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User: Jerf

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  1. Re:Wisdom is understanding on Convergence of Biology and Computers? · · Score: 1

    It's not logical--to me anyway--to support the idea of natural selection, discard the idea of purposeful design and then put an asterisk on natural selection (only on expressed genes).

    Watch it... you're confusing some things. "Expressed" in this context means any codon that has an effect on the individual, in that replacing that codon with another would have no perceptable effect. An unexpressed codon, by definition, has no effect, and while our current estimates of how much of the genome is expressed in one fashion or another may be off, it is impossible that the entire gene is expressed for various reasons involving the difficulty of "breaking" the chromosome during the reproduction process correctly. (It is beyond the scope of this message to get too deeply into that.)

    It is impossible (or illogical if you prefer) for natural selection to work on an unexpressed gene, because natural selection works by culling bad genes. (Not promoting good ones, mind you, eliminating bad ones.) If a gene is totally unexpressed, it is not bad, it's just neutral, and there are no ground to cull on the basis of having that gene, or refrain from culling on the basis of having that gene. If there is absolutely no effect, such that replacing the codon with another would have no effect on the creature, then natural selection can no more work on that gene then natural selection can work on a completely nonexistant gene; to natural selection, they are the same thing. Natural selection can only work on expressed genes.

    Now, the "expression" in this case is defined as "has an effect on the creature". Whether that's the conventional coding for a protein or some other more "exotic" effect isn't important at this level, the question is whether it has any effect.

    Thus, junk genes can not be affected directly by natural selection. One of the consequences I explored in one of my other messages is that as a result, if a gene is turned into junk, either because it is "turned off" or the activation effect of the gene is never experienced in the lifetime of the individual, the gene will degrade. Theoretically, one could imagine a species developing an immunity to some poison that some predator develops, and then the predator goes extinct. Over time, the species could well lose the immunity because it will not be selected for, so it will degrade without natural selection keeping it whole. If some other predator indepedently re-"discovers" that poison, the species may well still be vulnerable, and subsequently develop an entirely different defense against the poison.

    There is certainly junk on the genome. There are good reasons for the junk to be there and if they were important to life it would be impossible to ever conceive in the current manner.

    The question is how much. And that is up for debate. The existance of computationally meaningless sequences really isn't; they are there and there are a lot of them.

  2. Re:Godwin's law v2 on SCO Amends Suit, Clarifies "Violations", Triples Damages · · Score: 1

    If you're invoking Godwin's Law, the terrorists have already won!

    Don't ask me how. They just, uh, do. Yeah, just emotionally react to my claim without thinking about it.... uh....

    Won't somebody please think of the children?!?!? The children!

  3. Hurting my theory on SCO Amends Suit, Clarifies "Violations", Triples Damages · · Score: 1

    Addendum: Seriously hurting my theory is how stinkin' obvious this would be to the SEC. But for money, people do incredibly stupid things, sometimes even right out in public (especially since they may perceive the current Administration to be soft on this issue....).

  4. Still running on the stock scam theory on SCO Amends Suit, Clarifies "Violations", Triples Damages · · Score: 4, Interesting

    I'm still running on the stock scam theory. It explains the escalating shrillness of SCO (must stay in the news to affect the stock price) better then anything else.

    I'm not buying the Microsoft support conspiracy theory because whatever else you may think, you have to concede that Microsoft is a smart company and if they were going to indirectly support SCO in this, they would not leave an blatently obvious money trail to SCO. I think they licensed SCO's IP to just make them go away. Microsoft may have a huge legal team but odds are they are not sitting in Redmond twiddling their fingers; all else being equal even a company as large as Microsoft would probably prefer not to add another lawsuit to its plate.

    Without the Microsoft support (IMHO), the "trying to discredit Linux" isn't the motivation, it's just a side-effect of their need to continually ramp up the volume.

    If I'm right then we'll know in a bit; SCO can't maintain this volume much longer. I predict that in the next couple of weeks, SCO will unexpectedly drop the suit... and quite possible fold entirely.

  5. Re:How far we haven't come... on Hydrodemolition Robot Crushes With Water · · Score: 0, Flamebait

    You'd think they would have come up with a better way to break up asphalt than hitting it really hard by now.

    What better technology? Dropping acid on it? Genetically engineering bacteria to eat it? What, do you want nanomachines to tear it apart? That would be slow and quite wasteful of energy.

    Short of creating a robot to completely automate the human away, there's just no better way to remove concrete. Nothing can compete with this technique (physically whacking on the concrete), which produces no meaningful pollution, wastes little resources beyond the manufacturing of the equipment, and is absurdly efficient.

    You seem to be falling prey to sci-fi-induced misconceptions about technology, such as those promulgated by Star Trek. I suggest learning more about real engineering to repair your brain before you are rendered incapable of thinking about the real world meaningfully, if it's not already too late.

  6. Re:"Junk DNA" == Data stashes? on Convergence of Biology and Computers? · · Score: 1

    even stretches of dna in which the sequence is not important, but the length is in order to accomidate looping back and other various things

    Notice I said "replace with random code", not "delete".

    In fact even in the machine language metaphor you have to replace with random code, not delete, because even the computer jumps won't work.

  7. Re:Wisdom is understanding on Convergence of Biology and Computers? · · Score: 1

    In truth, I actually am a creationist, though I don't capitalize that because what most Slashdotters mean by the term is not exactly what I mean. (I hold the Creation Science institute in lower regard then even the average Slashdotter.)

    Nevertheless, it remains a mistake to attribute too much purpose to many actions. To the extent that Nature is random, those random processes do not have purpose. To the extent that Nature is not random, the purposes are not likely to be the ones that we humans are ascribing to them. Either way, you're better off not thinking of Nature in terms of "purpose". (Certainly the non-purposeful way of thinking provides a better model of what actuall happens.)

  8. Re:"Darwins Radio" by Greg Bear on Convergence of Biology and Computers? · · Score: 1

    Ever wondered why Gradualism in Evolutionarey theory is becoming less popular than Punctuated Equilibrium?

    For a more realistic answer... if you model evolution on a computer, it always comes out in the form of punctuated equilibrium, no matter what the model. Odd that way.

    Now, if you take the average of many runs against some criterion, the result will be a smooth curve, but each individual run will have fits and starts.

    It seems a more interesting question is "Why do we intuitively feel it should be smooth?", a question about our brains, much like "Why does the moon look larger near the horizon?" (Note: I'm not asking that question, I'm using it as an example.)

  9. Re:Pissing in the Well on SCO Terminates IBM's Unix License · · Score: 2, Interesting

    Copyright law is out to lunch on this issue.

    In general, copyright covers code better then patents (which is completely broken by trying to cover software), but even copyright law buckles here. It's one thing to talk about one paragraph dropped into a ten page work. It's another to talk about one paragraph dropped into a 100,000 page work (using a page as 1KB or so, which is reasonably standard). There's just a night-and-day difference here.

    Even if the original owner is entitled to compensation one questions the wisdom of the remedy consisting of yanking the legality from the entire work. If this were to get far enough I would not be surprised to see some sort of new doctrine come out of either Congress or the Supreme Court limiting the ability of one IP owner out of literally thousands to screw up the product, on the theory that its completely unfair to the other thousands of owners.

  10. Re:"Junk DNA" == Data stashes? on Convergence of Biology and Computers? · · Score: 1

    So you're equating "not being used to code for a protein" with "junk".

    Nope, not "equating", quite specifically "defining for the purposes of this conversation". And it's a simplification; another poster mentions "siRNA", but if it does something it's not junk.

    However, DNA that is always skipped over is, for the purposes of this conversation, junk. Given the rather good rationales for having this junk (such as decreasing the odds that during the creation of sperm or egg cells, the split will occur right in the middle of truly useful a gene), it is exceedingly unlikely that every single last codon will be useful, because if all the genes are "used" then these rationales don't work. Yes, some things currently though "junk" may be shown to be useful but it is almost certain that a lot of this is still "junk", in that changing it from C to T would have no perceptible effect on an organism, other then one less C and one more T.

  11. Re:Social cost=private costs + social cost on A Mighty Wind · · Score: 1

    I should have said "concentrate on the selling, not the buying".

    The idea of the lawsuits is to force the seller to raise the price, possible to infinity, which can work. The lawsuit is not trying to force everyone to not buy from the provider, which can't work.

    The selling can be controlled and various affects can be created by manipulating the selling price at various levels, but buying is much harder to (directly) control, and you can't really blame a buyer for buying something that is too cheap; one can't expect every buyer to examine everything they buy to see if it's too cheap. Look at the things that have tried, like boycotting Nike for unethical sweatshop practices: Miserable failures at anything other then making the boycotters feel good. If you really want to affect Nike you need to force them somehow (probably legally) to factor in higher wages to the people making the shoes... then things might change.

  12. Re:Wisdom is understanding on Convergence of Biology and Computers? · · Score: 2, Interesting

    From my original post: "The debate on its usefulness centers around the other physical implications of the existance of such DNA, and where it might have come from, but 'computationally' (in biological terms 'is it ever used to produce a protein?') it is indeed junk."

    Nothing you say contradicts that.

    Also, don't forget Nature is not purposeful. Putting useful stuff in the junk is not useful, because you're no more likely to mutate such that the formerly useful code is expressed then you are to mutate such that a truly useless portion is expressed. We can "comment out" code; there is no equivalent operation for nature, because "commenting out" is a purposeful act to preserve code for later. And the odds of "uncommenting" are too small to affect anything (the genome is huge).

    Also, natural selection only works on expressed genes. For every generation that a formerly-useful gene is not expressed, it is increasingly likely to be corrupted in an increasing portion of the gene pool until it effectively disappears, so the theory that the junk genes are "code libraries" on the long term is effectively twice debunked. On evolutionary scales, completely unexpressed genes are relatively quickly flushed completely out of the pool.

    Like I said, the other implications of junk genes are being explored and they are almost certainly not truly useless, but the consensus of the science is that the genes are not useful in what I am calling "computational" ways for the purposes of this discussion. It's really past the time for skepticism on this point, unless you really want to re-write modern genetics. (Which you may, but I doubt.)

  13. Re:"Junk DNA" == Data stashes? on Convergence of Biology and Computers? · · Score: 3, Informative

    It's junk DNA not because we don't know what it does, but because it's never accessed at all.

    The equivalent in computer science would be if you plotted every possible route through a program and some code is still never conceivably executed, that would be the equivalent of "junk DNA". Even if you went into the machine language code and replaced it with random values, the program would still never crash because it never executes.

    In the computer world we tend to call that "dead code".

    Thus, we do know that the "junk" is truly junk. The debate on its usefulness centers around the other physical implications of the existance of such DNA, and where it might have come from, but "computationally" (in biological terms "is it ever used to produce a protein?") it is indeed junk.

    Please consult any elementary (but up to date... the understanding of junk DNA has progressed a lot in the last decade) textbook on genetics.

  14. Re:An answer from a different perspective on Convergence of Biology and Computers? · · Score: 1

    Aside from the time issue (nerve conduction is blazingly fast), you would serve your function staying in silicon.

    Blazingly fast ? WTF? I think you meant to say that silicon conduction is blazingly fast.

    Nerve impulses can be measured in tens or hundreds miles per hour, pulses over wire or silicon is measured in tens of thousands of miles per second.

    This page is aimed at kids but happens to have a good chart of various speeds of various nerves; the top speed they show is about 225 mph, and they compare it to a commercial airplane, not the speed of light like electrical impulses are compared to.

    Why do you think our minimum reaction time is measured in tenths of a second, rather then nanoseconds, even when the reflex only takes one layer of nerves to activate (like spinal cord reflexes)?

  15. My opinion on Convergence of Biology and Computers? · · Score: 1

    Computing is already helping biology, like with protein folding. This is only going to get stronger.

    Biology may help build better computers, either by "growing" things like media, or with nanotechnology indistinguishable from biology being used to grow chips.

    However, the "ultimate" convergance of a biological computer is not going to happen, except perhaps in an isolated sense where it can be made cheaper to grow a computer. The problem with biological computing is that generally we want to compute, not be awed by the biology. (Far, far too many people when trying to imagine the future get sidetracked by the "awe" factor, but the "awe" factor is not a long-term factor.)

    "Pure" biological computing has an unavoidable disadvantage vs. non-biological computing: It's biological. Which is to say, you need an infrastructure to keep the biological part alive, which the non-biological solution does not need. This is an intrinsic flaw which can not be overcome except by leaving the biological realm. By the time we could build the "biopacks" seen in Voyager, we'll be able to build something much better that isn't biological. The part of the system keeping the biopack not only alive, but in the quite-likely narrow environment it will actually "work" in, would be better spent on actually doing the computation.

    Biological systems are astonishingly redundent, but that's just not necessary for non-living systems, where cracking the system open, repairing it, and reassembling it and expecting it to work isn't that big a deal. Do you think twice about repairing your car that way? Since it is of no particular consequence if a computer "dies" briefly, there's just no need for the astonishingly complex low-level redundency and healing capabilities in living systems.

    A pure, 50-50 convergance is a chimera. Both fields will be helping each other, computing probably helping biology more then the opposite, but total convergance is not going to happen. "Every discipline inevitably thinks of itself as the most fundamental." Computer science isn't exempt, and I know biologists feel that way. But a dispassionate examination shows there are fundamental differences such that the only way they are going to "merge" is if biology ends up being redefined to be the same as "nanotechnology" and includes things that we do not currently consider "biological".

    Which will probably happen, but it's not the sense you're asking about right now.

    BTW, "genetic" computing is mostly a side-show. It's practical significance is virtually nil. It looks cool, but it's slow as all hell and unreliable to boot. (What, slow you say? Yeah, it takes forever to set up the problem. Sure, it runs quickly after that, but it's disingenuous to dismiss the setup time, which while certainly possible to accelerate, will almost by definition take longer then checking the answer directly.) Current machines can already stomp the performance of any pure genetic computer you can imagine. (Note this very distinct from a machine that some genes may grow; be sure you know what these terms mean before you criticize this post, all you budding Slashdot biological computing experts. ;-)

    A lot of other existing "biological computing" is mostly a side-show too; cute, but it takes some serious trips into fantasy-land to come up with a practical application that will actually beat the non-biological competition.

    To the extent you care about my opinion, and remember, you asked, I would not advise getting too far involved in this field.

    (Now it's entirely possible that in the process of researching a pure biology computer that something interesting could be learned. I also think pure quantum computers are impossible but the research is useful and useful hybrid solutions will be developed, so the research is not a waste. But on a personal level, I would still not want to actively pursue something that's unlikely to be possible.)

  16. Re:Is this even legal? on 12/7 and Overtime on a Salary? · · Score: 4, Informative

    programmers are an exception to the Fair Labor Standards Act of 1938 - 29 USCA Â 213(17)

    I smelled BS on this but I was wrong: See the text of the FLSA, section 213, provision 17.

    Sorry for doubting you, pcwhalen. (Might want to link such things in the future, to help people like me who don't take Slashdot comments at face value. Which should be everyone...)

    That exemption really sticks out like a sore thumb, I think; take a look at the other exemptions and I think you'll agree this one doesn't fit in, except perhaps in the very limited domain of server operator (who may need to do something for 70 hours in a week, as a sailor might).

  17. Meta-advice on Storing Pictures While Backpack Travelling? · · Score: 2, Insightful

    Depending on just how serious you are about being without power for that long a period you may really need to consider an all-out power consumption analysis, as well as other more conventional factors.

    One thing that I really noticed was your thought about writing CDs, which consumes a non-trivial amount of battery power.

    I personally know almost nothing about how much power it takes to take one picture, or write 256MB onto a compact flash, or run a laptop, but you might need to find out. Batteries are heavy and basically dead weight (no value beyond their storage capacity), so you will want to minimize what you need to carry. Coming up with a fancy solution that requires thirty pounds of batteries to run for a week without contact with civilization is probably not useful. Also, you may get into trouble if you need fifty hours to recharge your battery set. ;-)

    Just a meta-thought.

  18. Re:Hypocrisy on A Mighty Wind · · Score: 3, Insightful

    Somewhere, sometime, highly populated states are going to realize that they are not entitled to simply purchase energy production from other states without suffering the drawbacks of that production.

    Yes, they are; the "drawbacks" that you refer to are, or should be, bundled into the price. In fact this sort of thing happens all the time, and is a perfectly normal part of capitalism. Paying for labor is nothing more and nothing less then paying somebody else for the "drawback" of having to work hard to assemble or create something.

    If the "drawbacks" aren't paid for it's the seller's fault for setting the price too low, not the buyer's fault, which you try to blame.

    Concentrate on the seller, not the buyer.

  19. Re:This is good, but... on Computing PageRank on your PC? · · Score: 1

    Here ya go:

    011

    Proper decompression is left an as exercise for the reader.

    Now, let us discuss payment schemes...

  20. Re:Quake is GPL. Where is the source? on Java Technology Demo Showcases Quake · · Score: 1

    Along with jrstewart's alternate licensing scenario, it is also possible the company simply used published documents on the format of the data files to produce a renderer all by themselves, which would produce an engine they would own fully.

    In which case it's only "fair" for them to own the final product, since that would be a lot of work.

  21. Nope... on Four-Dimensional Rubik's Cube Craziness · · Score: 2, Informative

    Those are only descriptions of a hypercube that is projected onto a three-dimensional space or intersected with a three-dimensional space.

    A real hypercube looks like a hypercube, not a cube with lines or anything else... of course you need to be five-dimensional to perceive the whole thing at once.

    In general you need N+1 dimensions to perceive an N-dimensional object; for example, we can only fully perceive two dimensional objects all at once. Three dimensional objects we only see a particular side of, and generally only the surface. A four-dimensional being could potentially see the entire three dimensional object all at once, just as we perceive two-dimensional objects all at once. A two-dimensional being only sees one dimension around him, and can only see a certain side of, say, a square.

    Note that there's nothing magical about any of this, or particularly unbelievable; if you're having trouble believing it's this simple your mind has been corrupted by bad sci-fi, probably Star Trek.

  22. Re:Tom raises several issues on Tales From The Perilous Realm · · Score: 1

    Wanna-be dualists should pay close attention to those words. Calling things "good" and "evil" implies an external standard which would then, as Bob Uhl says, collapse the dualism into a unified world.

    You can hold to dualism only if you refuse to elevate one morally over the other, in which case you're stuck with "A" and "1". I name them that because there is no way to order "A" and "1", unlike say "A" and "B" where "A" comes first.

    It's really difficult to hold to this philosophically (though perhaps not impossible; not being a dualist I would be unlikely to buy it anyhow), because without being able to distinguish between "A" and "1" meaningfully, how do you know there is not a third position? Or fourth position? Etc. It is extremely challenging to avoid a nihilistic philosophy where everything is equal, because of an unstoppable multiplicity of "forces", and therefore there are no distinctions at all; perhaps true but answering all philosophical questions with "Nothing" is not satisfying at all.

    Anyways, claims that Good can't exist without Evil are really kinda silly, like claiming Light can't exist without Darkness. Yes, it can, and in fact we believe there were periods in this universe's history when light did in fact exist without darkness, right at the beginning. Generally claiming the two must both exist stem from IMO poor definitions of good and evil, and even if you define the two in terms of opposition to each other (forming a circular system) it still doesn't imply that they both must exist; "Not a cowhorsedog" exists (everything is in fact not a cowhorsedog), but that does not mean that there is a cowhorsedog. (A cowhorsedog is of course an animal that is just like a cow, a horse, and a dog, except the three are physically one creature.)

    (Note that many people use dualism practically as an attempt to escape from morality, giving them an excuse to act "evil" and claim to themselves that they are just as justified acting "evil" as "good" since they are both equal. The way dualism as a philosophy tends to collapse into nihilism if followed to the logical conclusion and not carefully tended to shows why this philosophy can be so appealing to people trying to escape from constraints like morality, and indeed I observe a strong correlation between anti-authority types and dualists in real life. Also watch for people who try to slip "Balance" in the back door; if "Balance" is a desirable state and "Unbalance" is bad, then "Balance" is Good and "Unbalance" is Bad; this is a specific example of Dualism collapsing back to a unity system.)

  23. Re:There are lots of free workers on Offshore Outsourcing Threatens Offshore Outsourcing · · Score: 1

    Y'all missed the point. The claim was that open source workers work for free. My point was that while that work for free, they don't work for you for free, and there is one hell of a difference.

  24. Re:There are lots of free workers on Offshore Outsourcing Threatens Offshore Outsourcing · · Score: 4, Interesting

    Ever tried to force an open-source developer to change the design to meet your needs? Especially a large project not in a mode where they are begging for respect by pandering to anybody who will deign to email them.

  25. Re:Quite right! on Crime Prediction · · Score: 1

    Arms races, both literal and figurative, between cops and criminals are nothing new. You can never win, but that doesn't mean you shouldn't play the game.