Cavalcade of Mammals

This is why they call him “Silent” Jim Bunning.

Picture taken at a Senate committee meeting working on the health care bill.

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.

I want a pet book worm!

The North Auckland worm, Spenceriella gigantea, reportedly glows in the dark brightly enough to read by!

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
>Brachylophosaurus
GATGAPGIAGAPGFPGARGAPGPQGPSGAPGPKGVQGPPGPQGP--------------------------
GATGAPGIAGAPGFPGARGPSGPQGPSGAPGPKGVQGPPGPQGPRGLTGPIGPPGPAGAPGDKGEAGPPG
GATGAPGIAGAPGFPGARGPSGPQGPSGAPGPKGVQGPPGPQGPRGLTGPIGPPGPAGAPGDKGEAGPSG
                   **                                               * 

--------RGSAGPPGATGFPGAAGRGVVGLPGQR-----------------------------------
PAGPTGARRGSAGPPGATGFPGAAGRGVVGLPGQRGETGPAGPAGPPGPAGARGSNGEPGSAGPPGPAGL
PPGPTGAR-GSAGPPGATGFPGAAGR---------GETGPAGPAGPPGPAGARGSNGEPGSAGPPGPAGL
 *

-GLPGESGAVGPAGPPGSR
RGLPGESGAVGPAGPIGSR
RGLPGESGAVGPAGPPGSR
               *  

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!

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.

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.

Putting together the reading list for the seminar class this semester I ran across an odd corner of the human fertility industry that I never knew existed. I’m picking seminal papers in biotechnology and one of them is the 1992 paper, “Birth of a normal girl after in vitro fertilization and preimplantation diagnostic testing for cystic fibrosis” by Handyside et al. One of a pair of papers that first used PCR to test embryos for genetic disease so that the disease free ones can be implanted.

So I looked at where preimplantation diagnostic testing was available in Lexington. There is an IVF clinic that does preimplantation testing–not at the UK hospital, they seem shy of anything slightly controversial. What was odd, is ZDL, a company that sells fertility products for people to use at home, or send in for analysis. Home sperm counts, insemination devices, and more. Quite surprising!

I ran across a caloric restriction study being done with human volunteers. It is the CALERIE study (Comprehensive Assessment of Long-term Effects of Reducing Intake of Energy) being run by Eric Ravussin and Donald Williamson at the Pennington Biomedical Research Center in Baton Rouge, LA.

The study will put human volunteers on a diet with 25% less calories for two years to see of the effects of short term caloric restriction affect the body in ways similar to the effects in animals. In animals, 25% caloric restriction increases lifespan by 20-25% and reduces the incidence of many age-related diseases.

The results should be interesting. I hope they can recruit and keep enough participants on the low cal diet!

A was listening to Charles Darwin’s The Voyage of the Beagle, an incredible story of a round the world voyage of exploration that began in 1831 and continued for five years.

The end of the edition I was listening to had two appendices, the first being nautical stuff about the trip and the second being a reprint of the ship captain Robert Fitz Roy’s “Remarks with reference to the Deluge”. It’s basically a argument for literal biblical creationism by Fitz Roy, and it was pretty ironic to find it tacked on to the Voyage. I don’t know the which editions carried it, apparently the Voyage was published in several editions (wikipedia).

The strangest part of Fitz Roy’s argument was his attempt to describe a plausible way that the biblical Deluge, the business with the Ark and world covered by water, could have deposited the many layers of rock and sediment that compose the geological record and which he observed at locations around the globe. In his argument he mentions that the Library of Useful Knowledge, 1829 describes an experiment by Perkins that showed that at a depth of 3000 feet, water is compressed to 1/27 of its volume at the surface. Fitz Roy relates this to a sailor’s experience that in determining depth with a weight and a line, larger weights are required for deeper depths.

Fitz Roy then argues that sea water is very dense in the ocean depths, and that all sorts of objects immersed during the Deluge would sink to a depth where the water was dense enough to make then buoyant, different objects finding a different natural depth, and that these layers would be preserved as the Deluge ebbed.

This is quite remarkable. Water is known now to be nearly incompressible, around 2% at the bottom of the ocean, with the slight changes in ocean water density caused more by temperature and salinity than pressure. This means that Fitz Roy’s argument falls apart. More remarkable is that such a basic fact about water and the oceans was unknown in the 1830’s. Fitz Roy really believed there was a depth in the ocean where cannon balls float, accumulated from the world’s shipwrecks and banging around together in a layer where iron floats in the deep ocean.

I was listening to the NPR food show, The Splendid Table, and they ended the show with by having Dean Radin from the Institute for Noetic Sciences on to talk about how ‘thinking at’ chocolate makes it better. No, I’m not joking, and it wasn’t April Fools’ day. Ordinary fools day, I guess.

Looking at the Institute for Noetic Sciences (IONS) web site, it looks like this is the place where the California nuts collect. They are still doing psi studies, lots of ‘intentional’ studies which test various ways thinking at something changes it, from prayer and healing to remote viewing to psychokinesis. Not too surprisingly, Deepak Chopra is ‘associated faculty’.

The chocolate study guy, Dean Radin, is an interesting nut. He was a real engineer, then got a Ph.D in psychology from U of Illinois at Urbana-Champaign, then went off the deep end. It’s odd, he uses methods that look quite respectable–the chocolate study was double-blinded–to come to nutty conclusions, and publishes them in nutty niche journals. IONS has its own journal, “Explore: The Journal of Science and Healing”, and disturbingly the NIH’s Pubmed article indexing service includes its articles (see http://www.ncbi.nlm.nih.gov/pubmed/17905358). This is by far the craziest journal I’ve ever seen in Pubmed.