Tuesday, March 31, 2015

Low Albedo?

In back of the building in which my office is located, in a normally shady spot, there is still a sheet of ice, which I have been attacking piecemeal with an ice chopper. In places, fallen leaves have reduced the albedo of the ice, producing leaf-shaped holes in the ice:




It's a shame that the 3-D effect is not so apparent in the pictures because the holes look really cool up close:




I should go nuts and grab a bunch of leaves to strew over this ice sheet, but the damn things are hard to come by this time of year.

Monday, March 30, 2015

Gomez' Birthday

Today, I stick to my yearly tradition by wishing my baby brother, Gomez, a happy birthday. Mom will be traveling down to Gomez' house for Easter. Unfortunately, shipping an Easter Egg Ring down to his place really isn't that feasible... I don't think the eggs cooked into the ring would travel well in a USPS truck.

Happy Birthday, Gomez, and have fun with mom on Easter.

Sunday, March 29, 2015

Poor Little Starvelings

When I got to work this afternoon, I was greeted with the piteous cries of hungry cats. Oh, for shame, look at these poor little starvelings:



I've heard that the guy who's supposed to feed them is a bastard.

Edit: They just about "mugged" me when I fed them this afternoon. They really didn't want to give me a chance to open up a can of food for them. They've been in a pretty giddy mood lately, probably because it's finally decent out temperature-wise and they're finally getting a chance to be outside. I totally empathize with my little furry buddies.

Saturday, March 28, 2015

Rockstar Morality

I've been a big fan of the band Muse ever since hearing their song Starlight on a local college radio station. The best thing about the band is that they are totally a nerd band (no surprise, as frontman Matt Bellamy is the son of George Bellamy, rhythm guitarist of the Tornados, whose Telstar is a glorious bit of 1960s rocket-pop), whether referencing astrophysics in their music or channeling a gloriously cheesy science-fantasy kung-fu space western (a fantastic spoof of a cheap European knockoff of a gloriously cheesy science-fantasy samurai space western). Besides the band's impeccable nerd-cred, they also have released political songs urging listeners to break out of the mass-media propaganda bubble.

In the runup to the release of the band's upcoming album, Drones, Mr Bellamy took on the topic of drone warfare and the societal implications of their expanded use:


Now, speaking to Mac, Bellamy elaborated that the album was "a modern metaphor for what it is to lose empathy." He continued: "I think that through modern technology, and obviously through drone warfare in particular, it’s possible to actually do quite horrific things by remote control, at a great distance, without actually feeling any of the consequences, or even feeling responsible in some way."

"The next step in drones is gonna be autonomous drones, which actually make ‘kill’ decisions themselves, where no humans are involved," Bellamy added.



Heady stuff, coming from a "rockstar". Personally, my take on the use of drones is that they remove the danger of human casualties on the battlefield, but that the very depersonalization of warfare further lowers the bar for violence. If an operator can kill an individual while sitting in an air-conditioned room two thousand miles away, the very act of killing can become no more emotional than playing a video game is. In the case of autonomous drones, even the slightest moral element is removed from the act.

Of course, the moralist is also a rockstar, so here is a video of a badass live performance of the new song Reapers:





As a final note, our society has hit a pretty bad low when rock songs are a better source of information that the news media.

Friday, March 27, 2015

Sauce! Sauce! Sauce!

This week, I stopped by the H Mart Korean superstore in White Plains to pick up such staples as soy sauce, tofu, and kimchi. While shopping, I fell in love with an eight-and-a-half pound bottle of chili garlic sauce, which I absolutely had to buy:




This bottle of hot sauce is as large as my rather big head, a fact that will be apparent from this picture of me performing my locally infamous "bottle trick", where I use my long cranium and excellent sense of balance to dance with a bottle (or cup or book or what have you) on my head:




My preciousssssssssssssssssssssssssssss...




I predict it'll last me a couple of weeks. Title inspired by David Johansen's hilarious novelty track.

Thursday, March 26, 2015

Thanks Are in Order

Wow, I have to take a moment to express my gratitude to several people in the aftermath of last night's post. First of all, I have to thank Dr Christoper Mason, who sent me a text message to correct an inaccuracy in my post, regarding the pace at which genome sequencing halved in cost. Thank you, Dr Mason! Next, I want to thank the awesome Dr Evon Hekkala, who delivered an amazing Secret Science Club lecture back in April 2013. Dr Hekkala suggested that Dr Mason and I exchange contact information and "talked up" my blog... thanks, Dr Hekkala, you have been unfailingly supportive and 100% fantastic. I also want to thank Elisabeth Bik of Microbiome Digest, who sent a link to my blog post via Twitter. I knew something funny was going on when my post counter started "upticking" at 1AM. I have never met Ms. Bik, but count me as a member of her fan club... thank you!

It goes without saying that I am grateful to Margaret and Dorian, who make the whole Secret Science Club experience possible. Thank you one and all!

Wednesday, March 25, 2015

Secret Science Club Post-Lecture Recap: Talk Dirty to Us

Last night, I headed down to the beautiful Bell House, in the Gowanus section of Brooklyn, for this month's Secret Science Club lecture, featuring Dr Christopher Mason, assistant professor of physiology & biophysics and computational biomedicine at Weill Cornell Medical College and member of the Yale Law School Information Society Project (but not, to my knowledge, a member of the Information Society). He was also named a member of the brilliant ten by Popular Science magazine. Dr Mason created quite a stir locally when the results of his NYC subway system DNA collection project were revealed earlier this year. Dr Mason gained overnight notoriety when he answered, in response to a query about germs in the subway, "You wouldn't want to lick all the poles, even though you'd probably be fine." Now THAT is one thousand varieties of awesome!

Dr Mason began his lecture by stating that he was obsessed with sequencing DNA, the molecular "recipe" present from an individual's first cells. He described development as a symphony of DNA, RNA, and proteins, a combination of processes that occur at all times.

The last ten years of microbiology have been revolutionary. To illustrate the growth of processing power in the field of genome tracking, Dr Mason brought up Moore's Law and noted that the reduction in the cost of gene sequencing has vastly outpaced the general pace of technological development. In the period from 2006-2007, the cost to sequence a genome was cut in half every five months. This reduction in cost has led to "participatory genomics", embodied by such websites as "Patients Like Me", a social media site on which individuals can share genetic data. Genome guided medicine has arrived- medicines can be tailored to a patient's genetic profile. Dr Mason noted that more data equals more power, and that organizations such as Genspace are bringing microbiology to a wider audience. One of Genspace's projects is a study of the microbiome of the ultra-polluted Gowanus Canal, mere blocks from the beautiful Bell House. Dr Mason mentioned two genes that have a great effect on the health of an individual possessing them: CCR5-Δ32 provides HIV resistance, mutations decreasing myostatin can result in larger muscle mass, and LRP5 regulates bone mass.

Dr Mason then shifted to the topic of DNA patents. Until recently, DNA, once removed from the body, could be patented. The patenting of a DNA sequence such as the BRCA1 and BRCA2 genes, which are implicated in the development of breast cancer, had the potential to stymie medicine based on these gene sequences. Dr Mason likened gene patenting to "patenting the word because and claiming to own every book". The challenge to gene patenting took place on 4/15/2013 and the Supreme Court invalidated patents on BRCA1 and BRCA2 on 6/13/2013- claims on isolated DNA were rejected. The litigation finally ended in 2015, so you now have a right to look at DNA. Dr Mason quipped, "Your genome is free!"

Dr Mason moved on to the topic of the microbiome. Every individual has more than one genome- there is the human genome and there is the genome of an individual's microbiome. Dr Mason illustrated this concept with a political analogy: "In a genetic democracy, you are the minority party." Every human being plays host to three to five pounds of bacteria, and most of the genes in your body are not "yours". Dr Mason cited the work of the Human Microbiome Project, joking "You are your bacteria." One's bacterial symbionts provide about 90% of the body's serotonin and about 50% of the body's dopamine. As Dr Mason put it, "The nearest pharmacy is your gut." The human microbiome produces about 700 "drugs". Lab studies have shown that (WARNING: NYT LINK, SAVE YOUR CLICKS) gut bacteria transplanted to fat mice can slim them.

An individual "inherits" its bacteria buddies from its mother in a Maternal Microbiome Transfer- during birth, a newborn picks up some of its mother's vaginal microbiome. Later on, this major transference is supplemented during nursing. Babies delivered through a Caesarian section tend to have a higher incidence of disease later in life. Dr Mason likened the microbiome to an anti-disease "force field", then he flashed a news report of Boeing's new "force field" patent (gotta love interdisciplinary nerdery!). He also noted that exposure to cockroaches is good for infants with asthma, and that Fecal Microbiota Transplants can harness "the power of poop" to help individuals with certain gastrointestinal problems (Dr Martin Blaser's two Secret Science Club lectures also dealt with this subject). He then cited OpenBiome as the go-to place for potential stool donors, with their "give a shit" campaign.

Dr Mason had a brief digression about bacteriophobia, quoting Bertrand Russell: "To conquer fear is the beginning of wisdom." He showed the audience a couple of photos of his adorable daughter and mentioned her habit of putting toys in her mouth. When he took her to daycare, he observed the kids all putting the same toys in their mouths and passing their microbiota around. He likened it to the whole group "making out". This was the inspiration for the big "swabbing campaign" which led to the Pathomap.

The Pathomap is a "molecular view of the city", the goal of the project, which began on 7/15/2013, was to "seek out new life, new civilizations". The project has taken place over six different seasons, with 4,342 different data points in a subway system that transports 5.5 million riders daily. Samples were swabbed, annotated, and sequenced. 50% of the DNA belonged to no known organism (though the genomes of cockroaches have not been sequenced yet). Dr Mason described the subway system as a "rainforest to explore" in an interview with the NY Times. DNA from bacteria, eukaryotes, viruses, and "ambiguous" sources) was collected. A headline in The Atlantic proclaimed: "New York City Subways Are Covered in Microscopic Pizza". Despite the discovery of minute traces of anthrax, bubonic plague causing Yersinia pestis, and dysentery-causing bacteria, 88% of the bacteria on the subway were "friendlies". Out of the deleterious 12%, the most common were Enterococcus and Shigella. Despite headlines about everything "from beetles to bubonic plague" being found, Dr Mason noted that there is zero evidence that anyone is at risk from the subway bacteria. He noted that anthrax is caused by a soil bacteria and that the "anthrax DNA" that was found could belong to an unknown relative, and there is evidence that low levels of the "bad" bacteria in the subway are okay.

The greatest genetic diversity in the subway system was found in the Bronx, with Brooklyn ranking second. Dr Mason wryly noted, "Nothing soft comes from the Bronx." High diversity is a good thing, there is a lesser risk of any one organism accumulating in a dangerous concentration. Comparing the subway system's microbiome to the human microbiome, Dr Mason stated that the subway "looks like skin" with regards to the diversity of its biome. He noted the various incidence of bacteria associated with kimchi, sauerkraut, and noted that species diversity varies by area of the city. Areas of the subway affected by superstorm Sandy were characterized by bacteria not present elsewhere, including bacteria normally associated with the Antarctic. The hourly dynamics in the subway system vary in the course of a day- the periodic cleaning of the system is like a "forest fire", followed by a repopulation of the cleaned area.

Dr Mason provided a "greatest hits" summary of his various statements to the press, including such side-splitters as "the best thing to do with newborns is roll them like sushi on the subway ground" and the bit about licking the subway poles. The man has a knack for a soundbite.

On the topic of the genetic diversity of the system, Dr Mason indicated that the presence of DNA doesn't necessarily indicate that the organism it reveals the presence of is alive. Certain bacteria can produce antibiotics in order to compete with other bacteria. Among eukaryote genes, chickpea and cucumber genes were commonly found. Cockroach genomes not being sequenced, the mighty roaches of New York have yet to take their rightful place, now they are lumped in with the "unknowns". The amount of human DNA found varied from day-to-day... Dr Mason admitted that no swabbing was done on the day of the No-Pants Subway Ride. The human DNA that was found corresponds with census data- zooming in on the different areas of the Pathomap, one can predict the census results due to DNA matches. Humanity's "molecular echo" rings throughout the Pathomap.

Noting that the bacterial "map" of the subway system looked like an ad for Uber or a full-body condom, Dr Mason tackled the question, "Should I ride the subway?" He said, "It's okay, you're all healthy." He concluded that we should ride the subway.

The final section of the talk concerned future projects. The NYC subway system, with 1.7 billion riders, is the seventh busiest subway system in the world. The swabbing and mapping of subways in other cities has already begun. Another upcoming project is a Hospital Microbiome Project. An integration of molecular and technical data would result in a "smart city" in which pathogenic microbe alerts could be issued. Nanopore sequencing, measuring DNA as it passes through pores, is making genome sequencing even more rapid, which led to a discussion of the need for BIG DATA storage, with Dr Mason musing about Yottabytes of genetic data. He also mentioned the upcoming studies of the Kelley twins to determine the effects of space travel on identical twins (obligatory shout-out to the mad genii of Riddled!)

In the Q&A, some bastard in the audience asked if there was an appreciable difference between the outdoor stations, exposed as they are to UV rays and winter cold, and the sheltered underground stations. Dr Mason indicated that there was almost the same level of genetic diversity, but the outdoor stations had more plant DNA than the underground stations. Other topics addressed included probiotic deodorant sprays (the bacteria prevent the "stink producing" bacteria from proliferating, but showering washes the probiotics off). Regarding DNA sequencing and genome-based medicine, Dr Mason urged us not to run away from genetic information, but to be wary of a loss of privacy. On the "Ebola question", Dr Mason noted that Ebola is an RNA virus, and no testing for it has occurred. MRSA was found at three spots in the system. Dr Mason briefly touched on DHS pathogen detectors, using air filtration, but the feds don't typically share data. One wag, noting that Dr Mason was a charismatic, entertaining speaker, asked if he would be giving Neil Degrasse Tyson a run for his money as the great populizer of science, to which Dr Mason responded that he had met with Dr Tyson and had "exchanged microbiomes" by shaking his hand. For those of you fantasizing about hunky scientists hanging out, this isn't the first time that topic has been raised. Regarding the Gowanus, there are a lot of Archea there, talk about extremophiles!

At the end of the Q&A, Dr Mason mused about the use of bacteria to protect astronauts from radiation on long space flights, and about "microbiome synchronization" in the tight spaces astronauts would deal with. He ended by noting that the best hope for long-term human survival is space colonization. We won't be going along on to the "final frontier", we'll be travelling with trillions of our closest friends.

Once again, the Secret Science Club dished out a fantastic lecture, one that hit the "sweet spot" of imparting information, giving a look into the processes used by working scientists, a healthy dose of humor, and perhaps most important of all, a compelling local connection. Put succinctly, Dr Mason knocked it out of the park. Kudos to Dr Mason, Dorian and Margaret, and the staff of the beautiful Bell House. The ride home on the subway system was wonderful, I was able to bask in the rosy glow of knowing that I was traveling with a myriad of little buddies.

Here's a quick video featuring Dr Mason:





And, for extra measure, here's the Pathomap- be warned, though, you could spend many, many hours playing with it.