Replies

The Shannon definition for information (which I prefer to paraphrase as successful communication) is this: the reduction of uncertainty (Shannon entropy) in a receiver or molecular machine in going from a before state to an after state.

My computer does that too.

It is measured in bits – not binary – as the after entropy less the before entropy.

Bits *ARE* binary. "Bit" = "binary digit".

In nature, non-living and dead organisms do not communicate successfully, living organisms do communicate successfully.

Okay, I'll bite -- what is a "non-living organism"?

For that matter, please define "organism" in a way that does not circularly depends on a definition of the word "life".

Why "in nature"? What is "outside of nature"?

My computer "communicates successfully" -- is it alive? (Again, be sure not to beg the question by limiting your "definition of organism" in a way that circularly depends on the definition of life, or vice versa).

Therefore, I can define life mathematically by positive Shannon bits which occur in natural systems ---- and death/non-life by Shannon bits which occur in natural systems less than 1.

"Natural systems less than 1"? Huh?

My computer is natural -- it obeys all the laws of nature. Why is it not alive? (See: "please define natural" above).

A "dead" carcass in an acid bath exchanges Shannon information with the acid molecules. Is it therefore alive?

The measure can be taken by organism at space/time coordinate. It can also be applied to particular molecular machinery at space/time coordinate (brain dead, cardiovascular alive, etc.)

As opposed to "measure taken not at space/time coordinate"? Give an example of the latter.

Naturally, the space/time coordinate is necessary because the Shannon bits must be quantized in the continuum of space/time.

Well, "naturally"... Just as "naturally, the crystal energy is necessary because the cosmic vibration must be resonated in the continuum of the aura".

Got bits?

Binary bits, even.

Thank you for your reply!

me: It is measured in bits – not binary – as the after entropy less the before entropy.

you: Bits *ARE* binary. "Bit" = "binary digit".

That is the usual understanding of “bit” but it means something different in Shannon information theory:

Schneider: Glossary for Molecular Information Theory

bit: A binary digit, or the amount of information required to distinguish between two equally likely possibilities or choices. If I tell you that a coin is 'heads' then you learn one bit of information. It's like a knife slice between the possibilities: … Likewise, if a protein picks one of the 4 bases, then it makes a two bit choice ….

For 8 things it takes 3 bits. In simple cases the number of bits is the log base 2 of the number of choices or messages M: bits = log2M. Claude Shannon figured out how to compute the average information when the choices are not equally likely. The reason for using this measure is that when two communication systems are independent, the number of bits is additive. The log is the only mathematical measure that has this property! Both of the properties of averaging and additivity are important for sequence logos and sequence walkers. Even in the early days of computers and information theory people recognized that there were already two definitions of bit and that nothing could be done about it. The most common definition is 'binary digit', usually a 0 or a 1 in a computer. This definition allows only for two integer values. The definition that Shannon came up with is an average number of bits that describes an entire communication message (or, in molecular biology, a set of aligned protein sequences or nucleic-acid binding sites). This latter definition allows for real numbers. Fortunately the two definitions can be distinguished by context.

Or you can read about it yourself here: Shannon: Mathematical Theory of Communications(on page 2)

me: In nature, non-living and dead organisms do not communicate successfully, living organisms do communicate successfully.

you: Okay, I'll bite -- what is a "non-living organism"?

I should have used the term “non-life” an obvious noun instead of “non-living” which can be taken as an adjective, which you have done here.

Non-life includes such things as stars and rocks as distinguished from previously alive organisms which are now dead.

The "nature" term is key, which is why I kept repeating it. The object of the definition is to define life v non-life or death in nature. What constitutes “life” in artificial intelligence is for another discussion. Here we are speaking of the quantization of the continuum to define non-life v. life with regard to a theory of abiogenesis (life from non-life).

me: Therefore, I can define life mathematically by positive Shannon bits which occur in natural systems ---- and death/non-life by Shannon bits which occur in natural systems less than 1.

you: "Natural systems less than 1"? Huh?

To rephrase: if you calculate the Shannon bits for a “thing” which occurs in nature and the bits are >0 then it is alive. If the bits are <1 it is either non-life or dead (previously alive, now dead).

A "dead" carcass in an acid bath exchanges Shannon information with the acid molecules. Is it therefore alive?

A successful communication includes the following elements which are not present in your example: source, message, encoder, channel, noise, decoder, receiver. The state change of reducing uncertainty (entropy) in the receiver is the information – an action, not the message. It is measured in bits gained and is offset by a dissipation of energy into the local surroundings (thermodynamics).

Catalytic RNA fails the mark for the same reason. However, along with viruses and prions they would be considered an element of the model, i.e. “noise”. In the Shannon model applied to molecular biology, noise is often seen as the equivalent of “random mutations” – albeit “randomness” cannot be determined at that scale (one would have to look at the complete system) - noise is nevertheless the source of mutation.

me: The measure can be taken by organism at space/time coordinate. It can also be applied to particular molecular machinery at space/time coordinate (brain dead, cardiovascular alive, etc.)

you: As opposed to "measure taken not at space/time coordinate"? Give an example of the latter.

A measure not taken at a particular space/time coordinate would be one which applies to all of space/time as unity. In cosmology, the equivalent concept is Omega – or critical mass density of the universe, which is 1 for a universe that neither collapses on itself nor expands forever.

If we were to take the Shannon measure as a single number in the cosmos - unity, I suspect it would have a similar equilibrium as that appears to be a common thread, e.g. thermodynamics, critical mass density, matter v antimatter. AFAIK, noone has attempted such a universal model of Shannon entropy.

Nevertheless, I propose the meaningful application of Shannon is to an entity - existing at a specified space/time coordinate – to define that which is alive v that which is dead v that which is non-life.

IOW, you would measure as "alive" under the Shannon model today because you have bits greater than 0. Somewhere in the future, you will be dead and have no bits. Today, alive – tomorrow, dead. Shannon defines both at their unique point in space/time (a quanitization of the continuum).

One of the neat properties of a mathematical model is that it can be tested and applied across boundaries.

For instance, the Shannon theory can be applied both to the classic organism (e.g. the man) and to the component molecular machinery (e.g. the kidneys, brain, etc.). Thus we can say the kidneys are no longer successfully communicating within the body and are dead, yet the greater organism (the man) lives because successful communications are yet occuring at that level.

The same concept (at a particular slice of space/time) could be taken to quantum levels and cosmic levels to see its applicability.

For instance, at the quantum, we might ask if messenger bosons are a useful construct within Shannon communication theory? IOW, this is where we would look for a field-like "will to live" that permeates every cell which successfully communicates - either as an autonomous entity or within the molecular machinery of a greater organism.

Likewise, at the cosmic level, we might ask the information content of the universe, i.e. looking at the universe as a whole organism.

Perhaps that will make the quantizing issue more clear? When there is no successful communication at all, anywhere in space/time - there is no life. That is the beginning point for all theories of abiogenesis.

It, of course, has profound theological significance as well to the Judeo/Christian community because God spoke everything into being. We do, BTW, see sound wave artifacts in the CMB.

And, as we discussed on the other thread (and to which betty boop and I are preparing an article-response) - there are levels of willfulness, the least of which appears to be universal, the "will to live" which applies universally to individual cells regardless of organisms and collectives. The higher will, self-will, is unique to man. And beyond that is a spiritual longing ("ears to hear") which transcends space/time altogether and a presence in both simultaneously unique to those in whom the Spirit dwells. All of this is observed (though not by all men) and is Scriptural.

For Christian Lurkers: the concept of the creation (universe, physical realm) as a whole willful entity is contained in Romans 8.