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."

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."

"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."

2. Science *Is* anti-God. It seeks to disprove His existance every day!

With all due respect, do you REALLY believe that? If your answer is yes, then pull up a padded folding chair and a Diet Coke (Cheetos optional), and sit down.

According to dictionary.com, Science is defined in this case as "The observation, identification, description, experimental investigation, and theoretical explanation of phenomena." Or if you prefer, "Knowledge, especially that gained through experience."

Science as I understand it has to do with the quest for knowledge. Name any scientific discipline and it will have as its purpose the pursuit of knowledge within (and sometimes without) that discipline.

You and I would agree that God is Creator and knows everything. If God is Creator (and He is) and is all-knowing (that is, He has all knowledge), striving to learn more of what God has (facts) is NOT anti-God. Many founders of scientific disciplines were creationists, including Louis Pasteur (bacteriology), Francis Bacon (helped develop Scientific Method), Sir Isaac Newton (co-founder, calculus) and Gregor Mendel (genetics).

"Wait a minute!" you say. "Those evolutionists claim to be searching for facts, then deny God when they publish their findings!" That's true. But evolutionists, like creationists, interpret the facts through their worldview. The facts stay the same; the interpretation of those facts is the variable.

The key is: which interpretation is right?

Oh, probably some of the same reasons the Pope and Catholic Church do. Because it's painfully obvious from the available evidence. As most resonably well-educated adults are aware.

A broad question. Does the Pope believe in the Bible? How do you account for the Pope believing in both the bible and the Theory of Evolution?

I disagree with your premise that the Catholic Church maintains belief in evolution. First of all, this issue is not addressed directly in the Cathechism of the Catholic Church, but indirectly in passages relating to man's relationship to God and animals.

For instance, CC 371 - God created man and woman together and willed each for the other. The Word of God gives us to understand this through various features of the sacred text. "It is not good that the man should be alone. I will make him a helper fit for him." None of the animals can be man's partner. (Gen 2:18-20).

CC 2417 - God entrusted animals to the stewardship of those whom he created in his own image.

CC 2457 - Animals are entrusted to man's stewardship, he must show them kindness. They may be used to serve the just satisfaction of man's needs.

This from the Eternal World Television Network website:Evolution as Philosophy -------------------------------------------------------------------------------- What is the attitude of the Catholic Church towards the theory of evolution?

Considered strictly as a scientific theory, evolution starts with the hypothesis or conjecture that higher forms of life have developed from lower forms over a period of millions of years. The scientist then tries either to prove or disprove this hypothesis by searching for evidence to be found in the geological record. If he can show that there is a record in the rocks which shows the development of some lower form of animal into a higher form, he has proven his hypothesis. Consequently, there has been a great effort among scientists to search the geological record for evidence that modern man has indeed descended from the lower animals like the ape. There are, however, too many missing links in the record to allow any reputable scientist to claim that evolution is a proven fact.

Since, however, the cultural elite of today have a strong bent towards atheism or at least agnosticism, they push the theory of evolution as a proof that the world has not been created by God and that man is simply a higher animal without an immortal soul. In this propaganda effort they have taken a scientific hypothesis and turned it into a philosophy. They claim that their beliefs are somehow more rational or scientific than the belief of Christians. A true scientist, however, will recognize that physical science has nothing to do one way or another with proving or disproving the existence of God or the immortality of the soul. A true scientist will stick to his trade and recognize that such matters are beyond his competence as a scientist. If he is of the opinion that there is no God he will hold it as his personal belief and not as a proven scientific fact.

Obviously, those who embrace evolution as a philosophy oppose Christianity. Thus today there is a struggle in the public schools between the "Creationists" and the "Evolutionists." The Creationists, who are those Protestants holding for a strictly literal interpretation of the account of creation in the Bible, oppose evolution not only as a philosophy but as a scientific theory. Holding the God created man directly from the earth, they insist that the hypothesis of man descending from the apes must be wrong. Hence they regard the teaching of evolution even as a scientific hypothesis as anti-Christian.

The Catholic Church is united with these Christians in opposing evolution AS A PHILOSOPHY. With the Protestants, the Church insists that God created the world and that man has an immortal soul. The Church, however, does not oppose evolution AS A SCIENTIFIC THEORY. The reason is that she does not hold for an absolutely literal interpretation of those chapters of Genesis. Thus the Church sees no necessary conflict between the belief that God created the world from nothing and the scientific hypothesis that the world has evolved over millions of years. Again, the Church sees no necessary conflict between the belief that God created directly the souls of Adam and Eve and the scientific hypothesis that Adam and Eve descended from non-human ancestors. Thus even if can be proven scientifically beyond a reasonable doubt that man has descended from some lower animal like the ape, the Church will not have to change its position. Thus the Church is content to let the scientists go about their business and will only react when some step beyond the limits of science in making the claim that the theory of evolution has made Christianity obsolete. -------------------------------------------------------------------------------- Answered by Dr. Richard Geraghty, PhD

From HUMANI GENERIS (Concerning Some False Opinions Threatening to Undermine the Foundations of Catholic Doctrine) Excerpted from Pope Pius XII Encyclical Promulgated on 12 August 1950 To Our Venerable Brethren, Patriarchs, Primates, Archbishops, Bishops and other local Ordinaries Enjoying Peace and Communion with the Holy See.

Venerable Brethren, Greetings and Apostolic Benediction

If anyone examines the state of affairs outside the Christian fold, he will easily discover the principal trends that not a few learned men are following. Some imprudently and indiscreetly hold that evolution, which has not been fully proved even in the domain of natural sciences, explains the origin of all this, and audaciously support the monistic and pantheistic opinion that the world is in continual evolution. Communists gladly subscribed to this opinion so that, when the souls of men have been deprived of every idea of a personal God, they may the more efficaciously defend and propagate their dialectical materialism.

A long-standing challenge to evolutionary theory has been whether it can explain the origin of complex organismal features.

For 150 years the jokers of evolution have been saying that evolution is science but they have had no explanation for the development of organic features! Finally a truthful admission from an evolutionist!

We examined this issue using digital organisms—computer programs that self-replicate, mutate, compete and evolve. Populations of digital organisms often evolved the ability to perform complex logic functions requiring the coordinated execution of many genomic instructions. Complex functions evolved by building on simpler functions that had evolved earlier, provided that these were also selectively favoured.

A 'function' is an algorithm. No one has ever seen matter write either a function or an algorithm. So the question must be asked: how can this be a real life simulation of matter by itself creating complexity?

However, no particular intermediate stage was essential for evolving complex functions. The first genotypes able to perform complex functions differed from their non-performing parents by only one or two mutations, but differed from the ancestor by many mutations that were also crucial to the new functions. In some cases, mutations that were deleterious when they appeared served as stepping-stones in the evolution of complex features. These findings show how complex functions can originate by random mutation and natural selection.

It takes a lot of gibberish to hide the fact that the author is hiding a big problem in the experiment - the fitness cost of non-performing functions. According to evolution unfit functions must dissappear. However this program does not delete them as natural selection would, instead it lets them hang around without punishment.

This indeed is in real life one of the great problems of Darwinian evolution. How can an organism become increasingly fit through the large number of small steps required in gradual evolution at every point in the process. This is clearly impossible.

However, the question that this article raises is even more important than what it says: why cannot evolutionists give real evidence for their theory from real life? Why can they not find examples of these supposed processes occurring in living, breathing organisms?

Surely, we in the US have been spending uncounted billions on biological research for decades. There are millions of scientists throughout the world working on biological questions. How come none of these in the many decades of this intense biological research have been able to find the process of evolution actually occurring in any living thing?????????

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