Wednesday, January 07, 2015

The problem of the origin of life has been solved and creationists are terrified

You learn something new every day. Today I learned that a young physics professor at MIT has figured out how life originated without god(s). Salon let's us know about this amazing discovery: God is on the ropes: The brilliant new science that has creationists and the Christian right terrified.
The Christian right’s obsessive hatred of Darwin is a wonder to behold, but it could someday be rivaled by the hatred of someone you’ve probably never even heard of. Darwin earned their hatred because he explained the evolution of life in a way that doesn’t require the hand of God. Darwin didn’t exclude God, of course, though many creationists seem incapable of grasping this point. But he didn’t require God, either, and that was enough to drive some people mad.

Darwin also didn’t have anything to say about how life got started in the first place — which still leaves a mighty big role for God to play, for those who are so inclined. But that could be about to change, and things could get a whole lot worse for creationists because of Jeremy England, a young MIT professor who’s proposed a theory, based in thermodynamics, showing that the emergence of life was not accidental, but necessary. “[U]nder certain conditions, matter inexorably acquires the key physical attribute associated with life,” he was quoted as saying in an article in Quanta magazine early in 2014, that’s since been republished by Scientific American and, more recently, by Business Insider. In essence, he’s saying, life itself evolved out of simpler non-living systems.
Jerremy England's ideas are too complex for me. Watch this video to see for yourself.



54 comments :

  1. Color me whelmed. I haven't read the paper thoroughly but it looks to be an extension of Prigogine's theory which itself has been around for 50 years. Interesting but I'm not expecting the creationists to go over the cliff like lemmings anytime soon.

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  2. I know you are mocking the overblown hype of the title, but I'm pleased that the article mentions Ilya Prigogine, who kind of pioneered the whole idea of self-organization about 40 years ago and isn't claiming that England came up with idea himself. It's interesting stuff, but yeah, I kind of want actual biochemistry and not just physics in a convincing origin of life explanation.

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  3. Quite so. It's not the in principle problem of order emerging far from equilibrium, but the in practice problem of how this could credibly have been embodied using materials and concentrations possibly available on the early Earth

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    1. And perhaps more important, how this could credibly not have happened in other places or at other times where/when we have good reason to believe life didn't originate.

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  4. They are always trying to be the next prestigious intellectual figure-out-er of something important.
    Its laughable in its attempt. its boring!

    The writer says OBSESSIVE HATRED, of Darwin, is the a accurate profile of bible believing Christians and others who deny darwin figured it out.
    Darwin's express purpose was including the demonstrate that all physical and moral attributes of man was entirely from evolving from one stage to another.
    He wanted to have a complete equation, probably like Newtons perceived final conclusion on physics, on the origin of mankind and biology.
    He directly attacked any claims made that anything about people had a origin from a God creating us.
    not just biology but in our thinking.
    It was a direct attack on christianity and that christianity believing in the bible as the inspired word of God.
    People have never read his stuff. I have read, more, of his stuff then most people.
    he was goal oriented and the DESCENT OF MAN was his goal. Descent into muck as opposed from a origin from Gods creation and unique.
    Writers like this help my side because they are unreasonable.
    In fact they discredit themselves to even disinterested regular folk.

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    1. Boring? Christians are boring. You are boring

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    2. MissAthesist32
      Re are revolutionaries in history and present society and in these matters in science
      Such people are never boring.
      A subject is boring when its hopeless in its attempt to explain things without evidence of any value at all.
      Speculation even needs backup evidence.

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    3. @Robert Byers

      I rather enjoy watching you try to explain things without any evidence at all. It's not always boring but I do agree with you that it's hopeless.

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    4. Robert Byers: «A subject is boring when its hopeless in its attempt to explain things without evidence of any value at all.» - thus, christians (in their attempts to explain the natural world based on their god's actions) are (many times) boring...

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    5. My metaphorical hat is off to you MissAtheist32, you actually got Mr. Byers to respond directly to a comment, which is rare for IDiots in general and unprecedented for Robert Byers.

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  5. Big deal, physicists again to the rescue of biology. Like others, I am underwhelmed by this. If you want an argument for the inevitability of life I am more convinced by Stuart Kaufmann in The Origins of Order, though his analysis is not without its problems as well.

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  6. This must be a joke. This is all science got?

    http://www.evolutionnews.org/2015/01/on_the_origin_o_6092521.html

    "It's one thing to observe that energy keeps a machine running; it's quite another to claim energy produced the machine in the first place. You could shine light on random Scrabble tiles or disassembled computer components for billions of years, and you'll never produce a Shakespearean Sonnet or a functional computer. No wonder Harvard biophysicist Eugene Shakhnovich called England's proposals "extremely speculative, especially as applied to life phenomena."

    Despite the bluster of materialist science writers, many theorists have admitted no natural explanation for the origin of life.

    In 2011, Eugene Koonin, a senior scientist at the National Institutes of Health, starkly acknowledged that "the origin of life field is a failure -- we still do not have even a plausible coherent model, let alone a validated scenario, for the emergence of life on Earth." In his view, "A succession of exceedingly unlikely steps is essential for the origin of life, from the synthesis and accumulation of nucleotides to the origin of translation" making "the final outcome seem almost like a miracle.""

    "Dr. England's work, interesting though it may be, does not provide that insight. Sunlight -- or any known form of energy -- does not produce the genetic information life needs to build its complex machinery. In our experience, only one cause generates new language-based information or machine-like structures: intelligence."

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    1. If you really want to know how people with brains and gumption respond to a challenge, try reading Nick Lane's Life ascending. Or you can just call them "materialists."

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    2. sez unknown: "This must be a joke. This is all science got?"
      Yes, the origin of life is a topic about which real science doesn't have a whole lot of answers right now. Since you clearly think this lack of answers is a grievous flaw in real science, and you're an ID-pusher, could you tell us what answers ID has on the topic of the origin of life? I wasn't aware that ID had any answers on the topic of the origin of life, myself. But hey, I could be wrong, so how about it, unknown? What answers does ID have on the topic of the origin of life?

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  7. Is it true that unguided chemical processes cannot explain the origin of the genetic code?

    http://www.evolutionnews.org/2015/01/problem_2_ungui091111.html

    "the RNA world hypothesis does not explain the origin of the genetic code itself. In order to evolve into the DNA / protein-based life that exists today, the RNA world would need to evolve the ability to convert genetic information into proteins. However, this process of transcription and translation requires a large suite of proteins and molecular machines -- which themselves are encoded by genetic information. This poses a chicken-and-egg problem, where essential enzymes and molecular machines are needed to perform the very task that constructs them.

    To appreciate this problem, consider the origin of the first DVD and DVD player. DVDs are rich in information, but without the machinery of a DVD player to read the disk, process its information, and convert it into a picture and sound, the disk would be useless. But what if the instructions for building the first DVD player were only found encoded on a DVD? You could never play the DVD to learn how to build a DVD player. So how did the first disk and DVD player system arise? The answer is obvious: a goal directed process -- intelligent design -- is required to produce both the player and the disk at the same time.

    In living cells, information-carrying molecules (e.g. DNA or RNA) are like the DVD, and the cellular machinery which reads that information and converts it into proteins are like the DVD player. Just like the DVD analogy, genetic information can never be converted into proteins without the proper machinery. Yet in cells, the machines required for processing the genetic information in RNA or DNA are encoded by those same genetic molecules -- they perform and direct the very task that builds them.

    This system cannot exist unless both the genetic information and transcription / translation machinery are present at the same time, and unless both speak the same language."

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    1. Is it true that unguided chemical processes cannot explain the origin of the genetic code?

      No.

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    2. How amusing. Unknown claims the DVD player 'all of a sudden' sprung to life.

      But he seems to have 'forgotten' the long road of evolution leading from the first gramophone by Edison, 78 RPM discs, 45 RPM discs, reel tape recorders, eight tracks, cassette players, Beta/ VHS to the major (r)evolution (haha) the CD which in turn lead to the DVD player and now blu-ray.

      The DVD didn't all of a sudden spring into life. It came forth from machines capable of recording sounds in the beginning of the 1800s.

      The DVD analogue is like Paley's watch, yes it seems complex, but the DVD's (haha) creation is the culmination of not only sound/ video recording, but also the advances in lasers and laser optics, micro electronics, software, mechanics (electro motors) but also TV's.
      Also, don't forget, the CD player also uses a lot of the same, but also lacks, bit and pieces also used in DVD players.

      If the DVD was IC, we wouldn't have had Video-CD's, but lo and behold, we do.

      If the DVD were ID, the CD player wouldn't exist.

      The DVD analogue is Paley's watch, old wine in a new package.

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    3. A better analogy than the DVD is the computer. No computers are made nowadays without extensive computation in design and manufacture. Therefore computers are impossible without computers? Well, no. Likewise, proteins are now intimately involved in protein manufacture. Therefore proteins are impossible without proteins? Not as a matter of logic, nor as a matter of chemistry. Of course, the 'gotcha' response is that the first computer was designed by a person.

      Therefore proteins were also designed by people? No, intelligence dumbass! So (completely without evidence) you can have non-protein intelligence, but apparently you can't have non-protein protein synthesis.

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  8. Dr. Moran,
    The one thing that you said in this post that is respectable is, "Jerremy England's ideas are too complex for me."

    The other idea that seems too complex for you is the thought that genuine thinking people would look at the Darwinian evidence and simply find it unconvincing. I come from a software programmer's perspective. When I look at DNA,I see software -- because that is what it is. Its not a metaphor for software, the order of the DNA is software. The more I learn about the nature of biology, the harder it is for me to buy the theory that this stuff was produced one mistake at a time.

    As far as the origin of life problem being solved, well, how many times has this been the headline. C'mon, get real! Your credibility is badly tarnished when you retweat the rubble coming from Salon.

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    1. "I come from a software programmer's perspective. When I look at DNA,I see software -- because that is what it is."

      If human programmers built software with approximately 90% of the code broken, producing unwanted output or without function they would be fired on the spot.

      Also, it seems you have missed some key features of software programming, which have been around since the 1960's...
      And I quote:
      "Evolutionary algorithms are now used to solve multi-dimensional problems more efficiently than software produced by human designers, and also to optimise the design of systems.[5]"

      You continue:
      "the harder it is for me "

      Well, thank Thor, what you think and clearly not understand of biology and evolution isn't where main stream science is. Although 'it's harder for you to buy', without our current knowledge of evolution and biology we wouldn't understand how bacteria become resistant to anti-biotics, how mosquitos become resistant and how to combat virusses like HIV. And this is but a tip of the iceberg of the things we now understand about biology and evolution, because of a book an English bloke wrote in the 1800's.

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    2. "If human programmers built software with approximately 90% of the code broken, producing unwanted output or without function they would be fired on the spot."

      As software tester, I do run into these idiots from time though...

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  9. Bill Gates, “DNA is like a computer program but far, far more advanced than any software ever created.”

    Please feel free to fire him.

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    1. Where is that statement saying that Bill Gates is producing software that produces undesired output, has tons of lines that do nothing but make noise, etc? All I see is a metaphor for what DNA is, and we don't even know if Bill said such a thing, or if that was deformed by some creationist, as usual for most quotes brought about by creationists.

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    2. When did Bill Gates become an expert in genetics and biochemistry?

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    3. He did write something like that in "The Road Ahead", but of course it has been lifted out of its context. Gates was talking about high-school science teachers (good versus boring ones), not really about DNA, let alone "intelligent design". Here's a fuller quote:

      I had a great chemistry teacher in high school who made his subject immensely interesting. Chemistry seemed enthralling compared to biology. In biology, we were dissecting frogs - just hacking them to pieces, actually - and our teacher didn't explain why. My chemistry teacher sensationalized his subject a bit and promised that it would help us understand the world. When I was in my twenties, I read James D. Watson's "Molecular Biology of the Gene" and decided my high school experience had misled me. The understanding of life is a great subject. Biological information is the most important information we can discover, because over the next several decades it will revolutionize medicine. Human DNA is like a computer program but far, far more advanced than any software ever created. It seems amazing to me now that one great teacher made chemistry endlessly fascinating while I found biology totally boring.

      Needless to reiterate, he isn't an expert in biochemistry, and nowhere claims to be one.

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  10. photosynthesis, Google's top link for "Bill Gates DNA", http://www.goodreads.com/quotes/336336-dna-is-like-a-computer-program-but-far-far-more You could have found that yourself, rather than slander creationists.

    The question that needs to be asked is, "Is Bill Gates' assertion correct"?

    Whether from genotype or phenotype analysis I see it as being correct. About 3 gig of data (including any junk) defines a human being. There are 20,000 protein coding genes, but somewhere around 1 million protein variants in the human body. A cnc/3d print factory that could produce anything close to a working mouse would require far more than 3 gig of code. (Make sure the mouse can do the basics: find food, outsmart traps etc.) The more I look at DNA the more amazed I am at how superior the code is to anything that I have written -- and my work has won multiple national awards, and I have been issued multiple software patents.

    Please inform me of how simple DNA is. Please inform me of just how simple ATP synthase is, as it produces the primary energy used by all known life. How do I know? Had an extensive chat with a Ph.D. biologist who entered grad school as a comfortable atheist, did his thesis on ATP Synthase, and came out a confused agnostic.

    Don't look too close at what goes on inside the cell, it might amaze you.

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    1. "Don't look too close at what goes on inside the cell, it might amaze you."

      The general public is about 85-90% theist. Among scientists in general(all fields), this drops to about 50%. Among philosophers, this goes down to 30%. Among biologists and cosmologists, this drops to about 10%. Among evolutionary biologists, it's 98% atheists.

      Seems that the closer you look at how the world works, including biology, the less reason for god you find. Weird.

      Also, you don't know what neither the words agnostic or atheist means.

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    2. So what do you make of someone who did biochemistry to postgrad level and is now a jobbing computer programmer who thinks DNA resembles a program barely at all? That would be me, by the way. I entered grad school a 'comfortable atheist', and remain so, because there are certainly no fewer difficulties in getting a 'programmer' to ignite the spark of life than having gradients of electrochemical potential achieve it unaided. Those very same gradients seriously hamper the ability of said 'chemical programmer' to manipulate matter at single-atom level and get the ball rolling, in a way I doubt you fully appreciate.

      We could trade anecdotes and supposedly expert opinion (Bill Gates? An anonymous postdoc?) all day. It's basically meaningless. The basic question is: could nucleic acids arise uncoded? And MY opinion is, because of their unique stereochemistry, yes they could. Programs don't have stereochemical antiparallel symmetry, which appears to be a vital ingredient in the role of the nucleic acids, and has nothing whatever to do with programming.

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  11. Not one of you have taken even a simple whack at the question, "Is Bill Gates' assertion correct"?

    Mikkel Rumraket Rasmussen, "Also, you don't know what neither the words agnostic or atheist means." Oh, please enlighten me.

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    1. Not one of you have taken even a simple whack at the question, "Is Bill Gates' assertion correct"?

      I thought I had. No, his assertion is not correct. Mine is.

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    2. You said, "And MY opinion is, because of their unique stereochemistry, yes they could." Is this your response to Bill Gates' assertion?

      On software development, how is your assembly language skill? When you develop code in a high level language, do you have a reasonably clear picture of the resultant machine language? Do you have any experience with languages that cross the code/data barrier (execute data as code) such as LISP and fourth?

      I have never seen anything in DNA that resembles a stack. However, a change in the "code" produces changes in the resultant product (proteins.) This produces changes, very usually deleterious when in protein coding sections, to the resultant organism. This is the same as my computer software. When the code is changed, the subroutine is changed. A changed subroutine will change the way the program functions. If these changes are random, the result is most usually deleterious.

      As to your comment below, bFast = Gary? No.

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    3. The 'code' in translation produces a 3 dimensional physical structure, a protein. This is more like 3D printing than programming - though, again, I think one can get hopelessly misled by analogies. Proteins are nowhere near as brittle as computer programs. They have many degrees of freedom; they don't just bail out with a data exception at the first sign of trouble. The space of protein sequences surrounding any given protein sequence is stuffed with functional proteins; not so the space of 1-character amendments surrounding any piece of code. They are just different things.

      'Most' changes may be deleterious; evolution only has a problem when they ALL are.

      But anyway, what makes you think that protein is essential for life? Its universal presence in modern life is not contested, but we would see exactly what we see in a world where non-protein life had simply gone extinct, outcompeted by the superor catalysts produced by the protein world. Protein is certainly not the only material from which one can make biological catalysts.

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    4. "Proteins are nowhere near as brittle as computer programs. They have many degrees of freedom; they don't just bail out with a data exception at the first sign of trouble."

      This is an inexactitude, is it not? Many proteins, especially those of the core machinery of life, are ultra-conserved. It would stand to Darwinian reason that if a gene is ultra-conserved, it is because that gene is very brittle. I will agree that modern computer code is much more brittle than most proteins. However, there are many parts of a computer program that are not very brittle at all. If, for instance, the change is in a string that is intended to display on a screen, you will merely get a sqelling error.

      "But anyway, what makes you think that protein is essential for life?" Did I say that? As I reread my posts, the closest I got was to say that all life uses ATP, generated via ATP Synthase. This is a statement of current fact. I do not find RNA world research to be irrelevant, for instance.

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    5. By the way, that sentence quote-mined from Bill Gates is hardly an "assertion"; it's a mere obiter dictum -- surely not something Bill Gates intended to become a meme and start a life of its own on the Internet. As stupid people quote it after one another, they don't bother to check the context but never forget to appeal to authority -- "thus spake Bill Gates" -- as if it mattered a whit.

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    6. bFast says,

      Many proteins, especially those of the core machinery of life, are ultra-conserved.

      The most highly conserved proteins have about 35% sequence identity between eukaryotic and prokaryotic species. What that means is that in the best possible scenario 65% of the amino acids can be substituted without losing function.

      Most of the "core" proteins like ribosomal proteins, RNA polymerase, and metabolic enzymes show much less conservation and some aren't conserved at all.

      It would stand to Darwinian reason that if a gene is ultra-conserved, it is because that gene is very brittle.

      Conversely, if a gene is not ultra-conserved then it isn't very brittle. This is a case where nasty little facts spoil your beautiful theory. Too bad. Better luck next time.

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    7. This is an inexactitude, is it not? Many proteins, especially those of the core machinery of life, are ultra-conserved.

      OK, it is a generalisation.You made a very general statement that 'DNA is like code', I made an equally general statement along the lines of 'no, it is not', and you pick on the few genes that resemble code only in their apparent 'brittleness'!

      It would stand to Darwinian reason that if a gene is ultra-conserved, it is because that gene is very brittle

      Well, it would indicate that something is pinning that sequence in place other than vague 'function'. The most highly conserved proteins tend to be non-catalytic, and not especially complex. It is the case that certain sequences cannot be readily changed, because now a whole system exists around them. But there is nothing essential about their sequence; it's contingent. Ubiquitin, for instance, which tags proteins for destruction. It is 'brittle' in the way that "https://" is brittle. It is not the only sequence in the whole of protein space that could possibly function as a protein tag, it is one that (presumably) arose early and stuck. Once it became embedded, opportunities for amendment are severely curtailed. It hardly needed a master programmer to come up with it. Likewise histones, which could in principle have many forms but don't, because they are intimately connected with physical DNA and changes now tend to be fatal. This does not mean that changes would always have been fatal. Genes that don't evolve are hardly a major problem for evolution to explain!

      Me: "But anyway, what makes you think that protein is essential for life?" You: "Did I say that? As I reread my posts, the closest I got was to say that all life uses ATP, generated via ATP Synthase."

      Yes, in defense of your 'DNA is code' thesis, you immediately talked of protein and the assertion that "a change in the code produces a change in the resultant product (proteins)". However, the topic is the origin of life, and if the original organism did not have translation or anything like it, I'm not sure where that leaves the 'DNA is code' issue, other than something for Phase ll.

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    8. "However, the topic is the origin of life," We seem to be on slightly different wavelengths. I thought we were discussing the comparison between DNA and a computer, with Bill Gates' quote factored in.

      As far as origin of life goes, well I wasted an hour watching the attached video. I saw no one in the video suggest that they had solved the OOL problem. I saw a physicist propose a new direction for OOL search -- a direction that allows for selection without replication.

      As such I think Salon's claim, regurgitated by Dr. Moran, to be way off in left field. I find nothing in this thread that enhances the long debated discussion of OOL.

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    9. Apparently the sentiment that no one here actually thinks the origin of life was substantively solved in the video presentation was lost on you.

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    10. Actually, it would appear that Dr. Moran actually thinks that the origin of life was substantively solved in the video presentation -- or at least that's what his headline says.

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    11. "However, the topic is the origin of life," We seem to be on slightly different wavelengths. I thought we were discussing the comparison between DNA and a computer, with Bill Gates' quote factored in

      Well, that discussion goes no further than 'he thinks it is, I don't'.

      Presumably you are persuaded that life needed a programmer, so it matters whether one thinks that translation is the fundamental issue needing coding, or something else.

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    12. bFast says,

      Actually, it would appear that Dr. Moran actually thinks that the origin of life was substantively solved in the video presentation -- or at least that's what his headline says.

      Don't forget the part about creationists being terrified. bFast, are you terrified?

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  12. bFast:

    my work has won multiple national awards, and I have been issued multiple software patents.

    Gary? Is that you?

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  13. "Not one of you have taken even a simple whack at the question, "Is Bill Gates' assertion correct"?"

    That's because it is utterly irrelevant whether DNA is like "a computer program" to the question of how it arose.

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    1. Ok, fine, lets not deal with whether DNA is like a computer program. Lets deal with Gates' second assertion: "but far, far more advanced than any software ever created." Is this assertion true -- not for the simplest form of life, but for the most advanced. Is it realistic to assert that the human organism is far, far more advanced than any software Microsoft has ever created?"

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    2. So it's down to complexity? More DNA = organism is more complex? Like more software code = more complex computerprogram?

      Furthermore, you lightly skip over the fact, basically ignore actually, that +/- 90% of the human software prodcues nothing, broken output, wrong output. Do tell, would you hire a programmer with such crappy skills?
      And while windows 3.1 won't be winning the 'all time best computer program ever' award, it didn't contain 90% garbage.

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    3. "Is it realistic to assert that the human organism is far, far more advanced than any software Microsoft has ever created?"

      Define "advanced". Give me a way to measure "advancedness".

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    4. Ed, Mikkel Rumraket Rasmussen, well said.

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  14. And while we're on the subject of Bill's quotes:
    "I believe OS/2 is destined to be the most important operating system, and possibly program, of all time."

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