Maybe the counterbalancing would ease back pain?

This is how Sony is advertising some new gaming gadget. Somehow, I don’t think they’re trying to appeal to women gamers.


I also don’t think plunking the female form down deep into the Uncanny Valley like that is going to appeal to most well-adjusted males.

The other trope on display that I see a fair bit: showing just the torso while cutting off the model’s face. That’s one I sometimes see with male models, too — there’s nothing quite like obliterating the most expressive part of the human body to completely objectify your subject.

ENCODE gets a public reaming

I rarely laugh out loud when reading science papers, but sometimes one comes along that triggers the response automatically. Although, in this case, it wasn’t so much a belly laugh as an evil chortle, and an occasional grim snicker. Dan Graur and his colleagues have written a rebuttal to the claims of the ENCODE research consortium — the group that claimed to have identified function in 80% of the genome, but actually discovered that a formula of 80% hype gets you the attention of the world press. It was a sad event: a huge amount of work on analyzing the genome by hundreds of labs got sidetracked by a few clueless statements made up front in the primary paper, making it look like they were led by ignoramuses who had no conception of the biology behind their project.

Now Graur and friends haven’t just poked a hole in the balloon, they’ve set it on fire (the humanity!), pissed on the ashes, and dumped them in a cesspit. At times it feels a bit…excessive, you know, but still, they make some very strong arguments. And look, you can read the whole article, On the immortality of television sets: “function” in the human genome according to the evolution-free gospel of ENCODE, for free — it’s open source. So I’ll just mention a few of the highlights.

I’d originally criticized it because the ENCODE argument was patently ridiculous. Their claim to have assigned ‘function’ to 80% (and Ewan Birney even expected it to converge on 100%) of the genome boiled down to this:

The vast majority (80.4%) of the human genome participates in at least one biochemical RNA- and/or chromatin-associated event in at least one cell type.

So if ever a transcription factor ever, in any cell, bound however briefly to a stretch of DNA, they declared it to be functional. That’s nonsense. The activity of the cell is biochemical: it’s stochastic. Individual proteins will adhere to any isolated stretch of DNA that might have a sequence that matches a binding pocket, but that doesn’t necessarily mean that the constellation of enhancers and promoters are present and that the whole weight of the transcriptional machinery will regularly operate there. This is a noisy system.

The Graur paper rips into the ENCODE interpretations on many other grounds, however. Here’s the abstract to give you a summary of the violations of logic and evidence that ENCODE made, and also to give you a taste of the snark level in the rest of the paper.

A recent slew of ENCODE Consortium publications, specifically the article signed by all Consortium members, put forward the idea that more than 80% of the human genome is functional. This claim flies in the face of current estimates according to which the fraction of the genome that is evolutionarily conserved through purifying selection is under 10%. Thus, according to the ENCODE Consortium, a biological function can be maintained indefinitely without selection, which implies that at least 80 − 10 = 70% of the genome is perfectly invulnerable to deleterious mutations, either because no mutation can ever occur in these “functional” regions, or because no mutation in these regions can ever be deleterious. This absurd conclusion was reached through various means, chiefly (1) by employing the seldom used “causal role” definition of biological function and then applying it inconsistently to different biochemical properties, (2) by committing a logical fallacy known as “affirming the consequent,” (3) by failing to appreciate the crucial difference between “junk DNA” and “garbage DNA,” (4) by using analytical methods that yield biased errors and inflate estimates of functionality, (5) by favoring statistical sensitivity over specificity, and (6) by emphasizing statistical significance rather than the magnitude of the effect. Here, we detail the many logical and methodological transgressions involved in assigning functionality to almost every nucleotide in the human genome. The ENCODE results were predicted by one of its authors to necessitate the rewriting of textbooks. We agree, many textbooks dealing with marketing, mass-media hype, and public relations may well have to be rewritten.

You may be wondering about the curious title of the paper and its reference to immortal televisions. That comes from (1): that function has to be defined in a context, and that the only reasonable context for a gene sequence is to identify its contribution to evolutionary fitness.

The causal role concept of function can lead to bizarre outcomes in the biological sciences. For example, while the selected effect function of the heart can be stated unambiguously to be the pumping of blood, the heart may be assigned many additional causal role functions, such as adding 300 grams to body weight, producing sounds, and preventing the pericardium from deflating onto itself. As a result, most biologists use the selected effect concept of function, following the Dobzhanskyan dictum according to which biological sense can only be derived from evolutionary context.

The ENCODE group could only declare function for a sequence by ignoring all other context than the local and immediate effect of a chemical interaction — it was the work of short-sighted chemists who grind the organism into slime, or worse yet, only see it as a set of bits in a highly reduced form in a computer database.

From an evolutionary viewpoint, a function can be assigned to a DNA sequence if and only if it is possible to destroy it. All functional entities in the universe can be rendered nonfunctional by the ravages of time, entropy, mutation, and what have you. Unless a genomic functionality is actively protected by selection, it will accumulate deleterious mutations and will cease to be functional. The absurd alternative, which unfortunately was adopted by ENCODE, is to assume that no deleterious mutations can ever occur in the regions they have deemed to be functional. Such an assumption is akin to claiming that a television set left on and unattended will still be in working condition after a million years because no natural events, such as rust, erosion, static electricity, and earthquakes can affect it. The convoluted rationale for the decision to discard evolutionary conservation and constraint as the arbiters of functionality put forward by a lead ENCODE author (Stamatoyannopoulos 2012) is groundless and self-serving.

There is a lot of very useful material in the rest of the paper — in particular, if you’re not familiar with this stuff, it’s a very good primer in elementary genomics. The subtext here is that there are some dunces at ENCODE who need to be sat down and taught the basics of their field. I am not by any means a genomics expert, but I know enough to be embarrassed (and cruelly amused) at the dressing down being given.

One thing in particular leapt out at me is particularly fundamental and insightful, though. A common theme in these kinds of studies is the compromise between sensitivity and selectivity, between false positives and false negatives, between Type II and Type I errors. This isn’t just a failure to understand basic biology and biochemistry, but incomprehension about basic statistics.

At this point, we must ask ourselves, what is the aim of ENCODE: Is it to identify every possible functional element at the expense of increasing the number of elements that are falsely identified as functional? Or is it to create a list of functional elements that is as free of false positives as possible. If the former, then sensitivity should be favored over selectivity; if the latter then selectivity should be favored over sensitivity. ENCODE chose to bias its results by excessively favoring sensitivity over specificity. In fact, they could have saved millions of dollars and many thousands of research hours by ignoring selectivity altogether, and proclaiming a priori that 100% of the genome is functional. Not one functional element would have been missed by using this procedure.

This is a huge problem in ENCODE’s work. Reading Birney’s commentary on the process, you get a clear impression that they regarded it as a triumph every time they got even the slightest hint that a stretch of DNA might be bound by some protein — they were terribly uncritical and grasped at the feeblest straws to rationalize ‘function’ everywhere they looked. They wanted everything to be functional, and rather than taking the critical scientific view of trying to disprove their own claims, they went wild and accepted every feeble excuse to justify them.

The Intelligent Design creationists get a shout-out — they’ll be pleased and claim it confirms the validity of their contributions to real science. Unfortunately for the IDiots, it is not a kind mention, but a flat rejection.

We urge biologists not be afraid of junk DNA. The only people that should be afraid are those claiming that natural processes are insufficient to explain life and that evolutionary theory should be supplemented or supplanted by an intelligent designer (e.g., Dembski 1998; Wells 2004). ENCODE’s take-home message that everything has a function implies purpose, and purpose is the only thing that evolution cannot provide. Needless to say, in light of our investigation of the ENCODE publication, it is safe to state that the news concerning the death of “junk DNA” have been greatly exaggerated.

Another interesting point is the contrast between big science and small science. As a microscopically tiny science guy, getting by on a shoestring budget and undergraduate assistance, I like this summary.

The Editor-in-Chief of Science, Bruce Alberts, has recently expressed concern about the future of “small science,” given that ENCODE-style Big Science grabs the headlines that decision makers so dearly love (Alberts 2012). Actually, the main function of Big Science is to generate massive amounts of reliable and easily accessible data. The road from data to wisdom is quite long and convoluted (Royar 1994). Insight, understanding, and scientific progress are generally achieved by “small science.” The Human Genome Project is a marvelous example of “big science,” as are the Sloan Digital Sky Survey (Abazajian et al. 2009) and the Tree of Life Web Project (Maddison et al. 2007).

Probably the most controversial part of the paper, though, is that the authors conclude that ENCODE fails as a provider of Big Science.

Unfortunately, the ENCODE data are neither easily accessible nor very useful—without ENCODE, researchers would have had to examine 3.5 billion nucleotides in search of function, with ENCODE, they would have to sift through 2.7 billion nucleotides. ENCODE’s biggest scientific sin was not being satisfied with its role as data provider; it assumed the small-science role of interpreter of the data, thereby performing a kind of textual hermeneutics on a 3.5-billion-long DNA text. Unfortunately, ENCODE disregarded the rules of scientific interpretation and adopted a position common to many types of theological hermeneutics, whereby every letter in a text is assumed a priori to have a meaning.

Ouch. Did he just compare ENCODE to theology? Yes, he did. Which also explains why the Intelligent Design creationists are so happy with its bogus conclusions.

More boat than fish

How is it, living in the Anthropocene?

Sea levels will likely rise a few feet by the year 2100. Current fish wet biomass is about 2 billion tons, so removing them won’t make a dent either. (Marine fish biomass dropped by 80% over the last century, which—taking into consideration the growth rate of the world’s shipping fleet—leads to an odd conclusion: Sometime in the last few years, we reached a point where there are, by weight, more ships in the ocean than fish.)

The current world shipping fleet has a displacement of about 2.15 billion tons (most of which is oil and ore), so yeah, we humans are now bulking out more volume in the oceans than the fish do (we’ve got a long ways to go before we overtake invertebrates and bacteria, I suspect).

The other depressing point in the article is that global warming is adding more water to the oceans every second, and that every 16 hours we’re adding more than that 2 billion tons of water to the ocean.

Science proves me right!

I agree with the title of this article: Beards Keep You Young, Healthy & Handsome, Says Science. Furthermore, I find their conclusions totally copacetic.

Gentlemen, they’re not just for hipsters and the homeless any more. While both dead sexy and totally awesome, beards are also a boon to your overall health. Researchers discovered that men with beards and moustaches actually enjoy numerous benefits including, but not limited to, instant handsomeness.

A study from the University of Southern Queensland, published in the Radiation Protection Dosimetry Journal, found that beards block 90 to 95 percent of UV rays, thereby slowing the aging process and reducing the risk of skin cancer. Got asthma? Pollens and dust simply get stuck in that lustrous facial hair. Additionally, all that hair retains moisture and protects from the wind, keeping you looking young and fresh-faced. What’s more, shaving is usually the cause of ingrown hairs and bacterial infections that lead to acne.

Not noted, because their methodology was to leave bearded and unbearded mannequins in the bright sunlight of the Australian outback while measuring radiation absorption, is that they also keep your face warm in Minnesota winters.

Also not noted is that the way they make you more handsome is by hiding half your homely face.

Hey Bay Areans

With very little notice, I’m going to be in the Berkeley-Oakland area Tuesday and Wednesday, Feb. 26 & 27. My schedule is somewhat in flux at the moment what with borrowing cars and catching up with close friends and family I haven’t seen in too long, but should there be sufficient interest in a FlashHorde Beer Hour, I will carve out the time to make that happen. Discuss.

Roberts on Revkin on Keystone

I like reading David Roberts’ stuff on Grist, especially when I disagree with him. Sadly, there’s not a thing I disagree with in this piece rebutting Andrew Revkin on opposition to Keystone. (Perhaps excepting his characterization of Matt Nisbet as a “professional wanker,” which I find overly generous given that I have always found Nisbet sorely lacking in professionalism.)

This weekend, close to 50,000 people gathered for the biggest rally ever against climate change, a threat Revkin acknowledges is enormous, difficult, and urgent. Revkin and his council of wonks took to Twitter to argue that the rally and the campaign behind it are misdirected, absolutist, confused, and bereft of long-term strategy. They had this familiar conversation as the rally was unfolding.

As a result, Revkin suffered the grievous injury of a frustrated tweet from Wen Stephenson, a journalist who has crossed over to activism. This gave the wounded Revkin the opportunity to write yet another lament on the slings and arrows that face the Reasonable Man. He faced down the scourge of single-minded “my way or the highway environmentalism,” y’all, but don’t worry, he’s got a thick skin. He lived to tell the tale.

This is all for the benefit of an elite audience, mind you, for whom getting yelled at by activists is the sine qua non of seriousness. The only thing that boosts VSP cred more is getting yelled at by activists on Both Sides.

Nice line, that last one. Useful in SO many contexts.

Roberts’ casual slam against the Frameinator comes in response to this tweet, in which Nisbet chides types for not hewing to his own special brand of 13-dimensional chess:

What struck me about the thread that tweet came in was the overwhelming criticism of Keystone pipeline opponents for not having an overarching strategy that extends past stopping the Keystone pipeline as they mobilize people to oppose the Keystone pipeline. That criticism isn’t quite true:, for instance, is full of local student groups putting pressure on their colleges to divest from fossil fuel companies, in much the same fashion as the anti-apartheid divestment movement that hit U.S. campuses in the 1980s.

But there’s also an uncanny similarity between the objections voiced in that thread to Keystone opponents’ lack of a formal program, and objections we heard to the Occupy Wall Street folks way back in 2011. We heard back then that because OWS didn’t have, say, a 13-point program to adjust the schedule of lunches at quarterly SEC hearings, that they weren’t Very Serious People.

Which, of course, essentially translates to “your genuine groundswell of concern and subsequent activism threatens to undermine our position as experts.”

I used to get lots of letters and emails when I worked at Earth Island Institute from helpful people who thought somebody ought to start a campaign to do something. That something varied: take on the issue of overpopulation, plant redwood trees along the shore of San Francisco Bay, teach inner city children about marmots, whatever. The problem was that very few of these missives were phrased in the first person: “I would like to do this work.” It was almost always “…you should do this thing I think is important.”

I roundfiled those letters, but they kept coming.

Which all raises two questions for me:

  1. What is it with people declaring that movements like the opposition to the Keystone pipeline ought to do things a certain specific way, while notably refraining from offering to do any of the hard work of implementation with the group they’re criticizing?
  2. How the hell does Matthew Nisbet still have a job?

Where’s the solidarity?

Atheists are publicly chastised by Naima Washington.


It is a sad fact that people of color, particularly African American nonbelievers, are alienated within the secular community. Among the ‘faith’ communities, even those with the most racist and sexist doctrines, continue to do whatever it takes (and make no apologies) as they aggressively recruit and make space in their communities for people of color. Based on their disinterest in any recruiting efforts, the leadership of the secular community is apparently very proud of the fact that they, on the other hand, have few people of African descent in leadership positions as well as very few members. While there is no genuine intent or concerted plan to change this situation, many attempt to explain this phenomena by claiming that black folk are just too addicted to religion; otherwise, those of us who aren’t addicted to religion are either nominal or closet atheists, and therefore, need not be taken seriously. During the past 25 years, I belonged to many secular organizations; it was indeed a challenge to remain in them.

There is some effort to incorporate black Americans into atheist organizations; it’s not an active antipathy, but more an oblivious neglect. To make atheism relevant to black Americans will take, I think, structural changes: we need to openly recognize that issues of importance to the black community cannot be set aside as non-atheist issues.

It’s that nagging gate-keeping problem again. We need to realize that atheism and skepticism are universal ideals, not narrow ways to address a particular subset of questions. And it really is all about the questions: too many atheists think atheism is simply the answer, without doing the hard work of negotiating the human problems…and they get defensive when anyone tries to tell them that there are many concerns out there — social justice, feminism, black civil liberties, to name a few — that belong on the godless table. The current infighting that some people are moaning about is actually an example of the resentment of those holding the status quo: how dare we suggest that atheism has implications beyond just disbelieving in god and religion? How dare we try to expand the scope of atheism when we haven’t eradicated religion yet? How dare we suggest that the way to expand our base is to also consider the more pressing concerns of other people beyond our traditional white middle class conventionalities?

And so we watch the opportunities pass by, because our current constituencies simply don’t comprehend that women or black Americans or any other second-class group might be interested in something other than talking about how stupid the Bible is. Sometimes silence is as self-defeating as hostility.

When African American atheists attempt to expand their visibility and participation in the secular community by organizing with other nonbelievers—especially those who have been historically ignored by the leadership of the secular community—to publicly celebrate their freedom from religious dogma; when we ask everyone in the secular community to celebrate along with us, and we set aside one day out of the entire year to do so, there’s a problem! Last year, some very intelligent and insightful atheists declared efforts to organize a Day of Solidarity for Black Non-believers as segregation! Those same people are otherwise dead silent about the segregation, hostility, and alienation directed towards black atheists within the secular community year-round.

I didn’t see anything local to Morris happening on the Day of Solidarity (this Sunday, the 24th). I checked Minnesota Atheists to see if they had plans to honor the day this weekend, and no, they have nothing. Again, it’s not because their is an antipathy to black issues: it’s more of an absence of awareness. And hell no, the problem isn’t the black community, it’s the existing atheist community that seems unwilling to reach out.

Can we fix this? I don’t know. We might all start by looking locally to see if there are any Day of Solidarity events going on around you, and join in.

For my birthday? You shouldn’t have!

I just learned today about @MoFems and that they’re having a local conference on 9 March (yes, my birthday!): the F-Word Conference: What Role Do You Play in Redefining Gender and Culture?. I should probably look around my own neighborhood more often.

Speaking of local events…this weekend, starting today, is the Prairie Gate Literary Festival, and on Wednesday the 27th we have Barry Finzel visiting to give the honors lecture on Structural Biology and 3-D modeling, and on Tuesday the 26th Sylke Boyd will be telling us about sun dogs and northern lights and other exotic phenomena at Cafe Scientifique. This place is happening — I hope we can get more locals to stop on by.