tag:blogger.com,1999:blog-1513704378254120283.post1957094847722015697..comments2024-01-23T13:58:48.688-08:00Comments on The Trenches of Discovery: The human machine: biological batteries and motorsShaun Hotchkisshttp://www.blogger.com/profile/04832423210563130467noreply@blogger.comBlogger11125tag:blogger.com,1999:blog-1513704378254120283.post-42768222601430525282012-06-22T02:25:31.119-07:002012-06-22T02:25:31.119-07:00Fair enough.
I assume dark energy must be much bi...Fair enough.<br /><br />I assume dark energy must be much bigger in their part of the multiverse. Our universe's cosmological constant wouldn't be particularly useful as an evil force given that it wouldn't even come close to being able to lift the lightest feather.Shaun Hotchkisshttps://www.blogger.com/profile/04832423210563130467noreply@blogger.comtag:blogger.com,1999:blog-1513704378254120283.post-28910351773168244602012-06-22T01:15:55.216-07:002012-06-22T01:15:55.216-07:00"The first thing to understand about the Sith...<a href="http://www.sithacademy.com/2011/09/11/the-sith-path-an-invitation-to-the-dark-side/" rel="nofollow">"The first thing to understand about the Sith of this galaxy is that our arts manifest differently here than for the Sith of legend, because we exist in another part of the Multiverse which obeys different natural laws. In our universe, the Force may be thought of as Dark Energy, which doesn’t bind the galaxy together but drives all galaxies apart."</a>Mitchellhttps://www.blogger.com/profile/10768655514143252049noreply@blogger.comtag:blogger.com,1999:blog-1513704378254120283.post-62641332582360333742012-05-24T06:19:34.081-07:002012-05-24T06:19:34.081-07:00The Sith Lords are probably extracting power direc...The Sith Lords are probably extracting power directly from the vacuum or something using blah blah quantum key word blah blah zero point energy blah the force.Shaun Hotchkisshttps://www.blogger.com/profile/04832423210563130467noreply@blogger.comtag:blogger.com,1999:blog-1513704378254120283.post-22595816190694850222012-05-24T06:09:51.670-07:002012-05-24T06:09:51.670-07:00I've actually understated it a touch, ATP is P...I've actually understated it a touch, ATP is PART of RNA rather than just a precursor. RNA, like DNA, has 4 bases (A,C,G and U) - the A is just ATP minus two phosphate groups.<br /><br />So, just to check my working: <br />The hydrolysis of ATP to ADP+Pi has a Gibbs free energy of -30.5kJ/mol. ATP has a molecular weight of 507g/mol, so 70kg is just over 138 mol, which would therefore give 4211 kJ/day. This gives 48.7W power for a human at rest. <br /><br />I wanted to calculate how much time if would take for enough energy to flow through a human to power the kind of 'finger lightning' used by the Sith lords in Star Wars, but my physics wasn't quite up to it!<br /><br />Don't worry, you'll be in the acknowledgements.James Felcehttps://www.blogger.com/profile/14031758835739415241noreply@blogger.comtag:blogger.com,1999:blog-1513704378254120283.post-40550463646947249102012-05-24T05:47:12.529-07:002012-05-24T05:47:12.529-07:00Thanks James...
I hadn't appreciated that ATP...Thanks James...<br /><br />I hadn't appreciated that ATP played a role in RNA synthesis. That makes it much less surprising that it is the thing responsible for energy transfer.<br /><br />Also, it is agreed, the electron transport chain is cool. <br /><br />I wonder if I should go back and do a degree in Biochemistry...<br /><br />Finally, I wouldn't have believed you if you had claimed that the energy passing through my body in a life time was 25.5 megatons. I've just done my own calculation and for an 80 year lifespan that is the equivalent to 40 megawatts of power, which according to wikipedia is not that much less than the power of a small nuclear reactor). A corollary is that if we've both done our calculations correctly, a human being has about 40 watts of total power! That information must be shared...<br /><br />P.S... "your" novel..?Shaun Hotchkisshttps://www.blogger.com/profile/04832423210563130467noreply@blogger.comtag:blogger.com,1999:blog-1513704378254120283.post-37333398631991417512012-05-24T04:36:55.159-07:002012-05-24T04:36:55.159-07:00On a separate note linked to your comment about th...On a separate note linked to your comment about the MOAB; when I first did the calculation I went a bit wrong and came up with the conclusion that the energy that passes through your body over your lifetime is the equivalent of over 20 B83 nuclear bombs (i.e. 25.5 megatons, rather than 25.5 tons), which raised an eyebrow prompting me to check the figures. It would have been cool if true, though!James Felcehttps://www.blogger.com/profile/14031758835739415241noreply@blogger.comtag:blogger.com,1999:blog-1513704378254120283.post-70420422736060825712012-05-24T04:09:39.203-07:002012-05-24T04:09:39.203-07:00Saying that organisms with mitochondria 'rule ...Saying that organisms with mitochondria 'rule the planet' is a bit much, however, since the vast majority of lifeforms on Earth (in terms of both numbers and biomass) and prokaryotes and so have no mitochondria. One of the things evolutionary biologists are up to at the minute is comparing the mechanisms of ATP synthesis in different species of prokaryotes in the hope of shedding more light on the evolution of ATP synthase and the electron transport chain. One theory is that the bacteria that became mitochondria lived in an environment with a naturally occurring pH gradient that they then exploited (as some still do) to make ATP. When they were incorporated into another cell, the proton gradient had to be generated artificially and so got tied into sugar metabolism etc. <br /><br />3. I'm not trying to imply that ATP synthesis is inherently more 'quantum' than anything else - it can't be since it's made of the same components as the rest of the universe. I'm just pointing it out as an example of the point at which you can no longer explain biology with Newtonian physics. You can talk about antigen-recognition in Newtonian terms and it basically is correct, even though it's obviously just as quantum as anything else, but the electron transport chain would not work if electrons were entirely discrete particles with a finite position. I appreciate that the same is also true for all chemical reactions, but that's another area where most people think of it in conventional terms. The electron transport chain is just cool.<br /><br />4. If I do a mitochondrial back-story to my immunology novel then I think I'd have to include all other key moments in the evolution of cellular complexity! For this I'd recommend another of Nick Lane's books: 'Life Ascending: the ten great inventions of evolution'.<br /><br />5. Sure, I'll do a post in the not too distant post about what genetic engineering actually is and the (perceived and real) risks involved.James Felcehttps://www.blogger.com/profile/14031758835739415241noreply@blogger.comtag:blogger.com,1999:blog-1513704378254120283.post-25005660599936048072012-05-24T04:09:25.404-07:002012-05-24T04:09:25.404-07:00Ok, that's a lot to respond to. I'll go in...Ok, that's a lot to respond to. I'll go in the order you went in:<br /><br />1. It's true, ATP does look complicated, but it's actually not much more than a simple cyclic sugar to start with anyway; it just has the additional triphosphate and purine groups. The reason why it's used is almost certainly because it is a constituent of RNA synthesis. RNA was the primary organic molecule in very early life: it's thought that self-replicating RNA molecules were the first precursors to life. These RNAs would have a double function as the template for their own replication, and also the machinery by which it's achieved. Over time the system became more sophisticated and some RNAs would be free to take up new tasks, such as producing simple metabolic networks to allow more efficient self-replication. Eventually RNA was replaced by DNA in the data-storage capacity because of the greater chemical stability of DNA and also the need to partition transcription and translation to allow more subtle regulation of gene expression. Protein, on the other hand, took up the role of general cellular workhorse as it is made up of far more chemically diverse components and so is suited to a broader range of tasks. Nonetheless, RNA retained some catalytic role in the form of ribonucleoproteins and also reactive RNAs such as transfer RNA. The upshot of all this is that ATP and GTP (the two purinic RNA nucleotides) were originally used by catalytic RNAs in the production of more RNA and then later to power other reactions, and this is still the case today. ATP is by far the more important of the two but GTP is still required to catalyse some reactions, primarily phosphorylation reactions during cell signalling. ATP isn't inherently 'energetic', it's just that the cell keeps the ADP+Pi:ATP ratio a long way from equilibrium and so there's plenty of free energy to be extracted from its dephosphorylation.<br /><br />There are also lots of other examples of RNA nucleotides being used in important cofactors: e.g. Acetyl CoA, NADH, FADH2 etc.<br /><br />2. The role of mitochondria in all this is very interesting and is explained beautifully in Nick Lane's wonderful book: 'Power, Sex, Suicide: Mitochondria and the meaning of life'. The incorporation of mitochondria into a larger cells is arguably the most important step in the evolution of eukaryotic cells (i.e. us). Bacteria generate ATP in the same way as us, except that since they have no mitochondria they generate their proton gradient over their inner membrane, which places an inherent limit on their size because as they get bigger the surface area of their membrane decreases relative to their volume. For a cell to get large enough to have complex internal organisation the role of energy producer must be packaged up into subcellular compartments in order to get around the surface area:volume problem; i.e. mitochondria. The incorporation event is thought to have a been a one-off that then gave rise to all eukaryotes, but they had such an evolutionary advantage that they quickly diversified into myriad forms. A similar event then allowed the incorporation of a cyanobacteria into these proto-eukaryotes to give rise to chloroplasts and subsequently plants. It's worth noting, however, that both of these events will not have been clean-cut, and there was most likely a very long time where mitochondria existed partly as separate organisms and partly as symbiotes. Nick Lane gives a very nice explanation of the kind of stages that might have occurred to strengthen the symbiosis over a very long period of time.James Felcehttps://www.blogger.com/profile/14031758835739415241noreply@blogger.comtag:blogger.com,1999:blog-1513704378254120283.post-12952417183362408672012-05-23T11:17:35.117-07:002012-05-23T11:17:35.117-07:00Oh, also... if you're taking requests, how abo...Oh, also... if you're taking requests, how about genetic engineering, as well as the ethical implications of genetic engineering, and risks, etc.<br /><br />I'd be pretty keen to first read your thoughts and then ask you a bunch of questions about it. I'm not sure if it is within your range of specialisations though, so feel free to pass if it isn't.Shaun Hotchkisshttps://www.blogger.com/profile/04832423210563130467noreply@blogger.comtag:blogger.com,1999:blog-1513704378254120283.post-82631405298893128402012-05-23T09:33:11.125-07:002012-05-23T09:33:11.125-07:00Oh, also... the time when mitochondria gets absorb...Oh, also... the time when mitochondria gets absorbed into our evolutionary tree would make an awesome back-story for the novel, either in a prequel, or a story told by a character to provide context.<br /><br />BTW, I am now 20% sure that I am part of a living organism. I just have to work out what my role is...Shaun Hotchkisshttps://www.blogger.com/profile/04832423210563130467noreply@blogger.comtag:blogger.com,1999:blog-1513704378254120283.post-42991013625243701172012-05-23T09:21:55.436-07:002012-05-23T09:21:55.436-07:00And at last I reach the present...
I have quite a...And at last I reach the present...<br /><br />I have quite a few comments about this one:<br /><br />- At the moment, we only know one level under protons, that is, quarks. As far as we're aware, quarks don't have constituents. Although, there are theories where quarks are composite particles.<br />- I've always found it kind of surprising that the chemical we use to provide energy is so big and complicated. When life itself first evolved, I would have expected energy exchange to be one of the first, most important, things, so when all I knew about this was the burning of sugars I nodded my head comfortably. ATP however seems so fancy. Did mitochondria basically discover this method and then everyone else assimilated mitochondria because it was so ridiculously useful that anything that did assimilate mitochondria ruled the planet? How did mitochondria discover it? Is there any idea when, where "when" isn't so much measured in time but complexity of organisms around at the time (though time would be interesting too)?<br />- Did one organism assimilate mitochondria and then we're all descendants of that organism, or did "assimilate mitochondria" become a trait for a while, where organisms could find mitochondria and assimilate them and pass that trait to descendants? And then that trait become redundant once everyone had mitochondria in them? Or something?<br />-That MOAB really puts into perspective how explosive a nuclear bomb is. Even the "mother of all bombs" is more than a thousand times smaller than the *smallest* nuclear bombs<br />- electrons don't actually travel freely down a wire. <a href="http://en.wikipedia.org/wiki/Drift_velocity" rel="nofollow">They're surprisingly slow</a>. One electron will take hours to move one metre down a wire with a continuous current.<br /><br />I'm still confused (we've chatted about this before) about how quantum electrodynamics plays a particular role in ATP synthesis. All chemistry is based on quantum mechanics, so the bonding of all the elements in all of the molecules involved in life needs quantum mechanics. Surely, given that this stuff is occurring at the molecular scale, the passage of electrons down the chain is just a chemical process like all the rest and so no more or less "quantum". The electrons in a sugar molecule aren't ball-bearings hurtling around, but quantum wave-functions too. <br /><br />Also, it's not really full-blown QED that would be necessary to describe this process. QED certainly is the more general theory, but it is only really needed when there isn't a constant number of electrons (or photons if you're describing the light), so they must be treated as a field, rather than an individual particle. That might have been a bit confusing, I can elaborate if necessary. (by constant number of electrons I don't mean because some get lost, but because some get annihilated)<br /><br />I guess I'm nitpicking the specific mention that *this* is quantum. Everything you've talked about is quantum, because it is chemical. Even the immunology stuff is quantum, surely? The chemical processes by which T-cells recognise antigens is chemical and thus quantum, surely? How is this any more "quantum"?<br /><br />A non-quantum example would be the pressure in a blood-vein, or something...Shaun Hotchkisshttps://www.blogger.com/profile/04832423210563130467noreply@blogger.com