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Gould Op-Ed: Genes' Emergent Properties Matters 177

Posted by Hemos
from the interesting-take-on-things dept.
A reader writes "The New York Times has an op-ed piece in Monday's paper about the smaller-than-expected number of genes in the human genome (around 30,000 genes, versus 19,000 for a simple roundworm and the 100,000+ that were expected). With so few genes, it may be the case that the emergent properties of the combinations of genes, as much as the genes themselves, are contributing to our complexity. I suppose the honchos at Santa Fe Institute are rewriting their grant proposals already."
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Gould Op-Ed: Emergent Properties of Genes Matters

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  • Are biologists really no smarter than those managerial types that compute productivity by counting lines of code?

    So are you saying productivity should be measured by counting lines of output? ;-)

  • Am I the only person who saw this article on numerous news pages two weeks ago? I mean, a couple of days maybe, but weeks for a story like this to get noticed? I was thinking of submitting it, but then I'm way too lazy, and I still have to figure out how to make hyperlinks ;)

    You can make up your own mind as to whether I'm kidding or not.

  • Like hell I'm going to read every post here, so this has probably already been mentioned, but does it strike anyone as interesting the way that the article (or at least, the one I read two weeks ago) makes numerous, "scientific" references to things like "two million years ago, when apes and humans started to separate on their evolutionary paths..." I forget the exact statistics they were spouting, but that kind of thing was the general gist. Has this been proven? Is this paradigm regarded as fact? I surely hope not, considering how many times the "theory" of evolution has been examined, analysed, and refuted with real scientific methods and/or evidence. Just try a search on Google for evolution, and see how many pages you hit that disprove it pretty conclusively. Then try to find some that prove it. Make up your own mind.

    I'm not saying I believe in creation theory; I'm not religious, let alone a Christian (no offense to Christians -- I used to be one). But clearly the theory of evolution is far too flawed to be taken seriously, just as the theory of the staged moonlanding. Sorry to rant; I just hate it when people (especially scientists) stick to these stupid ideas. You'd think that if they can decode the human genome, they'd be smart enough to realise we didn't evolve from protazoa. There just wasn't enough time, even if it could happen. We know for a fact that the Earth is only around 4.5 billion years old -- if evolution happened we'd see animals changing practically overnight, considering that humans are supposed to have evolved from very basic mammals in only about 65 million years.

  • I love the fact that Steven J. Gould and company got so pumped up by the exploitation of fresh-off-the-farm boomer females in academia, that their brains exploded. With 70s pseudo-intellectual chicks who made it from the midwest to the Ivy League, the "genes don't matter" lines worked like a charm -- almost as good as lines of coke at the local disco. It worked so well that they are stuck emitting same sounds, like a poorly configured MP3 driver, over and over again.

    It's a new frigging millenium for crying out loud!

    What these herpes-ridden buggy-sound-driver-head wannabe-scientists don't get is that their sounds are now being emitted into a very different environment. The farmers daughters 70s intellectual wannabe chicks are in the throes of menopause. No one cares what they think anymore because no one wants to fuck them anymore so they are being "down-sized" out of the middle management harems into which they graduated from their "higher education". The only people left to listen to guys like Gould are young geeks to have been programming complex information systems since age 11. Gould probably wouldn't want to fuck them even if he could. But even if Gould's had a bunch of butch gay sons, for this new audience, saying that an alphabet of 30,000 characters is inadequate to write complex programs comes off like the drooling-idiocy-posing-as-science that guys like Gould are destined to emit until they die.

    Thank you, Dr. Gould. You are irreplaceable.

  • Your arguments only make sense if you think that the sole purpose of evolution is to produce a super-human that has no physical limitations whatsoever. We can't see in the dark? Blame it on the shortcomings of evolution. We can't leap over tall buildings in a single bound? Blame it on the shortcomings of nature.

    Name ONE problem on this planet that is the result of the poor workings of evolution. Before you answer, ask yourself: Is it a problem for life on this planet, or is it a problem for human beings? Is it a problem in the sense that the continued existence of our species is threatened, or is it a minor inconvenience? So I have to use glasses to improve my vision. Big deal. I don't see that as a threat to life on earth.

    I am not a mystical tree hugger. Mother nature can be a cold-hearted bitch at times. Evolution does not favor any one species. But here we are, the product of evolution, using electric lights and computers and all sorts of neat stuff. Evolution is responsible for designing these wonderful brains in our heads. So it took a few billion years to get here? So what.

    I'm not saying we should not, under any circumstances, create new life forms. I am saying that when we do it we should have a better reason than the fact that we need an interesting diversion. We should make damn sure we are not the ones being short-sighted. When the being with the neon green skin develops a horrible skin disease and dies a painful death, what will we say to asuage it? "Oops. My bad."???

    The ability to create new life is the ultimate tool. With it, we become gods. There is a lot of responsibility that comes with that job description. Before we sign up, let's just make sure we think it over first.
  • In the Unix philosphy, each little script is totally self-contained, its operation can be analyzed independently of the context, and combining several scripts will just yield the combination of their results.

    This may be true on the application level. The original analogy works when you consider the reuse of dynamically linked object-code on a modern *nix system. Context, in the case of *nix can be just as sensitive as that of a MS Windows - as anyone who has encountered glibc incompatabilities will tell you.
  • The author of that NYT piece is a Geologist, not a Biologist. For that, and other reasons, I wouldn't take it seriously.
  • One of the 'surprises' of the results of the mapping was that there is no difference between so-called races. Well, IANAG but I could have told them that.

    Why doesn't that surprise you? I think it's a real wonderful surprise that there is no prove of any significant intellectual differences between 'races'. I could easily picture it otherwise. What if here were still Neanderthalers around, provably a little bit less (or more) stupid then we are? The social problems we have now between different groups would be a lot worse I would guess!

    Luckily, the different races in humans seem to hardly vary in intellectual respect. Phew! The social problems of different environment alone are hard enough.

  • cool.

    Now write a program which thinks creatively, feels a range of emotions and learns spoken languages.

    Seriously, in the absence of knowledge about how genetic code works, it seemed reasonable to assume a certain size. Nobody would have denied that it could *possibly* be just 30,000 - they just expected a higher number. 30K happened to be over on the left side of the bell curve of probable outcomes given what was known at the time.

    I mean, what if we turned out to have fewer genes than some bacteria? Your argument would still apply but the finding would still be pretty unexpected no?
  • Actually, I said "So once again we find that we ourselves, and not our parents or our grandparents, are responsible for who we are and what we become..." I don't think that we'll ever explain it all; I don't believe in biological OR neurological reductionism and I think that there is an inherently Mysterious and Profound element to our humanity. We will always be responsible for our actions. The story of man has often been about the search for a scapegoat before whom we can lay responsibility for our evil deeds. From a philosophical stand-point we've always known that this is wrong-headed; now science is confirming what we've long known in our hearts.
  • what game is all this 'all your base' shit from?
    -
  • genes form a boolean net, a kind of cellular automaton, that is turing complete - i.e. the interaction of the genes *themselves* is equivalent to a computer program, and therefore quite possibly fundamentally unsolvable.

    this is because proteins that genes produce can do more than just go away and make stuff for bodily processes, they can affect (turn off, turn on, conditonally flip, etc) the action of other genes.

    so many people seem to have this idea that genes are just like a recipe, a linear list of stuff that goes to make up the organism. they're nothing like that.

    your genes are a program like the worst spaghetti code ever written, multiplied a billion-fold. every emergent property of the system will be used - there's nothing to tell evolution to Keep It Simple, Stupid.

    where does that leave the Human Genome Project? well, they know *something*. but my bet is that there are fundamental limits on the amount that we can ever actually know about how our genes work.

    check out the papers on this page [susx.ac.uk] for a fascinating example of how evolution can create things we don't understand, even in an extremely limited domain.

    also, Stuart Kauffman (of the Santa Fe Institute) has written a book "at home in the universe", the first part of which gives an excellent exposition of the above boolean net stuff. highly recommended.

    anyway, isn't it obvious that the complexity of a system bears no relationship the complexity of the rules of that system. think of Life for example: only three rules, but given a large enough arena to play in, those rules are sufficient to simulate any computer... start it off from a random state, and it's fundamentally impossible to predict what it's going to do!

  • "I suppose the honchos at Santa Fe Institute are rewriting their grant proposals already."

    Perhaps this should read: "... are rewriting their patent proposals already."

  • In the case of humans, that's a black box with 30000 2-bit inputs, an unknown number of outputs, and exponential order internal complexity.

    I trust you meant 30000 genes. There's a 2-bit input for each individual base (how many was that again?). 4^X = big friggin number :-)
  • The story of man has often been about the search for a scapegoat before whom we can lay responsibility for our evil deeds. From a philosophical stand-point we've always known that this is wrong-headed; now science is confirming what we've long known in our hearts

    We will always be responsible for our deeds, that's how we feel it, that is how humanity works. Science will never be able to change this. It might however be able one day to explain how it works. We shouldn't be afraid of understanding, it could never change the way we are. It might prove some religious feelings wrong though.

  • (around 30,000 genes, versus 19,000 for a simple roundworm and the 100,000+ that were expected) But with each additional gene, the number of interactions between its expression and the expressions of other genes rises exponentially, doesn't it?

    I think you are on to something. If there is perfect interaction among genes (all-to-all sort of relationship) then you could say that we are (4^30000 / 4^19000) = 4^11000 times more complex than a "simple roundworm". Of course, there may be some genes that appear to have a one-to-one relationship with some traits, but it seems unlikely or at least there may be unknown side effects of toggling this gene on or off. Either way, it just goes to show how pathetically little we REALLY know about the human genome. Sure, we now have a "map" but all this really gives us is a rough prototype of an immense data structure with no documentation. For all practical purposes, genetic research is probing a black box. In the case of humans, that's a black box with 30000 2-bit inputs, an unknown number of outputs, and exponential order internal complexity.

    There is no gene for the human spirit. -- Gattaca
  • by SIGFPE (97527) on Monday February 19, 2001 @09:20AM (#420170) Homepage
    ...this piece of code is 2 lines long and can produce more than 1000 lines of output: for (i = 0; i<1001; ++i)
    printf("%d\n",i);
    and yet this code: printf("1\n");
    printf("2\n");
    can only produce 2. So why should I be astonished when one genome can do more with 30,000 genes than another genome with 100,000? Are biologists really no smarter than those managerial types that compute productivity by counting lines of code?

    And am I to start using fancy schmancy language like 'emergent property' when I talk about ooh...so sophisticated coding techniques like looping and reusable subroutines?

    --
  • by The Other Dan (30260) on Monday February 19, 2001 @07:10AM (#420171)
    Come on, do you really understand biology? Where do you get off saying that we are are "so superior to the roundworm"? I'd like to see you try and self fertilize like roundworms can. Or completely metamorphose like a fly does. The fact is, there is no good measure of "complexity" and "simplicity" at the level of the entire organism. To simply assume that we are more complex than other animals is grounded in nothing more than ego. And finally, like Gould (and many, many others have emphasized) we can only understand developmental complexity by understanding how gene products interact. So even if we are somehow more complex, there is no reason to assume that such complexity would require more genes.
  • Nice troll. The gist of Gould's argument means that with the breakdown of the one gene --> one function paradigm, we have less hope now of acheiving what you are talking about than we did before. Which is a good thing if people like you think you know what "perfect forms" for organisms are ;)
  • But with each additional gene, the number of interactions between its expression and the expressions of other genes rises exponentially, doesn't it? If I'm surprised by anything, it's that people actually thought there might be a "gene for foo".

    What suprised me is that there are so many "genes for foo". Time and time again scientists have come across single genes that determine complex factors on their own. This suggests to me that genes are more important on their own than in combinations...

  • by Swordfish (86310) on Monday February 19, 2001 @07:13AM (#420174) Homepage

    I've been listening to this stuff about the lower-than-expected number of genes for a while now, and it is surprising to me that no one has mentioned the less of chaos theory. Chaos theory is the study of systems which have very simple equations of motion, but which have an extremely compilcated behaviour.

    So... even quite a simple creature, such as an insect, can have very complex behaviour, even with simple equations of motion. So it's really the system structure that matters, not the number of parameters in the system specification.

    And remember that computers are very simple indeed. They're just interconnected switches and things. But the program loaded into the hardware makes it complex. So the complexity of human beings comes from the ability to load programs and execute them.

  • by OlympicSponsor (236309) on Monday February 19, 2001 @07:15AM (#420175)
    "With so few genes, it may be the case that the emergent properties of the combinations of genes, as much as the genes themselves, are contributing to our complexity."

    Emergent properties is ALL genes do. Think this through:

    Genes don't literally MAKE, say, a nose. That is, they aren't out there with trowels and jackhammers building/carving your nose. Genes don't even DIRECT the making of your nose: ("Hey Gene, the nostrils are getting a little far apart, what do we do?").

    All genes do is encode proteins. The proteins react with each other and their environments creating byproducts and releasing energies. Anything that emerges is...well, emergent.

    You hear a lot of talk about genes "for" different specific features (nose shape, homosexuality, etc) but that's really a technical shorthand. A gene isn't solely responsible for a single feature. When we say a gene is "for" some feature we mean "the presence or absence of this gene can affect the presence or absence of the feature". This sounds like the same thing, but imagine the gene in isolation--it isn't going to produce a nose or "gayness" in a vacuum. A gene "for" homosexuality is a gene that produces a certain protein at a certain time. One of the (undoubtedly many) side-effects of the protein is the modification of a structure in the brain that causes processing to happen differently that causes, etc, etc, etc.

    People who are suprised by emergence-y in the field of genetics don't know what they are talking about. However, it's OK to be surprised by the LEVEL of emergence--that is, there's more "interference" among fewer genes than anyone thought.
    --
  • is that animation based in turn on some other joke? or is it just one of those things that gets forwarded everywhere and turns into a craze like the hampster dance or something?
  • Read the sig.
  • Wait!!! There's more!

    http://pub2.ezboard.com/fsobserverssobserversmai nf orum.showMessage?topicID=1491.topic

    I hope /. didn't munge that link. Trust me, there weren't any extra spaces in it when I pasted it in there. Apparently the first people to surrender their bases were people who play Unreal Tournament.

  • I woulda modded this up if I could...
    You should really learn what a gene actually is (it is not a base)(hint, a gene encodes a protein, 3 base pairs = 1 codon, 1 codon = 1 peptide, many peptides = protein). And there are only two possible base pairs, 4 bases, two base pairs.
    That is, genes are made up of many (many) base pairs and code for one type of protein each. The proteins are the root of most of the work done in a cell, IIRC. Roundworms could have thousands of genes that code for simple, useless proteins for all I know.

    Offtopic a little bit...one thing from my high school biology classes that struck me was how similar viruses in real life are to computer virus. (Duh, that's where the name comes from.) They are rouge pieces of DNA or RNA that code for proteins that protect them and help them spread. It's just neat, is all.

  • 'specially considering that they aren't 'designed' at all.
  • Thank you for going to the effort of finding that information.

    Drop your AC mask and get the up-moderation you deserve!

    FatPhil
    --
  • Ah, slashdot is so useful. You can make a controversial remark and know that someone who knows more about the topic than you will tell you exactly where to

    1. Shove it 2. Look for decent information.

    The latter was what I was hoping for. You think I have time to go through a huge generic search when you just told me exactly what to look for? Thankz for the help ;)

    Although, under preliminary examination, I still disagree with you...

  • Would you take your sick daughter to the mechanic?
    Would you take your broken car to the doctor?

    Why would you learn your biology from the pastor ?
  • So wouldn't that make genes more like Makefiles?

    Walter H. Trent "Muad'Dib"
    Padishah Emperor of the Known Universe, IMHO
  • Actually the DNA-RNA-Protein direction of information flow has absolutely *nothing* to do with the 30,000 vs 100,000 question, because the same information is encoded in all three formats, thus adding nothing to complexity (BTW: transcripts are RNA. Neither DNA nor protein are transcripts)

    The fact is, until about six months ago, biologists (including me) really did think that there were about 100,000 human genes. The media is *not* confused about that.
  • You obviously have no understanding of what "interaction" is. This is not simple set theory you know. (And I know what a power set is, and its size, I've done a bit of mathematics in my time)

    How many ways can a bowl and a banana "interact"?
    1) Bowl upright, banana inside it
    2) Bowl upside down covering bowl
    3) Bowl upside down, banana sitting on top
    4) Bowl nearly right way up, leaning on banana.

    These are all different situations, but are not _combinatorial_.

    I'm not saying genes are like bananas, but the "interactions" are certainly more "spacial" than "combinatorial".

    "FatPhil"

    --
  • The acceptance of sociobiology? Since when? Sociobiology is a great seller of books (walk into a bookstore and you'll see lots of books like "The Language Instinct" and "The Moral Animal", incidentally both written by non-biologists) But open up major scientific journals like Science and Nature and you'll find hardly any papers about it. While the sociobiologists and their Marxist critics like to duke it out in the popular press over Nature vs. Nuture, mainstream biologists have long since accepted Nature *and* Nuture.
  • So, it's the combination of a relatively compact set of instructions that makes everything happen... Isn't this a lot like having a lot of small programs that, when scripted together, can outperform a large, monolithic one?


    On the other hand, this makes creating 'killer roundworms' less justifiable to corporate bean counters. "But, Mr. Ackbar, for another ten thousand records we could create zero-gravity slaves."


    "But you don't understand! The world needs Aibo-eating roundworms".

  • Certainly chaos theory may be applicable to development and genetics, but it's not a magic wand [dannyreviews.com]. Also, the systems involved may not be deterministic enough for chaos theory to be applicable (people like Lewontin [dannyreviews.com] would argue for a significant role for randomness).

    Danny.

  • Chaos theory is the study of systems which have very simple equations of motion, but which have an extremely compilcated behaviour.

    Chaos theory is the study of systems with a behavior such that an arbitrarily small change in input parameters results in an output that is not at all close to the previous result. For example, a weather forecastor which, when given an input of 5 degrees, predicts a thunderstorm yet when given an input of 5.001 degrees predicts sunshine. In fact, Chaos theory was born from just such an example.

    Chaos is not about "simple equations of motion" although a number of these types of equations are used as examples.

    Devon

  • No es una moto, es un helicoptero
  • by Alien54 (180860) on Monday February 19, 2001 @06:42AM (#420192) Journal
    The obvious question is what this does to gene patents? Does it render them impotent?

    Or do you run into the situations when one company has patented nuts, and another company has patented bolts?

    Sometimes it would be better if they left things alone, and had not patented things in the first place.

  • It doesn't surprise me because the very idea that there is such a thing as different races has never been actually proved, and is now definitively disproved.
    The true meaning of the word 'racism' is the belief that there is such a thing as different races (and strictly speaking, racialism is the belief in the superiority of a so-called race). This theory, first propounded at the height of 19th Century imperialism as a justification for opression, has always been condemned and challenged since its inception by academics, intellectuals, scientists and others. Nevertheless there have been those who have worked extremely hard at defending the theory of racism. Hence the numerous studies of peoples skull measurements, nose sizes, skin pigmentation etc carried out by the Nazis. People knew Nazi science as bogus then, and it's no different now.
    There's only one race - the Human Race.
  • This is going to fundamentally change the approach scientists are taking toward understanding the genome. Instead of mass-replicating a particular segment, then seeing what protein it expresses (something they're getting quite good at), suddenly we have a notion of instructional code, telling the DNA how to express a protein. It seems to me the eventual solution to this problem is going to rely almost exclusively on computer processing techniques. At some point, genetics may become one specialized field of computer science. Too bad for the biologists, who were making nice headway with PCR and knockout-mice, among other techniques.
  • Common, human genome leads more likely to a (26000! / 13000!) times more complex being than a roundworm.

    Even in relation to mice, a (26000! / 25700!) times bigger complexity is possible.

    These complexity relations may be different, depending on the effect of control genes, but I'd bet that complexity grows much faster than #genes.

    chess
  • wasn't it ALWAYS someone else's code?

    Jaeger
    www.JohnQHacker.com
    GodHatesCalvinists.com
  • It's probably gzip'ed. Maybe being born is like booting a Linux kernel, it has to be uncompressed first.
  • by Goronguer (223202) on Monday February 19, 2001 @07:19AM (#420198)
    "short-sightedness of nature"???!!!

    Is there any thought or logic behind this phrase, or did you just think it sounded cool? Nature has given birth to myriad creatures of nearly infinite diversity, able to endure in nearly every climate found on the planet. Species come and go, but life endures. What, exactly, is it that you find so inadequate?

    I can think of nothing more short-sighted than humans using a "genetic compiler" to create living beings with "cool" features such as neon green skin for no greater purpose than to provide an "interesting diversion." When we play with fire, we must do so with the greatest caution.

    Nature sees the long term in ways you and I can only begin to imagine. In nature's view, we humans are expendable. Nature has all the time in the world. She can afford to wait.
  • This whole reductionist canard about genomes and phenomes is at least semi-mistaken. It's quite obvious to me that although fundamentally identical human genetic material has existed for many, many millenia, only comparatively recently did recognizably *human* social organizations emerge. the tendency towards civilisation is not innate -- it's in large part a product of social interaction. That's where a huge part of the emergent properties come from.

    That's the problem with inward-looking genetic reductionism and the simple-minded comparison of genetic code to computer programming. You have to look outward as well... to the interstitial spaces between genetic individuals. Foucault recognized this, or Jung.
  • It is simply not true that mammals are better designed than amphibians. As Gould is fond of pointing out, by any of the obvious criteria - biomass, number of species, number of individual organisms, robustness against disasters, etc. - single-celled diatoms are vastly more successfull than mammals. Gould's book Full House (Life's Grandeur outside the US) tackles this subject.

    Danny.

  • Right... that's all we need: biology based on current software engineering standards. Yah, I've got wings, but when I try to flap them and metabolize food at the same time, my heart crashes... oops. Maybe if I go into a coma and regain consciousness, the system will work okay. :)
  • It's called Zerowing. And it looks like the SomethingAwful forums have started a net-wide trend...

    ---
  • the very idea that there is such a thing as different races has never been actually proved, and is now definitively disproved.

    It seems obvious that there ARE different 'races' of humans. Look around, groups of people living in different areas have somewhat different physical (and perhaps mental) features.

    Instead of trying to apply the special, we-are-better-than-animals term of 'race', try the generic version, 'breed'.

    Some breeds have dark skin, some have light skin, some run faster, some are more suited to particular environmental conditions.

    Its kind of a dumb argument anyway, all breeds/species/etc are seperated by fine differences in genetic makeup, trying to draw specific divisions between them is not possible. There is a big difference between black and white, but its all shifting shades of grey in between, attempting to define each shade in more than general terms is largely a waste of time.

  • Gould is a paleontologist (and therefore a biologist). However, like the late Carl Sagan, Gould's professional reputation is far less impressive than his public popularity would suggest.
  • by Trinition (114758) on Monday February 19, 2001 @09:53AM (#420205) Homepage
    While I agree that their is more complexity to genetics than the genes by themselves, we seem to be overlooking another alternative that may at least partially play into this:

    Maybe we're ot as complex as we think ourselves.

    Perhaps if we were more humble we might see that we're less than 2 times the complexity of a common round worm after all.

  • While I'm no fan of Dennett -- he has absolutely no qualifications to write about evolution and is not a scientist at all, (unlike Gould who is quite qualified) I have to agree that Gould certainly likes to make waves: One of my most favorite science quotes is from David Hull and is quite appropriate:

    "From the beginning of their careers, scientists are presented with a dilemma. They can make their work look as conventional as possible -- just one more brick in the edifice of science -- or as novel and controversial as possible -- declaring a whole new theory or possibly even a whole new science ... From my own reading of the recent history of science, I see no strong correlation between my own estimates of the novelty of an idea and the strategy that an author adopts."
    --David Hull in Science as a Process (1988).
  • Lets see here - we have 30000 genes, so:
    Assuming genes are just on/off switches:

    We boil down to a 2^30,000 array of bits. Thats what, 30Kb?, or ~ 4KB?

    HAHAHAHA.

    2^30000 is still a goddamn HUGE number. Never mind that with all the interactions possible, it could be more like 100^30000.

    And the noble flatworm is 2^18000 bits? So
    2^30000/2^18000 makes humans 2^12000 TIMES more complicated than the flatworm.

    I don't think that's all that surprising, do you?
  • FWIW I'm pretty amazed it's only 30,000 genes. What I take issue with is that we have to use the kind of silly language that people at the Santa Fe Institute use to describe what are essentially simple phenomena. Given n genes, each of which might interact with n-1 others, it should be pretty obvious to anyone who's written code that a lot of stuff might happen. The guys at the Santa Fe Institute like to take these observations and dress them up in fancy language to make them seem profound. (At least that's the impression I get from reading some of the books that have come out of there - like the work of Stuart Kauffman.)
    --
  • by cduffy (652) <charles+slashdot@dyfis.net> on Monday February 19, 2001 @04:52PM (#420209)
    Nature is rather prone to suboptimization, no? Not that we'd necessarily do any better...
  • I'd like to see an in depth analysis of the differences between our own genetic and that of chimps (or Bobobos - our closest relative) with whom we share 98% of our DNA.

    98% of 30,000 genes only leaves 600 to distinguish us from chimps.... now imagine if a large part of that is actually junk DNA, or repsonsible for gross external anatomical features...

    It's gonna be pretty humbling if we find that our brain only differs from chimps as the result of the proteins generated by a few dozen genes!
  • Extremely funny. Where did I put those mod points?
  • Follow the link. It is at least as funny as PD implies.

    --
  • No reason why human beings should be more complex
    than other living beings, especially vertebrates,
    since we all experienced four billion years of
    evolution. Just different.
  • by maraist (68387) <`moc.maps0n.liam ... tsiaram.leahcim'> on Monday February 19, 2001 @10:26AM (#420214) Homepage
    I heard a great analogy on the Discovery channel one day (arguably aimed at kids):

    Nature invents each life form separately (I'm paraphrasing to fit my argument). In order to do this, it has a certain amount of money (resources). It can spend that money however it wishes. Some expenditures will be more fruitful than others. But you always only have a fixed amount.
    The show then went on to describe how some creatures had night vision (though there was some other trade off), others had the ability to fly, so on and so forth. Each attribute had a fundamental limitation.

    You will not be able to produce the super-being (the quisak sadarak?). Animals today don't see in the dark - they just have highly sensative eyes. If you put a cat in a locked room with no windows, it wouldn't see jack. Its vision is based on moon-light. One trade off is limited color-vision (more rods than cones). The flashlight requires, dun dun daa, batteries; A power-source. Now in order to achieve a power source great enough to luminesce, you've got to have a massive internal re-engineering. Most likely it would be some excessive use of ATP, which would in turn require massive cooling, storage, etc.

    How about temperature regulation? We use clothing today, so couldn't we make sheddable fur that's designable just like modern clothing? Possibly, but then you alter the texture of your base skin; that might not be too attractive or sexy (same with fire-retardant / weather resistant skin).

    Flight should be out for obvious reasons? Don't think anyone wants to go to weaker bones (especially foot-ball players).

    Want bones of steel? Well if we use iron, then we have a problem with rust, jaggad edges or general issue of toxic solubility. All of which require massive chemical modification for stability. Before countering this, understand the basic point that you can not trivially alter a system (i.e. replace calcium with Titanium). There are millions of variables which affect the dynamic system. Yes anything's possible, but often times at enormous trade-off-costs.

    Another important issue that separates biology from our mechanical world is adaptability. Sure a 747 can hold more, go faster, and withstand greater stresses, but it can't repair itself. A sheet of metal can only increase it's imperfections, where-as a grouping of cells can grow and repair weak-points. If we replaced some brain-cells with diamond lattice silicone, we'd be suceptible to E&M interfearance (as in an MRI scan), we'd risk fracturing the diamond over time, or tearing the surrounding tissue due to its rigidity.

    The point is that this is a non-polynomial problem. There is not single best solution, and most likely there's an infinite number of them. What's more, none of them are ideal for more than a handful of cases - They all have exploitable weaknesses. Nature has been kind to us in that we've managed a working set of genes that's been durable for a couple thousand years in lots of different environments (including space and underwater). The only way we'd be able to learn if a human designed (computer assisted) working set of genes is viable is to go through several life cycles in various environments. But I don't think human right's activists would let us treat babies like lab-rats. Sure we can simulate, but Nature's a little sneaky, the number of paracites and short-commings are much more numerous than a case-study tool can speculate. It's the same digitally controlled v.s. Analog argument as Vinyl Records sound better than [theoretical] infinite precision digital CD's (technically they do, and I'll mathematically demonstrate if you so require). Of course the trade-off here, is increased noise with each use.

    Terrestrian nature is the most resource intensive, longest running genetic search algorithm discovered to date. It would be kind of hard to top it with a few meager billion transistors.

    Note that you've referenced religious intentions. I would like to add that religion is not necessary for this argument. Instead this is practical caution. The best we can hope for is the identification of systems that are desirable and to make attempts to duplicate (with possible slight modifications) in subsequent generations. Doesn't this sound a lot like evolution?

    Now for those on the relgious side / anti-evolutionists, don't worry, I'm not attacking.. There's nothing to say that one or more super-beings didn't sit at their cray equivalent and play out similar NP guessing games, while making 'releases' every once in a while. Or that they didn't clean their .bashrc file on occasion. Even if their system is voice activated AI like Genesis suggests. :)

    -Michael
  • One reason why mammals have so few genes compared to, say, amphibians, is because we're better designed. Being warm-blooded, there's a controlled environment inside the body; so you only need enzymes that work for that environment.

    Amphibians need enzymes that work in all temperatures from about ten centigrade up. And because each enzyme only works in a limited range of temperatures, they need lots of different enzymes to do the same task; and these all need encoding. Hence the very large sequences.
  • >They also neglect to mention 97% of DNA is non-coding,
    >it's not used for protein production. So that 2% is a great difference.

    Not if the differences are evenly distributed,
    which they seem close to be.
    Also, last weeks results upped the 97% numebr to 99%.

  • Insightful, but I figured I'd give my $0.02.

    The transistors would be more like the nucleic acids. Of which there are obviously many orders of magnitude more than transistors in even a modern CPU.

    The genes would be more like the computer's functional units. Protein synthesis might be related to the bit-patterns in the registers. Though finite, it's a rather large set of possibilities. Thus through the reuse of various functional units, you can reproduce
    certain types of register bit combinations.
    Though it's kind of hard to relate protein synthesis - This doesn't totally fit the analogy since it seems that only one biological functional unit / gene can be used for a protein, unlike the computer with inter-connected units.

    Who knows, maybe this will be the next great discovery. I call first patent!!!

    -Michael
  • But isn't half the fun in life seeing what random kookie things that Windows does?

    Take the Win NT 4.0 show case, for example. It just made my week to see it crash during Bill Gates' demo.

    I'd take a brain damaged AI with incredible ... err.. personality any day over a cold / impersonal Solaris.

    -Michael

    p.s. For the feminist advocates out there, In real life I date a Linux Box, I just play the Windows whore on screen.
  • Is there any thought or logic behind this phrase, or did you just think it sounded cool?

    The logic behind this phrase is obvious, once you see the problems that exist on this planet because of the poor workings of evolution. The fact that we have to use technology at all to improve our rate of survival shows the falsehood of your mystical, earth-mother argument that "nature give the ability to endure in every climate on earth." The fact that I have to use an electric light to see at night is a sign that evolution hasn't gone far enough to improving our abilities.

    Also, how could you decry humans creating new lifeforms as "short-sighted"? It's simply a use of technology, one that will improve our ability to survive. Hell, we're already talking about changing Earth's orbit [slashdot.org] and climate engineering [slashdot.org], what makes this perticular use of technology so horrible (besides your own spiritualist clinging to false ideas about the sacredness of life?)


    --
  • by Thomas Miconi (85282) on Monday February 19, 2001 @07:36AM (#420238)
    You write: "Isn't this a lot like having a lot of small programs that, when scripted together, can outperform a large, monolithic one?"

    Alas, I fear it is the exact opposite :o)

    In the Unix philosphy, each little script is totally self-contained, its operation can be analyzed independently of the context, and combining several scripts will just yield the combination of their results.

    Our genes, on the other hand, are not independant from each other : the presence of one given gene can have significant influence on the expression of another gene. A genotype cannot be analyzed gene-by-gene: the result of a genotype cannot be predicted from the result of each gene taken separately.

    Which means that we are much more a MSWindows-like machinery, where in order to get any little thing working you must have tons of other programs / services / libraries installed and running in a very precise way - otherwise you're on your way to catastrophe. Every component is totally dependent on the context, and the context is the total sum of *all* other components.

    Sad, but true : from a software engineering perspective, we are a perfect example of brain-damaged design :o)

    Thomas Miconi
  • by gattaca (27954) on Monday February 19, 2001 @08:02AM (#420243)
    Right: First dogma of biochemistry:

    gene -> mRNA -> protein

    The problem is in the arrows. Lots of other stuff happens. so it's more like:

    gene-> lots of different mRNA -> even more different proteins -> more different proteins

    ...for a start. Secondly, one protein != one function.
    Thirdly, knowing the parts list doesn't tell you how to put a thing together together.

    Fourthly, even if 30,000 genes means 30,000 proteins, this gives a potential 450,000,000 pair wise interactions. But interactions aren't necessarily pairwise.

    Fifthly, genes interact with proteins that interact with small molecules that interact with other stimuli.

    Sixthly, Different genes do different things at different times.

    So it's all quite hard really...
  • Evolution doesn't really have "poor workings".
    It just happens, without cause or direction.

    For a random example, think of trout in some reagions of the Ukraine over the last 4 decades and industrial acidic discharges in to the rivers of the region -
    Are while species of trout dying "evolution working perfectly", as the non-fit have been eliminated.
    Or are trout dying "evolution failing totally", as it wasn't quick enough to let the trout survive?

    For everyone who shouts "failure" there will be one who shouts "success" and vica versa.

    I'm glad that I've evolved enough to turn on a lightbuld when I want to read in the dark. To me that's a good evolutive step! The problem is solved, it doesn't matter how. In this way inventing lightbulbs is as efficient evolutionary step as night-vision.

    FatPhil
    --
  • "How is the 3d matrix of bone cell division, encoded in the four bit code of dna?"

    Well, it's not a "four bit" code--not in the way you imply, anyway. That's a bit like saying that computers are amazing to represent the things they do, because they have only a "two bit" code.

    The complexity is represented by the X^4 combinations of nucleotides. When X is large, the DNA language is quite descriptive. What I'm trying to say, ultimately, is that I don't think there's that much compression going on. In fact, it's been pretty well established that evolutionary pressures usually don't optimize for size in complex organisms.
  • It is possibly correct to anthropomorphize genes, since it is they who are the driving force in life, and not indiviual humans (an individual of the species, apparently in response to an underlying stimulus, will sacrifice themselves for the good of the group... sometimes... we currently ascribe this behavior to genes), but to attribute a value judgement on a specific number of genes in relation to an 'inferior species' like the roundworm is anthropocentric, but with a twist, don't ya think?

    One might just as well conclude that evolving in the particular strain that we did required development of just the specific 30000 active genes that we 'kept'.

    The roundworm had to build slime genes and earth-digesting proteins and all that. We were smarter and ate the roundworms instead....

    ...thereby saving genes!

    But, seriously, folks, remember that all that junk DNA is theorized to come alive with mutations when the organism is under environmental stress.

  • The neo-Darwinists have shown (see Dennett's book, Darwin's Dangerous Idea) that this is not really different from mainstream evolution.

    Which Gould never denied, and it was a disgusting lie of Dennett's to ever claim that he did. Gould's real argument was against the "one-gene, one characteristic" model which Dawkins and Dennett needed to assume for lots of their highfalutin' conclusions about human behaviour. On this matter, he has been proved cataclysmically right.

  • The experiments with changing one so-called macro gene and causing eyes to appear all over the legs of fruit flies should make this pretty obvious. The genome is nano-molecular software, people! The ribosomes and other parts of the cell are the assembly machinery that follow it's instructions, but DNA is clearly turing complete. Think of all the cute little enzymes moving back and forth on RNA snippits, sometimes even changing and reordering the DNA.

    The genome is clearly software, and I imagine that their is a lot of code reuse. This only makes sense! If every part of the body was redundantly coded by simmilar genes, then a favorable mutation in one area would have no impact on the others; they might even end up incompatible! Think about it, if a creature evolved [or picked up via a passing bateriological plasmid or virus splice some favorable trait or genetic function from another species or even phyla [it happens]] a usefull new 'constructor' class for types of muscle tissue, would you expect it to only change the formation of muscle tissue in their left arm?

    The notion is ludicrous. Living things clearly are possess quite a hierarchy of coding. That any significant biologist could really have thought that every different substructure and detail of every part of the body was specifically detailed in the genome, they should have been laughed at.

    I suspect instead that gould is just being a pretentious semi-intellectual as usual. [Don't get me wrong, I love that he has so virtously stood up for evolution vs. creationism... but we should all expect a lot more then merely that in a real scientist, and his tendancy towards relativism and belittling the glory of mankinds mind have bothered me for a while ;) ]

    ---
  • Well said. Of course it's all about emergent phenomena

    But I really hate the way Gould always makes this 'emergency' into some sort of mysticism. That's also the gist of this article: Gould says triomphantically: I told you so! It's all a lot more complicated! As if anybody ever claimed to understand the lot.

    Gould's eternal enemy, Dawkins, has in my view a much saner approach: reductionism. Sure, the complexity is enormous, but if we don't try we'll never understand it. And of course the simple models we can make up using reductionism don't show the full spectrum, but at least it's a path to more knowledge. Instead of ridiculing them, as Gould does, you can improve them.

    Gould's remarks about religion and science not biting eachother clearly shows were he stands: he has a deep religous feeling about the underpinnings of the world we live in, and he would be truely disappointed if we would unravel too much of the mystery. Not a healthy attitude in science, I would say.

    Yes, this is prejudiced, based on the few things I read. I could be misguided...

  • by mc6809e (214243) on Monday February 19, 2001 @08:13AM (#420259)
    Consider the results of using evolutionary methods to design circuits for FPGA's.

    http://www.cogs.susx.ac.uk/users/adrianth/ade.html [susx.ac.uk]

    Nearly always, the circuits that evolve are smaller than those that are designed by an engineer. Here, the gates of an FPGA appear analogous to genes. It seems that these experiments with FPGA's might have predicted fewer human genes. I wonder what else these experiments might predict is going on in humans.

    These FPGA's have odd failure modes. Is there a connection with certain human diseases?

  • by SpinyNorman (33776) on Monday February 19, 2001 @08:20AM (#420263)
    To whoever modded me down to troll:

    Gene's code for proteins, not for your ass or brain. A single gene may interact with other genes to create a variety of proteins - this is combinatorial complexity, not emergence.

    Emergence is when a large collection of something has a property that wasn't present or predictable from the component elements. Put together a bunch of water molecules and you get a bulk water with it's emergent property of liquidity.

    Get the difference?
  • Another striking recent result is that commonality between the mammals is even closer than previously thought. Human and mouse are well above 90% DNA commonality.

    Once we get to the bottom of this, I suspect that we'll find 1) life is, at some level, much simpler than we thought, and 2) that's why evolution works. But we don't seem to be close to that insight yet.

    An interesting question is whether detailed knowledge about DNA will allow de-novo construction of life. It's hard to say. It may turn out, for example, that coarse-grained simulation of growth is too inaccurate and fine-grained simulation is too expensive, so "CAD for DNA" may be computationally infeasible. Computational chemistry has been struggling with that problem for years. The physics underlying chemistry is well understood, and experiment agrees with simulations based on the physics. But the computational load limits ab initio simulations to situations up to a dozen electrons or so. Beyond that, major simplifying assumptions have to be made, and the results start to diverge from reality quite quickly. Chemistry thus still requires experimentation.

  • I heard on the news the other day that this could mean that our complexity is more dependant on the proteins these genes produce rather than the genes themselves. I'm no expert, this is just what I heard...
  • It seems many human genes code for multiple proteins. In my naive view, this code easily solve the mystery; more complexity per gene instead of more genes....

    No need to review nature-nurture debates as Craig Venter suggests (although those debates are always nice...)

  • by jemfinch (94833) on Monday February 19, 2001 @11:53AM (#420273) Homepage
    No one has mentioned chaos theory because this isn't it.

    Chaos theory says that even with simple rules, systems can be unpredictable. It doesn't say more than that. It doesn't mention emergent systems because that's not covered by chaos theory.

    "the study of systems which have very simple equations of motion, but which have an extremely complicated behavior" is a perfect description of Complexity Theory. Complexity is the science of life at the edge of chaos and order, where complex systems emerge and adapt from a handful of simple rules.

    Check out the book "Complexity" by M. Mitchell Waldrop for an excellent Gleick-esque portrayal of the emergency (pun intended :)) of complexity as a science.

    Jeremy
    --
  • by Siqnal 11 (210012) on Monday February 19, 2001 @06:51AM (#420278) Homepage
    It's not a troll just because you don't get the joke.

    --
  • Whether it's 100000 genes or 30000 genes, it has always been clear that how those genes correspond to physical traits is at best a very complex proposition. After all, genes code for proteins, not for body parts. If that wasn't clear to Gould, maybe he should have paid more attention to molecular biology.

    The reason why many people believe that genes correspond to morphologies is because, despite the fact that genes code for proteins, it is empirically justified in a certain sense: genetic alterations in specific genes have been observed frequently to correspond to specific morphologies. Of course, that can be explained because those are the only alterations that are easily observed. It is likely that many other mutations have such widespread effects that they just cause death during development. And molecular biology has given us ample examples for the fact that many genes have many functions throughout development (e.g., "combinatorial codes").

    All this has been abundantly clear to many molecular biologists for decades, including Gould's colleagues at Harvard. Unfortunately, there seems to be a class of scientists that make a name for themselves by stating that everybody else in their field is plain dumb and then restating the obvious as if they were the first to think of it. Sorry, but as a far as I'm concerned, while Gould expresses things very well, he hasn't said anything of interest in many years.

  • It seems that it's a joke based on a bad Japanse to English translation. This should help you out a bit. It's damn funny.

    http://rmitz.org/AYB3.swf [rmitz.org]
  • by bcboy (4794)
    The "number of genes" they are calculating could be wrong. These are based on gene predictors, right? Which are just statistical models that try to guess where genes are. These thousands of genes have not actually been verified in a wet lab, and there could be many that aren't being seen by the predictors.
  • Actually, the number-of-genes calculation has been getting increasingly refined. Early rough guesses had it around 100k. This got revised down to 60k and we just let that stand pending actual sequencing of the genome. Now that that's been done, 60k turned out to be more like 32k once we ran the sequence through a computer to look for tell-tale signs of genes. Its not just statistical at this point, and I doubt there will be any further major revision of the number.

    On the complexity side, each of these genes on average can produce at least 2 different versions of its protein through alternative splicing, so the protein complexity remains up around 60k. And each of these proteins can have more than one function, and each function can be combined with the activity of more than one other protein...

  • The total number of genes in mammals seems to be
    not much more than twice that of invertibrates,
    but individually they've become more complex.
    Mammalian genes have more dead spots,
    code for multiple proteins, and so one.

    I was disappointed that there wasn't
    a good count of human genes yet,
    compared to the simpler genes of the fly and worm.
    But it is the complexity that isn't well understood yet.

  • The reason why there are 'fewer than expected' genes in the human genome is because over the last few years there has been a lot of bogus science claiming that all human behaviour is governed by our genes. Thus we saw claims that criminality, sexuality, poverty, being rich and even unemployment were somehow connected to genes. Strangely there was no-one postulating a 'right-wing bigot gene' or 'bogus scientist' gene. Although many challenged these claims on the basis of formal logic, research based on what has now proved to be erroneous (and in some cases fraudulent) assumptions still went on. Many were indeed getting concerned that the old Nazi 'science' of eugenics was making a comeback. One of the 'surprises' of the results of the mapping was that there is no difference between so-called races. Well, IANAG but I could have told them that.
    Perhaps people will now have to look at other causes for aggression, crime, unemployment, poverty et al, such as socio-political forces. But then again that might turn out to be just a little uncomfortable for some people.
  • by pohl (872) on Monday February 19, 2001 @06:52AM (#420294) Homepage
    I really can't see that a human is only half again as complex as a roundworm!

    But with each additional gene, the number of interactions between its expression and the expressions of other genes rises exponentially, doesn't it? If I'm surprised by anything, it's that people actually thought there might be a "gene for foo".

  • The research is pretty clear that there is a genetic component to many aspects of behavior. For example, twin studies have shown a genetic component to bipolar disorder. There is a 57% concordance of bipolar disorder in monozygotic twins, and a 14% concordance in dizygotic twins. Other behaviors linked to genetics include attention deficit, dyslexia, and male homosexuality.

    However, most behavior is influenced significantly by non-genetic factors that we don't understand...the other 43% non-concordance of bipolar disorder in monozygotic twins, for instance. In addition to that, there are very few behaviors that are dependent on a single gene mutation alone (Huntington's disease is the only one I can think of).

    For a good understanding of where we stand today with behavioral genetics, check out Toward Behavioral Genomics [missouri.edu].

    Many people link behavioural genomics with racism, but this is incredibly bogus. The strongly conserved genes that make up "racial identity" are limited to those evolved for survival in different environments (too much UV, not enough UV, etc.) Within the "races", there is plenty of genetic diversity and a wide range of different behaviors.

    Two things are for sure: if government becomes involved in how parents determing the genetic makeup of their children, there will be trouble.

    Secondly, there will be widespread access by parents to this kind of genetic behavioral information, and potentially mechanism to alter the genome of their child. Government won't be able to stop that, it will make the war on drugs look winnable. Reproduction is an exceedingly emotional subject, look at the abortion debate for example.
  • The metaphor has some value in looking at software design. But it fails to resolve any flame-wars over OS superiority.

    "In the Unix philosphy, each little script is totally self-contained, its operation can be analyzed independently of the context, and combining several scripts will just yield the combination of their results.

    "Our genes, on the other hand, are not independant from each other: the presence of one given gene can have significant influence on the expression of another gene. A genotype cannot be analyzed gene-by-gene: the result of a genotype cannot be predicted from the result of each gene taken separately."

    Complexity theory supposes that both of these things are true: That the individual parts of a complex whole are capable of being analyzed for their own simple behaviors AND that they can interact with each other in ways that cannot be totally predicted or understood from the behaviors of the individual parts.

    Note that I have not assumed that genes are prime exemplars of complex phenonena. I believe they are, and Gould has proposed one way in which they might be. But there are other ways in which they might produce complex results. And we do not know for sure whether genes are, in fact, complex phenomena as envisaged under complexity theory. And we certainly do not know, if they are complex phenomena, which of the many possible ways the complexity could arise are in fact true about genes.

    It is an interesting point to ponder (whether UNIX or Windows programming is more similar to our genes). But the level of abstraction at which interaction takes place does not answer the question in any final manner. We do not know yet how much one gene can become directly involved in the functioning of another gene.

    It is clear that both Windows and UNIX programs have some degree of interaction which is possible between programs. It is also clear the levels of interaction are generally different on the two platforms (although more by culture and economics than by operating-system fiat). What is not clear is whether the level of interaction between individual parts of programs in UNIX or in Windows is more conducive to emergent behavior.

    I think I can prove mathematically that both systems will necessarily produce complexity not found in their constituent parts. I don't believe I can prove which is better optimized for complexity.

    Perhaps a better question is whether the complexity is being produced efficiently by the code. Here it seems that the human-genome model is very efficient and non-bloated. This hints at some dissimilarity to Windows.

  • > Name ONE problem on this planet that is the result of the poor workings of evolution

    Humans. They destroy the planet and the life forms out there. We have no predators.

    If evolution worked well, we would have either bigger brain to be less stupid, or smaller brain so we didn't invent all the shit that is out there. Or we would have been stupid enough to kill ourself last century. This did not occured. Planet earth is doomed. Evolution at fault. Film at 11.

    Cheers,

    --fred
  • Well, with any luck, this will lead to the Holy Grail of a genetic compiler. I long for the day when we will be able to code life itself, when we can finally overcome the short-sightedness of nature and create the perfect forms for ourselves. Imagine just being able to code up a silicon-based life form, having the DNA assembled by nanites, and then being able to download your brain into it.

    Imagine growing a body who's natural metabolism is so great that you never have more than 2% body fat, or one with neon green skin, or something realy extravagent (like wings). Of course, no meat-flesh could ever possibly match the greatness that would come from being able to put your brain into a computer, but this could prove an interesting diversion, anyways.


    --
  • by Bluesee (173416) <michaelpatrickkenny@NOSPAM.yahoo.com> on Monday February 19, 2001 @07:02AM (#420308)
    Imagine if there were no patents granted for genes. Do you really think that research would stop? Way to get my goat this morning! That and the fact that I submitted a very similar story more than a week ago, before the public announcement, even.

    Well, lemme paraphrase what I submitted (*sigh*): it is even deeper than 'combinations' of genes. The word 'proteomics' may become bigger than the word 'genomics' as scientists discover that the array of proteins and the enzymes they create are more responsible for the differences in our make-up than the genes that merely create them. One might say that it's the products of the software, and not the hardware that constitutes the individual. I don't know much more about this subject, but would love to hear from someone who does understand this. If any of you seven or eight individuals are reading this, can you please elaborate for us? That would be great!

    Oh, there is an interesting, if a little technical, link on Proteomics here [incyte.com]. Check out the tour.
  • by Phillip2 (203612) on Monday February 19, 2001 @08:37AM (#420314)
    The problem with this whole debate is that 30,000 is just a simple straight forward number. Is it less than we expected? Well given that we had no real metric to measure against its hard to know what we expected. Worse given that we have no embracing definition of the "a gene" its kind of hard to trust the result.

    At the moment there is a lot of stuff being concluded from this simple number. But really they are totally unwarrented. There are not that many genes therefore perhaps genetic determinism is wrong said Venter recently. On what basis? How many genes would have been enough?

    The plain fact of the matter is that this number does not really advance us very much at all. The only reason that people are interested is that is something tangible and simple to come out of the human genome project. Its almost certain that anything actually useful which comes out of the genome data will not be simple, and will not fit into an easy sound bite.

    Phil

  • After all scientists expected 100,000 genes or so, and I think it's doubtful their initial estimates were that wrong.

    Ummm, of course, the initial estimate that the earth was flat, a plane could not fly, leeching, burning witches at the stake to get rid of the Devil in them were right on. Them crazy scientists are never wrong.

    -Spackler

    PSig: I was going to include the one about how masturbation caused infirmities, but I have had this odd facial tick lately.
  • by update() (217397) on Monday February 19, 2001 @08:40AM (#420317) Homepage
    Like a lot of Gould's writings, this piece broadly hints that:
    • Earlier scientists were wildly misguided, if not outright stupid or malevolent
    • Something entirely new is being presented here

    The "roughly 100,000" number was based on an off-the-cuff calculation of dividing the estimated genome size by the size of a "typical gene." There was no assumption that humans "had to have" lots more genes than other organisms.

    The idea that molecular biologists have been fixated on the presence or absence of a particular gene is ludicrous. Gene regulation, protein interactions, splice variants -- there have been thousands of labs studying these things for a decade.

    In the most reasonable and widely discussed mechanism, a single gene can make several messages because genes of multicellular organisms are not discrete strings, but composed of coding segments (exons) separated by noncoding regions (introns). The resulting signal that eventually assembles the protein consists only of exons spliced together after elimination of introns. If some exons are omitted, or if the order of splicing changes, then several distinct messages can be generated by each gene.

    Here's my prediction: splice variants will turn out to be nowhere near as important as he thinks. Other levels of regulation will be far more important. (It's not my impression that this is remotely "the most widely discussed mechanism," anyway.)

    On a completely different topic - the fact that a system has complex interactions doesn't necessarily make it chaotic. Chaos theory has great value but it's not the answer to all, or even most, complicated questions.

  • It is amusing to hear that now that we know that we have relatively few genes, we feel compelled to invoke some combinatorial arguments to differentiate ourselves from fruit flies. Most folks just want to 1) get laid, 2) acquire stuff 3) go to the bathroom. We read /. so we do need one more gene than our prokaryotic friends. These results should not come as a surprise.
  • Does having more genes make you superior?

    Rice has more genes than humans. Most people would consider themselves superior to rice. Even those who aren't.


    ________________________________________________ __
  • And remember that computers are very simple indeed.
    There are more transistors in 8086 [washington.edu] than genes in your body.

    And yet it's not exactly the cutting edge.

  • by Thomas Miconi (85282) on Monday February 19, 2001 @07:02AM (#420325)
    "Emergent properties of the combination of genes" have been known for decades to be the dominant factor in genotype-to-phenotype translation. AI computer scientists working on genetic algorithms have called this epistasis, borrowing the word from biology (see here [arizona.edu]), and giving it a slightly broader meaning:

    "You have epistasis when the expression of a given gene has a significant effect on the expression of other genes, thereby inducing the fact that a genotype of N genes cannot be analyzed by observing the effect of each gene separately". The unwritten corollary being: "which is quite a pain in the ass".

    Genetic algorithms work best (in comparison to other methods) when the problem space is highly-yet-not-too-highly epistatic. See this page [navy.mil] for extensive information, or just try a Google search [slashdot.org].

"Irrationality is the square root of all evil" -- Douglas Hofstadter

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