Smallest rotary motor in biology, the ATP synthase.

Smallest rotary motor in biology, the ATP synthase. All the work done in your body is fueled by breaking a chemical bond in ATP, the “currency of energy”. Did you know that you convert your body weight (or an estimated 50 kg) of ATP per day?!

Where does this ATP come from? It is synthesized by an incredibly sophisticated molecular machine, the ATP synthase, embedded in the inner membrane of our mitochondria. Energy from the oxidation of food results in protons being pumped across the membrane to create a proton gradient. The protons drive the rotation of a circular ring of proteins in the membrane that in turn move a central shaft. The shaft interacts sequentially with one of 3 catalytic sites within a hexamer, making ATP (little butterflies in the movie!). The ATP synthase rotates about 150 times/second

To visualize the rotation under a microscope, a very long fluorescent rod (actin filament) was chemically attached to the central shaft. Watch real movies (not animations!) of the enzyme spinning here:

Notice the rotation is slower with longer rods. The rotor produces a torque of 40 pN nm (40 pico Newtons x nanometer), irrespective of the load. This would be the force you would need to rotate a 500 m long rod while standing at the bottom of a large swimming pool at the rate shown in the movie.

How did this amazing rotor evolve? The hexameric structure is related to DNA helicases that rotate along the DNA double helix, using ATP to unzip the two strands apart. The H+ motor has precedence in flagella motors that use proton gradients to drive rotation of long filaments, allowing bacteria to tumble through their surroundings. At some point, a H+ driven motor came together with a helicase like hexamer to create a rotor driving the hexamer in reverse, to synthesize ATP.

The 1997 Nobel prize in Chemistry was awarded to John Walker and Paul Boyer for solving the structure and cyclical mechanism of the ATP synthase, respectively. This amazing enzyme was also the subject of my own Ph.D. thesis, and my first love!

For #ScienceSunday curated by Allison Sekuler and Robby Bowles .

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386 Responses to Smallest rotary motor in biology, the ATP synthase.

  1. Well done. This exceeds even the usually high-level content of G+, so I must give it an H+.

  2. DaFreak says:

    Here is H+ and he gives it a +1! Awesome ScienceSunday contribution!

  3. Wayne Eddy says:

    Finally. Good use of an animated gif!

  4. Tis a glorious gift you have given us Rajini

  5. Rajini Rao says:

    Thanks all, for the H+’s (looks like a hybrid of high five and +1) and sharing your positive comments 😉

  6. Glad to see you made good on your promise 😉 Very cool!

  7. lindos colores perooooo , porque los murcielagos

  8. Rehana Aniff says:

    ATP synthase…great animation!!

  9. Sherri Vance says:

    You’re an excellent teacher!

  10. Cool news for Rajini Rao – your post has made the “What’s Hot” list for Google+ — I love a social network where science generates so much interest! Thanks again for posting, Rajini 😉

  11. Rajini Rao says:

    Thanks, Allison Sekuler , who knew? I guess it takes cool science to become hot on G+!

  12. DaFreak says:

    omg and the ScienceSunday tag is in there! Rajini, I could kiss you! You are singlehandedly pushing #sciencesunday into #caturday territory! =D

  13. could someone explain about the 50 kg? where does that come from?

  14. awesome post!! ATP synthase is part of the electron transport chain of inner mitochondrial membrane.

  15. Amazing. Thank you so much for sharing.

  16. Rajini Rao says:

    Alex Chyrkov , that’s a conservative estimate. Because the ATP is constantly being broken and remade, at any one time, we may have only at most a few gms on hand. The number comes from how much energy in kilo calories an average person needs (say, 1,500 for a modestly active person), how much energy ATP releases (7 kcal/mole), then the conversion from moles of ATP to g of weight (507 g/mole). About 40% of energy from food is converted to ATP, rest is wasted as heat, etc. Back of the envelope calculations…that would give ~50 kg ATP.

  17. Rajini Rao says:

    Edward Woods , the evolution of this sophisticated machine took several billion years… a very long time 😉 It did not happen all at one time, and it did not happen by random chance. We see variations of this structure today (in different organisms) clearly showing diverging evolution along different paths…so we can actually track back the changes over time.

  18. How come you “know” this took billion years? This is a theory, nothing is proved, yet. Except this is real.

  19. Rajini Rao says:

    Secular Hermit , how do you know this is real? 😉 If you believe the science that brought you this, then you must also believe that the same science and the same analysis also has evidence for molecular evolution. There is plenty of proof, sign up for biology courses in college or read up on the experimentally obtained facts. If not, just enjoy a pretty gif.

  20. Nice post.

    Though I was also confused about by your statement that we consume our body weight of ATP per day. Well, I guess it makes sense with your explanation in the comments that they are broken and remade all the time but then I’m wondering what that figure is supposed to tell me in the first place.

  21. Rajini Rao says:

    Hi Daniel Furrer , the point was the huge “turnover” of ATP per day means that this enzyme is a real work horse! Consume=burn or break down.

  22. Shaun Orwell says:

    Holy fuck science is awesome.

  23. This is amazing!!! Can we grow artificially large pools of it? And can we harness the electrical power? Just wondering.

  24. Shaun Orwell says:

    Shah Auckburaully Only after we create AI and torch the sly

  25. Kyle Lehar says:

    That animated Gif creeps me out and I don’t know why.

  26. aaaaa ho ho ho ho ” holy fuck science ” has always been awesome and kind also to gift massive growth of population. now we know it.

  27. Shaun Orwell says:

    Zilmil Iloveu , you win the internet.

  28. Love this stuff. Thank you for sharing! It begs a designer.

  29. Tim Brys says:

    So ATP synthase evolved from something that needs ATP to function? How does that work?

  30. Rajini Rao says:

    Tim Brys , The ATP synthase is also full reversible and functions as an ATPase, i.e., it can break down ATP and generate a proton gradient. In this case, it will rotate in reverse. In the link I provided where you see the filament rotating, it is actually breaking down ATP not synthesizing it. In some bacteria, this reversibility is quite important (in the absence of oxygen), but in mitochondria there is a clever way that reversibility is blocked (by an inhibitor protein).

  31. Helpful analogy; didn’t quite sound right… but I’m hardly a science expert (barely passed o-chem in uni). Can current motor efficiency laws be applied to such a small scale?

  32. DNA rebuilt us. Retaining ideas is lastingly continuous. Life doesn’t end in death, begins in memories of all the rest.

  33. if this ATP synthase breaks down or if we block it, tons of heat is produces as a result of no ATP being produced. Just one of the way aspirin overdose can induces fever in us.

  34. Phil Wilcox says:

    RE: Rajini Rao to +Secular Hermit. So you’re saying that just because you saw this in a microscope then it logically follows that we have to believe your analysis of how it came into being and how long it took to come into being?

  35. DaFreak says:

    Actually the earth is “only” 4.5 billion years old, so I am not sure where you are getting seven billion from. Your argument is a god of the gaps argument. We used to explain all the sophisticated processes, from the rain, to lightning and the sun by calling upon our imagination and have gods create them for us. So far, everything we have learned turned out to be explainable and thus less sophisticated. We have already explained billions of things… What makes you think that the remaining questions won’t be answered? I am not saying that we will one day understand everything because we will just keep on pushing the boundary of knowledge outward forever but this does not mean that we are at the limit of understanding or that you have to pick the easy way out and just say that ‘god did it’.

    We have been pushing god into the gaps of knowledge since the first ape started walking upright but we have to learn to stop making this mistake. Instead we should just realize that we don’t know and get to work! It’s the only way to find out and to advance knowledge. Believing that it can’t be done or explained is equal to giving up.

    Do you think the information in the atom happened by random chance? ….just something to think about. 😉

    I am not sure if it was random, the laws of physics probably had something to do with it but ultimately it could be the case that our universe is just one of many and got its parameters “randomly” set by laws we have yet to grasp. Dragging gods into this won’t do anyone any good and it will not advance knowledge. Even if it would be random, how does that prove your point? Is randomness not the opposite of creation? Why would something write randomness into atoms? How would you even do such a thing? True randomness is just like nothing and god. We have never observed such a thing in nature yet. In general we describe randomness or chaos as something that is so complex, involving so many parameters that we can’t calculate its outcome but if you would have all those parameters, you could calculate the outcome. Even in quantum mechanics, people speak of a more truthful randomness but even there we are still talking about measurable probabilities. There might be a degree of randomness to what an individual atom does but a group can be predicted. We don’t understand QM very well yet so perhaps this too will be explained. Either way if true randomnes/chaos exists, I don’t see how it could give rise to so much order and if it exists it would be the opposite of creation because there would be no way of knowing the outcome at all in any given situation no matter how many parameters you get.

  36. yes yes yes! I loved learning about this stuff in bio last month! this is what i want to do for a living! ❤

  37. Hououin Kyoma yes by adding a phosphate group. thats how your body makes energy, by adding phosphates to ADP.

  38. I’m 66 yr old. My nearest encounter with your research is Watson and Cricke(sp.)

    Of course I want to know more!!

  39. Alex Snow says:

    Isn’t this just the neatest thing?

  40. DaFreak says:

    How is that not a god of the gaps argument? You don’t know how or what so you just go “god did it”. That is the definition of a god of the gaps argument. God doesn’t explain anything, and nobody uses that argument in any field of science. God is not more likely than invisible unicorns so unless they show a sign of existence you can’t use them as an explanation for anything which even if they existed wouldn’t do anyway.

    Neither do we know that information-rich systems are the result of intelligent causes… You are just making this up on the spot. A star or a lifeform is an information rich system. Look up stellar evolution, stellar nucleosynthesis and abiogenesis. We as well as the stars are the result of physical laws that are not intelligent and do not care about whether you go to mass on a Sunday. They also don’t entice hate or discriminate groups of people. Even if we were made by aliens/gods/laws, in a way they are all the same thing. You will always need to explain how they came to exist with the only difference that we know for sure that physical laws exist, we are pretty positive on aliens because of what we already know and god is a figment of our imagination until proven otherwise.

  41. Rajini Rao – now #1 on the G+ What’s Hot list 😉 — well done!

  42. Rajini Rao says:

    Dear Ben Menge , this is just a Google+ post. A social network site remember. I’m not giving a lecture here nor am I presenting a scientific paper at a conference. All my work is published, as are the work of hundreds of scientists whose work went into this single post. Please, lets keep things in perspective shall we? In the meanwhile, just enjoy the gif. It is pretty and it moves.

  43. DaFreak says:

    Ben Menge Just check wikipedia, they have a lot of free information. You can also check Stanford or MITcourses on youtube and search for biochemistry. You don’t have to go to university to understand how our body works on a molecular level… But however you choose to learn it, it will take a lot of time before your understanding, as well as mine, will be as deep as Rajini’s. People write vast tomes on this topic, you can’t expect to learn how all the pieces of the puzzle fit together from a single comment on google+

  44. NEY MELLO says:

    Rajini Rao, Thank you for your genial contribution to further understanding… Fantastic!

  45. I think your description should read “convert” rather than “consume” 50kg of ATP a day

  46. Hey, this is awesome, this animation was great, made me interested enough to read the story, which took me quite a while ’cause I’m not that much up on science. But any time I can be made to understand something this complicated I’m very appreciative. Thank you, Dr. Rao.

  47. Rajini Rao Your posts kindle in me the love of Science which lays embedded somewhere…inside…thank you…you rock my friend and this post ….”Absolute Magic” 🙂

  48. Rajini Rao says:

    Jonathan Beck , done. Thanks 🙂

  49. DaFreak says:

    Imagine a sentient puddle who wakes up one morning and thinks, “This is an interesting world I find myself in—an interesting hole I find myself in—fits me rather neatly, doesn’t it? In fact it fits me staggeringly well, must have been made to have me in it!” ~Douglas Adams

  50. That is just the most miraculous and beautiful thing. ~1/3 more efficient than anything we can make of a similar nature.

  51. What is the empty space from the animation filled with in reality? Water? Plasma? Saline?

  52. Blair Warner says:

    And people think this evolved randomly, with no guidance? the human body is absolutely amazing! Science discovers and recreates and harnesses, but NEVER creates, and it is not meant to prove origins, only “how things work”. Let science be science and philosophy and religion, and psychology, etc. deal with things that belong in their realms. Science confirms the later disciplines mentioned, at best.

  53. Irreducible Complexity. Sorry, but logically, continuously making mistakes (which is what molecular evolution proposes) could not get you the incredible complex molecule that is so elegantly portrayed in this animated gif. In point of fact, the components used to make this molecular machine cannot even be spontaneously reproduced, and the chirality alone suggests that random events would not be able to produce them. This is clear evidence, not for evolution, but for design (and by logical extension, for a designer). The animation is obviously the work of a gifted individual, how much more so the “molecular machine”.

  54. josem mo says:

    Google+ Mrs. Rajini Rao deserves for verified name, as I see she shares better scientific posts than (pardon) other verified scientists in G+ here.

    Ben Menge You need references? Please learn how to use Google search. And I’m enjoying how you insult your own intelligence, sorry.

  55. Rajini Rao says:

    Thank you for your defense, jose montarig . I used Google search too, to put together my’s pretty easy to find publications, lab web sites and information. FYI, research in my lab is on other (cool) proteins about which much less is known. Hope to bring you much more, thanks for tuning in 🙂

  56. Rajini Rao Beautiful post, very cool gif and lots of patience from you in these comments 🙂 Well done, and yes you truly do deserve a verified name from Google – I don’t think I could have been half as nice to the IDiots on this thread 😀

  57. Blair Warner says:

    I showed the .gif to my 11 year old son. He thought it was very cool, and it opened up a lot of discussion. Thanks for posting.

  58. Ida Steele says:

    Quiet interesting even if I did not fully understand Rajini Rao.

  59. Omar Saleem says:

    Haha. Studying for my finals right now in Biochemistry and thats one of the main topics. Need to understand each small mechanism within the synthase. Wish me luck!!

  60. Edward Woods Really? First you say the references for this post aren’t good enough and now you’re citing ‘Expelled’? That Ben Stein creationist piece of crap that was laughable at best, deceitful at worst? Wow.

  61. Rajini Rao says:

    Good luck Omar Saleem ! Please feel free to add any insights from your ATP synthase studies here 🙂

  62. Sheik Sheikh says:

    very clever illustration

  63. Amazing animation. Thanks for posting it. I will start following you. And, to echo the previous poster, I admire your patience with the the ID-ers and the self-proclaimed “sceptics”, who seem to see themselves as God’s little antibodies who swarm out to attack the threat to his existence posed by actual scientific knowledge.

    (I didn’t see how many intervening posts there were. The previous poster I was referring to was

    +Buddhini Samarasinghe)

  64. Rajini Rao says:

    Ben Menge , scientists are pretty passionate folks..we do very hard stuff for practically nothing in return. The only thing that motivates postdocs like Buddhini Samarasinghe is the search for truth because there is so much beauty and satisfaction in it. I know because I’ve been there myself. I’m older and more established, so I can afford to be cool about a lot of uninformed arguments we scientists encounter. I hope you appreciate that it is hard to argue with people who have not learned the alphabet, let alone read the book. Thanks for your comments, I appreciate them. 🙂

  65. ah ATP synthase…the single most important biochemical reaction. This is all we talk about in biochem…can’t avoid it.

  66. Rich Pollett says:

    Brilliant post! – loved the addition of the links to the real movies also. Thanks.

  67. Omar Saleem says:

    Thanks Dr. Rajini Rao

    My first thought was the fluid and impeccable engineering of the synthase. How the F1 hexamer forms a perfect sphere with the gamma shaft running through. An organic pump that efficiently as the conformational change takes place.

    I think the most amazing aspect of the synthase is its ability to produce the quantity of ATP that it does. Just puts into perspective how costly (in energy) many of our regular operations are.

  68. caleb perdue says:

    It looks like a brain function

  69. ATP => ADP It makes the world go ’round…sorta like love 😉

  70. Rajini Rao says:

    Omar Saleem , the top part of the gamma shaft is perfectly smooth and hydrophobic (greasy) so it runs smoothly within the hexameric core. I read somewhere that the instantaneous speed when it takes off from each of the three 120 degree pauses is as fast as the fastest man made rotor running in vacuum. As for quantity, there’s just tons of it..I used to purify 150 milligrams at a time from 13 liters of bacterial culture (smelly messy stuff). Cheers!

  71. DaFreak says:

    Rajini Rao Some wise life lessons for me in there as well. ^^

    I am only 25 and regularly find myself in heated discussions about gods / homeopathy / astrology / … I am pretty good at keeping my calm but I do invest way too much time in debating these issues and have not even once managed to get someone to see how silly and unproductive those ideas really are. I could and should invest my time more wisely. In the future I shall refrain myself from spamming your wonderfully educational posts by dragging out useless debate about such topics. I noticed that I end up derailing discussion and perhaps even detracts from the actual beauty of the science which is absolutely the last thing I would want to do.

    Thanks again for this awesome post and putting ScienceSunday on the map! 🙂

  72. Rajini Rao says:

    Koen De Paus , please don’t stop commenting..I’m counting on you 🙂 Absolutely not spam. Thanks for bugging me about ScienceSunday.

  73. Norman M. says:

    I love this! Not sure how this knowledge will creat in a few hundred of years…

  74. Koen De Paus — Don’t stop commenting. I am a christian and I don’t tend to agree with the idea that something this complex just happened by accident. But I believe that these discussions are very valuable for people on both sides of the issue. Too many on both sides don’t take the time to really examine the evidence.

    Ultimately, I don’t think most people are interested in believing in the Tooth Fairy. We all want the truth, and this is the only way we can pursue it. You may not sway anyone, or be swayed yourself… but the pursuit of truth as a community is too important to neglect. Have patience… the time you put in is well spent.

    …You are appreciated.

  75. powa moni says:

    wow thanks, in my profession it will help me lot. Will you do a animation about blood circulation process in heart? thanks in advance.

  76. Rajini Rao says:

    To anyone who believes in irreducible complexity, take a look at this paper that offers a pessimistic estimate of the time it takes for an eye to evolve: only a few hundred thousand years:

    The cool part is that we have examples of all stages in the evolution of the eye among animals today..from simple aggregates of photoreceptor cells to fully formed camera eyes. John Robertson , please take a look at the paper and give me your opinion. Remember, the complexity of the human eye is a favorite among proponents of ID. I’ll be happy to discuss the evolutionary intermediates in the ATP synthase as well, in fact I specifically cover that in my class.

  77. The ATP synthase is not part of the electron transport chain, but it’s indirectly coupled to it. I’m just studying about it 🙂

  78. Congrats Rajini Rao. You totally deserve it!

  79. Now Timmy, Grandma didn’t die, her apex seals just wore out.

  80. Nico Ward says:

    That’s so cool looking. What is the overall affect on the human bod?. In knowing this how can it change what we are able to do functionally as humans? What is the purpose of this discovery?

  81. DaFreak says:

    Matthew Johnson How is ‘god did it’ a caricature of your argument? You are talking about intelligent creation, whether that would be gods or aliens is just semantics. The reasoning ends there because there is no data to support it. It’s a dead end. You again mention “inference to the best explanation” which does not make any sense because god/aliens any kind of creator offers no explanation at all. It can’t be tested, it wouldn’t explain the creator, it can’t be falsified, it can’t advance knowledge or help us achieve new insights. Abiogenesis is a fact, biological intelligent design’s gap is closing fast, you have to move your ID wares to the realm of physics and start telling us about how gods write in subatomic particles instead of DNA.

    This brings me to my next point, your view of complexity, as Alex Ross stated is biased. Do you have any idea how complex the workings of a star really are? In a way, the barrier between life and other matter exists only in our minds. We are all made out of the same matter and energy organized in different patterns. Although life is indeed more complex than a rock, a rock is still complex even if you can’t see it. If you would have been a sentient star you would have thought of yourself as a complex being with all circumstances just right for you to be created. Tremendous pressure, insane temperatures, liquid metal storms, raging magnetic fields, quantum tunneling induced fusion, the creation of all elements and the birth mothers of planetary systems… There is a lot of interaction / information processing going on inside a star. It’s workings aren’t encoded in DNA but in how energy and matter interact on all conceivable scales, from the subatomic quantum world to the relativistic einstein world. Just like a human body can spontaneously assemble itself guided by the very same laws and its genetic makeup, so too can a star spontaneously assemble out of physical laws such as gravitational attraction which makes vast cloud of gas collapse in on themselves and ignite because of the pressure that such action generates. Its nuclear fusion process alone is maddeningly complex.

    The writings are on the wall, the intelligent design movement is starting to move away from biology and pointing its arrows of fail towards physics. Start practicing the following line “The universe is so fine tuned that it must have been intelligently designed” which should come easily since that is what I refer to with this being a god of the gaps arguments because your previous line was “this biomolecular machinery is so fine tuned that it must have been intelligently designed”. Don’t you guys ever get sick of moving the god to the next gap? Just give it up already. 😉

    Rajini Rao This was the last time I promise 😉

    Don’t worry about me not commenting, you wouldn’t even keep me away from these posts if you had a stick to beat me with. I would just like to see more attention go towards the science itself instead of always seeing it turn into a debate about gods. I tend to lurk around a lot and I appreciate the comments that learn me something (or at least try to ;)) a lot more than the ones who bring up gods.

  82. Jim Atienza says:

    Thanks for your description of the enzyme, your enthusiasm and appreciation for it is very clear. The animated gif is very educational, too. For me, the conjecture regarding the evolution of the rotor is less convincing than the notion that the enzyme was deliberately designed in toto.

  83. Rajini Rao — I am not a biochemist, but looking at the paper by Dan Nilsson, the paper seems to estimate the evolutionary timeframe for an eye, beginning with a small cluster of light sensitive cells. But it does not address the evolutionary timeframe to evolve the highly complex chain reaction of specialized proteins necessary to arrive at that first cluster of light sensitive cells.

    Having in place rhodopsin which transforms when struck by a photon, then interacting with transducin, which then releases GDP and GTP, which then latches onto the transformed rhodopsin, which then affects phosphodiesterase, which in turn affects cGMP… and on and on, and then is able to cycle back and reset itself.

    Evolving an eye isn’t so hard to explain once you have that process in place. But it’s a great deal harder to show how such a complex process could evolve in stages. It would either have to happen all at once, or not at all…unless it’s designed.

    Love this post though. Very interesting.

  84. Sherri Vance says:

    I’m an “IDer” and I admire your work exceedingly, Rajini. Because it prompts me to thankfulness, joy, and yes, even worship towards my God, that doesn’t take away from my appreciation for Rajini’s work or science in general.

    I wish evolutionists (yes, most scientists) and creationists could stop trying to convince each other. I don’t think design-vs-evolution is a “hill to die on” for Christians, because I believe God is capable of using and guiding processes — I don’t know what those processes might have been; I wasn’t there. But I also don’t see how my belief in and love for a divine being is a particular threat to science or scientists, the terrible assault some scientists seem to take it as. I support funding for science and research.

    I just want to be able to express grateful awe in the presence of a holiness that I feel when I read something like this post. I dare say many scientists feel awe and a kind of holiness as well. It’s just that I worship an ultimate Source with a name and personality.

  85. Tom Lee says:

    Rajini Rao Wow, what a great post. Fascinating info on the ATP. This post is one of hottest posts on G+ today. Congrats!

    Paris, Britney and Dolly’s posts can’t even come close. 🙂

  86. DaFreak says:

    You can be skeptical of actual data but you can accept intelligent creation without any data whatsoever… How does that make even the slightest bit of sense?

  87. Well done, Rajini Rao ! This looks much more interesting than how I had learned about mitochondrial ATP synthase in a book decades ago! ☺

  88. ATP is like the fuel for our cells

  89. Rajini Rao – To anyone who believes in irreducible complexity, take a look at this paper that offers a pessimistic estimate of the time it takes for an eye to evolve: only a few hundred thousand years:

    First let me thank you for an honest and fair invitation to discussion. Second as someone who has studied some of these issues for both work an interest, I am happy to continue the discussion.

    As I am familiar with the argument used in quoting Nilsson I will give you an excerpt of a critique of their work – in essence, they do not start from nothing, they start from something that is already incredibly complex(I cite the first page of your reference “we avoid the more inaccessible problem of photoreceptor evolution”), they then build on this incredibly complex substrate in a fashion that does not account for the small rate of favourable mutations, and the diminishing returns as less favourable genes are culled and the pool to draw from diminishes. It also does not take in to account the fact that according to darwinists, the eye has already been around since the very early fossils – to quote Land, M.F. and Nilsson, D.-E., Animal Eyes, Oxford University Press, New York, p. 1, 2005. “Specifically, the fossils show that vision originated ‘in the early Cambrian’, which Darwinists put at ‘some 530 million years ago’.” please see below

    However, Behe has shown that even a ‘simple’ light sensitive spot requires a dazzling array of biochemicals in the right place and time to function. He states that each of its ‘cells makes the complexity of a motorcycle or television set look paltry in comparison’ and describes a small part of what’s involved: When light first strikes the retina a photon interacts with a molecule called 11-cis-retinal, which rearranges within picoseconds to trans-retinal. (A picosecond [10–12 sec] is about the time it takes light to travel the breadth of a single human hair.) The change in the shape of the retinal molecule forces a change in the shape of the protein, rhodopsin, to which the retinal is tightly bound. The protein’s metamorphosis alters its behavior. Now called metarhodopsin II, the protein sticks to another protein, called transducin. Before bumping into metarhodopsin II, transducin had tightly bound a small molecule called GDP. But when transducin interacts with metarhodopsin II, the GDP falls off, and a molecule called GTP binds to transducin. (GTP is closely related to, but different from, GDP.) GTP-transducin-metarhodopsin II now binds to a protein called phosphodiesterase, located in the inner membrane of the cell. When attached to metarhodopsin II and its entourage, the phosphodiesterase acquires the chemical ability to “cut” a molecule called cGMP (a chemical relative of both GDP and GTP). Initially there are a lot of cGMP molecules in the cell, but the phosphodiesterase lowers its concentration, just as a pulled plug lowers the water level in a bathtub.

    This then is where Nilsson starts from, not at the beginning, not even close to the beginning, more like the final stages of assembly. And to follow:

    Mutation rate is very low—10–9–10–10 per nucleotide per generation. Of these, beneficial mutations are a small fraction—90–95% of mutations are harmful, 5–10% are neutral. And as discussed before, observed beneficial mutations are not the information-gaining type needed for evolution. The smaller the change, the smaller the selective advantage. This is expressed by the selection coefficient s. If a mutation has s = 0.001 or 0.1%, a supposedly typical value, then the number of surviving offspring is 0.1% greater for organisms with the mutant than without it. But the smaller the selective advantage, the more likely that random effects (e.g. genetic drift) will eliminate it—its probability of survival is about 2s.31 So the above mutation has only one chance in 500 of surviving, even though it is beneficial. Even if a beneficial mutation survives, for it to become fixed in a population, the organisms not carrying it must be eliminated. This is the cost of substitution. This limits the amount of substitution which can occur in a given time. This is known as Haldane’s Dilemma,32 after J.B.S. Haldane, one of the world’s leading evolutionists (and a Stalin-supporting communist for a while). He wanted evolution to work, but couldn’t get around his dilemma. Take a population of 100,000. If only a male and female pair have the new trait, natural selection must eliminate the other 99,998 and all their heirs. If there is perfect selection (s = 1), this can happen in one generation. But this means that for every new trait, 49,999 individuals must be eliminated without offspring. Then the population must be regenerated with these survivors. Anyway, even if evolution happened at the maximum speed for 10 million years, how many traits could be substituted in a creature with human-like generation times of say 20 years? Only 500,000. This small number of nucleotides is only a small fraction of the forty 500-page books worth of information (120 million base pairs) which are needed to transform an ape into a man. And in real life, selection is far less intense, meaning that only about 1700 substitutions could occur.

    Nilsson and Pelger did account for selection coefficients, although they chose s = 0.01 for each step in their simulation, larger than considered typical in nature. But they took no account of the tiny rate of favourable mutations. They merely assumed a certain variability in a population, and assumed that this would remain constant throughout. But in a real population, natural selection could select only from the variability in existing genes for the best vision, but culling those for inferior vision. This would reduce variability, because genes are eliminated. This is not the same as having mutations to produce better and better eyes. Neither did their simulation prove that simple mutations could continually produce 1% improvements. Somewhere along the way, totally new genes would be required.

  90. DaFreak says:

    I am sure it will be, like evolution or gravity, ‘just a theory’ in your opinion… Just like we are still working out the finer details of gravity we are are still working on exactly how life arose. It has already been experimentally verified that the basic building blocks of life, amino acids, can assemble themselves. They have even been found in space. How you get from tha to nucleic acid is being studied in labs all over the world and while there are many competing theories, theories that unlike your concept of “god did it” can be falsified, we still have a way to go. This is the closing gap I was talking about…

    Abiogenesis is at the moment the only scientific and logical explanation because unlike unicorns and god, it does not require a leap of faith, you don’t have to invent a god to make it possible, you are counting on nature, on reality to do the job for you. Although I am not a biochemist myself, just like I am not a climatologist, I trust the people who have studied these subjects all their lives. I am not up to date with the latest research but I trust scientists more than I trust my preacher.

  91. Disha Patel says:

    Nice Creation, Thanks

  92. Nathan Chang says:

    thats pretty cool.. and thanx too!! i could explain some of it to my science teacher to impress her a bit!!

  93. Abiogenesis is really just an extension of evolution. If we assume that God is absent, or doesn’t exist, then abiogenesis is all that is left.

    But there are still some seemingly enormous hurdles to get through before we can even begin to legitimately how life could spring from lifeless material without some kind of intentional intervention.

    The primary problem, in my opinion being that the conditions required to produce amino acids are also generally hostile to the formation of proteins. So it raises the issue, how can you get a single cell organism if amino acids can’t form into proteins? So far, abiogenesis has more dead ends than answers.

  94. but wt does ATP meanss???????????

  95. miller-urey explained how aminio acids would have been formed and there are several other experiments that showed how all the amino acids were formed and how they became proteins.

  96. Rajini why u want to add me ?

  97. Interesting…………..

  98. i really like the animation, it/

  99. Symon Smith says:

    Very nice animation, I’ve just finished a biochemistry course so its fantastic to see, knowing how much time went into discovering this, and thinking how many more discoveries are to come, and how this will improve lives.

    As for the people attacking the evolutionary interpretation, I’ve studied philosophy, so I could take apart step-by-step the rhetorical devices they are using to make science appear dogmatic (although I am aware some individual scientists may be a bit cranky, but as with any field:-)), but instead I’ll look at the concept of irreducable complexity.

    It is a poor argument as the “intelligent designer” would be irreducibly complex, if intelligent, and itself require an intelligent designer, and so forth, ad infinitum, an infinite sequence of creators, ultimately not resolving the paradox it purports to resolve of how complexity arose. This is implicitly, and obviously so, no references required, just the ability to reason at more than a rhetorical level and the courage to reject a poorly-formed point of view, even your own. That there is so much evidence in support of evolution is icing on the cake. Intelligent design is a concept that fails on its own terms.

  100. Joshua Schultz That’s just the problem, Miller-Urey was able to produce amino acids, but getting them to spontaneously form into proteins or useful polypeptide chains is another matter.

    What’s more, the ideal environment for creating the amino acids required very low levels of oxygen, and very little ultraviolet light… but O2 is essential for most living organisms, as is sunlight.

    So even if you got amino acids, and they formed into proteins, how do you get from there to living organisms, when the light, water and oxygen required for life would actually break down those proteins.

    It’s not a small problem, and many people have suggested some very intelligent (though incomplete) theories. But nothing has even come close to an answer yet.

  101. Jared Jensen says:

    So, I’m reading this and say out loud, “cool”. My wife’s attention perks and she looks over my shoulder. I start explaining this to her and she says, “You’d never see something like this on Facebook. It’s educational.” I turn to her and state, “Ya, that’s why I’m on Google+”.

  102. Kapil Kumar says:


  103. Looks amazing. But went over my head really. Can some one explain this from an engineer’s perspective?

  104. wow, thank you so much for sharing.

  105. sha! wondrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrr ful

  106. DaFreak says:

    Matthew Johnson Yes I “believe” in nature/reality and not magic… If you choose your invented god over the natural world. You are shutting your eyes to the wonders that surround you, the wonders that, in your opinion were created by your god. I am sure that you will create love and peace on earth by explaining this to other religions.

    Brian Overholt There actually was much less oxygen in the atmosphere in earth’s early days. Stromatolites, colonies of cyanobacteria pumped tons of oxygen into our atmosphere for millions of years. It’s the ability of cyanobacteria to perform oxygenic photosynthesis that is thought to have converted the early atmosphere into an oxidizing one, which in turn changed the composition of life forms on Earth by stimulating biodiversity and leading to the near-extinction of oxygen-intolerant organisms. Considering that the early atmosphere was probably very dense and cloudy because of volcanic eruptions and the impact of debris from space and that there was probably much less water on the surface because of all the heat and because that too is carried in from space over large periods of time, … Even if this for some reason doesn’t sound likely, how could it be less likely than having to create a god that came to earth to engineer and start life? Why would he create a little cell? Would he guide evolution all the way from that cell to fish > mammals > apes and eventually humans? We can explain how apes turned into man so why would you need his help at all during any step along the way?

  107. BORING!!!!!!!!!!!!!!!!!!

  108. RJ Matlock says:

    I love your first love…thanks for the info….Can I be your second love?

  109. this is really cool i like your atp presentation

  110. Yuvraj Brar says:

    I’m a physio student at UCLA, just wanted to say I really enjoyed reading your article. You touched on biomechanics, chem, and bio all in that little bit, opened my eyes. And that animation is awesome!

  111. DaFreak says:

    Lloyd Miller Abiogenesis consists of multiple theories that are being played out against each other. The fact that life is made of the same matter as everything else and not some magical substance points towards matter giving rise to life. Life exists today and we can’t use our imagination to just fill in the blanks which leads to life coming about through natural processes > abiogenesis. Gods are just figments of our imagination and have never, not even once shown themselves to be real! We have had 1000s of gods pass the revue already and not a single one turned out to be real deal. What makes you so sure that the one you believe in is different? You can’t and shouldn’t be sure. How can you be a scientist and choose to believe in something without facts or data? Especially when it relates to your own field of study? Gods are just as likely as anything else that you could possibly imagine and mankind’s imagination is infinite. We are still holding our breath for Russel’s Teapot.

  112. Raghu c says:

    Hey, Thank you for the info, shared, its really KNOWLEDGEABLE, I enjoyed….

  113. super..i didnt know…

  114. owww….nice…dat realy helpd ma’am!

  115. Shaun Orwell says:

    +Koen, the guy mixed up what the earlier guy said. He mistook “several” for “seven”.

  116. Lloyd Miller — Get off your high horse and drop the condescending drivel. We ALL can read, and therefore we all can discuss these matters. I agree that people who get their argument from should go read a scientific journal or two before they join the fray… but don’t go trying to tell people that they have to be a scientist before they can discuss these theories.

    You say “Don’t argue on things you have zero knowledge about.” I say that I am no scientist, but I have read the reports from many scientists, and know much more than zero. Even I, as a layman, have educated myself enough that I can read a report and see where a certain scientist has glossed over important problems. And just because I have no PhD, doesn’t preclude me from being able to call out a report or a theory on it’s weaknesses.

    Evolution very well might be real, and I have no problem with that if it is. But there are still many many holes and gaps. Endosymbiosis for one, is such an incomplete theory, it borders on magical. To a PhD that might sound stupid, but perhaps that’s more because they’ve come to firmly believe in their theory than that they actually have adequately answered the inherent problems in it. Scientists are not exempt from becoming biased.

    So just because I’m not a scientist doesn’t mean I can’t form an informed opinion based on the research of others. And just because a scientist’s opinion carries more authority than mine doesn’t mean it is above questioning, or that my own is not worth discussing.

  117. Ike Davis says:

    I remember the ATP Cycle from college, but I never actually understood how it produced power. It seems we murder plants and animals for their protons! 😉

  118. nice>>>>>>>>>>>>>>>>>>

  119. very nice Pic,But old photo is this,but minded girl,as iunderstand.

  120. shee vang says:

    so thats how it work

  121. kisanlal k says:

    its a miracle how body functions

  122. Lee P. Jr says:

    I wanted to put down some smart and pithy comment, but after reading a mass majority of the comments I’ll stick with, amazing. Simply Amazing!

  123. Koen De Paus “Gods are just figments of our imagination and have never, not even once shown themselves to be real!”

    Ah… You are an intelligent man, but that’s a very broad and sweeping, shall I say “unscientific” statement. Scientifically, statistically and logically you cannot rule him out.

    Disbelieve if you like. But I think spiritual phenomena and God have shown themselves to be very real many times over. The assertion they they have not shown themselves even once is both impossible to prove, and dismisses a huge category of human experience as mere superstition and self-imposed delusion… which is a fairly harsh (and somewhat elitist) position to take.

    I for one cannot start from the presumption that all spiritual experiences are illusions. That would mean that roughly 90% percent of humanity is essentially crazy. And while arguing for the existence of God seems like a convenient fantasy, there are as many logical problems for explaining reality without him as there are explaining reality with him.

  124. Jon Thrasher says:

    “At some point, a H+ driven motor came together with a helicase like hexamer to create a rotor driving the hexamer in reverse, to synthesize ATP.”

    I notice you don’t delineate the near infinite orders of magnitude comprising even conservative initial estimates of the probability of this result occuring from chance, or even under the influence of massively manifest mutations due to improbable scenarios of nuetrino emission even from supernovae nearby, so what to me is once again legitimate evidence that could lead to conclusions of advanced technological interposition in long practiced and applied bioengineering in evolving ecological field conditions, is all but ignored as an unfortunately intractable empirical nightmare, by cutting edge research, because it interferes with inculcated cultural conditioning against even CONSIDERING an hypothetical ‘panspermia’ framework for logical reductions to the improbability of this wondrously complicated mechanisms arising from the memes your lack of concern for origins seems to suggest. Yes?

  125. Rajini Rao 1167 shares! Wow that coffee must have worked. Anyway, John Bump asked if the bacterial flagellar motor was even smaller.

  126. P K sharma says:

    hi verry god luk thanks

  127. can we use this mechanism in real world, like green fuel engine mechanism 🙂

  128. Wonderful God’s creation !!!

  129. richa sharma says:

    Very interesting. Thanks,Ranjini. Was wondering whether energy generated kinetically such as motor can be substituted by non-motor generated energy such as enzyme reactions since that will ensure longivity because of no-moving parts and perhaps could be controlled better by providing optimised energy flow being highly objective to the load.

  130. I just wanted to say thanks for sharing this Rajini – I’ve recently heard of proton gradients mentioned in a BBC Discovery radio lecture by Sir Paul Nurse. Your article and animation has greatly increased my understanding and fascination of nature and life.

    I’ve also found another animation that illustrates how the ATP synthase fits in to the bigger picture of the electron transportation chain within a mitochrondria

  131. I can understand people that can not belive that there is a God who created all this complex systems. What I can not understand is how people can belive it happend by evolution. Its like taking 10’000’000 mechanical watches appart and giving them to apes and wait a very very long time and then think the have put all the peaces together in the right way and the watch would show the exact right time (atom watch) and having the right date as well.

    How likely do you think this is going to happen even if you would give them imaginary 4 billion years.

    It’s the same way with people who would not belive that there is eternity but in the same time tell me the world is 4.5 billion years old. To me if I would belive in the 4.5 billion years that kind of close to eternity 🙂


  132. Nanotechnology at its finest!

  133. nice picture huury………………………………….

  134. Aamir Mirza says:

    good h yarrrrrrrrrr tumhariiiiiiii tarah………

  135. Wow..that’s really amazing…..biochemistry concepts would have been really very easy n interestingy if they wud have been taught in this way.. …thanks for sharing this Ragini !!!

  136. Rajini Rao says:

    James Salsman , John Bump the bacterial version of the ATP synthase is only slightly smaller because it has fewer accessory/regulating subunits. The basic structure of the hexamer, shaft and rotating ring within the membrane are very similar and must have come from the same ancient genes.

  137. fantastic animation beyond imagination.

  138. Rahul Porwal says:

    Good work Rajni. Keep it up. We are proud of you.

  139. Saravanan M says:

    Interesting……. Thanks. Keep it up and all the best.

  140. Ram Prakash says:

    Sounds Very Interesting…

  141. Wow Interesting . Thanks

  142. Hi Rajini I wish your experiments lead you to the right path one day, that is the reality of life and our existence.

  143. Thank You Rajini Rao

    for the glance at “little” science from big scientists( including You ).

    Your first Love is very even energetic… ( :

  144. “This would be the force you would need to rotate a 500 m long rod while standing at the bottom of a large swimming pool at the rate shown in the movie.”? I don’t understand how 40 piconewton nanometers means anything other than 4.0e-20 Nm of torque? Can someone please elaborate on what this means?

  145. Andrew Johnston I disagree that rejection of evolution comes from lack of information per se. I think what happens is that you decide what feels right and then pick the evidence that supports that opinion and reject or question information that doesn’t fit that opinion.

    One difference between scientists who work on any science and laymen is that scientists know they don’t have all the answers, while laymen view science as knowing all. Holes or gaps in theories can be then used to reject any theory the don’t like. Therefore the massive amount of evidence for any theory can be rejected if there exists even a single unanswered question.

    You can spend all your energy trying to show people the evidence for evolution, but they will then just spend all their energy trying to find a question you can’t answer.

  146. devs josh says:

    how did you know that

  147. Tom French says:

    I am not reading 270 comments, but how the heck does a post about mitochondria devolve into a debate about evolution? Expand your focus people.

  148. Bill Seward says:

    Amazing Over my head!!

  149. Jaspal Singh says:


  150. Raul Valdez says:

    Did a college chemistry paper on this. Gotta love the Krebs Cycle!

  151. DaFreak says:

    Bob Schnatterly Perhaps you should read a real science book like the fundamentals of molecular evolution, written by people who actually studied molecular biology instead of a book written by 2 theologians who have never studied regular biology…

  152. DaFreak says:

    Matthew Johnson How many times are you going to keep bringing that up? Gods don’t explain anything, it’s just a label you use for things we don’t yet understand > A god of the gaps argument. What would gods explain? How would you explain gods? Why would gods create cells and not go for humans directly? What about machine software that learns? Nobody is programming it, yet its information density grows as a function of time and interaction with its environment. Even our brains increase in information content as we learn more about our environment, stars increase the number of different elements they hold, … Everything evolves. Change is the only constant. You can’t keep something the same for eternity. From the universe to stars, to planets, to atmospheres, to life, the brain, culture, … everything evolves! You assume that humans are something special, that we can create objects while nature can not. This is wrong. You are putting mankind on a pedestal and I applaud your engineering skills but we haven’t even come close to creating anything as complex as the stuff that nature has managed to produce. Do you think gods assist every baby to grow up? There are wonders all around us but if you look towards your god for answers, you will not find out anything about how it really came to be.

    If you read up on how the concept of god evolved and how gods evolved to become ever more powerful in an arms race between preachers and people that ask questions, you would see that the gods we have now have exploited niches that lie beyond the realm of reason / science / logic / reality / nature because all the other gaps have been shrinking since apes started walking upright.

  153. Andrew Johnston — I resent the notion that everyone who is critical of evolution as a complete theory for the origins of life must be ignorant of all the scientific fields you just mentioned. Yes, there are many who argue adamantly for creationism without any knowledge of the sciences. But it does not follow that intelligent people and scientists cannot also find large unanswered problems in evolution.

    On the contrary, it seems that people like yourself — who claim that evolution skeptics are merely less educated — are simply dismissing the problems with the theory as insignificant, rather than honestly admitting that evolution has not explained everything.

    I have read many books on several of the disciplines you mentioned, numerous peer reviewed articles, journals and studies regarding the various theories that are relevant to origins. I am a layperson, but with a higher than average understanding of all the disciplines you mentioned… and I have never read a Norm Geisler book, as somebody on here suggested we do.

    But my understanding has not lead me to acceptance of the theory of evolution as complete explanation. If anything, my understanding has allowed me to see the problems in it more clearly.

  154. Raja mass says:

    Life Science is always fascinating

  155. To Everyone, this is my last comment.

    An honest scientist who studies evolutionary biology and biochemistry will admit that there is much that has not yet been explained… perhaps much that is beyond our capability to determine at this point.

    A scientist who dismisses these facts betrays his bias. The holes in the theory are there. Saying they are insignificant is as biased a statement as the others who claim they are.

    You can say you have faith that we’ll eventually find the answers and evolution will continue to be confirmed with every discovery. That’s fine. But just recognize that for what it is… “faith” that evolution will be confirmed… and stop mocking the people who don’t share your faith, as if they’re idiots.

    You may think they are fools, but calling them so makes you an elitist. You may think them less intelligent… but saying so only betrays your prejudices. Be civil and respectful of those you disagree with (and that goes for you too, IDers).

  156. Stan G says:

    Didn’t they decide that little wonderful motors like this must have come through natural selection even before molecular biology was “discovered”?

  157. DaFreak says:

    Brian Overholt That’s a strawman. Nobody is saying we know everything and yet that is the position you choose to attack… It’s not because there are gaps in knowledge, that gods are the answer. It just means that we have to work out the finer details of how molecular biological evolution took place. Evolution has been confirmed. It is a fact just like gravity is a fact although both still need more work to figure out the finer details.

    On a sidenote, I too have had spiritual experiences. I will never forget that first time. I was 16, looked up at the stars and reality just hit me in the face. I can’t explain it. There was no milky way, just your everynight, light polluted sky but it all of a sudden became real. That was not a 2D background, I was looking out into a void of space and time. I made a connection with the stars and realized that those little specks I saw, were photons that had traveled millions of years to reach my eyeball. I got goosebumps, I cried, I had to sit down and felt connected with EVERYTHING. You don’t need gods for a spiritual experience. Nature is beautiful as it is and dragging in magic to say that nature is just the product of some human like vastly superior intellect diminishes its qualities, its complexity and our understanding.

  158. Rajini Rao says:

    Brian Overholt , thanks for your perspective. No scientist I’ve known ever claims to know that everything has been explained, so we are all honest by your definition. The problem, IMO, lies not with science trying to explain life on the basis of rigorous chemical, physical and mathematical laws, but with ID/creationists who have nothing testable to offer in return except some implicit belief or faith that the rest of us outgrew as we gained knowledge.

    Good to hear that you are a scientifically educated layperson. People like you should be the backbone of our society. Certainly I don’t think you’re a fool (I would not bother to engage with you if I did). However, for a fair and equal debate, you would need to match me, not in formal education, but in deep knowledge of the chemical basis of life…draw out a nucleobase and see how it compares to those recently found on asteroids, see how protein folds are conserved across multiple families, understand how phylogeny recapitulates function, appreciate the transition state of a chemical intermediate at an enzyme’s active site. If I told you that the archaeal ATP synthase subunit c (critical proton carrying subunit in the ring) branched off from a common ancestor shared by the eubacterial ATP synthase, and then diverged to give rise to the related V-type ATPase, would that make sense to you? It does to me, because I can see the shared sequences between chloroplast/mitochondrial ATP synthases and that of eubacteria because of their endosymbiotic relationship. And these phylogenetic relations would mirror those of many other proteins that I can find in GenBank. (I’m going easy on the geek talk here, trying to avoid talking about tandem duplication of subunit/loss of the critical aspartate in the V-ATPase with implications for loss of reversibility- a beautiful example of molecular evolution).

    I’m being totally honest here..without a deep understanding, you may not comprehend my arguments and we will be just talking past each other. In case you think I’m being elitist, I should clarify that I would not be able to adequately debate a particular solution to a complex math theorem, or argue the existence of the Higgs college level physics (now woefully out of date) or my reading of popular science does not put me in the same category as a physicist at CERN, for example. I’m not likely to challenge a theoretical physicist…not even on Google+ 🙂

  159. Koen De Paus — I guess I lied, I just couldn’t not answer you. You say that the position I argue against is a straw man… it sort of is. No scientist would officially go on record saying that everything has been explained. But when talking to people who are unconvinced that the theory of evolution is adequate to explain life, a lot of experts scoff at that position. But why would they scoff when they themselves know that science doesn’t yet explain everything about the origins life?

    There is so much that is completely beyond us at this point. Why is it so ridiculous to believe that natural explanations will always fall short, when so far they have?

    You have to admit that our ability to discover and explain has limits. I don’t think we’ll ever explain it all. And if we ever reach our limits of discovery, people will still postulate about how the remaining mysteries of life happened… and those who make the admiral effort to solve the puzzle with well formed naturalistic theories still will only have theories… which is also what theists have.

  160. Rajini Rao — I am honored that you responded to me, and I had one last thing to add after reading your response.

    Of course, as Koen De Paus pointed out, my characterization of dishonest scientists was a bit of a straw man. I wasn’t referring to any official position that a scientist has ever taken, so much as the way in which many experts have responded to skeptics. Some skeptics admittedly have an agenda to push, and that’s what the experts react to… it is just a bad situation we have created, that the debate has to be so heated… and creationists aren’t innocent either.

    Of course I would not debate you. As you pointed out, my self-obtained level of education does not equip me to argue with you on that level. I would rather LEARN from people like you, who take the time to explain the complicated processes and structures you study in somewhat simpler language that people from other disciplines can comprehend.

    As I read from you and other experts, and come to my own understanding, I can discuss that with others… not necessarily with you. I will leave you to your work, and if anyone is to debate you it would be another expert… and I would surely be interested in learning from that debate as well.

    Thanks for all your hard work, and your admittedly impressive expertise in this field. Everyone, even creationists, can find a lot of value in the work you are doing. 🙂

  161. Rajini Rao says:

    Matthew Johnson , I don’t have to accept these as facts, true. But I have no illusions about matching Hawking in a debate. There’s a difference, don’t you think?

  162. DaFreak says:

    “There is so much that is completely beyond us at this point. Why is it so ridiculous to believe that natural explanations will always fall short, when so far they have? ”

    This is very true and it will most likely and hopefully always be beyond us. I see the body of knowledge as an ever expanding light being cast outwards into an infinite darkness. The boundary of this light will be pushed onwards into new territory forever. The question why anything had to exist at all will forever be out of reach. But perhaps such a question is meaningless to ask if “nothing” does not exist. It is not ridiculous to believe that our explanations will always fall short, not at all! It is however ridiculous to assume that there is more to nature than nature. Nature is everything, as soon as we discover something new it becomes part of our knowledge of nature. Supernatural, supersupernatural, supersupersupernatural,… things don’t exist by definition because if they did they would be part of the natural. Now they just end up holding us back and detract from the real wonder that “normal” (crazy) nature has to offer.

  163. Matthew Johnson — Good points, but Hawking’s theories about a multiverse and the origin of our own universe are as untestable and philisophical in nature as a Theistic explanation would be.

    At least in biological evolution there are things the be studied, data to be measured, and experiments to be conducted. Much of evolution is potentially falsifiable… though much of it is also still beyond our ability to verify.

  164. Koen De Paus — I need to break this off, but I’ll say one more thing (I guess I’m a glutton for punishment like you). 🙂

    “It is however ridiculous to assume that there is more to nature than nature.”

    The thought that reality and existence transcends beyond time and space is an untestable assumption. But the thought that the natural world is all that exists is ALSO an untestable assumption. I am no more ridiculous in my belief than you are in yours… so let’s agree that neither position is ridiculous.

    Have a good one. You are certainly a worthy debate partner, and I respect your perspective, even though I might disagree. 🙂

  165. Rajini Rao says:

    Matthew Johnson , nope..have seen nothing in the evidence to consider deliberate “intelligence” driving or creating any of this. I don’t bring any philosophy, emotion, faith or personal beliefs to the table. Just data and verifiable facts. I have no vested interest in any particular version (if there is indeed a god, hallelujah! If there is none, so be it!). For the record, like many scientists, I came from an orthodox religious background..saw nothing to support it scientifically, OTOH, see the forces of evolution every day and every where. You can reserve skepticism, but unless you match my argument with specific molecularly accurate and experimentally verifiable counterarguments, I would see your stance as illogical. 🙂

  166. DaFreak says:

    Brian Overholt I guess this depends on how you define the word nature. I look at it as an infinite set that encompasses all that exists. Everything that we discover to be real becomes a part of the set. Even if we would discover gods, other universes, parallel dimensions or realms of existence so alien that we can’t even begin to fathom them, then they would just become part of what really exists, become a part of nature. That is why I look at the supernatural as per definition impossible.

    It’s nice to have a decent discussion about such topics! Most of them end up derailing into calling each other names. Peace! =)

  167. DaFreak says:

    Matthew Johnson “That is, we are claiming that we know from repeated experience that information arises exclusively from intelligent causes, so we posit this an explanation.”

    You are claiming that, you are reasoning from personal experience and “explain” a natural process by a label, a label that our minds produced, a label that is not defined and doesn’t end up explaining anything at all! I say it is simply not true and wrong that information arises exclusively through intelligent causes. I have shown you examples of information processes becoming more complex without the need of “intelligence”. Intelligence is not defined and not mathematically quantifiable, information content is. We see things spontaneously grow more complex, denser in information with no evidence of intelligence, such intelligence is not even required to “explain” these processes. If we were to posit that the universe was created by aliens… Would you settle for that? Can’t you see that it doesn’t really explain anything?

    “You can know the name of a bird in all the languages of the world, but when you’re finished, you’ll know absolutely nothing whatever about the bird… So let’s look at the bird and see what it’s doing — that’s what counts. I learned very early the difference between knowing the name of something and knowing something.” ~Richard Feynman

  168. Matthew Johnson, does this count as specified complexity?


    That’s a traditional Sri Lankan greeting. How about this?


    That’s a semi-random sequence of letters. How do you tell the difference, when you don’t know the answer in advance?

  169. Connor Wood says:

    Very interesting read, and amazing animation! Please, make more!

  170. Edward Woods, who are these “top evolutionists” who reject evolution? And, far more importantly, can you point to where in their writings they explain why they now reject evolution? After all, those reasons are important — if they don’t have good reasons, there’s no cause to believe them. Especially given the staggeringly good reasons to accept that evolution is true.

  171. John Midkiff says:

    Coolest molecular machine EVER

  172. Rajini Rao says:

    David Ratnasabapathy , there is no point in engaging Edward Woods on this topic. Overt religious rambling has no place in what was meant to be a scientific post. Thanks for trying, though. Any more preachy stuff from him will be deleted. There may be a place for it, but obviously not here.

  173. Excellent article – admit the technical points are beyond my knowledge – However, Dr. Rao, do you have other articles on ATP but identifying/including the interaction of CoEnzyme 1 in the production of ATP?

    many thanks.

  174. Jethro Reeve says:

    pretty cool. the complexity of this is one of the reasons i don’t believe that billions of years of evolution could have done it. it only makes sense for this to be intelligent design.

  175. Ok, here’s a longer phrase.



    Can you tell which of these contains specified complexity and which is random without knowing the answer in advance?

    About cellular DNA containing specified complexity: do you accept that DNA evolves, so that stretches of DNA that previously didn’t produce functional proteins, later do so?

  176. Jethro Reeve says:

    the key point is that new genetic information never arises through any known process. DNA appears to contain information that is not functional at the moment – sometimes incorrectly labelled ‘junk’ dna. It is nothing of the sort. We are only beginning to understand its purpose. God has created the genome of plants and animals with the amazing capacity for adaptation. We do not understand how this works. But the information is pre-existing and is a fascinating area of research. Evolutionary ideas have hindered scientific progress with the false notion of junk dna.

    The truth of the matter is that mutations are adding errors to the gene pool, and what we actually observe is devolution in progress. Note that noone has ever observed a mutation that adds genetic information. They are alway information neutral or lossy. Occasionally they may confer some benefit (such as wingless beetles on small islands, or bacterial resistance), but these benefits are the result of genetic loss.

    The notion of evolution giving rise to genetic complexity is scientifically bankrupt, and bereft of observational support. It is really a religious idea borne out of secular humanism and atheism.

  177. saman shwany says:

    so nice ,,,thanx also iam master student in Medical Biology in Gaziantep University / Turkey

    can you explain more than it….during fasting state and during normal feeding state the source and depend on what for getting this ATPs

  178. Fascinating, but I have seen smaller motors. Researchers developed a molecular-scale motor where the axle is a molecular bond.

  179. So many great responses, but also so many ignorant religious nutjobs talking out of their a** with childish spoon-fed opinions, like Edward and Jethro… Thank you for posting such a beautiful model of such an important process that has helped us learn so much about our evolutionary history.

  180. Jethro Reeve says:

    Cad’ika, if people have managed to create an even smaller motor, that is very clever, and testament to the fact that design comes about from an intelligent source!

  181. Matt Laroche says:

    Looks like someone filling a cone up with ice cream.

  182. hi rajini…

    v nice post by you….

  183. Thank you! Nicely explained!

  184. Nick Mack says:

    so much better than reading about Jersey Shore over on facebook

  185. You do give excellent explanations. I thank you. Most of the time I feel I need to hit my translate button but where else but G+ would I ever have a connection to this type of knowledge.

  186. Blake Caves says:

    I agree with Nelson, this is a pretty interesting motor.

  187. Well, I think the analogy you’re using for specified information is flawed because you can’t tell the difference between a random sequence of letters and a sequence which you think contains specified complexity. If you don’t have an objective method to identify specified complexity in a sequence of letters, you can’t really demonstrate it exists.

    I’m trying to understand your position, hence the 20 questions 🙂 In one of your posts above you wrote that “information arises exclusively from intelligent causes”. But if a stretch of DNA evolves a function using purely natural causes, then there we have information arising from a non-intelligent source.

    ETA: Matthew Johnson

  188. That is so incredible! Thank you for sharing I remember learning all about ATP in college. Love this!

  189. 袁瑞 says:

    I may appreciate that if I may have seen this illustration when I had my molecular biology class…..

  190. Being a biology major I LOVE THIS!!! =]

  191. Don Cameron says:

    Only three people used the word “breaking” in their posts, besides the original author and there is a flaw in the use here. A little research will reveal that breaking bonds always requires the input of energy. So to say we get energy due to breaking of bonds in ATP is not quite correct. We get energy from the formation of bonds, that may result from the original breaking of ATP (with some initiation). An easy way to get to this conclusion is the fact the products we kick out after metabolism (carbon dioxide and water), are not used as food sources by us, but require the input of energy (for example with photosynthesis), to create new STORES of energy. ATP stores energy in the same sense. When it is used, we release energy from the products that are “downhill” thermodynamically from the complex ATP molecule. Okay, not an easy concept, but as a teacher, every day I have to convince kids that the production of Nitrogen in explosions is the source of energy released.

  192. Rajini Rao says:

    All true, Don Cameron ..I should have said hydrolysis of the terminal phosphate bond of ATP but I’m trying to avoid chemical jargon here.

  193. John Ramirez says:

    Rajini Rao Simply, beautiful. This post (being short and illustrated) is a great example of how research and technology can really do great things to teach us all about Science. On another note, have the mechanical findings of ATP research been reproduced or utilized to some capacity? In other words, has any company used the synthase structure of energy consumption/conversion in modern technologies, or organizational production, etc?

    Anyone who likes the illustration and wants to know a bit more, go here ATP: Adenosine Triphosphate


  194. A very gud job,i did my UG & PG in Microniology

  195. My Mazda RX8 has a rotary engine. It was cool to check out this post and share. Thank you Rajini !!!!

  196. Rajini Rao says:

    That’s a great question, John Ramirez , thanks! There have been report of a nanomechanical device powered by a biomolecular rotor which drives a propeller:

    There is an overview in this free article:

    I don’t think they have reached commercial application yet, but some smart people are putting their minds to it!

  197. Rajini Rao says:

    Cad’ika Orade , that was a neat invention, but it was artificially (chemically) synthesized and had no biological function. But very cool, I agree! Here is a nice summary:

  198. John Ramirez says:

    Rajini Rao I’m already thinking about applying this mechanism to computer processes. I’m someone who assumes that research in biological evolution will allow humanity to find efficiency in current processes and technologies. Interestingly, I find that computers do have a similar structure to processing data. Thank you for the quick response. For a refresher, I’m watching the Khan academy video on ATP now and loving life.

  199. Hi, I’m interested that you display, when read on acid .. have we ever wondered how to overcome it .. so that energy produced by the body as lively as the active boy … Where acids, chemicals, food we eat .. because acid that is the cause of every disease I ..- a share for me as a child had found a solution malaysia .. malaysia created by a citizen.

  200. David Wales says:

    +Andrew Johnston

    Your question is a good one, but it merely highlights the characteristics of God. There are two possible answers. Either the intelligent designer does not exist, or the intelligent designer has always existed, outside of time and space. If one reads the biblical definition of God, God is described as having no beginning, thus negating your question.

    Ultimately, there has to be something which has no beginning, and is outside of time. The steady state theory suggested that rather than a god with no beginning, the universe itself had no beginning. Similarly, in an attempt to answer questions such as this, there have been several versions of the big bang theory which suggest that there have been infinite big bangs and reverse big bangs. (This is probably a simplistic way of putting it). The creation theory merely suggests that rather than a universe with no beginning, there is a god with no beginning.

  201. Ashwin Bhat says:

    I did not understand that, may need to read it again carefully, just in case, can anybody tell us in English what’s happening here?

  202. very cool explanation and representation of Mitochondrial ATP synthase.

  203. clever little bugga……..make you think just how small we really are

  204. khan anwar says:

    hai i am anwarkhan indian

  205. Rajini Rao – how awesome – this might be the most shared science post of all time 😉 Great work!

  206. Fahed says:

    Is it actual mechanical rotation? Is there mechanical wear on the components?

  207. sean steele says:

    Interesting that when recorded information is found any where in the world it is logically thought to be by design, except when that information is in a living cell. “Irreducibility of cell” research life through all facets of logic.

  208. That’s a weird looking piston.

  209. nice animation ……………..

  210. hey wats happening really naaku ardham kaledhu


  211. Nasrin Noor says:

    r u science student.

  212. Its an amazing presentation.ATP Adenosine Tri Phosphate is a 3 phosphate molecule which is produced in the mitochondria during cellular respiration which is used only by cells..many organelles in the cell use ATP energy to synthesis or break down molecules and required materials by cells and body

  213. Amit Rawal says:

    thanks for sharing this to us.

  214. Asif Sultan says:

    very interesting discovery about machinery in body.

  215. Saif Nirob says:

    I just excited to see that. Sometime I am thinking that is a Aquarium, and sometimes thinking that is a graphical magic.

    After all, its really a excellent moving color content… (!)

  216. Andrew R. says:

    a little late, but I can’t believe no one made this reference: I see your H+ and raise you an OH-

  217. Saravanan D says:

    thanks for the knowledgeable share

  218. Let me get this right. Is that rotation a by product? what is the use of the rotation? :S And is the rotation there when the cell is made the first time?

  219. Forget my earlier comment. Just understood its the rotation that move the molecules in the upper part. so this generates our 98.4F?

  220. prove that GOD existed! greatness of GOD, such a complex machine created from the early time.

  221. such a wonderful information that you gave!!!!!!!!!

  222. Manvir Clair says:

    With all the relevant information available easily i think its about time to start ignoring evolution deniers. they are trolling forums everywhere and reducing all interesting threads into evolution vs design. Please stop entertaining such people.

    Yes evolution is just an explanation and we may never be able to prove it conclusively enough to make other people adopt it. But the sheer brilliance and elegance of it is what appeals to the mind. Every new piece of information we find out about nature fits beautifully into this framework and makes us happy and content with it. I’m sure that if there is a higher order of intelligence that exists, it too must have accepted this powerful solution to explain its existence and with a greater majority because of the higher intelligence.

  223. Vinay Y S says:

    awesome. definitely +1 and added to my geek circle 🙂

    On a side note, G+ really needs slashdot style comment moderation system.

  224. Rajini Rao says:

    Tharaka Devinda , the purpose of the rotation is to release the newly formed ATP from the catalytic sites on the hexamer. The ATP is very tightly bound and the protein has to let go, so as to kick it out 🙂 The energy required to do this comes from the protons going down their gradient and rotating the shaft as they do so. Hope this helps.

  225. Endosymbiosis has played a role in evolution, and of course the mitochondria itself is an specific example of endosymbiosis. This connection always brings a chuckle since evolution deniers use this very cellular rotary motor as a basis to deny evolution.

  226. Ryan Chiechi says:

    Rajini Rao has innocently posted an animation of the structure of a complex molecular machine (which, incidentally is based on the probabilistic maps of electron density and is not what it “looks” like) and been sucked into debating the merits of the theory of evolution. Here is the problem: she is not arguing with people whose minds can be changed because they are based on belief, ignorance (of Science in general and the enormity of what they are arguing against), and misplaced skepticism of what they do not understand. Their conclusions are derived from faith, and then their understanding is in turn based on those conclusions. Scientists (of which I am one), in their professional capacity, derive conclusions from understanding which is turn based on empirical observations; our minds can be changed. So, keep it up, creationists, because there is a finite chance that you will change our minds (don’t hold your breath). But fellow scientists, if you are going to participate in social media, engaging creationists in debate is an exercise in futility… I do take exception, however, to the comment that scientists don’t create; I am a chemist, I create new forms of matter on a regular basis.

  227. One evolution denier (sorry, for not being able to specify his name) way back in this long comment thread, said that since evolution does not explain the origin of life (correct) that it is misleading to describe evolution as the explanation for the origin of species.

    At the time of the first unicellular organism way back then, in deep geologic time, there were no species. One life form can not constitute a species because it is the only one. When it stopped being the only life form and other species came into being, evolution of course, does explain that elegantly and with a ton of superb interlocking evidence from many scientific fields. Evolution, a robust, scientific theory unlike the god hypothesis, has both predicting and explanatory aspects of great potency.

    Evolution makes god redundant. It is of course possible that evolution is a redundant system. However, for many god believers, that is very psychologically perturbing to believe in a redundant god because that is why god belief mostly makes sense to them, that it is the only explanation for everything. For me, science explains some things, while religion explains nothing.

    It is also noteworthy to remember that in the Dover Trial, the judge, who happened to be a Christian, stated that Intelligent Design was religion, and therefore has no place in a science class. Equally noteworthy, is that science is not a democratic process and that an elite scientist is specifically one who has become proficient after many years studying a complex field, and not one who prevents others from doing the same, which in my mind, would constitute elitism.

  228. The functioning of a cell is beautifully complicated. The more you study about it the more u are filled with awe, actually u fall in love with Biology. The microscopic dimensions in which such complicated processes are taking place with absolute precision is mind boggling.

  229. Stewart Ball says:

    Thanks for sharing this. Having a visual of this process is so much better than reading about it!

  230. DaFreak says:

    thx Pedro Rodriguez Manzano, very interesting site indeed! > cell biology animations

  231. Rajini Rao says:

    I concur! Nicely done animations at You can see the ATP synthase in relation to the upstream events (electron transport chain). Thanks to both Pedro and Koen for finding and checking this site out.

  232. Rajini Rao forgot to mention in his post a detail that many probably know (necessarily all Biologists, Biochemists and Physicians) but if not considered could be lead to an apparent contradiction. I’m amazed nobody has yet mentioned the paradox after more than 400 comments. First I’ll expose the paradox in order to let those who don’t know yet the answer solve the mystery by themselves.

    Rajini wrote:

    Where does this ATP come from? It is synthesized by an incredibly sophisticated molecular machine, the ATP synthase, embedded in the inner membrane of our mitochondria…”

    How did this amazing rotor evolve? The hexameric structure is related to DNA helicases that rotate along the DNA double helix, using ATP to unzip the two strands apart. The H motor has precedence in flagella motors that use proton gradients to drive rotation of long filaments, allowing bacteria to tumble through their surroundings. At some point, a H driven motor came together with a helicase like hexamer to create a rotor driving the hexamer in reverse, to synthesize ATP.”


    So if ATP synthase is derived from an enzyme needed to modify the double-stranded DNA structure, then the ATP synthase can’t predate the synthesis and elongation of DNA. On the other hand, the synthesis of DNA requires deoxynucleoside triphosphates (dNTP) as substrate, and in their turn, the synthesis of dNTP requires ATP as substrate.

    Then, how the DNA was synthesized before the appearance of the DNA synthase in the history of life?

    In fact, our cells require ATP to synthesize pretty everything.


    The explanation is simple, there are other different processes to generate ATP, much simpler enzymatic reactions not coupled to a proton flow through a membrane induced by an electrochemical gradient. For instance, there’s some ATP synthesis in the glycolytic pathway that takes place in the cytosol. We (human cells) don’t even need of mitochondria to generate ATP, red blood cells don’t have mitochondria and yet they generate their own ATP, and some types of parasitic worms don’t even have mitochondria (nor ATP synthases).

  233. Jethro Reeve says:

    +Manvir Clair the theory of evolution most certainly does not fit into this ‘beautiful framework’ you talk of. every time something is discovered, evolutionist scientists would find some way to twist the evidence to make it seem as if it supports their religion (atheism). there are so many holes and ideas with no evidence in that theory. for example dark matter had absolutely no evidence for it. it makes much more sense to measure back and find how long it would have been without using the dark matter theory. that suggests only around 6000 years. if i were you, i would not be happy at each beautiful piece of information as it probably means another idea to think up for evolutionists. it is the theory of creation which each piece of evidence agrees with without any ideas with no evidence.

  234. Rajini Rao says:

    Zephyr López Cervilla , thank you for your comments. However, there is no paradox and it is indeed both well known and appreciated that single celled organisms can make do with only glycolysis and fermentation (such as yeast) although they have to switch to mitochondrial function when glucose runs out. Metazoans and higher organisms cannot survive and keep up with their energy requirement without mitochondria..95% of ATP comes from the ATP synthase. No human can survive without mitochondria..ATP synthase mutants with even a small reduction in function are lethal (Leighs disease, for example). Red cells are enucleate and have a limited/short life span for a specialized function.

  235. Rajini Rao says:

    Jethro Reeve , Most scientists bow to the flying spaghetti monster up in the big sky. He has been creating dark matter for at least 6000 years. I urge you to convert to pastafarianism immediately. RAmen!

  236. Rajini Rao, I referred to it as a paradox as it could look like apparently contradictory unless you had in mind that there’re other alternative pathways to generate ATP.

    A similar paradox to the need (current need) of a ribonucleoprotein complex for the generation of DNA polymerases, whereas in turn the translation of those ribonucleoproteins require of DNA as a template (via mRNA, and with tRNA and rRNA as substrates).

  237. DaFreak says:

    Bill O’Reilly is the host of the political commentary program The O’Reilly Factor on the Fox News Channel, which is the most watched cable news television program on American television.–es4FGwKQg

  238. Rajini Rao says:

    Koen De Paus , I bow to your noodliness for finding my favorite Colbert episode, and reminding me that there is “never a miscommunication”! I’m laughing so hard that my face hurts.

  239. Matthew Johnson Johnson, you wrote that there are two forms of complexity — specified complexity and mere complexity. The way I’m reading you, “mere” complexity is what is contained in stretches of DNA that are crafted by natural selection. “Specified” complexity is what is contained in functional, complicated stretches of DNA that weren’t crafted by natural selection, nor by humans. Is that correct? I’m trying to understand your viewpoint.

    The problem with this definition of specified complexity is that it’s a negative definition. It says specified complexity is anything that wasn’t evolved. So we can’t just look at a stretch of functional DNA and declare that it has specified complexity. We have to first prove that it cannot have evolved by natural selection and that it wasn’t made by humans.

    But it’s tough proving that a gene can’t have been built by natural selection. Because the DNA of organisms is scribbled all over with the signature of natural selection. Long stretches of DNA, for example, turn out to be modified versions of other stretches of DNA. That’s what we expect if they’re built by natural selection. When we group those stretches together by degree of similarity they fall into a groups within groups — the classic signature of slow evolution by natural selection. And given that we now know that genes are swapped between unrelated species, the presence of a complex gene unrelated to the other genes on a genome wouldn’t necessarily be un-natural. This again is a problem for identifying specified complexity, so long as it’s defined to be non-naturally made DNA.

    Perhaps I’m misunderstanding you. Is there a direct way we can detect specified complexity in a sequence of functional DNA?

    I’m confused by your your analogy. You say that if a string of letters has meaning in the English language, that is analogous to DNA having specified complexity. But you agree that new information (“mere” complexity) can be created by natural selection. So a cell’s functional DNA is a mixture of naturally and un-naturally crafted parts. Within the analogy, then, what parts of English don’t count as specified complexity?

    Would you say that short sentences are analogous to mere complexity, while long sentences have specified complexity? That would be excellent. Because see, that gives us a direct way to detect specified complexity! Just define what you mean by “long”. Is there a similar procedure available for DNA?

  240. Rajini Rao says:

    Sorry to have to moderate your comment out, Edward Woods , but I did make the point earlier that this is not the place to preach any religion whatsoever.

  241. Jethro Reeve says:

    Rajini Rao – i am afraid that you are wrong there. atheism is also a religion. though lots of people don’t think so, atheism/ evolution is full of religious beliefs.

  242. Rajini Rao says:

    Jethro Reeve , LOL yes, it’s called pastafarianism. 😉

  243. Atheists pursue their interests, certainly, but are irreligious in terms of worship and dogmatism. Scientists, on top of that, are the polar opposite of credulous, so to say that being both makes you ‘religious’ by definition is a bit farfetched. Please, do all the people who are here for the science a favor and spare us your personal annotations, they are irrelevant ;]

  244. José P. Llongueras —

    wor·ship /ˈwərSHip/

    Noun:The feeling or expression of reverence and adoration for a deity

    dog·ma /ˈdôgmə/

    Noun:A principle or set of principles laid down by an authority as incontrovertibly true

    I would suggest that the object of worship does not need to be a deity for the term to qualify, and in the case of the atheist the thing that replaces God is human reason. Human reason becomes the highest and most revered thing to be celebrated… or worshiped.

    And of course, the assertion that a God does not exist is just as much a dogma of atheism as any of the doctrines of Christianity. Atheism therefore has its own dogmas, just like any other category of religious belief.

    There is nothing inherently wrong with any of this. I only point this out to demonstrate that an atheistic conviction is just as much a religious bias as a conviction that God does exist.

    You can argue for evolution as an atheist or as a theist, but whichever one you choose is a philosophical conclusion, and the application of that conclusion to science is an exercise in biased interpretation of the evidence.

  245. DaFreak says:

    Isn’t that an obvious statement? In the old days people didn’t ask the right question because they thought that the sun was god or at least god’s doing. Thankfully, some people didn’t believe in gods and they did start asking the right questions. They figured it out, the gap got moved and so the gods had to move with it. There was no more room for older gods so mankind invented invisible gods beyond logic and now those gods are moving with the still existing gaps. IDers moved their god to the now rapidly closing gap in biology which means that just like our ancestors who couldn’t see the sun for what it really was because they chose their god over natural explanations, so IDers can’t see life for what it really is for the same reason. The sun was not some god or a 2D backdrop, it turned out to be a complex nuclear fusion engine. IDers can’t and don’t want to see the beauty of nature’s complexity that actually produced biology because it would mean that they would have to move their god to the next gap (physics & cosmology). As soon as you say “god did it” you stop looking for answers and just end up burying your head in the sand. That’s why we keep stressing you have to leave gods out of it. IDers think that just mentioning the word god explains something while it’s just a label that has no real meaning.

    As for references; amino acids have even been detected in space… The Miller–Urey experiment has shown that it’s pretty easy to create amino acids. When you have a bunch of atoms bumping into each other under violent conditions, interesting things are bound to happen.

  246. Rajini Rao says:

    Scott Hatch , thanks! I would only block someone if I feel threatened in a direct way, fortunately that has not happened to me here on G+. If I think a comment is totally inappropriate, I delete it. I don’t want to curtail free speech in any form, although I have learned from this experience and hope to better moderate the discussion in the future. Thanks for your support!

  247. LOL – I was about to respond to some one else’s responce to a previous coment of mine, but then realized that some how we went from ATP to DNA and whether or not it could happen on its own (which it obviously can – who knows about aliens coming down later to alter human DNA, I doubt it, but maybe – but amino acids, proteins, blah, blah, blah, LIFE can and probably did happen all by itself – but I digress). And I thought, I’m not going to bother, it has nothing to do with the topic and regardless of what I think, others believe just as strongly about what they think, and who am I to stop them. Then I read the three posts about people going off topic. That made me LOL, and now I LOL again as I realize I am still posting something off topic

  248. auuuugggggghhhh – the more I read comments I read the more I have to respond.

    DNA is not complex at all, its just something we dont have a 100% grasp on yet. by which I mean to say, DNA Itself is very very simple. What it does is what is complex. But its simple to understand how something so simple can become so complex.

    DNA can on only link together a few different ways – its like binary. Randomly hit your 0 & 1 button 8 times, and its gonna result in a number between 1 and 64 every single time. Lets say you need a 27 to get a single celled organism. If you randomly hit your 0 or your 1, just one number, once a day, every day, for 14 BILLION years, eventually you are going to get a 00100111, and then bam, and then 27 starts adding on, maybe it turns out if a 27 & 1 does nothing, 27 & 2 is weak, 27 & 3 is sluggish – but turns out 27 & 36 make it able to link together with other cells. Again, stretch this out for a billion years or so – eventually you end up with 27, 36, 52, 47, 19, 62 – or in binary, 00100111 00110110 01010010 01000111 00011001 01100010 – is it really complex? No, its just random crap. The good stuff is able to continue, the bad stuff either finds a nitch or dies off (or gets killed off). Its just been going on for a really really long time, and the actual list of 0’s and 1’s is quite a bit longer then this post, but thats all it is.

  249. Jethro Reeve says:

    Rajini Rao about as ridiculous to be honest. can you please tell me how to tag people in the comments? lol

  250. Rajini Rao Is there a way to speed up / increase the rate at which the bonds are broken without having to input work? I was thinking of it as a way to lose weight for those people who won’t take exercise.

  251. Rajini Rao says:

    I like the way you think, David Bennett ! Actually, the bond making/breaking step is not the energy requiring step, surprisingly, because of the way the molecule is held in the “transition state”. The energy cost comes from having to kick out the newly made ATP from its tightly bound state.

    In any case, this has nothing to do with your question. Your cells can indeed “burn” energy to produce heat without doing useful work. This is done in “brown fat” (found between our shoulder blades, in babies and hibernating animals). Brown fat is packed with mitochondria (which are brown) and contain a special uncoupling protein that shunts the proton gradient. If you remember, I mentioned that the ATP synthase is driven by a proton gradient (which in turn is generated during the course of oxidizing carbohydrate in the mitochondria). The protons gradient is dissipated by creating a hole in the membrane so that it can no longer be harnessed by the ATP synthase. It is quite a clever idea to produce heat. If we found a way to increase brown fat (instead of white fat), we could (in theory) merrily overindulge during the upcoming holidays and save on our heating bill as well 🙂

  252. daniel wyatt says:

    I happened purely by accident. The animation was working at the time…might i find it somewhere else (the moving model)?

    Im new to google and what is apparently your blog (at least that was a friends characterization), but was delighted by the content and wish to follow.

    You had a great quote about ‘the miraculous’, in the string/blog, but it took me some time to navigate back. I finally ‘searched’ ATP,and miracle of miracles, found the material.

    I dig it, hope u will continue to amaze, educate and, lastly, tell me of a better way to access the’blog’ less general than ‘search’.

    My name is Dan Wyatt, and you ar a phenom-thanks

  253. Rajini Rao says:

    Hi daniel wyatt , welcome to Google+. Since I’m in your circles, any content that I post will appear on your “stream” don’t need to search for it 🙂 Is the animated gif not working? I got it from the web page of Dr. John Walker:

    If you have any general Google+ questions, don’t be afraid to ask. Circle lots of interesting people for great content and enjoy.

  254. is it real? I mean it´s incredible!!

  255. Ye Sean says:

    Oh, There are two butterfly.

  256. Rajini Rao Sorry to take so long to come back to you on this – the film reminds me of flagella – the way they move – and don’t Finns have more brown fat than other Europeans?

  257. Rajini Rao says:

    David Bennett , I’ve been meaning to follow up on a lot of comments here too, but still have not got around to it. Flagella are much larger and even more complex although they do also use proton flow to drive the rotor.

    Do you think the Finns have more brown fat because they hibernate during the long cold winter? 🙂

  258. Tks for picture change. TORNADIC ACTION? Is This a pic or animation? Would like to correspond with you can you give me a email address?

  259. Rajini Rao says:

    Kasia Jarmołkowicz , Google it! 😉 Start with references in Wiki and go from there: Try it, it’s fun.

  260. Here comes it – my favorite ATP synthase from mitochondria. Thank you Rajini.

  261. Marc Cox says:

    Very interesting stuff …

    Hmmm… recalling ATP was part of photosynthesis( “Kreb’s cycle” ?) and Mitochondria have their own DNA separate from the central nuclear DNA which just now made me scratch my head and think wow – way too improbable for mere coincidence here …

    Well it seems has forwarded this theory advancing symbiotic coevolution :

    Ok, here’s some extra credit question 4u science geeks (nope I dunno the answers)

    A.) what, if any, is the difference between the cellular ATP cycle

    and the chloroplast ATP cycle both chemically and physically/physiologically ?

    B.) Do chloroplasts have Mitochondria ? If not why not ? (ok, only God knows the 2nd answer 4sure so defensible SWAGs are acceptable answers)

    C.) If chloroplasts DO have Mitochondria, run the maternal Mitochondrial DNA “clock”

    backward to project an approximate date of plants and animals common mother/ancestor.

    ( BONUS: If your projection predates the evolution of bacteria you get to email a REAL sarcastic and snarky letter ridiculing their theory ! )

    D.) Create a family tree of all bacterial/cellular structures (co)evolution in a timeline, especially highlighting the points of convergence or divergence of physical structures in the family tree.

    WOAH – I just noticed ATP synthase was the subject of +Rajini Rao ‘s Ph.D. thesis and was her “first love” so she may very well actually answer all this !

    That would be very cool !

    Ok noticed this from +Rajini Rao – “because .. can see the shared sequences between chloroplast/mitochondrial ATP synthases and that of eubacteria because of their endosymbiotic relationship.” – indicates she’s already ‘there’ to some extent ;

    STILL I’m pretty sure diagramming the actual MACROscopic TIMEline could raise some

    MORE interesting questions …


  262. Yong Tian says:

    It’s so interesting! I have learned it. But this is the first time to see it!

  263. I followed the link to the original article, but I can’t figure out the license that covers the image. I would like to put the image up on the article. Do you happen to know what license applies?

  264. Rajini Rao says:

    I love to teach this stuff, Aida Hazlan . Currently, I give lectures on ion pumps and channels to PhD and medical students 🙂

  265. Rajini Rao says:

    I have a nice calcium pump post with a similar animation..let me find it for you.

  266. Lars Mith says:

    And this molecular machine evolved ?

  267. Rajini Rao says:

    Yes, Lars Mith . Evolution occured over 3-4 billion years. That’s a lot longer ..than, say 6000 years 😉

  268. Rajini Rao: In a quick search this morning, I found myself reading an older post on photostable molecules in relation to the origins of life from; thus, I’ve been led to the dynamics of photoionization and the photoelectron spectra of adenine. Do you have any suggestions as to where I could find more information on such studies, as I am a budding philosopher of science, and recently found myself enthralled in ATP synthase? Hopefully this won’t prove to be a complete waste of your time.

  269. Rajini Rao says:

    How interesting, Erin-Kayla Love ! I can’t say that I’m an expert on photoionization. Do you have a link to the article you read on abiogenesis?

  270. Rajini Rao: The first post, which is the one I’ve previously mentioned, came from

    This article led me to photostable molecules, which I found minimal information (most likely due to my lack of experience in this field) in an older post from

  271. Congratulations to Sir John Walker and his team for this amazing discovery!

    “The Royal Society, the UK’s national academy of science, today (10 July 2012) announced that Professor Sir John Walker FRS has been awarded the Copley Medal, which is believed to be the world’s oldest scientific prize. Sir John receives the medal for his ground-breaking work in understanding what powers living cells.Congratulations to Sir John Walker and his team for this amazing discovery.” 

    Sir John Walker describes his life & work in an earlier interview :

  272. Rajini Rao says:

    Thanks for the information and link to the interview, Iain Macadair !

  273. So this is a funny picture I found a long time ago. The site had more of these, but this is one of the only I saved. Sadness. But here it is, for you all to see!

    (Totally relevant to this thread, by the way. And possibly NSFW due to strong language.)

  274. Rajini Rao says:

    Jacob Taylor , that was hilarious, thanks for the link. My thesis defense on ATP synthase was a bit more restrained 😉

  275. Rajini Rao Only a bit!? 😀

  276. Rajini Rao says:

    Haha, thankfully no video evidence in existence. You younger folks, Jacob Taylor , have to be more careful 🙂

  277. Rajini Rao says:

    Herrin Larkan , the comment thread was quite a wild ride 🙂

    To answer your question..there are many motors in biology that generate mechanical energy, if that is what you are asking? For example, myosin and kinesin move muscle filaments in muscle contraction and cargo along railroad tracks in the cell, respectively. If you mean generation of ATP, then the ATP synthase is the main source although small amounts are made as side products of breaking down glucose in glycolysis.

  278. wow!!!! that was fantastic!!

  279. Happy Birthday (soon) Rajini!!


  280. doc Jayson says:

    Although this post has been out for a while it still continues to be newly discovered for those recently introduced to G+ and science. Thank you Rajini Rao Allison Sekuler and Robby Bowles for maintaining the spark of science.

  281. Anand V.L. says:

    Not forgetting how mind-blowing this post is,, it’s so wonderful how all the fields of science come together here : thermodynamics, molecular biology, mechanics and physics. Reminds us that everything is the same.

  282. Sam Sharma says:

    #Science  is tooooo #cool  and this is why… #biology  is a fascinating subject.

  283. Awesome that this post is still getting +s and comments after all this time Rajini Rao !

  284. Sivam Sivam says:

    Realy impression all science info good

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