Monthly Archive: September 2009

The lost decade, or thanks for nothing!

Census data on median income change between 2000 and 2008 by way of USA Today:

Median income 2000-8

US GDP in constant dollars per capita grew 9.7% over this period, so the country grew 10% richer and if it was distributed evenly everyone’s income would have grown roughly 10%. But not–instead most of the $$ went to a small slice of the population, and that doesn’t show up in this table.

Book review: The Atrocity Archives and Concrete Jungle by Charles Stross

Atrocity Archives word cloud

Charles Stross has written the best new books I’ve read over the past few years.
Singularity Sky, Accelerando, Halting State, each excellent. And his books explore different ideas and are set in very different worlds. With the exception of the dismal Family Trade series, his writing has been excellent.

The Atrocity Archives and Concrete Jungle, two shorter works set in the same world are the first fantasy I’ve read by him, and they are crazy good. Halting State good, but these stories are modern fantasy integrated into the technological world, magic for hackers that participates in the modern world revolutionized by discoveries in mathematics, electronics, modern physics, and computers. A magical worldview that has confronted modern physics and considered the natural consequences of computers.

The book was a real page turner–errr, a virtual page turner that I read on computer. The Atrocity Archives is better than Concrete Jungle. Jungle seems constrained by its short length, the ending feels rushed. After Concrete Jungle I immediately sought a sequel and was glad to find The Jennifer Morgue.

Concrete Jungle word cloud

Soft tissue in dinosaur fossils

In 2005, a Schweitzer et al. reported that they had found soft tissue in the marrow of a T. rex. bone. Examination of the tissue showed evidence of cell-like structures that could indicate preserved cells. Also stuff was squishy like protein. It if held up, an incredible discovery.

In 2007, Schweitzer et al. followed it up with more extensive analysis that indicated the presence of collagen I protein. Most exciting, they used mass spec to sequence a few fragments of dinosaur protein. It was quite similar to chicken collagen, and of course birds are the closest living relatives of dinosaurs.

Then in 2008, Kaye et al. analyzed a number of fossils and found similar traces, but interpreted them as bacterial colonies, as biofilm. They even saw the cell-like traces in a fossil ammonite, a creature without blood cells.

This year, Schweitzer et al. doubled down, publishing collagen I protein sequence from a hadrosaur.


In total the two papers found protein sequences that cover 169 aa of collagen protein sequence. Here are the overlapping dinosaur sequences with the gaps removed aligned to chicken sequence. The dinosaur sequences differ from the chicken sequence at five positions.

It will be interesting to see if these results hold up. I would like to see replication by a second lab. Most convincing would be two labs given the same unknown sample and both finding the same new collagen protein sequence.

>Tyrannosaurus rex
>Gallus gallus
                   **                                               * 



Book review: Jurassic Park by Michael Crichton

I finally read the iconic dinosaur book by Michael Crichton. The book was very similar to the movie, closer than any other movie I’ve seen. In many ways the book reads as if it was written with the idea of turning it into a movie in mind. The plot is straightforward: rich old guy hires scientists to recreate dinosaurs from DNA preserved in fossils, then the dinosaurs get loose and eat people.

The science fiction idea than spawned the book is grand. Recreating dinosaurs! Real dinosaurs! That people can be see and watch and eventually run screaming from. The other part of the book, the horror movie bolt on plot, is naturally fit for a movie.

Surprisingly there isn’t much more to the book than what’s in the movie. And unfortunately the worst parts of the movie are the author’s invention. The ‘mathematician’ character, spouting ridiculous idea that chaos theory proves everything will go wrong and fall apart is all the author’s. Also, the annoying younger sister who alternates between fear, whining, and suicidal stupidity is all Crichton. She’s written worse in the book, the other characters mock whatever she has to say and keep telling her to shut up. The out of nowhere scene in the movie where she pops up as a computer system expert looks added in an attempt to give her character a positive side.

Still, dinosaurs!

cover pic

When the book was written, it was plausible to speculate that fossils millions of years old would contain bits of DNA. As it turns out, DNA degrades over hundreds of thousands of years, and no DNA has been recovered from samples millions of years old. In fact, chemical studies predict that DNA will degrade at such a rate that no original DNA remains in samples millions of years old. Today, alas, it seems unlikely that dinosaur DNA sequences will ever be recovered.

Jurassic Park word cloud

I am surfeit with hard drive capacity

Two terabyte hard drives were recently released, which to me means the day is nearing where a single computer with have all the storage space I can imagine ever using. This figures a typical computer with four hard drives. Here’s how I apportion a my complete storage needs:

1 TB, 100,000 books x 10 MB each, every book of which I’ve ever heard (or read).
1 TB, one million photos x 1 MB each, a lifetime of pictures and LOLcats.
1 TB, 200,000 songs x 5 MB each, every song I’ll every hear in my life.
7 TB, 200 TV shows x 50 episodes x 700 MB, complete runs for typical hour long TV shows.
12 TB, 3,000 movies x 4 GB each, one new movie a week for life.
Total: 20 TB

Four 5 TB drives add up to 20 TB, and 5 TB drives should be available in about 2-3 years. Backup and redundancy require extra storage not accounted for here, but becoming progressively easier.

As you can see, books and even audio are only a small fraction of the storage space. Start with a smaller video library–movies and TV seen so far, or only favorites–and four 2 TB drives would satisfy all personal storage requirements.

To use more personal storage someone needs to make some sort of digital diary, an elog, a continuous lifetime audio or video record.