Cavalcade of Mammals

Mars Underground by William_Hartmann. The book was a good read. It is set on Mars, at a time when thousands of people are on the planet, second stage exploration. People are beginning to think about colonization. The book is a mystery, with an administrator, Carter, his friend the resident artist, Philippe, and a newly arrived reporter, Annie Pohaku, investigating the disappearance of a Stafford, an exobiologist who’s one of the longest serving research scientists and explorers on Mars. Stafford had discovered traces indicating microbial life on Mars billions of years in the past.

The book starts very well, but then seems to stall out in the middle. The plot is uncomplicated and feels too bare. The characterization of the protagonist, Carter, is lacking. The description of Mars and the bases on the planet and Phobos are well done.

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.

Converting a single file:

faad -o - file.m4a | lame - file.mp3


Bash script for converting multiple files:

-----------------------
#!/bin/bash

for i in *.m4a; do
    echo "Converting: ${i%.m4a}.mp3"
    faad -o - "$i" | lame - "${i%.m4a}.mp3"
done
-----------------------


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.

The typical Republican answers yes to four of the questions in this survey* (or four out ten answer yes to all these questions, or some mix of the two). And people in the US used to worry about Russians slipping LSD in the water supply.

Question	Yes	No	Not Sure
Should Barack Obama be impeached?	39	32	29
Do you believe Barack Obama was born in the United States?	42	36	22
Do you think Barack Obama is a socialist?	63	21	16
Do you believe Barack Obama wants the terrorists to win?	24	43	33
Do you believe ACORN stole the2008 election?	21	24	55
Do you believe Sarah Palin is more qualified to be president than Barack Obama?	53	14	33
Do you believe Barack Obama is a racist who hates white people?	31	36	33
Do you believe your state should secede from the United States?	23	58	19
Should openly gay men and women be allowed to teach in public schools?	8	73	19
Should contraceptive use be outlawed?	31	56	13
Do you believe the birth control pill is abortion?	34	48	18

*Flipping yes/no for the gay teacher question.

Survey details here.

Or rather the lack of one. One after another, GOP statements on what they want in a budget hit the same points again and again. Republicans have decided this year that the federal budget deficit is terrible and must be curbed immediately. Ignore for a moment the Hooverism–that cutting federal spending today will prolong the recession and increase unemployment.

Look at the Republican plan–balance the budget by cutting taxes, increasing defense spending, and leaving Social Security and Medicare intact, and cutting other unspecified programs. The remaining budget, discretionary spending excluding defense only totals $5-600 billion and includes everything from road construction to federal courts to food stamps. With the permanent budget deficit about $600 billion (the 2008-9 bank bailouts and stimulus are one time costs), balancing the budget under the Republican plan doesn’t add up. Adding tax cuts and increased defense spending just make it extra impossible.

Sometimes the impossible can be done in small steps. The Senate voted this week on PAYGO, the deficit reduction measure that allowed Clinton to balance the federal budget in the 90’s. But no, every Republican voted against it.

Stan Collender sums it up in a blog post collecting GOP statements on the federal budget . Here are the bits:

Item 2. All Senate Republicans voted against re-establishing the pay-as-you go rules, which would have required that, with certain exceptions, any new mandatory spending or revenue legislation not increase the deficit. The rules were adopted with only Democratic support.

Item 4. Republican Chairman Michael Steele is saying so often that Republicans are against cuts in Medicare that it’s starting to sound like a mantra. Add to that their stated opposition to revenue increases (see #1 above), military spending reductions, homeland security reductions, and the extremely low possibility that, if Medicare is too hot to handle, they’ll go anywhere near Social Security, and the deficit reduction math becomes totally impossible.

There have been recent fantasy GOP budget proposals along these lines. See Tim Pawlenty’s (Gov. of MN and 2012 Presidential candidate) editorial in Politico. Or the budget proposal by Rep. Paul Ryan, ranking Republican on the House Budget Committee.

Even conservative economist Bruce Bartlett is unimpressed:

Like all Republicans these days, Pawlenty wants to have it every possible way: complain about the deficit while ignoring everything his party did to create it (Medicare Part D, two unfunded wars, TARP, earmarks galore, tax cuts up the wazoo, irresponsible regulatory and monetary policies that created the recession that created the deficit, etc.), illogically insisting that tax cuts are a necessary part of deficit reduction, and never proposing any specific spending cuts.

It would hardly be fair for me to fail the Republican proposals without offering my own. So here it is:
1) The federal government should spend an additional $600 billion a year until unemployment is down under 6%. Send at least half of it directly to states where it can be spent quickly, spend the rest on unemployment, food stamps, long neglected infrastructure, and a massive New Deal class jobs program.

2) Raise taxes. First, let the Bush tax cuts on income over $200K, capital gains, and large inheritances expire. Second, make the banks pay for their bailout with a combination of financial transaction taxes, an end the hedge fund income tax special treatment, etc, to total $150 billion a year. Third, add progressive tax brackets at the high end, and extra 1% for income over $1 million, $5 million, and $10 million. End a few of the large corporation tax breaks that leave many of them paying essentially no taxes. These modest tax increases are enough to put the budget in the green.

3) Cut total war/security/defense spending back so it equals what the entire rest of the world spends, about $500 billion a year–that would be a cut of $150 billion a year. End the Iraq and Afghanistan wars, saving $150 billion a year.

4) Whoa, now the federal budget has a $200 billion surplus!

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.