Epigenetics ain’t magic

I just got a notice of an Epigenetics Conference in Portland, Oregon. It made me cringe. It’s infuriating because epigenetics is actually a very important concept in development, but there’s this terrible misperception among the public that it’s a magical shortcut for evolution. I was also a bit primed for it by the mention of epigenetics on Larry Moran’s blog.

The Humanists of Greater Portland™ is supporting the 2014 Epigenetics Conference being held on Saturday 5 April 2014. Epigenetics is a relatively new field of science that looks at how the environment affects one’s genetic make up. In former times, it was thought that it took generations to change one’s genetic make up but studies now suggest it can happen over a matter of weeks or months. What one eats, their environment, their activities etc. all can alter ones genetic make up and this can greatly affect one’s health. Even the environment of the mother can affect the genetic make up of the baby in the womb.

No, it’s not new. Conrad Waddington coined the term “epigenetics” in the early 1940s. He was explaining how development is modulated by gene regulation, and that there is a multigenerational pattern of restriction of cell fates within a lineage…and that’s a concept that’s at least as old as Wilhelm Roux.

It’s broader than just environmental effects. We can talk about epigenetic modification within an embryo, as a consequence of a clocklike sequence of switches, for instance. It really is a well-known, long studied developmental process.

It does not change the “genetic makeup”. Epigenetics affects the expression of genes without modifying any sequence information. Thinking that it represents rapid evolutionary change is the major misconception that leads people to think the timing is somehow radical. It isn’t. A mutation changes the “genetic makeup” of a cell — for realz — in a fraction of a second. Get up and run a lap around the room, and you’ll get a rapid change in your physiological state in a fraction of a minute. Move from your flatland home to Denver (or vice versa) and you’ll get long term changes to the constitution of your blood in a matter of weeks. None of these represent a revolution in how we think about evolution.

You want to greatly affect your health, quickly? Don’t drink any water for a day. Or drink a couple of Big Gulps worth of sugar water. That’ll have about the same effect on evolution as epigenetic modulation.

Fortunately, it’s just the general blurb for the conference that set my teeth on edge. The descriptions of the presentations sound much more focused and of reasonable and appropriate scope. It should be informative. But please, pop culture summaries of epigenetics make PZ cry.

Some people are thinking I’m denying any role for epigenetics in evolution. No — it’s just not the role some less informed people think it is. What epigenetic modification does is broaden the range of phenotypes produced by a given genotype, allowing more genetic variation to persist in the population. That surely does have some effect on evolution, but it’s somewhat more indirect than the Lamarckian mode pop culture assigns to it.

It’s one thing that allows genetic assimilation to occur, for instance. But if you think people misunderstand epigenetics, just wait until you hear what they say about genetic assimilation.

If you’re still baffled, I wrote up an introduction to epigenetics a while back. I’ve also got a couple of examples of genetic assimilation.

Potential disasters pimpling the whole country

Your must-read article for the day is When the Rivers Run Black, the story of the Kingston, Tennessee coal ash spill. The walls of a gigantic reservoir pond containing toxic waste produced by a coal-fired power plant ruptured, pouring 5.4 million cubic yards of coal ash into the environment. It was the largest industrial accident in US history.

I was reading it and thinking about where my power is coming from — about half of Minnesota power comes from coal plants — and feeling grateful that none of those plants are anywhere near me. We like it when North Dakota builds their monster coal-burning plants over there in their weaker regulatory environment, and we just reap the benefits of cheaper electrical power over here. And then I read about the Kingston cleanup, and what they had to do with all the slimy sludge.

For months, train cars lined up to be loaded with sludge dredged from the river. The sludge was then carted down to Uniontown, Alabama, a mostly poor, mostly black county, where an enterprising commissioner decided that taking the waste was an economic opportunity. The county ended up taking about 4 million tons of it and dumped it in a landfill—for the price of just $4 million.

It is not unusual that a place like Uniontown ended up with the Kingston waste: Coal ash is almost always dumped in communities that don’t have the political or financial muscle to reject becoming other communities’ trashcans. According to a 2012 report, of the nearly six million Americans who live within three miles of a coal-fired power plant, 39 percent are minority, and the average per capita income is $18,400.

Damn. I am a privileged person, all right.

Fortunately, Minnesota is improving energy efficiency and regulating power plants more, so at least we’re slowly getting better. Although I notice now something in that happy report that was also discussed in the Kingston article: all that’s getting mentioned is emissions, not the accumulating solid waste from the plants. That waste is loaded with heavy metal poisons, but the EPA is dragging its heels, reluctant to even classify it as hazardous.

The paper they don’t want you to read!

The climate change denialists are a bit thin-skinned; they’ve also been exposed as a bit on the wacko side. The journal Frontiers in Psychology is about to retract a paper that found that denialists tend to have a cluster of weird beliefs (NASA faked the moon landings, the CIA was in charge of the assassination of political figures in the US, etc.) because the denialists screamed very loudly.

This outrage first arose in response to a paper, NASA faked the moon landing–Therefore (Climate) Science is a Hoax: An Anatomy of the Motivated Rejection of Science (pdf) which analyzed voluntary surveys submitted by readers of climate science blogs, in which the respondents freely admitted to having a collection of other beliefs, in addition to climate change denial. That paper found something else interesting, and was the primary correlation observed: a lot of denialists are libertarians. Are you surprised?

Rejection of climate science was strongly associated with endorsement of a laissez-faire view of unregulated free markets. This replicates previous work (e.g., Heath & Gifford, 2006) although the strength of association found here (r ~.80) exceeds that reported in any extant study. At least in part, this may reflect the use of SEM, which enables measurement of the associations between constructs free of measurement error (Fan, 2003).

A second variable that was associated with rejection of climate science as well as other scientific propositions was conspiracist ideation. Notably, this relationship emerged even though conspiracies that related to the queried scientific propositions (AIDS, climate change) did not contribute to the conspiracist construct. By implication, the role of conspiracist ideation in the rejection of science did not simply reflect “convenience” theories that provided specific alternative “explanations” for a scientific consensus. Instead, this finding suggests that a general propensity to endorse any of a number of conspiracy theories predisposes people to reject entirely unrelated scientific facts.

Oh, how they howled. Even libertarians seem to be embarrassed at being affiliated with libertarians, I guess. And conspiracy theorists, too? Why, the accusation itself is clearly evidence that there’s a conspiracy out to get them. They protested that because the respondents to the survey all found it through mainstream science blogs, all the responses were false flag operations put out by Big Climate.

What they didn’t realize was that they were generating more data to support the hypothesis. The authors of the first paper then wrote a second paper, the one that is now being retracted by the cowardly publisher, called Recursive Fury: Conspiracist Ideation in the Blogosphere in Response to Research on Conspiracist Ideation, in which they scanned public posts and comments on the first article, and analyzed the text for evidence of conspiracist tropes (it’s a nefarious scheme, they’re out to get us, it’s an organized movement to defeat us, etc.) and found that yes, conspiracist reasoning was quite common on climate change denial blogs.

They also rebutted some claims. The claim that the authors never bothered to contact the denialist blogs to host their survey was shot down pretty easily: they had the email, and further, they had replies from denialists who later claimed they never received any request to host the survey.

Initial attention of the blogosphere also focused on the method reported by LOG12, which stated: “Links were posted on 8 blogs (with a pro-science science stance but with a diverse audience); a further 5 “skeptic” (or “skeptic”-leaning) blogs were approached but none posted the link.” Speculation immediately focused on the identity of the 5 “skeptic” bloggers. Within short order, 25 “skeptical” bloggers had come publicly forward9 to state that they had not been approached by the researchers. Of those 25 public declarations, 5 were by individuals who were invited to post links to the study by LOG12 in 2010. Two of these bloggers had engaged in correspondence with the research assistant for further clarification.

Those emails were also revealed in a Freedom of Information Act request.

The squawking reached a new crescendo. Steve McIntyre wrote a strongly worded formal letter demanding that the defamatory article be removed, and accusing the authors of malice. Further, they complained that analyzing the content of blog posts and comments, public, openly accessible work, was an ethics violation.

Ludicrous as those claims are, Frontiers in Psychology is apparently about to fold to them. For shame.

You know, my university had a meeting with our institutional lawyers yesterday — I was called in to attend the information session for some reason, like having a reputation as a trouble-maker or something — and I was impressed with their professionalism and their commitment to actually defending the faculty and staff of the university. I guess not every organization is lucky enough to have good lawyers of principle.

Oh, well. All I can say is that, thanks to the denialist ratfuckers, now everyone is going to be far more interested in reading the two papers by Lewandowsky and others. I recommend that you read Motivated rejection of science (pdf) and Recursive fury(pdf) now, or anytime — they’re archived on the web. You might also stash away a copy yourself. You make a denialist cry every time you make a copy, you know.

The first author on the papers, Stephan Lewandowsky, has a few comments.

The strategies employed in those attacks follow a common playbook, regardless of which scientific proposition is being denied and regardless of who the targeted scientists are: There is cyber-bullying and public abuse by “trolling” (which recent research has linked to sadism); there is harassment by vexatious freedom-of-information (FOI) requests; there are the complaints to academic institutions; legal threats; and perhaps most troubling, there is the intimidation of journal editors and publishers who are acting on manuscripts that are considered inconvenient.

Watching Nate Silver squander his reputation

Nate Silver is putting together this journalism startup, and it’s already on the path to failure. I mentioned his oblivious sexism the other day, and now we learn the name of the ‘science’ writer he’s bringing to to cover the environment.

Nate Silver’s highly anticipated data-driven news site FiveThirtyEight launched on Monday, with a controversial figure covering science issues. Silver has brought on Roger Pielke, Jr., a professor of environmental studies at the University of Colorado Boulder, as a contributing writer – a political scientist who comes with a long history of data distortion and confrontations with climate scientists.

That last sentence is a lovely example of understatement. Pielke, both Jr. and Sr., are denialist kooks.

I don’t think I’ll bother reading FiveThirtyEight. “Data-driven,” hah.

That big physics announcement explained

You want more on the discovery of gravity waves from the Big Bang? It’s beyond my pay grade, so you’ll have to mosey on over to SciAm for the plain English summary.

Physicists have found a long-predicted twist in light from the Big Bang that represents the first image of ripples in the universe called gravitational waves, researchers announced today. The finding is direct proof of the theory of inflation, the idea that the universe expanded extremely quickly in the first fraction of a second after it was born. What’s more, the signal is coming through much more strongly than expected, ruling out a large class of inflation models and potentially pointing the way toward new theories of physics, experts say.

And why should we care?

The timing of inflation, in turn, tells physicists about the energy scale of the universe when inflation was going on. BICEP2’s value of r suggests that this was the same energy scale at which all the forces of nature except for gravity (the electromagnetic, strong and weak forces) might have been unified into a single force—an idea called grand unified theory. The finding bolsters the idea of grand unification and rules out a number of inflation models that do not feature such an energy scale. “This really collapses the space of plausible inflationary models by a huge amount,” Kamionkowski says. “Instead of looking for a needle in a haystack, we’ll be looking for a needle in a bucket of sand.” Grand unified theories suggest the existence of new fields that act similarly to the Higgs field associated with the Higgs boson particle discovered in 2012. These new fields, in turn, would indicate that other, heavier Higgs boson particles also exist, although with masses so high they would be impossible to create in any traditional particle accelerator. “This measurement is allowing us to use the early universe as a lab for new physics in energy ranges that are otherwise inaccessible to us,” Kamionkowski says.