
DNA Goes Binary 196
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."
Pernutation City (Score:2, Interesting)
I vote... (Score:3, Informative)
I'll be taking a look at Pernutation City. Thanks for the sugestion...
Re:Pernutation City (Score:2)
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.
Re:Pernutation City (Score:2)
http://www.boat-people.org [boat-people.org]
Didn't Church-Turing beat them to this? (Score:2, Interesting)
But... (Score:1)
thats what my bio teacher said, i think...
And.. (Score:2)
Re:But... Look at the YiJing (Score:3, Informative)
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.
Sortof, but that's not the point. (Score:2)
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).
Big deal... (Score:1)
And with binary, I can construct GCTA... and anything else as well.
This post brought to you by the numbers 1 and 0.
Does Morse not have three codes? (Score:2, Interesting)
TWW
Re:Does Morse not have three codes? (Score:2)
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.
Re:Does Morse not have three codes? (Score:2)
Bruce
Re:Does Morse not have three codes? (Score:2)
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)
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)
I'm Not Convinced (Score:4, Interesting)
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.
Re:I'm Not Convinced (Score:3, Insightful)
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)
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)
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.
Re:Not exactly. (Score:3, Insightful)
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.
Binary computers? How long before base4 computers? (Score:1, Offtopic)
This might be a "stepping stone" between traditional and quantum computing, or it might just be a posible avenue of progression never taken.
Re:Binary computers? How long before base4 compute (Score:1)
Re:Binary computers? How long before base4 compute (Score:1, Interesting)
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)
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.
Re:Binary computers? How long before base4 compute (Score:2)
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.
Re:Binary computers? How long before base4 compute (Score:2)
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.
Re:Binary computers? How long before base4 compute (Score:3, Interesting)
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.
Re:Binary computers? How long before base4 compute (Score:2)
Well, there's no reason you couldn't use a fixed-point fraction system for encoding floats, in which case the value would be exactly 0000000100000011, that is to say 1/3, using 8 bit components. You would just need to make adders/subtractors that worked with this format.
Re:Binary computers? How long before base4 compute (Score:2)
> 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".
Re:Binary computers? How long before base4 compute (Score:3, Informative)
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.
think about this: (Score:2)
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.
Re:think about this: (Score:2)
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.
Re:think about this: (Score:2)
Re:Binary computers? How long before base4 compute (Score:2)
Why 4 bases? (Score:2)
* "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)
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)
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.
Re:Why 4 bases? (Score:2)
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_.
Re:Why 4 bases? (Score:2)
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.
Re:Why 4 bases? (Score:2)
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.
bleh... (Score:2)
rational thinking and "why" (Score:2)
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.
Re:rational thinking and "why" (Score:2)
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.
Re:rational thinking and "why" (Score:2)
My world isn't nearly as empty as you might think it is... and all these opinions I have arrived to took years and years of cogitation while engaged in Physics/Math academia.
You should read a philosophy book or two, and maybe a book on logic.
True (1=1) , False (1=0)
To the question, "What is the truth?", there is therefor one single answer, or an inifinity: "The truth is 1=1".
Truth is determined by a predicate (in math). It assigns a 'value' to a statement. T("1=2") = false. If you do a bit of advanced math, quickly you will start seeing that "1=2" *IS* 0=1 *IS* false. Everything in math is the *same*. There is nothing generated apart from the 16 axioms of Real theory (or whatever theory you're using). Everything you do, including integrating fibonachi series, or whatever tickles you, IS those 16 axioms...
And in the same way, everything you do in physics derives from not axioms, but principles - postulates. The three tenets of thermodynamics for example. Everything in the world *is* those three tenets. If that is the truth you seek, I wonder how deep and real your world is.
I can already see you stirring in your chair thinking about the pretty little sun spots, and thinking how you learned in your physics class 101 how you can estimate the surface temp and luminosity of the sun by deriving from thermodynamics and what not... Good for you. You have not answered the Truth.
I will not try to argue anything with you, because this sort of realization takes years to come to, or for some, all of their lives, (you should actually read a bit of the discussion we were having on this thread with FnkMaster) but don't be fooled my friend that science 'generates' any truth. The truth of science is only observation. Existance or non existance. If a scientific formula generates 'a truth', and it doesn't fit observation, you revise the formula, not the world.
And really, as soon as you start asking questions which aren't 'a matter of fact', you are outside of the realm of truth/falshood that science has to offer you.
Don't get me wrong, science is a very powerful tool indeed. It's the ultimate use of one mankind's most cherished tools (logic/reasoning), but you're a fool if you think it answers any *real* question.
You quote Orwell, I quote Sartre: "When you have no character, all you can resort to is methodology" (it's from "La Nausee")... Be sure you never lose touch with your humanity by abandoning it to the methodology of science.
Re:rational thinking and "why" (Score:2)
It was further 'concluded' between me and said party that 'we' no longer had 'faith' in science to answer these said questions.
I never said science was a failing decadence... The only thing I did say, is that science won't answer certain questions, and people who believe they do are very very deeply deluding themselves. If you want a more explicit rehash: I said Science doesn't tell you the 'Truth' (truth in almost the religious sense, even though I'm quite convinced there is no god), ie. Science does not answer the question "why" (please read parent posts, I'm not going to re-elaborate)...
In you come with your banner of Philosophia Paternis. Of course I'm going to react the way I did...
You haven't added anything new to the discussion, and you've made me post two long replies. Did you read the parent thread?
The bottom line is this:
This makes them worth exploring, IMHO
I am quite happy for you. And in no way am I saying you shouldn't be doing what you are doing. However, don't delude yourself by saying you are answering the question "why". You aren't. Now, does that make you anything less than what you are? No.
End of discussion.
PS. Both Fnkmaster and I have relatively elaborate academic backgrounds in physics and math. Don't go picturing yourself a hick or some white trash troll somewhere in a basement.
Re:Why 4 bases? (Score:2)
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.
Re:Why 4 bases? (Score:2)
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".
Re:Why 4 bases? (Score:3, Informative)
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.
Re:Why 4 bases? (Score:2)
Re:Why 4 bases? (Score:2)
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.
Re:Why 4 bases? (Score:2)
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
Re:Why 4 bases? (Score:2)
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.
Re:Why 4 bases? (Score:2)
Re:Why 4 bases? (Score:2)
It's from Doctor Who. Google will help you on that.
Re:Why 4 bases? (Score:2)
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
e? (Score:2)
Re:e? (Score:2)
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).
Re:e? (Score:2)
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.
Intrest is an integral. (Score:2)
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.
10 fingers (Score:2)
Re:10 fingers (Score:2)
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
Reasons for fingers? (Score:2)
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.
Octal on The Simpsons (Score:2)
Fingers are also called digits Hmm. What significance would a different base have had on us?
A different base... Doesn't TV's The Simpsons make occasional octal jokes ("gimme four") about its characters, which lack pinky fingers?
Re:Octal on The Simpsons (Score:2)
Someone has enumerated Simpsons finger jokes. [snpp.com]
Supposedly the Simpsons God [tvtome.com] had five fingers.
Re:Why 4 bases? (Score:2)
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.
Re:Why 4 bases? (Score:2)
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)
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
No, Morse has only two symbols (Score:2)
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.
I think you're one level too low (Score:3, Interesting)
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 (Score:2)
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
Um, no... (Score:2)
Re:Morse has more than two symbols (Score:2)
Farnsworth is a deliberate distortion of the code timing that indeed helps one avoid the dreaded 10 WPM plateau. It sounds funny if you haven't been there, but dreaded is the right word. The problem is that below 10 WPM, you can think of code as dots and dashes. Above 10 WPM, you can't separate them in your head quickly enough to copy continuous code. You have to learn the sound, which is really forcing the recognition of the code into a different part of your brain. This forcing takes a good deal of discipline. I think it took me 60 days of copying the daily news for half an hour each morning and evening to get to be able to pass the 20 WPM test... barely. I could copy solid at 13 WPM, and at 20 I just wrote down all of the words after "is" and those were the test answers. I think ARRL actually made the test harder after I published how I passed it :-)
Be sure to visit nocode.org [nocode.org], code's fine on the air - let's just get it off that test!
K6BP
Actually (Score:3, Interesting)
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!
not really (Score:2)
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.
Comment removed (Score:3, Funny)
Two letters? (Score:1)
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)
Not really (Score:2)
Whats the most common /. DNA Type? (Score:1, Troll)
&
BO
Nothing like getting that grody feeling after sitting infront of that comp for days.
Merry X-Mas
Convergence of protein chemistry and A-life :-) (Score:2)
And would a 2-base minimalist "lifeform" have to be regarded as necessarily alien by 4-base life?
Space Considerations (Score:2)
Re:Space Considerations (Score:1)
Re:Space Considerations (Score:2)
Error correction in genetic codes is very ad-hoc because errors, codes, and correction are all done by molecules with idiosyncratic properties.
Re:Space Considerations (Score:2)
Similar to the Wired article.... (Score:2, Informative)
DNA of Famous People (Score:5, Funny)
A, T, G, C.
Bill Gates
A, B, C, D, E, F, G,
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
1 and 0.
Average
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.
Re: (Score:2)
space efficiency (Score:2)
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.
let me see if i understand... (Score:2)
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)
Re:Time for "expert" editors at Slashdot? (Score:2)
Its been that time for a long time, and it won't.. (Score:2)
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.
my resoning is thus: (Score:2)
There are lots of people who would do it, even for free. but whatever.
Slashdot has a lot of potential, but it's all wasted by the moron editors.
Something even cooler about DNA (Score:4, Informative)
You wanna see something cool... how about DNA having a parity bit?? Take a peek....
http://www.academicpress.com/inscight/09112002/gr
And another something else also cool... (Score:4, Interesting)
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.
Does anybody know... (Score:2)
Also, does DNA have any error-checking built into it?
I am disinclined to believe in this (Score:2)
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.
Re:what about GTCA? - RTFA (Score:2)
Re:what about GTCA? - RTFA (Score:1)