Cavalcade of Mammals

Here’s my list, not ten but as short as I could make it. It’s roughly in the order I read them. Ten books gets me through high school but doesn’t include all the books that had a big influence on me.

My list:
A kid’s biography of Thomas Edison. Sparked my interest in invention.

Commodore 64: Programmer’s Reference Guide. I taught myself programming on a VIC-20 and then a Commodore 64, then picked it back up again in graduate school to analyze mouse genomic DNA.

The Boy Scout Handbook. Learned lots of useful things!

Moon is a Harsh Mistress, Stranger in a Strange Land by Robert A. Heinlein. I became a space nut by reading science fiction. Heinlein was an early favorite.

The Best and the Brightest by David Halberstam. First big book on government I read.

A stack of old Scientific American magazines. I was given a few feet of Scientific American magazines and devoured the science review articles. This is where I found out biology was much more interesting than what was covered in high school. This is also where I discovered Martin Gardner’s Mathematical Games column and from that fractals and many more wonderful things.

Sleepless Nights in the Procrustean Bed, The Glass Teat, and short story collections by Harlan Ellison. I started reading Ellison’s short stories, then found his movie reviews in the Magazine of Fantasy and Science Fiction, then found his essays. He’s a master essayist.

Slaughterhouse-Five by Kurt Vonnegut. Eye opening.

Broca’s Brain, The Dragons of Eden, The Demon-Haunted World: Science as a Candle in the Dark by Carl Sagan. Taught me all sorts of science and started my love of general science books.

G̦del, Escher, Bach РAn Eternal Golden Braid by Douglas Hofstadter. A stunning book about math, music, recursion, and cognition.

The Fractal Geometry of Nature by Benoit B. Mandelbrot. Spent a summer reading this book. I wasn’t quite up to the math, but still it was fascinating.

Chaos by James Gleick. Fractals, chaos, deterministic but unpredictable systems, like weather. Good ideas, lots of interesting examples.

Science: Good, Bad, and Bogus by Martin Gardner. Pseudoscience and skepticism.

Extraordinary Popular Delusions and the Madness of Crowds by Charles MacKay (1841). Read this early on in college. The tulip madness, the South Sea Bubble, and other incredible episodes in the history of human folly.

Other books, ones that didn’t make the top 10 or that I read later.

The Lord of the Rings by J. R. R. Tolkien.

A Connecticut Yankee in King Arthur’s Court by Mark Twain. (interestingly, the technology an everyman Connecticut Yankee knows was all new to me).

The Crystal Cave by Mary Stewart. (the first book of her Arthurian legend series. Loved me some Arthur)

Neuromancer by Wiliam Gibson (sf, cyberspace!)

Knotted Doughnuts and Other Mathematical Entertainments, The Ambidextrous Universe: Mirror Asymmetry and Time-Reversed Worlds, Mathematical Circus by Martin Gardner. (recreational mathematics, puzzles, and oddities, mainly from his Mathematical Games column in Scientific American).

The Foundation Trilogy by Isaac Asimov. (sf, sociology as a super-science)

Animal Farm by George Orwell. (this rather than 1984, hearing so much about 1984 before I read it weakened the impact of 1984).

The Hitchhiker’s Guide to the Galaxy by Douglas Adams. (sf, funny, absurdist British sf)

Dune by Frank Herbert. (sf, a great tale integrating great sweeping ideas).

Fahrenheit 451 by Ray Bradbury.

Far Frontiers edited by Jerry Pournelle and Jim Baen. (I’ll let this stand as a representative of the non-fiction I read about prospects and plans for space development in books and in Analog. Read G. Harry Stine, Pournelle, Bova, Brin, Clark. “The Earth is the cradle of the mind, but we cannot live forever in a cradle”. –Konstantin E. Tsiolkovsky, Kaluga, 1911).

Shakespeare’s plays. (I thought in iambic pentameter for a few weeks in high school. A fun way to rewire your brain!).

Ender’s Game by Orson Scott Card. (sf)

Bruce Sterling, The Hacker Crackdown: Law and Disorder on the Electronic Frontier. (the history of computer hacking and the government’s alternately clueless and thugish reactions to it).

The Best of the Nebulas (sf, the best of the best).

Surely You’re Joking, Mr Feynman! by Richard Feynman

A People’s History of the United States by Howard Zinn. (an eye opener for me).

Bully for Brontosaurus by Stephen Jay Gould. (Gould’s rich essays on biology and natural history are amazing. I think this is the collection I started with).

Churchill’s Complex Variables and Applications (complex numbers are strange and wonderful).

The News That Didn’t Make the News and Why: the Project Censored Yearbook by Carl Jensen & Project Censored. (strangely enough, not all the news is fit for print).

Manufacturing Consent: The Political Economy of the Mass Media (with Edward Herman), Deterring Democracy by Noam Chomsky. (a different view of American government policy and actions, densely written and exhaustively sourced).

The Aquatic Ape by Elaine Morgan (read this in grad school, the thesis is that humans evolved through a semi-aquatic intermediate hominid. This turns out not to be true, but I found the idea of using biological features as evidence for human evolution very interesting. I grew up during the ‘man the upright walker’ period in human paleoanthropology).

The Mismeasure of Man by Stephen Jay Gould (scientific racism, history and arguments against, read this instead of the Bell Curve).

Douglas North and Roger Miller, Abortion, Baseball and Weed. (counterintuitive economics)

Anne Rice, Interview With the Vampire. (started me reading fantasy again)

The Mythical Man-Month by Fred Brooks. (software engineering and personnel management on large software projects)

Guns, Germs and Steel by Jared Diamond. (a sweeping explanation of the large-scale pattern of human history. Not proven, but a great approach to the question).

The Voyage of the Beagle by Charles Darwin. (incredible travelogue of his around the world voyage)

This is odd and sort of funny. And a little old. In Afghanistan, the US military has been conducting an offensive in Helmand Province. Apparently the propaganda push got a head of the facts. The official accounts had the US battling to clear the Taliban out of the Marjeh, a moderate size city of 80,000 to 125,000 people.

I ran across articles saying that the city didn’t exist. BAGnewsNotes had a picture of an isolated farm in Marjah, ostensibly showing that the place wasn’t a city.

BAGnewsNotes linked to a story on the truthout.com site. But this article didn’t have any pictures at all. Now this a story that really needs a picture, and there are easy sources, Google Maps for one. Here’s the farming village of Marjeh (or Marjah, or Marja, the name can be written different ways in english):

Just a collection of farms, no city at all.

Zooming out further shows that it is the biggest town in the area, so it makes sense that news of a big military operation in the area would talk about it happening in Marjeh, but it’s certainly no city.

Composite electron micrograph of the flagellum basal body and hook, produced by rotational averaging (Francis et al., 1994).

Stephen M. Barr has an article in First Things, The End of Intelligent Design?. Unfortunately, Barr is looking to rescue something from intelligent design (ID) so his criticisms are muted. His main interest is whether ID has been useful in advancing religion and theology. In a faux even-handed approach he criticizes ID for not proving it’s claims but then tosses in criticism of scientists for unspecified excesses. He also tries to win favor with a religious audience by claiming that “the ID movement has been treated atrociously and that it has been lied about by many scientists”, a judgment he doesn’t substantiate.

The readership of First Things is a strange group, many of the comments go off in philosophical directions but no one is talks about the central issue–whether ID is true or false. Is there good evidence for it? Is it likely to be true? Could it be true? Or is it known to be false?

Barr’s article starts well, it is true that there’s “not a single phenomenon that we understand better today” through ID. To restate that, there is no evidence at all for ID and that is the reason ID has been dismissed by biologists.

When the idea that certain biological structures are “irreducibly complex” was proposed several examples were given: the bacterial flagellum, the immune system, the blood clotting cascade, the vertebrate eye, the Krebs cycle, etc. In fact, biologists have evolutionary models and physical evidence of how each of these things has evolved. No “irreducibly complex” structures were proposed and then proven to be so. In truth, none of the proposed examples are even open questions, things that puzzle biologists that could possibly be shown to be “irreducibly complex” in the future.

And the case for ID is really worse that what I’ve described. It’s not that ID theorists proposed structures that biologists didn’t have good evolutionary models for, structures that could have turned out to be “irreducibly complex”. When these examples were given, there was already published research explaining the evolutionary origins of each example. For example, biologists reviewing Behe’s book were able to look up and reference the research discounting his examples. No better “irreducibly complex” examples have come to light since then.

Copied directly from the Calculated Risk blog, but too good to pass up!

The Mortgage Bankers Association … fell victim to the collapse of the market and sold its $90 million headquarters in downtown Washington on Friday for $41 million.
…
The Mortgage Bankers Association moved into the building in 2008 just as the real estate market was crashing …

Definition of irony…

In a meta discussion about AGW, Eric Raymond writes about how the term scientific consensus is used in public science debates. He seems to misunderstand it, and think it is an ‘appeal to authority’ type of argument and thus a sign that the party that raises it has no more convincing arguments.

It certainly can be that sort of poor argument, but typically when raised by scientists it is something different. The scientific consensus on a topic is mentioned as a shorthand way of communicating what’s understood by scientists working the field to the public. Scientists are trying to communicate that certain things are known, and that contrary arguments that pick one or two studies and argue that the contrary opinion is *really* true or at least that no consensus exists are misleading. Either the study is part of a technical debate in the field among researchers who all understand and believe the consensus that is being misconstrued or too much weight is being given to the opinion of a rare contrarian.

The contrarians can be further divided into 1) cranks of various sorts and 2) scientists working on a contrary idea who understand that the evidence still favors the consensus but hope to make discoveries that will eventually tip the balance of evidence in favor of their idea. The second scientist will happily talk up his idea if asked about it, but if asked about the consensus will acknowledge that it is currently overall the best explanation.

So scientists will mention the scientific consensus on an issue to the public to ground the discussion with the fundamentals of what is known. With the fundamentals set down, scientists can then explain the details of how things are known, what discussions within the field are about, or discuss contrarians.

Ever Since Darwin is book of essays by Stephen Jay Gould, originally written as columns for Natural History magazine.

This is Gould’s first collection of essays, published in 1977. It’s a great introduction to Gould’s writing. The essays are shorter and the ideas are simpler than those in some of his later collections. There are great essays on the life and times Darwin worked in, and on how evolutionary and developmental biology got worked out through fits and starts. The last few essays on sociobiology are kind of weak. I guess 30 years on, it’s hard to really understand the ground that was being fought over.

Overall, a great book!

I’ve put up a web site for exploring L-system images, L-system Iterator.

The snowflake shape is only one example of the pictures that can be drawn this way.

L-systems are simple iterated drawing rules. Simple rules for turning and drawing put together in this way make quite interesting and complicated patterns. The ones shown above are well known. From the the left, the Koch snowflake, the Sierpinski triangle, a kolam-like image, and a plant-like image. On the second row, the Heighway dragon, the Hilbert curve, and another plant.

The Heighway dragon has many interesting properties–for example, it can be tiled over the plane.

Some iterated objects are fractals–the Koch snowflake, Sierpinski triangle, and Hilbert curve are famous simple fractals.

L-systems can be quite complicated. The systems modeled on my web site use a single rotation angle and only one line width. More complicated models can make surprisingly realistic plants. Prusinkiewicz and Lindenmayer (the L in L-system) have developed detailed plant models.

The web site is based on the Perl code I wrote for my Biomorph evolution/selection web site. The images are generated using Postscript to draw the L-system, and then the ImageMagick convert program to change it to a PNG image. Images are given a file name that describes the L-system, effectively caching the image. The Prototype Javascript library is used to assist in making the popup boxes.

Each L-system variant has two changes from the current L-system. Some logic is used to keep the L-system in the same family–if there’s no Y equation, one isn’t added. Existing equations are grown or shrunk but not dropped. These images can take much longer to generate than the Biomorph images, so a number of limits are placed to keep the L-system from getting too complicated or taking too much CPU time.

The hardest part of the Postscript was getting the images scaled and centered appropriately. The images can extend in any direction and some are large, others small. The centering code generates the image twice, once to find out its dimensions and then a second time scaled and centered. Here’s the code to record the dimensions of each part of the image. It gets called before each stroke operation.

/max_path {
gsave initmatrix pathbbox grestore



ur_y false eq { /ur_y exch store } { dup ur_y gt { /ur_y exch store } { pop } ifelse } ifelse
ur_x false eq { /ur_x exch store } { dup ur_x gt { /ur_x exch store } { pop } ifelse } ifelse
ll_y false eq { /ll_y exch store } { dup ll_y lt { /ll_y exch store } { pop } ifelse } ifelse
ll_x false eq { /ll_x exch store } { dup ll_x lt { /ll_x exch store } { pop } ifelse } ifelse
} def

The ‘initmatrix’ command is required to reset things because of all the rotation operations.

The code for the site is linked on the L-system iterator home page.

Update: Added color variation as an option. And a reverse direction primitive.

Also, the code now runs under mod_perl.

Note for mod_perl users–mod_perl 2.0 has no way of handling alarms. select() doesn’t work either as a way of timing out pipes. The only usable method is prepending commands with ‘ulimit -t secs’ and letting the shell limit the system process.

To make the split color B&W images I used these ImageMagick commands:
convert -size 150x150 tile:color.png tile:bw.png ../temp/mask.png -composite split.png
using a half black, half white split image as the mask.

Then added the split line using:
convert -size 150x150 -fill white -stroke black -draw "line 0,0 150,150" split.png split_line.png

Here’s an idea for a game. It would be like the kid’s game Memory, where cards are turned over and matches are taken off the playing area. Instead of using identical pictures, images of different animals or plants would be used. Any pair could be matched by a player. The play would be quite similar to standard Memory.

The idea would be to match organisms by evolutionary similarity. So scoring would give maximum points for animals of the same species, next most for same genus, fewer points for animals in the same order, and no points for creatures in different phyla. The easiest implementation would be as a computer game with the computer dealing with scoring. Alternatively cards could be made the lineage described on the back. Each classification category could be displayed a different color or with a different symbol and the first/highest point matching lineage symbol give the points for the match.

This would make the play interesting as any pair could be matched but the player would have to decide if a pair was good enough to pick up or to wait for a better and higher scoring pair next turn.

The design aspect of picking a card set could make an easy set or a hard set, and two aspect of the choice would affect this. First, if animals fall into close pair groups that are distantly related (two parrots, two foxes) then the set would be easier. Having graduated and overlapping groups of cards make the set harder (dog, fox, skunk, weasel, otter, raccoon). Also, how much the player knows of these animals and their relationships can make a card set easier or harder. Some groups are obvious–birds, whales, bats–while other animals are either not as well known (i.e., coatis) or don’t have an obvious lineage (i.e., wolverine). And all these examples are mammals. Invertebrates would make a ridiculously hard game! So sets for kids could be easy and moderate to hard sets can be created.

Here are three game sets:
Mammals, butterflies, and marine invertebrates.

I have thought for years that it should be possible to regrow teeth. Teeth should be one of the easiest body parts to regrow. It seemed likely that the tooth bud, once formed, would receive signals from its local environment and grow into the correct type of tooth and emerge into place. That’s what happens during normal adult tooth development. So generating a tooth bud looks to be the key step. And indeed, in the past few years there have been reports of progress from research in this area. See this news article and this paper from the Yelick lab in São Paulo, Brazil.

But much easier than growing teeth should be killing tooth buds. Specifically, if the buds of wisdom teeth were killed then the painful, expensive surgery to remove wisdom teeth could be avoided.

Tooth buds form during fetal development. Wikipedia has a detailed overview. Wisdom teeth don’t begin to calcify until a person is 7 to 10 years of age. It should be fairly easy to kill the tooth bud at early stages. An injection into the tooth bud of a localized cytotoxin, either a general one or perhaps one specific to dividing cells would kill the stem cells that form of the core of the tooth bud. A toxin dose that kills cells within a 1-2 mm radius of the injection site should be effective. The gums will heal up and then the tooth bud will be gone. The dentist should be able to pick the injection location based on the expected eruption site. Inspection of x-rays may help pinpoint the bud location. A jig could be used to precisely position the needle tip.

Googling briefly I don’t see any other mention of this idea. It would be easy to test experimentally in animals if one can be found with late enough tooth development.

Putting video clips on my blog was a bit harder than I expected. I first tried converting the .MOV files the camera writes into .avi files using ffmegX and posting them using <embed> tag code. The files showed up great on my Mac but not at all on a Windows computer.

Flash format files, .flv, are the easiest cross-platform way to post video clips. Flash does require that the site supply a Flash player. There are many Flash players available. I tried OS FLV and it worked nicely.

To edit video files I used avidemux, then ffmegX to convert them to .flv, and I put them on the site using the ‘noscript’ <embed> code suggested by OS FLV with the OS FLV player.swf.