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To: Alamo-Girl
What Doctor Stochastic calls being “active” and what Ichneumon calls “operating” is what I have been reading as “information”, i.e. “successful communication”.

Information is distinct from communication, just as electrons are distinct from electricity. It doesn't help to blur the distinctions between the two, it only muddies the issue.

Both of you have prejudiced your verb choice with biochemical causation. But it seems to me that suggesting cause is circular reasoning and thus should not be a factor in answering the question,

Have you not "prejudiced your verb choice" with information? And is this thus circular reasoning?

especially since both the live and dead cells have the same basic chemical composition and DNA.

But not the same chemical *activity*, which is why we indicated that the activity was the key. In stating that "information" is the crux, you're on less solid ground since the "same basic chemical composition and DNA" indicates a similarity in information content.

"Activity" or "operation" are fairly close to "information"

I quite disagree.

but IMHO fall short in that you could shake a dead skin cell like a martini and it would still not be alive.

Vibration is not the same as "operating machinery". Shake an auto junkyard and the junked cars will not begin to run again.

IOW, such activity or operation must be also be autonomous and meaningful. Therefore, I prefer the word I see used most often to describe it: information (successful communication).

So a computer network is alive?

The dead skin cell has ceased to communicate.

I think you need to tighten up your definition here. With what does a tree "communicate"? Or a single-celled photosynthesizing algae?

And what is the distinction between "communication" and "exchange"? Is a decomposing cow corpse alive because it exchanges tissues and gases with the bacteria consuming it, and the surrounding environment? Is a dead whithering plant alive when it "communicates" its water content to the atmosphere?

723 posted on 07/07/2004 11:54:45 PM PDT by Ichneumon ("...she might as well have been a space alien." - Bill Clinton, on Hillary, "My Life", p. 182)
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To: Ichneumon; Sola Veritas
Thank you for your replies!

Information is distinct from communication, just as electrons are distinct from electricity. It doesn't help to blur the distinctions between the two, it only muddies the issue.

This is a common misunderstanding of the term "information" wrt information theory and molecular biology. Most people have a tendency to think of information like a sheet of paper or database or DNA – an informative “thing”. But information theory as it is used in molecular biology is more specific which is why I keep raising the name Shannon and give a paraphrased definition for information, i.e. information is successful communication. Which is to say that information is the successful communication per se and not the message by itself.

This might be a bit clearer by referring back to the links provided by Doctor Stochastic at post 674 and by me at post 684. From that post, here is the definition of information:

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

And here’s more to untangle the confusion:

I'm Confused: How Could Information Equal Entropy?

If someone says that information = uncertainty = entropy, then they are confused, or something was not stated that should have been. Those equalities lead to a contradiction, since entropy of a system increases as the system becomes more disordered. So information corresponds to disorder according to this confusion.

If you always take information to be a decrease in uncertainty at the receiver and you will get straightened out:

R = Hbefore - Hafter.

where H is the Shannon uncertainty:

H = - sum (from i = 1 to number of symbols) Pi log2 Pi (bits per symbol)

and Pi is the probability of the ith symbol. If you don't understand this, please refer to "Is There a Quick Introduction to Information Theory Somewhere?".

Imagine that we are in communication and that we have agreed on an alphabet. Before I send you a bunch of characters, you are uncertain (Hbefore) as to what I'm about to send. After you receive a character, your uncertainty goes down (to Hafter). Hafter is never zero because of noise in the communication system. Your decrease in uncertainty is the information (R) that you gain.

Since Hbefore and Hafter are state functions, this makes R a function of state. It allows you to lose information (it's called forgetting). You can put information into a computer and then remove it in a cycle.

Many of the statements in the early literature assumed a noiseless channel, so the uncertainty after receipt is zero (Hafter=0). This leads to the SPECIAL CASE where R = Hbefore. But Hbefore is NOT "the uncertainty", it is the uncertainty of the receiver BEFORE RECEIVING THE MESSAGE.

[snip]

You continued:

Have you not "prejudiced your verb choice" with information? And is this thus circular reasoning?

Not at all. I have not presumed a cause. In fact, the cause of such information is very much open research to this very day.

So a computer network is alive?

Computer networks are not autonomous. Artificial Intelligence researchers however seek to develop such an autonomous entity.

With what does a tree "communicate"? Or a single-celled photosynthesizing algae?

In both cases, itself and its environment.

And what is the distinction between "communication" and "exchange"? Is a decomposing cow corpse alive because it exchanges tissues and gases with the bacteria consuming it, and the surrounding environment?

The bacteria is alive because it has information (Shannon, paraphrased as successful communication) – the cow is dead, because it ceases such communication.

Is a dead whithering plant alive when it "communicates" its water content to the atmosphere?

The plant is not communicating with itself or its environment.

And on your other reply, you asked:

How is "dormant" different from "dead" (or "alive" for that matter)? I don't think that's going to be an easy one to answer without begging the question of the definition of "alive".

It all comes down to information (Shannon, paraphrased as successful communication). A spore is dormant but still has information. That means it is alive albeit in a very deep vegetative state. Once it detects a food source, the spore comes out of its dormant state. The anthrax spore is alive.

Bacillus anthracis is a relatively large (1-2 µm), Gram-positive, spore-forming, non-motile, non-flagellated facultative anaerobe. The spores are exceptionally stable under extreme conditions and can survive decades of dormancy. The microorganism grows readily on certain nutrient media, including those containing blood. The processes of sporulation [formation of spores] and capsule formation are observed only when the bacteria are cultivated on certain nutrient media and under certain conditions.

The life cycle of Bacillus anthracis has four major phases: vegetative phase (from spores to replicating bacteria), intense growth phase, stationary phase, and sporulation phase. Anthrax spores have a relatively high level of resistance to high temperatures and disinfectants.

Bacillus anthracis forms a poly-D-glutamic acid capsule while in the host animal, when grown with nutrient media containing blood or blood plasma, and in the presence of CO2. Bacillus anthracis does not sporulate in so-called "capsule-forming" media as efficiently as when it is cultivated in vivo. According to current knowledge, the capsule is neither immunogenic nor toxigenic, but is considered as a virulence factor as it protects anthrax vegetative cells from the bactericidal components of serum and phagocytosis. The capsule plays its most important role during the establishment of infection and is believed to be less significant in later stages of the disease, which are mediated by the anthrax toxin.

BTW, speaking of things coming out of a dormant state with a vengeance, here is the spooky life cycle of the Pfiesteria


852 posted on 07/08/2004 10:24:17 PM PDT by Alamo-Girl
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