Friday, February 28, 2014

David Carr Baird


I was talking to David and Margaret, his wife, a few days ago.  Now both in their eighties, they are currently helping a poor neighborhood forestall the building of a cell phone tower too close to a low income residence.  When I visited them last year, they were more than busy working to preserve the beautiful traditional architecture of Kingston, Ontario.  They have many friends, a number of whom are current and former faculty members of both the Royal Military College and Queen's University, including Agnes Hertzberg.

David is the former head of the Physics Department of the Royal Military College of Canada (RMC) where I obtained my first undergraduate degree (Honours Math and Physics).  He was my professor for a first year lab in experimentation.  He also taught me in a class on quantum and statistical physics.  So, about the picture.  David loved to use natural phenomena to teach his classes.  My first exposure to Young's Double Slit Experiment was with David putting up photos showing the interference of waves on Lake Ontario.  He had managed to find a spot where a river (the Cataraqui) interacted with "The Lake", resulting in a beautiful demonstration of double slit induced constructive and destructive interference.  The above photo approximates the delicious pictures that David used to introduce this concept.

I also clearly remember David introducing Fourier series and Gibb's phenonoma toward the construction of a square wave.  Another favorite was the visual representation of the sinc function and the squared sinc function.  He had an artistic flair in the presentation in his classes, a genuine warmth and a great sense of humor.  He was also a very rigorous scientist.  I never really understood just how rigorous until many years later.  I just remember really getting nailed when I had missed some concept like not getting the proper calculation of uncertainty.  There was a gravity to it.

Recently, David wrote a book on the history of RMC.  I'm currently reading it.  The book has some surprises such as these:

"At a time when personal contact between east and west was carefully supervised and rare, three prominent Russian physicists were authorized to make a closely monitored visit to Toronto to attend the 1960 International Conference on Low Temperature Physics.  They were B.N. Samoilov, V.P. Peshkov, celebrated as the discoverer in 1944 of second sound in liquid helium II, and B.I.Verkin after whom the low termperature laboratory of the National Academy of Sciences of Ukraine was named as the B. Verkin Institute for Low Temperature Physics and Engineering."  David and another professor hosted them in Kingston and even drove them to the Thousand Islands Bridge "so they could, at least, look across the international border at their Cold War adversary."

"The French-language teaching in the Physics Department had actually started in 1974.  Mukherjee, who since 1969 had been a Research Associate with Wiederick and Baird, was the only department member fluent in French (his early education in India had taken place in Pondicherry where the European language was French), and in the 1974-75 academic year he taught in French the entire set of Third Year physics courses in the Engineering Physics program - no mean feat for one's debut in professional duties."  [Mukherjee and Wiederick would eventually together focus their research on the characterization of dielectric and piezoelectric properties of materials.] [With extensive hiring from 1975 to 1977, the extension of French language teaching in the Physics Department to all four years was accomplished by 1977.]

David's official bio reads as follows:

David Carr Baird was born in Edinburgh where he attended George Watson's Boys' College and the University of Edinburgh.  His early interests included music, astronomy, researching historical sites for the Society of Antiquaries of Scotland, archaeological excavations, and mountain climbing.  While studying for his Ph.D. at St. Andrews University, he developed a lifelong love of flying while flying Tiger Moths as a member of the RAFVR Air Squadron at Leuchars.

In 1952 he joined the Physics Department at RMC to continue his research in superconductivity, and to participate actively in the development of physics curriculum at all levels from elementary to post-secondary.  He is the author of several physics texts that include Experimentation which has been in print since 1962.

Following his term as Head of the Department, he was appointed Dean of Science during a period of considerable change from 1980 to 1990.  During this decade the introduction of Space Science resulted in the creation of new research areas and educational programs.  In 1981 he became Director of an interdisciplinary team which constructed the first model in Canada of a superconducting motor for ship propulsion.

His early interest in archaeology was renewed when he undertook research as Visiting Scientist at the Laboratory for Archaeological Science and the History of Art at Oxford University (1980-95).

He encouraged his children [and his students] to follow their individual interests.


Update (March 1st):

Papers of B.N. Samoilov

Papers of V. P. Peshkov

Biography of B. Verkin

B. Verkin Institute for Low Temperature Physics and Engineering of the National Academy of Sciences of the Ukraine

Papers of B.K. Mukherjee

Wednesday, February 26, 2014

Lucky Numbers

from Surely You're Joking, Mr. Feynman
(Link)

One day at Princeton I was sitting in the lounge and overheard some mathematicians talking about the series for e^x, which is 1 + x + x^2/2! + x^3/3! + ... Each term you get by multiplying the preceding term by x and dividing by the next number. For example, to get the next term after x^4/4! you multiply that term by x and divide by 5. It's very simple.

When I was a kid I was excited by series, and had played with this thing. I had computed e using that series, and had seen how quickly the new terms became very small.

I mumbled something about how it was easy to calculate e to any power using that series (you just substitute the power for x).

"Oh yeah?" they said, "Well, then, what's e to the 3.3" said some joker - I think it was Tukey.

I say, "That's easy. It's 27.11."

Tukey knows it isn't so easy to compute all that in your head. "Hey, How'd you do that?"

Another guy says, "You know Feynman, he's just faking it. It's not really right."

They go to get a table, and while they're doing that, I put on a few more figures: "27.1126," I say.

They find it in the table. "It's right! But how'd you do it!"

"I just summed the series."

"Nobody can sum the series that fast. You must just happen to know that one. How about e to the 3?"

"Look," I say, "It's hard work! Only one a day!"

"Hay! It's a fake!" they say, happily.

"All right," I say, "It's 20.085."

They look in the book as I put a few more figures on. They're all excited now, because I got another one right.

Here are these great mathematicians of the day, puzzled at how I can compute e to any power! One of them says, "He just can't by substituting and summing - it's too hard. There's some trick. You couldn't do just any old number like e to the 1.4."

I say, "It's hard work, but for you, OK. It's 4.05."

As they're looking it up, I put on a few more digits and say, "And that's the last one for the day!" and walk out.

What happened was this: I happened to know three numbers - the logarithm of 10 to the base e (needed to convert numbers from base 10 to base e), which is 2.3026 (so I know that e to the 2.3 is very close to 10), and because of radioactivity (mean-live and half-life), I knew the log of 2 to the base e, which is 0.69315 (so I also knew that e to the 0.7 is nearly equal to 2). I also knew e (to the 1), which is 2.71828.

The first number they gave me was e to the 3.3, which is e to the 2.3 - ten - times e, or 27.18. While they were sweating about how I was doing it, I was correcting for the extra 0.0026 - 2.3026 is a little high.

I knew I couldn't do another one; that was sheer luck. But then the guy said e to the 3: that's e to the 2.3 times e to the 0.7, or ten times two. So I knew it was 20.something, and while they were worrying how I did it, I adjusted for the 0.693.

Now I was sure I couldn't do another one, because the last one was again by sheer luck. But the guy said e to the 1.4, which is e to the 0.7 times itself. So all I had to do is fix up 4 a little bit!

They never did figure out how I did it.

When I was at Los Alamos I found out that Hans Bethe was absolutely topnotch at calculating. For example, one time we were putting some numbers into a formula, and got to 48 squared. I reach for the Marchant calculator, and he says, "That's 2300." I begin to push the buttons, and he says, "If you want it exactly, it's 2304."

The machine says 2304. "Gee! That's pretty remarkable!" I say.

"Don't you know how to square numbers near 50?" he says. "You square 50 - that's 2500 - and subtract 100 times the difference of your number from 50 (in this case it's 2), so you have 2300. If you want the correction, square the difference and add it on. That makes 2304."

A few minutes later we need to take the cube root of 2 1/2. Now to take cube roots on the Marchant you had to use a table for the first approximation. I open the drawer to get the table - it takes a little longer this time - and he says, "It's about 1.35."

I try it out on the Marchant and it's right. "How did you do that one?" I ask. "Do you have a secret for taking cube roots of numbers?"

"Oh." he says, "the log of 2 1/2 is so-and-so. Now one-third of that log is between the logs of 1.3, which is this, and 1.4, which is that, so I interpolated."

So I found out something: first, he knows the log tables; second, the amount of arithmetic he did to make the interpolation alone would have to taken me longer to do than reach for the table and punch the buttons on the calculator. I was very impressed.

After that, I tried to do those things. I memorized a few logs, and began to notice things. For instance, if somebody says "What is 28 squared?" you notice that the square root of 2 is 1.4, and 28 is 20 times 1.4, so the square of 28 must be around 400 times 2, or 800. 

If somebody comes along and wants to divide 1 by 1.73, you can tell them immediately that it's 0.577, because you notice that 1.73 is nearly the square root of 3, so 1/1.73 must be one-third of the square root of 3. And if it's 1/1.75, that's equal to the inverse of 7/4, and you've memorized the repeating decimals for sevenths: 0.571428 . . .

I had a lot of fun trying to do arithmetic fast, by tricks, with Hans. It was very rare that I'd see something he didn't see and beat him to the answer, and he'd laugh his hearty laugh when I'd get one. He was nearly always able to get the answer to any problem within a percent. It was easy for him - every number was near something he knew.

One day I was feeling my oats. It was lunch time in the technical area, and I don't know how I got the idea, but I announced "I can work out in sixty seconds the answer to any problem that anybody can state in ten seconds, to 10 percent!"

People started giving me problems they thought were difficult, such as integrating a function like 1/(1+x^4), which hardly changed over the range they gave me. The hardest one somebody gave me was the binomial coefficient of x^10 in (1+x)^20; I got that just in time.

They were all giving me problems and I was feeling great, when Paul Olum walked by in the hall. Paul had worked with me for a while at Princeton before coming out to Los Alamos, and he was cleverer than I was. For instance, one day I was absent-mindedly playing with one of those measuring tapes that snap back into your hand when you push a button. The tape would always slap over and hit my hand, and it hurt a little bit. "Geez!" I exclaimed. "What a dope I am. I keep playing with this thing, and it hurts me every time."

He said, "You don't hold it right," and took the damn thing, pulled out the tape, pushed the button, and it came right back. No hurt.

"Wow! How do you do that?" I exclaimed.

"Figure it out!"

For the next two weeks I'm walking all around Princeton, snapping this tape back until my hand is absolutely raw. Finally I can't take it any longer. "Paul! I give up!  How do you hold it so it doesn't hurt?"

"Who says it doesn't hurt? It hurts me too!"

I felt so stupid. He had gotten me to go around and hurt my hand for two weeks!

So Paul is walking past the lunch place and these guys are all excited. "Hey, Paul!" they call out. "Feynman's terrific! We give him a problem that can be stated in ten seconds, and in a minute he gets the answer to 10 percent. Why don't you give him one?"

Without hardly stopping, he says, "The tangent of 10 to the 100th."

I was sunk: you have to divide by pi to 100 decimal places! It was hopeless.

One time I boasted, "I can do by other methods any integral anybody else needs contour integration to do."

So Paul puts up this tremendous damn integral he had obtained by starting out with a complex function that he knew the answer to, taking out the real part of it and leaving only the complex part. He had unwrapped it so it was only possible by contour integration! He was always deflating me like that. He was a very smart fellow.


Update (3/7/2014): A few of the calculations

e^3.3 = e^2.3 * e
e^3.0 = e^2.3 * e^0.7
e^1.4 = e^0.7 * e^0.7

Tuesday, February 25, 2014

Manifeste Refus Global (1948)

"Les voyages à l'étranger se multiplient. Paris exerce toute l'attraction. Trop étendu dans le temps et dans l'espace, trop mobile pour nos âmes timorées, il n'est souvent que l'occasion d'une vacance employée à parfaire une éducation sexuelle retardataire et à acquérir, du fait d'un séjour en France, l'autorité facile en vue de l'exploitation améliorée de la foule au retour. À bien peu d'exceptions près, nos médecins, par exemple, (qu'ils aient ou non voyagé) adoptent une conduite scandaleuse (il-faut-bien-n'est-ce-pas-payer-ces-longues-années-d'études!)

"Des oeuvres révolutionnaires, quand par hasard elles tombent sous la main, paraissent les fruits amers d'un groupe d'excentriques. L'activité académique a un autre prestige à notre manque de jugement.

"Ces voyages sont aussi dans le nombre l'exceptionnelle occasion d'un réveil.

"L'inviable s'infiltre partout. Les lectures défendues se répandent. Elles apportent un peu de baume et d'espoir.

"Des consciences s'éclairent au contact vivifiant des poètes maudits: ces hommes qui, sans être des monstres, osent exprimer haut et net ce que les plus malheureux d'entre nous étouffent tout bas dans la honte de soi et de la terreur d'être engloutis vivants. Un peu de lumière se fait à l'exemple de ces hommes qui acceptent les premiers les inquiétudes présentes, si douleureuses, si filles perdues. Les réponses qu'ils apportent ont une autre valeur de trouble, de précision, de fraîcheur que les sempiternelles rengaines proposées au pays du Québec et dans tous les séminaires du globe.

"Les frontières de nos rêves ne sont plus les memes . . ."

(Link)

Saturday, February 22, 2014

Wednesday, February 19, 2014

Violence Grows in the Ukraine

Panel session moderated by Michael Krasny of NPR's Forum on the growing crisis in the Ukraine.
(Link)

Thursday, February 13, 2014

Still Post Processing This . . .



I'm still processing this exchange.  I did read the ominous and darkly funny original post yesterday which appeared on the Bits of DNA blog. Without commenting on the full exchange and follow-up, I have to say that Lior's concern about the "Evidence for Abundant and Purifying Selection in Humans for Recently Acquired Regulatory Functions" paper seem to be worth merit:


Have to read the follow ups and corrections. Poor Reindeer. Poor Dogs. Poor Moo-moos. Poor Wolves. Poor us.


Update (2/16/2014):

1. It is highly worth reading the Why I read the network nonsense papers comments. In particular, a number of very well constructed comments are made by commenters who post under their real names:

Erik Van Nimwegen
Bioinformatics and System Biology
http://www.biozentrum.unibas.ch/~nimwegen/cgi-bin/page.cgi

Marc Robinson-Rechavi
Ecology and Evolution
http://www.unil.ch/dee/page22707_en.html

Gene Myers
Bioinformatics
http://www.homolog.us/blogs/

Nikolay Nicolov
Mathematical Institute
http://www.maths.ox.ac.uk/contact/details/nikolov

2. I note that as of tonight, Manoulis Kellis has responded to Lior Pachter. (pdf link) The response is also posted as comment 44 in the comment thread of the post on Why I read the network nonsense papers.

3. I look forward to those who are expert in the field of computational biology contributing their further thoughts.


Update (2/17/2014):
Adding:
Nicolas Bray
0.7535*Math + 0.6376*Biology + 0.5405*Statistics + 0.5320*CS + 0.4792
http://math.berkeley.edu/~nbray/

Sunday, February 9, 2014

North-South Ancient Admixture in Central-South Eurasia, Revisited

 
Quite early in the history of this blog, on November 3rd, 2010, I wrote a post discussing a minor "signal" I had noticed buried in the Dodecad admixture results for populations of Eastern Europe, the Middle East and South Asia.  The "signal" consisted of a combination of two Admixture components: "Northeast Asian" and "East Asian".  You can read about that early post here.  I've added a few thoughts on this topic recently, noting that the pattern is likely evidence of ancient bidirectional gene flow. (See Max Born on receiving the 1954 Nobel Prize . . ., Update, February 1, 2014.) 
 
In this post, I look at additional major components such as the "West Asian" component.
 
Reviewing observations from the previous posts, a number of deductions are possible:
 
1.  The "Northeast Asian"-"East Asian" admixture components are geographically correlated.
 
2.  The pattern extends from the Volga region of Southern Russia (Chuvash), into the Caucasus and Black Sea,  then into Pakistan, splitting westward through Syria into the Fertile Crescent, touching even into Egypt, and separately, trailing south through Pakistan extending west along the South Asian coast.
 
3.  The pattern is widely diffused compared to other admixture components.  In particular, it is much more widely diffused compared to the "North European" component and the "West Asian" component.  This wide diffusion is possibly indicative of great age since coalescence.
 
4.  As argued in the February 1st update of the post Max Born on receiving the 1954 Nobel Prize . . ., the "North European" component is likely correlated with pre-Ice Age hunter gatherers. 
 
5.  The "North European" component does not appear to be correlated with the "Northeast Asian"-"East Asian" pattern and is likely a superposition on it.
 
6.  The "Northeast Asian"-"East Asian" component does not appear to be present in the following populations considered in the Dodecad Admixture run:  Lithuanians, Cypriots, Spanish, French Basques, Tuscans, French, Northern Italians, Armenians, and Mozabite Berbers.  It is therefore uncorrelated with admixture in these populations.
 
In this post today, I look at three other major Admixture components with respect to the "Northeast Asian"-"East Asian" pattern.  These are the "West Asian", the "Southwest Asian" and the "Southern European" components.

Again, the data is normalized on the "Northeast Asian"-"East Asian" pattern. The remaining un-normalized components are allowed to float above this.  Figure 1 shows the zoomed in view with the normalization pattern running along the bottom.  This normalization approach corresponds with a North-South geographic pattern, as described in item "2." above.  Figure 2 shows the same data, but from a "zoomed out" perspective.  Populations are listed below Figure 2.

Figure 1:  Admixture components with normalized "Northeast Asian"-"East Asian" pattern show at bottom.  Components are arranged with highest "Northeast Asian" contribution on the left and highest "East Asian" contribution on the right.
 
Figure 2:  As in Figure 1, but "zoomed out" to fully show the un-normalized major components floating above the normalized "Northeast Asian"-"East Asian" pattern.
 
 Populations:
    1:  Chuvash
    2:  Lezgin
    3:  Georgian
    4:  Sindhi
    5:  Belorussian
    6:  Adygei
    7.  Pathan
    8:  Syrian
    9:  Turk
   10: Jordanian
   11: Romanian
   12: Ashkenazi
   13: North Kannadi
   14: Gujarati
   15: Uygur
   16: Burusho
   17: Egyptian

Looking at the above plots, the essential question to be asked is this:  Is there a correlation between the "Northeast Asian"-"East Asian" pattern and
 
1.  the "West Asian" component,
2.  the "Southwest Asian" component, or
3.  the "Southern European" component
 
?
 
The "West Asian" component is widely distributed.  In a few noticeable cases, such as the Chuvash, the Uygurs, the Burusho, and the North Kannadi, the "West Asian" component is only a very low level admixture component.  Based on this, it cannot be argued that the "West Asian" component is strongly correlated across the ancient "Northeast Asian"-"East Asian" pattern.  Moreover, the "West Asian" component is likely a superposition on this pre-existing population.  On the other hand, it has already been argued in another post that the point of coalescence of the "West Asian" component is somewhere in the Caucasus.   The distribution of the "West Asian" component centered about Georgians is vaguely apparent here.
 
The distributions of the other two major components "Southwest Asian" and "Southern European" are sparse and loosely distributed.   There does not appear to be an easily observable correlation between the ancient "Northeast Asian"-"East Asian" pattern and these components, at least from this data.


Saturday, February 8, 2014

The arrival of the frequent: how bias in genotype-phenotype maps can steer populations to local optima

Stephen Schaper and Ard A. Louis
(Link)

Abstract:

 
 
Figures:

 
 
 



 
 
Excerpts of interest:
 
Response when the population is too small compared to large populations:
 
 
Responses to environmental change:

 Phenotypes with a local high frequency fix at the expense of rare phenotypes:
 

Richard Feynman on the Double Slit Paradox: Particle or Wave?

 
    Richard Feynman's Double Slit Paradox Lecture (Cornell)
    (Link)

Thursday, February 6, 2014

The ocean's hidden waves show their power

  
Surprisingly, internal waves can sometimes be seen clearly in satellite imagery (like in the above image of the Luzon Strait). This is because the internal waves create alternating rough and smooth regions of the ocean that align with the crest of the internal wave. Sunlight reflects the smooth sections, appearing as white arcs, while the rough sections stay dark. MODIS data courtesy of NASA/Image processed at Global Ocean Associates.

David L. Chandler, MIT News Office
(Link)

““It’s an important missing piece of the puzzle in climate modeling,” Thomas Peacock [an associate professor of mechanical engineering at MIT] says. “Right now, global climate models are not able to capture these processes,” he says, but it is clearly important to do so: “You get a different answer … if you don’t account for these waves.” To help incorporate the new findings into these models, the researchers will meet in January with a climate-modeling team as part of an effort sponsored by the National Science Foundation to improve climate modeling.

“Beyond their effects on climate, internal waves can play a significant role in sustaining coral-reef ecosystems, which are considered vulnerable to climate change and to other environmental effects: Internal waves can bring nutrients up from ocean depths, Peacock says.”