Why I believe the theory of evolution

Logic is, fundamentally, the evidence for evolution.

The modern theory of evolution is based on a few simple postulates:

1) Living things reproduce.

2) In the reproductive process living things pass on inheritable traits through some mechanism of inheritance (which turned out to be DNA).

3) The inhertance mechanism is not perfect and variations are introduced through some mechanism (this turned out to be mutation of DNA, insertion, replacement, deletion, etc..).

4) Conditions of the environment of the organism coupled with internal and inheritable traits of the organism will combine to determine an organisms reproductive fitness (the ability of the individual organism to survive to reproduce thus incorporating any traits that the individual may have evolved through mutation into the gene pool of the species). (This last one is called natural selection).


The rest of the theory of evolution follows logically from these postulates. We can do a few simple thought experiments to make this clear. But I'd like to introduce a few concepts which are based on these postulates:

1) Evolution is a markov process. In statistics markov chains are stochastic mathematical models in which the future evolution of the system is based only on the system's current state, not on any previous states. This means that because evolution is a markov process, your genome was entirely based on the DNA you got from your parents' gametes. The genes of your grandparents likewise completely determined the genes of each of your parents, and you and a partner will completely determine the genes of your children. In a markov model each step directly influences ONLY the following step in the model's evolution. The genomes of my grandparents can be completely ignored in analyzing my genome's evolution from the DNA of my parents. I'll just state the implication here for those who might miss is. The implication of this fact is that evolution is a branching process. If we were to map out a tree of descent based on the fact that the genes of my grandparents are irrelevant to mine and future generations that come from me, then lines of my parents are drawn directly to me, and from me and my wife directly to each of my children, and directly from each of my children and their future partners to their future children. At that following step I'm completely left out and you can see how, since I have 2 children, my children produce two branches from my one branch.

2) The concept of genetic drift. Mutations are random, and thus subject to laws that govern random processes. One of these is the law of large numbers. This expresses itself in a concept referred to as genetic drift. In a large population of reproductively fit individuals the genes that are the most well distributed will, due to the law of large numbers, be most likely to remain most well distributed unless there is a drastic environmental change or a new mutation which introduces a dramatic improvement in reproductive fitness. This is why some populations appear to remain static for many hundreds or thoughts of generations. In small populations, though, novel new mutations are more likely to become dominant in a population in a relatively short amount of time because the law of large numbers doesn't have a chance to assert itself. It's like rolling a die 6 times. In that small sampling of this random event you may roll a sequence like 1, 3, 2, 4, 3, 1; which means you rolled 1 2/3 of the time. 3 2/3 of the time 2 1/6 of the time, 4 1/6 of the time 5 0/6 of the time and 6 0/6 of the time. each number, though had an equal probability (1/6) of coming up. If you rolled the dice 6000 times you'll likely see a probability distribution for each number approaching 1/6, and the distribution will come closer to 1/6 as you increase the number of dice rolls. This is the law of large numbers and this is why in a large population new mutations are more likely to be lost than to assert themselves, and why the opposite is true in smaller populations.
 
3) Reproductive isolation.  Two populations of the same species can be considered reproductively isolated if for any reason members of one of the populations cannot reproduce with members of the other and vice versa.  This is usually due to geographic isolation, members of one population have been brought to an island somehow, or they migrated to a different and remote area, or they've decided to occupy a different ecological niche, or they just don't like members of their population that share a trait (like maybe a patch of yellow fur) whatever is the cause, the two populations should, genetically, be perfectly capable of interbreeding but for some reason never do.
 
4) Sexual selection.  Sexual selection is derived from natural selection, except instead of something from the environment helping to determine reproductive fitness it's the reproductive preferences of members of the species themselves.


Now that I have explained these concepts, let's get on with the thought experiment.

Let's suppose that a population of species A exists.  It's a simple population with only a thousand representatives, and only one variety.  Let's say that 8 males and 13 females of this population become carried away from the general population by a flood into a new area and never find their way back to the original population.  This new area is a little different from their old area with many new food sources but some familiar ones.  Also mostly familiar predators and a few new ones.  So we now have populations A1 and A2.  The two populations are reproductively isolated.  So new mutations in each population will not be available to members of the other population.  Now there are a few new selective pressures on population A2, there are a few familiar food sources in the new area but not enough of those to sustain a large population of their species.  Either A2 mutates adaptations that will allow them to take advantage of the new food sources, or they eventually over reproduce and die of starvation as the new area doesn't have the resources to support a large population of A.  Because mutations are random it's always possible that no mutations will happen which allow A2 to take advantage of the available and abundant new food sources, but because of genetic drift and the fact that A2 is a small population if they do mutate the necessary new features there is a relatively high probability, esspecially given the advantages, that the new mutation will take firm hold in that population's gene pool.  Now let's assume that A2 evolves the new traits necessary to make use of the new food sources.  This will be traits not present in the other population.  We're already starting to see divergence.  We also introduced some new predators.  The population A2 will also face a strong selective pressure to evolve some strategy for dealing with these new predators.  Maybe claws, camouflage, sharp teeth, intimidation tactics, the ability to run fast, burrow deep, climb trees, whatever.  Over time, esspecially given the fact that the environment is not static, food sources will evolve to defend themselves from this new predator A2 and predators will evolve strategies for more effectively hunting this new prey A2.  Natural disasters may happen, sexual selection may favor interesting new but mostly nonfunctional adaptations in A2 and different such mutations in A1.  Eventually over thousands of generations the two populations of A will have diverged so much from one another as to not be recognizeable anymore as members of the same species.

It should also be noted that a population's gene pool can only allow for mutations on genes and genomes that are already present within the population.  An introduction of a novel new fully formed, fully functional, and advantageous gene into the population in a single generation, while not impossible, is so improbable as to be practically impossible.  The theory of evolution does not say that such a thing could never happen, but it does say that we can't make a habbit of assuming it did in any significant number of instances and in fact should proceed as though it never could have unless there is overwhelming evidence that suggests it did.

Also keep in mind that in a population an advantageous gene only has to evolve once.  After that it's passed on to future generations through the process of inheritance.

Essentially if you want to disprove the theory of evolution your best chance is to attack postulates 3 and 4.  Show that mutations don't happen or that natural selection doesn't happen.  The scientific method has already established very convincingly that mutations do happen and natural selection is a real process, though, so good luck.

Yahoo Answer again too long

I was answering this question:
http://answers.yahoo.com/question/index;_ylt=AoE1f2trPibL5RP1meAEbJ4jzKIX;_ylv=3?qid=20090124121806AANmIjB

"Is evolution a scientific theory ?


For a theory to be scientific it has to have repeatable experiments with a predicatable outcome. Evolution ( macro evolution ) is not repeatable as far as i know, so why do scientists then say that evolution is a scientific theory ? when they can not repeat an experiment where for instance a fish transforms into a bird ?



Honest answers only please.

Additional Details

3 days ago



i am aware of the fruit flies experiments. yet these are small changed ( micro evolution ), for macroevolution i do not know any repeatable experiments.



i strongly believe that experiments has to be repeatable , if not there is no point of makeing a theory out of it, since theories are used to predict the futur. it doesnt make sense to get rid of the "non repeatable experiments constraint" in a theory if it are only one time events ."
 
My Answer:

Evolution can't make predictions about how things will change only that things will change. Also evolution doesn't say that any species changes into another species, every succeeding generation is going to be a more specific representative of its current species. Over time differentiation of lineages from one ancestral population will result in the ancestral species being referred to as a genus.




No one would be able to induce a fish to evolve into a bird, in nature the pathways of evolution from fully aquatic fish, to tetrapod fish, to amphibious tetrapod, to full amphibian, to reptile, to therapod dinosaur, to bird took hundreds of millions of years. No laboratory has the time to repeat that. We also don't have the facilities to reproduce every environmental condition that might have served as timely selective pressures for specific changes, and we have no control over how genes will mutate. If we were to take the earth back in time 500 million years or so and let it play out again evolution most likely wouldn't progress along the same lines it has in our observable universe specifically because of certain completely random elements in gene mutation, specifically the effects of beta decay on DNA.



This doesn't mean, however, that we can't perform laboratory experiments that show us the process of evolution at work. If we understand that evolution works through inhertance and variability, natural selection and sexual selection, and genetic drift and reproductive isolation, then we only need show each part actually occurs in nature and the theory is confirmed if you can show these parts also are linked.



No one doubts that each generation inherits traits from its parents. This is a well established fact, so we can consider inheritability proven. Mutations are often wrongly disputed by creationists, though. In reality many beneficial mutations have been well documented and even reproduced in larboratories.



http://en.wikipedia.org/wiki/Nylon-eating_bacteria

http://en.wikipedia.org/wiki/E._coli_long-term_evolution_experiment#Results

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



Those are just three examples of many. These mutations added information to their respective genomes and were beneficial. They improved reproductive fitness and thus were more successful at being passed on to future generations. It's also interesting to note that all three of these mutations don't deal with enhanced survival through resistance to something that might harm them, but through the adaptation of a new pathway for metabolizing something found in their environments. Nylonase evolved a pathway for metabolizing the waste products of industrial nylon production, one of the e. coli colonies in the long term e.coli evolution experiment evolved a way to metabolize citrate which e. coli normally just cannot do at all. And the fungus evolved the ability to turn radiation into a source of energy similar to the way plants use sunlight.
 
From those experiments I think we can consider the fact that beneficial mutations occur to be an established fact. Well that and the fact that we can look at the genomes of the ancestral populations of all of these species and see that these genes just aren't there.




Natural and sexual selection deal with how selective pressures will help to determine what mutations including but not limited to mutations that render individual organisms unviable improve or harm or have no effect on reproductive fitness. Mutations that don't actually harm viability but which provide some other disadvantage due to environmental considerations are culled either because the individual is less likely to survival to reproduce or because the individual is not appealing to potential mates. This was demonstrated to work from the famous peppered moth experiments which many creationists wrongly attempt to discredit on completely irrelevant grounds. The color of the moths had no direct effect on the individual moth's viability, but in areas with lighter bark on the trees the black moth's pigment was a liability for them since it made them stand out to predators, while in sooty areas with darker bark on the trees the light colored moth's pigment was the liability. From this experiment and many others like it we can clearly see that natural selection is a force that really does operate in nature, and by observing bird populations esspecially we can clearly see sexual selection at work in plumage and coloration. From these facts I think it is safe to say that natural and sexual selection are real phenomena.



Now taking these facts into account we move on to reproductive isolation and genetic drift. These two aspects are completely logical, we can confirm them with a simple thought experiment. Whether or not you are satisfied with the evidence in favor of mutations or natural and sexual selection, let's just accept them as true for the sake of argument. Now evolution deals with gene pools within populations, not with individuals. With these assumptions just granted for the sake of argument (though I think I provided good evidence in favor of them all), it follows that within a given population if mutations happen and inheritance is always passed on from parents to offspring, that genetic drift will happen concerning which mutations make it into the general population and are inherited by all members of succeeding generations. This follows directly from how inheritance works. Evolution is a mathematical model known as a markov chain.



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



This basically means that it's the current state that determines how the next state will evolve and not any of the states before. This follows from the fact that we don't get our genes directly from our grand parents or great grandparents and so on, each individual will only inherit the genes that are present within their parent's genomes and mutate new traits from that limited pool. Because of this some genes can be lost from any given gene pool. Markov Chains are a statistical model and thus are subject to the law of large numbers. So in large populations the tendancy will be for there to be, for the most part, a sort of statis until or unless an adaptation is evolved into the gene pool that makes a very significant change in reproductive fitness, or something dramatic happens to the environment.



Reproductive isolation, however, is when a small subset of a species general population becomes isolated and no longer shares genes with the larger gene pool. In a smaller population genetic drift is more inclined to favor new mutations no matter how innocuous, but esspecially if they improve reproductive fitness even just a little bit. Over time, if two lineages of the same population never mix genes they will accumulate, through the inevitable random mutations, enough differences in their gene pools that they become noticeably distinct. Unless you can think of a reason why they shouldn't when we've granted the assumption that mutations happen. Keep in mind, though, that reproductive isolation doesn't mean the two populations can't mix for any biological reason, they could still interbreed if they could get together, but the isolation could be geologically imposed, or it could be ecologically imposed. It could even be imposed by bias in the whole sexual selection process (Like some birds preferring mates with lots of red feathers and others preferring mates with lots of green feathers).



So you see if we just prove that mutations happen and can be beneficial and that natural and sexual selection are real processes in nature, the rest follows logically. I leave inheritance out because I don't know anyone at all who disputes inheritability. The evidence from genetics, phylogenetics, the fossil record, etc, is just icing on the cake.

This is just...wow

I was perusing Yahoo Answers which, as you can see, has become almost a new hobby when I came across this question, which I'll just post a link to, since the question is a long one:

http://answers.yahoo.com/question/index;_ylt=Am2o3cl0GYvZ84__Wj.fSxbd7BR.;_ylv=3?qid=20081114204541AAwAKlx

While I was reading the answers I came across this gem:

By harry killwater:

"Here is what's up...

The Atheist has to hold onto the theory of evolution because if it is ever disproven then they have to acknowledge that there is a creator. Unfortunately the theory will never be disproven nor will the theory ever be proven. We are stuck with the "theory". It will always remain with us as a "possibility" and therefore will remain a convenient hiding place for the Atheist to roost.

Having once stood on the cliff as an Agnostic considering the precipice of Atheism, I have to confess that jumping in had a very seductive draw at that time in my life. Jumping off the cliff would guarantee me a lifetime position of intellectual superiority and the comfort of being right without having to prove anything. It would also have set me free from the burden of hard thinking and the weakness associated with not "understanding".

It would have been so easy to put my brain on a shelf and ignore the questions that plagued me. I could easily have spent the rest of my life using my intelligence to develop arguments to make fools out of the spiritulaists of all flavors. I would be very successful and would be greatly admired on this path.

But instead of jumping into the abyss, I chose to not ignore the obvious. The bumblebee and the tulip and the ameoba and the hummingbird and the giraffe and the turtle and the shark and the ant and the jellyfish and me and you could not have a common ancestor. This is irrational. There is not a thimblefull of evidence to support anything this ridiculous. When evolution is taken to it's logical conclusion, one has to accept that everything living has a common ancestor. Yet there are billions of missing links and the Atheist does not seem to care. Some become so delusional as to actually "believe" this insanity. It is a faith that protects them from having to admit that a god exists and that this god may actually want something to do with us.

So I turned away from the lure of hiding my weakness in a superiority complex and decided to go down the road of seeking the "god" that had to exist.

I do not think the rest of my spiritual story is relevant to your question so I will just stop here and say in summary...Atheism is the epitome of irrational thought hidden behind a veil of intellectual superiority used by people to hide their inability to confess their fear of trying to understand the reality of a god who could create everything that we see. In many cases with the new breed of Atheist, it also protects them from their fear that the majority of the godviews of man considers their behavior or thoughts to be immoral.

And life goes on....

agapefromnc"

Honestly one of the most unjustifiably arrogant things I have ever read.  The irony of these words is thick given that mr killwater is asserting that he chose not to become an atheist to avoid pretending to be "intellectually superior" and yet that is exactly the tone he attempts to strike here.  Even to the point of questioning the sanity of an atheist for believing evolution.

Of course this arrogance could have been justified had he actually attempted to construct some kind of rational argument that would back up his assertions that evolution is rediculous, but he never does.  The closest he comes is:
"The bumblebee and the tulip and the ameoba and the hummingbird and the giraffe and the turtle and the shark and the ant and the jellyfish and me and you could not have a common ancestor. This is irrational. There is not a thimblefull of evidence to support anything this ridiculous."
He follows that bald assertion up with this blatant misunderstanding:
"Yet there are billions of missing links and the Atheist does not seem to care."

He never goes on to explain why they could not have a common ancestor, I would love to see him try.  He asserts that this is irrational but doesn't explain why the arguments used to support common descent are irrational.  He asserts that there is not a thimbleful of evidence to support anything which he considers to be this rediculous but is obviously either thinking of an exceptionally large thimble, or is just demonstrating his ignorance of mountains of evidence that do in fact support such an actually not so rediculous observation.

He apparently missed the fact that the apparent relatedness of every living thing was first suggested by a creationist named Carl Linnaeus in the mid to late 1700's.  It was this observation, among several other observations, which lead Darwin to his theory of evolution by natural selection.  It is true that common descent is a logica conclusion.  That much mr killwater got right.  He doesn't leave much of a jumping off point for a correction since he makes such general assertions and offers no logical support for any of them here.  Really all I can say is I would love to see his evidence that backs up anything he said in that answer.

As for the "billions of missing links".  There's a reason why scientists don't use that term.  Missing links don't exist.  You can't link humans to apes through any progression at all because humans didn't evolve from apes.  Mr killwater seems blissfully ignorant of the many transitional fossils that have been found, though, which serve as part of the mountains of evidence supporting common descent.  The thing about fossils that mr killwater also must be woefully ignorant of, is that fossilization is rare.  Fossils only form under a few very specific sets of conditions that are not met everywhere and are not met often.  On top of that it becomes even less likely for fossils to survive until discovery.  This is all dependent upon erosion, people looking in the right place at the right time, and fossils are very delicate.  If the wrong person finds a fossil and doesn't know what it is or how to handle it properly that fossil is lost.  If someone goes running a bulldozer through earth where a fossil was near the surface, that fossil is lost.  I'll leave it to anyone reading this to think of any other scenarios that could easily result in lost fossils.  I think in the interest of setting the burden of proof to high for anyone to ever meet it, creationists are willfully ignoring how impressive the collection of transitional fossils we actually do have really is.  Of course we don't see every representative species between the first cell and any modern species, but we do see a lot of them, and more than enough of them to establish that transitional forms do exist.  This is why creationists are forced to resort to calling fossils hoaxes that are actually genuine.  Archeoptrix springs immediately to mind.  Yes there have been hoaxes, but scientists are adept at spotting hoaxes.  Archeotryx has been proven genuine and there is no debate about its authenticity among paleontologists despite many claims to the contrary that I keep hearing from creationists.  You can very firmly count the fossil record among the evidences for common descent.
Here, these links are wikipedia articles but they're as accurate as any introduction to the topic really needs to be:
http://en.wikipedia.org/wiki/Mammal_evolution
http://en.wikipedia.org/wiki/Reptile#Evolution
http://en.wikipedia.org/wiki/Hylonomus
http://en.wikipedia.org/wiki/Westlothiana
http://en.wikipedia.org/wiki/Petrolacosaurus
http://en.wikipedia.org/wiki/Mesosaurus
http://en.wikipedia.org/wiki/Edaphosaurus
http://en.wikipedia.org/wiki/Dimetrodon
http://en.wikipedia.org/wiki/Anapsid
http://en.wikipedia.org/wiki/Diapsid
http://en.wikipedia.org/wiki/Lepidosauria
http://en.wikipedia.org/wiki/Archosaur I esspecially like that living archosaurs are crocodilians and birds.
http://en.wikipedia.org/wiki/Synapsid which were reptiles but were the type of reptiles that mammals evolved from
http://en.wikipedia.org/wiki/Bird_evolution
http://en.wikipedia.org/wiki/Origin_of_birds
http://en.wikipedia.org/wiki/Whale_evolution whale evolution is interesting we've found many transitional fossils
http://en.wikipedia.org/wiki/Evolution_of_sirenians
http://en.wikipedia.org/wiki/Transitional_form This is also good for a general understanding of the subject of transitional forms, which is more accurate than "missing links".

The biggest problem with the term "missing links" is simply that it implies that evolution works in a way that no evolutionary biologist claims it does.

For more evidence of common descent check out this link:
http://www.talkorigins.org/faqs/comdesc/
You can also read this for more general and specific information about the theory of evolution:
http://www.talkorigins.org/origins/faqs-evolution.html

Then I found this line particularly funny:
"It is a faith that protects them from having to admit that a god exists and that this god may actually want something to do with us."

Hillarious is the assertion that it's faith that protects an atheist like me from having to admit the truth of a proposition I would have to support by faith.  That also is extremely ironic.  It takes faith not to have faith...what's the definition of faith here?  This reasoning really only serves to render the word faith effectively meaningless, which I find extremely funny.

"Atheism is the epitome of irrational thought hidden behind a veil of intellectual superiority used by people to hide their inability to confess their fear of trying to understand the reality of a god who could create everything that we see."
I, of course, also found this amusing.  The assumption here is, of course, atheists are afraid to try to understand that god is real and a real cause of everything we see.  The underlying assumption there is, of course that god is real.  Circular reasoning at its finest.  The entire assertion falls apart if god is not real.  If mr killwater tries to point at the fact that everything we see exists as proof that god is real the proof falls apart if god is in reality not real.  Circular reasoning is when a premise being used to support a conclusion depends on the truth of the conclusion it's trying to prove.  Arguments can't support themselves that way.  It's specifically for that reason that the existence of a god is anything but obvious.  It's certainly the easy way out as far as understanding the universe is concerned.  I'm not even saying it couldn't be correct, but it can't be proven.  Of course anyone is welcome to try to prove it.

Another Answer to a Yahoo answers question too long for yahoo answers.

The question is:
What exactly is Evolution and why do people care about it so much?
I heard a plethora of things about Evolution but what exactly is it? Why is it so vital for some people?

http://answers.yahoo.com/question/index;_ylt=Aj1m.kK8l66d1ZusFLoUmQ0jzKIX;_ylv=3?qid=20081112175258AAsrEff

My answer was too long so Yahoo wouldn't post it. So I copy and pasted it here and I intend to link to this blog entry in my new answer.

None of it true, I'm sure. Evolution is the theory that attempts to model how the fact of evolution (descent with modification) has resulted in the observed diversity of life on earth. The theory of evolution is based on observations by creationists like Linnaeus who noticed that all of life seemed to be classifiable in a sort of tree of related kinds. This was the beginning of our modern taxonomic system for classifying species. The observations between fossils extinct species and living species helped to give the impression that extinct animals are somehow related to now living species.Then along came Darwin who took this observation and observations from animal husbandry, namely the fact that we pick animals of the same species with traits that we like and breed them together to mold those traits in almost an art form. He talks about how expert pigeon breeders could even sculpt the shape of the beaks in a relatively few generations. He argued in favor of a mechanism of inheritance and then he applied this observed "artificial selection" to certain similar aspects of nature. In artificial selection it's us humans who decide which of our stock of animals are fit to breed, but in natural selection it becomes the specific survival requirements of nature that determine which of the stock of animals is fit to reproduce.Darwin also hypothesized the existence a mechanism for mutation, which would allow new inheritable traits to be introduced into the stock of animals. This was all long before we knew what the inside of a cell looked like. This was before we knew about genes and genetics so Darwin had no idea what the mechanism might be or how related biology was, on the cellular level to other existing disciplines such as chemistry.Darwin's idea was that natural selection definitely accounts for the observed variation within species in nature as artificial selection accounts for how a skilled breeder can sketch out a beak for a pigeon and in a relatively few generations breed a pigeon with that beak. He went a little further with this, though, to argue that, because it's also observed that all of the organisms alive and extinct share features that they may share a common ancestor and that all of the current species may have evolved through the mechanisms of mutation, inheritance and natural selection.Interestingly enough this hypothesis has only been confirmed through the discovery of the complexity of cells, genetics, biochemistry, embryology, etc. The phylogenetic tree is the tree that shows the evolutionary pathways of modern species from the very first cell. The phylogenetic tree's are developed by taking species that share characteristics and if they share all characteristics they are the same species, if they share more then they share a common ancestor, maybe not a unique common ancestor, but a common ancestor none the less. The more characteristics two species share in common the more recent the common ancestor. This is also confirmed by genetics, which shows us that two species that are phylogenetically similar are more genetically similar than two species that are less phylogenetically similar. This works because of the principle of inheritance. We can only inherit features that are present in our gene pools. So if you ever find an animal with a plant cell wall or chlorophyll you may have just falsified the entire theory of evolution. Those features are not shared by any common ancestor to animals and plants. They evolved independantly in plants long after our common ancestors branched, so they aren't in our shared gene pool, and mapping the gene pool has confirmed that they are indeed not in our genome. If you found haemoglobin in plants it would be the same situation. New features will evolve in the gene pool and if they're useful they'll stick around, much the way chlorophyll was useful for plants and vertebrae was useful for...well a lot of animals, heh.That was a basic primer, there's a lot more left to learn on the subject if you're honestly interested. As for why it's vital, I am extremely sure that evolution is correct based on the mountains of evidence that I have read in favor and the complete lack from all available sources of evidence that it is not correct. So from that standpoint I see it as vital to our existence, if it's correct, but not in any way that matters as we're already here. On the other hand it's not vital in any other way. If you want to have a chance of understanding the world we live in learning evolution can help. If you just want to believe something for reasons irrelevant to what's true, by all means ignore evolution or believe it's false.

Oops...I took too long answering and the question became resolved...that's why I couldn't post my answer...I wish Yahoo would tell you that. The generic "Yahoo Answers is taking a breather" error is getting annoying.

Another Answer to a Yahoo answers question too long for yahoo answers.

http://answers.yahoo.com/question/index;_ylt=Am_KvU1lyVWBPbWdSSK16P8jzKIX;_ylv=3?qid=20080905033254AACHBs4

Above is the question, below is my answer in full.

They are scientific theories thus many aspects of the theories are facts and the theories themselves are based on facts. The theory of evolution, for instance, is based on the fact of evolution. Evolution is simply defined as descent with modification. This basically means that every succeeding generation will not be a perfect genetic carbon copy of the preceding generation. These modifications can be neutral, beneficial or detrimental. The neutral modifications will have no noticeable effect or a bad or good effect depending on how the environment changes and only if the environment changes. Beneficial modifications will have a positive effect even if the environment stays the same. Detrimental mutations have a negative effect even if the environment stays the same.
Positive mutations are more likely to be selected for by natural selection because they will confer a survival advantage on the organism with the mutation making it more likely that the individual will survive and reproduce. When that individual reproduces it will pass on its beneficial mutation to its offspring. The theory of evolution suggests, with evidence, that eventually as these mutations accumulate new species can emerge even differentiating into new genuses and families, etc. You should try reading Darwin's The Origin of Species.
The evidence of this comes from fields that were already existent durring Darwin's lifetime and fields that were not yet existent durring Darwin's lifetime. There's paleontology. The fossil record confirms the evolution of, just to name a few examples, amphibians and reptiles from fish, the evolution of mammals from reptiles, the evolution of birds from reptiles, and the evolution of aquatic mammals from land mammals. It even shows a clear evolutionary pathway for specific species such as horses, elephants, pigs, humans, etc. The evolutionary theoy is also confirmed by genetics. A prediction of the theory of evolution for genetics would be that if the theory were correct you would expect to see a direct correlation between how closely related two species are and how similar their genomes are. This is exactly what we do, in fact, see. This is also only two examples of the evidence for evolution, there is much much more. I gave links.
Likewise the big bang is based on observations of the real world, for instance the fact that the universe is expanding. This is observed in the redshift of galaxies. Before this theory scientists believed that the universe was eternal and static, this model is known as the steady state model. Of course Einstein's theory of general relativity was the final nail in the coffin of the steady state model, even though there are still defenders of this now dead model. If gravity works the way that Einstein described, and countless experiments have confirmed that it does at least above the quantum scale, then there would have to be some special voodoo at work in the universe to keep the universe from collapsing in on itself. Of course if the universe is still expanding outward because of the force of what was initially thought of as a big bang that would explain why the universe isn't collapsing in on itself, in other words why all the galaxies aren't blue shifted. There's another reason why the theory of relativity marks the death of the steady state model, though, which Einstein himself advocated. Einstein's equations, taking the observed universe into account, when run backwards 13.7 billion years, gives us a big crunch. This would be the big bang in reverse. The interesting thing is that Einstein developed his equations with the assumption that the universe was eternal and static, he absolutely hated the idea that there could have been a beginning to the universe. But despite that his equations clearly show that the universe had a beginning which is referred to as the big bang.
Of course at the end of relativity's big crunch is a singularity. Because relativity assumes spacetime is continuous it crunches the universe down to infinite density, at which point the equations break down creating a singularity, which would be the equivilent of division by 0. The singularity is really just the point where the math becomes undefined. The common belief among cosmologists is that if we are going to understand the big bang we are going to need a quantum theory of gravity. One that brings quantum mechanics and relativity together.
One candidate is Loop Quantum Gravity, and you may be interested to hear that Loop Quantum Gravity predicts a model that changes the big bang to the big bounce. The mathematics of the theory only assumes the existence of spacetime atoms, which makes space not continuous and allows the math to be defined down to and before the moment of the big bang, allowing us to be able to understand what happened. Loop Quantum Gravity is still incomplete, but it's current state of readiness suggests that at extreme density (albiet finite density) the gravitational force changed from a weak attractive force to a very strong repulsive force causing rapid spacetime expansion as predicted by the inflationary model of the big bang. I'll provide a link to the article about the big bounce from scientific american as well.

http://evolution.berkeley.edu/evolibrary/article/0_0_0/lines_01http://www.gate.net/~rwms/EvoEvidence.htmlhttp://anthro.palomar.edu/evolve/evolve_3.htmhttp://www.talkorigins.org/faqs/comdesc/http://www.talkorigins.org/origins/faqs-evolution.html
http://www.sciam.com/article.cfm?id=big-bang-or-big-bounce

A very brief history of time

To answer this question in great detail would be long but I'll try to keep it brief. As far as the matter and energy that comprises the visible universe it has, as far as anyone knows, always existed. It is infinitely older than this universe. What that means about the universe before the big bang we do not know, the big bang itself destroyed all information about the universe before it. At least as far as we know, perhaps when we have a quantum theory of gravity we will be able to find out more, but currently we don't yet have such a theory, we have some good candidates for such a theory but they are still far too incomplete.
The big bang, contrary to popular belief, was not an explosion, it was a sudden and rapid expansion of space-time. As the universe became less dense it also became less hot, allowing the four fundamental forces of electromagnetism, gravity, and the strong and weak nuclear forces to separate (possibly) and for the formation of the two lightest atomic nuclei, Hydrogen and Helium. These formed around 100,000 years after the big bang. Gravity is actually the weakest force in the universe which we can easily confirm by dropping something from just about any height. The electromagnetic force is what keeps things from passing through each other and no matter how high something seems to fall from it never falls with enough force to break the electromagnetic force, but the electromagnetic force is more than strong enough to counteract gravity, just put two torus shaped magnets around a pole with the same poles toward each other and you will see one magnet levitate.
when the universe cooled off further hydrogen and helium nuclei started attracting electrons and making atoms. After further cooling gravity could begin to assert itself and the hydrogen and helium clouds started to collapse into stars, the galaxies we see are most likely the result of the universe in what appears to our current mathematical models to be a singularity, the point before the big bang when the entire universe was extremely dense, was "clumpy" it wasn't a smooth or perfect sphere, when it expanded the clumps just expanded too and now make up the galaxies.
So after the hydrogen and helium started collapsing into stars in those areas where things were clumpiest in the young universe, we know that stars work by nuclear fusion, they are so massive and dense that hydrogen in their cores is converted into helium, releasing energy in the form of photons, which is why our sun glows so bright. But when you fuse two hydrogen atoms you get a helium atom. Deep within a stars core there is also enough pressure and energy to fuse heavier atoms, in fact every element can be fused deep within the core of the most massive stars. The larger the star the shorter the lifespan, this is because more massive stars tend to burn hotter and so they tend to burn themselves out faster. These stars are also more likely to supernova. These supernovae would eject large amounts of heavier elements into the universe to be used in the formation of the next generations of stars. Our sun is a third or fourth generation star, it is only about 4.5 billion years old. The universe is about 13.7 billion years old. Our solar system's accretion disk also had a lot of heavier elements in it which while the disk was spinning was flung out to the outter edges of the disk as tends to happen, the majority of the matter was still concentrated in the center and formed into the sun, the planets solidified from the material that was imperfectly distributed along the outskirts.
There was, of course a lot of debris in the early solar system shortly after the earth formed, and an almost Mars sized celestial body impacted the earth around 4 billion years ago while the earth was still molten enough to reform after the collision which resulted in a chunk of the earth flying off and forming the moon. Meanwhile Jupiter and Saturn are working hard to attract as much inner slar system debris as possible but there is still a lot in the inner solar system which hits the earth as meteorites. Actually occasionally even to this day Jupiter and Saturn will accidentally fling something into the inner solar system, but for the most part their massive gravitational fields tend to attract meteors from the inner solar system to them.
Water is the most abundant chemical in the universe as hydrogen is the most abundant element in the universe and water is the simplest compound. Because of the nature of how objects collapse into planets and stars the earth acquires it's rotation. The denser elements will tend toward the center so we have a dense nickel iron core which is seperated into an inner and outter core, the inner core is hot and liquid due to the amount of pressure above it, seems paradoxical but that's how it is. The inner core rotates at a different rate than the outter core working like a dynamo and generating a massive megnetic field. It also, along with the molten mantle, helps to drive plate techtonics. Another source of energy that helps to drive plate techtonics is radiation from the decay of radioactive materials.
Meteorites and comets impacting the young earth's surface brought with them water and many of the biochemicals necessary for life. This was proven when scientists analyzed the crater of a meteorite to see what the meteor was made of and found many of the amino acids and nucleotides found in all life on earth. Then there is the even more recent analysis of the deep impact probe that crashed into a meteor in space and a spectrum analysis of the debris that flew off confirmed that the meteor did indeed have amino acids and nucleotides on it.
The early earth's atmosphere was supplied by the young planets geological processes, volcanoes and other processes that spewed lots of toxic gases into the atmosphere...toxic to us, that is. The early atmosphere had very little O2 and O3 in it and as a result the amonia and methane and hydrogen that did make up the majority of the early atmosphere couldn't bind to a lot of oxygen and become stable. The introduction of energy from the sun and from sources like lightning resulted in more of the biochemical compounds necessary for life forming. At this point our understanding is less certain about what followed. What we do know is that self replicating polypeptide chains form easily when the necessary amino acids are present. DNA and more simply RNA is a great way to streamline the process. Cells can exist without DNA or RNA but they would not have inheritable material in them. The DNA or RNA allows for inheritable material being introduced into cells which would be mutually beneficial to the DNA which is kept together and safe in the cell and to the cell which can now reproduce itself. How specifically all of this happened is the subject of an ongoing research subject called abiogenesis, though, and I don't know all of the current theories.
Once the first organism did come about with inheritable material, though, then it was a simple matter of natural selection. The first organisms would have just consumed amino acids and most likely repriduced asexually possibly getting genetic material from other organisms like themselves that they ate. Mutations happen from transcription errors or radiation. In more complex organisms entire sections of DNA may be added or deleted. Whole chromosomes may be duplicated or sometimes two chromosomes may be fused into one. Natural selection simply means that nature will determine which organisms survive and which do not. Those organisms which are unfit to compete in a given environment are less likely to survive to reproduce. Like bacteria in a petre dish, if you introduce penecillin, those bacteria with no genetic resistance will die and are less likely to reproduce, while those which are resistant are more likely to survive to reproduce. Over time random mutations will improve resistance until the bacteria are completely immune.
Over time these small changes accumulate and a new species emerges. Given more time more information will be added to the genome and even more complex structures will emerge. I could go into greater detail but this is long enough.

Expelled

I finally got to watch Expelled: No Intelligence Allowed last night. I have to tell you, the movie is aptly titled. But not for the reasons the creators of the film thought. The film opens up, after the initial credits, with Ben Stein sitting in his dressing room very thoughtfully going over a speech he is about to deliver, while it cuts away periodically to some quote mined phrases from some scientists who support evolution.
Dawkins: "the battle over Evolution is just one skirmish in a much larger war."
Dennett: "Science simply makes no use of the hypothesis of God."
PZ Myers: "Ask yourself what has Intelligent Design given us? Nothing."
"We cannot accept Intelligent Design as an alternative scientific theory."
"They will never accept that we have a better argument. They just pester us and they waste our time."

With all due respect to Dawkins I have to agree with what David Berlinski says later in the documentary. Dawkins does not appear to have the philosophical background to really back up his comments about religion which is what this quotation was certainly about. In Dawkin's opinion, as he confirms later in this film, Intelligent Design vs Evolution is really just a skirmish in the larger war of Religion vs Atheism. This is not an opinion that many scientists agree with. It's also not an opinion that I agree with. Of course the idea that Intelligent Design is a watered down version of creationism is not without foundation. Ben Stein himself confirms what he and the Discovery Institute spend the entire documentary trying to deny towards the end when he concludes "If the Intelligent Design people are right, God isn't hidden. We may even be able to encounter God through science."

Dennet's quotation is accurate, it is true that science makes no use of the hypothesis of God, and with good reason. Falsifiability is important to any scientific hypothesis. Due to the nature of the subjects being investigated by science it is impossible to prove anything correct directly, the only means of proving a scientific theory correct is to try to prove it wrong. Thus all scientific theories or hypotheses need to be falsifiable. How do you falsify the hypothesis of God? The very nature of the concept makes the concept impossible to disprove. The reason this is important is because it's also impossible to prove, thus the concept could be wrong, but its specific conceptualization makes it impossible to disprove. Thus we could waste an infinite amount of time pursuing this line of inquiry with no results if we ignore falsifiability and never have any reason to think we could be wrong. If science did not limit itself to those questions which can be falsified science would never make any progress. Scientists would find themselves bogged down with inquiries they could neither prove nor disprove. Yes science is today bogged down by inquiries it cannot prove, which is why it is essential that science be able to disprove them in order to eliminate those lines of inquiry that will never be productive. The quotation by Dennett here is intended to imply that there's no reason why science doesn't make use of the hypothesis of God. I hope that I've done a good job of dispelling that impression.

Concerning the quote by PZ Myers, it's a valid question, what has Intelligent Design given us? What predictions does Intelligent Design make? How is Intelligent Design applied to increase our standard of living? The theory of Evolution is behind countless advances in medical science. Contrary to Michael Egnor's post responding to the Alliance for Science essay contest that apparently really bothered him, evolution is taught in medical schools, for example in just about every course with the word "comparitive" in it.
http://www.pandasthumb.org/archives/2007/03/egnorance_combo_arrogance.html

And the as yet unknown scientist who said "We cannot accept Intelligent Design as an alternative scientific theory." Again the viewer is supposed to get an inaccurate impression from this statement. You're supposed to assume that the reason we cannot accept this is because scientists don't want us to. The reality is that we can't accept it because the "theory" or more accurately assertion or conjecture of Intelligent Design is not scientific. It's foundational assumption is that there is an intelligent designer, which is unfalsifiable. They may argue that this is the conclusion, but that would be false. We can put it another way, the foundational assumption is that there is design in nature, this implicitly assumes a designer. Thus their fundamental assumption is, implicitly, that there is an intelligent designer. Let's briefly explore this further. If a scientist were to approach the subject of intelligent design with no preexisting assumptions how would he proceed? Perhaps the best way to proceed would be to try to find evidence of design in nature. This seems to be what Intelligent Design proponents say they are doing. How do we go about finding evidence for design in nature, though? The way the Intelligent Design proponents do this is by making assumptions. They point to complexity and argue that complexity implies design. This could be true and it's easy to support the assertion with anecdotal evidence, such as a car engine or a watch, we know these are designed and we know these are complex. However We also know something about the process of designing a car and a watch, and we also know who designs cars or watches, generally. We have potentially first hand knowledge of the people responsible for these designs, and this in no way proves that complexity cannot be the process of complex and undirected processes. One could argue that this is the case even in human design, since the human thought is a complex undirected process. Human interaction even more so and most designs were joint projects or the process of improvement upon existing designs. One could even argue for a form of selection being responsible for the modern designs in the marketplaces, of watches, cars, anything. But that is not my intention here. The Intelligent Design advocates have to prove now that complexity is only possible if something is designed. How do they do that? Well so far they don't do that. In fact Intelligent Design advocates do nothing to try to convince scientists to take them seriously. They write books for the lay person, and lobby politicians to try to get schools to force them to be taken seriously. But they don't try to get the scientific community to take them seriously by doing real science. They don't generate testable hypothesis, they don't publish peer reviewed articles, they don't contribute anything that can be applied to do anything that might, for instance, improve our standard of living. I am aware of the Discovery Institute's list of peer reviewed articles on Intelligent Design if the list still exists. The articles in that list were either not about Intelligent Design, or not peer reviewed. Michael Behe's book, for instance, Darwin's Black Box, was not peer reviewed. Stephen C Meyer's article on the Cambrian Explosion that was published by Richard von Sternberg in the Proceedings of the Biological Society of Washington was not peer reviewed, if it had been peer reviewed it would not have been published, it was substandard work, but most importantly it was about the Cambrian Explosion (and more specifically bioinformatics, which is the origin of the higher phyla), which is not the topic of Proceedings of the Biological Society of Washington. That publication deals with Systematics which is the study of Taxonomy.

Then finally the last quote I also don't know who to attribute it to, "They will never accept that we have a better argument. They just pester us and they waste our time." This quote also is true. Intelligent Design advocates do willfully refuse to accept that evolution is a much better argument. They base their entire argument on flawed assumptions about complexity and design and negative attacks against evolution, essentially god-of-the-gaps arguments. But also a lot of straw man arguments, showing a lack of understanding of the theory they claim is so flawed. In reality if the theory of evolution actually said what they claim it says no one would believe it, but this is primarily what I meant when I said Intelligent Design advocates are not trying to convince the scientific community. Their goal is to convince people who don't understand evolution, people who will actually be inclined to believe their inaccurate characterizations of evolutionary arguments. And most importantly people who will not take the time to objectively research the assertions they make. Afterall why would they lie? Of course that question begs the question that they are lying, a sufficient reason to research all claims is to recognize that although these people claim to be experts they can still be mistaken. Take for instance Michael Egnor, again, he is a neurosurgeon. That's an impressive qualification, of course, so people are inclined to think he knows what he's talking about. Why? How does neurosurgeon qualify him to comment on evolution? William Dembski is a mathematician, that's impressive isn't it? But once again how does that qualify him to comment on evolution? Michael Behe is a molecular biologist, so he is somewhat more qualified to comment on evolution, but why can't he be wrong? Yes he studied the field, but did he understand it? How well did he have to understand it to be sufficiently good as a molecular biologist to be hired as a professor? How often do people ask these questions when a supposed expert gives them their opinion about a subject? In my experience not very often. Pointing at Behe and saying, "He's amolecular biologist and he doesn't believe in evolution" would be like pointing at Einstein and saying "He's a very brilliant physicist and he doesn't believe in quantum mechanics or the Big Bang." That's true, but so what? Einstein was still wrong, his own theory of relativity predicts the Big Bang, and quantum mechanics is a branch of science that relies on nothing unfalsifiable, makes predictions, and is applicable to improve our standard of living. Everyone reading this blog can thank quantum mechanics for that. The transitors that make your computer possible would not be possible without quantum mechanics. Thus if Einstein could be wrong about things so closely related to his own work, why can't Behe?

This has gotten long so I will conclude this post here will just the analysis of the opening quotations. I'll continue this analysis of the logic and accuracy of Expelled: No Intelligence Allowed in my next post.