Cavalcade of Mammals

Bit of local history I never knew about. I had noticed, but no one ever mentioned the court case…

“But the fight didn’t end there; it just moved to the courts and the states. The 1970s saw a tidal wave of high-profile civil rights lawsuits taking aim at restrictive zoning laws, virtually all of which were lost. Most crucially, in 1977 the Supreme Court upheld a law that banned apartment buildings in the Chicago suburb of Arlington Heights, denying an affordable housing developer’s claim that the law made integration almost impossible. (At the time, Arlington Heights had about 27 black residents out of a population of 64,000. In the nearly four decades since, its zoning has largely remained intact, and its black population is still under 1,000.)”

One of the best ways to fight inequality in cities: zoning By Daniel Hertz

I would like a source for science news articles that actually has the science. Biology articles that include gene names and what a study actually found. Stories that describe things with the correct technical terms, not ‘the internet is like a series of tubes’. News stories written at an old-time Scientific American level, at the level of medical or graduate school alumni magazines. Stories that link to the journal article, to the institution or lab’s page, the patent, that link to Wikipedia or a relevant site for background.

What I would really like a source that linked standard news accounts of science to an extra-science version of the news. This site could write the extra-science article, but no need for redundancy–if some other site has an account with the relevant details then this site would just link to it. ars technica’s Nobel Intent science news site often does the job, but of course they only cover some of the news and don’t provide the nexus–linking the weak tea news stories to their articles.

The nexus should facilitate the connection. Allow the user to enter the news site URL, story title, or a sentence of text and recognize the story and link to the extra-science article. Standard keyword searching would be useful as well. The Reeves lab had an almost perfect example of the empty science news story taped up: ‘Scientists clone brain gene. This discovery will lead to an understanding of how the brain works.’

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.

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.

Last October, NASA’s LCROSS mission slammed a spent rocket booster then the LCROSS spacecraft itself into the moon. No debris plume was seen from Earth, but observations from LCROSS of the booster hitting indicate the presence of water on the moon. How much water? Most news accounts don’t say, but the Science magazine article does.

100 kilograms of water was detected from an impact that created a crater estimated to be 20 m wide and 3 meters deep. So 100 kg water in about 500 m³ of regolith = 0.1 g/kg. (Googled a reference giving 2.3 to 2.6 g/cm³ as lunar regolith density).

The article gives a higher estimate for water, 0.1% to 10%, higher than my crude 0.01% estimate. Which is great–enough water to extract easily and live off. Best news for space exploration in thirty years!

(Credit: NASA)

So I have a box of motors scavenged from old electronic equipment. The first step was figuring out what I have.

I have four identical Pittman servo motors with attached optical encoders. They have two leads for motor control and four leads for the encoders, Vc, Gnd, quadrature A & B signals. So these motors need a sophisticated servo driver that can do PID (Proportional, Integral, Derivative) control. Basically the controller senses motor movement and direction by counting encoder tick marks and then juices the motor in the desired direction using a PWM (Pulse Width Modulation) applied driver voltage.

It’s common to run the these servos with PIC18 chips ($4.50). They have a built in quadrature encoder reader and can be programed to do PID.

Then the low power PWN signal gets run through a power driver like the L298 ($2.60). Here’s a well-documented L298 project. The L298 can driver two servo motors. A LMD18200 H-bridge ($12.50) is another power driver option, used in the Jeffery Kerr boards. Here’s a project using a PIC16 and the LMD18200 driver. The Allegro A3953 is another driver option.

Typically one PIC16 or PIC18 would control each servo motor. The recent dsPIC33 chips ($3.00) have dual encoders and should be able to run two servos. These chips came out in 2008 so I haven’t found any projects on the web describing dual servo projects.

The PIC18 and dsPIC33s are available as DIPs or as SMDs. They can interface to a computer through USB and so can be controlled directly, though connecting them to a programmable controller, a PIC, a BASIC stamp, an Arduino, etc is more common.

Hobby servos are much easier to drive and a single PIC18 can drive several, six to eight depending on the chip variation. Typically a hobby servo would not need a driver as the PWM is its control signal.

A UK Bible study group hosted a talk tonight by Dave Eakin, an Associate Professor in the Department of Biological Sciences at Eastern Kentucky University (EKU). I didn’t know quite what to expect coming in to the talk–was Eakin going to explain some biology to the Bible study group or was this going to be bog standard creationism? The talk turned out to be standard old Earth creationism. What an embarrassment he is to EKU!

An MP3 recording of the talk is available here.

I made notes during the talk, they give a flavor for it. My comments are in brackets:

3 groups: biblers, people with set minds…

Comments about apoliticalness and open mindedness.

Cartoon: candle representing science, “Hit it with the Bible”.

Chain of being cartoon.
He mentions he had a creationisty poster at the KAS meeting and no one gave him guff about it.

3 theories of evolution:
1. chemical evolution (abiogenesis)
2. general evolution “an extrapolation of Darwin’s natural selection”
3. natural evolution = special evolution [seems to be a ref to microevolution]

Behe’s Black Box book. [Darwin’s black box: the biochemical challenge to evolution
By Michael J. Behe]

It’s hard to tell if things are designed.
Creationists are blackballed, McCarthyism-type environment for creationists.

Paley-like are arguments are too simple/wrong, but Behe is more sophisticated [not clear how].
Watch, mouse trap, flagellum
[clotting cascade, eye, Krebs]
Eye
Trials for cats. [????]

Graduate of U. of Louisville! [figures!]

No one can solve these problems

Color blindness slide?
Can make it clear by increasing contrast…
“Evidence doesn’t support theories, theories support evidence” –Dr Dave.
Big Bang not current, has been replaced by String Theory

CSI example, making the point that evidence can be made to support whatever theory a person wants.

If 60,000 people believe a lie, it’s still a lie.

All his sick evolutionist friends ask him to pray for them.

Quote: when fossils are known all no more guessing. [missed the cite]

We doesn’t know everything so we know nothing.

Absence of life in pre-Cambrian, organisms suddenly appear, and…

Picture of single-celled microfossils, asks if anyone believes them.
Makes fun of certainty of Ph.Ds.

Something new from Discover mag, image of tree of life from single-celled organism.
Pisoliths from pre-oxy atmosphere Earth (pre 2.3 billion years), but they only occur in presence of oxy.
[Casting doubt on what we know.]

Stephen Jay Gould had a young Earth Creationist student. [meaning unclear…]
Quote from Gould, from Evolution’s Erratic Pace, Natural Hist May 1977, at 12, 14. about no transitional forms.

Erase all the lines from tree of life because we don’t know anything for sure.

Never presented Creationism in class. Wants student to think for themselves.
Quote from Colin Patterson (April 10, 1979) on how we don’t have any transitional fossils.
Quote by Tom Bethell in Harper’s February on how no one is willing to publicly talk about ‘questions’.

But what about Archaeopteryx? Small, unimportant. Just a reptile.
Eakin has reviewed many/most biology textbooks.
Says Archaeopteryx is often misrepresented, over interpreted.

Some point about lack of learned behavior in reptiles.
Figures of bird physiology. Pectoral muscles in bird/reptiles.

How did scales evolve into feathers? Unknown, too hard to imagine. [Evo-dev has been providing answers about this.]

How did birds start to fly? An irreducible jump.
We know in our hearts that transitional forms can’t happen.

Faith is… “the substance of things hoped for, the evidence of things not seen.”

My battery ran down at this point and the sound cut off the last minute or two of his talk and the extended Q&A afterward. He mentioned the audience was very respectful and had given him his say. Bible groups must usually be a rough audience!

In the Q&A, he also said that he had talked to many biologists and that 10-20% were creationists of some variety but unwilling to publicly talk about it. This is quite silly, an argument from popularity. Also it’s nonsense. Anonymous surveys of biologists have been done and almost no biologists are creationists. A 1987 Newsweek article reports a survey found 0.14% of earth scientists and biologists are creationists, and a survey reported in CSI pegs the number at 1-2 in about 2000, about 0.1%.

It was sad to find out that EKU has a creationist teaching biology. Oh, the poorly served students!

Most surprising was that Eakin gave his whole talk without ever describing the theory of evolution, in any of its forms, either the simple Darwinian version or the Modern Synthesis. His talk was instead the poorly thought out basket of criticisms of evolution with no case made for anything else. I’ve heard this described as common in creationist talks.

Eakin started his talk saying that evidence is never conclusive, that there’s always doubt, and that we can’t be sure of anything. I thought that would be the theme of his talk before he swerved into ordinary creationism.

Eakin’s talk was at least a decade out of date. One topic was Behe’s book and the argument of ‘irreducible complexity’. Eakin doesn’t seem to know that Behe’s featured examples, the flagellum and the eye, have been shown to have evolutionary precursors where part of the ‘irreducible’ structure exists and functions.

Eakin mentions Archaeopteryx and then makes an extended argument that the evolution of reptile ancestors into birds is impossible but doesn’t seem to know that additional transitional birds have been discovered, or the recent evidence of the relationship between scales and feathers.

Eakin also briefly mentioned his impression that few transitional horse fossils are known, and mentioned that the linear, gradual depiction of horse evolution was admitted by biologists to be false. This hoary creationist canard leaves so much out as to be plain dishonest. Eakin should known better.

In the early part of the 20th century, depictions of horse evolution presented a linear, gradual picture of horse evolution, but soon after more and more horse fossils were discovered and filled in a picture of horse evolution as a branching bush with over a score of Genera, many coexisting and all but a few now extinct. Talkorigins.org has a good page on this, though Stephen Jay Gould’s essay “Life’s Little Joke” collected in Bully for Brontosaurus is a better read. There are many transitional horse fossils, and the branching tree of horse evolution has been widely known for 70+ years.

The talk ended with a series of quotes from evolutionary biologists about the lack of transitional fossils and the difficulty of drawing conclusions. This was standard creationist quote mining, quite a laugh.

Eakin is a graduate of U of L. I know that won’t surprise anyone at UK.

Phil Agre ran the Red Rock Eater mailing list for many years, it was active during the 90’s. I think I started reading it in the late 90’s. The emails ran down to a trickle in 2002, in part I think due to Phil getting a permanent position at UCLA. The mailing list archive indicates it ran up to Jan 2005.

Phil Agre’s mailing list in essence was one of the first blogs. The content was mainly links and commentary by Phil with occasional longer essays. He was one of the best people thinking about what the internet could be used for and how it was changing the world.

After 2002, the Red Rock Eater list went into abeyance then seemed to have stopped for good. Phil Agre seems to have dropped off the net. In this comment thread a UCLA student says he was ill. I fear it is very serious to keep him off line so long.

His essays, “Advice for undergraduates considering graduate school” and “How to be a leader in your field” are internet classics.

Here is an essay I found interesting titled What Is Conservatism and What Is Wrong with It?

Update: He’s literally missing. This site is run by friends looking for him.
Update 1/31/09: UCLA police talked with him. He’s alive, though not well.

I gave the students in my upper level Biology of Aging class a pre-test to gauge their knowledge entering the class. I wanted to find out how much background explanation I’ll need to provide. The results:

1) How many human genes are there? That is, how many genes are in the human genome?

Answers (ordered from good to bad):
~30,000, millions, 2X a lot, 93, 2X 46, 36, 32, 26, 13 students left it blank.

2) What is the size of the human genome (in bps, Mbs, or Gbps)?
Answers (ordered from good to bad):
2X billions, Gbps, 12Mb or 12 Tb (not clear), 100 Mb, 54, 17 students left it blank.

3) How many amino acids are in a typical protein?
Answers (ordered from good to bad):
Proteins are composed of strings of amino acids so it varies, a lot, 42, 26, 21, 3X 20, 2X 12, 13, 3, 1, 10 students left it blank.

4) How many genes are unique to humans and not found in chimpanzees, dogs, mice, or other organisms?
Answers:
a few, 2X 1, 2, 5, 7, 12, 11%, 15 students left it blank.

5) Name four model organisms:
Number of reasonable answers:
3X 4, 2X 3, 1, 1 out of 3 animals, 16 students left it blank.

6) Order the following terms from least complex to highest complexity:
A. nucleotide
B. cell
C. lysosome Least complex:: ::Most complex
D. mRNA
E. proteasome Example: F, E, D, C, B, A
F. tissue
Answers (ordered from good to bad):
8X all good, 7X one pair switched, 3X -3, 2X -4, 2X -5, -6, 0 students left it blank.

7) What is the proteasome?
Answers (ordered from good to bad):
Every student left it blank.

8) Is dihydrogen monoxide a dangerous chemical?
Answers (ordered from good to bad):
20X water, 1 student left it blank, 1 student confused it with carbon dioxide, yes.

9) What does the mitochondrion do? What happens in mitochondria?
Answers (ordered from good to bad):
17X good (most commonly, ‘powerhouse of the cell’, many mentions of ATP or energy), 6X poor answer (a particle in the cell, RNA produces proteins, ?, blank).

10) What does it mean to say a gene is being expressed?
Answers (ordered from good to bad):
2X it is being actively translated into protein, 11X phenotype/trait/visible, that it exhibits a certain trait & it is a gene that is dominant, turned on & RNA made, like when your eyes are a certain color, organism with gene is not only a carrier but physically expresses the gene, genotype–the traits that you can see, the gene is active, 2 students left it blank.

11) What is a transgenic mouse?
Answers (ordered from good to bad):
3X genetically altered/genes inserted, a mouse that is genetically predisposed to having a desired condition to be studied, a mouse of several different genes, a mouse with reversible genes, 17 students left it blank.

12) How is a transgenic mouse made?
Answers (ordered from good to bad):
Every student left it blank.

13) If I say a gene is ‘knocked-out’ in a particular yeast strain, what do I mean?
Answers (ordered from good to bad):
Deleted from the genome, gene has been removed to test the activity or function of the gene, excised from the strain and not expressed, they cut it out, 7X it is removed or not used, eliminated from the sequence, mutation, taken out of the strand, you knocked out a recessive gene, not expressed, it is removed from or cultured where the gene is not expressed, 6 students left it blank.

14) What causes cancer?
Answers (ordered from good to bad):
2X a mutation within the cell that causes it to rapidly divide, [environmental factors] leads to mutations cause breaks in pathways that regulate growth and apoptosis, oncogenes caused to be expressed by [environmental factors], 4X uninhibited cell growth, malignant cells, free radicals & transcribing errors resulting in erronous tissue that self-propagates, 7X DNA mutations, 4X smoking/carcinogens/sunlight/everything, 2 students left it blank.

15) What causes Alzheimer’s disease?
Answers (ordered from good to bad):
2X deterioration of neuronal cells, heredity, 3X degradation of brain function, 2X deterioration of the brain & loss of myelination, 3X neurotransmitters [various], improper folding of a protein in the brain, 11 students left it blank.

16) What is a plasmid?
Answers (ordered from good to bad):
6X circular DNA, part of a cell containing genetic material, a small portion of genetic information, a tiny piece of DNA that can be inserted into a gene, cell marker, organelle, a form of transportation in the cell, transfers info from Trna to Rrna, 11 students left it blank.

17) How long ago did the last common ancestor of humans and gorillas live?
Answers (ordered from good to bad):
54 million years ago, 1.2 million years ago, 500,000 ya, 3X 100,000 ya, 50,000 ya, 10,000 ya, long time ago, they still do, that’s a personal belief–Ha!, 12 students left it blank.

18) How long ago did the last common ancestor of mammals live (roughly the same question as when did the last common ancestor of humans and mice live)?
Answers (ordered from good to bad):
54 million years ago, 1 million years ago, very long ago, 2X 500,000 ya, 100,000 ya, 50,000 ya, 16 students left it blank.

19) What does it mean to clone a gene?
Answers (ordered from good to bad):
20X copy/replicate it, 3 students left it blank.

20) Describe one way to clone the DNA for a gene?
Answers (ordered from good to bad):
Remove sample & grow in plasmid, 4X PCR, extract mRNA and duplicate it, transcription?, splicing DNA in half and transcribe it–semi-conservative model, 2X use stem cells, 13 students left it blank.

21) What is PCR?
Answers (ordered from good to bad):
2X Polymerase Chain Reaction–used to replicate DNA in large quantities for experiments, 2X process to make many copies of DNA from a small amount of starting material, small section of DNA is taken and lots of copies of it are made, Polymerase Chain Reaction, used for mRNA/DNA replication?, making copies of DNA in the lab, Poly, 14 students left it blank.

22) What is an antibody?
Answers (ordered from good to bad):
No good answer, no answer that mentions ‘protein’, many answers with the key words immune/foreign body/antigens/fights infection/invaders/defense, 3 students think it is a type of cell. Other answers: vaccine, a marker. 1 student left it blank.

23) What is a Southern blot?
Answers (ordered from good to bad):
Results of electrophoresis that shows chromosome size, a way of reading DNA to see what genes are present, a type of assay used to view lab findings, a way to test DNA, a mapping technique for the # of genes in a population, a chromatography process, to measure size of molecules, a way to determine how fast certain molecules travel through certain medians, a type of diagram used to examine a strand of mRNA with the exons and introns, a straining test, a genetic test, used for mRNA in genetics, 11 students left it blank.

24) In humans, do neuronal cells regularly die and get replaced with new neurons?
Answers (ordered from good to bad):
18X no, 3X yes, depends, 1 student left it blank.

25) In humans, do the cells lining the inside of the intestine regularly die and get replaced with new intestinal cells?
Answers (ordered from good to bad):
18X yes, 1 no, 3X students left it blank.

26) What is a chromosome?
Answers (ordered from good to bad):
11X DNA, 3X genetic material, makes up genes X & Y, part of DNA, part of the genome that makes animals unique, mitosis/meiosis element, a reproductive cell, on a gene, two chromosomes make up one strand of DNA, 3 students left it blank.

27) What is a telomere?
Answers (ordered from good to bad):
The cap at the end of DNA sequence, end of a chromosome, stop in DNA, 2X confused it with the mitotic spindle, 3X meiosis/mitosis element, 15 students left it blank.

28) What is a stem cell?
Answers (ordered from good to bad):
4X good answer, 2X an undifferentiated cell, immature/undeveloped cell in bone marrow, cell in spinal fluid, what is needed to clone an organism, a premature cell with no function, a cell with multiple functions, a basic cell easily replicated, DNA that makes new chromosomes, basic DNA, 9 students left it blank.

29) What is an allele?
Answers (ordered from good to bad):
2X different alleles give different phenotypes, 2X a form of a gene, 2X half a gene, 2X part of DNA, corresponding sections on chromosomal DNA, the location of a chromosome on a gene, a common gene, 12 students left it blank.

30) What is an enzyme?
Answers (ordered from good to bad):
2X good answer, 12X catalyst, 2X a protein, breaks down food, a metabolically functional chemical, helps with production of proteins, 4 students left it blank.

31) What is a transcription factor?
Answers (ordered from good to bad):
One OK answer, one cell pathways to activate genes, instructions for the cell on transcription, assists DNA replication, 4X answer reflects back ‘transcription’, 15 students left it blank.

32) Have you ever read a scientific paper from a research journal? Approximately how many journal articles have you read?
Answers (ordered from good to bad):
200, 2X 30+, lots, 3X 20+, 15, 8-10, 3X 3-5, 4X a few, 3X 0, 4 students left it blank.

33) What is your favorite book that discusses biology?
Answers (ordered from good to bad):
“Brave New World”, “Survival of the Sickest”, “Tinkerer’s Accomplice”, “The Man Who Mistook his Wife for a Hat”, 4X [a biology textbook], 5X none, never read one, 9 students left it blank.

34) What is the last book you read or are reading now?
Answers (ordered from good to bad):
“A Clockwork Orange”, “The Last Lecture”, “America in the Great Stoned Age: Can’t Find My Way Home”, “The Craft of Research”, “Les Miserables”, the 7th Harry Potter, a Wall Street book, the Bible, “Snow Crash”, “Duma Key”, “Fast Food Nation”, “Eclipse”, “Diary of a Madman”, “The Inferno”, none, “Under Sea, Over Stone”, “No Country for Old Men”, “Pride and Prejudice”, “The Woman with a Worm in Her Head”, 4 students left it blank.

What is your major and how many years have you been in college (Freshman = 1 yr)?
Senior/5th year: 3 students
Senior/4th year: 12 students
returning 5th year: 1 student
Junior/3rd year: 4 students
Sophomore/2nd year: 1 student
2nd year Pharmacy student: 2 students

19 Biology, Pharmacy 2, undecided 1, didn’t say 1

Which (if any) 300 or 400 level biology classes have you taken?
Only counting 304/315/350, several have had ecology, microbiology, 425, 395:
1 304/315/350
3 304/315
1 315/350
2 315
2 Biochem (2nd year Pharm students)
1 350
3 close to degree/transfer student
8 not 304/315/350
2 no answer

23 students took the pre-test. Currently, I have 33 students enrolled. Grades of these 33 students are:
BIO304 (genetics): 1 A, 4 B, 3 C, 1 D, 1 W
BIO315 (molecular biolgoy): 0 A, 2 B, 10 C, 3 D
BIO350 (physiology): 0 A, 1 B, 3 C, 1 D, 2 E
16 students haven’t taken 304/315/350

On 60 Minutes today, Andy Rooney talked about unemployment. Mr. Rooney heard that 10 million Americans are unemployed. Andy refuses to believe this–I guess his friends’ kids are working and his powers of observation don’t extend any further than that. He’s the Inspector Clouseau of commentary.

If many people *are* unemployed, Mr. Rooney knows why–people these days won’t work hard. Why, he worked in a paper mill (for a few months when in college) for $0.45/hour. Convert that from 1939 dollars to 2008 dollars and we have $7.08/hr, higher than today’s minimum wage of $6.55/hr. Of course today’s workers have more taken out for Social Security and Medicaid. In 1939 there was no Medicaid and the SS tax was 2% while today they are 15.3% combined, so today’s single worker takes home $5.97. Mr. Rooney’s short term college job is looking pretty good.

Andy Rooney is as out of touch as John McCain, who said in the Republican primary that American workers won’t take jobs picking lettuce for $50/hour, a whole collection of wrong ideas.