The First Lawyer of Behavior Genetics Speaks Out Against Plomin’s Blueprint

In his latest post, the behavioral psychologist Eric Turkheimer writes that in Blueprint, Robert Plomin appropriates his ideas without attribution and twists their meaning. You may have heard of the so-called First Law of Behavior Genetics: All human behavioral traits are heritable.” Turkheimer coined this and two further “laws” to point up ironies in the way behavior genetics was being practiced. “I wasn’t making the case that genes are the ultimate force that explains everything,” Turkheimer writes. “I was suggesting that if everything is heritable, maybe heritability is just an unsurprising part of the ordinary world, not a deep genetic insight into ‘what makes us human.’”

In effect, Turkheimer’s criticism of Blueprint is that its central thesis is based on a simplistic misreading of his (Turkheimer’s) work. This misreading makes Plomin’s book, Turkheimer writes, “simultaneously grandiose, boring and dangerous.” Ouch.

Here are the citations and links for Turkheimer’s original formulations of the “laws”:

 

Robert Plomin’s Use of My Ideas in “Blueprint”

The Eugenics Crusade, on PBS’s The American Experience

I and a large number of my smart and thoughtful colleagues are part of the latest episode of the PBS series The American Experience. This show is, “The Eugenics Crusade.” I’ve seen about half of it and it’s very well done. Television worth watching and getting outraged about!

It airs tonight, Oct. 16, 2018, at 9 pm Eastern and Pacific/8 Central on your local PBS station!

https://www.pbs.org/wgbh/americanexperience/films/eugenics-crusade/

Lies, damned lies, and GWAS

[Blueprint cover]

[Edited, lightly, 10/30/18]

Well, I provoked another kerfuffle in the pages of Nature. And it’s a troubling one, because it suggests a widening culture gap between the sciences and humanities—a gap I’ve spent a quarter-century-and-counting trying to bridge.

The piece in question is my review of Robert Plomin’s new book, Blueprint. I want here to give some context and fuller explanation for that piece, without the editorial constraints of a prestigious journal.

Plomin is a distinguished educational psychologist, American-born-and-raised, who works in the UK, at King’s College London. I have nothing for or against Plomin. I and my editors at Nature worked hard to keep ad hominem attacks out of the piece. Plomin’s book, however, is terrible.

  • “DNA isn’t all that matters, but it matters more than everything else put together” (ix).
  • “Nice parents have nice children because they are all nice genetically.” (83)
  • “The most important thing that parents give to their child is their genes.” (83)
  • “The less than 1 per cent of these DNA steps that differ between us is what makes us who we are as individuals” (9)
  • “These findings call for a radical rethink about parenting, education and the events that shape our lives.”(9)

I could go on—it’s teh Interwebs; people do—but you get the idea. However accurately he may represent the statistics, his statistics misrepresent the biology. With apologies to Benjamin Disraeli, there are three kinds of lies in genomics: Lies, damned lies, and GWAS.

*

Unless you’re some sort of third-rate hack, riding out your tenure on the strength of your rotation in a genetics lab in the mid-sixties, you know better than to say things like this. I presume that you, Gentle Reader, are not such a person. Plomin is not a hack scientifically, but as a writer he is. On the page, he is all exclamation points and pom-pons, thwacking the bass drum with his heel as he dances for DNA. DNA is everything. DNA is the Word. DNA is Love.

That’s a weirdly retrograde view in the postgenomic world. Again, see the above mainstream sciences. Either:

  1. Plomin is such a poor writer that he fails utterly to get across his putatively more nuanced understanding of the genome’s role in biology
  2. Plomin is a cynic, writing things he doesn’t believe in support of a repressive ideology that he does believe; or
  3. He is naive and genuinely doesn’t realize (or care) how this powerful new science is used.

I went with Door #3. As a reviewer of his book I took him at face value as a writer. I take him at his word when he says he is center-left, politically. (No conflict there with eugenic values. There’s a long tradition of leftist eugenics, back to the 19th C.) And I decided it would be unproductive to simply brand him an ideologue. Instead, I took the middle road, presumed innocence but naïveté. I gave him the benefit of the doubt in presuming innocence of intent, although I do think it an odd negligence on his part, given his express interest in using PGS to shape social policy. Seems to me that if you’re engaging with social policy you should be capable of thinking in terms of social policy.

Why is it dangerous? Because it enables and encourages social policy of biological control. That shit scares me. And it should scare you. Plomin is so caught up in his DNA delirium that he says that environmental interventions toward human betterment are futile. Parents, teachers, government officials: Relax, there’s nothing you can do that really makes a difference. DNA will out. Kids will be what they will be, regardless, so don’t waste your money and time. Let’s take that apart.

*

First, short-changing environmental and GxE (genes-by-environment) effects in human personality is literally the entire point of Plomin’s book. I’m not talking about his published, peer-reviewed studies, I’m talking about his latest book. Nor am I damning all sociogenomics work—not by a long-shot. I am damning the simplistic message of this particular book: “DNA makes you who you are.”

Second, then, hidden agenda or not, Plomin’s argument is socially dangerous. Sure, genes influence and shape complex behavior, but we have almost no idea how. At this point in time (late 2018), it’s the genetic contributions to complex behavior that are mostly random and unsystematic. Polygenic scores may suggest regions of the genome in which one might find causal genes, but we already know that the contribution of any one gene to complex behavior is minute. Thousands of genes are involved in personality traits and intelligence—and many of the same polymorphisms pop up in every polygenic study of complex behavior. Even if the polygenic scores were causal, it remains very much up in the air whether looking at the genes for complex behavior will ever really tell us very much about those behaviors.

In contrast—and contra Plomin—we have very good ideas about how environments shape behaviors. Taking educational attainment as an example (it’s a favorite of the PGS crowd—a proxy for IQ, whose reputation has become pretty tarnished in recent years), we know that kids do better in school when they have eaten breakfast. We know they do better if they aren’t abused. We know they do better when they have enriched environments, at home and in school.

We also know that DNA doesn’t act alone. Plomin neglects all post-transcriptional modification, epigenetics, microbiomics, and systems biology—sciences that show without a doubt that you can’t draw a straight line from genes to behavior. The more complex the trait in question, the more true that sentence becomes. And Plomin is talking about the most complex traits there are: human personality and intelligence.

Plomin’s argument is dangerous because it minimizes those absolutely robust findings. If you follow his advice, you go along with the Republicans and continue slowly strangling public education and vote for that euphemism for separate-but-equal education, “school choice.” You axe Head Start. You eliminate food stamps and school lunch programs. You go along with eliminating affirmative action programs, which are designed to remediate past social neglect; in other words, you vote to restore neglect of the under-privileged. Those kids with genetic gumption will rise out of their circumstances one way or another…like Clarence Thomas and Ben Carson or something, I guess. As for the rest, fuck ’em.

These environmental factors are “unsystematic” in exactly the same way that genetic factors are: They do not act in the same way with every child. A few kids will always fall on the long tails of the bell curve: Some will do well in school no matter what you throw at them; others will fail, no matter what they have for breakfast. But the mean shifts in a positive direction. Same is true for genetics. That is literally the entire point of polygenic scores! Every single one of the many thousands of variables that shape something like educational attainment is probabilistic. Genes or environment, we’re talking population averages and probabilities, not certainties. There is no certainty—Plomin himself makes this point repeatedly (and then promptly jumps back on the DNA wagon). To venerate genetics and derogate environment on grounds of being “unsystematic” is at best faulty reasoning and at worst hypocritical.

Plomin is spreading a simplistic and insidious doctrine that says “environmental intervention is futile.” I don’t care whether Plomin himself, in his heart of hearts, wants to ban public education; he gives ammunition to people who do want to ban it. “Race realists” and “human biodiversity” advocates—modern euphemisms for white supremacy—read this stuff avidly. I watched them swarm around the discussion of my review on Twitter, many of them newly created accounts, favoriting tweets from my critics, saving those messages for later arguments.

“But does that mean that EVERYONE using PGS is a white supremacist?” people ask me, their keyboards dripping with sarcasm. No, dummies: It means it’s a risk. I’m giving you a qualitative risk score, a probability. Can’t you apply your own logic to other situations? Again, whether you critics are being disingenuous or naive, the effect is the same.

“So does that mean we CAN’T DO this science? Are you a fascist, trying to stifle scientific inquiry?!?” others gently query me. Again, no, dummies: I’m saying if you do this stuff, a) get your genetic bias out of the way and look at genes and environment, and b) be candid and explicit about your intentions and the risks of misinterpreting the data.

*

The last point I want to make is about historical thinking. A lot of critics said and called me things that initially puzzled me. I had no evidence, they said. It wasn’t a review that I wrote, they complained. I didn’t engage with the book but merely promoted my ideology, they protested.

Eventually it dawned on me: These people don’t understand historical reasoning. They fail to see a historical argument as being evidentiary! After all these years, I still find it surprising that people with PhDs should fail to acknowledge an entire branch of knowledge, a fundamental way of explaining the world. But okay, communication, not war, is what I’m after, so let me lay it out, at least as I see it.

By and large, experimental science explains the world in terms of mechanisms, more or less eternal and independent of time and context. Historical reasoning explains the world through the three C’s: context, contingency, and cause-and-effect through time. Context means that science doesn’t occur in a vacuum. It mattered that Nazi Germany arose after Progressive-era Americans had advanced a scientific program of sterilization and institutionalization of the defective. The Germans, sensing the power of rigid social control founded on scientific authority and finding that authority in American eugenics, modeled their infamous sterilization law of 1932 on Harry Laughlin’s “Model Sterilization Law” of 1922. Contingency means that it matters who did what when. Contingency says, “It could have been otherwise: Why did things turn out as they did instead of some other way?” And by continuity and change I mean that when a historian tries to understand the present in terms of the past.

In short, my review used historical evidence to put Plomin’s book in historical and social context, rather than scientific context, and a number of critics cried “Foul!”, failing to even see historical evidence as evidence.

It’s not foul when a reviewer examines the central claims and aims of a book—you all (critics) just aren’t familiar with the way I did it. Especially with a field such as sociogenomics, which defines itself as interdisciplinary and aims to shape society. You may not read Plomin’s book in social context, but it’s a legitimate and—as attested by the many plaudits I’ve also received for the piece—an important one. Learn your damn history.

Historical thinking is not anti-scientific. Darwin was a historical thinker par excellence. Evolutionary biology, cosmology, geology, paleontology—these are historical sciences. To reason historically is by no means to refute the scientific method. In fact, I would wager that no person can get through life without employing historical reasoning). To do so is to refuse to learn from experience.

Because I did not primarily use scientific evidence in my review, some misguided and uncritical critics peg me as a radical relativist. You got the wrong guy, pal. I studied sociobiology and neuroethology as science for years, under some of the greats. Radical relativists do exist in the humanities and social sciences—I argue against them all the time.

Others, like Stuart Ritchie, bash away at me boneheadedly, picking at details of the piece that make no difference to my argument without the slightest effort try to understand what I am in fact saying. Playing “gotcha” is easier than real debate, but it wins you points with your yes-friends, I guess. Sad!

Historical thinking pulls your eye away from the microscope to look at science as an enterprise evolving over time. For really abstruse sciences, doing so may be mostly an intellectual exercise. But the more social salience a branch of science has, the more important it is to take the long view once in a while. And when you’re explicitly advocating using your science to shape society, it’s incumbent on you to do so.

I identify with distinguished, politically alert scientist-critics like Jonathan Beckwith and Richard Lewontin, who have critiqued their science (even their own science!) in order to make it better. I believe that in science as in politics, dissent is the sincerest form of patriotism.

*

In short, I don’t think sociogenomics is wrong; I think it’s being done wrong, and written about wrong, by people like Plomin. Some people are doing it right. In a forthcoming piece in the MIT Technology Review, I discuss the work of Graham Coop at UC Davis. I won’t go into detail here, but for examples of honest, candid, historically sensitive discussion of PGS research, see this and this. This post is my attempt to do for my critique of PGS what Coop did for his own PGS research (which, for the record, I admire). By and large, I think the biologists have been doing better at avoiding deterministic talk than the social scientists like Plomin—although some social scientists, like the sociologist Dalton Conley at Princeton, do at least have complex positions worth taking seriously.

Plomin does none of this. Instead, he gives us a simplistic and distorted view of the role of heredity in behavior that causes much social mischief. We can watch some of that mischief in real time as the white supremacist trolls swarm around this debate like yellow-jackets around an open soda. Other risks we can infer from careful comparison with historical examples—looking at both the similarities and the differences between Blueprint and previous attempts to use heredity to shape social policy. The argument in Blueprint—that “DNA makes us who we are” and environment “is important but it doesn’t matter”—is an idea grossly wrong on many levels. It’s not supported by the evidence and it’s socially dangerous.

And someone’s got to call bullshit on it.

TBT: Galàpagos Tortoise

I’m excited to learn that the entire 15-year back-catalog of the quirky and wonderful The Believer magazine is now online with no paywall. Here’s one of my favorite creative nonfiction pieces, written on the plane home from Quito in 2004. https://believermag.com/reptile-galapagos-tortoise/ 

 

Your DNA is Weirder than You Think

My review of She Has Her Mother’s LaughCarl Zimmer‘s wonderful new book on heredity, just appeared in the latest number of The Atlantic. The book casts a long shadow, covering history, science, medicine, and agriculture, all woven together by Zimmer’s energetic yet reflective reportage.

she-has-her-mother's-laugh-cover

My essay plucked just one theme out of many in the book— Genotopia readers will recognize my interest in destabilizing the textbook gene as the self-evident foundation of all life. Zimmer does this beautifully, describing not just one heredity but many, interwoven, flowing in many directions at once. It helps put heredity on a more equal footing with environment and experience; something that seems to me both politically important and profoundly true.

She Has Her Mother’s Laugh earns the Genotopia Anti-Deterministic Seal of Approval! 

Streamers

IMG_2134 sm
A spring outflow pouring into another pool. These small streams are home to rich communities of microbes.

These hot springs—often as clear as swimming pools, as though methodically poisoned to kill algae and small plants—are chocked with life. Even pools of boiling sulfuric acid have diverse communities of microbes. They drift invisibly in the crystal-clear center, down to depths of many meters. They can live without light or oxygen. Around the rims, colored bands of brown, red, yellow, and green are national borders. On one side, one kind of life thrives and repels its enemies; on the other, one of those enemies has found the tangy land of sour milk and rancid honey.

“There’s more diversity in these pools,” Everett Shock tells me, than all the macroscopic life you can see here at Yellowstone–pine trees, bison, bears, elk, shrubs, grass…all of it.”

The springs runneth over. The outflow finds the lowest point of exit from the pool and winds down the hill, where it braids with many others to form Geyser Creek. To the untrained eye, these outflows are unspectacular, compared to the pools. But Shock helps me learn to see. These outflows are rich with life and form laboratories for microbe hunters.

They present a wealth of different environments. At one spot that I’d been inclined to hop across, Shock pulled me close and made me look. Two outflows merged. One was acidic, the other basic. In a little wedge just above the confluence, was a patch of green, where photosynthetic bacteria thrived. “This boundary may represent the beginning of conditions under which photosynthesis is viable,” he said. “Looking at the bands is like going back in time.”

Two outflows merge, with a wedge of photosynthesis between them.
Two outflows merge, with a wedge of photosynthesis between them.

Here, you can often see the microbes—or at least their cities. The scientists call them “streamers.” The tiny bugs build ribbons of minerals that undulate like hair in the current. Some are pink, some green, others a nearly colorless grayish. The least pretty are some of the most interesting. Even though plenty of sunlight and oxygen is available to them, they don’t use it. They are anaerobic and draw their energy from hydrogen produced in the Earth’s mantle. I was not the first to think the colorless streamers looked like mucous; one pool particularly rich with them was called “Spent Kleenex.”

Let’s say you arrived on Earth to take samples, and you took an enormous bite out of a skyscraper—a couple hundred cubic feet, say. You load it onto your ship for analysis. Your instruments would record a lot of steel, glass, and plastic…and a small proportion of living material. Perhaps your scoop grabbed an administrator and a middle manager—no more than a few percent of the total mass of the sample. Would you taste it?

Nom nom nom.
Nom nom nom.

On an earlier field trip, apparently at a moment of boredom and certainly out of Shock’s earshot, one student pointed to some streamers and said to another, “I’ll give you a quarter if you eat one of those.” To the surprise and delight of the group, she plucked one out, blew on it a few times, and popped it into her mouth. Peals of laughter rang out through the field site. “How does it taste?” they asked, wanting to know.

“It’s flavorless,” she replied, “But it’s crunchy.”

When, several years later Shock’s group performed a chemical analysis on the streamers, they found that they contained only about two percent organic carbon. The streamer is unquestionably a product of biological processes, but almost all of the carbon in it comes from inorganic sources. It’s a mineral structure built by the community; it is their skyscraper.

What are the streamers for? The paleontologist Stephen Jay Gould was fond of pointing out the dangers of thinking that every biological structure must have a purpose, but it’s worth asking the question, judiciously. One possibility is that the streamer is simply sandy poop—not functional but merely a waste product resulting from their metabolism. The underlying geology in this region is heavily based on silica. If, for example, you needed to get rid of a lot of silica, it might stick together and remain bound up with the sticky, mucousy microbes.

Another possibility is that the streamer is a fishing net, a matrix that captures nutrients as they float past. Life and mineral could be inseparable; without their sandy sieve, the microbial community might not survive in the stream, which must feel a bit like a Himalayan peak to microbes accustomed to living in dark, toasty, anoxic pools of boiling sulfuric acid.

Streamers thus lead us to think of life as many astrobiologists do. We are all geo-biological systems. We are suffused with minerals, from the salt in our tears to the iron in our blood. The most ancient biological catalysts have metal centers, probably acquired from the surrounding rock in an undersea geothermal vent four billion years ago. Since then, ground rock and metal have cycled constantly through our bodies.

We are streamers, we are iron, and we’ve got to get ourselves back to the geothermal garden.

Microbe Safari II: Geyser Creek

20160723_134929
The Geyser Creek field of thermal pools, from a rise above.

This microbe safari is risky business. We are an hour’s bush-whacking off the trail, in the Yellowstone back-country, amid a field of geothermal pools. Most of the pools are at or near the boiling point. Some are alkaline, while others are as sour and corrosive as stomach acid. There was danger in nearly every step. The whole district is shot through with potholes, each one potentially deadly. Some are gurgle with boiling water. Some belch steam. To put a foot in one could mean vicious burns. To break the thin crust of silica and fall through would be deadly. (Someone died not far from here a month ago, straying off the boardwalk unguided. Fell into a pool. There were no remains to recover.) The place also smells like farts.

IMG_2123

Note the dangerous shelf on the far side. Approaching from that side, the ground appears solid right up to the thin, brittle edge.

After nearly twenty years of working around geothermal springs, Professor Everett Shock has developed a remarkable eye for reading these treacherous landscapes. Holes a few inches wide could be twenty or more feet deep and indicate thin ground. A particular kind of crusty formation on one side of a pool indicates danger, although similar crusts can be perfectly safe. One rule of thumb is to keep on the grass. Typically, as one approaches a pool, the soil becomes too harsh and hot to support macroscopic plants; a small, barren rock “beach” surrounds the pool. However, in some instances, grass may grow near the water while a barren but solid patch nearby is more secure. Shock can tell the difference. Soon we had all fallen into the habit of carefully checking each step before we took it. While moving, we kept our eyes down, scanning a radius of two yards or so around us for hazards. As we moved through the landscape, the ground burbled, glugged, steamed, spewed, belched, and boiled. It looked like a world out of Star Trek. Traversing it felt like crossing a minefield.

The pay-off for a microbe-hunter here, though, is huge. In this remote bit of the park, an area the size of a couple of football fields, one can find, Shock says, “a little bit of everything.” “This pool is acid,” he said, pointing as we gazed over the hot spring field, “that one right next to it is basic. One is spitting out iron, another is bright blue.” Some are as clear and inviting as a swimming pool, others are turbid and tinted, others are “mudpots,” boiling mud-puddles meters deep. One student, Melody, is doing her thesis on them. Melody judges the value of a site by its mudpots. IMG_2125 sm

“When we started,” Shock said, “we gave the pools simple names. Pool 1, pool 2, pool 3. But we found we couldn’t keep track of which was which. So we started giving them stupid names.” By “stupid” he means silly. Some are actually quite clever. A good name is mnemonic and funny–either witty or vulgar. Today we were sampling seven pools: Jackhammer boils violently and is surrounded by loose rocks the size of footballs. Bat Pool is vaguely bat-shaped. As we approached it, it shot up a burst of gas and water. “Hello, Bat Pool,” Shock said. “It’s nice to see you too.” St. Blucia is a milky blue. Spitting Croissant is crescent-shaped and harbors great colonies of mucousy microbes. Over the years, the pH and conductivity in Spitting Croissant have fluctuated wildly. Evolutionary theory would suggest that different species would flourish under the different conditions; physiology, however, offers the possibility that Spitting Croissant microbes are selected to tolerate a wide range of conditions. One of the students is working on finding an answer. The landscape here changes year to year. Last year, Dirty Donut was in fact donut-shaped. This year, we find the water has breached one of the walls, creating a wide outflow. Corner Thing I imagine being named at the end of a long day. Finally, lording over the other pools on the hill above, is the majestic Empress Pool.

IMG_2113 sm
As inviting as a spa…but deadly.

The technician, Vince—6’4”, about 220, decked out in a flannel shirt, aviator glasses, and a broad-brim hat with a jaunty long feather in the hatband—is integral to the operation. He carries the heaviest pack, keeps track of logistics, and watches over the group. Shock calls him “Uncle Vince.” Uncle Vince also had the painstaking job of collecting dissolved gases in the water samples. As the dry, thin mountain air warmed, sleeves rolled up, shirts came unbuttoned. Uncle Vince revealed a “Led Zeppelin Tour 1977” t-shirt. When I commented on it, Shock began singing “Whole Lotta Love” in a Robert Plant falsetto, playing air guitar as he puttered around, checking on the students’ progress. “Oohh baby, I ain’t foolin’/Gonna send you, back for schoolin’/Waaaay down inside…”

The sampling itself is simple enough, but it’s a delicate task. Many pools are undercut, leaving thin, treacherous ledges around part or all of the rim. Shock ensures that the students collect from a safe distance; the scoops have six-foot handles and can be extended to twelve feet. Usually one side of a pool is determined to be the sturdiest. Then the researchers have to work out a safe path across the minefield between camp and the pool. “Do you know the way to Jackhammer?” a student may ask, though the pool is in sight, as far away as a ten-year-old can throw a stone. Frequently, the answer is “Ask Everett.”

Shock’s students and technician, men and women alike dressed in variations of Early Indiana Jones, set up a field lab in a grassy spot with a bit of shade. Each member of the team got right to work on his or her designated task. One measured temperature, pH, and conductivity. Another collected water samples, which would be divvied up for later analysis: sulfur, hydrogen, various minerals, trace metals, organic and inorganic carbon, and small organic acids such as formate and acetate, which can be “bio-signatures”—characteristic products of life. Another student collected samples of the sediment in each pool. In the muck live microbes that don’t need oxygen or food. Sometimes the students shared samples. “Is there any leftover Spitting Croissant water?” is a question that makes sense here.

A typical biology lab is like a factory. The students are lined up at benches organized into “bays,” long tables jutting out from the walls with two student stations on each side. They work independently, bantering and listening to music as they carry out their often-repetitious tasks and shuttle between their bench and the instruments around the lab. Out in the field, the students arrayed themselves into a lumpy version of the lab, tucking themselves into niches, shady ones if possible, and often with bushes or scruffy trees demarcating the boundaries. They bantered as they carried out their repetitive tasks, while some picked their way carefully out to the next pool to collect their sample. Jokes and teasing were lobbed over the bushes like playful water balloons. The group killed about an hour seeing if they could name a mythical animal for each letter of the alphabet. Impressively, they could.

Shock presided over the operation like an orchestra conductor, keeping track of and checking in on each project, cueing the entrances and exits as necessary and then glancing out over the minefield and grabbing his walkie-talkie to warn a student of a hazard and suggest a safer route. Oddly, the group settles in a kind of normalcy, everyone at his or her task, the day ticking away. It’s just like being in the lab, except if you stray by a couple of steps you could literally melt on your way to getting a drink of water.

[next: Streamers]

Microbe Safari

We were an eleven-person ant-line marching down the boardwalk, laden with oversized, overstuffed backpacks, coolers, and tiny buckets on six-foot handles. The path to Artists’ Paintpot bore left, preparing to ascend. Steam plumed out of the Earth ahead on the right. Our leader veered left and stepped off onto spongy moss and plunged into scrubby pine forest. For the next hour, we bushwhacked our way around the mountain and up the adjacent valley. We pushed through the “green blizzard,” a limb-scratching forest of young pines. We scrambled over fields of fallen and rotting logs, as though we’d wandered into an over-sized game of pick-up-sticks. We crossed a laughing, bathtub-warm mountain stream and followed it through bogs and uphill. At last, we emerged into a primordial landscape—a barren field pocked with bubbling pools, steaming potholes, and boiling mud. One would not be surprised to see a Triceratops make its way gingerly across it. As we entered the field site, steam and water blasted out of a pile of rocks, a hundred feet into the air, as if saluting. “Hello, Avalanche Geyser,” said our leader, Dr. Everett Shock. “Nice to see you, too.”

Avalanche Geyser, Yellowstone National Park
Avalanche Geyser, Yellowstone National Park

I am trying to get a handle on the origin of life. One way to do that is to study organisms and environments in our world that approximate features of that ancient one. So I tagged along with Shock, to the back country of Yellowstone National Park. Its geothermal pools and springs are among the harshest habitable conditions on the planet. But in them life indeed thrives: diverse communities of microbes that most scientists place on the shortest, deepest branches of the tree of life. From them, Shock gleans clues to how early life may have coped with similar conditions. He goes to Yellowstone every summer with his group “GEOPIG,” the Group Exploring Organic Processes in Geochemistry.” The GEOPIGs’ motto is, “The biochemistry we have is the biochemistry Earth allows.”

Barring a time machine, anyone trying to think about the origin of life has to make assumptions. Everyone has their own model, which stresses certain variables and ignores others. In recent years, something approaching consensus has emerged that life probably arose in or around an undersea geothermal vent, about four billion years ago. Such vents still exist, at sites such as Lost City, a warm alkaline vent system in the mid-Atlantic. Some researchers study Lost City itself; others make model Lost Cities in the lab (see my previous piece about my visit to the lab of Laurie Barge and Mike Russell).

Hot springs provide another point of attack. Every summer, Shock comes to Yellowstone for two weeks to gather samples from about sixty pools in remote corners of the park. One pool is basic (high pH) while a few feet away lies one that is essentially boiling sulfuric acid. Temperatures range from the forties (centigrade) to the nineties. Conductivity, sulfur, chloride, metals, organic vs. inorganic carbon, dissolved hydrogen and oxygen, amount and quality of sediment, and other factors also vary widely. All of this data goes into a database that characterizes each pool in seventy-four-dimensional space. Analyzing the samples gathered during these two weeks keeps Shock’s team busy the other fifty.

[DO NOT try this at home, kids. Even with a back-country permit, it is foolish to go poking around these pools unless you know what you’re doing. Last month, a young man wandered off-trail and fell into a Yellowstone hot springThere were no remains to recover.]

While not identical to the early Earth, Yellowstone hot springs share some qualities with what many scientists believe were life’s initial conditions. Besides being high in temperature—similar to the “warm” hydrothermal vents that many think were the cradle of life—they are rich in the elements of the “Fe-S-C-H-O-N” system; iron, sulfur, carbon, hydrogen, oxygen, and nitrogen.

“What we’re doing is looking at the geochemical conditions that provide materials that life can take advantage of,” Shock told me, as the beautiful but deadly pools bubbled around us. “Maybe that can help us think clearly,” he said, about how some of the first organisms coped with similar environments. Life needs a carbon source, a constant source of energy, plenty of hydrogen, and important minerals such as iron, sulfur, and phosphorus. Good evidence exists that life emerged in water close to the boiling point, without free oxygen, and that it derived its energy by reducing CO2 to methane (CH4). After it became free-living, some microbes developed the ability to capture energy from sunlight rather than geothermal heat. The emergence of photosynthesis, about two billion years ago, was a huge game-changer: the oxygen that is a waste product of photosynthesis is poisonous to anaerobes. But life that could tolerate and then exploit oxygen survived the so-called Great Oxidation Event. Our modern world was off and running.

Much of this process is recapitulated in the Yellowstone pools. “There is more [genomic] diversity in these pools than in all the life you can see around us,” Shock said with an implicit sweep of the hand across the horizon. “Bison, Grizzlies, wolves, trees, grass, us,…everything.” (Indeed, one 1998 study found that none of 31 unique 16S ribosomal RNA sequences found in one pool matched that of any known organism.) Many microbes look similar under a microscope—they are the usual balls and rods and filaments. But in the 1970s, Carl Woese and George Fox showed that what used to be called the “Monera” in fact comprised two fundamentally different forms of life. Through a painstaking analysis of the RNA in ribosomes, Woese and Fox designated a new kingdom—later upgraded to a new category: domain—they called Archaea.[1] Although both a bacterium and an archaean are prokaryotic microbes, lacking a membrane-bound nucleus, they differ in the genes that encode and the proteins that compose some of life’s most ancient, fundamental structures. Among them are the various components of the ribosome itself, as well as membrane proteins key to metabolism and other cellular molecules present in some form in all organisms.

Shock’s approach, like every other in origin-of-life research, has its critics. How can you study the origin of life in an environment that’s already full of life?, some ask. How can you understand the early, oxygen-free world in pools with substantial levels of dissolved oxygen? Life has terraformed Earth almost beyond recognition. Just before the emergence of life, the Earth would have been mostly if not entirely ocean. There was little or no free oxygen, so the first life would have made its living anaerobically.

Shock doesn’t pretend that these pools and their inhabitants are identical to those at the dawn of life—he bristles at terms such as “primitive” or “living fossil.” Darwinism does not say that humans descended from chimpanzees; it says that we share a common ancestor that lived more recently than primates’ common ancestor with birds. Similarly, the microbes in Yellowstone hot springs are living very much in the present, but their lineage branched off the tree of life down close to the root. Studying them and their environments can help us understand how these deep lineages respond to particular conditions of heat, pH, mineral concentrations, and so forth, that were important in early evolution. This information can then inform models of how life’s basic biochemistry emerged.

Octopus spring, home of Thermus aquaticus.

The work would yield dividends even if it didn’t shed light on the origin of life. Our first day in Yellowstone, Shock took us to see Octopus Spring. Located just a few miles from Old Faithful, Octopus was the first pool where microbes were discovered living above the temperature at which life was thought to be sustainable, by the great microbiologist Thomas Brock, in 1966. Soon thereafter, and nearby at Mushroom Spring, Brock discovered Thermus aquaticus[2] In the early 1980s, the brilliant but eccentric chemist Kary Mullis, then working at Cetus, one of the early California biotech companies, used the DNA polymerase from T. aquaticus in developing one of the most potent tools in the history of biotechnology. Because it is adapted to high temperatures, the so-called taq (for “T. aquaticus”) polymerase was ideal for Mullis’s polymerase chain reaction, or PCR—one of the principal tools for amplifying a small sample of DNA up to billions of copies for analysis. Mullis received a Nobel Prize in Chemistry in 1993 for the invention.

[next: the pools at Geyser Creek]

[1] For a history of Woese’s work, see Jan Sapp’s The New Foundations of Evolution (2009).

[2] Brock, T. D., & Freeze, H. (1969). Thermus aquaticus gen. n. and sp. n., a nonsporulating extreme thermophile. J Bacteriol, 98(1), 289-297. See also Brock’s “The value of basic research: discovery of Thermus aquaticus and other extreme thermophiles” (1997).

Bison trouble

Just returned from a trip to Yellowstone National Park, where I tagged along with scientists as they bushwhacked into the back country to study geothermal pools and their microbial communities. It’s dangerous work; one of the hazards is hiking into a remote site, only to find that it’s overrun with bison. Or, maybe one is simply walking up the road in front of you, holding up traffic.

What can hot springs tell us about the origin of life? Stay tuned to find out…

[next: Microbe Safari]20160722_093857-1 20160722_094050

Wait, there’s a fly in my soup

My new piece in Nautilus Magazine is up. It’s on some exciting research going on at NASA’s Jet Propulsion Lab in Pasadena, on the origin of life. Most of us grew up with the “primordial soup.” Forget all that–hydrothermal vents are where it’s at. No one knows how life really started, of course, but this theory is pretty persuasive, because it obeys one of the central laws of the universe: entropy, the tendency for energy to go “downhill.” Take a look. 

Also, Nautilus Editor-in-Chief Michael Segal did an interview with me that’s now online. It’s a wide-ranging conversation, in which we talked about the history of science as a discipline, women in science, the Nobel Prize, and more. And it’s broken into nice, bite-sized pieces, perfect for brief lunch breaks and short attention spans.

Enjoy!

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