Tuesday, August 23, 2011

The Oldest Cells

I was going to write about the discovery of the oldest fossil cells but Jerry Coyne beat me to the punch [Newly found: the world’s oldest fossils!]. The new fossil bacteria are thought to be 3.4 billion years old and they were discovered in Australia only a few kilometers from the site where the so-called "cyanobacteria" fossils were discovered almost twenty years ago. Those fossils were reported to be even older (3.5 billion years) but the discovery has been completely discredited. The "fossils" aren't fossils [Did Life Arise 3.5 Billion Years Ago?]. That makes this discovery the oldest known cells (Wacey, 2011).

Interestingly, the senior author on this paper is Martin Brasier and he was one of the scientists who challenged the earlier result of William Schopf. Read all about it on Jerry Coyne's blog website.

The fossils are associated with a sulfur-rich mineral called pyrite. This mineral is produced by modern sulfate-reducing bacteria and it's reasonable to assume that the primitive bacteria detected in these ancient rocks also carried out sulfate reduction. That's not surprising since there wasn't much oxygen in the deep ocean 3.5 billion years ago.


Jerry Coyne didn't explain the biochemistry so let me give it a try. We need to start with a brief lesson on how modern living bacteria make ATP. The key to this understanding is a knowledge of Oxidation-Redution Reactions—one of the important basic concepts in biochemistry [see also Pushing Electrons].

Oxidation reactions are reactions where one or more electrons are given up. They are always coupled to reduction reactions that take up electrons. The direction of electron flow will depend on something called the "reduction potential" of the two half reactions. For our purposes we can think of the oxidation reaction as giving up "high energy" electrons that lose some of their energy before being taken up by the reduction reaction. It's this loss of energy that drives ATP synthesis.

Here's a simplified (!?) version of the electron transport pathway in the cell membranes of bacteria or mitochondria. The initial oxidation reaction is on the left below the membrane. NADH is a molecule produced during cell metabolism; notably glycolysis (degradation of glucose) and the citric acid cycle. NADH is the electron donor.


The electrons given up by NADH travel through various enzyme complexes that are embedded in the membrane (follow the red line). As the electrons give up some of their energy, the complexes pump protons from the inside of the cell to the outside. This sets up a proton gradient across the membrane and that gradient is used to drive ATP synthesis by ATP Synthase as the protons move back into the cell. This is the essence of chemiosmotic theory for which Peter Mitchell won the Nobel Prize in 1978. It's the most important pathway in all of biochemistry so every biochemist should know it intimately (they don't).

The electrons have to go somewhere eventually. The terminal electron acceptor in most modern species is molecular oxygen (O2) as shown in the figure. This is why we need oxygen to survive.

There are many modern species of bacteria that use different electron donors and electron acceptors to create the proton gradient. We're interested in those that use inorganic electron donors and something other than oxygen as an electron acceptor since those kind of bacteria are going to give us clues about the metabolism of primitive bacterial cells such as those preserved in the 3.4 billion year old rocks.

Here's a possible scheme based on what we know about modern sulfur-reducing bacteria.


The electron donor in this case is molecular hydrogen (H2). This avoids the need to use organic compounds such as NADH and glucose as a source of electrons. Hydrogen is just one of many possible electron donors but it happens to be one of the donors used by sulfur-reducing bacteria.

The electrons pass through various cytochrome complexes that are simplified versions of the ones in the first figure but they achieve the same purpose [Ubiquinone and the Proton Pump].

The electron acceptor is sulfate (SO42-). It is reduced (gaining electrons) to hydrogen sulfide (HS) which reacts with iron to produce the mineral pyrite. These bacteria do not need oxygen and they do not need an external source of energy in the form of a complex organic molecule.

We understand a lot about basic metabolism and bioenergetics and we can deduce the basic evolution of the modern complex pathways through studying unusual bacterial species that have adapted to unique environments, such as those that lack oxygen.


Wacey, D., Kilburn, M.R., Saudners, M., Cliff, J., and Brasier M.D. (2011) Microfossils of sulphur-metabolizing cells in 3.4-billion-year-old rocks of Western Australia. Nature Geoscience Published online Aug. 21, 20110 [doi:10.1038/ngeo1238]

26 comments:

  1. Just a clarification, when you say they do not need oxygen are you talking about molecular oxygen?

    I wonder what creationists are going to say about this discovery haha.

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  2. Remember to take your CoQ10.
    Especially if you are on statins.

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  3. Larry,

    Sulfur-reducing (the bacteria described in the paper) and sulfate-reducing (which you describe here) are not the same thing. These bacteria were reducing elemental sulfur, arising from sulfogenic photosynthesis (which predated oxygenic photosynthesis by perhaps almost 1 billion years).

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  4. @anaxyrus,

    In the paper they talk about sulfate-reducing bacteria, not sulfur-reducing bacteria. So that's what I described.

    Initially I thought they were describing a metabolism involving the oxidation of hydrogen sulfide and I thought it would be fun to describe a different electron donor in the electron transport chain.

    There's no evidence that these bacteria were capable of photosynthesis so I don't think we are considering that at all. We certainly don't expect the earliest forms of life to be capable of photosynthesis.

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  5. I'm linking to you for the biochemistry, so please update--sulphate or sulphur?

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  6. From the abstract:

    "We interpret the pyrite crystals as the metabolic by-products of these cells, which would have employed sulphate-reduction and sulphur-disproportionation pathways."

    So both, apparently.

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  7. Larry and Qetzal, thanks for the updates. My apologies, Larry.

    There has been a report (apparently not through peer review yet) of a mat community at 3.3 Ga with sulfogenic photosynthesizers on top and elemental sulfur reducers beneath.

    http://www.nature.com/news/2011/110706/full/news.2011.397.html?s=news_rss

    I agree that the first life was not likely photosynthetic, but at 3.4 life was at least 100 and perhaps many hundreds of millions of years on.

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  8. What I find fascinating about the electron transport chain is how the mitochondrion makes use of the laws of physics to perform its function.
    That is a general principle we can see throughout the intelligent functioning of the cell.

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  9. "This sets up a proton gradient across the membrane and that gradient is used to drive ATP synthesis by ATP Synthase as the protons move back into the cell."

    This is the heart of the process and the most striking use of the laws of physics by the mitochondrion.
    There must be many other uses of the laws of physics in the total process.
    Does anyone know of any articles or studies that analyzes cellular processes that way?
    I don't mean general descriptions of how processes occur but EXPLICITLY presenting how the steps make use of specific laws of physics.
    If so I would be very interested in seeing that material.

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  10. Anonymous writes:

    What I find fascinating about the electron transport chain is how the mitochondrion makes use of the laws of physics to perform its function.

    Umm - what other laws would you like it to use?

    Every single natural process and phenomenon in the universe "makes use of the laws of physics" to perform its function, from lightning strikes to stars shining to subatomic particles carrying forces and charges. Are they all intelligent, down to the subatomic particles?

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  11. Anonymous writes:

    Does anyone know of any articles or studies that analyzes cellular processes that way?

    Dr. Moran has co-authored a very large textbook chock-full of this stuff. You should buy it and read it.

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  12. What I find fascinating about the electron transport chain is how the mitochondrion makes use of the laws of physics to perform its function.

    Blink. Life is all about chemistry and energy. ie, physics. And really, it's largely about electrons. Their donation, receipt and sharing between atoms stabilises molecules.

    http://en.wikipedia.org/wiki/Ionic_bond

    http://en.wikipedia.org/wiki/Covalent_bond

    http://en.wikipedia.org/wiki/Hydrogen_bond

    These electron-mediated bonds (mostly the latter 2) form the stuff of life. Covalent bonding gives a stable structure to the DNA and protein backbones; hydrogen bonding allows DNA bases to pair in strict purine-pyrimidine linkage. This is at the heart of both replication (preservation of genotype) and translation/transcription (expression of phenotype) - ie, 'making use of the laws of physics'.

    Biological energetics is all about electrons. Steal them from water using the energy of the sun and you have a convertible energy source that you can store in a number of ways - in bonds, or as an electrochemical gradient that can turn the 'water wheel' that is the rotary ATPase, storing the energy in bonds. ATP is the stock energetic intermediate of the cell, and - no coincidence, and neatly circular - is the source of the informational "A" in the DNA base set A,T,C and G.

    All hail the electron!

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  13. Allan Miller, does it strike you as very interesting how the different levels all work together?
    Each level exists on its own (with its own rules and dynamics) but also integrates seamlessly across the levels.
    We all take this for granted but it is quite striking when you start to really focus on it.

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  14. "Allan Miller, does it strike you as very interesting how the different levels all work together?
    Each level exists on its own (with its own rules and dynamics) but also integrates seamlessly across the levels.
    We all take this for granted but it is quite striking when you start to really focus on it."


    Integrating across levels like that would be quite a challenge for human designers. If we ever tried it
    To think that that integration just happened without intent or intelligence is quite a leap of faith.
    It is more plausible and credible to conclude that intelligence and intent underlies it all.

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  15. It is more plausible and credible to conclude that intelligence and intent underlies it all.

    Not for me it ain't. I see complexity building up from blind integration of simpler subunits. There is certainly a hierarchy - Quarks, electrons, photons, energy and forces (thanks, Big Bang!) to protons and neutrons and atoms and the periodic table (cheers, Gravity!) to molecules to, in the right environment, replicators (good old Earth; good old Sun - thanks again, Gravity!) to phenotypically-assisted replication to cells to competitive/cooperative ecosystems to multicellular colonies to neural networks to intelligence (of a sort) to societies.

    There is no logic or plausibility to me in starting with intelligence and intent. Complexity arises from simplicity, not from even greater antecedent complexity. I know this means a lot to you, but I just don't buy it.

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  16. See this thread:
    http://sandwalk.blogspot.com/2011/02/facilitated-variation.html

    Some forms of complexity arise from simplicity. Like a complicated kludge.
    But not the kind of design we see in the operations we are talking about.

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  17. a complicated kludge

    Life, in a nutshell!

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  18. The design we see in the areas we are discussing are the opposite of kludges. Anyone who knows design principles can see that.
    But that is so obvious to those who know about such things that it is pointless to argue with others who do not know about these things.

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  19. The design we see in the areas we are discussing are the opposite of kludges. Anyone who knows design principles can see that.
    But that is so obvious to those who know about such things that it is pointless to argue with others who do not know about these things.


    Sorry Anon, but I think what I think; there is no point in getting snooty with me for my perspective. I work in software design and have a degree in molecular biology. So I think I'm reasonably placed to see the ways in which the genome does, and doesn't, adhere to principles of design.

    Fundamentally, I think Intelligent Design is bad philosophy and bad science.

    DNA is a bit like a book, or a computer program, organisms are a bit like machines, and all those things need designers, ergo ... ? Ergo nothing. Viable genomes are much less tightly-specified than books or programs, and organisms resemble machines barely at all. And just because one set of phenomena has intentional design does not justify the inference that this is a requirement for all phenomena you choose to lump in with them.

    You've got it the wrong way round. Intelligent Designers came on the scene with tool use and language. They create things that are a bit like the natural products of a designer-free world.

    Your Designer bears no resemblance to human designers - it is not made of physical stuff, and yet can interact with physical stuff by mechanisms unknown. And this complex entity came into existence by mechanisms that required no designer, pulled up by its own bootstraps?

    From a conviction that complexity and utility demand intent, ID solves a non-existent problem by the invention of an impossible entity, and scorns biology for not simply setting aside 160 years of data that confirms the current paradigm in spades.

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  20. For those who know about such things as simplicity and complexity that it is pointless to argue with others who do not know about these things.

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  21. For those who know about such things as simplicity and complexity it is pointless to argue with others who do not know about these things.

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  22. For those who know about such things as simplicity and complexity that it is pointless to argue with others who do not know about these things. (x2)

    Well, you're probably right, but I thought it was worth a try.

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  23. Allan Miller, please be aware that you are conversing in a friendly way with the individual who has been attacking me and my family and sending threatening messages to my home.

    If that is okay with you, then you are no better.

    That is your moral choice.

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  24. @Anonymous (not the real one)

    Behave!

    @Anonymous (the real one)

    There is a simple remedy for this kind of thing - pick an ID. Then no-one can masquerade as you.

    @Self

    Ba-hoo! I just don't know who I'm talking to anymore! Sob!

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  25. @Allan Miller
    Sorry.
    I reposted another Anonymous’ remark from Friday, September 02, 2011 4:05:00 PM on Saturday, September 03, 2011 5:16:00 PM and Saturday, September 03, 2011 5:17:00 PM.
    I do not know whether the Anonymous of Friday, September 02, 2011 4:05:00 PM and of Sunday, September 04, 2011 9:39:00 AM are the same Anonymous or not.

    @Anonymous of Sunday, September 04, 2011 9:39:00 AM
    I did not attack you or your family, or send threatening messages to your home.
    I do not know whether anyone attacked you or your family, or send threatening messages to your home.
    I do not understand whatever basis you can have for saying I did so.
    Could you lay off the rampant paranoia? In several comments you’ve been recommended to take mental counseling. That would be an eminently sensible course of action for you to take.

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  26. No,i can't do but if there are so magical oppertunity ,then when will i leave this chance.

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