Epistemological Question

[Hrvoje1]

Is there an analogy, and is there a difference, between the ability to perform a task based on stored information, that can be called knowledge, and the ability to perform work based on stored work, that can be called energy?

[FreeWill]

25 minutes ago, Hrvoje1 said:

perform work based on stored work, that can be called energy?

We perform work based on collected and stored knowledge and experiences, which is driving the genetic information based anatomic structure. 

That stored knowledge and experience could be count as (conscious) energy.

Edited June 22, 2019 by FreeWill

[Hrvoje1]

25 minutes ago, FreeWill said:

That stored knowledge and experience could be count as (conscious) energy.

So, you make more emphasis on the equivalence, than on the distinction between knowledge and energy? Because, I don't think these can be counted as any kind of energy, maybe as information, but not as energy. And that poses the further question of distinction between knowledge and information.

[dimreepr]

You're conflating apples and oranges.

[MigL]

Energy, the ability to do work, is a result of the configuration of a system.
As such, it is definitely information of that system.

I don't know if identifying that information with knowledge is conflation or confusion.

[Hrvoje1]

Probably both, but I don't think I made any of it, by examining the analogy between that kind of information, and the information that is stored for example in a brain, which FreeWill is talking about, or the one that is stored for example in DNA, and is used by enzymes to perform the task of protein synthesis.

[Sensei]

8 hours ago, Hrvoje1 said:

between the ability to perform a task based on stored information, that can be called knowledge,

Human, animal or plant is performing previously learned task (or encoded in DNA f.e. reflex action) in specific moment. i.e. escape (action) if there is danger (stimulus).

Non-reflex action can be controlled (also by learning and training). i.e. training how to not feel fear at high altitude, training how to not feel natural fear against wild predator animal etc.

8 hours ago, Hrvoje1 said:

and the ability to perform work based on stored work, that can be called energy? 

Chemical compound is going into reaction with other compound, if their molecules hit each other, and other environmental variables meet sufficient criteria. i.e. it happens spontaneously.

 

[Hrvoje1]

1 hour ago, Sensei said:

Chemical compound is going into reaction with other compound, if their molecules hit each other, and other environmental variables meet sufficient criteria. i.e. it happens spontaneously.

Now you are on the right track, when you mention spontaneity. Some chemical reactions are more spontaneous then the others, in that regard that they don't require catalysts to lower the activation energy, ie beat the energy barrier. For some, even that is not sufficient, they require another component that stores information and acts as a program for that catalyst, that is, sort of speaking, programmable. Such is case with the enzymes that synthesize proteins, they require DNA that contains the information based on which they operate. Without it, nucleotides would never assemble them selves spontaneously into proteins.

[Sensei]

On 6/22/2019 at 10:50 PM, Hrvoje1 said:

Now you are on the right track, when you mention spontaneity. Some chemical reactions are more spontaneous then the others, in that regard that they don't require catalysts to lower the activation energy, ie beat the energy barrier. For some, even that is not sufficient, they require another component that stores information and acts as a program for that catalyst, that is, sort of speaking, programmable. Such is case with the enzymes that synthesize proteins, they require DNA that contains the information based on which they operate. Without it, nucleotides would never assemble them selves spontaneously into proteins. 

It's easy to imagine how enzymes were introduced by random mutation to living organisms. If we have organisms without enzymes, it has worser yield of production of some compound, or processing nutrients etc. Random mutation (caused by radioactive decay of C-14 or K-40 etc., or cosmic rays, or radicals etc.) at some point of time, changed RNA/DNA in such a way, that new compound has been produced, compound which was/is accelerating some process, enzyme/catalyst of some sort. It was (and is) useful in getting better yield, so organism with such mutation was more successful in surviving, and spread that mutation to further generations, spread itself around the world. Organisms without mutation died or were forced to move to some niches in environment.

If we would make computer program which is going through the all possible states of memory with fixed size f.e. for 256 byte size memory, it's 256 ^256 states = 3.23e+616, one by one, and trying to execute it as program, at some moment, such loop would find some useful meaningful combinations of commands in the right order, doing something for real. It's just a matter of time by otherwise unaware, non-thinking algorithm, to find something useful, and interesting.

The all books on the Earth has fixed/limited number of pages, with fixed/limited number of characters used to make them. One could go through the all characters one by one, pages one by one, to fill them with randomly chosen characters. After some time (counted in probably billions+ of billions+ of years) it would get the all books ever written and not-yet-written by humans.

(examples of brute-force algorithm, which is very time consuming task for finding something useful from garbage of information)

On 6/22/2019 at 10:50 PM, Hrvoje1 said:

Some chemical reactions are more spontaneous then the others, in that regard that they don't require catalysts to lower the activation energy, ie beat the energy barrier.

Catalyst is just helping getting better yield. Reaction can be going without it, but at slower rate.

 

Edited June 24, 2019 by Sensei

[Hrvoje1]

OK, but how slower exactly? What is the ratio between protein synthesis rate when there is a normal concentration (density) of all required components present, and when there is for example no ribosomes, no RNA polymerase, no chaperones, and no DNA, but there is a sufficient supply of proteinogenic amino acids present in its usual concentration?

I believe that's the monomer stuff that gets assembled (and not nucleotides as I said previously) into proteins, which are polymer stuff made of those. I also probably shouldn't have mentioned other components, because most probably I didn't mention all that is required.

[Hrvoje1]

OK, maybe my question is such that you don't intend to answer. On the other hand, some people don't react unless notified about their quoting, or react very slowly, so to catalyze a bit your response:

On ‎6‎/‎24‎/‎2019 at 4:15 PM, Sensei said:

Catalyst is just helping getting better yield. Reaction can be going without it, but at slower rate.

 

[Hrvoje1]

I googled for "protein synthesis rate" and found a lot of interesting articles, but none of them answered the question.
Then I googled for "spontaneous protein synthesis", and found some interesting and relevant results.
First one is about answering the question: Is protein synthesis a spontaneous or a non-spontaneous process?
There, the second answer by Robert Bywater mentions that spontaneity is not very clearly defined notion in the context of that question.
But, whatever sensible way you define it, protein synthesis is definitely not spontaneous process. That doesn't mean that it requires some external factors that are not normally present in vivo medium, because that would not be sensible definition. But without the accuracy of a molecular machine called ribosome, how else could amino acids be assembled into a protein? And without information stored in DNA, and transcripted into mRNA, how would ribosome know what protein it is supposed to assemble, ie what needs to be translated into protein? Let alone amino acids by themselves, without the mentioned machinery?

Second one is about answering the question: How is the balance between protein synthesis and degradation achieved?
There it says:

Quote

For example, if we take a protein and break it down to its substituent amino acids, not even a small amount will reassemble spontaneously. Protein synthesis is the most expensive biosynthetic process known to us, and reconstruction in the absence of a great deal of free energy is extremely unlikely, but even if the energy were available, without a means of generating the appropriate sequence of amino acid subunits, as is done by mRNA during synthesis, the authentic peptide chain simply cannot be reconstituted.

So, I don't know how anything I said provoked you to tell me your story about how enzymes were introduced by random mutation to living organisms, but you might have noticed that this is a science discussion board, so what is easy to imagine to you, isn't necessarily representative or relevant. Relevant is only a scientific fact: proteins do not assemble themselves spontaneously, even if you give them all the time in the world. Right?

 

Edited July 8, 2019 by Hrvoje1

[Hrvoje1]

Accidents never happen, in a perfect world. Says Blondie. But Freud would most probably agree, at least with respect to slips and mistakes, he invented the whole theory about it. So, there is a reason why I mentioned nucleotides instead of proteinogenic amino acids. Namely, they are both categorized as "generic resources" in Constructor Theory of Life, by Deutsch and Marletto, and presented with the same letter N, in the model of self-reproducer, although the former appear as a substrate only in a copy phase (DNA replication), and the latter only in a construction phase (protein synthesis):

So, there is a difference in a raw material, that is not reflected in a detailed schema. At least that's the case in a currently only known implementation of life (Life v1.0).

Of course, that detail is intentionally abstracted from the picture, as not important, but those who talk about concrete implementation (as I did) should be aware of that.