2010: FTSOS in review, October to December

This is the fourth and final installment in the 2010 review of FTSOS. See the other three here and here and here.

October:
The most important post I think I have ever made was the one about Tyler Clementi. He was the Rutgers student who was outed as gay by his roommate. As a result – and as a result of a bigoted society – he killed himself. His death was an unnecessary tragedy that ought to bring shame to anyone who has ever voted against civil rights for gays or anyone who has ever made one moment of a gay person’s life more difficult directly because that person was gay.

October is Breast Cancer Awareness Month, so it was disconcerting to read that a few high school refs were being threatened with punishment for trying to support breast cancer research. They wore some pink whistles during football playoff games in order to raise awareness; they were later told they were in violation of some petty dress code and therefore may be facing suspension – including suspension of the pay they had planned to donate to the Susan G. Komen Foundation. After the blogosphere erupted, the organization that oversees refs in that area (Washington state) backed down.

I also went to some length to explain a few basic things about religion that conflict with science. Miracles, directed evolution, intercessory prayer, and the belief that faith is a virtue are all things which science rejects. It simply isn’t possible for someone to hold belief in any of those things and also logically claim he has no conflict with science.

November:
This was the month the board which oversees local quack Christopher Maloney agreed with me that by not referring to himself as a naturopathic doctor, he was creating confusion; people might think of him as a real doctor. Except for when he insists on putting himself in the spotlight or when there is a special occasion (such as this), I consider the issue he created to be done. He lost.

In this month I used the Socratic Method to explain our likely basis for morality. I largely pointed to our common ancestry and the obvious survival benefits that cooperation offers. I also talked about why we ought to act certain ways. We all use ultimately subjective reasoning, and that’s okay: Most of us share a number of values inherent in our nature. We use these values as our common basis for saying what is right or wrong. It’s sort of like a stand-in for objectivity. And we all have it.

I also used Edwin Hubble’s calculations for the age of the Universe to demonstrate a key point about science. One of the most enduring and annoying criticisms of science by people poorly versed in the sciences is that the practice has a history of being wrong. If it has been wrong about so many things in the past, why should anyone believe it now? Except science really doesn’t have the history everyone seems to think it does. The issue is with poor or limited data (such as what Hubble had). The scientific method actually has no limitations in and of itself. The limits come from our own minds.

I also discussed a paper from Nature which a number of creationists butchered. My focus was a particular creationist familiar to FTSOS readers, but a quick search at the time showed that a whole slew of creationists had fundamentally misunderstood the paper. This is understandable since it is unlikely any of them even read the paper (not that they would be able to understand most of it anyway), merely taking their cues from other creationists. In short, the paper was a study of how alleles become fixed in asexual populations versus sexually reproducing populations . In the former, alleles, if they are particularly advantageous, tend to spread through populations rapidly, quickly becoming fixed. But in drosophila, researchers found that for alleles to spread and become important, fixation was not necessarily required. Alleles act in much more complicated systems in sexually reproducing populations than in asexual organisms, so the way their frequency rises or falls is also more complicated.

December:
Since I mentioned FTSOS hitting the arbitrary number of 100,000 hits in an earlier installment of this review, I suppose I will also mention that it hit 200,000 hits in December. There isn’t much more to add to this, though, is there?

In a more significant post, I pointed out that the Catholic Church thinks (probably without realizing it) that Double Effect is wrong. The Church stripped a hospital in Arizona of its affiliation because the hospital made the correct choice to save a woman’s life at the expense of the not-a-human-being fetus she was carrying. This is pretty much the example textbooks give in order to illustrate the very concept of Double Effect.

I also wrote about a local (real) doctor who supports some quackery. Dustin Sulak is from Hallowell, Maine and he has been making a living making out marijuana prescriptions. That’s all fine and dandy (and I’m sure he is being responsible with his power), but he also supports Reiki. That whole ‘field’ is just a bunch of malarkey that has no place in medicine. I find it unfortunate that a perfectly qualified medical professional would lend credence to something so obviously made-up like that.

Finally, I lamented the fact that Republicans were holding up three extremely important bills this month. All three – the repeal of DADT, the New START treaty, and the 9/11 First Responders health care bill – were eventually passed or ratified. The whole hub-bub was a political creation: the Republicans want to embarrass the President, not get anything done. I don’t think the Democrats are by any means wonderful, but at least they tend to be at least half-way pragmatic. And they want 9/11 First Responders to have fucking health care.

So this concludes my review of FTSOS for 2010. Hopefully the next dozen months will be even better.

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Butchering science

Creationists hate science. They hate its conclusions, they hate its methods, they hate that it doesn’t support their silly beliefs. It’s that hatred that motivates them to butcher scientific articles and papers.

One recent butchering comes from Jack Hudson. I’m sure regulars here remember him. If not, it isn’t important. He’s a creationist with a background in introductory biology courses from 20 years ago. It’s doubtful he has much experience reading scientific papers, but that doesn’t stop him from trying.

In his post he butchers two articles. I’m going to focus on the first one, but I’ll briefly mention the second one. In that one researchers found that some negative mutations don’t change the protein sequence yet they are still negative. This one is simple. The entire sequence of a gene is not devoted to just the protein sequence. A mutation can therefore change one aspect of a gene without changing another – but it can still change another process that is important in forming proteins. Alter shape in one place and you have a good chance of seeing change somewhere else as a result. Biology is still all about shape.

The second paper, though. Woo. What a doozy of a butchering. First let me summarize the paper.

In asexual populations alleles can become fixed rather quickly. Their evolution is more straight forward because they aren’t mixing and matching genes. They produce offspring with the exact same genome, less there be a mutation. If there is a mutation, it can become fixed because things are generally less complicated with asexual populations and thus more black and white. Is this mutation good or bad? As the paper says and as Jack repeats upon hearing the term for the first time, alleles sweep through a population.

But when it comes to sexually reproducing populations, things become more complicated. And this is what the paper is about. The question is, do alleles sweep through populations in sexually reproducing populations like they do in asexual populations? The answer is no.

Now, if we’re to believe Jack, this means that evolution has failed because, why, evolution predicts an advantageous allele to reach 100% fixation, of course. Except it isn’t so black and white with sexually reproducing populations. (Nor does evolution predict that anyway.)

What the researchers did was study over 600 generations of fruit flies. They let them breed naturally, but then selected out the eggs which were produced the most quickly. This led to significantly faster reproducing populations. They then tracked specific alleles to see if they would become fixed. What they found was that they don’t.

Signatures of selection are qualitatively different than what has been observed in asexual species; in our sexual populations, adaptation is not associated with ‘classic’ sweeps whereby newly arising, unconditionally advantageous mutations become fixed. More parsimonious explanations include ‘incomplete’ sweep models, in which mutations have not had enough time to fix, and ‘soft’ sweep models, in which selection acts on pre-existing, common genetic variants. We conclude that, at least for life history characters such as development time, unconditionally advantageous alleles rarely arise, are associated with small net fitness gains or cannot fix because selection coefficients change over time.

The conclusion here is that selection for a particular trait in sexually reproducing populations acts upon many different aspects and genetic variants within the genome, not merely a single gene or SNP.

This suggests that selection does not readily expunge genetic variation in sexual populations, a finding which in turn should motivate efforts to discover why this is seemingly the case.

This is the actual conclusion of the paper. To put it another way (and to repeat myself), advantageous variants do not wipe out other genetic variants in a sexually reproducing population, instead acting on variation in a more subtle and complicated way. The big conclusion here is that there is a difference in how genes become fixed (or not fixed) in asexual populations versus sexually reproducing populations.

And Jack’s conclusion?

In short, if the activity failed to occur in the lab under optimal conditions, it is unlikely that traits are going to be transmitted this way in nature.

The traits are still being transmitted through natural selection working on variation. Jack’s conclusion has little to no connection to anything from the paper. In fact, it is abundantly clear that he read an article somewhere, figured out how to butcher it, and then went and read a few lines from the original paper.

I’ve said in the past that what takes a creationist 30 seconds to say takes an educated person 3 hours to correct. This post and the research required for it didn’t take that long, but the sentiment remains true – it’s a real hassle to untangle the carelessly mushed writings of a creationist.

Ancestral environments and reverse evolution

There’s been a long debate regarding whether evolution can be reversed or not. The general trend has been that it can not. The idea goes that once one evolutionary pathway has been crossed, it cannot be retraced back to its origins. It turns out that is not entirely true.

Says [researcher] Henrique, ‘In 2001 we showed that evolution is reversible in as far as phenotypes are concerned, but even then, only to a point. Indeed, not all the characteristics evolved back to the ancestral state. Furthermore, some characteristics reverse-evolved rapidly, while others took longer. Reverse evolution seems to stop when the populations of flies achieve adaptation to the ancestral environment, which may not coincide with the ancestral state.

What the researchers did was subject fruit flies to various selection pressure for multiple decades, i.e., they changed their environment over and over. The ‘end’ result was fruit flies that were markedly different in their traits as compared to the original specimens. That’s evolution. Children should understand that. What happened next was the researchers mimicked the original environment of the fruit flies from decades gone by. In response, the fruit flies adapted to those environments, possessing many of the same allele frequencies they originally had. What I find particularly interesting is that they did not evolve exactly the same, but they still evolved in a way that was similar to the original phenotypes. This helps to explain why sharks and horseshoe crabs remain so similar for so long: the gene pool of the population centers around certain allele frequencies because, well, they work. Change may happen – in fact, it certainly does – but ancestral pheno- and genotypes can evolve to such similar future counterparts as to make little difference in show, even though we know there to actually be differences, at least in contigency. It’s a bit like how two people of very different backgrounds and even different alleles can come to have the similar tones to their skin. Their evolutionary contigency, or histories, are different, but the result is virtually the same.

Another point of note here is that evolution can produce similar things, but it will almost never produce the exact same thing. The history of life, if rerun, would be much, much different in all likelihood. When exolife is discovered, we’ll have indirect confirmation of this. Until then, it should be important for people to realize that nothing in biology is inevitable – including humans.