Mon - July 18, 2005
Femtoreview: The Wisdom of Crowds, by James Surowiecki
This femtoreview is sort about the book: The
Wisdom of Crowds, by James
Surowiecki. However, in the grand book reviewing tradition, you will
find only cursory references to the actual
book.
"Groupthink" has been much maligned of late. We'll leave that just hanging out there—fortune-cookie-style—for you to adapt to your particular world view and political perspective. The plexus is not about politics.
What is it, and why is it so bad? First read the wikipedia's definition:
"Groupthink" has been much maligned of late. We'll leave that just hanging out there—fortune-cookie-style—for you to adapt to your particular world view and political perspective. The plexus is not about politics.
What is it, and why is it so bad? First read the wikipedia's definition:
Groupthink is a term coined by
psychologist
Irving
Janis in
1972
to describe a process by which a group can make bad or
irrational
decisions. In a groupthink situation, each member of the group attempts to
conform his or her opinions to what they believe to be the
consensus
of the group. In a general sense this seems to be a very rationalistic way to
approach the situation. However this results in a situation in which the group
ultimately agrees upon an action which each member might individually consider
to be unwise (the risky
shift).
It kind of reminds me of being a teenager. It seems to me that one of the main principles of groupthink is that the members of the group must in some way not be selfish. That is to say, they are willing to sacrifice their own outcome/reward in order to gain something from the group (or simply to retain their membership in the group). Were each member to insist on maximizing his or her immediate outcome, his or her acquiescence to the group would presumably be harder to tolerate.
Of course, James Surowiecki's book is not really about groupthink, since he would likely view it as a pathology—a local minimum that needs to be surpassed in order to restore the robust and efficient decision-making powers of a group.
This book is all about the counterintuitive observation that groups of otherwise non-experts can nevertheless arrive at "expert" decisions as long as their information "gene pool" is deep enough and that they are not trying to impress each other (i.e. they avoid groupthink). There are many fascinating examples in the book, and I really don't want to give them away. If you do start to read this book and find the idea of prediction markets intriguing, you might enjoy playing around at the NewsFutures site. It's totally free, and you cannot even spend money if you want to (there are other sites that allow this, and I'm sure you will not have difficulty finding them on your own).
Since the point of these reviews is to give the reader a little taste and then for us to give our general opinion, let us just say that there are some very interesting, and perhaps eerie parallels that we see as we try to view this book through the lens of the practicing scientist. For example, how are scientific facts assimilated into the body of knowledge? Is there a panel or an "académie"? Some people might point to the Science Citation Index (or Web of Science as it seems to be called these days) as a sort of disinterested arbiter of consent. After all, if my papers get thousands of citations, they are probably right, no?
One thing I see as I peer ever so gingerly into biology is that there seem to be ideas, theories, mechanisms, etc. that just "are" and are sort of accepted, and one might wonder whether it's all been proven or just taken to be the most plausible explanation. I certainly don't know enough to argue, and I imagine that physical scientists do pretty much the same thing, but it's still hard to know how much weight to give to all those lovely cartoons in the textbooks.
The point is simply that there is no question that scientific debates are carried out among people—social beings who for all their data and error analysis and controls studies, are just as susceptible to coercion and a desire to fit in as anyone else. We might be even worse, since unlike the non-academic science world, where one may derive a certain measure of success from financial reward, we are more likely to judge ourselves exclusively through the recognition of our peers. Perhaps this is an inevitable consequence of anything that is driven largely by fashion. I don't know.
What can we do about it? One thing that really resonated was a discussion in the book of just how little dissent is really necessary in order to force a group out of a badly taken decision. In other words, most of the member may have been in agreement, but only one—or a very small number—can actually be effective in moving the group to another option. This was actually portrayed on film a long time ago as 12 Angry Men. The idea I have for my group will be to discuss papers in that style. The exercise will be called "Reviewer #8" in homage to that great film (Henry Fonda played Juror #8: he who cast the sole not-guilty vote). The idea is that everyone reads the paper—as in a normal group paper discussion—but one member is instructed to disagree with some aspect of the paper. It might have to be a completely bogus or farfetched criticism (some papers are beyond reproach), but maybe not. Either way, in debating the complaints, we should all be forced to appreciate the experiment/theory/conclusions better. It could also be called "devil's advocate", but depending on one's views regarding the devil, this implicitly takes sides whereas "Reviewer #8" is only mostly anti-reviewer, and most of us should be able to bear that burden!
It kind of reminds me of being a teenager. It seems to me that one of the main principles of groupthink is that the members of the group must in some way not be selfish. That is to say, they are willing to sacrifice their own outcome/reward in order to gain something from the group (or simply to retain their membership in the group). Were each member to insist on maximizing his or her immediate outcome, his or her acquiescence to the group would presumably be harder to tolerate.
Of course, James Surowiecki's book is not really about groupthink, since he would likely view it as a pathology—a local minimum that needs to be surpassed in order to restore the robust and efficient decision-making powers of a group.
This book is all about the counterintuitive observation that groups of otherwise non-experts can nevertheless arrive at "expert" decisions as long as their information "gene pool" is deep enough and that they are not trying to impress each other (i.e. they avoid groupthink). There are many fascinating examples in the book, and I really don't want to give them away. If you do start to read this book and find the idea of prediction markets intriguing, you might enjoy playing around at the NewsFutures site. It's totally free, and you cannot even spend money if you want to (there are other sites that allow this, and I'm sure you will not have difficulty finding them on your own).
Since the point of these reviews is to give the reader a little taste and then for us to give our general opinion, let us just say that there are some very interesting, and perhaps eerie parallels that we see as we try to view this book through the lens of the practicing scientist. For example, how are scientific facts assimilated into the body of knowledge? Is there a panel or an "académie"? Some people might point to the Science Citation Index (or Web of Science as it seems to be called these days) as a sort of disinterested arbiter of consent. After all, if my papers get thousands of citations, they are probably right, no?
One thing I see as I peer ever so gingerly into biology is that there seem to be ideas, theories, mechanisms, etc. that just "are" and are sort of accepted, and one might wonder whether it's all been proven or just taken to be the most plausible explanation. I certainly don't know enough to argue, and I imagine that physical scientists do pretty much the same thing, but it's still hard to know how much weight to give to all those lovely cartoons in the textbooks.
The point is simply that there is no question that scientific debates are carried out among people—social beings who for all their data and error analysis and controls studies, are just as susceptible to coercion and a desire to fit in as anyone else. We might be even worse, since unlike the non-academic science world, where one may derive a certain measure of success from financial reward, we are more likely to judge ourselves exclusively through the recognition of our peers. Perhaps this is an inevitable consequence of anything that is driven largely by fashion. I don't know.
What can we do about it? One thing that really resonated was a discussion in the book of just how little dissent is really necessary in order to force a group out of a badly taken decision. In other words, most of the member may have been in agreement, but only one—or a very small number—can actually be effective in moving the group to another option. This was actually portrayed on film a long time ago as 12 Angry Men. The idea I have for my group will be to discuss papers in that style. The exercise will be called "Reviewer #8" in homage to that great film (Henry Fonda played Juror #8: he who cast the sole not-guilty vote). The idea is that everyone reads the paper—as in a normal group paper discussion—but one member is instructed to disagree with some aspect of the paper. It might have to be a completely bogus or farfetched criticism (some papers are beyond reproach), but maybe not. Either way, in debating the complaints, we should all be forced to appreciate the experiment/theory/conclusions better. It could also be called "devil's advocate", but depending on one's views regarding the devil, this implicitly takes sides whereas "Reviewer #8" is only mostly anti-reviewer, and most of us should be able to bear that burden!
Posted at 04:03 PM Read More |
Tue - June 21, 2005
MIT Biology Hypertextbook
Another resource that is in the same spirit as the
previous
post about Kimball's
Biology Pages, is the MIT Biology
Hypertextbook. The hypertextbook is a bit more bare-boned than the
Biology Pages, but it gets to the point quickly, so you can get on with your
life without getting tripped up by the endless jargon of biology. I wonder if
there is a correlation between language skills and a propensity to enter the
life sciences. Fortunately for me, my language skills are rather good (save
spelling, of course).
I was at a meeting of people who have funding through the Human Frontier Science Program last week (fortunately, I am one), and I was sitting there listening to what were surely some very top-notch bioscience peoples' talks. I was hoping for a little interdisciplinary inspiration, and I got some, but mostly I determined that the biologists were basically trying to impress each other. I would have been impressed if I understood one-tenth of what they were talking about. I've got hand it to them, though, because they have some funny terminology. I mean physicists are always inventing new particles with funny names, so there is some stiff competition in the amusing-terminology-department. But I heard one phrase that I think should be the goal of all science, and of all scientific talks: "nonsense suppression." If more scientists attempted to perform nonsense suppression, the world would be a better place. I presented a poster there that anyone in my field would have thought was for preschoolers, but I had a full audience for three hours. I made every attempt to suppress as much nonsense as possible!
(By the way, good luck searching for "nonsense suppression" in the hypertextbook, their search doesn't seem to work. Too bad.)
It turns out that a nonsense mutation is really cool. Basically it changes a coding series of bases (three bases code for a given amino acid) into one that is called a stop codon. A stop codon forces the apparatus that synthesizes polypeptides (or strings of amino acids) to...stop. It's like riding on a train, patiently waiting for your station when all of a sudden the train goes express and you're at your destination, and you get off. The only thing is that you weren't really there yet, so you're not home. What really happened was that the next stop was just labeled as your destination. A problem like this is clearly a catastrophe for a nascent polypeptide. A simple example is a mutation that changes CAG (that codes for glutamine) to TAG, a stop codon. Ouch.
Presumably, nonsense suppression fixes this, or stops if from occurring in the first place. I think I need to ask a real person, since most of the descriptions I read don't make any sense.
I was at a meeting of people who have funding through the Human Frontier Science Program last week (fortunately, I am one), and I was sitting there listening to what were surely some very top-notch bioscience peoples' talks. I was hoping for a little interdisciplinary inspiration, and I got some, but mostly I determined that the biologists were basically trying to impress each other. I would have been impressed if I understood one-tenth of what they were talking about. I've got hand it to them, though, because they have some funny terminology. I mean physicists are always inventing new particles with funny names, so there is some stiff competition in the amusing-terminology-department. But I heard one phrase that I think should be the goal of all science, and of all scientific talks: "nonsense suppression." If more scientists attempted to perform nonsense suppression, the world would be a better place. I presented a poster there that anyone in my field would have thought was for preschoolers, but I had a full audience for three hours. I made every attempt to suppress as much nonsense as possible!
(By the way, good luck searching for "nonsense suppression" in the hypertextbook, their search doesn't seem to work. Too bad.)
It turns out that a nonsense mutation is really cool. Basically it changes a coding series of bases (three bases code for a given amino acid) into one that is called a stop codon. A stop codon forces the apparatus that synthesizes polypeptides (or strings of amino acids) to...stop. It's like riding on a train, patiently waiting for your station when all of a sudden the train goes express and you're at your destination, and you get off. The only thing is that you weren't really there yet, so you're not home. What really happened was that the next stop was just labeled as your destination. A problem like this is clearly a catastrophe for a nascent polypeptide. A simple example is a mutation that changes CAG (that codes for glutamine) to TAG, a stop codon. Ouch.
Presumably, nonsense suppression fixes this, or stops if from occurring in the first place. I think I need to ask a real person, since most of the descriptions I read don't make any sense.
Posted at 11:06 AM Read More |
Tue - May 3, 2005
Plexus Blogger Gets Real Job
Although you might think that I already have a real
job—that of almost never updating this weblog—in fact, I am just a
postdoctoral fellow in France. All that will
change this fall, when I start as an assistant professor that the University of Michigan in the Chemistry department. I'm
very excited, and I hope to be able to live up to their very high expectations,
and I'm really looking forward to having students and to build up a lab. You can
see a little of what we are going to be doing on my incipient
website.
Posted at 12:32 PM Read More |
Fri - March 11, 2005
Tool: DEVONThink
If you're anything like me, you probably have a few
thousand PDF files living somewhere on your computer (hopefully reasonably well
organized). This is very convenient, and is a revolution in time-savings
compared to the old cycle of looking up a paper, going to the library to find
it, photocopying it and filing it somewhere (in physical space). Since I like
reading papers on the computer screen, I almost never actually print any
papers—in fact, I wrote my whole Ph D thesis without printing more than a
dozen papers. (I realize not everyone has the same
approach)
So here's the problem. What do you do to actually manage all this information? Due to the uncoordinated way in which electronic journals developed, no one ever bothered to include any kind of "meta data" in the files to help us index them at a later date (when we have thousands of them on our disks). Fortunately I (and no doubt many others) realized that some sort of logical naming system could help a little without being too annoying. What I did was to use a scheme like this:
nameabbrev-JournalAbbrev-vol-year-page.pdf
Then I would file these away in the folder for that author. Now, you might ask, "yeah, but which author?" And you'd have a very good point. I usually went with the big shot (she/he is more constant). What if someone who became a "big shot" later was once in a lab of another big shot? What if two big shots are collaborating? Should I copy papers into more than one folder?
This ridiculous system actually worked pretty well while I was a graduate student and I was deeply focused on one very particular subject. Now, I always tried to read stuff outside of my immediate hyper-specialty, but still, at the time, filing things by name worked pretty well.
Things got out of control as I went along in my postdoc. I started to branch way out and I was reading things about not just my particular area of physical chemistry, but also proteins and more biochemistry. So I started a separate filing system in parallel with the name-based one, only this one was subject-based. I was less interested in assembling the "collected works" of a particular big shot, than I was in learning about new subjects. What I really needed was a program to help sort this mess out.
I am sure there are many programs that are up to the task of organizing and viewing PDF and other format files, but I'll briefly describe one in particular, and you can think of this quasi-review as motivation for you to deal with the mounting information overload problem (you must have one too, no?). This program is only available on the Mac. Sorry, if there is something similar for Windows, good for you. We've been hearing this big lie for years about no software for the Mac; it wasn't true in the past, and it's not true now. Maybe some clever windows programmer can copy this program.
DEVONThink (DT) can be pretty complicated, but I'll just describe it at the level where I'm using it right now. DT can make a database of your files much the same way that, say iPhoto or iTunes does, but it does not require (or even encourage) you to copy the files to a special file structure. In fact, your files can stay put right where they are on your disk. Naturally, this means you're in a bit of a hole if you move or delete them on your computer. You can import them simply by dragging individual files, groups of files, or whole folders of files right into the DT window (what else would you expect). It will respect your files and treat them as "Groups" in DT (similar to playlists or folders in iTunes or iPhoto). You can have nested Groups (this was critical for me).
As your files are being imported, DT is actually indexing their contents as well. This is where the power really is. Of course, you can click on a file, and it will be displayed right away (no waiting for Preview to load the file), and it's really speedy about it. In addition to this basic functionality—which is almost already enough for me—there are four features that I really like and I will describe them below.
• Find across all files
• Classify
• See Also
• Wiki
You can type whatever you want in the ubiquitous find box (similar to Google box in Safari or other broswers, or the Finder). DT will quickly give you a list of all the files matching the criteria with a kind of ranking. This works very well and is very fast.
The "Classify" feature is a great surprise. When you are viewing a file, you can click the Classify button and it will show you a list of Groups that it thinks the file might belong in. It typically shows about ten groups. Not all of them are appropriate, but I think as the file collection grows, it will become more accurate. There is also an autoclassify option, but I don't trust it yet. Maybe I'll post an update about this later.
The "See Also" button is also a pleasant surprise. Here you will be presented with not a list of groups, but one of other files that DT thinks are relevant. Both of these features should allow you to download zillions of papers, and loosely file them away and then use DT to help you make connections between the different papers. Since finding connections between information from diverse subjects is the whole point of The Plexus, this program is certainly going to be one of our favorites.
The last feature is one that has been sort of sneaking up on me lately in several different contexts. This is the Wiki paradigm. Now, like you, I end up quite often finding myself at the wikipedia (usually through Google, but sometimes I right there first). Wiki is a user-modifiable documentation system that is very popular with open source projects, but also in school class projects. I've tried three different systems now: the original wikimedia, the wiki features in the online learning package called moodle, and finally in DT. DT's implementation is very simple.
In DT, doing wiki is really simple. You start with a blank RTF file, and you just type in it. After you write something (can be just notes or whatever), you highlight an important word or phase. You right click (or control-click) and choose "Make Link". Now it becomes a link. If your selected text is exactly the same as a group you have in your database, clicking on the (now created) link will immediately transport you to that group. If you don't have anything in your database to link to, DT will create a new RTF file when you click on that link. Now you start typing in that file and so on, and so on. Eventually you'll have a highly linked set of notes.
This has been a very long post, but I hope that by trying to explain my information overload problem, and by pointing out one approach to solve it that you will take heart that there is a path out of this mayhem-rich jungle. DT is not perfect, and things get a little funky once you realize that there is an internal filing system that DT will copy some files into (if you drag them directly in from, say, Preview). But really, it's no big deal. If you're lucky enough to use a Mac, you can download DEVONThink and try it for 15 days (of course I'm not affiliated with them in any way, I'm just a customer). It's not that expensive, and you'll save so much time. Now we can just start downloading files like crazy and make all kinds of new connections that we (or maybe no one) ever thought of!
(I would also like to point out that it is possible to attach files to bibliographic entries in EndNote and Bookends, I used to do this and it's too cumbersome. Nirvana would be automatically linking the PDFs in DT to either of these two reference managers. We can dream, can't we?)
So here's the problem. What do you do to actually manage all this information? Due to the uncoordinated way in which electronic journals developed, no one ever bothered to include any kind of "meta data" in the files to help us index them at a later date (when we have thousands of them on our disks). Fortunately I (and no doubt many others) realized that some sort of logical naming system could help a little without being too annoying. What I did was to use a scheme like this:
nameabbrev-JournalAbbrev-vol-year-page.pdf
Then I would file these away in the folder for that author. Now, you might ask, "yeah, but which author?" And you'd have a very good point. I usually went with the big shot (she/he is more constant). What if someone who became a "big shot" later was once in a lab of another big shot? What if two big shots are collaborating? Should I copy papers into more than one folder?
This ridiculous system actually worked pretty well while I was a graduate student and I was deeply focused on one very particular subject. Now, I always tried to read stuff outside of my immediate hyper-specialty, but still, at the time, filing things by name worked pretty well.
Things got out of control as I went along in my postdoc. I started to branch way out and I was reading things about not just my particular area of physical chemistry, but also proteins and more biochemistry. So I started a separate filing system in parallel with the name-based one, only this one was subject-based. I was less interested in assembling the "collected works" of a particular big shot, than I was in learning about new subjects. What I really needed was a program to help sort this mess out.
I am sure there are many programs that are up to the task of organizing and viewing PDF and other format files, but I'll briefly describe one in particular, and you can think of this quasi-review as motivation for you to deal with the mounting information overload problem (you must have one too, no?). This program is only available on the Mac. Sorry, if there is something similar for Windows, good for you. We've been hearing this big lie for years about no software for the Mac; it wasn't true in the past, and it's not true now. Maybe some clever windows programmer can copy this program.
DEVONThink (DT) can be pretty complicated, but I'll just describe it at the level where I'm using it right now. DT can make a database of your files much the same way that, say iPhoto or iTunes does, but it does not require (or even encourage) you to copy the files to a special file structure. In fact, your files can stay put right where they are on your disk. Naturally, this means you're in a bit of a hole if you move or delete them on your computer. You can import them simply by dragging individual files, groups of files, or whole folders of files right into the DT window (what else would you expect). It will respect your files and treat them as "Groups" in DT (similar to playlists or folders in iTunes or iPhoto). You can have nested Groups (this was critical for me).
As your files are being imported, DT is actually indexing their contents as well. This is where the power really is. Of course, you can click on a file, and it will be displayed right away (no waiting for Preview to load the file), and it's really speedy about it. In addition to this basic functionality—which is almost already enough for me—there are four features that I really like and I will describe them below.
• Find across all files
• Classify
• See Also
• Wiki
You can type whatever you want in the ubiquitous find box (similar to Google box in Safari or other broswers, or the Finder). DT will quickly give you a list of all the files matching the criteria with a kind of ranking. This works very well and is very fast.
The "Classify" feature is a great surprise. When you are viewing a file, you can click the Classify button and it will show you a list of Groups that it thinks the file might belong in. It typically shows about ten groups. Not all of them are appropriate, but I think as the file collection grows, it will become more accurate. There is also an autoclassify option, but I don't trust it yet. Maybe I'll post an update about this later.
The "See Also" button is also a pleasant surprise. Here you will be presented with not a list of groups, but one of other files that DT thinks are relevant. Both of these features should allow you to download zillions of papers, and loosely file them away and then use DT to help you make connections between the different papers. Since finding connections between information from diverse subjects is the whole point of The Plexus, this program is certainly going to be one of our favorites.
The last feature is one that has been sort of sneaking up on me lately in several different contexts. This is the Wiki paradigm. Now, like you, I end up quite often finding myself at the wikipedia (usually through Google, but sometimes I right there first). Wiki is a user-modifiable documentation system that is very popular with open source projects, but also in school class projects. I've tried three different systems now: the original wikimedia, the wiki features in the online learning package called moodle, and finally in DT. DT's implementation is very simple.
In DT, doing wiki is really simple. You start with a blank RTF file, and you just type in it. After you write something (can be just notes or whatever), you highlight an important word or phase. You right click (or control-click) and choose "Make Link". Now it becomes a link. If your selected text is exactly the same as a group you have in your database, clicking on the (now created) link will immediately transport you to that group. If you don't have anything in your database to link to, DT will create a new RTF file when you click on that link. Now you start typing in that file and so on, and so on. Eventually you'll have a highly linked set of notes.
This has been a very long post, but I hope that by trying to explain my information overload problem, and by pointing out one approach to solve it that you will take heart that there is a path out of this mayhem-rich jungle. DT is not perfect, and things get a little funky once you realize that there is an internal filing system that DT will copy some files into (if you drag them directly in from, say, Preview). But really, it's no big deal. If you're lucky enough to use a Mac, you can download DEVONThink and try it for 15 days (of course I'm not affiliated with them in any way, I'm just a customer). It's not that expensive, and you'll save so much time. Now we can just start downloading files like crazy and make all kinds of new connections that we (or maybe no one) ever thought of!
(I would also like to point out that it is possible to attach files to bibliographic entries in EndNote and Bookends, I used to do this and it's too cumbersome. Nirvana would be automatically linking the PDFs in DT to either of these two reference managers. We can dream, can't we?)
Posted at 09:39 PM Read More |
Tue - March 1, 2005
A Cornucopia of Interdiscipline: On ScienceWeek
Here are the topics covered this week (March 4
edition) by the online magazine ScienceWeek:
• History of Physics: Einstein, Lorentz, and the Ether
• Astrophysics: Star Disks and Planetary Systems
• Cell Biology: On Fast Recovery in Visual Pigments
• Plant Biology: On Movement in the Venus Flytrap
• Medical Biology: Antibiotics and Neurodegenerative Diseases
• Science Policy: On the Cost of Medial Education
The articles are quite different from your typical general audience treatment in journals like Science and C&E News. They usually present the main points brought up in a given article in a normal journal, give some references, and then a related story from previous ScienceWeek editions. From these point-form summaries, you will get a thumbnail sketch of the main questions, why they are important and what new conclusions have been drawn from the work cited. Unlike even the quasi-lay explanations in Science and Nature, these summaries actually explain potentially unfamiliar vocabulary and terms.
As you can see from the list above, ScienceWeek touches on a wide range of subjects. For example, the medical education story contains three stories: the principal one, another titled "Alarm over decline in number of US physician-scientists", and "On the evolution of medical school admissions testing." Each of these stories is about one screen-page long and you can read the main points very efficiently.
My only real problem with ScienceWeek is their annoying habit of using the hopelessly pompous "On..." structure. If you're Darwin, it's okay, otherwise, spare us the "On" and just start with the next word. I find a lot of prissy theory papers in the Journal of Chemical Physics use this "On" junk and I don't like it there either. Obviously your paper will be "On" whatever it is you put in the title. Maybe someone can write a perl script to parse the html and send all the offending "on's" to their rightful home in /dev/null/
Despite the overuse of a certain preposition that will not be named, ScienceWeek is a comprehensive and streamlined ezine that should be considered must-see-TV for those of us who are seeking interdiscipline. You can also subscribe to an email update of the titles. I find that this reminds me to check out the site. Also, I would recommend typing in your favorite subject into their search box to see what you've missed (or written for that matter).
• History of Physics: Einstein, Lorentz, and the Ether
• Astrophysics: Star Disks and Planetary Systems
• Cell Biology: On Fast Recovery in Visual Pigments
• Plant Biology: On Movement in the Venus Flytrap
• Medical Biology: Antibiotics and Neurodegenerative Diseases
• Science Policy: On the Cost of Medial Education
The articles are quite different from your typical general audience treatment in journals like Science and C&E News. They usually present the main points brought up in a given article in a normal journal, give some references, and then a related story from previous ScienceWeek editions. From these point-form summaries, you will get a thumbnail sketch of the main questions, why they are important and what new conclusions have been drawn from the work cited. Unlike even the quasi-lay explanations in Science and Nature, these summaries actually explain potentially unfamiliar vocabulary and terms.
As you can see from the list above, ScienceWeek touches on a wide range of subjects. For example, the medical education story contains three stories: the principal one, another titled "Alarm over decline in number of US physician-scientists", and "On the evolution of medical school admissions testing." Each of these stories is about one screen-page long and you can read the main points very efficiently.
My only real problem with ScienceWeek is their annoying habit of using the hopelessly pompous "On..." structure. If you're Darwin, it's okay, otherwise, spare us the "On" and just start with the next word. I find a lot of prissy theory papers in the Journal of Chemical Physics use this "On" junk and I don't like it there either. Obviously your paper will be "On" whatever it is you put in the title. Maybe someone can write a perl script to parse the html and send all the offending "on's" to their rightful home in /dev/null/
Despite the overuse of a certain preposition that will not be named, ScienceWeek is a comprehensive and streamlined ezine that should be considered must-see-TV for those of us who are seeking interdiscipline. You can also subscribe to an email update of the titles. I find that this reminds me to check out the site. Also, I would recommend typing in your favorite subject into their search box to see what you've missed (or written for that matter).
Posted at 11:05 AM Read More |
Mon - January 24, 2005
Larry Summers: Turning Back the Clock
[Update, Feb.
18, 2005: apparently, the "off-the-record"
remarks were not entirely "off-the-record". They were in fact, "recorded" on
some sort of tape recorder. Using this off-the-record record, the full
transcript was made available by Harvard. Since they have the Q&A
that followed, one can assume that Summers' speech is what he said, rather than
what he had prepared. Either way, it is now clear to the whole world that the
president of Harvard University has no capacity whatsoever to speak in clear
language that cannot be
misinterpreted.]
If he had suggested that blacks might be genetically unsuited for science, he'd be packing his bags already. Instead, Harvard president, Larry Summers, let one slip about women—also known as "the 'minority' that's OK to riff on." This is a very bad sign, indeed, as it means that those in power are even starting to forget how to pretend that minorities and women are equals.
There are several accounts of the top-secret, off-the-record remarks in the New York Times, Boston Globe, and Slate. (By the way, since when are conferences off the record? I mean isn't that why Gordon conferences are unusual?)
There are well-documented physiological and neuroanatomical differences between male and female humans, as there surely are between male and female wombats, tree shrews, and lemurs.
The Times article captures most of what I think (and, in fact, I deleted most of what I wrote after having read it in full). But I would just like to highlight one quote by UCSB economist Dr. Catherine Weinberger:
Surveying a representative population of working scientists and engineers, Dr. Weinberger has discovered that the women were likelier than the men to have very high test scores. "Women are more cautious about entering these professions unless they have very high scores to begin with," she said.
And why is that? Could it that women have been hearing the kind of bull that Larry Summers is spewing their whole lives? Unlike boys, girls have to earn every compliment they get.
My wife, a gifted physicist, has a very poorly developed sense of self-evaluation and she constantly relies on external approval. I think that she is a perfect example of what happens to women who pass through our system.
Harlem: A Dream Deferred
What happens to a dream deferred?
Does it dry up
like a raisin in the sun
Or fester like a sore—
And then run?
Does it stink like rotten meat?
Or crust and sugar over—
Like a syrupy sweet?
Maybe it just sags
like a heavy load.
Or does it explode?
–Langston Hughes
If he had suggested that blacks might be genetically unsuited for science, he'd be packing his bags already. Instead, Harvard president, Larry Summers, let one slip about women—also known as "the 'minority' that's OK to riff on." This is a very bad sign, indeed, as it means that those in power are even starting to forget how to pretend that minorities and women are equals.
There are several accounts of the top-secret, off-the-record remarks in the New York Times, Boston Globe, and Slate. (By the way, since when are conferences off the record? I mean isn't that why Gordon conferences are unusual?)
There are well-documented physiological and neuroanatomical differences between male and female humans, as there surely are between male and female wombats, tree shrews, and lemurs.
The Times article captures most of what I think (and, in fact, I deleted most of what I wrote after having read it in full). But I would just like to highlight one quote by UCSB economist Dr. Catherine Weinberger:
Surveying a representative population of working scientists and engineers, Dr. Weinberger has discovered that the women were likelier than the men to have very high test scores. "Women are more cautious about entering these professions unless they have very high scores to begin with," she said.
And why is that? Could it that women have been hearing the kind of bull that Larry Summers is spewing their whole lives? Unlike boys, girls have to earn every compliment they get.
My wife, a gifted physicist, has a very poorly developed sense of self-evaluation and she constantly relies on external approval. I think that she is a perfect example of what happens to women who pass through our system.
Harlem: A Dream Deferred
What happens to a dream deferred?
Does it dry up
like a raisin in the sun
Or fester like a sore—
And then run?
Does it stink like rotten meat?
Or crust and sugar over—
Like a syrupy sweet?
Maybe it just sags
like a heavy load.
Or does it explode?
–Langston Hughes
Posted at 12:08 AM Read More |
Fri - December 17, 2004
Two Articles on Interdiscipline
Two recent articles discuss–rather cursorily
I would say—the problems and challenges facing those who gravitate towards
interdisciplinary research. One of
these is in Science, and the
other is in the American Chemical Society's weekly bulletin, Chemical and Engineering
News (as usual, you'll need subscriptions, sorry). One of the main
problems is the fact that although research is becoming increasingly
interdisciplinary, professional academic science is still built around
traditional department structures. Many new faculty avoid venturing too far
afield for fear that they will not maintain a solid home base of support. It
goes something like this: if you do
Xical Y
(or Yical
X) research, then you are not fully a member of either the X or the Y
departments, and you need good personal support when the tenure decision
approaches. The way one department chair put it to me was that if you're a
jointly appointed professor in two departments, you kind of have to get tenure
twice, i.e. in both departments.
This is all sensible, and I realize that tenure decisions and departmental identities are slow to change. I discount, however, the notion that you must take a big risk in order to do interdisciplinary research. What you must do is constantly force yourself to pick up new subject areas that are outside of your formal classroom training, and you must be flexible in designing your projects so that they will have several levels of success while consciously building in fallback options and "consolation prizes." But why is this any different from any other description of a successful research program? If you're not doing those things, you're probably stagnating anyway.
One thing I've noticed in my not-extensive-enough visits to different departments is how parochial they can all be. At one place I asked a lot about the physics department while I was in the chemistry department, and I was rather surprised to sense almost no contact between them. At another, it was the biochemistry department with which they (the chemists) had little contact. I find this rather peculiar since neither of these universities was so physically large that it would require more than a five minute walk to go from one building to the other, yet they had very little interaction.
So the point of this latter comment is that one of the unrecognized roles of those in interdisciplinary research is that of the uniter. By being bold and naive at the same time, we can forge (or reinforce, if we're lucky) links between departments that are often out of touch with each other. Why is this important? Budget cuts, or at least cost cutting, are becoming rampant in publicly funded education. While it is always possible to whine about it, there is an alternate approach: find value where it has not been noticed before.
Science is about creating knowledge and expanding the imagination of those who ask new questions in order to create new knowledge. I can't believe that there is anyone who would object to this functional definition. So, in order to create knowledge today—now that all the really simple questions have been answered—we need to rely more on networks rather than solitary toil. Networks, however are not necessarily linear. I'm no computer scientist, but I can draw simple diagrams. If we just look at a series:
where the greenish dots represent nodes of the network (or in our case, researchers) and the numbers show how many connections there are. So it turns out that the formula can be found that tells you how many connections there are. It's called the combination (sometimes written nCk). Since there's a formula, we can plot it. Below I've plotted the number of "collaborations" involving two researchers as a function of the total number of researchers (same as number of lines as a function of the number of dots).
The blue curve shows the number of two-person collaborations, while the green curve generalizes the idea a little in order to include three-person collaborations. Clearly, these curves are not linear. Just how nonlinear they are, however, depends on the number of researchers. Let's look at marginal increases.
Here we plot the percentage increase in the number of collaborations due to adding one new researcher. This can be calculated by taking the difference in new collaborations and old ones and dividing by the old ones. OK, so this shows that for any department, adding one researcher increases the total number of collaborators less and less as a fraction of previous collaborations. For example, if you have 20 researchers, you only increase the total number of collaborations by 20, and 20/(the old total) is about 10%.
The conclusion is that assuming all collaborations are within the same department, based solely on number of collaborations only relatively small increases in new knowledge creation can be expected with new hires.
What this model ignores, however, is interdisciplinary collaborations—especially in cases where departments are mutually alienated and have no hope at all of collaborating with each other. What if the new hire could collaborate with a whole different department? Here's a simplified and probably ludicrous scenario (but it's interesting anyway). Imagine a department of 40 researchers, and they hire one new person who can collaborate with another department of 40 and in so doing, breaks through old barriers, while permitting all of his or her "home" department to collaborate with all the others. This would amount to a 40-person department adding 41 new potential collaborators. The total increase in collaborations would be 2460, or a 315% increase. The 40-person department adding one person with no ability to go "abroad" would yield just 40 new collaborations, for an increase of 5%.
This is a very simple model of reality, but it does suggest one very important thing: adding interdisciplinary researchers actually should add value to the university in a disproportionate way since it permits more effective use of resources the university already had but was not exploiting. I'd bet economists have a name for this effect, since it must come up often in discussing the benefits of free trade.
This is all sensible, and I realize that tenure decisions and departmental identities are slow to change. I discount, however, the notion that you must take a big risk in order to do interdisciplinary research. What you must do is constantly force yourself to pick up new subject areas that are outside of your formal classroom training, and you must be flexible in designing your projects so that they will have several levels of success while consciously building in fallback options and "consolation prizes." But why is this any different from any other description of a successful research program? If you're not doing those things, you're probably stagnating anyway.
One thing I've noticed in my not-extensive-enough visits to different departments is how parochial they can all be. At one place I asked a lot about the physics department while I was in the chemistry department, and I was rather surprised to sense almost no contact between them. At another, it was the biochemistry department with which they (the chemists) had little contact. I find this rather peculiar since neither of these universities was so physically large that it would require more than a five minute walk to go from one building to the other, yet they had very little interaction.
So the point of this latter comment is that one of the unrecognized roles of those in interdisciplinary research is that of the uniter. By being bold and naive at the same time, we can forge (or reinforce, if we're lucky) links between departments that are often out of touch with each other. Why is this important? Budget cuts, or at least cost cutting, are becoming rampant in publicly funded education. While it is always possible to whine about it, there is an alternate approach: find value where it has not been noticed before.
Science is about creating knowledge and expanding the imagination of those who ask new questions in order to create new knowledge. I can't believe that there is anyone who would object to this functional definition. So, in order to create knowledge today—now that all the really simple questions have been answered—we need to rely more on networks rather than solitary toil. Networks, however are not necessarily linear. I'm no computer scientist, but I can draw simple diagrams. If we just look at a series:
where the greenish dots represent nodes of the network (or in our case, researchers) and the numbers show how many connections there are. So it turns out that the formula can be found that tells you how many connections there are. It's called the combination (sometimes written nCk). Since there's a formula, we can plot it. Below I've plotted the number of "collaborations" involving two researchers as a function of the total number of researchers (same as number of lines as a function of the number of dots).
The blue curve shows the number of two-person collaborations, while the green curve generalizes the idea a little in order to include three-person collaborations. Clearly, these curves are not linear. Just how nonlinear they are, however, depends on the number of researchers. Let's look at marginal increases.
Here we plot the percentage increase in the number of collaborations due to adding one new researcher. This can be calculated by taking the difference in new collaborations and old ones and dividing by the old ones. OK, so this shows that for any department, adding one researcher increases the total number of collaborators less and less as a fraction of previous collaborations. For example, if you have 20 researchers, you only increase the total number of collaborations by 20, and 20/(the old total) is about 10%.
The conclusion is that assuming all collaborations are within the same department, based solely on number of collaborations only relatively small increases in new knowledge creation can be expected with new hires.
What this model ignores, however, is interdisciplinary collaborations—especially in cases where departments are mutually alienated and have no hope at all of collaborating with each other. What if the new hire could collaborate with a whole different department? Here's a simplified and probably ludicrous scenario (but it's interesting anyway). Imagine a department of 40 researchers, and they hire one new person who can collaborate with another department of 40 and in so doing, breaks through old barriers, while permitting all of his or her "home" department to collaborate with all the others. This would amount to a 40-person department adding 41 new potential collaborators. The total increase in collaborations would be 2460, or a 315% increase. The 40-person department adding one person with no ability to go "abroad" would yield just 40 new collaborations, for an increase of 5%.
This is a very simple model of reality, but it does suggest one very important thing: adding interdisciplinary researchers actually should add value to the university in a disproportionate way since it permits more effective use of resources the university already had but was not exploiting. I'd bet economists have a name for this effect, since it must come up often in discussing the benefits of free trade.
Posted at 01:56 PM Read More |
Tue - November 30, 2004
Three Online "Textbooks"
Textbooks can be great resources, but they are
costly, hard to search, and, let's face it, they're heavy. For a free,
searchable, and virtually weightless alternative, there are several online
resources I've found recently that I think are worth adding to our "Tools"
category.
HyperPhysics
The 20th Century saw a lot of changes to the framework of physics, but at the same time, some concepts remain essentially fixed, and sometimes all you need is a quick reminder. Like, "what is the formula for blackbody radiation exactly?" HyperPhysics has just about any topic you would normally find in a textbook, but with all the added value of links between topics. It even has sections on chemistry, geophysics, biology, and math (although for math, I'm not sure anyone can beat Mathworld from Wolfram Research).
Image source: HyperPhysics
HyperPhysics is maintained by the Department of Physics and Astronomy at Georgia State University. The results from the site often show up in google searches, but you can also use google to search the site directly by using google's domain constraint. For example if you want to search for "phase" you would type the following google:
phase site:hyperphysics.phy-astr.gsu.edu
We will try to put in links to HyperPhysics when we mention physics topics so that those seeking interdiscipline from other fields will not be stymied by vocabulary (as we so often are when we read biological things).
Kimball's Biology Pages
Not knowing much about biology, but being fascinated by it and its molecules, we at the plexus are always looking for useful resources to help in our own quest for interdiscipline. I was reading a story about transcription factors, and I had no idea what they are so I did a search and up came with this nice page on gene regulation from Kimball's Biology Pages. There are so many links you could probably spend way too long following a thread, but I like the way you can really get a feel for the interconnectedness of biology. Reading a linear textbook never really captures this sense. The only problem I have with this site is one that I have in general with biological things, I can never figure out how general an idea is. They give a concept and then they give one example and move on. I guess that's just the way things are when there are so many exceptions and special cases. Anyway, all I'm saying is that I find it much harder to get a big picture first and then to dive into the details. Maybe if you're more bottom up, you'll do better.
The maintainer of this site, Dr. John W. Kimball, is described on the site:
John W. Kimball has retired from a lifetime of teaching biology. A graduate of Harvard College, he began his teaching career at the secondary level, teaching chemistry and biology to students at Phillips Academy, an independent school in Andover, Massachusetts. In 1969, he returned to Harvard to study immunology with the late Professor A. M. Pappenheimer. After receiving his Ph.D. there, he went on to teach introductory biology (in both majors and nonmajors courses) and immunology at Tufts University where he became a tenured professor. In 1982 he returned again to Harvard where he taught immunology and also participated in teaching the introductory course for majors.
The Basics of NMR
This is a topic I never thought was very interesting. In organic chemistry, they showed us tiny little molecules and said how there was spin and that if you think of other nuclei as little magnets they can couple to other spins and that how many peaks you get depends on how many different kinds of nuclei there were and what they were connected to, and blah, blah, blah. I never figured it out and would usually just guess which peaks corresponded to which nuclei and usually I was wrong.
This reflects one of the problems of interdiscipline. Often one is forced to use ideas and techniques one is simply not prepared to fully comprehend. We didn't know anything about Hamiltonians and basis functions and coupling and all the whatnot that you need in order to really know what all those peaks mean.
Fast-forward about ten years. Using ultrafast laser pulses, we can exploit the same ideas that people have been using for years to study spins, only we can do it with vibrational and electronic energy levels. Now I see why NMR is important, because we can just change the states, the Hamiltonians, and the couplings and use all the stuff they've already figured out to do our new spectroscopy tricks. One problem is that a lot of us thought NMR was boring, so we don't know it very well. Hence our interest in The Basics of NMR. This is a real textbook on the web, complete with animations and full-out equations. I think that between this site and Richard Ernst's great book Principles of Nuclear Magnetic Resonance in One and Two Dimensions, we will be well on our way to understanding this powerful methodology—so we can shamelessly steal whatever we can.
Image source: The Basics of NMR
The author is Joseph P. Hornak, a professor of Chemistry and Imaging Science at the Rochester Institute of Technology.
HyperPhysics
The 20th Century saw a lot of changes to the framework of physics, but at the same time, some concepts remain essentially fixed, and sometimes all you need is a quick reminder. Like, "what is the formula for blackbody radiation exactly?" HyperPhysics has just about any topic you would normally find in a textbook, but with all the added value of links between topics. It even has sections on chemistry, geophysics, biology, and math (although for math, I'm not sure anyone can beat Mathworld from Wolfram Research).
Image source: HyperPhysics
HyperPhysics is maintained by the Department of Physics and Astronomy at Georgia State University. The results from the site often show up in google searches, but you can also use google to search the site directly by using google's domain constraint. For example if you want to search for "phase" you would type the following google:
phase site:hyperphysics.phy-astr.gsu.edu
We will try to put in links to HyperPhysics when we mention physics topics so that those seeking interdiscipline from other fields will not be stymied by vocabulary (as we so often are when we read biological things).
Kimball's Biology Pages
Not knowing much about biology, but being fascinated by it and its molecules, we at the plexus are always looking for useful resources to help in our own quest for interdiscipline. I was reading a story about transcription factors, and I had no idea what they are so I did a search and up came with this nice page on gene regulation from Kimball's Biology Pages. There are so many links you could probably spend way too long following a thread, but I like the way you can really get a feel for the interconnectedness of biology. Reading a linear textbook never really captures this sense. The only problem I have with this site is one that I have in general with biological things, I can never figure out how general an idea is. They give a concept and then they give one example and move on. I guess that's just the way things are when there are so many exceptions and special cases. Anyway, all I'm saying is that I find it much harder to get a big picture first and then to dive into the details. Maybe if you're more bottom up, you'll do better.
The maintainer of this site, Dr. John W. Kimball, is described on the site:
John W. Kimball has retired from a lifetime of teaching biology. A graduate of Harvard College, he began his teaching career at the secondary level, teaching chemistry and biology to students at Phillips Academy, an independent school in Andover, Massachusetts. In 1969, he returned to Harvard to study immunology with the late Professor A. M. Pappenheimer. After receiving his Ph.D. there, he went on to teach introductory biology (in both majors and nonmajors courses) and immunology at Tufts University where he became a tenured professor. In 1982 he returned again to Harvard where he taught immunology and also participated in teaching the introductory course for majors.
The Basics of NMR
This is a topic I never thought was very interesting. In organic chemistry, they showed us tiny little molecules and said how there was spin and that if you think of other nuclei as little magnets they can couple to other spins and that how many peaks you get depends on how many different kinds of nuclei there were and what they were connected to, and blah, blah, blah. I never figured it out and would usually just guess which peaks corresponded to which nuclei and usually I was wrong.
This reflects one of the problems of interdiscipline. Often one is forced to use ideas and techniques one is simply not prepared to fully comprehend. We didn't know anything about Hamiltonians and basis functions and coupling and all the whatnot that you need in order to really know what all those peaks mean.
Fast-forward about ten years. Using ultrafast laser pulses, we can exploit the same ideas that people have been using for years to study spins, only we can do it with vibrational and electronic energy levels. Now I see why NMR is important, because we can just change the states, the Hamiltonians, and the couplings and use all the stuff they've already figured out to do our new spectroscopy tricks. One problem is that a lot of us thought NMR was boring, so we don't know it very well. Hence our interest in The Basics of NMR. This is a real textbook on the web, complete with animations and full-out equations. I think that between this site and Richard Ernst's great book Principles of Nuclear Magnetic Resonance in One and Two Dimensions, we will be well on our way to understanding this powerful methodology—so we can shamelessly steal whatever we can.
Image source: The Basics of NMR
The author is Joseph P. Hornak, a professor of Chemistry and Imaging Science at the Rochester Institute of Technology.
Posted at 12:23 PM Read More |
Fri - November 26, 2004
Google Scholar
OK, so I went to google scholar as soon as I found
out about it (on an AP story). It was impressive, but it is really not ready for
prime-time. I'm sorry, but I have papers with more than 30 citations, and they
were barely showing up. If it can't search all the literature, it's still just a
research toy, like "regalur" google (which I use all the time--except for
literature searches).
Here's an example (I'm not being vain, just I know my own work better than anyone else's, naturally):
Dif f ractive optics implementation of six-wave mixing
V Astinov, KJ Kubarych, CJ Milne, RJD Miller - Cited by 10
... Dif f ractive optics implementation of six-wave mixing. ... (050.1970) Diffraction and
gratings : Diffractive optics (300.6450) Spectroscopy : Spectroscopy, Raman. ...
Optics Letters, 2000 - ol.osa.org - adsabs.harvard.edu
OK, so we'll forgive the strange formatting, but "Cited by 10" is totally insane, this paper has 33 citations according to Web of Science. Another paper we did, which has 26 citations according to Web of Science, only garners 5 according to Google:
Diffractive optics-based six-wave mixing: Heterodyne detection of the full χ tensor of liquid CS
KJ Kubarych, CJ Milne, S Lin, V Astinov, RJD … - Cited by 5
... KJ Kubarych, CJ Milne, S. Lin, V. Astinov, RJD Miller. Abstract. This work exploits
the passive phase stabilization of diffractive optics to implement heterodyne ...
The Journal of Chemical Physics, 2002 - link.aip.org - adsabs.harvard.edu
So is Google Scholar a worthwhile tool? I don't know. But I will continue to use it and we will post to the plexus from time to time with thoughts on the usage of this new research tool. I use normal pleb google all the time, even for non-pleb science stuff, so we can only hope that "scholar" will become something usefull. In any case, if your school can't front the cash for the journals, you're not going to benefit from this new search tool—other than to feel crappy knowing that so many other institutions have much more access than you do. Personally, I suspect that google scholar will further perpetuate the Nature/Science/PNAS/PRL mythology for us physical scientists—what it does for you "other" folk, I don't know.
Here's an example (I'm not being vain, just I know my own work better than anyone else's, naturally):
Dif f ractive optics implementation of six-wave mixing
V Astinov, KJ Kubarych, CJ Milne, RJD Miller - Cited by 10
... Dif f ractive optics implementation of six-wave mixing. ... (050.1970) Diffraction and
gratings : Diffractive optics (300.6450) Spectroscopy : Spectroscopy, Raman. ...
Optics Letters, 2000 - ol.osa.org - adsabs.harvard.edu
OK, so we'll forgive the strange formatting, but "Cited by 10" is totally insane, this paper has 33 citations according to Web of Science. Another paper we did, which has 26 citations according to Web of Science, only garners 5 according to Google:
Diffractive optics-based six-wave mixing: Heterodyne detection of the full χ tensor of liquid CS
KJ Kubarych, CJ Milne, S Lin, V Astinov, RJD … - Cited by 5
... KJ Kubarych, CJ Milne, S. Lin, V. Astinov, RJD Miller. Abstract. This work exploits
the passive phase stabilization of diffractive optics to implement heterodyne ...
The Journal of Chemical Physics, 2002 - link.aip.org - adsabs.harvard.edu
So is Google Scholar a worthwhile tool? I don't know. But I will continue to use it and we will post to the plexus from time to time with thoughts on the usage of this new research tool. I use normal pleb google all the time, even for non-pleb science stuff, so we can only hope that "scholar" will become something usefull. In any case, if your school can't front the cash for the journals, you're not going to benefit from this new search tool—other than to feel crappy knowing that so many other institutions have much more access than you do. Personally, I suspect that google scholar will further perpetuate the Nature/Science/PNAS/PRL mythology for us physical scientists—what it does for you "other" folk, I don't know.
Posted at 12:08 AM Read More |
Mon - November 22, 2004
The Jesus Lizard
Heard on this week on CBC Radio's weekly science show, Quirks and Quarks, is a truly
amazing story about how the Basilisk lizard walks on water. You can find more
links, and most importantly the audio of the broadcast on the November 20, 2004
archive page.
Image source: S. Tonia Hsieh
Image source: S. Tonia Hsieh
Posted at 06:28 PM Read More |
Thu - November 18, 2004
Tool: Virtual Journal of Biological Physics Reserach
Tools will be a recurring feature on the plexus.
These are things that lend aid to those seeking interdiscipline. The first one
is a kind of meta journal where papers are listed that are relevant to a certain
topic—in this case biological physics—and you download them through
this edited list. Of course, you must have a subscription to the journal, or
your university/company has to have one. I realize that this is pretty useless
for anyone who doesn't have this access. The editor is none other than Robert H. Austin, by far
one of the most entertaining and irreverent scientists I've ever
read.
The Virtual Journal of Biological Physics Research has papers ranging from reviews to letters, from liquid theory to microscope instrumentation, and lots of proteins, and you better believe that they're a-foldin'. This thing oozes interdiscipline. In fact, I can be much lazier now that I have found this VJ since I had already downloaded about a dozen papers on the list, but I had to do it at each site separately.
The Virtual Journal of Biological Physics Research has papers ranging from reviews to letters, from liquid theory to microscope instrumentation, and lots of proteins, and you better believe that they're a-foldin'. This thing oozes interdiscipline. In fact, I can be much lazier now that I have found this VJ since I had already downloaded about a dozen papers on the list, but I had to do it at each site separately.
Posted at 11:10 PM Read More |
Wed - November 17, 2004
Femtoreview: A Century of Nature: Twenty-One Discoveries that Changed the World
Living, as we do, in Paris, France, my wife and I
have a hard time finding good English language science books. We do find them
every once in a while at W. H. Smith, but we were spoiled as grad students where
we had a really killer campus bookstore. Anyway, on a recent trip back to
Canada, we stopped into another campus bookstore
and—comment
dire?—pigged out. If I can get through
some of the other books, I'll do Femtoreviews of them
too.
The first book is called A Century of Nature: Twenty-One Discoveries that Changed the World, edited by Laura Garwin, Tim Lincoln, and Steven Weinberg. The editors have chosen 21 papers from the prestigious journal, Nature, and they reproduce each one with an introductory commentary written by someone important in the field.
OK, now it's always problematic when people make lists of Best this or Worst Dressed that. That said, David Letterman is living proof that people cannot get enough of these lists. We will count ourselves among their number and submit willfully to the pleasures of this great little book.
Anyway, what struck me as particularly amusing while I was reading this book was how short were the actual articles and how long were the commentaries. For example, the paper by Ted Maiman about the first laser was about one page in the book, while Charles Townes' goes on for pages. The other thing that was striking, was how non-used-car-salesman the old articles were. Today, even the most boring methods paper has to be written like it will change the course of history. Here we have some papers that actually did change the course of history, and they are written with cold detachment.
I am not going to tell you what I think about all the papers, there are 21 of them, and they range in understandability, while the commentaries are all very well-written and clear for a typical scientist. I'm not sure how enjoyable this book would be for a non-scientist, though. Maybe for them, they could consider the real papers as museum artifacts: to be appreciated, but let's face it, the little description of the thing is all you really need to know. The commentaries provide enough of a challenge.
I would like to point out a couple highlights:
- Davisson and Germer experiment: by far one of the coolest mistakes in science, and their description is terrific.
- Myoglobin: paper by Kendrew et al. Started it all, and with Perutz, put the LMB in a special place in the history of science. Our children will look back on this work in awe (assuming they do science!). The work required to solve the structure is so astronomically more difficult than anything people do today, it will blow your mind. Put another way: they used the first computer to help them analyze the data.
- First laser: if the number of popular science books about a subject correlated in any way to the subject's importance in our lives (or even in science), you would think that we scan groceries and send information over the internet using String Theory. Alas, this knotty notion of "physics" is so insanely oversold, I can't even stand it anymore. Even if it turns out to be "right," it's irrelevant because you have to be a freak of nature to understand all the math (and that comes from someone who is not at all unhappy in Liouville space). That said, lasers are important, they embody quantum mechanics, uncertainty and all that other jazz that purchasers of Brian Greene and, ahem, Steven Weinberg, so crave. For whatever reason, there are a hundred books on String Theory, and like two on lasers. The difference? Laser are real, testable, and useful. Hmm. This one-page paper by Maiman is worth fifty on String Theory.
- MRI: read the paper, then revisit the controversy. I guess that was last year's controversy. Anyway, you can see for yourself, on the Nobel website. Lauterbur is a clever man, a great orator, however, he is not.
- Bunch of important biological things. I hope to understand them better (that's one of the points of this site).
This book should be on your shelf. You can show the articles to students or colleagues. You'd be surprised how many people don't bother to read the original papers in their field.
I would like to start the list of papers that didn't make the cut with the following:
C. V. Raman and K. S. Krishnan, Nature 121 (1928) 501: "A New Type of Secondary Radiation"
(note that the discovery of the Raman effect predated that of the laser by 32 years.)
The first book is called A Century of Nature: Twenty-One Discoveries that Changed the World, edited by Laura Garwin, Tim Lincoln, and Steven Weinberg. The editors have chosen 21 papers from the prestigious journal, Nature, and they reproduce each one with an introductory commentary written by someone important in the field.
OK, now it's always problematic when people make lists of Best this or Worst Dressed that. That said, David Letterman is living proof that people cannot get enough of these lists. We will count ourselves among their number and submit willfully to the pleasures of this great little book.
Anyway, what struck me as particularly amusing while I was reading this book was how short were the actual articles and how long were the commentaries. For example, the paper by Ted Maiman about the first laser was about one page in the book, while Charles Townes' goes on for pages. The other thing that was striking, was how non-used-car-salesman the old articles were. Today, even the most boring methods paper has to be written like it will change the course of history. Here we have some papers that actually did change the course of history, and they are written with cold detachment.
I am not going to tell you what I think about all the papers, there are 21 of them, and they range in understandability, while the commentaries are all very well-written and clear for a typical scientist. I'm not sure how enjoyable this book would be for a non-scientist, though. Maybe for them, they could consider the real papers as museum artifacts: to be appreciated, but let's face it, the little description of the thing is all you really need to know. The commentaries provide enough of a challenge.
I would like to point out a couple highlights:
- Davisson and Germer experiment: by far one of the coolest mistakes in science, and their description is terrific.
- Myoglobin: paper by Kendrew et al. Started it all, and with Perutz, put the LMB in a special place in the history of science. Our children will look back on this work in awe (assuming they do science!). The work required to solve the structure is so astronomically more difficult than anything people do today, it will blow your mind. Put another way: they used the first computer to help them analyze the data.
- First laser: if the number of popular science books about a subject correlated in any way to the subject's importance in our lives (or even in science), you would think that we scan groceries and send information over the internet using String Theory. Alas, this knotty notion of "physics" is so insanely oversold, I can't even stand it anymore. Even if it turns out to be "right," it's irrelevant because you have to be a freak of nature to understand all the math (and that comes from someone who is not at all unhappy in Liouville space). That said, lasers are important, they embody quantum mechanics, uncertainty and all that other jazz that purchasers of Brian Greene and, ahem, Steven Weinberg, so crave. For whatever reason, there are a hundred books on String Theory, and like two on lasers. The difference? Laser are real, testable, and useful. Hmm. This one-page paper by Maiman is worth fifty on String Theory.
- MRI: read the paper, then revisit the controversy. I guess that was last year's controversy. Anyway, you can see for yourself, on the Nobel website. Lauterbur is a clever man, a great orator, however, he is not.
- Bunch of important biological things. I hope to understand them better (that's one of the points of this site).
This book should be on your shelf. You can show the articles to students or colleagues. You'd be surprised how many people don't bother to read the original papers in their field.
I would like to start the list of papers that didn't make the cut with the following:
C. V. Raman and K. S. Krishnan, Nature 121 (1928) 501: "A New Type of Secondary Radiation"
(note that the discovery of the Raman effect predated that of the laser by 32 years.)
Posted at 05:03 PM Read More |
Tue - November 16, 2004
Profile: Janet Rossant
For the first installment in the celebrity
scientist profiles, I decided to head back up north, to Canada. This is the
beautiful country where I did my PhD, and they are not sufficiently
recognized.
Biography [from ISI Highly Cited]
Janet Rossant
Born: UK
Citizenship: Canada, UK
FRS, FRSC
PhD: Cambridge University, 1976 in Mammalian development
BA: Oxford in Zoology
Image source: CIHR
Career Path:
Postdoc: Oxford (1975-1977)
Assist. Prof.: Brock University, Biological Sciences (1977-1981)
Assoc. Prof.: Brock University, Biological Sciences (1981-1985)
Adjunct Prof.: McMaster University, Pathology (1981-1985)
Assoc. Prof.: University of Toronto, Medical Genetics (1985-1988)
Senior Investigator: Samuel Lunenefeld Research Institute (1985-Present)
Prof.: University of Toronto, Molecular and Medical Genetics (1988-Present)
Joint Head: Samuel Lunenefeld Research Institute, Program in Development and Fetal Health (1994-2002)
Prof.: University of Toronto, Obstetrics and Gynecology (1995-Present)
University Prof.: University of Toronto (2001-Present)
She has a full armoire of awards.
Here's her research description from the ISI Highly Cited page:
My research interests centre on understanding the genetic control of normal and abnormal development in the early mouse embryo using both cellular and genetic manipulation techniques. Recently, my research has moved in two new directions. First, stem cell research, with the discovery of a novel placental stem cell type, the trophoblast stem cell. Second, genome-wide functional genomics. I direct the Centre for Modelling Human Disease in Toronto, which is undertaking genome-wide mutagenesis in mice to develop new mouse models of human disease.
The unparalleled CBC Radio program Quirks and Quarks (which we will be linking to habitually) had Dr. Rossant on the show December 1, 2001 following the announcement by Advanced Cell Technology (ACT) that they had succeeded in cloning a human embryo. I know that is a little out of date given the recent work by the Korean group, but it's nice if you're just getting into stem cells (intersections, right?).
Dr. Rossant's most cited paper is called "Failure of blood-island formation and vasculogenesis in Flk-1 deficient mice" (F. Shalaby, et al, Nature, 376 (1995) 62-66). 1353 citations.
This paper looks at what happens when you generate mice that lack the gene encoding a protein necessary for the formation of blood vessels. The receptor, tyrosine kinase Flk-1 binds vascular endothelial growth factor (VEGF). You can read more about this receptor ligand pair here. Dr. Rossant's group found that the mice lacking the gene were unable to make blood vessels and the ingredients necessary for haematopoiesis (also hematopoiesis)—making blood cells—were also greatly reduced. The method they used to make these mice is known as homologous recombination.
The x-ray structure of the Flt-1/VEGF complex is available on from the Protein Data Bank (PDB) under the code 1FLT.
According to this blurb on the website for the International Vascular Biology Meeting:
...[H]er research has moved to two new directions. First, stem cell research, with her discovery of a novel placental stem cell type, the trophoblast stem cell and second, genome-wide functional genomics. She directs the Centre for Modeling Human Disease in Toronto, which is undertaking genome-wide mutagenesis in mice to develop new mouse models of human disease. Her work has had major influences in developmental biology, stem cells and cell lineage.
...Dr. Rossant has been a pioneer in the use of chimeric mouse embryos, embryonic stem cells, in situ markers and lineage specific ablation strategies to effectively study developmental processes and analyze mutants. Her laboratory was first to demonstrate that murine embryonic stem cells can alone give rise to an intact mouse.
So, that's a nice intro to a very successful scientist, and I hope you find enough links to things you don't know much about—I had no idea what half these words meant before putting together this post. That's a really big problem with biology from a physical science point of view: it's so much vocabulary and not all of it can be derived from having a good handle on etymology. Fortunately, Google solves almost all the problems of translation.
Finally, can stem cells be any hotter? They were even debated during the presidential election.
Biography [from ISI Highly Cited]
Janet Rossant
Born: UK
Citizenship: Canada, UK
FRS, FRSC
PhD: Cambridge University, 1976 in Mammalian development
BA: Oxford in Zoology
Image source: CIHR
Career Path:
Postdoc: Oxford (1975-1977)
Assist. Prof.: Brock University, Biological Sciences (1977-1981)
Assoc. Prof.: Brock University, Biological Sciences (1981-1985)
Adjunct Prof.: McMaster University, Pathology (1981-1985)
Assoc. Prof.: University of Toronto, Medical Genetics (1985-1988)
Senior Investigator: Samuel Lunenefeld Research Institute (1985-Present)
Prof.: University of Toronto, Molecular and Medical Genetics (1988-Present)
Joint Head: Samuel Lunenefeld Research Institute, Program in Development and Fetal Health (1994-2002)
Prof.: University of Toronto, Obstetrics and Gynecology (1995-Present)
University Prof.: University of Toronto (2001-Present)
She has a full armoire of awards.
Here's her research description from the ISI Highly Cited page:
My research interests centre on understanding the genetic control of normal and abnormal development in the early mouse embryo using both cellular and genetic manipulation techniques. Recently, my research has moved in two new directions. First, stem cell research, with the discovery of a novel placental stem cell type, the trophoblast stem cell. Second, genome-wide functional genomics. I direct the Centre for Modelling Human Disease in Toronto, which is undertaking genome-wide mutagenesis in mice to develop new mouse models of human disease.
The unparalleled CBC Radio program Quirks and Quarks (which we will be linking to habitually) had Dr. Rossant on the show December 1, 2001 following the announcement by Advanced Cell Technology (ACT) that they had succeeded in cloning a human embryo. I know that is a little out of date given the recent work by the Korean group, but it's nice if you're just getting into stem cells (intersections, right?).
Dr. Rossant's most cited paper is called "Failure of blood-island formation and vasculogenesis in Flk-1 deficient mice" (F. Shalaby, et al, Nature, 376 (1995) 62-66). 1353 citations.
This paper looks at what happens when you generate mice that lack the gene encoding a protein necessary for the formation of blood vessels. The receptor, tyrosine kinase Flk-1 binds vascular endothelial growth factor (VEGF). You can read more about this receptor ligand pair here. Dr. Rossant's group found that the mice lacking the gene were unable to make blood vessels and the ingredients necessary for haematopoiesis (also hematopoiesis)—making blood cells—were also greatly reduced. The method they used to make these mice is known as homologous recombination.
The x-ray structure of the Flt-1/VEGF complex is available on from the Protein Data Bank (PDB) under the code 1FLT.
According to this blurb on the website for the International Vascular Biology Meeting:
...[H]er research has moved to two new directions. First, stem cell research, with her discovery of a novel placental stem cell type, the trophoblast stem cell and second, genome-wide functional genomics. She directs the Centre for Modeling Human Disease in Toronto, which is undertaking genome-wide mutagenesis in mice to develop new mouse models of human disease. Her work has had major influences in developmental biology, stem cells and cell lineage.
...Dr. Rossant has been a pioneer in the use of chimeric mouse embryos, embryonic stem cells, in situ markers and lineage specific ablation strategies to effectively study developmental processes and analyze mutants. Her laboratory was first to demonstrate that murine embryonic stem cells can alone give rise to an intact mouse.
So, that's a nice intro to a very successful scientist, and I hope you find enough links to things you don't know much about—I had no idea what half these words meant before putting together this post. That's a really big problem with biology from a physical science point of view: it's so much vocabulary and not all of it can be derived from having a good handle on etymology. Fortunately, Google solves almost all the problems of translation.
Finally, can stem cells be any hotter? They were even debated during the presidential election.
Posted at 12:36 PM Read More |
Mon - November 15, 2004
Rough outline of the plexus
There are a few things I want to do with this blog.
One of them is to put down my thoughts about things I read relating to science
and to my formation as an interdisciplined researcher. To motivate this, I'm
going to do profiles of well-known and not-so-well known (but very successful)
scientists in hopes of discovering some of the organizing principles of doing
science well.
I will draw on two main sources for this on-going investigation. The first is the list of Nobel laureates. There is no question that the single most visible side of science is how we award our most prominent members. I bet people who only watch two movies all year still tune into the Academy Awards. I know that the Nobel is a very political prize—and maybe we can get into that—but it is still the clearest way to find truly exceptional scientists. And many of them are or were very well interdisciplined.
The second source is far less well-known outside of the professional science community, and even then I'm not so sure if people are aware of this. It's from the people who do the Web of Science, and it's called ISI Highly Cited. The first time I read that, I thought it was a joke since I read it as sort of scientific street slang: "Yo, check it: is I highly cited?" Then I realized that it wasn't another instance of Ali G infiltrating further into our inner sanctums.
These profiles will be listed under the, er, "Profiles" category.
I will draw on two main sources for this on-going investigation. The first is the list of Nobel laureates. There is no question that the single most visible side of science is how we award our most prominent members. I bet people who only watch two movies all year still tune into the Academy Awards. I know that the Nobel is a very political prize—and maybe we can get into that—but it is still the clearest way to find truly exceptional scientists. And many of them are or were very well interdisciplined.
The second source is far less well-known outside of the professional science community, and even then I'm not so sure if people are aware of this. It's from the people who do the Web of Science, and it's called ISI Highly Cited. The first time I read that, I thought it was a joke since I read it as sort of scientific street slang: "Yo, check it: is I highly cited?" Then I realized that it wasn't another instance of Ali G infiltrating further into our inner sanctums.
These profiles will be listed under the, er, "Profiles" category.
Posted at 04:52 PM Read More |
the plexus — a new science-centric blog
Shine a laser at a protein, and it may very well
react in some way--it might change shape, or something might pop off of it. Run
a gel and extract a mutated protein that has a totally different enzymatic
activity than the wild type. Pull a coiled DNA segment and you just might be
able to measure the microscopic forces using a very unmicroscopic microscope.
Compute a molecular dynamics simulation of a protein bound to a stretch of DNA
and you might learn something about translation factors.
Who are you in each of these scenarios? I think we all know the canonical answers. Physicists use lasers, don't they?
Science is arcane, and is now more hyperspecialized than ever. I see no signs of any abatement, either. It is obvious to me, however, that the most interesting discoveries are taking place at the overlaps and intersections between historically disparate disciplines. Another word for this is "plexus":
plex•us n. pl. pelxus or plex•us•es
1. A structure in the form of a network, especially of nerves, blood vessels, or lymphatics: the cardiac plexus; the pelvic plexus.
2. A combination of interlaced parts; a network.
[New Latin, from Latin, braid, from the past participle of plectere, to plait, See also plek- in Indo-European Roots.]
I hope to make the plexus a blog that takes a look at how the sciences are intermingling. Sometimes there will be questions, sometimes advice. I also intend to put my own fully unformed thoughts about papers and research topics I find interesting. We are taught scientific "discipline" very well in our education system, but it seems as though we need to teach ourselves interdiscipline.
So there you have it: the plexus, a blog for scientific interdiscipline.
Wish me luck!
Who are you in each of these scenarios? I think we all know the canonical answers. Physicists use lasers, don't they?
Science is arcane, and is now more hyperspecialized than ever. I see no signs of any abatement, either. It is obvious to me, however, that the most interesting discoveries are taking place at the overlaps and intersections between historically disparate disciplines. Another word for this is "plexus":
plex•us n. pl. pelxus or plex•us•es
1. A structure in the form of a network, especially of nerves, blood vessels, or lymphatics: the cardiac plexus; the pelvic plexus.
2. A combination of interlaced parts; a network.
[New Latin, from Latin, braid, from the past participle of plectere, to plait, See also plek- in Indo-European Roots.]
I hope to make the plexus a blog that takes a look at how the sciences are intermingling. Sometimes there will be questions, sometimes advice. I also intend to put my own fully unformed thoughts about papers and research topics I find interesting. We are taught scientific "discipline" very well in our education system, but it seems as though we need to teach ourselves interdiscipline.
So there you have it: the plexus, a blog for scientific interdiscipline.
Wish me luck!
Posted at 03:46 PM Read More |
Calendar
| Sun | Mon | Tue | Wed | Thu | Fri | Sat |
Categories
Archives
XML/RSS Feed
Comments powered by
Statistics
Total entries in this blog:
Published On: Jul 18, 2005 04:17 PM
Published On: Jul 18, 2005 04:17 PM
