Cavalcade of Mammals

Today Slashdot had an ‘Ask Slashdot’ post asking the question “Mathematics Reading List For High School Students?” Slashdot reader comments usually start are typically dismal and often worse. The only useful comments I’ve seen come to questions both technical and obscure. Looking for a Scheme compiler for the Commodore 64 or tools for hacking a router and Slashdot commenters can help.

But today a rare gem, an interesting question of general interest on /. worth reading. Here’s a summary of the suggestions:

(the obvious: Flatland, GEB)

How to Lie with Statistics by Darrell Huff, 1954
Men of Mathematics by E. T. Bell
How to Think Like a Mathematician: A Companion to Undergraduate Mathematics by Kevin Houston
All the Mathematics You Missed But Need to Know for Graduate School by Thomas A. Garrity
Prisoner’s Dilemma by William Poundstone
Schaum’s Outline of Linear Algebra by Seymour Lipschutz
The Feynmann Lectures on Physics by Richard Feynman, Robert Leighton, and Matthew Sands
Surely You’re Joking, Mr. Feynman by Richard Feynman
Bringing Down the House: The Inside Story of Six M.I.T. Students Who Took Vegas for Millions by Ben Mezrich
The Golden Ratio: The Story of PHI, the World’s Most Astonishing Number by Mario Livio
Fermat’s Last Theorem by Simon Singh
The Code Book: The Science of Secrecy from Ancient Egypt to Quantum Cryptography by Simon Singh
The Codebreakers: The Comprehensive Story of Secret Communication from Ancient Times to the Internet by David Kahn
Against the Gods: The Remarkable Story of Risk by Peter Bernstein
Knots : Mathematics with a Twist by A. B. Sossinsky
The Little Schemer by Daniel P. Friedman and Matthias Felleisen
The Pleasures of Counting by Thomas William Körner
Innumeracy and A Mathematician reads the Newspaper by John Allen Paulos
The Shape of Space by Jeff Weeks
‘e’: The Story of A Number by Eli Maor
What is mathematics? by Courant and Robbins
A Pathway Into Number Theory by R. P. Burn
Zero: The Biography of a Dangerous Idea by Charles Seife
A Long Way From Euclid by Constance Reid

and to add a few not mentioned:
Chaos by James Gleick
Five Equations That Changed the World: The Power and Poetry of Mathematics by Michael Guillen
Mathematical People: Profiles and Interviews by Donald J. Albers and Gerald L. Alexanderson

And last and best, any of the books of Martin Gardner’s Recreational Mathematics columns from Scientific American.

I read a review of Michael Brooks’s 13 Things That Don’t Make Sense on the Uncertain Principles blog. I haven’t read the book, but the review tickled me enough that I looked around for more info and found Jennifer Ouellette’s review in The New Scientist where Brooks is a contributor.

Both Chad Orzel and Jennifer Ouellette give Brooks weak “this book has some weak parts but also some good parts” reviews. Just from the reviews and blurbs I can tell Brooks book is destructive, part worthless speculation on the meaning of anomalous results that are almost certainly erroneous and part flattering discussion of pseudoscience.

Why are people giving Brooks such gentle reviews? The physics results are typical of the lot. John Webb’s fine-structure result is of the same sort as the Viking experiment result. Interesting if true, but not reproduced and instead contradicted by other experiments and thus uninteresting.

Brooks doesn’t understand that for something to not ‘Make Sense’ it has to be true. Anomalous *verified* results, results that can’t be explained theoretically or seem to contradict existing results are the kinds of things that ‘Don’t Make Sense’ but could be cool. These are the kinds of things that Brooks should be writing about.

One of Brooks’s topics is the mimivirus, a virus with the largest genome known so far (1.2 Mb). I can’t imagine anything particularly Earth shaking about it–it’s really big for a virus, but that’s it. Biology is littered with oddities and weird exceptions. No one tell Brooks about ttn-1, a titin protein 57X larger than the average worm protein. Or about the ostrich.

The placebo effect has two components, self-delusion and a poorly understood mechanism whereby the state of mind can affect the body. The mind->body connection is true and poorly understood, the proper subject of Brook’s book.

In Jennifer Ouellette’s review she says that Brooks includes homeopathy because of its relation to the placebo effect. This is ridiculous–any of the thousands of worthless ‘medical’ treatments known from blood letting to magic spells have this property.

Brooks’s inclusion of homeopathy and death is complete nonsense. Homeopathy is pseudoscience, bunkum. And there well understood evolutionary reasons why organisms die, death (and aging) are not even anomalous.

Twee.

I had an idea for a game. It’s a memory game, the idea is to flash a molecule on the screen for a few seconds in the left hand window, then in the window to right the player builds the molecule. That’s basically the game. The player learns to recognize interesting chemicals, learns to break down larger molecules into functional groups as a way of remembering them, and perhaps learns what they are.

As the molecule fades it would be replaced with a picture that goes with the molecule–oranges for citric acid, as a memory aid or a clue for the chemically astute player.

The game could be made easier by having the molecule fade out slowly, or flashing on periodically, or visible through a port.

I don’t really want to write a molecule editor myself, that would take a lot of time and also it turns out to have been done by chemist/programmers many times. Yeah! Some very good molecular editors are out there. I was particularly impressed with Molinspiration WebME editor. Two problems though, it’s 2D and not open source.

Looking further, I found BKchem and molsKetch both of which look good and are GPL licensed but are 2D. Jamberoo is Java based but the molecule editing worked too slowly for a game.

Avogadro is 3D, is GPL licensed so the source code is available, and works on Linux/OSX/Win. It looks good and works well, so I think it would make a good starting point for a game.

Vitamin C in Avogadro:

Pepper spray has been around for years now, but there is not commonly available antidote. And we know how the active ingredient, capsaicin acts to active, or hold open, the ion channels that transduce pain signals. In fact, a quick Google shows that capsaicin binds and activates a receptor called the vanilloid receptor subtype 1 (VR1), a member of a group of related receptors called TRP ion channels that are activated by temperature changes.

Capsaicin chemical structure (from Wikipedia)

So an antidote would be an inhibitor of the VR1 receptor, and such a thing should be easy to find, or create, and in fact another Google shows that several have been created. Capsazepine was the first inhibitor discovered, way back in 1994. Activators and inhibitors of this receptor have many potential uses as analgesics and anti-inflammation compounds so there is a lot of research interest.

Capsaicin inhibitor capsazepine (from Wikipedia)

A spray containing one of these inhibitors should be an effective antidote for pepper spray. But surprisingly no such inhibitor is available! The small quantities of purified inhibitors are available in small quantities for research purposes (i.e. capsazepine, 50mg for $455 but I can’t find anyone who has made an antidote preparation. This should be safe and fairly easy. Safe, because it would be applied mainly externally, and because pepper spray is itself fairly safe–aside from the pain and shock it is used to cause. It doesn’t have other, non-specific side effects. And relatively easy to make because the literature describes the synthesis of inhibitors from capsaicin itself. So the starting product used to make an inhibitor can be capsaicin, and capsaicin is readily available in large quantities!

Update:
Wikipedia: Discovery and development of TRPV1 antagonists

I find it fascinating that things part of common knowledge today were discovered relatively recently. Here is something not known in the 1860s, from Darwin’s Origin of the Species, p 29-30:

I do not believe, as we shall presently see, that all our dogs have descended from any one wild species; but, in the case of some other domestic races, there is presumptive, or even strong, evidence in favour of this view.
…
The whole subject must, I think, remain vague; nevertheless, I may, without here entering on any details, state that, from geographical and other considerations, I think it highly probable that our domestic dogs have descended from several wild species.

We now know that all dog breeds are descended from wolves through a domestication event or several closely spaced domestication events about 100,000 years ago. This explains why dogs are found with aboriginal human groups throughout the world.

This is from a section describing how in most domesticated animals have many breeds or varieties yet are descended from a single wild species. In the 1860s, the the evidence pointed to more than one wild ancestor for dogs.

I was thinking about Godel, Escher, Bach – An Eternal Golden Braid because I started up my ant farm. It’s an incredible book, a work of genius that blew my mind when I read it in HS. Turns out Douglas Hofstadter, the author, has a new book out that is described as covering similar ground titled I Am a Strange Loop. So I wanted to reread GEB. I looked around and checked my book list, but no GEB. I’ve really got to pick up a copy!

Quote from The Origin of the Species Introduction:

In considering the Origin of Species, it is quite conceivable that a naturalist, reflecting on the mutual affinities of organic beings, on their embryological relations, their geographical distribution, geological succession, and other such facts, might come to the conclusion that each species had not been independently created, but had descended, like varieties, from other species. Nevertheless, such a conclusion, even if well founded, would be unsatisfactory, until it could be shown how the innumerable species inhabiting this world have been modified, so as to acquire that perfection of structure and coadaptation which most justly excites our admiration.

The first paragraph of Charles Darwin’s Origin of the Species:

INTRODUCTION
WHEN on board H.M.S. Beagle, as naturalist, I was much struck with certain facts in the distribution of the inhabitants of South America, and in the geological relations of the present to the past inhabitants of that continent. These facts seemed to me to throw some light on the origin of species?–that mystery of mysteries, as it has been called by one of our greatest philosophers. On my return home, it occurred to me, in 1837, that something might perhaps be made out on this question by patiently accumulating and reflecting on all sorts of facts which could possibly have any bearing on it. After five years’ work I allowed myself to speculate on the subject, and drew up some short notes; these I enlarged in 1844 into a sketch of the conclusions, which then seemed to me probable: from that period to the present day I have steadily pursued the same object. I hope that I may be excused for entering on these personal details, as I give them to show that I have not been
hasty in coming to a decision.

I’ve never read Origin, having thought of it as mainly of historical interest and not relevant today. But it does have a wealth of examples and descriptions of animals and their niches that now seems interesting to me so I’m having a go it. The Voyage of the Beagle should have even more of this sort of thing, but I figure it makes sense to read Origin first.

It’s funny that Darwin starts his book protesting that he is not hasty. He is the least hasty scientist of which I’ve ever read.