Here I Stand; I Can Do No Other

I weigh in on Google Glass at KCET.

The gist:

Some of us come out to the desert to escape the Panopticon that life in the city already is, increasingly. In Los Angeles, Google Glass might be just one more increment of invasion in a landscape already thoroughly colonized by surveillance cameras, red light cameras, random private webcams, smart phone videographers and other such prying eyes. But there are places out here that don’t even have 4G yet. In fact — and you might want to sit down here and swallow that mouthful of coffee — there are some places out here where even the 3G coverage is spotty. We are in the back of beyond here in much of Eastern California.

And we like it that way, mostly.

So by all means, come on out and visit the desert. Bring your recording equipment, whether it’s a shoulder-mounted Steadicam or this latest bit of geek lust from Google sitting on your face. Document your hike. Record that coyote begging for sandwiches. Take video of that gorgeous desert bloom backlit by sunrise. The desert needs all the documentation it can get.

But if you’re talking to me, take that Google Glass off and put it away. If I’m speaking in public — which I do from time to time, offering lectures and poetry readings and such — and see you’re in my audience wearing Google Glass and you haven’t cleared it with me first, I will stop what I’m doing and ask you to put it away or leave. If you’re at an adjacent cafe table facing me and recording in my direction, I will write something derogatory in Sharpie on a sheet of paper and hold it up. I may escalate from there. And I’m not alone.

Read the whole thing.

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The argument from eyelid development

This is a new one for me. Earlier today I was summoned on Twitter to address an assertion by a creationist, @jarrydtrokis. I was slightly boggled.

He was baffled by eyelid development. It seems he thinks it requires…intelligent design!.

… Here’s one for you to ponder :) Eye lids in the womb… How are they formed? #IntelligentDesign?

Wait, what? What’s mystifying about eyelid formation?

The section of skin in the middle dies… How does it know to do that? And in a perfectly straight line???

Oh. It forms a straight line. Whoa. And he claims to have done research to get the answer.

The research I’ve done shows the scientists are at a loss for an explanation….

Gosh. I can do research, too. It’s easy to explain, with pictures even.

The eyelids separate in a straight seam because of how they got that way. The eyelids form by expansion of two epithelial sheets from above and below that meet in the middle. When you see how the eyelids develop, it’s easy to see how they separate in a straight line later. This is a series of images over the course of about a day in mouse development. In the first, you can see the eye sans eyelid, but ringed by epithelia. In the second, you can see that epithelium growing, expanding in a sheet over the eye. In the third, the sheet is beginning to close in a line over the middle, and in the fourth it has completely closed, but leaving a seam or scar in a straight line across it.

mouse_eyelid_sem

Wait, you say inquisitively, I’d like a closer look at that seam. Can you show me what is going on postnatally, as the eyelids separate? Sure can.

mouse_eyelid_tem

The first panel is 5 days postnatal in the mouse; the eyelids are still fused. But you can see a difference in the histology of the junctional region (J), and a depression at the arrowhead (you can also see the layers of keratin there). There’s something different in this area.

In the second panel, 10 days postnatally, the depression at the junctional region is deepening and you can see a stratum granulosum (SG) at the seam, while you can also see hair follicles (HF) forming in the adjacent portions of the lid.

The third and fourth panels are at 12 days, and now the keratin layers have extended into the depression from both the inside and outside, completing the separation of the two lids.

Now @jarrydtrokis might be tempted to say that Jesus did the separating, but that’s only true if Jesus is a polypeptide called epidermal growth factor, or EGF. EGF is a molecule that triggers growth and differentiation of keratinocytes, and it turns out that if you treat baby mice with EGF it accelerates the rate of eyelid separation.

I’m sorry, @jarrydtrokis, but your argument from ignorance wasn’t very persuasive, and your talents at ‘research’ are rather pathetic, since the paper describing all that was trivial to find. But then, isn’t this always the case with creationists? There are none so blind as those who will not see.

Findlater GS, McDougall RD, Kaufman MH (1993) Eyelid development, fusion and subsequent reopening in the mouse. J Anat. 183(1):121-9.

Gizmodo fails again

There’s a whole lot wrong with this Gizmodo piece on the proposed Palen Solar Electric Generating System. In fact, the fuckup per sentence ratio is higher than in any piece I’ve seen this month outside of Mercola.com. The Solar Energy Zone “Initiative” wasn’t “signed into law” by Obama — it was a record of decision issued by the Interior Department on an agency program as the culmination of an environmental assessment, rather than a bill passed by Congress and sent to the President’s desk. (Which means Obama didn’t sign it and it’s not a law.) Palen will very likely not start construction this year: the California Energy Commission is casting a sober eye at contractor BrightSource’s technology on its proposed Hidden Hills project, which is much closer to approval. The towers at Hidden Hills will be just as tall as those at Palen, if either plant ever gets built, and Hidden Hills will likely go up first, meaning that the Gizmodo headline is wrong.

Like I said: many, many errors. But this one’s the worst, and it’s the very first paragraph:

The US government holds vast tracts of public lands—more than a 654 million acres, in fact—for public use such as national parks as well as for military use like test ranges and proving grounds. But most of the time, much of that land is left to rot when it could be producing clean solar energy for our ever-increasing power needs.

“Left to rot.”

By way of comparison

“Left to rot.”

ashford

“Left to rot.”

marching

What is it with some of these tech writers? Any landscape that doesn’t look like fucking Trantor is useless to them, sounds like.

What I taught today: those oddball critters, the vertebrates

We’ve been talking about flies nonstop for the last month — it’s been nothing but developmental genetics and epistasis and gene regulation in weird ol’ Drosophila — so I’m changing things up a bit, starting today. We talked about vertebrates in a general way, giving an overview of major landmarks in embryology, and a little historical perspective.

We take a very bottom-up approach to studying fly development: typically, fly freaks start with genes, modifying and mutating them and then looking at phenotype. Historically, vertebrate embryology goes the other way, starting with variations in the phenotype and inferring mechanisms (this has been changing for the last decade or two; we often start with a gene, sometimes from a fly, and use that as a probe to hook into the genetic mechanisms driving developmental processes). What that means is the 19th and early 20th century literature on embryology is often comparative morphology, looking at different species or different stages and trying to extract the commonalities or differences, or it’s experimental morphology, making modifications (usually not genetic) to the embryo and asking what happens next. Genes were not hot topics of discussion until the last half of the 20th century, and even then it took a few decades for the tools to percolate into the developmental biologists’ armory.

And much of 19th century embryology went lurching down a dead end. We talked about Haeckel, the grand sidetracker of the age. There was a deep desire to integrate development and evolution, but they lacked the necessary bridge of genetics, so Haeckel borrowed one, his theory of ontogenetic recapitulation. A theory that quickly went down in flames in the scientific community (jebus, Karl Ernst von Baer had eviscerated it 50 years before Haeckel resurrected it). We actually spent a fair amount of class time going over arguments for and against, and modern interpretations of phylotypy — it isn’t recapitulation, it’s convergence on a conserved network of global spatial genes that define the rough outlines of the vertebrate body plan.

Finally, I gave them a whirlwind tour of basic developmental stages of a few common vertebrate models: frog, fish, chick, and mouse. We’re going to talk quite a bit about early axis specification events in vertebrates (next week), and gastrulation (probably the week after), so I had to introduce them to the essential terminology and events. I think they can see the fundamental morphological events now — next, β-catenin and nodal and Nieuwkoop centers and all that fun stuff!

(Today’s slides (pdf))

Science makes you good! (Sometimes.)

You’ve probably heard this explanation for the virtue of religion: that even if god doesn’t exist, belief in god (or some other monitoring authority) makes people behave more morally. There have been many experiments that have actually shown that people are nicer or more generous when exposed to religious concepts, such as this one by Norenzayan and Shariff.

In one of their own studies, they primed half the participants with a spirituality-themed word jumble (including the words divine and God) and gave the other half the same task with nonspiritual words. Then, they gave all the participants $10 each and told them that they could either keep it or share their cash reward with another (anonymous) subject. Ultimately, the spiritual-jumble group parted with more than twice as much money as the control. Norenzayan and Shariff suggest that this lopsided outcome is the result of an evolutionary imperative to care about one’s reputation. If you think about God, you believe someone is watching. This argument is bolstered by other research that they review showing that people are more generous and less likely to cheat when others are around. More surprisingly, people also behave better when exposed to posters with eyes on them.

One explanation is that simply alerting people to the possibility of surveillance makes them more careful. God is just the most popular boogeyman.

But here’s an interesting twist on the Norenzayan and Shariff study, with very similar protocols. Ma-Kellams and Blascovich also had subjects do a word scramble before sharing a money reward, and also had them make moral judgments after reading a story about date rape, and assessed their opinion on a certain controversial subject.

The twist: the word scramble contained science terms (“logical,” “hypothesis,” “laboratory,” “scientists,” “theory”), and the controversial subject was science.

I think you can guess where this is going. Thinking about science makes you more moral!

Across the four studies presented here, we demonstrated the morally normative effects of thinking about science. Priming lay notions of science leads individuals to endorse more stringent moral norms (Studies 1, 2), report greater prosocial intentions (Study 3), and exhibit more morally normative behavior (Study 4). The moralizing effects of science were observed both by using naturalistic measures of exposure to science (e.g., field of study) as well as laboratory manipulations of thought-accessibility, and emerged across a broad array of domains, including interpersonal violations (Study 1), academic dishonesty (Studies 2), prosocial behaviors (Study 3), and economic exploitation (Study 4).

It is important to note that the primes used across all studies activated broad, general, lay notions of science rather than specific scientific findings. The key words used the science primes (logical, hypothesis, laboratory, scientists, and theory) were likely associated with semantic notions of rationality, impartiality and progress–notions that are a part of the broader moral view of science as a way of building a mutually beneficial society in which rational tools are used to improve the human condition.

Another important caveat is that it’s a typical psychology study, using a small pool of undergraduates at the University of California Santa Barbara, so they’re actually tapping into very narrow cultural norms. A group of students who were familiar with the Tuskegee syphilis study, to name just one exception, might respond to priming with science words very differently, while people from a less science-dependent culture might find the exercise meaningless.

But still, I don’t think those keywords would prompt concerns about being monitored and compelling people to police their behavior more carefully — they might instead switch people into slightly different modes of thought, where, as the authors suggest, different values are emphasized more. And maybe that’s what culture is actually doing: it’s reinforcing desirable associations in people’s minds to subtly shape their behavior. Clearly, though, we don’t need religion to do that. As a vehicle for positive values, anything can work: religion, football, stamp collecting, Pokemon, comedy, technology, television, or science (similarly, I think it’s also obvious that those media can also be vehicles for destructive values).

If you’re going to make anything an agent of virtue, though, it would help if it had the advantage of being fundamentally true in the first place…which is where religion falls down hard. If one of the values we want to enhance is honesty, for instance, you can’t do it with a medium that is a tissue of lies.

I am not alone!

I guess I’m not the only one bemused by the recent weird backlash among some scientists against philosophy. Michael Krämer also defends philosophy.

So then, should we physicists listen to philosophers?

An emphatic "No!", if philosophers want to impose their preconceptions of how science should be done. I do not subscribe to Feyerabend’s provocative claim that "anything goes" in science, but I believe that many things go, and certainly many things should be tried.

But then, "Yes!", we should listen, as philosophy can provide a critical assessment of our methods, in particular if we consider physics to be more than predicting numbers and collecting data, but rather an attempt to understand and explain the world. And even if philosophy might be of no direct help to science, it may be of help to scientists through its educational role, and sharpen our awareness of conceptional problems in our research.

Unfortunately, he also sounds like he’s got the physicist’s disease of sounding like physics is the only science in the world. Every word also applies to biology, chemistry, psychology, you name it…

We need a sociologist of science…or a philosopher

There’s another paper out debunking the ENCODE consortium’s absurd interpretation of their data. ENCODE, you may recall, published a rather controversial paper in which they claimed to have found that 80% of the human genome was ‘functional’ — for an extraordinarily loose definition of function — and further revealed that several of the project leaders were working with the peculiar assumption that 100% must be functional. It was a godawful mess, and compromised the value of a huge investment in big science.

Now W. Ford Doolittle has joined the ranks of many scientists who immediately leapt into the argument. He has published “Is junk DNA bunk? A critique of ENCODE” in PNAS.

Do data from the Encyclopedia Of DNA Elements (ENCODE) project render the notion of junk DNA obsolete? Here, I review older arguments for junk grounded in the C-value paradox and propose a thought experiment to challenge ENCODE’s ontology. Specifically, what would we expect for the number of functional elements (as ENCODE defines them) in genomes much larger than our own genome? If the number were to stay more or less constant, it would seem sensible to consider the rest of the DNA of larger genomes to be junk or, at least, assign it a different sort of role (structural rather than informational). If, however, the number of functional elements were to rise significantly with C-value then, (i) organisms with genomes larger than our genome are more complex phenotypically than we are, (ii) ENCODE’s definition of functional element identifies many sites that would not be considered functional or phenotype-determining by standard uses in biology, or (iii) the same phenotypic functions are often determined in a more diffuse fashion in larger-genomed organisms. Good cases can be made for propositions ii and iii. A larger theoretical framework, embracing informational and structural roles for DNA, neutral as well as adaptive causes of complexity, and selection as a multilevel phenomenon, is needed.

In the paper, he makes an argument similar to one T. Ryan Gregory has made many times before. There are organisms that have much larger genomes than humans; lungfish, for example, have 130 billion base pairs, compared to the 3 billion humans have. If the ENCODE consortium had studied lungfish instead, would they still be arguing that the organism had function for 104 billion bases (80% of 130 billion)? Or would they be suggesting that yes, lungfish were full of junk DNA?

If they claim that lungfish that lungfish have 44 times as much functional sequence as we do, well, what is it doing? Does that imply that lungfish are far more phenotypically complex than we are? And if they grant that junk DNA exists in great abundance in some species, just not in ours, does that imply that we’re somehow sitting in the perfect sweet spot of genetic optimality? If that’s the case, what about species like fugu, that have genomes one eighth the size of ours?

It’s really a devastating argument, but then, all of the arguments against ENCODE’s interpretations have been solid and knock the whole thing out of the park. It’s been solidly demonstrated that the conclusions of the ENCODE program were shit.

yalejunk

So why, Yale, why? The Winter edition of the Yale Medicine magazine features as a cover article Junk No More, an awful piece of PR fluff that announces in the first line “R.I.P., junk DNA” and goes on to tout the same nonsense that every paper published since the ENCODE announcement has refuted.

The consortium found biological activity in 80 percent of the genome and identified about 4 million sites that play a role in regulating genes. Some noncoding sections, as had long been known, regulate genes. Some noncoding regions bind regulatory proteins, while others code for strands of RNA that regulate gene expression. Yale scientists, who played a key role in this project, also found “fossils,” genes that date to our nonhuman ancestors and may still have a function. Mark B. Gerstein, Ph.D., the Albert L. Williams Professor of Biomedical Informatics and professor of molecular biophysics and biochemistry, and computer science, led a team that unraveled the network of connections between coding and noncoding sections of the genome.

Arguably the project’s greatest achievement is the repository of new information that will give scientists a stronger grasp of human biology and disease, and pave the way for novel medical treatments. Once verified for accuracy, the data sets generated by the project are posted on the Internet, available to anyone. Even before the project’s September announcement, more than 150 scientists not connected to ENCODE had used its data in their research.

“We’ve come a long way,” said Ewan Birney, Ph.D., of the European Bioinformatics Institute (EBI) in the United Kingdom, lead analysis coordinator for ENCODE. “By carefully piecing together a simply staggering variety of data, we’ve shown that the human genome is simply alive with switches, turning our genes on and off and controlling when and where proteins are produced. ENCODE has taken our knowledge of the genome to the next level, and all of that knowledge is being shared openly.”

Oh, Christ. Not only is it claiming that the 80% figure is for biological activity (it isn’t), but it trots out the usual university press relations crap about how the study is all about medicine. It wasn’t and isn’t. It’s just that dumbasses can only think of one way to explain biological research to the public, and that is to suggest that it will cure cancer.

As for Birney’s remarks, they are offensively ignorant. No, the ENCODE research did not show that the human genome is actively regulated. We’ve known that for fifty years.

That’s not the only ahistorical part of the article. They also claim that the idea of junk DNA has been discredited for years.

Some early press coverage credited ENCODE with discovering that so-called junk DNA has a function, but that was old news. The term had been floating around since the 1990s and suggested that the bulk of noncoding DNA serves no purpose; however, articles in scholarly journals had reported for decades that DNA in these “junk” regions does play a regulatory role. In a 2007 issue of Genome Research, Gerstein had suggested that the ENCODE project might prompt a new definition of what a gene is, based on “the discrepancy between our previous protein-centric view of the gene and one that is revealed by the extensive transcriptional activity of the genome.” Researchers had known for some time that the noncoding regions are alive with activity. ENCODE demonstrated just how much action there is and defined what is happening in 80 percent of the genome. That is not to say that 80 percent was found to have a regulatory function, only that some biochemical activity is going on. The space between genes was also found to contain sites where DNA transcription into RNA begins and areas that encode RNA transcripts that might have regulatory roles even though they are not translated into proteins.

I swear, I’m reading this article and finding it indistinguishable from the kind of bad science I’d see from ICR or Answers in Genesis.

I have to mention one other revelation from the article. There has been a tendency to throw a lot of the blame for the inane 80% number on Ewan Birney alone…he threw in that interpretation in the lead paper, but it wasn’t endorsed by every participant in the project. But look at this:

The day in September that the news embargo on the ENCODE project’s findings was lifted, Gerstein saw an article about the project in The New York Times on his smartphone. There was a problem. A graphic hadn’t been reproduced accurately. “I was just so panicked,” he recalled. “I was literally walking around Sterling Hall of Medicine between meetings talking with The Times on the phone.” He finally reached a graphics editor who fixed it.

So Gerstein was so concerned about accuracy that he panicked over an article in the popular press, but had no problem with the big claim in the Birney paper, the one that would utterly undermine confidence in the whole body of work, did not perturb him? And now months later, he’s collaborating with the Yale PR department on a puff piece that blithely sails past all the objections people have raised? Remarkable.

This is what boggles my mind, and why I hope some sociologist of science is studying this whole process right now. It’s a revealing peek at the politics and culture of science. We have a body of very well funded, high ranking scientists working at prestigious institutions who are actively and obviously fitting the data to a set of unworkable theoretical presuppositions, and completely ignoring the rebuttals that are appearing at a rapid clip. The idea that the entirety of the genome is both functional and adaptive is untenable and unsupportable; we instead have hundreds of scientists who have been bamboozled into treating noise as evidence of function. It’s looking like N rays or polywater on a large and extremely richly budgeted level. And it’s going on right now.

If we can’t have a sociologist making an academic study of it all, can we at least have a science journalist writing a book about it? This stuff is fascinating.

I have my own explanation for what is going on. What I think we’re seeing is an emerging clash between scientists and technicians. I’ve seen a lot of biomedical grad students going through training in pushing buttons and running gels and sucking numerical data out of machines, and we’ve got the tools to generate so much data right now that we need people who can manage that. But it’s not science. It’s technology. There’s a difference.

A scientist has to be able to think about the data they’re generating, put it into a larger context, and ask the kinds of questions that probe deeper than a superficial analysis can deliver. A scientist has to be more broadly trained than the person who runs the gadgetry.

This might get me burned at the stake worse than sneering at ENCODE, but a good scientist has to be…a philosopher. They may not have formal training in philosophy, but the good ones have to be at least roughly intuitive natural philosophers (ooh, I’ve heard that phrase somewhere before). If I were designing a biology curriculum today, I’d want to make at least some basic introduction to the philosophy of science an essential and early part of the training.

I know, I’m going against the grain — there have been a lot of big name scientists who openly dismiss philosophy. Richard Feynman, for instance, said “Philosophy of science is about as useful to scientists as ornithology is to birds.” But Feynman was wrong, and ironically so. Reading Feynman is actually like reading philosophy — a strange kind of philosophy that squirms and wiggles trying to avoid the hated label, but it’s still philosophy.

I think the conflict arises because, like everything, 90% of philosophy is garbage, and scientists don’t want to be associated with a lot of the masturbatory nonsense some philosophers pump out. But let’s not lose sight of the fact that some science, like ENCODE, is nonsense, too — and the quantity of garbage is only going to rise if we don’t pay attention to understanding as much as we do accumulating data. We need the input of philosophy.