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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."
Ever read it? By Greg Egan, THE most imaginative SF author ever
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)
TWW
"Encyclopedia" is to "Wikipedia" what "Library" is to "Some people at a bus stop"
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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.
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
But these [four] bases aren't easy to make from the chemical constituents of the early Earth, point out Reader and Joyce.
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...
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.
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?
"The question of whether machines can think is no more interesting than [] whether submarines can swim" - Dijkstra
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.
You can't judge a book by the way it wears its hair.
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.
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I'll be taking a look at Pernutation City. Thanks for the sugestion...
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.
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.
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.
He painted a unicorn in outer space. I'm askin' ya, what's it breathin'?
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.
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?
Will I retire or break 10K?
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!
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.
If C only links with G, and A with D, isn't it already Binary? Because there are two possible combinations.
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.
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?
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
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.
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"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
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.
You can't judge a book by the way it wears its hair.
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.
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.
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
Bruce Perens.
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).
autopr0n is like, down and stuff.
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.
autopr0n is like, down and stuff.
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.
autopr0n is like, down and stuff.
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?
autopr0n is like, down and stuff.
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.
autopr0n is like, down and stuff.
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.
autopr0n is like, down and stuff.
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.
autopr0n is like, down and stuff.
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.
autopr0n is like, down and stuff.
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.
Working for necessity's mother.
> 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".
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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.
autopr0n is like, down and stuff.
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.
autopr0n is like, down and stuff.