Monday, 19 January 2015

Jurassic Park IV on the horizon....


Ancient, or prehistoric DNA (usually abbreviated to aDNA) has been of interest to palaeontologists ever since the remote possibility that it might be recovered began to be entertained. The improvement of molecular biological techniques such as the polymerase chain reaction (PCR) and the development of laboratory equipment for dealing with and sequencing DNA has greatly expanded the scope of possible research on aDNA, with the result that the field is presently one of active exploration.

Sadly, the breakdown of DNA from a dead organism, over long periods of time, leaves the original molecules separated into multiple short sections. These remnant sections may number only a few hundred base pairs out of hundreds of millions in the original sequence, and the remnant sections themselves may feature damage of various kinds. To recover a fragmentary DNA sequence from one chromosome in a fossil is thus a very long way from recovering an entire genome complete in every chromosome, just as the recovery of one sentence or even a word, is not the same as having the entire works of William Shakespeare. This matter of short sequences versus a complete genome is a primary separation of reality from Jurassic Park.  

Another division between Jurassic Park’s scenario and reality is the durability of DNA, given it is truley the 'delicate molecule of life'. Can aDNA last for hundreds of millions of years? Ancient DNA studies were launched in 1984, when Berkeley researchers collected DNA from an 150 year old museum specimen of a recently extinct Zebra relative, the quagga (Equus quagga quagga). This was the beginning of a quest into the past for DNA, which had been thought to deteriorate too badly for study soon after death. Researcher Svante Paabo became a major pioneer of this field. He applied DNA extraction techniques to Egyptian mummies and other ancient human remains, successfully producing sequences from bodies thousands of years old. DNA from animals dead a few thousand years, such as extinct moas (Dinornis robustus and Dinornis novaezelandiae), has allowed for comparisons with living species in order to determine the evolutionary distance from living relatives.

When an organism shuffles off its coil, its DNA is subject to breakdown due to the nuclease enzymes naturally occurring within the cells, and the end result of this process if completed would be the complete reduction of DNA to mononucleotides, the links from which the chain was made. At that point all the DNA information would be destroyed. However, several factors can slow-down nuclease activity and DNA breakdown: cold temperatures, rapid drying, and salt are primary conserving influences. However, even under optimal conditions, DNA continues to break down through oxidation and other chemical processes, until finally its identity is erased or so blurred that it could have originated from a Blue Whale (Balaenotera musculus) or my brother (Stevenus manningii)!

So, once again we will creep toward a summer of speculation as folks claim to have dinosaur DNA in their impeccably preserved samples....but for me, if the movie sparks an interest in science for another generation, it has done a splendid job!

Wednesday, 17 December 2014

I see dead things....

The white noise of the Stanford synchrotron has started to lullaby me to sleep....this helped by the metronomic back and forth of the sample stage, like some high-tech macabre hypnotist act performing to the Borg. The first 6 days of beam time were straight forward, but this should have been 10 ten days of scanning prior to this point. Alas, one of the beam lines on which we were meant to work had a slight 'leak' of radiation...so we were unable to give our fossil samples an EXAFS bath that they all required...this will now have to wait till Spring 2015. Today we switched from the 'hard' 13.5 KeV x-rays to to the softer 3.15 KeV....this to gently tease a sulfur signal from our samples and tweak energies between the multiple oxidation states via XANES of this splendidly useful element within organic molecules. This lighter side of our elemental analyses is cloaked in an atmosphere of helium, adding to the degree of complexity that consists the sample stage. All told, we are sleep deprived...light deprived...but very happy with the steady stream of data from the XRF rapid scanning stage.


Friday, 21 November 2014

Dinosaurs, sculptures, field jackets, museums and PhD's....

This has been one of those weeks that simply evaporated. I touched down in Newark last Saturday and it is suddenly Friday....there seems to have been a rip in the space-time continuum that has seemingly navigated me through several museums collections, an animal menagerie and a PhD committee meeting at the University of Pennsylvania. I am once again back at the American Museum of Natural History (New York) sat in the prep lab, being serenaded by the gentle hum of pneumatic pens as millions of years of sediment is gently teased from stunning dinosaur bones...all the way from Mongolia. At the far end of the prep lab sits a vast field jacket....fruits of our Summer labours in Montana. It was delivered last week (see image below) and the collections curator (Carl Mehling) was called by the delivery bay folks and told, "Your sculpture has arrived".... The 2575 pound field jacket is the largest to enter the AMNH in a few years...its secrets will soon be unlocked by the splendidly skilled preparators who work within these hallowed halls. My time in New York is nearly done, until the next visit, off to the airport again....

Prehistoric 'sculpture' arriving arrives at the AMNH!