DNA Goes Binary

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."

Comments

what about GTCA?

[Anonymous Coward]

isint 4 letters simple? why go two?

first 10 posts at least? ;p

Pernutation City

[lisle]

Ever read it? By Greg Egan, THE most imaginative SF author ever

Re:Pernutation City

[shess]

"Permutation City", right?

I'll admit he's imaginative, but every book of his I've read started out good throught he first half, then ... lost it. Basically, they stopped making sense. All the sentences were made up of correct words, but the plotlines ceased to relate to each other or earlier plotlines. Maybe it's that he's feeding a line that's just too sophisticated for me, but I'm fairly well-read, so I doubt that.

My personal suspicion is that he needs a good editor. A lot of current science fiction needs a good editor. Not only to catch little stupidities (grammatical problems, mixing up a name, etc), but also larger issues, like indicating which plotlines just aren't pulling the book forward, or which characters are too shallow, whatever. But just as CEOs write their own email nowadays, authors seem to handle their editting in-house...

Later,
scott

Re:Pernutation City

[Vryl]

'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.

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

[Vryl]

hrrrm ...

http://www.boat-people.org

Didn't Church-Turing beat them to this?

[Strike]

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)

Re:Didn't Church-Turing beat them to this?

[Anonymous Coward]

Hooray for metamoderators on crack modding an unrated post as "overrated" before anyone even had a chance to look at it.

Re:Didn't Church-Turing beat them to this?

[Anonymous Coward]

Sounds like it should say that researchers created a 1-bit DNA to contrast our traditional 2-bit implementation. ;)

Neat trick to guess what the building blocks might have been, long after they have been out-competed into oblivion. Makes me wonder if a higher-order-bit DNA is yet to evolve--or perhaps they have but turned out to be less competitive than good-'ol 2-bit.

Re:Didn't Church-Turing beat them to this?

[p3d0]

Man, you don't even have a rudimentary understanding of this, do you?

Hint: it's not computer science. It's biology.

But...

[unterderbrucke]

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

Re:But...

[Anonymous Coward]

Coming soon, the motion picture: DUUD, Where's My GATTACA?, starring Ethan Hawke and Ashton Kutcher.

Big deal...

[dietlein]

... 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.

Re:Big deal...

[Anonymous Coward]

Okay, smartass, what proteins can you make? Make me a gram, right now!

Re:Big deal...

[Anonymous Coward]

This post brought to you by the numbers 1 and 0.

Okay, sorry buddy, but you gotta pay up now: Microsoft Patents Ones, Zeroes

Does Morse not have three codes?

[nagora]

How is a space represented in Morse? I thought the codes were "dot", "dash" and "pause".

TWW

Re:Does Morse not have three codes?

[pVoid]

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.

Re:Does Morse not have three codes?

[Bruce Perens]

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

Bruce

Re:Does Morse not have three codes?

[pete-classic]

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.

Re:Does Morse not have three codes?

[pVoid]

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.

Comment removed

[account_deleted]

Comment removed based on user account deletion

Not exactly.

[The Monster]

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.

[Ieshan]

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.

Re:Not exactly.

[MillionthMonkey]

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. :)

Binary computers? How long before base4 computers?

[SHEENmaster]

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.

Why 4 bases?

[UnknownSoldier]

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?

[pVoid]

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?

[Fnkmaster]

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. :)

Re:Why 4 bases?

[pVoid]

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_.

Re:Why 4 bases?

[g4dget]

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.

Re:Why 4 bases?

[joe_bruin]

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.

Re:Why 4 bases?

[Fnkmaster]

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".

Re:Why 4 bases?

[Fnkmaster]

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.

Re:Why 4 bases?

[Hadlock]

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.

Re:Why 4 bases?

[pVoid]

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.

Re:Why 4 bases?

[Twirlip of the Mists]

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.

Re:Why 4 bases?

[joe_bruin]

thanks for your intelligent reply. you make a good point, i will revise my definition of the anthropic principle.

Re:Why 4 bases?

[pVoid]

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.

Re:Why 4 bases?

[pVoid]

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.

Re:Why 4 bases?

[Anonymous Coward]

Actually anthropic principle is basically *all* selection biases we humans have *because we are who we are*, not just those about intelligent life. Only some of this biases are not worthy of uber-c00l names like "anthropic principle" and just called self-selection bias. The problem is, it is not clear at all which ones qualify for anthropic principle name. I wish Hawking made the distinction -if there is any- between the two when he chose to popularize the statement.

Re:Why 4 bases?

[Mac Degger]

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 :)

Re:Why 4 bases?

[Mac Degger]

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

Re:Why 4 bases?

[Mac Degger]

Now that's a nice quote! Bit of Kubla Kahn mixed in with a dash of Douglas Adams (just got The Salmon of Doubt :) ). Would you care to tell us who the quotee is?

Re:Why 4 bases?

[Anonymous Coward]

...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".

That would be Pascal. And you misquoted, it is actually more like "even if there isn't a god, it is in my best interest to act as if there is." His idea was that even if there isn't a god, you have nothing to lose by believing. But if there is a god, and you don't believe, then you're screwed.

So you believe, just in case.

Re:Why 4 bases?

[pVoid]

Ahh, sorry, I frogot...

It's from Doctor Who. Google will help you on that.

Re:what about GTCA? - RTFA

[pVoid]

But these [four] bases aren't easy to make from the chemical constituents of the early Earth, point out Reader and Joyce.

Morse has more than two symbols

[Bruce Perens]

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

Re:Morse has more than two symbols

[GigsVT]

As someone with a basic knowledge in CW (enough to pass the FCC test for general class at least, which isn't saying much these days), I'd say your description is kinda off.

Those rules might make valid enough code to read, but there are a lot more things going into it than that, especially at high speeds. A lot of people do farnsworth these days, especially when starting out, which means the character rates are going to be a lot higher than the overall symbol rate. Basically, very fast symbols with longish spaces inbetween. Anyone who learns at true very low speeds is just screwing themselves over later, so most people learn at a minimum 13wpm character rate with 5wpm spacing.

Re:Morse has more than two symbols

[Bruce Perens]

Yes, I trained with Farnsworth, with characters at around 28 WPM and with word spacing appropriate to my copying speed at the time. I got my Extra from the ARRL VECs operating at Travis California, around 1993, and then put away the key :-)

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, code's fine on the air - let's just get it off that test!

K6BP

Re:Morse has more than two symbols

[GigsVT]

Heh, that's how I passed the 5wpm, just made sure to copy everything after IS well enough to figure out which multiple choice fit. They've done away with multiple choice now, so it is a little more difficult. I didn't learn enough to be comfortable operating on the air, and now that it's been a few years without practice, I doubt I could even copy much of anything anymore.

I didn't know you were a ham, that's pretty cool. I signed up for the nocode.org but I won't be able to contribute right now, money is tight. I do agree that morse is an artificial barrier to entry that has little to do with "advancing radio technology".

If you get a chance, stop by #electronics or #hamradio on irc.freenode.net.

Re:what about GTCA? - RTFA

[Superfarstucker]

so does this mean i can turn people off !!! 0 you batard 0!! LoL

Actually

[Spyffe]

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!

Won't fit in my sig

[gymbrall]

Screw the geek code 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... ;)

Forgot the Last Stage

[jimmyCarter]

1. Simplify the language of life
2. ???
3. Profit

Re:Forgot the Last Stage

[cryms0n]

In Soviet Russia, the language simplifies YOU.

Re:Binary computers? How long before base4 compute

[CableModemSniper]

At first glance, this post looks like a troll. However on second glance, one realizes the poster is just clueless.

Two letters?

[toupsie]

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...

Re:Binary computers? How long before base4 compute

[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?

Making the leap from Binary to Quaternary

[Grendol]

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.

Whats the most common /. DNA Type?

[Chris_Stankowitz]

PU

&

BO

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

Merry X-Mas

Re:Whats the most common /. DNA Type?

[Anonymous Coward]

Troll? ok, mabye its not that funny, but it not even close to trolling.

Reminds me ..

[Anonymous Coward]

..of the classic joke:

There are 10 kinds of people in this world;
those who understand binary, and those who don't

Convergence of protein chemistry and A-life :-)

[Morgaine]

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? :-)

not really

[SHEENmaster]

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.

Re:Binary computers? How long before base4 compute

[Jester99]

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.

Re:Binary computers? How long before base4 compute

[rebelcool]

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.

...can you

[Anonymous Coward]

liberate me ex inferis?

I vote...

[Eric_Cartman_South_P]

...for Jack Vance. Anyone ever read Demon Princes? Pure gold.

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

Shizzolate That Shit.

[Anonymous Coward]

Yeah, Boy-eeeee...

"Linus Torvalds": Absurd Liberal Myth

[Anonymous Coward]

It amazes me that so many reputable people and organisations have fallen for the ridiculous myth that there is some sort of Finnish student who has single-handedly created something that threatens to overthrow the current software distribution system as we know it. I find it particularly absurd that he is lauded as some sort of super overlord throughout hackerdom. Even generally reliable sources have fallen for this ridiculous scam. The concept that one youth from Central Europe could sow the seed for an operating system which frightens Microsoft is risible at best. It has taken Microsoft a decade to produce an OS which is even reasonably reliable and stands alone. So what makes you think that in the short time span from 1991 to the present day that a fictional character could produce an operating system which is more stable than Windows?

Obviously, this "Linus Torvalds" must be some sort of superhuman to have done such a thing. But we all know that there is no such thing as a superhuman. As such it must be plain for all to see that this "Linus Torvalds" is some sort of fabrication. It is the only way to explain why Linus keeps such a low profile, and that the main bit of evidence to even suggest his existence is the testimony of his mother and the strange posts "he" makes on obscure message boards. The fact that an entire community of "warez doods" has sprung up, proclaiming that "LUNIX RULEZZZ" is such a flimsy piece of evidence it must be discounted. But if "Linus Torvalds" does not actually exist, then who has conjured up his existence? There is only one possible person who could get away with such a fraud. Mikke Torvalds, "his" supposed birth parent.

Mrs. Torvalds may have a lot to say about her son, but this does not excuse the fact that he does not exist. When you consider this, is it genuinely surprising that she found him "easy to raise"? Of course, there is one immediate objection which will no doubt be raised. "If Linus Torvalds doesn't really exist," I hear you ask, "then who wrote Linux?" That is a good question, but it is very obvious to see who. If you take a look around here for a while, you will hear names like Alan Cox, Richard Stallman, and Eric Raymond being bandied about. Obviously, it is immensely skilled coders and hackers such as these people who have made the wonderful OS Linux what it is today. The person who first made that post on comp.os.minix was in fact Linus' mother, who, frustrated by the ludicrous restrictions imposed upon her by Minix, posted a message under a partial pseudonym, asking for help building a new operating system. All she wanted was someone to help her use her PC to print out her recipes, but before she knew it she was in way over her head. Pretty soon Linux had hit 1.0 and strangers like Tanenbaum were talking about and cussing it.

Fortunately, Mikke had released the kernel under the GPL from the start, so she was able to dump it onto the shoulders of other people without arousing too much suspicion. Now she only has to make periodic appearances on Usenet and the like to avoid arousing the interest of news-hungry geeks and ZDNet reporters. "But what about the conferences?" you cry. "We have photographic evidence!" Well, that isn't Linus. Are you sure you'd like me to tell you who it is? OK. The person whom you have all been worshipping for eleven years is in fact Richard Stallman, a man simultaneously venerated and vilified by the Slashdot community. When Linux started to become famous, Mikke knew that she was in deep water and that her hoax might be uncovered, so she decided to contact the most trustworthy man in the open source world. RMS was happy to cooperate, especially when he knew that Linux had completely overwhelmed the Hurd and that he might as well help; after all, if Linux was exposed as a giant falsification, mightn't his beloved GNU project be considered a hoax also? Neither could take the chance, and for that reason Stallman was perfectly happy to quickly purchase a cheap rubber mask and shave off some of his bodily hair.

Fast forward to 2002, and GNU/Linux is very stealthily taking over the server market. Mikke Torvalds' simple request has turned into a multi-million dollar industry, and Stallman's hobby and grand vision has actually begun to come to fruition. This is why, despite the fact that Linus Torvalds is actually a figment of our collective imagination, we should all honour him for being a prime symbol of our steadfast belief and ability to do what must be done. May his memory live on forever.

Re:"Linus Torvalds": Absurd Liberal Myth

[Anonymous Coward]

OK, I'm confused.
Finland is in Central Europe?
I thought that Finland was in Northern Europe.
I believe this to be a major flaw in your argument, which causes it to come crashing down like a 2002 stock market.

Space Considerations

[m0rph3us0]

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.

Re:Space Considerations

[D iz a n k Meister]

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.

Re:Space Considerations

[g4dget]

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.

Re:Space Considerations

[D iz a n k Meister]

I think to guarantee reception without retransmission of a word with less than x errors, you need a prime field.

Of course, one can check for errors in many different ways, and then ask for a retransmission, or discard the word.

Re:Space Considerations

[g4dget]

In short, no. There are many ways of constructing forward error correcting codes. Galois fields just happen to be one convenient way that generates codes that are useful for very specific channel models. And those channel models don't even apply for genetic information.

Re:Space Considerations

[Anonymous Coward]

Since the single parity check is GF(2), and DNA has been shown to use spc, you may want to reconsider.

Re:Space Considerations

[Anonymous Coward]

Since the single parity check is GF(2), and DNA has been shown to use spc, you may want to reconsider.

Is that what they teach engineers? Fact is, DNA does not use single parity check.

Reasons for fingers?

[MacAndrew]

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 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.

Re:Reasons for fingers?

[D iz a n k Meister]

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

Well, we have base-10 arithemetic. Thanks to rigorous analysis, topology, and modern, or abstract, algebra, math has been abstracted away from the arithemetic. Thus all calculations in any other base would be just as valid and possible. I don't think the *base* is of any real significance.

Re:Reasons for fingers?

[MacAndrew]

I don't know. I wasn't thinking about calculations so much as human nature preferring round numbers. If 10 were 12 then a decade would be longer -- kind of like a quart and a liter are treated the same, though one is larger. And socially -- if we had a different number of digits our obscene gestures would all be different.

Humorously, but I wonder.

Re:Binary computers? How long before base4 compute

[D iz a n k Meister]

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.

Similar to the Wired article....

[berniecase]

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

Octal on The Simpsons

[yerricde]

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

[StormcallerESC]

I'd be rather disappointed if ease of animation is nature's excuse too.

Re:Octal on The Simpsons

[MacAndrew]

Doonesbury's always had 5. And other serious strips.

Someone has enumerated Simpsons finger jokes.

Supposedly the Simpsons God had five fingers.

DNA of Famous People

[Jugalator]

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.

Re:DNA of Famous People

[shepd]

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

Order yours now! Call 1-800-ABCDEFG and have your credit card ready! (Kids, ask your parents for help before calling). Sorry, no Personal Cheques or CODs.

(For all those outside North America)

"Doh!"

[Anonymous Coward]

"Doh!" exlaims the bible thumper.

Darwin wins again.

Re:"Doh!"

[Anonymous Coward]

Now, that's uncalled for :-O :-)

space efficiency

[TheSHAD0W]

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.

And..

[redcliffe]

If C only links with G, and A with D, isn't it already Binary? Because there are two possible combinations.

Re:And..

[martyn s]

Well, an "A-T" pair is different than a "T-A" pair. The other strand is really there just for structural integrity.

decimal is evil...

[Anonymous Coward]

Stop using decimal. It is bad.

No, Morse has only two symbols

[redelm]

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.

Re:No, Morse has only two symbols

[Anonymous Coward]

well, yeah, any alphabet of symbols can be reduced to bits. this is obvious, the entire internet with it's richness of ASCII, Unicode, etc, is just high/low voltage levels on the wire.

in information theory the bits are a measure of how much information is present, not the number of symbols in the alphabet. that's a different level of abstraction.

Re:No, Morse has only two symbols

[Anonymous Coward]

Sorry redelm, but ASCII Code has only two symbols. ON and OFF.

... Hey, that applies equally well to any well-defined communications protocol that can be transmitted over a wire!

If you read a defintion of Morse Code, it will mention 2 specific symbols, dot and dash, and at least one kind of "pause" symbol is implicit. An elementary homework assignment in communication theory is re-encode a language to transmit the same set of messages using fewer symbols and longer strings. That's what you were just doing.

Re:No, Morse has only two symbols

[Anonymous Coward]

"the bits are a measure of how much information is present"

Since you said "a measure", not "the measure", yo're right. Even if you ignore noise bits, significant information content is determined by context (including compression), contextual costs/values (including compression), and a-priori likelihood, I'd think.

slashdotters only like decimal .

[Anonymous Coward]

They are too stupid to understand anything else. I've been saying this a long time.

only two letters

[Anonymous Coward]

> Like Morse or binary code, it has only two letters

DUUD!

OOps!!

[D iz a n k Meister]

error checking != error correcting

sorry.

let me see if i understand...

[constantnormal]

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).

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?

[immerrath]

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 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!

Re:Time for "expert" editors at Slashdot?

[BitHive]

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 ;-)

Re:Time for "expert" editors at Slashdot?

[Anonymous Coward]

Huh. But Slashdot is Taco's plaything. How can you take away Taco's plaything? Keep your mutts off of Taco's plaything!

Re:Time for "expert" editors at Slashdot?

[rebelcool]

you'll find that most slashdotters don't know all that much about computers, either.

See a post below about some guy claiming that all computers moving to 'quadnary' would be faster than binary. Anyone with a minimum education in logic design can point out a half dozen reasons why that's not likely to happen.

It is rather remarkable though at the sheer number of people who's highest accomplishment is a confusing looking shell script assume they're the genius on everything.

you forgot something

[Anonymous Coward]

12. PROPHET!!

Re:you forgot something

[Anonymous Coward]

Funniest fucking thing I've ever seen. You r0x0r.

Re:You forgot something

[Anonymous Coward]

The obligatory:

6. ???
7. Profit

Sorry, I had to...

Re:You forgot something

[Anonymous Coward]

The obligatory:

8. ???
9. Profit

Sorry, I had to...

Re:You forgot something

[Anonymous Coward]

The obligatory:

10. ???
11. Profit

Sorry, I had to...

Re:You forgot something

[Anonymous Coward]

The obligatory:

12. ???
13. Profit

Sorry, I had to...

Re:You forgot something

[Anonymous Coward]

The obligatory:

14. ???
15. Profit

Sorry, I had to...

I'm Not Convinced

[Anonymous Coward]

* 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.

Re:I'm Not Convinced

[Twirlip of the Mists]

I hereby moderate this post -1, Too Smart; Made Us All Look Bad.

Re:I'm Not Convinced

[Anonymous Coward]

I'm going to be an asshole (AND an anonymous coward) but get lost

Re:I'm Not Convinced

[Jennifer E. Elaan]

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.

Re:I'm Not Convinced

[Anonymous Coward]

"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."

I respect your opinion, and I agree that the whole point was likely a *proof of concept*. However while in vitro evolution is a neat biochemical trick, that is suredly _not_ how life began.

The incorporation of diaminopurine (which I assume was 2,6-diaminopurine, the article doesn't say) in place of guanine (2-amino-6-oxypurine) and adenine (6-aminopurine) to yield a marginal catalytic activity doesn't seem to me to be that much. My guess is that diaminopurine was used as it can both 1.) hydrogen bond with uracil via the 6-amino moiety (necessary for the II structure and catalytic activity of the ribozyme), and 2.) can act as an electron donor in the ligase reaction in place of the naturally occurring guanine residues.

Don't get me wrong, I think that the authors do interesting biochemical work, but I look at it no further than that when it comes to the chemical evolution of life.

what?

[Anonymous Coward]

You can convert any four-character alphabet to two symbols:

A, B, C, D => AA, AB, BB, BA

furinstance

can I get a big grant now?

Grasping at Straws

[ATN]

Lot's of coulds, maybes, and probablys. Not exactly thrilling or scientific. Sounds more like working with an agenda.

Something even cooler about DNA

[frenchs]

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

Obligatory Binary Joke

[Anonymous Coward]

There are 10 types of people in the world. Those who understand binary, and those who don't.

Re:Obligatory Binary Joke

[Anonymous Coward]

There is only 1 type of person who could have posted the parent comment. Total fucking dumbass.

Re:PerMutation City

[Anonymous Coward]

I think you mean Permutation City. Not Pernutation.

Re:Binary computers? How long before base4 compute

[rebelcool]

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.

And another something else also cool...

[Guppy]

"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.

Re:And another something else also cool...

[Anonymous Coward]

I found your post interesting. However, D. radiodurans according to this page, has four "distinct" circular chromosomes (i.e., they are not the same). This, along with a highly efficient RecA, suggests that the organism does not really represent a RAID array, but is more akin to having backups, with a recombination/repair system on the loose.

I wonder how he saw the light

[Anonymous Coward]

when there was apparently nothing off of which for the photons to bounce. Oh, and the planet is spherical and it revolves around the sun. Sorry religious fools.

Re:I wonder how he saw the light

[Anonymous Coward]

Are you implying that GOD, Father of all Creation, has retinas just like you and me, and needs them to detect light?

Re:But... Look at the YiJing

[daoist]

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 yourself.

So all you need is Yin and Yang. Binary.

Re:Binary computers? How long before base4 compute

[Twirlip of the Mists]

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.

Merry Christmas!

[Anonymous Coward]

Channel memory, now.

I invented UDDU!

[Anonymous Coward]

Now to milk it!

think about this:

[SHEENmaster]

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.

Re:think about this:

[rebelcool]

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 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:

[Gordonjcp]

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.

single parity checks can go multidimensional

[Anonymous Coward]

... like so-called "hypercodes" and n-dimensional spc-based product codes. The hypercode model fits the dna string closest because it interleaves convolutionally and so potentially endlessly, but folding could bring in product coding too, I guess.

I think you're one level too low

[Bruce Perens]

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

Somebody better tell Reed And Solomon

[Anonymous Coward]

Because 2 is prime, you can use extension fields and base the code on symbols with 2^n bits and codewords with practically any number of symbols. This is used in CDs, etc.
Doesn't everybody know that?

Re:Binary computers? How long before base4 compute

[m1a1]

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.

RE: "In Soviet Russia" jokes

[some guy I know]

In Soviet Russia, the same tired joke over and over again tells some unimaginative loser.

I'm sorry, but this joke got old about a billion times faster than the "All your base are belong to us" variations.
(Sorry, "Us are belong to all your base".)

Re: "In Soviet Russia" jokes

[cryms0n]

Well, I only got into this joke a couple of days ago.

Not everyone moves on the same joke calendar!

Re:Binary computers? How long before base4 compute

[shepd]

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

Okay, if there's no mathematical reason, tell me the value of 0.3 in binary to the last digit. ;-)

Typo alert

[Bruce Perens]

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

Re: "In Soviet Russia" jokes

[Anonymous Coward]

Yes, there are always the retards who think old jokes is still funny.

You forgot something

[Anonymous Coward]

The obligatory:

4. ???
5. Profit

Sorry, I had to...

Um, no, not at all..

[autopr0n]

First of The article is about microbiology, and about how some researchers developed a dual base pair kind of 'dna' that could actually work (i.e. replicate itself, make proteins, etc). It says absolutely nothing 'computability' of DNA.

Secondly, you can use a unary base for computation. For example, 3 = 000, 4 = 0000, etc. All possible inputs for various equations and the like can be created as unary numbers. In fact, if you had any idea with regards to what you are talking about, you would know that Church numbers (introduced in Church's breakthrough paper) are basically unary.

So in other words, you obviously didn't read the article, and you obviously don't understand anything about the Church-Turing thesis.

Sortof, but that's not the point.

[autopr0n]

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).

Re:Binary computers? How long before base4 compute

[autopr0n]

Okay, if there's no mathematical reason, tell me the value of 0.3 in binary to the last digit. ;-)

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.

10 fingers

[autopr0n]

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.

Re:10 fingers

[Mac Degger]

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 :)

e?

[autopr0n]

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?

[pVoid]

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).

Re:e?

[Jennifer E. Elaan]

e^(i*pi)+1=0

Which succinctly relates the 5 most important numbers in math, e, pi, i, 1 and 0.

Re:e?

[Fnkmaster]

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.

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.

bleh...

[autopr0n]

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.

Um, no...

[autopr0n]

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.

Not really

[autopr0n]

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.

Its been that time for a long time, and it won't..

[autopr0n]

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 (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.

rational thinking and "why"

[guybarr]

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.

Re:rational thinking and "why"

[pVoid]

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.

Re:rational thinking and "why"

[guybarr]

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

whose formal manifestation is the scientific method ...

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).

let's not get into chicken-egg style debates. We both agree that the body of models and definitions is an essential part of science. I just remark
in passing that the hirarchical structure of these models and definitions
allows you to ask answerable questions of high level of complexity.

IOW, these models shape and extend the way we think, allowing us to
investigate things you couldn't w/o . This is, of course, dangerous,
but so is every useful tool.

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

This kind of thinking is insane. Of course there are fuzzy questions
and fuzzy issues. But there are many issues which can be rigourously treated.

The sun's luminosity (at some place/time) is not subjective. You
can measure it and what you predict (within error bounds) will be rigourously TRUE/FALSE. This is truth. It is not subjective.

Don't mistake the idea that not _all_ questions can be answered objectively with saying (as you do) that _no_ question can be
answered objectively.

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

I don't belive anyone actually belives that, but if you do, you seem to have quite a limited, empty world. You cannot learn, or evolve, or
change the world. Just be. Even a mushroom does more than just "being".

(I'm not saying you are such a "mushroom", I'm saying you should perhaps rethink your world-view)

Like Orwell wrote: Freedom is the right to say, "2+2=4"

Enough. Time for some truth-finding.

Re:rational thinking and "why"

[pVoid]

I think you overestimate both yourself, and your precious little Science.

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"

[CodeShark]

A minor quible perhaps, but I am begging to differ with your statement as well. I think it would be more accurate to restate your premise as follows.

"Historically. the human race's only truth verifying method is reasoning and intellect", instead of "truth finding method".

I can't count how many articles and books which I have read in terms of the major "society influencing" technologies have come from a science-minded individual having a unique but unscientific (at the time) view of a particular phenomenon, making an important discovery from a "flash of intuition", or "leap of faith", or coming up with the "right answer" from any number of blatantly unscientific sources (dreams anyone, luck sometimes... given a bit of time I can probably evn come up with instances where the "truth" became known first as an "answer to prayer" -- can't get much more *cough* irrational than that, right?)

Under the heading of luck, for example, the bio-organism we know that is now used to create Penicillin was a useless mold -- until Dr. Fleming found that it killed a particular bacterium in his lab. He could have just as easily cursed his bad luck, written off the experiment, washed the petri dish, and started over. Instead, he used his reasoning and intellect to conduct a scientific experiment to answer a specific question: I wonder what other assorted nasties (at the germ level) this particular mold can kill, or was it just a one time thing...? Once his reasoning established that Penicillin was in fact a great germ killer, then a whole raft of scientific experiments took place based on the hard evidence from the foundational "I wonder...", so add those two words to each of these questions, and see what science actually did:

• ...this weird green stuff can kill other bacteria that cause human illness...
• ..if this germ killer can be developed into a medicine... Experimentally proven answer: yes.
• ...what is the dosage that kills the germ but not the patient.... Experimentally proven answer(s) threshhold and low toxicity dosing levels?
• ...how to create enough of this new wonder drug to keep a person alive? (don't remember the intervening experiments, but ultimately a weak corn liquor was the right answer).

More personally, I had a totally illogical but now proven insight that most stomach ulcers had a bacterial origin -- literally years before Helicobacter pylori (H. pylori) was proven to be the guilty culprit (within the last decade IIRC). What I didn't have was the scientific training or tools to follow the intuition with experiments to the stage of medical proof.

Re:rational thinking and "why"

[guybarr]

I think you overestimate both yourself

That is very probably true. Academically, I am a research student.

and your precious little Science

Science isn't mine, it's the human race's, and yes, I believe it's precious, although, like every human construction, not unflawed.

... snipped some trivial logics definitions, and reduction of math to axioms, and physics to postulates ...

I think that when you say everything you do in real theory is those 16 axioms you make the same mistake as a biologist saying:
"everything you are is nothing more than the result of applying a certain DNA sequence with a certain set of external stimuly"
These two sayings are in some way true, but they are not very useful.

It is true, that some of what science generates are predictions which have testable truth-value. Only these can be treated as "truth". But what you are ignoring is that the set of such observations, possible with current science and technology, is continually expanding.

IOW, the set of known 'matter of fact' questions is expanding in quite unpredictable and beautiful ways, exactly through the scientific process.

This makes them worth exploring, IMHO.

Are those all the questions in existance ? No. Neither did I claim so.
Are those the _only_ questions worth exploring ? I, at least, don't claim that.
Are those *real* questions ? well, this depends on semantics and I really won't go there this time of night.

As for character, that is, IMHO, not gained by talking.

And one final remark, perhaps so trivial you've ignored it: the scientific methodology is a part of my humanity and of humanity at large. I agree it should not consume all other parts, (nor do I think it completely possible), but one should also not let it die in uninhibited mysticism, or relativism, as well.

Re:rational thinking and "why"

[pVoid]

You know, if you look up at the parent threads, this discussion was between me and Fnkmaster, regarding how some things weren't answerable by science (like why we have 10 fingers).

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:Binary computers? How long before base4 compute

[perfects]

> 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".

Re:Binary computers? How long before base4 compute

[Anonymous Coward]

We haven't have the luxury of playing with +5V logic at work for the past 6 years... These days logic levels are low swing signals at +/- 100mV amplitude. The voltage swing are tiny so that we can switch it quickly without a large dV/Dt (bad!). Nothing wrong with that as long as it is engineered correctly.

Re:Binary computers? How long before base4 compute

[Jennifer E. Elaan]

Adders aren't constant time, they're O(nlogn) even in hardware, using something better than ripple-carry anyhow.

Switching to a balanced-ternary system would be possible, since ternary works well with a split-rail supply, but any more than 3 states and it starts to act more like an analog computer than a digital. Noise becomes a real problem.

Binary is used because it uses so little area to implement. More complex systems start requiring window comparators, which use very nontrivial area. For a MSI (medium scale integration) system, it could be done, although noise is problematic still. For VLSI, there is just no reason.

Greg Egan spoiler alert

[Anonymous Coward]

Perhaps Egan's site explaining his works will be of help: http://www.netspace.net.au/~gregegan/

Re:Its been that time for a long time, and it won'

[p3d0]

The Slashdot editors are addicted to their own power...

To paraphrase: never attribute to malice what can easily be explained by apathy.

The editors are not evil tyrants; they're basically kids who made a web site for their own reasons and have no interest in being journalists. The site thrives without the editors' expending any effort in this direction, so why should they start now?

Comment removed

[account_deleted]

Comment removed based on user account deletion

my resoning is thus:

[autopr0n]

If they don't care, then they should give the jobs to people who do care. The only reason they dont, as far as I can tell, is that they are adicted to the power that running /. gives them, and don't want to share it with people would make them look like fools in comparison.

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.

Intrest is an integral.

[autopr0n]

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.

Re:Binary computers? How long before base4 compute

[tgrigsby]

And to be clear, the current binary chips have to determine a voltage high or voltage low from a *range* of voltages. You almost never get an exact high or an exact zero. And the problem with fuzzy voltages increases as traces get smaller and clocks run faster. As chip development evolves, the problem of determining whether a transistor holds a one or zero becomes more difficult. If you attempt to introduce a chip which, while perfectly feasible, requires more than two voltages, you increase by orders of magnitude the difficulty in determining which voltage a transistor holds.