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Archive for December, 2008

Better than LOLcats?

Tuesday, December 23rd, 2008

This is what the internet is for, I love this site. It’s been up for a few years and they never run out of pictures.

Workers over aligator pit

Report & short

Monday, December 22nd, 2008

The fracture of the US financial system gives me an idea for a new business model.

1) Raise some capital.

2) Use a tiny fraction to hire a few business/finance reporters, and have them find a company riddled with fraudulent business practices. How hard can it be–this stuff is common and not very well hidden. Look at Enron, Halliburton, the Madoff Ponzi scheme.

3) Then short the company’s stock, send the evidence to the appropriate regulatory and oversight agencies, feed the info to the press, and profit!

Bigfoot and cheap cameras

Monday, December 22nd, 2008

You would think someone would have caught a photo of bigfoot by now considering how much more common cameras have become in the past decade. Point-and-click cameras and cell phone cameras are in everyone’s pocket. Instead, ‘peak Bigfoot’ was in the 50’s and 60’s, when cheap movie cameras became available to the hoaxing public…


Monday, December 22nd, 2008

China is building like mad. China is making (and using) 8X as much cement as the US. I’ve seen images of the construction boom in coastal Chinese cities, but I wouldn’t have guessed at this level of production.

World cement production
Annual production of cement by country in billions of metric tons. By way of, Source USGS 2006 report and the USGS 2008 report.

Biology pre-test

Monday, December 22nd, 2008

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?
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
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

Hobbiest scale prototyping?

Tuesday, December 16th, 2008

One of the coolest technologies around are the rapid prototyping technologies: CNCs, Laser scanning, and Stereolithography. I first ran into stereolithography at a UK campus fair soon after I arrived, I forget which one.

In stereolithography a 3D computer model gets formed into a actually plastic part using a process in which heat from a laser polymerizes a liquid. Each pass forms a layer, and layers of under 0.1 mm are added to build the complete part. This technology was developed in the late 1980’s and is now fairly common though very expensive. The machines are $50-150k, and shops will turn out a part for a few hundred dollars. Incredible stuff.

Part made with stereolithography

The University of Kentucky has a Rapid Prototyping shop with a Stereolithography machine on campus.

Two things make this tech expensive, the monomer plastic ($200+ per liter) and the machines. The monomer is magic stuff, 21st century chemistry, and can’t substituted.

Can a machine be made more cheaply? Perhaps. Instead of the UV laser and X/Y scanning optics, how about using a DLP and a UV bulb? The DLP (an array of computer controlled mirrors, the display tech for bright computer projectors) directs the UV light to the correct part of the work area, the monomer polymerizes, the part is lowered, and the cycle repeats.

Could this work? It seems plausible. Best as I can tell, the monomer needs to be heated 20-30°C to polymerize. This is done in ~100μs by the laser, so a UV bulb shining for longer might be able to polymerize the monomer. The UV laser (100mW typically) has an intensity equivalent to 10,000W shining on a small 2cm x 2cm work area, so a 200W or 400W UV bulb (commercially available) shining for 1/10 of a second should in theory work. Losses due to heat dissipation may make a longer light pulse necessary, but it would likely still be under a second if this will work at all. The monomer could be preheated to the highest temperature where polymerization doesn’t occur to help polymerization along.

The result would be a simple and cheap stereolithography device with a small working area (2cmx2cmx15cm)! It could be built for very little ($200 UV bulb, $100 old DLP projector, $200 lenses and misc parts), with the high cost of the plastic monomer the biggest limitation. A DLP chip with 1000×1000 mirrors would have a 0.02 mm resolution. If UV intensity required for polymerization isn’t limiting, at 0.075 mm resolution a standard DLP would give a 7.5cm x 7.5cm working area and allow larger parts to be built.

What is the cost in plastic monomer for the parts? About 15c to 50c for a small Lego size piece, compared to the 5c a block cost for Legos.


Update: I had a look around for cheaper & more accessible plastic monomer. Two turned up–rubber stamp photopolymer resin and screen printing photopolymer emulsion.

The rubber stamp photopolymer is inexpensive and would likely UV cure in under a minute (1s or 60s is hard to gauge). Unfortunately, the resin is quite viscous, 60,000 cps, quite thicker than honey. So likely too thick for adding a thin layer at a time.

Screen printing photopolymer emulsion appears more promising. It polyvinyl alcohol or polyvinyl acetate with diazo or SBQ crosslinking initiators. It forms a plastic that is fairly weak and not water resistant but which can be hardened with secondary UV curing and hardening agents. UV polymerization typically takes a few minutes (with a source of 1-2 W/cm2); a strong UV source should reduce the time to under a minute. These photopolymer emulsions typically have viscosities of 3,500 to 12,000 cps, much more suitable!

Signs of progress

Tuesday, December 16th, 2008

Heard from a chorus of conservative pundits… “It’s a sign of progress in Iraq that Iraqi reporter Muntader al-Zaidi felt safe enough to throw a shoe at President Bush”. Or at least it will be if he survives the reported beatings and torture he is enduring.

Note to movie and TV writers: this would be an appropriate use of the word quantum, as in, “This is a sign of a quantum of progress in Iraq.”

Words I like

Saturday, December 6th, 2008