Tuesday, April 16, 2013

Where Do Organisms Get Their Energy?

I've been thinking a lot about fundamental concepts in biochemistry. One of them has to be energy—where do cells and organisms get the energy to grow and divide?

Most of the metabolism section of biochemistry courses in North America are taught from an anthropomorphic, fuel metabolism perspective. That's understandable since the purpose of such courses is mostly to prepare students for the MCAT exam. (Medical school entrance exam.) I prefer an evolutionary approach to teaching biochemistry but that's not very popular these days.

By the time the course is over, students will have learned that humans get their energy from food, especially glucose. The next step is to ask where the glucose comes from. The simple answer is that food (i.e. glucose) comes from plants. The next question is where do plants get the energy to make glucose? The answer is, of course, sunlight. This should lead to an explanation of photosynthesis but that rarely happens in introductory biochemistry courses.

This description leads to the classic "food chain" as shown in the figure (above) from FT Exploring Science and Technology [The Flow of Energy Through Plants and Animals]. This is conceptually sound biochemistry as far as it goes. As long as students understand how sunlight can be used to make ATP and how ATP can be used to make macromolecules (including glucose), then they will understand that humans ultimately get their energy from sunlight. I would be happy if all biochemistry students could explain this food chain at the molecular level.

But in order to make sure that students really understand this process, I go one step further. I explain that there are many species of bacteria that are chemoautotrophs. Chemoautotrophs are incapable of photosynthesis yet they are able to grow and divide in the absence of any organic compounds. Their carbon source is CO2, just like photosynthetic organisms. These bacteria have a basic metabolism that teaches us what primitive life forms must have been like. Knowing how they get their energy helps students understand evolution.

Where do chemoautotrophs get their energy? I'm interested in knowing how many readers have taken biochemistry and are able to answer that question. Please let me know in the comments before you read the answer in these posts [Carbon Dioxide Fixation in the Dark Ocean] [Core Concepts: Pathways and Transformations of Energy and Matter] [Ubiquinone and the Proton Pump].


69 comments:

  1. I have only a limited background and it was many years ago, but I think chemoautotrophs use various chemical compounds as energy sources to drive their metabolisms. An example might be sulfur reducing bacteria (maybe)

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  2. I never had any formal course in Biochem (I'm a Geologist by background who moved on to Microbial Ecology at PhD level). Basically chemoautotrophs get their energy from different forms of litothrophic metabolism. They oxidize inorganic substances with O2 and/or other more exotic compounds (Fe2+, etc). Organic compounds can also sometimes be used as electron acceptors. They get their ATP from those redox reactions. They then use that for Carbon fixation.

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    1. That's exactly right. They get their energy from inorganic oxidation-reduction reactions using a variety of common molecules as electron donors. The most common ones are H2, NH4+, NO2-, H2S, S, and Fe2+.

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  3. Interestingly, have read a statement by professor John Brobeck who observed: “A scientist is no longer able to say honestly something is impossible. He can only say it is improbable. But he may be able to say something is impossible to explain in terms of our present knowledge. If something appears impossible to us, the professor went on to say, one thing that needs to be added is a source of energy unknown to us in our biological and physiological sciences."

    I wonder what your thoughts are on this.

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    1. What if John Brobeck was a plumber ?

      Why is it important to you that he is a professor ?

      Could it be that you are used to accepting statements of fact based on the authority and title of the one making the statement and as a result are overly enamoured with titles ?

      Science always works in probabilities and a degree of belief is assigned to any explanation of a phenomenon commensurate to the supporting evidence.

      So I don't know what scientists John Brobeck has in mind, perhaps he is referring to those employed by the Discovery Institute.

      Delete
    2. Steve, don't feed this Watchtower troll.

      Delete
  4. Cells get energy from creating proton gradient, which is used to create ATP from ADP.
    Proton gradient is made thanks to electron transport(*). Those electrons are absorbed by oxygen in aerobic organisms.
    In anaerobic respiration sulfur or something other is used instead of oxygen to absorb electrons.

    That's what I remember (but I have read "Ubiquinone and the Proton Pump" some time ago). I don't have any background in biochemistry.

    Looking at Wikipedia, that "something other" may be iron (or other metals), nitrate, sulfate, carbon dioxide or fumarate.

    (*) - I have also read Oxidation-Reduction Reactions and I have question:
    Is it correct to say (simplifying), that cells get their energy in the same way as batteries?

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    1. You can be a chemoautotroph and still use O2 as electron acceptor. Being an aerobe or anaerobe as nothing to do with it.

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  5. Based on the title (Carbon Dioxide Fixation in the Dark Ocean) of one of the articles, distant and misty memories waft just past the edge of my consciousness from decades ago when I took 2nd year biochemistry.

    Something about sulfur and thermal vents.

    As Curly said, "I'm trying to think but nothing happens."

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  6. This should lead to an explanation of photosynthesis but that rarely happens in introductory biochemistry courses.

    What, really? The most important chemical reaction on the planet, and it is not shown in many introductory biochemistry courses? That is odd. Of course, my own university education had other shortcomings (philosophy of science was nonexistent, for example), but this we went over often enough.

    Where do chemoautotrophs get their energy?

    By breaking down energy-rich anorganic compounds - whose energy, however, must also ultimately have come somewhere...

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    1. Many North American schools teach biochemistry from a medical perspective. In America, the objective of many biochemistry courses is to prepare students for the MCAT and photosynthesis is not a high priority.

      I bet that only a small percentage of biochemistry course in Canada and the USA teach photosynthesis. Photosynthesis was dropped as soon as I stopped teaching introductory biochemistry in my department. We are graduating a thousand life science students per year who have never learned about photosynthesis.

      Isn't that sad?

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    2. Sad, and ironic as well, given that medical colleges are increasingly broadening their entrance criteria. McMaster, for instance, which some consider to be the Canada's best med school, does not require any science courses for admission, and only considers the verbal reasoning section of the MCAT.

      Delete
  7. From what I thought I understood (with no special reading before answering) is that chemoautotrophs use hydrogen sulfide, at least at hydrothermal vents. And the energy to break that down comes from other compounds, but now that I think about it, I'm not sure. Do they get some energy from heat?

    I am a new (but not young) high school biology teacher and I will always make sure that students understand all of our energy comes from the sun, I don't know how far I should go with another source of energy. What do readers here think high school students should understand?

    I've never taken a biochemistry course--isn't it enough that I'm a Sandwalk reader? ;-)

    Now off to learn more--working on it slowly.

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    1. Actually, some of the energy used by life is from geothermal sources not the sun; someone above mentioned geothermal vents providing sulfur compounds to support chemotrophs.

      But, on the subject of being a reader of Sandwalk, it certainly has been educational for me, which is why I return.

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    2. Lynn,

      I'd say students could usefully learn about something like this (overlooking the sonorous movie-trailer voiceover): http://ocean.si.edu/ocean-videos/hydrothermal-vent-creatures . It is a useful addition to teaching about ecosystems - barely a joule enters from the sun. Understanding energy flows through such systems could be usefully tied into the thermodynamics learnt in chemistry class.

      One slight quibble: the voiceover talks of 'converting inorganic compounds into energy', and careless wording might also give the impression that heat (involved in bringing fresh substrate) is somehow involved in the energy flow. Both would be inaccurate - energy is released when electrons rearrange in response to the differential 'pull' of other atoms, destabilising their current arrangement. Life taps that flow. Photosynthesis uses light to boot electrons thermodynamically 'uphill'. Chemotrophs utilise molecules in which, relative to the terminal electron acceptor, the electrons are already 'uphill'.

      Delete
    3. Thanks a lot Allan. I can't watch the video yet, but it seems as if it would fit into a class.
      I agree with the problems with the misconception you mention. I even showed some of that in my comment above. But you have made things more clear--"Life taps that flow." and your last sentence. Very helpful.

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  8. As long as students understand how sunlight can be used to make ATP and how ATP can be used to make macromolecules

    But the unasked, “elephant-in-the-room” question is, how could ATP which is needed to make ATP possibly have evolved? I’ve searched and searched, but just can’t find any kind of Darwinian explanation for this paradox. Could someone please tell me how one “gradually” solves a circular dependency via an undirected process?

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    1. It seems there's only one possible solution to that conondrum, doeesn't it?

      That ATP isn't actually needed to make ATP, only that the extant process has evolved to be dependent on it from something else.

      Delete
    2. jcc,

      Is it worth even attempting to correct your misinformation about ATP synthase as Larry did below? I gave you lots to think and you did not even try. Why should we think that you would try and understand this time around?

      You truly don't care. You're just looking for something that has not been explained to keep yourself from reasoning with what we do know.

      Delete
    3. Rumraket:

      It seems there's only one possible solution to that conondrum, doeesn't it?

      That ATP
      isn't actually needed to make ATP, only that the extant process has evolved to be dependent on it from something else.

      Seriously? You’re saying that the original process didn’t require ATP? Do you realize how absurd you’ve just made yourself sound? Do you realize that you’ve just invoked the “Darwin of the gaps” rationale without supplying any scientific evidence? This is classic! This is worse than magic… “oh, don’t worry how it came about, it just evolved... somehow…” Never mind the physical, chemical and biological limitations involved, or the ridiculous implausibilities it asserts: “Evolution is true because people like Moran believe it’s true, an’ I believe what Larry says…”

      And you still think this blog is all about "science?"

      Delete
    4. You asked a question by building an absolutist claim into your question. I simply solved the problem by postulating that your absolutist claim isn't true. Turns out I was right, that ATP ISN'T needed to make ATP.

      Speculation is part of science. I'm not asking you to believe something without evidence as fact, though you yourself shouldn't be making absolutist claims that you don't know for a fact are true either.

      Delete
    5. Also, calling speculation worse than magic is pure projection. You're the one postulating magical creation, not me. I would offer a mechanism, and I would be clear about what parts were speculatory, then I'd suggest ways to test it.
      You would then say "I find that to be pure speculation and unconvincing, therefore I'm going to continue to believe that a magic man must have done it". No mechanism offered. Just *poof* grand design out of nowhere. Nobody knows how or why, what magic is or how it works. Divine miraculous magic - it just works, don't think about it. Can't be tested either, never have been.

      But you believe it anyway, and you have the never to deride me for for suggesting your absolutist claim of a logical conondrum might not be so absolutely true after all.

      It's funny how skeptical you are of science that conflicts with your religious beliefs. But when were your beliefs ever tested? When did a supernatural designer ever sit in a lab and *poof* fully formed, exquisitely detailed and complex living organisms into existence? Where do you nutcases even get the idea that this is possible?

      Human designers haven't created life by magic, ever. They haven't actually ever created anything by magic at all. There's no evidence that your blind faith alternative is possible and it's fundamentally untestable because you numbnuts keep making up shitty excuses for why spacewizard won't subject himself to testing.

      Delete
  9. Clarification:

    In my haste, I wrote the inaccurate and poorly worded question, how could ATP which is needed to make ATP possibly have evolved?

    Knowing that the rabid nit-pickers will descend on that like vultures on day-old carrion, let me be more precise: how could the ATP synthase mechanism, which needs ATP to make ATP, possibly have evolved?"

    There, that's much better! :)

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    1. Troll,

      Do you know how chemoautrophs get their energy? Stop trolling and answer yes or no.

      Delete
    2. In case there's any confusion, I want to make it very clear that what jcc says is wrong.

      Here's a description of the ATP synthase reaction. The substrates are ADP and inorganic phosphate (Pi). The are hundreds of other reactions inside the cell that result in ATP synthesis from ADP + Pi.

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    3. I'm not even surprised I was right without knowing it. XD

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    4. Larry:

      In case there's any confusion, I want to make it very clear that what jcc says is wrong.

      Let me clear up the confusion you just caused amongst your lackeys. They’re very impressionable you know, and just because you say something is true, doesn’t automatically make it true—in fact, it’s a pretty sure bet that you’re wrong a lot.

      Let’s start from the beginning, shall we? Life, all life depends on ATP as it’s constituted—not ADP, not GTP, not any other compound. Cell respiration requires glycolysis and glycolysis requires ATP. As you know, ATP is required in the first step of glycolysis. Without it, glycolysis wouldn’t take place and as a result, neither would the ATP synthase. It’s a classic chicken and egg conundrum.

      But you already knew that. It’s one of those “inconvenient truths” of your trade that your cognitive dissonance has successfully repressed. In fact, your sloppy blogging habits have betrayed your compartmentalization. Your “ATP synthase” hyperlink above goes to Wikipedia’s “Exception that proves the rule” page! Geee, I wonder why you needed to look that one up?

      Really, Larry, if you’re gonna play the ultimate authority here, then don’t ya think you’d better cover your tracks better than that?—especially when you’ve been caught with your pants down on an issue that you know you’re wrong about?

      Face it. You Darwinists have no explanation for the ATP-ATP causal circularity—and that’s just one of many that exist in your field of “expertise.” You have to ask yourself, “How could ATP evolve and where are the many transitional forms required to evolve the complex ATP molecule?” No feasible candidates exist and none can exist because only a perfect ATP molecule can properly carry out its role in the cell. In addition, a potential ATP candidate molecule would not be selected for by evolution until it was functional and life could not exist without ATP or a similar molecule that would have the same function.

      Your relig—eh, “theory” is taking on water faster than you can bail.

      Delete
    5. jcc,

      Let's see, you made a mistake, and admitted so, here:
      how could ATP which is needed to make ATP possibly have evolved?

      And corrected that to read:
      let me be more precise: how could the ATP synthase mechanism, which needs ATP to make ATP, possibly have evolved?

      ATP synthase does not need ATP to make ATP. You exhibited your ignorance twice, only to then consult and come back and change completely the scenery to claim that it is Larry who was "caught with his pants down," when it is you who is trying to hide his sorry ass by changing what you said for a second time.

      I am not surprised. You lack the most basic honesty.

      As interesting as talking about how "circles" arise in evolution could be, you loaded your new question trying hard to compound many questions into one just to make sure that this time no simple answer could come. You also loaded it with so much misinformation that I would not know where to start without leaving something open for your basic dishonesty to take and deform further. Then again, why bother? You demonstrated in that other thread that you don't give a damn about answers. You will shield your intellect from any possible understanding because you can't face the reality that you believe some quite stupid fantasies. There's also the problem that as soon as somebody tries to give you an answer you will change the question again claiming that you caught somebody with their pants down.

      In the meantime, the many facts you can't deny about evolution are right there for all to witness. Move towards questions in quantum mechanics if you wish, you will still have common ancestry with most-if-not-all of the rest of life. Your god will continue to be a nonsensical joke. You will continue to be the exemplar of the deep dishonesty necessary to remain a creationist in the face of a reality that refuses to bend to your desires. Live with it ass-hole.

      Delete
    6. JCC,

      You cannot bluff your way out of the hole you dug yourself into. Everyone here can tell you know virtually no molecular biology.

      You are trying to cover for your blunders by the use of jargon, but you use it incorrectly, and this audience can't be bluffed by the INCORRECT use of jargon.

      Whichever creationist website you learned your biochem from, whether AIG or more likely CMI, that's not the same as formal training. We can tell the difference.

      e.g. you write "You have to ask yourself, “How could ATP evolve and where are the many transitional forms required to evolve the complex ATP molecule?”"

      This is painful to read. Why is it so important to you to pretend you know science? Why do you need to pretend? Why? Is it so bad being a non-scientist? Do you hate being normal?

      Delete
    7. Anyway, naturally occurring pyrophosphates seem to be promising candidates as ATP precursors, cf. here.

      Delete
    8. That is an interesting possibility, Piotr. The complexities of ATP relate mainly to its role in nucleic acids, not to its general energetic properties. There are many groups that could be jabbed onto inorganic phosphate, but only a small set has the shape/charge complementarity that characterises the nucleobases. They 'select' each other, since inter-chain hydrogen bonding enhances stability for both.

      The first issue that jcc raised - ATP consumption during the initiation step in glycolysis - relates to a post-carbohydrate-biosynthesis world, ATP already embedded. The second - enzymatic ATPase - relates to a post-ribosomal world. Both of these systems in modern organisms originate in nucleic acid, and that, rather than imaginary metabolic chickens and energetic eggs, is where jcc should focus their denial-energy.

      No-one is glossing over the actual issues or ignoring chemical reality - quite the opposite. Precursor systems, and definitive answers, are thin on the ground, but understanding the actual chemical territory would help jcc's critiques enormously.

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    9. Your “ATP synthase” hyperlink above goes to Wikipedia’s “Exception that proves the rule” page!

      Oops! That was a link for another comment I was writing. Sorry 'bout that. Here's the real link: How Cells Make ATP: ATP Synthase.

      Delete
    10. Modern cells contain several "high energy" compounds that can be directly coupled to ATP synthesis (substrate-level phosphorylation). Some of them are good candidates for the standard energy currency of primitive cells (e.g. 1,3-bisphosphoglycerate, phosphoenolpyruvate, phosphocreatine, phosphoarginine). These are all discussed in standard biochemistry textbooks in the sections on phosphoryl group transfer.

      I agree that pyrophosphate likely played a key role in metabolism before ATP was "invented."

      I don't understand why people like jcc think they know more about this subject than the experts. What sort of mentality breeds that kind of arrogance?

      Delete
    11. Piotr's link is quite interesting, worth a read.

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    12. Abstract: The discovery that photosynthetic bacterial membrane-bound inorganic pyro- phosphatase (PPase) catalyzed light-induced phosphorylation of orthophosphate (Pi) to pyrophosphate (PPi) and the capability of PPi to drive energy requiring dark reactions supported PPi as a possible early alternative to ATP. Like the proton-pumping ATPase, the corresponding membrane-bound PPase also is a H+-pump, and like the Na+-pumping ATPase, it can be a Na+-pump, both in archaeal and bacterial membranes. We suggest that PPi and Na+ transport preceded ATP and H+ transport in association with geochemistry of the Earth at the time of the origin and early evolution of life. Life may have started in connection with early plate tectonic processes coupled to alkaline hydrothermal activity. A hydrothermal environment in which Na+ is abundant exists in sediment-starved subduction zones, like the Mariana forearc in the W Pacific Ocean. It is considered to mimic the Archean Earth. The forearc pore fluids have a pH up to 12.6, a Na+ -concentration of 0.7 mol/kg seawater. PPi could have been formed during early subduction of oceanic lithosphere by dehydration of protonated orthophosphates. A key to PPi formation in these geological environments is a low local activity of water. [Links Between Hydrothermal Environments, Pyrophosphate, Na+, and Early Evolution. Nils G. Holm & Herrick Baltscheffsky. Orig Life Evol Biosph (2011) 41:483–493.]

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    13. Larry,

      Modern cells contain several "high energy" compounds that can be directly coupled to ATP synthesis (substrate-level phosphorylation). Some of them are good candidates...

      Candidiates??? You don’t know for sure?

      These are all discussed in standard biochemistry textbooks...

      And “standard biochemistry textbooks” know for a fact that cell energy currency evolved into the ATP-ATP circularity? And by the way, don’t think I overlooked the fact that you did not deny that the ATP-ATP causal circularity exists.

      I don't understand why people like jcc think they know more about this subject than the experts.

      What “experts?” You, or any other “expert” can’t say for a fact that this causal circularity “evolved,” yet you’re convinced that it somehow did—and you have the unabashed temerity to call me “arrogant?”

      Perhaps if you were an engineer you’d appreciate the existential significance that a causal circularity conundrum represents. Any second year software engineering student can tell you that you cannot make a reference in a software package to the one you’re currently writing or modifying. It's a circular dependency that the compiler cannot resolve. It’s a logical conflict. The only way it could work is for the compiler to somehow be able to reference the package you're currently designing as if it were complete and fully functioning. And this isn't just a software issue—it's an overall design issue. Just like the ATP-ATP circularity conundrum, it cannot be “gradually” resolved—it’s a physical limitation and a logical impossibility to think that it could.

      Delete
    14. @jcc

      I don't know for sure because it happened a long time ago and my memory isn't as good as it used to be when I was an adolescent like you.

      Delete
    15. Wow. Once again, when an atheist gets backed into a corner and can't respond to the questions asked of him, he resorts to taking personal shots at the questioner...

      Delete
    16. Just like the ATP-ATP circularity conundrum, it cannot be “gradually” resolved—it’s a physical limitation and a logical impossibility to think that it could.

      The way you put it, no cyclic process can ever emerge spontaneously in the Universe. All you are saying is just a trivial restatement of the chicken and egg conundrum.

      Delete
    17. Piotr Gasiorowski:

      The way you put it, no cyclic process can ever emerge spontaneously in the Universe.

      Not when the end product requires itself for the process to begin.

      All you are saying is just a trivial restatement of the chicken and egg conundrum.

      Exactly! As I’ve demonstrated, it’s unequivocally, a design issue.

      Delete
    18. It's an "irreducible complexity issue" -- a dead horse, not even worth flogging. What you are saying implies that non-equilibrium thermodynamics and chemistry are impossible and that oscillating reactions can't occur naturally. You need more education.

      Delete
    19. @jcc

      Any second year software engineering student can tell you that you cannot make a reference in a software package to the one you’re currently writing or modifying.

      Aha, finally something I can address.

      jcc, you're full of shit.

      Just ask any compiler developer, this is exactly the way compilers are developed.

      The process is called bootstrapping and is the process of writing a compiler (or assembler) in the target programming language which it is intended to compile.

      Delete
    20. One more time jcc. ATP synthesis as we know it just needs a proton gradient to generate ATP from ADP and Pi. The entire glycolysis to ox-phos game did not appear as a complete system, as you are claiming.

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

      Delete
    21. @jcc
      While your reasoning is valid, all you have to do is ask, what would happen outside of a cell; which leads to the origin of life-fortunately. This means that the living cell has to be alive FIRST to perform all those processes because in the atheistic soup it can't. No way!

      Delete
    22. Piotr Gasiorowski:

      It's an "irreducible complexity issue"

      Yes, it is. How astute of you.

      -- a dead horse, not even worth flogging.

      Only to a closed-minded Luddite.

      What you are saying implies that non-equilibrium thermodynamics and chemistry are impossible and that oscillating reactions can't occur naturally.

      Um, no. I didn’t say that at all. Please don’t put words in my mouth. I am saying that functioning systems that possess and use specified, complex information such as living cells that use the ATP-glycolysis-ATP cycle, could not have gradually developed into the systems we observe today without the intervention of an intelligent agent.

      You need more education.

      Yes, as do you—including learning some basic manners.

      Delete
    23. Um, no. I didn’t say that at all. Please don’t put words in my mouth. I am saying that functioning systems that possess and use specified, complex information such as living cells that use the ATP-glycolysis-ATP cycle, could not have gradually developed into the systems we observe today without the intervention of an intelligent agent.

      I'm not putting words in your mouth. You said simply this, without mentioning "specified, complex information":

      Not when the end product requires itself for the process to begin.

      Which is obviously false. But be my guest, move the goalposts.

      As for "specified, complex information", you have nowhere proved it is unevolvable. You just declare it is; but your personal incredulity is your own problem.


      Delete
    24. steve oberski:

      Aha, finally something I can address.

      jcc, you're full of shit.


      Too bad you chose not to do it politely.

      The process is called bootstrapping and is the process of writing a compiler (or assembler) in the target programming language which it is intended to compile.

      I guess I have to point out the obvious: um, who is doing the writing there? I’ve never heard of compilers self-coding themselves into existence, have you? Your analogy fails dismally. But back to my point; since when have you been able to put in a #include (or an import) for an object that had a dependency on the package you were currently working on and were able to get it to compile, huh?

      Delete
    25. jcc,

      You seem obsessed with glycolysis as the primordial ATP-generating system. A simple way out of your imagined conundrum: what if it wasn't?

      Bear in mind that glycolysis starts with glucose, which is typically biosynthesised, with the consumption of yet more ATP. You imagine there was just all this glucose lying around?

      Delete
    26. Dominic Nikel:

      While your reasoning is valid, all you have to do is ask, what would happen outside of a cell; which leads to the origin of life-fortunately. This means that the living cell has to be alive FIRST to perform all those processes because in the atheistic soup it can't. No way!

      Please don’t confuse the issue with sound reasoning and impeccable logic. It makes it that much harder to obfuscate the argument for those who want their worldview to be true.

      Delete
    27. Allan Miller:

      You seem obsessed with glycolysis as the primordial ATP-generating system.

      No more so than all the atheists here who are hell-bent on denying the possibility of an intelligent designer.

      A simple way out of your imagined conundrum: what if it wasn't?

      Ok, so in that case it ought to be simple enough for intelligent creatures such as us to devise a set of reductionist experiments that demonstrate how it could have occurred.

      Bear in mind that glycolysis starts with glucose, which is typically biosynthesised, with the consumption of yet more ATP. You imagine there was just all this glucose lying around?

      Sounds like you’re lending credence to my whole causal circularity argument…

      Please explain to me exactly how, in a Darwinian sense, does a system that contains such a circular dependency gradually modify itself beyond its original configuration without losing its original functionality or destroying itself?

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    28. @jcc

      "Please don’t confuse the issue with sound reasoning and impeccable logic. It makes it that much harder to obfuscate the argument for those who want their worldview to be true."

      What can I say? I'm glad you are here:) I especially enjoy your your sarcasm seasoned with a good sense of humor;) You made me laugh to tears lol

      Delete
    29. Dominic Nikel:

      I'm glad you are here:)

      Thank you and likewise. As you know, when you’re in hostile territory, it’s nice to have someone simpatico.

      You made me laugh to tears lol

      You’re too kind. If only the atheists would lighten up when given a dose of their own medicine. :)

      Delete
    30. jcc,

      Why did you ignore my comment? Not able to withstand being evidenced as a dishonest ass-hole? Let me give you a few more items to think about:

      Candidiates??? You don’t know for sure?

      Don't be an ass-hole. That there's plenty of molecules that can act as energy carriers means that there's plenty of ways in which the ATP "circle" could have evolved from a system relying on other molecule(s).

      And “standard biochemistry textbooks” know for a fact that cell energy currency evolved into the ATP-ATP circularity?

      As I said, you changed your claim at least twice because you did not know what you were talking about (and still don't know, otherwise you would know of many other stupid mistakes you made, like talking of the evolution of ATP, obviously you don't know what ATP is, other than being used and produced in glycolysis).

      And by the way, don’t think I overlooked the fact that you did not deny that the ATP-ATP causal circularity exists.

      If by that you mean that ATP is used and produced in glycolysis, why should Larry deny such a thing? Why exactly? In these discussions, the ones who rather lie are the creationists like yourself, who is pretending that knows more than you really know.

      What “experts?” You, or any other “expert” can’t say for a fact that this causal circularity “evolved,” yet you’re convinced that it somehow did—and you have the unabashed temerity to call me “arrogant?”

      We call you arrogant because you try and presume to know yet make stupid mistakes, like changing from ATP used to make ATP to ATP synthase's mechanism needing ATP (which it doesn't), then changed to ATP used in glycolysis which produces ATP. You are an ignorant fool who does not know any biochemistry trying to teach biochemistry to a biochemist, just because you misread some claims about ATP in some creationist source.

      Any second year software engineering student can tell you that you cannot make a reference in a software package to the one you’re currently writing or modifying. It's a circular dependency that the compiler cannot resolve ...

      Well, any software engineer would be able to tell you that UNIX was written in B once (or A, my memory might not be too clear about it), then C was invented and developed, and then UNIX rewritten in C. A circle "evolved" out of having a precursor language for writing software. Since there's plenty of molecules that can carry energy there's plenty of molecules that could have been "A" or "B" before the circle evolved. Not only that, there are many ways to produce ATP. Mammal biochemistry is not the only one biochemistry existing among life forms. You talk about this "problem" as if there was just one kind of metabolism, and just one way of extracting energy from glucose, and as if glucose was the only molecule where energy could be extracted from.

      You are plainly an arrogant fool. You forget that life has many forms. You think that a single example of metabolism presents enormous problems for evolution to occur. All based on your self-impossed ignorance. You have ways to know much better, but you rather avoid thinking about it properly. Man, you make it clear that creationism is a sickness that destroys the individual's character and most basic honesty.

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    31. jcc,

      Thank you and likewise. As you know, when you’re in hostile territory, it’s nice to have someone simpatico.

      Which can only be someone as ignorant as yourself. Otherwise this would be a creationist telling you not to ridicule other creationists with your obvious, and arrogant, ignorance.

      You’re too kind. If only the atheists would lighten up when given a dose of their own medicine. :)

      As far as I have seen, we don't lie to you. We present you with answers that you just dismiss trying hard not to think about them. You are far from lightening up. Your tone shows you to be an ass-hole proud to be incredibly ignorant in favour of holding you your stupid fantasies about there being some god. You rather misuse your intellect than allow yourself to understand. Presented with clear answers you run away from them by presenting other questions. You lack the guts to face reality. You have no character and no honesty, not even honesty to yourself.

      I am really so glad those aren't my problems.

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    32. Negative Maturity:

      Why did you ignore my comment?

      Let’s see, what part of, "I don’t converse with people who call me: 'an ass-hole,' 'a dishonest ass-hole,' and 'an arrogant fool'" don’t you understand?

      Adios (again).

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    33. Me Bear in mind that glycolysis starts with glucose, which is typically biosynthesised, with the consumption of yet more ATP. You imagine there was just all this glucose lying around?

      jcc Sounds like you’re lending credence to my whole causal circularity argument…

      Nope - merely trying to focus you on real issues instead of imaginary ones. "Here's some causal circularity!! ATP consumed in glycolysis!!!". er... well glucose is manufactured using ATP. "OK - THERE'S some causal circularity!!!" er ... no, the ATP that is consumed in glucose manufacture is not made by metabolising glucose, but by photo/chemosynthesis. "OK, THERE's your circularity - enzymes involved in electron transport are made using ATP!!!". Indeed, right now, after 4 billion years of evolution, they are. Does this mean that the proton-gradient mechanism of ATP synthesis is impossible without enzymes? That is an open question.

      jcc: Please explain to me exactly how, in a Darwinian sense, does a system that contains such a circular dependency gradually modify itself beyond its original configuration without losing its original functionality or destroying itself?

      It does not contain such a circular dependency, would be one way out of the conundrum. I write computer programs on a computer, via a computer program. How could computer programs ever have come into existence? (Just to head you off at the pass, making something of the involvement of intelligence in computation would be somewhat to miss the point).

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    34. Allan Miller:

      Nope - merely trying to focus you on real issues instead of imaginary ones.

      Yes, the fact that it’s not just the ATP circularity, but the entire metabolic cycle that is inextricably circular-dependent is an, ahem, imaginary issue.

      How could computer programs ever have come into existence? (Just to head you off at the pass, making something of the involvement of intelligence in computation would be somewhat to miss the point).

      Yes, the intervention of intelligent agency in the computer analogy is to only “somewhat miss the point.” And therein lies the real problem with attempting to have a reasoned discussion with them—their denial of the obvious. “Look! What’s that bright thing up in the sky?—it looks like the sun has come up. It is time it did,” said the theist. “Oh, not necessarily so. It’s more like the North Koreans have finally launched and detonated a nuke,” said the atheist.

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    35. jcc - you have a knack for missing the point. If you blether on about circularity in glycolysis, you are going to look a fool to an educated audience. Nor is the entire metabolic cycle 'circularly dependent'. It is a cycle, not a circle. Everybody agrees that this cycle must have had a commencement.

      ATP is a nucleic acid monomer. That is its most fundamental role: it supplies the energy for its own polymerisation. It happens also (nowadays) to function as the prime 'energy currency' of the cell, with the other nucleic acid monomers also having important roles, and a huge role for catalytic proteins built by ATP-containing ribosomes and driven by both ATP and GTP. But there is no reason to suppose that ribosomes, nor even very much of what one would describe as cellular metabolism, were necessary at the start.

      If you don't think you can have a reasoned discussion with people who understand the fundamentals of a subject, when you don't, it is less likely to be a failing on their part than yours.

      I'm merely urging you to stop bullshitting. You think people have not noticed the fundamental relationship between ATP and both metabolism and nucleic acid construction? But this has nothing to do with glycolysis, or protein coding. Your determination to find something for God to do leads you to underthink the issues, IMO. You leap upon the first circularity YOU perceive as the fundamental one, and berate 'atheist ideologues' for not clasping you tearfully to their bosom for your insight.

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    36. jcc,

      I did not ask why don't you have a conversation with me. I asked why did you ignore the comments. In other words, we have answers, you choose ignorance and imbecilic dishonesty. That's why I call you an ass-hole. Remember that whether you want it or not, you are representing not just your religion, but the intellectual bankruptcy required to believe as you do.

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    37. Negative Entropy:

      I did not ask why don't you have a conversation with me.

      To address your comments would be to engage you in conversation—but unfortunately, given your predilection for prideful arrogance, bigotry, intolerance and hatred, that would only result in an exercise in futility.

      In my last post to you, I altered your moniker to “Negative Maturity,” not to be a smart aleck, but to accurately indicate to you just how childish you are. You clearly have a great deal of maturing to do before you can earn the respect of whom you’re addressing, and as a result, earn the right to be listened to.

      I’ve read your responses to my posts and found that you are not interested in engaging in any kind of mature, intelligent discussion on the topics at hand. All that comes across in what you write is a profane, seething, infantile hatred of anyone who holds a different opinion than you. I pray that someday very soon you’ll realize that the tactics you employ are counterproductive to any hope you may have of convincing anyone of the validity of your opinions. I also pray that someday, you’ll allow God’s Holy Spirit to speak His truth to you. If and when that day comes, then I would enjoy nothing more than to get to know you personally and hear your life story.

      May God bless you.

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    38. jcc,

      Since I perceive you as an ass-hole, and tell you so in unambiguous terms, I decided above not to make it a point to complain about your remark about my maturity. But since you bring it back, what surprises me is that you would turn around and write what you wrote, because it shows how blind you are to your own behaviour. I do not know how anybody would consider it a sign of maturity to come and ask questions like yours, firmly rooted in ignorance, while pretending to know more than you do. For you to see me as immature, you should have some ground to do so. Yet, it seems like you judge without looking at yourself in the mirror. I admit that I am not the prime example of maturity, but if you looked carefully and honestly, you would notice that I gave you answers and things to think about. That I also described correctly the tactics you were using not to engage your intellect thus avoiding to deal with answers that were making sense, but you rather not hear.

      There's plenty of examples: the way you changed your first ATP question into a wrong one about ATP synthase, and how when caught to be wrong, you changed it into ATP being used in the first part of glycolysis, insulting Larry for a mistake that you made, only to then pretend that you meant that all the time, then pretending that you know something by loading that comment with questions that betrayed how little you understood about biochemistry and evolution. Yet, in your view, I am the one who has a "predilection for prideful arrogance, bigotry, intolerance and hatred." So I would ask, why would you insult Larry for not guessing that you would want to change the question after noticing that the ATP synthase mechanism does not use ATP, if not out of "prideful arrogance, bigotry, intolerance and hatred"? Why would you not pay attention to any answers and move the goal posts each time you are answered if not out of "prideful arrogance, bigotry, intolerance and hatred"?

      I don't think that you have any right to tell me that I have such predilections until you are able to show that you can engage with answers without displaying such predilections yourself.

      I normally am very aggressive, but try not to insult a believer (the few who remain honest in conversation, who listen even if they are not convinced, could attest to this). But as soon as the believer behaves as you do, then they earn it. So far you have only confirmed that you deserve such treatment. Not once have you tried to understand anything but my tone. I don't need your respect. I'd rather have you respecting yourself.

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    39. To address your comments would be to engage you in conversation

      But I did not ask you to address them. It's clear that you ignored them because you continued to make the very same kinds of mistakes that you could have avoided if you were paying attention. But you do the same with anybody's comments. You just ignore them looking for some words you can use before moving the goal posts and avoid any understanding on your part.

      How seriously can I take your "I also pray that someday, you’ll allow God’s Holy Spirit to speak His truth to you" if I witness such deep dishonesty emanating from you?

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  10. I'm interested in knowing how many readers have taken biochemistry and are able to answer that question. Please let me know in the comments before you read the answer in these posts

    They pass electrons from inorganic electron donors down chains of serial electronegativity differential, ultimately to terminal electron acceptors. As there is a free energy change associated with the transfer of electrons, each step in the cascade releases an increment of energy which is used to pump protons across a membrane, creating a physical gradient with an osmotic and an electrical component. Allowing the protons to equilibrate drives ATP synthesis, storing the energy in the phosphate bond.

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    1. You pass! :-)

      Just a minor quibble. The free energy of ATP hydrolysis can't really be localized to a particular phosphate bond. See The Demise of the Squiggle.

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    2. I've just read your post on ATP hydrolysis. Fascinating stuff, very different from what I was taught in secondary school (in the mid-1970s).

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    3. OK, I stand educated! My biochemistry fundamentals date from the late 70's...

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  11. Biochemistry and Microbiology Undergraduate.
    Chemoautotrophs get their energy from oxidizing compounds such as sulphur ( the green and purple sulfur bacteria) and ammonia ( nitrosifiers and nitrifiers- both bacteria)

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  12. Vet, Medical microbiology at PhD level.
    Oxidation of sulfur, nitrogen or other inorganic substrate. The electron aceptor can be, in addition to oxygen, other organic and inorganic compounds.
    Thanks for a great post and comments!
    Pablo Nart

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    1. More of the same - echo what Pablo (and others) have come up with.
      First degree Biochemistry (Sheffield U).
      Done other things since so I am more than a touch 'rusty'.
      Robert.

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