Cavalcade of Mammals

The first papers from the ENCODE Project: ENCyclopedia Of DNA Elements came out in Nature and Genome Research this week. The project’s goal is to understand non-coding DNA seqeunces by focusing in on 1% of the genome with multiple experimental approaches.

It’s not getting described well in the press. This news article is quite giddy: link

DNA study challenges basic ideas in genetics
Genome ‘junk’ appears essential

By Colin Nickerson, Globe Staff | June 14, 2007

A massive international study of the human genome has caused scientists to rethink some of the most basic concepts of cellular function. Genes, it turns out, may be relatively minor players in genetic processes that are far more subtle and complicated than previously imagined.

Among the critical findings: A huge amount of DNA long regarded as useless — and dismissively labeled “junk DNA” — now appears to be essential to the regulatory processes that control cells. Also, the regions of DNA lying between genes may be powerful triggers for diseases — and may hold the key for potential cures.

The details are interesting for biologists but not super surprising. Here’s an overview of non-coding DNA:

2% of the human genome encodes proteins. A difficult problem is to figure out what the the remainder, the non-coding DNA, does. About 1% is clearly involved in regulating protein expression, and a few additional percent have other known functions. An additional 2% are conserved non-coding sequences, DNA that has kept its sequence for tens of millions of years. The function of most of these conserved non-coding sequences is not known but their DNA has been retained because it has a function.

While it is hard to prove a negative, most of the remaining 90+% is likely non-functional (’junk DNA’) or very weakly functional. Some bits are likely spacers the sequence of which is unimportant. About 1/2 the human genome is transposons, bits of DNA that have copied themselves over and over (it is like the genomic inbox is full of spam).

The most interesting finding is that some non-coding non-conserved DNA is functional. Exactly how this works biologically is not clear–so very new, very cool. Ultimately, this adds another 1-2% to the functional non-coding class of DNA.

So it is interesting to hear that a new function for a bit of the non-coding DNA has been discovered–there will be a lot of cool new biology working out what bits of this do. Still, most of the genome is junk DNA.

The amount of junk DNA in a genome can vary a lot. There are some frogs and salamanders with genomes ten times larger than humans. These animals likely have about the same number of genes as humans. They are thought to just have a *lot* more junk DNA.

The recent development of the 1TB hard drive reminded me of my first thoughts about the end of the hard drive expansion. Back when the 1 GB drives came out I calculated my total lifetime media need. It came out under 10TB and half of that was video:

1TB 200,000 books at 5MB/book (every book I’ll read or know about)
1TB 200,000 songs, 5MB/song (every song I’ll ever hear)
3TB 3000 movies, 1GB/movie (every movie I’ll watch or desire to watch)
1TB 300 TV show seasons, 3GB each (ditto)

Personal records:
1TB 500,000 photos, 2MB/photo (every photo I’ll take or see)
1TB 2000 hours home video, 500MB/hr (fun to shoot, but who will watch it?)
0.001 TB (every word I’ll write, email, publish)
0.1TB 1GB/year (saved email and internet cruft, LOL cats, etc.)

It sums up to 8TB/life. And indexes, you definitely need indexes, so say 1TB for indexes.

This will expand as high res video/photos phase in but even that won’t push this out much beyond 100TB.

300 TB would allow you to record your entire life in video for 16hr/day for 100 years at 500MB/hr (one camera angle). No compression for time spent watching your self-video is assumed. :)

Saw this colored peg low res image and was reminded again I want to do something similar with black and white ping pong balls. I would work up a Lego bot to drop the balls in.

And then I had a cooler idea–I’ve seen a programmed water drop device used to make images. A related idea would be to drop water onto piano strings. The drops would strike the strings and make sound instead of images. The drops would fall a distance so you would see the music visually–see the notes coming before they hit.

Thinking more, there’s a good chance this wouldn’t work–the water drops wouldn’t have enough force. Worth a try though. :)

It was announced today that the full genomes of James D. Watson (and Craig Venter, though for much more than $1,000,000) have been sequenced. The NYT article had this bioethics blurb:

Dr. Watson and Dr. Venter are both taking a considerable personal risk in making their genomes publicly available. As is probably true for everyone, their genomes are likely to contain mutations that could lead to disease, revealing possibly unfavorable information about themselves and their relatives.

For Venter this is clearly untrue. He’s rich and can self insure with no problem. Likely Watson has enough dough this isn’t a risk either. For their poorer relatives, yes there is risk. I don’t think the writer of the NYT article, Nicholas Wade, gave this any thought–genetic knowledge insurance/employment risk is a standard story line, and the writer plugged it into this article.

I heard NASA head Michael Griffin interviewed on NPR this morning. He was asked about global warming and after a bit of prodding said that while he knew it was happening and human caused he didn’t see it as a problem. He said that the current global temp might not be ‘optimal’ for humans and thought some warming might be a good thing. Classic second stage global warming denial.

This is a zombie argument–wrong and long proven to be wrong but it keeps popping up. A good site for rebuttal of global warming denial zombie arguments is at Gristmill. Griffin’s zombie is handled here.

Every few months I run across an anecdote about how horrible Canada’s or UK’s national health system is (but never about any of the other European health systems, hmm). Anecdotes may cause you to consider an argument, but you need to turn to data to draw conclusions.

US/Canada health system comparisons:
Big study, clearly written: http://www.pnhp.org/canadastudy/
And a 2007 Commonwealth Fund study:
http://www.washingtonmonthly.com/archives/individual/2007_05/011316.php
Med. student review of the literature: http://www.amsa.org/studytours/WaitingTimes_primer.pdf

BTW, the Canada comparison is the one in which the US looks best, several of the European national health systems are *much better* and *much cheaper*. US citizens with top-of-the-line employer provided health plans get care as good as in the best European systems (just more expensive).

Conclusion: US has the worst and by far the most expensive health system among Western nations.

Evolution question from the first Republican presidential debate, torture question from the second debate. The others believe in evolution (at least to some degree) and did not answer the torture question at the second debate.

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/