Slashdot Mirror
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."
Comment removed based on user account deletion
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
[100% ISO 646 Compliant]
SVM, ERGO MONSTRO.
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
Bruce Perens.
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!
Sigmentation fault - core dumped
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...
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).
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.
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.
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.
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.
-
I'll be taking a look at Pernutation City. Thanks for the sugestion...
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.
Normal human
... oh, you get the picture.
/.-er
/. Editor
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.
Beware: In C++, your friends can see your privates!
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!
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.
Ya ya, who cares. I'm a biology minor, and computer science major, and this article wasn't particullarly interesting to me even. ;)
a phb.htm
You wanna see something cool... how about DNA having a parity bit?? Take a peek....
http://www.academicpress.com/inscight/09112002/gr
"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.
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.
That which is, is not.
That which is not, is.
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.
I write in my journal
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.
I write in my journal
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
Bruce Perens.