New Deep-Sea Hydrothermal Vents, Life Form Discovered

A new "black smoker"--an undersea mineral chimney emitting hot springs of iron-darkened water--has been discovered at 8,500-foot depths by an expedition funded by the National Science Foundation (NSF) to explore the Pacific Ocean floor off Costa Rica.

Scientists from Duke University, the Universities of New Hampshire and South Carolina, and the Woods Hole Oceanographic Institution in Massachusetts have named their discovery the Medusa Hydrothermal Vent Field.

The researchers chose that name to highlight the presence there of a unique pink form of the jellyfish order stauromedusae. The jellyfish resemble "the serpent-haired Medusa of Greek myth," said expedition leader Emily Klein, a geologist at Duke University.

The bell-shaped jellyfish sighted near the vents may be of a new species "because no one has seen this color before," said Karen Von Damm, a geologist at the University of New Hampshire.

According to Von Damm, stauromedusae are usually found away from high-temperature hydrothermal vents, where the fluids are a little bit cooler, not close to the vents as these are.

Aboard the Research Vessel (R/V) Atlantis, the researchers are studying ocean floor geology of the East Pacific Rise, one of the mid-ocean ridge systems where new crust is made as the earth spreads apart to release molten lava.

"Each new vent site has the potential to reveal new discoveries in interactions between hot rocks beneath the seafloor, the fluids that interact with those rocks and the oceans above, as well as a rich biosphere that depends on vent processes," said Adam Schultz, program director in NSF's Division of Ocean Sciences, which funded the expedition through its Ridge 2000 program. "This discovery has implications for understanding the origin of Earth's crust, its evolution over time and how living organisms adapt to extreme environmental conditions."

Jason II, a remotely-controlled robotic vehicle the scientists are using to probe the vent field, logged water temperatures of 330 degrees Celsius (626 degrees Fahrenheit) at the mouth of one of the vents. Jason II subsequently found a second vent about 100 yards away.

Von Damm said that heat-tolerant tubeworms found living on Medusa's chimneys, a type known as alvinellids, are commonplace in the equatorial Pacific and thrive on high-iron fluids. Jason also has retrieved two other types of tubeworms--tevnia and riftia--from the vent area.

In addition, the camera-studded robot, which can collect biological specimens with the aid of the mechanical arms it uses to remove rock samples, has gathered samples of mussels from the vent area.

According to Von Damm, wherever there are mid-ocean ridges, scientists frequently find geothermal vents warmed by heat energy from underlying volcanic conduits.

"Each new vent sparks fresh excitement, because each one is different. Every vent has a different chemistry, and that helps us understand the processes going on in the ocean crust. Each one gives us a different piece of the puzzle," Von Damm said.

More than 500 new species have been found at vents since they were first discovered in 1977.

"After looking at relatively barren lava flows for several days on this expedition," said geologist Scott White of the University of South Carolina, "we all knew it would be special when we found creatures living at this new vent field."

Vigorous Exercise Keeps People Thin with Age

The old adage “use it or lose it” is truer than ever. People who maintain a vigorously active lifestyle as they age gain less weight than people who exercise at more moderate levels, according to a first-of-its-kind study that tracked a large group of runners who kept the same exercise regimen as they grew older.

The study also found that maintaining exercise with age is particularly effective in preventing extreme weight gain, which is associated with high blood pressure, high cholesterol, diabetes, and other diseases.

The study, conducted by Paul Williams of the U.S. Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab), followed 6,119 men and 2,221 women who maintained their weekly running mileage (to within three miles per week) over a seven-year period. On average, the men and women who ran over 30 miles per week gained half the weight of those who ran less than 15 miles per week.

“To my knowledge, this is the only study of its type,” says Williams, a staff scientist in Berkeley Lab’s Life Sciences Division. “Other studies have tracked exercise over time, but the majority of people will have changed their exercise habits considerably.”

The research is the latest report from the National Runners' Health Study, a 20-year research initiative started by Williams that includes more than 120,000 runners. It appears in the May 3 issue of the journal Medicine and Science in Sports and Exercise.

Specifically, between the time subjects entered the study and when they were re-contacted seven years later, 25-to-34-year-old men gained 1.4 pounds annually if they ran less than 15 miles per week. In addition, male runners gained 0.8 pounds annually if they ran between 15 and 30 miles per week, and 0.6 pounds annually if they ran more than 30 miles per week.

This trend is mirrored in women. Women between the ages of 18 and 25 gained about two pounds annually if they ran less than 15 miles per week, 1.4 pounds annually if they ran 15 to 30 miles per week, and slightly more than three-quarters of a pound annually if they ran more than 30 miles per week. Other benefits to running more miles each week included fewer inches gained around the waist in both men and women, and fewer added inches to the hips in women.

“As these runners aged, the benefits of exercise were not in the changes they saw in their bodies, but how they didn’t change like the people around them,” says Williams.

Although growing older and gaining weight is something of a package deal, it isn’t the same in everyone. The lucky few remain lean as they age, most people pack on several pounds, and some people become obese. The latter group is particularly at risk for high blood pressure, high cholesterol, and diabetes. Fortunately, Williams’ results show that maintaining exercise can combat such extreme weight gain.

“Getting people to commit to a vigorously active lifestyle while young and lean will go a long way to reducing the obesity epidemic in this country,” says Williams.

Another paper published in the November 2006 issue of the journal Obesity by Williams and Paul Thompson of Hartford (CT) Hospital found that runners who increased their running mileage gained less weight than those who remained sedentary, and runners that quit running became fatter.

“The time to think about exercise is before you think you need it,” says Williams. “The medical journals are full of reports on how difficult it is to regain the slenderness of youth. The trick is not to get fat.”

Williams’ research was funded by the National Heart, Lung and Blood Institute. The May 3 paper in the journal Medicine and Science in Sports and Exercise is entitled Maintaining Vigorous Activity Attenuates 7-yr Weight Gain in 8,340 Runners.

Berkeley Lab is a U.S. Department of Energy national laboratory located in Berkeley, California. It conducts unclassified scientific research and is managed by the University of California.

Is the Brain a Spintronic Device?

Is the Brain a Spintronic Device?

Spintronics is a new paradigm of electronics based on the spin degree of freedom of the electron. Either adding the spin degree of freedom to conventional charge-based electronic devices or using the spin alone has the potential advantages of nonvolatility, increased data processing speed, decreased electric power consumption, and increased integration densities compared with conventional semiconductor devices.

All spintronic devices act according to the simple scheme: (1) information is stored (written) into spins as a particular spin orientation (up or down), (2) the spins, being attached to mobile electrons, carry the information along a wire, and (3) the information is read at a terminal. Spin orientation of conduction electrons survives for a relatively long time (nanoseconds, compared to tens of femtoseconds during which electron momentum decays), which makes spintronic devices particularly attractive for memory storage and magnetic sensors applications, and, potentially for quantum computing where electron spin would represent a bit (called qubit) of information.

Given the incredible intricacies of the brain's ultrastructure and the billions of years it has had to evolve, it is certainly conceivable that the brain may utilize spintronics. Of course, any talk of quantum mechanical effects in the brain is often greeted with scepticism, thanks to the shameless shenanigans of Roger Penrose and Stuart Hameroff involving Bose-Einstein condensates and microtubules. However, there may be a role for quantum mechanical effects in neural computation yet, and it may be spintronics. The idea is speculative, but definitely worth further consideration, bearing in mind that one potential problem with spintronics is whether spin states are stable long enough to be used in neural computation.

Another Neural Prediction Challenge!

In a previous post, I noted that Jack Gallant had issued a Neural Prediction Challenge. Now, we have another challenge, this time from the Gerstner lab:

Here is our Challenge, open to everybody in in neural modeling, machine learning, or similar fields:

- Is it possible to predict the timing
of every spike that a neuron emits with 2 ms precision?
- Is it possible to predict the subthreshold membrane potential
with a precision of 2 mV for arbitrary input?

Annotated training data and test stimuli from several
cells under different stimulation conditions are available
at
http://icwww.epfl.ch/~gerstner/QuantNeuronMod2007/challenge.html

Important dates
* Data set available by March 16.
* Participants must submit their prediction by June 1st.
* Winner announced around June 10 .
* Winning results will be presented at the workshop June 25/26
Quantitative Neuron Modeling: Predicting every spike?


Competition and Prizes
The competition is organized in several categories, called A,B,C,D.
Participants may run in one or several categories

* 1st prize :

o 4 nights of hotel in Lausanne at the Lake of Geneva,
June 23-27.
o Free participation in the Quantitative Neuron Modeling
workshop June 25/26
o 35-minute-slot for talk as an
Invited Speaker at the workshop.

* 2nd prize:

o Free participation in the
Quantitative Neuron Modeling workshop June 25/26
o Poster presentation and poster spotlight in the workshop.


Methods and Models:
The only aspect that counts for us is the quality of the prediction
on the test set. In terms of methods, anything goes
(Machine learning, compartmental model, integrate-and-fire model,
systems identification etc)



We hope that many people will take up the challenge.
Let the best model win!

Synapse Resolution Whole-Brain Atlases

It is well-known that the highest resolution whole brain atlases are currently at BrainMaps.org, which has been compared to a Google Maps for the brain. However, these atlases are 0.46 microns per pixel, and are not sufficient to discern individual synapses, which require nanometer resolution. So in this post, I will consider the problems associated with constructing a synapse resolution (nanometer resolution) whole-brain atlas.

There seem to be two fundamental hurdles to constructing a synapse resolution whole-brain atlas: 1) image acquisition, and 2) digital technologies for working with the images and serving them over a network.

The first hurdle encompasses the time bottleneck and section preparation. If each section is 50 nm thick, then for a 10 mm mouse brain, 20,000 sections are needed, thus requiring some type of automation for section preparation. If we consider the time to scan a single 10mmx10mm section at 1MHz, it comes out to 46 days, which is unacceptable. Even with 20,000 TEMs (transmission electron microscopes) in parallel, one for each section, it will take 46 days for the complete scan. An alternative is offered by way of virtual microscopy solutions offered for light microscopy. One way would be to scan over the section, acquiring one column at a time instead of a patchwork of small images for montaging. Another alternative would be to construct a TEM with parallel scanning capabilities (having parallel magnetic lenses and electron beams), so that the entire section could be scanned at once, instead of scanning each little image patch in serial. This solution requires constructing a special type of TEM which implements certain features found in current day virtual microscopy systems for LM (light microscopy), and thus requires a team of hardware and software specialists to specially design, in addition to some physicists who are intimately acquianted with the physics behind TEM.

The second hurdle involves digital technologies, and the observation that even if a whole mouse brain was able to be acquired through TEM, that digital technologies currently would not be able to deal with that much data (8 x 10^17 pixels, or 2.4 10^18 megabytes (uncompressed)). A single section is 4 x 10^12 pixels, which comes out to 12 x 10^12 megabytes or 12,000 petabytes (uncompressed), which is still not feasible using today's digital technologies.

Let's consider a less ambitious proposal: TEM montaging of a 1mm x 2mm area at 2.5 nm resolution. TEMs typically acquire images in 2kx2k patches, which means that each patch is 5 microns x 5 microns. So for 2mmx1mm, it's 80,000 patches, and the montaged image size would be 800k x 400k, which is already a problem since there are file format size limitations on common formats like TIFF and JPG, and so to acquire such a large image would necessitate using a non-standard file format, which makes the issue of making the images web accessible more problematic. The largest images, say at BrainMaps.org, are 120k x 100k, which works out to 3 GB as a JPG-compressed TIFF file (or 30 GB uncompressed), and which is already near the limit for the TIFF file format (which is 4 GB), which means that images much exceeding 120k x 100k are already going to present a problem.

In conclusion, for purposes of obtaining information about whole-brain connectivity, a nanometer-resolution whole-brain scan is required, and current-day tracer experiments are suboptimal and will always leave room for ambiguities that can only be resolved by completely mapping every synapse and axon in the brain. However, constructing a synapse resolution (or nanometer resolution) whole-brain atlas for even a mouse brain is so formidable as to be seemingly beyond today's technological capabilities. Maybe in 10-20 years.

Wednesday, February 07, 2007

Pubmed Pet Peeves

Suggestions for the Pubmed developers:

1) Assign a unique author ID so that you can pull up all publications for a given individual as opposed to all individuals who happen to have the same name.

2) Ability to export references to Bibtex format. (Google Scholar does this already).

3) Include number of times cited. (Google Scholar does this also).

What is a Brain Area?

What is a "brain area"? More recently, I have become aware of the inadequateness of the concept of "brain area", or at any rate, to call into question the basis for such a concept. This basis is three-fold, as noted by Felleman/van Essen: cortical areas (or in general, brain areas) are defined by 1) connectivity, 2) functional maps, and 3) chemical or architectonic signatures. However, for the most part, parcellations of the primate (and non-primate) brain have been based on studies using Nissl- or myelin-stained material that are over a century old, and investigators have come up with widely different parcellation schemes for the brain, which in my opinion, is a prominent warning sign that the notion of "cortical area" is ill-defined. Further anatomical studies of the brain have confirmed this point to me. And so, while I recognize the utility to conventionally naming different brain areas on the basis of Nissl-stained material or otherwise, I do not believe we currently possess an adequate conceptual understanding of what really constitutes a "brain area". In early sensori-motor areas, this concept seems applicable since we are talking about mappings from sensory receptor sheets onto the cortex, which get mapped onto well-defined areas of the brain, but other areas of the brain are not like this, and there is no reason a priori to expect that these association and limbic parts of the brain should be nicely parcellated into anything like discrete non-overlapping brain areas.

Part of the problem involves considering useful alteratives to this notion of discrete non-overlapping brain areas which is prevalent in the neuroscience community, and which heavily biases interpretions of experiments. It is largely a conceptual problem, but I am confident that a revolution in our notion of "brain area" will be forthcoming in the near future. Such an overhaul in this precious concept is requisite to a better understanding of the brain.

What I find amusing is that neuroscience textbooks never address this conceptual issue, though it is widely recognized by many prominent neuroscientists as a central problem. This has the peculiar effect that students of neuroscience often learn about their subject, thinking that all of the fundamental conceptual issues have been worked out and that the field of neuroscience rests on a firm foundation. This is not the case, and I would not be surprised if this shaky foundation crumbles, and that many of the "mysteries" of the brain's organization and function, when viewed in a new light and a new foundation, do not seem that mysterious after all, but rather obey a very precise and well-defined logic and reason.

The observation that the concept of "brain area" is ill-defined means, in part, that current attempts to analyze whole-brain connectivity using graph theory are based on incorrect data and incorrect assumptions, since we may legitimately question whether the nodes in the graph have any real meaning. So claims like "the brain is a small-world network" purported by some are empty, and are merely the consequence of following the recent fad in "network science", where anyone and everyone attempts to show that their favorite system is a so-called small-world network. How unoriginal and blase! If only these people could think for themselves instead of parroting the latest fad. The worst part of it is when these people actually publish such nonsense since it misleads other people (usually laymen, but also some neuroscientists) who don't know any better.

She Blinded Me with Science

A dream is a wish your blog makes

I've really let this blog go over the last while, haven't I? There are so many great new blogs out there that I haven't had the chance to link to. First off, I wanted to thank everyone who commented on my DOI post; the tips have made thesis-ing go a tad more smoothly. Second, I wanted to let everyone know what I'll be up to next. Soon, I'll no longer be qualified to write from the point of view of a grad student. I've been offered an Assistant Editor position with Chemical and Engineering News. I'm looking forward to getting started, even though the production schedule will mean that the bloggers will scoop me more often than not. :) It's likely that from now on, I'll be posting from meetings, and in another forum. So for now, "She Blinded Me with Science" will be on an indefinite hiatus, while I format margins, apartment hunt in DuPont Circle, and hone my craft at C&EN.*
I'll leave you with a deconstruction of one of the more hilarious commercials I've seen lately. Go to this link, then click the "see the Zoom! TV commercial" box, and prepare to be blown away.
Choice quotes:
"..an advance so profound, it took a team of scientists years to create."
This was noteworthy because apparently, a lot of scientific advances can be sorted out in a fortnight.
"the patented Zoom! light"
Can you really patent light? Can you forbid, say, the use of the 254nm wavelength without paying extensive royalties? My guess is that they've patented whatever lamp generates the UV light at a controlled intensity that's used in the procedure, but feel free to correct me if I'm wrong.
"breaking down the stains' double bonds"
I love how they threw that in there just to be sciencey. Evidently, the radicals generated by the Fenton reaction (which means the gel contains hydrogen peroxide and some kind of iron or other catalyst) are changing the structure of the stains so they no longer appear colored.

aside: I just did some demonstrations yesterday for 8th graders. Among other things, we bleached shredded carrots (aka, got rid of some of the double bonds.)

I'm really just concerned about the fallout for double bonds everywhere. I hope no one starts a smear campaign. (Double bonds aren't all bad, people! Gleevec's got 'em, hey, even Viagra's got 'em.)

Lastly, I know that when I go to the dentist's office, I wear my slinky little black dress. The black dress is, after all, a wardrobe staple.

Thanks for reading, everyone.

* If you do a Google Image Search for C&EN, you will find pictures that appeared in Chembark, Carbon-Based Curiosities, and the Lieber group webpage in the top hits.

Thursday, April 05, 2007

Just try it.

Try googling "masamune effect". It has to be in quotes for this to work. I was looking for a specific reference and was too lazy to go to Web of Science right away. I got a good chuckle for my efforts, but little else.
Sorry I haven't blogged in a bit. I'm recovering from an unfortunate turn of events that I'd prefer not to post about, and my computer time's being eaten up by other things these days.

..when you're done with that, read the real references, if you're so inclined. (I did have to go outside of Google to find them, since this work is mentioned offhand in many more recent papers.)
(a)W. Choy, L. A. Redd III., S. Masamune, J. Org. Chem. 1983, 48, 1137-1139;
(b) S. Masamune, L. A. Reed III., J. T. Davis, W. Choy, J. Org. Chem. 1983, 48, 4441-4444.

Satoru Masamune, while a professor of chemistry at MIT, made many contributions to the field of chemical synthesis. These two papers describe some of his contributions to the Diels-Alder reaction, one of my adviser's favorites.
The Diels-Alder reaction is artistic (it can let us sculpt 3D molecules out of flat precursors), it's green (no waste atoms lying around after the reaction, with just a few exceptions), and chemists have gotten pretty good at controlling and predicting its power.

Back to Masamune's papers. This work describes a small reactant with a defined 3D structure, which reacts very well at low temperatures, catalyst-free (green again, low energy requirement) with a variety of partners. The best part about this reactant was that one could predict the 3D structure of the products for the reaction. Masamune surmised that this was made possible by hydrogen bonding interactions occurring over the course of the reaction. That's a strategy taken straight out of the enzyme's playbook.

I picked the picture because I've always been fascinated by those desk toys. If you could turn the magnet on and off at will, I think it's a pretty decent basic illustration of the concept of building 3D things from flat things.

Wednesday, March 21, 2007

Whither the protecting group?

Kudos to Phil Baran's group, who have just published in the journal Nature describing protecting-group (PG) free syntheses of members of the hapalindole, fischerindole, welwitindolinone and ambiguine families.
the ref: Nature 2007, 446, 404-408.
His group has published the enantioselective total synthesis of some of these compounds before (see, for instance, JACS 2005, 127, 15394-96.) but I'm guessing Nature deemed this worthy because of its unified application of a few big philosophies of organic synthesis (ie, atom economy and convergency) while trying to evaluate the pros and cons of going PG-free, as well as its overarching call for hearkening back to the early days, when men were men and syntheses were PG-free. That, and they optimized the routes to welwitindolinone and fischerindole to get higher yields.
So what is a protecting group? For organic chemists, they are a way of reining in the more unruly sections of the molecule you happen to be making. To be more specific, it's necessary to mask parts of the molecule that are likely to behave in some way other than what you'd like, or that refuse to "go along quietly" when some other part of your molecule needs attention.
For a great description, take a look here for Dylan Stiles' (aka Tenderbutton's) rather prescient article about the protecting group and some classic examples thereof.
Is the "PG-free way" really Mother Nature's way? If not, is her favorite protecting group the MOM group?
I think that some masked chemical reactivity exists in the biological world. I hope that my more scientifically inclined readers won't take offense at my stretching an analogy just a bit for the sake of a blog entry.
Take enzymes like proteases. Proteases break the bonds that link up the fundamental building blocks in proteins, and they're involved in many important roles in the body, from blood clotting to cell death. It's extremely important that proteases be exquisitely regulated, so that they don't start chopping up proteins willy-nilly. The "protecting groups" for proteases are in place at the beginning, during their production. Proteases are built as inactive forms known as zymogens, and in order to reveal the active protease, there's a little sliver of protein (called a peptide) that's got to get lopped off.
the ref: Nature 1999, 402, 373-376.
That isn't the only mechanism for regulating proteolysis. You can imagine that if a protease somehow gets activated at the wrong time, or in an out-of-control way, there would be dire consequences (ie, too much protease activity could contribute to stroke or alzheimer's).
When that happens, one natural defense mechanism is the serpin class of proteins. Serpins permanantly (covalently) inhibit proteases, mostly the serine type.

Incidentally, this is the most chemistry I've ever seen in an issue of Nature. Besides the Baran paper and the intro to it by Porco, there's a great piece by Bergman on C-H activation and a review by Toste. Plus, there's an article about chemistry in the NatureJobs section.
UPDATE 3/24: I should've realized Nature did that to coincide with the ACS national meeting.

Will DOI cure what ails me?

As I mentioned on my last post, I've been busy reformatting tons of references, adapting something I've written before to satisfy a slightly different format.
Non-scientists, non-scholarly types: It's like writing that 8th grade term paper all over again, times 100. You know, the one where each of your sources for your bibliography had to be on a separate index card, and you had to get your mom to drive you to the Hackettstown Library to search (are you ready now?) the Readers' Guide to Periodical Literature for information on The Manhattan Project. I can't remember why I chose to write a term paper about the A-bomb at the tender age of 14, but a lot of what I read about for that paper still comes up.
But I digress.
The point is that reformatting references is unbelievably mundane work.
There is some computer software out there that's meant to take care of all that for you. The one I had started using is called EndNote. Endnote interfaces with Word, and it's smart enough to know that when you move text around, the numbers of your references will change if the order's been changed. It has templates for bibliographies in many different journals and can (supposedly) instantly reformat your references to a new journal.
Endnote didn't work well for me at all. I was working with a library of a couple hundred references for this review paper back in 2005. Unfortunately, I couldn't figure out a way to make the software format my references according to the specifications of the particular journal. So, once I was sure I was done shuffling text around, I switched my references to text-only and reformatted them manually, and now I'm reformatting once again.
Is there other, better software out there?
The biggest difference between now and when I was in eighth grade is the ease of access to the internet. One of the handiest technologies for keeping track of the scholarly literature is The Digital Object Identifier System, or DOI. DOI is like a homing device for a journal article, so that no matter where the content moves on the web, looking it up using a DOI locates it and retrieves it.
Recently, some Elsevier journals changed their web and old links no longer worked. If I'd set those links to the DOI of the journal article, they'd still be intact. That reminds me; I need to change my research group's "Publications" page so that everything is indexed by DOI.
What I'm wondering is whether there will come a point where DOI will become the universal reference citation standard, including in print. If that happened, I'd never have to worry about whether I should be using bold or italic font, or whether the authors' surnames come first or last, ever again. Just a simple URL would be all I'd need. However, part of me thinks that if journals (or is it the ACS Style Guidepeople?) were ever going to adopt uniform, URL-based standards, they would have done it a few years ago, at the relative "dawn" of the internet age.
What are the barriers to this, if any? Is it a content searching issue?
If you were going to pick a universal reference style, what would it be and why?

If I were going to Chicago...

If I were going to Chicago, I'd probably be inspired to post something a little more imaginative.
I've been working on a research proposal (read: reformatting references) all week. My brain hurts.

It won't surprise anyone who knows me that I'd want to attend talks that walk the chemistry-biology tightrope. (Read: Jon Clardy, Dale Boger, Laura Kiessling, Sam Gellman, Carolyn Bertozzi, Anna Mapp, Xiaowei Zhuang, etc.)
Here are some of my less obvious go-to talks.

Sunday all day (intermittently): AGFD: Natural Products, Diets and Cancer Prevention. A friend from my last lab always made time to go to the talks from the Ag. and Food chemistry division. I like them, too, because, to me, they have a more "generalist" vibe, and sometimes there are some really interesting chemical structures that they throw up on a slide. You never know where the inspiration for the next target will come from. Not too long ago, there was a postdoc in my group who spent part of his Ph.D. synthesizing a molecule found in Roquefort cheese.

Monday AM: MEDI: Drugs from Academia: Marketed Drugs Discovered in Academic Labs
I'm curious what Bob Holton's going to do with the taxol $$. That, and I have to cheer on Princeton's own Edward C. "Ted" Taylor.

Monday lunch: CHED: Undergraduate Research Poster Session: Organic Chemistry
Mad props to Mike, my little bro, for being the first in the family to present a poster at an ACS meeting. I should probably have gotten more work done.

Monday PM: CHED: Research in Chemical Education
My friend Angie is a teaching postdoc and she's giving a talk about how to keep a lecture hall's worth of sophomores engaged in the organic chem course's subject material. My favorite quote from her teaching experiences is on my Facebook wall. "Sigh....I'm introducing the concept of "backside attack" to 260 college sophomores today. Pray for me." At her postdoc interview she had a week's notice to prepare a lecture on her assigned topic for another ~300 students.

Tuesday AM: PHYS: Xiaowei Zhuang's talk in ACS National Awards in Physical Chemistry
I know I said I wouldn't discuss an obvious one, but I've always really been intrigued by the idea of single molecule imaging studies. I was too afraid of math to take the plunge in a group like that, though. I like to think that one day we'll be able to make movies like this one. I don't think I've linked to that movie yet.

Wednesday AM:
9:55-10:35 ORGN: Biomimetic Natural and Unnatural Products Synthesis
Not a surprise that I'd go here. :)
I think the boss is talking about some new alkaloid-related work, but I'm not sure.

Wednesday PM: INOR: Coordination Chemistry: Characterization and Application
I want to listen to my friends Karl and Eli give talks about their work (or at least, my rudimentary, pop-science understanding of their work, judging by the link).

At some point: run up to Lincoln Park to get breakfast at The Bourgeois Pig, followed by research on, um, surface science at the Bliss Spa, paid for by my imaginary money.

Thursday PM: Nanoparticles: Synthesis, Passivation, Stabilization, and Functionalization
Nanotubes, biosensors, and a talk from someone in Chad Mirkin's group. What's not to like?
Chad Mirkin was here at Princeton a while ago and I regret skipping his talk because of labwork. His science reaches in so many directions.

Note to Anonymous

this started as a reply to a comment on my last post, but it got so long i figured it deserved a post of its own. paul, excuse the lack of caps. i wrote this in the heat of the moment. i know how to diagram sentences, i swear. :)
anonymous,
i do agree with you that for grads busting their asses to pass quals (or get into a good group, or just getting stuff to work for once), the wining and dining days of recruiting are a distant memory. it's definitely true that fewer and fewer upper year students take part in the festivities, and with good reason...
i think that potential chemgrads need to go in well-informed about precisely what you said, and be open to (gasp!) other options. if you really really really want an industry job, they are tough to get these days. maybe the pendulum will swing back, maybe not.
and you're right, a survey can't be comprehensive if everyone isn't polled or doesn't respond, and they're reporting on survey data, so hopefully people trained as scientists know to take it with a grain of salt.
"The 2006 survey involved mailing questionnaires
to a random sample of 24,000
ACS members who were most likely to be
in the domestic workforce. They all resided
in the U.S., were under 70 years of age, and
were not in the emeritus, retired, or student
member categories." -C&EN 9/18/2006
The ACS has over 150,000 members, and it's been discussed at length in the blogs that many chemists don't join ACS at all, or their employers pay for it, so there's some overrepresentation there.
without real poll data, you risk jumping into that nebulous trend story fad. see here and here. so maybe their hands are tied to some extent. i don't think the stories on the survey data should be portrayed as indicative of anything wider. the question is, how could a good poll be properly conducted? with the status of postdocs being different almost everywhere, to cite one example, it would require extensive red-tape wading to reach everyone. on the other hand, since a lot of the job market stuff comes through word of mouth anyway, we could argue about where the best place is to disseminate this information in the first place. federal labor statistics?
i hear about industrial sites that are only hiring one person or two a year, and everybody has a fantastic pedigree. so, what happens to the others? some people are having to take a risk and take a job at a tiny company where they'd really need to stand out to ever be hired by a big guy.there are probably some success stories there, but i don't know as many working chemists as other bloggers. derek's situation is difficult, as well. it's economics driving that, plus perhaps preferring to train someone with less experience in your company's particular way of doing things?
when i got to grad school, i had blinders on. it's partially due to the fact that i went to a small school and didn't know any grad students, and that i had my "eyes on the prize" and didn't stop to think about the fact that i might be good at more than chemistry. my academic work was inextricably linked to my self-esteem back then. i think you can still go to grad school and work in a lab because you like chemistry. that's perfectly OK, but i think that people in this modern economy have to realize that a ph.d. in chemistry can be useful in plenty of different jobs, despite the traditionalists who regard those careers as "alternatives". i struggled with that idea for some time, but i keep hearing about my friends in the grad program that are going to go into consulting or work as a patent agent, two jobs i didn't know existed till grad school. some of them think that they might miss the lab, but maybe not. i even know someone who returned to the lab from an editorial position. it's tough, and you need to work hard to get back into the groove, but it's possible. reading "the world is flat" made me realize that everyone's going to have to work smarter and be creative in order to stay afloat.
the easiest jobs to look at are the ones for which you are supposedly directly trained. med school-> doctor. business school-> executive. law school-> lawyer. sally struthers school->medical assistant, electrician, business management, or accounting. chemistry grad school-> professor or lab chemist? yes, it's true that the other professions don't have the same kind of supply/demand issue in their job markets, but it's not something individuals have much control over, so i went for something different. maybe that's why when i hear about disgruntled grad students first thinking about other professions, those are often the things they gravitate toward at first. it takes real soul-searching to look beyond that. months and months of it, in my case, and if i'm not happy when i start working, i'm not afraid to start the process all over again.
i think the hardest part of the problem is that it's hard to explain this to the young-uns, because they think they have the answers and it won't happen to them, because we have somehow "failed" as chemists. i doubt i would have listened if "future me" went back in time to warn "young, idealistic, slightly cocky me" about such things.

whew. that's a manifesto-length post. speaking of which, if you haven't read milkshake's post, get thee to org prep daily. i learned a lot from it.

It's recruiting season at Princeton.
Typically, prospective students don't actually visit our department until they're already admitted, meaning that the department pulls out all the stops to bring in plenty of great people. I was admitted in the first year that Princeton started having a full recruiting weekend, instead of ad hoc visits to the department, and it made a huge difference (we had 1.5 times more people start than what had been common for the past 5 or 6 years). Every department does recruiting differently and presumably tries to do something distinctive/memorable, although I feel like most students come for a certain faculty member or two, not the department as a whole. Back when I was a senior in college, I remember that I had dinner at Yale's Peabody Museum (with the dinosaurs), but I think I heard that that hasn't been done in recent years. True? Also, does anybody know whether MIT still does the lobster bake? I've been told that TSRI does interview its students before admitting them, so the process is a little different there. What are some of the other well-known/ unique/ offbeat recruiting traditions?
The really interesting stuff happens after recruiting, when students commit to the university and then have to join a group. This tends to fuel the gossip for the better part of the fall semester. Who's going where, how many people is so-and-so taking, and the like. The department doesn't allow anyone to officially join a group until the end of November, although many students will start working in their lab of choice the summer before. During the fall semester, all first years attend all the research talks given by the faculty in one of our lecture halls. Unfortunately, as my years here have progressed, I've started to notice that the department's been providing less and less food at these events (we got free lunch and baked goods, the next year it was just baked goods, the year after that nothing at all.) My understanding is that at some places, the research talks are more of an "open house" setup, where interested parties listen to the faculty member discuss what's going on in the group. I've seen some of David Liu's open house posters, for instance. I understand why the department asks everyone to attend every talk, since there have been several occasions where students have switched fields completely at the beginning of grad school, and it's important to know what's going on outside of your field, but I also think that in an open house situation, there's likely to be more lively discussion, because everyone who's attending wants to be there.

Too bad Apple's got that name locked up

I gravitated toward this paper's title, "Reversible, Erasable, and Rewritable Nanorecording on an H2 Rotaxane Thin Film".
the ref: JACS 2007 129, 2204-2205.
This paper's about a new material that makes a promising step toward atom-scale data storage devices. As computers store more and more large files (and I don't just mean home movies from your family trip to the world's largest ball of twine, I'm talking government use, scientific number crunching, and the like), the logical progression points to further miniaturized data drives.

Computers store data in bits and bytes, and the system boils everything down to a string of digits with only two possible values: zero or one. Because of this, the fundamental storage unit needs to be capable of switching reversibly between two different forms.

The authors of the paper pulled that feat off by making their new material from a molecule called a rotaxane, which is mechanically interlocked, like those metal toy puzzles that drive me crazy. Basically, the ring can move to each side of the dumbbell.

The "recording device", a scanning tunneling microscope, reminds me of a tiny turntable needle. This kind of microscope is a little different from the ones in every high school science classroom. It's used to measure properties at surfaces down to the nanometer (billionth of a meter) scale, and with an applied voltage, it can manipulate material down to individual atoms and molecules. Those school microscopes couldn't come close to being able to "see" something that small, and there's no voltage involved with them, either.


Put those two things together and the tiny tip can "move" the ring on the dumbbell molecule reversibly, which would translate to recording and erasing.

These researchers published a similar paper last year, but the new work tweaks the molecular structure of the dumbbell that makes erasing "data" easier. The next questions are ones of lifetime (how long-lasting is this material and how stable is the switch once it's put in position? etc.)

Ten year plan for Australasian science

Ten year plan for Australasian science

Karen Harries-Rees/Melbourne, Australia

Australian scientists have launched a vision that sets out the next 10 years of synchrotron science in the country. Australia's synchrotron, which will open this year, will be a jewel in Australian and New Zealand science, they predict.

The 10-year plan, Accelerating the future - a plan for Australian synchrotron based science 2007-2017, was developed over two years by an expert committee and has been endorsed by the Australian Academy of Science, the Australian Academy of Technological Sciences and Engineering, and the Royal Society of New Zealand. It was launched by the committee's chair, Keith Nugent, professor of optics at the University of Melbourne.

Jewel in Australia's scientific crown © Australian Synchrotron

Nugent said the plan is ambitious but achievable. It aims to put Australia in world leading status in some areas, such as phase-contrast imaging, in which Australia has a real strength, he said.

There is no funding allocated to achieving the plan. 'We took the view that we were not going to worry about where the funding would come from. We wanted to have a plan for where the priorities lie and use that as a basis for lobbying for further funding,' said Nugent.

The plan has been well received by Australia's researchers. 'While it is not possible for everybody to be pleased by any developmental plan, the vast majority of the scientific community do appear to appreciate the structure and direction of the plan,' said Andrea Gerson, director of the applied centre for structural and synchrotron studies at the University of South Australia. 'The next few years will be very important for the Australian synchrotron as it consolidates on the first nine beamlines and recognises the growing needs in other scientific areas.'

Peter Lay, from the University of Sydney's school of chemistry, said that the way the synchrotron is funded and managed in future will either make or break the facility.

The science, not art, of management

The science, not art, of management

WHAT THEY DON`T TEACH YOU AT B-SCHOOL

Suman Srivastava

What don’t they teach you at B-school? I have a two-word answer to this question: street smartness.

Business school taught me how to read balance sheets, but didn’t tell me how to motivate people to give their best. It taught me how to structure the organisation for maximum productivity, but not how to deal with a person who thinks her boss is a creep. My management degree taught me how to create an excellent marketing strategy, but not how to sell it to a client who is insecure about his job.

Business schools tend to be very left-brained. Very analytical, quantitative and structured. Which is a good thing because the Indian education system is not very good at teaching us to be analytical, quantitative or structured. The school system basically teaches us to learn by rote. The best business schools force you to unlearn that.

In the process, they tend to put the quantitative approach to a problem on a pedestal, ignoring the qualitative and “feel” aspects of managing people. If management is both a science and an art, then B-schools teach the science but ignore the art.

Life, unfortunately, is all about art. Success comes to those who learn to deal with people best. Those who learn to understand the fears and motivations that people have, understand their joys and sorrows. The role of a leader is to inspire, provide direction and keep people motivated. Other professional skills are taken for granted.

One can argue, perhaps with justification, that nobody can teach the art. That may be true, but where business schools tend to err is in leaving their management students with a feeling that the art doesn’t really matter.

I had to wait until my hair turned grey before I understood that the art does matter.

But perhaps, I am just a slow learner.

News Release

UW Science Education Takes First STEP June 11, 2007 -- Recent graduate Christopher Harnden says a new University of Wyoming program pairing College of Education undergraduates with graduate researchers gave him a competitive edge. Harnden, of Worland, participated in the launch of the Science Teacher Education Program (STEP) sponsored by Wyoming National Science Foundation EPSCoR (Experimental Program to Stimulate Competitive Research). The program gives secondary science education majors an opportunity for hand-on research experience at the college level. It also supports them in creating lesson plans based on the research to use in their student teaching residency. "I wasn't even planning to do the program and then a friend convinced me to get involved because it would help with my student teaching," Harnden says. "It was one of the best educational opportunities I've had at UW." STEP fellowships are awarded to science education majors the spring semester of their junior year. The three-semester program carries a stipend for both the STEP fellow and the mentor graduate student. Funding is also available to the secondary school for lab equipment associated with the STEP lesson plan, which remains with the classroom for future use. The program begins in the summer when the science educator assists during six weeks of summer graduate research. Harnden was paired with UW zoology and physiology graduate student Lusha Tronstad to assist her with her research into the illegal introduction of lake trout into Yellowstone National Park. Previous to STEP, Harnden had no experience with research or the scientific method at the college level. "STEP provided me with credibility. I was no longer a science educator going into the classroom trying to portray concepts without having a single day of experience in the lab," Harnden says, jokingly adding, "and the practical application eliminated the students from asking, 'When am I ever going to use this&?apos;" The program benefitted students in Harden’s temporary Laramie junior high and high school classrooms, too. "The biology class I was placed in was more health focused, but I was able to use STEP to apply the research and scientific methods and do lesson planning. Lusha also came in as a guest and talked about her research, which really impressed the students," Harnden says. Before his exposure to the hard science at UW, Harnden says he was unaware of the important research going on at his own university. "Being part of STEP opened my eyes to what the university is doing in terms of research and opportunities available to students outside of the College of Education," he says. "STEP is an incredible program and one that all science educators need to have."