Nature abhors a gradient
November 4, 2005 4:09 AM Subscribe
Nature abhors a gradient. So I was reading about the latest developments in the Behe Panda trial and I came across a link to this way of thinking, in essence that the 2nd law of thermodynamics is the guiding force behind complexity (summarised here). Like any good scientific theory, they have a blog but can they explain the Tuatara, which seems a little lacking in contemporary gradient reduction?
Surely He could have done better, unless He has a bizarre and malevolent sense of humor.
I prefer to think He is not malevolent, but I don't put bizarre past Him. A bizarre sense of humour would explain a lot.
posted by three blind mice at 4:22 AM on November 4, 2005
I prefer to think He is not malevolent, but I don't put bizarre past Him. A bizarre sense of humour would explain a lot.
posted by three blind mice at 4:22 AM on November 4, 2005
The question was, to be honest, a little flip, but what I meant was a creature that has changed little in 225 million years might be a case against a guiding force in evolution. I'm no scientist, however, and I hoped any metafilter boffins present might assist me in separating wheat from chaff.
In an unrelated note that I figured wasn't worth FPhood (live or die on it own merits kind of thing), but is mildly interesting, one of the authors is Carl Sagan's kid, Dorion.
posted by Sparx at 4:29 AM on November 4, 2005
In an unrelated note that I figured wasn't worth FPhood (live or die on it own merits kind of thing), but is mildly interesting, one of the authors is Carl Sagan's kid, Dorion.
posted by Sparx at 4:29 AM on November 4, 2005
A creature that "hasn't changed in 225 million years" is simply one that has found a survival niche that happens to have lasted for that long. It's not to be expected for most species, but there's nothing rule-breaking about it.
posted by rxrfrx at 4:42 AM on November 4, 2005
posted by rxrfrx at 4:42 AM on November 4, 2005
I'm wondering how this is different from Schroedinger's Negative Entropy model, from his book "What Is Life?"
posted by gsb at 5:03 AM on November 4, 2005
posted by gsb at 5:03 AM on November 4, 2005
Why does energy-based entropy dissipation outweigh matter-based entropy dissipation?
posted by sandking at 5:39 AM on November 4, 2005
posted by sandking at 5:39 AM on November 4, 2005
By far the most interesting part of life for me is the self-organizing principle of hydrophobic membranes within polar environments. Everyone "knows" that fatty things abhor water and tend to clump together, but understanding why they do this is a lot more difficult. It has to do with local changes in entropy, basically altering the solvation shell of polarised water molecules within a bounded volume drives the system. Basically, it's a higher entropy state to have lots of water molecules aligned roughly uniformly along a single vast membrane rather than to have a system consisting of many millions of tiny solvation shells aligned sphewrically around billions of lipid molecules.
The way that a drive towards greater disorder can paradoxically "create" local ordered membranes because of water's minute local polarity is to me a magnificent and subtlye example of how barely comprehensible atomic structures affect the macroscopic world. That it can also have to do with the partial formation or transformation between planar and tetrahedral electron orbitals demonstrates that natural selection is sensitive even to the exquisitely abstruse facets of quantum chemistry. Which is pretty damn impressive.
I also suspect that local thermodynamics can account for some anomalous membrane protein flippings and other highly improbable events. And I still don't really get how it is that ion channels can discharge their positive ions against a concentration gradient without an obvious influx of energy. I suspect, again, local solvation dynamics providing the probability "hump" for the transaction.
posted by meehawl at 5:44 AM on November 4, 2005
The way that a drive towards greater disorder can paradoxically "create" local ordered membranes because of water's minute local polarity is to me a magnificent and subtlye example of how barely comprehensible atomic structures affect the macroscopic world. That it can also have to do with the partial formation or transformation between planar and tetrahedral electron orbitals demonstrates that natural selection is sensitive even to the exquisitely abstruse facets of quantum chemistry. Which is pretty damn impressive.
I also suspect that local thermodynamics can account for some anomalous membrane protein flippings and other highly improbable events. And I still don't really get how it is that ion channels can discharge their positive ions against a concentration gradient without an obvious influx of energy. I suspect, again, local solvation dynamics providing the probability "hump" for the transaction.
posted by meehawl at 5:44 AM on November 4, 2005
This is an interesting theory that I haven't heard much about. Thanks for the links, Sparx.
To answer the question, I don't really see how living fossils somehow undermine the case made about evolution and the 2nd law of thermodynamics. As far as I know, evolution says nothing of the necessity of change, it just explains why certain change occurs.
That said, the dominant form of life on earth hasn't changed appreciably over a period much longer than 225 million years. Because we are such macrofauna, we are completely biased in our attention towards species of similar scale, to say nothing of our affinity for vertebrates, or even mammals. This leads us to largely ignore what is unquestionably the dominant form of life on the planet. Evolution may lead to new and fantastic designs on our scale, but I don't think we should forget what is by far the most successful life on earth. In biomass, it exceeds all other life, in diversity, unmatched. It inhabits every conceivable niche in which life is known to exist. It is also far older than all other life on earth. Bacteria is the dominant life form on Earth.
I must admit, before my first year microbiology class enlightened me, I failed to understand the depth of my multicellular chauvinism. Now, of course, I realise that in order to understand the mind of god, we have to understand god's plan for life. From this, I can only conclude that we are some bizarre, gargantuan, overspecialised and chronically self absorbed side effect.
God chose bacteria to rule this world, and so it has been, from the earliest days of life. This is abundantly clear. Adjust your belief systems accordingly.
Thank you, that is all.
posted by [expletive deleted] at 5:45 AM on November 4, 2005
To answer the question, I don't really see how living fossils somehow undermine the case made about evolution and the 2nd law of thermodynamics. As far as I know, evolution says nothing of the necessity of change, it just explains why certain change occurs.
That said, the dominant form of life on earth hasn't changed appreciably over a period much longer than 225 million years. Because we are such macrofauna, we are completely biased in our attention towards species of similar scale, to say nothing of our affinity for vertebrates, or even mammals. This leads us to largely ignore what is unquestionably the dominant form of life on the planet. Evolution may lead to new and fantastic designs on our scale, but I don't think we should forget what is by far the most successful life on earth. In biomass, it exceeds all other life, in diversity, unmatched. It inhabits every conceivable niche in which life is known to exist. It is also far older than all other life on earth. Bacteria is the dominant life form on Earth.
I must admit, before my first year microbiology class enlightened me, I failed to understand the depth of my multicellular chauvinism. Now, of course, I realise that in order to understand the mind of god, we have to understand god's plan for life. From this, I can only conclude that we are some bizarre, gargantuan, overspecialised and chronically self absorbed side effect.
God chose bacteria to rule this world, and so it has been, from the earliest days of life. This is abundantly clear. Adjust your belief systems accordingly.
Thank you, that is all.
posted by [expletive deleted] at 5:45 AM on November 4, 2005
meehawl- I don't think it's really so amazing that you create "ordered" structures like membranes by increasing total microscopic entropy, because those structures are only "ordered" when you look from very far away. I mean, in reality, if you could look close enough, you'd only need to look at the inside of the bilayer and the area just outside to see that there's a whole lot of motion going on on the aqueous side, and that's not exactly very "ordered."
posted by rxrfrx at 5:51 AM on November 4, 2005
posted by rxrfrx at 5:51 AM on November 4, 2005
Also {insert comment here about watching laymen discuss science on the internet}
posted by rxrfrx at 5:52 AM on November 4, 2005
posted by rxrfrx at 5:52 AM on November 4, 2005
I believe the question was whether a living fossil disproved the existence of a guiding force in evolution, and this I assume to mean: does it disprove ID?
Well, shit, what doesn't?
posted by mek at 6:01 AM on November 4, 2005
Well, shit, what doesn't?
posted by mek at 6:01 AM on November 4, 2005
does it disprove ID?
I was under the impression that most creationists don't believe the earth is anywhere near 225 million years old, so it's kind of a moot point.
posted by rxrfrx at 6:03 AM on November 4, 2005
I was under the impression that most creationists don't believe the earth is anywhere near 225 million years old, so it's kind of a moot point.
posted by rxrfrx at 6:03 AM on November 4, 2005
Don't conflate ID and strict biblical creationism, or any sense of creationism for that matter.
posted by mek at 6:21 AM on November 4, 2005
posted by mek at 6:21 AM on November 4, 2005
Don't conflate ID and strict biblical creationism, or any sense of creationism for that matter.
I will, in fact, do the latter. Are you arguing that we should believe the universe was "designed" but not "created" by a supernatural force?
posted by rxrfrx at 6:27 AM on November 4, 2005
I will, in fact, do the latter. Are you arguing that we should believe the universe was "designed" but not "created" by a supernatural force?
posted by rxrfrx at 6:27 AM on November 4, 2005
Also {insert comment here about watching laymen discuss science on the internet}
Ok, there was this guy and he came to an online forum and while he had no credentials he said, "maybe since entropy is just another physical phenomenon, like heat, the negative entropy associated with evolutionary genetic improvement isn't as great an absolute quantity as the positive entropy associated with a compost heap"
posted by nervousfritz at 6:27 AM on November 4, 2005
Ok, there was this guy and he came to an online forum and while he had no credentials he said, "maybe since entropy is just another physical phenomenon, like heat, the negative entropy associated with evolutionary genetic improvement isn't as great an absolute quantity as the positive entropy associated with a compost heap"
posted by nervousfritz at 6:27 AM on November 4, 2005
I mean, in reality, if you could look close enough, you'd only need to look at the inside of the bilayer and the area just outside to see that there's a whole lot of motion going on on the aqueous side, and that's not exactly very "ordered."
That's why I said it was paradoxical. How it comes to be that from a microscopic perturbation in the relative quantity of disorder on either side of a bilayer only a few hundred atoms thick we arrive at you, posting on metafilter, is a wonder. And the fact that the local environment of a bilayer is by its nature asymmetric and dissimilar is also fascinating. I refer you here for some of the unanswered questions about membrane evolution":
Replicating vesicles as models of primitive cell growth and division.
I'm amazed at how people take bilayers for granted. Their genesis and evolution is still far from completely understood. Which came first, RNA or bilayer? Or did they both emerge. Can bilayers code for their replication without nucleic acids or precursors? Do they require the increasing osmotic pressure from replicating nucleic acids to drive their budding, and eventual evolution? Could there have been a "bilayer world" before the RNA world?
And in the end it is, as I mentioned, driven by changes in the entropic microstates within local domains. I'm impressed that you have such a gut feel for the mechanisms of entropy and its consequences, but I remain in wonder. I suppose next you're going to tell me that protein folding is "no big thing"?
posted by meehawl at 6:30 AM on November 4, 2005
That's why I said it was paradoxical. How it comes to be that from a microscopic perturbation in the relative quantity of disorder on either side of a bilayer only a few hundred atoms thick we arrive at you, posting on metafilter, is a wonder. And the fact that the local environment of a bilayer is by its nature asymmetric and dissimilar is also fascinating. I refer you here for some of the unanswered questions about membrane evolution":
Replicating vesicles as models of primitive cell growth and division.
I'm amazed at how people take bilayers for granted. Their genesis and evolution is still far from completely understood. Which came first, RNA or bilayer? Or did they both emerge. Can bilayers code for their replication without nucleic acids or precursors? Do they require the increasing osmotic pressure from replicating nucleic acids to drive their budding, and eventual evolution? Could there have been a "bilayer world" before the RNA world?
And in the end it is, as I mentioned, driven by changes in the entropic microstates within local domains. I'm impressed that you have such a gut feel for the mechanisms of entropy and its consequences, but I remain in wonder. I suppose next you're going to tell me that protein folding is "no big thing"?
posted by meehawl at 6:30 AM on November 4, 2005
k, there was this guy and he came to an online forum and while he had no credentials he said
hey that guy was like cool and stuff.
I suppose next you're going to tell me that protein folding is "no big thing"?
First of all, physics definitely blows my mind. What is matter? What is energy? Do we "really exist?" I have no fucking clue. It always makes my head hurt when I think about it.
However, having said that, once we take certain physical principles for granted (e.g. conservation of mass/energy, thermodynamic rules), protein folding and lipid layer organization doesn't seem like a big thing at all. I mean, it's cool and everything, but it doesn't seem any more special than a delicious sandwich.
posted by rxrfrx at 6:36 AM on November 4, 2005
hey that guy was like cool and stuff.
I suppose next you're going to tell me that protein folding is "no big thing"?
First of all, physics definitely blows my mind. What is matter? What is energy? Do we "really exist?" I have no fucking clue. It always makes my head hurt when I think about it.
However, having said that, once we take certain physical principles for granted (e.g. conservation of mass/energy, thermodynamic rules), protein folding and lipid layer organization doesn't seem like a big thing at all. I mean, it's cool and everything, but it doesn't seem any more special than a delicious sandwich.
posted by rxrfrx at 6:36 AM on November 4, 2005
I will, in fact, do the latter. Are you arguing that we should believe the universe was "designed" but not "created" by a supernatural force?
I'm not arguing for any form of ID, but what's any more absurd about making that specific argument? Say someone believes in ID and believes the universe is infinitely old. Seems consistent enough. Anyway, metaphysical wanking.
posted by mek at 6:56 AM on November 4, 2005
I'm not arguing for any form of ID, but what's any more absurd about making that specific argument? Say someone believes in ID and believes the universe is infinitely old. Seems consistent enough. Anyway, metaphysical wanking.
posted by mek at 6:56 AM on November 4, 2005
I also suspect that local thermodynamics can account for some anomalous membrane protein flipping and other highly improbable events.
Remember, Entropy of a state basically means 'the number of microstates in a macrostate'.
Think of a tray of 64 pennies. The most entropicaly favorable state is to have 32 heads up and 32 tails up. There are a huge number of possible arrangements of I think it's something like 231, but I could be way off.
Now, on the other hand, there are only 64 arrangements with just one penny face up, and only one arraignment with all pennies face up.
But, the fewer pennies you have, the fewer total microstates you'll have. There are 2n total micro states.
So, if you have only 3 pennies, the probability of having all of them face up is only 1/8.
It's the same with molecules. The fewer molecules involved in a system, the lest 'thermodynamically' it behaves.
posted by delmoi at 7:06 AM on November 4, 2005
Remember, Entropy of a state basically means 'the number of microstates in a macrostate'.
Think of a tray of 64 pennies. The most entropicaly favorable state is to have 32 heads up and 32 tails up. There are a huge number of possible arrangements of I think it's something like 231, but I could be way off.
Now, on the other hand, there are only 64 arrangements with just one penny face up, and only one arraignment with all pennies face up.
But, the fewer pennies you have, the fewer total microstates you'll have. There are 2n total micro states.
So, if you have only 3 pennies, the probability of having all of them face up is only 1/8.
It's the same with molecules. The fewer molecules involved in a system, the lest 'thermodynamically' it behaves.
posted by delmoi at 7:06 AM on November 4, 2005
However, having said that, once we take certain physical principles for granted (e.g. conservation of mass/energy, thermodynamic rules), protein folding and lipid layer organization doesn't seem like a big thing at all. I mean, it's cool and everything, but it doesn't seem any more special than a delicious sandwich.
I agree.
posted by delmoi at 7:07 AM on November 4, 2005
I agree.
posted by delmoi at 7:07 AM on November 4, 2005
I think we're all ignoring the improbability postulate here. It's clear from Scheinhuffs work that only an inversion on the entropic axis could possibly generate these sorts of results. I'd be hesitant to draw any conclusions, but it looks like a classic Weinfred curve response. If you want more information check out Smith & Weinbergers research at MIT (sorry, can't find a decent link right now).
posted by blue_beetle at 12:16 PM on November 4, 2005
posted by blue_beetle at 12:16 PM on November 4, 2005
What if you reversed the polarity of the neutron flow?
posted by growli at 12:59 PM on November 4, 2005
posted by growli at 12:59 PM on November 4, 2005
Very funny blue beetle.
it doesn't seem any more special than a delicious sandwich
Oh such jaded people.,
Sandwichs don't spontaneously invert and interconvert their conformation. But I still haven't seen a good explanation for how, say, dolichol phosphate manages to flip so quickly through multiple layers, especially when you consider the torque resulting from all the carbs hanging off it.
It's all very well to say "oh it's entropically favourable", but so what? That doesn't tell you anything about the kinetics. Life happens at a perceptible rate because the organic reactions are happening at a rate many, many, many orders of magnitude above where they would be without exquisitely shaped molecules leveraging bizarre and spooky quantum effects. That is the real mystery of life, and to imagine that it's easily explainable at our current stage of knowledge is just postmodern hubris.
posted by meehawl at 1:14 PM on November 4, 2005
it doesn't seem any more special than a delicious sandwich
Oh such jaded people.,
Sandwichs don't spontaneously invert and interconvert their conformation. But I still haven't seen a good explanation for how, say, dolichol phosphate manages to flip so quickly through multiple layers, especially when you consider the torque resulting from all the carbs hanging off it.
It's all very well to say "oh it's entropically favourable", but so what? That doesn't tell you anything about the kinetics. Life happens at a perceptible rate because the organic reactions are happening at a rate many, many, many orders of magnitude above where they would be without exquisitely shaped molecules leveraging bizarre and spooky quantum effects. That is the real mystery of life, and to imagine that it's easily explainable at our current stage of knowledge is just postmodern hubris.
posted by meehawl at 1:14 PM on November 4, 2005
meehawl writes "Life happens at a perceptible rate because the organic reactions are happening at a rate many, many, many orders of magnitude above where they would be without exquisitely shaped molecules leveraging bizarre and spooky quantum effects. "
Wha? Catalysis is pretty well understood, and you don't need any "bizarre and spooky quantum effects" to explain it. Briefly, the catalyst stabilizes the transition state (which says everything about kinetics). Those molecules are "exquisitely shaped" because this stabilization often comes in the form of a geometric arrangement that's favorable to the transition state.
posted by mr_roboto at 2:36 PM on November 4, 2005
Wha? Catalysis is pretty well understood, and you don't need any "bizarre and spooky quantum effects" to explain it. Briefly, the catalyst stabilizes the transition state (which says everything about kinetics). Those molecules are "exquisitely shaped" because this stabilization often comes in the form of a geometric arrangement that's favorable to the transition state.
posted by mr_roboto at 2:36 PM on November 4, 2005
I'm aware of the transition state analog theory for catalytic mechanism, and of the Hammond Postulate.
I must say that it impresses me immensely that the author of such papers as A smart microfluidic affinity chromatography matrix composed of poly(N-isopropylacrylamide)-coated beads and Molecular basis for asymmetrical growth in two-dimensional streptavidin crystals has managed to keep his sense of wonder about the natural world relatively intact. Well done Sir! I applaud you.
posted by meehawl at 8:31 PM on November 4, 2005
I must say that it impresses me immensely that the author of such papers as A smart microfluidic affinity chromatography matrix composed of poly(N-isopropylacrylamide)-coated beads and Molecular basis for asymmetrical growth in two-dimensional streptavidin crystals has managed to keep his sense of wonder about the natural world relatively intact. Well done Sir! I applaud you.
posted by meehawl at 8:31 PM on November 4, 2005
I'm aware of the transition state analog theory for catalytic mechanism, and of the Hammond Postulate.
I must say that it impresses me immensely that the author of such papers as A smart microfluidic affinity chromatography matrix composed of poly(N-isopropylacrylamide)-coated beads and Molecular basis for asymmetrical growth in two-dimensional streptavidin crystals has managed to keep his sense of wonder about the natural world relatively intact. Well done Sir! I applaud you. May your battle against adjectives long continue.
posted by meehawl at 8:33 PM on November 4, 2005
I must say that it impresses me immensely that the author of such papers as A smart microfluidic affinity chromatography matrix composed of poly(N-isopropylacrylamide)-coated beads and Molecular basis for asymmetrical growth in two-dimensional streptavidin crystals has managed to keep his sense of wonder about the natural world relatively intact. Well done Sir! I applaud you. May your battle against adjectives long continue.
posted by meehawl at 8:33 PM on November 4, 2005
Double post. So sorry. Exhibiting, I might add, a slight degree of aptameric evolution.
posted by meehawl at 8:34 PM on November 4, 2005
posted by meehawl at 8:34 PM on November 4, 2005
meehawl, going back to your comment about "oh it's entropically favourable" and "so what." I think it's important to remember that entropy can be measured, and that its relationship with several variables is well known -- regarding Gibbs Free Energy.
Also, quantum effects are important, but so far the methodology to dissect transition states are valid and testable, despite the lack of quantum information. I don't think it's possible to stop at any point and say we know everything, and I have yet to meet a scientist who believes that. Then again, there are many mysteries, as you mention, but tractable solutions to these mysteries are important and *do occur*.
posted by gsb at 10:20 PM on November 4, 2005
Also, quantum effects are important, but so far the methodology to dissect transition states are valid and testable, despite the lack of quantum information. I don't think it's possible to stop at any point and say we know everything, and I have yet to meet a scientist who believes that. Then again, there are many mysteries, as you mention, but tractable solutions to these mysteries are important and *do occur*.
posted by gsb at 10:20 PM on November 4, 2005
meehawl writes "I'm aware of the transition state analog theory for catalytic mechanism, and of the Hammond Postulate."
Why were you acting like you aren't, then?
Of course, if you have done work that proves current theory is insufficient, and that catalysis must be explained by "bizarre and spooky quantum effects", science eagerly awaits your revolution....
ps. My next paper is going to be about lipids!!!!
pps. That "adjectives" thing went totally over my head. Sorry.
posted by mr_roboto at 10:59 PM on November 4, 2005
Why were you acting like you aren't, then?
Of course, if you have done work that proves current theory is insufficient, and that catalysis must be explained by "bizarre and spooky quantum effects", science eagerly awaits your revolution....
ps. My next paper is going to be about lipids!!!!
pps. That "adjectives" thing went totally over my head. Sorry.
posted by mr_roboto at 10:59 PM on November 4, 2005
Why were you acting like you aren't, then
I think you have me confused with someone else.
"bizarre and spooky quantum effects"
That "adjectives" thing went totally over my head
Even though I often work with those fiddly little things, I personally have never ceased to find the behaviour of atoms and electrons bizarre and spooky. Then again, I often find myself marvelling at the fluid flow from the kitchen tap, much to the annoyance of my wife. YMMV.
Let me see, I saw couple of papers recently about spin coupling and its possibly relation to ligand binding that illustrates nicely how "spooky" effects can influence something as mundane as haemoglobin affinity...
A direct method for locating minimum-energy crossing points (MECPs) in spin-forbidden transitions and nonadiabatic reactions.
Ground- and excited-state electronic structure of an iron-containing molecular spin photoswitch.
--
Then again, there are many mysteries, as you mention
Yes. For example, one of them was how the classic Phillips mechanism for lysozyme could function as efficiently as it does. I believe this problem was somewhat resolved several years ago when it was discovered that the Asparagine 52 residue was actually forming an intermediate covalent bond and not just relying on weak interactions to perform cleavage. This mechanism is probably shared by many or most serine proteases. That is progress.
posted by meehawl at 6:58 AM on November 5, 2005
I think you have me confused with someone else.
"bizarre and spooky quantum effects"
That "adjectives" thing went totally over my head
Even though I often work with those fiddly little things, I personally have never ceased to find the behaviour of atoms and electrons bizarre and spooky. Then again, I often find myself marvelling at the fluid flow from the kitchen tap, much to the annoyance of my wife. YMMV.
Let me see, I saw couple of papers recently about spin coupling and its possibly relation to ligand binding that illustrates nicely how "spooky" effects can influence something as mundane as haemoglobin affinity...
A direct method for locating minimum-energy crossing points (MECPs) in spin-forbidden transitions and nonadiabatic reactions.
Ground- and excited-state electronic structure of an iron-containing molecular spin photoswitch.
--
Then again, there are many mysteries, as you mention
Yes. For example, one of them was how the classic Phillips mechanism for lysozyme could function as efficiently as it does. I believe this problem was somewhat resolved several years ago when it was discovered that the Asparagine 52 residue was actually forming an intermediate covalent bond and not just relying on weak interactions to perform cleavage. This mechanism is probably shared by many or most serine proteases. That is progress.
posted by meehawl at 6:58 AM on November 5, 2005
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posted by rxrfrx at 4:22 AM on November 4, 2005