Author: russhodge

I am a science writer at the Max Delbrück Center for Molecular Medicine in Berlin, author of fiction and popular science books, an artist, and a professional musician who performs on the viola da gamba and Medieval and Renaissance stringed instruments. I edit manuscripts of all types and teach the full range of scientific communication skills. I am doing theoretical work in this subject - see for example https://goodsciencewriting.wordpress.com/2018/03/11/ghosts-models-and-meaning-in-science/

My work in early music

For those of you who don’t know about my other professional career, the “Anglistenchor” of the University of Heidelberg and my instrumental ensemble “Syntagma” are performing the second of two concerts under the title “Strike the viol” in Heidelberg this Sunday, July 27, 7pm at the Peterskirche. If you want to hear Baroque music like you’ve never heard it before, come by! Tickets can be purchased on-line or directly at the concert. You can see a short interview with me and the conductor and a member of the choir here. This time the composers are JS Bach, Purcell, and their contemporaries.

…and now back to science…

Another “before and after” text from a new science writer

Jon Paul Hildahl, a postdoctoral researcher at the University of Oslo, wanted to try some popular science writing and produced this text. We worked on it a bit together and then he revised it. Here are the “before” and “after” versions. I’ll provide some commentary in the next post. The main issues were editing – removing redundant or unnecessary language, unraveling a bit of the science, and providing illuminating explanations for a more general audience. Thanks for providing this, Jon – you truly have a future as a science writer (alongside your own excellent research, of course). Jon currently works in the group of Gareth Griffiths at the University of Oslo, where I conduct a week-long course every December for Masters’ students. It’s always one of the highlights of my year. Thanks to Jon for letting me post this, with his name.

BEFORE:

Regulation of immunity and disease resistance by commensal microbes and chromatin modifications during zebrafish development
Jorge Galindo-Villegas et al 2012 PNAS

It is obvious that we are not alone in this world, but it is becoming increasingly clear that we are not even alone in our own bodies. We are covered inside and out by small critters called microbes that include many helpful bacteria, archaea and fungi, collectively called commensals. The resident population that we carry throughout much of our life is called our microbiome. It is very abundant; our body contains 10 times as many microbial cells as human cells. It is not surprising then that these cohabitants play an important role in human health. Indeed their effect on animal health is an area of active research. In particular, it is becoming clear that a little dirt is good for you, especially in your early formative years. It has been shown in multiple animal models that microbes in the environment during early development can help establish the immune system and protect the host from attack by disease causing bacteria. This study helps to clarify the mechanisms by which this initial microbial exposure is controlled at the cellular and genetic level using a powerful fish model.

These researchers have used two powerful models to delineate the role of commensal bacteria during development of the immune system: 1.) germ free condition in 2.) the zebrafish model. Many studies of the role of environmental bacteria use germ free models. This provides a reference to what would happen in the absence of resident microbes. This can then be compared to the natural situation of exposure and colonization by commensals. Fish are exposed to a rich microbial ecosystem in their aquatic environment, which suggests that they have evolved ways to deal with environmental microbes both good and bad. You might ask, however, what a fish can tell us about human biology? Luckily, many if not most developmental processes are conserved among distantly related animal groups. Additionally, the zebrafish have many advantages as a research animal since they develop quickly in transparent eggs that can be easily followed and manipulated. They also have a well-characterized genome and sophisticated genetic tools that allow researchers to add or subtract gene products and measure the level of gene expression. It is known that the initial and fast acting (also called innate) immune system develops within days and before hatching for zebrafish.

In this study, the authors were able to follow the immune response of zebrafish from the time they hatch, at around two days after fertilization, and for the first days of exposure to the external environment when commensal colonization is believed to occur. They showed that zebrafish have a rapid and punctuated innate immune response after hatching, peaking after one day and then decreasing. This initial activity improves the response of early immune cells, providing a better protection against pathogenic bacterial infection and tissue damage compared to fish reared in germ free conditions. The researchers were also able to show that innate immune cells respond by a conserved mechanism, involving a intracellular response pathway by the myeloid differentiation primary response protein 88, MyD88. Another important finding from this study is that epigenetic regulation, which modifies the ability of genes to be expressed, modifies the immune response such that a robust emergency response is in place in case of infection or injury, while reducing the risk of adverse immune effects due to excessive inflammation by providing initial responders (antimicrobial effector proteins) that are not limited by epigenetic regulation.

AFTER:

The ying and yang of germ warfare

None of us go through life alone – not even within our own bodies. We are covered inside and out by microbes that include many helpful bacteria, archaea and fungi, collectively called commensals. The resident population that we carry throughout much of our life is called our microbiome. It is very abundant; each body contains 10 times as many microbial cells as human cells. It is not surprising then that these cohabitants play an important role in human health, an area of active research. One of the results is to show that a little “dirt” is good for you, especially in your early formative years. Studies using several animal models show that during early development, environmental microbes help establish the immune system and protect the host from disease-causing bacteria. A recent paper entitled, “Regulation of immunity and disease resistance by commensal microbes and chromatin modifications during zebrafish development” uses a powerful fish model to provide new insights into the mechanisms by which this early microbial exposure mediates cellular and genetic responses.

Jorge Galindo-Villegas and colleagues at the University of Murcia in Spain have compared zebrafish in two settings to clarify the role of commensal bacteria during immune system development: fish raised in a normal environment, and those raised in germ-free conditions. Germ-free models are commonly used to simulate what might happen in the absence of resident microbes, compared to the natural situation of exposure and colonization by commensals. Fish are normally exposed to a rich microbial ecosystem in their aquatic environment, which suggests that they have evolved ways to deal with environmental microbes that have both good and bad effects.

What, you may ask, can a fish tell us about human biology? Luckily, most significant developmental processes are conserved among distantly related animal groups. And zebrafish have many advantages as a research animal: They develop quickly in transparent eggs that can be easily observed and manipulated. Their well-characterized genome and sophisticated genetic tools allow researchers to add or subtract molecules and measure how genes – including the components of the immune system – respond. Another advantage is that the initial, fast-acting (“innate”) part of the immune system develops within days – even before zebrafish hatch.

The authors of this study followed the immune response of zebrafish from the time they hatch (at around two days after fertilization) through the first days of exposure to the external environment, when most commensal colonization is believed to occur. They showed that zebrafish have a rapid and punctuated innate immune response after hatching, which peaks after one day and then decreases. This initial activity improves the response of early immune cells, providing better protection against later pathogenic bacterial infections and tissue damage than is observed in fish reared in germ-free conditions. The researchers also showed that innate immune cells respond to these early infections using a mechanism that is found in many other animals, including humans. The response activates a biochemical signaling pathway in cells involving the myeloid differentiation primary response protein 88, or MyD88, which helps recognize microbes and initiate a immune response.

Another important finding from the study is that during early development, factors that influence the way DNA is packaged alter the patterns by which genes typically respond to stimuli. While fish that are exposed possess the same genes as fish that are not, early infections and environmental conditions cause their cells to establish patterns in which certain genes become active and others remain silent. The effect of this type of “epigenetic” regulation is to provide an extra level of control, giving cells the ability to mount a robust emergency response in case of infection or injury, but without the adverse immune effects – which can happen when inflammation reaches a serious level. Even fish raised under germ-free conditions mounted a slight immune response by this means. In contrast, antimicrobial effector proteins, which provide the fish with a fast-acting initial response system, have sustained high expression that is not limited by epigenetic regulation. Altogether, this study nicely demonstrates how commensal bacteria are closely intertwined with the development of the their host’s immune system.

Author: Jon Paul Hildahl
Link to the free full text of the original article

Searching for Oslo: a non-hypothesis-driven approach

Note: I will be speaking at a conference on science communication in Oslo in September. This is not the talk I will give there; however, it was inspired by the invitation.

First let me thank the conference organizers for this wonderful event and inviting me to this lovely city. I’ve been to Oslo many times and have always enjoyed it, but I’m not the type of tourist who studies up on a place before he goes. In fact, and this is embarrassing to admit, I’m not even sure exactly where I am. I told one of my kids I was coming to Oslo and she said, “Where exactly is Oslo, anyway?”

“It’s up, and to the left,” I told her.

Actually I didn’t have the slightest idea. I’d never looked it up on a map. I realized that I hardly ever use maps anymore. Almost nobody does. You don’t need to. You just go to the airport on time, go to the right gate, and the airlines and trains take care of the rest. Or you have an iPhone. You tell it where you want to go and it calculates your route, starting with your exact current position. Your iPhone says: “Go out the door. Turn left. Walk 1,213 kilometers. Turn right.”

If you’re going to go looking for something, it’s a good idea to start out with a general idea of its location. In the case of Oslo, it’s helpful to know that it is located in the Milky Way galaxy. It helps more to know it’s in our own solar system, even right here on our planet. It’s hard to calculate the odds of that happening; we’d need to know more about the state of the early universe at 0.00001 seconds after the Big Bang. However Oslo got here on Earth, its location is convenient. If it were anywhere else in the solar system, for example on Mars, we probably wouldn’t know it existed.

Once you have narrowed the search area to Earth, you’re getting close. At that point my knowledge of geography starts to get fuzzy, so you should just stop somebody and ask for directions.

But a little more information can help. I knew Oslo was in Scandinavia, which means you won’t waste a lot of time looking for it in the Pacific Ocean, or South America. I would like to note, here, that Scandinavia is a concept I don’t fully understand. We usually give names to continents, or countries, or hurricanes, or new species. As far as I can tell Scandinavia doesn’t fit into one of those categories, so I’m not sure why it needs a special name. On the other hand, if people want to call themselves Scandinavians, I guess there’s no law against it. At least they picked a nice name. Usually these things are decided in a committee, and you know how committees are. If you let a committee pick the name, Scandinavia would probably be called “Roger”.

I don’t know if you’ve ever seen a map of Scandinavia, but it’s huge. And there are a lot of blank areas. Many of these appear to be isolated regions that have never been explored. Scandinavia is so large that there could be 10 Oslos hiding out there, and you could spend your whole life looking for them, especially if they didn’t want to be found. Plus, we’re lacking a lot of information that would have been helpful. It is unclear how many groups have gone off searching for Oslo and failed to find it. These were negative results, so they couldn’t get their papers published. In other cases, groups found one Oslo and then broke off the search, never considering that there might be 9 more Oslos out there. So the data may be skewed toward one Oslo that happens to be easiest to find.

Today you should never start any scientific project without an exhaustive search of the literature, for example, by typing “Oslo” into Google. Here you find one fact that can significantly narrow the search area: Oslo is located in Norway. With that piece of information alone you can eliminate 2/3rds of Scandinavia from the search area. So it would only take 0.33333… lifetimes to search the remaining area and find 10 Oslos. The probability of finding only 1 Oslo would be a tenth of that, so you ought to calculate 3.3333… lifetimes. In a grant application, that comes to three full-time positions and one third-time position, probably a technician.

Now I think it’s reasonable to invest that much effort in searching for Oslo, especially since you might find other things while you were at it. Who knows what remains to be discovered in these large, unexplored areas of the country? You might find a species of Archaea that evolved 3 billion years ago in a thermal vent on the ocean floor. It’s a long ways from that deep ocean vent to a valley in Norway, but you can crawl a long way in 3 billion years. Especially if the colony is being driven by a male Archaea, who doesn’t waste time seeing the sights along the way, and keeps the pit stops as short as possible. You might also find the last surviving tribe of Yeti. Or secret UFO landing sites. You should keep your eye out for these things. If you find one of them, you should mention it in your supplemental data.

It’s quite common in science to start looking for one thing and end up finding something else. In fact, sometimes you find things when you aren’t looking for anything particular at all. You know how it is: you come into the lab on a Sunday, just to putter around a bit, and suddenly, lying there in your Petri dish, is the ribosome.

This is the type of science we call non-hypothesis driven research. You grope around in the dark and suddenly your hands grasp onto something. Please don’t think of this as a reference to some sort of sexual activity because it is not. In any case, in non-hypothesis-driven research, you should always be prepared for surprises. You’re out in the field looking for Oslo, or maybe a new species of Archaea, and suddenly you find a Yeti. You’ll never get a Yeti back to the lab in a Petri dish. So when you’re doing non-hypothesis driven research, you should always take along a big net. And some tranquilizer darts.

It’s hard to get funding for this kind of research. When you apply for a grant they always ask what you’re expecting to find. This is kind of silly, because if you already knew, you wouldn’t need their money to find it. So when you’re applying for a grant you just sort of pretend that you don’t know what you’re going to find.

That’s harder to do when you’re trying to get funding for non-hypothesis-driven research. Under the section on “Expected results and impact,” you can’t just write, “I have absolutely no idea.” Instead you should say something like, “We expect to find either a new species of Archaea, the city of Oslo, or a Yeti.” It’s wise not to mention secret UFO landing sites in grant applications.

You work hard to finish the application, send it off, and then you start waiting. You wait for years and years, and you never hear back from the grant commission. The entire system is biased against non-hypothesis-driven research.

But think where we’d be without it. I don’t know who the first person was who discovered Oslo, but he certainly didn’t find it by using a map. Without that bold pioneer, we wouldn’t be here. We’d be somewhere else. Probably in Stockholm.

A novel, non-hypothesis-driven method to determine the location of Oslo

Abstract. Traditional methods of locating large foreign cities involve a time-consuming, manual inspection of maps, sometimes with the aid of a magnifying glass. Recent years have seen the development of automated, high-throughput technologies such as Google Maps. These methods, however, are of limited applicability in cases where you don’t have the right map, or when you are at Starbucks and the Internet server crashes. Here we use Oslo as a model system to develop a novel, non-hypothesis-driven approach for determining the location of any large object on Earth. The method can easily be adapted to find other cities as well as smaller entities, such as new species of Archaea, or Yeti.

On the publication of “Remote sensing” by the magazine Occulto

Some remarks given on May 31, in Berlin, on the presentation of the newest edition of Occulto…

My name is Russ Hodge, and I’m honored that Occulto is publishing my short story “Remote Sensing” in the new issue. I believe this is the first time the magazine has published a short piece of fiction, and I hope it won’t do any permanent damage.

Originally I had hoped the story would come up here on stage with me. I would just introduce it and step back and let it speak for itself. But at the last minute it got cold feet. “You go ahead,” it said, “I’ll just wait here at the bar.” A lot of stories are shy in public, and the authors are to blame. Some writers bring their stories on stage and undress them, right there in front of everyone. As if stories don’t have feelings. Well, they can experience humiliation like anybody else. They can also be quite passionate. Check into a hotel room with a story sometime, order some champagne, light some candles, and you’ll see what I mean.

Stories shouldn’t need much introduction because they are small, complete worlds, self-contained and self-sufficient, like a universe within a snow globe. Inside a story, the normal rules of logic and even the laws of physics don’t necessarily apply. You wouldn’t want this strange reality to leak out into the real world. Suppose, for instance, you put some antimatter into a story. If it escaped it could cause what physicists call a naked singularity. I don’t know what that means, or why it’s naked, but I do know that a naked singularity could cause the end of the world, which one should avoid whenever possible.

This story is probably safe. There are no genetically modified organisms that might escape and destroy the world. There is a small amount of radioactive material, but it is handled with extreme care.

The topic is the relationship between a young man and his grandfather, during the last few months of his grandfather’s life. The story ends before anyone actually dies, which avoids a lot of medical terminology, gruesome details about the autopsy, or all the ways lawyers earn money on a fresh corpse. Some authors write on and on about these things, but that’s not my style. I killed a character one time and it made some of my friends so mad that they stopped talking to me.

That happened in another story, which was about a man who got bitten by two snakes. The first bite occurred immediately before the story began and the second came right at the end. Basically, by the first sentence, the guy was already dying. I did my best to save him, and he put in some effort himself, but it was no use.

Neither of us saw the second snake, hiding under a rock on the last page. Suddenly it was just there, and it scared the hell out of both of us. Now I’m a great believer in the craft of writing, and I know people who plan a story down to every detail. I’m not like that. Hemingway said, “If in a story there’s a gun hanging over the fireplace, it had better go off.” But you have to plan these things. Somebody grabs the gun and tries to shoot it, only to discover that the author forgot to buy any bullets.

But a lot of the process of writing is still a mystery to me. I start with a character, and a first sentence, and they seem to take over from there. Just about anything can happen. Like that second snake. Suddenly there it was, and it seemed inevitable. The same thing happened with this story: the final sentence appeared out of nowhere, through a process that I don’t understand. But you know it is exactly the right ending.

Well, my friends didn’t agree about the snake. The story was only about 10 pages long, but that was enough for them to develop a deep emotional attachment to this character. I tried to tell them that he was purely a fictional construct, and that he didn’t really exist. They would have nothing of it. You’d think I’d murdered a family member. A family member they got along with.

“You can’t kill him,” they said. “You’ve got to change the ending!” I apologized, but told them the matter was out of my hands. “It’s a story about a guy who gets bitten by two snakes,” I said. “That’s just how it is.”

This incident taught me an important lesson. Now I try not to kill anyone in a story unless it’s absolutely necessary. I also try to follow this principle in my daily life. Going around murdering people just for the entertainment value of it can cause all kinds of complications.

Well, I promise you there are no snakes in this story in Occulto at all. Which is really a bit odd, considering that the story is set in my home state of Kansas. I can tell you first-hand that we have plenty of dangerous snakes. Copperheads, rattlesnakes, water moccasins. The copperheads like leafy spots in the shade, rattlesnakes lie on rocks in the sun, and water moccasins hang out in the lakes and rivers. Basically, you’re not safe anywhere. All right, you could hide in your mailbox. You won’t find any snakes there, because the mailboxes are already occupied. By black widow spiders.

I never considered myself a “regional” writer until I moved to Europe and lived here for about 20 years. One morning I woke up and found all my stories moving back to Kansas. Maybe it’s nostalgia. Or some sort of neurodegenerative disease that is wiping out my short-term memory. Maybe I’ll wake up someday and believe that it’s 1966 and I’m in the second grade.

What I really think is that I’m experiencing a universal law of physics, or an old folk saying – it’s one of those two, I can’t remember which: You never fully appreciate something until it’s lost. That’s certainly true of our health, and of many more things. For example, your car keys. And life itself. The only people who can totally enjoy life are dead people. And the rule also applies to your mother-in-law. You never really appreciate her absence until she comes for a visit.

So maybe I should say a few words about Kansas. This is totally unnecessary in understanding the story, but I don’t know what else to talk about.

Kansas occupies the exact geographical center of the continental United States. On the maps they show us in grade school, the US is at the center of the world. This is somewhat inconvenient for the Russians, whose country is split in half, and to get from East Moscow to West Moscow you have to travel across the whole world, but we paid for the map.

In cosmological terms, astronomers tell us that all the galaxies in the sky are flying away from us at tremendous speeds. Put all this information together and you discover that Kansas lies at the navel of the universe.

People are proud of this location but we don’t make a big deal out of it. You have to remember we didn’t choose to live there. A long time ago when the government drew Kansas on a map, that’s where they stuck us. We would have preferred to be closer to one ocean or the other, but nobody asked. Somebody has to live at the center of the universe, and it just happens to be us. Anyway, we have lots of other things to be proud of. Right at the moment I can’t think of any, but ask me again in a couple of weeks. I’ll do some research.

This location is why so many aliens visit Kansas: imagine you’re traveling from one end of the universe to the other, at warp speeds; at some point you need a pit stop. We’re conveniently and centrally located. We have clean bathrooms, good coffee, and really good steaks. About a quarter of Kansans claim to have been abducted by aliens. The aliens don’t intend us any harm. They take you for a few hours, and subject you to strange experiments, hoping to find a steak in you somewhere. When the experiments show that you aren’t a cow, they let you go again.

Some facts about Kansas: the state flower is the sunflower, the state bird the Meadowlark, and our state song is “Home on the Range.” We learn it in the first grade, and it goes like this:

Oh give me a home where the buffalo roam
And the deer and the antelope play…

When they teach us this song you think, this doesn’t sound like the Kansas I know. Sure, we have a lot of deer. If you live in the outer suburbs they come right into your yard. In deer season, you can hunt them right from the back porch. But you have to be careful. It’s easy to mistake your neighbors’ lawn ornaments for a deer, and people are awfully sensitive about having their lawn ornaments shot to pieces. In deer season it is not unusual to see garden gnomes, plaster statues of the Virgin Mary, and bird feeders outfitted in fluorescent orange hunting jackets.

But there are strange things about this song. Where the deer and the antelope play. Now we know that the plural form of deer is deer. Nobody, even in Kansas, puts an –s on deer. But the antelope… We’re not so sure about that one. “Antelopes” sounds fine to me. So in the song, they’re either talking about one specific deer and one specific antelope, or a bunch of deer and that one particular antelope.

Try as I might, I have never seen that animal. And I’ve looked for it, believe me. Every time I’ve driven through my state, I have kept a sharp eye out. But I’ve never seen the antelope.

And where are the buffalo that are supposedly roaming around all over the place? Your teacher says, “We killed them all.” Doesn’t seem like nice behavior towards an animal featured right there in the first line of your state song, but there you have it.

And the song neglects other prominent species in our state. Right now, for example, Kansas is up to its neck in llamas. Everywhere you go these days, somebody’s started a llama farm. I don’t think you can milk one, and their eggs are inedible, but a llama must be good for something. Whatever it is, we should consider changing the state song. For example,

Oh give me a home where the buffalo used to roam
And the deer and the camelids play…

The song goes on to say,

…Where seldom is heard
a discouraging word
and the skies are not cloudy all day.

Here, we’re talking outright lies. I’ve heard a lot of discouraging words in my time – a lot, it is true, from foreigners from places like Paris, and Nebraska, but every once in a while a native will rip you with a criticism. And we do have clouds. There is the tall and majestic variety, which look like clipper ships, or six-packs of beer, or Snoopy on his Sopwith Camel, and other times they’re low and grey, hiding tornadoes and hail and all sorts of other unpleasantness.

Or perhaps I’ve misinterpreted this line. Maybe the song intends to say, “The skies are not cloudy all day long.” In other words: “Okay, we have clouds, but they never stay in the sky all day long, because eventually the wind pushes them into Missouri.” In any case, you have to admit, the original is either a lie or is misleadingly ambiguous.

The state motto is Ad astra per aspera, which is Latin, which is interesting considering that the number of Latin speakers in Kansas is approximately the same as the number of ancient Romans. If you say it really fast, with a Kansas twang, it sounds like “a disaster for aspirin,” but you can run it through Google Translate. Our motto means, “To the stars with difficulty.”

They got that right. It’s difficult for anybody to get to the stars, but it’s a special challenge in Kansas. We don’t have any mountains. If you climb a mountain the stars are still far away, but they’re just a little bit closer. States with mountains have an unfair advantage when it comes to going to the stars.

The science story that has it all

Some scientific stories – think of Watson and Crick’s discovery of the structure of DNA – are so electrifying that you instantly realize they’re bound for a Nobel prize or some other lofty pinnacle of greatness. This wasn’t one of them. My first impression was that it was free-falling rapidly in the other direction. If nobody has put it up it for an IgNobel yet, you may consider this article an official nomination.

It’s one of those quirky little pieces that make you think, “Wow, you can obtain funding for anything if it’s crazy enough,” or “The guy who wrote this grant must be a genius; let’s hire him,” or “There are waaay too many people getting PhDs these days.” But then you bite into it, the way you might try a hamburger made of soybeans, just to please your girlfriend, and you realize that it’s the gift that keeps on giving, if only in the form of several days of gastrointestinal distress.

I’m speaking, of course, of the invention of 3D eyeglasses for praying mantises. If you haven’t seen the pictures, visit this site and prepare not to get much work done for the next few hours.

The project is the work of Jenny Read, from the Institute of Neuroscience at Newcastle University. The story issued by their press office doesn’t mention publication in a peer-reviewed journal, but it does say that the group received £1 million pounds from a certain Trust, so who cares? (I’m not naming the Trust until I’ve sent them five grant applications that I’ve been hanging onto, waiting for just the right funding body; I found the story, so I have the right to a head start.) In case you were wondering, £1 million pounds amounts to 1.23 million Euros at today’s rate of exchange.
Besides, who cares about getting a paper published when your work produces a video that will go instantly viral? Or maybe the lab was about to be scooped, and had to get the story out there.

I will return to the fascinating scientific aspects of this story, and its wonderful potential for industrial applications, but first let me say that this is obviously one of those projects that started in a pub. They caught a praying mantis by trapping it in a beer glass; everybody gathered around, and somebody said, “Hey, I bet to that bug, we look like we’re on a huge IMAX screen.”

A lot of British studies, particularly from psychological research, start in a pub and spend millions proving things we already know. Remember the classic paper proving that “Men and women who have consumed a moderate amount of alcohol find the faces of members of the opposite sex 25% more attractive than their sober counterparts.” That one got its support from the Universities of St. Andrews and Glasgow, which were probably closest to the pub.

This type of research is much harder than it sounds. It requires a particular skill set: you have to be able to do statistics, or at least count, while drunk. Then you have to remember to save all the soggy napkins and beer coasters that you’ve been using to gather statistical data. Finally, you must be able to read your own handwriting in the morning. It’s worth cultivating these talents as you work on your PhD; they’ll practically guarantee you a position in a lab in the UK.

But back to the praying mantis. One intriguing part of the story is that, as opposed to other insects, this species already has 3D vision. That’s because they have smooth eyes, as opposed to the eyes of certain dragonflies and moths, which are broken up into 30,000 or so bubble-like ommatidia. I guess that means they have 30,000D vision, which probably makes it hard to see anything at all. It’s a good thing such insects don’t drive cars, because they’d need a lot of mirrors – all of which would be labeled, “Objects in the mirror are fewer than they appear.” Now those are insects that could really use 3D glasses, just to watch normal TV, but it would take a farm of Cray supercomputers 12 billion years to work out the optics and design the things, and by that time the dragonflies would have evolved into helicopters.

How do you attach glasses to a praying mantis? With beeswax, of course. You grab a mantis, glue some glasses to its eyes, and stick it in front of a computer monitor which is showing The Fast and the Furious 17, or whatever number they’ve gotten to these days. If the mantis jumps back to avoid getting mashed on the grill of an oncoming car, you know that the glasses work. Another good piece of evidence is if the mantis tries to grab Paul Walker, mate with him, bite off his head, and eat him. I’ve known a few human women who respond the same way when they see Paul Walker in 3D.

One of the researchers involved in this project was a certain Dr. Vivek Nityananda; say it three times in a row, fast, and you really have to wonder if Newcastle is pulling our leg. He proclaims: “This is a really exciting project to be working on. So much is still waiting to be discovered in this system. If we find that the way mantises process 3D vision is very different to the way humans do it, then that could open up all kinds of possibilities to create much simpler algorithms for programming 3D vision into robots.”

I find this somewhat enthusiastic, but molecular biologists say such things, too; translated into their discipline it comes out: “3D glasses attached to the eyes of praying mantises present a promising new target for potential cancer therapies.” Particularly cancer of the eyeball, I suppose.

Dr. Vivek Nityananda doesn’t mention the fact that the research should also result in a lot more customers attending the local IMAX. You could fit 1,980,722,314,222 praying mantises into the theater, although it’s unclear how they will pay, unless the research subjects are getting a cut of that £1 million pounds.

For a writer there’s an even more compelling reason to be interested in this project. Garrison Keillor, the great American humorist, once said that a great story has five elements: a mystery, religion, money, sex, and family relationships. In a Nov. 8, 1997 broadcast of A Prairie Home Companion, he managed to capture them all in just twelve words, although it’s 14 if you expand the contractions:

“God,” said the banker’s daughter, “I’m pregnant. I wonder who’s the father?”

By extension, the perfect science story would have those elements, too, plus a bit of technology. That’s rare, but here we have them all, if you think about the mating practices of female praying mantises, usually with males from their own species, or perhaps with Paul Walker. Add this story’s elements of murder and cannibalism, and I foresee a book, a screenplay, and a feature film. I’m currently trying to buy the rights to the story. There’s still time to get in on this; just send me a mail and I’ll tell you where to send your contribution.

The sun has a sibling – but are they holding hands?

I guess the birth announcement got lost in the mail, which is understandable given the fact that it happened a few billion years ago, somewhat before the invention of e-mail or even a postal system. In case you haven’t heard: our Sun has a sibling! And it’s a girl!

She’s called HD 162826, which will give her some grief during grade school, but probably not as much as if she had been named Moon Unit Zappa, Elbow (3 children were given that name in 2009), Hotdog (2 in 2012), or Freak (34 in 1995). I don’t know how you determine the sex of a star, but apparently someone can, because everybody says HD 162826 is a sister. I’d love to send my congratulations to the parents, but their identity is somewhat vague.

In any case, the discovery of the Sun’s sister has triggered an outpouring of emotional responses and some typically wild speculations on the part of the press. The first article I saw on this was here, and this piece is interesting for a number of reasons. It gets off to a great start with this sentence:

“Researchers from the University of Texas at Austin has discovered that a previously known star may actually be the sibling of our own Sun.”

“Researchers… has discovered” is a little strange, but maybe that’s how they talk in Texas. All right, in the excitement it seems petty to quibble about the conjugation of verbs. The article continues:

“The possible solar system is located a mere 110 light years away from the solar system.”

This sentence is also intriguingly strange. First off, there’s nothing “mere” about “110 light years away,” at least if you’re using Google Maps to plan your trip. (I tried, and the closest hit is Hd’s Mesa, an employment agency on 1826 W. Broadway Road, Mesa, Arizona, a mere 9,100 km from my present location.)

A light year is 9.4605284 × 1015 meters. It would take the Voyager 1 spacecraft, which is traveling at a maximum rate of 62,136 km/h, at least 1,909,787,303,382.4 years to get there. That’s only if Voyager 1 is pointed exactly in the right direction, which I kind of doubt, and only if I’ve done the math right. If you find an error in my calculations, let me know.

Of course you have to take into account that 1,909,787,303,382.4 years is about 138 times longer than the current age of the universe (depending, of course, on the date at which you are reading this.) In 1.9 trillion years the universe will either still be expanding, or collapsing in on itself, depending on your feelings on the topic of dark matter. In the expanding universe scenario, some scientists calculate that the universe might double its size in 11.4 billion years. It’s unclear how things will go after that, but Voyager 1 will clearly need somewhat longer to arrive. If, on the other hand, you’re a proponent of universal contraction, everything will be closer together, so the trip won’t take quite as long. Maybe Voyager 1 should just park somewhere and wait.

But the intriguingly strange sentence above (“The possible solar system is located a mere 110 light years away from the solar system”) has more to offer. I suppose “the possible solar system” means that the sibling sun might also have a solar system, and “the solar system” at the end of the sentence presumably means “our solar system.” If I’m wrong, and these two phrases refer to the same solar system, I don’t quite understand how a thing can be 110 light years away from itself. Unless you are talking about some sort of weird, alternate reality. Of course, physicists like that kind of thing – remember Schrödinger’s cat, which demonstrates not only the possible existence of parallel universes, but also that Erwin Schrödinger had some serious issues with cats.

The idea that our planets might have long-lost siblings is old news. Earth’s first sibling was found in 2007, as you can read here. I’ve covered that story in an earlier article. A second sibling was found this year. The first candidate, Gliese 581c, is a mere 20 light years away, while Kepler 186f is 500 light years from us. That’s just how it goes: “children” (or planets, in this contorted world of familial metaphors) grow up, relocate to distant places, attend the university, and acquire huge amounts of debt before moving back home to live in the basement.

Both of these planets are “sisters.” It’s easier to tell the sex of a planet, I suppose; at least you can get closer and inspect them, without getting burned to a crisp.

* * * * *

In case you hadn’t noticed, I could go on talking about unusual grammar and interstellar sex determination all day. But the discovery of our “sister sun” has also prompted some scientific speculations that are worth considering. Consider this from the Tech Times article I cited above:

“Aside from being a potential sister star to the Sun, Ramirez and his colleagues also believe that there is a very small chance that the HD 162826 system could have planets suitable for life. While the chances may be small, the researchers are certain that the odds are not zero.”

I can’t resist one linguistic point here: the first sentence implies that the potential sister star is Ramirez and his colleagues. This is a common grammatical mistake called a “dangling participle.” The problem becomes clear if you consider a sentence such as, “Hanging from a tree, the firemen rescued a cat.” But more intriguing is the comment, “the researchers are certain that the odds are not zero.” It’s hard to find just about anything for which the odds are truly zero (rather than 0.0000000…00001); try it sometime and you’ll see.

Another article about the finding puts it this way:

“One of the most exciting consequences… is the likelihood that these stars support planets, and possibly even life. Back when the Sun’s siblings were all hanging out in their nursery together, there would have been a robust, inter-system exchange of planetary material and chemical runoff. Enriched chunks of early Earth could have been launched into other fledgling solar systems, seeding the potential for life on other planets.”

Now I don’t know how this passage strikes you, but there’s a point at which you have to be cautious about metaphors. There’s some serious hanky-panky going on in this nursery school. “Exchange of planetary material and chemical runoff” are clearly euphemistic references to some sort of bodily fluids. If you’re generous you might think the topic is spilling KoolAid, but then you get to the part about launching “enriched chunks of early Earth,” and it’s hard not to think about kids throwing around poop. Finally we get to “seeding the potential for life” – a figurative climax, if not a literal one. If by that point you haven’t figured out what the author is talking about… Let’s just say it’s not the kind of day care I’d consider for my kids.

Coming back to the science, one should remember that this nursery probably existed over 4 billion years ago, when things were pretty hot, and I’d say the limb that supports these speculations is a pretty long one. But some notable scientists – Berzelius, Kelvin, Hermann von Helmholtz, Francis Crick, and Stephen Hawking – have promoted this type of panspermia hypothesis, and I’m not one to argue with such bright bulbs.

This second piece from motherboard.vice.com (clearly one of the first places you’d go to check out the latest findings from research) goes on to say:

“The idea that we might have genuine biological relatives on planets orbiting distant solar siblings is certainly tantalizing.”

I don’t quite know what they mean by “genuine biological relatives,” unless they’re referring to Vulcans, or a long-lost cousin named Bob, but it’s safe to say that the idea is tantalizing. Most things are, to somebody.

I’d like to jump into the fray of wild speculations by suggesting that our Sun and its sibling might be holding hands. That happens sometimes, as shown by the recent birth of twins. On Mother’s Day, at that. What are the odds of that? Certainly not zero.

Fundamentalist math: another outtake from the Science Cabaret

People are always inventing new ways to tell if someone is possessed by the devil. One way is to catch a grasshopper. We have a lot of them in Kansas. Catch one and count the legs. You count six? It says right there in the Bible that they only have four. Satan is a sneaky guy, always making your eyes play tricks on you. Six legs? Hah. Those huge dinosaur fossils? They’re not really there.

But these methods aren’t foolproof. When somebody looks at a grasshopper and counts six legs, maybe he’s just forgotten his reading glasses.

Counting legs requires some basic skills in math, which people generally learn in school, but a lot of fundamentalist Christians have decided to home-school their kids so they won’t learn a lot of liberal nonsense. In fact, some of these households promote a sort of Neo-fundamentalist version of creation which attempts to reconcile scientific discoveries with the Bible. Doing so requires an alternative form of math.

God obviously counts differently than human beings. For one thing, He really does know what number lies at the end of infinity. Our minds aren’t big enough. Think of the largest number you possibly can, you can still add 1 to it. Our brains just about get there, but we always fall a few numbers short.

God’s infinite Powers also give him the ability to bend time, and to change numbers to mean different numbers. One day a six will mean six, another day it will be 2πr.

Those seven days in the book of Genesis? Everything works out fine if each of those days lasted 500 million years. Years, on the other hand, were a lot shorter in Biblical times. Methuselah lived for 969 years? Without antibiotics? Come on. It’s obvious: One year for Methuselah was ten of ours. The dimensions of Noah’s ark? Just raise all those numbers to a higher power. An ark capable of holding all the species on Earth would have to be roughly the size of Texas.

So God counts things differently than people. Maybe what is 1 grasshopper leg for us is .6666 grasshopper legs for God.

In Kansas people use the grasshopper test to see if you’re possessed by the Devil. But in ancient times there were other tests. During the Middle Ages, for instance, there was the joke test.

The joke test arose from a huge theological debate. It probably started in a bar, as most of these things do. When people have one too many, or ten too many (another example of alternative counting systems), they get philosophical. Somebody says, I wonder if God has a sense of humor?

Back in the Middle Ages you couldn’t just let a comment like that go; you had to look into it. The debate over this issue became an awfully big deal. One faction said, God can’t have a sense of humor because what would he laugh at? He created EVERYTHING, and made it PERFECT. So he couldn’t have created something just to laugh at.

In the Medieval period they obviously didn’t know about the platypus. If Europeans had the platypus, which is obviously ridiculous, they would have known that God has a sense of humor. Why else would You create something that odd?

One faction of Christians had no sense of humor at all and so they decided that God couldn’t have one, either. That meant humor must have been invented by the devil, making it perfect material for a test. If somebody told a joke, you had grounds for burning them at the stake. Which is pretty funny if you think about it. Actually, it’s not funny. It’s ironic. Can God have a sense of irony? I’m not really asking. I don’t want to start something here, particularly if it will lead to a pile of wood and a book of matches.

Eventually the Middle Ages were over. People could finally giggle in public again, which required a new test to detect the presence of Satan. Some brilliant church committee came up with the water dunking test. If people suspected you of being a witch, they tied you to a board and dunked you in the river. After about two or three hours they brought you back up. If you survived they knew, Yup, that’s a witch. If you died… well, experiments sometimes produce negative results. But they’re hard to publish, so people kept using the method for a long time.

That test still exists, by the way, but today we call it the Guantanamo test.

The Renaissance saw the beginnings of modern science, which was pure atheism, so it provided lots of material for new tests. They took you out in the middle of a field and made you look at the sun. Tell us, they’d say, does the Sun revolve around the Earth or the Earth around the sun?

Since your life is at stake, it occurs to you that this might be a trick question. So you stall for time. You say, It depends – are we on Daylight Savings Time? In the process you become blind, but you don’t need eyes anyway. They just trick you all the time.

Even fundamentalist math won’t help you answer questions about planetary motion. That topic belongs to the domains of physics, and geometry, and so we’ll save it for another time.

American football, cheerleaders, and science communication

Recently I heard someone compare science communication to a sport. I didn’t catch which sport he meant, but he was fairly drunk, so it probably doesn’t matter. Maybe it was a dumb idea anyway, but there’s no law against metaphors. A metaphor is a way of saying one thing when you are thinking about something else, such as when you’re talking to your wife about the shopping list but your mind is actually entirely focused on your Facebook page. There are good metaphors and bad metaphors. For example, the upcoming visit of your mother-in-law could be compared to an inspection by a human rights organization, an invasion of kudsu, or a hostile takeover on Wall Street; one of these will fit your particular situation better than the others.

I do remember that the general topic of the conversation was differences between the way Americans and people from other countries communicate science. Now some people attribute this to the fact that a lot of American universities offer their scientists courses and workshops in writing and giving presentations. But the reality is, at an early stage in development, kids started playing different kinds of football. That causes fundamental changes in the way their neurons are wired. Then when you play football, you kill some neurons off again. But you kill off different ones. These changes in brain architecture spill over into other types of behavior, such as science communication.

American football is simple. One team has the ball, and it lines up against the other team. Then they crash into each other. When the dust clears, you look for the ball. Wherever it is, that’s where the teams line up to do it all over again. The goal is to carry it the ball over the goal line, but you have to be upright when you get there. So if the ball comes your way, look out, because everybody on the other team will try to break your legs.

If you make it to the End Zone, your team gets six points. I don’t know how they arrived at this number. One point ought to be fine, unless the total reflects some sort of risk factor. It’s true, for example, that your chances of reaching the End Zone alive are about one in six. But that wouldn’t explain why a shot in tennis can be worth 15 points, or the absurd scores you get for throwing a dart in a pub, unless there are a lot of dart fatalities they aren’t telling us about.

Anyway, American football teams have a sort of mascot called a coach, a combination of army drill sergeant and evangelist preacher who speaks in tongues, a genetic cross between a pit bull and a Neandertal, whose vocabulary consists of 100 words of which 90 are profanities, who has to be kept on a leash at games. Otherwise he will assault the referees, people in the stands, cameramen, or players from either team, sometimes biting them. This individual is usually a former football star who has been hit on the head so many times that he believes he is preparing troops for the invasion of Normandy, the defense of Stalingrad, or some other situation involving the fascist pursuit of world domination.

On your first day of practice, this coach takes you down to one end of the field and shows you where to stand. Then he puts his face 1cm from yours and gives you a whiff of breath that would permit you, if your football field is equipped with a mass spectrometer, to conduct a precise analysis of his diet and the metabolic status of various internal organs. But you wouldn’t have time because he immediately begins shouting in your face.

“You, scumbag!” he shouts.

“Yessir!” you scream.

“You see that goal down there?” he shouts.

“Yessir!”

“That there is our goal, and this here behind you is their goal.”

“Yessir!”

“You stand here and wait until the ball comes flying through the air. You catch it and you run straight for our goal, you hear?”

“Yessir!”

“If something gets in your way, just run over it! No matter what it is! If it’s somebody from the other team, run over him! If your grandma comes onto the field, run over her! If a 7-Tesla MRI scanner weighing about 6 tons suddenly drops out of the sky, just run over it!”

“Yessir!” you scream.

This all sounds simple enough. So you stand there a while and sure enough, here comes the ball. You catch it and all hell breaks lose. You run toward the goal and half the people on the field are trying to break your legs, whereas your teammates are trying to break the legs of the other team before they get to you. Beginners sometimes get disoriented and start running the wrong way. Then things really go wild: your own team starts chasing you while the other team tries to knock them down. If you switch and run backwards and forwards a few times in a row, the result is total anarchy. It’s like mixing up willy-nilly a bunch of promoters and inhibitors and glopping them onto cells. Both football players and biochemical pathways will get confused, sometimes at the same time, respectively. This state of chaos has one benefit: the person with the ball might slip through unnoticed. In some ways this resembles the way cancer cells evade the immune system, and in other ways it doesn’t. That’s completely irrelevant here, but I just thought I’d mention it.

Eventually an American football player gets hit on the head so many times that he forgets about the option of running backwards. It’s at this point that American football might be used as a metaphor for science communication. Just in case the topic ever comes up, for example in a bar.

Say you’re standing in front of an audience with some sort of scientific result in your hands. If we consider this information the ball, then the goal is to run it straight to the End Zone (into the minds of the audience), along the most direct route possible. If your path is blocked by some nuisance, like contradictory results, or mean comments from a reviewer, or a Coke can somebody put in your electron microscope, just push it out of the way, using brute force, a control experiment, or some sort of complicated explanation. Whatever happens, keep heading for the End Zone, and try not to get your legs broken along the way.

Now earlier I mentioned that there are good metaphors and bad metaphors. In Europe they play a different form of football, which ignorant people call soccer. A lot of people apparently use this game as a model for communicating science, which leads to a lot of games with no score.
I admit that I don’t completely understand the sport, but I’ve observed it a few times. It mainly involves a lot of guys standing around kicking a ball. They kick it forward and back, and left and right, unless a person from the other team is in the way, and then they kick him. This sort of aimless kicking usually goes on for about 20 or 30 minutes. At that point a member of your team says, Hey, look down there at the other end of the field. Somebody’s put up a net. I wonder if you could hit that with the ball? What would happen? Somebody tries it, and the whole stadium goes nuts.

I don’t know how many scientific talks you’ve been to, but I often feel like the speaker starts out in the backfield kicking a ball over here, and over there, sometimes getting in a few kicks on his competitors. If you get lucky, at some point the speaker discovers that there’s some sort of goal to aim for. If he hits it, usually by accident, everybody goes crazy.
Another reason European football isn’t a very apt metaphor is that there’s no good scientific equivalent for rowdy fanatics who get drunk, rush onto the field, and tear down the goalposts, unless you count behavior at scientific conferences. Incidentally, that’s the only context in which scientists typically switch jerseys. When you wake up in the hotel room of another person attending the conference, you might grab the wrong clothes.

This behavior is a little less common in American football. We have other nuisances to distract people from the game, but even they have parallels in science: cheerleaders (the reviewers who accepted your paper), marching bands (animated graphics in PowerPoint presentations), advertisements (funding from the pharmaceutical industry), and the emergency rescue teams that rush in to scrape people off the field (acknowledgements). Impact points clearly have a significance in American football. In that sport you do actually kick the ball sometimes, to get an extra point, which is like supplemental data. So it’s a complex metaphor. I’m not sure how helmets and faceguards fit in yet, but I’m working on it.

Juggling molecules while balancing the brain

Research highlight from the MDC
(visit www.mdc-berlin.de to see more highlights from MDC research)

People with a mental illness are sometimes described as being “unbalanced” or “having a screw loose.” These expressions may not be very polite, but they capture two important aspects of mental and physical health. First, organs such as the brain need to maintain an overall balance as we experience stress and engage in various types of activity. Ultimately this state depends on the functions of fundamental components in our cells – not screws, of course, but proteins and other molecules. A frenetic activity at this vastly smaller scale is required to ensure the stability of cells and tissues. While it is often extremely difficult to connect these levels of biological structure, the lab of Jochen Meier has established a new link. In a recent study in the Journal of Clinical Investigation, the group has connected a molecule called the glycine receptor (GlyR) to the operation of networks of neurons – and the way they are disrupted in epilepsy.

Jochen and his colleagues had already found an association between GlyR and brain disorders. They had carried out a molecular analysis of brain tissue from epilepsy patients. This disease is caused by an overexcitation of certain neurons, particularly in a region of the brain called the hippocampus. “We found that hippocampal cells produce unusually high proportions of a specific form of GlyR,” Jochen says. “The current project aimed to show how this molecule contributes to higher brain functions and eventually causes symptoms related to the disease.”

GlyR has one function that is clearly related to signal transmission between brain cells: it acts as a receptor for a neurotransmitter called glycine. Neurons release neurotransmitters into synapses, tiny gaps that separate them from their neighbors. These small molecules typically dock onto receptor proteins on other cells (postsynaptic) or on presynaptic receptors of the original cell. Depending on the type of neurotransmitter receptor and type of neuron, this either inhibits or promotes the signal.

The GlyR can be composed of two different proteins called alpha and beta subunits. Our genome encodes only one beta protein, but cells pick and choose between different genes for the alpha subunit. It may be combined with the beta subunit to create the GlyR; however, single cells sometimes produce GlyRs composed of alpha subunits only.

Like all proteins, the GlyR alpha3 subunit (GlyR-a3) is produced when the information in its gene is transcribed into an RNA molecule. Later the RNA is translated into protein. Along the way bits and pieces of the RNA may be removed in a process called splicing, creating proteins of different lengths, containing different functional modules – a bit like adding or removing wagons from a train.

GlyR-a3 RNA sometimes undergoes yet another change that affects its chemistry and functions. During a process called RNA editing, one letter of the molecule is swapped for another. This causes a corresponding change in the chemistry of GlyR-a3 protein and makes it work more efficiently. What Jochen’s team had discovered in epilepsy patients was an unusually high proportion of “long” spliced forms, and they also observed a swap in one letter of its chemical alphabet.

GlyR-a3 is known to inhibit the firing of neurons in the spinal cord, which can block the transmission of signals related to pain. This might mean that the form of GlyR-a3 found by Jochen’s team (the long spliced form, changed by RNA editing) was tuning down the excitability of neural networks in epileptic patients. To find out, the lab needed to observe the behavior of the altered molecule in an animal’s brain. Aline Winkelmann and other members of Jochen’s lab developed a strain of mouse in which particular cells in the hippocampus – called glutamatergic excitatory neurons – produce high amounts of this version of GlyR-a3.

Now they measured the way the change affected the animals in various ways: checking whether it affected the structure of neurons, the excitability of neural networks, cognition, memory, and mood-related behavior. Unexpectedly, they discovered that the altered form of GlyR-a3 caused an overexcitation of the system – and an important reason why.

“The long spliced form of GlyR-a3 is packed up with presynaptic vesicles,” Jochen says. “These are bubble-like packages that neurotransmitters are placed into before cells release them. Put this association together with an increased sensitivity to the neurotransmitter – and even some spontaneous activity due to the change in the receptor’s chemistry – and the neurons were prone to release more neurotransmitters. This had measurable effects on behavior: it disturbed the animals’ cognitive functions and some forms of memory.”

The study yielded another extremely interesting and wholly unexpected finding. The scientists discovered that in another type of cell, parvalbumin-positive inhibitory interneurons, higher amounts of the molecule had completely different effects on network excitability and behavior.
“Here the result was reduced network excitability, because it was enhancing the functions of this type of neuron,” Jochen says. “The change triggered anxiety-related behavior in the animals. But it did not cause any changes in cognitive function.”

A close scrutiny of the animals’ neurons and hippocampus didn’t reveal any significant changes in overall structure. In other words, higher amounts of this form of the GlyR-a3 molecule weren’t “rewiring” the animals’ brain network. Instead, they were persistently changing the overall balance of neural networks by enhancing the neuronal output.

“What we’ve done is to identify a mechanism at the level of molecules that is linked to the release of neurotransmitters and identifies two critical types of neurons that can cause an imbalance in the brain,” Jochen says. “We think this helps explain both changes in excitability of the brain network in epilepsy and the neuropsychiatric symptoms of some types of anxiety that are often associated with the disease.”

– Russ Hodge

Reference:

Winkelmann A, Maggio N, Eller J, Caliskan G, Semtner M, Häussler U, Jüttner R, Dugladze T, Smolinsky B, Kowalczyk S, Chronowska E, Schwarz G, Rathjen FG, Rechavi G, Haas CA, Kulik A, Gloveli T, Heinemann U, Meier JC. Changes in neural network homeostasis trigger neuropsychiatric symptoms. J Clin Invest. 2014 Feb 3;124(2):696-711.

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Ontogeny recapitulates sobriety:

From the Archaeal origins of life
to the pinnacle of evolution – a PhD

Some remarks made upon the award of the title Dr. to Dr. David Fournier

Considering the evolution of life on Earth, and the evolution of David Fournier in particular, aren’t you just smacked in the head by Haeckel’s famous principle, “Ontogeny recapitulates phylogeny”? Since that first twinkle in his father’s eye, well, actually since about four minutes after that first twinkle, David has passed through all the stages. He has made the transition from one-celled organism to undifferentiated clump of cells, worm, fish, tadpole, and rat, sometimes in the space of a single weekend. On another weekend David passed through the phases of Civil War reenactor, clownfish, and a member of the French Olympic curling team, but that’s another story. At every stage of his life, David has been curious. He was a curious tadpole. Among PhD students, he has a uniquely philosophical attitude; you can stop him on the street and discuss theories of the universe that turn out to be completely false, but are so elegantly constructed that it takes you a long time to figure that out. If you call David at three a.m. he will quote from the works of George Wilhelm Friedrich Hegel, with footnotes.

Anyway, if evolution were a ladder, which it is not, and don’t let anyone tell you otherwise, but if it were, David now stands at the summit. Along with other members of homo molecularbiologicus, and the even more highly developed member of its clade, homo bioinformaticus. The relationship between these species almost perfectly reflects that of Neandertals and modern humans. You may interpret that however you like.

After he passed through a pupal stage in school, David was squeezed by the French university system into a Wurst-like form, a saucisson, a sort of cocoon, sucking him in like a black hole in a box, although it is difficult to see how wormholes might fit into this analogy, unless it is a box of donuts. In any case, after many sleepless nights, David experienced some sort of cerebral event that made him run for ridiculously long distances, and if you stopped and offered him a ride, he’d say, “No, thank you very much.” Where I come from, you see a man running like that, he’s running away from something, but I didn’t see anybody behind him. Did David believe invisible people were chasing him? It’s not the kind of thing you can just come out and ask.

At some point David discovered the secret to success known to all graduate students: If you drink enough coffee, interspersed with a Red Bull every once in a while just for variety, the affinity between your conscious mind and body becomes very weak; they dissociate, and your mind drifts away. Your body becomes this robot that goes to work while your mind is sitting on a beach somewhere, sipping a margherita. Every once in a while a thought sort of floats into your consciousness. You say it out loud, and far away the robot body types it down and eventually you’ve collected enough strange and unrelated facts to make up a whole dissertation. You send the robot body to your thesis defense and it stands in front of your committee receiving signals from your mind, which is located on some remote planet. Every once in a while there’s a small interruption in the transmission and the robot suffers a blackout. You think aliens might be disrupting the signal. Or it might not be aliens. It could be other things, for example, coconut crabs. Somehow.

You remain in this dissociative state for three or four years before taking the next step of development and becoming a fully mature scientist with a PhD. Providing you don’t have any dangerous genetic defects, particularly monogenic traits like a cleft chin. If you do, you’ll develop along an alternative route. You may become an ice fisherman, or a garbage collector in Naples, or a person who carves butter into the shape of The Last Supper by Leonardo da Vinci.

But if everything goes normally, there you are, cruising down the hill in your doctoral cannister, becoming increasingly specialized, like a ball rolling down the Waddington model, except there’s nothing downhill at all about a PhD, it’s more like climbing up Mount Waddington, and free-climbing at that, without oxygen cannisters. Anyway, at some point a receptor on the surface of the container senses a molecule, probably a pheromone, and this triggers a massive epigenetic … well, let’s call it a process, I’m not a scientist, I don’t know the technical term for it. And I can’t say a lot more about it here, because it’s part of a massive secret international project called Systems Biology. This is so secret that even scientists don’t know what it really is. No one has the complete picture. It’s been split it up into little parts and each person is given just a little piece to work on. You feel like you’re some little part of a big network, and you’re not even a very interesting part, like a diode, or a RAM, or beta-catenin. We suspect it is a huge conspiracy. I probably shouldn’t be telling you this.

This epigentic event comes right at the conclusion of your PhD and it’s like setting off some sort of developmental IED, a roadside bomb filled with shrapnel. The shrapnel are microRNAs. They fly around everywhere and derepress a pathway involving canonical Wnt signaling, or non-canonical Wnt signaling, or some other type of Wnt signaling, simultaneously or in various combinations, and as a result we have 393, 217, or 655 potential new targets for cancer research, respectively.

microRNAs are so dangerous that any cell that sets them off would have to be an idiot, because that cell is always the first to get blown to pieces. Of course, your average cell is not generally noted for its intelligence, even though its DNA might encode a complete play by William Shakespeare. You can also inscribe Shakespeare onto a grain of rice, but that doesn’t make the rice smart, despite its massive genome, which is many times larger than that of humans. No, the true sign of intelligence is to learn from your mistakes, but if you mess around with microRNAs you won’t learn anything at all, because you’ll undergo apoptosis. Letting microRNAs loose is like putting a bunch of cats and raccoons together in a cage. You might do it once, but you certainly wouldn’t climb in with them. It’s not a pretty sight.

Now for several paragraphs this piece has been headed for a point, but then it got sidetracked during a long metaphor, like meeting a woman in a bar, and then walking her home, and I won’t go into detail about what comes next, we’ll just take a little pause at this moment so that each of you can individually complete that scenario using your own imagination.

The real point is that with the award of his PhD, David Fournier has reached scientific maturity. It’s like puberty, it’s like a butterfly, two concepts which can never be combined in one sentence without sounding creepy. Yes, even if we’re talking about reaching puberty in a metaphorical, scientific type of way, some people will automatically think of sex. Especially mentally disturbed people. If you’re thinking about sex now, you should stop, and perhaps consult a psychiatrist. And last but not least (not really, but it just felt like time to throw in a common but meaningless transition device), if you started reading this piece thinking that it would contain a discussion of David’s sexual phenotype, you can think again. This is not that type of magazine.

* * * *

So here David Fournier stands at the summit of human evolution, and at the peak of his maturity, both scientific and sexual, and he’s wearing a funny hat. For just a brief moment, he feels immortal. And then he is struck by a vision, that moment of clarity that comes to everyone upon reaching the top of a ladder: the realization that there’s only one way to go from here. At some point on the way down he’ll discover Viagra, which is a mixed blessing. It improves your potency but tends to have the opposite effect on a scientific career.

Sure, you hear these rumors about guys going on to become professors, but where’s the evidence? Professors are supposed to be in their lab, or a classroom, or in their office, but when you go looking for them, they’re never there. That calls to mind something David read while doing research for his dissertation. He found a quote from the great Ernst Haeckel, who had some not-very-nice things to say about professors before becoming one himself:

Es ist eigentümlich, daß sich gerade diejenigen Professoren am meisten gegen die Abstammung vom Affen sträuben, die sich bezüglich ihrer Gehirnentwicklung am wenigsten von demselben entfernt haben.

Now David’s knowledge of German is somewhat limited, restricted exclusively to the works of Hegel, who was really French (on his mother’s side; they pronounce the name Hégelle), so I have thoughtfully provided a rather loose translation into English:

It is appropriate that those professors are the sharpest critics of the idea of the descent of man whose brains have evolved least since the apes.

David actually put this quote into his dissertation, deep in the discussion, sort of a test to make sure the committee actually read the thing, like putting a jalapeno in a piece of pie. In English the quote comes out sounding a little mean, a little superficial, completely lacking the gravitas and resonance of the German original. When my own writing suffers from these problems, often right after lunch, I run it through Google translate and see if it doesn’t sound better in some other language. Here’s the quote in Basque:

Bitxia da, hain zuzen, tximinoak jaitsiera aurka gehienek badakite irakasleek, gutxiago ikusten duten hori kendu garunaren bera garapenean.

That automatically adds some intellectual depth, because you have to be a genius to learn Basque. I can’t provide a literal translation, but when you hear it out loud it sounds terribly dark and mournful. You automatically sense that it’s talking about death: either that of the professor, or the ape, and whichever one is left is throwing a wake for the one that died. Indisputably, the best wakes are thrown by the Irish, so here’s the Gaelic version, in the form of a toast delivered in a pub:

Tá fiosracht, i gcoinne pheaca, mar shiombail de na múinteoirí, ina choinne aon.

The first time David ever heard this, he thought it was French, and I won’t tell you what he thought he heard, because in French this sounds incredibly obscene. I thought the person was speaking English, perhaps with an Italian accent, and I heard this:

Gee I feels wrecked. I’m gonna puke marshmellows in a minute onna your chinna, hon.

But that’s just ridiculous. In Irish it’s a lot better; after a literal translation back into English you get this:

Curiosity is against sin, as a symbol of the teachers, against any.

This statement has an aura of mystery, like a Zen koan, or a Communist slogan, or the kind of thing a cabdriver would say to you. Probably a foreign cabdriver, for instance someone from Belgium.

* * * *

Successfully completing his doctorate required that David learn the Secret Formula for Success in a PhD, which can be purchased on-line, providing no one has hacked your PayPal account. The program guarantees success if you buy it, rather than downloading the bootleg copy, as David did, and then religiously follow all 12 steps. It’s true that 12-step programs have become popular in many scientific fields, such as Alcoholics Anonymous, and astrology, but any similarities between their lists and this one is just one of those bizarre coincidences that sometimes happen when you live in a random, chaotic universe.

1. We admitted we were powerless over science—that our lives had become unmanageable.
2. Came to believe that a power greater than ourselves (our group leader) could restore us to sanity, despite having no good reason for believing this.
3. Made a decision to turn our will and our lives over to the care of God (our group leader) as we understood Him.
4. Made a searching and fearless moral inventory of ourselves, our lab benches, and the bottom drawer where He keeps the emergency bottle.
5. Admitted to God (our group leader), to ourselves, and to another human being, for example, a postdoc, or our psychiatrist, or just some random person in the street, the exact nature of the mistakes we made in our experiments.
6. Were entirely ready to have God (our group leader) remove all these defects of character, using only a pipette and many cover slips.
7. Humbly asked Him to remove our shortcomings, by docking our pay, or making us clean out the mouse cages.
8. Made a list of all persons whose experiments we had ruined, and offered to repeat them all, on weekends, in exchange for authorship somewhere deep in the middle of the list.
9. Made direct amends to our competitors wherever possible, except when to do so would injure them or others, unless we would get more impact points by sticking it to them.
10. Continued to take personal inventory, and when we were wrong, promptly admitted it, preferably before the paper had been submitted, in which case we snuck it in during the review process.
11. Sought through prayer and meditation and incredible amounts of caffeine and late-night phone calls to improve our conscious contact with God (our group leader) as we understood Him, praying only for knowledge of His will for us, hopefully sent by email, and the power to carry that out if we have high-throughput technology platforms and if we feel like it.
12. Having had a spiritual awakening as the result of these steps, we tried to carry this message to the next generation of predocs, by making their lives just as miserable as our had been, and to practice these principles in all our affairs.

The twelfth step is hardest, especially if you have a minor genetic defect like a conscience, or a soul, and only a few truly master it. Which way will David’s ball roll? At what point will he reach his finally differentiated form? Will fundamental discoveries in stem cell research permit him to de-differentiate if he decides, at the age of 70, to start a new career playing the pan-pipe with a band of South American street musicians? Will he ascend to the Académie Française, and then be buried alongside Voltaire in the Panthéon in Paris, after they remove his heart and brain, as they did with Voltaire? Or will he end up under a parking garage in England, like Richard III? Only the future will tell. Further research is necessary. Although we do have some promising lead compounds.

– Russ Hodge