Cavalcade of Mammals

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.’

Forwarded my blog from my old server to this one. Added a Rewrite rule to httpd.conf on the old server in the main site <VirtualHost *:80> section:

RewriteEngine On
RewriteRule ^.*/blog(.*)$ http://jimlund.org/blog/$1


The Northwest Passage, the sea route from the East coast to Alaska along the shore of North America is open! This is the third straight year it’s been open after being ice bound for something like 6,000 to 8,500 years.

I expect that for kids growing up now it will always be open, and only news if a particularly cold year closes it.

Shakepeare’s Sister posted on the very cover of The Overton Window, a thriller by Glenn Beck. I haven’t read it, but the plot is described as weak Randianism dumped in a Mixmaster with a thrillerish suppression of conservatives by the establishment and counterrevolution story.

He points out the the Statue of Liberty has been turned into a man. But it gets odder than that!

The other really strange thing is the viewpoint. It’s the back of the statue. And it’s been turned to face Manhattan. Why? I did a search of pictures of the Statue of Liberty and none of the first hundred were a back view. All showed the face, either full on or from the side to include Manhattan. I don’t know what to make of it, but it creeps me out!