Sunday, December 13, 2009
Wednesday, December 9, 2009
We're still in the principle photography phase here on the set of THE BEARDOME, but we've collected enough footage to release a full-length theatrical trailer. We're still on track for a December 2009 release, although Jake is refusing to grow a beard on only the left half of his face for a key scene in the film. We're in negotiations with his agent, stay tuned.
Friday, December 4, 2009
Here at Hydrocalypse Industries headquarters we're hard at work on our latest film project. The budget is bigger than for any previous video we've ever done, and we blew most it on this teaser trailer. Stay tuned for more updates from the set.
Wednesday, December 2, 2009
We've recently been inspired by the diversity, the power, and the biological importance of beards. We have begun a new and exciting project in beard science, cataloging the microflora of the beard phenotypically, genetically, genomically, and a whole-lotta-other-omically. More to come...
Posted by Christina at 11:45 AM
Tuesday, December 1, 2009
Emirates has developed our favorite iPhone app. iLingual is a great program that helps you learn a new language (French, German, or Arabic), get around in a foreign country, and annoy everyone during lab coffee breaks. Best of all, it's free! Check out the video to see it in action!
Posted by Christina at 1:54 PM
Thursday, November 19, 2009
Just in time for the holidays! Official Hydrocalypse Industries merchandise! Not sure what to get for your child? How about a nifty hydrocalypse.com sticker for his lunchbox! Looking for a personal gift for that special someone? Try our his and hers line of underwear! Check out our store at Cafe Press, the only place to get official Hydrocalypse Industries products!
The Hydrocalypse Industries store at Cafe Press
Posted by Patrick at 4:14 PM
Tuesday, November 17, 2009
Thursday, October 29, 2009
Tuesday, October 27, 2009
Friday, October 23, 2009
The power struggle that raged during the redesign is over. Christina, Jake, and I retained our rank as Unicorns of the Hydrocalypse. Michael, however, who has returned to his native Dutch land was demoted from Unicorn to Horse. He remains an important part of the Hydrocalypse Industries family in his reduced role, but there must always be four Unicorns. In recent days someone has risen to fill Michael's place. The identity of the fourth Unicorn will not be revealed today, but we are ready to release footage of this person in action.
Tuesday, October 13, 2009
Tuesday, October 6, 2009
Monday, September 14, 2009
Saturday, September 5, 2009
Tuesday, August 25, 2009
Everyone is familiar with hyperbole-laden sports commercials, especially those made by Gatorade. What people are less familiar with is that the Unicorns were approached to make a special commercial for the "What's G" campaign featuring a scientist. Since we're big fans of avoiding dehydration and Lil' Wayne, we agreed. Gerald, our resident
German Austrian scientist with a name that starts with G, stars. (The following video is also available in glorious HD)
Posted by Patrick at 10:28 AM
Wednesday, August 12, 2009
Sunday, August 9, 2009
Monday, July 27, 2009
Everything is more fun when it's a mean-spirited competition, so we decided to have a little miniprep challenge in lab (minipreps are ways to isolate circular pieces of DNA from bacterial cells). Everything is even more fun when it is culturally insensitive, so we decided to compete against all the German (and Austrian) students in our lab. Unicorns (and USA) vs. Germans, in all-out plasmid prep battle...CAN...YOU...HANDLE...IT!!!?!??!?!!!
We decided that we couldn't just compete on time, because cutting corners can reduce the DNA yield. Our final measure was nanograms of DNA isolated over seconds of miniprep time. If you think you can beat the Unicorns, we did eight five milliliter minipreps of the pCDF-Duet vector, a low copy plasmid from Novagen. Try just beating us on time though, I dare ya.
Respond to the video on youtube or comment on this post if you think your lab is awesomer (ha!), or if you are a Qiagen representative and want to give us free stuff/a lucrative sponsorship.
Posted by Christina at 8:15 AM
Monday, June 29, 2009
Before there were genomes, DNA, or confocal microscopes, there were dudes doing synthetic biology in France. Despite what almost every single paper on synthetic biology says, the term was actually coined in the early 20th century by Stéphane Leduc, who spent all of his time mixing together various salts and chemicals and seeing how osmosis (left) could mimic the properties of "real life" (right). Maybe in 100 years when everyone knows better they will ignore our treatises as well.
Posted by Christina at 6:57 AM
Monday, June 22, 2009
Friday, May 15, 2009
Monday, May 11, 2009
No, this isn't another post about Star Trek. This is about my new favorite photo, chock full of famous synthetic biologists. I'm hoping it is the first in a series of us posing with celebrity scientists.
Special thanks to David Jeruzalmi for taking this marvelous photo, Craig Venter for having a good sense of humor, and George Church for making that crazy face off to the side.
Posted by Christina at 6:46 PM
Sunday, May 10, 2009
Friday, May 8, 2009
Thursday, May 7, 2009
We at the Hydrocalypse have a passion for design. When it comes to agarose gel electrophoresis, we know that good science can be beautiful, and beauty is truth. Our design philosophy acknowledges the metaphysical continuity from science to engineering, function, form and art.
Our colleague and Friend of the Unicorns, Buz Barstow, has recently auteured these sketches for an agarose gel mold.
Clean lines, modern design, all calibrated to within one micron. Brought to you by the Unicorns of the Hydrocalypse.
Posted by JAKE at 11:35 AM
With the Unicorn's exclusive viewing of the new Star Trek movie only hours away (Pre-Review: its going to be awesome), the blog content explosion must continue. Today, we analyze another biology themed TNG episode: "Identity Crisis."
As Synthetic Biologists™ we know that completely rewriting the DNA of an organism is fun and anyone can do it. All you need is years of expertise and millions of dollars. In the future, any yahoo with a tricorder and a Galaxy-class starship can do the same.
On stardate 44664.5, we discover that members of Geordi LaForge's old crew abord the USS Victory are mysteriously disappearing. Upon realizing that all those disappearing were all members of a mission to an unexplored planet, Geordi and the Enterprise return to investigate (always a bad idea). They find a planet full of mysterious aliens that are invisible to the naked eye. Here's the shocking twist: some of those aliens are actually the former crew members, who got infected when they visited the planet. The aliens reproduce by a method much more efficient than sexual reproduction: infected visitors have their DNA rewritten over a number of years, and once the transformation is nigh, the infected people experience an uncontrollable urge to return to the planet. During the investigation, Geordi transforms into an alien, ditches his clothes, and runs around naked on the planet's surface. With time running out in the episode, Data decides that its time he gets involved, devises a way to detect the invisible aliens, and Dr. Crusher resets all of Geordi's DNA to its original state in time for supper.
Lessons learned about rewriting DNA:
- Why have sex when you can create an overly elaborate virus? (the aliens must have been lovelorn synthetic biologists)
- It can make you invisible (I believe that this was accomplished via GFP and the Lac promoter)
- It can induce uncontrollable urges (there's a Pon Farr joke in there somewhere)
- Its easy to do and undo (we're still working on the second part)
Wednesday, May 6, 2009
I know what you're thinking: how is it possible to make two awesome videos in one week? Well, it takes hard work, patience, and inspiration. This time, in the form of Craig Venter and his amazing boat. For those of you who may not know, Craig Venter has been described as "The Justin Timberlake of synthetic biology;" he is one of the co-sequencers of the original human genome sequence, and is currently working on building whole genomes from scratch. At the same time, he goes yachting with sequencing machines so that he can "find cool stuff" in the ocean and "get a tan." To you, sir, we tip our hats.
And don't worry, we haven't forgotten about star trek week. Here is a video of me killing Klingons in 1990.
Posted by Christina at 5:07 PM
We must briefly interrupt Star Trek week with important news. Taking some time out of our normal research, we've isolated the original animal from which the current swine flu outbreak started. Footage below.
Stay tuned for more Star Trek and more videos....
Posted by Patrick at 3:24 PM
Tuesday, May 5, 2009
The events of 47653.2 should be an example to those of us in the Synthetic Biology community. For our (presumably few) readers unfamiliar with stardates, I am referring to the tragedy that befell the Enterprise D in 2370 as she tracked a stray torpedo through the Typhon Expanse.
The story is painful to recall, even hundreds of years before it will happen. Lieutenant Barclay gets the Urodelan flu, so Dr. Crusher activates his dormant genes with a synthetic T-cell for treatment. But Dr. Crusher, getting sloppy, misinterprets her agarose gels and fucks up the T-cell transfections. So naturally the cells run amok on the Enterprise, activating the crew's secret introns and causing them to devolve into whatever weirdo animals their species evolved from. Long story short, Barclay devolves into a spider, Dr. Crusher gets sprayed with venom, Data's cat turns into an iguana for some reason, and Ensign Dern is gored by a space-crab.
So what lessons can scientists draw from this? The first lesson is obviously to avoid over-medication. As is well known, the Urodelan flu is generally mild. Even in the 24th century, fluids and bed rest are the best medicine.
Second lesson: All engineered organisms eventually escape and run amok. So what are you going to do about it when it happens? Lysine contingency? Suicide gene? Release a new organism, deadlier still, to hunt and kill the first thing? I don't have all the answers, so I'm happy to leave this thorny question to the appallingly uninformed voters.
Thirdly, what is all this iguana and spider DNA doing in the human genome? Do you want monkeys in your introns? Gross! I propose that we use Synthetic Genomics, sister-discipline of Synthetic Biology, to rewrite the human genome and eliminate all non-human DNA. This kind of thing is already working for viruses, therefore humans are the next logical step. If we can get it done by 47653.2, we may be in time to save Ensign Dern.
Monday, May 4, 2009
Posted by Patrick at 11:04 AM
Unless you live under a rock you know that the new Star Trek movie is coming out this week (and if you do, please collect some dirt samples for us). For this wonderful week, we will honor our love of Star Trek through blogging from our special futuristic biology point of view.
To get started, I just want to mention what is probably the best known of the Star Trek biological breakthroughs: Khan Noonien Singh. Khan may be "the product of late 20th century genetic engineering," but that chest, my friends, is simply a work of art.
Posted by Christina at 8:40 AM
Thursday, April 23, 2009
The attempt to demystify science isn't new. In the seventies, the young French philosopher (this is already sounding awesome, right?) Bruno Latour spent two years in a neuroendocrinology lab at the Salk Institute. The book that he wrote on his experience, Laboratory Life: The Construction of Scientific Facts, details his observations of the scientists as if he were an anthropologist studying a mysterious foreign "tribe." Through spending time with the tribespeople and learning to think and speak like them, he was able to uncover how scientists collect, learn about, talk about, and present scientific data.
I can't tell you why you should read this book any better than Jonas Salk himself did in the book's introduction so I'm just going to copy some of the good parts of that from here.
"Scientists often have an aversion to what nonscientists say about science. Scientific criticism by nonscientists is not practiced in the same way as literary criticism by those who are not novelists or poets...
A love-hate relationship exists toward scientists in some segments of society. This is evident in accounts that deal with facets ranging from tremendously high expectations of scientific studies to their cost and their dangers--all of which ignore the content and process of scientific work itself...However, the present book is somewhat different from accounts usually written by nonscientists about science...[Latour] has tried to to observe scientists with the same cold and unblinking eye with which cells, or hormones, or chemical reactions are studied...
I am now convinced that this kind of direct examination of scientists at work should be extended and should be encouraged by scientists themselves in our own best interest, and in the best interest of society...If the public could be helped to understand how scientific knowledge is generated and could understand that it is comprehensible and no more extraordinary than any other field of endeavor, they would not expect more of scientists than they are capable of delivering, nor would they fear scientists as much as they do. This would clarify not only the social position of scientists in society, but also the public understanding of the substance of science, of scientific pursuits and of the creation of scientific knowledge. It is sometimes discouraging that although we dedicate our lives to the extension of knowledge, to shedding light and exemplifying rationality in the world, the work of individual scientists, or the work of scientists in general, is often understood only in a sort of magical or mystical way.
Even if we do not agree with the details of this book, or if we find it slightly uncomfortable or even painful in places, the present work seems to me to be a step in the right direction toward dissipating the mystery that is believed to surround our activity."
Seriously, read this book.
Tuesday, April 21, 2009
Sunday, April 19, 2009
One of my goals for our blog is to show (to the few people who may read this who don't know us personally) that scientists are just like regular people whose job happens to be mixing together clear liquids all day. For this reason, I am pretty interested in DIYbio, a group that aims to make science, and biology in particular, more accessible to people who are interested in viewing the world around them scientifically but maybe don't have a degree in science. [What follows is probably the most serious/boring post we have on here, but believe it or not, we are serious sometimes and this is something I feel is important enough to go into excruciating detail about. Feel free to skip this and go back to looking up cusses in scholarly journals.]
I think it is totally awesome that people who don't have a lot of experience with science think that biology is cool enough to meet at bars to talk about, and it is great that people want to do experiments. However, in the process of demystifying biology so that amateurs can interact with things like bacteria, DNA, and even genomes, DIYbio often ends up pushing "traditional" science further into the abstract ivory tower. This is especially true I think in the discussions around how to do DNA electrophoresis (separating different pieces of DNA based on their size). In seeing what DIYbio is proposing as methods for doing this common lab technique, it is clear that the people who do it every day (grad students, post docs, and technicians working in labs everywhere) haven't done a really good job of explaining how the data that is finally presented to the public is "made"; that is, how the experiments are actually done. What people end up seeing is what biotech companies that want you to buy their $1000+ electrophoresis setups are saying.
I hope that in showing how we do DNA electrophoresis in our lab (at the ivoriest of all towers, harvard) I can show how experimental biology is often hacked together and DIY (which makes it really fun and sometimes frustrating) and has a lot more to offer than the final reports of what we make of the experimental results, and way more to offer than the bio-rad website. I'm not going to go through all of the DIYbio proposals on how to do gels, because the discussion boards listed above already go into good detail about what would work and what wouldn't and why. My goal is just to show that the way that we do it is already pretty cheap and is actually quite similar to some of the final proposals for the DIY gel box from Pearl Biotech.
So here's my method for making DNA gels, illustrated with some fancy cell phone camerawork. First, I weigh out some agarose, mix it with saline, and microwave it for two minutes. Agarose is relatively expensive at $420 for 500 grams, but you only need 1 gram per gel so it should last for a long time.
While the agarose is microwaving I put together my gel tray. We use a simple piece of plastic put together for us by the harvard machine shop wrapped with masking tape (really) around the bottom so that the melted agarose doesn't fall out. A small plastic comb makes the wells where I'll put the DNA.
Now my agarose is melted, and here comes the tricky part. We add ethidium bromide here, a super toxic, absolutely (maybe) will kill you DNA stain that allows us to see where the DNA is. This stuff is difficult to dispose of safely, and there are some other options for DNA stains that are more expensive, but probably better if you're going to be doing this someplace that doesn't have OSHA people all over it.
Now I've poured my gel into my prepared gel tray and let it harden, it's time to load my DNA.
I put it into a plastic box, also made by the machine shop. This box is filled with the same saline solution I used to dissolve my agar, and has a wire running through it that can be connected to any power source. I mix the DNA with a solution of glycerol and a dye. The dye lets you see how far your sample has run through the gel, and the glycerol is heavier than water so it lets the DNA fall into the wells that the comb made in the gel.
After running a voltage through the gel for about 20 minutes the gel is ready to look at under UV light. This makes the ethidium bromide glow where it has bound to the DNA and you can take a picture of the gel.
Tada! I hope that this shows that lab scientists and home scientists have a lot in common when we have similar goals, in this case separating out some DNA. I think if what people saw about DNA wasn't on CSI, Gattaca-like tests that gave you statistically suspect percentages for disease risk, or $500 canvases with DNA fingerprints that people wouldn't think scientists are so weird, and maybe would be even more interested in talking about biology at a bar. If you think this is a good idea, let us know. If you think it's boring, let us know; we can go back to talking about Star Trek and poop.
Posted by Christina at 6:22 PM
Sunday, April 12, 2009
This is a good first pass at the data, but we know that power law distributions are all the rage these days, so we need to make the data look more power-law-y. Randomly adding parameters to our model revealed a missing parameter that completes our graph:
Much better. A thoughtful scientist would want to delve deeper into the data to discover the mechanisms through which swears end up on PubMed. Running a hidden-Markov chain model on the data classified the causes of bad words on PubMed into the following categories:
A mutant crp allele that differentially activates the operons of the fuc regulon in Escherichia coli.
Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, Massachusetts 02115.
L-Fucose is used by Escherichia coli through an inducible pathway mediated by a fucP-encoded permease, a fucI-encoded isomerase, a fucK-encoded kinase, and a fucA-encoded aldolase. The adolase catalyzes the formation of dihydroxyacetone phosphate and L-lactaldehyde. Anaerobically, lactaldehyde is converted by a fucO-encoded oxidoreductase to L-1,2-propanediol, which is excreted. The fuc genes belong to a regulon comprising four linked operons: fucO, fucA, fucPIK, and fucR. The positive regulator encoded by fucR responds to fuculose 1-phosphate as the effector. Mutants serially selected for aerobic growth on propanediol became constitutive in fucO and fucA [fucO(Con) fucA(Con)], but noninducible in fucPIK [fucPIK(Non)]. An external suppressor mutation that restored growth on fucose caused constitutive expression of fucPIK. Results from this study indicate that this suppressor mutation occurred in crp, which encodes the cyclic AMP-binding (or receptor) protein. When the suppressor allele (crp-201) was transduced into wild-type strains, the recipient became fucose negative and fucose sensitive (with glycerol as the carbon and energy source) because of impaired expression of fucA. The fucPIK operon became hyperinducible. The growth rate on maltose was significantly reduced, but growth on L-rhamnose, D-galactose, L-arabinose, glycerol, or glycerol 3-phosphate was close to normal. Lysogenization of fuc+ crp-201 cells by a lambda bacteriophage bearing crp+ restored normal growth ability on fucose. In contrast, lysogenization of [fucO(Con)fucA(Con)fucPIK(Non)crp-201] cells by the same phage retarded their growth on fucose.
Automatic analysis of signals with symbolic content.
Department of Applied Physics, University of La Laguna, C/ Astrofísico Sánchez. Ed. de Física y Matemáticas, CP 38200, La Laguna, Spain.
This paper presents a set of methods for helping in the analysis of signals with particular features that admit a symbolic description. The methodology is based on a general discrete model for a symbolic processing subsystem, which is fuzzyfied by means of a fuzzy inference system. In this framework a number of design problems have been approached. The curse of dimensionality problem and the specification of adequate membership functions are the main ones. In addition, other strategies, which make the design process simpler and more robust, are introduced. Their goals are automating the production of the rule base of the fuzzy system and composing complex systems from simpler subsystems under symbolic constrains. These techniques are applied to the analysis of wakefulness episodes in the sleep EEG. In order to solve the practical difficulty of finding remarkable situations from the outputs of the symbolic subsystems an unsupervised adaptive learning technique (FART network) has been applied.
Ovarian teratoma in a bitch.
Department of Preventive Veterinary Medicine, Universidade Estadual de Landline, Londrina, Paraná 86051-990, Brazil.
Scientific writing doesn't often inspire poetry, but this paper is beautiful in its simplicity and directness. Feel free to recite this at your next poetry slam:
Ovarian teratoma in a bitch.
Posted by Patrick at 9:14 PM
Tuesday, March 24, 2009
Today is Ada Lovelace Day, where the internet celebrates all the Sassy Bitches of Technology.
All over the internet there are awesome blog posts about sassy bitches doing their part for science and technology, including my new favorite, the awesomely sassy Grace Murray Hopper:
Have a sassy day everyone, and get ready for Sassy Bitches of Science: Rosalind Franklin--coming soon!
Posted by Christina at 11:10 AM
Friday, March 20, 2009
If you only saw this blog, you would think that we spend most of our time thinking about television and getting famous. While this is true, we also spend a lot of time thinking about science and how to bring the hydrocalypse. Most of our work focuses on trying to artificially evolve hydrogen-producing enzymes to be stronger. Another huge area of effort is coming up with acronyms. For example, this artificial evolution strategy is referred to as the "Hydrogenase Isolating Life-form: A Novel Directed Evolution Reactor," or:
There can be only one.
Posted by Christina at 7:36 AM
Tuesday, March 17, 2009
For our new sitcom "The Lab," we decided to start with casting and go from there. There's a lot of people in the lab, so we started with the people in the two bays that house the bloggers, the boss, and people we constantly make fun of.
First, the boss-
And our good friends who have a good sense of humor when we make jokes about them-
Please pass this along to any friends in the industry!
Posted by Christina at 1:31 PM