Wet Monomers shouldn't become polymers - but ...

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Re: Wet Monomers shouldn't become polymers - but ...

Postby BioWizard on August 12th, 2017, 10:29 am 

scientificphilosophe » 04 Aug 2017 02:31 am wrote:Hi BioWizard

Apologies for the delay in replying.
This is for several reasons. Firstly I have been away for a few days, but more importantly I still, genuinely, do not understand several aspects of your replies, and I am becoming concerned that our conversation is mismatched because I am somehow not articulating myself in the right way.

I am therefore trying to consult with a colleague who is now away for a few weeks (on conference and then holiday) so it may take me a while to respond again on this subject.


This is fine.

scientificphilosophe wrote:While I do understand the basic nature of the reversible reactions you are focusing on I feel that we cannot say that a polymer has been formed until it has reached a stable condition. A momentary existence before it reverts back to its constituent monomers (or worse) is not, in my layman's opinion, truly forming the polymer because it has to be usable in a practical way.


>Exactly<

You got it. This is actually one of the very points that I was trying to convey to you. Things aren't so cut and dried at the molecular level, and tend to exist on a continuum. As such, a polymer's stability is a function of both its formation and reversion rates. When we colloquially say that a "polymer forms", what we're actually saying is that "the formation rate is sufficiently larger than the reversion rate for the polymer to last long enough for us to measure its presence (or utility of sorts)". Conversely, colloquially saying that a "polymer does not form" is not very different from saying that "the reversion rate is sufficiently higher than the formation rate that no polymer forms and lasts long enough for us to measure its presence (or utility)".

By extension of this, the stability of a polymer can be modulated by altering the formation and reversion rates with respect to each other. If you make the formation rate much higher, you make the polymer more stable. If you make the reversion rate much higher, you decrease the stability of the polymer - and if you keep going there will be a point where the polymer's existence is as good as none, and we say the polymer doesn't form.

scientificphilosophe wrote:You are implying that formation and reversal is constant - which it might well be in the lab, or possibly even in a primal ocean. If correct, the polymers must be harvested at the right moment to become usable. Without the human element, how is that to be done in a natural process?


This might come as a shock to you, but these processes are a lot more dynamic inside cells than we can ever hope to recreate in the lab at present.

Let's say you put a DNA polymer in a buffered solution in a test tube today. You measure its length tomorrow and you find out its still the same. You measure it the day after that and it is still the same. So you conclude that the polymer is stable. But when if you measure it in ten years? A hundred years? A thousand years? You will suddenly start to measure significant decomposition. Suddenly, the process isn't so static anymore. Why? Because you started to observe it at the time scale that matches its slow dynamics.

Alternatively, you can add an enzyme that degrades DNA. Now your DNA polymer will start decomposing in a matter of minutes. If you measure its length tomorrow, it will seem like it disappeared in an instant. But it didn't. It disappeared gradually over a matter of minutes. And if you want to measure that disappearance dynamically, you would have to do your measurements every few minute or seconds after you add the enzyme. Because the enzyme has changed the rates of the process (by speeding up the rate of reversion), and the timescale of your observation needs to match the new dynamics of the system.

Nothing is fixed, everything is contextual. To understand the stability of a polymer, you need to understand the formation and reversion rates, and the factors influencing them.

scientificphilosophe wrote:What we see in living cells is that the polymers are stable and do not reverse instantly. They are preserved ready for use elsewhere in the cell.


Correct. The reversion rates are slow enough that the polymers in cell can perform measurable functions and "do not reverse instantly". But when happens as cells grow and divide? These structures are turned over and recycled in a dynamic process.

Since we're on the subject, do you know that cells move themselves round specifically by modulating polymerization dynamics? Here's an (incredibly simplified example): To move to the right side, a cell causes polymerization of its cytoskeleton in the right direction and depolymerization of its cytoskeleton in the left direction. The net outcome is that the cell shimmies to the right. How can polymerization and depolymerization be locally controlled within the very same cell? Enzymes. How is the process done regulated directionally? You send enzymes that stabilize polymerization to the right, and enzymes that de-stabilize polymerization to the left side.

These processes are very dynamic and occurring all the time. If you measure them instantly, you won't catch the dynamics. If you measure them over time, you will find that all these polymers are constantly forming and breaking down as the cell responds to its environment, grows, divides, migrates, and so on.

scientificphilosophe wrote:Overall, even with a constantly reversing process, you are still implying that the right conditions have to be created in order to 'shift a balance' and produce more/many polymers. So we are still back to creating the right conditions for assembly not disassembly. Again I am puzzled why you do not focus on answering the point about assembly. This may be where my colleague can help me to re-phrase my point.


Because assembly is only 50% of the process. If these polymers were as stable as you seem to think, cells wouldn't be able to divide, grow, migrate, polarize, and so on. Cells would be frozen down. The stability of these polymers is constantly manipulated inside cells to allow all these processes to occur. In fact, some cancer drugs, such as taxol, capitalize on this - they increase the stability of intracellular polymers to the point that it becomes detrimental for the cell's survival. Others, such as Cytochalasin, do the opposite - they mess up with cells by destabilizing polymers.

Here, read this: https://en.wikipedia.org/wiki/Cytoskeletal_drugs

It's all in the balance between the two process. I would be stunned if you still don't see that by now.

scientificphilosophe wrote:When you say...

Consider these two statements:
1- A polymer doesn't form because the monomers never come together
2- A polymer doesn't form because the monomers fall apart as soon as (or faster than) they come together

While these two statements may sound different to you (and apparently they do), they are actually the same from a chemical/thermodynamic viewpoint. The outcome is the same in both: a polymer fails to form.


The two statements are not the same even from a thermodynamic viewpoint. We may not even get the same outcome.

If only one monomer is present it can only react with ions in the water (if at all) and not with another monomer.
If two monomers are present and react, before then disassembling, it is a very different reaction and depending on the background level of heat and other chemicals/ions present, might produce something else - possibly wit ha change of energy levels in an exothermic/endothermic reaction.

We are back again to determining the right conditions for assembly and stability.



Wait. Didn't you yourself earlier say:

scientificphilosophe wrote:While I do understand the basic nature of the reversible reactions you are focusing on I feel that we cannot say that a polymer has been formed until it has reached a stable condition. A momentary existence before it reverts back to its constituent monomers (or worse) is not, in my layman's opinion, truly forming the polymer because it has to be usable in a practical way.


You literally said "a momentary existence......is not truly forming". Are you saying that this makes sense to you when it suits you, and doesn't make sense when it does not suit you?
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Re: Wet Monomers shouldn't become polymers - but ...

Postby BioWizard on August 12th, 2017, 10:57 am 

scientificphilosophe wrote:While you may wish to respond to this in the near future I won't be able to respond again until I have consulted my colleague,


No worries, take your time.

so can I ask you to revert again to the other topic of 'Origin and Evolution' where there are many unanswered points?


scientificphilosophe I prefer to do one thread at a time, due to time constrains. I look forward to getting back to the other thread - after we finish with this one.
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Re: Wet Monomers shouldn't become polymers - but ...

Postby neuro on August 21st, 2017, 1:33 pm 

Ehi, BioWiz,
just to be picky... :°)
BioWizard » August 12th, 2017, 2:28 pm wrote:ATP synthase, for instance, harnesses the flow of electrons across the membrane to shift the equilibrium from ADP + P towards ATP.

It actually harnesses the flow of protons across the membrane...
(the flow of electrons from donors to acceptors down to oxygen fuels the transmembrane transport of such protons, which then flow back through the ATP-synthase).

But I must admit that - although I took care of specifying "a single reaction" - you are right: an enzyme can drive a single reaction in one direction by harvesting energy from a physical process (such as a photon) instead of a coupled chemical process:
Other enzymes can harness light radiation. And so on.

And, BTW, sorry about diverting the topic... :°)
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Re: Wet Monomers shouldn't become polymers - but ...

Postby BioWizard on August 21st, 2017, 7:45 pm 

Neuro,

While one can argue that the flow of electrons is the source the proton gradient and therefore posit that the statement isn't in essence incorrect, that was admittedly not my intended meaning. I was indeed thinking of the H+ flow through complex V, but for some reason typed "electrons" instead =) I was going to talk about the ETC but decided to ommit that part, and the rest is histo... freudian? Thanks for the correction.
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Re: Wet Monomers shouldn't become polymers - but ...

Postby scientificphilosophe on October 23rd, 2017, 8:49 am 

Hi Biowizard

Again - apologies for the delay in responding to you.

I remain puzzled by a number of your statements and really would like to resolve them in my mind, because as a non-expert they beg a number of questions which I think would benefit everybody.

They come back to the central themes of assembly (not disassembly); purpose; direction; and origin. As a result if we can get to the bottom of these things we may resolve much broader questions.

You constantly avoid the question of assembly, but I don't know why. Is it because you can't answer it?
We all know, in broad terms, that there is a chemical balance to be struck between the observed processes of assembly and disassembly, but to focus exclusively on disassembly is wrong.

Bryson (under the guidance of his contributor) mentioned that many biological processes contravened the Mass Action Law, and this is indeed confirmed on other websites incl. Wikipedia.
There are hints that this is resolved by 'macromolecular crowding' - but this seems to be an observation not an explanation.
Is there a chemical way to overcome the contravention in the law?

Another obvious point is the way in which enzymes are just thrown into the mix as a way to resolve the thermodynamic aspects of polymer building, without any explanation of how they miraculously emerged to do this so conveniently in these situations. As I understand things, they work partly because of their chemical make up and partly because of their shape - which effectively has to exactly fit into certain niches in the target/emerging polymers (substrates). So if a polymer with a particular shape and chemistry needs an enzyme that also has a particular (and sometimes flexible) shape and chemistry, we are in a Chicken and egg situation - or is this just a happy miraculous coincidence... ?

All of this is even more surprising when you layer-on the fact that a negligible number of proteins, (compared to the number of permutations available), are actually useful, and even then only have use in the context of a cell/body which didn't originally exist. What was the driving force to focus on these particular happy marriages?

Finally there is the issue of purpose. These things work together in a seemingly co-ordinated way, with an objective.
Like the complex ways in which cells communicate electronically, or the example given by yourself that cells change direction via a complex set of chemical processes, they do this seemingly with an objective in mind but nothing to give the chemical bits an instruction. Are they really chemically inevitable?


To answer some of the specific points you made earlier:

My challenge to your own original example of 'disassembly in two ways', was nothing to do with the (possible) breaking apart of an emerging polymer, but on the point of assembly - there were two potentially very different outcomes in terms of assembly. Can't you see that? Your examples are not the same by any means.

When you say that 'assembly is only 50% of the process' I have to disagree because cells and bodies exist to create and sustain life. That is the objective we are talking about. We are not talking about a partially successful test tube operation.

Assembly and stability are the focus. Please answer those points. We would all benefit by you doing so.
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Re: Wet Monomers shouldn't become polymers - but ...

Postby BioWizard on October 23rd, 2017, 11:20 am 

We would all benefit by you doing so.


scientificphilosophe, I think I've spent a lot more time and effort trying to teach about polymerization dynamics and energetics than I am willing to do for free. I'm afraid beyond this point I will have to charge you for my time. If you're willing to pay me, I am be willing to continue. If not, then you need to go and try to learn those concepts on your own, starting with the wealth of informational leads that I and others have provided. Attempting to understand phenomena using only half of the concepts that apply to them IS what leads to the kind of difficulties and confusions that you are facing. While I'm happy to answer your questions, I'm not willing to go in circles forever simply because you want to pick and choose which laws of nature you want to incorporate into your interpretations. It doesn't work that way.

What we would all benefit from is for you to not pick and choose the subset of reality that yields an interpretation suiting your agenda. You have everything you need to learn about the relevant concepts here in this thread already. If you want to go around and make a genuine effort to learn it, and then return to ask questions that do not show willful ignorance, be my guest. If you'd like me to hold your hand through it, I may do it - for the right fee. Otherwise, if you just want to go in circles and insist you want to focus on forward kinetics and ignore reverse kinetics, then the answer is no. I have neither the time nor the desire to uselessly go in circles.
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Re: Wet Monomers shouldn't become polymers - but ...

Postby scientificphilosophe on October 23rd, 2017, 11:29 am 

Biowizard

I honestly don't see how this is 'going round in circles'.
I have acknowledged the significance of disassembly, but you have not addressed the points of assembly.
I have given you the specifics of the Mass Action Law and the nature of enzymes to comment on, but you don't wish to do so.

That's fine, but they remain valid points which must therefore remain open
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Re: Wet Monomers shouldn't become polymers - but ...

Postby BioWizard on October 23rd, 2017, 11:35 am 

Sorry to shut you down more forcefully this time, but your references to “purpose” and “miraculous appearance” gave you away. This is a science board. If you want to talk god, purpose, and magic, please find a different place to do that.

You made no valid points, at least none that we are interested to discuss scientifically. No offense, it’s just not what this specific board is for. Now please move it along.
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Re: Wet Monomers shouldn't become polymers - but ...

Postby scientificphilosophe on October 23rd, 2017, 12:23 pm 

Biowizard

I have no intention of bringing God into this.
And if you cannot see the sarcasm in the way I deployed "miraculous coincidence" then you need to stop looking for conspiracies, and lighten up.

I have said many times that I am not a creationist or any such like.
As scientists - should we ignore / run away from valid questions?
No.

When I have been asked, I do not have the answers. It seems that you don't either.
Fine. Be honest enough to say you don't know.
But don't accuse me of things I am not.

My questions are specific, and they remain.
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Re: Wet Monomers shouldn't become polymers - but ...

Postby BioWizard on October 23rd, 2017, 12:31 pm 

No you don't get to twist this around, not when you make statements like this:

scientificphilosophe wrote:When you say that 'assembly is only 50% of the process' I have to disagree because cells and bodies exist to create and sustain life. That is the objective we are talking about. We are not talking about a partially successful test tube operation.


You're far from carrying out a sincere scientific inquiry, let alone being a scientist, so please don't give yourself that credit. I figured you out a very long ago and was humoring you for the sake of clarifying the scientific concepts to others who might be reading. And you were behaved enough that it was marginally worth it. But now you're flat out pushing willful ignorance as if it was valid reasoning, and accusing me of being unscientific because I'm refusing you engage you on it. It may or may not be intentional, but I'm not going to allow it either way. If you lie one more time and claim that I am the one refusing to be scientific about this, you're going to get banned. You don't get to troll us.
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Re: Wet Monomers shouldn't become polymers - but ...

Postby scientificphilosophe on October 23rd, 2017, 1:02 pm 

I am persisting with this because I respect you as as a scientist.
I absolutely do not say that you're being unscientific in any way, and I don't know why you say that.
The only thing I have said is that you don't appear to have answered my points.

I honestly don't - and I have tried my best to tell you what I don't understand.

This is a sincere inquiry - I have never made any claim to being an expert in this field.
That is why I have questions. It is not 'willful ignorance' - I simply don't understand

In terms of the quote, I honestly believed (still believe) that cells generate proteins with a much higher level of success than 50%
If that's wrong then I'm very glad to know it, but wouldn't have thought that cells could survive on a lesser percentage.
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Re: Wet Monomers shouldn't become polymers - but ...

Postby BioWizard on October 23rd, 2017, 5:23 pm 

I'm no longer interested in helping you - sorry.

Do your own research and arrive at your own conclusions. Or, you know, arrive at your conclusions, and then cherry pick subsets of information that make them look valid to you. Whichever floats your boat. I'm done here.
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Re: Wet Monomers shouldn't become polymers - but ...

Postby scientificphilosophe on October 23rd, 2017, 6:23 pm 

Seems like the subject has been released for others to comment.

The initial premise was that the formation of polymers in a water-based environment doesn't happen outside living bodies. If correct then there would seem to be something special about what happens in a living cell. If not, then chemistry should explain everything.

The conversation so far has shown that there are differing opinions because questions remain unanswered.

On the one hand we see real mechanisms performing dehydration reactions in a water-based solution, on the other we need special circumstances and specially tailored chemicals to do this (such as enzymes). Some of the issues have been highlighted above, concerning biological organisms apparently breaking the mass action law.

I do not know if a proper explanation has been achieved for this. I have seen references to macromolecular crowding but is this an observation or has this effect been chemically explained?

Do dehydration reactions occur in a water-based environment anywhere else on Earth outside a living cell, barring the lab?

As they are so closely tailored, would both enzymes and proteins have to emerge simultaneously before the first cells existed?

Can anyone else offer some insights into the perceived problems of assembling proteins and other polymers in an aqueous environment?
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