Saturday, February 28, 2009

Waaah, I have a lot of money!

From a recent post by Andrew Sullivan:
I've worked hard and earned the American dream - and now have to work for the government for well over half the year (a government that still persecutes me for being an HIV-survivor). Obama will take more of my money - and much, much more in the future. Liberalism believes in punishing hard-working successful people in this manner - and the more you succeed, the more they will punish you.

This is a pretty self-serving view of liberalism. Quite simply, Obama's liberalism has some faint idea that government deficits are too high, and thus the government has to find some way of increasing its revenue. As we just heard over and over during the stimulus debate, it is better to keep money in the pockets of poor people, as they are much more likely to spend it, creating a bigger multiplier effect, etc. Thus, if the money can't come from poor people it must come from rich people.

I also find it pretty damn galling that Sullivan phrases liberalism's purpose as "punishing hard-working successful people" -- if he actually believes that then he is a fool, and if is writing that for its shock value then he is dishonest. Liberalism believes that there are some things the government can and should provide for its citizens, and what differentiates conservatives from liberals is the scope of those services. While I certainly sympathize with his persecution by (mostly-conservative) anti-gay elements, the very drugs keeping him alive were largely the product of government sponsored research -- which needs to get paid for somehow, and which liberals have championed far more than conservatives.

Thursday, February 26, 2009


Apparently the Germans beat me to the punch of scooping Nate Silver:

You know it was bad....

when The Metro, the free newspaper available at subway stops in Boston (and other local version available in many cities) decides to run an article about how bad it was. It, in this case, is Bobby Jindal's response to Obama's quasi-State of the Union address the other night. I can count on one finger the number of times the response has been good (Jim Webb in 2007) and I can remember many responses that have been boring or pointless or whatever (Nancy Pelosi and Tim Kaine spring to mind) but I can't remember the last time it as so bad that it became a story in and of itself.

Now, part of what makes this a story is that Jindal has had the aura of 'rising star' in the GOP. We've heard that he is smart and electable and hey, even better for the GOP's image, he is not white. But he is also, apparently, a Muppet. Dooh, Muppetism! I really question the judgement of those who had met Jindal and decided that a goofy looking guy who goes by Bobby is someone that the American people would elect as president.

As for Obama's speech, it was certainly a strong one, with a good pacing for a State of the Union. He got in a few good digs at Republicans, rightly pointing out that it is a bit odd them to all of a sudden start worrying about deficits (he didn't quite put it that way). And closing with the "look at all these inspirational Americans" was well-done, but those are kinda hard to screw up.

Friday, February 20, 2009

Electoral College change?

Next week the bill to allow DC an actual, voting Congressman comes up. This might or might now pass, but one stipulation of the bill is that, to get Republicans on board, an extra Congressman would also be given to Utah. What I haven't seen mentioned at all is how this would affect the electoral college. Given that Utah would now have another Congressman, wouldn't their EV total go from 5 to 6? But DC is already at 3, and I don't think it would become 4... perhaps I should register the domain name to scoop Nate Silver...

A guy who knows these things writes in:
Yes, the current DC plan will change the electoral vote totals:

(1) The plan calls for a permanent increase in the size of the House to 437 (including the new DC seat and the new non-DC seat). Until the next census, the extra non-DC seat will go to Utah. After the 2010 census (and for the 2012 congressional and presidential election), the non-DC seat will be reapportioned under the normal method, so it is not obvious which state will benefit.

(2) DC, under the 23rd amendment, already gets the number of electoral votes it would get if it were a state, and in any case cannot have more electoral votes than the least populous state. So DC will not be getting another EV.

(3) All of this is immaterial. The Constitution clearly says (twice) that DC is not a state, and unambiguously says that Representatives are drawn from States and that Representatives must be inhabitants of the States which they represent. The entire argument of the pro-DC side --- that Congress has unlimited power over the affairs of DC, Constitution be damned --- is silly. It implies that Congress could ban free speech or start a tax-supported church in DC if it so desired. I'm all for DC voting rights, but the only workable solutions I see are (a) statehood, (b) retrocession to Maryland, or (c) Constitutional amendment similar to the 23rd, but for congressional representation.

Especially agree on the third point, in that there's really no way to argue that the Constitution is unclear on this. Yes, DC residents should have voting rights, but in order to get them, the Constitution will probably need to be amended. I had no idea that retrocession was a word, but I'm glad it is.

Wednesday, February 18, 2009

Mr. February

Conditional probability can sometimes be useful in genetics, so I came up with a problem for my students to solve. In you're itching to see how much you remember from stats in college, here's your shot:

You go to Fenway Park for a Red Sox - Yankees game. 80% of the fans there are Red Sox fans, while 20% are Yankees fans. Further, 10% of Red Sox fans are obnoxious, while 100% of Yankees fan are obnoxious. An obnoxious person is sitting behind you. What are the chances he is a Red Sox fan? Answer below.

But what I'm really interested in is the 'battle' for Red Sox SS -- as in, who will combine with Varitek to form the worst bottom-of-the-order combo in baseball this year? I mentioned earlier that apparently Lugo had committed himself this offseason to getting his tape worm removed, and it looks the Dominican witch doctor who was treating him came up with the correct blend of herbs, spices, and vodoo chants, as Mr. Lugo is looking much less emaciated this year.

Couple this data point with recent statements by Francona, and I'm pretty sure that Lugo will trot out there on Opening Day, while Lowrie serves as Mr. Super Sub, bouncing around between 3B, SS, and 2B to give time off to the regulars. Since Lowrie is white, I assume that he will also take over pinch-bunting duties, which the Red Sox never do, but Tim McCarver will call for during all nationally televised games.

If things break right for the Sox -- meaning Saito is healthy, Penny is effective, and Ramon Ramirez can handle the KC-to-Boston transition (he's the guy they got for Coco) -- the Sox could have the best pitching staff in all of baseball, with a solid rotation and a shut-down pen. But this is not a team that is going to score a ton of runs, certainly not to the level of days of yore, when Mark Bellhorn was leading the offense to ~950 runs a year. Their offense is by no means anemic, but especially if Ellsbury doesn't improve his game, it is an offense that has several easy outs.

So to solve the problem, we use Bayes Theorum:

We want to know P(A:B), the probability of a Red Sox fan given it is an obnoxious fan.

P(A) = probability of a Red Sox fan = 0.80
P(A') = probability of not a Red Sox fan = 0.20
P(B:A) = probability of an obnoxious fan given it is a Red Sox fan = 0.10
P(B:A') = probability of an obnoxious fan given it is not a Red Sox fan = 1.00

P(A:B) = P(B:A)*P(A) / [P(B:A)*P(A) + P(B:A')*P(A')] = 28.6%

I like those odds. You should throw your beer in his face and pop him in the nose before even getting a glimpse at his ball cap.

Saturday, February 14, 2009

We have a winner!

After much searching, I've found a suitable (& free) replacement for VectorNTI, A Plasmid Editor by a guy at the University of Utah. It reads GenBank files, so you can easily import your VectorNTI files. It works on both Windows and Macs, and unlike VectorNTI, it doesn't hide away your files in a database, so you can easily work on stuff both at home and in lab. Further, it reads ABI trace files (which I don't believe VectorNTI does), performs alignments, and even speaks text out-loud, which can be really useful if you're, say, comparing your sequence to something printed out. It only took a few minutes of poking around to become familiar with its intuitive interface. This was clearly designed by someone who has actually cloned stuff before: an excellent program.

PS Just discovered that you can make a reverse complement of an ABI trace file (and immediately align it) -- very useful if you sequenced something with a reverse primer.

Friday, February 13, 2009

BUMA (Bi-Partisan Unity My Ass)

I've been a dedicated reader of The Votemaster for about five years now (I don't think I've ever missed a post) and this is the most impassioned I've ever seen him (Feb. 13 post):

All this talk about bipartisanship is overrated. Yes, the tone of politics could be better. It used to be that senators could disagree strongly on the floor of the Senate and then go off and enjoy a mint julep together. But there are serious, deep, irreconcilable differences between Democrats and Republicans on a host of issues. On the whole, Democrats believe that government is the solution; Republicans believe it is the problem. You can't paper over this with nice talk about "bipartisanship." That's why we have two parties and elections. Somebody wins and somebody loses and the winner is expected to carry out his program. When Al Gore got more votes than George Bush in 2000, nobody was demanding (or expecting) Bush to cede half (or any other fraction) of his power to Gore. The Democrats got one cabinet slot, and a fairly minor one at that (Transportation). People who moan that the politicians should work together to solve the country's problems don't seem to realize that both the Democrats and Republicans want to solve the country's problems--but their solutions are totally incompatible.

Nothing he's saying here is groundbreaking, and it is certainly something that many have said before. But if you're used to reading his daily posts, this is a big change in tone. Come 2010 & 2012, Democrats will do well at the polls if their plans are working, and they will lose seats if their plans are not. No one will say, well, I lost my job and house, but hey, there are three Republicans in the cabinet, I guess I'll stick with the Dems!

Thursday, February 12, 2009

This rule goes into effect once I'm done violating it

Coach Dale passes along an essay from the NY Times earlier this week. General gist:
Science has marched on. But evolution can seem uniquely stuck on its founder. We don’t call astronomy Copernicism, nor gravity Newtonism. “Darwinism” implies an ideology adhering to one man’s dictates, like Marxism. And “isms” (capitalism, Catholicism, racism) are not science. “Darwinism” implies that biological scientists “believe in” Darwin’s “theory.” It’s as if, since 1860, scientists have just ditto-headed Darwin rather than challenging and testing his ideas, or adding vast new knowledge.

This would be an astute observation... were it true. The problem arises earlier in the essay, when the author writes:
By propounding “Darwinism,” even scientists and science writers perpetuate an impression that evolution is about one man, one book, one “theory.”

I can't remember the last time I heard a scientist use the phrase "Darwinism." Science writers, however, use it all the time. In the same way that one wouldn't confuse "baseball players" with "baseball writers" we really shouldn't lump these two professions into one group. Whether a journalist, a writer, or a radio talk-show host, the folks who communicate about what other folks are actually doing generally have their own agenda, and for popular media, that agenda is generally conflict.

Further, it is not like the American public's resistance to full acceptance of evolution is a branding issue. Does this guy really think that were we to all just be more careful and use evolution instead of Darwinism that the unwashed masses would suddenly start believing that they are descended from monkeys?

Evolution Polls

Bishop "Soapy Sam" Wilberforce writes in (this is only part of the email, but gets the point across):
I actually think polling on belief in evolution is not credible, for a few reasons.

1) no one ever seems to define "evolution" in the polling. It's beyond obvious that the world is more than 6000 years old. It's slightly less obvious (but still beyond obvious) that "beaks of finches" is true and that natural selection occurs. It's somewhat less obvious (but still obvious) that man has a common ancestry with other mammals. It's not particularly obvious how the first living creates appeared on Earth. And it's even less obvious if God exists.

The point is that when people answer the evolution question in polls, they are answering one of the above questions. We just don't which one. It irks me to no end that we do polling on evolution, report the answers, but fail to report that some people thought we asked if the earth was created 6000 yeras ago, some thought we asked if natural selection exists, some thought we meant human evolution, and some thought we were talking about whether there's a God. The whole topic has been hopelessly transformed into an implicit argument about God. Which is dumb.

I agree that polls can be quite misleading, especially based on how the question is phrased, so I dug around and found some other polls that might shed some light on this. For example, a Gallup poll from last year asked:
"Which of the following statements comes closest to your views on the origin and development of human beings? (1) Human beings have developed over millions of years from less advanced forms of life, but God guided this process. (2) Human beings have developed over millions of years from less advanced forms of life, but God had no part in this process. (3) God created human beings pretty much in their present form at one time within the last 10,000 years or so."

Notice how the word 'evolution' doesn't appear in the question. "Guided by God" scored 36%, "God had no part" got 14%, and "God created in present form" got 44%. Of course, by focusing on God's role, this poll muddies the water in the exact way that Soapy (and I) thinks is dumb. But other polls on that site phrase the question in other ways as well, so in aggregate one can certainly say that the percentage of Americans who believe in evolution is still pretty small, certainly smaller than a fillibuster-proof majority. This is a problem because this is not a question where there's room for disagreement, any more than there is room for disagreement about the structure of the atom or the laws of gravity.

I'll readily admit that there is room for debate about the mechanism of how life got started. And in all honesty, that is somewhat of an academic argument. But the fact that humans share common ancestors with monkeys, worms and fungus is not up for debate, and the acceptance of that fact has profound implications in all sorts of non-academic pursuits (you're entitled to you own opinions, but not your own facts).

Darwin & Lincoln

Today is the 200th anniversary of both Darwin's & Lincoln's birthdays, a historical coincidence only rivaled by John Adams and Thomas Jefferson both dying on the 50th anniversary of July 4, 1776.

Unfortunately, while Lincoln's contribution of preserving the Union an abolishing slavery has caught on, Darwin's achievement is thought to be true by only 39% of Americans. Sigh. The good news is that, by age cohort, young folks are by far the most likely to believe in evolution, with over 50% 'buying' it.

It is amazing that Darwin was able to postulate evolution 100 years before anyone knew what DNA was. And it is further amazing that the widespread sequencing of many genomes over the past 10 years has provided the final proof that evolution is clearly occurring. Anyone who doubts this just a damn fool.

Monday, February 9, 2009

My DNA made me do it

Charles Q. Wilson has an interesting article on politics and DNA, going over research that a decent chunk of our political ideology has a genetic component. The majority of these findings are based on twin studies:
There are two common ways of reaching this conclusion. One is to compare adopted children’s traits with those of their biological parents, on the one hand, and with those of their adoptive parents, on the other. If a closer correlation exists with the biological parents’ traits, then we say that the trait is to that degree inherited.

The other method is to compare identical twins’ similarity, with respect to some trait, with the similarity of fraternal twins, or even of two ordinary siblings. Identical twins are genetic duplicates, while fraternal twins share only about half their genes and are no more genetically alike than ordinary siblings are. If identical twins are more alike than fraternal twins, therefore, we conclude that the trait under consideration is to some degree inherited.

There's nothing controversial (at least scientifically) with these studies -- twin studies are used all the time to study these sorts of problems (and, to my level of satisfaction, have proven that homosexuality, at least in men, has a strong genetic component).

Interestingly, Wilson mentions a study that looks at the genetic basis of why people do or don't vote, which is something I've written on in the past:
Genes also influence how frequently we vote. Voting has always puzzled scholars: How is it rational to wait in line on a cold November afternoon when there is almost no chance that your ballot will make any difference? Apparently, people who vote often feel a strong sense of civic duty or like to express themselves. But who are these people? James Fowler, Laura Baker, and Christopher Dawes studied political participation in Los Angeles by comparing voting among identical and fraternal twins. Their conclusion: among registered voters, genetic factors explain about 60 percent of the difference between those who vote and those who do not.

What to expect (when you're expecting)

Someone who knows these sorts of things provides this very helpful run down of how the reconciling process occurs, assuming that the Senate does pass the stimulus bill later today:
1) Speaker picks the House conferees.
2) Senate can elect conferees, but usually just puts it in the hands of the majority leader by unanimous consent.
3) Politics tends to control who is on the committee.
4) It's highly unlikely that anyone who voted against the bill will be on the committee. It's not crazy, however, to think that the centrists will be represented --- they may have demanded it as part of the bargain. I would imagine Nelson will be on it at a minimum.
5) The number of conferees is not restricted, nor do House and Senate have to have same number.
6) The conference report has to be accepted by a majority of conferees from both chambers before it goes back to the full bodies.
7) sometimes the chambers try to "instruct" the conferees, but these instructions aren't binding.
8) That said, conferees cannot add stuff that's not in either bill. They have to work with what is there.

As for the politics, it is key to remember that a conference committee delegation doesn't represent a political party, especially in the Senate. It represents the final deal worked out in the chamber. the conferees may not be the biggest proponents of the bill, but they know that if they fail to hold the bill in a form that will keep the deal set, they are going to be in the majority leader's doghouse for a good while.

But more to your point, the Senate almost always has the leverage. Definitely true now: since there is zero chance that the current Senate bill would fail an up/down vote in the House, the House has little but cheap talk to bring to the bargaining table. The Senators will basically argue that any change to their bill will jeopardize their ability to break a filibuster of the conference report --- which may or may not be true, but is certainly a plausible possibility. The final bill out of conference will lean toward the Senate version, but there will be concessions both ways. The Senate moderates know this. It would take something pretty big to turn Collins/Specter/Nelson against the bill all of a sudden. And thus a lot of the Senate argument in conference is just bluster. And everyone knows it. So they'll split the difference on a lot of stuff (remember, much of this is basic numbers haggling), and the Senate will win more than the House. But expect something about 2/3 or 3/4 of the way toward the Senate bill form the House bill. That's typical.

Friday, February 6, 2009

In space, no one can hear you scream

Getting back to the why are we here, how did we get here, and is it beer hour yet? Continuing on the atheism vs. agnosticism theme, another reader comment:
Somehow, both the atheists and theists seem to think that they get to be null hypothesis. Especially the atheists. That they are the null hypothesis --- there is no God -- and the theists have to prove that there is one. Since there is no evidence, the null hypothesis can't be rejected.

But that's dumb hypothesis testing. We don't allow null hypotheses that are unproven. The true null hypothesis is "I'm not sure if there is a God." Given that, we need evidence one way or another. And we just don't have it. That points toward the null being agnosticism. And it's a decent working definition, too.

But I think there's a greater obscurity here. Because atheists seem to want to rest the proposition of where the universe came from on the question of whether there is a God or not. They seem to think that if there is no God, then their version of universe history is correct. But again, that's biasing a particular null hypothesis. You can't say, "I found some candy under my pillow last night. And since you can't prove there is an Easter Bunny, then the candy must have appeared there via natural evolution."

In regard to time being long, we wrap back to my favorite atheist brain teaser: the aliens. Most secular humanist atheists seem to believe that aliens must exists, because the universe is far too big, and time far too long for them not to exist. But we don't have any evidence whatsoever. So under atheistic reasoning, we can't reject the null that they don't exist. But if aliens don't exist, all of a sudden the case for God gets a lot, lot stronger. The universe is very large, remember, and time is very long.

My reply to this is essentially the purple monkey reply, as in, I don't believe that the true null hypothesis on whether there is or is not a purple monkey living on the moon is that we don't know. At some point one needs to acknowledge that the tremendous body of ever-growing knowledge from the science community about evolution and its ramifactions and its proven testable hypotheses is not in any way comparable to religious traditions that are hundreds if not thousands of years old, when solar eclipses were crap-your-pants events. To ignore the historical context for where each of the hypotheses -- there is a god, there isn't a god -- or to shrug one's shoulders and say, eh, they're equal, well, that's too much of postmodern relativism for my taste (and as the purple-monkey analogy provider noted, not really consistent with how anyone actually lives their life).

Now, the alien bit, that's interesting. It immediately reminded me of an article I read in Technology Review a little while back about The Great Filter (no link to it, but I have the PDF if you're interested in reading the whole thing). The author starts with this statement:
The next decade might see a Mars Sample Return mission, which would use robotic systems to collect samples of Martian rocks, soils, and atmosphere and return them to Earth. We could then analyze the samples to see if they contain any traces of life, whether extinct or still active. Such a discovery would be of tremendous scientific significance. What could be more fascinating than discovering life that had evolved entirely independently of life here on Earth? Many people would also find it heartening to learn that we are not entirely alone in this vast, cold cosmos. But I hope that our Mars probes discover nothing. It would be good news if we find Mars to be sterile. Dead rocks and lifeless sands would lift my spirit. Conversely, if we discovered traces of some simple, extinct life-form--some bacteria, some algae--it would be bad news. If we found fossils of something more advanced, perhaps something that looked like the remnants of a trilobite or even the skeleton of a small mammal, it would be very bad news. The more complex the life-form we found, the more depressing the news would be. I would find it interesting, certainly--but a bad omen for the future of the human race.

Essentially, the author argues that, because we haven't seen any traces of life elsewhere yet, life must be rare. And there are two ways in which life can be rare, which he calls the Great Filter:
The filter consists of one or more evolutionary transitions or steps that must be traversed at great odds in order for an Earth-like planet to produce a civilization capable of exploring distant solar systems. You start with billions and billions of potential germination points for life, and you end up with a sum total of zero extraterrestrial civilizations that we can observe. The Great Filter must therefore be sufficiently powerful--which is to say, passing the critical points must be sufficiently improbable--that even with many billions of rolls of the dice, one ends up with nothing: no aliens, no spacecraft, no signals. At least, none that we can detect in our neck of the woods.

In other words, let's say that the Great Filter is behind us -- perhaps the transition from prokaryotic to eukaryotic is literally a once-in-a-universe event. Then that's good for us, because it suggests that doom does not lie around the corner. But if the Great Filter is in front of us -- say, every civilization that advances close to the point of space travel ends up blowing themselves up with incredibly powerful weapons -- well, that's obviously bad news.

While I do find fault in some of the arguments of the author, and while this article doesn't comment on the relative merits of atheism or agnosticism, it does make an interesting point that we should really hope that we are all alone. But getting back on track, I don't think our uniqueness or lack thereof in the universe really argues either way for the existence of god. Sure, if aliens landed tomorrow and laughed themselves silly at the idea of Jesus being the son of god, yeah, I could see how that could be problematic for the faith of a lot of Christians. Conversely, if aliens landed and had with them their own copy of the King James Bible, well, I'd probably need to hit up the confessional (assuming, of course, that the aliens weren't using the religiousity of our species as a way of infiltrating, controlling, and eventually enslaving us). I guess what I don't understand is how the the existence or non-existence of other civilizations really informs the god debate one way or the other.

Thursday, February 5, 2009

I think he's talking to you

Obama has penned an Op-Ed for the Washington Post today. Probably worth reading, and appreciate the fact that we have a literate president who actually feels the need to explain himself to the public. How novel. I particularly enjoy the tag line at the bottom:
The writer is president of the United States.

Wednesday, February 4, 2009


From the most recent issue of Nature, I feel the authors don't place enough emphasis on the fact that they found a snake 42 feet long! (or roughly twice the size of the shark in Jaws). One could certainly imagine scientists received more funding if they'd hype their work a bit more...

Giant boid snake from the Palaeocene neotropics reveals hotter pastequatorial temperatures
The discovery of the world's largest snake has important implicationsfor our understanding of the evolution of global climate. The snake, a relative of the boa constrictor, was 13 metres long and would have weighed more than a tonne. It lived in tropical South America around 60 million years ago. A snake this size would have required mean annual temperatures between 30-34 deg. C, higher than the tropics today.

Cloners of the world, unite

I'm currently in a dispute with the biotech company Invitrogen, a big company that keeps getting bigger, having recently acquired Applied Biosystems. Here's a recent back-and-forth I've had with them regarding their decision to no longer allow academics to freely use a plasmid design & database program of theirs. Apparently this is having somewhat of an effect, in that the Invitrogen accounts reps have been hearing complaints from their clients at Harvard and MIT. I suppose my next step is to make announcements at various beer hours in the area, which has the benefit of allowing me to visit various beer hours in the area.

My original email:
Sent: Wed Jan 28 09:16:34 2009
Subject: vector nti

Hi Invitrogen corporation people,

I've been a long-time user of VectorNTI, and I'm quite disappointed with Invitrogen's decision to no longer allow free use to the academic community. I further take offense at what I consider to be disingenuous statements put out by the company regarding this decision. Upon announcing that VectorNTI 10 would no longer function, Invitrogen stated something along the lines of "affordable academic pricing" -- I see that a one year license costs $825. I can't think of any other program that costs this much, and this is only the price for one year! Additionally, Invitrogen stated that, because of the release of Vector NTI 11, it would no longer support Vector NTI 10, "as is standard software practice." This is false -- when Microsoft releases a new version of Word my old copy doesn't suddenly lock up. If you don't want to support version 10 then that is fine, but to essentially terminate the use of version 10 is most certainly not standard software practice. Finally, Invitrogen's tactic of offering something for free, getting people invested in its use, and then starting to charge exorbitant fees is a practice generally reserved for those selling cocaine, not a company "committed to unparalleled excellence and responsible stewardship."

I hope that Invitrogen revisits this issue. It would certainly be reasonable for Invitrogen simply to offer a non-expiring license for those using Vector NTI 10, with the caveat of no additional technical support.


Their reply:
Sent: Wed, Jan 28, 2009 at 3:41 PM
Subject: RE: vector nti

Dear Dr. XXXX,

Thank you for contacting Invitrogen. We take feedback from our customers seriously and I have forwarded your email to the Product Manager. I have attached instructions for how to export your files into Genbank format if you would like to use freeware or another software package. If your license expired, please use this trial license to access your data (expires 3/31/2009)

Please feel free to contact us at, if you need any assistance.


And the beginning of the "screw you" phase of negotiations, carbon-copied to all my scientist-friends:
Sent: Tue, Feb 3, 2009 at 8:53 AM
Subject: Re: vector nti

Thanks for the password to unlock the program. However, I still feel that Invitrogen's decision to prevent academics from using previous versions of VectorNTI "as is standard software practice" is condescending and disingenuous.

I just checked my lab's order list. In the first month of 2009, we ordered over $1000 of products from Invitrogen, the vast majority of which could easily be purchased from competitors, simple products like enzymes, vectors, chemicals, etc. I'm going to recommend to my labmates that we boycott Invitrogen's products; indeed, I'll make it easy on them by suggesting substitute vendors, such as NEB for enzymes, Clontech for vectors, Invivogen for selective media, etc. I'll be sure to mention this idea to other labs in the building, as no one wants to ask his or her boss for an extra ~$1000 to buy a computer program, especially in this tight funding environment. I'll also carbon-copy this email to friends from graduate school, and urge them to pass it around their current institutions.

Invitrogen should realize that very few biomed companies have a monopoly on any particular product, and the vendor of choice for the vast majority of scientists is the vendor that treats them right -- decent prices, good documentation, and a general sense of not being a giant Evil Company. Invitrogen is certainly in danger of becoming such a behemoth.


Obama's Fortnight

We've had a new president just over two weeks now, which is apparently how long it takes for Maureen Down to write a snippy column (no link, screw her). I really can't stand her, never have -- to steal from The Family Guy, she insists on herself.

The first order of business was a bunch of executive orders. Obviously I was for pretty much all of them (closing Gitmo, etc.) and I'm glad he acted quickly on these matters. Long-term, though, I really hope Obama realizes that executive orders are a poor substitute for going through the legislature, as having executive orders made and then overturned and then made again with every change of president is not conducive to the general welfare.

The major legislative battle is the stimulus package, which (kinda) is tied to the bailout, at least in terms of "stuff on the mind of the American public." If it has any teeth to it, I'm pleased with Obama's proclamation today limiting executive pay for banks that receive federal funds, but already some are carping that there are too many loopholes. We'll see. I'm all for measures such as this, and wouldn't mind seeing them harsher, because we cannot as a society be in the business of privatizing gains while socializing loss. And you can already see some statements from the right and various financial types, whining about how they'll lose talented people, etc. etc. but if they were that talented, would they have needed a giant bailout?

The stimulus package, i.e. the actual bill that is going through our actual Congress, well, I'm lukewarm on it. From either a governance or a politics perspective, I'm not really sure what Obama is doing in terms of recruiting bipartisan support. I mean, in general, I'm all for that, but bipartisanship should not be the primary goal -- an effective bill should be. I just worry that, in order to get a few Republicans to vote for it, the bill will end up having the wrong priorities (too many tax cuts and highway spending) and not work, in which case Obama/Democrats get all the blame come 2010. As Krugman pointed out the other day:

You see, this isn’t a brainstorming session — it’s a collision of fundamentally incompatible world views. If one thing is clear from the stimulus debate, it’s that the two parties have utterly different economic doctrines. Democrats believe in something more or less like standard textbook macroeconomics; Republicans believe in a doctrine under which tax cuts are the universal elixir, and government spending is almost always bad.

So here's a case where I'd like to see Obama & Harry Reid roll up his sleeves and dare the Republicans to fillibuster a good stimulus. But remember the campaign itself -- Obama is not the sort of guy who responds quickly or fights back or what have you -- he is calm, patient, and lets things play out. We're seeing that in his handling of the stimulus so far, but it will be interesting to see if does come out swinging at some point.

Monday, February 2, 2009

XLIII recap

Now 6 of the last 10 Super Bowls have been exciting. I don't know if last night will go down as a great game -- way too many penalties, for starters -- but it was certainly a very exciting game. The play of the game was the 100 yard INT for a TD at the end of the first half, which was at least a 10 point swing and probably a 14 point swing. It seems like the Steelers have one of those plays every game, something weird, improbable, whatever -- like the punt bouncing off the head of a Chargers blocker in the Divisional round. But that's what good teams do.

Remarkable that Kurt Warner now has the three highest passing yardage games in Super Bowl history. And while he's only 1 for 3 in the big game, he's twice been the victim of his defense failing to stop the other team's final drive (and was almost a victim of that in his one victory, as Tennessee came within one yard of winning that game). While the pro football Hall of Fame is a more mysterious process, and certainly less talked about than baseball's version, I gotta imagine that both QBs earned their entry last night. Warner has led two different teams to the Super Bowl, played great all three times, and has won league MVP twice. Put it this way, it is hard to argue that Peyton Manning (1 Super Bowl appearance, 1 win) is a hall of famer and then not include Warner (I should actually check the stats on that). As for Big Ben, only 1 QB has won two Super Bowls and isn't in the Hall of Fame (Jim Plunkett), so even if he doesn't win another, his odds are pretty good.

Sunday, February 1, 2009

Super Bowl XLIII

Okay, Cardinals - Steelers, going for their first and sixth Super Bowl titles. First, a trivia question (no I didn't make this up myself). Name the two franchises that have won three Super Bowls with three different starting QBs, and name the QBs. Barring a pre-game injury to Roethlisburger (I'm not looking up how to spell that correctly) and a start and win by Leftwich, the Steelers are not one of the teams. Answer at the bottom of this post.

My Super Bowl past has been dominated by games that aren't close. The first Super Bowl I remember was Dan Marino's first and only, Super Bowl XIX, 49ers-Dolphins. This game was a blow out, 38-16. So was the next one, Bears over the Patriots 46-10. And the next, 39-20 Giants over Broncos. Then Redskins 42, Broncos 10. Finally, the 1988 Super Bowl produced a close one, with Montana-to-Taylor besting Boomer and Icky Woods and the Bengals, 20-16. 9 of the next 10 Super Bowls were largely uninteresting -- as in, the final 5 minutes of the game were essentially meaningless -- with the exception of Giants-Bills in '90, the Norwood game. Some of the games in this span were over before they started, such as the Cowboys 52-17 over the Bills in Super Bowl XXVII (I think this was the Don Beebe/Leon Lett game), and the 49ers over the Chargers 49-26 in 1994, where Steve Young hit Jerry Rice for a bomb on just about the first play of the game.

It wasn't until the Rams held off the Titans on the 1-yard line in Super Bowl XXXIV that the big game started getting interesting again, triggering a run of quite a few nailbiters: Patriots in '01, '03, and '04 were all close games, as was last year's game. That's 5 great games out of the past 9.

In general (last year being a notable exception), the sports public is pretty good at predicting what kind of game it is going to be. In other words, for some games, the general consensus is, gee, I just hope [Team X] keeps it close and makes it interesting. For other games, people are genuinely divided over who's going to win. This year's match-up seems to be much more along the lines of the former than the latter. Not a lot of folks think the Cardinals are going to win, and most are just hoping that Warner stays vertical long enough to keep it close.

One thing that must be taken into account, though, is that the best experts are a team's fans, and I don't know any Cardinals fans. Lemme tell you what I mean... in 2001, no one gave the Patriots a shot, but they pulled off a huge upset, and I wasn't terribly surprised -- I had seen them play all year and I thought they had a shot (a similar thing occurred for the 1996 Syracuse Orangemen, led by John Wallace to the NCAA Finals, where they lost to Kentucky -- sometime you just know that your team has a shot). Around Christmas time my brother-in-law, a Steelers fan, didn't seem overly enthused by their chances, but then again, I can't remember the last time I saw him terribly enthused about anything.

Immediately after the NFC & NFC Championship games concluded, I asked a few football fans what they thought the spread would be, and the near-universal answer was 10 points. Vegas, however, opened at ~7, and hasn't really budged. I suppose one could interpret this as meaning that they want people to take the Steelers.

In terms of how the teams got here, neither team was really tested in the playoffs. The Cardinals played a home game against a rookie QB, then faced the Panthers in what might be the worst game ever played by a QB, and finally played another home game against the Eagles, who are really good at losing Championship games with Reid and McNabb (1-4 or 1-5, I think). Likewise, the Steelers didn't have to face either the Colts or the Titans, who were probably the top challengers in the AFC.

Anyway, while I want the Cards to win, I think the Steelers will win and cover (putting 50 on them, although regardless I'll finish in the negative this postseason).

Of most importance, though, is what will Bruce play during the halftime show? The consensus appears to be 4 songs, although I'm not sure if that is set in stone. Born to Run seems pretty obvious, so we should assume he'll play that. A lot of people seem to think Glory Days will make an appearance, but I'd rather hear Badlands, which is probably his most high energy live song. Will there be something off the new album? If so, it'd be either My Lucky Day or Working on a Dream. I'll guess:
Promised Land, Working on a Dream, Badlands, Born to Run. But I have no idea.

Trivia Answer:
NY Giants: Simms (86), Hostetler (90), Manning (07)
Redskins: Theismann (82), Williams (87), Rypien (91)