Science magazine has an article today on extracting and sequencing proteins from T. rex bones, and I’m already getting email from people wondering whether this is believable, whether it challenges the stated age of dinosaurs, whether this means we can soon reconstruct dinosaurs from preserved genetic information, and even a few creationists claiming this is proof of a young earth. Short answers: it looks like meticulous and entirely credible work to me, these fossil bones are really 68 million years old, and it represents a special case with limits to how far it can be expanded, so scratch “reassemble dinosaur from fragments” off your to-do list.

First thing I have to mention, though, is that this work is precise quantitative chemistry, not biology, and it’s a bit far from my expertise. The authors are using mass spectrometry of very tiny samples of greatly fragmented proteins to get sequences of short peptides. It’s tricky work, because not only are the proteins in very low concentration, but they are degraded and modified by chemical processes, and they are contaminated with minerals and material from the decay and fossilization processes. The peptides they do get are in extremely low concentration, requiring very precise techniques for analysis.

The data isn’t quite as glamorous or easy to grasp as a great honkin’ big dinosaur bone. They wash out and purify an extremely dilute broth from the fossil, run it through a machine, and produce charts like this one.

(click for larger image)
The LC/MS/MS fragmentation pattern from a 68-million-year-old T. rex peptide. (A) The experimental MS/MS spectrum for the T. rex doubly charged hydroxylated tryptic peptide sequence GVQPP(OH)GPQGPR from femur bone extract identified by LC/MS/MS. (B) The synthetic version of the same sequence. All major fragment ions from the experimental spectrum are in very good alignment with ions from the synthetic version, confirming the sequence. This molecular sequencing evidence of protein from a 68-million-year-old fossilized bone demonstrates excellent preservation of the T. rex femur and the high sensitivity of state-of-the-art MS technology.

What it is is a plot of the fragments coming through the mass spec, from which the sequence of that 12-amino-acid peptide can be measured. In this case, they also made a synthetic version of the peptide to show that the pattern of peaks was the same.

The researchers end up with a collection of fragmentary protein sequences, not the whole sequence of the protein, and then they compare those short sequences to a database of protein sequences from extant animals to identify partial matches. Then they ask which organisms have the greatest overall similarity to the selection of short sequences.

The T. rex peptide fragments had the greatest similarity to chicken peptides, but also had differences—some fragments matched up better with newt, fish, or frog sequences. That’s actually a good thing: if there weren’t those differences, there would be a strong suspicion of contamination from modern sources. If, for instance, someone had spilled chicken soup on the sample, we would see overwhelming similarity to chickens but not to newts or frogs (the probability that someone spilled their bowl of newt, frog, and chicken noodle soup is considered very, very low).

I’m persuaded that this T. rex bone contained degraded bits of T. rex protein imbedded in it. There are still some limitations, though. The protein they’re identifying is collagen; 90% of the proteins found in bone are collagen, a relatively simple and conserved molecule, so they’ve started with a highly enriched source 98 million years ago and are washing out a few dilute and broken scraps of the molecules now. It’s an impressive accomplishment, but we aren’t going to be reconstructing muscle anatomy and cell and tissue organization from this, or even getting a good sampling of different gene products for phylogenetic analysis. It’s one protein, and it’s a mess, but it’s really there.

There is promise for the future, though.

As technologies become more refined and protein extraction techniques are optimized, more informative material may be recovered. This holds promise for future work on other fossil material showing similar preservation, but also demonstrates a method for obtaining protein sequences from rare or endangered extant organisms whose genomes have note been sequenced. The MS- and bioinformatics-based approach we have used can be applied not only to obtain sequences from extinct organisms, but also to obtain protein sequences from extant organisms whose genomes have not been sequenced and to discover mutations in diseased tissues such as cancers.

That’s the right perspective, I think: they have a technique that is so good, that they can pluck out a signal even from the highly degraded core of a piece of fossilized bone, there are opportunities for extracting sequences from microsamples of other, less exotic tissues.

Asara JM, Schweitzer MH, Freimark LM, Phillips M, Cantley LC (2007) Protein Sequences from Mastodon and Tyrannosaurus Rex Revealed by Mass Spectrometry. Science 316(5822): 280-285.