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Science

DNA Goes Binary 196

Posted by michael from the speak-l337 dept.
Anonymous Coward writes "Chemists in the United States have constructed the simplest possible genetic language. Like Morse or binary code, it has only two letters - but it can orchestrate some of the basic molecular reactions needed for life to evolve."
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DNA Goes Binary More

DNA Goes Binary

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  • Pernutation City (Score:2, Interesting)

    by lisle ( 66482 )
    Ever read it? By Greg Egan, THE most imaginative SF author ever

    • I vote... (Score:3, Informative)

      by Eric_Cartman_South_P ( 594330 )
      ...for Jack Vance. Anyone ever read Demon Princes? Pure gold.

      I'll be taking a look at Pernutation City. Thanks for the sugestion...

    • 'Permutation City' is damn weird, even for Greg Egan. 'Diaspora' is amazing, however. The time-scale of the book continued to blow me away as I read it. I was having to get up and walk around the room to sort of 'cool off' and get my bearings. Not many books can do that to you.

      Btw, Greg is an all-round good guy. Check out: http:\\www.boat-people.org [http].

      At one point, you could go to the site, and send your mailing address, and Greg would send you a 'We are all boat people' T-Shirt. I have one.
  • I mean, theoretically, the Church-Turing thesis states that any algorithm (which, I would hope includes evolution) can be done with the "Turing Machine", which as we all know can be implemented in binary code. So, isn't this basically old news dressed up a different way? (Alternatively, old news with a new perspective for application)
  • doesn't DNA have 4 letters only anyway?
    thats what my bio teacher said, i think...
    • If C only links with G, and A with D, isn't it already Binary? Because there are two possible combinations.

    • doesn't DNA have 4 letters only anyway?
      thats what my bio teacher said, i think...

      The Yijing has Yin and Yang. It comes up with 64 permutations, of which Hexagram # 24 [ Standard Sequence ] corresponds to Codon UAA, which just happens to be a representation of "stop". The most common english word for Hexagram # 24 is return.

      For more on that topic go read Johnson F Yan DNA and the I Ching, Martin Schonberger The I Ching and the Genetic Code and Kayta Walter Tao of Chaos. Go hunt for them at Powell's [powells.com] yourself.

      So all you need is Yin and Yang. Binary.

    • IIRC G or T is replaced with U in RNA. I really should remember, since it was in the article. Oh well.

      But anyway, the point is that the components of this two pair stuff were more readily available on the primordial earth (and more heat resistant).
  • ... with Morse code, I can construct G, C, T, and A!

    And with binary, I can construct GCTA... and anything else as well.

    This post brought to you by the numbers 1 and 0.
  • How is a space represented in Morse? I thought the codes were "dot", "dash" and "pause".

    TWW

    • Pause doesn't really 'exist' in morse.

      In fact it's very interesting, how in the beginning of math, '0' didn't exist either. It was nothing. But they had to come up with a symbol to represent nothingness.

      In short: 'Pause' in Morse would be the end of your binary-DNA molecule.

      • See my comment above. I think Morse actually has 5 symbols. And it's not really a clocked code.

        Bruce

        • I'm not too sure about that...

          Morse has design principles in it that make it that there are very few ambiguities (sp?) in distinguishing different letters... Just like the error correction codes on CDs: if you've ever thought of it, how tha f*ck does an audio CD reader know where the stream starts, and where it ends?

          Morse is meant to be fast bursts... the messages are brief and kurt, with little room for confusion, and don't convey anything that isn't essential. Just like life at a cellular level.

    • Re:Does Morse not have three codes? (Score:4, Informative)

      by pete-classic ( 75983 ) <hutnick@gmail.com> on Tuesday December 24, 2002 @08:03PM (#4955040) Homepage Journal
      It's a synchronous protocol. It is also a binary protocol. The line is either high or nominally zero. A dit is a short interval of current. A dah is an interval of current about three times as long as a dit. A dit length pause represents a space between characters, a three dit pause between words, and a seven dit length pause represents a space between sentences.

      How long a dit is depends on the skill of the operator(s).

      My only qualifications are that 1. I look at a portrait of S. Morse all day* and 2. I can STFW.

      -Peter

      *Really. I'm currently weathering the tech job crunch as a security guard at First Data Corp, of which Western Union is a subsidiary.

  • Comment removed (Score:5, Informative)

    by account_deleted ( 4530225 ) on Tuesday December 24, 2002 @07:49PM (#4954984)
    Comment removed based on user account deletion

    • I'm Not Convinced (Score:4, Interesting)

      by Anonymous Coward on Tuesday December 24, 2002 @09:47PM (#4955323)
      * The more likely operator during those early days would have been something with only 2 bases.

      This is pure conjecture. The *early days* could have well been a mixture of many purines and pyrimidines, and the AGCT and U won out in the replication arena due to the thermodynamic stability/instability of their base pairing (A+T, G+C in DNA and A+U, G+C and G+U in RNA). If diaminopurine was a major player, then it should have survived. It didn't, so there is really no reason to believe that it ever was a major (if any) player in the genetic game.

      • It IS pure conjecture, that's the whole point. They are trying to model early life processes, to show that it COULD happen this way. Right now, we have no solid theory on the evolution of DNA, which is the "missing link" in the general theory of evolution.

        Remember, these are chemists, not paleobiologists, so they used diaminopurine, presumably because it was easier to artificially create the strands using it. Historical accuracy is not the point, this is a proof of concept.

  • Not exactly. (Score:4, Interesting)

    by The Monster ( 227884 ) on Tuesday December 24, 2002 @07:51PM (#4954990) Homepage
    Chemists in the United States have constructed the simplest possible genetic language.
    What they've found is that they can build a functional ribozyme out of diaminopurine and uracil.

    We've all probably seen perfectly valid i86 machine code entirely composed of printable ASCII, too, (I recall one which could be used to convert binaries to emailable text, which was used to post DOS utilities back in the day) but that doesn't make it a 'language' that the processor understands

    • Re:Not exactly. (Score:4, Insightful)

      by Ieshan ( 409693 ) <ieshan@g[ ]l.com ['mai' in gap]> on Tuesday December 24, 2002 @09:56PM (#4955366) Homepage Journal
      You're missing the point. You changed the form of the thing when you tried to fit it into a computer analogy.

      It's a serious biological discovery, in some respects - it makes the DNA system more plausible on early earth, and it's a much simpler system which DNA could have grown out of.

      Your analogy makes this sound like wasted effort "just to prove it's possible", their work is part of research to explain the evolution of the genome.
    • We've all probably seen perfectly valid i86 machine code entirely composed of printable ASCII, too

      Remember Code Red? Whoever wrote that one managed to embed x86 machine code instructions in a frigging URL!
      I hate to say it, but that impressed me deeply. :)

  • All our technology is either analog or binary, but why not try octal or hexadecimal computing? It would allow for for faster computers even if the cost would be the redesign of a LOT of chips.

    This might be a "stepping stone" between traditional and quantum computing, or it might just be a posible avenue of progression never taken.
    • At first glance, this post looks like a troll. However on second glance, one realizes the poster is just clueless.

    • Re:Binary computers? How long before base4 compute (Score:1, Interesting)

      by Anonymous Coward
      Why not? This question is raised by most CS students when they get an introduction in chip-design.

      Because its hard. You'd have to create transistors (or whatever) that operate on several volt-levels, instead of on/off. Actually on/off is not that clean; there are flanks to the signal. Could you differentiate between the flank from 3 to 0, and a 1 or 2?

    • Re:Binary computers? How long before base4 compute (Score:4, Informative)

      by Jester99 ( 23135 ) on Tuesday December 24, 2002 @08:13PM (#4955083) Homepage
      The problem is one of line noise. In binary computing, your lines are either conveying a 1 (voltage high) or a zero (voltage nil).

      If you were to go to four states, now instead of having +0V and +5V, you now also have +1.5V and +3.5V representing different states of the quad-bit.

      Fluxuations in the system's power do not easily switch a line from +5 to 0, or vice versa, but could easily switch 3.5 to 5. The more signals you try to carry on a given line, the more suceptible that line is to noise. Obviously, by increasing your max voltage, you could separate your signals more, and take care of it that way, but that's not a solution; you'd be less power-efficient, you'd generate a lot more heat, and all sorts of bad things would happen.

      In short, binary is Simple. And that's why it works. Once you start trying to get into multiple voltage levels, you make things far trickier.
      • Binary is not only Simple, any Language using a larger Alphabet could be encoded using binary. That means that anything that is possible on a baseWhatever computer is possible on a binary computer. So you better have a really, really good reason to switch from binary computing.

        As far a quantumn computing goes(not that I have any real credibility in that area) the advantage is that you can have a qubit in 2 states at the same point in time, which I think implies that you can actually execute multiple instructions at the same time. So you are still basically using binary computing, just the ammount of finite work that can be accomplished at one time is bigger.
        • hardware wise switching would be a fool's errand.

          I put some thought into this about, if you could create a hypothetic quadnary system with roughly the same 'speed' as a binary, I still don't see why it would be faster. Since every operation a computer does is either an add or a shift, how would going from base 2 to base 4 really be any faster? I suppose less quad bits to shift, but the adder would be more complicated. I dont even want to think about how one would design a quadnary adder.

        • Binary is not only Simple, any Language using a larger Alphabet could be encoded using binary.

          Uhm. I don't have any proof to back this up, but it seems obvious to me that any symbolic system can be encoded using any other symbolic system, as long as both systems are non-degenerate. It's all about arbitrary base arithmetic, right?

          So, technical challenges aside, there's no purely mathematical reason why base 2 makes more sense than any other base.

          Personally, I prefer to do all my math with base 1 arithmetic. It's a lot easier. 111 + 11111 = 11111111.
      • > In short, binary is Simple. And that's why
        > it works. Once you start trying to get into
        > multiple voltage levels, you make things far
        > trickier

        Exactly. And for a computer, it's a bad thing when errors occur.

        But for evolution, errors are necessary. Errors = mutations = progress.

        Maybe the reason that DNA uses 4 states instead of 2 is because it introduces errors more frequently, leading to faster evolution. At some point a primitive binary system probably evolved into a 4-state system, which was superior. And perhaps DNA uses 4 instead of 6 because 6 introduces too many errors and the system falls apart.

        Four may simply be the "sweet spot".

    • That's not a novel idea, as someone else said, beginning logic students always ask this. Then once they learn how logic design works, this kind of idea is something to send shivers up a chip designer's spine.


      It would allow for for faster computers

      Not likely. The complexity increase would slow things down alot. Especially since fact in every circuit you'd have to have something measure the voltage at every gate...

      Not only would they be slower, they'd be far more unreliable, consume vastly more power, and the circuits would be enormous.

      • By using voltages 0,1.5,3.5. and 5 you would actually be using less power in most datasets.

        By 'faster' I was reffering to data transfer rate; not calculations. If a single bit in my system could hold two of yours then mine would be twice as fast.

        Unreliability wouldn't be a problem so long as you keep the inductance of the wiring down; myistereo is hardly "unreliable" and it has inifinite voltage states.

        I understand the "beauty of binary", but we don't think that way, our programs don't think that way(a boolean takes a byte or more for addressing), and it seems like a waste.

        I neither have the equipment nor the knowledge to build such a system. If I made it out of multistate relays(my inspiration for this idea) then it would, in fact, be enormous and consume more power. But then again so would binary electronics.
        • data transmission is even worse for this because of errors and line noise. In order to keep the errors to a minimum not only is parity used, but the very waveform of transmission is a way of keeping things in check.

          Most transmission waveforms do NOT translate 10101 and so on as high-low-high-low-high pulses because of the potential for error. This is true for all transmission lengths, both short and long.

          As an example, Ethernet uses Manchester [brighton.ac.uk] encoding. There are many, many other schemes for this that accomplish the same basic task.

          In short, nobody uses straight binary pulses for data transfer because its unreliable. Using shifting voltages would compound the problem.

          • One of the reasons for using Manchester coding is that Ethernet interfaces have an isolating transformer at either end. So the signal needs to be AC for that to work. Plain vanilla serial just uses a normal mark/space system though, and it works fairly well even in noisy environments. Especially RS423, which is balanced - noise is coupled into both lines equally, but can be cancelled out.
    • This would have no noticable impact as any value can already be represented in binary. If you have 12 values, you also have to have the sensitivity to distinguish between those 12 values and transmit them across any given medium. This is too tedious, and leaves a lot of chance for error. By computing in binary you simplify it. You have +5v and -5V, on or off, +5 or +0, etc.
  • As the article points out, RNA and DNA both are constructed of 4 amino acids *: A, C, G, T/U. Is there a reason for why nature used four instead of 2 ? I'm curious as to the scientific answer why we have 10 fingers as well. Both 4 and 10 seem arbritary, or are they?

    * "Escher, Bach, Godel" shows an interesting link between Biology, Music, Philosophy, and Computer Science.

    Cheers

    --
    Political speeches are like steer horns. A point here, a point there, and a lot of bull inbetween.
    ~ Alfred E. Neuman

    • Re:Why 4 bases? (Score:3, Insightful)

      by pVoid ( 607584 )
      There is a concept in scientific reasoning which I forget the name...

      It basically goes: it's no use thinking of such 'arbitrary' things, because you know what, if it had been base 2, and we all had 12 fingers, your post would have been:

      As the article points out, RNA and DNA both are constructed of 2 amino acids *: X, Y. Is there a reason for why nature used two instead of 4 ? I'm curious as to the scientific answer why we have 12 fingers as well. Both 4 and 10 seem arbritary, or are they?

      There are certain things that have a 'scientific explanation', like why all life is most likely carbon based (because Carbon is a 'small atom', and has a very very complicated structure allowing it to form very varied types of bonds (tripple, double, single), which allow for long chains of molecules -- it has been argued in fact that Silicium, which is very similar to Carbon in all respect apart from it's not being a 'small' atom wouldn't be suitable because it wouldn't be as flexible as carbon based chains, and hence they would break easily... anyways, offtopic).

      • Re:Why 4 bases? (Score:4, Insightful)

        by Fnkmaster ( 89084 ) on Tuesday December 24, 2002 @08:33PM (#4955146)
        What you are doing is applying the anthropic principle, so-called because it is essentially an appeal to the fact that it is the way it is because we are here to ask it. Perhaps that sounds silly when reduced to its essence, but fundamentally what you are saying follows this basic pattern. The problem with this is trying to figure out what things, numbers or observations in our universe should be open to 'scientific explanation' and which should be written off to the anthropic principle. If you accept such a principle, it seems like you can essentially draw any arbitrary line and call the things on one side of the line open to scientific inquiry and the others not ("they just are that way" "why?" "just cuz." or "cuz you are here to ask why they are that way").


        As a physicist by training (though not by profession), I take issue with this basic principle. The fine structure constant, e, pi, hbar, c.... these are all "weird" constants we observe in various places in the universe. Some of them have deeper meaning that we have discovered, or at least relationships that connect otherwise seemingly disparate areas of math, physics, or whatever. Some, as far as we know, are still arbitrary free parameters. As I remember it, the Standard Model currently has something like 5 or 6 free parameters in it.... if you fix these, you get all of modern physics to pop out (well, roughly like that). Are these random? Are they arbitrary? We don't know yet, but we shouldn't stop asking the questions.


        Also, I know there are different forms of the anthropic principle (weak and strong) - I forget the exact distinction, and I believe what we are describing more or less corresponds to the strong form. The weak form is more watered down and palatable to a general scientific audience. :)

        • Very interesting.

          See, my point of view is not that we should all sit in silence like Skeptics would have us (because there is no line to draw)... but rather not ask the question 'Why?'... Science, and physics answers 'How?' rather than 'Why?'.

          There was a very famous press release done with Feynmann around the 50s (Feynmann is one of the most renowned Physics professors in the world)...

          A journalist asked him some simple question like "why is there lightning?" or something like that. To which Feynmann started saying "because...", and the journalist would then say "well, why is that that electrons do that"... and Feynmann would continue explaining EM theory... and in the end, Feynmann gave this loooong speach and left the journalist dumb-founded. Anyways, it's just a point to show that "why?" isn't always the good question to ask, because ultimately, the answer is "because.".

          In essence, Why implies 'intention'... "Why did scientists do this? so that they could have a simpler model to work with"... Asking that question to the world of physics, is ultimately believing that the world has intentions - ie. a creation of some being. (which I don't believe personally, but that's OT).

          As for the constants you talk about, you are absolutely right. There definitely are 'more special numbers' than others, but it still doesn't give _meaning_.

          • Agreed fully. And now you have stumbled on the reason that I left physics, and I couldn't have stated it better myself. In fact, I have over the years explained to many friends, including folks in the software industry why I didn't pursue physics, and it precisely the inability at its fundamental levels to answer the 'why's. I mean, we can understand lightning (I think we can say we know 'why' lightning happens, but we don't really know why all the other things are the way they are SUCH THAT lightning happens). And we can elucidate the rules and postulates of quantum mechanics and general relativity. But physics can't tell us 'why 3 space and 1 time dimensions that are perceptible' or 'why is the Ricci tensor the correct description of our space time'. I mean, you have to basically posit a model and show that the model results in describing observed phenomena. At such a fundamental level, you really lose the ability to answer 'why'. I had hoped that perhaps string theory or other theoretical paths would lead to a better understanding of why, but then I realized after studying physics for a while that you never really get to the why, you just come up with more abstract, unified models that admittedly might be more aesthetically pleasing, but don't really get you anywhere in terms of real understanding. But if you stopped asking 'why', you'd never get to at least understanding 'how'. I think that most physicists accept that at the core of their discipline, there are some unanswerable 'why' questions, which require an appeal to religion, or the anthropic principle, or just an acceptance of the fact that they are. But if we had just accepted 'intention' as the heart of everything, we would never have bothered pursuing science... 'why is there lightning'... 'because there is and the gods will it'. The 'why' questions are what I think drives us, so they are useful to ask, but also frustrating since they are, at the heart of it, unanswerable.


            Also note that the most miserable group of fellows I've ever met in my life were the Harvard physics faculty. I always believed it was because they had set out in their youth to answer why and discovered that they could only answer how, and usually only for such a small esoteric part of reality that nobody much cared outside of their specialty.

            • I'm very fascinated really to have stumbled on someone with such a similar story as mine. I started off being the science lover, and started my university as a pure Physics major. All throughout highschool, I had been several years ahead of my fellows in both physics and math. But after one year of physics, I decided Math must be the thing for me at univ. That eventually turned to comp sci - believe it or not, I was for a while infatuated with the idea of being the god of my programming realm. Eventually, the drunkeness of that omnipotence on a computer faded away.

              Strangely enough, just in the recent couple of years, I've almost completely moved onto the arts. I've accepted a certain fatalism and determinism in the world, but it doesn't mean I'm mystic, or religious... having had so many years of scientific training makes that I'm always clear minded about why things happen. I've just stopped looking for a reason because, as one philosopher says (I forget which) "even if there is god, it's in my best interest to act as if there isn't".

              In the end, I've found it incredible how the same impulse that was in me to ask the question 'why' is what drives my artistic aspiration. It's a 1:1 correspondance really, an isomorphism of the same thing. The act of creating anything that is 'harmonious' gives me the same joy that would the answer of a 'why'.

              I just recently got a christmas present for a friend of mine, it's "40 years of pictures with Jeanloup Sieff" (he was a very famous french photograph)... in his intro, he says there is no art... only artists who have an urge to create - and their creations.

            • If all the questions were already answered, what would be the point in learning it? We are at the point where we can explain for a long time on any question inside the realm of human experiance, and a great deal more. But, I don't see why you should expect us to know everything, and be omnipotent.
          • IMHO, the only possible rational answer to "why" is discussing the question in a more exact or complex model.

            Physics, and science in general, are rational, which means they deal with modelling numerical relationships, and testing these models theoretically and experimentally.

            So, IMHO, a constructive response to the question "why" is not assigning intent to nature, but saying something like:

            "This is what we know, this is what we speculate, your phenomena [fits to | is predicted by] this branch of human models of nature. If you disagree, please construct a disproving test, or a better model, and we'll all learn something new"

            To summarize my view:
            The serious answer to "why" is "This fits theories X_1..X_n in ways Y_1..Y_n".

            All this is not a reason to despair from science, in spite of it's limitations, it's still the best truth-finding method the human race has.

            • I beg to differ...

              The Human race's only 'truth' finding method is reasoning and intellect.

              Science, is as the name implies, knowledge. Think of Science as a vast library of past experiences the collective human race has had (add to that some models that have been developed that fit these observations).

              Truth is an entirely subjective concept... and thus can only be resolved in the subjective realm.

              In the world, there is only being and not being. No truth.

        • perhaps you should consider a new line of study.

          the anthropic principle should be applied to things things that happen by probabilistic chance and have no 'why' explanation.

          why did this particular subatomic particle decay yesterday and not today (given reasonable halflife parameters)?

          why is the universe made of matter, not antimatter, if equal parts were made during the big bang (yes, there are some arguments to the truth of this statement, but let's not get into that)?

          why did this snowflake end up looking just this shape?

          why do we have 10 fingers?

          the answer: it just happened that way. we could just as easily have had 8 or 12 fingers if not for some random mutation at some point. if it didn't, you wouldn't be asking about it. hence, the anthropic principle.
          • Perhaps you should consider taking your foot out of your mouth. If you have to resort to an ad hominem attack in your first sentence when we (pVoid and myself) are engaged in an otherwise civil discussion of the philosophy of science. This has very little to do with the pursuit or practice of physics or computer science, two areas in which I am somewhat accomplished, probably substantially more so than yourself.


            The entire point of my post, if you cared to or took the time to read it, is that determining which things "happen by probabilistic chance" as you so eloquently explain it, and which do not is not nearly as easy as you posit. Clearly, we CURRENTLY believe that which subatomic particle decayed at any point in time is a random, probabilistic event, described by quantum mechanics. In fact, the indistinguishability of these particles is one of the basic tenets of traditional QM (and probably of modern QM variants as well), as you can find in any basic QM textbook.


            But even this basic theory has its challengers. People who have posited non-local theories, hidden variable theories and so on. These include reputable theoretical physicists over the years, and the point is that they didn't take the fact that there was no "why" as a given, they questioned it.


            With your other examples, there are definitely possible scientific explanations for these facts. The fact that we have 10 figers - an evolutionary argument can be made that the opposable thumb, plus at least 2 other fingers is required for minimal tool handling, and by biomechanical modeling, one might show why 5 fingers per hand is a partcularly efficient construction. Snowflake shapes - one could examine ice crystal formation to explain how ice crystals are able to form under certain conditions. Obviously, random molecular motion and configurations still have substantial effects on the exact final configuration of any given snowflake in a statistical sampling of snowflakes. (Again, get yourself a physics textbook - statistical mechanics and thermodynamics do have something to offer in understanding these kinds of systems). And the matter-antimatter question I won't even address since it involves possible symmetry breaking discussion which I am simply not qualfied to have, but suffice it to say that the discovery of CPT symmetry breaking has led to at least one or two Nobel prizes in the last 40 years. Thank god those scientists didn't accept your explanation that it's "just cause, and don't bother asking".

          • Actually, none of these is an example of the anthropic principle. The anthropic principle is kind of a reverse causality; it says that X is true because if it were false, intelligent life in the universe (or on Earth, or in South Boston, or whatever your reference frame may be) could not exist. The fact that intelligent life does exist in that reference frame necessarily dictates (post hoc) that X be true.

            For example, one might ask the question, "Why is gravity not an inverse cube relation instead of an inverse square relation?" Application of the weak anthropic principle would result in the conclusion that a universe in which gravity works along the inverse cube would be unable to support intelligent life, so if that were the case there would be no beings around to observe the fact. The fact that we are here making observations about gravity necessarily means-- though purely in an after-the-fact kind of way-- that gravity couldn't have acted along the inverse cube.

            The question of particle decay can't be addressed by the anthropic principle. Whether the particle decayed today or yesterday would have no bearing on the existence of intelligent life in the universe, so it could have gone either way. We don't know why it happened yesterday and not today, but there's no evidence that it had to happen one way or the other.

            The one about snowflakes actually has an answer. The structure of a snowflake is governed by its environment: air currents, particulate matter, instantaneous pressure and temperature on the microscopic scale: all of these things affect crystal formation. A snowflake looks just that way because of the sum of all the forces acting on it during its formation. Again, the anthropic principle doesn't apply.

            As to why we have 10 fingers, the answer is even simpler: we have 10 fingers because our ancestors had 10 fingers, and they managed to live long enough to pass on their genes to us. If some outside force had made life hard for the 10-fingered among them, then some other group with a different number of fingers would have been better able to pass their genes on to their offspring, and as a result we'd have a different number of fingers today. It is, in fact, entirely possible that this may have happened at some point in the distant past, although I don't think the fossil record has anything to say on the subject.

            The anthropic principle doesn't apply here because if having 10 fingers had been a liability in the past, there would still be somebody here to have this discussion. Having 10 fingers is not, as far as we know, a necessity for the existence of intelligent life.

            Really, the weak anthropic principle by itself isn't terribly insightful. If you combine it with Everett's work in branching time and parallel universes, though, it starts to make a sort of sense. See, there is a universe out there for every possible state. There's a universe where gravity is an inverse cube relation. There's a universe where there is no gravity at all. There's a universe where gravity repels rather than attracts. The question arises, then, as to why we're in this universe and not any of those. The weak anthropic principle says that we exist in this universe because none of those other universes could have developed intelligent life. They're all possible in the absolute sense, but it's not possible for us to exist in them, so from our frame of reference, they're impossible.

            Ultimately, this is navel-gazing. But it's entertaining navel-gazing.
            • thanks for your intelligent reply. you make a good point, i will revise my definition of the anthropic principle.
            • I must add one thing though Twirlip,

              As to why we have 10 fingers, the answer is even simpler: we have 10 fingers because our ancestors had 10 fingers

              This comes back to what we were discussing earlier with Fnkmaster, you are here answering the 'how' it came to be that we have 10 fingers. Not the 'why'.

              The difference is subtle, but it's there... a chain of events may explain the current state of the world, but it doesn't add 'meaning' to it... or as I was saying earlier 'intent'. Intent comes with conscious being with wills (like humans - or gods). And that's what I came to realize (and what Fnkmaster too, it seems) over the years, that asking the question is a very human trait, and the answer only lies in the realm of humaness... not the absolute.

              Very entertaining indeed.

              • Exactly. I think this says it best: no known proces in the universe is goal driven; so why should life be goal driven?

                This you should take to mean as much as "there is no meaning to life unless you make that meaning", not 'life is meaningless, go kill yourself' :)

                Well, I hope you get what I mean...xmas eve has scrambled my usual elucidating self :p
          • Gentelmen, the blade of the grim reaper (/. archiver) approaches...

            And as I search for something witty to adjourn this nice discussion, my brain pulls a blank on this christmas morning, at 3.45 in the AM.

            So I leave the wit to others, and paste you this quote:

            There are worlds out there where the sky is burning, and the sea's asleep, and the rivers dream. People made of smoke and cities made of song. Somewhere there's danger, somewhere there's injustice, somewhere else the tea is getting cold.

          • Actually, one answer to the question "why do we have 10 fingers" is because nature is fractal. We have a body with 5 apendages (1 head, 2legs, 2 arms). On those appendages, we have 5 sub apendages: 5 fingers :)

            Of course, then you end up with why 5 nd not 4, but hey, you can't have it all :)

            And as an aside, I'd say that the antropomorphic principle should be applied more...reason being, we do exist. Therefore, the universe in which we exist is one which allows for us to exist (anything else, and we wouldn't be here to aks stupid questions :) ). Which means we CAN answer some questions about the universe with answers wich relate (somehow) to us, because if we couldn't, we wouldn't be here in the first place :)

        • e? (Score:2)

          by autopr0n ( 534291 )
          Isn't e just a 'convenience' number? I mean, since int(x^e) = x^e, while x^[other numbers] are a bitch to calculate. So, we throw e into all types of exponential equations just to make them easy to integrate/differentiate?

          • Re:e? (Score:2)

            by pVoid ( 607584 )
            Did you know there is a relatively simple equation that relates e to pi?

            I'd have to dig it up, don't make me... I'm lazy... but it's a rather simple integral...

            I think the integral of f(x)=e^(x^2) over (-inf;+inf)... Or something. I'm too lazy.

            The point is there are numbers that have definite 'speciality' in the world (of math).

          • The beauty of it is that, yes, that is in fact one place where e pops up. But it's not the only place where e pops up. I mean, perhaps you can connect all the other problems where e arises to its role in integration, but I'm not sure - and it arises in areas such as continuous compounding of interest, the formula that relates the sine and cosine functions to e, which leads to the strange, almost mystical relation e^(i*pi)+1 = 0. You can find more historical depth on e in places like this [st-and.ac.uk].


            Anyway, I think my point is that calling it a convenience number seems to trivialize it, though of course the relation you describe is one of the several true basic statements you can make about e, it's definitely not the only one.


            Also, your site, autopr0n.com, rocks. I just wanted to take this brief offtopic chance to thank you and the autopr0n mods for giving the world good, fresh TGP links, and the new rating system rocks. I always refer friends to your site.

            • The reason e pops up while doing compound intrest stuff is because it's an exponential integral. The money you've made is n*i^t, where n and i are constants. So obviously the integral would have e in it, otherwise it would be a bitch to find :P.

              the e^(ipi) thing is a result of e^(ix) = sin x + cos x or something, so you end up with sin(pi)+cos(pi). Or something. Not really that special, IMO.
      • Well, we have 10 fingers because all vertebre(sp?) have them. Otoh, some early animals had more and less then 5 apendages, but 5 fingers is what we 'stablized' too, so obviously there is some kind of reason.
        • Well, according to Stephen J Gould, the answer here is as simple as "because!". And I subscribe to his point of view; if evolution where run again (as in rewound and played back), we'd probably not even be here. Or if vertabrates did manage to produce human being again, we might have 3, or 6 appendages. Evolution is nothing more than the fosilisation (as in the realisation of the actual) of random chance. That's because evolution is a name we've given to a process entailing the random combination of chromosomes...the combination giving us more brain mass also happened to have the combination for having 5 and not 4 fingers. Play the whole thing out again, and it might combine differently...hell, brains might not hold up as well as brawn, and in the next go we'd not make it as we got out skulls bashed in.

          Screw this, I shouldn't be allowed to post on the night after xmas eve...just go read Gould and you'll get what I mean :)
    • Nature has a lot of adaptations but no reasons.

      At least if you take the secular view. :)

      Ten fingers is hardly the only solution on our planet, others have been "tried" and perhaps will be tried. Hemingway's 6-toed cats are a famous example that breed true, and humans occasionally are born with an extra digit or two. Some mammals like horses fuse five fingers into one, or another number. Our ancestors may have had more. Try this PBS article [pbs.org] on evolution of digits.

      We have 10 fingers and base-10 math. Fingers are also called digits Hmm. What significance would a different base have had on us?

      I fall into the "why do we have..." trap myself. There are no whys exactly, just some way that something is well adapted and selected-for or not; and even that is a gross oversimplification.

      By the way, here we have 5 bases (only 4 used at a time), not the 20 (?) amino acids used in protein biosynthesis.
    • Four bases may be a good engineering compromise: they give you more "storage density" than two bases, but are less susceptible to mismatches and require less machinery to maintain than six or more.

      Pentadactyly (having five fingers) probably evolved somewhere in our early amphibian ancestors, for reasons that have nothing to do with us. However, it seems to work reasonably well for many animals, and those that have different requirements (hooves, wings, etc.) have modified how fingers are used.

      In general, biology probably makes many of the same engineering compromises we see in man-made systems. And as in man-made systems, biology often has to live with something that was a good idea long ago, designed under constraints that no longer apply. And often, designs are kept because they basically work and aren't causing any major problems.

    • well techincally the 6 finger gene is dominant, it's just that for whatever reason, 5 fingers have an evolutionary advantage in either survival, or mating. i'm sure there's a 4 finger gene, and maybe even a 3 finger gene, but for whatever reason, be it picking fruit or killing prey, it didn't work out that well.

      of course, there's the possibility that it has to do with cellular growth patterns, and if that's the case, you might want to check out this phenomenon [nasa.gov].

  • Morse has more than two symbols (Score:3, Interesting)

    by Bruce Perens ( 3872 ) <bruce@perens.com> on Tuesday December 24, 2002 @07:55PM (#4955006) Homepage Journal
    Morse uses a logic on-off combined with time to generate more than two symbols. The symbols are:
    Dot (short on)

    Dash (on for length of three dots)
    Character-internal Space (off for length of dot)
    Inter-character space (off for length of dash)
    Long space (length of several dashes, I think)

    There is also something called swing that is a function of time parameter changes in hand keying and can itself convey contextual information like emotion.

    Bruce

    • Sorry Bruce, but Morse Code has only two symbols. ON and OFF. Symbols have a very precise meaning in communications theory -- a symbol is a communications element [state of the wire] that exists at a particular position [time] in a communications stream.

      Increasing the number of symbols used is a popular way to increase the information flow of a spped-limited channel. Modems went above 2400 baud (symbols per second) mostly by increasing the symbol constellation. 56kbps is 15 bits per symbol at only 3750 Hz.

      Even given the need for timing synchronization, Morse Code isn't every efficient even with it's primative compression.

      • Let's be careful to separate Morse code from the data link below it. You are talking about the data link of the radio telegraph, one layer down in the stack. Your answer is correct for figuring out modulation and bandwidth.

        Morse is a code that is overlaid on that data link, and has its own symbols that can be expressed as strings of data link on or off bits, only approximately, because Morse is not a clocked code. How many data link one bits there are to a dot has to do with the ratio of a dot length that the operator is sending at that moment (remember he's hand-keying) to the time constant of the key-ckick filter.

        Bruce

        • Typo alert: that's key-click filter.

          I found a reference that claims a dot is a Baud. I don't agree. Using the recommended time constant for the key-click filter, I think a dot fits in two Baud. But note that the key-click filter is generally set too fast - the manufacturer doesn't know what top speed the operator might have, and thus most operators send a dot of more than two Bauds in length.

          Bruce

      • Symbols arn't in time, they are indexed in a string. You simply can't encode morse with just ones and zeros, unless you use unary to represent the time. You might as well just enumrate the thing and use unary to denote the number and claim that morse code is unary. You could also say morse code uses symbols based on the spelling of the terms 'dotditditdotdotdots1dots2dits3' etc, and claim it had 8 symbols. Either way would be idiotic.

  • Actually (Score:3, Interesting)

    by Spyffe ( 32976 ) on Tuesday December 24, 2002 @07:58PM (#4955019) Homepage
    It doesn't matter what base you're writing your DNA code in (base-4, base-2, you name it). What's difficult is creating the ribosomes that will actually do the DNA-protein conversion. If you can do that, you're in business.
    Otherwise, it's useful as a theoretical tool but not much else. Still, a synthesis of computers and biological systems just got a little closer. Here's hoping for cyborgs by 2020!
    • Tt's a binary DNA system, not a binary electrical system. Analog computer accessories such as audio-tape drives on the C64/C128/AppleII/IBMXT/etc worked because of the ability or read/write the medium directly. Reading/Writing DNA would help make people that coould interface with computers; but wouldn't be necessary in the actual cyborg.

      Nervous systems 'evolve' inside the actual organism and are not completely planned in advance by DNA. Some sort or AI code would be necessary in the cybernetic hardware to adapt ittself to the user's nervous system. Until we can make something like that, reliable cybernetics will never be producable.

  • Won't fit in my sig (Score:3, Funny)

    by gymbrall ( 585532 ) <gymbrall.gmail@com> on Tuesday December 24, 2002 @07:59PM (#4955025)
    Screw the geek code [geekcode.com] I'm putting my genetic code in my sig.
    Now all I need is a cloning program that reads from standard input.
    (before anyone suggests it, I know sex works, but I'm a geek, what are my odds... ;)
  • Like Morse or binary code, it has only two letters

    Neither Morse or binary code have letters. Dots, dashes, ones and zeros but no vowels or constanants. Picky, picky.

    Merry Christmas...

  • Making the leap from Binary to Quaternary (Score:3, Insightful)

    by Grendol ( 583881 ) on Tuesday December 24, 2002 @08:03PM (#4955043)
    If the original genetic material was 'binary', this is going to create quite a debate on how the shift to 'quaternary' genetic material happened into being. Possible arguments are that two different systems of genetic material merged, It made the 'evolutionary step' (insert miracle or magic here). Other interesting debate will set up about what the benefits and detractors are with each 'File system'. What metabolic implications are there to the reproductive process if there is possibly an alternate genetic 'file system'. The metabolic implications could be a significant reason due to the fact that reproduction is such an energy consuming activity in almost all species that I know of. Maybe there were both a binary and a quaternary system around and due to energy/metabolic needs one died out. Some other interesting issues would be error correcting properties of a genetic file system. Some quaternary DNA is fairly robust I have been told. Capable of replacing missing bits. Which could be handy in the mitosis process which could be frought with errors due to environmental factors such as cell chemistry, viral issues, radiation, cell wall capabilities and strengths, etc. It will be interesting to follow up on the Binary related implications and their quaternary comparisons.
    • Since the two types of base pairs can be mixed, It dosn't really seem like it would pose that much of a question. In fact, the DU pairs, IIRC are compatable with AT pairs.
  • PU

    &

    BO

    Nothing like getting that grody feeling after sitting infront of that comp for days. :)

    Merry X-Mas
  • I wonder at what point the random processes of in vitro evolution in the lab's chemical soups would constitute something that could be called life, using a minimalist interpretation of the term? As soon as any form of self-replication is achieved? It will already have environmentally-directed behaviour after all, thanks to catalysis.

    And would a 2-base minimalist "lifeform" have to be regarded as necessarily alien by 4-base life? :-)
  • Four letter combinations save considerable space, I believe you can store 2 times more information with a four letter system than with a binary system. Also I think some of the error checking "code" could be more easily implimented with the four letter sequences than with the two letter sequences. Something about some letters not matching up beside each other. Which could also be important when the genes from two entities combine (ie. reproduction). Just a few hunches of mine, no scientific data to back me up.
    • IIRC, error checking codes need to be based on a prime field(a field with a prime number of elements). Thus 4 is a no go.
      • No, that's false. You can build many kinds of error correcting codes. The ones based on prime fields just happen to have some properties that some people find algorithmically or theoretically appealing.

        Error correction in genetic codes is very ad-hoc because errors, codes, and correction are all done by molecules with idiosyncratic properties.

  • I first read about the concept of this language in Wired 10.12 [wired.com]. They go on in the article talking about how all life is information and how all living matter computes in some way or another.

  • DNA of Famous People (Score:5, Funny)

    by Jugalator ( 259273 ) on Tuesday December 24, 2002 @08:41PM (#4955166) Journal
    Normal human
    A, T, G, C.

    Bill Gates
    A, B, C, D, E, F, G, ... oh, you get the picture.

    Linus Torvalds
    A and T only, since G can be encoded with an AT pair and C with TA. Consequently, G and C are redundant if we allow a special escape character between the codes, such as A|T|AT|TA. Thereby, we save one code since only three would be required in total.

    Average /.-er
    1 and 0.

    Average /. Editor
    A, A, T, T, G, G, C and C.

    Ellen Feiss
    0.

    The people of SOVIET RUSSIA
    C, G, T and A.

    Hilary Rosen
    D, M, C and A.
  • I think the reason we evolved using a system of four possible base-pairs was to conserve space on the genome and pack more information along a shorter distance.

    Right now, it takes only three base-pairs along a strand of RNA to code for the next amino acid in the protein chain being constructed. If there were only two possible combinations for base-pairs, then it would take six of them to code for that amino acid. The transfer RNA would have to match up to 6 positions, not three, and there would be that much more room for error.

    In addition, if there is a mismatch in base-pairs between the mRNA and tRNA, the difference in attraction between two and three bonds is greater than the difference between five and six bonds, and it would be more difficult to build a ribosome that could reliably construct proteins.
  • They've managed to create some simple RNA-like code sequences using only two codes. Hence it's a string of bits.

    Short RNA sequences have recently been the focus of interest as a potential control mechanism for gene expression (Science Magazine's Highlight Of 2002 [slashdot.org]).

    Does this mean that our DNA is being run on a binary RNA VM, and that the Turing test was met before it was described?

  • Time for "expert" editors at Slashdot? (Score:3, Insightful)

    by immerrath ( 607098 ) on Tuesday December 24, 2002 @09:38PM (#4955306)
    This is the second time in the past week I've winced after reading the title of a story here at Slashdot. The first, of course, was the story [slashdot.org] about Science choosing small RNAs as their story of the year. I'm a biologist, and both of these stories are so obviously written by people who didnt understand them, that it is embarassing to read them. Atleast thats how it seemed to me. Slashdot is mostly a computer geek hangout, and so the stories have to placed in geek-terms, I guess, but they dont have to be WRONG and OVER-simplified! A lot of the comments are factually incorrect too. What I'm getting at is a proposal: Appoint Slashdotters who are qualified in various fields: Biology, Physics and other specialized areas to edit stories about those topics, and decide whether a story is worth posting. This story for example, is not Slashdot-news-worthy in the least, and biologists here will agree -- its more a cool technical result than "binary DNA"; sheesh!
    • Mod parent up. The only problem I can see in this proposal is appointing gurus for computer-related fields, since we're all experts here ;-)
    • The Slashdot editors are addicted to their own power, and seem to have zero interest in accuracy or professionalism. There are obviously slashdotters who are far more knowledgeable in their fields (including CS and CE) who would love to be editors, but aren't given the opportunity. Rather we get lots of dupes and bogus stories being posted.

      But, you can take the sorce, or better yet scoop [kuro5hin.org] (the software that runs kuro5hin) and make your own site. In fact, I think some bio/sci people have done so, although I don't know about any off the top of my head.

  • Something even cooler about DNA (Score:4, Informative)

    by frenchs ( 42465 ) on Tuesday December 24, 2002 @10:04PM (#4955394) Homepage
    Ya ya, who cares. I'm a biology minor, and computer science major, and this article wasn't particullarly interesting to me even. ;)

    You wanna see something cool... how about DNA having a parity bit?? Take a peek....
    http://www.academicpress.com/inscight/09112002/gra phb.htm [academicpress.com]

    • And another something else also cool... (Score:4, Interesting)

      by Guppy ( 12314 ) on Tuesday December 24, 2002 @11:09PM (#4955546)
      "You wanna see something cool... how about DNA having a parity bit?? Take a peek...."

      Here's another something else interesting -- the equivalent of a DNA RAID Array, found in the microbe Deinococcus radiodurans. This particular bacterium has the distinction of being the most radiation-resistant organism known.

      D. radiodurans posses four copies of its circular chromosome, stacked together like a roll of Lifesavers. This alignment allows for fast and efficient repair of any errors.

  • What is the advantage in having a 4x3 language for DNA (4 bases * 3 bases/aminoacids)? Why is the code for some aminoacids redundant, but not for others? (Are the first ones more important?)

    Also, does DNA have any error-checking built into it?
  • Because in Nature there are four bases not two.

    I don't think Nature would use four anything where two will suffice. The sexes are an example.

    Disclaimer - I'm not a geneticist and only a lame Computer Scientist. I could be, and probably am, totally wrong.

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