Artificial Life Experiments Show How Complex Functions Can Evolve

NSF ^ | May 8, 2003 | Staff

[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."

[PatrickHenry]

1601 placemarker.

[gore3000]

[Nowhere does Gould say, or even imply, that the Cambrian explosion is, in your words, "unexplainable".]

First of all I have already answered your statement and why it is a lie. My statement was that Gould stated that the Cambrian refuted gradual Darwinian evolution. I have quoted the passage twice and it is quite clear to any honest person with a third grade understanding of English:

Contrary to Darwin's expectation that new data would reveal gradualistic continuity with slow and steady expansion, all major discoveries of the past century have only heightened the massiveness and geological abruptness of this formative event..." (Gould, Stephen J., Nature, vol. 377, October 1995, p.682.)

Your disgraceful dishonesty in willfully mistating what I have said and ignoring the proof given for them as if it had not been given shows quite well that you are not interested in the truth and will shamelessly lie repeatedly in the hope that repetion will make your words true.

You are just another evolutionist loser.

[longshadow]

g3k was originally calling for examples of "matter self-assembling without human intervention" but is disallowing any proffered example because there is "no [human] assembly required."

Well, he's never let a little thing like a contradiction stop him before -- no reason to think he'd change now.

[gore3000]

This humble creationoid research center

Aaah, the stalking slimer strikes again. Patrick Henry, dedicating his life to insulting those who disagree with him.

When are you are insulting friends going to answer the question asked by me some 500 posts ago:

IF EVOLUTION IS SCIENCE, WHY CANNOT THEY PROVE IT FROM REAL LIFE? WHY MUST THEY GO FOR PROOF TO PHONY, CONCOCTED 'SIMULATAIONS'? SCIENCE IS ABOUT REAL LIFE, NOT ABOUT COMPUTER GAMES.

[gore3000]

Vertebrates are chordates, but chordates are not vertebrates. -ME-

No kidding, bunky, which is why I had to correct you on that point.

Lying as always. I said that Vertebrates is a phyla, not that they are not chordates. Chordates is a more general term than vertebrates, it is not the name of a phylum. So your statement above is another one of your usual lies by misquotation and misreference. Your total dishonesty continues to show through.

[gore3000]

Fission is, or course, a nuclear process, not a "chemical reaction." And, as well you know, the sun produces light by fusion of light nuclei, not fission of Uranium.

The usual semantic nonsense from evolutionists and a plain lie. Nuclear fision or fusion is a property of the chemical element uranium. Call it what you will, it requires no assembly. I also never mentioned whether the reaction is fusion or fission, so that "refutation" is a total lie since it implies I said something I never said. So much your nonsense. The fact remains the example of Dr. Stochastic was no example of self assembly, but a good example of the evolutionist practice of link-o-lying.

[longshadow]

Nuclear fision [sic] or fusion is a property of the chemical element uranium.

No comment necessary. You'ved just proved our point once more.

[gore3000]

4. PE does not require any unique explanatory mechanism (e.g. macromutation or saltation).

PE does not require anything except an atheist turn of mind. It denies the need for evidence since there is no way to tell that anything transformed itself into something else. It just 'happens'. It is therefore not science, but absolute garbage.

The problem of a whole species, or a large portion of it evolving at once is a difficulty which evolutionists have not explained very well. The problem of random changes spreading through a population is quite difficult. Even Darwin thought that evolution could more easily take place in small populations. The problem is that any change has to be small so that the individuals can still mate with each other. The changes also have to occur evenly throughout the population. In other words, the whole species sort of has to evolve together. This is all much easier said than done, this is especially problematic when we come to sexual reproduction. In fact, this problem by itself, seems to me to completely destroy Gould's punk-eek.

[gore3000]

t is I who many posts ago (Post# 1329) asked you to show how abiogenesis was possible:

Indeed you did,

Now you remember. Then you go on to insulting me for bad memory when it was you who in post# 1538 said "Of course, the issue is that the you support abiogensis". Clearly you cannot meet the challenge of showing a single theory that can overcome the three problems which real science has shown make life from non-life utterly impossible. Stop the insults, stop the excuses, stop the doubletalk, stop the misrepresentation of my position and discuss the facts.

[gore3000]

is disallowing any proffered example because there is "no [human] assembly required."

I did not say that human assembly is required. I am asking for examples of matter assembling itself into complex things. The 'nuclear reactor' merely requires a large concentration of uranium. This does not require any complex thing occurring. Further, for life to have occurred from matter some very complex assembly was necessary. The DNA for example has no sequential chemical or other affinity to cause it to assemble in the way that life arose. For atheists and materialists to propose such a thing they certainly have to show some very complex self-asembly of non-living matter. The other problems that need to be surmounted in order to achieve life from non-life are detailed and explained in Post# 1558 .

[gore3000]

A nice story but the readers will note that there is a complete absence of examples and facts supporting the claims made by it. Science requires facts not pretty stories.

Here is an example of the problem:

Coevolution is often seen in a number of species of flowering plants that coevolved with specific pollinators (insects, bats, etc). The pollinator gets a reward such as nectar for pollinating the plant. Moth-pollinated plants often have spurs or tubes the exact length of a certain moth’s “tongue.” For example, Charles Darwin predicted the existance of a moth in Madagascar based on the size and shape of a flower he saw there. The moth was actually discovered about 40 years later. The common snapdragons that many people plant in their gardens are designed for a bumblebee of just the right weight to trip the opening mechanism.

From: Coevolution and Pollination

Note Darwin's remark that there had to be a specific insect that fed on this plant. Well here we see the problem, the insect could not live without the plant and the plant could not live without the insect. In fact, the plant had to be the correct shape, etc. for the insect to feed on it. Just saying that flowers coevolved with specific pollinators does not answer the question of how such a thing could occur. All it does is state the insurmountable problem and its unexplainability. Now tall stories are no problem for evolutionists, but what has to be taken into account is that it takes time, lots of time, for the proper mutations to arise and plants (like all species) have to continue reproducing throught this long time. Without the insect, and a specific constitution to allow this insect to spread its pollen, the plant would not have survived for a single generation more. This makes the evolutionary explanation of the rise of plants total nonsense.

Time, there is no infinite time, there is no billions of years for a species to go through the necessary mutations to survive. Species have to reproduce, eat and survive on a daily basis, and this gives absolutely no time for the changes required for this 'coevolution' or for many other changes postulated by evolutionists.

[gore3000]

The weak force is the force that induces beta decay via interaction with neutrinos.

Thanks for the detailed explanation of how the sun nuclear process works. As you show, this is a natural function due to the chemical and nuclear constitution of the elements involved. This process has nothing to do with the 'assembly' of anything as claimed by Dr. Stochastic. Thanks for the clarification.

[Doctor Stochastic]

The quote from the website plainly says that if there is enough uranium concentrated in one spot a chemical reaction is likely to occur. We believe that that is how the sun produces light

Your first sentence does not reflect the contents of the web site.

Perhaps you could give the names of anyone else (except your) that believes that the Sun produces light by chemical reactions of uranium.

[Doctor Stochastic]

As I showed (and no one wishes to address) the simulation did not punish unneeded and useless functions which natural selection certainly does.

The simulation did punish unneeded and useless functions by having these useless functions consume limited resources. The simulated organism dies if it runs out of resources. If you had read the paper, you would have known this.

[gore3000]

Your first sentence does not reflect the contents of the web site.

Your semantic nonsense does not cut it. You claimed the site showed an example of self assembly. All it shows is a natural process which is well known and requires no assembly. Further, you used the plural 'examples'. There was only one example. It was therefore another example of evolutionist lying-by-links in the hope that no one would catch their lie.

[gore3000]

The simulation did punish unneeded and useless functions by having these useless functions consume limited resources.

Another bald faced lie from you. It says no such thing in the article above and that is why you cannot give a quote which says that. It is a completely a figment of your imagination. A totally made up statement with no basis in fact. Since it was completely concocted out of thin air, it is legitimate to call it a lie and not an error.

As I quoted before, the program clearly did not punish useless functions:

Some mutations that cause damage in the short term ultimately become a positive force in the genetic pedigree of a complex organism.-article-

As I have shown that is the problem with real life evolution, it does punish bad and useless functions and waste of resources - as your statement above tacitly admits. So my statement is correct and continues unrefuted - the program 'tweaked' reality in order to prove through a concocted program what it could not prove in real life.

[Doctor Stochastic]

Calling me a liar doesn't change the paper in Nature. (Lenski, Ofria, Pennock, & Adami, "The evolutinary origin of complex features.")

[PatrickHenry]

Stalking, sliming, insulting PLACEMARKER

[Junior]

A "30 seconds on Google could save him hours of embarrasment" placemarker.

[PatrickHenry]

30 seconds on Google

Man, you just don't get it. The creationoid technique proceeds from knowing The Truth! ahead of time, and posting accordingly. When some sliming, insulting, hellbound eeeevoooluuushunist dares to post a satanic "fact" that contracticts you, then you go to Google for 30 seconds, not to learn anything, because you already know everything, but in order to snatch some useless, out-of-context quote from somewhere, anywhere, so you can do a fast cut & paste into the thread and then claim victory.