You're comparing apples to oranges. If you're trying to use genetic algorithms to achieve a specific goal, you need to use a fitness function that corresponds to what you want. For example, if you want to evolve a sorting program, the fitness of your program is (typically) how close to the right order you get; if you choose something unrelated, there's nothing to favour programs with the desired trait. The biological equivalent would be selective breeding of animals (e.g. dogs) for a specific task (e.g. herding sheep).

The long-term natural evolution scenario could be considered to be (very roughly) equivalent to a genetic algorithm where the fitness function is, essentially, capability to survive and reproduce in whatever environment the organism is in.

The point here, anyway, was to illustrate that a wide range of goals can be met by evolutionary processes, not that genetic algorithms are always equivalent to the evolution of life on Earth.

The problem with that counter-argument is that it's not really true. Considering the sheer amount of genetically different individuals of our species alone (with different strengths and weaknesses)...

...compared to the large amount of species of bacteria with billions of identical individuals, I'd say that complexity does not limit diversity.

Dembski's reasoning (or at least this particular part) would be a sensible argument against evolution if, for example, bacteria must have flagella to survive (many don't). The argument against Dembski is that life needn't be like we see it; there is a huge amount of possibilities, and the probability of a specific mechanism appearing is irrelevant.

Ok, perhaps for that particular example. The evolutionary idea, though, is that animals under environmental distress / selection pressure will fairly quickly evolve in order to survive. The fossil record shows stasis. Most preserved animals seem to come from nowhere, live for X million years, then dissapear from the fossil record altogther. This is the rule rather than the exception.

The problem I have with this is that Crocs are considered "living fossils" with little to no morphical change through the millenia and their ancesteral, fossilized remains supposidly date back  ~80 million years. The dinosaurs supposidly died around 60 million years ago due to a massive global extinction event (meteor or comet collision) yet crocs didn't? Then you have the famed ice age animals of wooly mammoths and saber toothed tiger remains that are believed to have lived  from 4.8 million years ago to around 3,500 years ago. Crocs happily lived through this epoch as well? We know from modern crocodial and alligator studies that these animals live in specific temperate climates.. Their eggs in particular produce male or female offspring depending upon the temperature they are incubated at.

http://en.wikipedia.org/wiki/Crocodilia

The Regis example represents 26 letters of the alphabet and a mere 15 character combination. In living cells, protiens are built from 20 possible amino acids and the "simplest" protien is around 50 amino acids long. (Most folded protiens are hundreds of amino acids in length.) These are then  placed in a specifc order, and folded into a precise 3 dementional shape.

Now, we have found that the amino acid sequence can vary to some degree and some amino acid positions can in fact be substituted. But there are many positions where only one specific amino acid will work in order to get a folded protien. And keep in mind that our diverese cellular structues, such as hair, finger nails, blood, liver tissue, brain  tissue etc. are made from many *different * and many *combinations* of protiens.

http://en.wikipedia.org/wiki/Protien

Every one of us has a unique immune system. Our immune systems are built with a large amount of jumping genes or mobile genetic elements. This is why I may have allergies where you may not.

Let's say a super flu hit the world and killed 90% of human population leaving 10% to survive and carry on the species. In a sense this is evolution via. natural selection. The flu resistant people didn't evolve to cope with the flu epidemic ,but rather some of the population was already immune, thus not affected. Also every survivor is not a new species of human. So, even though this *may* be a benefical genetic mutation, it says nothing about the morphilogical changes darwinian evolution predicts.

Some evidence, such as the fact that six out of thirteen allozyme loci are different, that hawthorn flies mature later in the season and take longer to mature than apple flies; and that there is little evidence of interbreeding (researchers have documented a 4-6% hybridization rate) suggests that this is occurring. The emergence of the new hawthorn fly is an example of evolution in progress.[http://www.pnas.org/cgi/content/full/94/21/11417]

Let me try to explain in another way.. Chance evolution predicts that elephants and dolphins could have just as easily recieved the equivilant of the human brain and we could have easily remained an ape species indefinately. But isn't it odd that the one species that recieved the human type brain has the nessicary tools to go along with it? Could dolphins or elephants smelt metals, design intricate machines, explore space etc. with a trunk or a pair of flippers instead of hands with opposible thumbs?

So an animal cannot evolve in 100 years time?

Why did they die? Not one transitional species linking phyla survives to this day ,even though we have millions of animal species living?

Palentologists use cladistics to compare bone structures and determine an evolutionary heredity. There are problems with this approach:

Imagine if bulldogs, chiuauas, and great danes were only known from the fossil record. What do you think palentologists would conclude? How about egg laying, duck-billed platypus with poisionus talons? Or what if butterflies and caterpillars were only known in the fossil record?

Also, most often, complete skeletons are not found, leaving much to the imagiantion of the reconstructing palentologist.

Scientists link animals on strange premises. For example from yor wiki link,

http://en.wikipedia.org/wiki/Pakicetus

These are the precursors to dolphins because they share a similar feature in the ear?

(And notice how some of the links remain blank and many other links have wikipedia quality warnings to boot)

And I count a whopping 47 transitional species listed on that wiki page. Darwin himself expected to find countless millions of animals to fill in the gaps in the years ahead of him.

Except that "most likely" isn't a convincing scientific piece of evidence and amounts to nothing more than a "just-so" story designed to explain evolution.

It's not like these structures have been assembled at random from nothing at all. They've been gradually built up step by step during billions of years.

But how exactly do these structures get built step by step? Complex organs for instance need to have everything pretty much working all at once. What good is a muscle without a blood supply, bones to move and control wiring? And what good is blood without a transport system, a pump and lungs (or gills) to supply oxygen? Bones would be useless without all of the above. etc.

The evolution in these links isn't outside the realm of microevolution (changes due to breeding alone). I'm not disputing microevolution. The problem is that microevolution has limits and can only change an existing species so far. This has been proven through artifical animal breeding.

From your link:

Around 10 million years ago the earth's climate entered a cooler and drier phase, which led eventually to the ice ages. One consequence of this was that the north African tropical forest began to retreat, being replaced first by open grasslands and eventually by desert (the modern Sahara). This forced tree-dwelling animals to adapt to their new environment or die out. As their environment changed from continuous forest to patches of forest separated by expanses of grassland, some primates adapted to a partly or fully ground-dwelling life. Here they were exposed to predators, such as the big cats, from whom they had previously been safe.

Man I'd like to take a ride in this guy's time machine. We just don't know what happend for sure and to suggest otherwise is just plain arrogant to me.

Why did the transitory animals "...most likely lived for a short time..." exactly? Is your reason for "most likely" because of the fact that we are not finding them in the fossil bearing strata? This seems like circular reasoning to me.

I do consider Archeopteryx a very plausible missing link. I just can't help wonder why we have so few examples of this calibur.

http://en.wikipedia.org/wiki/Archeopteryx

Cave may hold missing link
"It represents a kind of stepping stone between very primitive insects and praying mantids," he said. "Or it might be a completely new kind of insect."

A fossil of a newly-discovered, chipmunk-sized mammal that roamed the world with the dinosaurs 125 million years ago provides a missing link in the evolution of the middle ear, according to a researcher at the Carnegie Museum of Natural History.

A Missing Link in Membrane Protein Evolution
How do integral membrane proteins evolve in size and complexity? Using the small multidrug-resistance protein EmrE from Escherichia coli as a model, we experimentally demonstrated that the evolution of membrane proteins composed of two homologous but oppositely oriented domains can occur in a small number of steps[...]

It could be a "missing link" to the evolution of cuttlefish, squids, and octopus.

It's kinda weak to me.. Too bad the links to "ectotympanic bone " and "auditory bulla" don't have articles yet.

The shape of the ear region in Pakicetus is highly unusual and only resembles the skulls of whales. The feature is diagnostic for cetaceans and is found in no other species.
According to Thewissen, the teeth of Pakicetus also resemble the teeth of fossil whales, which is another link to more modern whales.[3]

The Tiktaalik is interesting but shouldn't we remember the lessons of the Coelacanth?
http://en.wikipedia.org/wiki/Coelacanth

This fish wast hyped as one of the de facto icons of evolution. We thought it went extinct for 80 million years ago then it turned up living off the coast of Africa. Once we studied the living examples with very little morpic changes over eons of time, we found out it wasn't the land walking proto vertibrate we once thought. No this wasn't a walking fish that represented the move from the ocean to dry land by vertibrates. We have no reason to suspect that the ancient Coelacanth is anything more than it really is, an oily, boney fish with some unique features.

I'm not a scientist either and you are right, they could have survived, and that might indeed be the case. I just think that the Crocs represent what we see in the fossil record, stasis. We see species living virtually unchanged for millions upon millions of years. Multicellular life was thought to only have arisen 550 to 600 million years ago and yet this amount of time is quickly gobbled up with many, many examples of stasis.

Yes and this is the same story Darwin presented in his classic writing "On Origin of Species." But what does it take to get a photosensitive cell?

Let us return to the question, how do we see? Although to Darwin the primary event of vision was a black box, through the efforts of many biochemists an answer to the question of sight is at hand. 4 When light strikes the retina a photon is absorbed by an organic molecule called 11-cis-retinal, causing it to rearrange within picoseconds to trans-retinal. The change in shape of retinal forces a corresponding change in shape of the protein, rhodopsin, to which it is tightly bound. As a consequence of the protein's metamorphosis, the behavior of the protein changes in a very specific way. The altered protein can now interact with another protein called transducin. Before associating with rhodopsin, transducin is tightly bound to a small organic molecule called GDP, but when it binds to rhodopsin the GDP dissociates itself from transducin and a molecule called GTP, which is closely related to, but critically different from, GDP, binds to transducin.

The exchange of GTP for GDP in the transducinrhodopsin complex alters its behavior. GTP-transducinrhodopsin binds to a protein called phosphodiesterase, located in the inner membrane of the cell. When bound by rhodopsin and its entourage, the phosphodiesterase acquires the ability to chemically cleave a molecule called cGMP. Initially there are a lot of cGMP molecules in the cell, but the action of the phosphodiesterase lowers the concentration of cGMP. Activating the phosphodiesterase can be likened to pulling the plug in a bathtub, lowering the level of water.

A second membrane protein which binds cGMP, called an ion channel, can be thought of as a special gateway regulating the number of sodium ions in the cell. The ion channel normally allows sodium ions to flow into the cell, while a separate protein actively pumps them out again. The dual action of the ion channel and pump proteins keeps the level of sodium ions in the cell within a narrow range. When the concentration of cGMP is reduced from its normal value through cleavage by the phosphodiesterase, many channels close, resulting in a reduced cellular concentration of positively charged sodium ions. This causes an imbalance of charges across the cell membrane which, finally, causes a current to be transmitted down the optic nerve to the brain: the result, when interpreted by the brain, is vision.

The photoreceptor signals its absorption of photons through a release of the neurotransmitter glutamate to bipolar cells at its axon terminal. Since the photoreceptor is depolarized in the dark, a high amount of glutamate is being released to bipolar cells in the dark. Absorption of a photon will hyperpolarize the photoreceptor and therefore result in the release of less glutamate at the postsynaptic terminal to the bipolar cell.

This would be so much more plausible with some real, empircal science.

But that's the problem bro, animals show abrupt arrival and millions of years of stasis in the fossil record, not a steady, constant stream of intermediates of which Darwin predicted.

Of course it's not, in fact Evolution needs breeding changes. Darwin's microevolution of finch beaks is a coner stone to his theory.The problem is that no matter how much we breed animals they don't change in unexpected ways. Although we can achieve some very interesting breeds, it only goes so far. So big, so small.

This is interesting and I have read a bit about this particular example previously. Seems this could be reproduced in a lab.

This looks a little "just-so" to me. Interesting idea, but I'd feel much more comfortable with such a scenario with some hard, empirical science.

Whatever the cause of bipedality, it eventually led to the development of higher intelligence. Darwin's theory is that with the freed up hands that bipedality allows, hominids would be able to use tools, and the use of tools led to the development of greater intelligence.

Agreed 100%, but when we start going lightyears beyond the scientific data and completely speculate around a single prevailing idea (to the exclusion of any other possible competeing explanations) it's a bit arrogant. At least to me.

I'm pressed tonite, but this caught my eye.

http://www.livescience.com/animalworld/top10_vestigial_organs.html

 10) Flightless birds. Show me one flightless bird that doesn't use it's wings.. Every species has a use wether from courtship, to diving in the water, to balancing themselves on fast runs, camoflague.. You name it, they use them and they are FAR from useless.

Vestigial structures are anatomical structures of organisms in a species, which have lost much or all of their original function through evolution. They are typically in a degenerate, atrophied, or rudimentary condition. They are often called vestigial organs, although not all of them are actually organs.

Although structures usually called "vestigial" are largely or entirely functionless, a vestigial structure may retain lesser functions or develop new ones.[1] Thus, a "vestigial wing" is one useless for flight, but may serve some other purpose.

9) Hind legs in whale. First, note how blurry the un-clicakble inlay is, even though it instructs you to view the inlay. Second, they've only found two specimines total that looked anything like a leg bone, not beyond the realm of a tumor or anomolus genetic defect. Third: These uniform bones in modern whales are important anchors for the reproductive organs.

There are many cases where whales have been found with rudimentary hind limbs in the wild, and have been found in baleen whales, humpback whales, and in many specimens of sperm whales. Most of these examples are of whales that had only leg bones, but there were some that included feet with complete digits.

8 ) erector pili . Or goosebumps. These are VERY important to sex in humans. Imagine if your girl didn't get erect nipples. Need I say more? (Sorry if this is a family show.)

7) human tailbone : Important anchor for buttox muscles.

6)The Blind Fish Astyanax : I'm not sure that absolute darkness wouldn't do this to many species.

5)  Wisdom Teeth : I'm not sure this isn't an inbred genetic trait in humans. A) It doesn't affect all people. B) Inbred hicks often have messed up teeth.

4)Dandelions. Have sex organs which they "don't use" but clone themseleves instead. A) They do use them to attract bees and ants which benefit from their pollen and B) in turn they are protected from other insects. C) I'm not so sure they don't use them for normal flower sex as well. D ) There are species of Dandelion that do reproduce normally.

3) Fake lizard sex: No comment, interesting. Some species of sea fish actually are all female and one of the dominant females begins producing testosterone and becomes the male, litterally.

2) Male breast tissue(nipples). It is my understanding that we are all female in the womb untill the DNA codes differentiate us as sexes. So not all tissue is removed. Saying it is vestigial seems to imply that humans will evolve and lose them. I don't think that will happen.

1) Human Appendix : The Encyclopedia Britainica (forget  wich year, sometime in the 90's described the appendix as the place where digestive, immune responses start. I'll see if I can find a link.

We both link Wikipedia articles but this should be noted.

http://en.wikipedia.org/wiki/Criticism_of_Wikipedia

Wikipedia isn't the most reliable source of information.