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."
Really? Inanimate matter can by itself create a turing machine? So kindly explain to us how this miraculous thing occurs without intelligent intervention.
I see you have a low self-esteem. Don't be so hard on yourself.
First, I deal with what you write, not with what you wish you had written. Which was --->
In this case, it made a cubic function generator circuit which outperforms the best that all electronic engineers were capable of producing in all the history of electronics.
The circuit at the top was patented in 2000, and is the current state of the art. The circuit at the bottom was produced by pure unaided evolution, and outperforms the human version.
Clearly, you now admit there is still no evidence for your claim.
True, it's not the same circuit.
Second, you have no problems jumping to conclusions
The researchers appear to have topped their prior "personal best" and produced an even better circuit, which they presented in their later paper.
But fail to see the facts.-->Circuits are simulated using SPICE (Quarles, Pederson, Newton, Sangiovanni-Vincentelli 1994).
Third, simulations are not the real thing. We lost several Mars probes, all of which were run through simulations.
Fourth, you use hyperbole erroneously again.
If transistors et all were as unpredictable as you imply, they couldn't even be used to make reliable circuits at all.
I did not imply anything about transistors. I did imply that simulations are not real.
Fifth, the circuit designers and I know that a junction transistor can be used as a diode. They did not choose to do so. The circuit was changed.
Sixth, unterminated runs act as antennae and at high frequencies provide signal loss. I have no doubt that you would select a just-so story over the real thing, but that does not qualify as evidence for the embodiment of the just-so story to perform the required tasks.
For any real application I'd choose the evolved circuit over the patented one any day.
At this point, your assertions are still hanging.
I did mention frogs with glass asses.
The theory of evolution is about prokariotes or better, as you know.
Still saying that evolution is about bacteria. It is about all living things descending from each other. AND IT DOES NOT WORK FOR THE REASON GIVEN - fitness, natural selection, the supposed agency of evolution will make it impossible to achieve the numerous gradual changes required for a species to transform itself into a more complex species because fitness/natural selection requires (as you have already admitted) that each and every change provide increased viability or it will destroy those with the new change.
In your own words:
It's a truism of entomology (been demonstrated in sealed mason jars thousands of times) that when two nearly identical species occupy nearly the same contained biological nitche, one or the other will eventually prevail entirely, no matter how tiny its differential advantage.
1,012 posted on 05/09/2003 9:59 PM PDT by donh ).
You have been trying to dance around this for over three hundred posts and continue to fail to address it. Without natural selection there is no 'how' to evolution, with natural selection evolution is impossible.
Total nonsense. First of all the Universe does not have a 'will', nothing it does is either pleasing or displeasing to it. It also has no feelings. This is more than a quible when speaking with materialists who think that only inanimate matter exists. More important though the fact that we can predict the phases of the moon shows that the Universe does not behave randomly. The fact that the speed of light is constant and that we can predict the actions of numerous natural forces, make formulas of how they act and repeatedly confirm their actions, shows that matter does indeed act according to specific rules. We are constantly discovering more and more rules by which matter works. It is because these rules do work that we can build things from bridges to atom bombs, from planes to internal combustion engines. If matter behaved randomly none of the engineering feats of the modern world would be possible.
and hasn't the slightest demonstrated notion of what a law is to constrain it.
Yes, not being able to think it does not know that it is constrained in what it can do. Not being able to think though makes it impossible for it to intelligently arrange itself. However, as shows above matter is nevertheless constrained whether it knows it or not.
I have often pointed out that materialism is anti-science, thanks for proving my point.
I see you have a low self-esteem. Don't be so hard on yourself.
That was lame even for you.
Clearly, you now admit there is still no evidence for your claim.
Clearly, you're delusional. I stand by my statement and evidence has already been given. Your hand-waving doesn't make it go away.
Second, you have no problems jumping to conclusions The researchers appear to have topped their prior "personal best" and produced an even better circuit, which they presented in their later paper.
What part of "appear" was unclear to you? I clearly labeled it as speculation, not a "conclusion", you goof.
But fail to see the facts.-->Circuits are simulated using SPICE (Quarles, Pederson, Newton, Sangiovanni-Vincentelli 1994).
During the evolutionary process, yes. This hardly precludes them from doing a quick breadboard of their final designs, does it? In any case, that's an attempt on your part to hairsplit the results, for the several reasons I gave, which you have not even attempted to deal with. Evade much?
Third, simulations are not the real thing. We lost several Mars probes, all of which were run through simulations.
Lame. I made a specific point about the known ability of circuit simulations to accurately analyze the real results of circuit topologies, which is not invalidated by your red herring about the failure of experimental craft performing never-before-attempted maneuvers millions of miles from assistance.
[If transistors et all were as unpredictable as you imply, they couldn't even be used to make reliable circuits at all.]
I did not imply anything about transistors. I did imply that simulations are not real.
Of course they aren't "real", but that wasn't your point at all. Your point was the implication that simulated performance may not match real performance. I quite logically pointed out that, yes it does (for these types of analyses), and it did so precisely because the behavior of transistors is well known and highly predictable, unlike your implication that they are somehow likely to exhibit surprising behavior in variance to their models.
In short, your point was invalid, and you have done nothing to salvage it by blathering about simulations not being "real".
Fifth, the circuit designers and I know that a junction transistor can be used as a diode.
No, you didn't. Don't even try to lie about it. You wrote:
I found the patent and examined the circuit and it involves 5 transistors and 4 diodes. The circuit used in the "runoff" has 9 transistors. Somebody changed something.No, they didn't, because a transistor wired that way *is* a diode. QED. If you understood that you wouldn't have blathered on about "someone changed something", because you'd know that that "change" was no "change" at all.
They did not choose to do so. The circuit was changed.
Ok, fine, Mr. Wizard, please explain to us how a transistor wired in such a manner *differs* in behavior from a diode. We'll wait.
Sixth, unterminated runs act as antennae and at high frequencies provide signal loss.
Wow, what a really random sentence. And this has *what* to do with the circuits in question, please? Be specific, this ought to be really amusing.
I have no doubt that you would select a just-so story over the real thing, but that does not qualify as evidence for the embodiment of the just-so story to perform the required tasks.
Yet again, you cluelessly imply that circuit simulation software is in some manner grossly defective in a way that has managed to elude electronic engineers for the past few decades. Perhaps you would like to tell them exactly *why* a computer-analyzed result of a circuit design allegedly would differ significantly from actual performance? We await your blinding revelations.
At this point, your assertions are still hanging.
At this point, I'm ready to hang myself before I bother with any more of your red herrings and cheap excuses again.
I made several other points that I note you didn't even attempt to address.
I declare this game of cat-and-mouse over, and you lost it through dishonesty and troll-like behavior. You clearly don't want to deal with the actual issues raised by experiments of this kind, and so I won't push you on the matter. You may continue to fail to learn from the evidence as you wish. Goodbye.
It shows that on the scale of observation that the Moon does not behave randomly. A study of Brownian motion and radioactive decay shows that these phenomena do act randomly (using "randomly" rather loosely.) We do know the laws of both Brownian motion and of radioactive decay: these laws predict random behavior; such behavior is observed.
You can declare all you want, but that does not make it so. We are discussing other declarations of yours that are still hanging.
You made specific statements concerning specific circuits. I asked for the evidence backing those specific statements. They are still not backed up despite your red herring.
What part of "appear" was unclear to you? I clearly labeled it as speculation, not a "conclusion", you goof.
If it is speculation then it is not evidence of anything. You used it as an argument for the fact that the circuit in the paper is not the circuit in SciAm. You now say you didn't mean anything by it. So be it.
which is not invalidated by your red herring about the failure of experimental craft performing never-before-attempted maneuvers millions of miles from assistance.
Calling my valid statement, which demonstrates that simulations fail, a red herring does not make it so. The measurements were simulations. More importantly the Mars probes failed because the simulations did not take into account different units being used by one team and, in another case, failed to consider the transient response of a hall effect proximity detector on the software that shuts off the engines.
No, you didn't. Don't even try to lie about it
Yes, I did know about the transistor use. You don't know what I know. I know circuit design shortcuts. I know that you can use a transistor as a diode in a pinch. After all, it "consists" of back-to-back diodes in a sense.
From my post 829--- . There are a total of 9 semiconductor elements in the design, five NPN transistors and 4 diodes. The genetic design "competed" against the patented circuit in a modified version. It introduced 2 resistors and used transistors to act as diodes. This will have an effect on the operation of the circuit.
I also know that there exists parasitic capacitance in bipolar junction transistors and that unnecessary transistors floating around will affect circuit performance at high frequencies due to this characteristic.
Ok, fine, Mr. Wizard, please explain to us how a transistor wired in such a manner *differs* in behavior from a diode
See parasitic capacitance above.
And this has *what* to do with the circuits in question, please? Be specific, this ought to be really amusing. (concerning antennae)
Its operation at high frequencies.
In conclusion, your hyperbolic assertions remain hyperbolic assertions.
I'm not actually sliming you. I'm telling the truth.
You make a statement, then you lie about it. Then you pretend you have some other "questions". Then you slime me. Typical left-wing, atheist dribble.
Logically all that's left is that you must be selling your twaddle for cash. You might as well admit it.
According to Gould, the fact that there are thousands of potential shell shapes in the world, but only a half dozen actual shell forms, is evidence of natural selection. Not so, says Wolfram. He's discovered a mathematical error in Gould's argument, and that, in fact, there are only six possible shell shapes, and all of them exist in the world.
In other words, you don't need natural selection to pare down evolution to a few robust forms. Rather, organisms evolve outward to fill all the possible forms available to them by the rules of cellular automata. Complexity is destiny—and Darwin becomes a footnote. "I've come to believe," says Wolfram, "that natural selection is not all that important."
Wolfram says "there's no place for God" in his new science. But what about just outside? What will theologians say when they see a theory that proposes that the entire universe—with its perplexing combination of good and evil, order and chaos, light and dark—could have been started by a First Mover using a dozen rules?
Gregory Chaitin groans when he hears this. "Academic politics and scientific politics are as hardball as anything in Washington. When someone goes off in a different direction like this, people get upset. It's the same in every field. It's only after they are good and dead that we declare them geniuses."
Did you mean "peeing"?? ;)
Mise le meas.
RWP
You will note. I have argued specifically. There are no straws in my evidence. Now your general comments are a distraction to what I have been arguing. I did not make a statement on the general utility of evolutionary programming. I asked for evidence backing up specific assertions. You did provide evidence in good faith, however that evidence does not sustain the assertions that were made(not by you).
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