Scientific Meanings of the Term "Agent"

[BillTre]

In considering possible scenarios invoked to explain the origin of life, I find myself searching for a general term which can be applied to the first units on the way to becoming living cells.

Currently, I am using the term "entity", but am unsatisfied with it because I consider it about the most generalized way to talk about "thing" (like an inert rock).
What I am want to discuss are things with active processes intrinsic to their structure.

Alternatively, I am considering using the term "agent". This would seem to be able to actively take action. However, I don't want terms that could lead to too much confusion with other already established terms.
In biology, the term agent is used in discussions of disease causation (as in infectious agents). This a more advanced biological state than what I am looking for, but one I am OK with explaining around.

A thermodynamic animate agent can impose some thermodynamic operation which could in theory drive a system in ways contrary to normal thermodynamic predictions.
I guess a Maxwellian demon would be an example of this, but it has a well established, rather fantastic (meaning not real world) usage. Thus I am leaning to not using it.

Overall I like the agent term, because it indicates that biology seems to have the ability to work around "standard" thermodynamic limits which non-animate entities adhere to.
This not meant as a violation of thermodynamics, but as a work around that arises naturally.

I am wondering what others on the forum think of the potential uses of these terms in the context of early animated matter.
In particular, since I am not particularly well versed in the intricacies of thermodynamics, I am interested in how agent is used in that field, and whether there are particular uses of "agent" in non-equilibrium thermodynamics (which I know little of)?

 

[jedishrfu]

I found this paper which uses the word agent in the form of multi-agent systems.

https://link.springer.com/article/10.3103/S0146411615080398

Perhaps by scanning it you'll see how agent is used in that context.

 

[mcastillo356]

https://en.wikipedia.org/wiki/Abiogenesis
Maybe "organic compound"?
Greetings

 

[Borek]

Maybe "organic compound"?

As far as I understand what @BillTre wrote that won't work.

Organic compound has a very well defined meaning and is several steps lower on the "organizational ladder" than the "agent". Organic compound is a single compound (all molecules identical), "agent" can (or perhaps even must) consist of numerous compounds (several types of molecules).

 

[BillTre]

As far as I understand what @BillTre wrote that won't work.

Organic compound has a very well defined meaning and is several steps lower on the "organizational ladder" than the "agent". Organic compound is a single compound (all molecules identical), "agent" can (or perhaps even must) consist of numerous compounds (several types of molecules).

Yes. Exactly!

To be more specific and clear, I am talking about something (assembled from molecules) which is able to:

• acquire energy from its environment
• maintain its molecular components distinct from its environment (containment physically speaking)
• produce its own molecular components
• make functional replicas of itself

The most simple list of requirements would be:

• a cell membrane (or its equivalent)
• a relationship with its environment so that it can acquire energy (probably chemical)
• a metabolism, so the acquired energy is directed to productive uses for the entity
• a way to make functional copies of itself

This requires more than a single kind of molecule, and probably many molecules of most of the different types. The molecules would also have a particular organization in space.

The essence of living things (or maybe animated matter) is the functional organization of things from the molecular level up, in order to produce replicas.
The simplest such thing commonly considered is usually something like a dumbed down prokaryotic cell, arising in some energy rich environment. Just sitting there making copies of itself.
There are several scenarios, each with many steps.

Once, powered up, if this thing reproduces more rapidly than it is destroyed (through whatever entropic processes confront it), it will acquire (through selective mechanisms involved in reproducing entities) abilities (far beyond normal molecules) to deal with environmental changes (as it arises into the world of the living).
It that sense, to me, it seems like an agent taking care of its business.

Where exactly, its agent-ness kicks is not yet clear to me.
For example, can it just roll on blindly, in an unchanging environment, making copies and be an agent?
My first impression is yes. Its like a computer going through a list of tasks to make a copy.

Alternatively, does an agent have to make a decisions to do something (do this process, or do that process)?
My impression is that following through to do a series of processes when involved (by its particular molecular situation) would be enough for it to be an IT type agent.

Whether this concept is in conflict with some other meaning of agent I don't know.
I could use a modifier like biological --> biological agent, but that is too much connected with medical and disease meanings. Unappealing.

 

[jim mcnamara]

So what you are looking at is either overlapping or the immediate precursor for the hypothetical "RNA world"?

https://en.wikipedia.org/wiki/RNA_world

How about circRNA? (open access!) as a branch point:
https://link.springer.com/article/10.1186/s12943-017-0630-y

 

[BillTre]

So what you are looking at is either overlapping or the immediate precursor for the hypothetical "RNA world"?

Yes, except I avoid "RNA world" since other things (molecularly speaking) would most likely be going at the same time (not exclusively RNA).

Containment would seem to essential for any chemical system.
Otherwise any molecules would float away and production being lost to the productive entity, would be fruitless.
Concentrations (driving chemical reactions) would drop to levels too low to significantly drive a reaction.
Some call it the RNA, membrane, metabolism world.

There are different proposed molecular mechanisms for sequestering from the environment:

• membrane (bi-lipid layers, like cells have now)
• protein layer; some viruses have protein shells with no lipids, but this would probably initially not be so well structured
• Some kind of sequestering by differential adhesion between the molecules in a pahse separation kind of way (like oil and water sequester from each other). Non-membrane delimited cytoplasmic regions have recently been discovered, presumably based on differential adhesion between their molecular components.

In addition, an initial source for organic molecules would have to exist. Either from some external source, or from some form of molecular production with in the pre-biological entity. Most assumptions about this are that a variety of molecules would be produced, lipids, peptides (perhaps sequence skewed in some way), small molecules involved in some of the most basic metabolic pathways (some basic metabolic pathway reactions seem be able to proceed without catalysis).
It may be relatively easy for metabolism to begin.

This is all way before what is considered to be the last common universal ancestor (of all current (non-viral (meaning cellular) life).
Traits based largely on the commonalities between bacteria and archaea (look like bacteria, but are genetically distinct) include:
a delimiting cellular membrane
DNA (but not the DNA synthesizing enzymes which are different between archaea and bacteria). Therefore, the protein enzymes to produce DNA were most likely evolved after the universal last common ancestor (just before the separation point, in evolution, between the bacteria and archaea). RNA gene perhaps?
A very complicated electron transfer system which pumps protons (H⁺) across the cell membrane, creating a difference in (H⁺) concentration across the membrane. This in turn, is used to drive a large molecular turbine (driven by (H⁺) going back across the membrane), to make ATP from ADP inside the cell, by making some use of the rotation energy to force the bound molecules ADP and P to react and form ATP.
These alone require several large genes that work together (so these would have to be kept together for future success, implies improvements in genetic transmission between generations).
Genetic system and something like a ribosome (a DNA-protein machine, nucleic acid sequence dependent protein production system) would be needed to produce these things.
The membrane lipids are also different between the two groups. This means that lipid synthetic enzyme genes were probably different.
The earliest membranes are usually thought to be composed of whatever lipids (probably a mix) were generated from whatever the process was initially supplying organic molecules to the life development site.
Therefore, different set of synthetic enzyme genes probably arose (probably as something like RNA genes) in the two different lines that lead to the archaea and bacteria.

So all this stuff (and probably some others I am not now remembering) was present (or (in the case of DNA synthetic enzymes) soon after the archaea-bacteria split).
These were very well developed complex molecular systems, well adapted to using environmental energy to make replicas of themselves, which out-competed their more poorly adapted neighbors.

What I thinking about are to simplest molecular things that could fulfill these requirements (which are very complex in the last universal ancestor).
What should they be called?
Agents?
Seems to be more than just an entity to me.

 

[Ygggdrasil]

Yes. Exactly!

To be more specific and clear, I am talking about something (assembled from molecules) which is able to:

• acquire energy from its environment
• maintain its molecular components distinct from its environment (containment physically speaking)
• produce its own molecular components
• make functional replicas of itself

The most simple list of requirements would be:

• a cell membrane (or its equivalent)
• a relationship with its environment so that it can acquire energy (probably chemical)
• a metabolism, so the acquired energy is directed to productive uses for the entity
• a way to make functional copies of itself

I have heard the term protocell used to describe something like this (perhaps having its basis on Jack Szostak's work on replicating vesicles).

 

[BillTre]

I have heard the term protocell used to describe something like this (perhaps having its basis on Jack Szostak's work on replicating vesicles).

I have also considered terms like those. However, they imply a limiting bi-lipid membrane (actually what my favorite process of life arising).

However, there are possible scenarios that make use of other isolation mechanisms.
To not limit the possible limiting mechanisms, such as a membrane-like function from enveloping peptides, or a differential adhesion basis of isolating components, I would rather avoid words implying biochemical details like a normal cellular membrane, even though that directly to membranes seems the most likely path that things on Earth might have followed.

 

[Ygggdrasil]

BTW, for those generally interested in the topic of the origin of life, the University of Chicago has been hosting an interdisciplinary seminar series on this topic: https://physicalsciences.uchicago.edu/events/origins-of-life-speaker-series/

The lectures are hosted on Zoom and open to the public (the last lecture in the series is tomorrow) and videos of the lectures are freely available on YouTube (the videos can be accessed from the link above). I'd recommend John Sutherland's talk about prebiotic chemistry as one of my favorites of the series, but there are some that may be more relevant to the topic of this thread (e.g. Anna Wang's talk).

 

[BillTre]

BTW, for those generally interested in the topic of the origin of life, the University of Chicago has been hosting an interdisciplinary seminar series on this topic: https://physicalsciences.uchicago.edu/events/origins-of-life-speaker-series/

The lectures are hosted on Zoom and open to the public (the last lecture in the series is tomorrow) and videos of the lectures are freely available on YouTube (the videos can be accessed from the link above). I'd recommend John Sutherland's talk about prebiotic chemistry as one of my favorites of the series, but there are some that may be more relevant to the topic of this thread (e.g. Anna Wang's talk).

Well that sounds GREAT!
Now I have several hours of videos to watch on something I'm very interested in.

They also seem to have two talks about a facet of this issue which I feel I have limited knowledge of: the delivery of organic molecules from space, as opposed to them being generated by various possible processes on earth. To me this process seems so small in volume and not concentrated at specific sites life origination that I have doubts about its import. Maybe I will learn something.