Skip to comments.Artificial Life Experiments Show How Complex Functions Can Evolve
Posted on 05/08/2003 10:11:06 AM PDT by Nebullis
Arlington, Va.If the evolution of complex organisms were a road trip, then the simple country drives are what get you there. And sometimes even potholes along the way are important.
An interdisciplinary team of scientists at Michigan State University and the California Institute of Technology, with the help of powerful computers, has used a kind of artificial life, or ALife, to create a road map detailing the evolution of complex organisms, an old problem in biology.
In an article in the May 8 issue of the international journal Nature, Richard Lenski, Charles Ofria, Robert Pennock, and Christoph Adami report that the path to complex organisms is paved with a long series of simple functions, each unremarkable if viewed in isolation. "This project addresses a fundamental criticism of the theory of evolution, how complex functions arise from mutation and natural selection," said Sam Scheiner, program director in the division of environmental biology at the National Science Foundation (NSF), which funded the research through its Biocomplexity in the Environment initiative. "These simulations will help direct research on living systems and will provide understanding of the origins of biocomplexity."
Some mutations that cause damage in the short term ultimately become a positive force in the genetic pedigree of a complex organism. "The little things, they definitely count," said Lenski of Michigan State, the paper's lead author. "Our work allowed us to see how the most complex functions are built up from simpler and simpler functions. We also saw that some mutations looked like bad events when they happened, but turned out to be really important for the evolution of the population over a long period of time."
In the key phrase, "a long period of time," lies the magic of ALife. Lenski teamed up with Adami, a scientist at Caltech's Jet Propulsion Laboratory and Ofria, a Michigan State computer scientist, to further explore ALife.
Pennock, a Michigan State philosopher, joined the team to study an artificial world inside a computer, a world in which computer programs take the place of living organisms. These computer programs go forth and multiply, they mutate and they adapt by natural selection.
The program, called Avida, is an artificial petri dish in which organisms not only reproduce, but also perform mathematical calculations to obtain rewards. Their reward is more computer time that they can use for making copies of themselves. Avida randomly adds mutations to the copies, thus spurring natural selection and evolution. The research team watched how these "bugs" adapted and evolved in different environments inside their artificial world.
Avida is the biologist's race car - a really souped up one. To watch the evolution of most living organisms would require thousands of years without blinking. The digital bugs evolve at lightening speed, and they leave tracks for scientists to study.
"The cool thing is that we can trace the line of descent," Lenski said. "Out of a big population of organisms you can work back to see the pivotal mutations that really mattered during the evolutionary history of the population. The human mind can't sort through so much data, but we developed a tool to find these pivotal events."
There are no missing links with this technology.
Evolutionary theory sometimes struggles to explain the most complex features of organisms. Lenski uses the human eye as an example. It's obviously used for seeing, and it has all sorts of parts - like a lens that can be focused at different distances - that make it well suited for that use. But how did something so complicated as the eye come to be?
Since Charles Darwin, biologists have concluded that such features must have arisen through lots of intermediates and, moreover, that these intermediate structures may once have served different functions from what we see today. The crystalline proteins that make up the lens of the eye, for example, are related to those that serve enzymatic functions unrelated to vision. So, the theory goes, evolution borrowed an existing protein and used it for a new function.
"Over time," Lenski said, "an old structure could be tweaked here and there to improve it for its new function, and that's a lot easier than inventing something entirely new."
That's where ALife sheds light.
"Darwinian evolution is a process that doesn't specify exactly how the evolving information is coded," says Adami, who leads the Digital Life Laboratory at Caltech. "It affects DNA and computer code in much the same way, which allows us to study evolution in this electronic medium."
Many computer scientists and engineers are now using processes based on principles of genetics and evolution to solve complex problems, design working robots, and more. Ofria says that "we can then apply these concepts when trying to decide how best to solve computational problems."
"Evolutionary design," says Pennock, "can often solve problems better than we can using our own intelligence."
What did you expect from someone who thinks that nuclear fission is a "chemical reaction"?
Now you've done it..... how many times have you been warned at the Darwin Central Committee Secret Agent Briefings never to post comm protocol details in the clear?
"Close cover before striking...."
We now return you to the regularly scheduled encrypted message:
"John has a large moustache..... John has a large moustache......."
I expect that he would attempt a campaign to drive his debate opponents from the website. Observe this one from another gentleman creationist:
The king of slime works in not-so-mysterious ways. The personal attacks [no irony there!] are one thing, but the constant thread derailments and childish bantering, along with the stomach-turning games of "slap-ass" he and his 'buddies' play are almost enough to drive people away from this forum.Do they seriously imagine that this makes me look bad, or that such behavior will support the cause of creation "science"?
1,699 posted on 05/21/2003 10:34 AM EDT by Michael_Michaelangelo
Yawn. Andrew, you're clearly getting more and more shrill and strident with each passing post.
Your words ---> I think you're misreading the point being made. A transistor is "back-to-back diodes" in the sense of its internal construction at the semi-conductor level. A diode is a single PN junction:
You even put quotes around the back-to-back.
Yes I did, because I was quoting verbatim earlier uses of that phrase. Now was that so hard to figure out? Well, for you, I guess it was.
As for "in the sense", I was pointing out that we were discussing the term in the sense of the internal construction of the transistor, and not in the sense of wiring discrete components together with solder as you were attempting to dishonestly shift the topic to. That's quite different from your own earlier attempt to use "in a sense" to try to minimize your admission that an earlier point of yours was moot.
Don't fault me for using the phrase honestly just because you misused it and I called you on it.
What a hypocrite.
What a troll.
Andrew, you lost the discussion with your trolling dishonesty a week ago, and now you've just plain lost it all together.
Andrew, if all you have left is insults which attempt to mischaracterize what I write in so transparent a fashion in order to give you a cheap excuse to falsely call me a "liar", give it up. I'm not impressed. Quite the contrary, in fact, my opinion of your intellectly honesty *and* your intelligence drops with each post of yours.
I have better things to do than repeatedly correct the staccato accusations of crybabies. If you insist on continuing to attack me just to try to salvage your own wounded pride, I'm going to get the moderators involved. Your childish behavior has gone on long enough. Get a grip.
Still trying the red herring. I stated it won't work. In a sense, means in a sense. Junction transistors are not fabricated by putting two diodes back-to-back. They are fabricated by a process of doping(appropriate to you) and redoping(still appropriate to you) a silicon wafer(newer techniques exist).
Now, transparently lacking any rational backing for your red herring position you threaten. Well, go ahead call on the Moderator. I used in a sense honestly and I will reiterate, After all, it "consists" of back-to-back diodes in a sense. --- post 1435
Your words---I was pointing out that we were discussing the term in the sense of the internal construction of the transistor
general, talk sense into this troll, if you can. I can't.
The point the troll was attempting to make was that I did not know what I was talking about. I knew that a transistor could be used as a diode and I knew that it could be considered as two diodes back-to-back. But two diodes back-to-back do not in every sense make a transistor, which he apparently was trying to imply with --- Trollish Behavior #9: Not only "in a sense", Troll, but in actuality. Stop squirming, Troll.
Good, so you agree with me after all, despite your continued bitching about it for a WEEK now. And of course that doesn't stop you from then launching into a ridiculous tirade against me anyway:
Your transparent attempt at squirming out of your hypocritical and B.S. revision of the clear meaning of actuality does not work. I added another method of adjoining diodes since you cannot fathom soldering despite your alleged E.E. training. You could superglue the things togther if you like.
Blah blah blah.
Give it up, son. You're just making a monumental ass of yourself.
And your red herring attempt at changing the discussion to mating semiconductor layers won't work.
It's not a "change", or a "red herring", as you well know. It was the original context which you yourself were invoking when you said, and I quote you, "Which, of course, makes my original statement, that a transistor was in a sense two diodes back-to-back, entirely correct".
But then, of course, when I used that *same* fact to undercut a point you thought you were bolstering with it, suddenly it's time for you to spend a week prancing around distracting attention from your own statement by going off on a ridiculous tangent about "soldering leads together", which is a different thing altogether, as you well know. Well you're not fooling me, and I doubt you're fooling anyone else.
But then, that's your tactic, isn't it? On these threads I've repeatedly seen you treat any point you might be losing ground on as a red-hot fire poker -- your constant method of dealing with that is to divert the topic into some side issue or nitpicking subtopic, again and again as necessary to keep the argument running off in every direction but back to the issue(s) you'd rather not talk about. Getting you to stay on topic is like trying to nail Jell-O to the wall: We want to talk about the capabilities of evolved circuits, so you want to talk about the accuracy of simulations. Okay, we'll talk about the accuracy of simulations, so you want to talk about "unterminated leads". Okay, we ask you to evaluate just how much/little the "unterminated lead" in that circuit is likely to affect its performance, so you want to talk about whether a transistor with base/collector wired together is a suitable subtitute for a diode. Fine, we point out that given the internal structure of a transistor, wiring a transistor that way reduces it *to* a diode. Rather than deal with that point, you about-face and begin to argue that contrary to your earlier claim of being "entirely correct" about transistors being back-to-back diodes internally, suddenly you want to confuse the point and switch to the straw man about diodes "soldered" together not forming a transistor (as if that had anything to do with the original point *YOU* were the first to raise). Fine, then we point out your shift of topic, and you spend the next week blustering about how *we're* the ones who tried to shift the topic, and you've managed to flog that dead horse so long that you don't even need to shift topic anymore, because you've become so devoid of actual substance that your namecalling is its own diversion.
My only regret is that I've allowed you to get away with it by playing your "chase the topic" game around in circles for so long.
But I note that this is pretty par for the course for creationists -- they seem to know they can't win on a head-to-head discussion of the evidence, so they constantly play either the "shift the topic repeatedly" troll game, or the "act like a bonehead on the most simple of points so that 1000 posts go by just trying to get them to admit that 2+2=4 after all" troll game.
It may be childish, but it often works. Not only does it disgust lurkers so much that they bail out early and never return, but it keeps the evolutionists so busy playing "whack-a-troll" that they spend far less time making posts presenting the actual evidence.
But it doesn't make it any less dishonest or childish.
Methinks someone is a little paranoid.
How would you know?
I made the original statement. It was you that started the argument about it by accusing me of being a troll in making the statement. Now you say we agree and further say this
Give it up, son. You're just making a monumental ass of yourself.
Your statement actually describes yourself.
In a sense, you should insist on a refund. A transistor is a transistor. Absent the potential of a bias on the base your "back to back diodes" are as useless as a tit on a bull.
That's a nice straw man you've got there. "Absent the potential of a bias on the base" my hind end. Yeah, and "absent a battery a radio is just a hunk of metal and plastic". Like that disproves that radios work? Your squirming aside, if you take two PN junctions (diodes) and join them P-to-P or N-to-N, you will indeed have constructed a working transistor (although not a practical one if the middle of the "sandwich" is too thick). I presented specific facts and argument in the post to which you are responding, and I note you haven't attempted to refute a single one of them -- the best you can do is mouth off and make personally insulting remarks. Typical.
Take your sophistry elsewhere, we're not in the market today.
Did you take a course on "bull" in college as well? I hope the doping lecture was for the benefit of the general public because if it was intended for me, I can only chuckle.
I'm sure that *is* all you can do. Many of the rest of us are capable of a higher level of discourse, however.
I don't know what your problem is, but kindly do not continue to share it with us unless you've got something worthwhile to add to the conversation.
No doubt that is how you use it or many others. But then why address it to all, more than one, or any other specific person(unless it is just convenient) when it is much easier to just leave the "to line" blank?
It seems to me that part of judging the quality of arguments involves some knowledge of the topic at hand. (This is not a criticism of you, merely a statement of opinion.)
You don't have the requisite male anatomy to admit when you're wrong.
A battery is the source of potential dipstick, the base or gate of a transistor is an inherent component of same.
I repeat, get a refund forthwith.
I studied college level EE for five years, but that was 30 years ago, and I've been doing mostly micro-electro-mechanical systems (MEMS) for the last 20 years.
Like General_re, I've forgotten most of what I knew.
The core argument isn't a quibble about diodes and transisitors, it's whether a useful circuit can be designed by an evolutionary process.
The answer to that question is yes.
Well, it may be to you, but here we are discussing a specific circuit. Since you have a background in the subject, you might have some opinion as to the evolved circuit and how it functions. Specifically, how it functions compared to the patented circuit in the environment and uses for which it was designed.
Well, your honesty and integrity cannot be challenged.
In a million turn 10K pot.
Computers are very good at iteration given a problem, a desired solution, a dbase and a good programmer.
Artificial life in an artificially created environment with artificial intelligence endowed by its creator. Evolutionary?
I'd hate to end-to-end test the darn thing for linearity.
Even so, you must know claims that a transistor "is in a sense two diodes tied back to back" clearly misses the mark and establishes the claimee as dabbling outside his field of expertise.
Hint, control the temperature, as that will change the measured value.
Hint 2, use kelvin contacts (four leads - two to drive the test current, two to measure the voltage drop) to avoid contact resistance problems.
Or buy a 7K carbon resistor and a jeweler's file, measure the resistor and start filing a notch in it until the value rises to 9.4115K. Protect the cut with shellac or nail polish...
Yup, and given a new not too hostile environment, a selection for better addapted members of a population, and a few ten's of thousands of generations, evolution/natural selection will result in a new species...
Or someone trying to explain it to a tyro...