Author: russhodge

Photos taken by Mehrnoosh Rayner

Getting warmed up. That thing on my face isn’t food – just a microphone. Felt like a little UFO hovering around my mouth the whole evening.

Half-way in and nobody dead yet. So far so good.

With Jochen Wittbrodt, developmental biologist extraordinaire, and Ken Holmes, founding father of synchrotron radiation in structural biology extraordinaire.

Have you noticed how anything that happens on Mars, or in outer space, or even at a really high altitude, such as the top row of bookshelves in the library, is ecstatically portrayed by the media as evidence of extraterrestrial life? Don’t get me wrong, I’m all for extraterrestrial life. I’ve been actively looking for it since I was a child. The closest I’ve ever come is the discovery of an Unidentified Swimming Object (USO) in a bowl of soup purchased in the Gare du Nord in Paris, France, but further investigation suggested a terrestrial origin, that it had evolved from the green fungus on the horse steak (Plat du Jour), crawled over the rim of the bowl, and rapidly adapted to an aquatic environment. Take-home message: never order the 14,- Euro ménu in the Gare du Nord – unless you care to repeat this experiment.

Two weeks ago we saw the surfacing of a new trend whereby the media (and apparently a few scientists) interpret the discovery of anything spherical in space, or from space, as evidence of extraterrestrial life. This is not entirely unreasonable. After all, the Death Star was spherical, wasn’t it? I’m not completely clear about the species assignment of Darth Vader or Carrie Fischer – they certainly look human rather than alien (except for Carrie’s hair, or Darth Vader’s brain after being partially lobotomized by a light saber), but since they came from a Galaxy Far, Far Away they were certainly extraterrestrials, by definition…

Of course, there are a few spherical objects in space that aren’t necessarily evidence of E.T.s (the moon, stars, planets without atmospheres) – but whenever a new sphere pops up, you have to ask yourself the question. If it happens once, surely a certain degree of skepticism is called for. But twice in one week?? And then a third time??? Science requires an open mind… Let’s review the evidence.

Case number 1: Water on a really fast hat

This week astronomers discovered a spectral signature of water on HAT-P-11b, a “Neptune-sized planet” (in other words, a really, really large ball) orbiting a sun in the constellation Cygnus. In my opinion they could have found a simpler name for the planet, one that was more aesthetically pleasing, like “Giovanni”, or “Mergatroid”, but then, I’m not an astronomer. Not that biologists are any better; they probably would have called the planet Seven-up, Bruno or Oskar, or Big Momma Stem Cell, or something equally strange.

I particularly like the title of one of the media reports on this story: “Hot Wet Alien World discovered in constellation Cygnus.” Talk about blatant attempts to draw hits to your website… If a person types “hot wet alien” into the Google search box – which surely happens all the time – guess what pops up first?

Interestingly, none of the reports (including the abstract of the article in Nature) tell us precisely which star this planet is orbiting, perhaps to keep us from flying out there and taking a look ourselves. A word of caution if you’re contemplating a road trip. What looks like a nice, tidy constellation from here on Earth is actually spread out over some considerable distances. One of the stars in Cygnus is about 11.4 light years from us, and another is 3200 light years away. So don’t leave home without a full tank of gas, or plasma or whatever, and a whole bunch of NASA freeze-dried ice cream.

The authors of the paper cagily tell us that the planet lies at a distance of about 120 light years from Earth, so if you’re willing to do a bit of research, you can probably figure out the identity of the culprit star. They also say that the planet orbits its sun about every five days. And that it’s atmosphere is “surprisingly clear.”

I don’t find this atmospheric clarity surprising at all on a planet four times the size of the Earth, whizzing around its sun in a year that lasts only five days. At that speed you’d need to hang onto your HAT-P-11b. This planet is really moving. If you’ve ever ridden down the German Autobahn at 250 kph in a convertible with the top down, you’ll know that any fog inside the car tends to dissipate rather quickly. It’s also rather hard to breathe. You do, on the other hand, accumulate a lot of smashed bugs, which suggests that any aliens on HAT-P-11b are probably hunkered down on land, holding on for dear life, and have evolved seatbelts, or at least the sort of glue by which Earthly barnacles attach themselves to ships.

The E.T. aspect of this story wasn’t played up as much as in the past, when the merest whiff of water outside our solar system has consistently caused a sort of media feeding frenzy, or at least a bar crawl. You may recall the story I reported on here, in which a certain Prof. Vogt claimed that life was “certain to exist” on a planet called Gliese 581g. His reasoning went something like this: the planet lay in the so-called “habitable sphere” (yes, another ball) around its star, which made it likely to have water, which led to Vogt’s extraordinary and somewhat inscrutable statement during a press briefing:

“Personally, given the ubiquity and propensity of life to flourish wherever it can, I would say, my own personal feeling is that the chances of life on this planet are 100 percent. I have almost no doubt about it.”

We’ll just pause here for a moment so that you can puzzle over the intricacies of that statement. As you do, keep in mind the fact that two weeks later, Michael Mayor and his exoplanet-mythbusting team from Switzerland suggested that Gliese 581g might not exist at all – it could merely have been a glitch in “noisy” spectroscopic data, or someone who forgot to clean his eyeglasses. I couldn’t find a response from Prof. Vogt. In fact, I haven’t heard much mention of him at all recently.

Case number 2: A ball on Mars.

This one is really impressive; check out the image. That pesky rover Curiosity keeps taking pictures of odd things as it rolls across the surface of Mars. Remember the space rat it photographed in May, last year? NASA says it was just a rock – of course they’d say that, otherwise they’d have to tell us the truth about Area 51 and Steve Jobs and a lot of reverse-engineered alien technology, such as the iPhone 6. This week Curiosity photographed a perfect little sphere, just sitting out there on a rock, minding its own business. The official explanation proposes that it was carved out by water, but there are winds on Mars, and it surely would have rolled away by now.

I actually have a hypothesis about this: I think it’s a golf ball, most likely hit by one of two people: Alan Shepard or Tiger Woods. I have this on good authority from my father, Ed Hodge, who has turned the discovery of lost golf balls into an art, if not a science, and a lucrative source of retirement income.
If this artifact on Mars is Shepard’s golf ball, it was launched from the surface of the moon on Feb. 6, 1971. On that date astronaut Alan Shepard climbed out of the lunar capsule of Apollo 14 with a golf club and two golf balls. One news report says he had smuggled them aboard in his “space suit.” Where in a suit could you hide a long, pole-shaped object and two balls? Here we’ll take another brief pause so that you can consider that one…

Just remember that security measures were a bit more lax in 1971. Today you’d never get them past airport security, let alone onto a Saturn V rocket. People have been known to try to smuggle 62 poisonous snakes through security, but a golf club? And two balls?

Anyway, is it conceivable that one of Shepard’s two balls (yes, I am referring to the golf balls, for those of you with perverse imaginations) reached escape velocity and, through a combination of careful aim, dumb luck and Newtonian physics reached this precise spot on Mars, to land 43 years later right in the path of Curiosity? To answer this question we need to consider a couple of factors (actually a lot more, but let’s keep things simple).

First: escape velocity on the moon is 2.4 km per second. Could Alan Shepard have hit a golf ball that fast? On Earth, they say, most golfers achieve a swing that is 160 km per hour. That works out to about 0.044 km/sec. In his prime, Tiger Woods achieved a swing of about 0.056 km/sec, and he didn’t have to smuggle anything onto the course in his pants to do it (well, actually…). Anyway, most of Tiger Woods’ tournaments have taken place on Earth, at least those that we know about, whose escape velocity is 11.2 km/sec. Tiger Woods would have to hit the ball 200 times faster to send it out of Earth’s atmosphere toward Mars, and there are all kinds of other things to take into consideration, such as resistance posed by the atmosphere and its ability to evade all sorts of obstacles: birds, airplanes, innocent bystanders (remember President Gerald Ford?) and the 500,000 pieces of space junk floating in Earth orbit.

Alan Shepard, on the other hand, would only have had to hit the ball 60 times harder to send it on its way to Mars. Consider that his swing was unencumbered by any wind resistance on the lunar surface. It was, however, perhaps encumbered by his bulky space suit, which would probably be like playing golf in one of those Sumo wrestler costumes. The one time I put one of those on I was almost smothered by a Portuguese woman who was 5’2” tall and weighed 85 pounds, but then we had gravity to contend with. Taking all of these factors into consideration, I think the evidence tips things in favor of Shepard.

One should perhaps note here that the average speed of a bullet leaving a .44 Magnum, as can be observed in the classic movies of Clint Eastwood, is approximately .40 – .475 km per second, which means that Alan would only have had to hit the ball about six times the speed of Clint’s bullet in order to propel the thing out of lunar gravity and toward its current location. Is this more likely than an alien leaving little round spheres on Mars, perhaps in the form of rodent droppings? You decide.

Case number 3. Conspicuous clay ovoids.

I love space programs, despite the fact that they are funded at a level of about a million times that of cancer research, but it turns out you can find Martians without ever leaving Earth at all. The third story about aliens is another tale of cracking open a meteorite and finding – no, not the Higgs boson, although I don’t think this can be definitively ruled out – something that (sort of) (maybe) might (possibly) resemble a cell.

I am speaking, of course, of the “conspicuous clay ovoid” discovered this week in a meteorite named Nakhla (a much cooler name than HAT-P-11b). Nakhla was ejected from the surface of Mars (there is no evidence that a golf club was involved), flew off into space, and collided with Egypt. It also collided with a dog, which was vaporized instantly, leaving no traces, not even dog DNA. I especially like the logic by which this event is reported on the website of NASA’s Jet Propulsion Laboratory:

“This dog story did lead directly to the recovery of several fragments of the Nakhla meteorite. The meteorites are very real, so there’s no reason to doubt the dog story.”

Decades later, scientists in Greece and the UK began slicing Nakhla up into tiny slivers, oblivious to the fact that they might be cutting up tiny little Martians, and in the process they came upon a mysterious little sphere that they call a “conspicuous biomorphic ovoid structure.” Biomorphic means “resembling or suggesting the forms of living organisms,” and “ovoid” is defined as “shaped like an egg,” which gives anyone reading the article all sorts of reasons to think of aliens, and makes you wonder about the wisdom of slicing up meteorites. I mean, the thing might hatch.

The news widely reported this as evidence of a “cell structure,” “more evidence of the possibility of life on Mars,” or even that “Mars is still habitable.” All very promising, until you carefully read the paper, which provides a more sobering view.

The first citation from the paper starts out promising, but fades out toward the end: “One reason why we carried out this investigation into the origin of the ovoid structure in Nakhla is because the conspicuous rounded shape of the structure is somewhat reminiscent of a terrestrial cellular microorganism… Despite the conspicuous shape and structure, the ovoid is very large, and martian microorganisms are expected to be chemotrophic and therefore probably very small (<1 μm) in size.”

If you’re patient enough to read all the way to the end, or at least past the first 140 characters, a skill which seems to evade most journalists, the biological hypothesis receives a pretty good dousing: “The consideration of possible biotic scenarios for the origin of the ovoid structure in Nakhla currently lacks any sort of compelling evidence. Therefore, based on the available data that we have obtained on the nature of this conspicuous ovoid structure in Nakhla, we conclude that the most reasonable explanation for its origin is that it formed through abiotic processes.” Abiotic meaning that this is not the ball of an E.T.

Alas, alas, having balls is not sufficient evidence for all of this week’s wonderful speculation about E.T.s. But please keep looking, guys. There are a lot more spheres out there in space to investigate. Probably more rodents as well. Maybe even a Yeti. (After all, if you find a Yeti in Norway, as I have suggested in another piece, it must have come from somewhere.) Or at least a pyramid carved in the shape of a face. After all, Nakhla was aimed at Egypt, and aimed specifically at a dog. Sort of a Martian meteorite drone. We know that rodents on Earth don’t particularly like dogs; why should they be any different on Mars?

Naturally, these three reports could be simply a random set of bizarre coincidences whose occurrence within a single week defies logic and all kinds of probabilities which are difficult to estimate without knowing what dark matter is, or the current whereabouts of the elusive Higgs boson. But I take my responsibilities as a science writer seriously. Somebody has to connect the dots. Or in this case, the balls.

(Getting evolution wrong, once again)

Recently the Mother Nature Network (not to be interpreted as the Mother of the Nature scientific publications, as far as I can tell) posted an article by Michael Graham Richard entitled “What will humans look like in 100,000 years?” (You can find it here.) The result is another case of an interesting question that gets convoluted by some rather strange assumptions about how evolution works.

The image that is presented represents the work of “artist and researcher Nickolay Lamm … with help from Dr. Alan Kwan,” a PhD in computational genomics. Richard’s article doesn’t state whether the piece is based on an actual scientific publication or not. I couldn’t find either name on PubMed, which means that the paper on the topic hasn’t been published yet, or has been rejected many times, or is in some nebulous state in between. Maybe they’ll have a better chance of finding a journal in 100,000 years, when their hypothesis can finally be tested.

I was immediately alarmed by the fact that the man and woman in the picture are Caucasians. If current demographic trends continue, I doubt there will be many “Caucasians” left in 100,000 years, if there are any at all. Lamm gets around this with the statement, “we shouldn’t read too much into the fact that the man and woman are Caucasian because those were just the best models he could find.” All right, we’ll give him a pass on that one.

The head of the man of the future is a bit more triangular than that of most people nowadays. This is explained by the “Heads are a bit bigger to accommodate larger brains,” the article explains. Well, to me, the shape of the man’s head has changed, but the woman’s hasn’t really. Will only men have larger brains? Will they be born that way? Will women need larger hips to bear them?

It’s true that that the female model they used to begin with has an unusual face to begin with: her eyes are set higher than normal in the face, if you go by classical rules of drawing that tell you to place them equidistant from the top of the head and the bottom of the chin. So it may look like her forehead has stretched upwards – maybe, though, her eyes have just migrated down to a more normal position in the face.

And is it true that we will really need larger brains? Won’t I have an iPhone able to store petabytes of data, or some kind of chip located at the base of my brain that can immediately access Wikipedia and Facebook (everyone will be friends with everyone in 100,000 years, all 100 billion of us)? Not to mention direct, on-line streaming. These gadgets would allow us to “outsource” most of the information we currently have to store in our brains. So a good argument can be made that our brains might shrink – it’s already happening, to judge from a lot of daily experiences I have with other humans.

The biggest difference in Lamm’s humans of the distant future is the size of the eyes, which have grown to make people look like cartoon characters. “Manga-style eyes,” to quote the article. It states, “Lamm speculates that this would be a result of human colonization of the solar system, with people living father away from the sun where there is less light.” He goes on to say that these conditions might promote the development of a sideways blink (that would be cool) and thicker eyelids to offer protection from cosmic rays on the fringes of our solar system.

To insinuate these features into the population at large and influence its evolution, the original mutants would have to live on Neptune or Pluto or wherever for a loooong time, probably thousands of generations, and have oodles of very fertile kids who would then come back and mate (very successfully) with the founder population on Earth. Of course, other people might be living on Venus, or Mercury, where there’s a lot MORE light, so presumably they’d have smaller eyes. Or maybe their eyes will develop built-in sunglasses, where our lenses get darker when exposed to bright sources of light. Sort of like the eyeglasses we wore back in the 70’s, which were supposed to turn grey in the light. At some point they usually got stuck in “grey mode,” which meant that all of our family pictures look like Mafia reunions.

Lamm even adds yellow rings to the eyes, “special lenses that act kind of like Google Glass does today, but in a much more powerful way.” Constant access to the Internet (right there on your eyeballs) will reduce the amount of information we need to access in our brains; we won’t need to store anything that’s instantly available on-line. This is another argument for the smaller-brain trend.

Of course, evolutionary innovations in eyeballs will pose some social challenges: it will be hard, for example, to keep people from cheating during tests. And you’ll be able to watch movies on your contact lenses while doing other things, such as driving, unless society has solved the problem of automobiles. Maybe you’ll have to remove the lenses during these activities, or switch them off, but that will probably be illegal. The business lobby will be tracking the motion of your eyeballs and people will be recording what you’re seeing for marketing research, and they’ll have a huge lobby to pass profitable laws.

I was in Oslo recently, which experiences long periods of decreased daylight in the winter months. That’s the kind of place where you’d expect to see the birth of huge eyes, if they arise by chance and somehow lead their owners to have a lot more kids. I didn’t notice any of these cartoon people walking around. But maybe it was just too dark to really notice. Next time I’ll keep my eyes open.

This is the introduction to a talk I gave in Oslo last Friday, Sept. 12, 2014, at a conference on science communications. A video of the complete talk, including the more serious part, can be seen at this link. It’s the last two film segments on the page.

Thank you Unni for that very kind introduction. It was all true, even the parts that sounded like some weird movie that you would probably never recommend to your friends. My name is Russ Hodge and it’s a great pleasure to speak at this wonderful event. I’ve been to Oslo many times and always enjoy the trip to your beautiful city. I come here every year the first week of December to teach a course on presentations skills to molecular biologists. I don’t know how successful it is, but nobody has ever died during it, or even been seriously injured, and they keep inviting me back, so you may draw your own conclusions.

I couldn’t remember exactly how many times I have been to Oslo, so last night I sat down and tried to figure it out. I came the first time in 2007, and have come one time every year since, so I could apply this formula:

2014 –  2007 = 7

I use the same formula when somebody asks me how old I am. Here, of course, the calculation doesn’t work out; you have to add another trip to include both 2007 and 2008. Subtraction can be sneaky that way.

Now this is a biological problem (the migratory patterns of a human being, me), and I used a calculator on my computer to solve it. That makes it an example of bioinformatics. Everyone says bioinformatics is really hard, but I didn’t find it that bad at all. Of course it depends on the methods you use. For example, bioinformaticians sometimes use Markov models or Monte Carlo simulations, but those would have been a whole lot harder, especially since I don’t know what they are. So I just used basic subtraction. (By the way, I have to do the same thing when somebody asks me how old I am.)

Russ, puzzling over a problem in bioinformatics

Of course these results don’t have any statistical validity, so I added this:

(2014 –  2007) + 1 = 8    (p < 0.05)

I know even less about statistics than bioinformatics, but I do know that statisticans always put a p in there somewhere, and it’s always greater or lesser than some other number, so there you go. If you want to know more about this, we’ll be hearing later from a biostatistician, Jo Røslien, and I’m sure he’ll be glad to explain it to you.

Eight trips to Oslo, wow. There aren’t many places in the world I’ve been eight times. I’ve probably been home a few more times than that. If you ask my wife, she might not agree, but then, she’s not a bioinformatician.

When you’ve been to a place eight times you’re practically a native. That’s how I feel about Oslo. Of course, I don’t speak a single word of Norwegian, which makes me a strange sort of native. Sort of a foreign native. Still, Oslo has some surprises even for a native. For example, when I arrived yesterday, Oslo looked DIFFERENT. Was there more than one Oslo? Had I flown to the wrong one? It took me a while to figure out the problem, but I finally did: all my other trips have been in DECEMBER. I don’t know if you’ve noticed this, but it’s DARK in December. I arrive in Norway, get off the plane, and I just automatically say, “Would somebody please turn on the lights?”

In science, the hardest part of finding an answer is sometimes clearly identifying the problem, and that was certainly true in this case. Once I knew that Oslo was too bright, there was a simple solution – just put on some sunglasses.

So once again, thank you for inviting me to Oslo, where I feel like a native, but a special kind of native, who only comes out in the dark and has poor communication skills. Maybe a native Norwegian bioinformatician. Or a native Norwegian vampire. Or a native Norwegian bioinformatician vampire. If you have any of those in Norway, that’s exactly how I feel.

* * * *

Science communication is serious business, and I do have some serious things to say about it, and I promise I will. But one of the most important things I have to say about it is that we ought to have more FUN at it. I’ve been a professional science communicator for 17 years. It’s a great job, but sometimes it’s hard. You run up against a lot of walls. If you could see them coming, you could avoid them, but they’re sneaky, and they’re mostly invisible. You’re writing an article, or you’re talking to someone, and boom, you run against an invisible wall, and you go flying on your ass. Over and over again.

I’m going to talk quite a bit about invisible walls today. These walls are in the minds of scientists, and in the minds of science communicators, and in the minds of the people we’re trying to talk to. I’m going to talk about ways to make invisible walls visible, and what that means for science and science communication.

But first let me say that if you see somebody run along, and he bangs into an invisible wall and falls down, and then he gets up and starts running and it happens all over again, you’re probably going to laugh. It’s not so funny when it happens to yourself… Well, why not? Why not laugh at ourselves a little bit? So I decided to start a CRUSADE to make science communication more FUN.

Now the crusades of history involved huge armies of religious people setting out to take over a foreign country. I’m not religious, and my crusade is very small; in fact, there are no followers except for a few people who read my blog and may be seriously disturbed. But a lot of great ideas start small. That’s also true of bad ideas, I know. The trick is to tell the difference. How? Only time will tell. I’m still at the very beginning of my crusade, the early planning phase, sort of the grant application phase. For example, I haven’t picked which country this crusade will invade. Maybe Norway? We’ll see.

So today I’m going to talk about invisible walls, and making science communication fun, and hopefully say something useful along the way. We’ll see.

* * * *

Sometimes I think science communication is difficult because we’ve gotten ourselves into a box and we need to get out. This inspired the title of my talk, LETTING SCIENCE COMMUNICATION OUT OF THE BOX, in case you’ve forgotten. There’s also a CAT in the title, which you may also have forgotten, but that’s okay, I’ve just reminded you.

I’m sure most of you realize I’m alluding to a famous experiment proposed by the physicist Erwin Schrödinger. In fact, one of the speakers this afternoon, Chris Vøløy, is involved in a project called Schrödinger’s cat. Actually his project is called “Schrødingers katt” , which is Norwegian, so I might be translating it wrong. For all I know, in Norwegian this might mean “Einstein’s parrot.” Chris, are you here? Did I get this right?

Schrödinger’s cat is a THOUGHT experiment, which means the cat is an imaginary cat. Now if a biologist were to do an experiment with an imaginary animal, he’d face a challenge getting his paper published, but in physics you can get away with these things.

Nobody has ever done Schrödinger’s experiment, or if they have, they won’t tell you about it, because it would violate all kinds of regulations about the ethical treatment of animals. Okay, it’s a metaphorical cat, but even metaphorical animals deserve some respect.

Erwin Schrödinger and his cat

Schrödinger’s experiment also violates all kinds of rules of common sense (for example, the difficulty of getting a cat into a box). Again, in a thought experiment that doesn’t matter. For example, in a thought experiment I could be the King of Norway. Or the Queen of Norway.

Anyway, Schrödinger’s experiment with the cat is interesting for science communication because it’s unethical, illegal, probably impossible, and on top of that, NOBODY UNDERSTANDS WHAT IT MEANS. Well, it meant that Erwin Schrödinger didn’t like cats very much. But other than that nobody really understands it. And yet 79 years later here we are still talking about it. If that’s not successful science communication, I don’t know what is.

Basically the experiment involves locking up a cat in a steel box with one atom of a radioactive substance that would decay after a certain period. Now it’s a bit irritating that Schrödinger leaves some details of the experiment vague, and others he explains in great detail. For example, he doesn’t mention what type of atom you should pick, or how you capture only one atom, or how you know you’ve got the right one. Another detail he doesn’t explain is whether in this experiment, he is the King of Norway or not.

But he does go into detail about the placement of the atom in a Geiger counter. Once everything is in place, if the atom decays, “the counter tube discharges and through a relay releases a hammer that shatters a small flask of hydrocyanic acid.” In case you don’t know, that’s a particularly nasty type of poison. Anyway, you’re not supposed to look into the box. The question is this: At some point, the half-life of the radioactive substance, there is a 50 percent chance that the cat will be alive. Schrödinger doesn’t tell us what the probability is that the cat will be dead, but there’s a formula for this somewhere; you can find it on the Internet.

With all of this Schrödinger wanted to make a specific point. Schrödinger says that until somebody opens the box, the cat is in an indeterminate state. It’s not really alive and not really dead. Actually he puts it a different way, and if you ask me, it’s a pretty disgusting. He says, “The living and dead cat (pardon the expression) [will be] mixed or smeared out in equal parts.”

This is why I said it’s important to choose the right radioactive substance. If you have a substance that decays in one hour, that’s fine. But suppose you pick a substance that takes longer to decay, a lot longer. Maybe weeks or years. I don’t know if you’ve ever kept a cat in a box for a really long time, but I’m telling you, it smells bad. It smells bad whether the cat is dead or alive, but those are different kinds of bad smells. You’ll definitely know. And even if you don’t, the cat will know.

Now as I said, this is a thought experiment, so we don’t have to care that much about the methods, or the results, or the discussion. Today Schrödinger would never get this published, except on a blog, or in The Journal of Impossible, Ridiculous, and Pretty Disgusting Thought Experiments. Well, maybe not. I know the editors of that journal personally and they might not even publish it.

In fact, there is a group of people in California who are actually doing this experiment, or at least an experiment that’s pretty close. I’m sure you’ve heard of them. I’m talking about those companies that offer cryopreservation. You pay the company a lot of money and when you die, they will wrap you up in tin foil and freeze you. The idea is that in 100 or 200 years, or 1000 years, or a million years, scientists will be able to cure the disease that killed you. They’ll even be able to cure it after you’re dead, which is pretty wonderful.

This is supposing, of course, that in one million years the company will still exist, and that California will still exist, rather than sinking in an earthquake, and that in one million years there has never been a power blackout in California. Right. In a state that elected Arnold Schwarzenneger governor. Good luck. In fact, there have already been blackouts. You have to hope the company has some big batteries somewhere, with a lifetime somewhat longer than the battery on your laptop.

Anyway, if the electricity has stayed on all the time, and if somebody remembers the human popsicles stored in the freezer in the basement, and if science learns to cure cancer and Alzheimer’s disease and develops some sort of nanotechnology to repair the damage that being frozen for a million years causes to a human body, maybe those people will be revived. You can pop them into the microwave. But first remove the aluminum foil. You shouldn’t put aluminum foil into a microwave. I’ve tried, and the results are not pretty.

The frozen people will probably wake up in some sort of Star Trek universe, where there’s all kinds of new technology they have to learn. The iPhone one million point five. People who use Macs will have an advantage. I’m sure we’ll still have Macs in a million years. But we won’t have PCs. PCs will have become extinct, like dinosaurs, maybe because of an asteroid strike.

Well, until all that happens, those people in California are in a state like that of Schrödinger’s cat. Except for the part about being mixed or smeared out. That’s might happen if the electricity goes out. But if everything goes well for a million years, we hope they’ll be reasonably intact. It’s hard to say. They’ll probably be fatter – water swells a bit when it turns to ice – but they’ll have been transformed from a state of death to a state of life. So yes, I guess you can say that currently, those people are in an indeterminate state like Schrödinger’s imaginary cat.

The Jentsch lab and the FMP Screening Unit identify a long-sought channel that helps cells reduce their volume

Some important scientific questions resist a solution for years, until a new technology appears that seems to put an answer within reach. Success depends on creativity – finding a way to translate an old question into a form that can be handled by the new method – but also on timing. And a bit of luck never hurts.
About four years ago Thomas Jentsch thought that the time had come for an all-out assault on a question that had teased biologists for decades. The campus had been acquiring instruments that might be the key to the solution. But the clock was ticking; other labs had the technology, too, and were interested in the same question: How do cells reduce their volume?

All types of cells undergo alternating phases of expansion and shrinkage as they divide, specialize, migrate, and cope with changes in their surroundings. In a liquid environment without any barriers, particles move from areas of high concentration to low. This applies also to water “particles”, which tend to diffuse until they have reached the same concentration everywhere. Water will flow from regions of high concentration (where it is diluted by a low concentration of osmolytes like ions, the constituents of salt, or other particles) to areas of low water concentration (where it is diluted by a high concentration of salt or other particles). So if cells are exposed to a hypoosmolar solution (which contains fewer osmolytes), water will flow into the cell, which now contains more osmolytes than its extracellular environment. But because the cell is enclosed by a membrane, the particles within it cannot simply be diluted to reach an equilibrium with extracellular concentrations. Instead, osmotic pressure will build up inside.

The same accumulation of internal water can occur when the number of internal particles increases through a breakdown of organic molecules, like glycogen to sugar, and cells may expand until the membrane is stretched to its limits. In order to keep from bursting, the cell needs to lose particles such as chloride or potassium ions, or organic osmolytes such as the amino acid taurine.

The loss of these particles decreases their internal concentration, which eventually becomes lower than in the external medium. This leads to a reversal of water flow, cell shrinkage and a recovery of the previous, normal cell volume and shape – called regulatory volume decrease. This volume decrease was known to be associated by a loss of negatively charged chloride ions (anions) from the cell through a channel.

Many aspects of the transport of chloride and other ions are well understood thanks to years of research on the part of Thomas’ lab and many others. This type of work has exposed hundreds of types of ion channels in cell membranes. These pore-like structures are composed of proteins woven through the membrane in a way that allows them to open and close. Channels are highly specialized to admit specific ions or other particles in response to changes in electrical charge, pressure, or other conditions. Their behavior is usually regulated by intricate biochemical networks. Most ion channels are so essential that any flaw in their components or their regulation can cause serious diseases – Thomas’ lab has established many such connections.

Much less was known about the outward passage of anions like chloride and other particles as cells shrink. Scientists postulated the existence of a specialized channel and had even given it a name: the volume-regulated anion channel, or VRAC. “VRAC was a hot topic,” Thomas says. “Hundreds of papers were being written about it and it was the subject of major international conferences.”

Despite all the interest, and the fact that the biophysical properties of the channel and some of its important functions were known, no one was able to actually find the channel protein. Occasionally a lab claimed to have identified a protein that belonged to it, but one by one, these candidates were discredited. While a number of drugs interfered with the channel’s behavior, they also disrupted other cellular processes. Without identifying a specific protein, scientists could understand neither these effects, nor the way swelling triggered changes in the channel’s behavior.

Part of the interest – aside from the fact that the channel served an important basic function in all types of cells – arose from observations that it, too, seemed to be linked to serious diseases. In any case, Thomas doubted that VRAC could hide much longer. The sequencing of the genomes of humans and other organisms had led to the development of technologies that permitted scientists to scan the DNA sequence for molecules with specific functions. Recent papers by other groups hinted that they were using these methods to search for the channel.

“Identifying the VRAC would finally give us a handle on some of these questions,” Thomas says. “Basically, it would open up an entirely new field.”

* * * * *

Until fairly recently, the study of gene functions almost always required an arduous, molecule-by-molecule approach. The earliest methods involved forward genetics: a scientist found an organism with a specific variant of a feature or a defect, then studied patterns of inheritance to establish that a single gene was involved. You might not identify it for years, or decades, but at least you knew it existed.

Modern biochemistry made it possible to do reverse genetics, through which scientists interfered with a specific gene and then studied the consequences for an organism. Most of these approaches depended on physically removing or altering genes, and thus eliminating the proteins they encoded.

The 1990s brought a powerful new alternative based on introducing artificial molecules called small interfering RNAs (siRNAs) into cells. siRNAs are composed of nucleotides, like other RNAs and DNA. This means that strands with complementary sequences will dock onto each other, which is the reason for the double-stranded helix structure of DNA. RNAs are usually single-stranded, but if an siRNA docks onto a complementary mRNA it produces a short, double-stranded region. Cells normally take notice and dismantle the molecule before it is used to make proteins. So artificially introducing siRNAs into cells has become a new, effective way of “knocking down” particular molecules by interrupting the flow of information from gene to RNA to protein.

Since the first applications of siRNAs in plants and simple model organisms, researchers have adapted them for use in human cells. The completion of the human genome revealed the entire set of mRNAs encoded in it, and scientists working in companies began constructing vast “libraries” of siRNAs to target them all. Theoretically this could be used to block the production of every human protein, one-by-one. Along the way, you would probably hit a molecule required for a particular function – such as the VRAC – and shut it down.

Humans have over 22,000 genes, meaning that the project would require at least that many experiments – actually the number would be much higher. There is no way to predict with certainty that a particular siRNA will work reasonably well within a cell. The way to get around this was to develop multiple siRNAs for each target and then challenge cells with two or three different versions; one of them would usually work.

But 22,000 experiments – let alone two or three times that number – could not be performed by hand. Robots and automation would be required at each step: to prepare samples, perform experiments and collect the data, and sophisticated software to analyze the results.

In the genome age, the technology and software needed for genome-wide siRNA screens began coming together, leading to several successful projects that have produced fascinating new insights into the functions of genes.

Several years ago the FMP created a Screening Unit, now jointly operated with the MDC, and acquired high-throughput, automated equipment to manage such large-scale projects. Headed by Jens von Kries, the facility has made significant contributions to a number of campus projects, many drawing on the tens of thousands of compounds that the unit has collected from researchers, pharmaceutical companies, and other sources. A typical use of this vast library is to challenge cells with substance after substance, hoping to disrupt a specific process in cells – with the aim of further developing the “hit” into a research tool, possibly even a drug. Chemists associated with the Unit then step in to tinker with a successful substance to strengthen its effects, make it less toxic for cells, or lend it other desirable properties.

The Screening Unit had also acquired a library of siRNAs that targets every known gene and then, through grants including a successful application from Thomas to the European Research Council (ERC), also a machine called FLIPR that was needed for following the time course of hundreds of experiments in parallel. So the necessary tools were on hand to search for VRAC components. “But first an extremely reliable experimental procedure had to be developed to detect the opening of the VRAC channel upon cell swelling,” Thomas says. “Any test that will be carried out tens or hundreds of thousands of times has to deliver clear, dependable results.”

Postdoc Tobias Stauber and PhD student Felizia Voss took the first steps toward developing a robust experimental protocol. This required almost two years, and as Thomas says, “There was no guarantee that we would find VRAC, even with this whole-genome approach, and certainly no guarantee that we would find it first.” Failure would have been particularly hard on Felizia, who was devoting her entire time to the project, and other PhD students who had become involved. Positive results would provide an impressive story for their dissertations; no one wanted to consider the alternative.

Tobias and Felizia began by growing cultures of human embryonic kidney cells – a favorite model for genetic research because the cells readily take up foreign molecules such as siRNAs. First they equipped cells with a yellow fluorescent “reporter” protein that would reveal whether cells changed their concentration of anions upon swelling. The cells were placed in a diluted medium in the presence of the ion iodide, which entered the cells through the opened VRAC channel and quenched the fluorescence. Although VRAC opening leads to a net loss of cellular chloride and volume regulation, the addition of external iodide, which is not present in the interior of the cell, leads to a net influx of iodide – channels are like “holes” that allow movement in both directions. The basic idea was that an siRNA that blocked the production of VRAC within the cell would abolish, or at least reduce, the loss of fluorescence upon exposure to a diluted medium containing iodide.

“This entire approach depended on an assumption that simply might not turn out to be correct,” Thomas says. “If a single specific molecule were required for VRAC, we might find it in the experiments. But if several molecules formed VRAC together, and each of them could be functionally replaced by another one, we might never find it with this approach. In fact, we discovered that VRAC has five components, and only one is absolutely required – we were lucky that only four of the subunits can replace each other.”

The scientists optimized the transfection of siRNAs and other aspects of the experiments, such as the number of cells, and established appropriate controls. Once this had been accomplished, it was time to scale up the experiment for a genome-wide search for VRAC components, trying to eliminate one essential component of the channel.

Now Katina Lazarow, a postdoc with the Screening Unit, stepped in to adapt the procedure to the instrumentation. Each step of the pipeline of experimentation and analysis had to be adapted to the specific question the scientists were trying to answer. This required many months of intense work – often through the weekends. The actual screen would also take about two months of work, once again including weekends.

* * * * *

Such a large experiment required automation for the preparation of cell cultures, introducing a different siRNA into each one, then capturing images that would show whether the intervention had any effect on VRAC. These steps were performed in a specialized piece of machinery called the FLIPR, acquired second-hand with funds from Thomas’ grant and the Screening Unit.

The machine has become an important addition to the Screening Unit because it allows scientists to prepare experiments in all 384 “wells” of a assay plate in parallel, and follow changes in fluorescence over time, also in all the wells in parallel. The scientists needed to follow the exact time course of a decrease in fluorescence, because it is a measure of the flow of anions through VRAC.

Applied to the whole genome, this produced more than 130,000 fluorescence curves to analyze – a step that obviously required bioinformatic analysis. Miguel Andrade’s group at the MDC took on the task.

“We specified the parameters necessary to distinguish possible VRAC components from all the other proteins that didn’t affect the transport of chloride ions out of the cell,” Thomas says. “In the end we were left with a list of about 200 proteins that might be involved.”

More analysis and experiments were required to whittle the list down to just a few – hopefully just one – candidate. Part of this could be done by a computational analysis of the proteins’ sequences. The main goal was to find molecules with patterns indicating they were likely inserted into membranes. But other types of molecules might be worth investigating as well. A biochemical signal – passed along by a specific protein – might be required to operate the channel, even if that protein wasn’t a direct component of VRAC. Blocking it might shut down the channel just as well as eliminating one of the membrane proteins. The data collected in the experiments may eventually shed light on these processes. “We now have a treasure trove of data that remain to be analyzed; first we were concentrating on candidates for channel components,” Thomas says.

Felizia, Tobias and Thomas took on the list of candidate membrane proteins and began sorting through everything that was known about the functions of the candidates, from other experiments. The aim was to distinguish promising proteins from those that were less so – “And you had to be careful not to discard any molecule that might turn out to be the real one!” Thomas says.

After this analytical effort, over 80 proteins remained for one-by-one investigation through more experiments. Using the same experimental protocol, they challenged the cells with new siRNAs directed against those same 80 genes. The scientists dug in for another period of hard work.

This time, disruptions of only one molecule – a protein called LRRC8A – continued to interfere with VRAC. “So far we had only covered one aspect of VRAC function, the cells’ uptake of iodide,” Thomas says. “Now we wanted to explore another aspect – to measure its effects on electrical currents. We did this using a method called patch-clamp.” Two PhD students from Thomas’ lab, Florian Ulrich and Jonas Münch, joined the team and worked for about a year on the analysis of VRAC. They discovered that the knock-down of LRRC8A also reduced chloride currents. This meant that LRRC8A was either a direct component of the channel, or it exercised a firm control on VRAC functions. Thomas’ lab began the next round of experiments to find out.

* * * * *

“Proving that LRRC8A protein was a direct component of the channel required a number of steps,” Thomas says. “Upon a closer look we saw that it fulfilled a number of important criteria. First, it was expressed by many types of cells in the body, all of which need to regulate their volume and are thought to express VRAC. And a study of its sequence showed that it had regions that would be embedded in membranes – but was it really present in the plasma membrane that encloses cells?” The scientists generated antibodies that attached themselves to LRRC8A and observed under the microscope that LRRC8A indeed moved to its expected position at the outer membrane.

So far, so good – but was LRRC8A the channel itself? The scientists overproduced the protein in cells and measured currents activated by swelling. “Of course we had hoped that this would boost swelling-activated currents way beyond those in normal cells,” Florian says. “But were dismayed to see that rather than increasing currents, overproducing LRRC8A actually decreased currents!”

Thomas had an explanation for this behavior: “Channels are often composed of multiple proteins woven together in the membrane,” he says. “LRRC8A might form a channel together in a complex with other proteins, and if we had too much of LRRC8A, it may assemble with these other proteins at the wrong ratio, leading to complexes that cannot pass currents.”

What might those proteins be? Obvious candidates were molecules that were very closely related to LRRC8A. The cells of humans and other animals have many such “homologs”: far back in evolutionary history, in ancestral organisms, biochemical mistakes occasionally produced multiple copies of many genes. In the species in which they originally occurred, the copies would be redundant. That meant they could be lost again, which often happened as the genes naturally underwent mutations.
In some cases, however, spontaneous mutations enabled the copies to develop new functions. So the human genome contains four other versions of LRRC8 (labeled LRRC8B through E) that may function in a similar fashion.

“Databases containing information from other experiments showed that these molecules, too, are widely expressed in various types of cells,” Thomas says. “When we began to study these molecules individually, by introducing them into cultured cells, we noticed something interesting. Most of them remain inside the cell, in the cytoplasm. But if we introduced them along with LRRC8A, they move to the membrane.”

This indicated that LRRC8A binds to these related LRRC8 proteins, and that certain combinations of LRRC8s might be required to create the channel. Another round of experiments removed and restored various combinations of the proteins. Since siRNAs usually achieve only a partial blockage of a given protein, and might affect other molecules than the intended target, it was necessary to turn to another method. Here the scientists used a new technique called CRISPR-Cas, which interferes with genes directly at the level of DNA rather than its messenger RNA products. CRISPR-Cas allows scientists to make a physical cut in the genome and eliminate a specific gene. The results replicated the findings of the siRNA experiments and importantly showed other LRRC8s were involved in VRAC, but always in combination with LRRC8A.

The scientists found that each of the other LRRC8 proteins, B-E, could be deleted alone without abolishing VRAC currents. But when B-E were eliminated together, VRAC currents were gone just as if LRRC8A itself had been removed. “This showed that LRRC8A needs at least one of the other subunits to form a channel, but that LRRC8B through E are redundant – in other words, they can replace each other,” Felizia says. “And we even generated a cell line lacking all the forms A through E. Currents could only be restored when expressing A with at least one of the other family members.”

Importantly, different combinations of proteins yielded channels with different biophysical properties. “These are intrinsic channel properties,” Tobias says, “which demonstrates that LRRC8 proteins are not just involved in the signaling system that opens the channel upon cell swelling, but are an integral part of the channel itself.” This observation solved another enigma in the field – VRAC currents seemed to vary in different cells and tissues. “Our work now explains the variability of currents because different cells in the body make different amounts of these proteins. The different combinations may serve cell-specific functions.”

The project also provided hints toward answering another interesting question about channels involved in cell shrinkage. “The loss of volume involves expelling small organic molecules such as taurine,” Thomas says. “There was a controversy among experts – some claimed that these molecules exited via the VRAC, whereas others thought they might use yet another channel.”

Further experiments revealed that VRAC accomplishes both functions. The lab used to a radioactive form of taurine whose export from the cell could be tracked. Darius Lutter of Thomas’ group adapted a test that would measure its efflux, and the scientists found that taurine’s behavior aligned with the presence or absence of various LRRC8 molecules and VRAC behavior.

“All in all, these experiments reveal that the channel is directly constructed from combinations of LRRC8A and other LRRC8 forms,” Thomas says. “They give us the first clear route to explore the mechanisms by which cells shrink and shed particles in response to swelling. Those functions are crucial in the context of all types of cells, and this work provides the basis for understanding how they become defective in a number of serious diseases.”

Even with the well-coordinated collaboration and intensive efforts on the part of Thomas’ labs and the Screening Unit, the group’s search for the VRAC took four years. But the race would only officially be won if his team was first to publish on the subject. The scientists quickly wrote up a paper on the project and submitted it to a major journal.

All the way along, Thomas had been worried that other groups might be working on the problem; after four years, getting scooped would be a hard blow. Those concerns turned out to be justified. On the very same day that the article appeared in Science, another lab published a paper in the journal Cell that identified LRRC8A as a component of VRAC. That work did not, however, demonstrate that the “A” form had to be combined with another LRRC8 to create the channel.

“Our work puts the whole field of cell volume regulation on firm ground,” Thomas says. “The signals that connect an increase of cell volume to the opening of the VRAC are enigmatic, and we now have a handle to investigate them. We have suspected that defects in VRAC are involved in a number of diseases, and now we can develop mouse models to confirm those roles and look for other functions of the channel.”

Reference:
Voss FK, Ullrich F, Münch J, Lazarow K, Lutter D, Mah N, Andrade-Navarro MA, von Kries JP, Stauber T, Jentsch. Identification of LRRC8 heteromers as an essential component of the volume-regulated anion channel VRAC. TJ.Science. 2014 May 9;344(6184):634-8. doi: 10.1126/science.1252826. Epub 2014 Apr 10.