Evolution explained.

Evolution

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By JT Eberhard

Start with this simple “TOP 10 MYTHS ABOUT EVOLUTION” from the Skeptics Society to get a brief overview in just a few minutes.
It should be noted that the contents of this post represent only a very, very small portion of the evidence for biological evolution – as Daniel Dennett put it, most people do not realize that Evolution is as firmly established as the fact that water is made up of two Hydrogen atoms and one Oxygen. There is much, much more evidence than I could ever fit into hundreds of books. Fortunately, it is all out there for the reading. Google and your local library are your best friends here if you really want to familiarize yourself with this, the fundamental principle of Biology. Scientists have no qualms with making their experiments, research, and conclusions available for everybody and anybody to read and critique. Such is the confidence one can draw from basing their ideas about the way reality works on logic and evidence.

What is science?

“All evolution in thought and conduct must at first appear as heresy and misconduct.”
~ George Bernard Shaw
Science works under only one assumption: that the universe obeys a set of rules. If this assumption is true, then we should be able to observe the behavior resultant of these rules.
Here’s an example: we observe something falling, and we notice that it falls more quickly as it approaches the Earth. After making this observation we can generate equations to explain these motions and use them in the future to predict how objects will fall. Guess what: it works! As a matter of fact, it works so well that our current understanding of gravitation allows us to fire objects with uncanny accuracy to certain points even beyond our solar system. This confirms our assumption and very, very strongly suggests that reality is following a set of rules. Moreover, it indicates that we can deduce them.
That is a very simple example, but I’m sure you’re aware that more complex iterations of the scientific method are all around you. The computer you’re reading this on right now is the product of hundreds of years dedicated to ascertaining the nature of electricity. It could not function if not for an understanding of how certain particles operate on a microscopic level. Both of these are revealed only through observation and the predictability of living in a universe bound by rules. When his computer breaks, I’d wager that even the Pope will likely call somebody who understands the rules operant in making his computer function. Any business peddling their ability to pray computers back into working order will find themselves declaring bankruptcy in short order.
In science, it is never noble to pretend to know things you do not know, while religion depends on such self-deception. While you will receive a fair amount of praise in a church for claiming to have knowledge about the origin of the cosmos that no cosmologist has, science plays by considerably higher standards. If, in the course of an experiment or in the process of peer-review, you purport to have knowledge you do not have, you will be caught and swiftly penalized. Science depends on what you can establish; it is interested in seeing the world how it truly is, not how we wish it was.

What Evolution is Not.

If, at any time, somebody insinuates that evolution posits where life came from, then they have just exposed their lack of knowledge surrounding the theory. The theory of evolution deals only with how life arrived at the point it has, and it makes no claims about the origins of life.

That is not to say that we have no science regarding abiogenetic chemistry – we do. We have several models explaining how the first self-replicating molecule could have arisen and catalyzed evolution, all of which are compliant with known science (the most widely accepted model is called the RNA World model). Abiogenesis is just a question that evolution does not tackle (though it does necessitate abiogenesis).

Is Evolution Disprovable?

Yes. If we were to find a fossilized rabbit in soil from the Triassic, that would disprove evolution. Every time we uncover some new science, or uncover a new fossil, evolution faces a potential challenge. For instance, when we discovered genetics, if genetics contradicted evolution, the theory would have failed. However, every new discovery we have made, such as genetics, has corroborated the theory of evolution, not contradicted it.

Distinctions in Terminology.

Macroevolution
Those who reject evolution often say they accept “Microevolution” but deny “Macroevolution.” Such a distinction is like saying that one believes in inches but not miles. Small changes over enough time become big changes. While there are some notable differences between the two, it does not detract from the fact that the main difference between the two is how much time they have had in which to work.
The key point in this debate seems to be whether or not evolution can produce new species, so a sizable portion of this essay will deal primarily with the idea of speciation.
There are several books and peer-reviewed articles on the subject of speciation (such as the aptly-titled, Speciation). Beyond that, all of the forthcoming information is, and always has been, easily found on the internet. Those who reject evolution because they believe there is no evidence for it have failed to take the 10 seconds necessary to google it.
Theory
While I may have a theory regarding what two cards my opponent is holding at the poker table, this is not the way scientists use the word. A theory is a hypothesis or collection of hypotheses, which has stood up to repeated rigorous testing and passed the test. A theory explains all relevant facts and is contradicted by none.
The difference between a scientific theory and a scientific law is not their degree of acceptance or explanatory power. It is typically (there are a few exceptions) whether or not they include an equation explaining the phenomenon in question. That’s it.
For instance, on one hand we have theories like germ theory or the theory of gravity. On the other hand, we have something like Newton’s Second Law of Motion:
The relationship between an object’s mass m, its acceleration a, and the applied force F is F = ma.
See the difference? Is germ theory really more or less accepted than Newton’s Laws of Motion? Not at all.
Christians and other religious people determined to see their personal creation myths of choice stand unopposed, even by reality, will continue to assert that evolution is “just a theory.” However, all of them are unlikely to walk off the top of a skyscraper any time soon because gravity is “just a theory.”

Should we defer to experts?

The following argument originated with philosopher and scientist Daniel Dennett, mine is only a variation. It is a very key aspect to this argument that is often overlooked.
Consider the following proposition:  Трава типично зелена
I believe the above statement is true. I also confess that I have no idea what it means. Frankly, I don’t even know how to pronounce it.
So why do I believe it? I believe it because I asked a Russian-speaking friend of mine to give me a sentence of Russian. I told her not to tell me what it means, and I said that no matter what the sentence is, it has to be true. So even though I have no clue what it says, I believe it – and I would be willing to bet a tremendous amount of money that it is true. I am willing to place my “faith” in an expert.
Let’s consider another proposition:  e=mc^2.
Do you believe it’s true?
Do you understand it?
I’d wager that most people would answer “yes” to the former and “no” to the latter – which is fine. In the case of both this example and in the Russian proposition, it doesn’t matter if we understand it – it only matters that the experts do. This is very useful – even scientists utilize equations they couldn’t personally extract any meaning from in their work.
We all do this. By taking a ride in an airplane, you are deferring to the expertise of physicists; by eating a cheeseburger, you are laying your well-being at the feet of people who understand bacteria; and every time you get a flu shot, you are eagerly embracing our understanding of how germs evolve – otherwise, you would not need a new shot every year for the same diseases.
The point is that you should not worry about deferring to the consensus opinions of experts – particularly in a field such as science. The universe is so vast that one cannot even imagine its size without invoking logarithmic scales, let alone even begin to imagine all of the stuff within it. Every human being who has ever lived, myself included, is ignorant of almost everything there is to know. It is through our dependence on experts in various fields that mankind, as a whole, can begin to construct a map of reality that is in-keeping with all of the facts we have revealed.
However, in this one lone instance when discussing the scientific concept of Evolution, we have people, virtually all of whom are non-experts, denying the breadth of our understanding of a subject. This is done exclusively out of deference to a myth that carries none of the evidential weight its followers demand of science. While science, as always, is up to the challenge, this is an unfair fight in which many of those denying evolution have not arrived at their particular world view through objectivity or consideration of tangible evidence – and you cannot reason somebody out of a position they did not reason their way into.

What drives Evolution?

Evolution is engineered by the same key forces that generate new order everywhere in our universe without the need for any appeal to god. They are:
1. Mutation.
2. Reproduction.
3. Competition.
That’s it. If you have these three catalysts in place working over time, order and often improved functionality are inevitably the end result. This goes for life on this planet and for the evolution of stellar bodies in galaxies light years beyond it.
While it is clear that human beings enjoy (or suffer through) reproduction and competition, as does almost every other animal, many people do not understand how mutation works. Mutations in DNA are actually more common than you might think, as Larry Moran explains:
“The haploid human genome is about 3 × 10 to the 9th base pairs in size. Every time this genome is replicated about 0.3 mutations, on average, will be passed on to one of the daughter cells. We are interested in knowing how many mutations are passed on to the fertilized egg (zygote) from its parents. In order to calculate this number we need to know how many DNA replications there are between the time that one parental zygote was formed and the time that the egg or sperm cell that unite to form the progeny zygote are produced.
In the case of females, this number is about 30, which means that each of a females eggs is the product of 30 cell divisions from the time the zygote was formed (Vogel and Rathenberg, 1975). Human females have about 500 eggs. In males, the number of cell divisions leading to mature sperm in a 30 year old male is about 400 (Vogel and Motulsky, 1997). This means that about 9 mutations (0.3 × 30) accumulate in the egg and about 120 mutations (0.3 × 400) accumulate in a sperm cell. Thus, each newly formed human zygote has approximately 129 new spontaneous mutations.”
The long and short of it is that each of us is trotting around with well over 100 “birth defects.” While most of them are completely neutral, you must remember that we are spreading these mutations out over a vast population, which means we can expect microevolutional changes in every generation, with speciation and other macroevolutional changes over many generations.

Testable Hypothesis and other Evidences for Evolution.

The fossil record
Which transition are you interested in? Let’s start with early reptiles to mammals (this is going to be very long – we have a lot of transitional fossils including Human transitional fossils); later in this essay, Amber will discuss how we can view this piece of the fossil record in the human brain.
Anyway, we’ll start with Paleothyris, and every subsequent transitional fossil will transition to the next transitional fossil. Most of these were found using predictions such as those used by Dr. Neil Shubin (more on him in the next section), we knew the age that such creatures must have existed in, went to places with dirt that old, and ‘lo and behold we found them. It should be noted that this is only a tiny fraction of the fossil record, and that the fossil record is only a fraction of the overall evidence for evolution.
Paleothyris
Protoclepsydrops
Clepsydrops
Archaeothyrisy
Varanops
Haptodus
Dimetrodon
Sphenacodon
Biarmosuchia
Procynosuchus
Dvinia
Thrinaxodon
Cynognathus
Diademodon (of the group Eucynodontia)
Probelesodon (of the Chiniquodon group)
Probainognathus
Exaeretodon
Oligokyphus
Kayentatherium
Pachygenelus (1)
Diarthrognathus (2)
Adelobasileus
Sinoconodon
Kuehneotherium (an example of a Haramiyidan)
Eozostrodon
Morganucodon
Haldanodon (Very similar to Castorocauda similis)
Peramus
Endotherium
Kielantherium
Aegialodon
Steropodon
Vincelestes
Pariadens (the first known marsupial, but only by the skin of his teeth – literally)
Kennalestes
Cimolestes
Procerberus
Gypsonictops
This list is just a drop in the transitional fossil bucket. We have plenty to peruse.

Tiktaalik, a testable hypothesis in Evolutionary theory
Tiktaalik is a transitional species that is part of the fossil record between early amphibians from bony fish. It is the link between Eusthenopteron (which arguably precedes Sterropterygion) and Panderichthys.
Tiktaalik was discovered by a team led by paleontologist Neil Shubin of the Univesity of Chicago. Shubin describes how evolution was used to predict the location of Tiktaalik this way:
“What evolution enables us to do is to make specific predictions about what we should find in the fossil record. The prediction in this case is clear-cut. That is, if we go to rocks of the right age, and the rocks of the right type, we should find transitions between two great forms of life, between fish and amphibian.”
And that transition is precisely what they found.

Observed instances of speciation and the creation of new features

Speciation is a very lengthy process, which is likely why Creationists often employ statements such as:
“What we haven’t seen is any species evolve to become an entire new species that can’t reproduce with the former species.”
Of course, when was the last time you saw any of the steps of stellar evolution occur (these tend to run in the millions and billions of years)? Do you deny their validity on the basis that they take a lot of time to complete? Of course you don’t. We can see evidence of all the different stages and can extract a plethora of other evidences for how they function. The evidence that such stages occur in stars is so vast as to be undeniable by anybody who has studied the subject. The same is true with speciation. (It should also be noted that most people in America who deny evolution on the supposed lack of evidence also believe that a man lived inside the belly of a fish for three days without being consumed by the beast’s stomach acids. One cannot help but wonder what can be done to change somebody’s mind at that point.)
Thankfully, we have several instances of observed speciation to fall back on. The most recent is the controlled experiment in evolution with the lizard species Podarcis sicula, in which the species developed a Cecal Valve, a new feature not present in the ancestral population. The old population of Podarcis sicula was still around and breeding, yet they had branched off to create a new animal that, though still a lizard, was a new species with adapted behaviors and features.
A few other noted instances of Macroevolution include: Culex pipiens, Rhagoletis pomonella, and Mimulus.

Genetic evidence

One of the early arguments against the fact that mankind has evolved from earlier primates was the fact that we have 23 pairs of chromosomes – all great apes have 24. If we evolved from apes, we should expect to have at least 24 pairs. Acknowledging that such a fact would contradict all relevant facts about biology, scientists began to imagine where the 24th chromosome went. Their first hypothesis (notice how the hypothesis flows from what we already know) was that somewhere along the line a pair of chromosomes fused. So how can we tell whether or not this happened?
On the end of all chromosomes reside features called “telomeres.” Telomeres function as a kind of genetic marker, indicating that the chromosome has ended. In the middle of chromosomes, there is another genetic marker called a “centromere.” That means a simplified version of a chromosome would look like this (T=Telomere, C=Centromere):
T ——– C ——– T
However, the second chromosome is unique in that it looks like this:
T ——– C ——– T ——– C ——– T
What this indicates is that at one point two of our predecessor’s twenty-four chromosomes fused to create our second. Science created a hypothesis, tested it, and came up with a confirmation. What was an argument against evolution quickly became another brick in the wall of evidence for the theory.
Additionally, PZ Myers does a brilliant job of explaining the basics of synteny, one of the many types of genetic evidence, here.

Things that Evolution explains elegantly

And what comedian designer configured the region between our legs-an entertainment complex built around a sewage system? ~ Neil deGrasse Tyson, Astrophysicist
There are many things that fit into evolutionary theory succinctly, but that make absolutely no sense if a god designed the universe. This includes things like why men have nipples, why we see in color like most lizards do (though most mammals do not), and why we have 32 teeth rather than the 36 of most great apes.
Conversely, the presence of literally millions of engineering flaws simple enough for humans to notice helps to refute the idea that a designer more observant than human beings had a hand in producing them. Here are just a few of the big ones.
DNA:
The DNA molecule is prone to a high number of errors due to its awkward nature. The numerous flaws in DNA replication result in cancer, down syndrome, and a host of other conditions far too lengthy to list. It is hard to imagine an intelligent designer utilizing such an unstable system, let alone a flawless one.
The presence of the appendix:
The appendix is a very useful organ in many animals. However, humans are not one of those animals. In human beings, the appendix produces an insignificant amount of white blood cells, but we can do just fine without the appendix, since other organs produce more than enough. The appendix itself makes us vulnerable to several types of infections, some of them fatal. It also poses the threat of rupturing which, according to those who have suffered a ruptured appendix, really, really hurts.
If a designer did include the appendix in the human design, he is most assuredly not a loving god, but rather a malicious one. On the other hand, a vestigial remnant like the appendix makes perfect sense within the evolutionary model.
Vestigial appendages:
Did you know that many snakes, such as pythons and boa constrictors, have hind leg bones? It’s true:
See the bump where the bones are? Many whales also have them.
Speaking of sea life, did you know that many deep sea life forms like the cave-dwelling tetra fish (Astyanax mexicanus) are blind? They have eyes; the eyes just do not work. Why would an intelligent designer provide them with those organs? Evolution though, can explain them succinctly.
“Genetic mutations that hamper eye development also may increase the number of taste buds. Thus, mutations that happened to give the fish an advantage in tasting and smelling—a huge benefit in a dark environment—might also have inadvertently, and harmlessly, caused the degeneration of their eyes.”
PZ Myers explains it in greater detail:
“What’s actually going on is that there is an increased expression of a gene called Sonic hedgehog, which causes an expansion of jaw tissue, including both the bones of the jaw and the array of sensory structures on the ventral surface — this is an adaptation that produces stronger jaws and more sensitive skin, what the fish finds useful when rooting about in the dark at the bottom of underground rivers to find food. The expansion of Shh has a side effect of inhibiting expression of another gene, Pax-6, which is the master regulator of eye development. Loss of eyes is a harmless (if you’re living in the dark) consequence of selection for better tactile reception.”
As explained above, humans have an appendix, which is a vestigial appendage. We also have the coccyx (human beings have leftover tails), prectores pilorum (the muscles that cause goose bumps), and wisdom teeth. All of these make no sense if human beings were designed, but they make perfect sense if we evolved.

Conclusion

There are simply no reasons in terms of either philosophy or science to deny the fact that evolution has been occurring for a very long time and is still occurring today, while there is a wellspring of evidence to believe that it has, and still is occurring.

For an excellent overview of the facts and mechanisms of evolution, we highly recommend these videos from the Cassiopeia Project.

THIS ARTICLE WAS COPIED AND PASTED FROM AN ATHEISMRESOURCE.COM.  I THOUGHT THE ARTICLE REALLY HAMMERED THE FACTS.   FOR THE ORIGINAL ARTICLE WITH LINKS, PICTURES AND VIDEOS, CLICK HERE.