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."
Happy
Mother's
Day!
It's just pointless disruption for disruption's sake. It only succeeds if you respond.
Blather on all you want, there is still no evidence of the 17 transistor circuit outperforming a specific patented theory. Your red herring won't work. Produce the evidence for the specific topic or slink away.
You made these statements
Are you not aware that pending patent applications cannot be searched, only granted patents?
According to my husband, who has been a patent examiner for 15 years, and is a Primary Examiner, you cannot search applications for pending patents.
You did not write.
Are you not aware that pending patent applications, in some cases, cannot be searched?
Nor did you write.
According to my husband, who has been a patent examiner for 15 years, and is a Primary Examiner, you cannot search applications for all pending patents.
It is pointless to you, because, of course, you cannot produce the evidence for the assertion that was made. That request is common. Back up what you assert. Now the question concerns specific circuits and a specific assertion. "Put up or shut up" is a common rejoinder. The fact that you pot shot from the sidelines is evidence of your lack of character.
Another pirouette! You are the one that mentioned patent applications first.
Why otherwise would you write the following erroneous statement?
Are you not aware that pending patent applications cannot be searched, only granted patents?
Boldly trying another red herring tack, are you?
Still with no, zip, zero, nada, evidence for the specific assertion made on specific circuits, in a specific article. I'm sure they have something but what is it? This is akin to the rapid speciating worms that didn't.
Almost funny, you need work on your patter!
No doubt you think the following is true despite the evidence that I produced.
... pending patent applications cannot be searched, only granted patents?
Okay, but the statement did not limit itself. In any case, the original topics of discussions were two. One involving the cubic function and a granted patent to a human designed circuit. This assertion was made by a poster
Deal with it. 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.
I asked for evidence of this performance edge. None has been produced. 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. Despite this not one graph comparing the two circuits has been produced here. I suspect that the performance edge is a paper product. Something that the emulating program has produced. Why do I surmise that? Because in evolving the circuit I doubt that each individual circuit was constructed in order to measure its performance of the cubic function. That would be impractical.
From the article ---A genetic programming run typically spawns a population of tens or hundreds of thousands of individuals that evolve over dozens or hundreds of generations. A weeklong run on a laptop computer is sufficient to produce half of the human-competitive results listed in the box on the preceding page; however, all six of the inventions patented after 2000 required more horsepower than that.
The second topic relates to the assertion that many patents have been issued for inventions produced by genetic programming. The same article that had the cubic function circuit in it also made mention of a patent application ---
We have filed a patent application that covers both the new rules and the new controller topologies. If (as we expect) the patent is granted, we believe that it will be the first one granted for an invention created by genetic programming.
This was in the article with the date of February 2003. Clearly, it has not been granted. It does not matter if it is still pending for it to be evidence that there are no patents for inventions created by genetic programming. That still leaves the ability to produce the evidence of many such inventions, but no one has done that.
They never try to evolve a "TUNABLE INTEGRATED ACTIVE FILTER" using rocks, ham sandwiches, and walnuts with a blow torch as the energy source. Ever wonder why?
There are genetic programming patents, but they involve genetic programming. There is even a recent application from L'Oreal that is so broadly written so that if the patent is granted they can charge anybody with patent infringement for any type of computed advice. They included genetic programming, soft programming, heuristic programming, and the kitchen sink. As to the genetic programming patents, they are for Koza's techniques and implementation of the genetic software.
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