This isn't really all that surprising a discovery, though it's nice to see gene expression finally getting its due attention.

For the computer programmers in the audience, the simple way to understand it is that every gene is a conditional statement (i.e. IF (foo) THEN {bar}). Under such-and-such a condition gene X does Y, which of course can include nested conditionals and function calls in the form of a cascade of expression on other genes. If you've done any programming at all, you know that making a simple change in the conditionals can have a profound effect on the way a program behaves.

Understood this way, the whole thing becomes very "well duh!" and you're left wondering why anyone was ever puzzled by how a 2% difference in coding sections of the genome could result in such a significant phenotypic difference. But then most people don't have the software background, and those who do sometimes get bogged down over the eye-glazing molecular chemistry stuff. (This is roughly akin to being bombarded with details about the physical properties of transistors and magnetic platters. Substrate is irrelevant if you're just interested in the algorithm!)

Incidentally, this is another nail in the coffin for the notion that the past 10,000 years or so hasn't been enough time for human populations to evolve significantly. Tiny mutations can make a big diff, and selection is ubiquitous...

Also, the analogy presents a good way of making sense of some very confused nature/nurture arguments. Innateness and plasticity in the brain, for example, aren't in conflict but are orthogonal to eachother -- you could have a highly specified brain structure mapped out in the genetic code, combined with routines enabling a high degree of neural rewiring. Organisms can also be programmed to react and develop differently in different environments.

Ten trillion cells full of proteins. Quite a system to model. (Not to mention the trillions of bacteria living on our skin and in our digestive system.) We'll need quantum computers to model the entire system.

"Goedel, Escher, and Bach" discussed this issue about 30 years ago. Still a good read - in fact I am working on it now.

"How is evolution kind of like the famous TV show "Iron Chef"?"

Actually now that i think about it, Creationism has some striking similarities to the Iron Chef as well. Think about it, benevolant aristocrat builds a castle for all the action to take place in. You are left to your own devices for a time, and then at the end you get judged... by a minor Japenese politician, a B movie star, a grouchy restaurant critic, and sometimes Yokozuna. Now that sounds damn familiar, although i'll allow i nodded off quite a bit during Sunday School and had some odd dreams.

"Still, we'll never get to the answers if we don't pursue the ideas in a scientific manner, and look for them properly."
- Some things we will learn by looking at specific genes, but some things we will not for a long time, because of this complexity of interactions. We should be looking at the systemic process instead of individual genes: we cannot learn which way evolution pulls a species just by studying the actions and the intent of individual members, and we cannot predict the effect of a free market system simply by looking at the goals of individual buyers and sellers.

It might be better to look at the systemic system of rewards and punishments for individuals in a marketplace, and similarly it might be better to look for certain external conditions for a species that trigger genes, and the process of adaptation, to understand genetics.

For example, when a species faces strong adversity and is almost wiped out, that is when an evolutionary change is triggered. Why? Because a) the number of members is smaller, making new gene propogation quicker b) the strong external pressure ensures that a small difference in survivability will make a big difference (when all members survive, there is no difference between the "stronger" and the "weaker").

There might also be specific chemical conditions in an individual that have an impact on which kind of genes get triggered, and which do not. There might be combinations of genes which could be grouped together as logical units in terms of interaction with other genes. Etc.

Scientists sometimes do not look at the whole system when studying problems, and focus on individual actions/genes to understand the whole.

#6 "We should be looking at the systemic process instead of individual genes:"

George -

I assure you this is exactly what the field of genomics deals with. It is the macroeconomics to genetic's microeconomics. Compartive genomics, functional genomics, population genetics, etc.. all work in concert together to tackle these problems and more. The synergies are just beggining to materialize.

What is even more exciting is the addition of computer scientists to this field of study.

The question should be: Can you be a Republican while supporting evolution? Or will you be forever in the closet? (kind of like log cabin Republicans)

Sorry, but even with degrees in forestry (the biology angle) and computers (the logic angle), evolution seems illogical and biologically unlikely. Let's tackle the logic angle. My daughter's biology textbook puts the first appearance of mammalian life at about 220 million years ago. Usually this is presented to be some sort of shrew-like animal. Now, I look at man and see no noticeable changes for, say, the last 5000 years (size doesn't count - a bigger human is still a human, just like a super-sized order of fries is still fries). So, I divide 220 million by 5000 and I get 44,000. 44K iterations of a period that shows little change (actually, no change, IMHO) is supposed to result in a shrew evolving into a human (not to mention all the other thousands of mammalian species)? Really? Even allowing for accelerated evolutionary periods (and where's evidence for that?), I'm sorry but I can't buy it. And the argument that our evolution has slowed seems to beg the point - where was it proven to be faster?
I haven't yet had a cogent response to this from supporters of evolution. One responder claimed an evolutionary improvement in the voice box could have accelerated the process. I maintain that if the initial shrew was fluent in five languages, the given time frame still isn't sufficient to account for all the necessary changes.

"My daughter's biology textbook puts the first appearance of mammalian life at about 220 million years ago. Usually this is presented to be some sort of shrew-like animal. Now, I look at man and see no noticeable changes for, say, the last 5000 years (size doesn't count - a bigger human is still a human, just like a super-sized order of fries is still fries). So, I divide 220 million by 5000 and I get 44,000."

So you are taking one particular case (modern humans) and their 5000 year history and applying that to 220 million years? That is .002% of the timeline, any chance modern humans in that tiny spectrum might be anamolous in some way? It occurs to me, for one thing, that you have also chosen one of the most wildly successful creatures in nature in the apex of its acendency. In other words, humans had little reason for radical evolutionary changes to be favored. They were spreading like wild-fire as is. Now in isolated habitat evolutary pressures would be expected to play more significant roles- and they did such as the various pigmy communities in the Pacific. A hobbit-like human sub-species certainly seems reasonably radical to me within the last 12,000 years.
I cant help the pun: forestry degree or no, I dont think you are seeing the forest for the trees. Apologies to everyone for that.

Roger -- Lots of species seem apparently unchanged for millions of years. And with humans spread out over the entire world with relatively limited interbreeding over the last 5000 years, there has been no way to spread changes over the entire species. But there is also a lot of evidence for rapid change, especially with small isolated species in a changing environment.

There is a good amount of fossil evidence with well-dated fossils showing bursts of change and long periods of stasis. Stephen Jay Gould popularized this as "punctuated equilibrium" and his books are a good read on this. (He is, justifiably I think, criticized for claiming invention rather than just emphasis of this phenomenon.)

We know from domesticated animals how quickly populations can change under selection pressures. Yes, it is conscious selection pressure, but it does demonstrate how quickly change is possible and how much genetic diversity resides in a species. That Lhasa Apso is descended from wolves in the last 5000 years.

Lots of laboratory experiments with quick-breeding species can produce astounding rates of change with just various environmental variations.

I'm curious -- do you have, or know of, any reasonable alternative explanations? We know -- incontrovertibly, I'd say -- that selection pressures can produce significant biological changes within a species. Darwin's theory fundamentally just says that this same effect is responsible for larger changes such as speciation as well. Do you think there is some threshold at which another effect -- natural or supernatural -- has to kick in?

"I'm sorry but I can't buy it. And the argument that our evolution has slowed seems to beg the point - where was it proven to be faster?"

Dog breeding? Somehow the British mastiff was changed from a 100 pound dog of war into a 40 pound pug unable to reproduce without human intervention all within a few hundred years.

Well, Eros, you're apparently another one of those arrogant lefties who believes "intelligent conservative," to say nothing of "conservative intellectual," is an oxymoron. But the answer to your question is yes. A Republican can accept that the theory of evolution is the best explanation we have for the facts we have (I guess you could call that "supporting" evolution, though a natural process needs no "support" from anyone, conservative or liberal). We Catholics can also be religious and accept evolution thanks to Augustine (see "On the Literal Interpretation of Genesis") and Aquinas. I think you might want to expand your circle and meet some actual conservatives rather than knee-jerk stereotyping us.

Curt and Mark - thanks for both of your responses - well, except for that trees pun - further proof that, if anything, we're devolving...actually, I had to leave forestry for computers because my bark was worse than my bytes...

Let me take this a step further, using some of each of our suppositions. Say we have this 44K iterations, again. Let's say half of those iterations are 'hyper', i.e., change occurs at 2 to 3 times the pace of 'normal' periods (this seems generous IMHO). In effect, that would mean you 'increase' your iterations to 88-132K times. Still having trouble seeing how you get from a non-talking, non-thumbed, first generation shrew to modern man (and the many other diverse mammals). Can you tell me sincerely that this doesn't trip you up even just a little bit?

As far as the dog breeding goes - not meaning to sound snarky/smart alecky, but how many breeding cycles before you get a non-dog? Given all the breeding that's gone on with them for thousands of years, isn't it interesting that no matter what breed, when I see it, I don't think "What kind of animal is that?". From the smallest to the biggest, the least hairless to the most, they're still dogs. Even wild-bred dogs look remarkably similar to the most domesticated (for example, wolves and German shepherds).

Looking forward to your responses.

"...actually, I had to leave forestry for computers because my bark was worse than my bytes..."

Bytes? Oy vey Roger, you're such a character. [rimshot]

Awful jokes aside, Roger, since you have the computer background you should be able to grok my analogy above in comment #1. Small changes make a big diff. Even setting aside the highly variable rate of evolution, you're falling into the fallacy of assuming that it takes big changes on the genome to result in big changes in the phenotype. But it just ain't so. That's the whole point of this story.

You really ought to learn a bit of genetics before you start wandering into this stuff. You are approximately in the position of someone who looks at the history of computers and claims he has no idea how you could have gotten from the Manchester Mark I to Blue Gene in a mere 50 years. Mirabile dictu, it happened.

"I had to leave forestry for computers because my bark was worse than my bytes..."

Ohh thats low. Outstanding.

" Say we have this 44K iterations, again. Let's say half of those iterations are 'hyper', i.e., change occurs at 2 to 3 times the pace of 'normal' periods (this seems generous IMHO). In effect, that would mean you 'increase' your iterations to 88-132K times. Still having trouble seeing how you get from a non-talking, non-thumbed, first generation shrew to modern man (and the many other diverse mammals). Can you tell me sincerely that this doesn't trip you up even just a little bit?"

It trips me out plenty but a whole lot of things in nature do as well that are true. The problem I have with your scenario is that when you spit ball numbers like this chances are you are going to go wildly astray. You say 44k iterations, but as the first mammals spread out (possibly extremely quickly, we see how fast new or foriegn species can invade an ecosystem) you develop divergent populations almost exponentially. So to put it in electronics terms there is a huge amount of parrallel processing going on over millions of generations and wildly varying circumstances. Until a stasis is reached you are going to see a burst of development that just isnt comparable to contemporary times.

"As far as the dog breeding goes - not meaning to sound snarky/smart alecky, but how many breeding cycles before you get a non-dog? Given all the breeding that's gone on with them for thousands of years, isn't it interesting that no matter what breed, when I see it, I don't think "What kind of animal is that?".

Because we've only seen a few thousand years or so of breeding, and moreoever it is being directed to intentionally remain 'dog-like' in certain regards. My question back to you is what was the first cave man thinking 10,000 years ago when he said 'where the hell did that wolf go and what is this new thing?' My answer is- probably nothing because the change was subtle and across still signifcant swathes of time. I think people expect speciation to be radical in 'human time' and its not necessarilly the case. Look at a wolf compared to a husky, the difference is subtle and probably indestinguishable if dogs wernt omnipresent in human life. Of course a few hundred years later you have a Mexican Hairless that looks like something from BetaCrom VII. You tell me which species the huskey looks like it belongs to given that comparison.

Where has evolution proven to be faster? Um, duh - try germs.

A good deal of the science that keeps major epidemics et. al. at bay right now, and may save our lives going forward, is heavily predicated on the theory of evolution. Reverting to any other explanation that could not account for and offer mental tools to deal with the rapid mutation and transformation of pathogens and viruses would be dangerous almost beyond words (do the words "antibiotic resistant strain" mean anything to you?).

It's one thing to offer a better theory that gives us such tools. But a know-nothing "I don't believe it" pose, well... until you have a better and more useful explanation, allow me to offer an Arab saying: "the dogs bark, but the caravan moves on."

And thank goodness for that, for all our health.

One might look at the evolution of Ashkenazi Jews and why they are about 1 standard deviation smarter than the average human population.

This change in population intellegence took place over a period of about 500 years. The advance was about 1 IQ point per generation.

Roger, when you say "2 to 3 times the pace of 'normal' periods (this seems generous IMHO)", I think you've got it very wrong here. In certain periods, change can be hundreds of times faster than in periods of relative stasis. A significant change in the environment, whether because of movement and isolation of a population, or something like climate change, can cause a radical change in effective selection criteria, with a correspondingly quick change in the genotype of the population.

Roger,

Your post got me thinking about gradual vs. punctuated evolutionary models - here are a couple of reasons, offhand, why generalized adaptation in humans might be subtle, rather than dramatic (though I don't think that your premise that, to paraphrase, 'the last 5000 years have shown stable evolution, therefore the last 44K sets of 5000 years must've been stable' holds water - geology suggests dramatically different average conditions in earlier eras, during which selection pressures could've been correspondingly different). And of course, if you don't believe in evolutionary biology, then the following arguments are irrelevant, as you don't beleive in genetics, geology, chemistry, physics, or modern medicine, since these fields are consilient (ie., based on concordant theories and shared, cumulative empirical observations). Still, thanks for starting the discussion.

> allowing for accelerated evolutionary periods (and where's evidence for that?),

google Cambrian explosion. Transitional fossils (winged lizards, stumpy snakes) might also suggest punctuated evolution, if they cluster during specific geological periods. For humans, googling the timelines of various extinct sub-species pf homionids may be informative in this regard. There is also some evidence in the humnan genetic evolutionary record for quite dramatic, relatively recent changes (say... ah, here http://www.newscientist.com/article.ns?id=dn7539 or here http://www.nature.com/nature/journal/v437/n7055/full/nature04101.html;jsessionid=85830CD0823FD3AD06A08A32ED3ABA2E)

With a nod to Joe (post #17), there is currently strong selection for hiv resistance at the T-cell receptor level in sub-Saharan Africa. This selection is very strong, but at the level of the phenotype, opaque (ie., you can see it through x-ray crystallography or immunostaining, but to all appearances these strongly selected for human variants are just people who have the phenotype of "not dying from hiv". A crucial survival adaptation that will be invisible in the fossil record may be the rule rather than the exception.

The absence of visible changes during recent human development may not be as significant, particularly if humans are in an ESS (evolutionary stable state). If "typical" modern humans are sufficiently successful at reproducing, then, like the fossil record of sharks (who have a much, much longer duration as a species than us), most of the observed adaptations will be in size (ie., bigger to take advantage of abundant/large prey, smaller for the converse).

The relative complexity of human reproduction at the molecular level may also result in a more "brittle"/less flexible genome (due to imprinting, which as far as I know is limited to higher primates). That's just a swag (scientific wild-ass guess), tho.

Another possibility is that, since humans as a species(currently and historically) practice infanticide/tribal genocide, there may be strong selective pressure against radical human variation. On a less existentially horrific note, there are over 320 reported mutations that affect human facial appearance http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM&cmd=search&term=craniofacial+), but few that seem to improve human reproductive success. Human variants like being blue (Diaphorase deficiency), tailed, crab-handed, and extremely hairy exist, but they'd better have great personalities! A tendency towards visceral aversion to even relatively trivial differences (or a preference structure biased towards the average during sexual selection) may tend to keep social primates like humans closer to a baseline norm.