Cavalcade of Mammals

The artificial sweetener aspartame is about 200 times sweeter than sugar. It is widely consumed in large quantities–diet sodas contain 140-185mg per 12 oz., so a person drinking a lot of diet soda may consume a gram a day. The FDA recommends 40mg per kg body weight as a safe daily dose–about 2 grams per day for a average sized person.

In the human gut aspartame breaks down into three components: two amino acids, phenylalanine and aspartic acid, and methanol. Phenylalanine and aspartic acid, being amino acids, are a normal part of the human diet. Methanol is absorbed from the gut and converted by the liver to into formaldehyde and formic acid, both nasty but non-specific poisons. In the small amounts formed from aspartame they are thought to not be dangerous. Some foods, some normal body processes, and alcohol consumption produce methanol, though I don’t have figures as to how much.

There has been some controversy over whether aspartame is safe. There have been a few studies showing some cancer risk in animals, three recent mouse studies from Soffritti et. al. being the most convincing. Any cancer risk is thought to come from the methanol. Recent studies in animals seem to running about 10:1 no cancer:cancer. As aspartame has been in food for thirty years, there have been some large human studies, and none of them show increased cancer due to eating aspartame.

Here are American Cancer Society and National Cancer Institute pages assessing aspartame.

The other concern brought up is whether the phenylalanine and aspartic acid that aspartame breaks down into have an effect on the nervous system. In addition to being used for making protein, these amino acids are also feedstock for making catecholamine neurotransmitters. There is some evidence that a large ingestion of these two amino acids alone might throw off normal neurotransmitter levels. It’s not clear what, if any, effect this has on human brains–it clearly has no striking consequence. Any effect is of course relative–aspartame is often consumed with caffeine, a substance that clearly effects brain function. :)

This 2008 review article makes a number of alarmist suggestions but has almost no actual evidence. It’s a very odd article. A large human dose of aspartame is about 1 gram a day. The RDA for protein consumption is 0.8 g / kg day, which contains about 2 grams of phenylalanine and aspartic acid. Not all foods have an even balance of amino acids, so animals must have fair ability to buffer a diet rich in one or another.

Aspartame has been well-studied and is safe. It is still being studied–it may turn out to be a very weak carcinogen, too weak to show up clearly in the studies so far. Or have a subtle effect that screws up the rare person’s brain. Risks are relative–aspartame is certainly much better for a person’s health than the sugar it replaces. On the other hand, you can’t go wrong drinking water.

How to connect a PIC microprocessor to a computer’s USB interface.

Links:
Microchip forums
a PIC USB project
a PIC USB library
Microchip forum on a Nuts ‘n Volts article on PIC USB using the SDCC compiler
PUF: PIC USB Framework
Nuts ‘n Volts HID demo Rebuilt
SDCC – Small Device C Compiler

A small GPS tracker able to report its position would be useful. It could be used as a LoJack style property tag. There are a number of ways to do this of varying difficulty and expense.

GPS modules are fairly inexpensive, selling for $50-100. The harder part is communications. There are three main ways to have a GPS report its postion: 1) cell phone text messages, 2) radio, or 3) using open wireless internet nodes. 3) is unreliable, there may not be a open access point where it is needed. 2) is hard–the way it would work is to have a radio transmitter with a 1 to 10 mile range send location info through a ham repeater onto the internet. This requires a ham license and roughly $100 for the controller and radio electronics.

The easiest way turns out to be 1). In fact, there are cell phones available that have GPS and of course text message and/or data capability. Some of these phones allow the phone to run custom software. And in fact, groups have written this software already.

One is TrekBuddy. It can be combined with a cheap cell phone with GPS. Using a prepaid phone, the cheapest plans are about $0.20 – $0.35 a day, about $6 – $11 a month.

There is also Mologogo, a site with a custom tracking app that sends data to the mologogo.com site and displays the position on a map.

Other similar services:
iTag
InstaMapper
AccuTracking

How to download flash video.

Try the UnPlug Firefox extension first. If it works it is the easy way.

If that doesn’t work, here’s a way of downloading flash video.

1) Install tshark, a network monitoring tool.

2) Run tshark from a command line:
tshark -e http.host -e http.request.uri -T fields tcp port 80 > sites.txt

3) Load or reload the web page with the flash, let the video start to play. Then you can stop tshark.
tshark logs all the files that get called to load the web page.

4) Look in the sites.txt file. Search for files with the .flv extension:
flash.video.worldnow.co /wand/WAND_20101010210218823AB.flv

Put together the web site and file path like so (the ‘m’ in com was cut off):

5) Download this file. I use wget:
wget http://flash.video.worldnow.com/wand/WAND_20101010210218823AB.flv

6) The file can be viewed with a flash video player (like VLC) or converted to .avi with ffmpeg:
ffmpeg -i WAND_20101010210218823AB.flv video_file.avi

Great article at the Pathogens: Genes and Genomes blog.

The technology generation after next-gen (next-next-gen?) is getting close!

And here’s an article from 2009, the first using single molecule sequencing to sequence a human genome. Helicos short read tech was used, and the reagent cost was $50k. Pushkarev, Neff, and Quake.

The Li and Wang News and Views summary of the Pushkarev article has a good overview of next-gen sequencing.

Articel on yeast article
A yeast cells will only divide a certain number of times before it stops–it senesces. When yeast cells divide, the mother and daughter are asymmetric, and the daughter cell has it’s division clock reset. At least part of this is due to extrachromosomal rRNA circles (ERCs) being retained by the mother cell.

New research finds that the septin ring between mother and daughter cells is a selective barrier for membrane proteins. The ERCs can’t pass the septin ring, and are likely linked to a membrane protein.

Z. Shcheprova et al., “A mechanism for asymmetric segregation of age during yeast budding,” Nature, 454:728–34, 2008

A drug that activates telomerase

A team of biotech and academic researchers has found a natural product compound, TA-65, that activates telomerase. Activating telomerase for short period is a way to renew cell populations that stop dividing. This diminishment of renewing cell populations causes some of the human aging phenotypes. If telomerase was turned on all the time, it would lead to cancer. The idea is that short term telomerase activation may have the benefits of renewal without increasing cancer incidence. TA-65 has only had one pilot human pharmacokinetic study where it seemed to have an effect on T-cells.

A Natural Product Telomerase Activator As Part of a Health Maintenance Program. Harley et al. Rejuvenation Research. doi:10.1089/rej.2010.1085. Online Ahead of Print: September 7, 2010

Great Harry Potter fan fiction. Harry Potter reimagined as a rationalist encountering Rowling’s world of magic.

Harry Potter and the Methods of Rationality PDF

I’ve had trouble finding info. A google search on “crystal binding proteins” sorta worked.

IgA binds to cholesterol crystals:
Cholesterol crystal binding of biliary immunoglobulin A: visualization by fluorescence light microscopy. Lammert et al. World J Gastroenterol. 2001 Apr;7(2):198-202.

There no doubt are proteins that bind to calcium carbonate shells material, but I couldn’t find info on them. I think shell is formed like bone, by cells increasing the local concentration of Ca++ so it crystallizes out of solution rather than by direct enzymatic action.

Collected references on DNA sequencing by synthesis and related next-gen sequencing technologies:

SBS history page at Harvard

• Pubmed search
• Four-color DNA sequencing with 3′-O-modified nucleotide reversible terminators and chemically cleavable fluorescent dideoxynucleotides. Guo et al. PNAS July 8, 2008 vol. 105 no. 27 9145-9150.
• Four-color DNA sequencing by synthesis using cleavable fluorescent nucleotide reversible terminators. Ju et al. PNAS December 26, 2006 vol. 103 no. 52 19635-19640.
• Design and synthesis of a 3′-O-allyl photocleavable fluorescent nucleotide as a reversible terminator for DNA sequencing by synthesis. Ruparel et al. PNAS April 26, 2005 vol. 102 no. 17 5932-5937.
• Design and Synthesis of a Photocleavable Fluorescent Nucleotide 3‘-O-Allyl-dGTP-PC-Bodipy-FL-510 as a Reversible Terminator for DNA Sequencing by Synthesis. Meng et al. J. Org. Chem., 2006, 71 (8), pp 3248–3252.
• Four-color DNA sequencing by synthesis on a chip using photocleavable fluorescent nucleotides. Seo et al. PNAS April 26, 2005 vol. 102 no. 17 5926-5931.

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.’