Prospect-gate 2016: Or, how I’m learning to stop worrying and trust Neal Huntington

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.

Ruminating on the Loss of Neil Walker

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?

Maybe President Trump Wouldn’t Be Too Bad?

In addition to baseball and biology (in that order), I also nurse an interest in politics. This primary season has really fascinated me, particularly because of the cast of characters that the GOP trotted out there. So, of course, I’m going to talk about Donald Trump and why hypothetical President Trump might not be as bad as anyone thinks he could be.

Before we really get started, there are two things I want to make clear off the rip. First, I do not support Donald Trump as a presidential candidate. I think that the xenophobic, sexist, and generally unenlightened remarks that he has made throughout his primary campaign are disqualifying; someone who has said those things into a microphone should not represent our nation to the world.

Second, I do not think that Donald Trump has any real chance of being president in January. This election will likely be Clinton’s coronation, and it seemed like it would be that way months ago. But the fact is that Trump will almost certainly be the Republican nominee, putting him mere electoral college votes away from being the “most powerful man in the world.”

This hooligan’s proximity to the Oval Office has put me in a bit of an existential rut lately, and it took a lot of introspection to pull myself out of that hole. But it finally dawned on me: I don’t think President Trump would be too terrible. I know, but hear me out. The president has power, but the office is not a dictatorship. Trump would still have to work within the confines of our republic, particularly with a Congress that would likely stymie anything he might try to do (and hey, We the People are used to that after the last eight years).

In addition to the checks and balances built into the system that would keep hypothetical President Trump from Trump-ing out too much as the Commander in Chief, there is also the inertia of the bureaucratic systems built around the presidency that carry over from administration to administration. For example, the intelligence officials who brief the president daily to keep him or her up to speed on global situations would have their own agenda from day one. It is likely that their advice would keep President Trump from marching down to Mexico City and slapping an invoice down on Peña Nieto’s desk for the newly erected border wall.

There is certainly damage that can be done. The worst that Trump can do might be to rile up unstable members of our society who have been waiting for “strong” president to “say what everyone is thinking” and “not give a damn about being politically correct.” We have all seen what can happen when certain individuals are emboldened by political rhetoric to take matters into their own hands. If hypothetical President Trump would continue talking about the Mexican people, women, and other groups like he has done in the past, it may convince someone to do something. He would be the president, after all.

But all of this might be ridiculous to contemplate. Trump just isn’t a general election candidate. Sure, he cleaned up in the primaries, but that is because the primaries select for the most “out there” candidates, who then have to tack back to the middle to be viable in November. Trump certainly can’t do that, right? But maybe there is reason to worry about a viable Trump general election candidacy. Consider that the Trump rhetoric has seemed to dull a bit lately. After knocking Cruz out of the primary in Indiana (all but assuring his own GOP nomination), Trump even seemed respectful of his competitor Cruz. He has also been avoiding some of the over-the-top offensive speech topics that he gained notoriety (and a ton of free media coverage) for earlier in the primaries, probably due to the influence of new political handlers that he has brought into the campaign in preparation for a run at the Oval Office in November.

Taken all together, this can be terrifying for those of use who never wanted, nor expected, Trump to have any chance in November. He still has to go up against the Clinton political machine, and who knows how offensive his rhetoric might become in a contest against a strong woman candidate. Heck, he has already suggested that Clinton is only polling high because she holds the “woman card.” In other words, he still has time to screw this all up. But even if he doesn’t, hey, maybe it wouldn’t be too bad. This time next year, we might all be wearing matching hairpieces. I, for one, welcome our new overlord.

Update: The NY Times posted a piece that made some of the same points that I made at around the same time that I put this piece up, so go have yourself a look-see over there if the spirit moves you to do so.

Another Zika Structure…and a Mea Culpa

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.

FiveThirtyEight, Elo, and Baseball

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:

The Complete History of the MLB, an interactive, Elo rating-based way to compare teams throughout baseball history.

2016 MLB Predictions (along with an explanation) also uses Elo, but this time to project the remainder of each team’s performance this season. A nice touch is that this one updates after each game.

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.

Scientists Publish Zika Snapshot

(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:

Life Graph

biographI 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.