Freethought & Rationalism Archive

DNAunion · 07-31-2002, 06:14 PM

Quote:

DNAunion: The thread-starter dealt with the second law as it applies to biology: i.e., does biological evolution violate the second law?

This question does not deal with cosmomology (i.e., the origin, evolution, or large-scale structure of the Universe).

It also is not about physics itself, or thermodynamics itself. We aren't talking about a steam engine, or the cooling of a hot cup of tea, etc.

The question is about organisms undergoing biological evolution and how the second law applies. Note that two disciplines are involved: biology being one. Now, what area of science is devoted to the study of biology and its energy transformations? Could it be bioenergetics? You bet.

Oh, and, just for you............I WIN. :-)

Quote:

Scientiae: Oh, and you started this thread by responding directly to the challenge of whether creationists could recall the other laws of thermodynamics.

DNAunion: You seem to forget that my very first post in this thread also contained these statements:

Quote:

DNAunion: Anyway, as others here stated, no, life does not violate the second law of thermodynamics. All living organisms are open systems, taking in matter/energy from their surroundings (for example, we take in food that our bodies then catabolize for energy, which is needed to maintain - or increase - the highly ordered state of our bodies).

DNAunion: Hmmmm...do you see anything in there about the second law and biology????

[ July 31, 2002: Message edited by: DNAunion ]

Undercurrent · 08-01-2002, 07:32 AM

Quote:

Originally posted by Starboy:

I agree a frozen hamster would have lower entropy then a live one. The same thing would be true for a brick.

Yes, the laws of thermodynamics pay no heed to the living/non-living status of the systems they describe.

Quote:

The way I am using order, I think it would be somewhat proportional to the inverse of entropy. So as order increases entropy decreases. A perfect crystalline structure at absolute zero is maximally ordered, but its entropy is defined to be zero. When I say that the transition from living to the dead decreases order what I am trying to say is that such a transition increases entropy.

Yes. But so far all you've done is said it. Entropy is a perfectly good (although a bit hard to compute) number. "The function which assigns entropy values in a body to times has a jump discontinuity at the moment of death" is also a very specific statement.

If I am to understand your statement, you would be saying that the entropy of the unfortuate hamster would decrease as it is being flash frozen, but somehere in the middle of the process at "the moment of death" it would jump up and continue to fall from that point. To I understand your argument?

Interestingly, your "discontinuity in entropy" would serve quite well as a definition of "moment of death." It would certainly be helpful to the loved ones of a person on life support to then have "entropy monitors" set up around the dying. After the jump occurs, the family should have no wonderings about whether or not it would be right to remove the life support. As it is, for such people, there really is no well-defined moment of death, and people are always left wondering.

m.

Supramolecular · 08-01-2002, 08:56 AM

Hi Lentic Catachresis,

You said:
The chemical interactions between water and oil have a greater influence over the system than entropy does.

I said:
When an oil molecule is placed in water, it causes the water molecules around it to become more ordered than they would be in the bulk liquid.
When two such oil molecules come together in water they dispel several relatively ordered water molecules (due to the smaller surface area of the molecules together) thus increasing the entropy of the system.

This process is almost totally entropy driven.

You said:
If the hydrophobic effect isn't a chemical interaction then can you state why

I said:
The hydrophobic effect is an effect rather than a chemical interaction. Examples of chemical interactions between molecules are hydrogen bonds, ionic, Van Der Waals, dipole-dipole, pi-pi etc. Some of the interactions could be attractive or repulsive.
I see what you�re saying re chemical interactions, but between oil and water there are no chemical interactions apart from weak Van der Waals interactions, so there is no enthalpic benefit of an interaction between oil and water, only an entropic benefit from the release of �ordered� water.

You said:
BTW. I see you are a research scientist. What field do you work in.
And my post must be quite controversial for you to make your first post in half a year.

I said:
I don�t find your post controversial par se, only your comment that chemical interactions between water and oil have a greater influence over the system than entropy does. This process is totally entropy driven as outlined by myself and tronvillain. My PhD was in Supramolecular chemistry although now I research the solid state (polymorphism etc.)

Thanks though for prompting me to post as not only was that my first post in half a year but my first post ever on Infidels after a 12 month period of heavy lurking.

So, hello everyone. Think I�ll go and introduce myself in the introductions forum.

Starboy · 08-01-2002, 03:48 PM

Quote:

Originally posted by Michael:


Yes. But so far all you've done is said it. Entropy is a perfectly good (although a bit hard to compute) number. "The function which assigns entropy values in a body to times has a jump discontinuity at the moment of death" is also a very specific statement.

If I am to understand your statement, you would be saying that the entropy of the unfortuate hamster would decrease as it is being flash frozen, but somehere in the middle of the process at "the moment of death" it would jump up and continue to fall from that point. To I understand your argument?

Interestingly, your "discontinuity in entropy" would serve quite well as a definition of "moment of death." It would certainly be helpful to the loved ones of a person on life support to then have "entropy monitors" set up around the dying. After the jump occurs, the family should have no wonderings about whether or not it would be right to remove the life support. As it is, for such people, there really is no well-defined moment of death, and people are always left wondering.

m.

Greetings Michael,

It has been a couple of decades since I have done any statistical mechanics, so please excuse me if I am short on proof. What I am stating is as an idea and will gladly consider any argument for or against. The only thing I would add to your understanding is that the discontinuity might be in the first or higher derivatives of entropy. My na�ve reasoning for this idea is to consider the entropy of a living system to include a component that represents the order of the process of living. My intuition leads me to think that a machine that is running smoothly is more ordered than one that is running poorly or not at all. Using this primitive concept it seems natural to think that going from a running to non-running state would result and some form of discontinuity in entropy.

Starboy

DNAunion · 08-01-2002, 05:03 PM

Starboy: My naive reasoning for this idea is to consider the entropy of a living system to include a component that represents the order of the process of living. My intuition leads me to think that a machine that is running smoothly is more ordered than one that is running poorly or not at all. Using this primitive concept it seems natural to think that going from a running to non-running state would result [in] some form of discontinuity in entropy.

DNAunion: Coming more from a molecular cell biology/bioenergetics angle, I agree.

For example, a protein is more ordered than are its free constituents (amino acids) and so has a lower entropy than its individual components. If a formerly functional protein is decomposed to any degree (such as it might be at the time of death), then its entropy has increased relative to its normal state. Same goes for other biopolymers.

Living cells are highly ordered and must continually “fight” against their natural tendency to become disordered, and against the natural tendency of their chemical reactions reaching equilibrium.

Starboy · 08-01-2002, 05:20 PM

Hi DNAunion,

Yes I would agree but I am saying more than that. In the example you give, that cell that contained the protein would have lower entropy when the machinery of that cell is active (cell is alive) then that of a cell that has stopped functioning (cell is dead). This may not make sense at the cellular level since the machinery of the cell is chemistry, but maybe it makes sense if there is such a thing as ordered chemistry vs. disordered chemistry. I think at the level of an organism it may make more sense. What do you think?

Starboy

Lentic Catachresis · 08-01-2002, 05:47 PM

Hi Supramolecular:

I think the point I was trying to make, perhaps not to well in retrospect (i used the first example that came to my head), was that there are others factors to consider rather than just entropy. That is to say we cant just think of atoms/molecules as behaving in an entirely "random" manner.

I think my main point was that water/oil don't mix due to chemical interactions (or lack of) ie repulsion towards each other.
Whilst i can see my entropy/ethalpy statement is wrong I still think that my original comment that other factors influence biomolecular processes apart from entrophy still stands, and there are instances where enthalphy has a greater influence than entrophy on biological systems.

DNAunion · 08-01-2002, 06:03 PM

Quote:

Starboy: Yes I would agree but I am saying more than that. In the example you give, that cell that contained the protein would have lower entropy when the machinery of that cell is active (cell is alive) then that of a cell that has stopped functioning (cell is dead). This may not make sense at the cellular level since the machinery of the cell is chemistry, but maybe it makes sense if there is such a thing as ordered chemistry vs. disordered chemistry. I think at the level of an organism it may make more sense. What do you think?

DNAunion: I believe it was Richard Dawkins who stated “There are many more ways to be dead than there are to be alive” (or close to that). This statement applies not only to whole organisms, but to any individual cell that comprises a multicelluar organism (or to an entire unicellular organism). Doesn't this statement alone indicate, statistically, that living is a more highly ordered state than is non-living?

As far as whether or not there is such a thing as ordered chemistry, yes, there is: the “biochemistry” of a living cell is ordered chemistry.

For example, in aerobic organisms, the “infamous” FoF1-ATP synthase (which helps produce ATP during oxidative phosphorylation) is a complex molecular machine composed of multiple protein parts, which have different shapes and serve different functions. Some parts are stationary while others rotate; some parts serve as conduits for the flow of protons (which generates the rotation of the other parts); some parts bind substrates and then catalyze their conversion to ATP; some parts anchor the bottom of the machine to the membrane; and some parts fasten the top of the machine to the bottom, anchored part to prevent the whole unit from simply rotating within the membrane. And all of this relies on there being an electrochemical gradient across the membrane in which the FoF1-ATP synthase is found (a leaky membrane shuts down oxidative phosphorylation). If the highly ordered state of that molecular machine is disrupted, the cell can/will die. Same goes for other molecular machines.

Even biochemistry not directly reliant upon a molecular machine is ordered. Take glycolysis. There are (in the standard pathway) ten steps that occur during the conversion of glucose into pyruvate, and each step requires a different enzyme. And each enzyme is matched specifically to its substrate(s) by its precise, complementary three-dimensional conformation. This is ordered chemistry, and if it becomes disrupted, the cell can/will die.

Quote:

"We might, in fact, define life as a continual struggle to maintain a myriad of cellular reactions in positions far from equilibrium because at equilibrium no net reactions are possible, no energy can be released, no work can be done, and the thermodynamically improbable order of the living state cannot be maintained." (Wayne M. Becker, Jane B. Reece, & Martin F. Poenie, The World of the Cell: Third Edition, Benjamin/Cummings Publishing Co., 1996, p133)

Quote:

"Thus, life is possible only because living cells maintain themselves in a steady state far from thermodynamic equilibrium. ... This state, in turn, is possible only because a cell is an open system and receives large amounts of energy from its environment. If the cell were a closed system, all its reactions would gradually run to equilibrium and the cell would come inexorably to a state of minimum free energy, after which no further changes could occur, no work could be accomplished, and life would cease. The steady state so vital to life is possible only because the cell is able to take up energy continuously from its environment, whether in the form of light or preformed organic food molecules. This continuous uptake of energy and the accompanying flow of matter make possible the maintenance of a steady state in which all the reactants and products of cellular chemistry are kept far enough from equilibrium to ensure that the thermodynamic drive toward equilibrium can be harnessed by the cell to perform useful work, thereby maintaining and extending its activities and structural complexity." (Wayne M. Becker, Jane B. Reece, & Martin F. Poenie, The World of the Cell: Third Edition, Benjamin/Cummings Publishing Co., 1996, p133)

Quote:

"However improbable a structure may be because of its order, it can always be generated if sufficient energy and information are available. Energy and information are, in other words, two indispensable prerequisites for the existence of life. Order can be brought about, maintained, and even extended in biological systems provided that adequate information and energy are available. The information is required to specify what form that order should take, and the energy is needed to drive the reactions and processes that lead to the order." (Wayne M. Becker, Jane B. Reece, & Martin F. Poenie, The World of the Cell: Third Edition, Benjamin/Cummings Publishing Co., 1996, p112)

Note that I am not saying that this notion of the machinery of life being more ordered in a living organism than in a dead organisms cannot be taken to higher levels.

[ August 01, 2002: Message edited by: DNAunion ]

[ August 01, 2002: Message edited by: DNAunion ]

Starboy · 08-01-2002, 07:10 PM

DNAunion,

Are you saying that bio-organic chemical processes are alive in some sense? If so how would they die? Or does death have no meaning at this level because it is reversable?

Starboy

Supramolecular · 08-02-2002, 01:52 PM

Lentic Catachresis
Quote:
"Whilst i can see my entropy/ethalpy statement is wrong I still think that my original comment that other factors influence biomolecular processes apart from entrophy still stands, and there are instances where enthalphy has a greater influence than entrophy on biological systems."

Me:
That's definitely true Lentic.

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08-01-2002, 08:56 AM	#53
Supramolecular Junior Member Join Date: Jan 2002 Location: UK Posts: 45	Hi Lentic Catachresis, You said: The chemical interactions between water and oil have a greater influence over the system than entropy does. I said: When an oil molecule is placed in water, it causes the water molecules around it to become more ordered than they would be in the bulk liquid. When two such oil molecules come together in water they dispel several relatively ordered water molecules (due to the smaller surface area of the molecules together) thus increasing the entropy of the system. This process is almost totally entropy driven. You said: If the hydrophobic effect isn't a chemical interaction then can you state why I said: The hydrophobic effect is an effect rather than a chemical interaction. Examples of chemical interactions between molecules are hydrogen bonds, ionic, Van Der Waals, dipole-dipole, pi-pi etc. Some of the interactions could be attractive or repulsive. I see what you�re saying re chemical interactions, but between oil and water there are no chemical interactions apart from weak Van der Waals interactions, so there is no enthalpic benefit of an interaction between oil and water, only an entropic benefit from the release of �ordered� water. You said: BTW. I see you are a research scientist. What field do you work in. And my post must be quite controversial for you to make your first post in half a year. I said: I don�t find your post controversial par se, only your comment that chemical interactions between water and oil have a greater influence over the system than entropy does. This process is totally entropy driven as outlined by myself and tronvillain. My PhD was in Supramolecular chemistry although now I research the solid state (polymorphism etc.) Thanks though for prompting me to post as not only was that my first post in half a year but my first post ever on Infidels after a 12 month period of heavy lurking. So, hello everyone. Think I�ll go and introduce myself in the introductions forum.

08-01-2002, 05:03 PM	#55
DNAunion Veteran Member Join Date: Jan 2001 Location: USA Posts: 1,072	Starboy: My naive reasoning for this idea is to consider the entropy of a living system to include a component that represents the order of the process of living. My intuition leads me to think that a machine that is running smoothly is more ordered than one that is running poorly or not at all. Using this primitive concept it seems natural to think that going from a running to non-running state would result [in] some form of discontinuity in entropy. DNAunion: Coming more from a molecular cell biology/bioenergetics angle, I agree. For example, a protein is more ordered than are its free constituents (amino acids) and so has a lower entropy than its individual components. If a formerly functional protein is decomposed to any degree (such as it might be at the time of death), then its entropy has increased relative to its normal state. Same goes for other biopolymers. Living cells are highly ordered and must continually “fight” against their natural tendency to become disordered, and against the natural tendency of their chemical reactions reaching equilibrium.

08-01-2002, 05:20 PM	#56
Starboy Banned Join Date: Jun 2002 Location: Tallahassee, FL Reality Adventurer Posts: 5,276	Hi DNAunion, Yes I would agree but I am saying more than that. In the example you give, that cell that contained the protein would have lower entropy when the machinery of that cell is active (cell is alive) then that of a cell that has stopped functioning (cell is dead). This may not make sense at the cellular level since the machinery of the cell is chemistry, but maybe it makes sense if there is such a thing as ordered chemistry vs. disordered chemistry. I think at the level of an organism it may make more sense. What do you think? Starboy

08-01-2002, 05:47 PM	#57
Lentic Catachresis Junior Member Join Date: Aug 2001 Location: UK Posts: 26	Hi Supramolecular: I think the point I was trying to make, perhaps not to well in retrospect (i used the first example that came to my head), was that there are others factors to consider rather than just entropy. That is to say we cant just think of atoms/molecules as behaving in an entirely "random" manner. I think my main point was that water/oil don't mix due to chemical interactions (or lack of) ie repulsion towards each other. Whilst i can see my entropy/ethalpy statement is wrong I still think that my original comment that other factors influence biomolecular processes apart from entrophy still stands, and there are instances where enthalphy has a greater influence than entrophy on biological systems.

08-01-2002, 07:10 PM	#59
Starboy Banned Join Date: Jun 2002 Location: Tallahassee, FL Reality Adventurer Posts: 5,276	DNAunion, Are you saying that bio-organic chemical processes are alive in some sense? If so how would they die? Or does death have no meaning at this level because it is reversable? Starboy

08-02-2002, 01:52 PM	#60
Supramolecular Junior Member Join Date: Jan 2002 Location: UK Posts: 45	Lentic Catachresis Quote: "Whilst i can see my entropy/ethalpy statement is wrong I still think that my original comment that other factors influence biomolecular processes apart from entrophy still stands, and there are instances where enthalphy has a greater influence than entrophy on biological systems." Me: That's definitely true Lentic.

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