Cavalcade of Mammals

BTW, the previous article comes by way of a link to an article in VentureBeat. Contentwise the article is nothing special, a thinly written industry conference talk/press release. But the author Mark Coker and VentureBeat understand online journalism. The article has what every web news story ought to have but few do–relevant and appropriate links. The article links to a detailed article on the technology, the company, and the conference. This is great!

Unfortunately most news organizations haven’t got this figured out yet. They will report on (summarize) say a report by the FDA without linking to the report. Many/most of these are now on the web–the reporter read it there in many cases–but the article doesn’t link to it. Or to the FDA press release.

Science news never links to the journal article. Or to the less technical journal News and Views summary, or to the non-technical University press release.

It a real opportunity for a news organization. If I knew the McClatchy (formerly Knight-Ridder) news service did this I would seek out their articles over AP’s or the New York Times. I haven’t seen any grab for this brass ring.

A company has developed a new reading technology called Live Ink (paper here). The idea is to improve the way text is displayed to improve reading comprehension. The way the brain perceives a page of text is as small region at a time. Words from several lines get picked up at the same time. This confuses the parts of the brain that comprehend words and sentences. Live Ink proposed to spread text out to avoid this mental confusion to improve reading comprehension.

There’s a kernal of a good idea there–electronic text allows reformatting to increase comprehension. But their solution sucks. It takes up too much space and it only partially helps with the problem of line confusion. The syntactic breakup may be helpful. Here’s an image of it:

Computer formatting is a good idea. Here is my idea of how to do it. Fuzz out the lines before and after the current line. This could be done one of two ways. If eye movement tracking is available, follow the eye and only make the line being looked at visible with the others fuzzed out. Without eye tracking make this a timed system (like traditional light bar reading trainers). Start it on a section of text and make one line at a time is visible moving through the text. Controls would be needed to pause and go back a few lines, and flip it off.

By fuzz out the rest of the page I mean alter it so the brain doesn’t think it is text and try to decode it. Whether making it out of focus is enough or if another kind of noise needs to be added would need to be determined by trials. It would be important to leave enough information that the presence of text blocks and formatting is visible. These provide visual landmarks needed for good reading.

Technically, this could be easy–a web browser extension or perhaps as simple as some Javascript added to a page with overlay images fuzzing the text and moving as needed.

Well done site that explains stem cells to the public:
http://www.tellmeaboutstemcells.org/

To reset a wordpress password, first generate the hash:

perl -e 'use Digest::MD5(md5_hex);print md5_hex("the_password"),"n";'

then update the password in the database:

mysql
mysql>select * from wp_users;
mysql>update wp_users set user_pass='the_hash_string' where ID=xx;
mysql>exit


I looked up Jerry Pournelle’s site and he was worrying about the US getting overwhelmed with immigrants. To start with, it looks like he’s using scare numbers, 100 million US immigrants in the next 20 years. The US has recently naturalized 1/2 million to a million immigrants a year (pdf). The base value is about a 1/2 million with the figure doubling during amnesty periods.

So how high was immigration into the US in the past? I recall the last big wave was in the early 1900’s. Googling brought up the census numbers. The 1990 US Census estimates 19.8 million foreign born citizens in a population of 248.7 million, 8.0% of the US population. At the peak of the last wave of immigration, there were 13.5 million foreign born citizens in a US pop of 92.2 million, making up 14.6% the country. And this wasn’t an isolated peak, the foreign-born percentage was 9.5% in 1850, 13.1% in 1860, 13.4% in 1880 picking the earliest figures I found and then the other high points (pdf, pdf).

So the rate of immigration into the US is not near the historical high. And in context and with regard to assimilation I would expect current immigrants are easier to assimilate. Typical immigrants today come to the US knowing quite a bit about the country, and already familar with many aspects of the culture from the movies, TV, and books that the US exports around the world. The immigrants coming from Southern and Eastern Europe in the early 1900’s knew much less about the US.

Old doggerel, but new to me:

“Let’s consider the concept of niche-
If I knew what it meant I’d be rich.
Its dimensions are n
But a knowledge of Zen
Is required to fathom the bitch.”

Archaeologists push back the date of the invention of noodles to 4,000 BP:
BBC NEWS

The 50cm-long, yellow strands were found in a pot that had probably been buried during a catastrophic flood.

Radiocarbon dating of the material taken from the Lajia archaeological site on the Yellow River indicates the food was about 4,000 years old.

Scientists tell the journal Nature that the noodles were made using grains from millet grass – unlike modern noodles, which are made with wheat flour.

The discovery goes a long way to settling the old argument over who first created the string-like food.

Professor Houyuan Lu said: “Prior to the discovery of noodles at Lajia, the earliest written record of noodles is traced to a book written during the East Han Dynasty sometime between AD 25 and 220, although it remained a subject of debate whether the Chinese, the Italians, or the Arabs invented it first.

Great science writing too–packed with detailed information yet succinct. I’ve never read a molecular biology news article as good.

A compter security hack has appropriated the word nematode to describe “good” network worms. Dave Aitel says

“We don’t want people to think this is impossible. It’s entirely possible to create and use beneficial worms and it’s something businesses will be deploying in the future.”

So much for ever being able to Google “nematode” again! Spoiler! Bastard! And it’s so wrong. Aitel has a apparently heard of Caenorhabditis elegans, everyone’s favorite worm and entirely harmless, and jumped to the conclusion that every nematode is beneficial to humans. So wrong, so sad; a little knowledge is a dangerous thing. If this is the depth of his thinking I certainly wouldn’t take his advice on computer security.

I just read a review on cutting-edge new sequencing technology (Shendure et al., 2004). There are several approaches that were new to me. One that caught my imagination incorporates “polony technology,in which PCR is performed in situ in an acrylamide gel” for DNA amplification. A related technique using emulsion has been developed by the Volgelstein lab.

My idea of developing a method using reversibly terminating nucleotides has also occurred to many other people! Apparently finding a way to do the reversibly termination has been a roadblock. I certainly didn’t have a way to do it. They have worked out approaches to detection of incoration, the other half of the method, and also a part I didn’t develop.

Very interesting tech. According to the paper, even nanopore sequencing is close to working!

The paper talks a bit about using ULCS for personal genome sequencing (PGP, everthing gets an acronym), about the whys and what it will mean. It contain the usual throw away consideration of ethics and consequences. The papers says this “will require high levels of informed consent and security”. In practice, your personal seq info and related disease susceptibility info *will* get spread to interested parties. Just look at who calls the shots; after more than a decade of attention to genetic privacy and overwhelming public support, “no US federal laws that ban genetic discrimination for medical insurance or in the workplace”.

How I would love to seqeunce 1Gb a week!

From PZ Myers, unsourced:

“0.1% of all the species that have existed are currently extant, and the average lifetime of a species is roughly 10 million years”

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