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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."
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?
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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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/. 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.
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.
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.
Nature is rather prone to suboptimization, no? Not that we'd necessarily do any better...
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.
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...
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?
It's not a troll just because you don't get the joke.
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You are a fucking moron.
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.
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...
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
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.
"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.