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Artificial Life Experiments Show How Complex Functions Can Evolve
NSF ^ | May 8, 2003 | Staff

Posted on 05/08/2003 10:11:06 AM PDT by Nebullis

Artificial Life Experiments Show How Complex Functions Can Evolve

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."


TOPICS: Culture/Society; Miscellaneous; News/Current Events
KEYWORDS: ai; crevolist
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To: gore3000
Yup. Essentially, atheists know that God exists but hate to admit it.

prove it.

1,301 posted on 05/13/2003 10:16:10 AM PDT by donh
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To: gore3000
Each time I say abiogenesis is impossible you argue with me.

For me to argue with you, you'd have to actually pay attention. I have yet to see your proof, or even your hint, as to why I should suppose prokariotes, which is what you are describing, could only have sprung up out of organic junk instantaneously.

1,302 posted on 05/13/2003 10:18:59 AM PDT by donh
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To: gore3000
Well, since you claim to have read the book, kindly tell us exactly what particles of matter can generate turing machines. This I need to see, I can use a good laugh.

Where did I claim that, exactly? Please show me before we go on--I'm pretty tired of you making stuff up that I've supposedly said and then putting on these supercelious tap-dancing shows when asked to produce the evidence from my own mouth.

In other words donh, I am asking you to back up your statement.

You have postulated that abiogenesis is categorically impossible. Yours the claim that needs backing up. My claim is quite a modest, but apposite one: that you haven't demonstrated compelling--even vaguely tempting, really--evidence, much less proof, of these ambitious universal claims.

1,303 posted on 05/13/2003 10:27:11 AM PDT by donh
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To: HalfFull
btt
1,304 posted on 05/13/2003 10:29:44 AM PDT by HalfFull
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To: gore3000
.In what manner is this a relevant response to the extract quoted?

Seems quite obvious to me that matter cannot reason

Which is, to repeat myself, since I was apparently ignored, relevant to what I said how?

1,305 posted on 05/13/2003 11:00:37 AM PDT by donh
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To: Dataman
No need to get angry. I'm only pointing out an inconsistency in your thinking. That doesn't translate to an attack or a threat or a put-down.

Let's get our emotional responses in order here. The problem is not anger, it is annoyance over what looks like obtuseness out of refusal to think about what is being read. As, for example, when you come right back with the same lazy, unresponsive misstatement of your deponents position, as you have just now done.

1,306 posted on 05/13/2003 11:04:28 AM PDT by donh
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To: Michael121
But the idea of evolution came after faith and religion. So the disproving is up to your side.

Apparently, you do not understand what the word "faith" means. "Faith" is the proud claim that you haven't proved diddly. Like science, I've no interest in the saturday night grudge match you've arranged between God and science. Science doesn't care about God, one way or another--God is not within science's domain of competence.

1,307 posted on 05/13/2003 11:08:59 AM PDT by donh
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To: gore3000
My argument against evolution is concicely stated in post#1265 just above.

So, apparently, you don't understand what "concise" means either. You have simply found an incredibly longwinded way to reject my suggestion that evolution did not always work the way it works in prokariotes. So it is just a restatement of your basic theme--that prokariotes had to leap into existence out of junk. This is the entire basis of your argument, absurd as it is, and you have simply window-dressed it to make it look more impressive than it is. It is likely that the rules governing meat machines are not going the be the rules for what went on before meat machines. My supposed contradiction is simply the fruit of me being willing to talk about pre- and post- meat machine paradigms--compounded by your inability to hone in on the precise details of any argument, busy as you are re-arranging your canned lecture yet again.

Pick and choose what you are arguing about and we can discuss that. Stop trying to purposely confuse the issues by saying that the argument against evolution does not apply to abiogenesis and that the argument against abiogenesis does not apply to evolution.

Take 5 seconds from your busy schedule to notice what I am actually arguing about regarding there being both a pre- and post- meat machine era, with distinct rules, and I'll consider discussing this further. Never mind agreeing or disagreeing with me--lets just see if you even understand.

1,308 posted on 05/13/2003 11:22:32 AM PDT by donh
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To: AndrewC
freeper4u: "Programming a robot (or simulation of a robot) to walk in a real physical environment is hard problem"

AndrewC: "Don't you see the contradiction in your statement and how it relates to the rest of your statement?"

No.
1,309 posted on 05/13/2003 12:08:18 PM PDT by freeper4u
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To: freeper4u
No.

A simulation does not walk in a real physical environment. Programs are concepts as demonstrated in all of the virtual creatures that were "created" in the link you cited. IOW nothing that you presented as evidence was a material object.


1,310 posted on 05/13/2003 12:20:22 PM PDT by AndrewC
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To: AndrewC
Andrew,

In this example, the point I set out to make, and I think it was proved in the paper is that many problems that would be hard to solve by direct computation can be easily solved indirectly by genetic algorithms.

No simulation will ever be as good as the real world. But you can still learn a lot about the real world from a simulation.

Of course there are a zillion other hard problems that real creatures need to solve in the real world, but the Sims simulation effectively singled out a few of them and successfully showed they can be addressed quite effectively by genetic algorithms instead of a solution arrived at by direct design.
1,311 posted on 05/13/2003 12:40:52 PM PDT by freeper4u
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To: freeper4u
No simulation will ever be as good as the real world. But you can still learn a lot about the real world from a simulation.

You mean like the global warming models??

1,312 posted on 05/13/2003 12:45:29 PM PDT by colorado tanker
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To: freeper4u
but the Sims simulation effectively singled out a few of them and successfully showed they can be addressed quite effectively by genetic algorithms instead of a solution arrived at by direct design.

What was demonstrated was virtual. Real joints, with real motive elements requiring real energy sources and real raw materials occuring in a hostile environment was not demonstrated.

1,313 posted on 05/13/2003 12:47:24 PM PDT by AndrewC
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To: AndrewC
Andrew,

All that was shown in the Sims simulation was the question of whether or not it is possible for any kind of sensors, motors, and joints to be represented in a binary string, whether a sequence of binary operations on that string can improve the operations of those sensors, motors, and joints in a given environment for a given goal, and whether that binary string is sufficiently small enough that it does not rule out the possibility for a real DNA to represent the same information encoded by the simulation.

Even though that question is far different from the one of: "did real creatures evolve" and even "can real creatures evolve", it is still a very important question, and the result was positive, meaning that the next set of questions can be asked in the context of the hypothesis proved by this first experiment.

That is how science marches forward. It will never prove real creatures did evolve, but successive successful experiments show that it is more likely that evolution alone cannot be precluded as a possible explanation for the genesis of life on earth.
1,314 posted on 05/13/2003 1:25:01 PM PDT by freeper4u
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To: freeper4u
All that was shown in the Sims simulation was the question of whether or not it is possible for any kind of sensors, motors, and joints to be represented in a binary string, whether a sequence of binary operations on that string can improve the operations of those sensors, motors, and joints in a given environment for a given goal, and whether that binary string is sufficiently small enough that it does not rule out the possibility for a real DNA to represent the same information encoded by the simulation.

That is all well and good, but we represent things all of the time when we draw it, write about it, speak about it or think about it. We can even imagine improving it. The fact is everything that man has built started out as a concept. Even a rock used as a weapon had to be conceived even if it was initially picked up to be used as food.

As for DNA coding, anything can be used to represent something else because representation is a concept(written while moving salt shaker to the left and stating this is New York). Eyeblinks were used to send a message by a POW. You want to code the human genome by drumbeats, it can be done, but you better have a lot of time to waste.

You want to use DNA to code a program? That is easy. With 4 bases ,

  1. Adenilne (A)
  2. Cytosine (C)
  3. Guanine (G)
  4. Thymine (T) or Uracil (U)
you have a four level code. You can match the bases to 2 bits in this manner for an example.

Pentium instruction INT 7 has a hex value of CD07 or in binary

1100110100000111

In DNA code mapped as above this would be

TATCAACT

As you can see each byte takes up 4 bases, so that a DNA the size of the Human genome could code a program of about 750 megabytes. In this day and age it may seem like a trivial amount of data since it will easily fit on a DVD. However, going through all of the progrms that could be written in that amount of memory would take a very long time. Here is a previous calculation giving an indication of the information that can be coded by the DNA.

The number of different items represented by that 6 billion bit sequence as I stated before is 26000000000. In base 10 that would be 101806179974. Now there are 60 seconds/minute * 60 minutes/hour * 24 hours/day * 366 days/year * 15,000,000,000 years = 4.74336E+17 (or 1017.67608609) seconds since the purported start of the universe. We will assume this full time is available to generate the sequences represented by the 6 billion bit sequence. The huge number represented by 101806179974 breaks all my calculators so I must use logs. If we divide the number of items (101806179974) by the time available (1017.67608609) we end up with 101806179956 combinations/second. Clearly that is a huge amount of "information".

1,315 posted on 05/13/2003 2:41:52 PM PDT by AndrewC
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To: AndrewC
Proofread better

Adenilne = Adenoid Adenine

1,316 posted on 05/13/2003 2:45:52 PM PDT by AndrewC
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To: donh
Well let me set you straight. I made a comment. Someone did not like it. I like an argument so I kept it going.

The thing is this is non winnable to either side. Not that one side will not be proven correct. But that neither side will convince the other in my lifetime. Once my life is over, I guess I shall then see if faith was warrented.

If not then I have lost nothing. Science is cool. But what I see is that politics get involved way too much and in a lot of cases it appears, whether or not it does in actuality, to influence results. I like pure science that catters not to political pressures and PCism. If the science is real then it as also true.

Whether the science is geo-, bio-, or not there is a truth. The problem is we have to wait for one conclusion with political overtones. Before someone without politics gives the real answers.

There was a reporter after Columbine, who wanted to see how easy it was to get a gun at shows or on the WEB. He went into this with certain expectations. That is he thought it would be so easy to obtain a gun. He was proved wrong. The only person who would actually sell him a gun wanted him to drive 100+ miles to meet and make the sale in person, at a gun shop which could do a background check.

One example but there are hundreds like this based on science. Arts. Politics. Archeology. etc...

Politics is needed, and funny. It does however get in the way too often.
1,317 posted on 05/13/2003 4:45:45 PM PDT by Michael121
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To: PatrickHenry
multi-spectral moron alert placemarker
1,318 posted on 05/13/2003 4:47:29 PM PDT by longshadow
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To: AndrewC
Andrew,

The beauty of genetic algorithms is that the encoding format of a DNA string is independent from the process of evolution because the agent making changes to the string has no idea what it is doing.

As in real evolution, the Sims experiment used a random process to mate the genes of its virtual creatures, so it doesn't matter how the encoded creature are represented. That is, it is not necessary for anyone to "design" a particular representation that enables genetic algorithms to evolve a string that decodes to a creature that improves its results in the fitness test.
1,319 posted on 05/13/2003 5:02:21 PM PDT by freeper4u
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To: AndrewC
[Why don't you answer the question?]

You have not provided the evidence for the assertion that the evolved circuit performs better than the patented circuit even in its modified form. Not one measurement, not one graph, not one number.

Sigh -- just how many new pointless "objections" are you going to pull out of your hat in an endless parade of lame excuses to avoid having to actually deal with the questions that have been put to you, and the issues raised?

You're not fooling anyone with this game-playing. Except for perhaps yourself.

But just to give you one less cheap excuse to avoid the issue, here's more information on the evolved circuit: "Evolving Inventions", John R. Koza, Martin A. Keane and Matthew J. Streeter, "Scientific American", Feb. 2003. For a more technical treatment, see: Matthew J. Streeter, Martin A. Keane, John R. Koza: Routine Duplication of Post-2000 Patented Inventions by Means of Genetic Programming. EuroGP 2002: 26-36.

So what's your excuse going to be *now*, Mr. Evasive?

While you're at it, you might want to take a gander at the following and explain why evolution doesn't actually work in *these* research projects either, even though it certainly seems to perform just fine:

The above can be found in the publication: William B. Langdon, Erick Cantú-Paz, Keith E. Mathias, Rajkumar Roy, David Davis, Riccardo Poli, Karthik Balakrishnan, Vasant Honavar, Günter Rudolph, Joachim Wegener, Larry Bull, Mitchell A. Potter, Alan C. Schultz, J. F. Miller, E. Burke, Natasa Jonoska (Eds.): GECCO 2002: Proceedings of the Genetic and Evolutionary Computation Conference, New York, USA, 9-13 July 2002. Morgan Kaufmann 2002, ISBN 1-55860-878-8

Give it up, Andrew, you're just looking silly. There's a whole world of significant evolutionary research results out there that you can't just make go away by wishing hard enough, or being evasive enough.
1,320 posted on 05/13/2003 5:46:03 PM PDT by Ichneumon
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