This is what happens when you don’t declare potential conflicts of interest

Senator Grassley of Iowa is demanding that the American Psychiatric Association be transparent about its financial relationship with pharmaceutical companies:

The worry is that this money may subtly alter psychiatrists’ choices of which drugs to prescribe.

An analysis of Minnesota data by The New York Times last year found that on average, psychiatrists who received at least $5,000 from makers of newer-generation antipsychotic drugs appear to have written three times as many prescriptions to children for the drugs as psychiatrists who received less money or none. The drugs are not approved for most uses in children, who appear to be especially susceptible to the side effects, including rapid weight gain.

Senator Grassley’s investigations have not only detailed how lucrative those arrangements can be but have also shown that some top psychiatrists failed to report all their earnings as required

–IP

Mathematician donates Wolf prize money to Bir-Zeit

The algebraic geometer David Mumford, one of the three winners of the Wolf prize this year, is donating his share of the prize money to Birzeit University – a Palestinian university, and Gisha — an organisation that promotes Palestinian freedom of movement. From the Haaretz article:

“I decided to donate my share of the Wolf Prize to enable the academic community in occupied Palestine to survive and thrive,” Mumford told Haaretz. “I am very grateful for the prize, but I believe that Palestinian students should have an opportunity to go elsewhere to acquire an education. Students in the West Bank and Gaza today do not have an opportunity to do that.”

[...]

“The achievements I accomplished in mathematics were made possible thanks to my being able to move freely and exchange ideas with other scholars,” he said. “It would not have been possible without an international consensus on an exchange of ideas. Mathematics works best when people can move and get together. That’s its elixir of life. But the people of occupied Palestine don’t have an opportunity to do that. The school system is fighting for its life, and mobility is very limited.”

–IP

A pleasant surprise

I got a small research grant for an academic project. My very first grant. I keep looking at the letter and I can’t stop smiling.

–IP

John Wheeler

John Wheeler passed away yesterday morning, at the grand old age of 96.  His work on nuclear fission, black holes, and relativity will be commented on by others, I’m sure, and I’ll leave that to physicists.  I pulled this quote from the NYTimes obituary because I liked it, and it’s consistent with the discriptions I’ve heard of his character from his colleagues and students:

Dr. Wheeler described his own view of his role to an interviewer 25 years ago.

“If there’s one thing in physics I feel more responsible for than any other, it’s this perception of how everything fits together,” he said. “I like to think of myself as having a sense of judgment. I’m willing to go anywhere, talk to anybody, ask any question that will make headway.

“I confess to being an optimist about things, especially about someday being able to understand how things are put together. So many young people are forced to specialize in one line or another that a young person can’t afford to try and cover this waterfront — only an old fogy who can afford to make a fool of himself.

“If I don’t, who will?”

Image description:  mugshot of John Wheeler standing in front of a chalkboard that has two graphs on it, and several numbers and mathematical symbols written on it.

Image courtesy of New York Times.  (Hat tip to Clifford.)

–IP

I wants me a sonic screwdriver

I’m in quite a bit of pain due to arthritis right now, am taking max doses of NSAIDs, and am feeling every bit of 903 Gallifreyan years old.  Blogging may be sparse for a while.

In the meantime, you should all rejoice in the fact that a new season of Doctor Who started last Saturday.  That’s much more exciting than my blog, surely.  You can watch the last episode online for seven days after each show.

–IP

Eclipse tonight

Via Clifford, who is careful to keep us informed of stuff.  There is to be a total lunar eclipse tonight/tomorrow, which should be visible from most of North and South America, Western Europe, Africa, and Western Asia.  NASA has more info, including diagrams and times for different time zones.

The eclipse should start about 8.40 pm on Wednesday 20th, and reach totality at 10.00 pm  in EST.  That’s 1.40 am on Thursday 21st and reaching totality at 3.00 am in GMT.

Enjoy!

–IP

Sometimes you can tell I’m a geek

Have been watching some Star Trek re-runs, including the episode “Qpid” in which Picard and some of the Enterprise crew end up in Sherwood Forest as Robin Hood’s gang. The episode includes this classic moment, which had me in stiches, and which will no doubt provide me with a reason to continue giggling for the rest of the day:

Image description: Lieutenant Worf dressed as Will Scarlet, exclaiming “Sir, I must protest! I am not a merry man!”.

Image of Worf is courtesy of Alpha Memory, published under the terms stated there.

–IP

Lord of the physics

Via Clifford, someone has been working out how far the balrog and Gandalf fall in the film of The Two Towers, what the air resistance of your average balrog is, and some discussion of terminal velocities.

In other news, I am mostly settled in my new flat, with the obligatory pictures on the wall (and none of them are of LotR).  The Cute Toddler hugged me at breakfast this morning, or at least I thought she was hugging me, but it turned out she was actually trying a sneaky manoeuvre involving her wiping her very snotty nose on my trousers.  Once on each knee.  But she’s too cute for me to mind.

–IP

On garden paths and what I want to be if I grow up

There are times when we realise things about ourselves that other people have known for ages.

In my first term at university, I came home from my first Logic lecture and burst into tears because I was convinced that it was hard and I couldn’t do it. But it was required course so I went back. Three weeks later I was reading everything I could get my hands on that had formal semantics in the title. When I started computer science, I again panicked about it being new and hard, and then found that I loved hearing about logic and language processing from three openly antagonistic perspectives. I knew I would enjoy linguistics, but I hadn’t yet found the kind of linguistics that really made me buzz.

Now, a few years on, I picked my linguistics courses this year on the basis of what fit my timetable, and on the basis that some empirical research methods couldn’t hurt (the courses I really wanted to do where all held at the same times as my required courses).  So I didn’t expect to become quite so captivated  by the course I picked.  And now I’m awake at night wanting to take apart the cogs and wheels of every linguistic study I’ve read to see how the numbers work, where they come from, what they mean. I want to hold each token in my hand and watch what it’s doing and why. I want to know its formal purpose, but I also want to know its social purpose. What do we pay attention to? But more precisely, how does we pay attention to it? How do we pick up on the things that signal social and linguistic differences? How to we process that stuff? Where does variation come into it, and why?

The week before submitting my project I was working 10+ days on 5 hours of sleep while feeling crap. What I wanted to do most was go to bed for at least a week. But after that, what I most wanted to do was find out what the next result was. I’m not sure I could have maintained that kind of drive and focus in those circumstances with philosophy or computer science or even with another branch of linguistics. I still just want to go back to my numbers and my tokens — to tinker with the little cogs and wheels, and maybe supplement them with formal semantics and garden paths and parsers.

I have to make some serious decisions in the next two weeks or so. I have to decide where I’m going with this stuff in terms of dissertations. I think I know now I’m not really a straight philosopher. I’ve tried it on for size, I’ve enjoyed it. I’ve spent hours upon hours thinking about philosophical stuff. But I need my numbers and cogs and wheels and facts. Which makes me a scientist, I think. As for informatics, I think I just don’t really care enough about the artifical intelligence models and cognitive science models. At least not right now. Maybe I just don’t know enough about them — that’s always a possibility. But I want to know what real people do with real language. I expect philosophy and informatics to continue playing a part in what I do, but I’m thinking that right now, linguistics is what I want to focus on.

Does that make any sort of sense?

–IP

GoldVarb bring-and-share

People with answers to GoldVarb X¹ issues, or with other GoldVarb questions should feel free to post them in this thread.

(Tangentially, maybe I should have a series of “tips and tricks” type posts for academic programs.)

Anyway, this post is based on my experience of working with GoldVarb X on a Mac and also on PCs. Mandatory caveat: I have not done extensive testing on GoldVarb, this post is based solely on my experience of working with it during the last semester. The tips I propose are meant in good faith, but they are not guaranteed solutions. The management of Modus Dopens accepts no responsibility for lost or cocked-up files. No tokens were harmed in the making of this post.

Right. The first thing to note is that there are far fewer compatibility issues with Macs. Yet another reason why Macs are just sexier. Files created on a Mac can be open and run on that Mac just fine, and files created on a Mac can usually be transferred to a PC and run on the PC without problems, but the inverse does not hold. I have not experimented with transferring files from one Mac to another, however. Files created on a PC are highly problematic to transfer to another PC or to a Mac, and can then either not be opened, or the computer does not identify them as GoldVarb files, and will identify them as executables or other odd things. Sometimes the files get reformatted (eg, with apostrophes replaced with other symbols), and I haven’t worked out a way around this yet. The answer might be to save as .txt rather than .rtf in step (1) below, although I have not tried this myself — when I used the steps below, I saved as .rtf.

Usually the safest is to do the following:

1. Copy the contents of the token file to a simple text editor (eg TextEdit) and save as .rtf or .txt. Be sure to have saved your factor specifications before you do this. Do the same with the the condition file, but save it as a separate document. (And the same with your results file if you’re wanting to save and transfer it).

2. Zip the .txt or .rtf and the GoldVarb versions of the files (since you might be lucky), and transfer.

3. On the machine you’re transfering to, unzip the files.

4. Launch GoldVarb. From GoldVarb, go to File -> Open and select the GoldVarb version of your token file. (NB, if you’re trying to open a condition file, ignore the previous sentence. Instead, go to the directory to which the file is saved, not from within GoldVarb, and double click on the file to open). If the file doesn’t immediately open as a GoldVarb file, it’s probably not worth continuing to try to open the GoldVarb versions of the files.

5. If (4) is unsuccessful: open the text versions of the files. Launch GoldVarb if you haven’t already. Go to File -> New -> New Tokens and copy and paste your tokens into the token file. Save. Scroll down to the bottom of the token file and check to see whether your factor specifications have been copied over as well. If they are showing up as text in the token file, you may need to re-enter the factor specificiations into the factor specification dialogue (but this should be easy as you can copy and paste from the text at the bottom of the token file). Delete the text from the bottom of the token file before you try to run any analyses. If your factor specs are not showing up in the bottom of the copied tokens, check your factor spec dialogue. They may have copied over anyway, but often they don’t. If you lose the factor specs you’ll just have to enter them again.

6. Go to Tokens -> No Recode to get a new condition file. Copy and paste the conditions from the text file into the new condition file and save.

7. If you will be transferring GoldVarb files between those machines more than once, it’s worth saving your token file to the machine you transferred to as a GoldVarb .tkn file. That way, the next time you transfer files to that machine, if you lose your factor specs and the factor specs are the same, you can open this token file, delete the tokens, copy in the new transferred tokens, and select File -> Save As and rename the file. NB, if you do an ordinary save or you do not rename, you will lose the old token file!

–IP

¹Sankoff, David, Sali Tagliamonte, Eric Smith. (2005). Goldvarb X: A variable rule application for Macintosh and Windows. Department of Linguistics, University of Toronto.

A question of identification

I’m feeling mostly better. I am sufficiently better as to be getting some work done, and when I’m feeling not-up-to-work I am up to reading. I’m reading Frank McCourt’s Angela’s Ashes, and have come across a wonderful passage in which the author describes his introduction to geometry:

He draws two lines side by side and tells us these are parallel lines. And the magical and mysterious thing is that they never meet. Not if they were to be extended to infinity, not if they were to be extended to infinity, not if they were extended to God’s shoulders. And that, boys, is a long way though there is a German Jew who is upsetting the whole world with his ideas on parallel lines.¹

Is it Einstein? Johnny von Neumann is also the right time period.

–IP

¹McCourt, F. 1996 Angela’s Ashes. London: HarperCollins Publishers. pp 169-70

In which I laugh maniacally

A friend wrote to complain that every time I email her to let her know of interesting astronomic whatsits worth waiting outside in your slippers for, it clouds over. Thus, she maintains, I must be transatlantically internet teleporting Scottish weather on purpose. All I can say is that that’s all part of ….My Master Plan.

Mwuahahahahahahahahahahah.

–IP

“Unscientific” does not mean “controversial”

No, really, it doesn’t. I looked both words up in a dictionary just to double check, and nope, they don’t mean the same thing:

Unscientific:

1. not scientific; not employed in science: an unscientific measuring device.
2. not conforming to the principles or methods of science: an unscientific approach to a problem.
3. not demonstrating scientific knowledge or scientific methods: an unscientific report.

Controversial:

1. of, pertaining to, or characteristic of controversy; polemical: a controversial book.
2. subject to controversy; debatable: a controversial decision.
3. given to controversy; disputatious.

(Courtesy of Dictionary.com*)

Scientists shouldn’t be afraid of tackling contravertial issues. Science shouldn’t be limited by social controversy. Academic freedom means being able to talk in a scholarly manner about things that may be controversial. And yes, if you are a scientist, then offering an unscientific opinion about science is unscholarly.

What science should be limited by is science. That is, science should be limited by the definition of what constitutes scientific research. If a study is unscientific and unscholarly, then it’s not science. If something is not scientific, then scientists shouldn’t be concened about it (in their scientific capacity).

What am I talking about?

James Watson. Larry Summers. The IQ debates. Jensen and Galton. Is-science-PC discussions. The perennial is-gayness-genetic question. Intelligent Design, for that matter. But specifically I’m taing about the reaction to James Watson’s genes-in-mouth debacle.

I was disappointed. Not by James Watson, because frankly, it’s not as if we didn’t know before that he’s chauvinist down to his bootstraps. I was dissapointed by all the people who defended him on the basis of academic freedom, that thus win prizes for phenomenally missing the point of academic freedom.

Quoth Watson:

James Watson provoked widespread outrage with his comments to The Sunday Times, which quoted the 79-year-old American as saying he was “inherently gloomy about the prospect of Africa” because “all our social policies are based on the fact that their intelligence is the same as ours — whereas all the testing says not really.”

He told the paper he hoped that everyone was equal, but added: “people who have to deal with black employees find this not true.”

Watson was later suspended from his post at Cold Springs Harbour Lab, and uninvited by at least one university a which he was scheduled to give a lecture.

Over at Harry’s Place, Alec McPherson responded:

I don’t think this was even refusing to allow him to promulgate his wretched views instead of publicly repudiating them, which would be questionable enough. This strikes as silencing him in one field, where he may well excel, because of his opinions in another, which we are told is unrelated. As so often is said in the hallowed pages of Harry’s Place, this is the Stalinist approach to debate.

PZ Meyers commented:

It’s a sign, though, that CSHL will not be administered by anyone willing to assert controversy, and that’s too bad.

It’s worth reading Zuska’s take on the matter, by the way (not quoted because the quotes would be too long, just hop on over and read).

I would argue that Myers and McPherson have simply missed the point of the controversy about Watson’s comments, since it wasn’t the case that Watson was drawing a scientifically justified conclusion. He was just expressing racism. It wasn’t scholarly, it wasn’t scientific, it wasn’t academic. It’s not a matter of academic freedom. In what way is Watson being silenced in genetics? He was suspended from Cold Spring Harbor Lab, that’s true. That was a post he got because of his scientific acheivements, and since his suspension was a response his talking about social policy in an unscientific and unscholarly manner. Suspension may or may not have been the appropriate response, but it hardly prevents Watson from talking about his field in a scientific and scholarly manner, especially since the post he was suspended from was not an academic post but an administrative one. It’s not his scientific career that’s suspended, it’s his administrative tasks.

He was also uninvited to give a lecture, that’s true, but having freedom of speech doesn’t mean people have to give you a platform if they think you will use it for speaking about unscholarly unscientific matter. So yes, one has the right to spout any old nonsense one fancies, but that doesn’t mean you’re automatically entitled to a platform.

I think crying academic freedom in this case is not only misguided, it is also irresponsible. To do so is to conflate science with social policy. Supporting Watson’s unscientific comments while attempting to distance onesself from the sentiment they express does nothing to highlight the fact that his statements were not based in science. Basically, the message is “his comments are valid even if I don’t like them”. But Watson’s comments are not valid — they are prejudice masqerading as science. We should be criticising the lack of scientific rigour in his conclusions and the prejudice that led him to his conclusions. That’s not an attack on academic freedom – it’s upholding scientific standards.
–IP

*Dictionary.com Unabridged (v 1.1). Retrieved October 27, 2007, from Dictionary.com website: http://dictionary.reference.com/browse/controversial and http://dictionary.reference.com/browse/unscientific.

Mole Day

Today is Mole Day, from 6.02 am to 6.02 pm, commemorating Avogadro’s Constant:

N = 6.02 * 10²³ mol ^-1

(to two decimal places) where N is the number of atom per mol.

–IP

Orionids

Via Clifford, the Orionids are coming to town today and tomorrow. NASA explains that Orionids are meteor showers that appear to be coming from the direction of Orion, a constalation made distinctive by a straight line of three stars that appear to be quite close together but equally spaced. Orionids are caused by the Earth pasing through dust and particles shed by Haley’s Comet on its orbit.

We’ve probably missed most of them already, the shower was supposed to peak in the wee hours of this morning (California time), which is mid-morning in the UK. We might see a few more tonight though, if it’s clear out, so look out for them. And check out the NASA page for more explanations, diagrams, and tips for viewing the meteors.

–IP