On Plato, the Early Church, and Modern Science: An Eclectic Meditation

November 30, 2004 | Jean F. Drew

[Alamo-Girl]

Thank you for your reply!

Unclear. Do you mean "what is life, in natural systems as they exist in fact today," or "what is life, in natural systems as they have ever existed in fact," or "what is life, as it could exist in natural systems in principle"? We can't answer the first question, and then dismiss the abiogenesis question as if that first answer also satisfies the second and third questions.

We are speaking to life, in natural systems as they exist in fact today from the level of our minds, senses and sight - or higher, with regard to the universe.

We are not looking downward to constituent continuums of inorganic corpuscles, fields or geometry. We are not looking backward in time as to how such life came to be. We are not looking forward in time as to how it might be simulated.

The principles of natural life are on the table to the extent they are within the reach of our minds.

The entire inquiry of abiogenesis is erased from our blackboard because it is a waste of time. IOW, many here have already said the result would be "idle speculation" on the grounds of the fallacy of quantizing the continuum. So why bother?

Obvious, yes. And likewise, only an arrant fool would suggest that there's any difficulty in separating snakes from lizards. But again, there is no definition of "snake" that will unambiguously separate snakes from lizards at all times in the past, no matter how self-evident the distinction is today.

Again, we are not looking for a definition of life which would apply backwards in time or to lower tiers of continuum. We are looking at the level of our vision and minds, here and now, and only with regard to natural life.

The "snake/lizard and continuum of the geologic record" item is quite interesting in that it explores the fallacy of quantizing the continuum and the theory of evolution. But we are trying to keep any discussions of evolution off this thread because they tend to become confrontational. This thread, on the other hand, is characterized by mutual respect and a sincere desire to understand one another and the questions before us.

It doesn't seem to me that viruses meet this definition. If they do, then I submit that many computer programs and chain letters also do.

I was giving a shorthand summary of betty boop's post at 753. In context of the exanded verbiage on her post, manufactured intelligence with today's technology would fail Bauer's characterization on various points (thermodynamics, sensitiviity, etc.)

[Alamo-Girl]

Again the metaphor returns to me of scientists fumbling with keys convinced that one of them will fit the lock all the while not actually looking at the lock itself; perhaps if they did they would notice it is a combination lock.

Thank you for all of your posts which ever encourage us to look!

[Matchett-PI]

Oh, my goodness - how rude of me! As I was going through some of my older pings, I just now realized that I forgot to follow up on your response here in # 525 to my questions. I don't have time to get to it right now, but wanted to let you know that I will hopefully get the time to make my reply to your post later on today.

[js1138]

I am truly amazed that the question of ”what is life?” meets with such obfuscation.

I would call it clarification rather than obfusction. Your (and Betty's)examples of live vs dead have been rigged to make the question seem absurd, but the question isn't absurd.

You have presented us with two quite different criteria for distinguishing life from non-life. One is abstract and relies on structure and behavior; the other depends on the history of the object (is it natural?).

What would be the status of an entity that looks and behaves like a bacteria, but which is manufactured from "non-living" materials and which utilizes amino-acids not found in "natural" living things?

What would be that status of an albatros whose heart hs not beaten in the last 30 seconds?

[Alamo-Girl]

Thank you for your reply!

Your (and Betty's)examples of live vs dead have been rigged to make the question seem absurd, but the question isn't absurd.

Neither betty boop nor I are "rigging" the question or making the question "absurd".

At least as early as Pearson it became a question for science. Bauer addressed the question through scientific observations. Pattee asked the same question from the aspect of physics and noted the lack of interest by biologists. Schneider's work in molecular biology for cancer research points to a clear distinction based on Shannon-Weaver.

You have presented us with two quite different criteria for distinguishing life from non-life. One is abstract and relies on structure and behavior; the other depends on the history of the object (is it natural?).

We presented both, but they are not either/or. The Shannon model allows us to measure information in laboratory conditions so that natural life (if you accept the Shannon derived definition) can be objectively and scientifically detected - and it does not conflict with Bauer's characterizations.

What would be the status of an entity that looks and behaves like a bacteria, but which is manufactured from "non-living" materials and which utilizes amino-acids not found in "natural" living things?

Again, we are only looking at the here-and-now, not the future possibilities. The closest thing you have in the here-and-now is the laboratory manufacture of the polio virus, which was indeed alive. It was however made from existing natural life (Shannon definition) and thus there is no bright line distinction.

What would be that status of an albatros whose heart hs not beaten in the last 30 seconds?

Truly, I'm not sure whether a 30 second pause in communications of the molecular machinery of the albatros' heart would be sufficient to preclude subsequent communications (reduction of uncertainty of a receiver, a molecular machine in going from a before state to an after state). If so, that molecular machinery is dead - and the lack of successful communications would likely spread to the interrelated molecular machinery comprising the bird, causing the death of the global organism, the bird.

In humans, a myocardial infarction will result in cell death (no more cellular successful communications) in certain physical areas of the heart. If successful communications within the molecular machinery can continue at the reduced rate, the machinery will eventually route blood flow around the dead cells and continue functioning, i.e. successfully communicating, reduction of uncertainty in the receiver, in molecular machines going from a before state to an after state.

It's when the communication ceases in the entire molecular machinery, that it may (if the function of the molecular machine is vital) spread to other molecular machinery and death of the globally governing organism, the man, ensues. IOW, the body of the man reaches the point where none of the vital molecular machinery communcates.

The definition of what is "vital" molecular machinery determines the legal and clinical definition of "death". Currently I believe the definition hinges on the heart, i.e. a person can be brain dead and nevertheless clinically alive because the heart continues with assistance of a respirator simulating the machinery of the brain for that particular molecular machinery, i.e. forcing air into/out of the lungs rather than communicating to the lungs to expand/contract.

[js1138]

I'm curious what it would take o have something that was not made from existing natural life. Are you referring to the blueprint? Is anything that copies an existing structure automatical natural? Are you referring to the manufacturing machinery?

What specifically is it that makes something natural?

[js1138]

I am not trying to hijack the thread or divert it into a ditch. I was pinged to it at a point where a question that is interesting to me was being posed.

It seems to me that to have a conversation you need to agree on basic torms, or at least pause while those definitions are being considered. I am not aware of any universally accepted definition of life. I would say that your proposed definitions are valuable subsets of such a definition, but are not exhaustive. In particular, they fail to distinguish between natural and synthetic in cases where the history is unknown. They also fail to distinguish hard cases, such as those presented by prions, viruses, and bacterial spores.

There is no particular reason to have an elaborate and abstract definition of life to distinguish complex living organisms from dead tissue. The need for a definition arises in hard cases, such as those presented by the prospect of laboratory biogenesis, or the prospect of cybernetic intlligence. A definition must necessarily be free of historical context, because history makes the definition unnecessary.

[Alamo-Girl]

Thank you for your reply!

I'm curious what it would take o have something that was not made from existing natural life. Are you referring to the blueprint? Is anything that copies an existing structure automatical natural? Are you referring to the manufacturing machinery?

In the polio virus example, naturally existing biological life was used for parts and medium in its manufacturer in a test tube. At the root, the organism was naturally alive as would be a cloned sheep, an organism with altered DNA, a man with a heart transplant or a brain dead person on a respirator.

In your next post, you said:

I am not aware of any universally accepted definition of life. I would say that your proposed definitions are valuable subsets of such a definition, but are not exhaustive.

If you have a more exhaustive definition, I'd certainly like to hear it!

I am not aware of any universally accepted definition of life. I would say that your proposed definitions are valuable subsets of such a definition, but are not exhaustive. In particular, they fail to distinguish between natural and synthetic in cases where the history is unknown. They also fail to distinguish hard cases, such as those presented by prions, viruses, and bacterial spores.

The Shannon definition clearly includes all life cycles and forms: viruses, bacteria, spores and prions (a single cell lifeform). In particular, the Shannon information definition helps us to understand miscommunication of prions and viruses and noise in the channel that can cause mutations, cancers, etc. AFAIK, there is no more elegant or useful definition of life v non-life/death than Shannon information.

There is no particular reason to have an elaborate and abstract definition of life to distinguish complex living organisms from dead tissue. The need for a definition arises in hard cases, such as those presented by the prospect of laboratory biogenesis, or the prospect of cybernetic intlligence.

The Shannon definition is not abstract or elaborate, it is the mathematics of communications. The purpose of a definition goes to biology, medicine, cosmology, physics, philosophy, theology as well as artificial intelligence.

A definition must necessarily be free of historical context, because history makes the definition unnecessary.

Causation seems to be a stumbling block for you though it is not part of the question at all. On the previous post you asked:

What specifically is it that makes something natural?

It occurs in nature. Nature is the primitive, untouched state of the material world.

If it would help to make the posters more comfortable with the subject, perhaps we could separate the issue of natural life which is involuntary - i.e. not the result of discernible intent other than the indirect desire for sex - from natural life which results from intention - i.e. God as Creator, collective consciousness of the universe, scientists making polio viruses, altering DNA, substituting molecular machinery, etc.

IOW, intention could be raised as subject number "next" after we first answer: "in the natural world, what is life?" unless of course one believes there can be no life without intent.

[js1138]

Prions, viruses and bacterial spores are metabolically stable. At least they do not metabolize.

Am I wrong about this?

[Alamo-Girl]

As I recall, spores do indeed metabolize and viral metabolization is a symbiosis with its host. I believe the virus model is akin to prion metabolism.

In any case, the Shannon-Weaver model works well to integrate their life cycle with the host, i.e. as a miscommunication. Metabolism is not a factor in Shannon-Weaver.

[Alamo-Girl]

Metabolism is not a factor in Shannon-Weaver.

Rats. I should have explained.

The Shannon-Weaver does not concern itself at all with the value of the message itself - only the mathematics of the communication. Whether the message tends to health or mad cow disease - the math is the same.

[js1138]

Is the "aliveness" of a virus intrinsic, or is it alive only in relation to its host?

Regarding spores, I found this:

"Many bacteria form a single spore when their food supply runs low. Most of the water is removed from the spore and metabolism ceases. Spores are so resistant to adverse conditions of dryness and temperature that they may remain viable even after 50 years of dormancy."

http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/E/Eubacteria.html

[Doctor Stochastic]

To be absolutely clear, the question is "in natural systems, what is life?"What is an "unnatural" system? I know that the Greens define everything that isn't human as "natura" and human created objects as pollution. Are not humans and their constructs every bit as natural as anyting else?

[Doctor Stochastic]

Actually, viruses use a different method from prions.

Viruses feed their own genetic data to a "host" reproducing machine; the host then reproduces the virus. Viruses work by means of normal genetic pathways. People do not (at least I can't find an example) spontaneously generate viral infections.

Prions are just proteins that crystallize differently. Prions do not use genetic mechanisms for infection. Also, unlike viruses, prion-like diseases may form spontaneously in people (and probably other mammals.) The tendency to form prions is genetic; but the prion's infection does not spread by genetic means. If a person is susceptible to prion infection, getting a prion into the relevant tissue (brain, nerve) triggers crystallization sort of like a seed cry stall does in a saturated sugar solution. Prions are (so far) the only infectious agents that do not contain genetic material. This make them hard to de-ativate. Keywords: Creuzfeld-Jacobsen, Scrappie, Alpers, inter alia. Vide.

[Alamo-Girl]

Thank y’all so much for your replies and the fascinating links!

But once again I must stress that the Shannon-Weaver model is the mathematics of communications and does not address the value of the message at all. So under Shannon-Weaver it doesn’t matter that prions are only proteins, that mycoplasmas have no cell walls, that viroids are RNA without a protein coat. They fit within the communication model. The model addresses source, message, encoder, channel, decoder, receiver and noise. Noise can result in a miscommunication of an intended message and therefore, a malfunction (or perhaps improvement) in the molecular machine.

The bottom line to Shannon-Weaver is information, the reduction of uncertainty of the receiver in going from a before state to an after state. It is all about communications and all of these “lifeforms” are part of the communications (or miscommunications) in molecular machines.

If we were to proceed down the path of questioning whether the lowly virus, prion and viroid are “alive” – then we would be appealing to definitions of life which make “cuts” based on biochemical boundaries. Such cuts open the door for other types of arguments such as the following:

Evidence for Creation

There are those who see an unbroken continuum between living and nonliving matter. If this is so, the question of life's origin becomes a moot point. Viruses, prions, mycoplasmas, rickettsiae and chlamidiae are offered as examples of organisms that bridge the chasm between living and nonliving. But the differences between living and nonliving matter are in fact so great that this chasm cannot be spanned.

Although viruses and prions are made from biopolymers, they are no more alive than the enzyme additives in some detergents. Viruses are lifeless complexes of proteins and nucleic acids. The biological activity of viruses, including their replication, is completely dependent on the metabolic activity of the infected cell. Prions are unique proteins that alter the structure of certain other proteins. The newly changed proteins in turn acquire prion-type activity, creating a domino effect of protein alteration. This property of prions renders them infectious. For reproduction, prions, like viruses, are wholly dependent on live cells.

Rickettsiae, chlamidiae and mycoplasmas, on the other hand, are among the smallest known living organisms, and are very much alive. The fact that chlamidiae and rickettsiae are obligate intracellular parasites only means that they have serious metabolic deficiencies. A clear distinction between living entities and nonliving substances is essential for a consideration of whether it is possible to go from one state to the other. For this reason we need to descend into the submicroscopic world of matter.

The elemental compositions of living and nonliving matter differ greatly.4 The actual chemical determination of living matter is done on "once-living matter". Before chemists can analyze living matter, they have to take it apart to isolate its individual components, thereby killing it. Thus the actual phenomenon of "life" is not amenable to detailed chemical scrutiny. In the very process of laying hold of isolated "purified" components of living matter, "life" slips out between the chemists' fingers, and what remains is an inert, "lifeless" substance. This is so because living cells are composed of lifeless, nonliving components. The implication is that the difference between life and death is a question of how biomatter is organized. Therefore, it should be possible to reverse the killing of cells by restoring them to their pre-disruption state. Why this has not yet been done in the laboratory will be discussed in the next chapter.

… In presenting a case for a tight logical link between analyzing the molecular aspects of life and the creationist paradigm, it is not enough to enumerate the components of living matter. Simply knowing the components of living matter is not enough to account for its biological activity.

Living matter behaves differently than its isolated components. Living cells incorporate selected substances and utilize them either for energy or as building blocks for growth. They also secrete metabolic waste. Living cells grow and divide into daughter cells. Lastly, when cells recognize unfavorable environmental conditions, they make metabolic adjustments to preserve their existence.1 Living matter gives every indication that it "wants" to stay alive. This is a property of the complex network of components in living matter. The whole seems to be more than the sum of its parts.

If we collect all of the ingredients from live cells, lace them in a membrane-enclosed vesicle, we have an inert, "lifeless" assembly of biomatter. This bag may be stored indefinitely in an environment hospitable for life, without the actual emergence of life. If we periodically analyzed the contents of this artificial "cell", we would find little change in its chemical composition. Such an arrangement of matter is called equilibrium.2

If we sampled the composition of life cells growing in a defined laboratory setting, surprisingly, the results would be similar, that is, we would find the chemical composition of live cells quite constant. But instead of the term "equilibrium", we say that matter in live cells is in a "steady state system". The significant difference between the two is the dynamic flux of matter through live cells.

A mechanical illustration of this difference is shown in Figure 3.1. Here, the contents of both vessels remain unchanged over time, but there is constant movement of liquid through vessel A. The flow of molecules through cells is an essential feature of life. (In contrast, the liquid in container B is stagnant.) The movement of water through a compartment, representing the flux of matter through the cell, is an oversimplification of what actually occurs. In reality matter changes as it travels through the cell. The incoming precursors (biomonomers) are simple substances which are gradually built up to successively more complex structures.

I can certainly understand the desire of some to answer ”in nature, what is life?” by describing the biochemical characteristics.

However, I do not believe that approach is adequate because it does indeed toss prions, viroids and viruses into the non-living bucket whereas they are the channel (or noise) for mutation (or miscommunications) in living systems.

IOW, excluding them from the model for "what is life v non-life/death" also puts the mechanism for evolution off the table – which evidently is the intent of the above article.

Shannon-Weaver, OTOH, does not disturb even the classic model of evolution which I personally find out-of-date, nor does it disturb any of the newer von Neumann based models, nor does it speak yeah or nay to abiogenesis, nor does it preclude either Intelligent Design or Young Earth Creationist. It is ideologically and theologically neutral on top of being elegant.

However, if the consensus here is to go with a biochemical definition - then I'm "game" for trying to nail the characteristics.

[betty boop]

Hello Alamo-Girl!

js1138 writes: I am not aware of any universally accepted definition of life. I would say that your proposed definitions are valuable subsets of such a definition, but are not exhaustive. In particular, they fail to distinguish between natural and synthetic in cases where the history is unknown. They also fail to distinguish hard cases, such as those presented by prions, viruses, and bacterial spores.

To which you replied: If you have a more exhaustive definition, I'd certainly like to hear it!

You can ditto me on that, A-G!!! I just love it: here we have a thread that is unambiguously devoted to the great subject of being (that is, life), and we have to quibble over whether being is natural, or might it be artificial? Quibbles are also raised about the sufficiency of proposed basic qualities or characteristics of life. One is informed that they are useless because they can’t instantly “distinguish [and answer] the hard cases.”

Good grief! It seems to me (and I’m sure many of our friends here will find this controversial) that if the “hard AI” guys want to build an intelligent machine to the standard of von Neumann’s probe then the very first thing they need to do is to figure out how Nature creates a living system.

Actually, I imagine that Bauer’s observations (rigorously, relentlessly reduced to mathematics) about processes and qualities of living systems shed light even on the hard cases — which a person might notice if he’s paying attention.

Since I don’t read German, Russian, or Hungarian – the only languages in which he is published -- Bauer’s work has been translated to me by a friend. The formulae are the same from text to text I gather – ah, mathematics, sublime universal language!!! [More of your “unreasonable effectiveness of math” here, Alamo-Girl!]

But since we have been chasing down phantasms most recently – in particular the by-now famous Fallacy of the Quantized Continuum, as perfect a description of how to arrange an entirely pointless exercise that I can imagine – we’ve wandered far from the original mission.

I think it’s time for course correction. How shall we proceed? You note that Shannon information theory is not concerned (or even interested, it seems), in the “message” being communicated. Ultimately the theory drives to the status of the receiver after the message has been communicated. The communication is said to be “successful” if it produces a “reduction of uncertainty” in the receiver.

We have many possibilities for further discussion here. The first pertains to the sender: the source of the message being communicated; second, the nature, quality, or meaning of the message (its semiotic quality); third, the physical route by which it is transmitted and received; and fourth, what the receiver “does with it” so that communication is successful at the receiver’s end (such that a reduction in uncertainty will occur, facilitating the life interest of the receiver by suitably “informing” its choices. Not very scientifically put; but I think it’s an accurate description).

Where shall we go from here?

Oh, a last thought, though a depressing one. Just a little cite from Levins and Lewontin, 1985:

Evolutionists believe organic evolution to be the negation of physical evolution. **

This statement seems twisted to me. Why these guys think biology is so privileged as to be exempt from the physical processes which make it possible is beyond me. FWIW it seems such models look like very poor candidates for the explication of life. Maybe that’s why some of our friends now tell us “don’t ask” about life (unless it’s artificial life, of course, and then it would be O.K….) on the grounds that we humans can’t tell life and non-life apart, because life is not something that can be observed in the first place, according to the scientific method (???)….

Well, good night dear Alamo-Girl, and good night all! God bless everyone reading these lines.

** Pace Levins and Lewontin; but to me, this statement is inane, and headed straight for anomie at the speed of light.

I can’t imagine, for instance, how it is possible to account for biological evolution without taking the evolution of the physical universe into account. For the “biosphere” appears to be a subsystem of this larger system. And the universe itself has evolved. Physical science tells us that certain “arrangements” very needful to the “contingent” emergence of biological systems occurred in the early universe (living organisms came ever so much later on -- just within the past 4 billion years ago, in a universe whose age is estimated at somewhere around 14 billion).

And so it seems reasonable if a person wishes to speculate about issues of teleology, which we’ll remember is the science of ends, purposes, goals – the very word “evolution” suggests development towards an end, or at the very least to a state “higher” than that achieved at present. (“Higher” also suggests the idea of an “end” in the sense of a rational or objective measure by which something can be adjudged ‘higher” or “lower.”)

[Alamo-Girl]

Thank you so very much for your excellent post!

I had no idea that Bauer's was a mathematical model. For me, the mathematics is the most objective approach - hence, the appeal of Shannon-Weaver. Perhaps we ought to take a closer look at how Bauer expressed his findings mathematically to see if it is a better model.

Math is indeed unreasonably effective, remarkably so with physics. Therefore, when a mathematical model fits, my confidence soars. Conversely, I would always wonder if a non-mathematical answer could be transportable or applied universally.

Or if you'd rather not take up Bauer, we could resume with Schneider and take an exhaustive tour of the Shannon-Weaver model. A basic chart is at post 341. A summary is at post 491. The key formulae are posted between the two.

This statement seems twisted to me. Why these guys think biology is so privileged as to be exempt from the physical processes which make it possible is beyond me. FWIW it seems such models look like very poor candidates for the explication of life. Maybe that’s why some of our friends now tell us “don’t ask” about life (unless it’s artificial life, of course, and then it would be O.K….) on the grounds that we humans can’t tell life and non-life apart, because life is not something that can be observed in the first place, according to the scientific method (???)….

LOLOLOL! Very strange indeed.

And so it seems reasonable if a person wishes to speculate about issues of teleology, which we’ll remember is the science of ends, purposes, goals – the very word “evolution” suggests development towards an end, or at the very least to a state “higher” than that achieved at present. (“Higher” also suggests the idea of an “end” in the sense of a rational or objective measure by which something can be adjudged ‘higher” or “lower.”)

So very true. Perhaps this ought to be the course correction rather than pulling out the magnifying glasses again?

I'm wondering what issues are the most important to other posters and Lurkers...

[marron]

we have to quibble over whether being is natural, or might it be artificial?

...that if the “hard AI” guys want to build an intelligent machine to the standard of von Neumann’s probe then the very first thing they need to do is to figure out how Nature creates a living system.

Actually, whether or not a living system is artificial or natural should be a side issue. As you point out, one of the things we learn from living systems is how to build such a system. In the course of attempting this, we will learn a lot about what the differences are between mechanisms that are "alive" versus those that are not.

At the simplest level, the differences can be fuzzy. But one of the ways we would recognize something as being "alive" is its ability to at least temporarily work against normal entropy, to repair itself and reproduce itself. Without this ability, if we are building them one by one, and repairing them the same way, its just a machine.

At the higher end, we would look at the kinds of things AI would be interested in, which is the mechanism's ability to rewrite portions of its own software set, which would give it some self-directed autonomy. But even at that, even if it had that ability, it would still be a machine if it could not repair and reproduce itself.

[js1138]

Evolutionists believe organic evolution to be the negation of physical evolution.

This appears to be another quote mine nugget. I haven't found the quote in context online, but it appears in the usual expected places for out-of-context quotes. Are we back to arguing Second Law stuff?

What do you take this quote to mean?

I'll take a stab at it. It means that living things have, locally, the appearance of violating thermodynamics. I would have to point out that they do this just by living, even if they don't evolve.

I have to say that this thread reminds me of how Chomsky talks about language. He tried to reduce human language to a system of symbols and syntax. He argued that syntax was built into the brain. He opposed the notion that the rules of language were learned. His view is remarkably like the view that life evolves from inner principles without any significant input from selection.

Of course his analysis only works on well formed sentences and completely disregards quirks of language such as connotation.

To get the flavor of how this works, consider a simple statement, "The dog bit John". Where is the information? Suppose there are two listeners or receivers. One has a pet pekinese that is friendly and cuddly. The other receiver is recovering from an attack by a pit bull. Is the information the same for both? Is there any way to know what the message is without having detailed knowledge of the receiver?

I am curious how you can embed information in a system that will evolve properties that are not known in advance. It would seem to me that that the shape of a Wolfram automata cannot be known in advance.

[Alamo-Girl]

Thanks for your post, js1138!

Information is not the value of the message for the very reason you describe. Meaning is derived from context.

Unfortunately, many people have a difficult time separating the two. In common usage, information implies value or meaning. However, in the mathematics of communication --- the "information" in "information theory" --- the value or meaning of a message is not an issue. That is why the Shannon theory is portable to a great many disciplines.

Information is measured as the reduction of uncertainty in the receiver. It is an action, or transaction, not a static "thing".

In the following charts, information is expressed as the structure of the transaction – the arrows between the boxes. The relationships are highly mathematical and bear out in observations of molecular machines:

From the Shannon-Weaver Model

Claude Shannon and Warren Weaver produced a general model of communication:

This is now known after them as the Shannon-Weaver Model…. The Shannon-Weaver Model (1947) proposes that all communication must include six elements:

• a source
• an encoder
• a message
• a channel
• a decoder
• a receiver

These six elements are shown graphically in the model… The emphasis here is very much on the transmission and reception of information. 'Information' is understood rather differently from the way you and I would normally use the term, as well. This model is often referred to as an 'information model' of communication.

Shannon (as applied to molecular information theory): A Glossary for Molecular Information Theory and the Delila System

information: Information is measured as the decrease in uncertainty of a receiver or molecular machine in going from the before state to the after state.

"In spite of this dependence on the coordinate system the entropy concept is as important in the continuous case as the discrete case. This is due to the fact that the derived concepts of information rate and channel capacity depend on the difference of two entropies and this difference does not depend on the coordinate frame, each of the two terms being changed by the same amount." --- Claude Shannon, A Mathematical Theory of Communication, Part III, section 20, number 3

Information is usually measured in bits per second or bits per molecular machine operation.

molecular machine: The definition given in Channel Capacity of Molecular Machines is:

1. A molecular machine is a single macromolecule or macromolecular complex.
2. A molecular machine performs a specific function for a living system.
3. A molecular machine is usually primed by an energy source.
4. A molecular machine dissipates energy as it does something specific.
5. A molecular machine `gains' information by selecting between two or more after states.
6. Molecular machines are isothermal engines.