Author: jlolds

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

Monday Routine at Krasnow–the Seminar

I rarely delve into the day to day here at the Institute, but, mostly to give a flavor of the scientific program, here goes:

Please join us for the next Krasnow Monday Seminar TODAY
Refreshments will be served at 3:30pm.  Come chat with colleagues and like-minded researchers and students prior to the talk at 4pm.

SPEAKER:  Iosif Vaisman,
Professor and Director of the Ph.D. Program,
Department of Bioinformatics and Computational Biology,
George Mason University

Protein function analysis using computational mutagenesis:

Proteins exhibit a wide range of functional consequences upon mutation.
Accurate predictive models for the impact of single amino acid
substitutions on protein stability and activity provide important insights
into protein structure and function. Such models are also valuable for the
design and engineering of new proteins. This talk will focus on a
computational mutagenesis technique based on a four-body, knowledge-based,
statistical contact potential and machine learning methods. For any
mutation due to a single amino acid replacement in a protein, the method
provides an empirical normalized measure of the ensuing environmental
perturbation occurring at every residue position. The predictive
mutagenesis models are evaluated using large training sets of mutants
derived from diverse proteins that have been experimentally studied and
described. These predictive models are either comparable to, or in many
cases signicantly outperform, alternative approaches.

Hat tip to Carolyn Payne and our support staff…

Innovation, Steve Johnson’s perspective

Entrepreneur and author Steve Johnson has a piece in today’s Sunday NY Times on innovation here. His point is that a whole lot of what most of us would consider the core of technology innovation doesn’t come from corporate R&D (writ large) but rather from a combination of academic, government-sponsored and even amateur sectors–a investment area he calls “the fourth quadrant”.

That’s true, but regardless, there’s a lot of chaff to separate from the wheat!

I think the core question is not where the innovation is coming from, but rather how to identify true paradigm-breaking discovery from the same old same old. It’s not entirely obvious to me. There was an obscure predecessor to the Web called gopher that, in the infancy of the Internet, had many of the features of the Web, but with more of a hierarchical text focus. It sure seemed innovative at the time. But of course, most of AS’s loyal readers wont have heard about it. Somehow, it was innovative, but not innovative enough.

By the same token, the early Web browsers (e.g. Mosaic) were incredibly clunky. But the seed for a paradigm shift was there in Mosaic 1.0 and, in the end, it wasn’t in gopher.

How to Balance Science With Compliance?

It’s a fact that the compliance burden (often in the form of unfunded mandates) continues to increase on U.S. scientists and those who support the scientific enterprise here. This increased burden is, to some extent, of our own making as their have been several high profile missteps by U.S. scientists and science institutions which to say the least, has been embarrassing.  But the burden has also been rising inexorably because of the increasing awareness of the taxpayers’ right to have oversight over how taxpayer dollars are put to work for science progress. The end result of this burden is that U.S. scientists have less time at the bench, less time at the bed-side and increasingly are looking at attractive offers from overseas.

What can we do to balance these two often conflicting demands?

It seems to me one thing is to make sure we educate the mid-level compliance officers who are assigned the unenviable job of watching over the practicing scientists to a common mutually agreed upon level–so that there is some degree of certainty of what will be actually be required. This is especially true between different institutions. The notion of one institution, one grant is somewhat quaint. Increasingly, a successful approach, requires a multi-disciplinary team assembled across multiple institutions.

The second, is to educate our trainees that performing compliance requirements is part and parcel of the ethical and responsible conduct of science. All too often, there is a cultural gestalt, passed down by those of us in faculty positions, that all of this is just so much “noise” and that often the best response is to simply ignore a compliance request (in the hopes that it just goes away). Obviously, this is wrong and, more dangerously, puts institutions at risk.

The third, is to work with elected officials and policy decision-makers towards a workable middle-road,  such that there is an understanding that what might be appropriate oversight for the likes of a defense contractor operating in theater, is very different from the oversight required for a typical bench-top scientist PI at an American academic institution. One size definitely doesn’t fit all.

In short, compliance has become a tripping hazard of American-style science. It’s important to begin a larger societal conversation about this issue before the tripping hazard turns into a brain drain.

Thanks to the Organizers of DOM VI

DOM VI is now history–it was a terrific scientific conclave with some absolutely incredible talks. A short blog post then to thank the organizers– in particular Kenneth Kwok –for their superb pulling it all together. Here Ken and I are posed in front of one of Singapore’s iconic science locations, brain sculptures make the photo.

I’m back in DC after a mind-boggling 18 hr, 10,000 mile non-stop to New York directly over the Pacific Ocean.

Live Blogging from DOM 6

Kenichiro  Mongi from Sony showed the following viral video from TED on human leadership behavior:

Right now John Weng from Michigan State is telling us about his view that there are 5 chunks of a brain-mind model: development,  architecture, area, space and time. His mantra: you need a deep understanding of  computer to understand the brain. Hmmm.

Does the brain have a Von Neumann Architecture: DOM VI Update

Yesterday’s talks had an underlying debate about the very nature of the brain, namely does it have a Von Neumann architecture, has it evolved to compute or did it evolve to be something more of a Rube Goldberg machine? Pushing the latter view was Duke’s Dale Purves, the former position was taken by Rutger’s Randy Gallistel with Stanford’s Jay McClelland coming down somewhere in the middle.

Central to the debate was the question of whether there is a biological substrate for the required read/write addressable memory in the brain (in species ranging from ants to humans).

My own view is that the CA3 field of mammalian hippocampus at least offers the possibility of serving as the biological substrate as evidenced by its circuitry, the plasticity of its synapses and the possibility of mechanisms other than pure spike time dependent plasticity providing the ability to address specific synapses.

My former Mason colleague Maria Kozhevnikov (now at the National University of Singapore and Harvard Medical School) gave a wonderful talk on performance differences produced by immersing human subjects in immersed 3-D environments.

I had the honor of opening up DOM VI with an overview of the initiative.

Singapore Bling (Decade of the Mind VI)

I’m up at 4AM again. Jet lag for me goes away as a step function. I’m at a plateau right now. Up at 4 and really sleepy by around 9PM. Today (Sunday) we’ll dialog with some of the principals in combination a tour and dinner. We’re gathering in the late afternoon for a tour of the Peranakan Museum (the culture before the British got here–descendants of the Chinese and South-Asian communities that formed a hybrid culture) and then a festive dinner at a restaurant near by.
Yesterday I took in the full Orchard Road shopping experience. Imagine an eastern asian version of Rodeo Drive and Fifth Avenue rolled into a single massive tree-line boulevard. Or for those loyal readers from the Washington Area, Imagine malls like Tysons –except they are like the iceberg that the Titanic hit–the part above ground is dwarfed by what’s below the street level. At one of the most iconic of these shopping palaces (Ion) you’ll not only find access to the MRT (Singapore’s version of Metro) but also stores like Marks and Spencer, Burrberry and oddly enough for my Ann Arbor friends, a version of Borders Books that harkens back to the glory days.
And of course the food courts, which go on and on and forever and for which my colleague Tyler Cowen has provided much better reviews than I ever can (I believe his next book is on the economics of food!).
I ended up spending some money on some gifts; the Singapore dollars is right now at about .77 of the US dollar, so even though it’s absolutely not true, my neuroeconomic brain was making feel like the country was on-sale.
Our Hotel, Traders, is proximal to the leafy quiet neighborhood at the end of Orchard Road near the Botanical Gardens. It’s also quite near the U.S. Embassy (it looks impregnable by the way). So it’s not surprising really that the hotel is connected to a much smaller Mall which caters to the ex-pat scene. There is a clone of Whole Foods that was filled with people who could easily have been teleported from the one I usually go to in Clarendon. I have to say the prices, on average, were a bit better–although that could still be cognitive dissonance of using the Singapore dollar.
We’re near the equator. The last place this hot that I visited, Curacao, was also very near the equator. I suspect I mentioned that in a 2005 blog entry. So as I’m hearing about crisp Fall weather from the States, I’m a bit envious.
Tomorrow I’ll kick off the conference with an overview of the Decade of the Mind Project and where I hope it can go, both within the US and internationally. Then we’ll hear talks from Dale Purves, Randy Galistel and Maria Kozhevnikov. With luck (and wi-fi), I’ll be live blogging.

Blogging from Singapore

So I’m in Singapore a few days early, to get over the jet-lag (I’m a believer in Melatonin) and for some scientific meetings tomorrow. The Decade of the Mind Conference doesn’t begin until Sunday. In the meantime some observations: the non-stop from Newark to Singapore didn’t go over the Pole. Instead it took a route that led across the Atlantic, Northern Europe, Russia, Afghanistan, Pakistan, India, The Bay of Bengal and on in to the Island State. We took the most interesting circuitous route across both Afghanistan and Pakistan with intricate direction turns–makes one think there might be some concerns about where commercial jets can safely go–or not. And there was some very exciting turbulence over the Indian Ocean as we got close. But all told, it was a great flight and definitely the fastest way to East Asia from the US east coast.

The food here–so far–is great. I had an amazing fish curry for breakfast.

Great news on the Chilean miners. We got the text messages of the successful rescue on the plane.