I've written a lot about my skepticism about evolution, and here's a post on The Loom about mutations in the HIV virus that will serve as an illustration of of one of the assumptions that evolutionists make without, in my opinion, much merit: that genetic similarity implies common ancestry. Carl Zimmer -- who undoubtedly knows more about biological evolution than I do, since I'm a computer scientist who only simulates evolution -- displays and explains several charts that show how various strands of HIV are related to each other and to SIV (Simian Immunodeficiency Virus).
I have no doubt that human DNA is similar to chimp DNA, and that what Mr. Zimmer calls "microevolution" (a term originally created by skeptics of evolution?) occurs. In small time scales, changes can be traced between SIV and HIV, and their relationship can be observed and tested. However, the "wall" that Mr. Zimmer refers to is that of time, and it's a fact that any common ancestry between chimps and humans can only be inferred, not proven or even reproduced in a scientific manner (without a time machine). There's a gaping chasm between demonstrating genetic similarity and proving common ancestry that science cannot hope to bridge. The only difference between those who believe that God created life and those who believe it evolved is that the latter tend to fill in the holes with deception rather than faith.
Random mutation and natural selection are real and can be observed, but there's very little evidence to suggest that they are capable of explaining the origin of life. Predictions based on evolution are often very wrong. Just like everyone else, scientists have agendas and research tends to follow the grant money. (All that means is that you have to abandon the illusion of scientific objectivity and be prepared to consider the motivations and prejudices behind everything that's published (including this site, of course).)
Finally, I'll add a note from my own research and simulations. In my experience, similarity seems to be the rule for evolutionary systems. I've run countless simulations with non-interbreeding species with randomly generated genomes in NS+M environments (natural selection plus mutation), and their genomes almost always converge. Why? Because evolution is an optimization algorithm, and if it's implemented properly it will find an optimal solution to whatever evaluation criteria is applied to it. There are often local maximums that can trap poor implementations (perhaps analogous to "niches" in a biosphere), but over time these get shaken out and the result is uniformity, not diversity.
Update:
Phelps comments and posts and link to an fascinating story about plants that defy normal laws of heredity.
Challenging a scientific law of inheritance that has stood for 150 years, scientists say plants sometimes select better bits of DNA in order to develop normally even when their predecessors carried genetic flaws. ...In the Purdue experiment, researchers found that a watercress plant sometimes corrects the genetic code it inherited from its flawed parents and grows normally like its grandparents and other ancestors.
There's a lot we don't understand yet, and much of what we think we understand is probably wrong.
MW said: "The only difference between those who believe that God created life and those who believe it evolved is that the latter tend to fill in the holes with deception rather than faith."
That is a broad statement... with far too much bias and far too little fact. So only those who believe in evolution are deceptive or employing deception? Or, perhaps, those who believe in evolution are far more likely to employ deception? What a ridiculous conclusion to draw.
I don't believe in God as the creator of life... but I don't believe in evolution either. I think they both leave a lot of unanswered questions.
Have you seen the latest news on plant hybrids? They've now observed hybrids apparently repairing mutations a full generation past the last good genetic code. To me, this puts a huge load of doubt on even microevolution.
Mark: Well, it doesn't take deception to believe in pure "creationism", since God can do whatever he wants for any reason. Although everyone is deceptive to some extent, there's not a lot of money floating around for creationist research.
Phelps: Wow, I hadn't seen that, that's incredible.
Great achievement has no roadmap. The X-ray is pretty good and so is penicillin.. and neither were discovered with a practical objective in mind.
I'll be the first to admit that too much of the scientific research we do is profit-driven. That's not to say that profit-driven research is without merit or benefit to society... but there's something to be said for ignoring an avenue of exploration simply because there's no money to be made from anything discovered along that path. I think we sell ourselves short too often in that regard.
Mark: Grant money isn't profit... profit depends on getting actual practical results. Grant money is just whatever some guy feels like spending, so it doesn't even represent any market other that that.
Yeah, I know that grant money is different.... but it is still an example of what I was talking about in my previous post... ignoring avenues of exploration because, in the case of grant money, no one wants to pay for the research and, subsequently, there's the same potential to sell ourselves short.
The water cress experiment shouldn't cause you to doubt evolution, really. Do you expect that the correction is made through some miracle, or is it just some normal feature of genetics previously undocumented? MW: as a computer scientist, you must be aware of such things as CRC checking and so on. There are many ways this correction might occur. As the article author says, inheritance happens more flexibly than we might have believed.
Evolution, even biological evolution, is an optimization process as you say, but the target is moving. An important element of a creature's environment is all the other creatures! I'm guessing in your simulation the species you are optimising do not affect one another (except when you come to judge their relative methods), whereas in biology one species hunts another, they compete for resources, they can set up symbiotic relationships etc. This is where niches emerge, and from them diversity.
jez: The point of the water cress thing is that we don't know as much as we think we do. That's exactly what I said about it.
As for my experiments, yes of course the species interacted with each other. Moving equilibriums are very rare, they almost always stablize.
Moving equilibriums are rare...because the environment isn't changing. Earth, last I checked, doesn't have that issue.
One question in regards to the NS+M simulations you've run - do they ever include a mechanisim for mutations which make inter-breeding impossible. For example, you start with Species A. Mutation occurs (say, doubling of genetic code, polyploidy) which creates Offspring B which cannot interbreed with Species A, but can interbreed with other Offspring B if they occur. I ask because this is a phenomenon that has been observed in nature, so it would make sense to include it. It would also potentially address the issue of moving equilibriums, even without artifically changing the environment, as new species occuring would be an environmental change on their own. Perhaps I am simply showing my ignorance of these experiments. You do state that you start with non-interbreeding species so it may not change the simulation greatly.
As for genetic convergence, the danger of converging genomes in real life are obvious. If you have a changing environment where genetic convergence means wiped out populations, and you change the environemnt enough, you probably won't get equilibrium. And of course if you do, and you change the environment so it is no longer optimal, you'll either see a mutation or existing species begin to dominate, or if the environment change/genetic convergence is too great, you'll see the complete destruction of the "optimum" species. If the galapagos islands suddenly sunk under the ocean, I don't know how many of those species would survive.
Oh, and scientists aren't filling in the holes with deception, but further study, exploration, analysis, etc. The God Squad just has one big hole, into which they crammed one big deception, dusted their hands off and said "well, thats the end of that!"
http://science.nasa.gov/headlines/y2004/10sep_radmicrobe.htm
Interesting article about a similar mechanisim for DNA repair that scientists have been studying for years.
I didn't notice before, but the "Predictions based on evolution are very often wrong" statement links to a discussion of a short piece by Stephen Meyer, a notable "Intelligent Design" proponent. It seems the entire basis of the statement is "Meyer says so" with only anecdotal evidence and no citations.
Anyway, an article by Meyer was linked as well, so I thought I'd link to a pretty thorough rebuttal here:
http://www.pandasthumb.org/pt-archives/000430.html
My favorite part is the reference to the "peer reviewed" aspect of his article:
The Proceedings of the Biological Society of Washington (PBSW) is a respected, if somewhat obscure, biological journal specializing in papers of a systematic and taxonomic nature, such as the description of new species. A review of issues in evolutionary theory is decidedly not its typical fare, even disregarding the creationist nature of Meyer’s paper. The fact that the paper is both out of the journal’s typical sphere of publication, as well as dismal scientifically, raises the question of how it made it past peer review. The answer probably lies in the editor, Richard von Sternberg. Sternberg happens to be a creationist and ID fellow traveler who is on the editorial board of the Baraminology Study Group at Bryan College in Tennessee. (The BSG is a research group devoted to the determination of the created kinds of Genesis. We are NOT making this up!) Sternberg was also a signatory of the Discovery Institute’s “100 Scientists Who Doubt Darwinism” statement. [3]
I don't really understand why, but both you and Meyer have completely failed to do even the most basic research on evolution as a theory, or at least have failed to grasp most of it. Meyer at least has the excuse that he's trying to become famous, or push his ID agenda, but I don't understand it from you.