Author: jlolds

Native Angeleno, professor of Neuroscience and Public Policy at George Mason University

Whole genome strategies for brain diseases

I’ve linked to a list of recent articles using a whole genome approach to studying diseases. Essentially this is a classic example of the post-Popperian approach to biomedical research–rather than treat the question as a detective story, carefully putting together a series of hypotheses to test a theory, we instead simply “print” out all of the genetic information and see what’s different. Of course is the case of many brain diseases this may obscure the role for the environment in the etiologies…but the advocates of this industrial style of science are gaining a good deal of strength (look at the journals where these article are published).

I do see a tremendous utility in such research from the standpoint of adding new potential therapeutic targets and also giving us clues outside a disease’s conventional dogma.

In the meantime, happy 2007.

Jim

The Neuroscience of Music

In today’s Sunday NYT: a very interesting portrait of neuroscientist Daniel Levitin (one of several neuroscientists with a real musical background) on his theory of how our brains are wired to enjoy music. Some of it is a bit far fetched, but it’s intriguing nonetheless.

Money quote:

This summer he published “This Is Your Brain on Music” (Dutton), a layperson’s guide to the emerging neuroscience of music. Dr. Levitin is an unusually deft interpreter, full of striking scientific trivia. For example we learn that babies begin life with synesthesia, the trippy confusion that makes people experience sounds as smells or tastes as colors. Or that the cerebellum, a part of the brain that helps govern movement, is also wired to the ears and produces some of our emotional responses to music. His experiments have even suggested that watching a musician perform affects brain chemistry differently from listening to a recording.

This is the last blogpost here for 2006. Happy New Year to all of my readers and we’ll look forward to a productive 2007.

Jim

Some items for the New Year

With the new year soon upon us, I thought I would telegraph some of the significant events for the next semester. I'll be off to the the SICB meeting in Phoenix in the first week of January to chair the editorial board meeting for The Biological Bulletin. I'll try to take some pictures from the road and post them (although I suspect my digital images from trips to Austria and China later in the year will be more interesting). Then on January 11 and 12, the Institute will hold its annual scientific retreat, this year organized by Professor Layne Kalbfleisch. I've written about the retreat before–it's a chance for all of us to get together to talk about our scientific research off-site. In future years, we'll be moving the retreat to the end of the Spring semester, to allow us to coordinate overlap with the Institute's two advisory boards.

Also during January we'll be interviewing candidates for the various PI searches that are on-going. I'm looking forward to meeting with the finalists. These interviews will continue into February. The anticipation is that there will be three new PI's joining the Institute at the beginning of next academic year.

Later in the Spring, we'll be hosting the Decade of the Mind Symposium. The keynote speaker list looks spectacular. More about that later.

Jim

End of the semester

Today marks the last day of the Fall semester. For me, the high point
has been the remarkable scientific productivity among our PI's and
the tremendous dedication of our wonderful support staff. But the
success at Krasnow is really, more than anything else, a team effort:
our graduate students, postdocs and external advisory board members
have also contributed mightily to the dynamism and scientific
excitement at this Institute…12 miles perhaps (as the bird flies)
from the U.S. Congress that ultimately supports so much of our work
and 100 holiday seasons since the seminal Nobel Prize of Cajal that
serves so many of us as inspiration.

Jim

Dissertation III: How much do you own your work?

One common tension in the thesis work is the often unstated conflict between the major professor’s view on ownership versus that of the graduate student. As a matter of fact, the graduate student author generally holds copyright on the words and figures in the thesis; the major professor is generally viewed as owning the data and having rights to senior authorship on the resultant publications. However there are many complexities involved and any real understanding of the issues (at least in the biosciences) must be nuanced.

From my viewpoint, the stumbling block often really lies with the question of who has the right to pursue future follow-on research resulting from the thesis (the graduate student or the major professor). The newly minted Ph.D. understandably feels that she or he has done the experiments, has become the world’s expert on that small area of science , has just completed a tome (i.e. the thesis) on the subject and therefore has the rights to the future research based on the thesis findings.

However, in a typical NIH-funded lab, in my opinion, the PI owns the actual raw data (not the graduate student) and it is generally assumed that the intellectual kernel of the thesis came from the PI (at least as much as from the graduate student). This is less clear in the case of non-federally funded research of course.

The key is that the thread of research in the thesis usually exists within the larger context of that of the major professor and his/her laboratory. Thus the argument is made that the follow-on research stays within that larger context of the PI’s lab while the graduate student goes on to different (and hopefully more interesting) projects during the postdoctoral years.

In practice, conflicts have usually been resolved in favor on the major professor as opposed to the graduate student.

So my recommendation is: enjoy the very real ownership of your dissertation itself…and look forward to all the future science you can do, once you are an independent investigator.

Jim

The dissertation: II

Today I’m going to write about the choice of the thesis project. This is nominally a collaborative choice between graduate student and mentor, although in the sciences, it’s often really the province of the dissertation advisor. The fundamental reason for this is that there are no givens in scientific research–it’s not cookbook. Essentially, the success of the thesis project is somewhat stochastic, although with expertise this can be minimized.

Thus, ultimately one of the most important criteria for choosing a major professor, is their ability to pick good dissertation projects. And typically professors become better at picking projects as they gain experience with supervising dissertations. Hence, one of the principle disadvantages of choosing a newly-minted assistant professor relates to the possibility that they might pick a very bad thesis project.

So what makes a good thesis project? First, I believe that it should have a very high probability of yielding publishable results no matter which way the experiments turn out. At the same time, it should be very much hypothesis-driven. At first, this might sound like a paradox. But at least in the biosciences, this is often true (most successful NIH RO1 applications are designed this way).

The second very important characteristic, is that the entire experimental scope of the thesis experiments should be able to be conducted within a reasonably compact period of time. It’s a bad thesis project that wont get its first pilot data for five or so years (think longitudinal studies such as the famous Framingham Project on blood pressure).

It’s also very important to have the experiments manifest practicality. If getting your data requires space on a mission to Saturn–something your proposed advisor has no experience with, then probably something is very wrong with the choice of thesis project (not to mention that the trip to Saturn will take a bit of time).

Finally, I always believe that there should be some aspects of a thesis project that can be “cut out” from the professor’s research program and published potentially independently by the graduate student. As an example, one of my students has such a chapter in his thesis where he developed a new computational methodology for solving differential equations in neuroscience simulations. This is a topic that might be easily “cut out” into a separate paper from his thesis as a single author unit. The advantage with this strategy is that it gives the trainee early evidence of independence–something that will be crucial for career advancement later.

Jim

The dissertation: I

Over the next several posts, I’ll put forward some of my ideas about what a successful science thesis should encompass. First some general comments:

The dissertation or thesis is of course the culmination of a graduate students work towards the Ph.D. degree. For the sciences, in general we are looking for original and potentially publishable work. That the work could be published (and usually will be) implies that it advances scientific knowledge in the disciplinary area of the dissertation.

Typically, the research leading up to the thesis takes on the order of 2-3 years and represents a coherent body of experiments, which taken together, form the basis of the thesis chapters. A thesis also typically includes a comprehensive literature review and a somewhat speculative discussion chapter (often the last time a scientist gets to be reasonably speculative in print until they reach the rank of full professor).

There is some debate as to whether the middle chapters of a thesis should be essentially separable as distinct publishable papers (the staple 4 papers together concept) or whether it’s better to have an integrated tome. I have my opinion on this which I’ll reserve for one of the next posts.

Of course a thesis must be defended–usually including a public seminar given by the degree candidate, and an examination session with the thesis committee where, in some European universities, any question at all is fair game–even if not related to the thesis. In the US the defense is often somewhat pro forma–we basically don’t allow someone to defend if it’s likely that they will fail.

Jim

Washington DC "tis the season"

A strange aspect of living in Washington is how, come the holiday season, the weather turns actually winter-like (as if on cue) and how there seem to be an endless stream of holiday parties that successively pile up on the days as if they were storm waves crashing up on a beach. So it is this year living along side the Potomac River.

I gave a talk yesterday on artificial intelligence–a topic that I get asked about quite a bit, but one that I’ve always felt somewhat removed from, given my own work in neuroscience. And yet, the field of AI has made great strides since Marvin Minsky–although my take is we’re not anywhere near the “strong AI” that was sold last century. One way new way to think about AI I suppose may be to go beyond the Turing Test towards some deeper understanding of our own consciousness and what it means to be self-aware.

And so we return to the topic of studying consciousness and the mind–which is the raison d’etre of the Krasnow Institute for Advanced Study.

Happy Holidays,
Jim

NIH to allow multiple PI’s on grants

This is pretty big news for those of us who collaborate extensively:

Money quote:

Beginning with research grant applications submitted for February 2007 receipt dates, the NIH will allow applicants and their institutions to identify more than one Principal Investigator (PI). The Multiple PI option will be extended to most research grant applications submitted electronically through Grants.gov (http://www.grants.gov/) using the SF424 R&R application package. Grant applications that will accommodate more than one PI beginning in February include: R01, R03, R13/U13, R15, R18/U18, R21, R21/R33, R25, R33, R34, R41, R42, R43, R44, and C06/UC6 (see http://era.nih.gov/ElectronicReceipt/strategy_timeline.htm). Some types of applications including individual career awards (K08, K23, etc.), individual fellowships (F31, F32, etc.), Dissertation Grants (R36), Director’s Pioneer Awards (DP1), and Shared Instrumentation Grants (S10) will not accommodate more than a single PI. The restriction to a single PI will be described in announcements for those programs.