In the summer of 2012, I was a precocious undergraduate spending the summer at a certain Ivy League institution as a research assistant in the laboratory of a certain Nobel Prize winner. I plugged away at the microscope all day, with Earl Sweatshirt’s early shit blasting in my ears, the steady minimalist beats fueling me through my grueling days. But then I would come home, and unwind in front of my computer like any good millennial. One day the Curiosity rover landed to much fanfare, and I stayed up on my computer late into the night to watch it. Something about space is so inspirational to anyone with any real interest in science. We have run out of things to explore; those greedy colonialist pigs circled the globe long before I ever got the chance (and made a real mess of things by doing so). And space itself isn’t something new: JFK inspired the US to reach for the stars decades ago, while the USSR was also looking upward. Since then, it seems like every country has a space program. Maybe space is just mundane now? Maybe resupplying the International Space Station is like the monthly trip to Costco? But I think there is still some mystique in it. Because the night that Curiosity landed on Mars, I watched with wonder–and I was not the only one. We keep having these moments as a society where the space programs of our planet manage to keep us interested long after people were supposed to have gotten bored with space. I started to wonder if NASA is just getting better at marketing. Did they hire some big PR firm to drum up public support–and maybe secure a half a percent more of the next federal budget. Maybe it makes more sense that this wonder was never really gone. Because now Elon Musk is promising to send people to Mars and I want to be first in line. The truth is that the rational part of me doesn’t believe that SpaceX will ever send a soul to Mars. Hell, they can’t even get a resupply rocket off of the ground. But the idea is just so human. There’s nothing left for us to explore. So why not pile into aluminum tubes and blast off (or up) for the heavens, why not see what we can find out there? This monkey is ready to blast off into space, man.
I was obsessively following trade deadline Twitter chatter up to and past the deadline, so I caught the Liriano trade as it happened. We’re out from under Liriano? Sounds great to me, I thought. Then the details started to pour in. Instead of just Liriano, we were giving up AA prospects Harold Ramirez and Reese McGuire. All for a quad-A starter. I was livid. I cursed Neal Huntington up and down, texted everyone I knew who I thought might give a damn (not many people), and scoured Twitter for someone, anyone, trying to spin the trade in a positive light (no one). I had a sandwich and a beer at a local bar to calm my nerves and started walking home. Maybe it was something about the cool evening air mixing with my slight alcoholic buzz, but the trade suddenly made sense to me. Please allow me to explain.
The trade only makes sense if you assume that the Pirates so wanted to be out from under Liriano that they were willing to part with Ramirez in order to convince Toronto to take on that contract. Ramirez is a decent outfield prospect, but his stock has slipped lately. Tim Williams of Pirates Prospects suggested on Twitter that it is not crazy to think that Ramirez will never see the light of PNC Park. So those two pieces of the trade cancel out, and we are left with Reese McGuire for Drew Hutchison. Unlike Ramirez, McGuire has a really clear path to the bigs in a Pirate uniform, and it is hard to justify dealing him for Hutchison. However, that is my hypothesis. It seems like the Pirates think that Hutchison can be a solid rotation piece by next year, so this makes some sense as a one-for-one trade.
All of this is a tough pill to swallow, though. I went to an Altoona Curve game last week and got a front row seat right behind home plate. Reese McGuire kept taking warm up swings in front of me, and I kept watching the man work. The whole time I thought, this guy is going to be catching Taillon and Glasnow at PNC Park before we know it. I am sad to think that I will never see that come to pass. But I wish those guys the best in Toronto, for our sake and for the sake of Huntington’s credibility.
Neil Walker returns to Pittsburgh this week for the first time since being traded to the New York Mets last December for Jonathan Niese. I was born and bred a Pittsburgher, so I love to weigh in on the Pirates front office decisions. It is probably too early to reflect on that trade, but I’m going to do so anyway.
Walker played with the Pirates from 2009 to 2015, and throughout that time he was a pretty dismal defensive second baseman. During that seven year window, Walker racked up -11 defensive runs saved (DRS) and -31.6 ultimate zone rating (UZR). Compare that to the MLB average DRS of 10.9 and UZR of 8.3 over that same period for qualified second basemen. So let’s face it: Walker was never a defensive second baseman. In fact, I might go so far as to compare him to Chase Utley (“He’s a power hitting second baseman. You know how rare that is in the national league?”). Walker had always been there to hit. But if you really compare Walker during his heyday in Pittsburgh to his second base contemporaries, his run production was right around that of other decent second basemen: he was right in the middle of qualifying second basemen between 2012 and 2015 when taking into account DRS and weighted runs created plus (wRC+) (somehow I knew Chase Utley would pop up as a fellow In-Betweener).
With Pirate infield depth waiting in the wings, it wasn’t hard to believe that the Pirates chose to cash out the Neil Walker chip. Josh Harrison has been a more than capable replacement: FanGraphs has Harrison at 0.9 wins above replacement so far this season, with a 0.350 on base percentage and a 4 DRS that puts him comfortably in the top half of second basemen this year. But I will admit that I feel a twinge of nostalgia when I remember the days when the Pittsburgh Kid actually played in Pittsburgh. We had seven beautiful years, Pittsburgh. Nothing lasts forever. And Neil: glad to hear that you finally joined the ranks of those of us who wised up and left Pittsburgh for the greener pastures of New York. Looking for a roommate?
From time to time, I make a mistake by failing to keep up with the primary scientific literature as closely as I should. If I had been on my grind, I would have noticed that another Zika structure was published in Science at around the same time as the Nature structure that I blogged about earlier. The group that put together this structure also compared the Zika particle to related viruses, this time choosing to focus on a region of the viral protein coat that is especially dissimilar to related viruses. The authors go on to suggest that this region of the coat may be involved in attaching to host cells, which could explain how transmissible Zika is compared to its relatives.
Now is as good a time as any to say how big of a FiveThirtyEight fan I am. Nate Silver’s site publishes the best data-driven stories on the web (NY Times’ Upshot is another good one to check out if you’re interested, but it has a decidedly more economic bent). Silver and his colleagues do an amazing job of bring data to bear on any question they can think up, and lucky for me that often includes baseball. If you want to see what I mean, take a look at the pieces that they published in the last 24 hours:
FiveThirtyEight has gotten some real mileage out of using Elo ratings to compare basketball and football teams, but this looks like the biggest project they have tackled using the rating system, working with data going back over 100 years.
I plan on keeping my eyes on the 2016 predictions for the rest of the season, and I have already had a ton of fun going back and comparing teams from 100 years ago. So far, it looks like my own Pittsburgh Pirates still haven’t managed to reach their apogee of the turn of the 20th century, even with the recent run of competitive teams. Adding to my frustration, the damnable Chicago Cubs have the highest stock that they’ve had in decades. Everyone gets their moment in the sun, I suppose.
(Image credit: Kostyuchenko et al. (2016) Nature.)
Update (4/27/2016): Science also published a Zika structure, drawing complementary conclusions from it. I thought it would be a good idea to post a small blurb about it here.
A group in Singapore published a structure of the Zika virus particle in Nature on Wednesday. Zika, which the Centers for Disease Control recently concluded is responsible for birth defects in children of infected mothers, has become a growing public health concern.
Victor A. Kostyuchenko and his colleagues at the Duke-National University of Singapore Medical School used cryo-electron microscopy to see the structure of Zika particles incubated at different temperatures. Importantly, the scientists found that the Zika particle is stable over a broader range of temperatures than other related viruses. On a practical level, this could mean that the virus is more transmissible than related viruses, and may be more challenging to control.
Virus particles are simply genetic material–either DNA or RNA–surrounded by a protein coat that protects and transports the genetic material. When the protein coat comes into contact with a susceptible cell, the virus can inject its genetic material into the host. The virus then uses its own genetic material to take over the cell’s own protein-producing machinery in order to produce more viruses. Eventually, those new viruses will be released and go on to infect other cells.
The authors note that their structural model can allow others to find drugs that may destabilize the virus. The hardiness of the Zika particle is almost certainly due to a tough protein coat, but certain drugs may make that protein coat more susceptible to degradation at higher temperatures or other harsh environments. All of this can be used to help stem the transmission of the virus.
For more information, check out the article at Nature: http://www.nature.com/nature/journal/vnfv/ncurrent/full/nature17994.html
I got bored in a genetics lecture a couple of days ago and started to doodle a graph of my perceived biology knowledge and reasoning over the course of my life. “Perceived biology knowledge” is in arbitrary units, and parts of my life are binned into “childhood,” “high school,” “college,” and “grad school” along the x-axis. One caveat is that I am perhaps too biased to reliably perceive my own knowledge and reasoning at any point in my life. Memory is also imperfect, so the early life data-points are probably hard to believe.
In spite of the problems with trying to turn this type of subjective introspection into something data-driven, the general trajectory of the plot and the relative magnitudes within the x-axis bins are likely reliable: the biphasic linear growth through childhood and high school seems reasonable, and the large gains going into college and grad school should be unsurprising to anyone who has had the pleasure of going through those experiences. In fact, one of the major conclusions that I draw from this thought experiment is the effect of disruptive events on my scientific reasoning and knowledge. I was learning a bit and growing throughout childhood and high school, but the real gains came from first going to college–and getting thrown into the deep end with rigorous science classes first semester–and the similarly disruptive first year of grad school. This seems to argue in favor of the conventional wisdom that getting out of one’s comfort zone is the only way to truly grow and improve. To extrapolate a little advice out of this: Don’t be afraid to be in over your head, I guess.