Science Interviews

Interview

Sat, 29th Oct 2011

Fossil Proteins - Planet Earth Online

Roy Wogelius, University of Manchester

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Roy -   What we're looking at now is a very, very small, probably juvenile reptile from the green river formation, that's about 50 million years old and about 5 centimetres long.  It's only part of an organism and we think this poor unfortunate little critter probably got bitten in half and that's why it's ended up in the fossil record.

Richard -   If we look at it, there's almost a long tail and two legs,Tyrannosaurus rex I guess, almost like frog’s legs but probably about half the length of my finger imbedded in this quite thin, sandy, almost like a slate [material].

Roy -   That's right.  You can see a long central tail and then you can see where the legs join in, where the pelvic region is and then the organism is truncated.  Mostly what you can see is the skin.  And if you look at it very, very closely you can actually see that there is some of the patterning left in the skin.

Richard -   It is mottled isn't it?

Roy -   Yes that's right, and that's the scale pattern.  And that's why we thought this would be a tremendous specimen to look for the residue and patterning of proteins.

Richard -   You're actually looking for remnants of proteins of the molecules that made up the skin?

Roy -   Some remnants of the original chemistry.

Richard -   After 50 million years.

Roy -   That's exactly right.  It's the chemical fossil.  Now that seems like an outrageous thing to propose doesn't it? Yet we have absolutely no problem thinking about organic molecules being preserved as long as we don't think about what species they've come from or from exactly where they're from.  We just put them in our gas tanks or petrol tank and burn them.  This is a chance, using some of these very, very sophisticated techniques to track back and find some of these very, very robust organic molecules and trace them back to the their source and indeed, we were able to do that.

Richard -   So what did you do?  It's a very different process to the sorts of things palaeontologists normally get up to.

Roy -   And that's why I describe myself as a geochemist.  Usually, palaeontologists look at bone and then they look at structures.  What we wanted to get to was using chemical techniques and we had this idea of using a different part of the electromagnetic spectrum.  It's a very, very simple thing that we did: we just used infrared light rather than visible light.  Now, infrared light gives you an idea about the presence of organic molecules because an awful lot of the infrared spectrum will cause vibrations in the organic components.  And by that, what that means is that we can identify specific parts of organic molecules and the specific parts of the organic molecules that are present within this fossilised lizard skin are extremely similar to the organic molecular fragments that are present in beta carotene from existing lizard skin.

And so, we did a comparison of the distribution and types of these organic - we'll call them functional groups.  We mapped these organic functional groups and compared them from this fossilized skin to skin taken from a present day gecko and the distribution patterns map very, very nicely.

Richard -   So what can you conclude then?

Roy -   What that showed us is that the protein residue derived from the original skin still has some of the character of the original proteins and the distribution of it is controlled by the original biological structure.  It can and it will have a big, big impact on understanding evolution because we can get down to these protein sequence levels.  Preservation of DNA, that's just not going to back into deep geological time, but the preservation of some of these proteins from these soft tissues does.

Richard -   And this has applications beyond just understanding evolution.

Roy -   One of the things I'm very interested in, in fact the other side of my research has to do with radioactive waste disposal and how we can safely sequester radioactive waste.  Now, the safety cases, for most countries, have to demonstrate containment for between 100,000 and a million years.  Well this is a 50-million year experiment between trace metal contaminants and organic compounds that tells us one way that nature has been able to sequester organic compounds and trace metals in place and that's very, very useful information for us.

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I believe they are. I have a theory that there is a lot more left of dinosaurs then just bones turned to stone. I feel that when an animal is fossilized the materials that made up the flesh of the animal do not completely vanish, but spread out into the rock matrix like a drop of ink on a wet sponge. If there was some way to dissolve all of the minerals then what is left would be remains of muscle and sinew. Just spread out extremely thin. I am not saying dna is preserved. Just saying that the animal is pretty much still there, just spread out and very diluted with rock. OokieWonderslug, Wed, 2nd Nov 2011



Unfortunately, ookie, organic chemicals are high energy materials that will gradually decompose to water, carbon dioxide or graphite, and nitrogen gas, as the lowest energy forms of C, O, H, and N elements respectively. The process would be extremely slow in ambient surface conditions, except that hungry microörganisms will speed it up significantly, particularly through greedily devouring organic nitrogen for their own growth/multiplication requirements. Protein is ingested for this purpose. Carbohydrate is also ingested to meet the energy requirements for the metabolism of these microorganisms. We have all witnessed how the remains of dead livestock become bleached bones within a couple of years, and leave almost no trace of organic matter. damocles, Wed, 2nd Nov 2011



Unfortunately, ookie, organic chemicals are high energy materials that will gradually decompose to water, carbon dioxide or graphite, and nitrogen gas, as the lowest energy forms of C, O, H, and N elements respectively. The process would be extremely slow in ambient surface conditions, except that hungry microörganisms will speed it up significantly, particularly through greedily devouring organic nitrogen for their own growth/multiplication requirements. Protein is ingested for this purpose. Carbohydrate is also ingested to meet the energy requirements for the metabolism of these microorganisms. We have all witnessed how the remains of dead livestock become bleached bones within a couple of years, and leave almost no trace of organic matter.


But Damocles - don't we also have superb evidence (everytime we go to a petrol station) that complex high energy high energy hydrocarbons of previous eras can remain - they are our coal, oil, and gas reserves imatfaal, Thu, 3rd Nov 2011

From Imatfaal:


The evidence that we have is of coal -- which very roughly approximates to graphite plus water (already flagged as low energy chemicals) -- and hydrocarbons, which could be seen as low energy in an oxygen-poor medium. Oil arises almost exclusively from animal remains, and is the product of geodegradation of fats. Plant remains, and protein and carbohydrate more generally produce coal.

It is a serious error to regard fossil fuels as high energy chemicals. The high energy is associated with the oxygen gas that we use to burn them. Hydrocarbons, even relatively complex hydrocarbons, can be found in abundance on the low energy moons and planets of the outer solar system. In a rational world, we would regard the fuel as free, and charge for the use of atmospheric oxygen  . Well it does take a little exploration and labour to prepare the materials that allow us to exploit the high energy of atmospheric oxygen gas, I suppose.

One way of getting a handle of the fact that the energy resides in the oxygen and not the fuel, is that an anaerobic process can only get about 20% as much energy per gram from a sugar as the aerobic process does.

I suppose that the other point is that any complex organic materials that might remain in or near dinosaur fossils will have a lot more "microörganism character" than "dinosaur character". damocles, Thu, 3rd Nov 2011

damolces - yu seem to be trying to have it both ways - in consecutive posts you said that the carbohydrates that make up the dinosaur flesh are hi-energy and thus can no longer exist - but then said i was wrong to refer to hydrocarbons as high energy. 

Is there really that much difference in joules per kilo between a chunk of dinosaur flesh and crude oil?  Frankly the water that makes up a decent proportion of any body and is just a tiny fraction of crude oil make me think that you will get a load more energy from oil or gas per kilo. crude oil has an energy density of over 40Mjoules per kilo - and whilst hydrogen rocket fuel is much higher - that is a pretty heavy energy density, and natural gas is even higher. 

And whilst oxygen is necessary to liberate large proportions of the that energy quickly - that applies in equal measures to the dead dinosaur and the crude oil. 

you said that dinosaur flesh could not remain cos it is high energy and will end up as co2 h2o etc and heat - but I still contend that we have huge amounts of prehistoric material that has a distinct ability to be burnt very energetically to give off co2 h20 etc,, which has remained.  I can quite believe that any recognizable dinosaur bits of flesh will have gone  imatfaal, Thu, 3rd Nov 2011

Caught out on the "having it both ways"! Well, partly anyway.

However, the comments about oxygen stand. In the planetary formation process, where a state fairly close to chemical equilibrium is produced as the result of wide sampling of the sub-yellow-heat temperature range, and slow cooling, gaseous oxygen is never produced in quantity. Oxygen, the third most abundant element present after hydrogen and helium, is completely tied up in oxides of the various other elements.

If heptane -- C7H16 degrades to its lowest energy products in the absence of oxygen, specifically
    C7H16 → 4 CH4 + 3 C (as graphite)
the total energy produced is 1.12 kJ/g

But the presence of gaseous oxygen changes this to
    C7H16 + 15 O2 → 7 CO2 + 8 H2O (as liquid)
with a total energy produced of  48.57 kJ/g

So gaseous oxygen does not only speed up the release of energy from a fuel, it is also the source of most of that energy. In the case of a typical hydrocarbon fuel -- n-heptane -- that amounts to about 97% of it! In the previous post my claim of 80% of the energy was based on a similar calculation for sugar, which is a genuinely high energy organic compound, as opposed to hydrocarbons which are low energy. damocles, Thu, 3rd Nov 2011

You are blinding me with greater scientific knowledge - unfair! 

I stick to my point entirely though.  The oxygen point is either superfluous or lost on me; I understand how heptane will decay to graphite and methane in the absence of 02 and burn to co2 and water in the presence - but my point is that neither of these have happened to most of the longchain hydrocarbons in crude oil.  so why must it have happened to dinosaur flesh?  the oxygen levels at the time of the dinosaurs and today are not the same - but they are well within an order of magnitude and the variance is not enough to change decay paths

and on the low energy high energy debate - how are you defining a sugar as higher energy than crude oil?  i presume the idea of energy density works on the amount of joules you can get from kilo of stuff that is combusted in the most efficient way.  is it really the case that sugar is higher than crude oil in this case?  imatfaal, Fri, 4th Nov 2011

No, sugar is not higher than crude oil on the normal "fuel value" scale. But that is because this scale assumes an infinite supply of gaseous oxygen. Sugar is much higher than crude oil when the fuel value is calculated per unit of oxygen consumed. The only gaseous oxygen that is present on Earth has been produced, over the ages, as a small surplus in the energy account of plant photosynthesis, reduced by its exploitation by other living organisms. We are never going to run out of oxygen or coal, and there is no need to worry about oxygen gas conservation, but it must clearly be the case that there is not enough oxygen gas on earth to be able to burn up all the coal and organic matter on Earth.

Moreover when flesh is undergoing transformation to fossil, it is doing so in anaerobic conditions. So high energy/low energy works only in terms of reactions in absence of oxygen gas

The real point about dinosaur flesh is that it has all undergone chemical reaction and degradation. Crude oil is a long lived intermediate product in the degradation of fats in an anaerobic situation; coal is an end product of the degradation of carbohydrates and protein, with protein being responsible for the high nitrogen and sulfur content of some coal, and natural gas is an end product of nearly everything (a mixture of methane, other hydrocarbon gases, hydrogen, nitrogen, traces of sulfurous gases and, in many cases, intermixed with radiogenic geological helium and argon. As I pointed out before, any protein that might have survived will surely have more microorganism than dinosaur character.
damocles, Fri, 4th Nov 2011

Interesting concept that the energy is in the oxygen.  Certainly methanogens are anaerobic bacteria that take long chain hydrocarbons and generate energy by breaking them down to methane.

But...  you should think of chemical energy as the combination of an oxidizer and a reducer.

Is Iron Oxide (RUST) high energy?

It can be used as an oxidizer for metallic aluminum to create a very violent reaction.

As far as the dinosaurs, I find it extraordinary that fossils can be demineralized to recover some of the original multimillion year old proteins.  And the research above indicates that we not only can recover bone associated proteins, but also skin associated proteins.  And, of course, the proteins can be reverse engineered to recover DNA fragments.  But, we are very far from recovering a complete set of dino proteins. 

Petroleum Oil is very different from organic oils, with more cyclic structures, and fewer carboxylic acids and active regions.  However, if the theory is that it is of organic origin, perhaps it would be a good source for ancient proteins... if there was a good way to separate the proteins from the inorganic oils. 
CliffordK, Sat, 5th Nov 2011

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