Cavalcade of Mammals

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.

With next generation sequencing technologies that have become available over the last two years, there is enough DNA sequencing machines that their combined capacity is, at a guesstimate, about 30,000 Gb per year.

How much DNA sequencing is that? Enough to sequence the genomes of 10,000 people per year. In other terms, enough capacity today to sequence every bacteria and virus species in a single year, or every the genome of every species on the planet in 300 years, bacterial genomes being small.

The sequencing technology is improving at a fast clip and I expect that in ten years or so it will be 1000X better (faster and higher capacity sequencing machines). So in ten years, it will be possible to sequence every species on the planet in a single year.

Scanners can be used for macro photography, at least the ones with a great depth of focus. The scanners with CCD sensors tend to have a good depth of focus while the thin scanners with a CIS sensor can only focus on objects a mm or two from the glass.

I collected a list of scanners recommended for macro photography.

from here:
EPSON Perfection 3170
from here.
Microtek ScanMaker X6 EPP
Artec AM12S, AM 2400-U Pro
Epson Expression 836XL
3D Pro Scanner
Memtek Memorex SCF 9360P 3D
from here:
Epson Perfection 1240U Scanner
Epson Perfection 1200U

Checking specs, these also look well suited:
Epson Perfection 2480
Epson Perfection V300
Epson Perfection 2450
Epson Perfection 3490

Parasitic diseases are common in the eastern Kentucky Appalachian region. This is one of the topics of a report in June 2008 PLoS Neglected Tropical Diseases.

The diseases mentioned, Strongyloidiasis and Ascariasis, are parasitic nematode infections!

Strongyloides stercoralis

Ascaris lumbricoides

And the Ascaris lifecycle. The Ascaris worms are huge, 20-49 cm long!

I saw an article of the problems Univerity Presses are having these days, the problems of an industry facing a changing market combined with university budget cutting during the recession. I think University Presses should embrace change. To me, the Univerity Press looks like the easiest segment of the publishing industry to move completely online. Most of their books are published by academics and mailed to university libraries where they sit bulky and using expensive floor space, rarely read. And for an academic, the electronic book has plenty of advantages, easy searching, cut&paste for quotes and organizing digital research notes, etc.

The physical book is unnecessary, and the price could easily drop several fold. Libraries would save money both buying the books and on shelf space. Without physical books, the main cost is in Univeristy Press is acquisitions and editing staff. The only things holding the Press to physical books are old academics who can’t/won’t use computers (few), the norms of what counts as a book for academic advancement, and inertia.