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
Humbug is a hot issue at a time of bugs and irreproducibility in science, fake news in social media, and a sense of mistrust in the solutions of the COVID 19 crisis. Trust in science calls for a language that is understood. Some fundamental terms, symbols, and units at the basis of counting and measuring are presented as a Canonical Carol from medium to message to meaning, to crack the code for communication from physical and chemical sciences to molecular biology and mitochondrial physiology. The theme is: BAH! Humbug! The meaning of BAH! will be explained extempore, the retrograde and self-referential meaning of Humbug! is: back to Humbug ― the end and the beginning. • 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
- 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).
- 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.
- 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«
- This extroduction is the external or executive introduction to the Canonical Carol.
Extroductory Canons on quantities, symbols, and units. A composition composed in the spirit of Douglas Hofstadter
- 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 and species 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 to the why should I 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, while the Canonical Carol is written in different Staves. 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
H: Historical stories, novels and philisophical bestsellers. BAH! Humbug!
- BAH! Humbug! ― is the theme of the canonical carol on terminology that found its roots in Charls Dickens novella A Christmas Carol (1843) (Figure 1) and L Frank Baum’s The Wonderful Wizard of Oz (Figure 2). But first of all BAH is inspired by a canonical Carroll: Lewis Carroll’s novel Through the Looking-Glass (Figures 3 and 4), the sequel to Alice's Adventures in Wonderland (1865) referred to by Douglas Richard Hofstadter in his book Gödel, Escher, Bach: An eternal golden braid. A metaphorical fugue on minds and machines in the spirit of Lewis Carroll (1979). MC Escher’s Dragon ― the Ouroboros (Figure 5) ― is a canonical self-referential symbol that penetrates BAH from beginning to end and from the end to the beginning: when the Highest-level system H devours itself and becomes its own Bit B, and backwards when Bit B creates its own system B, when the object Body B inflates into its own system Body B ― when the medium is the message. The book The Medium is the Massage (1967) was co-created by Herbert Marshall McLuhan and Quentin Fiore (Figure 6).
- In practical language we cannot but use a dualistic terminology for objects. Does a term describe the object of our investigation? Or is the term an object, worthwhile of canonical investigation? Extroductory Canon Voice B major is all about dualistic terminology, with a different twist.
B major: Taking part in an X mass party
- Subtle dualistic meaning of a term is at the heart of a good joke: the meaning of a term in one context takes us by surprise when pushed into a different box with a paradoxical result.
- BAH! Humbug! — This cannot be completely useless, it can serve as a bad example.
- Except at infinity: Parallel lines cannot know what they have in common. They never meet.
- On return from infinity: Parallel lines know what they have in common. That's why they never meet.
- Honestly: I am the author of a new term: "plagiarism".
- Through the looking glass: Looking into a mirror I can see myself looking.
- I and I dont need a mirror: I, for one, like Roman numerals.
- A practical guide to units: Doctor: "I'm sorry but you suffer from a terminal illness and have only ten to live." — Patient: "What do you mean, ten? Ten what? Months? Weeks?!" — Doctor: "Nine."
- Henny Youngman: When I read about the evils of drinking, I gave up reading.
- Subtle dualistic meaning of a term is at the heart of a good joke: the meaning of a term in one context takes us by surprise when pushed into a different box with a paradoxical result.
- In the Practical-Technical world, dualistic terminology is neither funny nor disturbing. Taking part in an X mass party may be funny and disturbing. If you are Practically focused only on your body mass and BMI, without Theoretical interest in count, volume, and mass, you may skip the Body of Voice B major and continue with B minor. But don't mix with a biologist, a sport scientist, and a chemist.
- An X mass party pops up in the Highest-level Hut H with a capacity of 60 Bodies B, most of them Biologists. One cell biologist just finished a respirometric experiment with cultured cells. Since she wanted to express respiratory rate as O2 flow per cell IO2/ce [amol·s-1·x-1] and O2 flux per cell mass IO2/mce expressed in SI-units [mol·s-1·kg-1], she counted the cells for normalization by cell count, and measured the cell mass for normalization by cell mass. As a cell biologist and Mitochondrial phyiologist M, she was trained to consider the cell count Nce as the number of unit-entities of entity-type X = ce. And for measurement of cell mass, mX = mce, she needed a really large number Nce of cells. That's why she was among the latest group to join the X mass party.
- Mitochondrial biologist M: My name is Magda M. Hello, sorry for being late. Three more Biologists B are with me, and it's kind of you that you other two did not mind waiting a bit.
- Sport scientist S: Servus, my name is Stefanie S. Never mind, we really did not a bit mind this kind of waiting.
- Chemist C: Good evening, my name is Christina C. Would you mind me pointing out, that this wating time was a bit too long? Now we cannot walk up to system H, but have to Assemble in an Airway car of the gondola lift; otherwise the High-level Hut would close until we pop up there.
- Sport scientist S: That's OK. We are all well trained at an average Body mass of 60 kg. So let's make an exception this night and pop up into the Airway car A as a party of 6, to pop up at the Hut in time.
- Chemist C: But do we all fit into a single system A?
- Mitochondrial biologist M: Easy! The Airway car can take a weight of 400 kg, we are a party of six buddies B NB = 6xB, therefore, our weight is less than 400 kg.
- Sport scientist S: Biologists should be more clear, we talk about Body mass, not weight.
- Chemist C: I remember from physics, that weight is what matters in the Airway car. This will make a difference when a future X mass party will take place on Haumea in the Kuiper Belt near Pluto.
- Mitochondrial biologist M: Sure, we use an approximation under ‘practical’ conditions; wet weight or dry weight should be wet mass or dry mass. There are ongoing discussions, if we should use wet or dry mass for our cells. Anyway, my living cells are dead when I measure their mass.
- Sport scientist S: Your Body mass is certainly not yet dead when we measure your BMI. We are all fit, since our BMI is about 20 kg∙m-2.
- Chemist C: .. and we all fit into system A. let's pop up after all. I cannot wait until our party of six joins the party in the Hut.
- Mitochondrial biologist M: Due to my cell mass measurements, we are the last Airway car to arrive. Look here, this is the last empty table, the Hut is full, and the party goes on as a party of 60 with 10 parties of 6.
- Chemist C: This makes an X mass party of 3600 kg body mass.
- Sport scientist S: But can you explain the meaning of X?
- Chemist C: Every scientist should know this. In the International System of Units, countable elementary entities get the symbol X.
- Sport scientist S: Does that mean, that you make an X for YOU, when I measure your Body mass?
- Mitochondrial biologist M: We should not get too personal. Since the majority at our X mass party are Biologists, we could use the symbol B for our Buddies, such that for you, her, and me we insert generally X = B.
- Chemist C: Wait a minute. IUPAC defines the 'amount of substance concentration' as cB = nB·V-1 [mol·m-3]. X = B then means, that we talk about substance B; entities X can be particles, ions, molecules, ..
- Sport scientist S: .. and a Body X = B ..
- Mitochondrial biologist M: .. and all my cells X = ce.
- Sport scientist S: Why do you say 'cells' and not 'cell'?
- Mitochondrial biologist M: Because I am counting the cells, I don't count a cell.
- Sport scientist S: I don't count Bodies, I just put you on the mass balance.
- Chemist C: But your mass balance measures, it does not count and does not know how many bodies you have sampled for your mass determination.
- Sport scientist S: ??? .. We need more Beers. One per B on our table A.
- Chemist C: How many moles of B? - {They get 6 Beers}
- Mitochondrial biologist M: Don't push down to the unit mole for amount, let's stick to the count. I count NB = 6 Beers in our system A, and NB = 6 Bodies; divide the Beers by the Bodies, then you have 1 Beer.
- Chemist C: You forgot the units.
- Sport scientist S: Who cares about units? Beer is Beer, Body is Body.
- Mitochondrial biologist M: Only when you count, not when you measure mass or volume. My Weizen is a 0.5 L beer, your Pils is a 0.33 L beer.
- Chemist C: According to SI, you should use Base SI units, to express volume in the unit [m-3].
- Mitochondrial biologist M: We are practical and use the liter [L]. I don't care about [m3].
- Sport scientist S: Now it is me who cares. Since we express the BMI in SI units [kg·m-2], this normalization for Area [m3] is closer to [m3] than [L].
- Chemist C: But this is trivial, 1 L = 1 dm3. And one mole ..
the scientist remembers that she had joined these parties already six times, and always presented a Christmas Carol. Before she contemplates on how many liters of Beer per B have been consumed (Extroductory Canon Voice B minor), she discusses her cell mass mce, the body mass of B in A, and her Body mass in herself. With 'her cell mass' she did not refer to her cells in B, nor to her cells cultured in the lab, but to some cell type ce cultured in her lab. This was understood implicitly by all biologists on her table. Therefore, she had to explain the difference between 'her cell mass' and 'her Body mass' by the explicit statement, that this was not a type of Body mass studied in her lab, but clearly 'her Body mass in herself'. With less Beer and a Black board instead, she would have written the symbols and units according to BEC 2020.1:
- mce [kg] — the mass of all cultured cells of entity-type ce in the sample, which was used to measure the cell mass
- mB in system A [kg] — the mass of all biologists of entity-type B in the party of NB = 6, who entered the Airway car A; mB = 360 kg
- MUB [kg·x-1] — the mass of a unit-entity UB of entity-type B, where B was 'herself'.
B: To drink or not to drink Beer
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.
- YES, then H(O2k[D{atlab}])
- NO, then H(O2k, D[atlab])
- 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>}])
- 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 NK = 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 NX, 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:
- Manual F(DatLab, Assembly, Operation[Add cells], Disassembly) — failed, take an alternative thread, mining and grinding on the same level without pushing:
- Manual F(DatLab[Add cells], Assembly, Operation) — failed, give up grinding and pop up
- D(adtlab, F[DatLab, Assembly, Operation, Disassembly]) — ?? — switch from system D to system PC, where you have installed DatLab and DatLab is running
- PC(DatLab[DL-Protocols{F<How to Find instructions in F, Add cells>}]) — Found !!
- 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:
- 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:
- HHH: push down taking all you need out of the box or copy the software.
- O2k↔PC(DatLab): pop up (set up) the instrumental system with your PC and DatLab connected to the O2k.
- 2K: pop up (insert) the instrumental chambers into the O2k
- 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.
- 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'.
- 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:
- 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:
- 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,
- 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}])
- 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:
- 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 Nce of the experimental sample is identical to the cell count Npce of the negative control. The cell viability index IVce = Nvce·Nce-1 of the experimental group and the cell viability index IVpce = Nvce·Npce-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.
M: MitoEAGLE states and rates and mitochondrial physiology — a coral on canonical and practical
C: A puzzle on pine Cones
References
- 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.
- 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.
- Gallavotti G (2014) Nonequilibrium and irreversibility. Springer, Heidelberg, New York, London.
- Bureau International des Poids et Mesures (2019) The International System of Units (SI). 9th edition:117-216 ISBN 978-92-822-2272-0.
- 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.
- 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.
- 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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Preparation: Intact organism, Permeabilized cells, Homogenate, Isolated mitochondria, Enzyme, Intact cells
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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
