the possible scenarios come up woefully short. I'd be interested in any other cogent thoughts as to how it might have happened, and then we can run calculations, based on those assumptions. But I'm not too impressed with what is now a decades-long "just wait, we'll think of something" argument. At the end of the day, even if you hold out hope that someone will discover some new law of chemistry or physics or some new property of matter that has eluded us to date which will make it more probable, I understand that, for now, your position is that no-one knows how life could come about through natural processes. That is good. Now we just have to get you the rest of the way: acknowledging that there is a known cause which is fully capable of (and regularly observed doing so) creating complex, specified information-rich systems: namely intelligent agents. C'mon, one more step -- you're almost on board! :)Eric Anderson_{September 8, 2011
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True there has to be evidence of feasibility before one can calculate the probability. And to date no one has shown the OoL via stochastic processes is even feasible.Joseph_{September 8, 2011
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I don't have a mac on my jet, but I do have a 50,000 volume library.CannuckianYankee_{September 8, 2011
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A huge LOLOLOL!!!CannuckianYankee_{September 8, 2011
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No, I'm not hiding behind anything. And no, I don't think we are in agreement substantively - it's not the exactness of the number I'm talking about but the fact (I believe it to be a fact) that such a calculation is meaningless, because you do not know, and cannot know, that what the "probability space" is. To take an example - let's say that someone observes that lightning strikes the same tree twice in the same year. There's a saying that "lightning never strikes in the same place twice", implying that any given piece of the earth has an equal chance of being struck. So the person calculates what the odds are of the lightning striking twice in the same place, given the frequency of lightning strikes and the number of places it could hit, and finds that indeed the chances of lightning hitting the same tree twice is infinitesimally small. And concludes that Jove must have it in for that tree. Then Benjamin Franklin or someone turns up and demonstrates that certain spots, particularly certain high spots, like trees, are much more likely to be struck than other spots because of the way that unlike charges attract each other. Suddenly, the probability calculation looks very different, because we now have additional information. The problem is that if you do a probability calculation you have to be very clear what it is the probability of, given what. Now Koonin may be correct that the probability of the particular scenario he posits is indeed very low, given his assumptions, and his assumptions may or may not be correct. Or he may not be correct because while his assumptions may be correct, there may be some other factor that he has not considered at all, because we do not yet know of it. Or he may be correct that abiogenesis is extremely unlikely to have happened in the way he posits, but much more likely to have happened in some other way, that he does not posit, because he does not know of it. In other words, all we can say, from a calculation that shows that a certain scenario is extremely improbable given certain assumptions, is that the assumptions are wrong, that the thing didn't happen that way, or that there have been more opportunities for it to happen than we have assumed. In other words that we don't know how it happened. And we don't. Maybe there was divine intervention at that point. But we can't conclude that any more than we can conclude anything else. Which also leaves open the possibility that abiogenesis did occur, but not in the way that anyone - or anyone considered by Koonin - has so far postulated. And there is no probability calculation that will tell us how likely that is.Elizabeth Liddle_{September 8, 2011
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Ouch. It was free the other day when I downloaded it. Was that just a one day free download period?Eric Anderson_{September 8, 2011
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Elizabeth: Again, you say the calculation is impossible. Fine. Everyone agrees that the calculation is impossible, at least in terms of coming up with the exact, precise, unequivocal number. But that is a straw man concern, which is why I feel you are hiding behind it. The real question for OOL is: given all manner of unbelievable assumptions (meaning -- read this very carefully -- *we don't need to know the probabilities of these factors; we assume they are 1*), what are the odds of life arising with the factors that remain? In other words, let's reduce the calculation to those factors we can put a reasonable handle on. That is a perfectly legitimate exercise, and the takeaway lesson is that even with all manner of favorable assumptions, the likelihood of life arising by chance is vanishingly small. And it is almost certainly much worse because we have given up all kinds of assumptions. I can't tell if we are in agreement substantively and you are just focusing on the technical point that there isn't an exact number, so let me ask this: Do you ackwnowledge that the odds of life arising by chance are astronomically small, or are you saying that because we don't know the *exact* number, we can't say precisely unlikely it is and, therefore, it might in fact be likely?Eric Anderson_{September 8, 2011
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It was free for me. http://www.amazon.com/Logic-Chance-Biological-Evolution-ebook/dp/B0058I5U2CPetrushka_{September 8, 2011
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The book cost $42 on kindle, so this is not what I called a "free book"...Kyrilluk_{September 8, 2011
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I'm not "hid[ing] behind" anything - don't ask loaded questions! The calculation is impossible because we don't know the relevant probability distributions, or even the "probability space". What Koonin seems to have done (and from what I've read of it, the rest of the book seems excellent) is to calculate the probability of one particular scenario, with a few assumptions. That's not the probability of life, even if the assumptions are accurate, which we don't know. It's the probability of one scenario. If his assumptions are valid, then it's probably not what happened. But you can't quantify the pdf of unknown factors.Elizabeth Liddle_{September 8, 2011
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"He then goes on to handwave the criticism away by referencing how Darwin ‘dealt’ with this by showing how the eye could evolve… " Oh, brother. Darwin's eye evolution nonsense is even worse than Matzke's "detailed explanation" for the evolution of the bacterial flagellum. Surely Koonin can understand Darwin did not adequately deal with the evolution of the eye, so he must be paying obligatory obeisance at Darwin's grave (and bashing ID in the process) in order to not get into too much trouble with the establishment.Eric Anderson_{September 7, 2011
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Elizabeth, why do you hide behind the "calculation is impossible" for the idea that the probability of life originating by chance is exceedingly improbable. It is almost certain that Koonin's probability is incorrect. Not because it is too infavorable, but because the calculations assume all the most favorable conditions, which almost certainly didn't obtain at the same time and place. In reality, the odds are much worse. No-one is saying that we know an exact calculation. What we are saying is that *even given all manner of favorable assumptions* what we can calculate is that the likelihood of life arising by chance (shoot, even a handful of the needed proteins) is so ridiculously unlikely that we can, on a perfectly logical and reasonable basis, conclude that it did not happen by chance.Eric Anderson_{September 7, 2011
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A little I suppose. I use Kindle for Mac while on my jet, and PC on my helicopter. The iPhone mostly comes in handy in my limousine. Otherwise one of my entourage reads to me during my meals or massage. xpmaterial.infantacy_{September 7, 2011
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I'm 3% into the book and when referencing some of the proposed problems for Darwinism he mentions irreducible complexity, and in the footnotes says "Of course ID is malicious nonsense". He then goes on to handwave the criticism away by referencing how Darwin 'dealt' with this by showing how the eye could evolve... It's an interesting read so far, and it is pointing out the insufficiency of strictly Darwinian mechanisms, but it seems he aims to deal with the problems by creatively filling the gaps the way most pop-evolutionary theorists do, which is with a lot of stories, mathematical models, speculation etc.illegit_{September 7, 2011
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The 'inadequacy of natural selection as even a main mode' etc. Is this gut trying to overthrow Darwin. Fine but is it this guy. What does he contribute or prove. Got a hunch its nothing. If its okay to diss natural selection then it must be okay for creationists and okay to quote this book to this end. As long as evolutionary biology and geology presumptions are in place these writers might as well not publish as their contributions will perish. YEC and maybe iD creationisms are more likely to figure things out smartly because of accurate presumptions and boundaries . These evolutionists are not going to contribute any smart idea to figure things out. They are wasting their time and lives on impossible to check speculations. Correcting Darwin on points isn't anymore the way to go for prestige of discovery.Robert Byers_{September 7, 2011
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He says the chances are 1 in 10^1018. On the Earth only, 1 chance in 10^1042. Among other things, this means that all origin of life attempts are all doomned to failure, and tthat this research is another boondoggle.
Well, no, it doesn't mean this. It could also mean that Koonin's probability calculation is incorrect. As such a probability calculation is impossible, my assumption would be that it is incorrect.Elizabeth Liddle_{September 7, 2011
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"He says the chances are 1 in 10^1018. On the Earth only, 1 chance in 10^1042." Interesting; I'll have to check it out. These odds are *much* better than many other estimates (ranging, for example, up to 1 in 10^40,000). Either way it vastly outstrips the probabilistic resources of the known universe, but I'll have to go through his calculations carefully to know why his estimate is many orders of magnitude below others. The multiverse as an explanation for life is silly. Why can't otherwise intelligent people see that? Here's the rub: it doesn't matter if there are other universes. *Given* our universe and the laws of chemistry and physics that exist in our universe, what are the odds that life arose by chance? Not only are other universes pure speculation, but they just aren't relevant to the calculation. Finally, just to nip things in the bud a bit more, even if we somehow think the multiverse is relevant, let's be clear about how many universes we are talking about. The probabilistic resources of our universe are something on the order of 10^139 +- (Dembski rounded up to 10^150, for good measure). If Koonin is saying that the odds of life arising are 1 in 10^1018, then he must be postulating something like 10^868 universes, way more universes than particles in our universe. C'mon, talk about outrageous probabilities. And the multiverse is supposed to be some kind of saving "explanation"? People need to face the facts: it is much more probable (and, therefore, we are much more justified in believing) that the sun will abruptly cease to shine tomorrow at noon, or that gravity will fail tonight at midnight than that life came about by chance. Believing in chance as an explanation for life is not blind faith (that would be a discredit to the term faith, even blind faith). It is an unfounded, incoherent, entirely irrational belief.Eric Anderson_{September 6, 2011
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At any rate, you left off the context:
The model considered here is not supposed to be realistic, by any account. It only illustrates the difference in the demands on chance for the origin of different versions of the breakthrough system and, hence, the connections between this version and different cosmological models of the universe. Koonin, Eugene V. (2011-06-23). The Logic of Chance: The Nature and Origin of Biological Evolution (FT Press Science) (Kindle Locations 7070-7072). FT Press. Kindle Edition.
The huge improbability illustrates the problem with a particular "toy" model, and is not intended to rule out all models.Petrushka_{September 6, 2011
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I seems more reasonable to me simply to say we don't know and to wish the researchers good luck. In my case it wouldn't be sarcastic. There have been problems in science that took hundreds of years to work out. This one is generally regarded as the toughest of all.Petrushka_{September 6, 2011
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Well now aren't we privileged? :)CannuckianYankee_{September 6, 2011
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The most remarkable single thing about Koonin's book is the appendix. In it he gives the probability of naturalistic abiogeneis. He cosiders the simplest forms of life could arising through naturalistic chemical processses, given 14 billion years and the ENTIRE known universe. He says the chances are 1 in 10^1018. On the Earth only, 1 chance in 10^1042. Among other things, this means that all origin of life attempts are all doomned to failure, and tthat this research is another boondoggle. Koonin still believes in a naturalistic origin of life. He postualtes the usual infinite multiverse, to take care of the probability problem. It seems to me that naturalism is in big trouble, when a top prof like Koonin needs an infiite mutiverse to explain how life began.chris haynes_{September 6, 2011
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Future publication dates are actually pretty common. The goal is to point to the tip of the marketing push, so it never feels like you are pushing an "old" book.johnnyb_{September 6, 2011
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mel, It's a brand new book with a publication date of 2012 (which I found odd). It's not yet available in print form - only as an eBook. Perhaps it will take some more time before it becomes available in your area on Amazon. Incidentally, News, I'm now on the 2nd Chapter and it appears that it's not exactly a "Darwin-free book." Koonin appears to have more of a problem with the "Hardness" and dogmatism of the modern synthesis; thus the Preface: "Toward a Postmodern Synthesis of Evolutionary Biology." He praises Darwin and those who further praise Darwin; even mentioning Dobzhansky's famous "Nothing in biology makes sense except in the light of evolution," not once, but twice for emphasis. One thing I can tell you about the book - it's very well written and easy to follow. He's not so much interested in the fine details as he is in the "big picture." He states at the beginning that he first intended it to be a popular Tome like that of Hawking, but later revised it to be a bit more "scientific" but not technical.CannuckianYankee_{September 6, 2011
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Additionally, bookmarks, highlights, etc., will be automatically sync'd between the various Kindle app platforms. I'm really getting a kick out of reading on my PC, Mac, and iPhone -- the same book at different times, depending on where I am at any moment. This previous eBook skeptic is now a proselyte.material.infantacy_{September 6, 2011
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Boo-Hoo! Seems I don't get the free book here in the UK. Perhaps if UD gives it a good review I'll buy the hard copy. MV.melvinvines_{September 6, 2011
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I mentioned this in another thread, but another option is to download Kindle to your PC or mac: PC: http://www.amazon.com/gp/feature.html/ref=kcp_pc_mkt_lnd?docId=1000426311 MAC: http://www.amazon.com/gp/feature.html/ref=kcp_mac_mkt_lnd?docId=1000464931 Once you've downloaded the software, any free book offered on Amazon; and there are thousands of them in public domain are simply a click away.CannuckianYankee_{September 6, 2011
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"Also works on the Android Kindle app, for those who don’t have a Kindle."
I love reading Kindle books on the iPhone (don't own a Kindle). It's much more enjoyable than I suspected before trying it. Thanks for the book!material.infantacy_{September 6, 2011
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I just got it. You don't have to have a Kindle. You can download a free reader for nearly any device.Petrushka_{September 6, 2011
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