On The Margins

Monday January 09, 2006

[ Science ] Food as Medicine

This simple graphics is from The Wall Street Journal article on Dr. Akira Endo.

Last Thursday, my family and I went to a Chinese restaurant recommended by my daughters' piano teacher. We ordered a course for four, and I chose a mushroom dish as one of the four dishes which we could order as part of the deal but I didn't touch the mushrooms until my wife served me a large piece of the top, which looked like two round pieces attached together. I ate it with little thought but in about half-an-hour, I experienced an amazing, almost overwhelming change. After a long, tiring day, I had suddenly become more clear and alert. My eyes, which are usually equiped with glasses, seemed to be viewing a further and wider scope, and I seemed to be present in the moment with a pleasant sensation throughout my body. When I talked about this to my wife and daughters, they dismissed it with a laugh but after some insistence on my part, we started looking at the table to search for what had affected me. Other than the duck tongues, I had had everything else before in some setting. The only thing new was the mushrooms. We summoned the floor manager, and asked him about the mushrooms. They were Reishi mushrooms (Ganoderma Lucidum / Ling Zhi). On our return home, my wife looked up the Net for information on these and found a wealth of material refering to their medicinal effects.

And this morning, just before departing home, I spotted a Wall Street Journal article on Dr. Akira Endo, a Japanese scientist who has cultivated fungi for their medicinal, anti-cholesterol and other effects since the 1960s. ("Stalking Cholesterol: How One Scientist Intrigued by Molds Found First Statin — Feat of Japan's Dr. Endo Led To Heart-Care Revolution But Brought Him Nothing — Nature as a Drug Laboratory" Peter Landers, WSJ, January 9, 2006; Page A1.)

Dr. Endo's research led to the discovery of some of the first anti-cholestral drugs, and his techniques were used by giant drug companies to discover other drugs of the same family. The main point of the article is that many artificial drugs have tremendously negative side effects but that, ever more, drug discovery efforts in giant companies are turning their attention to discovery of materials in nature. With all the tools and techniques of modern science (and science is little else without these techniques and tools), we can only discover a fraction of all that is offered in nature and that can be found useful to medicine and human beings. This should be enough to invoke a feeling of wonder, awe and respect.

Returning to Reishi, much useful information can be found on the web. For example, see references by Dylan Kosma and Daniel J. Royse. It is also mentioned by the Taoists as the "Elixir of Life". People interested in Reishi might also be interested in Lichens. UC Davis, where I spent 7 years doing graduate work, offers a course in edible mushroom cultivation.

2006-01-09 14:52:15.0 -- Comments [2] ; Permalink ; Trackback.

Friday October 28, 2005

[ Science ] Isotherm Contours on Earth

NASA's World Wind application can produce isotherm pictures for the earth's surface.

2005-10-28 22:58:44.0 -- ; Permalink ; Trackback.

Wednesday September 21, 2005

[ Science ] Satellite Images for Rita

In the next few days, you should be able to view Hurricane Rita off the Gulf Coast on the satellite images available at the website of National Oceanic and Atmospheric Administration's Weather Service. (Click the "Satellite" tab on that website.) The image below may or may not have Rita on it depending on when you visit. There are a great number of other fantastic atmospheric images provided by NOAA. To me, it all shows the amazing power of the earth and its atmosphere. In a multitude of ways, the earth seems like a living creature and it might be understood far better if viewers saw it in those terms.

By the way, in case you're wondering why I've written so much about hurricanes, I should add that I have more than just a common curiosity that moves with the news. After all, a good portion of my engineering Ph.D. dissertation (completed in 1989-1990) was devoted to the theoretical and computational study of vortex-vortex interactions at high Reynolds numbers.

2005-09-21 22:13:17.0 -- Comments [0] ; Permalink ; Trackback.

Tuesday August 30, 2005

[ Science ] Being in the World vs. Being in the Mind

At the end of his little book On the Internet, one of the leading contemporary philosophers, Hubert Dreyfus, laments

In sum, as long as we continue to affirm our bodies, the Net can be useful to us in spite of its tendency to offer the worst of a series of asymmetric trade-offs: economy over efficiency in education, the virtual over the real in our relation to things and people, and anonymity over commitment in our lives. But, in using it, we have to remember that our culture has already fallen twice for the Platonic/Christian temptation to try to get rid of our vulnerable bodies, and has ended in nihilism. This time around, we must resist this temptation and affirm our bodies, not in spite of their finitude and vulnerability, but because, without our bodies, as Nietzsche saw, we would be literally nothing. As Nietzsche has Zarathustra say: 'I want to speak to the despisers of the body. I would not have them learn and teach differently, but merely say farewell to their own bodies—and thus become silent.'

Simpler (possibly indirect) indications of these claims are scattered everywhere for us to see. For example, consider this little note on the importance of physical being and exercise to the health of one's memory, the quintessential aspect of mind, or read the report in today's Wall Street Journal on "Exploring the Bicycle-Brain Connection: How Exercise Boosts Cognitive Function." (The Journal requires a paid subscription for access to its online edition.)

Of course, examples such as these are simply reminders of something more significant. What Dreyfus says in his various writings, including those on Heidegger and on artificial intelligence, is actually much deeper. The claim is that the understanding of (and coming to terms with) our status in the world is impossible without our physical interaction and being in it. In fact, there is a tight connection between the two. For example, we learn quite differently (in quality and experience) as we shake a hand in a meeting room, leaf through a book on a coach or write in a note book under a tree using the pen held by our fingers than when we do something similar to all these things through the use of different physical environment such as the screen of a VDT, a mouse and a keyboard. The state of physical being and the form of interaction is actually not immaterial despite what some might like to think.

Internet, Philosophy, Body, Mind.

2005-08-30 14:27:31.0 -- Comments [0] ; Permalink ; Trackback.

Monday August 22, 2005

[ Science ] Efficient Attack on SHA-0

Xiaoyun Wang is the lead author of a recent paper on a new attack on SHA-0 (and others regarding similar methods of attack on SHA-1). John Markoff of The New York Times tells the story of how she was unable to make it to the Crypto 2005 conference due to visa restrictions that slowed her application.

Cryptography, Visas.

2005-08-22 17:52:00.0 -- Comments [0] ; Permalink ; Trackback.

Friday August 19, 2005

[ Science ] Circadian Oscillator

Yesterday, I wrote a little entry on jet lag prevention. Genome Informatics ( 15(1): 3-12 (2004)) has published an interesting paper by researchers at Humboldt University, Berlin, on the cricadian oscillator, or the biological clock of mammals (Becker-Weimann, S., Wolf, J., Kramer, A. and Herzel, H. "A Model of the Mammalian Circadian Oscillator Including the REV-ERBα Module"). In the introduction to the paper, we read: In almost all organisms, an internal circadian clock with a period of about 24 hours has evolved that allows timekeeping even without external stimuli. This clock organizes the temporal order of molecular, physiological and behavioral processes and thereby contributes to their optimal adaptation to certain daytimes. In several tissues about 10% of mRNA concentrations have been found to be oscillating with a 24 hour period, demonstrating the vast influence of the clock on cellular processes. While many tissues contain a molecular clock, in mammals the master clock that coordinates the others is located in the suprachiasmatic nuclei (SCN) in the hypothalamus.

It was interesting to me that jeg lag actually manifests in the body through the autonomous oscillations in proteins and mRNA concentrations. This paper points to other research that examine "extensive and divergent circadian gene expression in liver and heart" (Nature, 417:78-83, 2002).

The paper also points to a book, by Leon Glass and Michael C. Mackey, which seems worth a thorough study: From Clocks to Chaos: The Rhythms of Life. In fact, I think I'll be ordering it very soon as the topic continues to fascinate me whether it concerns the importance of certain temporal rythms in religious rituals or my own personal experience and scientific background.

One thing I've noticed in my personal life. In the last five years, my family and I have travelled across 11 to 12 time zones and back, every summer, and I've observed that my youngest daughter has always taken the longest to get over her jet lag and that the older members of the family have suffered from more severe lingering oscillations in attempting to re-adjust their biological time.

For those interested in further study, McGill University hosts a multi-university Center for Nonlinear Dynamics in Physiology and Medicine.

Biology, Time, Genomics.

2005-08-19 09:20:00.0 -- Comments [0] ; Permalink ; Trackback.

Tuesday January 18, 2005

[ Science ] Numerical Simulation of Indian Ocean Tsunami of December 26, 2004

Cornell University researchers have released a video rendition of a numerical simulation for the recent Indian Ocean Tsunami of December 26, 2004:

. . . 7 MB version of the multigrid coupled tsunami simulation.

. . . 43 MB version of the multigrid coupled tsunami simulation.

According to Cornell's news release: The video compresses 10 hours and 30 minutes in the life of the tidal wave into one minute, showing in contrasting colors the advancing high water and the trough behind it, as well as the receding waters observed along coastlines near the epicenter before the wave struck. It shows high water in red and low in blue. The more intense the color, the greater the displacement from sea level. A clock in the animation starts at the moment of the Sumatra earthquake.

2005-01-18 12:11:28.0 -- Comments [2] ; Permalink ; Trackback.

Thursday January 13, 2005

[ Science ] Tsunami Waves 7,000 Kilometers from Epicenter

The BBC reports today of the effect of 3 meter high tsunami waves as far away as the fishing settlement of Hafun, in north-east Somalia, which is located more than 7,000km (4,000 miles) from the epicenter of the earthquake. Pictures from Hafun are available here, and a simple tsunami wave diagram can be found here.

University of Alaska, Fairbanks, has a short note on tsunami waves and the factors affecting their rate of travel and dispersion. However, the focus of this elementary note is on storm-generated waves.

The University of Washington, Seattle, maintains a page on general tsunami information, including a multi-media documentation of recent tsunami events, but no readily available information appears there for calculating the speed and rate of dispersion from a single observation of the wave at a known distance form the epicenter. From what I know about the physics of water waves it should be possible to come up with rough but very useful speed and dispersion estimates based on such (single point w.r.t. epicenter) information. There is a link to tsunami research centers in the U.S. which I didn't have time to pursue in detail.

The USC Tsunami Research Center seems to be the most web-friendly and promising online source of material on tsunami research. It is worthy of further exploration. See, for example, video clips of some simulations for a tsunami event off the coast of California. (If the video simulations included wave amplitude and time progression (or relevant non-dimensional numbers), some non-dimensional analysis could allow rough extensions to similar cases.) Some of the research publications of this center on the analytics of tsunamis should be useful for extracting a simple model to compute speed and dispersion rates. For example, this paper may be start but it considers the case of shallow water wave amplitude evolution. The reference in the paper to "Lamb" is probably to Sir Horace Lamb's seminal work Hydrodynamics of 1879, chapter VIII of which is devoted to the analytical study of tidal waves of various kinds. (I believe Ludwig Wittgenstein studied with Sir Lamb before starting his work with Bertrand Russell.)

While the more fancy analytics and high-compute simulations taking account of coast-line land formations may be of great interest to property insurers and pure scientists, conservative back-of-the-envelope estimates for speed and dispersion of tsunami should still be possible for any middle-schooler to perform and for any fluid dynamics student to explain.

2005-01-13 08:56:19.0 -- Comments [0] ; Permalink ; Trackback.

Friday October 15, 2004

[ Science ] Will People Be Burried With It?

Note: To see the image, you may need to sign-on to the online edition of The New York Times.

The Food and Drug Administration has cleared the way for a Florida company to market implantable chips that would provide easy access to individual medical records . . . "We haven't even sorted out the appropriateness of a RFID tag that goes on a pallet of tomatoes," Mr. Crews said, "much less one that can go under a person's skin."

"Identity Badge Worn Under Skin Approved for Use in Health Care," The New York Times, October 14, 2004.

Clyde Wayne Crews Jr. is the director of technology studies at the Competitive Enterprise Institute, a regulatory research group in Washington.

Will people be burried with it? Will future archaeologists and anthropologists be able to use it? Will it be used to track the outcast and the unwanted? How much harder will it become to deal with cases of identity theft and masquerading in the implants' security and identity "applications"?

2004-10-15 10:27:07.0 -- ; Permalink ; Trackback.

Tuesday September 07, 2004

[ Science ] What Edison Helped Take from Us

Inventions in science and technology are not all about progress.

Every technical invention seems to take something from us in return for what it gives.

With the invention and propagation of basic electric lighting, ultimately brought to every office and home in every city and small town, something sacred was taken from most people--a serene night's sky, which most urbanized people can now see only through the sanitized and limited version that comes to them as images telescopes have viewed, processed and recorded according to their own limitations.

No longer do we need to feel, on a nightly basis, a deep wonder about our place in the universe. The problem has been solved and put to rest.

2004-09-07 15:09:21.0 -- ; Permalink ; Trackback.

Sunday July 04, 2004

[ Science ] Structural Analysis of Proteins

In a recent paper, computer science professor Yuan-Fang Wang of UC Santa Barbara, describes a tool based on 3-D Java for fast protein visualization.

The 3-D structure of proteins determines their biochemical operation.

For example, a great deal of effort was used to map the 3-D structure of Hemoglobin, the main ingredient of our red blood cells, in order to discover and explain how it fixes oxygen.

Computer visualization is only one aspect of structural analysis. In fact, it is one of the last steps in the the geometric analysis of a protein. (The ultimate goal being the actual biochemical function and relationships.)

Another important (and more fundamental) aspect is the actual determination of the geometric structure given a protein's amino acid sequence.

Such determination involves an optimization problem which searches for geometric positioning of protein backbone such that the lowest potential energy state is attained.

This procedure follows from the basic physical principle that all structures prefer the geometry that leads to the lowest potential energy.

The potential engergy can be determined by adding all potential energies due to interactions among the amino acid molecules that have been strung together in a protein.

There is a whole separate art in writing the potential energy equation as a function of molecular positioning and solving it for its lowest value in the hyperdimensional space of the molecular distances. The optimization problem can be solved in a number of ways. Since this is a large-dimension problem, it is important to use some heuristics to start the problem with the protein geometry in a realistic initial state. Following this initial state, the computation searches for neighboring states that have lower potential energy. This sequence is repeated until lowest potential energy "neighborhood" in the hyper-dimensional space of molecular distance vectors is found.

2004-07-04 00:25:27.0 -- ; Permalink ; Trackback.

Saturday June 26, 2004

[ Science ] RoboCup--Robotic Soccer

Robotic soccer has many converts, including Iran, which won the 2nd place in the 2004 German Open's Middle Size league.

There were many German entries, and the first winners come from Osnabruck, Germany, the city of my sister-in-law's family.

RoboCup itself is a larger organization.

At one point, when I was studying with Hubert Dreyfus, I planned to write an essay on whether it was possible for robots to play real soccer.

Well, here is RoboCup's goal: By the year 2050, develop a team of fully autonomous humanoid robots that can win against the human world soccer champion team.

It's a lofty goal, and to what degree it will be accomplished is worth watching.

Unless the robots are allowed to injure people, I doubt they'll win . . .

Now, it is time for me to run for my weekend soccer game on the Stanford compus!

Have a wonderful JavaOne and watch for those robots and don't let them beat you ! ! !

2004-06-26 08:30:01.0 -- ; Permalink ; Trackback.