Seyfarth EA (2006). Julius Bernstein (1839-1917): pioneer neurobiologist and biophysicist. Biological cybernetics, 94 (1), 2-8 PMID: 16341542

We at Sick Papes do not operate under the illusion that we are only the folks that love a dank ‘ticle. But it’s rare to find a practicing researcher who also takes the time to investigate the important historical exploits of his/her field. Throughout his career, Ernst-August Seyfarth has done just that, authoring several papes about relatively obscure hero neurobiologists such as Ludwig Mauthner (1840-1894), who discovered the infamous Mauthner cell, Julia B. Platt (1857-1935), one of the first comparative neuro-embryologists, Tilly Edinger (1897-1967), an early paleoneurologist, and Johann Flögel (1834-1918), one of the first insect neuroanatomists. At the same time, Dr. Seyfarth sustained a thriving research program studying mechanosensation in spider slit sensilla, as well as spider behavior (at one point, investigating the origin of spider push-ups).

My favorite of Seyfarth’s historical narratives is the story of Julius Bernstein, a bad-ass German physiologist who was the first to describe the action potential (despite this noteworthy achievement, I had never heard of the guy). Bernstein was born in Berlin, where, after completing medical school, he returned to do a post-doc with the perpetually belligerent Hermann von Helmholtz, a pioneer of physics, physiology, philosophy, and competitive lifelong moustache consistency. While trying to best his boss with a blend of buffed bald-head/bushy beard, Bernstein developed a brilliant contraption called a differential rheotome, or “time slicer”.

The rheotome (shown above) was a sort of “ballistic galvanometer” that consisted of a turntable that opened and closed two circuits as it rotated. One circuit transiently stimulated the nerve, and the other instantaneously recorded its response. Both the stimulation and recording periods lasted only a fraction of a millisecond, depending on the speed of the turntable. The temporal offset of the stimulus and recording epochs could also be changed by adjusting the angle between the two switches. By varying these parameters and averaging over many trials, Bernstein built up a full picture of a single action potential in a frog nerve.

After this achievement, Seyfarth describes how Bernstein went on to formulate an eerily prescient “Membrane Theory of Electrical Potentials”, based on the predictions of the hauntingly familiar Nernst equation. It’s insane how right Bernstein was most of the time. Maybe it’s just that his stupid ideas and shitty experiments were forgotten? It’s hard to say, but Seyfarth attributes Bernstein’s stellar accomplishments to his unflappable attention to detail.

Bernstein is great, but Seyfarth deserves a boatload of credit here too, for illuminating Bernstein’s illustrious career and writing it down in this sick historical pape. Now that he’s retired, I hope that Dr. Seyfarth returns to the archives to dig up more sick historical anecdotes about neurobiologists of yore.

Contributed by butthill

Sick Papes Interviews Jonathan Tang

Sick Papes sat down with Jonathan Tang to discuss his recent paper “A Nanobody-Based System Using Fluorescent Proteins as Scaffolds for Cell-Specific Gene Manipulation.” Sick Papes also did this interview the old fashioned way, like an idiot, by recording and transcribing rather than emailing and relaxing.  Hence the big delay.  But like rediscovering a bottle of once lost liquor in your dirty clothes pile, you should be excited: Jonathan took advantage of antibodies from a camel to make GFP – the head honcho fluorescent protein for cellular visualization – friggin’ functional, as the key scaffolding ingredient in a threesome of transcriptional hedonism. He calls these nanobodies “transcription devices” and if you F with GFP, you better start getting creative. 


Jonathan Tang et al. 2013. A Nanobody-Based System Using Fluorescent Proteins as Scaffolds for Cell-Specific Gene Manipulation. Cell 154, 928–939

 SP: I’d like to start this interview with a quote from the movie Nacho Libre.  Have you ever seen Nacho Libre?

 JT: No.

 SP: Okay well it’s a movie where Jack Black plays a Mexican wrestler and at one very important point in the movie he says, “Under the clothes we find the man and beneath the man we find… his nucleus.” What type of man are you and what’s up with your nucleus?

 JT: Okay. I guess on the surface I’m pretty shy person.  Underneath I am someone who wants to change the world.  And my nucleus? I hope it’s functioning well, with little UV induced damages.

 SP: You’ve invented a technology for retrofitting transgenic organisms called “transcription devices dependent on GFP.” Can you explain GFP and “transcription devices” to our readership?

 JT: GFP stands for green fluorescent protein, it was discovered in a jellyfish 40-50 years ago and emits green fluorescent light. GFP has been put to use as a tool in molecular biology since 1994, allowing researchers to tag proteins and visualize cellular processes. This has been a powerful, Nobel prize winning tool for researchers. Regarding “transcription devices,” that’s a fancy name I gave to an engineered, hybrid transcription factor.  The idea is to make the device activate transcription, but only when its two independent protein parts are tethered to GFP. If GFP is present in the cell, the device be fully formed and functional to initiate transcription in a downstream gene of interest. 

 SP: Most SP readers have a 3rd grade education.  How would you explain this technology to a 3rd grader?

 JT: I don’t know if a 3rd grader would understand genes, but here it goes: the transcription devices are present throughout an organism but remain inactive except in cells with GFP.  In these cells, devices tether themselves to GFP and initiate events inside cells to turn on other genes. 

 SP: How does this interaction actually work?

 JT: It’s based on protein-protein interactions. The devices are binding proteins derived from camel antibodies that bind to GFP with high affinity.  The reason why we use camel antibodies is because the antigen recognition domain is contained in a single peptide segment. Conventional antibodies are hard to express in cells as they are made of two proteins joined by a breakable disulfide bond. I found that there were pairs of the these camel antibodies that recognized different parts of GFP and could co-occupy GFP.  This allows one to simultaneously tether different protein domains on to GFP.  In this case, I tethered a DNA binding domain with one camel antibody and a transcription activation domain with another. GFP is then the scaffold for forming an active transcription factor which can then initiate transcription of any gene of interest downstream of its genome binding site. 

 SP: It seems like you kind of owe the camel a lot. Pretend I’m a camel.  What would you like to say to me?

 JT: I guess for the sake of the next Nature paper, tell me why you evolved single chain antigen binding domains.  Please tell me that. If you do, I’ll pay you back with a lot of water.

 SP: Like middle-author type water?

 JT: Like a gallon of water.  Other than that, thank you very much you solved my problem.

 SP: At any point in your project, did you make a scale model of GFP in your kitchen to try and identify where the transcription devices would bind?

 JT: Not quite like that, but I did do a look at a lot of crystal structures and computational models of GFP structure, along with the structures of the GFP binding nanobodies.  I just kept trying to fit them together. Turns out it was a waste of my time, because in the end I had to empirically pair-wise test all 6 nanobodies. 

 SP: How happy were you when you found a pair that worked ?

 JT: I was pretty happy actually.  I was in the lab at like 5 o’clock in the morning (editors note, JT is a confirmed night owl) and there was nobody around.  I was just so happy, but there was no one to tell.  Then my adrenaline went up and I walked around the building looking for people to tell but there was still no one.  So I went back to work. 

SP: That was a breakthrough moment in the project?

JT: Yes. There was no way to know if the system would work at all.  I only had the six nanobodies which were generously given to us.

SP: It’s amazing how a couple of hours of positivity can energize us to wade through a swamp of disappointment that can last years.

JT: That’s true.  Prior to that moment there was a lot of disappointment.

SP: Did you try other systems?

JT: Yes, I tried to make a Cre recombinase into a GFP-dependent into Cre recombinase.  It was a naïve idea. But those experiments were helpful, as they did told me that the nanobodies could direct GFP to distinct compartments in the cell.  That was the first clue the reagents I had could tether GFP.

SP: How do you think about, or visualize, these high affinity interactions between the nanobody devices and GFP? Like a key in a lock? Bugs on a windshield?

JT: Yes, I think of them as locks and keys, they simply come together.  Without the high affinity, I don’t think it would work very well. 

SP: One of my favorite things about this paper is that the technology that’s developed is not only an important proof of concept, but is immediately of practical use.  What is the current utility of your GFP nano-bodies? Where do you see this technology going forward?

JT: One of the exciting applications is for retrofitting transgenic GFP animals. Many GFP lines have been engineered to express GFP in genetically defined populations of cells.  For example, the GENSAT ( project has over 1,500 mouse lines for labeling neuron populations in the brain and retina.  Now the question is can we use these nanobody devices to perturb function in GFP expressing cells.  One idea would be to turn on the light-sensitive ion channel channelrhodopsin in GFP expressing brain cells to make these neurons fire action potentials with light.  As we show in the paper, with this technology you can probe the downstream brain circuitry from the cells that were previously only visualizable. In the long term, this paper suggests that GFP itself is a great transgene.  Because it can be used for anything.  You can imagine building many types of synthetic systems that use GFP to turn on or off different cellular processes, by mating GFP animals to other animals carrying nanobody devices or by introducing these devices with viruses. 

SP:  Have you thought about targeting your transcriptional devices to other proteins too?

JT: You mean using other proteins for turning on the system? That’s something that we’re looking into doing.

SP: One more question for you, on behalf of the molecular aficionado readership: In your paper, you note that there are pros and cons to your devices vs. traditional recombinases for manipulating genomes. Can you explain those pros and cons?

 JT: The current system uses three components to form the hybrid transcription factor.  While this is not as efficient as functional single molecules like Cre, it does have the ability to achieve more specificity through intersectional expression of the individual components. The other problem we experienced was having too much GFP, which sequesters individual nano-devices without the paired binding necessary for transcriptional activation.  So the nano-devices have to be tested with each transgenic line.  Unlike with Cre, which tends to enact permanent changes in a cell and its progeny, this system can also be reversible, dependent on the continued presence of GFP.

Thanks Jonathan you’re the man!

Contributed by yourbodyismytemp-pal


Supplemental Text 1 from:

Deshpande, G., Zhou, K., Wan, J.Y., Friedrich, J., Jourjine, N., Smith, D., Schedl, P., 2013. The hedgehog Pathway Gene shifted Functions together with the hmgcr-Dependent Isoprenoid Biosynthetic Pathway to Orchestrate Germ Cell Migration. PLoS Genet. 9, e1003720.

Like many people, I have conflicted views about the reams of Supplemental Data that accompany the online versions of most papers published these days. At its worst, Supplemental Data is nothing more than a grainy video of a bat performing fellatio, overdubbed with thumping techno.  At it’s best, however, a truly great Supplemental Figure reminds me of the famous scene in When Harry Met Sally where Meg Ryan loudly fakes an orgasm in a crowded restaurant, except that for me, the orgasm is real, and in those moments of ecstasy I am neither woman nor man but purely divine flesh of the GodBody incarnate. This Supplemental Text Document right here is one of those good ones which make me very glad to be living in the “Era of Supplemental Data,” as it was recently dubbed by Francis, the first pro-Open Access Pope.

To be real with you, I’ve never seen a Supplemental Document quite like this one. While Supplemental Data most often includes extra methodological details, additional controls, large datasets, or tangential experiments requested by reviewers, this one is a long-form prose essay about a decade-old scientific disagreement between these authors and a different lab. We here at SickPapes don’t take sides in this quagmire - both of these labs are outrageously hot and time-tested - but we find it surprisingly compelling to read such an emotionally honest and open piece about a genuine scientific disagreement. 

Our story begins in 2001, when Paul Schedl’s lab published a paper in Cell providing evidence that a secreted protein called hedgehog is involved in guiding embryonic germ cells as they migrate towards the future gonad. In one key set of experiments, they ectopically expressed hedgehog in abnormal locations, and showed that germ cells migrated incorrectly. This was interpreted to suggest that hedgehog is sufficient to influence germ cell migration.

As far as the public was concerned, the next thing that happened was In 2007, when Ruth Lehmann’s lab published a rebuttal, with the unambiguous title “hedgehog does not guide migrating Drosophila germ cells.” In the Lehmann lab, the hedgehog ectopic expression simply did not affect germ cell migration as it did in the hands of the Schedl lab members. This was not a matter of subtle differences in methods, this was literally a direct repeat of a simple experiment, giving different answers. Both labs are highly respected, and this discrepancy was hard to explain without getting a tad bit disrespectful. 

Which brings us to explaining why this new Supplemental Essay from Schedl’s lab is so sick: it explains what was happening behind the scenes at Cell the whole time. First, they reveal that the Lehmann lab’s 2007 paper actually originated as a technical comment sent to Cell in 2002 in response to the original 2001 article. The Cell editors asked the Schedl lab if they wanted to retract their paper, and the Schedl lab said “No.” Instead, they came to an agreement with Cell that an outside, independent researcher would repeat the hedgehog experiments, communicating only with Cell and not with either of the labs in question (Shout out to Stephen DiNardo, stepping in to do a major solid for the scientific community without any personal glory).

After an extended drum-roll, Dr. DiNardo told Cell that his independent experiments confirmed the original results from the 2001 Schedl lab paper, not the Lehmann results. So, what does Cell do with this important finding? Nothing. Instead of publishing this informative back-and-forth, they didn’t make any of this public, and just let everyone gossip for a decade. And, according to the Schedl lab in this Supplemental Text, this gossip-filled silence has “undermined [their] credibility in the scientific community, jeopardizing [their] careers.” Damn, Cell - that is some cold shit. I wish more folks would publish Supplemental Emotionally Honest Essays detailing the strife that various journals put them through. At the least, this might add fuel to Randy Schekman’s dope protest against journals like Cell.

With that, we here at SickPapes wish to salute any and all Sick Supplemental Data, and wish you a very happy 2014!

Contributed by benewencampen


Clarke et al (2013). Detection and learning of floral electric fields by bumblebees. Science 340 (6128): 66-69

Greggers et al (2013). Reception and learning of electric fields in bees. Proc R Soc B 280 (1759).

Year in and year out since the beginning of time, the amber fields of research programs across this great land are sprinkled with NSF fertilizer and grow the science crops that feed our hungry brain-mouths. While most days we feed our bloated carcasses on the high fructose corn syrup of the mind, every once in a while, you fill your cow horns with the right kind of manure, nail the astrological planting cycle and BLAMMO! - when the research harvest comes in, it comes in big. Well, it’s a boom year and the organic veggie du jour is bee learning and cognition. Here’s just one hors d’eouvre to whet your appetite:


My most vivid memories of childhood summers come from wandering along the Maine coast listening to my Aunt describe the auras of unwitting passersby, from “deep-blue” for the kid on a skateboard, “wispy green” for the owner of the Life is Good shop, and “surprisingly rectangular camo-colored” for the potbelly-sporting middle-aged man with a warm Budweiser and a Kiss lunchbox. Like these divine beach-goers, all living things (including the most heartless beasts of all creation: plants) give off subtle electrical fields. Despite its profound implications for literally everything, research on electric field perception has been mainly restricted to publications in Frontiers in Quack Science and F1000’s “What the $&*% do we know?” section. Two recent papers, though, are finally lending heft to the otherworldly electro-perceptational abilities of bees.

Up first is a sick pape showing that bees can sense electric fields created by plants. By creating artificial flowers (“E-flowers”, or E-cigarettes for bees) where they could measure and manipulate the electric field, Clarke and friends showed that bees can learn to differentiate between flowers that are completely identical except for their electric field. Mind-blowingly, the mere presence of the bee near a flower also changes the flower’s electrical pattern, so bees may be able to use their aura-sniffing abilities to figure out which flowers have been recently cleaned out by some other nectar-hungry bee.

While this study definitively showed the presence of the Third Eye in bees, more questions are raised than answered: Does the third eye align with the seventh chakra? Can the NSA use it to track my Private Browsing content? What causes Third Eye Blindness?

Thankfully, in a case of cosmic alignment, within a couple of weeks of this pape coming out, YET ANOTHER sick pape from a totally separate group gave us insight into how this might work. Coulomb’s law states that two charged particles will exert a physical force upon each other. Since insect antennae carry a charge, they could theoretically move in the presence of an electric field, allowing bees to perceive these electric fields.

In a beautiful series of “set em up and knock em down” experiments in our second sick pape, Greggers and amigos showed that bee antennae move in response to electric fields and that these movements juice up some specific neural pathways that allow the bee brains to perceive electricity. Indubitably sick.

Contributed by jamescrall

We here at SickPapes have obviously spent the past several years reaching out to a wide variety of porno mags, with hopes of initiating a collaboration. Our goal was simple: to use our vast fame and influence in the scientific community (and beyond) to call bullshit on the troves of “evolutionary psychology” pop-science out there about human sexual behavior, which we feel often lacks a certain je sais exactly quoi called “data.”  

When we finally met MOMMA TRIED, we were ecstatic. MOMMA TRIED is a “literary nudie mag” which aims to appeal to all sexualities and types of people out there. 

For their first ever issue, we interviewed Dr. Vincent Lynch about the evolutionary ideas surrounding the female orgasm, particularly on the elaborate just-so stories that societies have concocted to explain the apparent differences between the male and female orgasm. Dr. Lynch is an outrageously sick molecular biologist who has given birth to a beautiful series of papes on human evo-devo, many about the evolution of pregnancy. As a graduate student, he wrote a single-author take-down of a particularly suspect dataset, and it was incredibly rad of him to sit down with us.

To read this exclusive interview, you’ll have to order this physical, glossy, nudie mag from this website. Or, if you’re in New Orleans on November 23, 2013, you can go to their launch party!

Have fun everyone!!

Contributed by benewencampen

Dunlap, K. and Mowrer, O. H. (1930). Head movements and eye functions of birds. J. Comp. Psychol. 11, 99–113.

People make a lot of hay out of the series of photographs by Eadweard Muybridge that Governor Leland Stanford commissioned to figure out whether all four hooves of a galloping horse are airborne at the same time. Muybridge ingeniously used an array of cameras that were triggered sequentially by the horse busting through a series of trip wires. The result of this experiment was that there was definitely a moment in the horse’s gait when all four feet were off the ground. (Stanford went on to found the university that produced Olympic water polo player Tony Azevedo; Muybridge ended up shooting a man who slept with his wife, but was acquitted on grounds of “justifiable homicide”.)

Now I don’t want to dump on the birth of cinema, but I’ve just been out watching horses gallop around all morning, and I’m pretty sure that I could reproduce Muybridge’s experiment with some study drugs and a mug of properly mulled cider. Things are always clearer in hindsight, but it didn’t take much squinting to convince me that horses are airborne every quarter second or so. Perhaps Muybridge and Stanford were half blind from living in an era before proper sunglasses, or maybe horses were faster in the 19th century because there were no clocks and all the conductors had to count continuous Mississippis to keep the trains on time.

Whether or not the Muybridge horse study was necessary, subsequent developments in rapid picture-taking have proven incredibly useful for the study of biomechanics. Today I want to discuss an early example of how the camera can be used to compensate for the inability of us humans to fully appreciate animals. 

Many people have wondered, “What’s up with pigeons bobbing their heads all crazy while they walk”, but most people are too afraid to blog about it. As Dunlap and Mowrer, the authors of today’s sick pape, put it, “The forward and apparent backward movements of the head which pigeons, chickens, and certain other fowls display while walking have been commented on by various persons orally, but seldom in print.” 

It may have occurred to you that this jerky head movement is an accident of the pigeons walking gait, perhaps analogous to the swinging of a human’s arms. But this is wrong. In 1930, Dunlap and Mowrer took some great photos that proved that bird head bobbing is just an illusion. In fact, it is you, the viewer, who is lurching ferociously back and forth, and the bird is perfectly motionless! That’s not actually true. What is really happening, Dunlap and Mowrer found, is that when the bird’s body is moving, the head is completely still. In other words, the head is locked in position relative to the forward moving body. Then, when the body stops for a brief moment, the head thrusts rapidly forward to a new position. So, overall, the head is maintained in a stable position relative to the body. The stroboscopic photo above, from a sick follow-up pape by B.J. Frost in 1978, illustrates this nicely.

This head stabilization has obvious benefits for vision, as it is much more difficult to analyze a visual scene when your head is shaking. Another set of experiments by B.J. Frost in the 70’s clearly demonstrated that head-bobbing is controlled by vision, as pigeons walking on treadmills don’t bob at all (because the visual scene is stationary).

The findings of Dunlap and Mowrey in 1930, and subsequent work by B.J. Frost and other enthusiastic bird bio-mechanics, are a superb example of how the world is incredibly fast and confusing, and only photographic magic and detailed quantification can distill truth from all the chaos.

Contributed by butthill

Sick Papes salutes those review article figures which take a Daoist approach to cellular biophysics and molecular mechanics (Larkum Nat Neuro 2013)

Contributed by yourbodyismytemp-pal

"Making snail smoothies in Hell"

An Interview with Jon Sanders, co-first author on:

Sanders, J.G., Beinart, R.A., Stewart, F.J., Delong, E.F., and Girguis, P.R. 2013. Metatranscriptomics reveal differences in in situ energy and nitrogen metabolism among hydrothermal vent snail symbionts. The ISME Journal, 1-12. doi:10.1038/ismej.2013.45

There once was a pape, and that pape had a hot title: "We Have Never Been Individuals." And in that pape lay a dopely articulated argument. And that argument was that although it has been experimentally and conceptually helpful to pretend that we are all individual organisms, discrete in our genomes and metabolism, this is just simply not true. The very first multicellular organisms evolved into a world that had already been dominated by microbes for like a billion years, and our biologies have always been interpenetratin’. And these symbioses with microbes are not superficial or disposable. These dudes point out that, although It was helpful to ignore (or not know) this fact in the past so that geniuses could figure out how genes work, the time has come to acknowledge that animal-microbe symbioses are “the rule, not the exception.” 

Nowhere is the importance of microbial symbiosis more striking that at the deepest darkest bottom of the motherfucking ocean, where the only way that any animals can survive is by givin’-and-gettin’ all night long with the chemosynthetic bacteria that can eat the toxic chemicals spewing out of deep sea vents. 

I recently sat down with an American Hero named Jon Sanders and asked him what happened behind the scenes of an incredibly sick pape he recently spewed forth from the depths of Hell.  In this pape, Sanders and his co-first author Roxie Beinart invented a new way to collect and sequence fresh RNA from both microbes and animal (snail) at the bottom of the ocean, using an insane and terrifying blender.

1) Describe a day in the life on a boat during a research “cruise.” What’s the Work:Sleep:Insanity ratio?

Close your eyes. Say “I’m on a cruise in the South Pacific.” It’s basically the opposite of that, for two months.

Dominant adjectives for my experience include, “frigid,” “exhausing,” and “loud.” In packing, I foolishly failed to account for the world’s most powerful air conditioning. They keep the inside of the boat at what feels like just above freezing, probably to dry out the air, or maybe to cull the infirm. This led to a frantic search for a sweater when we put in for resupply on the island of Nuku’alofa in Tonga. If you thought that warm clothing would be difficult to find in a place where 50°F is the lowest temperature ever recorded, you would be correct. 

Sleep wasn’t much of a consideration. You might get one shot at a research cruise during your PhD, so you try to make the most of it. For the first month at sea, Roxie Beinart (the co-first author of the paper and my partner in crime on this cruise) and I probably slept 2-4 hours a day. We tried to do a preposterous amount of work. 

Everything is defined by the ROV’s (ROV stands for Robot Of Vengeance) dive schedule. ROV goes to the bottom of the ocean, ROV comes up with a box of alien deep-sea stuff. The robot’s crew fish it out of the water with incredible crane-ninja skills. Then you need to process that alien stuff, much of which has only been seen by a handful of humans ever in history. Or maybe you’re the first one. I would usually spend 3-5 hours after dives doing dissections. Roxie was running experiments on live animals, which required constant sampling and monitoring. In between, we mostly broke things and then tried to fix them.

I think they still call it a “cruise” (instead of something more descriptive, like “vomit-inducing labor camp”) to lure in naive graduate students like me. I lost 10% of my body weight on that first month. I would do it again tomorrow. I wouldn’t even hesitate. 

2) What was the month leading up to the cruise like? What lab equipment did you bring on the boat with you?

Preparation was almost as frantic as the cruise. Roxie and I helped our advisor build a mobile laboratory in a refrigerated shipping container. (In the world of oceanography, these are referred to as “reefer vans.”) We outfit our reefer van with a bunch of stuff to help us replicate the conditions at the bottom of the seafloor. This involves mixing seawater with toxic (hydrogen sulfide) or explosive (hydrogen) gases, then using industrial pumps to force the water at obscene pressures through enormously heavy “aquaria” (basically stainless steel bomb casings). We can use these to run experiments on live animals to help us understand their insane and counterintuitive physiologies. 

So for the months before the cruise, we did a lot of plumbing, wiring, and construction. We got crash courses on pump maintenance and operation of mass spectrometers. We organized a lot of various kinds of fittings. Then we packed the van full of crap and sent it on a truck to a train to a ship to Samoa, where we searched frantically for a crane capable of lifting it onto the deck of the research ship.

3) Can you describe, for some of our more thick-headed readers, how there can be a food-chain at the bottom of the sea, where there is zero sunlight to get the primary producers poppin’? Where does the energy come from to fix carbon? Where do the free electrons wind up?

Basically you get life when you take high energy electrons from an electron donor, extract that energy by moving them to a lower energy state in an electron acceptor, and use the liberated energy to self-organize matter in a way that temporarily contravenes God’s obvious thermodynamic will for the universe to become an undifferentiated soup of entropy. 

Up here, plants hijack electromagnetic energy from the giant thermonuclear explosion at the center of our solar system to charge up electrons and store them in delicious sugar. We heterotrophic animals do His will by consuming these exquisitely crafted, high-energy carbon rings and turning them into shit, dumping the electrons all the way down the redox scale by splitting oxygen into water.

Under the bottom of the ocean, water in the earth’s crust is heated by the fires of Hell (Editor’s Note: this has been fact-checked). This performs a job somewhat analogous to sunlight by charging up electrons and producing reduced chemicals like hydrogen and hydrogen sulfide. Different microbes pass those electrons down a long chain of different electron acceptors to get energy for fixing carbon, eventually culminating in oxygen from the deep bottom water. (Note that this oxygen is largely a product of photosynthesis, so much of vent life is still dependent in a way on sunlight.) However, most microbes are really small, and so don’t have simultaneous access to both the energy-rich reduced vent fluid and the oxygen-rich bottom water a few centimeters away. These free-living microbes have to make do with a little slice of that big redox gradient. 

Some microbes, though, have figured out how to cheat (no doubt aided by their proximity to Satan) by corrupting normally-heterotrophic animals. Animals are big and have circulatory systems and respiratory pigments, so can access and transport both reductants and oxidants to their microbial overlords. They are rewarded for this with a constant stream of nutritive compounds. Consequently, many of these ‘autotrophic’ animals have, in their sloth, lost the ability even to participate in the sacred animal duties of Eating and Shitting. 

Canonically, chemoautotrophic vent symbioses get their energetic electrons from hydrogen sulfide and dump them into oxygen. These days we’re discovering that it’s way more complicated than that. Different symbioses may utilize different sulfur species or even hydrogen as electron donors. In our paper, we found hints that some symbiotic bacteria may also be using alternatives to oxygens, like nitrate, as electron acceptors. 

4) Do you know how and when people first figured out that symbiotic bacterial were the key to animal life in the deep sea? 

A professor in my department, Colleen Cavanaugh did it as a first year graduate student. It was unbelievably insightful. People had just discovered all this insane animal biomass  where it absolutely shouldn’t have been in 1977. Biologists got their first crack at the vents in 1979. Then two years later this upstart and incredibly badass young woman comes along and publishes the answer to the mystery in Science. She just schooled the whole world. 

5) It is profoundly sick to collect RNA at the very bottom of the ocean and to turn that into data. Tell me how the ISMASH machine works.

Mostly it didn’t. When I started my PhD, my coadvisor Pete Girguis was like, “Jon, I want you to build a deep sea blender.” I was like, “sweet.” I had no idea what I was doing. 

The concept is actually pretty simple. You want to 1) stop transcription, and 2) stabilize the RNA. Saturated solutions of ammonium sulfate are pretty good at doing both, since they precipitate the shit of RNA degrading enzymes and basically everything else. 

 The problem is that big animals can do a lot of transcription and RNA degradation before the preservative can make it into all the tissues. Molluscs are even worse, since they have shells. If you just dunk a snail or clam in RNAlater you might get an RNA profile of “suffocating slowly in horrible chemicals” instead of “happily oxidizing sulfide.” Which would suck. Thus Pete decided to just blend the shit out of them. 

So me and this amazing guy Chris DiPerna spend a bunch of time in his buddy Paul’s shop in Southie fabricating a prototype. It plugs into the submarine’s hydraulics system to spin a motor to spin a literal set of Waring brand blender blades. Of course we have no way to really test it out so we pack it all up in the van and send it off to the South Pacific and just hope. 

On the boat people think it’s just ludicrous, which of course it is, but how can’t you love it? You’re making snail smoothies in Hell. We plug it in and send it down and cross our fingers, and the amazing ROV pilots snag a snail and drop it in there and close the lid and hit ‘blend.’ All of this is being directed from the control van, which is sort of like the illegitimate love child between the bridge from the Starship Enterprise and a satellite news truck. (You can follow along at home in the online Virtual Van []. Just pick the 2009 Fisher_LauBasin cruise on the left, click ‘virtual van’ and type in ‘blender’ in the search bar and hit ‘find.’) That first time it was the middle of the night and there were a ton of people in there, and everyone cheered. Or at least that’s how I remember it. But we couldn’t really tell if it worked until the submarine came up hours later. 

Of course it didn’t work. I had no idea what I was doing. 

So amongst all the other craziness me and the ROV guys (without whom none of this would have happened) keep hacking on these blenders trying to get them to work. The low point comes when we try to blend this wimpy diaphanous sea cucumber for an easy win. It came up looking like a very heavily used condom but otherwise intact [Editor’s note: LOL]

Eventually I take the advice of the guy who was literally driving the sub when they found the Titanic. We bolt some plastic rods to the insides of the blenders to break up the vortex, and BAM! Snail smoothies. We had just enough dives left to get the four samples that ended up in the paper. 

6) Of the transcripts that you identified, only 12-13% of the eukaryotic genes matched known proteins. Do you think that’s because the sequencing reads you were getting were relatively short, or because these deep sea snails have radically different genomes from us land-lovers?

Probably the former, or something similar to that. That’s the neat thing about symbiosis: these animals get to acquire utterly unthinkable abilities without having to drastically modify their boring eukaryotic genomes. They’re actually pretty closely related to those orgy snails (aka slipper snails, Crepidula fornicata) you find on the beach here in the Northeast.

We really didn’t focus on the eukaryotic portion of the transcripts because of the sequencing depth — on average about a third of the reads were from the bacteria, but since the bacteria have about an order of magnitude fewer genes overall, the coverage was quite a bit higher. But there’s probably still some useful science to be done with those reads, for anyone interested. Available now for the low low price of free on MG-RAST. 

When you think about it, it’s kind of insane that literally a third of mRNAs in these organisms are bacterial. I wonder what it would look like if you blended me whole and sequenced it?

7) Can you please vibe out with me for a minute about how incredible it is to go from live animals on the deep sea floor, to collecting them in a blender, to isolating the RNA, to sequencing the RNA, to generating a massive text file with all the raw sequence data, to actually putting all that into the framework of metabolic pathways, to actually understanding something about how energy is being created and used within cells at the bottom of the ocean?

It’s true. I had no idea what I was doing - Wouldn’t have happened without a ton of help. That’s what I love about science: on the one hand you’re standing on the shoulders of these intellectual giants, people who are good at writing code for the bioinformatics and people like Colleen Cavanaugh who have these incredible insights that open up entire fields and people doing all this insanely careful genetics work to figure out what all these genes actually do.

And on the other hand none of it works if you don’t know a guy in Southie who’s a crack hand welding aluminum or if you don’t listen to the sub pilot who discovered the freaking Titanic who’s telling you how to fix your goddamn vortex problem with a piece of plastic. Wouldn’t have happened without  the molecular expertise of my awesome coauthor Roxanne Beinart or without Pete Girguis’s hyperproductive, hyperimaginitive deep sea fever dreams. Wouldn’t have happened without my mom and dad encouraging me to build stuff in the garage and to break the family computer over and over again while I figured out how to Linux in middle school. 

You do all that and you go out on a boat and you figure out that this snail can basically eat hydrogen and breathe fertilizer. And that’s happening right now, on this stupid planet. You know nothing, Jon Snow. 

8) What does “holobiont” mean?

These snails seem to be able to swap out their bacterial symbionts for different superpowers, depending on the local chemistry. Or, alternatively, the bacteria seem to be able to swap out their meatsuits. We think of ourselves as animals, so we tend to identify with the snail side of things. People want to know, what species of snail are you talking about? But if it’s really the bacteria that interface with the geochemistry, isn’t the identity of the bacteria actually the more important feature? And it’s even more confusing, since some snails only seem to partner with one type of bacteria, while others are more promiscuous (Alviniconcha/bacteria Facebook status: “It’s complicated”). 

“Holobiont” tries to simplify things by taking the specific combination of partners as the unit of identity, rather than having to go through all these contortions about who’s hosting whom. I mean, jesus, they’re 1/3 bacterial RNA anyway. It’s also an attempt to subvert the dominant paradigm. #bacteriaforlife #euksareboring #YOLObiont


Contributed by benewencampen

Yen, J.H., Barr, A.R., 1973. The etiological agent of cytoplasmic incompatibility in Culex pipiens. J. Invertebr. Pathol. 22, 242–250.

Since our last post, two months ago, we here at Sick Papes have been riding the highs and lows of an almost indescribable emotional voyage from which we have only recently emerged, bursting with joy and self-knowledge.

It all began, like most of our emotional experiences, while we were blasting the Chances With Wolves radio show (which, in case you don’t know, plays the best music on the planet) at full volume while dissecting crickets under a microscope. All of a sudden, a song by Jonathan Richman called "Fly Into the Mystery" came on. This song, like many others by Jonathan Richman, is about the beauty and longing of summer nights in Boston. And it began to haunt me.

Driven by an unknown urge, I embarked on a literature search of other beautiful things that have happened on Boston summer evenings. This obviously led me to this 1924 pape, where two dudes took a break from their Great Gatsy-era shennanigans to look through a microscope for one GodDamn second an observe a strange bacteria living inside the ovary cells of the mosquitoes living around Boston and Brookline. These bacteria, subsequently named Wolbachia, remained mostly a curiosity for the next 60 years, thought to only exist in a handful of insect species. It wasn’t until the 1990s, when dudes figured out how to use molecular methods to identity cryptic bacterial species, that the trippy truth emerged: Wolbachia infect ~1 million species of insects (and other arthropods and nematodes), and are probably the most abundant endosymbiotic bacteria on the planet. And more importantly, their insane evolutionary success is largely because they can directly manipulate the reproductive behavior of their hosts. 

Somes jokes, like the one about re-captioning every single New Yorker cartoon with “Christ, what an asshole!” stay hilarious no matter how many times you hear them. And it’s the same for some research topics: as far as I can tell, every pape that has ever dropped about Wolbachia is fucking amazing. It was in the vortex of insanely hot papes about Wolbachia that we have been trapped for the past two months, unable to stop clinking through to other hot references. It’s pointless to try to pick the best of the bunch, but this 1972 pape right here is straight up astounding. (OK, Wolbachia weren’t totally ignored until the 1990s, but they were definitely a left-field kinda thing.)

The background is that different populations of mosquitoes from around the world often can’t successfully mate with each other. This isn’t really a mind-blower - it’s the early stages of speciation, where the different populations still look like the same species, but their genomes have independently evolved to the point that they can no longer fit together quite right when they mate.

What IS a mind-blower is that, in this case, the reason these different populations can’t reproduce is because of the specific strains of Wolbachia that live in the ovaries of the different populations. If you simply feed the mosquitoes antibiotics, all of a sudden they can reproduce with the other populations. In other words, the Wolbachia bacteria is causing the formation of new insect species. This is also the case in Nasonia wasps, where three totally different species instantly become interfertile if you give them antibiotics

The bigger, and more insane, picture is that Wolbachia are passed from mother to offspring directly through the egg cell, and so to ensure their continued reproduction, the bacteria basically take control of the host insect’s reproduction. These examples of Wolbachia-driven sterility are one result of this evolutionary pressure: Wolbachia prevent any mosquitoes which don’t carry the same strain of Wolbachia from mating, thereby promoting the reproduction exclusively of those hosts which harbor the self-same bacteria. And if this wasn’t wild enough, Wolbachia can also kill all male embryos (which they don’t like because only the female insects transmit Wolbachia), can directly increase the egg-laying of infected insects, and apparently live in specific cells of the insect brain, doing God-knows-what.

We are relieved that we finally escaped this two month-long, late-night pape-reading vision-quest, but DAMN if it wasn’t sweet.

Contributed by benewencampen

Engreitz, J. M., Pandya-Jones, A., McDonel, P., Shishkin, A., Sirokman, K., Surka, C., et al. (2013). The Xist lncRNA Exploits Three-Dimensional Genome Architecture to Spread Across the X Chromosome. Science. doi:10.1126/science.1237973

If you ask me, one of the stupidest ideas out there is that of the “Man Cave.” The fact that a mainstream portion of my society thinks that the definition of manhood involves sitting in a specific room and watching TV and burning these remote-control-themed scented candles (or these ones) is nauseating, and I ask you to join me in weeping for the future generations of boy-children who will be raised with this double-whammy addiction to football and fucked-up aromatherapy. 

Scientists (on the whole), like all members of our society, have a truly awful track-record of handling the differences between the sexes. It is depressingly easy to find overwhelming evidence of rampant sexism in how science is practiced on a daily basishow it is taught, and in what it chooses to study and the language it uses to describe those findings. We here at Sick Papes strongly encourage all of you to destroy the Patriarchy and all other forms of inequality (not kidding).

That said, I’ll be DAMNED if there isn’t some seriously dope-ass research out there about some of the (actual) differences between men and women, and X-chromosome inactivation has got be near the top of the Hot column in this century’s “Research Topics: Hot-or-Not” list.

In mammals, XY individuals - those we often call “males” - carry a Y-chromosome, which contains a gene that initiates the cascade of developmental events leading to the growth of a male (including the development of male-specific organ known as the Butt). This is fine (and dandy), but because of this, females have twice as many X chromosomes in every one of their cells, which is not necessarily dandy because twice the chromosome means twice the mRNA levels of every gene on that chromosome, which could really harsh one’s mellow. In order to balance out the amount of transcription from genes on the X-chromosomes, every cell in the embryo of a female mammal shuts down one of the two X-chromosomes, completely silencing its expression. This is X-chromosome inactivation.

Probably the most famous manifestation of X-chromosome inactivation in action is the Calico Cat (editors note: complex internal rhyme unintended). The beautiful colors that besplotch the majestic Calico result from fact that pigmentation genes are located on the X-chromosome. During development, random cells throughout the cat inactivate either one or the other X-chromosome (each of contains a specific pigmentation gene), leading to the differential expression of pigment alleles in random patches of color on the adult’s fur. (Thus, all Calico cats are female, a fact that may surprise some of our readers who don’t already subscribe to Cat Fancy magazine).

The present pape addresses the molecular mechanism by which the X-chromosome shuts down. This process is known to involve a long, non-coding RNA (i.e. it doesn’t encode a protein product, but instead performs its biochemical handjob as an RNA) called Xist. Xist is transcribed from a specific location on the X-chromosome and then, in a bit of particularly trippy biological mystery, spreads to cover the entire chromosome over a period of hours like an iTunes visualizer, correlating with the cessation of transcription.

In this pape, a couple of major players in the game with, from what I can tell, infinity money, developed a technique to do time-lapse, deep-sequencing-based analysis of how the Xist RNA spreads to cover the X-chromosome during the process of X-chromosome inactivation. The first surprising thing is that Xist RNA doesn’t just leak outwards from its source along the length of the chromosome (like, for example, a two-dimensional pee stain on one’s shorts), but rather accumulates in very defined, specific spots across the chromosome (much like, for another example, forming a careful pee pattern in a snowbank). 

The truly sick part of this pape, though, is that the regions where the Xist RNA accumulates are in fact the closest regions of the X chromosome in 3D physical space (not in 2D sequence space)! Because remember: the chromosome is packed into the nucleus like a crazily efficient, unknotted brick of uncooked Ramen noodles, so two points that are physically close in the nucleus may not actually be next to each other along the linear length of the chromosome. The model that the authors propose from their data provides quite heady visuals indeed, and we thank the authors for the opportunity to heartily update our mental imagery of one of the trillions of incredibly small machines working away in our cells.

Contributed by benewencampen
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