[Fis] Reopening of the Reclosure of the Closure of the Bionetwork Discuss

Dear Jerry and FIS colleagues,

Thank you for the emotionally coloured clarification of the subject of our debate. In effect you say, if I understand you correctly: “Hey Karl, what’s up? Do you labour on indigestion or did you not understand the facts? If you have an opinion behind stating that what I said is false, so speak up and give good reasons.

The facts are /I still try to re-express you so we get to the core problem/:

Atomic numbers were created by the chemists for logical descriptions of empirical material observations of networks of relations, both biological and non-biological relations. Our understanding of these numbers lead directly to our understanding of DNA as the genetic material and as a source of genesis of life itself.
…
Firstly, I view all chemical processes as electrical flows. … Have you not heard of batteries?

Secondly, the language of chemistry was developed by the chemical community to express empirical observations. … you should show … that the the information of DNA can be calculated using Shannon information, or, … can calculate the number of isomers of organic molecules or that biological species are distinguishable in such language.

In other words, the absence of correspondence between arithmetic operations of mathematics and the operations of valence and covalent bond re-arrangements are well known. Or, have you solved these problems, Karl?

With regard to the third issue raised by Karl, you ignored the word, "typically". Please read more carefully.

With regard to the fourth issue, Karl, please give us your methods of calculating the information content of DNA as a molecule participating in the genesis of a biomolecular network.
Give us your reasoning…!”

So far my understanding of what you have said. Now I shall answer.
Answer starts here:
To your point :
(1)Atomic numbers were created by the chemists for logical descriptions of empirical material observations of networks of relations, both biological and non-biological relations. Our understanding of these numbers lead directly to our understanding of DNA as the genetic material and as a source of genesis of life itself.

Perfectly in agreement. In epistemology, chemical elements are logical constants. As logical constants, they obey some – highly complicated – combinatorial rules. (If elements a and b are concurrently present, molecule c will develop + x corollaries more.)
The chemical elements are logical building blocks. Here, I introduce a philosophical half-breed, some few steps back from the Kantian object as such. That idea of an object as such is generated by peeling off the particularities until the generality itself remains. While abstracting from Grandma’s blue easy-chair, one would go while un-clothing the particularity of this object along following steps: something of anyone’s, a long as it is such a blue easy-chair as Grandma’s; something of anyone if it is a blue easy-chair, …, an easy-chair, …, a chair, …, anything to sit on, …, anything at all.
The iso-propyl-3,4-etc-12butane something is, after all, a particularities-ridden Kantian object as such. Peeling the specificities off, one arrives at the intermediate idea: many building blocks plus glue plus structure plus rules (maybe: plus symbols). Of these, the many building blocks are the pure elements. The glue plus structure plus rules are what Jerry talks about saying this is not the same mathematics as the math behind the building blocks. And here is where I say yes it is the same mathematics but a bit more complicated. Or not complicated but unusual, maybe giving one the feeling of visceral nervousness.

To your point
(2) Firstly, I view all chemical processes as electrical flows. … Have you not heard of batteries?
We have discussed originally whether life was an interplay between electrical and chemical representations of the same-identical state, but if you restrict your assertion to that chemical processes are by and large electrical flows, I am quite ready to discuss that point too.

The example of batteries shows that a state and a process are interlinked. If the battery is in its physiological melee in state A it may discharge electrical tension according to measurements set Q. If the battery is in state B it may discharge electrical tension according to measurement set W.

Exactly what I say. The feed-back interplay between a momentary state (the state A is contemporal, now) and a sequential process (the discharge will happen along time. It would pervert the idea of a battery if it exploded in the course of a discharge.) is what we talk about. But one needs the yang to the yin. One cannot say that the process is exactly that what we discuss. We discuss the interplay between that on what the process takes place and the process.

Let us complicate the battery example into a picture of ecology: we discuss the weather over a continent. Jerry states that the weather is the pattern of clouds, donner, blitz, rain, snow. I say that it also the swamp, forest, ocean, river on the Earth, too. Close the loop, Jerry. The material is the battery, the swamp, the process is the electrical flow, the rain. They influence each other. One is the logical consequence of the other.

Therefore, I would say: the sentence “chemical processes are basically electrical flows” is not true (.f. not grammatically, but does not fit into the pattern of explanational statements). The right way of putting this would be imho “chemical processes are the interplay of constraints on possible states where one set of constraints are electrical flows which interact with the other set of constraints which detail densities on possible places.”

To your point
(3) Secondly, the language of chemistry was developed by the chemical community to express empirical observations. … you should show … that the the information of DNA can be calculated using Shannon information, or, … can calculate the number of isomers of organic molecules or that biological species are distinguishable in such language.

The language of predictably sure densities was developed by the social research community to answer to needs of politicians and businessmen. We shall put a supermarket (road, school, fire station, etc.) there only if there will be at least x units with probability of occurrence 1.0. The units you count in and the units an infrastructure-planning statistician (sociologist) counts in are the same. You know that you are certain about the occurrency of some specific types of units and that they mix among each other causing much trouble and havoc. If the cross-selling among visitors to a Multiplex and a bowling hall and a parking lot does not function, you get confronted with manifold actual consequences of the empirical observations (as opposed to predictions). We use the same methods as you. What is for you an element, for me is a certainity. What for you chemical valences, for me types of interaction.

The information in the DNA is well understood. If there are n units in a sequence there can be up to n! different sequences. This is pure and simple Shannon.
That what Shannon has not looked into is the transmission of information by means of non-sequenced media. He quite wisely did not do so, because up to 32 you can transmit more information by sequentially arranging them. He could not have dreamt that there is this freakish number theoretical anomaly which makes biology (and, generally, it appears, everything) work. Even now it is hard to recognise that we can of course transmit messages by the overlap structure of symbols. There are for demonstration purposes childrens’s toys made (like Sudoku it can be understood.)

In the FIS salon, openness of mind is encouraged. So maybe we can work on the combinatorics of overlap structures. Take k*10 pieces of paper and draw some symbols on each of the units in a group of 10. If you made the symbols randomly, chances are high that among the k messages not two will be the same, structure-wise.

Now we discuss which types of structures will appear certainly (and these are the elements) and which types of structures will appear probably and so on. This leads one – after lots of combinatorics and huge tables – to predicting the properties of a complicated structure made up of certainities with properties combined. Yes, the job can be done. Your requirement is: “calculate the number of isomers of organic molecules or that biological species are distinguishable in such language”
and exactly this is what the project delivers.

To your point (4)
In other words, the absence of correspondence between arithmetic operations of mathematics and the operations of valence and covalent bond re-arrangements are well known. Or, have you solved these problems, Karl?

Allow me to repeat that this is the reason why I happen to be in this room: to keep insisting that indeed I have solved these problems. Yes, I actually mean that I do have something new to say.
 

To your point (5)
With regard to the third issue raised by Karl, you ignored the word, "typically". Please read more carefully.

Let me repeat that our disagreement was on:
The language of bionetworks, the language of individuals and species, is remote from the typical language of philosophy and logic
which I regret to keep evaluating as a statement which is not true. If we could not express our thoughts about bionetworks then it would be far from what we can understand. Wittgenstein has shown that the grammar must allow for the sentence to make sense. Then, if bionetworks are subject to rational thought, they must be expressable by logical sentences. Maybe the difference between us is that I do believe that bionetworks are rational, understandable, explainable, reproducible, in one word, within the domain of rational relations. In your philosophy, there appears to be a segment of reasonable concepts, and then, unconnected, all those strange things that happen in bionetworks. Here, our opinions do differ.

To your point (6)
With regard to the fourth issue, Karl, please give us your methods of calculating the information content of DNA as a molecule participating in the genesis of a biomolecular network.

The triplet in question we encounter in the numeric table of partitions into four (distinct) summands. There, it can be interpreted as the increase in the jump of the difference of the present state with regard to the next state. The walk happens along the number-of-objects dimension. The sequence constrains growth (mass, something that can be counted on N). The kind of the added object can be read off the kinds of sub-segments on N where this specific extent of increase is likely to such a degree (degree of prob of an attribute to be present: type of object). Then, we get into Lego.

The exchange between you and me allows focusing on what we find hard to communicate. I keep saying that there is an outlandish freak of two combinatorial functions cutting each other twice and this appears to be the answer to everything and all. Among other practical uses, it allows creating mathematical objects with a-priori properties (just like your chemical elements) out of thin air logically. The original density of the logical space has been found in pure additions. Using the freakish number theoretical interrelation one can show that the average addition is not quite exact, but it is inexact to the tune of some 0,000 … 0003 %, where … stands for some 57 more Zeroes. This inexactitude is what explains – or at least does not exclude the explanation of – as good as every phaenomenon mathematicians have said heretofore “well, this is outside math, this is physics or chemistry or biology”. Information is what we disregard as we conduct an addition. As we say 2+2=4, we thr!
 ow away the distinction between 2 and 2 vs. 4 on one hand, and between 1+3 and 2+2 (which also could have been) on the other hand. In a closed logical system one cannot throw or wish away slight differences of matter /space/ and continuity and diversity. They come back and haunt you as chemical valences or isomers’ puzzling properties or black holes or magnetism. We oversimplify for the children with additions and no one at University gets around to sitting down with the kids and say “well, you remember we said that 2+2 is exactly 4. Now, on closer look, maybe we do find some hairs to split.”

Hope that this contribution is not too long. Thanks again for insisting on clarification.

Karl

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Received on Tue Feb 28 21:26:52 2006