Berkeley CSUA MOTD:Entry 18573
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2018/10/16 [General] UID:1000 Activity:popular
10/16   

2000/6/30-7/3 [Science/Biology, Computer/Theory] UID:18573 Activity:very high
6/30    Now that the human genome appears to be all but decoded. Is
        there any method to measure the number of bits that are encoded
        in the genome. IE how does it compare to a modern operating system.
        \_ Well, the encoding system is using a power of two, so there is
           a very easy conversion.  The problem is that it's not always
           easy to see where code ends and garbage begins in DNA.
           \_ ONE HUMAN ~ 4 TERABYTES
                \_ Uh, I don't have my biochem text with me (on vacation),
                   but I seem to recall the human genome being 2,000,000 kbp
                   (kilobase pairs), or 4 Gbits of data (2 bits/bp). -nweaver
                \_ That's just the program text. The Interesting Question(tm)
                   is How much does it take at runtime?
              \_ The number is actually much less than that, since the
                 bitstring is EXTREMELY structured. Which means less bits. If
                 I were to guess, you're off by a factor of 100-1000. Maybe
                 worse. That doesn't mean anything however, since we know next
                 to nothing about the structure, and won't for quite a while
                 \_ ONE HUMAN ~ 4 TERABYTES NO COMPRESSION, PUNY HUMAN
           \_ once the genome is there, the interesting stuff begins.  For the
              next 30-50 years, I think scientists will be working on the grand
                   \_ try 300-500; popular press is just listening to what the
                      funding proposals are babbling; anyone actually writing
                      them makes sure the timespan predicted is long enough
                      "so that i won't be around to be held responsible" but
                      short enough as to not to discourage investment. sad,
                      but true.
              unification theory of DNA.  A physical/biology/mathetical model
              of the interaction of the different genes.  Imagine running a
              simulation of a new lifeform created by artifically pieceing
              different genes!  The complexity of such a simulation is beyond
              anything we've done.  Today's supercomputers used to simulate
              nuclear explosions will look like toys next to computers
              simulating artificial lifeforms.  Who wants to guess on the
              computational power needed to run a simulation of a single cell?
              \_This is the typical clueless CompSci answer to biochemical
              problems.  I remember once one of my advisors said that the
              problem with working with computer scientists on biological
              simulation in actual living cells. Just pick your favority
              problems was that they just didn't get it. I guess he had a
              point.  Why waste your time trying simulate a complete cell at
              such a granular level on a computer? We can simply run the
              simulation in actual living cells.
              \_ Why bother running simulations of rockets, and atomic
                 bombs? Oh yeah, that's right, if you find something
                 *really* interesting, **THOUSANDS/MILLIONS** OF PEOPLE
                 **DIE**.
                 Apparrently, its true that those who can't do, teach.
                 \_ What are you trying to say?  This makes no sense.
              Just pick your favorite
              organism and transform them. DNA is cheap and plentiful to
              reproduce with a little lambda phage, plasmid, and PCR.  Also,
              simulation of a single cell, albeit interesting, isn't exactly
                        \_ >80 column idiocy fixed.  Get a clue.  -tom
              completely useful. Since we are mainly interested in
              multicellular organisms, a simulation of intercellular
              interactions would be much more valuable. i.e. what exactly is
              involved in the complex interaction of cell signalling during
              embryonic growth, and how that interrelates to differentiated
              cells.  A more realistic goal is to use pattern recognition
              techniques to be able to predict tertiary/quarternary structure
              of proteins and enzymes from DNA, and probably one which is much
              more profitable than trying to simulate organisms when the
              actual organisms can be produced cheaply. Go buy yourself a copy
              of Maniatis.  -williamc.
              \_ If you take a pure scientific view, there is lots of value
                 to understanding how cellular processes work, and being able
                 to model them means a huge step toward fully understanding
                 the schemes (algorithms if you will) nature has come up with.
                 From a practical viewpoint, you want to be able to model
                 a cell so you can design your own cellular signalling pathways
                 What you're saying, William, is that there is no value in
                 understanding the inner working of cells, that nuclear
                 transport, mRNA regulation, vessicle trafficking is not impt.
                 Thats a very narrow minded view.
                 \_ What he's saying is that full simulation is infeasible,
                    and suggesting a viable alternative. Get a clue.
                        \_ see below
                \_ More than Moore's law can produce for you even if it lasts
                 through 2500 A.D.. Without a new computational paradigm, or a
                 better abstraction than sheer chemistry, this will not be
                 practical (in all likelihood) until well past the predicted
                 lifespan of the Homo sapiens species, or even genus Homo.
                 \_ Dude.  Do you realize how LARGE the number
                    current_computational_speeds * 2 ^ (500 / 1.5) is?
                    \_ Yes I do. Do you realize that modeling a physical
                       system on quantum level is considered non-polytime on
                       a classical computer? And do you realize how many atoms
                       a cell contains?
                        \_ In something like 8 iterations of Moore's Law
                           (12 years) you'll be able to read 4 terabytes
                           (the DNA sequence) into RAM.  The rest of the
                           cell structure is simple relative to DNA and
                           doesn't need to be fully modeled.  By the time
                           you can read DNA into RAM, processors will be
                           running at 256 Ghz, with who knows how many
                           instructions per cycle.  That's far more
                           processing power than a cell has.  The only
                           computational barrier at that point will be
                           writing the code to model it correctly; that's
                           hard for a cell and much harder for a full
                           organism.  -tom
                           \_ "The rest of the cell structure is simple
                               relative to DNA"? Get a clue, cs boy. You
                               can read the damn bytes into RAM, but you won't
                               know what the fuck to do with them. Predicting
                               "everything" from DNA, or even a small subset
                               of it such as the general protein problem
                               (folding, interaction, binding sites, etc), may
                               easily, to the best of mankind's current
                               knowledge, turn out to be, oh, say,
                               EXPSPACE-hard. All your Moore's law ramblings
                               aren't worth crap until we know SOME fully
                               encapsulated localization structure in the
                               problem (be it DNA, protein, life, etc). Which
                               doesn't seem too plausible.
                       \_ It would be stupid and _unnecessary_ to model the
                          individual atoms to model a cell or dna.  For example,
                          weather modeling gets better everyday and they're
                          certainly not modeling every atom in a storm.
                          \_ See above.
                 \_ And do you honestly think we'll still be computing on
                    silicon then?
                    \_ The above was predicated on "no change of paradigm"
              \_ But can distributed computer help, like what SETI@home does?
                 -- yuen
                \_ Probably not; seti@home relies on the fact that an
                   arbitrarily large amount of computation can be done by
                   any node without needing input from any other ongoing
                   calculations; a cellular model would be much more
                   interactive.  Still, I think the assertion that we'll
                   never have enough computing power to model a cell is
                   silly and unfounded.  -tom
                   \_ 3 words for you -- "think avogadro's number"
                   \_ "No one would ever need more than 640k".
                \_ I have to agree with william. You don't start a
                   computationally intensive calculation at the lowest
                   possible level of understanding. For instance, if you
                   ever want to see a result, you would not start a model
                   of even a modest polypeptide by doing ab intitio
                   calculations on the interactions between individual
                   electrons and nuclei. Modeling an entire cell based on
                   molecular interactions is similarly too complex and
                   really unnecessary.
                   \_I dont understand this fixation with atoms.  You dont
                     need to model atoms, just the kinetics and thermodynamics
                     of interactions.  Duh, anyone thats knows anything knows
                     theyre not going to figure out interactions in the cell
                     from scratch.  We have 100+ years of abstraction to work
                     with.
                \_ Nobody is talking about simulating cells at the atomic
                   level, dumbass.  As for "why not try it on a real cell?"
                   It's a stupid question.  It's always more economical to
                   simulate something first rather than try it first.  You
                   can change your simulation parameters faster than you can
                   change your real-world experiment.
                        \_ this is utterly false.  -tom
                           \_ this is the first intelligent thing you've
                              said in this thread, tom
                   How do you think we
                   build cars and airplains and computers?  We break it down
                   into components, build models in computers, simulate them,
                   and then build small scale models.  Drugs can be synthesized
                   in a computer faster than in real life.  I'd love to see
                   how a particular drug will affect a cell even before
                   the drug exit in real life. Science fiction?  maybe. But
                   then again, who would have thought of the internet 100
                   years ago?
        \_ what is human gnome, and is it better than kde?
        \_ alot of you missed a point made above, DNA isn't enough!  The cell
           itself carries much info that isn't in the DNA (via already synthed
           proteins, sugars, biochemical microenvironents, mitochondria and
           their DNA, imprinting (which the genome project is ignoring), as
           well as other molecules that we probably don't realize are
           necessary in a model).  Yes, much will be able to be done, but the
           necessary in a model).
                \_ the total amount of cell information not contained in DNA
                   is almost certainly less than the amount of information
                   contained in the DNA.  So call it 8 terabytes and 13
                   iterations of Moore's Law.  -tom
           Yes, much will be able to be done, but the
           system will have holes and leave a lot to interpretation.  That's
           not to say that phages, bacterial sims, YACS, . . . are the answer,
           they also have many, many flaws, but we are getting closer.  And
           it is probably the marriage of the techniques that will produce
           the answers we are stiving for, with the great aid of human
           intuition and analytical skills.
           Anyhow, the 4TB, GB, whatever, of DNA isn't enough.  Just
           imprinting alone would add 2 bits to every base pair (methylated or
           glycosylated), now add on everything else you forgot to consider.
           Oh, and don't forget you need the environments of all surrounding
           systems, i.e. in birth you need the mother, her DNA, and so forth
           to get it all right.  Bottom line, an approximation is better than
           nothing, but don't get your hopes up too high!
           \_ The first challenge is simulating an amoeba.  -tom
2018/10/16 [General] UID:1000 Activity:popular
10/16   

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