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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."
So are you saying productivity should be measured by counting lines of output? ;-)
-- ;-)
Kuro5hin.org: where the good times never end.
You can make up your own mind as to whether I'm kidding or not.
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.
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.
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.
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?
Vidi, Vici, Veni
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?
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I'd rather have a bottle in front of me than a frontal lobotomy.
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 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!
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
Vidi, Vici, Veni
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
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.
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...
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
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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
Read the sig.
Where's the submit button??
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.
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
--
Also FatPhil on SoylentNews, id 863
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"
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Also FatPhil on SoylentNews, id 863
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.
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".
Carefree highway, let me slip away on you.
No es una moto, es un helicoptero
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"
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.
"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.
Da Blog
Danny.
I have written over 900 book reviews
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 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.
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).
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?
Don't like my sig? I don't either.
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
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Learn the rules so you know how to break them properly.
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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.
IANAGeneticist, but 30000 combinations of the four possible base pairs works out to 4^30000 possible combinations. Not only is that much greater than the number of people who have ever lived, it's also greater than the estimated number of atoms in the universe (which I've seen estimated as less than 2^65536).
20 January 2017: the End of an Error.
Well, I think the scientists have it right, anyway. It seems obvious to me that Mother Nature is very good at compression. When a cell divides, the DNA must be copied. The protein that does this is called a telomere, and it does so at 200 bases per second. There are many telomeres operating at once to copy your DNA, but the fact that there are Billions of base pairs means that it takes a long time.
Amoebas and other small bacteria get round this by starting to copy the DNA's copy before the Cell has even split, so that it is copying the next generations DHA ahead of time.
Despite this, it is clear that Mother Nature has a vested interest in compressing data to a great degree. Considering that we are composed of, effectively, nanotechnology beyond our wildest dreams, it wouldn't surprise me if the compression technology is equally advanced. Why waste resources, and more importantly, time?
As the DNA mechanism was in its present form, more or less, several Billion years ago, before multi cellular life arose, we can see that our peculiar DNA compression technology is a hangover from the time of single cellular life, when time was short and DNA had to copy itself quickly.
Of course, much of what I say is speculation, but I consider it very interesting speculation.
--
Clarity does not require the absence of impurities,
/* And you'll never guess what the dog had */
/* in its mouth... */
--Larry Wall in stab.c from perl
There is plenty of evidence to support microevolution; no one is debating this. However, macroevolution is an entirely different matter. Even given that a species can change from an ape into a human, which is probably just inside the scope of credibility, although I seriously doubt the conditions were present to force such a change, I would still have a pretty hard time working out how all that life happened in the first place. Like the previous post says, the "simple" cell is a most complicated thing. In fact, all experiments attempting to cause spontaneous "cell generation", involving a duplicate of the conditions that were present when the Earth was young and evolution supposedly started to happen when organic molecules started randomly interacting, have failed completely. It is not that we do not know the theory of how it should happen; we do. It's not that we can't accelerate the process or even give it much better conditions. We can. It simply won't happen. In fact, the probability of a cell spontaneously generating out of a primordial soup have been calculated at about the same as if I took a sledgehammer to my Swiss watch, dumped the bits into a box, shook it once or twice, and pulled the watch out in perfect working order, telling the correct time. This is roughly equatable to a ratio of 1:10^40000 which, if you understand a thing about mathematics, you will realise is an extremely large number; ie an incredibly low probability. Oh sure, it could happen, but then for that one cell to survive long enough in the rather inhospitable primordial soup to replicate and make more of itself, and for them to become more sophisticated, and write new DNA structures...and now I'm getting out of my league so I'll shut up in case I do an M$ spokesperson stunt (open mouth, insert foot). The point of all this is that evolution could, theoretically, happen. But to say the chances are infinitesimal barely does it justice. Scientifically, I believe that the probablity I quoted is so close to 0 that it is zero to all intents and purposes. What evidence do I have about what did happen? Well, if I told you that, you'd simply laugh, so what's the point? Besides, it would take me all night, and you'd fall asleep after the first paragraph.
return 0;
According to whom? There's lots of evidence of intelligent design in the universe.
Would you reject the concept of a designer because it conflicts with your philosophy or preconceived notions?
But Herr Heisenberg, how does the electron know when I'm looking?
What you are looking for is the field of bio-informatics, which integrates mathmatics, computer science, and biology. (With some chemistry, physics, and philosophy thrown in for good measure.)
As far as self-analysis goes, it's something that human beings do every day, which is "code" that analyzes itself.
Don Armstrong -".naidnE elttiL etah I"
http://www.donarmstrong.com
>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%.
What is complexity?
1) What is(are) the timing mechanism(s)?
2) what is the programming sequence that creates a certain structure correctly?
3) How do we control the process so that birth defects/organ damage can be avoided while not interfering with the natural processes of mutation and evolution?
4) Will we be a happier society in having the benefit of genetic correction of certain defects (ie. will we be more appreciative of what we have without the little natural reminders of just how precious life is)? Will we be as driven to succeed without certain adversity? (Would Stephen Hawking be as awesome/well known/driven/smart if he were not physically disabled?)
"Do not be swept up in the momentum of mediocrity." - anon
You're actually almost on the right path.
;-))]
Post translational modification is quite common in almost all eukaryotes. (I think it may even be present in prokaryotes, but I'm not as familiar with them.)
Intron splicing via spliceosomes is modulated by factors such as U2AF (U2 Associated Factor) and proteins such as Sxl (Sex-less [Drosophila]) to produce active and inactive proteins from a single mRNA transcript.
We even see a different type of event called RNA editing in apoB protein, which you probably know forms VLDL's. It can be post-transcriptionally edited by editosomes to generate abortive aboB proteins that make cholomicrons (the super small liposomes). [If I remember correctly, C6666 is turned into an Inosine which turns a ACG into an AUG stop codon. (Sure about the C6666 part, but not about the intervening sequence.
Of course, this is all even before the post-translational modification that we know can take place (addtion of sugars, protein cleave (Ig, Pesinogen, etc...)).
Don Armstrong -".naidnE elttiL etah I"
http://www.donarmstrong.com
actually, i was reading about proteins for my biochemistry class (and according to my studies this article is pretty much full of shit, or at least the "discovery" aspect) and much more interesting than the number of genes, is the way proteins are put together. one word: modular. now, before all you bio/chem types say that proteins are pretty much a direct transcription of RNA, i agree with that. however, it seems that many chunks of proteins share similar components, and many of them are modified by post-translational mechanisms (proteins or organelles). Thus, it seems possible that some genes may encode modular (object oriented even, haha) proteins which are subsequently assembled by other proteins. Thus, one gene that encodes these modular proteins could actually produce through post-translational modification many, many different kinds of protein. One example of this could be gamma alpha beta membrane receptor complexes. anyway... what do you think?
Well :) thanks but no thanks, you don't answer my question :) :) and I'm defenitely not in bio-anyting :) :)
What I want is mahematics and computer science nothing else
I'm talking about something I think I saw at school (loong time ago *sigh*)
And self-analyzing is aboslutely not something human beings do everyday (I'm talking about succesful self-analyzing (i.e. you actually find out "what is this all about")) I'm pretty sure nobody suceeded there
thanx anyway...
cheerz..
Yes, ok, racism is luckily quite convincingly disproved (quite a while ago), but why doesn't that surprise you? It could easily have been otherwise!
And about the science of racism: it can be done well. There is nothing wrong with measuring skull sizes etc. and trying to correlate it with race and things like intelligence. It only gets wrong if you have prejudices about it, and it gets outragious if you base politics on dubious claims. But asking the question should be allright. BTW, it was not only Nazis that believed in racism; all 19th century books I've read were quite 'racistic'.
As an aside, by the law in my country, I am not even allowed to correlate race with anything. Racism is illegal here. Luckily the science backs it up, finding anything else is illegal!
To make it clear how ridiculous that can get: we had a new rule here that made it compulsary for some dog-races to be muled (pittbull etc.). There were some demonstrations which disproved against racism wrt dogs! Racism for dogs in is quite appropriate i would say.
(Yes of course I see the dangers of racism. I just want to point out racism is a question of science, you shouldn't be to dogmatic about it (pun intended). Probably I underestimate the dangers of racism in the current educuated age, and I should be more weary of it).
I think this is one of the fundamental flaws of genetic engineering right now. A bunch of (vary knowledgeable) scientists and/or doctors (who think they now more than they actually do) start mucking with genetics because they've noticed a pattern between the presence or absence of a given gene and some property of the life form they are studying.
There is a whole field of bioinformatics, which applies information theory and statistical methods to gene sequencing. This is a branch of science that (like "chaos theory") is trying to escape the reductionist paradigm that Gould points out as being rather arrogant.
Bingo Foo
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taken! (by Davidleeroth) Thanks Bingo Foo!
Anyway, many posts deal with the fact that it might be disapointing that we are "so simply" encoded and where can the understanding of this coding could lead us to. I also see many posts making an anology between ADN and computer code.
I think I remember it is proven that you cannot write a code that can analyze itself (something like that)
I'd appreciate if someone could *enlight* me with this self-understanding problem
If the mathematical proof does exist (I think it does, but, again, I couldn't find it), then it will have some very interesting consequences:
- - Is this a proof there is no way we can actually understand ou genetic code ? (don't think so)
- - If we get to understand it then:
- - The states machine analogy is (at best) incomplete
:)
anyone ?- There is "something else" about us we still can't have a grasp on (soul ?)
- The proof was wrong (unlikely)
- The proof I'm talking about doesn't exist and I was mistaken in the first place (sigh) (hope no)
You're pulling your maths from thin air. Put that factorial away, it's doesn't belong here.
Side note - I believe there are some frogs with more than twice the number of genes as humans - can anyone verify that for the list?
The "complexity" of what can be achieved with a certain number of genes is more closely related to some kind of busy beaver function.
The inverse function is far more interesting:
Q - What is the "complexity" of our genes' "behaviour"? (I'm thinking of Kolmogorov complexity, or equivalent)
A - It is less than or equal to the number of genes we have. (Oooh, a bit like the Chaitin length?)
So a practical challenge is for people to come up with a model for the behaviour with the smallest complexity, not the other way round.
(I'm not suggesting that anyone will do it for anything apart from simple bacteria and suchlike for quite a while. Having said that, if they've done it for E.Coli, then they're on the way already...)
FatPhil
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Also FatPhil on SoylentNews, id 863
Geez, what ever happened to good old fashioned combinatorial complexity, and Occam's razor ("keep it simple, dumb ass")?
It sounds like Hemos just read about complexity, and didn't quite get it.
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.
But isn't the genome actually comprised of about five individuals? If so, it's going to be jolly difficult to spot inter-gene relationships etc... Garbage In, Garbage Out...
Really, it shouldn't be so surprising that the genetic makeup of a roundworm is that close to that of a human. In fact, there is only a 1% difference in the DNA makeup of an ape as compared to that of a human.
This fact has allowed many genertic-research/manipulation techniques to be perfected such as somatic cell hybridization) on non-human organisms without becoming entangled in the ever-so-present moral and ethical implications of such research (playing God).
The only caveat to this, of course, has been mentioned several times times in this article's threads: it's not the number of genes but the number of combinations. (Adding only 100 genes to a particular genome increases the number of combinations exponentially.)
I wouldn't be surprised at all.
Does having more genes make you superior?
what's he really talking about here? to gould this is part of the debate of "punctuated" vs. "gradual" evolution. it's about the cambrian explosion -- was the resulting biological diversity an accident? was the resulting development of intelligence in homo sapiens a similar cosmic accident? gould answers "yes" to both of these questions and therefore believes that human beings may be the sole intelligent residents of the milky way. [see, among other books, "here be dragons" by simon levay and david koerner]
i agree that the key to human development is "more combinations and interactions generated by fewer units of code." but, let's not overstate the consequences. history and chance certainly played a role in the development of complexity, and the development of intelligence, but its impact was more likely on the timing of the development and not on ultimate emergence of the traits.
nature doesn't do anything just once.
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
Yes, roundworms have different behavior patterns and capabilities when compared to people, and comparing them is like comparing apples to oranges. But you CAN make observations noting the number of behaviors possible, and compare those numbers.
In other words, observe the number of different states obtainable in a given environment, and observe how many different environments result in different states. You can argue about what defines a "state" or an "environment", but even a rough estimate is enough to show that there is a significant difference in complexity between people and roundworms.
Complexity in definitely not a linear function of the number of genes, but it is reasonable to presume that more complex behaviors require more genes.
What I meant to say was 'Eat this combinatorial explosion, bitch.'
The "cue the foo posts in 3, 2, 1..." posts will commence with no subsequent foo posts in 3, 2, 1...
"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.
when we can finally overcome the short-sightedness of nature and create the perfect forms....
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....
This is 'Exhibit A' of the very hubris Gould was talking about.
Bingo Foo
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taken! (by Davidleeroth) Thanks Bingo Foo!
?
and the difference is ?
"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." Probably the case. Perhaps like binary? Every additional bit added to a binary number doubles the resolution of that number. 8 bit gives 256 discrete steps, 9 bit gives 512, 16 bit gives 65536, etc. Perhaps that theory is true. The interaction between different genes giving different effects.
War crimes, torture, lies, illegal spying... Would someone give Bush a blowjob, already, so he can be impeached?
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.
Recent discoveries show many genes code for up to 10 proteins. These proteins all have start codons on different parts of the same gene. Earlier estimates of gene count were often base on the number of start codons, that's one of the reasons for the appearant over estimation.
Humans are clearly more complex than roundworms. If we have hardly more genes then roundworms, then the complexity must stem from other reasons. Craig Venter suggested in his press release environmental factors are more important. That's too short a call for me. I agree, in the 70's everything was attributed to environmental factors. Since then, we've seen the acceptance of socio-biology, and maybe an overstressing of biological factors. But comparing with a roundworm, we clearly need some biological explanations.
If the number of genes is about the same, this complexity must lie in the complexity per gene, or in the complexity of how genes interact. Well, both show plenty of possibility for the missing complexity. Multiple proteins per genes is obvious; the intricacies of complex gene interactions is also a large potential source of ingenious heritage of information. Too be complete, junk maybe not junk. And for a real stretch: maybe some organization in egg-cells other than DNA is passed as information to offspring-cells.
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?
As Gould points out in his editorial, one of the best results of this discovery is that it sounds death knell of reductionist biology. As usual, the human body turns out to be more complicated than anyone could have imagined. ("Gee, we really still haven't explained it all? Gosh darnit!")
I have always thought it was silly to ascribe artistic talent, criminal behaviour, musical aptitude or computer savvy to the foibles of some particular single gene. Now here's independent confirmation of my opinion. Goody! I love being right all the time.
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...
These "comparisons" are in someways useful, but in otherways useless.
For argument's sake let's say that 50% of the silicon in my Psion 5 is the same as the silicon in my Mobile phone (very similar ARM processor core). Is this a useful statement?
Similarly, there's probably a vast amount of the PPC in a Mac that's the same as the PentiumIII in a PC, as they both use well known methods for implementing register files, caches, multipliers etc. The Mac and the PC also both share a PCI bus as well?
Similarly, a linux PC can have 99% of the same hardware as a Windows PC (can easily be 100%).
See the measurements can be made, but they paint such an incomplete picture that they really don't say that much.
You should probably not have dropped science - a good science teacher should teach you a) how to judge and b) how and where to use these "facts".
Even if you don't like what it says, learn it, so that you can argue against it from a more informed view.
FatPhil
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Also FatPhil on SoylentNews, id 863
Now I'm not a bio-tech geek but I'll try to explain. Your genes are stored in the nucleus of your cells. Genes are composed of DNA. In order to make a protein, a section of your DNA is copied into RNA in a process called transcription. (think of it as copying and pasting a section of code) The RNA is then transported out into little protein factories in your cells and the information contained in the RNA is translated into a protein sequence. (think of translating as changing the code from Perl to C) Proteins are encoded differently than genes so there is a translation process to get the information from one to the other.
Now to get back on topic, there are about 30,000 or so genes in the human body and there are effectively 3 gene transcripts for each gene due to the transport mechanism. Coincidentally this number is about 100,000. So what people are getting confused about is that someone didn't understand the difference between a gene transcript and a gene.
Ultimately understanding gene transcripts and how they form proteins will ultimately be much more important in creating therapies for diseases.
I think that the scientists may have missed something in their rush to get to the end of the human genome, because I really can't see that a human is only half again as complex as a roundworm! I mean come on, the human brain on its own is a marvel of complexity far superior to anything else we've discovered. To ascribe this to such a rediculously small number of genes is a sure sign that they've overlooked something.
Are they really sure that they've got everything? I mean most of the DNA is so-called "junk DNA", but maybe it's time to take another look at it. After all scientists expected 100,000 genes or so, and I think it's doubtful their initial estimates were that wrong.
In a way this is a good thing. Now that we've got this problem, scientists will have to search for more clues, and will make new discoveries about life. Somewhere out there has got to be what makes us so superior to the roundworm.
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...
In terms of "popping into existence simultaneously," no. This is your misunderstanding of evolution. There is no popping into existence simultaneously in evolution. There are steps and stages, and the organism is a complete functional whole at any given time. It's not the case of an organism lacking pieces of a later system. This makes it seem like the whole system needs to pop in at once. Really, it's just that the systems start out only needing one thing, and then gain a optional part by some mutation. Later, due to another mutation, that optional part becomes indispensable. The process repeats itself, and the system gets more built up. So in retrospect, we see all these systems that we think are "irreducibly complex" when really, they're not.
Plus, just so you know, your claim that "this is STILL baby's play compared to a multicellular organism" is pretty inaccurate. In terms of complexity, the amount seen within a cell far outranks multicellular systems and organisms.
If you really want to learn more about this, and how it relates to the evolution of a cell, try looking in an evolutionary textbook (look up origins of life, RNA world). However, it seems like you're already pretty sure about what you'd like to believe.
No need to review nature-nurture debates as Craig Venter suggests (although those debates are always nice...)
Then why does the bifurcation ratio of our arteries from our aortas down to the tiny capilary that feeds each cell, conform to Fiegenbaums ratio 4.669i.
Biology has not sussed the mathematics of morphogenesis yet. How is the 3d matrix of bone cell division, encoded in the four bit code of dna?
The thing that amazes me is the information compression ratio. Represented by the chromosomal library. There is a place to find congruences in math, the Mandlebrot set is a good example, basically the Mandlebrot works like it does because of the irrational fracton. Morphogenesis might be pulling the same trick. Biological mathematics work different to human mathematics.
Peter.
It's called an elephant's trunk whereas it is in fact, an elephant's nose, a nose by any other name would smell as sweet
Gould seems to want to show that evolution by natural selection is not really all there is to it (religion notwithstanding), and this article is more of his wishful thinking that there is more to humans than just the product of eons of evolution. His line of thinking seems to be: "We require "emergent" properties, so we humans are more special than all the other animals and plants that are 'simply' the product of evolution by natural selection."
Alternatively, Gould just wants to make a big splash and get some fame. He is a good writer after all, so maybe he is addicted to fame?
What exactly do you mean by spontaneous cell generation, and it failing? That a cell failed to "pop into existence"? Is this supposed to be surprising? Evolution doesn't assert this.
In contrast, if you mean the experiments that have been performed to generate organic precursors to biological molecules, (think Stanley Miller, of U Chicago - is oldest, many replications to date), then you're wrong, because these have worked, and been replicated using different substrates and they have generated a variety of amino acids and biological molecules (Miller's was within a week, btw).
While there are many postulations about the next step in the origin of life: the generation of a self-replicating molecule, all of them are still speculation. So your claim that we "know the theory of what should happen" is incorrect. In fact, most scientists do not claim to know _the_ theory of "what happened" without generating scientific proof in the form of experiments. So your claim that we could know the theory but not be able to do any experiments to prove it true is illogical, from a scientific standpoint.
The probability that you quote (from?) seems to be for the chance that a modern cell will pop up in its entirety all at once. Again, not surprising that it's practically zero.
Your statement about _one_ cell surviving in the inhospitable environment long enough to replicate suggests that you have a different opinion than the general speculation that self-replicating molecules came first, and cellular membranes and cells later.
Doesn't really matter though, since you're not going to tell me your theories anyway. Mmmm, wow, glad you have that much confidence in them that you think I'd laugh.
The Evolutionists will point to this as proff that we all evolved from the same microbes milenia ago.
The creationists will claim this as evidence of a single and extreamly eficent creator.
I will say they are both correct. I.e. Evolution would not have produced the variety and complexity of lifeforms by accident.
--= Isn't it surprising how badly I spell ?
It could easily have been otherwise!
Not at all. It was intellectually bereft and demonstrably so.
There is nothing wrong with measuring skull sizes etc.
and trying to correlate it with race and things like intelligence
Yes there is. For a start 'intelligence' is itself ill-defined. Secondly, trying to correlate race with intelligence is absolutely wrong, precisely because it is actively seeking to establish a basis for racial superiority. And although many 19th century books took the theory of race as a given, it was also questioned at the time and massively rejected during the 20th century.
I just want to point out racism is a question of science
No, it isn't. And it never was. The racists had a theory and then set out to prove it. They never set out to disprove it. That is in itself unscientific. For in depth explanations try looking at the work of Stephen J Gould who nails their kind of pseudo science to wall.
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.
I just hope this means people will stop blaming my mom for my lack of hair.
Someone hates these cans.
Imagine just being able to code up a silicon-based life form
Yeah! Way cool... With that coders will be able to create REAL bugs!
People could probably use a future version of perl to code something like a Platapus, which is:
"Proof that God gets stoned" -- Robin Williams
Keep Trollin' in your Honda punk.
Someone hates these cans.
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.
It's the usenet of the gods. Once the basic DNA coding was done and distributed, spam began to clog the works. Software bloat, the whole enchilada.
Half-heartedly hidden in the object code you can find "!seineew era sreenigne tfosorciM"
SOMEBODY SET UP US THE BOMB
not
THEY SET US UP THE BOMB
Sheesh. k1dZ.
First they ignore you.
Then they laugh at you.
Obliteracy: Words with explosions
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.
Ok, so the scientists thought it would orignaly be around 100,000 genes, but who came up with that number... It was most likley based on some early experiments done on the human genome when they were just guessing at how many it could be. Leave it to the human race to jump to conclusions way too early, probably some over zealous scientist that wanted to be the one to calculate the number of genes. This just proves that they still dont know what the human genome does and there is a lot more work that needs to be done before they go making any other predictions.
I'll be glad to continue this discussion if you're willing to not be an AC.
Email me at tom_cooper at bigfoot dot com for more information.
Regards,
Anomaly
But Herr Heisenberg, how does the electron know when I'm looking?
I recall my 4th grade science teacher saying there was a 98% similarity in DNA between humans and apes, and a 70% similarity in DNA between humans and earthworms. I dropped science at the begging of the next grade.
It can be post-transcriptionally edited by editosomes to generate abortive aboB proteins that make cholomicrons (the super small liposomes) if a drug company could grow some special proteins that enzymatically "fix" defective proteins in diseases like diabetes (eg. insulin and it's associates). i'm not sure how feasible this is, or even how useful it would be, but at least all your bases aren't belong to me.
wow, that was in coherent! >=-}
"How did bacteria end up in here?"
Game: Player 'Donald J Trump' now has AI skill level 'experimental'.
While the complex interaction between genes is an amazing example of an efficient design for storing information, it should not necessarily be taken as the sole source of human complexity.
Obviously we can't reduce development to just what is stored 1-1 in the genome. But explaining away reductionism by saying humans are too complex for a simple genome, ignores the known importance of the environment and makes for an incomplete argument.
"It takes an uncommon mind to think of these things." --Calvin
Even if you ignore the effects of proteins feeding back to gene expression the number of combinations of genes grows exponentially. That they do at least occasionally feed back probably allows an increase in organism complexity to grow factorially with gene expression. To make things more complex, genes are not just on or off, but can be promoted to different levels of expression, which is why many of the cells in your body can be so different from each other.
The prediction of 100,000 genes was a very simplistic guess based on the total number of nucleotides and average gene length. There was little reason to believe that it would give much more than an order of magnitude, and guesses as to the actual number of genes in the academic community ranged over an order of magnitude themselves... because they just didn't know. In fact some would say we still don't know the expressed number, and you can still bet on it:
http://www.ensembl.org/Genesweep/
mitochondrial DNA doesn't count!
"And last June, in the journal Nature Genetics, two teams of scientists independently presented studies with estimates in the range of 28,000 to 35,000 genes".
Still, I think that even scientists have a hard time with combinatorial explosions. For example, it's hard to believe that 256bit encryption takes as many times longer than 128bit to guess at (ideally) as 128bit takes from knowing the answer to start with. Exponentials really don't seem intuitive so usually we use logarithms to simplify things.
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
'nuff said.
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Obviousness is always the enemy of correctness. -- Bertrand Russell
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.
"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.
On that note, it makes me breathe a sigh of relief that genticists won't be able to just 'select' against autism, various neurophysiological conditions, etc...
Gattaca seems to be falling behind schedule, and I am pretty much okay with that.
Jaeger
www.JohnQHacker.com
GodHatesCalvinists.com