Thursday, July 31, 2008

Genealogies, of the academic variety

Neurotree is a really cool website that aims to create and store the training relationships between neuroscientists. From it, I learned that on one side of my family, the Bean side, I am 6 steps from Charles Sherrington (below, from Wikimedia), the English physiologist who coined the term "nociceptor" (yup, I actually read his book The Integrative Action of the Nervous System, where he used that term. How come that wasn't on the damn book list meme, eh?). Sherrington shared the 1932 Nobel with Lord Adrian for their work on neuronal physiology, and trained three Nobelists as well: Eccles, Granit and Florey.

The other half of my tree, the Clapham side (hmm, I am Bean-Clapham spawn! Something about that makes me chuckle. In an uncomfortable way), brings me to a distinct group of physiologists, with Erwin Neher (gulp, another Laureate), up to Haldan Keffer Hartline (another Laureate) , who himself trained with Werner Heisenberg!. Wow, I didn't know that! For those of you keeping score at home, that's another Laureate, this time in Physics.

Great; now I can fail to live up to my academic parents' expectations, as well as my real life ones! :) Ok, my real parents always said they'd be happy with whatever I chose to do. Hopefully my academic parents agree!

The other cool thing about Neurotree is the cluster analysis of neuroscientists, which reflects the relatedness of the various subdisciplines within neuroscience. Having some way of tracking the changes in this through time would be pretty cool. I wonder if you had the information about how those clusters changed through time, would you be able to pinpoint the early papers and workers who led this shift? They are real pioneers of new clusters. Could you also tie that into people's published works? I wonder how those papers that signal the birth of a new cluster would rate on the citation analysis metrics some people are so worried about?

Now anyone can browse the tree, so go check it out. If you're a neuroscientist and haven't been added, then go make an account and fill in some details.

Wednesday, July 30, 2008

The Book Meme

Alrighty, let's not get all serious and stuff in here, with the science and whatnot. Let's do a meme! It's 2008, memes are the new worm, and juniorprof tagged me with the 100 book meme. Here's the list below, with completed reads in bold and partial reads in italics.

1 Pride and Prejudice - Jane Austen
2 The Lord of the Rings - JRR Tolkien
3 Jane Eyre - Charlotte Bronte
4 Harry Potter series - JK Rowling
5 To Kill a Mockingbird - Harper Lee
6 The Bible -
7 Wuthering Heights - Emily Bronte
8 Nineteen Eighty-Four - George Orwell
9 His Dark Materials - Philip Pullman
10 Great Expectations - Charles Dickens
11 Little Women - Louisa M Alcott
12 Tess of the D’Urbervilles - Thomas Hardy
13 Catch 22 - Joseph Heller
14 Complete Works of Shakespeare -
15 Rebecca - Daphne Du Maurier
16 The Hobbit - JRR Tolkien
17 Birdsong - Sebastian Faulks
18 Catcher in the Rye - JD Salinger
19 The Time Traveller’s Wife - Audrey Niffenegger
20 Middlemarch - George Eliot
21 Gone With The Wind - Margaret Mitchell
22 The Great Gatsby - F Scott Fitzgerald
23 Bleak House - Charles Dickens
24 War and Peace - Leo Tolstoy
25 The Hitch Hiker’s Guide to the Galaxy - Douglas Adams
26 Brideshead Revisited - Evelyn Waugh
27 Crime and Punishment - Fyodor Dostoyevsky
28 Grapes of Wrath - John Steinbeck
29 Alice in Wonderland - Lewis Carroll
30 The Wind in the Willows - Kenneth Grahame
31 Anna Karenina - Leo Tolstoy
32 David Copperfield - Charles Dickens
33 Chronicles of Narnia - CS Lewis
34 Emma - Jane Austen
35 Persuasion - Jane Austen
36 The Lion, The Witch and The Wardrobe - CS Lewis
37 The Kite Runner - Khaled Hosseini
38 Captain Corelli’s Mandolin - Louis De Bernieres - They made a book out of that crap Nick Cage movie? Who knew?
39 Memoirs of a Geisha - Arthur Golden
40 Winnie the Pooh - AA Milne
41 Animal Farm - George Orwell
42 The Da Vinci Code - Dan Brown
43 One Hundred Years of Solitude - Gabriel Garcia Marquez
44 A Prayer for Owen Meany - John Irving
45 The Woman in White - Wilkie Collins
46 Anne of Green Gables - LM Montgomery
47 Far From The Madding Crowd - Thomas Hardy
48 The Handmaid’s Tale - Margaret Atwood
49 Lord of the Flies - William Golding
50 Atonement - Ian McEwan
51 Life of Pi - Yann Martel. Well, the wife read it. Does that count?
52 Dune - Frank Herbert - Yeah, I read the trilogy. Multiple times. It's still sorta whack though.
53 Cold Comfort Farm - Stella Gibbons
54 Sense and Sensibility - Jane Austen - What is UP with the Jane Austen on this list?
55 A Suitable Boy - Vikram Seth
56 The Shadow of the Wind - Carlos Ruiz Zafon
57 A Tale Of Two Cities - Charles Dickens - And the Dickens. What the hell?
58 Brave New World - Aldous Huxley
59 The Curious Incident of the Dog in the Night-time - Mark Haddon
60 Love In The Time Of Cholera - Gabriel Garcia Marquez
61 Of Mice and Men - John Steinbeck
62 Lolita - Vladimir Nabokov
63 The Secret History - Donna Tartt
64 The Lovely Bones - Alice Sebold
65 Count of Monte Cristo - Alexandre Dumas
66 On The Road - Jack Kerouac
67 Jude the Obscure - Thomas Hardy
68 Bridget Jones’s Diary - Helen Fielding
69 Midnight’s Children - Salman Rushdie
70 Moby Dick - Herman Melville
71 Oliver Twist - Charles Dickens - Listen, whoever wrote this list, 19th century British novels are not my thing. You've proved it, ok. Are you happy now?
72 Dracula - Bram Stoker
73 The Secret Garden - Frances Hodgson Burnett
74 Notes From A Small Island - Bill Bryson
75 Ulysses - James Joyce - I'll take The Dubliners or Portrait…please.
76 The Bell Jar - Sylvia Plath
77 Swallows and Amazons - Arthur Ransome
78 Germinal - Emile Zola
79 Vanity Fair - William Makepeace Thackeray
80 Possession - AS Byatt
81 A Christmas Carol - Charles Dickens - I sat through Scrooged.
82 Cloud Atlas - David Mitchell
83 The Color Purple - Alice Walker
84 The Remains of the Day - Kazuo Ishiguro
85 Madame Bovary - Gustave Flaubert
86 A Fine Balance - Rohinton Mistry
87 Charlotte’s Web - EB White - I find "Elements of Style" to have a much better plotline
88 The Five People You Meet In Heaven - Mitch Albom
89 Adventures of Sherlock Holmes - Sir Arthur Conan Doyle
90 The Faraway Tree Collection
91 Heart of Darkness - Joseph Conrad
92 The Little Prince - Antoine De Saint-Exupery
93 The Wasp Factory - Iain Banks
94 Watership Down - Richard Adams - Somehow couldn't get into it. Watched the cartoon on TV with my dad though.
95 A Confederacy of Dunces - John Kennedy Toole
96 A Town Like Alice - Nevil Shute
97 The Three Musketeers - Alexandre Dumas
98 Hamlet - William Shakespeare
99 Charlie and the Chocolate Factory - Roald Dahl And James and the Giant Peach and The Twits and have read some of his non kid stuff.
100 Les Miserables - Victor Hugo

Wow, 13 completed reads, and 7 partial reads. 20 per cent! Still, this proves two things. Nat doesn't read fiction. Which I freely admit. I am much more of a non-fiction creature. Secondly, overwrought and needlessly wordy 19th century fiction sucks. What a waste of time!

There are actually very few books on this list I haven't read that I actually wish I had. I count only 1984 and One Hundred Years of Solitude on that list. If you got an argument as to why any of the others is a must read, with which I should edify myself, let me hear it.

I won't tag anyone, but if you're reading this, feel free to put your own up, in the comments here if you have nowhere else to put it.

Tuesday, July 15, 2008

David Linden starts as Editor in Chief of Journal of Neurophysiology

Linden is professor of neuroscience at Johns Hopkins, and an electrophysiologist to boot! He replaces Eve Marder (Brandeis) another electrophysiologist (we izz in ur science, recording ur currentz!), as the Editor-in-Chief.

In his opening editorial, he says some things I like to hear. Here's a snippet:

I've always greatly admired the scientific ethos of the Journal of Neurophysiology. Reading the Journal reminds me of what I like best about science. I like that it publishes full-length reports, which are still being cited 20 or 30 years on. I like that each paper can stand on its own, without 10 supplemental online figures...I like that the Journal of Neurophysiology has been guided solely by publishing excellent and interesting science, regardless of perceived "sexiness" or "impact factor."
Hoo-ray! I like the sentiments, that's easy to see. Turns out Linden is actually a pretty funny guy, who has a blog, The Accidental Blog, where I found a link to a podcast of neuroscientists, Neuroscientists Talk Shop. Sounds interesting, and it's getting loaded onto the MP3 player as we speak. Yay, more geek talk!

Course, I haven't published in J. Neurophys. But it's always been on my watch list.

Friday, July 11, 2008

Dreaming of heaven...of the electrophysiologist's type

I've often said that in electrophysiologist's heaven, there's no series resistance, and you have an infinite number of solutions in a special magic fridge/shelf, containing every possible permutation of divalents, weird anions, or whatever.

Cause dealing with the lack of those two things is a series pain in the ass.


Thursday, July 10, 2008

What are the 'bibles' of your field?

Dr. Jekyll & Mrs. Hyde had a quick post on about how she doesn't read too many science books anymore (she's a postdoc), leading to the question of what's the point of a book length treatment when the science is always progressing? That's a good question, so go over there and comment on what you think is the proper role for science books.

But it's obvious that there are some books which most scientists in a given field own, and have read, and have incorporated into their thought process.

You know, the bibles of the field.

They're the books that everyone has on their shelf, the ones you spent your book money on as a grad student, the ones you point younger scientists to when they have a question, the ones you just know in your gut will have the answer once you peruse the table of contents. Some are methodological bibles, some are conceptual bibles, and some blend the two.

For electrophysiology, I can immediately think of three main bibles. They are, in no particular order:

"Ion(ic) channels of Excitable Membranes", by Bertil Hille, currently in its third edition. If it's a question about some fundamental basic property relating to ion channel function, or you want a good overview of the squid action potential, then this is the place to start. Still a favorite, though I have to say I prefer the 1992 2nd edition, for the tactile sensation of its cover, it's wonderfully incorrect title, as well as its modest overall size. The third edition sadly fails each of these criteria.

"Single-Channel Recording", 2nd edition, edited by Erwin Neher and Bert Sakmann. Maybe you've heard of them, having won the Nobel in 1991 for their development and use of the patch clamp technique. The book is largely covers methodological questions, though it's title is a misnomer; it covers a lot more than just single channel recording.

"The Axon Guide" edited by Rivka Sherman-Gold. Published by Axon Instruments (now owned by Molecular Devices), it covers a lot of basic material as well as more detailed questions in an accessible, easy manner. It was out of print for some time, and then Axon made it freely available in pdf form. You can download it from the Overlord Master Molecular Devices here. Everybody I train in patch clamp gets this, and I quiz em about it. I especially like its treatment of filters and digitization, two topics which many young biologists haven't heard much about. And series resistance. Oh the series resistance. That my friends is a post in itself.

So, what are the bibles of your field?

Yeah yeah, Maniatis, ok whatever. What else ya got? Cause that's bor-ing!

Wednesday, July 9, 2008

Wednesday quick hits

When blogging has been nonexistent for years, is it fair to say that recent blogging has been "light"? Still, things have been quite busy around here lately, mostly as we work to firm up the shape of a manuscript looking at the regulation of TRPC5 channels (Hmm...seems like a post describing TRP channels more generally is in order - put it in the hopper, which is already bursting at the seams). But in between bouts of analyzing current amplitudes and looking for series resistance errors (pine away you molecular and cell biologists, but remember, you made your choice, wrong as it was), I have been following some interesting science related blog posts and whatnot.

Yaroslav Nikolaev posted an interesting picture of scientific progress. Not sure I agree that the real bottleneck is always assessment stage but check it out. Hmm, it seems I should list 'epistemology' as a hobby in my social networking personae. Whoa, geek overload coming!

The Amazon Kindle looks pretty cool, anyone out there using it? Because I'm in the process of totally phasing out paper printouts of journals (which is going pretty well), so maybe I could expand the scope even further.

Sigh, research misconduct is such a downer. How prevalent is it really, and in what ways is the current architecture of science promote it?

What online reference managers are people out there using? I've been using Connotea, but have also checked out CiteULike a little bit. And I've tried Zotero as well, but it was SLOW. None of these have really grabbed me, so does anyone have a killer app they want to suggest? And no, please don't mention Papers. We're non Mac type in Junction Potential land.

AutoHotKey is an awesome little free app that let's you easily make shortcuts, etc. I don't think I could live without it now.

It's been a few weeks, but my brother and I hit the Iron Maiden show they played in Massachusetts at the Comcast center. Yeah, it was as awesome as it sounds. And yeah, I can hear the jealousy out there.

Wednesday, July 2, 2008

Conceptual and experimental innovators in science and Galenson's creative types

I just read the Wired article "What Kind of Genius are You?" by Daniel H. Pink from 2006 about University of Chicago economist David Galenson's then recently published book "Old Masters and Young Geniuses: The Two Life Cycles of Artistic Creativity". It's a tad old, and I have lost the source of the link, but it's definitely worth reading, and I just had to write a blog post about it.

Reading the article, I felt intellectually buffeted by the force of Galenson's hypothesis and its apparent explanatory power, similar to the way I felt the first time I read Kuhn's "The Structure of Scientific Revolutions." Galenson's idea arises from studies of artists' lifetime production (well, he is a economist) and is this: there are two essential types of creative artists, the "conceptual" innovators" and the "experimental innovators". The conceptual innovators make dramatic leaps in their fields, often doing so at early ages after which their production declines. The second type, "experimental innovators" instead often take much longer to develop their most significant output, spending a long time developing and experimenting with techniques. Conceptual innovators seem to 'know' where they're going and where they want to take the field, whereas experimental innovators don't, and evolve bit by bit, letting the work develop and seeing where it takes them:

Picasso and Cézanne represent radically different approaches to creation. Picasso thought through his works carefully before he put brush to paper. Like most conceptualists, he figured out in advance what he was trying to create. The underlying idea was what mattered; the rest was mere execution. The hallmark of conceptualists is certainty. They know what they want. And they know when they’ve created it. Cézanne was different. He rarely preconceived a work. He figured out what he was painting by actually painting it. “Picasso signed virtually everything he ever did immediately,” Galenson says. “Cézanne signed less than 10 percent.”

Experimentalists never know when their work is finished. As one critic wrote of Cézanne, the realization of his goal “was an asymptote toward which he was forever approaching without ever quite reaching.” (p.2).
Now, I immediately starting thinking about how this might apply to different scientists. I am convinced that there are many parallels between how artists work and how scientists work. That's not suprising, as both are intensely creative human endeavors, and probably many scientists would agree. Could this be another region where there are significant parallels between artists and scientists?

I say yes, but exactly how meaningful these categories are remain to be examined (and is rife with all the difficulties of measuring the output of scientists). But I definitely think there are conceptual and experimental innovator types among scientists, at times manifested in their approach to questions. There are those who are good at coming up with new hypotheses and models when the hard data to make any of those connections is weak or even non-existant. This might lead to a lot of negative experiments, but if you can do it right and you hit on something new, then significant progress can be made. In fact this led me back to Kuhn, regarding those scientists who develop the new paradigm must buy into it before there is significant data to show it's better than the current (think Copernicus pushing the heliocentric model of the solar system before it performed better than the Ptolemaic model-it took ~80 years and Kepler to make the heliocentric model perform better).

But the other approach is to take a subject of interest, and just start doing experiments, and try and let the results 'talk' to you, leading you to the next experiment. At some point, if you're lucky and perceptive, you have a decent shot of seeing something that isn't expected, and is the first step in the path towards a significant advance forward.

I'll be the first to admit that I am firmly in the second camp, and am an avowed experimentalist (hard to call myself an innovator). For just about all the projects I've worked on, I've decided on a particular subject or subfield, and then started to do experiments.

In my view, both of the approaches are valid and useful, and in principle I don't think either has an inherent greater probability of leading to something "new." I sometimes wonder though whether the slow approach, might produce something in the end which is perceived as being less shocking simply by virtue of the fact that all of the preceding experiments made the final result likely, or even inevitable. With the conceptual innovator, it's more obvious when "before" and "after" occurred. In that case, is the conceptual approach more likely to garner the attention needed for publication in a high profile journal? This might be taking things too far, but I suspect there is something to it.

Of course, the dichotomy between the two types isn't anywhere near complete. Conceptualists aren't making up things willy-nilly, totally disregarding all that has come before. And experimentalists must have some sort of model, however implicit, or else how would they choose among the infinite number of possible experiments. Galenson himself has said there are certainly people who straddle the extremes. Yet there are strong tendencies, and I wonder how far the concept can be extended to scientists.

So, my small and somewhat reticent readers: Are you a conceptual or an experimental innovator?