Saturday, May 30, 2009 by Professor Kool-Aid.

An introduction:My name is Rod, and my story is a peculiar one. To be honest, it is funny how I was raised in the African American Baptist tradition which was Arminian, and then at the end of my undergrad days, I became a Calvinist just to fit in with my friends who were part of Reformed University Fellowship.  They had all of the answers, the cool Christian parties, and the right looks.  All of my life, I had never fit in anywhere, even refused to join a fraternity in college.  But I guess I was exhausted of being the outcast, that man like Mr. Manhattan of the Watchman series, you know, the dark colored, super-intelligent being who just does not look like your average human rocket scientist.  I still get that Mr. Manhattan feeling sometime, but today, I can proudly say, I am my own man, and I am accountable to God alone.  Below are two pieces that explain my  experience. I hope that I can elaborate on these in the weeks and months ahead.Cage StageWhy I Kissed Calvinism Goodbye (full article)

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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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Monday, May 25, 2009 by angel.

a submission to the coming out g-dless project.

my ascent to a humanist perspective has been a slow and painful journey. raised independent fundamentalist baptist (IFB), i very deeply believed in jesus, the virgin birth, heaven, hell, a literal creation, and a literal translation of scripture all of my life. basically, if it was in the king james bible, i soaked it in. i was saved at 4, baptized at 7, led my first convert to christ at 10, and attended bible college at 18.

after bible college, it made sense to me to study scripture from the jewish perspective; so i enrolled in the judaic studies program at UCF. i must confess that a big part of the draw was to learn how to better convert jews. don’t listen to what other evangelicals may tell you, we totally get extra points for the chosen people.

instead of finding a community of people lost and empty in their own self-deceit, everyone seemed dispappointingly normal. what’s more, a lot of them were atheists, and no one seemed to have a problem with that. i had been brought up to believe that “humanists” and “atheists” were under literal demonic influence and part of a vast evil plot by satan to destroy humanity.

imagine my surprise when the exorcisms failed.

i’ll spare you the details of my lengthy discussions with professors, rabbis, pastors, physicists, and my cosmically important friendship with a reformed jew turned atheist over the next few years.

intellectually, the evidence was clear. a fundamentalist view of the world stops working the minute you look beyond the few resources approved by your tiny sect.

emotionally, this was all very hard to accept. i had to take the chance that this was some elaborate scheme of satan’s to deceive me. in the end, it seemed to me that a religion worth believing in should stand up to a little objective scrutiny.

from beginning to end, it took me 5 years to drag myself out of fundamentalism completely, and another 2 years to tell anyone about it. i was 27. when my mother found out she cried, fumed, prayed, and kept my atheism as her shameful secret. i led a double life to save face for her.

the election in November changed that for me. for the first time in a long time, i cared about something. i liked the feeling and decided it shouldn’t stop. i will no longer feel like an outcast because i’m not religious, and i refuse to be quiet about gay rights, stem cell research, evolution, abortion, or anything else i’m passionate about because it may offend someone else’s beliefs.

it seems to me that there was some unspoken rule i had agreed to. that because i don’t have a g-d or imaginary elf associated with my beliefs, they’re somehow less important. that’s simply not true. i do not need a g-d to validate me. i do not need a hell to scare me into being a good person. i handle that all on my own.

i’m g-dless, i’m out, and i’m proud.

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Saturday, May 23, 2009 by giodasilva.

Science and religion have been at constant odds. I believe that religion was the first method humans had to explain how something worked. It likely goes back to the moment where humans were able to create things, taking the liberty to use “create” as a synonym for “manufacture”. I can only imagine (without evidence, of course, because imagination requires no evidence) that when early humans manufactured tools or were able to harness the power to generate fire, one question would come to the primitive mind: if we made these things and we control them, then what/who made us and controls us? Taking the liberty to imagine myself as an early Homosapien, I would likely see the creator (me) as more powerful than the things that I “created” and could easily destroy. The inference being that there is something more powerful out there that can make us and destroy us.

One basic religious concept that is universal, whether you are discussing the Judeo-Christian tradition or an Eastern religion, is that there was creation. A moment in time when from nothing, the Universe as we know it came to be. Religion across the globe continued this sort of general explanation about the birth and fate of the Universe for many centuries, relying mostly on Aristotelian reasoning (or lack thereof). In an interesting twist of fate, very religious men and women, often funded by the Catholic Church, began to question the workings of the Universe based upon observation and the primitive mathematics available after the Dark Ages. The consequence of which was a friction that would last to this day. As the bastard child of religion, science stopped caring about why, instead focusing on how the Universe worked. Religion is the architect and science is the engineer; one relies upon the other.

The topic of this series is one of the most elegant and often misinterpreted scientific theories in the history of science thus far. When Charles Darwin published The Origin of Species, the devout Christian gentleman set forth a debate that cuts to the very core of humanity: the need to belong. What Darwin unwillingly and unknowingly managed to do was to strike a very sensitive nerve in Western faith. Adam and Eve were no longer viable allegories for the birth of humanity, and now we could explain in detail how humans, or any species on earth, came to be. Evolution unintentionally challenged the concept of a humanity created in the image of the Old Testament God.

As a scientist, I recognize the enormous disconnect between scientific discoveries and their communication to the general public. Perhaps people are turned off by our society’s stereotype of a scientist: the socially-awkward, creepy, reclusive, and often not-so-attractive individual (think Quasi Moto). Looking around at my peers, I generally agree. But stereotypes should not inhibit scientific discourse and understanding. That’s why I’ve written this series about the theory of evolution.

This is not an attempt to persuade or dissuade anyone’s opinion. Rather, it’s an attempt to address misconceptions and offer a clear picture the Theory of Evolution as it stands today. While not scholarly in the traditional sense, I hope that the series perks your interest and inspires you to research this topic. I will be very glad to field any questions in terms of hard science and detailed explanations about the experimental process on an individual basis.

Let’s begin!

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Friday, May 22, 2009 by admin.

We are former religious fundamentalists. Our journeys are each unique, and we have come to vastly different conclusions about spirituality. What we have in common is that each of us studied, thought, questioned, strolled or clawed our way out of a strict fundamentalist view of the world. We hope that our stories, our thoughts and the difficult questions we have faced will help other former fundies out there. We want you to know that you are not alone, you are not condemned, and it’s ok to touch your genitals. We all do (even monkeys).

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