Saturday, February 27, 2010

Grad Students Making a Difference

So it has been a long time since I last posted. Aside from being busy in the lab, I have been debating AIDS denialists or as they call themselves dissidents under the name Kevin Sullivan (not my real name). A few months ago I heard of a documentary called House of Numbers that was making the rounds at film festivals and stirring up controversy. House of Numbers is a documentary that advances an agenda of a small but quite vocal minority of people who deny the existence of HIV and therefore the existence of AIDS as well. One group in particular, the Perth Group has gone so far as to defend a man who knowingly infected others with HIV in a court of law by arguing the virus does not exist. Fortunately, they were defeated. When I hear things like this I normally just facepalm and try to ignore such arguments. A couple of weeks ago a friend linked me to an ongoing discussion, taking place on the House of Numbers facebook page. A grad student sent a letter to the producer of the movie trying to explain that advancing such an agenda is irresponsible and quite dangerous (grad students trying to change the world \m/). She offered to try her best to inform them of the mountains of scientific data arguing that HIV and AIDS are quite real and do kill people. The letter was posted on the facebook page and a long discussion ensued. The discussion was picked up by the Perth Group and they entered the discussion. Although she was outnumbered and not in the most friendly environment she did an awesome job of taking a high ground and treating her misguided attackers with respect. More importantly she did an equally awesome job of taking the scientific evidence and breaking it down so that non-scientists could understand it. I am sure she was aware that she was not going to change the minds of the film crew, the Perth Group, or the vocal supporters on the House of Numbers facebook page. That said, I think what she did do was appeal to the people who were on the fence reading the discussion but not posting. Lets face it, science is 99% failure and scientists rarely get to see their work make a real difference in anyone’s lives. Its not every day a grad student has the opportunity to make a difference in the world. If Silvia was able to convince one person to continue to practice safe sex or continue to take their life-extending medicines her efforts will have had more impact than many scientists experience in a lifetime. We need more people like her.

Her story has been picked up by other blogs like erv. Its really cool to see the scientific community coming out to support her.

Friday, February 19, 2010

Friday Fish tank - Pseudocrenilabrus nicholsi

I really wish these guys would sit still for more than two seconds. I had to resort to using the flash, ending up with this murky picture. At least it will give you an idea of their amazing coloring. There's also a pair of Laetacara curviceps in the back - who probably show up one Friday here as well if I can get a good enough shot.

Thursday, February 18, 2010

YAY Data!!!!!

Something didn't fail miserably in the lab? Astonished!
Nevermind what the picture actually is for now, but trust me, it looks better in all its 16 bit TIFF glory.

Endless forms most bizarre

Enjoy this cool photo list of the 50 weirdest organisms. Admittingly, it set me off on a frantic wikipedia search to read more on quite a few of these. My favorite though, goes out to that mottled lump of a monkfish or the indignant looking batfish, so awesome.

Thursday, February 11, 2010

Rachel Maddow on global warming

Visit for breaking news, world news, and news about the economy

With the added bonus of Bill Nye!

Science fiction

Lemurs on a raft!

“Any event that is not absolutely impossible ... becomes probable if enough time elapses”.

-George Gaylord Simpson

Madagascar is one of the world’s richest biological hotspots. It is home to 5% of the world’s flora and fauna, 80% of which are endemic, or only found on the island nation. One question that has been raised over and over is how did all these creatures get to Madagascar in the first place? This is especially true for Malagasy mammals. Excluding those introduced by humans, all native terrestrial mammals are found nowhere else in the world.

A few theories have been cast about attempting to explain this natural mystery. Could the mammals all have been present on the Gondwanan supercontinent and then separated over geological time? Perhaps they crossed on a land bridge left by shallow seas. While all possible, there is currently a lack of geological evidence to support these theories. If these scenarios were true, then we would expect to see more “typical” African mammals on the island – which is the exact opposite of what is found. The fossil record too for example does not support either of the above models - it only dates back a few thousand years for mammals on Madagascar. Meaning, we have no trace of ancestors from modern populations. Most surprisingly, the relatively recent appearance of mammals in the fossil records means they must have arrived long after the opening of the Mozambique Channel, a 430km physical barrier separating Madagascar from Africa.

While the fossil record is scarce for mammals, molecular dating from mammalian population on Madagascar shines a more complete light on their ancestry. Molecular systematics and divergence ages puts the founding populations for different groups arriving independently from Africa between 60-20 million years ago. Still long after Madagascar became an island.

A rather fanciful idea that has always floated around was that animals could have rafted from the continent to the island. Hell, even the Creation Museum uses that idea to justify how animals colonized the world after The Flood. But in the case of Madagascar, it may actually be true. In Nature this month, new computer models of Eocene ocean currents (and most likely throughout the Oligocene and Miocene) lends support for a rafting scenario. During this period which corresponds with the molecular dating of founding populations, not only were currents especially strong in the southwest Indian Ocean and Mozambique Channel, they were also much different directionally than their modern counterparts. Flowing from northwest to southeast and at a ripping 20cm/s at times, matted vegetation could have been transported from Africa to Madagascar in as little as 25-30days. And as the currents changed through time to their modern patterns, further colonization would have been cut off. This makes the superficially silly notion that animals surfed their way between islands, currently our best explanation. Don’t you love how science works in weird, cool ways like that? This work is however very preliminary, with the authors of the paper underscoring that a further 1-3 years of coupled models running on a supercomputer will be necessary for a more complete simulation. Nevertheless, this may lead to a more robust theory of how terrestrial organisms came to populate land separated by huge marine barriers independent of typical biogeographical models.


Ali, J. R., and M. Huber. Mammalian biodiversity on Madagascar controlled by ocean currents. Nature 463:653-656.

Tuesday, February 9, 2010

More industry opposition to science

Too often, politics trumps science. And sadly most pols think only in election years or term lengths while the consequences of their (in)actions can far outlive them. Support for climate change legislation however defies the usual trend. Here, politicians are undertaking the cause, which is firmly backed by science, to divert a looming global disaster.

Passing legislation to curb our emissions means businesses will have to upgrade their technology and clean up their act – all of which costs money. This of course brings out all the denialist kooks in Washington. Major opposition to climate change legislation comes from the right in this country, which more often than the left, has the backing of agricultural and industrial sectors, those who would be hit the hardest by new regulations.

Recently, the EPA deemed increased atmospheric CO2 levels were a threat to human health and ruled CO2 emissions should be regulated under the Clean Air Act. This will be no easy task however. Politico reports that the same forces that helped weaken climate change legislation in Congress are launching an assault on the EPA. With 1,170 businesses and interests from agriculture and industry throwing lobbyists into the fray, they hope to challenge the EPA’s authority in regulating CO2 emissions and thus sending regulatory power back to Congress where politicians, hungry for campaign backing, lend a much friendlier ear.

And according to the report:

“But even if the agency can defend its pragmatism, it may not escape a trial on global warming science.

The National Cattlemen’s Beef Association and the Massey Energy Co. and other mining interests already have filed a petition for court review of the EPA’s endangerment finding. “We think the EPA had a pre-selected outcome, then shaped the science to fit that outcome,” says lawyer Paul Phillips of the Holland & Hart law firm in Denver.”

Projection much?

The story continues:

“The EPA will have some powerful allies if such a challenge is filed. At least 16 states and four major environmental organizations have asked for court permission to join the case on the agency’s behalf. The latter group reprises much of the coalition that proved successful in the 2007 Supreme Court case that found greenhouse gases were a pollutant under the Clean Air Act, paving the way for EPA regulation"

Saturday, February 6, 2010

Whale war wages on

We’re only into February of 2010 and the clashes between anti-whaling activists and Japanese fishermen are already heating up in Antarctica’s icy waters. This week marked the second of the year’s two collisions between the rivaling forces. Left with a 3 foot gash in its hull the Bob Barker, named after the greatest game show host ever(!) and long time animal rights activist, who donated millions to Sea Shepherd so combat whaling fleets, was forced to temporarily abandon its pursuit of the whaling ships. While there were no injuries, the confrontations are becoming increasingly aggressive and likely only a matter of time before serious injury and death occur.

In January, another of Sea Shepherd’s vessels, the Andy Gil (which looks more like the Batmobile, or something from a James Bond movie), was rammed by a Japanese ship. Though like in this month’s incident, both sides are blaming the others. The video of the collision (here and here) does not make clear just who was at fault.

Honestly, why can’t we just live by Jon Anderson’s words (listen to that bass as well!)?

Dig it?

Friday, February 5, 2010

Friday Fish tank - Dwarf Gourami

Registration now open for NECSS

The Northeast Conference on Science and Skepticism will be held in NYC on Saturday April 17. This year's conference has a hell of a speaker list - including James Randi who could not attend last year due to health reasons. With only 400 spots available, its best to register early.

Tuesday, February 2, 2010

Trim5a- Guardian of the Genome:

As you can see from the title, the first factor I am going to blog about in the series on host restriction factors is Trim5a (T5a). Before I jump right into it, I want to give a little background I forgot to give in my introductory post, specifically what do viruses do? Viruses can’t do a whole lot, they are just balls of protein, nucleic acid (DNA or RNA), and maybe lipid and some sugars. They need a cell and it’s machinery for every step of its life cycle. The life cycle starts when I virus is floating around and finds something that makes it stick to a cell. If the virus binds to a specific receptor the virus can enter that cell, if the receptor is not there the virus cannot get in. This is the first block to infection. Next all viruses enter the cell and the genetic material must got to the right place. At this point the virus makes viral proteins and copies its genome. Once all the components to assemble new viruses are present, progeny viruses are mande and these new viruses leave the cell to infect others. You may be able think of many steps in this process where a cell can try to defend itself. I am going to focus on proteins that block entry, freeing of genetic material, leaving the cell, and infecting the next cell in this series.

Trim proteins are named for their tripartite motif comprised of a RING, B-Box and coiled-coil domains. A RING domain is a domain that similar to those of E3 ubiquitin ligases. These enzymes help add ubiquitin (a protein) to a target protein. Ubiquitin is most commonly a tag that makes a protein for degradation. The coiled-coil domain mediates the multimerization of proteins. The B box is thought to enhance both of the previously mentioned functions. An additional domain, SPRY/B30.2 is added through alternative splicing to generate Trim5a, the antiviral form of the protein. Conceptually this protein consists of two parts, the TRIM and SPRY. The TRIM domain gives it its effector function while the SPRY domain gives it its specificity. Evidence suggests that the SPRY domain recognizes features on the N-Terminal domain of the capsid protein (shell around the viral RNA/DNA). Although the precise mechanism behind T5a mediated restriction is unknown, evidence suggests that restriction occurs through two processes: destabilization of the capsid core before the completion of reverse transcription and degradation of the core-T5a complex. Retroviruses have an additional step in their life cycle, they copy their RNA into DNA. For viruses like HIV this takes place after it enters the cell. This requires that the capsid (shell) stays mostly intact. Its almost like making a hard boiled egg, if you boil an egg in its shell you get breakfast, if you break the egg in boiling water you get mush. T5a does exactly that, turns retroviruses into mush. T5α has a short half-life in the cell possibly due to autoubiquitination from theTrim motif. Rapid turnover targets the core-T5a complex for degradation. In a nutshell, T5a breaks the virus open too soon and takes out the trash. Understanding how these two processes work individually or in concert is the subject of intense investigation.

With that background done, I am going to talk about why these proteins are cool and what they teach us about evolution and selection pressure. Of all the factors on the list only Trim5a (T5a) acts as a post entry, preintegration block to initial infection of retroviruses. It can render viruses 10-100 (possibly more) less infectious. Considering this crucial function, the great diversity among homologs and orthologs at the T5a locus is to be expected. For example every species of primate tested has a unique T5a. They are not different all over. Instead the diversity is mostly limited to the specific amino acids that allow T5a to recognize a viral capsid (see figure from Newman et al. 2006). These hot spots of mutations highlight the idea of the Red Queen. Whenever a T5a protein that can block a specific virus is selected for, the virus must evolve around this block. Now getting around one T5a

is difficult enough, but in some species like rhesus macaques there are anywhere from 6-11 T5a alleles circulating in the population (as a spoiler, yes retroviruses get around all of them). So what about us? As it turns out there is actually very little variation in humans. The only really different one we have found is broken. There are a number of possibilities for why we are so homogeneous, we are a young species, we have gone through many bottlenecks and our radiation out of Africa is has resulted in founder effects. We know humans get retroviruses, HIV-1, HIV-2, SIVmac, HTLV-1 and 2, XMRV, and Foamy virus, so our T5a can’t be the most amazing block ever conceived. Could it be possible that one virus nearly wiped us out. We have come close to the brink of extinction on a number of occasions in the past. Did this one T5a allele win the Red Queen arms race? We can only speculate, but you can be sure that in some ways the T5a in every one of your cells has been shaped from battles with ancient or maybe not so ancient retroviruses.


Vestigial organs and features are well known evidence for common ancestry and macroevolution.Similar in concept to anatomic vestiges, another quirk of common ancestry is that DNA preserves the blueprints for many “lost” features but are not expressed during normal development. Occasionally though, an organism will be born with what’s called an atavistic structure. Much like its literary definition, biological atavism is some phenotypic reversion to an ancestral form.

Atavistic features may commonly be observed during early life stages since many organisms share similar embryonic forms. For example, human fetuses having tails then eventually losing them during development. The amazing strength of evolutionary theory is that we can use it to make predictions. For instance, we understand how whales evolved supported by a long list of transitional forms. So we can reasonably make the prediction that we would sometimes expect there to be a mutation in living whales to express some atavistic feature. And evolution is once again confirmed by observations in nature. Whales and dolphins have occasionally been caught possessing rudimentary hind limbs, a testament to their terrestrial past.

Hind limbs on cetaceans are nonfunctional though, often very small in size – likely to the ancestral species’ gradual reduction in size and loss over time. They also vary in their complexity. Some may be present only beneath the skin and attached to the pelvic bone (a vestigial structure), while others as buds protruding on the skin to full leg-like structures. The skeletal remains also confirm that these limbs are also not just random malformations, but actual primitive limbs. On the rare specimens that have been analyzed, individual bones can be identified including femur, tibia and metatarsus. Cetacean hind limbs are also much like human tails in embryonic stages. Whales too form hind limb buds during development but the cells degenerate during later stages.

From vestigial bones, atavistic features and an abundance of transitional forms, all the lines of evidence points to cetaceans having a common quadrupedal terrestrial ancestor and the power of evolution. There is one more Atavism of note though, the Slough Feg album of the same name with the song below coincidentally being about natural selection and evolution. Anyone else agree we need more metal songs about science?