[nasamn777]

You may have noticed the words "closed system" a couple of times above. Consider simply a black bucket of water initially at the same temperature as the air around it. If the bucket is placed in bright sunlight, it will absorb heat from the sun, as black things do. Now the water becomes warmer than the air around it, and the available energy has increased. Has entropy decreased? Has energy that was previously unavailable become available, in a closed system? No, this example is only an apparent violation of the second law. Because sunlight was admitted, the local system was not closed; the energy of sunlight was supplied from outside the local system. If we consider the larger system, including the sun, available energy has decreased and entropy has increased as required.

Your example here is somewhat unclear. It confuses some important distinctions. For example, your system is transient but moving toward equilibrium. Energy of the overall system is being dissipated. It does not capture the nonspontaneous processes related to the development of lifeforms. For example, if I had a gas that had energy flowing into the system from outside, I would not expect to see one volume of air at one temperature and the other volume of air at another temperature. The air would tend to mix together and the heat would flow through the colder wall. There would be a distribution of temperature within the fluid based on known laws. A finite element analysis of the fluid could be done to obtain the air temperature distribution if the boundary conditions are known over the given time. There is no apparent violation of the Second Law in your example, because the system is at nonequilibrium and the system is moving toward equilibrium as expected. The natural tendency (spontaneous process) is for the water to heat up due to the sunlight. A nonspontaneous process would be for ice to form on one side of the water due to the heat of the sun. Now if we had a solar collector connected to a Stirling heat engine that drives a Stirling cooler, we might see ice forming in the water. We have the thermodynamic mechanism that allows this nonspontaneous process: without the mechanism this will not happen.

The notion of the thermodynamic mechanism has relation to Dembski's conservation of information and applies to open systems.

Iin + I machine [due to constrained boundary conditions} >= Iout

An example is a computer. The computer utilizes energy to perform nonspontaneous processes. It acts as a thermodynamic mechanism. There is an informational content related to the boundary conditions of the computer. Also, the user may add an input of information by, for example, programming the computer. The sum of information into the computer plus the information associated with the thermodynamic mechanism is less than the information out. Information consequently has a relation to thermodynamic entropy.

Concerning the thermodynamic mechanism: in nature there are some simple thermodynamic mechanisms. One example is a waterfall. The water is heated due to the fact that the kinetic energy (due to the falling water) is converted to thermal energy. The water experiences a slight rise in temperature. Other natural mechanisms are self-organizing systems. These systems are very limited and are constrained due to the physics of the system. We do not expect these systems to produce stone mosaics!

[Alamo-Girl]

Thank you for your reply!

The problem with Dembski’s theory as with Manfred Eigen’s challenges to “information theory and molecular biology” is the very, very common misinterpretation of what information “is”.

In common-speak, information is the message. But that is inaccurate wrt to "information theory and molecular biology". Claude E. Shannon, the father of information theory describes information as the action, the successful communication, the reduction of uncertainty (entropy) in the receiver ---- not the message. In fact, the message is entirely beside the point which is the reason his theory is broadly applicable across many disciplines.

Here is the original Shannon theory: A Mathematical Theory of Communication

Schneider reduces it for us as follows:

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.

Geometrically speaking, it is best visualized as spheres – Shannon spheres – the collection of which would look like a gumball machine. A Glossary for Molecular Information Theory

In the Shannon-Weaver model, what Dembski and others call "information" is the "message" or "information content". Applying it to biological systems, that would put the focus on the DNA or RNA - whereas the actual dissipation of energy into the local surroundings (thermodynamics) is the consequence of the reduction of uncertainty or entropy - the communication (activity of state change).

The DNA and RNA are evidence of the semiosis, the encoding/decoding - the functional complexification in biological systems. That is a most significant area of investigation to be sure, but the greater mystery is the communication itself.

I posted the following to an earlier thread to help explain the difference:

Review of Yockey’s book

DNA as a message

In his book, Yockey uses communication theory to study the DNA-RNA-protein system in living organisms. Yockey uses the theory of communication systems not only as a metaphor, but also as a theory to describe, explain and predict phenomena in molecular biology. Here we have a communication system (telephone or CD player)

in the engineer's world:

Message in source code

Encoder Transmitter

channel

channel code Noise

channel

Decoder Receiver

Message in destination code

in the biological world:

				genetic noise: mutations		noise in genetic code. tRNA
Genetic message in DNA including tRNA		transcription into mRNA	channel	mRNA code	channel	translation into protein		Genetic message in protein code   tRNA
tRNA		independent channel (cytoplasma?)

(the independent channel is not in Yockey's book)

Continuing now with my comments…

The reviewer claims that there is no encoding process in the biological world. I believe Rocha would disagree with him. The reviewer claims that the biological world only decodes, that the genetic code is the decoder device. If it is not encoded, then why would there be any decoding...

But going back to the question of what we are looking for. It is a type of “complexity” in that we are seeking to find the source of the communication itself – in the above charts, the arrows which are connecting the boxes. The other part that we are seeking is the source for the semiosis – the language – the syntax – in the encoding and the decoding boxes. Or if one insists that no encoding has/is taking place, then the semiosis in the decoding box.

The message which is being transmitted in the graphic is the DNA. It is often called “information” but that is not the kind of information we are looking for – we are looking for what is causing the reduction of uncertainity in the receiver – the Shannon information, successful communication. The DNA itself – like the chemicals themselves – is as good dead as alive. IOW, once that successful communications ends, the biological system is dead.