Thursday, May 28, 2009 by giodasilva.

A major misconception about the theory of evolution is that humans come from monkeys. That is absolutely wrong and a travesty to the actual nature of how evolution works.

The correct statement is that in terms of primate genetic relationships, we are related.

However, here is another misconception: not only are all primates related, but all mammals are positively genetically related also. Oh, and not only mammals but also all forms of animal life!

At one point in time the common ancestor, whatever it was, changed; and by point I do not mean second, minute, day, nor week; by one point in time I mean evolutionary time which generally falls in the scale of geological timelines (thousands to tens of thousands of years). Now, short of taking a course in genetics, it is hard to fathom how some species can be 99% identical in terms of genetic makeup, yet so different in terms of morphology (how they physically look). The clarification is simple and something the general public likely does not know.

Of the billions of nucleotide base pairs which make up our genetic material only a very small percentage codes for physical traits.

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Thursday, May 28, 2009 by giodasilva.

I can see how religion would have a problem with such randomness; the universe according to Aristotle was supposed to be a very ordered place. Suddenly the Earth is no longer the center of our Solar system, and the existence of humanity seems like pure chance.

Those are truths.

The fear of not belonging, of being alone, cuts to the core of humanity. We are social beings with close ties to our parental male/female pairs. But to keep drawing the evolutionary line back in time and find something that is neither human nor ape, nor anything we can recognize, makes it seem like we are left in a random mess.

Would God do that to us?

The answer is yes.

Here is the reason: the Theory of Evolution does not explain and cannot explain creation; it only attempts to explain how the machinery of life has moved forward and adapted to the ever-changing landscape of the earth. How much more powerful is a god that creates a self-evolving machine than a god that snaps its divine fingers and makes things happen?

I’ll put it this way: have you ever seen your old VW Beetle suddenly transform itself into a gorgeous new BMW? I bet that would be far more interesting than trying to buy a BMW outright! Certainly, you would be more impressed with the engineer of such a vehicle.

People reconcile faith with the facts of science every day. The Catholic Church has issued statements admitting to the fact evolution is real. Recently the Anglican Church announced a public apology to Darwin (I guess better late than never) realizing the folly in its criticism.

A good scientist will never try to prove nor disprove the existence of a god. Science relies on the ability to design experiments to prove or disprove a hypothesis. No such experiment can be devised to prove or disprove God (yet).

However, thousands of experiments have been performed and are now routine techniques (which will likely be updated and revised over the course of scientific progress) which have shown beyond a shadow of a doubt that evolution is a fact.

No matter how many revisions take place, mutations will happen in random spots at a constant rate, and the selection process will determine which of those are viable or not.

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Thursday, May 28, 2009 by giodasilva.

Along with evolution comes a very closely related process: selection. Mutations or changes in the genetic material will happen at a constant rate and generally are non-deleterious. Why would that be? Well, if it is not broken, there is not a need to fix it, but nothing is wrong with a little tweaking! Now here comes the catch: mutations can cause some very serious changes. A single amino acid mutation in hemoglobin causes sickle-cell anemia, a serious genetic disorder. Animal life has been evolving for millions of years on land and sea. With each passing generation it is the “survival of the fittest” concept that promotes successful vs. deleterious mutations to the life of the organism.

Nature selects which mutations are successful by simply exposing those mutations to the environment.

It is wrong to think that the environment makes the gene change; that process would be far too efficient at selecting genes and cause overpopulation (think of it as never picking the fat kid to join your team – btw, I was that fat kid and it still hurts). Instead, even though the mutation rate is constant, the nucleotides which mutate are random. There are probabilities that go along with the randomness but in statistics there are no absolutes, so no single nucleotide is safe. Once a random mutation happens that, for example, results in a longer neck where the vegetation up high happens to be quite abundant, the animals with longer necks face less competition for food and are able to more easily pass on their mutated genes, rinse and repeat for generations and eventually you have a giraffe. Meanwhile the shorter necked ancestors eventually die out from starvation. That is the impact of the environment. The environment only offers a “brick wall” or a “sieve” so that only those mutations which are viable for the survival of the organism persist.

These are scientific facts which are proven daily in biology and biochemistry labs across the world. No single evidence has been found to refute this process.

Now with every scientific theory or law, there are revisions which take place as we learn more. For example, not until Stephen Jay Gould presented the theory of evolution did it make total sense to me in the form of Punctuated Equilibrium.

To sum it up, the processes which lead to morphological and physiological changes are due to mutations in single nucleotides in the genome of an organism (there are other mechanisms like exon shuffling and genome duplication events but this is not an evolutionary biology book so we will stick with the basics). Because the genetic code is degenerate, mutations can accumulate for decades, centuries, or even millions of years before changes are observed in species. Evolution as a process is not linear in time; it is marked by long stagnate plateaus of apparent inactivity, and decorated by spikes of small, or even major changes. There is no way to predict what will occur.

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Thursday, May 28, 2009 by giodasilva.

Change is constant.

This is a simple yet encompassing statement. No matter what, no single moment in time is like the other. Every day is composed of 24 hours, but each of those is undeniably different. Each Monday is so inherently unlike the other, and some are even good ones. The same is true on the molecular level. To understand how, you’ll need the following far-to-brief crash-course in biochemistry (further research is highly encouraged!):

Inside of the nuclei of each cell that contains one (some cells do not), billions of nucleotides arrange themselves linearly and in base pairs in a sequence. The sequence may seem random, but in reality it is the famous DNA double-helix. The central dogma of biochemistry states that DNA codes for RNA (a type of messenger and primordial genetic and catalytic molecule), which in turn codes for proteins. Proteins, in turn, are made up of amino acids. This is a very clever molecular bureaucracy because it allows for stringent regulation of processes. Tight regulation is a good thing. Imagine not knowing exactly if you will have to get a haircut 5 minutes after you just got one!

The four nucleotides which code for the animal genome (and plant as well) are aligned in groups of three, called codons. Each codon in DNA can be transcribed to a corresponding set in RNA, and in turn translated into one of the 20 amino acids. Even though there are only 20 commonly occurring amino acids, there are 64 codons. The more specialized amino acids have fewer codons and the less functionally important amino acids have more codons; the system is therefore degenerate, yielding a sort of flexibility in coding. A good comparison is a chess set where there are more pawns than knights and so on.

Billions of these codons make up our DNA. With each passing generation and through the variation in population migration patterns and our choices in mating partners, the chromosomes of each offspring become slightly different. Scientists can measure this mutation rate (how often changes in codons or just in any base pair happen), and we know that the rate is constant, much like we know there are 60 seconds in one minute. However not all mutations cause changes in our morphology or physiology, in other words, not all changes are visible. Remember that the genetic code is degenerate, so there is room for error. One thing to keep in mind is that no machine is perfect; all of them malfunction. This is where natural selection comes in.

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