Sunday, February 3, 2013

A couple of good reads

I recently read and enjoyed three excellent books:

  • George Saunders' The tenth of December - The best fiction I have read in a long time. I was drawn to this book by a wonderful article in the NY Times article (George Saunders has written the best book you'll read this year). The book completely lives up to the hype. I couldn't put it down. I am currently reading another of his books (CivilWarLand in bad decline). Check out two of his excerpted short stories from tenth of December and you'll see what I mean (1 and 2).
  • Jim Holt Why does the world exist?: an existential detective story - A wonderful read on why there is something and not nothing. This book goes well with two others I've read in recent years (Brian Greene The hidden reality and Lawrence Krauss A universe from nothing). Holt's approach is more philosophical, and he does a wonderful job framing the problem from this perspective. I was surprised that he even provides his own ontological justification for why there is something rather than nothing and why we could rationally expect that something to be utterly mediocre.
  • Julian Barnes The sense of an ending - Barnes' engaging (meta-)commentary on the narrative impulse. The book's self-referential title says it all. We need crave the sense of an ending just as we crave the sense of a reason in an unreasonable world. This is all succinctly put by Barnes when he has a character quote: "History is that certainty produced at the point where the imperfections of memory meet the inadequacies of documentation."

 Currently reading

  • Oliver Sacks Hallucinations - excellent book that resonates with two questions that I can't shake: what is the physical basis of the subjective (first-person) experience and how different can it become. If you haven't read Sacks' Altered States in the New Yorker you really must. 

Tuesday, December 18, 2012

A very fractal christmas

Multivariable Calculus Class Does Christmas (fractals)

Please respond using the survey below to choose your favorite!

Sunday, September 23, 2012

Updates on The Junot Diaz Challenge and a new book club!

On September 29, 2011, I set the goal of reading 100 books in a year. The goal was a large one and pushed me to do a lot of reading that I definitely would not have done otherwise! However, in case you are wondering, I totally failed at this goal by pretty much any measure, despite my best intentions:
In case you are counting, you will notice that I am a bit behind my pace: we are one month down and I have read 5 books (off my 6 books a month pace while teaching). Not to worry, I am still working hard on this project and will be back on top of my rate in no time. Stay tuned!
Over the course of the year, I have occasionally posted about my readings, but recently, I have been kind of radio-silent! This is the long overdue post to update you on my progress.

In November, I encountered what would become a major flaw in the 100 books in a year ideal and subsequently my inability to set a new goal: the very real time restraints imposed by my teaching schedule combined with a rather arbitrary restriction (that I read a book); and what is a book? Certainly not a chapter, article, blog post. Do short books count equally as well as long books? So we are penalizing longer books with this system? What about podcasts, do these count not at all?

Basically, I reset my goal to find interesting questions to consider and just do that with my free time as much as possible (limiting time spent doing things that distracted me from this goal).

I have had a wonderful time with the challenge I set for myself and over the course of the year I learned about a lot of really cool stuff!

Here is a partial list of things I thought about, learned and read:





Blogs/Articles (noteworthy)

Good source of books off copyright

Excellent PDF about the creativity needed to do real mathematics

I have started an Evidenced-based education group at St. Andrew's and am looking forward to reading a couple good books (Sahlberg and Perkins) on the subject as well as studies

Reading now

Check out the book club that John Burk started about this book!

Dawkins is still at the top of his game!

Monday, November 28, 2011

Travels with Charley (JDC #11)

Steinbeck left us a lively record of an ancient US

I had a great treat reading Nana and Poppi's (my grandparent's), 1962 version of this book. Steinbeck takes us along with his dog Charley on a trip through the US during a period characterized by the nation's racial growing pains. 

When I was in Salinas this summer with Neemu, we visited Rocinante, his truck and home during this journey, at The National Steinbeck Center (the link is to another blogger's page with some nice shots of the center - one is included below):

A journey is a person in itself; no two are alike. And all plans, safeguards, policing, and coercion are fruitless. We find after years of struggle that we do not take a trip; a trip takes us.

My wayward spirit makes me a natural consumer of a book like this and Steinbeck did not let me down. I love travel literature*, and if you do too, check it out^!  

* Other books I have enjoyed that remind me of this one include: A Walk in the Woods (thank you India D.), On the Road, Zen and the Art of Motorcycle Maintenance, Big Sur, Dharma Bums, Fear and Loathing in Las Vegas, The Sun Also Rises, The Grapes of Wrath, and My Antonia.

^ You may have read a recent NY Times article that raised questions about the authenticity of Steinbeck's account. Check that article out if you haven't. It seems appropriate to quote Steinbeck here. On page 125, he appears to believe that impulse for investigation to reconstruct the past is simultaneously impossible to deny and necessarily insufficient to fully form an account of another person. After burning another man's lost court order to pay overdue alimony, he says: "Good Lord, the trails we leave! Suppose someone, finding [my journalling detritus], tried to reconstruct me from my notes."

Saturday, November 26, 2011

The Moral Landscape (JDC - #10)

The philosophical basis for the science of morality

Unlike many of the other books I read, I didn't enjoy this book as much as I expected to. While the book raised a number of interesting philosophical questions (which I had almost without exception encountered elsewhere), Harris did not (and could not in the short book) engage much of the relevant philosophical literature on ethics. Of the scientific and anti-religious material he discussed, the book was at times engaging but, too often, poorly organized. 

Ultimately, Harris's motivation to ground discussion of morality in science is one to which I am very sympathetic. It is a motivation that results from his belief that moral questions are ought not be answered by religion*, to which Steven Jay Gould surrendered them with his non-overlapping magisteria. To the extent that I believe that religious evidence is irrelevant to questions in general, I agree with Harris (and Dawkins and others of the new and old atheists who have made this point). The most compelling frameworks we use to organize our experiences are those that are compatible with scientific/naturalistic explanations of the world. This includes moral and cultural values.

That said, we are a very long way from proving which code of conduct will yield the most "well-being" for two people, let alone two cultures (comprising billions of people in the world).^ It is probable that, like many interesting problems (deriving economic forecasts, predicting a chemical reaction from the first principles of quantum mechanics, solving the protein-folding problem in biology, proving or disproving that P = NP in computer science, or demonstrating the truth of a statement in a formal system), it is, in a general sense, intractable. If this is the case, there may be no obvious better system than making corrections to a free-market economy in a liberal democracy via scientific discoveries.**

There may be no chance of (stable) unconditional cooperation among man

Harris correctly points out that without cooperation his dream of higher and higher levels of well-being among nations will not be possible. There have been simulations of repeated interactions among agents that show that while unconditional cooperation is a destination for some game theories, it is often not a final destination.

Martin Nowak does an excellent job of describing the expected long term strategies in repeated games. What he finds in his model is not one final best policy of conduct but instead a repeating cycle of unconditional competition -> tit-for-tat -> generous tit-for-tat -> unconditional cooperation then back to unconditional competition, and on and on. 

Check out his lecture to the Royal Society:

I hope to read his book, Supercooperators next.

There are a number of reviews of the Moral Landscape if you are interested in points of view other than mine.
* Typically when scientists rail against religion they are particularly angry with Western religions (the God of Abraham). If by religion we are willing to include Baruch Spinoza's "religion as naturalism" (God = Nature), then the two are completely overlapping (are one magisterium). Most religious people I know would consider Spinoza to be an atheist and as such would be unpalatable. Eastern religions can be even more compatible with naturalistic values, but these are typically not considered.

^ The fact that we do not even have a good definition of "well-being" was discussed in the book, but is perhaps a more important limitation than we fully grasp. Furthermore, even if we had a good definition that was universally accepted (not likely until we have a world without religion - ahem), we will have the problem of intractability. John von Neuman's, minimax theorem works for two people in a zero-sum game, but this is not one of those.

** To claim that there is a better solution would require an argument much more convincing than Harris has proffered. Other objections to any policy are: the problem of unintended consequences (Harris acknowledges), the problem of logistics (any solution relying on cooperation will have cheaters), the problem of evil, the problem of intractability (mentioned in previous footnote); and the problem of learned helplessness (via aid); to name a few. Check out Dead Aid to see possible unintended consequences of even our most humanitarian altruistic impulses:

Tuesday, November 22, 2011

#9: Incompleteness by Rebecca Goldstein

The proof and paradox of Kurt Gödel

I have admired Gödel since I read Hofstadter's: Gödel, Escher, Bach: an eternal golden braid. I hadn't read his work as a logician, but would talk with friends about it (and its implications) informally. That is, until I was chatting with Suman in 2008. He could tell that I would benefit from reading a popularization of his incompleteness theorems that dealt more directly with the content of his proof, so he and Anjali gifted me this book for my birthday (Harvey-mas).

The book was a joy to read (man have I been lucky with these books - I seem to say that they all are great). I enjoyed learning about Gödel's life - his life in Vienna, his work on the proofs, and his cherished walks with Einstein, another scientist who Rebecca Goldstein argues is intellectually exiled* by his theories/proofs - and the proof itself.

When I was an undergraduate in an introductory course on philosophy and discussing a number of important proofs, I found myself wishing for an airtight proof that the axioms of an argument were correct. Could there be assurance that I was using the right axioms? If not, I might come to the completely wrong conclusion despite using a rational argument. As you know, in any argument, the conclusions follow from the premises via rules of inference

At the time, I constructed an argument by analogy that no such proof existed since we could not imagine removing a condition, which we could not imagine removing (e.g. one could not imagine removing from the set of axioms that a human mind is a prerequisite for rational argument). Just as a fish would not have a concept for water (since it had always been fully surrounded by water and there had never been not water for it), so too, we humans could be fully immersed in some set of beliefs or conditions which would be impossible to imagine going without. 

Via Gödel's incompleteness theorems**, Gödel proved that such a program was useless: we cannot justify a set of premises in a logical system using the logic alone. If you are interested in the context from which Gödel's work arose, check out: Hilbert's program, and the Liar's paradox (i.e. "This sentence is false".

Implications of incompleteness

While many others extended the incompleteness theorems to the humanities, the computer sciences, and intelligence research (see Penrose for example), Gödel himself was more reticent to extend his theories. He does have this to say about the differences between men and machines though:

Either the human mind surpasses all machines (to be more precise it can decide more number theoretical questions than any machine) or else there exist number theoretical questions undecidable for the human mind.

By this, Gödel seems to suggest that either we are not like a machine (because our decision mechanism is not, at base, mechanical), and we have access to truths that a formal system would find unprovable; or else, we are at base complicated machines that have deluded ourselves into believing we have access to unformalizable mathematical truths.
* While both Einstein and Gödel achieved a large degree of fame for their discoveries, Goldstein argues that it was the world's subjectivist interpretations of each man's theory that lead to their respective marginalization. For Einstein and Gödel, their work bespoke the objectivist reality of Physics (physical realism) and Mathematics (Platonism).

** From Wikipedia: "For any formal effectively generated theory T including basic arithmetical truths and also certain truths about formal provability, T includes a statement of its own consistency if and only if T is inconsistent."

Sunday, November 20, 2011

QED (Richard Feynman) and The Price of Altruism (Oren Harman) - JDC: #7 and #8)

Richard Feynman describes strangeness better than anyone

If you can't explain it to a six year old, you don't really understand it. 

Before QED, "Surely your joking Mr. Feynman" and "What do you care what other people think?", his autobiographical works, were all I had read. 

However, I was excited to read a slightly more technical work because no one puts complicated physical phenomena so simply. His wonderful humility, sparkling sense of humor and highest standards of explication are unmatched among the science writers I have read. 

It was a joy to learn how the probabilistic nature of photons lead to our everyday experience with light: it moves in straight lines, it bends (or slows down) in different media such as water, white light can be decomposed into its various colors when passed through a prism or diffraction grating, plus many more.

Some unanswered questions remain. I don't understand the origin of the complex component of the amplitude vector that Feynman gives to each photon in his vector diagrams. Although this was not a focus of his teaching in the book, it was something I would like to investigate further. This, combined with my excitement to learn more from whatever has been published of his masterful teaching, lead me to purchase the complete "Feynman Lectures on Physics." I doubt they will fall under the purview of the current Junot Diaz Challenge postings, but perhaps I will write some thoughts as I have them, here.

Altruism <= game theory + (multi-level) selection

Oren Harman's book about George Price is a very engaging, in-depth, discussion of the history of the science of evolution after Darwin. Two central questions of the book, and indeed, evolutionary biologists in the 20th century were: what is it that nature selects (genes, organisms, groups, populations)? What explains that a self-interested evolving unit (gene, organism, group) acts, at times, altruistically (accepting a cost to itself to benefit another)? Examples discussed in the book that shed light on these questions include: The sex-ratio in organisms (selection at the level of the individual should result in 1:1 and often does), virulence of viruses (natural processes of attenuation imply group selection may be at work), and the life-cycle of slime mold. Starving slime molds consist of single-celled amoeba which die for others (creating a stalk of dead cells) to allow other amoeba to climb and create a fruiting body (cells of amoeba higher up) which will be transported by animals or the wind to live another day (check out a nice movie of the process below).

(Fascinatingly, it was found that in the wild, these stalks are typically formed from a single clone. That is, the amoeba that group together are identical. They share the same genome and are therefore not anymore altruistic than a cell in my arm, which sacrifices itself after absorbing a toxin from the environment to protect a cell in my liver, or brain or any other integral organ to improve my survival chances and thus the chances that I will pass-on my genes - the very same genes that include instructions for reproducing that sacrificial skin cell.)

My history-myth about multilevel selection

George Price, among many others described in this book, were entranced by questions of how best to apply the ideas of evolution to solve evolutionary riddles. In particular, could altruism among units of evolution (genes and/or individuals and/or groups) be understood best by analyzing the problem at the level of the gene or higher up or both. 

Richard Dawkin's own wonderful book, The Selfish Gene, argues that the gene is the only necessary unit to consider when trying to understand a given phenomena. He envisions each individual as a vehicle or husk, for its genes. The gene is in a fight against all other genes to reproduce itself most effectively. The gene will only form alliances if that means that it will improve its reproductive success (as in the case of multicellular organisms).

This gene's-eye view of evolution is a powerful way to understand the evolutionary solutions to biological problems, and it, combined with William Hamilton's cost benefit equation*, can explain a wide-range of phenomena. Among these are wonderful game theoretic problems (introduced as a mathematical discipline by John von Neumann^ and popularized by many others including John Nash) such as the prisoner's dilemma that cast multi-agent problems in a mathematical frame (finding evolutionary stable strategies in a population).

However, it was found that the gene's-eye view is not mutually-incompatible with the view that group selection can also occur. Just as the laws of physics must always be obeyed when one employs a biological or chemical law to solve a biological problem (since the equivalent physical statement of the problem may be intractable or represent an inefficient solution path), so too rules of genetic selection must be obeyed (including the laws of chemistry and physics!) when one uses individual or group selection ideas to solve a problem. Harman summarizes David Sloan Wilson's work** on group selection as follows: began to become clear that the unit of selection [gene, individual or group] and the level of selection [gene, individual or group] depended entirely on different criteria. Of course genes were replicators, and clear units of permanence. But whether a certain level of life could be viewed by selection depended not on permanence but on where fitness differences resided in the biological hierarchy. Here is why: If a population is viewed as a nested hierarchy of units, with genes existing within populations and so on, fitness differences can exist at any or all levels of the hierarchy because heritable variation can exist at all these levels... Despite all the history and hype, the gene's-eye view and group selection are not, an never should have been, antithetical.

Price's mathematical treatment of trait change in evolution

George Price's work is a wonderful addition to this discussion because he provides the mathematical relationship that allows us to account for the average trait change in evolution due to selection and transmission. 

Here, Harman has used z and z(overlined) to mean a character (e.g. a phenotype) and its respective average value; w is the fitness of the character; and the covariance, Cov, and expected value, E, functions are as they are typically defined mathematically. However, if one wants to consider the resultant trait change due to transmission one level down (e.g. from organism to gene), we can consider the nested version:

where the right hand side is inputed iteratively as many times as needed (for each level). With enough data, we can imagine determining which of the terms in the sum is most important and attribute the relative importance of group or individual or gene selection. I have to admit that I have not seen this done, but would love to see an example of this to more fully appreciate its value. 

Overall, Harman's treatment of the history of evolutionary biology and his biography of George Price's life (of which I have not commented here) is excellent. I really enjoyed considering some of these wonderful problems and hope you will too if you have the inclination and the time. Thank you Scott and Veena for this thoughtful present.*^

* Hamilton's cost benefit equation states that an organism is willing to incur a cost, C if the aggregate benefits, B, to its kin, defined by r, are greater (rB > C). Ideal relatedness can be calculated: a parent or sibling shares 1/2 of genes (r = 0.5), each grandparent or uncle shares 1/4 (r = 0.25), each first cousin shares 1/8 (r = 0.125). Note these assume that there is no incest. The calculation is simple in that for every line drawn as a consequence of sexual reproduction, one simply needs to multiply the previous relatedness by 1/2. If there are multiple ways to reach a family member, the two paths are added (e.g. for a sister, 1/2 * 1/2 + 1/2 * 1/2 = 1/2 since I can think of the connection from me between mom and sister or dad and sister). Note that for half siblings, r = 0.25. Thus J.B.S. Haldane famously quipped:
I would lay down my life for two brothers or eight cousins.
Note that Hamilton's cost-benefit equation is being applied by J.B.S. Haldane at the level of the individual instead of the gene. Dawkins does this often in his book as well.

^ Incidentally, John von Neumann also provided the mathematical basis of quantum theory and is therefore the godfather of both of these books.

** For a nice review article on multilevel selection by David Sloane Wilson and E. O. Wilson check out this pdf.

*^Scott Johnson and Veena Reddy, now members of my family, gave this book as a gift to me a few years ago (this shows you how many books I still need to read) after I told them about my proposal to work with two microorganisms (distinct single-knockout mutants) in the lab to see if they could evolve to cooperate over time. With this platform technology (i.e. knock-outs which via natural evolutionary process maximize fitness through cooperation), one could engineer "multicellular" cooperative microbe populations that solve important problems (e.g. photosynthesize light and create biofuels [cooperation between algae and engineered yeast]).