X-mass Carol

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X-mass Carol

Gnaiger Erich (2020) A canonical carol on quantities, symbols, and units. MitoFit Preprint Arch 2020.4.v0.

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Abstract: Pre-preprint version 0 (v0.1) (2020-06-13) last update 2020-06-14 • Keywords: Amount of substance, Bit, Body mass, Cell respiration, Buglish, Canonical and practical, Canonical ensemble, Concentration, Count, Dimension, Entity, Extroduction, Flow, Flux, Format, IUPAC, International System of Units, Isolated mitochondria, Living cells, Mass, Measure, MitoPedia, Molar mass, Normalization of rate, Object, Organism, Permeabilized cells, Publish, Sample, System, Unit, Volume

Extroduction

1. This article aims at providing a new understanding of the concepts of counting and measuring. Although we are familiar with the concepts of counting and measuring — or we are counting and measuring without the need to be familiar with these concepts —, established systems of quantities, symbols, and units do not sufficiently reflect the fact that quantities for measurement of size (mass [kg], volume [L]) are opposite to a group of quantities that are strictly linked to counting (count [x], amount [mol], charge [C]). The units 'mole' for amount and 'coulomb' for charge are connected to the unit 'counting-unit' [x] for count by fixed stoichiometries, but [x] is not part of the International System of Units (SI).
2. This article is relevant to all areas of science and philosophy and all disciplines that are involved with counting and measuring. However, for strictly Practical-Technical Realists R(PT), the Canonical Carol is too theoretical. For Technical-Theoretical Nerds N(TT), the Canonical Carol is too practical. If you identify yourself as a PTC-type of the Brave person B(PTC) — Practical&Technical-Theoretical&Canonical — then pop up to the PDF of the Canonical Carol.
3. The Canonical Carol is written in recursive form about recursive systems, where an experimental system is contained in an instrumental system, an extroduction introduces the introduction, and the quantity 'count' devours its own physicochemical unit x. Enjoy the Canonical Carol from beginning to end, the Carolical Canon from end to beginning, to realize that the beginning is not in the introduction, and the beginning is not in the Canonical Carol — the beginning is at a Higher-level H in the canon, and level H is the extroduction.

This extroduction is the external or executive introduction to the Canonical Carol.

• Push down to »Extroduction«

Extroductory Canons on quantities, symbols, and units. A composition composed in the spirit of Douglas Hofstadter

• Push down or pull up to »Hofstadter DR (1979) Gödel, Escher, Bach: An eternal golden braid. A metaphorical fugue on minds and machines in the spirit of Lewis Carroll. Harvester Press:499 pp.«

While there exists only one single Canonical Carol, there is a potential maximum number of Extroductory Canons set by the global number of counting human people or by the number of groups of counting human people. Babies can count before being taught to count and before talking, and the ability to count is not restricted to the human species. For each group of persons a different pattern triggers counting. This trigger-pattern should be encoded into each specific variation or voice of Extroductory Canons. Such a large number of Extroductions cannot be included within the Canonical Carol, since it would blow up its word count beyond a reasonable number of words allowed in a scientific system of publication. The word-count expansion in the extroduction aims at introducing different PTC-audiences the why to open the box, and to the how to read it's contents. The Extroduction is the manual for the Canonical Carol written in different Voices. As usual, this manual for the Canonical Carol cannot be well understood without reading the Canonical Carol, which should be used as a manual for the Extroductory Canons. As always, read the manual first.

Table of extroductory contents

Voice	Title
H	Historical stories, novels and philisophical bestsellers. BAH! Humbug!
B	To drink or not to drink Beer
X	Taking part in an X mass party
P	Are you a Practical&Technical-Theoretical&Canonical person who can switch to PTC-mode?
O	A Canonical O2k-Manual for high-resolution respirometry: why the living cells died and dyed
M	MitoEAGLE states and rates — a coral on canonical and practical
C	A puzzle on pine Cones

P: Are you a Practical&Technical-Theoretical&Canonical person who can switch to PTC-mode?

The question is, who you are and how you are, if you enter the jukebox of the Canonical Carol.

PTC: Are you a canonical PTC-person who enjoys pushing and popping? Do you like taking things apart, finding new interests in the parts and pushing down further, without loosing the Assembly code? Are you not satisfied with exploring parts B when taking A Apart? Are you trained in the skill to perceive and store the Assembly code for popping back up to the Assembly A?

TT: A TT-personality engages with a deeper-and-deeper Technical-Theoretical interest in pushing down from bodies to cells to bioblasts to molecules to atoms to quarks, without taking note of the canonical assembly code.

PT: A PT-person uses the computer in the best Practical&Technical way, but does not take it apart. The PT-personality uses an instrument and software, without curiosity about software code, neither writing software nor assembly instructions. This PT-approach is vitally important to complete an experiment. If you would switch to PTC-mode in the lab, the living cells on the bench would be dead cells before their respiratory rate is measured.

TC: How you proceed as a TC-Irrealist that has no Practical personality, you find out when proceeding to the Extroductory Canon Voice O.

O: A Canonical O2k-Manual for high-resolution respirometry: why the living cells died and dyed

Q1: The question is, who you are and how you are, if you enter the Canoncal O2k-Manual in the jukebox of the Canonical Carol.

Q1(Q2): Is the DatLab software of the high-resolution respirometer HRR (which is installed on my PC [that is connected to my O2k]) part of the O2k?

In the O2k-Catalogue, DatLab is listed as part of the O2k, which was shipped in a Hardware box H, that contained the hardware O2k H(O2k), and a separate USB-flashDrive, which is the Software box D. After assembly of the O2k, H is unfortunately empty, since there is no instruction on how to copy the O2k before taking it out of the box — this would be a most economical approach to the Power-O2k. This is different with the Software box D, since there is an instruction to copy DatLab rather than taking it out of the box D, such that DatLab stays inside the box D containing DatLab, represented as D(atLab).

Before opening box H, it is instructive to clarify the canonical representation of H, to address question Q1(Q2), if DatLab is part of the O2k.

1. YES, then H(O2k[D{atlab}])
2. NO, then H(O2k, D[atlab])
3. Before deciding too quickly, consider the important higher-level question in this nested network: Is H part of the O2k? — O2k(H[O2k{D<atLab>}])
4. Postpone the decision and think of your living-dying cells on the bench - now we are a bit practical even in Theoretical&Canonical TC-mode.

Q1(Q2[Q3]): Is the instruction 'Add cells' in the O2k-Manual F(Add cells) part of the O2k-Hardware or Software, and where is the F.. manual?

We should add the cells into the O2k for HRR measurements. If I proceed with the perception that DatLab is part of the O2k-system, then the part of the O2k-Manual that instructs me to add the cells into the O2k should explicitly (canonically) define, into which part the cells are to be addded, else a TC-user may try to add the cells into the USB-flashDrive D(atlab). It goes without saying that the proper part where to add the sample are the O2k-Chambers 2K (for the German 'Kammer' for chamber, and there are N_K = 2 x K chambers used in the O2k). The O2k-Manual says, that the O2k should be taken out of the Hardware-box H, DatLab should be copied from the Software-box D(atlab) to be installed on my PC, and — BINGO! Here is the answer to Q1(Q2) in Voice O: DatLab is not part of my O2k, the O2k-Catalogue should get this right for all TC-users (neither PT-Realists nor TT-Nerds would care).

The O2k-Manual shows in a video, how two O2k-Chambers are taken out of the Assembly box A(3K) → A(1K) + 2K, pushing down from system A to entity K, leaving one spare O2k-Chamber in box A(1K). This is followed by popping up 2K to the O2k-System S. In my TC-mode there is a Theoretical voice that says: Think of normalization, count the cells first. The Technical side transfers a subsample of cells to the cell counter. and here comes the Canonical again.

Do the instructions of the cell counter include the unit 'counting-unit' [x] in their system of units? Does the cell counter manual introduce properly the quantity 'count' with symbol N_X, meaning 'number of unit-entities of unit-type X, expressed in the unit 'counting-unit' with symbol [x], where in the cell counter X = ce? If I do not re-write the cell counter manual at this stage, since the living cells are dying on the bench, I should nevertheless update the 'Add cells' instructions in the O2k-Manual.

Where is the O2k-Manual F (pronounced as 'the F.. manual')? The instruction says: H(O2k, D[adtlab, F{DatLab, Assembly, Operation, Disassembly}]) ↓ push down to find the USB-FlashDrive D(adtlab, F[DatLab, Assembly, Operation, Disassembly]) in box H and copy the Manual F(Assembly, Operation, DatLab). But since the living cells are dying on the bench, there is no time to read the F.. manual. Just look for 'Add cells'. ↓ push down to find 'Add cells'. There are several options for pushing, with failures and problems:

1. Manual F(DatLab, Assembly, Operation[Add cells], Disassembly) — failed, take an alternative thread, mining and grinding on the same level without pushing:
2. Manual F(DatLab[Add cells], Assembly, Operation) — failed, give up grinding and pop up
3. D(adtlab, F[DatLab, Assembly, Operation, Disassembly]) — ?? — switch from system D to system PC, where you have installed DatLab and DatLab is running
4. PC(DatLab[DL-Protocols{F<How to Find instructions in F, Add cells>}]) — Found !!

The great success to find the instruction 'Add cells' is a great testimony to the fact, that the O2k-Manual is the most simple, logical, practical, easy-to-use, userfriendly instrumental manual of type F in the world. There exists no simpler, logical, easy-to-use structure of F:

1. HHH: push down taking all you need out of the box or copy the software.
2. O2k↔PC(DatLab): pop up (set up) the instrumental system with your PC and DatLab connected to the O2k.
3. 2K: pop up (insert) the instrumental chambers into the O2k
4. H: get started with High-resolution respirometry: switch on the O2k, connect DatLab, select a DL-Protocol for 'cells', define the experimental temperature of your experimental system, add mitochondrial respiration medium.
5. DatLab(DL-Protocols[F{How to Find instructions in F, Add cells}]): In DatLab, the selected DL-Protocols designed for 'cells' as a sample type, include within the DL-Protocol the F-Manual, which provides instructions how to Find help, and where you find the instruction on 'Add cells'.

There is no way to make this structure of the nested system simpler, more logical, easy-to-use. So how do you find this structure? You may find it to be useful, but in the first place you do not find the structure at all. When trying to Find the instruction 'Add cells', we are not trying to find information on how to Find, but without any choice we have to use the structure of F to Find 'Add cells'. We cannot best use a structure of a nested system, if we are not pushing down into the instructions to find instructions, without forgetting to pop up back to the current task. If you have time to play pusing and popping, even complex structures will precipitate. This is how learn using a new software when we like to play with it, and the more PTC- one adds to a PT-approach, the more sophisticated and error-free applications are possible. Any sophistication of TC-mode does not help in using or designing a nested structure, if the practical side is missing. Therefore, diversity of operation- and cognition-modes is the key to innovation of design and success of application, based on gender balance, cultural diversity, Extroductory Voices in the team — if only they can communicate.

Of course, there is of simplifying the structure of O2k-Manual F and making it even more logical and canonical. Oroboros, please stack all Operation instructions into DatLab, such that failures and problems 1-3 above will not happen, even without thinking about the structure of F. Change from:

1. D(adtlab[DL-Protocols{F<How to Find instructions in F, Add cells> F[DatLab, Assembly, Operation, Disassembly]), to let all external F disappear altogether, devoured by DatLab itself, to obtain the linear thread,
2. D(adtlab[DL-Protocols{F<How to Find instructions in F, Assembly, Operations<How to operate DatLab, How to operate the O2k»Add cells«>, Disassembly}])

No more frustration in Finding everything on the O2k in DatLab and everything on DatLab in DatLab. With its self-referencing, retrograde structure this linear thread gets fuzzy on recursive nodes, and canonical perfection can never be achieved in a perfectly linear structure: If all instructions on the O2k and DatLab are nested in DatLab, where do you find the instruction how to find DatLab? The instruction on how to open the box must not be popped into the box. F on F nested in the box implies infinite regress without bottoming out, and all you need is falling in love with the Extroduction that contemplates about the system in the box and out of the box.

With too much obsession by the Extroduction, the living cells have died on the bench and their nuclei dyed in the cell counter. At this stage, exclusively continued TC-mode of the Unrealist provides escape. I have a living cell preparation on the bench, but all are dying, without application of any mild detergent to permeabilize the plasma membranes enabling the dying of all nuclei in a cell viability test. Being aware of this theoretical question, I prepared a parallel subsample as a negative control for the cell viability test: experimental sample 'ce' = living cells; negative control sample 'pce' = experimentally permeabilized cells using digitonin. In the TC-approach all living cells were dying, such that sample 'ce' is not intact any more when it should be popped into the 2K of the O2k. The cell count N_ce of the experimental sample is identical to the cell count N_pce of the negative control. The cell viability index IV_ce = N_vce·N_ce^-1 of the experimental group and the cell viability index IV_pce = N_vce·N_pce^-1 of the negative control group are identical, both are exactly zero, since subscript 'vce' indicates 'viable cells'. This is fine for the pce-control cells. But an appropriate term is required for the ce-experimental cells. These living cells ce are not intact any longer — they are certainly not intact cells. But these living cells are not viable cells at a viability = 0. But this experimental sample ce should have a viability >0.95 in a more Practical and less Canonical approach. This is where Mitochondrial physiology bottoms out BEC 2020.1.

References

1. Ioannidis JP, Greenland S, Hlatky MA, Khoury MJ, Macleod MR, Moher D, Schulz KF, Tibshirani R (2014) Increasing value and reducing waste in research design, conduct, and analysis. Lancet 383:166-75.
2. Boltzmann L (1877) Über die Beziehung zwischen dem zweiten Hauptsatze der mechanischen Wärmetheorie und der Wahrscheinlichkeitsrechnung, respektive den Sätzen über das Wäremegleichgewicht. Sitzb d Kaiserlichen Akademie der Wissenschaften mathematich-naturwissen Cl LXXVI, Abt II:373-435.
3. Gallavotti G (2014) Nonequilibrium and irreversibility. Springer, Heidelberg, New York, London.
4. Bureau International des Poids et Mesures (2019) The International System of Units (SI). 9th edition:117-216 ISBN 978-92-822-2272-0.
5. Cohen ER, Cvitas T, Frey JG, Holmström B, Kuchitsu K, Marquardt R, Mills I, Pavese F, Quack M, Stohner J, Strauss HL, Takami M, Thor HL (2008) Quantities, Units and Symbols in Physical Chemistry. IUPAC Green Book 3rd Edition, 2nd Printing, IUPAC & RSC Publishing, Cambridge.
6. Hofstadter DR (1979) Gödel, Escher, Bach: An eternal golden braid. A metaphorical fugue on minds and machines in the spirit of Lewis Carroll. Harvester Press:499 pp.
7. Gnaiger Erich et al ― MitoEAGLE Task Group (2020) Mitochondrial physiology. Bioenerg Commun 2020.1. doi:10.26124/bec:2020-0001.v1.

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Amount of substance, Bit, Body mass, Cell respiration, Buglish, Canonical and practical, Canonical ensemble, Concentration, Count, Dimension, Entity, Extroduction, Flow, Flux, Format, IUPAC, International System of Units, Isolated mitochondria, Living cells, Mass, Measure, MitoPedia, Molar mass, Normalization of rate, Object, Organism, Permeabilized cells, Publish, Sample, System, Unit, Volume