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Gould Op-Ed: Genes' Emergent Properties Matters
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."
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.
Seastead this.
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.
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?
Vidi, Vici, Veni
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
Vidi, Vici, Veni
(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
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?
---- SIGFPE
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.
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.
"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.
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Non-meta-modded "Overrated" mods are killing Slashdot
(Hey Ryan! Here's your proof!)
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?
Vidi, Vici, Veni
Wait!!! There's more!
i nf orum.showMessage?topicID=1491.topic
/. 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.
http://pub2.ezboard.com/fsobserverssobserversma
I hope
If tits were wings it'd be flying around.
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.
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.
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 is a greater offense to steal men's labor, than their clothes"
"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.
Danny.
I have written over 900 book reviews
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.
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 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."
"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
--David Hull in Science as a Process (1988).
Nature is rather prone to suboptimization, no? Not that we'd necessarily do any better...
Extremely funny. Where did I put those mod points?
Follow the link. It is at least as funny as PD implies.
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E_NOSIG
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.
I heard a great analogy on the Discovery channel one day (arguably aimed at kids):
.bashrc file on occasion. Even if their system is voice activated AI like Genesis suggests. :)
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
-Michael
-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%.
But isn't half the fun in life seeing what random kookie things that Windows does?
... err.. personality any day over a cold / impersonal Solaris.
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
-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.
-Michael
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 and climate engineering, what makes this perticular use of technology so horrible (besides your own spiritualist clinging to false ideas about the sacredness of life?)
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Feminism is the wild notion that women are human beings.
You write: "Isn't this a lot like having a lot of small programs that, when scripted together, can outperform a large, monolithic one?"
:o)
:o)
Alas, I fear it is the exact opposite
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
Thomas Miconi
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
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Also FatPhil on SoylentNews, id 863
"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.
Let's try not to let fact interfere with our speculation here, OK?
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.
SDMI: Finally! Music that won't rip or burn! Brought to you by the fine folks at RIAA.
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 most controversial site on the Web
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
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the pen is mightier then the sword. the sword is mightier then the court. the court is mightier then the pen.
http://www.cogs.susx.ac.uk/users/adrianth/ade.html
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?
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?
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...
No need to review nature-nurture debates as Craig Venter suggests (although those debates are always nice...)
It's not a troll just because you don't get the joke.
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You are a fucking moron.
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
If tits were wings it'd be flying around.
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.
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.
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 "cue the foo posts in 3, 2, 1..." posts will commence with no subsequent foo posts in 3, 2, 1...
The metaphor has some value in looking at software design. But it fails to resolve any flame-wars over OS superiority.
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.
Eternal vigilance only works if you look in every direction.
> 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
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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.
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Feminism is the wild notion that women are human beings.
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.
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.
Rice has more genes than humans. Most people would consider themselves superior to rice. Even those who aren't.
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"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), 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 for extensive information, or just try a Google search.