Thursday, 25 July 2013

Nature's Chemical Laboratory

The brilliant 18th Century chemist, Antoine Lavoisier (1771-1794), is quoted as saying, 'I consider nature a vast chemical laboratory in which all kinds of composition and decompositions are formed.' It is often folly to paraphrase the accepted genius of Lavoisier, but the work that we undertake at particle accelerators (such as Diamond and SSRL) has enabled us to extend this chemical insight to life through deep time. It might now be fair to say, 'We consider nature, both past and present, a vast chemical laboratory in which all kinds of composition and decompositions are formed, which are occasionally preserved as fossils'.

What organic signals might remain in a fossil...even those not locked in amber?
The study of decaying bodies has provided useful data on the various stages of decomposition that might give clues to the time and type of burial environment.  It is remarkable that as soon as a heart stops beating, oxygen that was so critical to life process ceased to circulate and internal anoxic conditions rapidly develop. In the absence of oxygen cells began their auto-destruct sequence, this is called autolysis. Here the cells self-destruct courtesy of enzymatic digestion. While the tissues of an organism are still relatively soft, prior to rigor mortis setting in, blow and flesh flies all take there chance to colonise a corpse with their eggs and soon to be voracious larvae (who we know and love as maggots).  
Tissue chemistry of living animals provides a useful elemental recipe to diagnose and then identify in fossils.
If there are no scavengers around to chomp through our dead body, fly maggots will soon compensate for this. Within 24 hours flesh can often be moving again, not in a zombie-like state, but with the writhing bodies of maggots, feasting on rotting flesh. Maybe I should have suggested at the beginning of this blog that you not read this close to meal times? Whilst the maggots are munching from within a carcass, soil microbes start the process of multiplying on the new food source beginning to ooze from the various orifices of a body into the underlying soil. Microbial communities that were once symbiotic with an animal in life, living in the respiratory system, gut and intestine, also begin to multiply and consume their host. This is the ultimate in organo-recycling systems. The organic acids and gases (including methane and hydrogen sulphide) generated as by-products of the microbes metabolism soon begin to change carcass colour and start to bloat the body, accompanied by the distinctive rotting my anatomist friend Dr. Dino Frey might say, 'It has all gone soft and soupy'.....we all have days like that!

Decaying modern carcasses can provide evidence as to how fossils might preserve delicate organic molecules.
The combined efforts of insects, microbes and possibly scavengers would make short work of our deceased beastie. Most of the body fluids would soon be 'released' into the surrounding soil, causing an initial dye-off of vegetation (due to nitrogen toxicity), leaving a deathly halo around the body. The maggots would pupate soon after having eaten their fill. All is quiet on the recycling front to the causal observer, but not to the geochemist, as things have only just started to get interesting. Depending on the soil porosity and permeability beneath a body, the sediments would also be directly affected by the gentle ebb of decay juices from the body...yum! As the soil microbes get a free dinner, they also begin to process the vast influx of nutrients from the carcass. Metabolic by-products of the microbes also begin to alter pore-water chemistry, giving rise to the precipitation of early mineral cements to bind the soil particles. The stink of decay marks the availability of reactive chemistry. The once living animal is now entering the immortal realm of fossilisation.  The bodies of all living organisms are a wonderful store for elements that once released (or partly released) from their biological bonds can complex to form different species of mineral. Here is the paradox. Release too many of the organic building blocks to the inorganic processes and you reduce the amount of organism that remains to be fossilised. This is a bizarre 'two-horse' race between decay and that we rely on being a close draw.... especially if we are to search any fossil remains for a whiff of original biochemistry that might still lurk within the mineralogical straight-jacket. This is precisely why we need to use some of the most sensitive imaging technology in the world to tease-out this astoundingly dilute organic signal, through working at synchrotrons light sources such as Diamond and SSRL. Splendid fun!

Tuesday, 23 July 2013

Diamond is a Palaeontologists best friend....

I can already hear the gentle hum of nudged particles circumnavigating the vast Diamond storage ring at relativistic speeds....yes, once more the Manchester Palaeontology Research Group are headed to the UK Synchrotron facility. We have spent the last few weeks preparing our prehistoric samples for the ultimate examination, one that takes place at the atomic scale. We aim to tease dilute traces of past biochemistry from our fossils using the astoundingly bright monochromatic x-ray light that only an accelerator can generate.

This weekend we will be working in the realm of Extended X-ray Absorption Fine Structure spectroscopy (or EXAFS for short). EXAFS spectroscopy is sensitive to the electronic structure of the probed central absorber atom, and is especially able to accurately quantify distances from one shell of electrons to the next surrounding an atoms nucleus. This technique provides a great deal of information as to the atoms biological or geochemical context. In other words, was the atom emplaced within the organism while it was still alive, or did a geological process place a strategic atom to later bamboozle palaeontologists. This is of huge importance when trying to understand the chemical ghosts of extinct organisms, given each atom has its own diagnostic fingerprint....and its our task to run those prints!

Tuesday, 9 July 2013

Another splendid year!

The class of 2013 from the School of Earth, Atmospheric and Environmental Science...I am the rather brightly clad chap at the front!

Friday, 5 July 2013

So you want to name a new species of dinosaur?

We often take for granted the elegant simplicity that a species name might take.  However, a name often provides the tag from which we can hang the evolutionary relationships and classification of an organism… so, it is worth explaining how and why we name beasties. To start somewhere we are all familiar with, a popular name. Palaeontologists have the rather fun habit of giving dinosaurs a nickname when excavating a skeleton…especially when the said remains are either rare, complete or both. The T. rex skeletons of Sue and Stan were named after their respective finders. The name for the mummified hadrosaur dinosaur that Tyler Lyson and I excavated a few years back, was based on the simple fact of its geographical provenance ('Dakota'). However, all types of birds, mammals (including ourselves), fish, amphibians, reptiles, crustaceans to bacteria have at least two 'official' names that follow internationally accepted codes for naming plants and animals. These are the International Code for Zoological Nomenclature (ICZN) and the International Code for Botanical Nomenclature (ICBN). Within these two books are the rules of naming a new species. A new name is given only when the plant or animal that has been discovered is shown to be distinct from any known species. The animal, its morphology, fossil and/or structure is then formally described and published within a peer-reviewed journal (that is usually the fun part!). A new species is then ‘born’ unto the blinding light of the scientific world, and often makes a brief appearance in the wider world, via the media….usually hailed at the end of the news programme by the words ‘And finally’…'And finally scientists at the University of Dunking Buckets have discovered the fossil remains of a new species of predatory dinosaur with feathers, etc. etc.’ Having feathers and being a predatory dinosaur usually ensures such stardom.

The classification of specific plants and animals into distinct groups or tribes is also worth a quick review. Carl Linnaeus (his name was really von Linne, but he even translated his own name into latin!) devised the binomial ('two-name') system applied to naming plants and animals in his splendid work Systema Naturae, published in 1735. Linnaeus subdivided a name into first the genus and then species names, for example you are Homo sapian (written always in italics). The Linnaean system allowed species to be classified within a hierarchical structure, starting with kingdoms. Kingdoms were divided into Classes, then Orders, which were further divided into Genera, eventually divided into Species. The classification was based upon observable characters, meaning that many early classifications resulted in very strange family trees. The more specimens and morphological characters you have, usually the more robust the family tree...but this does not stop single bones representing a whole species. However, a new fossil or living beastie that possesses a very distinct character, say a theropod dinosaur with feathers and a peg-leg, can have an impact that is far from proportional to its evolutionary ‘importance’ in the fossil record of all life (such is the draw of toothy beasties with pirate tendencies).

Our own evolutionary path parted with the ancestors of dinosaurs some time in Carboniferous Period, when the diapsids (reptiles and later to include birds) and synapsids (to become mammals) parted evolutionary company. However, the basic tetrapod (‘four-feet’) skeletal plan is still recognizable, shared between vertebrates…even palaeontologists! I love taking my undergraduate class to The Manchester Museum across the road from my University Department in which I teach. Getting students to recognise the five fingers in the hand (pectoral fin) of a sperm whale (Physeter mcrocephalus), the vestigial hips (ilia) and seven neck (cervical) vertebrae and to compare with elephants (Loxodonta sp.), antelopes (Antilope sp.) and chimpanzees (Pan troglodytes), the conservative skeletal blueprint is such a splendid example of such shared relationships. The evolutionary distance between one animal to another is beautifully displayed by their morphological 'distance', a function of the selective pressures that have often dictated the survival of a species. There is no vim divinam at work, purely the elegant simplicity of ‘decent with modification' so eloquently put by Charles Darwin.