Part 2 book “The cell language theory – Connecting mind and matter” has contents: Applications of the cell language theory to biomedical sciences, the universality of the planckian distribution equation, the universality of the irreducible triadic relation, the philosophical implications of the cell language theory, conclusions.
“6x9” b2861 The Cell Language Theory: Connecting Mind and Matter Chapter Applications of the Cell Language Theory to Biomedical Sciences Most, if not all, human diseases, both somatic and mental, can be said to arise from miscommunication and disregulation of metabolism within individual cells (i.e., intracellular semiosis) or between cells (i.e., intercellular semiosis) in the human body Hence, the cell language theory and medical sciences are intimately related The cell language theory is one of the four major theoretical building blocks underlying the theoretical model of the living cell known as the Bhopalator discussed in Chapter The four components of the Bhopalator, i.e., cell language, cell force, intracellular dissipative structures (IDSs), and conformons, are depicted in Figure 7.1 as the four nodes of a bodycentered tetrahedron (BCT) whose center is occupied by the cell model One unique feature of the tetrahedron is that its four nodes are all equivalent and in simultaneous contact with one another, which is used in Figure 7.1 as a topological means to symbolize the essentiality and the interconnectedness of the four theoretical components of the living cell In other words, these four theoretical building blocks constitute the irreducible tetrad of the cell (ITC) The principle of ITC implies that the cell structure and function cannot be completely accounted for without implicating all of the four theoretical components, although, at any given time, only one or two of them may be prescinded (i.e., selected out or highlighted for 289 b2861_Ch-07.indd 289 17-10-2017 12:06:22 PM b2861 The Cell Language Theory: Connecting Mind and Matter “6x9” 290 The Cell Language Theory: Connecting Mind and Matter ŽŶĨŽƌŵŽŶƐ ŚŽƉĂůĂƚŽƌ Ğůů>ĂŶŐƵĂŐĞ /^Ɛ Ğůů&ŽƌĐĞ Figure 7.1 Cell language as one of the four major building blocks of the theoretical model of the living cell, the Bhopalator The geometric figure employed here is called the BCT (Body-Centered Tetrahedron) (see Figure 10.15) that has been found to provide a useful template for modeling many processes and structures in the Universe (see Section 10.17) emphasis, temporarily ignoring the rest of the components, for the convenience of thought) As we attempt to apply the cell language theory in this chapter to solve practical problems in biomedical sciences, our emphasis will be placed on the intercellular or intracellular communications (or semiosis) mediated by the cell language, but this does not mean that the other three theoretical components are not involved in one way or another 7.1 The Need for a New Paradigm in Biomedical Sciences H H Heng, the author of Debating Cancer [297], recently stated that: The explosion of genomic information has generated both excitement and confusion The paradox of knowing more about cancer’s genetic landscape yet understanding less of its common molecular basis represents such an example It was believed or hoped by many that the cancer genome sequencing project would once and for all solve the mystery of cancer, without anticipating that the powerful technology b2861_Ch-07.indd 290 17-10-2017 12:06:23 PM “6x9” b2861 The Cell Language Theory: Connecting Mind and Matter Applications of the Cell Language Theory to Biomedical Sciences 291 would further add to the unmanageable complexity of the picture Following the high hopes of the development and utilization of various large scale -omics technologies, the long expected clear-cut understanding of cancer is actually fading away… What is the real problem? Not enough molecular data yet? No suitable model for data analyses? Or on an even more serious note, has there been a wrong conceptual framework all along? (7.1) Of the three possible explanations for the “cancer paradox” that Heng is conceptualizing, I think that the last possibility is the most likely explanation, i.e., a wrong conceptual framework for not only cancer research, but also for the biomedical science research and education, in general 7.1.1 The Inefficiency of the Current Methods of Drug Development One evidence for the “wrong conceptual framework” of the contemporary biomedical science, I think, is provided by the inefficiency of the current drug development research According to Bain & Company [298], the cost of developing a new drug is estimated to be $1.7 billion and it takes 12–16 years to complete a drug development process from the compound discovery stage to marketing The overall attrition rate for developing a drug is calculated to be 10,000:1 According to another survey, the United States invested a total of $25 billion in 2000 on the research and development for pharmaceuticals and produced only 11 new drugs on the market in that year, costing the US pharmaceutical industry $2.3 billion per new drug In addition, once a drug is approved by the FDA, the success rate of drug treatment is only 30–60% [299]: Only about 50% of the patients treated with drugs respond favorably 7.1.2 Precision Medicine In his State of the Union Address on January 30, 2015, President Obama launched the Precision Medicine Initiative with the following statement: Doctors have always recognized that every patient is unique, and doctors have always tried to tailor their treatments as best they can to individuals You can match a blood transfusion to a blood type — that was an important discovery What if matching a cancer cure to our b2861_Ch-07.indd 291 17-10-2017 12:06:23 PM b2861 The Cell Language Theory: Connecting Mind and Matter “6x9” 292 The Cell Language Theory: Connecting Mind and Matter genetic code was just as easy, just as standard? What if figuring out the right dose of medicine was as simple as taking our temperature? (7.2) The cell language and associated biological theories described in this book suggest one possible strategy for implementing the Mission Statement (Figure 7.2(b)) of the Precision Medicine Initiative, as briefly summarized in Figure 7.2(c) and 7.2(d) and in the figure legend (a) President Obama Retrieved from https://www.whitehouse.gov/precision-medicine on 01/04/2016 (b) The Mission Statement: “To enable a new era of medicine through research, technology, and policies that empower patients, researchers, and providers to work together toward development of individualized treatments.” (c) Efficient Drug Development Precision Medicine Personalized Medicine (d) Precision Medicine = PDE + Microarray Technology + the Bhopalator/Piscatawaytor (2015) (2008) (1995) (1985-1991) Figure 7.2 A possible strategy for implementing the Precision Medicine is based on: (i) the cell language theory (i.e., the Bhopalator model of the cell), (ii) the microarray technology, and (iii) PDE (as a quantitative method for classifying the normal and disease states of the human body (see Section 7.3 for specific examples), the theoretical model of which being the Piscatawaytor (formulated in 1991) b2861_Ch-07.indd 292 06-11-2017 01:01:36 PM “6x9” b2861 The Cell Language Theory: Connecting Mind and Matter Applications of the Cell Language Theory to Biomedical Sciences 293 The proposed strategy of implementing the Precision Medicine Initiative (PMI) is based on three components: (i) the cell language-based model of the living cell, the Bhopalator, and the human body, the Piscatawaytor (see Section 3.2.20), (ii) the microarray technique for measuring mRNA levels in cells and tissues (see Section 7.2), and (iii) the Planckian distribution equation (PDE) (described in Chapter 8) that introduces a new quantitative method for classifying long-tailed histograms of mRNA levels measured from both normal and diseased cells and tissues Since the microarray technique plays a fundamental role not only in the proposed strategy for implementing PMI, but also in possibly ushering in a paradigm shift in cell biology and medicine, this method and its implications in biology are discussed in some detail in the following sections 7.2 Ribonoscopy The term “ribonoscopy” was coined in 2012 [25] to indicate the scientific study of mRNA levels in living cells and tissues measured with DNA microarrays, in analogy to spectroscopy which is the study of optical spectra of atoms and molecules using spectrometers [300] “Ribonoscopy” is an experimental method by which We can study living cells using RNA molecules and their copy number variations as molecular reporters of intracellular events. (7.3) 7.2.1 DNA Microarrays A microarray consists of a microscopic slide (or its equivalent), about cm by cm in dimension, divided into, typically, 10,000 squares or spots, to each of which is covalently attached a fragment of DNA (i.e., cDNA, or oligonucleotides) that is complementary to a stretch of the genome encoding an RNA molecule Thus, using one microarray, it is possible to measure simultaneously the levels of 10,000 RNA molecules or more in a biological sample Before the development of the microarray technique, it was possible to study only a small number of RNA molecules at a time The experimental procedures involved in DNA microarray measurements are schematically summarized in Figure 7.3 and its legend A typical microarray experiment implicates the following steps: b2861_Ch-07.indd 293 17-10-2017 12:06:24 PM b2861 The Cell Language Theory: Connecting Mind and Matter “6x9” 294 The Cell Language Theory: Connecting Mind and Matter (a) (b) (c) (d) Figure 7.3 The microarray experiment and typical results (a) The mRNA isolated from a biological sample is transformed into complementary DNA (cDNA) using reverse transcriptase and labeled nucleotides which is then hybridized with the probe DNA previously attached to the microarray surface Image reproduced from [301, 302] (b) In two-color or two-channel microarray experiments, complementary DNA molecules are prepared from two samples to be compared, e.g., cancer vs normal cells, with differential labeling The fluorescent dyes commonly used for cDNA labeling include Cy3 (cyanine dye 3), which fluoresces at 570 nm (corresponding to the green color), and Cy5 which fluoresces at 670 nm (corresponding to the red color) The two Cy-labeled cDNA samples are mixed and hybridized to a single microarray that is then scanned in a microarray scanner to visualize fluorescence of the two fluorophores by exciting with a laser beam or 570 or 670 nm wavelength The relative intensities of each fluorophore are analyzed based on a ratiobased method [303] after proper normalization [304] to identify up-regulated and b2861_Ch-07.indd 294 17-10-2017 12:06:26 PM “6x9” b2861 The Cell Language Theory: Connecting Mind and Matter Applications of the Cell Language Theory to Biomedical Sciences 295 Isolate mRNA from broken cells Synthesize fluorescently labeled cDNA from mRNA using reverse transcriptase and fluorescent nucleotides Prepare a microarray either with DNA fragments or oligonucleotides synthesized on the microarray surface Pour the fluorescently labeled cDNA preparations over the microarray surface to effect hybridization Wash off excess debris Measure fluorescently labeled cDNA using a computer-assisted fluorescence microscope The final result is a table of numbers, each number registering the fluorescent intensity which is in turn assumed to be proportional to the concentration of cDNA (and ultimately mRNA in the cell) located at row x and column y, the row indicating the identity of genes, and y the conditions under which the mRNA levels are measured (see Table 7.2) Another example of microarray measurements of RNA is shown in Figure 7.4 The term RNA here refers to not only mRNA, but all other forms of RNA including RNA complementary to the introns, promoters, ribosomal RNA, small interfering RNA, and non-coding RNA The data in Figure 7.4 were measured by Garcia-Martinez et al [315] from budding yeast Saccharomyces cerevisiae undergoing glucose–galactose shift at six time points: 0, 5, 120, 360, 450, and 850 after the nutritional shift Each data point is the average of three measurements The overall quality of the kinetic data, as evident in the smooth and coherent trajectory exhibited by each gene, increases our confidence in the microarray experimental method Figure 7.3 down-regulated mRNA levels The image is adopted from [305] (c) The mRNA fold changes (y-axis) in breast tumor tissues of 20 patients (x-axis) before (BE) treatment relative to control (N) Each profile represents the mRNA level changes encoded by one gene The figure contains 50 genes out of ~5000 genes analyzed (d) The mRNA fold changes of tumor in 20 breast cancer patients before (BE) and after (AF) treating with doxorubicin for 16 weeks RAT2N indicates mRNA level ratio with red channel (or channel 2) normalized [306] b2861_Ch-07.indd 295 17-10-2017 12:06:26 PM b2861 The Cell Language Theory: Connecting Mind and Matter “6x9” 296 The Cell Language Theory: Connecting Mind and Matter Dissipative Structures (Glycolysis) Transcript Levels (Relative) 250 YPL075W YNL199C YMR205C YGL256W YGL253W YJL052W YBR221C YNL071W YER178W YMR083W YDR081C YGR193C YCL040W 200 150 100 50 -200 200 400 600 800 1000 Time (Minutes) Figure 7.4 RNA dissipative structures (or dissipatons) encoding glycolytic enzymes The intracellular levels of the RNA molecules encoding glycolytic enzymes are measured in budding yeast using DNA arrays by a Garcia-Martinez et al in Valencia [315] at t = 0, 5, 120, 360, 450, and 850 after switching glucose with galactose Of the 13 trajectories shown, the one labeled YCL040W (light blue) exhibits an unusual behavior of increasing (rather than decreasing) between and 120 One possible explanation for this observation is that the degradation of the YCL040W transcript is selectively suppressed following the nutritional shift The advent of the microarray technique in molecular biology in the mid-1990s [307–313] marks an important turning point in the history of cell biology, comparable to the discovery of DNA double helix in 1953 Although there remain many challenging problems, both methodological [314] and biological [301], this novel technology possesses a great potential to make fundamental contributions to advancing our basic knowledge about the workings of the living cell, with important consequences in medicine, biotechnology, and pharmaceutical industry 7.2.2 The Microarray Data Interpretation Problem It is unfortunate that, from the beginning of the microarray era, leaders in the field have created the impression that the microarray technique allows b2861_Ch-07.indd 296 17-10-2017 12:06:26 PM “6x9” b2861 The Cell Language Theory: Connecting Mind and Matter Applications of the Cell Language Theory to Biomedical Sciences 297 biologists to measure rates of gene expressions (denoted as TR, transcription rates [315]) by measuring mRNA levels (denoted as TL, transcript levels [315]) In other words, they have created the scientific atmosphere in which it is deemed legitimate to accept a simple one-to-one correspondence between TL and TR The following quotations reflect such a lax attitude in the microarray field (emphasis is mine): “… Microarrays prepared by high-speed robotic printing of complementary DNAs on glass were used for quantitative expression measurements of the corresponding genes….” [308]. (7.4) “Oligonucleotide arrays can provide a broad picture of the state of the cell, by monitoring the expression level of thousands of genes at the same time….” [312]. (7.5) “… DNA microarrays, permits the simultaneous monitoring of thousands of genes….” [313]. (7.6) These statements would be correct if the term “genes” (in italics) were replaced by “mRNA levels” or “transcripts” In other words, workers in this field routinely conflate “genes” with “gene transcripts” and Transcription Rate (TR) with Transcript Level (TL), leading to numerous false-positive and false-negative conclusions in interpreting microarray data Most investigators in the field seem to think that there is no harm in using the terms “gene expression” and “mRNA levels” interchangeably, but the investigations by Garcia-Martinez et al [315] and Fan et al [316] have now clearly demonstrated that the mixing of these two terms can lead to erroneous conclusions [317–319] Because of the experimental difficulties involved in measuring TR, it was not until 2004 that J Perez-Ortin and his colleagues in Valencia, Spain, succeeded in measuring both the TR and TL values simultaneously of the whole genome of budding yeast subjected to glucose–galactose shift [320– 322] It is well known that when budding yeast cells are deprived of glucose, they undergo a profound metabolic transition from fermentation (converting glucose into ethanol) to respiration (converting ethanol to carbon dioxide and water) known as the diauxic shift [322] When these TR values are plotted against the TL values, highly nonlinear trajectories were obtained as shown in Figure 7.5 Previously investigators routinely assumed b2861_Ch-07.indd 297 17-10-2017 12:06:27 PM “6x9” b2861 The Cell Language Theory: Connecting Mind and Matter 298 The Cell Language Theory: Connecting Mind and Matter fTL-fTR Plot 1.2 Fold Changes in TR Fold Changes in TR fTL-fTR Plot 1 0.8 0.6 0.4 0.2 0.5 1.5 1.2 0.8 0.6 0.4 0.2 0 Fold Changes in TL Fold Changes in TR Fold Changes in TR fTL-fTR Plot 10 1.2 1 0.8 0.6 0.4 0.2 0 Fold changes in TL Fold Changes in TL fTL-fTR 19 1.5 1 0.5 0 0.5 1.5 Fold Changes in TL Figure 7.5 Plots of fold changes in TR and TL of budding yeast during metabolic transitions caused by glucose–galactose shift These four examples (for mRNA molecules encoded in genes #1, #3, #10, and #19) were chosen randomly out of the 5184 mRNA molecules investigated by Perez-Ortin and his coworkers [315] Fold change in TL, denoted by fTL, is defined as the ratio of TL at time t over the TL at t = 0, i.e., fTL = TL/ TL0 Each plot shows the results of six measurements at t = 0, 5, 120, 360, 450, and 850 after glucose was replaced with galactose in the growth medium that TR would be a simple linear function of TL, but as can be seen here, TR is clearly not linearly related to TL in about half of the time (The components of the TL–TR trajectories that are parallel to a straight line with a slope of about indicate linear correlations between TL and TR.) Experimental evidence indicates that TL is determined by the balance of two opposing processes — the transcription of genes into RNA or mRNA (i.e., TR) and the degradation of mRNA into shorter fragments (whose rate is denoted as TD, transcript degradation rates) [548], so that the following relation holds: d(aTL)/dt = b(TR) – c(TD) (7.7) where a, b, and c are the parameters whose magnitude may or may not depend on individual mRNA nucleotide sequences If we assume that a b2861_Ch-07.indd 298 17-10-2017 12:06:27 PM “6x9” b2861 The Cell Language Theory: Connecting Mind and Matter Index 565 Enzyme free energy level quantization of, 338 Epistemic cut, 209 Epistemology, 281, 529 Equation algebraic, theory of, 200–201 Boltzmann distribution, 81 Fifth degree polynomial, 200–201 Fourth degree polynomial, 200–201 Planckian distribution, 3, 20, 35, 64, 159, 236, 338, 341, 347, 356, 360, 368, 441, 489 Equilibron equilibrium structure, 4, 241, 250–251, 328 Essentiality, 23–24, 289, 393, 396, 527, 537–538, 545 Evolution biological, 29, 33, 42, 96, 234, 250, 283, 287, 426, 447, 451, 483 cosmological, 101, 362, 368, 447, 481 Darwin’s theory of, 8, 53 Exclusivity, 23–24, 393, 396, 527, 530–531, 538, 545 Exosomeas molecular texts, 6, 235 F Fermion decipehring, with digital CymaScope, 235 F0F1–ATP synthase internal structure of, 133 rotary conformational waves in, 75 F1 proton gradient-driven rotation of, 130, 135 F0, 86, 152, 335 b2861_Index.indd 565 Feeling, 34, 265, 271, 273, 287, 380, 414 Fermentation, 297, 301 Flesh ontology, 260, 396 Fibonacci number, 386–389 Fibonacci series, 381, 386, 388 Final cause, 101, 457 Firstness, 34, 51–52, 106, 263–266, 268, 271–272, 277, 281, 287, 380, 398–399, 404, 414–415, 419–420, 425, 429, 431, 433, 435–436, 444, 448, 450–451, 456, 465, 476, 478 First Law of transcriptomics, 330 Force cell, 2, 8, 31–32, 53, 102, 175, 178, 289 elastic electrical, 461 electroweak, 178, 217, 225, 269 gravitational, 457 mechanical, 170 strong, 9, 32, 102, 105, 463 torsional, 136, 160 weak, 105, 178 Force generating mechanism chemical reaction-induced, 160, 162 proton gradient-induced, 122 Form, 16, 21, 23, 28, 36, 46, 52, 54, 59, 61–62, 66, 80, 82–83, 92, 97, 109, 111, 116, 119, 137–138, 141, 147, 153–155, 164, 175, 177, 188–191, 197, 200, 206, 211, 213, 217, 223–224, 230, 232, 272, 274–275, 281, 321, 334, 366, 369–370, 379–380, 386, 392, 396, 398–399, 411, 414–416, 433, 436, 442, 446, 449, 452, 454, 463, 478, 547, 554, 556 17-10-2017 11:33:07 AM b2861 The Cell Language Theory: Connecting Mind and Matter “6x9” 566 Index Formal cause, 101 Four causes doctrine of Aristotle, 102 Fourier principle, 64 theorem, 63, 68, 213, 229, 327, 361, 408 Functor quantitative, 481 qualitative, 481 Franck-Condon principle generalized, 2, 29, 69, 163, 256, 426 Frustration, 206 Funtional magnetic resonance imaging (fMRI), 236, 335, 346, 348, 353–354, 360, 366, 462 G Galois, E., 200–201 Gaussian distribution, 315, 347, 356–357, 359 Gene expression, 32, 54, 161, 255, 263, 301, 331, 384, 391, 400, 428, 434, 469 Watson–Crick, 201, 203, 241–242, 248–249 Gene as a molecular machine, 461 Genetic code fifth, 240–241 first, 239–340 fourth, 240 second, 240 third, 240 Genetic network, 185, 465 Genotype, 14, 100, 251, 313, 384 Glotometrics, 236, 476 Gnergy tetrahedron, 2–3, 6, 402, 421, 424, 432, 444–448, 471–473, 477–479 b2861_Index.indd 566 Gnergy principle of the Universe, 423 Geometry Euclidean, 464 Global village, 45–46 Glycolysis, 29, 58, 124, 296 God, 281, 380, 385, 392, 399, 434, 452 Golden ratio, 381, 383–388, 391–392 Gradient Ca++ ion, 56 concentration, 27, 31, 58, 99, 133, 186, 190, 225, 257 ion, 3, 58, 74, 181, 190 pH, 115, 118, 124, 141–142 potential, 190 proton concentration, 58, 133 stress, 181, 190 transmembrane, 190 Grammar generative, 188–189 Grotthuss mechanism, 4, 43, 46 Group theory, 200–201 Growth, 161, 257, 298, 387, 389 H Hanoverator, the, 259 Hard drive, 99 Heredity, 265 Hereditary transmission, 287 Herz–Rosen–Pattee model of reality, 416 Herz model of reality, 416–417 Hieroglyphs, 191–198, 221–222, 225–226, 228 High-resolution X-ray structure, 44, 115, 118, 132, 143 Hinduism, 380, 392 Histogram codon usage profile, 352 decision-time, 335, 356, 360 17-10-2017 11:33:07 AM “6x9” b2861 The Cell Language Theory: Connecting Mind and Matter Index 567 long tailed, 20, 26, 41, 236, 293, 315, 327, 335, 341, 351, 359, 441, 462 mRNA, 319, 322, 326 protein-length frequency distribution, 352 sentence-length frequency, 354, 462 single-molecule enzyme kinetic, 31, 336, 349, 360 T-cell receptor variable region sequence diversity frequency distribution, 350 US annual income distribution, 358, 462 word-length frequency distribution, 335, 355, 462 Holy spirit, 281, 385, 392 Homeostasis ion, 112 Hormone sex, 108 stress, 113 Homo sapiens, 107, 285, 400, 445, 451, 458–459 Human knowledge, 7, 12, 51, 53, 178, 281, 286, 410–411, 413, 425, 428, 456, 464–465, 468–469, 478, 484, 529 Human genome map, 192–193 Human genome, 190–193, 196, 303, 335, 346, 352–353 Hydration Hydration shell primary, 240 reorganization, 224 secondary, 240 Hylomorph, 281, 380, 392, 396, 399 Hyperstructure, 29, 58, 98, 299 Hypostatic abstraction, 383 b2861_Index.indd 567 Hypothalamic control, 113 releasing factors, 108 I I-Ching, 244–248 I-Ching hexagrams, 245–246, 248 Iconic Model of Reality, 454–456 Identity-within-difference, 396, 524, 533 Ideogram, 191–192 IDS-cell function identity hypothesis, 56, 312 Induced-fit hypothesis, 2, 8, 53, 79–82, 94, 140, 230 mechanism, 43, 69, 77 Infoknowledge, 470–471 Informatics first law of, the, 363, 365, 440–441 Information flow constructor theory of, 14 genetic, 14, 28, 54, 56, 80, 96, 153, 192, 197, 211, 250, 257, 283, 381, 391, 426, 451 meaningful, 14 meaningless, 14 negative, 441 parametric definition of, 20, 379 Peircean, 4, 15, 19, 379, 391, 414, 475 Planckian (IP), 8, 18, 348, 352, 362, 368, 379, 441 positive, 441 Shannon, 9, 13, 15, 18, 242, 379, 412, 435, 440 theory, 19, 103, 175, 226, 365, 371, 380, 390, 411, 476 uncertainty-reducing, 439 17-10-2017 11:33:07 AM b2861 The Cell Language Theory: Connecting Mind and Matter “6x9” 568 Index Information-energy complementarity, 58, 94, 97, 104, 268, 383, 445–446, 449, 556, 558 complementarity theory of protein folding, 94, 97, 335, 347, 390, 462 Information-life, 446–449 information-life supplementarity, 446–447, 449 Infostatistical mechanics, 364, 371–373, 375 Intracellular dissipative structures (IDS), 2–3, 31, 54–56, 186–187, 190, 256–257, 289, 332 Interference, 68 Interferon, 108 Interleukin, 108 Interpretant, 13–14, 19, 51–52, 175, 192–193, 226–228, 266, 271–273, 275–277, 281–283, 314, 365, 377, 378–380, 392, 401, 403, 418–419, 420, 425, 450, 453, 476, 478 Ion activity, 302 antiport, 139 gradient, 3, 58, 74, 181, 190 hydride, 86, 90, 92 transport channel, 62 transport, 138 Irreducible triadic relation (ITR), 3, 13, 103, 176, 222, 225, 228, 251, 280, 365, 377, 379, 409, 410, 453, 475, 477, 478, 481–482 J James, William, 20–21, 268, 456 Josephson conjecture, 174, 177, 179, 286, 466, 469 Judgement, 124, 310 b2861_Index.indd 568 K Kinematics, 116, 145, 147 KroeplinGlyphs, 212–213 L Language iconic, 450 cosmic, 5, 212, 227, 252, 483 mental, 457, 460 material, 460 molecular, 3, 185, 248, 251 cell, 5, 32, 110, 176, 179, 188, 197, 259, 290 human, 3, 5, 32, 45, 105, 109, 179, 183, 188, 192, 197, 227, 252 Lao-tzu, 410 Law of requisite varierty (LRV), 258 Legisign, 266, 271–273, 276–277, 282–283, 420, 468 Lexicon, 8, 53, 186, 188, 527 Life cosmological, 458 individual, 422 universal, 103 Liformation, 424, 473, 477 Ligand amount of, 72 activity of, 70 binding, 29, 70–71, 73, 77–80, 94 binding affinity, 73 Light Amplification based on Stimulated Emission of Radiation (LASER), 339, 340 Ling, G N., 1, 4, 35–37, 41, 43, 45, 149 17-10-2017 11:33:07 AM “6x9” b2861 The Cell Language Theory: Connecting Mind and Matter Index 569 linkage pseudo, 114 true, 84–85, 88 Linking number (LK), 154–156 Ling–Pollack water structures (LPWSs), 39, 149–150 Logic complementarian, 22–24, 400, 433, 435, 455–456, 548 triune, 24, 397, 524, 538, 540 Lyman series, 305 M Machine macroscopic, 33 molecular, 8, 33, 54, 84, 112, 160, 169, 210–212, 244, 257, 305, 398, 432, 434, 461 Newtonian, 160, 162, 169, 372, 400, 446 self-organzing whenever and wherever needed (SOWAWN), 27 Macroglyphs, 194 Macroscopic motion, 191 scale, 174, 557 Macrosemiotics, 211, 264, 267, 468 Madisonator model of mitochondrial structure and function, 114 Mass, 14, 23, 30, 160, 210, 269–270, 275, 361, 457 Material cause, 101 Matter observed, 455 observing, 455 Mattergy, 22, 424, 446, 470–471, 473, 477 Matter–energy, 470 b2861_Index.indd 569 Matter-symbol complementarity, 33–34, 201–202, 204–205, 556–558 matter-sign complementarity Von Neumann–Pattee principle of, 34, 202, 557 McLuhan equation, 45–46, 212–213, 215, 225 Meaning, 2, 4, 6, 14-16, 18, 33, 56–57, 145, 150, 161, 173, 183, 186, 188, 197, 199, 215, 222, 225–226, 237, 245, 257, 276–277, 278, 304, 314, 362, 368, 372, 398, 421–422, 424, 427, 430, 439–442, 447, 449 Measurement, 22, 24, 28, 52, 166, 169, 293, 295, 298, 337, 353, 369, 412, 415, 438, 530, 539–540, 549 Mechanical energy, 9, 31–33, 58, 61, 104, 115, 130, 148, 152, 156, 159, 162, 167, 170, 191, 197, 204, 206, 256, 391, 456 tension, 104 Mechanics classical, 435 infostatistical, 364, 371, 375 Newtonian, 9, 160, 169, 400, 410 quantum, 3, 8, 28, 33, 53, 177, 179, 256, 327, 333, 369–371, 400, 412, 415, 435, 447, 467, 483, 523, 529, 538 statistical, 9, 18, 53, 92, 364, 371, 375, 434 Mechanism active transport, 60 circle, 35–36 enzyme catalysis, 2, 8, 14, 29, 42, 44, 63, 70, 74, 103, 229, 335, 339, 350, 390, 425, 461 17-10-2017 11:33:07 AM b2861 The Cell Language Theory: Connecting Mind and Matter “6x9” 570 Index muscle contraction, 165 of oxidative phosphorylation, 59, 115, 162 passive transport, 62 Rochester–Noji–Helsinki (RoNoH) model of oxphos, 121 table, 307–308, 311 Mediation, 124, 265 Membrane cell, 7, 37, 52, 58, 99, 219, 229, 231 mitochondrial, 58, 128, 163 plasma, 7, 82, 124 potential, 55, 59, 118, 120, 135, 142, 190, 257 Memory primary, 99 secondary, 99 Merleau-Ponty, Maurice, 183, 260, 268, 281, 380, 396–397, 433–434, 484, 523, 527, 532, 535, 541, 544, 546, 550 Metabolic module, 305 Metabolism Metabolic pathways, 8, 53, 185, 315–319, 465 Metabolon, 185 Microscopic reversibility, 79, 92 scale, 174 Microglyphs, 194 Microsemiotics, 10, 175, 255, 259, 264, 267, 282, 285, 403, 468 Mind and matter, 174 Mitchell, Peter, 58, 64, 88, 115, 123–124, 128, 130–132, 136–137 Mitochondrion, 111–112, 138, 250 b2861_Index.indd 570 Mitochondrial control, 62, 64, 122, 131, 149, 164, 243 DNA, energy transduction, 58, 67, 117, 144 matrix, 124, 142 membrane, 37, 44, 55, 61, 64, 71, 74, 88, 115, 118, 128, 133, 142, 164 response to stress, 113 Möbius pentad, 405–407 relation, 405, 449 Models of consciousness, 6, 475, 479 computing, 558 Module, 98, 299–300, 305 Molecular mechanisms, 1, 75, 114–115, 120, 126, 130, 144, 160, 176, 186, 211, 221, 250, 350–352, 383–384 Molecular machines, 8, 33, 54–56, 112, 160, 163, 169, 210, 244, 257, 305, 398, 432, 434, 461 Mona Lisa, 385, 387 Morphism, 424, 464 Motion bodily, 107 Brownian, 2, 43, 69–72, 80, 83, 92, 119, 121, 159, 167, 230, 233, 351, 372, 380 cellular, 113–114, 317, 331, 351, 445 goal-directed, 31 molecular, 116, 151, 158 oscillatory, 250, 253 periodic, 26, 63, 68, 219, 229, 460 17-10-2017 11:33:07 AM “6x9” b2861 The Cell Language Theory: Connecting Mind and Matter Index 571 random, 161 rotary, 92, 119, 125, 132, 151 rotational, 63, 122, 461 thermal, 82–83, 159, 163, 208–209, 232 translational, 166 vibrational, 63–64, 68, 92, 460 voluntary, 107 Muscle contraction, 115–116, 128, 131, 164, 166, 170, 230 Music, 45, 214, 244, 373 Musical instrument self-organizing, 408, 460 Mutation genetic, 55 Myosin, 32, 68, 94, 165–167, 169, 170–171 N Naturalized phenomenology, 397 Negentropy as negative entropy, 363 Network dynamic, 274 dynamic molecular, 56 NewBrunswickator, the, 259 New Jersey theory of mind (NJTM), 404, 406–407 NewJerseyator, the, 439 Noise, 211, 317 Nothing, 278, 420, 451 O Object, 13–14, 19, 21, 35, 51–52, 101, 150, 166, 175, 182, 192–194, 210, 226–228, 262–263, 266, 273, 275–277, 281–283, 287, 333, 365, 375, 377–379, 381, 401, 403, 409, b2861_Index.indd 571 415, 418, 420, 425, 437, 449–450, 453, 456, 470, 472, 476, 478, 484 Organic Cosmological Principle (OCP), 458–459 organization dis-, 363, 369 gnergy principle of (GPO), 33, 111, 423 other-, 27–28, 374 self-, 8–9, 27, 33, 58, 95, 105, 109, 179, 258–259, 267, 281, 382, 404, 457, 482, 555 oscillation, 150, 219, 226, 251, 460 oscillator self-organzing, 439 oxidative phosphorylation, 1–2, 44, 58–62, 64, 74, 89, 111–112, 114–116, 122–123, 126, 128, 131, 151, 161–162 oxphos, 1–2, 60, 63, 74, 78, 87, 111–112, 115, 121, 124–127, 131–132, 136–137, 140, 144, 148 oxphosome, 63, 66–67, 74, 86, 88, 92 P President Obama, 291–292 Paradigm shift in biomedical sciences, 94–95, 293, 478, 485 Parthenon, 385 Petoukhov coincidence, 239, 242, 244, 249 Petoukhov hypothesis, 461 Peirce, Charles Sanders, 261 Peircean definition of sign, 261, 378 Peircean metaphysics, 281, 380, 414–415, 429, 432, 475, 478 08-11-2017 09:37:18 AM b2861 The Cell Language Theory: Connecting Mind and Matter “6x9” 572 Index Peircean sign, quark model of, 192–193, 226–228, 263–264, 266, 269–270, 274, 276–278, 280, 370, 377, 378, 383, 402-403, 407, 418, 432, 442–443, 449, 463, 465–466 Peirce’s simple concepts (PSC), 280, 379 Periodic table, 8, 53, 281, 433 Personalized medicine, 292, 306, 314, 328 Petoukhov coincidence, 239, 242, 244, 249 pH regulation, 112 gradient, 115, 118, 124, 142 Phaneron, 425 Phaneroscopy, 28, 425 Philosophical table of information, entropy and energy, 434 Phonetics, 186 Phenotype, 14, 100, 251, 309–312, 314–315, 321–322, 326–328, 384 Phonograms, 191–196 Phonons, 98 Photon, 26, 98, 270, 333, 340–341, 447, 482 Photosynthesis, 140 Phosphate fluxes, 90 Phosphorons, 63, 86–90, 92, 144, 145, 148–149, 167 Photoelectric effect, 380 Physiosemiosis, 284–286 Phytosemiosis, 284–285 Planckian distribution equation, 3, 18, 20, 31, 35, 64, 150, 159, 235–236, 293, 333, 335, 338, 341, 361–364, 367–369, 382, 441, 462, 475, 481–482 b2861_Index.indd 572 Planck radiation equation, 27, 159, 315, 326, 333, 368–370, 475 Planck radiation formula, 347, 462 Poisson distribution, 310, 313 Pollack, Gerald, 4, 7, 37, 39, 41, 43, 45, 149–150 Potential action, 104, 106, 251, 256, 265, 374, 433 membrane, 55, 59, 118, 120, 135, 142, 190, 257 PPM model of human knowledge, 413 Practopoiesis, 391–392, 425–427, 429 Pragmatics, 16, 441 Parameter free, 20, 315, 338, 354, 362, 368, 476 infological, 362, 370, 402 Precision medicine, 291–293, 306 Pre-fit hypothesis, 2, 8, 74, 77, 79, 81, 94, 230, 232 mechanism, 43, 68–69, 77–79, 166 Prigogine, 27, 37, 54–55, 213, 250, 258, 305, 374, 383, 386, 389 Prigoginean mechanism of encoding time into matter (PMETM), 383–384, 386 Princetonator, 205–209, 259, 407 Principle generalized Franck–Condon, 2, 29, 42, 69, 163, 166, 211, 256, 390, 426 Le Chatelier, 78, 140 maximum information, 9, 198–199 06-11-2017 11:02:24 AM “6x9” b2861 The Cell Language Theory: Connecting Mind and Matter Index 573 of microscopic reversibility, 79, 92 of recursion, 435 of slow and fast processes, 2, 29, 70, 229 thermodynamic, 63, 348, 365, 368, 386, 403, 434, 437 Process spontaneous chemical, 65 coupled, 74–75 electrochemical, 58, 118, 122 electromechanochemical, 58–59, 67, 119 endergonic, 148, 161 exergonic, 148, 158–159, 161 fast, 2, 29, 70, 229 formal, 207 irreversible, 301 physical, 128, 176, 267, 283, 359, 537 physicochemical, 4, 28, 33, 41, 55, 104, 158, 176, 253, 341, 349, 408, 539 Planckian, 4, 35, 150, 341, 355, 359, 362, 368, 380 reversible, 93, 124, 130, 232, 301 slow, 2, 29, 70, 428 Prostaglandin, 108 Protein complexes configuration, 24, 81, 139, 151, 203 conformation, 24, 32, 59, 67, 70, 82 degradation, 298 folding funnel, 94–96 folding, 44, 96 synthesis, 185 Proton transfer Bohr, 546 b2861_Index.indd 573 coupled electron transfer, 74, 87, 144 Extramembrane, 124 Intramembrane, 62, 64, 88, 124 Mitchell, 88–89, 92, 124, 136–137 motive force, 122, 126, 162, 404 sink, 144 transfer chain, 91, 149 transfer complex, 63, 88, 118 Williams, 136–137 Proton-coupled electron transport (PCET), 144 Pseudolinkage first-order, 64 second-order, 88 Wyman’s, 89, 92 Q Qualisign, 266, 271–272, 276–277, 282–283, 420, 468 Quality, 24, 34, 248, 265–266, 271, 277, 285, 287, 295, 366, 393, 420, 481 Quantity, 16, 119, 248, 285, 393, 439, 481 Quantization of conformational energy of biopolymers, 131, 159 energy, 338–339 free energy, 341 Quantum of action, 9, 30–31, 303, 305, 358, 368, 457, 526, 530–531 mechanics, 3, 9, 28, 30, 41, 53, 177, 180, 256, 369, 371, 400, 412, 428, 435, 469, 529, 537 17-10-2017 11:33:07 AM b2861 The Cell Language Theory: Connecting Mind and Matter “6x9” 574 Index Quarks, 102, 178, 269–270, 272, 274–278, 395, 418–419, 421 Quons, 23, 395–396, 473 R Racker–Stőckenius experiment, 148 RASER model of enzyme catalysis, 339, 360 Rate Amplification based on the Substrate-Enhanced reaction Rates (RASER), 339–340 Reaction Belousov–Zhabotinsky, 32 biochemical, 44 chemical, 8, 14, 27, 41, 44, 53, 56, 64, 86, 90, 99, 117, 120, 128, 481 coordinate, 69 diffusion system, 56, 205, 258–259 rate, 41, 339–340 self-organizing chemical, 56, 258, 389–390, 425–426, 482 Reality ultimate, 2–3, 22, 267, 279, 392, 448, 456, 474, 541, 548 Reason, 11, 83, 99, 101, 105, 132, 183–184, 189, 266, 272, 279, 301, 347, 368, 421, 439, 445, 458 Reasoning, 23, 34, 104–106, 280, 424, 454, 458, 472 Receiver, 13–16, 108, 183, 192, 365, 402 Recursivity, 435 Resonance wave, 64, 68, 213, 253 Relation entropy-information information-energy-entropy, 437 irrational, 451 b2861_Index.indd 574 ITR, 222 modeling, 290 paradigmatic, 182, 371, 452, 548 rational, 105, 219, 277, 406, 435 syntagmatic, 182, 452 irreducible triadicity, 3, 13, 34, 379, 410 sign, 14, 19, 43, 179, 192 Relativity special, 21, 446, 449, 483 generalized Franck–Condon, 29, 63, 166, 256, 426 Replication with variations, 386–389 Representamen, 14, 192, 227–228, 262–263, 271–273, 275, 277, 281–283, 365, 378–380, 392, 401, 403, 418–420, 425, 450, 453 Representation, 2, 12–13, 19, 22, 24, 34, 36, 40, 55, 66, 71, 85, 98, 158, 165, 176, 179, 188, 193, 228, 246– 247, 249, 265, 271, 274, 378–379, 386, 389, 401–402, 413, 427, 442, 446, 448, 465–466, 47 Resonance signal generator, 242 Respiration state 3, 66–67, 79, 167, 340 state 4, 66–67 Respirasome, 62–63, 85–87, 91 Respiratory chain, 61, 64 control, 65–67 enzyme, 122, 124 substrate, 63 Rheme, 266, 271–273, 283, 420, 469 Ribbons, 304–305 Ribosome, 52, 240–241 Ribozyme, 28, 99 17-10-2017 11:33:07 AM “6x9” b2861 The Cell Language Theory: Connecting Mind and Matter Index 575 RNA soup, 204, 208 Rochester–Noji–Helsinki (RoNoH) model of oxphos, 121, 129, 131–132, 144, 148 Rosen’s modeling relation, 418 Rosetta stone, 190–195, 197–198, 221–222, 226 Rotational degrees of freedom, 63 Rotational propagation, 132 Rule-governed creativity, 181, 198, 201, 276, 428 S Saccharomyces cerevisiae, 295 Saussure, Ferdinand de, 8, 53, 176, 179, 182, 447, 452 Schwan’s cell theory, 54 Science energy, 467 gnergy, 467 information, 467 Second law of thermodynamics, molecularized, 81, 94, 162–163, 166, 433, 435 Secondness, 34, 51–52, 106, 263–266, 268, 271–272, 277, 281, 287, 380, 398–399, 404, 414–415, 419–420, 425, 429, 431, 433, 435–436, 404 Self-knowing Universe, 457–460 Self-organizing musical instrument (SOMI), 408, 460 Semantic axis Semantic force, 178 Semanticity, traditional, 198–199 Semantics of the Universe, 16, 186, 188, 195, 245, 403, 441 Semiotic force, 178 Semiotic theory of everything (S-TOE), 483 b2861_Index.indd 575 Semiotics Peircean, 4, 192, 269, 280, 287, 391, 410, 421, 483 neo-, 278, 280, 287, 410 Semiosis real, 283 virtual, 283–284 Sentence linguistic, 8, 53, 176, 202, 263, 371 molecular, 49, 187, 216 Seoulator, the, 259, 279–281 Sex hormone, 108 Shannon formula, 183, 250 entropy, 17–18, 362, 366, 435, 441 information, 9, 13, 15, 199, 242, 250, 412, 435, 440–441 Shillongator, the, 6, 259, 279, 423, 444, 453, 457, 477, 483 Shiva, 380, 392 Sinsign, 266, 271–273, 276–277, 282–283, 418, 420, 468 Stress-Induced Duplex Destabilization, SIDDs, 157, 191, 303 SID–TEM–TOF, signal-induced deactivation of thermally excited metastable state TO function, 4, 150, 340, 349, 351, 360 Sign c-sign, 270, 272, 274 e-sign, 270, 272, 274 composite, 275–276, 465 definition of, 261, 378, 401, 442, 453 elementary, 272, 275, 414, 465 iconic, 23, 194, 262, 441, 454, 464 17-10-2017 11:33:07 AM b2861 The Cell Language Theory: Connecting Mind and Matter “6x9” 576 Index interpretant-less, 276–277, 418, 420 indexical, 262, 442, 469 object-less, 277, 418–420 symbolic, 23, 262, 454 triad, 263 Peircean, 263, 266, 270, 277, 280, 370, 378, 402, 418, 442, 463 processor, 264–265, 274, 284–285, 401, 403, 450 Sign interpretation, 14, 19, 175, 228, 378, 390, 425 Sign production, 14, 19, 28, 175, 228, 378, 380, 390, 425 Signal transduction, 8, 53, 105, 183, 230, 255, 431, 465 transduction pathways, 8, 53, 465 Signified, 183 Signifier, 183 Signless, 278, 418, 420–421 Simplex of 3-dimensional space, 101, 107, 446 Single-molecule enzymology manipulation technique, 165 Somatic mutation theory (SMT), 327 Space Hilbert, 464, 466 Peirce, 443, 464, 466 sign, 466 semantic, 403 Spacetime curved, 9, 14 flat, 14 Spectra atomic blackbody radiation, 333, 336, 347, 361 hydrogen atom, 302 water, 214, 216 b2861_Index.indd 576 Spectral shift, 142 Spin glass, 196, 203 Spin glass Hammiltonian, 203 Spink’s sign pyramid, 402, 446 Spinoza, 268, 281, 380, 392, 396, 399, 433 Spirituality, 259–260, 279 Stoichiometry H+/electron, 124–125 H+/ATP, 124–125 Structures dissipative, 2, 9, 27, 54, 104, 186, 190, 221, 257, 296, 328, 374, 555 dynamic, 55, 190, 257 intracellular dissipative, 2–3, 54, 56, 190, 256, 332 transient, 383, 389 Supermolecule, 60, 62–63, 66–67, 74, 88 Superstring, 430, 463, 465, 467, 483 symmetry a-, 447, 474, 544 anti-, 471–472, 474 breaking, 34–35, 128, 363, 474, 484, 547–549 making, 475 Syntactics, 16, 441 System circulatory, 105, 110, 450 endocrine, 105, 450 formal, 3, 182, 204, 418, 470, 472 immune, 105, 188, 450 motion, 107, 450 natural, 3, 418, 470 nervous, 105, 330, 450, 531 Systome system plus environment, 26 medicine, 4, 41, 43 17-10-2017 11:33:07 AM “6x9” b2861 The Cell Language Theory: Connecting Mind and Matter Index 577 T T-cell receptor, 27, 335, 348, 350–351, 360, 476 Taj Mahal, 385 Tao, the, 22–23, 281, 399, 411, 421 Tarragonator, the, 557–558, 201, 305, 402, 449, 453–454, 483 Testosterone, 108 Tetrahedon body-centered, 2, 6, 101, 106, 290, 402, 450, 453, 471, 483 gnergy, 2–3, 6, 421, 444, 447, 477, 479 Theory category, 3, 8, 11, 264, 382, 413, 463, 471 cell language, 254, 333 group, 200–201 kinetic, 8–9, 53 molecular information, 10, 255, 267, 447 of consciousness, 408 of everything (TOE), 179, 201, 286, 305 quantum field, 37, 47 set, 463–466 Thermodynamics First law of, 128, 328, 330, 469–470 Second Law of, 81, 94, 162, 166, 433, 435 Third Law of, 363, 441 Thirdness, 34, 51–52, 105–106, 264–266, 268, 271–272, 277, 281, 287, 380, 398–399, 404, 414–415, 419–420, 425, 431, 433, 435–436, 448, 450–451, 456, 465, 476, 478 Thylakoid membrane, 138–139 b2861_Index.indd 577 Thought, 6, 23, 37, 42, 47, 59, 61–62, 65–66, 69, 77, 83, , 88, 90, 93, 95, 103, 106–107, 118, 135, 149, 152, 163, 167, 173, 187, 191–192, 195, 207, 213, 223, 252, 257, 265, 268, 272, 278, 280–281, 286–287, 290, 321, 338–339, 341, 370, 380, 383, 388, 391–392, 396, 398–399, 403, 410–411, 414–416, 428, 430, 432–433, 440, 444, 454, 475–476, 478, 481–482 Thoughton, 401, 403, 404 Time, 4, 8, 21, 25–27, 29, 43, 45–46, 53, 56, 59, 66, 70, 82, 93, 101, 103, 105–106, 116, 133, 139, 145, 152, 163, 166, 169, 177, 186–189, 192, 204, 211, 214, 223, 251, 257, 260, 270, 275, 279, 286, 289, 293, 295– 298, 300, 305, 310, 335, 339, 341, 344, 346, 349–350, 356, 357, 360, 366, 372, 383, 407, 414, 416–417, 426, 428, 431, 437–438, 447, 462, 482, 531–532, 537, 541–542 Tissue culture, 306 Tissue organization field theory (TOFT), 327 Transcendentality, 23–24, 277, 393, 396, 538, 539 Transcription, 8, 14, 52, 55, 103, 192, 250, 297–298, 300, 303, 317, 330–332, 391, 427 Translation, 14, 52, 55, 63, 68, 70–72, 103, 166, 240, 250, 391, 421, 427, 461 Translational degrees of freedom, 63, 242, 461 Transcript level, 296–297, 330 Transcription rate, 297 Transcript degradation, 298 17-10-2017 11:33:07 AM b2861 The Cell Language Theory: Connecting Mind and Matter “6x9” 578 Index Transcriptomics, 330 Transmembrane gradient, 73 Transhydrogenase, 65, 86, 88, 91, 118, 138 Transprotonase, 62, 65, 67, 88, 118 Triad fundamental, 56, 464, 466 Irreducible, 103, 192, 225, 227, 252, 365, 448, 453, 467, 474, 481 named, 56 Peircean, 409, 448, 456 possibility-probability-model (PPM), 413 sign, 13 systome-system-environment, 74 Triadic architectonics of human knowledge, 410–411 Triadic model of the World, 408, 454 Triadic monism, 4, 469, 474–475 Tweezer optical, 166, 169 laser, 166, 169 Twist, Tw, 154–156 U Universality of triadicity, 399 Uncertainty, 15, 17–18, 362, 437–440, 539 Unified theory of physics, biology and philosophy, 305 Universum sapiens, 457, 459 Unmoved mover, 256, 451 V Variation, 287, 293, 381, 386–389, 432 Vertebrate mitochondrial code, 243, 250 b2861_Index.indd 578 Vibration, 5, 63, 68, 174, 213, 215–219, 226, 229, 334, 341, 460, 476 Vibrational energy level, 30 Vibrational degrees of freedom, 63, 461 Vishnu, 380, 392 Von Neumann limit, 207, 209 Von Neumann exponent, 209 W Water as the medium of cell language, bulk-phase, 38 cell, 4, 43–44 dissipative structures of, 4, 47, 49, 229 exclusion zone (EZ), 38–39 fourth phase, the, 37–39 Ling–Pollack, 39, 149–150 structured, surface, 49 Water thesis, 5, 222–226 Watson–Crick pairing, 203 Watson–Crick base pairs, 248 Wave chemical conentration, 68 electromagnetic, 39 gravitational, 68 mechanical, 67 packet, 75, 151, 361 particle duality, 3, 41, 64, 98, 244, 266, 360, 369, 475 postulate of cell functions, 68 standing, 49, 68, 70, 187, 213, 221, 231, 359, 361, 462, 476 water, 48–49, 110, 223, 230 Wave–particle duality in biology, 361 biomedical sciences, 67 physics, 537 17-10-2017 11:33:07 AM “6x9” b2861 The Cell Language Theory: Connecting Mind and Matter Index 579 Weaver, Werner, 3, 18, 326, 370, 372 White formula, 151 Writhe, Wr, 154–155 Z Zeroness, 276–277, 281, 287, 419, 463 zoösemiosis, 284–285 Y Yin-yang doctrine, Yin-yang pairs, 242–243, 248–249 b2861_Index.indd 579 17-10-2017 11:33:07 AM ... (ΔT) Drug (ΔD) -2 2.5 ~ 22 .5 + 22 .6 ~ 67.5 + + 67.6 ~ 1 12. 5 + 1 12. 6 ~ 157.5 - + 157.6 ~ 20 2.5 - 20 2.6 ~ 24 9.5 - - 24 9.6 ~ 29 2.5 - 29 2.6 ~ 22 .5 + - Defined as the mean ± 10% of the range of angles... tumor and drug treatment on the b2861_Ch-07.indd 309 1 7-1 0 -2 017 12: 06: 32 PM b2861 The Cell Language Theory: Connecting Mind and Matter “6x9” 310 The Cell Language Theory: Connecting Mind and. .. about the b2861_Ch-07.indd 301 0 6-1 1 -2 017 01:01:40 PM b2861 The Cell Language Theory: Connecting Mind and Matter “6x9” 3 02 The Cell Language Theory: Connecting Mind and Matter Figure 7.7 The