Let’s talk about…things

I accidentally found this post by Massimo Pigllucci about metaphysics. I have no opinion about metaphysics. I only find the way philosophers talk amusing. Philosophy is probably the only academic discipline which uses the word “thing” as a professional jargon. The first time I saw the Heideggerian term “things themselves”, the image of giggling south cal teenagers came to mind.

“So, let’s talk about, like things and stuff, and you know, themselves…”

“Fer sur. I’m like totally into, you know, things surrounding us that exist…”

I mean, other branches of philosophy came up with difficult sounding words like différance. The best you can do is…things? Come on, guys. This is bad PR. The only impression I have about metaphysics is that it is the study of things.

PS: Massimo Pigllucci has some good stuff on his blog. This post is about libertarianism. I always found the word libertarianism, as it is used in the USA, confusing because it seems to be applied to contradictory things. As it turns out, that is because it is! Anarcho-syndicalism? anarcho-capitalists? People do love big words, don’t they…

The science of dog coats

Jerry Coyne’s blog has a good post (written by guest blogger Matthew Cobb) summarizing a new Science paper about the genetics of dog coats. [link]

I find the following most interesting:

However, although they open their article by pointing out that dogs and humans have lived together for around 15,000 years, they point out in their conclusion that dog “breeds” are an incredibly recent invention – less than 200 years. Inother words, in a couple of hundred year, artificial selection on just three genes has produced an incredibly variety of phenotypes. Furthermore, that selection may have focused on different characters, such as aggressivity or size, the genes for which may be linked to the coat genes. They conclude, “Consequently, in domesticated species, the appearance of phenotypic complexity can be created through combinations of genes of major effect, providing a pathway for rapid evolution that is unparalleled in natural systems.”

PS: I am finishing up a paper that I should have finished a year ago. Won’t post anything (except for short links) until the paper is submitted.

It’s Christmas (for paleoanthropologists)

Everybody is talking about the “new” hominid fossil, Ardipithecus. Carl Zimmer has a great write-up. [link]

Big Brain – by Gary Lynch and Richard Granger

A reader once asked me to recommend a popular book on the evolution of the brain. I suggested John Allman’s The Evolving Brain but I found it unsatisfying for many reasons. It is very broad in scope but doesn’t say too much about the human brain. I recently found Big Brain by Gary Lynch and Richard Granger and I am very happy to report that it is an excellent book. It includes a very good chapter that compares the brain sizes of various primates and hominids.

The evolution of the brain is a very important scientific question in its own right. The Big Brain includes several bold theories. I am very intrigued by the idea that the mammalian cortex is an elaboration of the ancestral olfactory system while the DVR (dorsal ventricular ridge) of the birds is an expansion of the ancestral visual system.

However, here I only want to mention something that’s tangentially related to the intent of the book. From the point of view of defending the theory of evolution, I think it is rather unfortunate that all popular books (for example, The Greatest Show on Earth) say nothing about the evolution of the brain. You can talk all day about e coli, plants, and insects, but people aren’t impressed by those. I hear it all the time. Evolution doesn’t explain really complicated things, like the brain. It’s about time educators and science writers devote some chapters on this topic.

Down Under (2)

I have mixed feelings about Bill Bryson. On one hand, he is a superb story teller. He captures the history and the culture of Australia so vividly and so effortlessly in Down Under that I wish he wrote a book about every country in the world. On the other hand, he is boring when he actually writes about his travels (which is kind of ironic for a travel writer). He is prone to cheap humor and exaggeration whenever he tries to transform his rather mundane trips into standup routines.

But I truly appreciate how much he loves nature. There probably is a naturalist in Bill Bryson. You simply don’t expect reading about the following things in a travelogue:

* The Giant Gippsland Earthworm. This earthworm can grow to 3 meters in length! I’ve been to Gippsland a few times but I never heard about this monster.

* Nothomyrmecia macrops, a very primitive ant. The story of how this species was discovered is remarkable.

* The Edicara biota discovered by Australian geologist Reg Sprigg. This is a collection of fossils more ancient than the Cambrian explosion. How come people don’t talk about the Edicara biota in evolution/creation debates?

The computation of congruent numbers

Wow. A note on number theory in Science. That doesn’t happen very often. I don’t know a thing about congruent numbers but it’s really exciting to see that the Fast Fourier Transform finds its way into number theory! From the article:

Both calculations used a staple in large-scale scientific computation known as the Fast Fourier Transform, adapted for number theory. In general, the transform streamlines otherwise unwieldy computations by systematically partitioning the data. It has been used, for example, in computing the first trillion digits of pi.

That is really amazing. The Fast Fourier Transform usually deals with continuous functions. How can you possibly use it in number theory? Boggles the mind. I remember I had a book on Harmonic Analysis (which I only read the first chapter) which spends most of the chapters developing the fourier transform for abstract algebras. I didn’t understand why anyone wants to undertake such a challenge. Why, maybe this is the answer.

If anyone can point me to a paper describing the “Fast Fourier Transform, adapted for number theory”, I’d be most grateful.

“A night vision neuron gets a day job”

I always suspected that part of the rod pathway in the retina is involved in photopic vision. It’s great to see my pet theory confirmed. See “A night vision neuron gets a day job” in Nature Neuroscience [link].

Down Under

I read Down Under by travel writer Bill Bryson while I was in Sydney for a short vacation. I found this story from the book irresistible. In short, somewhere in the 1980s, Australian scientists detected an unusual earthquake in the middle of a unpopulated desert. The waveform was unlike anything that was recorded and geologists couldn’t explain what it was. Nomads living near that area reported bright flashes in the sky. Four years later, after the Aum Shinrikyo Cult in Japan (the one whose members released Sarin gas in a tokyo train station) was busted, it was discovered that the cult owned a large property in Australian outback. The site happened to be where the earthquake was. Australian police raided that area and found a secret lab with sophisticated equipments and traces of radioactive materials. It was suspected that the Aum Shinrikyo Cult tested a small atomic bomb there.

I am very skeptical about the story because of Bryson’s tendency of exaggeration, but it captures the myth of Australian outback so well that I’ll pretend it is true.

Bryson made some very insightful observations about Australia:

1. The country is so big and so sparsely populated that you can detonate a baby nuke undetected.

2. The country is so isolated from the rest of the world that people outside Australian don’t hear about weird things like this.

Green-Tao Theorem

I have never been too crazy about number theory, but the Green-Tao Theorem (first proved in 2004) recently caught my attention. It states that the sequence of prime numbers contains arbitrarily long arithmetic progressions. It is very surprising to me because my impression is that prime numbers get sparse very rapidly. You’d think evenly spaced points can’t possibly all land on prime numbers. Intuitively, you need something like geometric sequences.

The Green-Tao proof was an existence theorem. It doesn’t tell us how to find those sequences. I can’t imagine how but mathematicians actually managed to find some finite-length arithmetic sequences that are all primes. For example,

6171054912832631 + 366384*223092870*n, for n = 0 to 24

That’s it? I was hoping for something very exotic, like numbers so large you need specialized notations to express them.

PS: I am fascinated by Graham’s Number. It has nothing to do with Green-Tao Theorem. I just like the idea of a number so large you need a specialized notation.

PPS: The other brilliant mathematical hack is Bill Gosper’s algorithm for doing arithmetic with continued fractions. One of these days I’ll figure it out and write a program to demonstrate how it works. Here’s an implementation in c.

PPPS: The Mathematica Demonstration Project is doing a terrific job popularizing mathematics. I want to see two demonstrations: 1. Bill Gospher’s continued fraction algorithm. 2. The Helmholtz decomposition of vector fields. They are among the most beautiful things in mathematics that I’ve encountered.

L’Archéologie du Savoir (V)

The last issue(vol 15. no 1) of the Skeptic magazine features an interesting article titled “Crazy Ideas 101″. The author Scott Calvin teaches a very inventive class on critical thinking. The fringe theories that he talks about in class includes a curious “theory” called Time Cube. I never heard of it so I looked it up in the wikipedia. yadi yadi yada … Time Cube is pretty much your average (perhaps I am being too generous here) crazy/incoherent cargo-cult science. But check out this line:

Bei Dawei of Hsuan Chuang University in Taiwan has written an exploration of Time Cube. In “Proving Human Stupidity: Time Cube, Gnosis, and the Challenge of Radical Cosmology”, he draws analogies between Ray’s achievements and those of the Greek astronomer Hipparchus.

Cool! A Taiwanese who is the world’s expert on Time Cube? Mr. Bei, I’ll buy you a beer for that.

PS: I can’t seem to find a copy of the paper. But here’s the abstract:

Nature’s Harmonic Time Cube Creation Principle (“Time Cube”) is the discovery of that complex and unique American thinker, Dr. Gene Ray, Cubic. His claim to have “squared the circle and cubed earth’s sphere” through a higher order of mathematical reasoning, curiously recalls previous moments of cosmological paradigm shift which were similarly accompanied by a compelling sense of renewed salvific wisdom, or gnosis, in opposition to a previous aeon of ignorance and servitude. At the same time, Time Cube represents a radical reordering of traditional hierarchies of knowledge and scholarship, as well as an excellent example of what amounts to a formidable contemporary wave of internet-based cosmological populism. We, Dr. Ray charges, were “educated stupid.”

The tone of the abstract doesn’t sound quite right.

PS: I got a copy of Bei Dawei’s “paper”. I am sorry. This is pure bullshit.

Darwin and literature

Jerry Coyne posted an interesting entry about literature and the theory of evolution. Since I am passionate about both, you’d think this is exactly the kind of thing that I want to see. I’ve been very critical about the uncrtical attitude towards Freudian psychoanalysis in humanities. Isn’t a darwinian approach to literary criticism a positive development? At least it’s based on science, not pseudoscience? Nope. Absolutely not.

1. As Jerry pointed out in his post, it is very unlikely that evolution has too much to say about literature. There is no literature module in the brain. There isn’t enough time to evolve one. A modular brain theory which aims to explain every single aspect of human endeavor is hopeless.

2. Do we really want professors of literature to speculate on fitness and adaptation? They simply don’t have the training to do so. Evolutionary psychologists are already bad enough.

3. I said many times in this blog: very soon, maybe in our lifetime, no scholars in humanities will be able to make a comment on human nature without mentioning evolution. However, it does not follow that every fruit of human endeavor requires a darwinian explanation. For example, evolution might (eventually) have a lot to say about creativity, but it doesn’t follow that every product of creativity requires an evolutionary interpretation.

The wikipedia has an entry about Darwinian literary studies (yes, such a beast does exist). It says:

A good example of applied Darwinian criticism is Joseph Carroll’s reading of Pride and Prejudice, which shows how the fundamental biological problem of mate choice informs the plot of Austen’s novel. In this view, the novel narrates a social order in which males compete on the basis of socioeconomic attributes such as money and rank, whereas females compete according to ‘personal’ attributes such as youth and beauty.

This is even worse than a Freudian reading of Pride and Prejudice. Why does anyone want to read Pride and Prejudice from this point of view? We already know the principles of evolution. If I want to see how it applies to the human society, I’ll read a paper or conduct a controlled experiment. Why do I want to read Jane Austen for this purpose? Or, you can turn this around and claim that we don’t read Jane Austen in order to illustrate evolution. Rather, we use the theory of evolution to understand Jane Austen. This is very problematic. Unless you can identify some special features in Pride and Prejudice that are uniquely Darwinian, this approach eventually lead to a position which says that all fictions, at least to some degree, are “about” the principle of evolution. I think it really misses the point.

I’ll try to put it another way. The theory of evolution is a valid tool in biology, because it is true. It works for biologists because it is how biology works. Why do we expect evolution to inform the plot of a novel? The world of a novel is not real. The development of characters, the dynamics of relationships are not real. They are the product of imagination, which is not bound by physical laws or biological laws. Unless the author intend to develop the plot as an allegory of evolution, there is no reason to expect darwinian themes in a work of fiction.

The only way out, it seems to me, is to insist that the imagination of an author is not unbounded. The job of a darwinian literary critic is then to demonstrate that no matter how hard an author try, in order for her work to be convincing, it cannot avoid darwinian themes. Two problems:

1. This is a scientific goal, not an artistic/interpretative goal. I would like to see a scientific theory of creativity. But to achieve it, we should do more experiments, not read more Jane Austen.

2. Assuming 1 is scientifically true, darwinian criticism will become as boring as pointing out that nowhere in the world of Pride and Prejudice does the law of gravity fail to operate. No shit.

L’Archéologie du Savoir (IV)

Check this out! It is wiki-azing.

The Vegetable Lamb of Tartary is a legendary plant of central Asia, believed to grow sheep as its fruit. The sheep were connected to the plant by an umbilical cord and grazed the land around the plant. When all the plants were gone, both the plant and sheep died.

Although it owed its currency in medieval thought as a way of explaining the existence of cotton, underlying the myth is a real plant, Cibotium barometz, a fern of the genus Cibotium. It was known under various other names including the Scythian Lamb, the Borometz, Barometz and the Borametz (pronounced Baranetz, from Russian baran (ram)). This plant produces a woolly mass supported by a number of stems. The Tradescant Museum of Garden History has one under glass.

L’Archéologie du Savoir (III)

Oskar Vogt (1870-1959) was one of the pioneers of cortex research. He was the first person who distinguished the isocortex (ie. the neocortex) and the allocortex. Here’s an interesting titbit about the history of neuroscience found in wikipedia:

In 1924, Vogt was one of the neurologists asked to consult on Lenin’s illness and was given his brain for histological study after Lenin’s death. Lenin’s brain showed a great number of “giant cells”, which Vogt saw as a sign of superior mental function. “The giant cells” were cortical pyramidal cells of unusual size. There were also particularities in layer 3.

In 1925 Vogt accepted an invitation to Moscow where he was assigned the establishment of an institute for brain research under the auspices of the health ministry in Moscow. In 1945 Lenin’s brain was still in the Institute of Berlin. According to claims of two Belgians, L. Van Bogaert and A. Dewulf, the Soviets carried out a military operation specifically to retrieve the brain before the Americans obtained it, and succeeded in doing so. The brain is now at Moscow’s Institute.

This version is somehow not exactly the same as the one I’ve been told. I heard that Vogt concluded that Lenin’s brain was unremarkable in every way, which offended the russians so much that he had to escape the country.

A mathematical fantasy inspired by Dr. Who

In the Dr. Who TV series (which is brilliant, by the way), a TARDIS is a spacecraft/time machine whose interior is larger than its exterior. Question: Is there a geometrical/topological object with this property? I never learned enough differential geometry in college to formulate this question more precisely, but intuitively this is impossible. Intuitively, the surface area of the two sides of a orientable manifold must be the same, although I don’t recall a theorem about it. Maybe it’s possible to formulate a geometry such that each manifold is associated with two metrics, one for the interior, the other the exterior. A TARDIS-like geometry seems to be possible (if not trivial) in this scenario.

Suppose that a TARDIS-like geometry can be formulated, the next question is, can you put a TARDIS inside a TARDIS? Consider a fractal in euclidean geometry. A fractal is a mathematical object consisting of smaller version of itself. In TARDIS-geometry, maybe it is possible to construct an object consisting of infinite, but exact copies of itself. Since I am apparently the first person who came up with this idea, I shall call this imaginary object… tarctal.

PS: The other question is, can you bring a TARDIS out of its mother TARDIS? Ie. Can you find a transformation (homeomorphism??) that project from the interior to the exterior of a TARDIS-like manifold?

The Locus Control Region of human r/g pigments

I started to read some classic papers about the genetics of color vision. Having very little formal training in molecular biology, I am hoping that this exercise will help me understand how this type of research is conducted.

The first topic I’m interested in is the regulation of red and green pigments in human retina. Red cones only express red pigments. Green cones only express green pigments. How is this done? The first paper I read is about the Locus Control Region (LCR), which is a short sequence upstream to the red pigment gene. The classic paper is

Wang et al. (1992) A Locus Control Region adjacent to the Human Red and Green Visual Pigment Genes. Neuron (9) 429-440.

This is a very good paper for physiologists with no genetics background to read because it is fairly self-contained. It relies on very few previous results and uses basic tools. The conclusion is straightforward: You need the LCR to express the red and green pigments. Without the LCR, none of the two is expressed. Patients with genetic defects which delete or mutate the LCR are monochromatic, having only the blue cones.

You’d think the most straightforward strategy is to remove the LCR from the genome of an animal, and see if the animal has only blue cones. I’m not sure if this is possible. Probably yes but not easy. But the critical issue is that mice don’t have the three cones that we have, so you have to use humans (or old world monkeys) to execute this plan.

This paper did something like this. You first construct a DNA sequence with a segment in front of the human red cone (which includes the LCR and other important things such as the promoter) and a reporter gene (beta-gal in this case). You insert this into the genome of a mouse, and see if the reporter gene is expressed in the cones of the mouse. If yes, you know that there is something in the cones of the retina that recognizes the LCR and causes the expression of the gene following the LCR. Since in human the genes following the LCR are the red and the green pigment, we know that the LCR is involved in the expression the red and the green pigments. You can then construct another sequence without the LCR, send it into an animal and see if the reporter gene is still expressed. If you delete the LCR and see no beta-gal expressed in the retina, you have proved your case.

The LCR was probably isolated with standard PCR and then it was fused with the beta-gal gene in a plasmid. The next step is to create a transgenic mouse. The sequence is injected to mice embryos. The offsprings have the sequence integrated into the genome of every cells. You look at the retina, and indeed, the blue beta-gal gene is only expressed in the cones of the animal. Note that the mouse has two types of cones. beta-gal is expressed in both. It is not expressed in rods and other types of retinal cells.

If the LCR is deleted, beta-gal is not expressed. The author also showed that the LCR is very conservative. It is present in genomes of mouse and bovine.

How is this related to the regulation of the red and the green cones? I’ll write about it in the next post in this series.

Stanley Fish is an idiot

[via PZ]

PZ does this thing in his blog. If someone says something stupid, he quotes it in Comic Sans font with a background of Monty Python’s Gumby character. I can’t tell you how much joy I get seeing Stanley Fish get the Gumby treatment. Yes, I wasted some of my youth in a department of literature where Stanley Fish was considered an important person. Now if you are scratching your head asking yourself, how is that even possible? I don’t know.

I am forced to conclude that an education in literature is bad for you, because it makes you say things like this:

Griffiths builds on the religious tradition in which curiosity is condemned because it distracts men from the study and worship of God, shackling them, says Augustine, “to an inferior love.” But curiosity can also distract men from secular obligations by so occupying their minds that there is no room left for other considerations. These men (and women) fail to register the pain of animals subjected to experiments in the name of knowledge, pay no heed to the social consequences of their investigations, and take no heed of the warnings issued in Marlowe’s “Dr. Faustus,” Mary Shelley’s “Frankenstein,” H.G. Wells’ “The Island of Dr. Moreau” and Robert Louis Stevenson’s “Dr. Jekyll and Mr. Hyde” (not to mention the myth of Pandora and the Incredible Hulk).

You see, curiosity is bad, because people who write stories say so. The logic is impeccable.

Brain Surgery

Since I’ve been doing lots of surgery this year, I find the Brain Surgery sketch by Mitchell and Webb irresistible.

What is the difference between a doctor and a brain surgeon? One is not exactly brain surgery. The other IS brain surgery!

Does evolution explain human nature?

“Obviously, says the monkey.”

I like this article written by primatologist Frans de Waal for the Templeton Foundation.

Money quote:

These primates show hints of a moral order, and yet most people still prefer to view nature as “red in tooth and claw.” We never seem to doubt that there is continuity between humans and other animals with respect to negative behavior—when humans maim and kill each other, we are quick to call them “animals” — but we prefer to claim noble traits exclusively for ourselves. When it comes to the study of human nature, this is a losing strategy, however, because it excludes about half of our background. Short of appealing to divine intervention as an explanation, this more attractive half is also the product of evolution, a view now increasingly supported by animal research.

This insight hardly subtracts from human dignity. To the contrary, what could be more dignified than primates who use their natural gifts to build a humane society?

李家同又亂放炮了!

李家同寫了一篇荒謬的文章, 叫 “如果Turing是中國人！“. 荒謬在哪裡?

1. 英國首相跟 Turning 道歉, 意義在於社會正義與人權. 李家同綁架這個新聞, 借機用來發表他膚淺的社會評論. 是什麼樣的公眾學者, 在這種場合不流下人道主義的淚水, 反而冷血的大談產業發展?

2. 李家同大幅簡化了 Turing 對基礎科學的貢獻, 他的感歎完全抓不到重點. 對解決他所關心的問題沒有幫助.

3. 他連基本的史實都搞錯.

好在有專家批評, 我就不多嘴了. 請大家參考以下兩篇:

* 關於英首相向 Turing 致歉

* 創意 v.s. 基本功？

L’Archéologie du Savoir (II)

Who is Paula Nancy Millstone Jennings? Paula, of course, composed the worst poetry in the entire universe.

Vogon Poetry is of course the third worst in the Universe. The second worst is that of the Azgoths of Kria. During a recitation by their poet master Grunthos the Flatulent of his poem, Ode To A Small Lump of Green Putty I Found In My Armpit One Midsummer Morning, four of his audience died of internal haemorrhaging, and the President of the Mid-Galactic Arts Nobbling Council survived by gnawing one of his own legs off … The very worst poetry of all perished along with its creator Paula Nancy Millstone Jennings of Greenbridge, Essex, England in the destruction of the planet Earth.

Douglas Adams, The Hitchhiker’s Guide to the Galaxy.

I read The Hitchhiker’s Guide before the internet. As the only person in the college who was nerdy enough to read this book (you see, Douglas Adams isn’t that popular in Asia), I had no one to turn to for one of the most burning questions I had in my youth: Who is Paula Nancy Millstone Jennings and how bad is her poetry? I probably wasted a year taking classes in The Department of Literature, just to prepare myself. I had to make sure that I know bad poetry when I am confronted with bad poetry. I read my share of T. S. Elliot and Ezra Pound but I wasn’t impressed. There has to be poetry worse than The Waste Land. A lot worse. I have to find me some Paula Nancy Milstone Jennings.

As it turns out, Paula Nancy Millstone Jennings of Greenbridge, Essex is based on Paul Neil Milne Johnstone of Redbridge, Essex, a classmate of Douglas Adams. The following, apparently, is the worse poem in the universe.

The dead swans lay in the stagnant pool.
They lay. They rotted. They turned
Around occasionally.
Bits of flesh dropped off them from
Time to time.
And sank into the pool’s mire.
They also smelt a great deal.