The Naked Scientists

The Naked Scientists Forum

Author Topic: Can we detect fossilised proteins?  (Read 4548 times)

Offline thedoc

  • Forum Admin
  • Administrator
  • Sr. Member
  • *****
  • Posts: 511
  • Thanked: 12 times
    • View Profile
Can we detect fossilised proteins?
« on: 02/11/2011 13:52:38 »
You’ll remember, in the film Jurassic Park scientists manage to reconstruct dinosaurs from DNA preserved for tens of millions of years. Sadly for killer dinosaur fans, DNA doesn’t appear to last that long…but it turns out that proteins do...
Read a transcript of the interview by clicking here

or Listen to it now or [download as MP3]
« Last Edit: 02/11/2011 13:52:38 by _system »


 

Offline OokieWonderslug

  • Full Member
  • ***
  • Posts: 93
    • View Profile
Can we detect fossilised proteins?
« Reply #1 on: 02/11/2011 18:45:44 »
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.
 

Offline damocles

  • Hero Member
  • *****
  • Posts: 756
  • Thanked: 1 times
    • View Profile
Can we detect fossilised proteins?
« Reply #2 on: 02/11/2011 23:44:46 »
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.

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.
 

Offline imatfaal

  • Neilep Level Member
  • ******
  • Posts: 2787
  • rouge moderator
    • View Profile
Can we detect fossilised proteins?
« Reply #3 on: 03/11/2011 08:57:49 »
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.

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
 

Offline damocles

  • Hero Member
  • *****
  • Posts: 756
  • Thanked: 1 times
    • View Profile
Can we detect fossilised proteins?
« Reply #4 on: 03/11/2011 12:28:50 »
From Imatfaal:
Quote
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

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  ;D. 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".
 

Offline imatfaal

  • Neilep Level Member
  • ******
  • Posts: 2787
  • rouge moderator
    • View Profile
Can we detect fossilised proteins?
« Reply #5 on: 03/11/2011 14:39:33 »
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 
 

Offline damocles

  • Hero Member
  • *****
  • Posts: 756
  • Thanked: 1 times
    • View Profile
Can we detect fossilised proteins?
« Reply #6 on: 03/11/2011 21:21:40 »
Caught out on the "having it both ways"! [:I] 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.
 

Offline imatfaal

  • Neilep Level Member
  • ******
  • Posts: 2787
  • rouge moderator
    • View Profile
Can we detect fossilised proteins?
« Reply #7 on: 04/11/2011 10:24:37 »
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? 
 

Offline damocles

  • Hero Member
  • *****
  • Posts: 756
  • Thanked: 1 times
    • View Profile
Can we detect fossilised proteins?
« Reply #8 on: 04/11/2011 15:13:35 »
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.
 

Offline CliffordK

  • Neilep Level Member
  • ******
  • Posts: 6321
  • Thanked: 3 times
  • Site Moderator
    • View Profile
Can we detect fossilised proteins?
« Reply #9 on: 05/11/2011 10:37:02 »
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. 
 

The Naked Scientists Forum

Can we detect fossilised proteins?
« Reply #9 on: 05/11/2011 10:37:02 »

 

SMF 2.0.10 | SMF © 2015, Simple Machines
SMFAds for Free Forums