Abiognesis: excerpt from a book.

[nobahar]

Hello!
I'm reading a book titled Abiogenesis: How Life Began. The Origins and Search for Life. I was hoping someone would be able to explain the following. Its based on the theory that life emerged around hydrothermal vents:

"The real entropic output of life then is not the complex organic molecules that constitute life and enable the processing, but those waste products closer to equilibrium than the reactants, such as methane, acetate and certain sulfides and oxides as well as the recalcitrant stable organic molecules such as the hydrocarbons that tend to be interred within the sedimentary piles." (my own emphasis).

This makes no sense to me. Particularly the bolded part.
Any help at all is appreciated.
Thanks in advance.

 

[Ryan_m_b]

The exert is talking about entropy, in that respect is it saying that the waste products increase the entropy of the system. Do you understand this?

Also if you are interested in abiogenesis this video is very good



https://www.youtube.com/watch?v=U6QYDdgP9eg

 

[nobahar]

Thanks for the response Ryan. I appreciate the principle of entropy, but this bit in particular I am confused about:

"those waste products closer to equilibrium than the reactants"

I am not sure what reactants the sentence is referring to. Surely the equilibirum is dependent on the reactants as well. I do not see how the waste products can be closer to equilibrium without the reactants also approaching equilibrium...

 

[Ryan_m_b]

"those waste products closer to equilibrium than the reactants"

Perhaps it meant "those waste products closer to equilibrium than the reactants they came from". So it's comparing the waste products of the reaction to the reactants that were there at the start, does that make sense?

 

[JorgeLobo]

Entropy as used here means there's less energyin in a system available to do work. That is, complex molecules have been metabolized leaving waste products with less avalable energy.

 

[nobahar]

Thanks again Ryan.
So its a comparison across time? As in: there is some conc of the reactants at t=0, the reaction proceeds, approaching equilibrium, and the waste products are being considered at this later time, comparing the conc of the waste products at this later time to the conc of the reactants at t=0. Which has an associated increase in entropy, which apparently drives the process to a large extent.

 

[Ryan_m_b]

There are no"experts" in abiogenesis - all are merely speculators since one have achieve this. The video is garbage. It's merely a rejection of creationism, preaching to the scientific choir, and as there is no accepted theory for the initiation of life the rest is mere pedantic speculation.

Entropy as used here means there's less energyin in a system available to do work. That is, complex molecules have been metabolized leaving waste products with less avalable energy.

This is not true and misleading. There is a wealth of scientific evidence and study pertaining to abiogenesis. You are displaying an ignorance here, whilst there is no comprehensive Theory of Abiogenesis there is far more investigation than simply "pedantic speculation".

Thanks again Ryan.
So its a comparison across time? As in: there is some conc of the reactants at t=0, the reaction proceeds, approaching equilibrium, and the waste products are being considered at this later time, comparing the conc of the waste products at this later time to the conc of the reactants at t=0. Which has an associated increase in entropy, which apparently drives the process to a large extent.

I guess so, that's all I can make from that statement.

 

[nobahar]

There are no"experts" in abiogenesis - all are merely speculators since one have achieve this. The video is garbage. It's merely a rejection of creationism, preaching to the scientific choir, and as there is no accepted theory for the initiation of life the rest is mere pedantic speculation.

Entropy as used here means there's less energyin in a system available to do work. That is, complex molecules have been metabolized leaving waste products with less avalable energy.

Thanks Jorge, not experts but excerpt, as in a short extract.
Can't entropy be associated with an increase in energy. Indeed, the book does state a movement towards less energy, but can that really be taken from the use of the word entropy here?

 

[nobahar]

I guess so, that's all I can make from that statement.

Thanks Ryan, thank goodness its not only me (that finds it ambiguous), then!

 

[JorgeLobo]

Think so nobahar - entropy is a property that can be used to determine the thermodynamic energy in a system available for work. I had a bit of trouble understanding what this has to do with abiogenesis in this brief extract.

 

[Pythagorean]

Work is a physics term. biological systems are physical systems. The system must take matter from the environment and metabolize it. It then uses that matter (and energy, coincidentally) to send signals, build structures, replicate itself. This all requires "work" to move matter in specific ways like this.

An example of energy that's not work would be heat byproduct. The heat must go from source to sink for us to extract energy in a usable way. The byproduct is the heat that doesn't go into work, but goes to the sink (see image in link below)

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

 

[bobze]

Ryan is on the right path here. They are referring to, I believe, that more complex organics can build up over time (particularly hydrocarbons) through various chemical processes. Life then in this instance, though complex itself, would increase the total entropy of the system by metabolizing those more complex natural molecules. While the life maybe "complex", remember that it is the net change here we are worried about. Its important to remember that even in something like a theoretical isolated system you can have local decreases in entropy, so long as your net change is 0 or increasing.

There seems to be an idea, a hypothesis if you will, growing in popularity amongst prebiotic chemists involving RNA polymerization and UV light--Which when RNA polymerizes in the presence of UV light it turns out to be good at increasing the entropy of the system. This maybe one of the ways that earlier "trial and error" nucleotide permutations eventually formed the first replicators.

Edit: Just to address something that seems to have been taken care of so everyone (particularly the OP) is getting good information; there certainly are experts when it comes to abiogenesis. Prebiotic chemistry is their field of study and there are many cataloged facts and observations left over from those yesteryears that those experts and scientists explain and seek to explain. Certain processes have left more information about the early Earth than many people realize and there is data there for science to be preformed on. Contrary to certain posters ill-founded beliefs, such areas are not a lot of "guess work". Little self education could go a long way.

 

[nobahar]

Thanks for the response bobze.

...when RNA polymerizes in the presence of UV light it turns out to be good at increasing the entropy of the system. This maybe one of the ways that earlier "trial and error" nucleotide permutations eventually formed the first replicators.

Can you elaborate on this bit? According to the University of Southern Mississippi website, polymerization is almost always associated with a decrease in entropy.

 

[mishrashubham]

"The real entropic output of life then is not the complex organic molecules that constitute life and enable the processing, but those waste products closer to equilibrium than the reactants, such as methane, acetate and certain sulfides and oxides as well as the recalcitrant stable organic molecules such as the hydrocarbons that tend to be interred within the sedimentary piles." (my own emphasis).

Equilibrium is associated with the entire reaction and not only its reactants or products. But 'equilibrium' over here does not talk about any reaction, but a state of high entropy or a more 'probable state'.

Can you elaborate on this bit? According to the University of Southern Mississippi website, polymerization is almost always associated with a decrease in entropy.

Yes while the polymerization does decrease the local entropy, the energy released in the reaction increases the entropy of the surroundings, resulting in a net increase in entropy of the system. That is what Bobze wrote.

Which when RNA polymerizes in the presence of UV light it turns out to be good at increasing the entropy of the system.

{emphasis mine}

 

[jackmell]

"The real entropic output of life then is not the complex organic molecules that constitute life and enable the processing, but those waste products closer to equilibrium than the reactants, such as methane, acetate and certain sulfides and oxides as well as the recalcitrant stable organic molecules such as the hydrocarbons that tend to be interred within the sedimentary piles." (my own emphasis).

This makes no sense to me. Particularly the bolded part.
Any help at all is appreciated.
Thanks in advance.

Lemme' take a shot at that ok?

You'll agree that at equilibrium, we have the maximum entropy. The second law has driven the system to maximum disorder and free-energy to do work is at a minimum. But life is an ordered system that is constantly being bomb-barded by the second law to become disorded. To stay alive then, life must continuously feed on order in the form of ordered molecules. Those ordered molecules represent negative entropy. Life feeds on this order by "riding" the free-energy trajectory during the process of converting these high-ordered molecules into smaller, more disordered ones like water and CO2. These smaller, low-energy molecules represent an increase in entropy and thus are closer to equilibrium. Life, to persist then, creates entropy during this order-conversion and it does so by pushing chemical processes closser to equlibrium like in the conversion of a high-ordered sugar molecule to low-order and greater entropy of water and CO2

If it were a test question, that's what I'm goin' with. Figure it's a B maybe.

 

[JorgeLobo]

Dispute there are "experts" in a phenomenon no one understands or has replicated in whole or in validated part. There are hypotheses only for abiogenesis.

 

[Ryan_m_b]

Dispute there are "experts" in a phenomenon no one understands or has replicated in whole or in validated part. There are hypotheses only for abiogenesis.

An expert is simply someone who has extensive knowledge of the field (most often because they have long time experience working within it) regardless of how complete the field is.

 

[jackmell]

Dispute there are "experts" in a phenomenon no one understands or has replicated in whole or in validated part. There are hypotheses only for abiogenesis.

You kinda' don't believe it huh? Chemistry is really very beautiful. Life too. And if you study them for a long time, things begin to emerge about them. Your ideas about them become more than just the sum of all that you've learned. It's a slap in the face to chemistry to doubt it can, all by it's lonesome, create something wonderful like life. That's part of the beauty and that's part of what emerges I think. But it's not easy for someone to just blindly accept that without going through the painstaking synthesis of reaching that conclusion through emergence. There are things you can only know by living a long time and for me at least, I find it easy to accept that chemistry can create life all by itself.

 

[JorgeLobo]

Extensive knowledge? In chemistry associated with hypotheses but not in abiogenesis where science sees no theory prevailing.
An expert in building and understanding roads can tell you nothing about the destination until he gets there.

 

[Ryan_m_b]

An expert in building and understanding roads can tell you nothing about the destination until he gets there.

(Emphasis mine)

Why would he need to? He's an expert in building and understanding roads.

 

[JorgeLobo]

Exactly - why would the chemist need to understand or claim expertise in abiogenesis - he's only running reactions, tho' his observations may indeed be part of the reveal when it is understood.

 

[Ryan_m_b]

Exactly - why would the chemist need to understand or claim expertise in abiogenesis - he's only running reactions, tho' his observations may indeed be part of the reveal when it is understood.

Again you are getting round to this odd point that you can't be an expert in something until it's met an arbitrary measure of knowledge. If you work in abiogenesis research and you are one of the top of the field then you are an expert in abiogenesis. Simples.

 

[JorgeLobo]

Not an arbitary measure of knowledge but any valid knowledge and I doubt the folks identified would even call themseves expert in abiogenesis. Th subject is abiogenesis - not chemistry of proposed reactions and, to this point, their approach is no more valid than folks claiming aliens left life on earh.

 

[jackmell]

Exactly - why would the chemist need to understand or claim expertise in abiogenesis - he's only running reactions, tho' his observations may indeed be part of the reveal when it is understood.

I believe chemistry background is essential in understanding life. Personally, I cannot imagine anyone studying abiogenesis without being a chemist. No offense to the Biologist but it's really all chemistry.

 

[Ryan_m_b]

Not an arbitary measure of knowledge but any valid knowledge and I doubt the folks identified would even call themseves expert in abiogenesis. Th subject is abiogenesis - not chemistry of proposed reactions and, to this point, their approach is no more valid than folks claiming aliens left life on earh.

That last statement of yours is utterly ridiculous. Suggesting that abiogenesis is as unsubstantiated or as limited as the idea of aliens seeding Earth represents a massive ignorance of a field.

I believe chemistry background is essential in understanding life. Personally, I cannot imagine anyone studying abiogenesis without being a chemist. No offense to the Biologist but it's really all chemistry.

Why do you assume that biologists these days don't have a significant understanding of chemistry (HINT: Ever heard of biochemistry)? I did my undergrad in biology and I can't think of a single module I did that did not involve chemistry in one form or another and yes abiogenesis did come up more than once.

 

[Pythagorean]

Difficult: formulating and developing a theory. Requires and expert who has years of training and experience in the subject via their mentors who were also experts.

Easy: sitting back and ambiguously criticizing theory. Requires only minimal English skills.

 

[jackmell]

I think we should get back on topic. The thread author asked about entropy and I feel my B-level performance up there did a good job of answering his question. That's ok. No need to thank me. I was happy to help.

 

[Pythagorean]

I was sticking to the thermodynamic definition of entropy on my post about "work". This is the context in which Jorge asked about it. It's not so cleanly about order/disorder. It's defined very specifically around the temperature of the system.

Of course, I believe thermodynamic entropy is just a subset of a more general information entropy, but we can avoid speculation by just talking about thermodynamic entropy for now.

 

[Pythagorean]

Jorge, the tone of the video is unfortunate but the content was not "pedantic speculation". It's a very reasonable guess as to how life could have started. The point I only that magic or supernatural wasn't required for life. That we can take a cause/effect approach.

I guess, realistically one could complain that the video provoked religious discussion and is therefore a violation of PF.

Im an atheist, so I perhaps selfishly never realized this, I just ignored the anti-theist tones. Because again, I'm an atheist, not an anti theist.

 

[nobahar]

I think we should get back on topic. The thread author asked about entropy and I feel my B-level performance up there did a good job of answering his question. That's ok. No need to thank me. I was happy to help.

Bit difficult to thank you if I haven't been online. Great explanation. Perhaps a B-level, if lenient. Since you don't want a thank you, I shall save it for someone else.

Not sure why creationism has crept in...

 

[nobahar]

Jorge, the tone of the video is unfortunate but the content was not "pedantic speculation". It's a very reasonable guess as to how life could have started. The point I only that magic or supernatural wasn't required for life. That we can take a cause/effect approach.

I guess, realistically one could complain that the video provoked religious discussion and is therefore a violation of PF.

Im an atheist, so I perhaps selfishly never realized this, I just ignored the anti-theist tones. Because again, I'm an atheist, not an anti theist.

I found the video useful, I wouldn't consider it anti-theist, since it attacked the arguments of theists, not theists themselves.

 

[JorgeLobo]

As a biologist who has written on this subject as well as the proper place for religious concepts such as creation as philosophy and not as science and who has never pushed creationism in this forum or any other, let me explain.

Science has not (yet) created life in the lab - so there are no "experts" in the creation of life from the inanimate - abiogenesis. The path pursued to study this phenomenon is the best scientists can think of now - but it is only speculation, only hypothesis, and an unsuccessful one to this point. Remember - this is the creation of life, not more complex molecules that folks speculate could be life's presurcors by some unknown process to establish vitality. In fact, the failure to produce life by the scientific concepts pursued to this point may well indicate these folks are on the wrong track.
A video dramatizing this unvalidated hypothesis is distrubing as it communicates an ynvalidated hypothesis as having substance and is consistent with the natural philosophy concept that preceeded the development of the scientific process. Dumbed down - this concept says wise folks can imagine the answer cause they're wise. Science says they answer is in the experiment and so far there is no experiment that produced life.
As science assumes all is knowable - we will one day know the answer but as Hamlet said, there are more things on heven and Earth than are dreamt of in your (natural) philosophy. So it may well be a concept not considered to this point.

 

[bobze]

As a biologist who has written on this subject as well as the proper place for religious concepts such as creation as philosophy and not as science and who has never pushed creationism in this forum or any other, let me explain.

Science has not (yet) created life in the lab - so there are no "experts" in the creation of life from the inanimate - abiogenesis. The path pursued to study this phenomenon is the best scientists can think of now - but it is only speculation, only hypothesis, and an unsuccessful one to this point. Remember - this is the creation of life, not more complex molecules that folks speculate could be life's presurcors by some unknown process to establish vitality. In fact, the failure to produce life by the scientific concepts pursued to this point may well indicate these folks are on the wrong track.
A video dramatizing this unvalidated hypothesis is distrubing as it communicates an ynvalidated hypothesis as having substance and is consistent with the natural philosophy concept that preceeded the development of the scientific process. Dumbed down - this concept says wise folks can imagine the answer cause they're wise. Science says they answer is in the experiment and so far there is no experiment that produced life.
As science assumes all is knowable - we will one day know the answer but as Hamlet said, there are more things on heven and Earth than are dreamt of in your (natural) philosophy. So it may well be a concept not considered to this point.

The problem in your assumptions here Jorge is that "life" or rather the origin of life doesn't exist in a bubble. If it did, I'd certainly agree with you that there are no abiogenesis experts. But that isn't the case.

Abiogenesis describes the field of science that studies how abiotic agents can become biotic replicating agents. Certainly no one has ever done that in a lab, that doesn't mean however there aren't experts in the different areas of the field. Such as say--on the molecular biology of autocatalysis or prebiotic chemistry or something like say, the thermodynamics of chemical systems. As these, and many more subjects, are required to the field of study in question--There can be experts (ex·pert/ˈekspərt/
Noun: A person who has a comprehensive and authoritative knowledge of or skill in a particular area.) in the field of and science of abiogenesis.

I agree about the video though (though I didn't watch it, but I'll take your word for its misrepresentation of science), but then again dumbed down: Being a "biologist" who has "written" on the subject is just a nice little ol example of argument from authority. Being the science-type then, I think you should be equally as weary of any such argument made on the basis of said appeal for its lack of credibility as the video--No? (of course turning those cunning skills to introspective purposes is always much harder than flexing them extrospectively :tongue:)

 

[JorgeLobo]

Sure - define it as you will - knowing a lot about chemistry that hasn't established initiation of lifebut that was what they were hoping.

Truth is not arrogance. The credentials were offered largely in response to the claim of pushing creationism.

 

[Quickless]

Abiogenesis originally showed promise at the level of logic but has to date been a sterile research agenda.

"There is a wealth of scientific "EVIDENCE" ... pertaining to abiogenesis." I found this statement to be rather ambitious.

Can anyone site any current work on the topic?