The Case for Junk DNA

Most of our DNA probably doesn't really do anything and could be dispensed with. Some may find that statement to be surprising, but there are good reasons to believe it. "The Case for Junk DNA," published a couple of months ago at PLoS Genetics, explains some of the history behind the idea of junk DNA as well as experimental and observational support. (A layman's explanation is provided by Carl Zimmer here.) The argument rests on a few basic facts:

1. Much of our (and other organisms') genome is made up of repetitive sequences, broken genes, bits and pieces of viruses and other self-replicating virus-like elements. A few may have secondarily taken on function in helping to regulate genes, or even create new genes, but attributing some kind of essential function to most of it would be like saying that the phrase "copy and paste me" peppered throughout Shakespeare's works serves a narrative function.

2. There is no correlation between genome size and organismal complexity. As illustrated by the image below, genome size can vary widely, even between closely related lineages. (Millions of bases shown on a log scale, with the star indicating humans.)

Let that sink in for a second. Salamanders have genomes that are over 10 times as large as ours. (Insert joke about the salamander's letters.)

3. If you assume that most of the genome is functional, then the mutation rate in humans (or other organisms) ought to be causing 'mutational meltdown' because our collective genomes are being hit with deleterious mutations faster than natural selection can remove them.

There is also experimental support, such as a 2004 experiment where a large section of a mouse's genome was deleted with no apparent effect.

When you put it all together, I think the evidence strongly suggests that much of our genome is expendable. T. Ryan Gregory, one of the authors, has blogged and published on this issue for a long time. If you think of a reason for why we need all that 'junk' DNA, Gregory asks that you submit it to 'the onion test,' which is simply:

...if most eukaryotic DNA is functional at the organism level, be it for gene regulation, protection against mutations, maintenance of chromosome structure, or any other such role, then why does an onion require five times more of it than a human?

---

Continue reading...

On the Origin of Hitler

About a month ago I was browsing through Science and noticed a review of a recent book by historian Peter Bowler. (The review requires a subscription, so instead I'll direct interested readers here for a roughly equivalent review.) His book, Darwin Deleted, imagines a world where Darwin did not exist, as a device for illuminating other ideas about evolution. Apparently he argues that if Darwin had not existed, evolution might not have been as contentious of an issue. This is because, while many religious people weren't particularly thrilled with the idea of evolution, it was natural selection as a mechanism that really got their dander up. It was just too materialistic--even for some scientists. In fact, during the early twentieth century natural selection took a back seat until the modern synthesis of the 1940s put it back in the center. As I understand it, Bowler imagines a world where evolution was accepted relatively peacefully, with natural selection being discovered later.

Bowler also argues that the atrocities of World War II would still have occurred without Darwin. This seems completely obvious to me, but a staple of anti-evolution propaganda is to blame Darwin for Hitler. In fact, just last week the Discovery Institute posted a video on YouTube doing just that. At first glance you can see why the argument appears convincing. Darwin said that evolution occurs by survival of the best adapted, so Hitler took Darwin's theory to the logical conclusion by attempting to eliminate the weak.

I can accept that some people just repeat this kind of thing because that's what they heard, but it's harder for me to believe that thinking people take such things seriously. It seems transparently nasty and dumb to me. For one thing, even if Darwin did serve as a source of Hitler's inspiration, that fact wouldn't have any logical consequence for the validity of Darwin's ideas about how nature works. (I bet the German artillery loved Newton's ideas too!) Moreover, we could hardly hold Darwin responsible for the deeds of a future sociopath. But what I find more annoying is that people who say this must ignore or forget known facts and social currents that existed independent of Darwin.

For example, animals were bred for desired traits for centuries and millennia before Darwin. Darwin himself drew on artificial selection--i.e. breeding--for his insight of natural selection. Consider the following quote:

… Experience has long since taught mankind the necessity of observing certain natural laws in the propagation of animals, or the stock will degenerate and finally become extinct. But strange to say, in regard to the human animal, these laws, except in certain particulars, are more or less disregarded in these latter times. The inevitable consequence is, the race is degenerating, new diseases are introduced, while effeminacy and barrenness are on the increase: and worse than all, this evil condition of the body has its effects upon the mind…

That was George Q. Cannon writing in 1857, three years before he was called as an Apostle and a year before Darwin published Origin of Species. You could just as easily say that Hitler was applying widely accepted principles of animal breeding to humans. It simply doesn't take a theory of species formation to decide that your race (however defined) is better than others, or to hate Jews, or to be nationalist, or to think the "weak" are a drain on society, and so on. The Nazis appropriated anything that seemed to lend support to their ideology. If Darwin's theory was one of those, then that's unfortunate but it's hardly Darwin's fault (he died in 1882, for heaven's sake) and means nothing for its validity as science.

One more thing: the idea that species progress was not Darwin's. Darwin understood that natural selection would result in adaptation to environmental circumstances, not the production of some kind of platonic ideal. Thus, to argue that elimination of the weak was necessary for human evolutionary progress would be a bastardization of Darwinian evolution. As I mentioned above, Darwinian evolution was eclipsed for a while by other ideas about evolution, some of which involved progress. (If blame is to be laid, I would bet those ideas had more influence.)

In their zeal to cast aspersions on evolution, anti-evolutionists also often go a step further and say that Darwin himself was a supporter of social Darwinism. To the extent that is true it is unfortunate although, again, it doesn't matter what Darwin thought with respect to the validity of his theory. But although he was a product of his time, Darwin was relatively progressive in some of his views (eloquently opposing slavery, for example) and it seems that detractors have a difficult time making their case without distorting his writings. For example, in The Descent of Man he wrote:

At some future period, not very distant as measured by centuries, the civilised races of man will almost certainly exterminate, and replace, the savage races throughout the world.

Oh, that's terrible! Except when you look at the context you see that the sentence is the first half of a hypothetical he uses to make a point about how extinction erases the gradations between species. And considering Europe's colonial enterprise Darwin's statement probably seemed like an unremarkable prediction [1]. It's rather uncharitable to rip that sentence out of context and present it as though Darwin hoped for the extinction of other races, as the DI video does, but that's the kind of garbage I've come to expect from them.

Social Darwinism and the eugenics movement, to say nothing of the Nazis, were wrong. If we pawn it all off on Darwin, however, then we miss important lessons about the naturalistic fallacy, the naive application of science, human rights, ethics, the golden rule, economics, and so on. When it comes to Hitler, Darwin is a distraction.


Notes:
1. Americans weren't innocent either. Manifest destiny, anyone?

---

Continue reading...

Blessed Are the Nerds

My Saturday web surfing alerted me to a small controversy over the role of nerds in American culture. National Review's July cover story was a piece by Charles C. W. Cooke attacking scientist Neil deGrasse Tyson and America's sanctimonious nerds. To the extent that the piece is a reminder that smart people can fall prey to their own biases and that data alone cannot drive decisions, I suppose it is a useful commentary. But I have to say that, to my eye, the whole piece drips of bitterness and projection.

One part insecure hipsterism, one part unwarranted condescension, the two defining characteristics of self-professed nerds are (a) the belief that one can discover all of the secrets of human experience through differential equations and (b) the unlovely tendency to presume themselves to be smarter than everybody else in the world. Prominent examples include MSNBC’s Melissa Harris-Perry, Rachel Maddow, Steve Kornacki, and Chris Hayes; Vox’s Ezra Klein, Dylan Matthews, and Matt Yglesias; the sabermetrician Nate Silver; the economist Paul Krugman; the atheist Richard Dawkins; former vice president Al Gore; celebrity scientist Bill Nye; and, really, anybody who conforms to the Left’s social and moral precepts while wearing glasses and babbling about statistics.

No condescension here! You might also notice that all of the nerds mentioned come from the Left [1]. I guess that makes sense on the article's own terms because Cooke asserts that "First and foremost, then, “nerd” has become a political designation." That the word had been redefined to carry primarily political meaning was news to me, but since I only moderately identified with the term in the first place, I don't have much investment in the definition. Someone should inform high school students, though.

How smug are the nerds?

These are the people who insisted until they were blue in the face that George W. Bush was a “theocrat” eternally hostile toward “evidence,” and that, despite all information to the contrary, Attorney General Ashcroft had covered up the Spirit of Justice statue at the Department of Justice because he was a prude. These are the people who will explain to other human beings without any irony that they are part of the “reality-based community,” and who want you to know how aw-shucks excited they are to look through the new jobs numbers.

I can see how calling yourself "reality-based" might be off-putting. On the other hand, maybe it should be pointed out that the term was coined by a Bush aide (thought to be Karl Rove) as a term of derision.

The aide said that guys like me were "in what we call the reality-based community," which he defined as people who "believe that solutions emerge from your judicious study of discernible reality." ... "That's not the way the world really works anymore," he continued. "We're an empire now, and when we act, we create our own reality. And while you're studying that reality—judiciously, as you will—we'll act again, creating other new realities, which you can study too, and that's how things will sort out. We're history's actors…and you, all of you, will be left to just study what we do."

Given the history, is it any wonder that "reality-based community" has been adopted by nerds as a term of honor?

Cooke's piece has come in for criticism, but I guess you would expect that from those jerk-nerds of the Left. Personally, I liked this bit from Andrew Leonard at Salon:

Cooke argues that leftists are embracing the nerd-designation because it says to the world what they are not: “… which is southern, politically conservative, culturally traditional, religious in some sense, patriotic, driven by principle rather than the pivot tables of Microsoft Excel, and in any way attached to the past.”

Oh NO! Cooke dares attack nerdish chart-love! That really stings. But you know what? It’s not the fault of liberal nerds that Ken Hamm’s Creation Museum, which claims that dinosaurs were wiped out in a flood 4300 years ago, is in the South. And for better or worse, it’s not the fault of liberal nerds that large swathes of Republican politicians in the South have lined up behind the breath-taking rejection of the scientific method that is symbolized by the Creation Museum.

I might also add that those are some gratuitous assertions on Cooke's part.

Cooke ridicules nerd identification as a fad adopted by posers.

“Ignorance,” a popular Tyson meme holds, “is a virus. Once it starts spreading, it can only be cured by reason. For the sake of humanity, we must be that cure.” This rather unspecific message is a call to arms, aimed at those who believe wholeheartedly they are included in the elect “we.” Thus do we see unexceptional liberal-arts students lecturing other people about things they don’t understand themselves and terming the dissenters “flat-earthers.” Thus do we see people who have never in their lives read a single academic paper clinging to the mantle of “science” as might Albert Einstein. Thus do we see residents of Brooklyn who are unable to tell you at what temperature water boils rolling their eyes at Bjørn Lomborg or Roger Pielke Jr. because he disagrees with Harry Reid on climate change.

This is interesting. My wife's education was in the liberal arts, so I guess she isn't allowed to assert the value of childhood vaccination to her stay-at-home-mom peers. But more interesting is that Cooke chose to pit Bjørn Lomborg or Roger Pielke Jr. against Harry Reid. Really? I think what Cooke meant to say was "rolling their eyes at Bjørn Lomborg or Roger Pielke Jr. because he disagrees with many climate scientists and economists, whose work has informed Harry Reid's views." You see, nerds would know that Lomborg and Pielke's reputations have very little to do with what Harry Reid thinks. (As an aside, Cooke seems to have taken Pielke's departure from Nate Silver's FiveThirtyEight as a personal slight. In searching the web for information about Pielke, I found this note by Cooke lamenting the terrible vitriol of the Left. It's not the Left's fault Cooke apparently crushed on a guy that has gained a reputation for distortion.)

Cooke also calls out progressives for themselves believing some unscientific things:

Progressives not only believe all sorts of unscientific things — that Medicaid, the VA, and Head Start work; that school choice does not; that abortion carries with it few important medical questions; that GM crops make the world worse; that one can attribute every hurricane, wildfire, and heat wave to “climate change”; that it’s feasible that renewable energy will take over from fossil fuels anytime soon — but also do their level best to block investigation into any area that they consider too delicate.

First of all, I thought we were talking about nerds, not progressives in general. Second, just this last week Chris Mooney at that lefty magazine Mother Jones highlighted a video of Neil deGrasse Tyson--the man Cooke chose as his nerd symbol--telling anti-GMO folks to "chill out." Also, nerds would not simplistically attribute every hurricane, wildfire, or heat wave to climate change. Rather, they would bend over backwards to explain that climate change will statistically increase the frequency and severity. Unfortunately such efforts seem to be lost on Cooke and his non-nerds and, for their part, they like to use every snow storm or regional cold snap as an opportunity to remind everyone that Al Gore was wrong [2]. What is it with them and Al Gore?

Look, if conservatives like Cooke are losing out to the nerds, it's mostly their own fault. In the wake of the Great Recession and the election of Barack Obama, the Right has run to the fever swamps, leaving behind (or actively expelling) politicians and commentators who refuse to follow (i.e. "RINOs"). If you've lost the nerds, maybe that should tell you something.


Notes:
1. More or less.

2. I did a quick search to see if Cooke had ever done something like that. He had. Granted he was more nuanced in his commentary than most, but I took an interest in this claim: "The 1990 IPCC Report promised an increase in sea level of around 120 millimeters [or 12 cm] by 2014." A nerd might have a copy of the 1990 IPCC report and bother to look up what it said. Would it surprise you if the only justification I can find for Cooke's statement is an uncharitable reading of a graph? What the report actually says is, "Under the Business-as-Usual scenario, the best estimate is that, for the year 2030, global sea level would be 18cm higher than today. Given the stated range of uncertainty in the contributing factors, the rise could be as little as 8cm or as high as 29cm."

---

Continue reading...

What Is the Deal with the Ebola Outbreak?

This week I caught some of The Diane Rehm Show on NPR, which had a very interesting discussion about the current Ebola outbreak. (Audio and transcript here; also available as a free podcast on iTunes.) Panelists included Dr. Anthony Fauci and Laurie Garrett.

As a brief side note, Ebola helped launch me onto my career path in microbiology and immunology. During my senior year as an undergraduate I took a virology course that, along with some outside reading, led me to pursue microbiology in graduate school. Ebola was the exotic virus of the day. One of the books I (mostly) read as part of my extra-curricular reading was The Coming Plague by none other than Laurie Garrett. (For some reason I never did read The Hot Zone, though.)

Anyway, I thought that Garrett said some of the most interesting things in the discussion. For example, one surprising feature of the outbreak is that it is exacerbated by the resistance of the very people that need help. Why?

GARRETT
...first of all, these countries have an average adult illiteracy rate of 50 percent. Then you take in what's functional literacy versus the ability to read anything that actually tries to describe what a virus is, you're talking about a very small percentage of these populations.

And for most people, the germ theory of disease is not a real concept....

In the case of Ebola, we're really up against cultural beliefs that when a disease hits a given family, it's because your ancestors committed some sin against some other family and they have leveled evil spirits against you. It's a kind of sense of an endless set of circles of retribution and revenge for deeds committed by someone against someone else. Well, now add to it, they just came out of these heinous civil wars where indeed evil deeds were done on almost every single family by somebody during the course of the 1985 to 2003 outbreak of violence.

And so you have a situation where outsiders are trying to say to people, there's a virus. And this virus causes this disease. And we are outsiders dressed in space suits and we don't look like you and you should believe us. And meanwhile the average person doesn't even have a concept of what a virus is....

FAUCI
This is nothing new. It's not new to HIV, it's not new to Ebola. History is replete with examples of when there are major outbreaks and plagues. The fear, the terror that is stricken into people has people almost intuitively look to someone to blame, someone, some group, some class, some religion, some country. There always needs to be a reason for things. And if you don't understand, as Laurie was saying correctly, the subtleties of the germ theory of infection, then you're looking to blame people and blame nations and blame groups that have nothing to do with it. So you're absolutely correct, it's a very difficult situation.

This next part gets at something I have felt deeply for quite a while, which is the importance of public health to our prosperity and standard of living. I don't think people in first-world countries appreciate what they have, which is why things like the anti-vaccine movement, slashing of budgets for programs that undergird our medical knowledge and capabilities, or cultural forces that disparage or twist science make me angry.

GARRETT
Quick thing is the average per capita spending, according to the World Bank on health care per person in these countries is a high of $18 a year, a low of $7. So there's not a lot of health care delivery available if you're spending $7 per person per year on all health services combined. And as far as the question -- I'm very glad the caller brought this up -- from Ann Arbor. Thank you. Funding and WHO -- WHO is in severe budget crisis. Has been now for almost four years.

They've laid off 20 percent of total personnel of the institution. And their disease response capacity has seen its budget slashed. I know that the average listener imagines that there's this huge SWAT Team of health providers sitting in WHO Headquarters in Geneva. And at the snap of a finger the director general deploys them where needed. This is absolutely untrue. In fact, WHO goes around begging for people like Dr. Fischer to -- at the expense of somebody else, the U.S. government, for example -- to go in under the WHO flag where needed.

And our own CDC has seen our budget cut for international response capacity, pandemic response and surveillance. So actually we're less prepared today then we were perhaps 10 years ago, in terms of the budgetary constraints of the major responders.

For more on the virus and what kinds of conditions the doctors treating infected people labor under, listen to or read the whole thing.

---

Continue reading...