2010: FTSOS in review, July to September

This is the third installment of the 2010 review of FTSOS. See the first two here and here.

July:
Some of the smaller posts I’ve made that I think deserve a little more attention are the ones where I emphasize that biology is all about shape. The article I wrote about the fight against HIV is one of those posts. Research earlier this year found at least one location on HIV molecules that remains a consistent shape between individual viruses. This is important because HIV’s ability to be differently shaped in different parts of a single body makes it difficult to combat.

I also wrote about the difference between atheists, new atheists, and anti-theists. One of the public relation problems for atheism is that it is viewed as a dirty word. People assume it means absolute certainty, and that is seen as arrogant. It’s ironic because belief in God usually comes with certainty and that isn’t seen as being so arrogant, but I digress. Atheism is not certainty. Furthermore, where it is involved in new atheism and anti-theism, atheism acts as a descriptive base; new atheism and anti-theism are normative positions.

One of my all-time favorite posts is the one about photolyase and cancer. Photolyase is a protein that captures light and uses two of its constituents (a single proton and single electron) to force contorted nucleotides back into place. It is not present in humans, but is common in plants and other animals, helping to keep their genes functioning properly. This may be one reason we’re more susceptible to cancer than many of our fellow organisms.

August:
This was a skimpy month for FTSOS. I was away on a couple vacations for the bulk of the month, so the majority of the posts were either from my “Thought of the day” series or they were pictures/YouTube videos. But for what was there, I couldn’t resist pointing out and expanding on a fantastic quote from the judge who said Prop 8 in California is unconstitutional. In his quote he said a ban on gays getting married fails to advance any rational cause. I compared that sentiment to the idea that the majority cannot be allowed to discriminate simply because it is the majority.

I also made a post about a website devoted to philosophical thought experiments. The thought experiment I chose to highlight was Judith Jarvis Thompson’s Trolley Problem. My big motivator was a recent discussion with another blogger who laughably claimed that the trolley experiment was merely a logistical exercise, not an exercise about morality. To date he is still the only person in the world to believe that.

I also went through a few theistic arguments that are obviously failures. The most notable in my mind is the argument that says everything has a cause, therefore the Universe had a cause. There are two major problems with this. First, then why not just say a sort of ‘exo-nature’ caused the Universe? There is no need for consciousness – in fact, that only makes the theistic argument less probable. Second, the whole basis for this argument rests in the idea that forces result in reactions. For instance, if I push a chair, that chair moves; I applied a force. This is basic physics. But the whole shebang of forces and equal and opposite reactions? We’re talking about the science of what we know that happens within the Universe. And all we know necessarily breaks down prior to the Big Bang. The First Cause argument cannot be used because it rests about an unwarranted extension of science. Religion abusing science? Crazy, I know.

September:
The beginning of September was just as skimpy as the end of August because I was still on vacation. But while I never gave a huge post on the subject, the defining moment of the month (and year and decade and…) for me was my hike of Kilimanjaro. I have started writing about it at this point – just not for FTSOS. But in lieu of that you can read the account of the journey from my fellow group member and current Facebook buddy Jim Hodgson.

I also gave a very lengthy post on why prostitution ought to be legal. No one seemed to care, but I put a lot of effort into, so I thought I would mention it here. Basically, we make the practice illegal because of our own discomfort with sex as a society. We also draw false correlations between it and other illegal activities: of course one illegal thing will bring with it other illegal things if it’s something people want. Finally, for the safety and health of all involved, it would be better to legalize and regulate prostitution than keep the old system we have now.

One of the most popular posts on FTSOS that people found via search engines was the one where I lamented low science and math scores in the United States. A lack of funding relative to other areas, hostility towards science, and a general anti-intellectual trend in the U.S. all contribute to the decline of America on the world stage in education.

Another lament was my post about the anti-vax crowd causing deaths. The fact is, people who advocate against vaccines or for made-up alternatives to vaccines are making the world a more dangerous place, making people sick and even causing deaths. Get vaccinated – and, if you have them, especially get your children vaccinated.

Once again I really want to highlight a fourth post here. In this case, it is the one I made about the Problem of Evil. This has forever been an issue that no Christian (or other relevant believer) has been able to resolve. If God is good and evil exists, then we need to answer why. Appealing to free will fails because while God is necessarily good, free will does not need to necessarily exist. In other words, God is required to be good; he is not required to create free will.

Expect October to December tomorrow.

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Photolyase and cancer

Upon arriving at the beach yesterday, I lathered on the sun screen. Being relatively fair-skinned, I’ve learned my lesson in forgetting or not using enough of the stuff, and I wasn’t about to get all burned up. I don’t like eating lobster; I certainly don’t want to look like one.

But that isn’t the only reason I throw the stuff on so heavily. I’m also well aware of the tenacity and, if such a word is appropriate, vulgarity of cancer. Tanning is just a bad idea unless someone really wants to be diseased. It may look good (and not always), but I doubt that has ever brought solace to any cancer patients. Laying out in the sun without protection (as I saw a few people doing all day – it was at least 85 F, not a cloud in the sky) or jumping in one of those tanning cancer tubes is a sure-fire way to cause potentially deadly somatic cell mutations.

The way this works is that UV light slaps into the double helix structure of DNA causing an incorrect fusion in base pairs on the same side of the helix. Imagine – and apologies for the violence of it all – getting punched in the mouth. Instead of your teeth vertically matching as they do now (at least relatively), a couple teeth on the bottom row are now horizontal and facing each other. This calls for a dentist.

Different organisms have different mechanisms (dentists) for correcting damaged DNA. Naked mole rats, for example, have two genes for contact inhibition instead of the single gene virtually all other mammals have. This has resulted in no one ever recording an instance of cancer in the ugly little critters. If humans had this mechanism, cancer probably wouldn’t be nearly the problem it is.

Instead we get a number of repair mechanisms, chief among them base excision, nucleotide excision, and mismatch repair. (The mechanism in naked mole rats doesn’t repair mutated cells; it merely stops them from proliferating.) Unfortunately, the repair fidelity, just like the copying fidelity, of DNA is not perfect. Mistakes are made, mistakes are missed. We get cancer.

Part of our plight arises from something we’ve lost over evolutionary time. Most plants and other animals have a protein called photolyase which specifically seeks out UV damaged DNA.

Researchers at Ohio State University were recently able to observe exactly how photolyases perform their protective duty. The photolyase protein captures energy from visible light and uses it to project a single proton and a single electron towards a dimer in DNA. The two tiny particles then initiate a series of reactions that knock the contorted nucleotides back into place across the ladder, without needing to remove them like normal human proteins do. A proton and electron finally return to the photolyase protein, presumably so it can dash off to fix the next dimer it finds.

In other words, this dentist isn’t very gentle. He just punches your contorted teeth back into position. (Okay, it’s more elegant than that, but I had to finish the analogy.)

The article goes on to speculate as to the potential utilization of this protein in humans.

Given that photolyases were lost in evolution, it was possible that other proteins in the cell that allowed photolyases to do their job were also lost. But mice that were given the gene for the photolyase protein showed remarkable protection from UV damage. This means that in mice, the rest of the cellular infrastructure that photolyases need is still there. Chances are good that it’s there for humans as well.

There are other instances of mice being able to utilize genes not otherwise found in them, almost as if they’ve had them all along. For example, when injected with snippets of DNA for making red photo-pigment, normally dichromatic mice suddenly had trichromatic vision. This indicates an earlier evolved ability to see colors in the mammalian line that was later lost. In all likelihood, the appropriate gene(s) was probably just turned off out of a lack of need, leaving in place much of the cellular machinery needed to utilize red photo-pigment. I suspect the same is true with photolyase. If this can be extended to humans, a significant leap in the fight against many skin cancers may be on the horizon.