G Model

BIO 3469 18

ARTICLE IN PRESS
BioSystems xxx (2014) xxxxxx

Contents lists available at ScienceDirect

BioSystems
journal homepage: www.elsevier.com/locate/biosystems

Time rescaling and pattern formation in biological evolution

Q1

2 3 4

Abir U. Igamberdiev
Department of Biology, Memorial University of Newfoundland, St. Johns, NL A1B 3X9, Canada

5 19 6 7 8 9 10 11 12 13 14 15 16 17 18

a r t i c l e

i n f o

a b s t r a c t
Biological evolution is analyzed as a process of continuous measurement in which biosystems interpret themselves in the environment resulting in changes of both. This leads to rescaling of internal time (heterochrony) followed by spatial reconstructions of morphology (heterotopy). The logical precondition of evolution is the incompleteness of biosystems internal description, while the physical precondition is the uncertainty of quantum measurement. The process of evolution is based on perpetual changes in interpretation of information in the changing world. In this interpretation the external biospheric gradients are used for establishment of new features of organization. It is concluded that biological evolution involves the anticipatory epigenetic changes in the interpretation of genetic symbolism which cannot generally be forecasted but can provide canalization of structural transformations dened by the existing organization and leading to predictable patterns of form generation. 2014 Published by Elsevier Ireland Ltd.

Article history: Received 5 February 2014 Received in revised form 14 March 2014 Accepted 20 March 2014 Keywords: Biospreading Epigenetic change Heterochrony Heterotopy Quantum measurement Uncertainty

20

1. Introduction

The evolutionary process is commonly analyzed as occurring in the external time and space and arising from the pre-existing 22 complexity at the level of elements constituting complex systems. 23 Such approach generates paradoxes and contradictions of the scale 24 exceeding signicantly the inconsistencies inherent to the New25 tonian mechanics and leads to the appearance of evolutionary 26 theories contravening in their basic foundations, contradicting each 27 other and denying any compromise. The opposite view claiming 28 that time and space intrinsically result from relations between 29 observers is not fully explored with regard to biological evolution. 30 This relational approach arises to Lebniz and was introduced to 31 modern biology by Robert Rosen. It describes the loop causality 32 described by two domains, one being related to the undifferentiated 33 unitary whole and another to the differentiated selected local 34 spacetime, and characterized by the complementarity between 35 the statement that the general geometry of spacetime causes local 36 spacetime to emerge, and the statement that local spacetime 37 interactions produce the general geometry (Rosen, 1991). 38 In previous papers I developed the concept of internal quantum 39 state (IQS) shielded by error-correction and keeping the identity 40 41Q2 of macroscopic system at the quantum level (Igamberdiev, 2004, 2007; Igamberdiev, 2008). The IQS percolates from the level of 42 macromolecules to the unity of a complex multicellular organism, 43
21

Tel.: +1 709 864 4567; fax: +1 709 864 3018. E-mail address: igamberdiev@mun.ca http://dx.doi.org/10.1016/j.biosystems.2014.03.002 0303-2647/ 2014 Published by Elsevier Ireland Ltd.

and at higher levels of organization through the system of microtubules of nervous system. The dual unity of the coherent internal state and of mechanical movement of the macroscopic body underlies the morphogenetic events (Igamberdiev, 2012). In the evolutionary process we move beyond the individual organism and its intrinsic IQS. This means that the no-cloning theorem, stated by Wootters and Zurek (1982) and Dieks (1982), imposes limitations that forbid creation of the identical copies of an arbitrary unknown quantum state. However, although perfect copies of an unknown quantum state are prohibited by this theorem, it does not prohibit the production of imperfect copies. This opens a possibility of multiplication and evolution of quantum systems via coupling a larger auxiliary system to the system undergoing cloning and applying a unitary transformation to the combined system. In case of tting choice of the unitary transformation, some components of the combined system will evolve into approximate copies of the original system. Thus evolution occurs as a transformation of the quantum system coupled to its environment. The internal observers, acting as measuring agents, constitute a network of interactions between organisms mediated by the environment, in which the renement of the wave function generates objective patterns corresponding to perception of the reality of external world (Igamberdiev, 2008). The imperfect cloning means also interruption and multiplication of the agency establishing and holding IQS. A misunderstanding, which often arises in analysing quantum measurement, comes from postulating the necessity of conscious observer for xing measurement result. This postulation is not supported even at the level of brain. Benjamin Libets experiments suggest that consciousness appears as the epiphenomenon of brain

44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72

Please cite this article in press as: Igamberdiev, A.U., Time rescaling and pattern formation in biological evolution. BioSystems (2014), http://dx.doi.org/10.1016/j.biosystems.2014.03.002

G Model
BIO 3469 18 2
73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93

ARTICLE IN PRESS
A.U. Igamberdiev / BioSystems xxx (2014) xxxxxx

states while the reduction of uncertainty in volition acts takes place in the unconscious prior to their awareness (Libet, 1985). Several examples of the unconscious choice in behavior of animals of different levels of organization were established in research of Gunji group (see e.g. Fukano et al., 2004; Migita et al., 2005). The result of measurement can be xed not as a conscious phenomenon but as a consistent history representing soft decoherence event having semiotic value. A modication of the consistent histories interpretation of quantum mechanics, dened as the semiotic interpretation by Christiansen (1985), introduces semiosis as a driving force of decoherence and evolution of quantum systems. The semiotic interpretation is based on the understanding of quantum measurement as an internal process where the measuring device is included into the measured reality, thus establishing a semiotic relation between the device and the quantum system interpreted by the observing agent. In this interpretation decoherent histories are rened through their signicative validity; moreover, the formation of sign itself is equivalent to this reduction. The relational view introduces dual time reference frames (intrinsic and observational) and leads to the comprehension of evolution as a self-growing Logos in the sense of Heraclitus.

94

2. Quantum measurement, time, and growth of complexity

In modern theoretical biology the internal measurement concept is suggested as a background for explanation of the phe96 nomenon of life (Pattee, 1989; Igamberdiev, 1993; Matsuno, 1995). 97 The quantum measurement is an irreversible phenomenon exhibit98 ing itself as a reduction of the potential eld. Its relation to 99 irreversibility of time was discussed earlier (Igamberdiev, 1985, 100 1993; Shiokawa and Hu, 1995). However the collapse of wave 101 function is not equivalent to time because it does not generate a 102 measurable duration. The quantum measurement represents the 103 action of a measuring device on the measured system. When the 104 measuring device is a part of measured system, the measurement 105 proceeds internally in relation to the whole system and the latter 106 becomes more complex as a result of measurement itself. This leads 107 to an iterative recursive process which appears as the develop108 ment and evolution of the system. The quantum measuring device 109 can be organized in such way that it encodes the system in the 110 course of interaction with the measured object and makes it possi111 112 ble for the measurement to proceed in a regular way. In this case, 113 a system can memorize the evolutionary complication of organi114 zation and evolve further, in other words it contains an internal 115 description memorizing the measurement result. The evolution116 ary increase of complexity becomes possible when the genotype 117 appears as a system distinct from the phenotype and embed118 ded into it, which separates energy-degenerate rate-independent 119 genetic symbols from the rate-dependent dynamics of construction 120 Q3 that they control (Pattee, 2001). 121 The internal measuring device measures, among other elements 122 of the measured system, itself in the state of measuring, which lim123 its possible accuracy of quantum measurement and manifests itself 124 as the uncertainty principle (Matsuno, 1992). The increase in com125 plexity as a result of quantum measurement corresponds to the 126 increase in complexity of living organisms in the course of evo127 lution. Indeed, evolution can be viewed as a potentially innite 128 recursive embedding process, where life evolves as measurement 129 of environment, and, through living organisms, becomes embedded 130 into this environment, which affects its further development by its 131 own presence (Rojdestvenski and Igamberdiev, 1999). According 132 to Magdalef (1996), a measurement (observation) of the environ133 ment becomes a source of evolution of the living system itself. The 134 complexity of environment increases as a result of life itself, which, 135 in turn, produces more complexity in life as reection of this fact
95

in the course of measurement at the next level of recursion. Uncertainty comes about as a necessary consequence of such embedding measurement. Thus the increase in complexity occurs simply as a result of quantum measurement. Biological evolution, viewed as adaptation to the tness landscape changing in the course of evolution, becomes its own cause, a universal property of the living world. The appearance of measurable time occurs in the systems that perform quantum measurements in a regular way, with low dissipation of energy (Igamberdiev, 1993, 2004). These systems are modeled as hypercycles, which we dene as the structures appearing when the subset of a substrate set of the catalytic system happens to be the matrix for generating and reproducing the set of catalysts itself (Igamberdiev, 1999). This denition keeps the main features of the original notion of hypercycle given by Eigen and Schuster (1979). The hypercyclic system is closed in the way that all of the catalysts needed for an organism to stay alive (representing an efcient causation according to Aristotle and forming organisms spatiotemporal structure) must be produced by the organism itself, only relying on matter and energy from outside (Letelier et al., 2011). When hypercycles appear, time becomes an independent measurable variable due to internal reproducible changes. Eigens hypercycle is a formalized representation of the autopoietic system of Maturana and Varela or Rosens (M, R) system (Leteiler et al., Q4 2011). The system becomes an internal autonomous clock that distinguishes the past (memory), the present (life), and the future (anticipation based on the reproducible model), so the modeling and logic become possible within the system (Rosen, 1985). The hypercycle having own embedded description, becomes a structure that realizes computation in accordance with its internal logic dened by the embedded description. The latter has a property of incompleteness which is reected in the fact that quantum correlations of the systems states are associated with undecidable logic theories, i.e. can potentially generate statements not dened within the system. The undecidability can be interpreted in the sense similar to Gdels incompleteness theorem, meaning that there exist propositions, expressible in the formal logic, which cannot be proven or disproven (Van den Nest and Briegel, 2008; Briegel et al., 2009). From the quantum mechanical point of view, the emergence of a new statement can acquire a new error-correction meaning to support the internal quantum state (IQS) (Igamberdiev, 2004, 2007). The IQS keeps the system organizationally invariant. It is supported by the set of error-correcting commands that aim to keep IQS free from external demolitions which corresponds to its low effective temperature of a nanokelvin range shielded from external thermal inuences (Igamberdiev, 2007, 2012). A new statement makes the system more complex, with its all spatiotemporal organizational invariance be rescaled. In the course of evolution, an available element of a formal system (similarly to a word when used as a metaphor) can acquire another (in addition to already existing) value that contributes to formation of a new level of organization in the system. The logical basis of this action is the incompleteness of existing formal system that allows assigning arbitrary values to the statements non-provable within that system, while the physical basis is a quantum uncertainty arising in quantum measurement (Fig. 1). A new statement can arise from existing elements by acquiring a double function, however, for xation of this new statement via expansion of existing formal system, some redundancy of the system is needed, which can be achieved by multiplication of some of its elements. The creation of meta-statement will lead to time rescaling in the system. The phenomenon of rescaling of the internal time in systems with nite number of states was analyzed by Rojdestvenski and Cottam (2000) in the context of the internal measurement concept in biology. They established a connection between time rescaling and generalized statistics and suggested to

136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201

Please cite this article in press as: Igamberdiev, A.U., Time rescaling and pattern formation in biological evolution. BioSystems (2014), http://dx.doi.org/10.1016/j.biosystems.2014.03.002

G Model
BIO 3469 18

ARTICLE IN PRESS
A.U. Igamberdiev / BioSystems xxx (2014) xxxxxx 3
247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301

Fig. 1. Physical and logical processes underlying biological evolution.

use a generalized notion of entropy to set the time rescaling parameter. Thus the growth of complexity comes from inseparability of 203 the measuring device from the measured system, and results in 204 increasing of complexity of both the system and the environment. 205 When Gdel numbers are introduced, empowered by a new 206 value, the reduction of uncertainty takes place and separation of 207 contradictory statements is realized. The internal semiotic activ208 ity attaining new values appears as an endo-observer agency that 209 internalizes Gdel numbers. As a consequence, even without addi210 tion of new elements, the division in internal temporal scale takes 211 place, and the whole time of the system is rescaled, which results 212 in reduction of uncertainty and increase of complexity. This pro213 Q5 cess corresponds to increase in external work, which, according 214 to Bauer (1935), is the main characteristic feature of the evolu215 tionary process. It aims to exploit additional resources to maintain 216 living state of evolving biosystem. The increase of external work 217 is observed also in the social evolution due to continuous tech218 nical progress. While the future in the structure of internal time 219 is incorporated as anticipation according to the model generated 220 from embedded description, time rescaling will result in a change 221 of the model of anticipation, generally in its development toward 222 enhancement and better exibility. Thus evolution is the change 223 of the model of anticipation due to empowering of new mean224 ings to Gdel statements. The act of anticipation can be considered 225 as a prior condition for the appearance of a new endo-observer 226 agency of internal measurement. The emergence of a new level of 227 organization cannot be recursively described; it is a process simi228 lar to creating a new formula, which was not present initially. The 229 irreversibility of evolution can be explained in terms of its logical 230 foundations. It is determined by the fact that the Gdel formula set231 ting the truth value cannot be obtained through a set of reversible 232 logical operations. 233 The notion of past in the system, represented in the embedded 234 description as a memory, can be described as an asynchronous com235 munication in which the transmitter and the receiver are separated 236 by the time interval. In fact, time is an engine to separate contradic237 tory statements (Gunji, 1994) and the inequality of the statement 238 Q6 of the transmitter and of the receiver is the example of such sepa239 ration. Gunji and Kusunoki (1997) suggested a model of interaction 240 generating emergent phenomena based on incomplete identica241 tion consisting of alternate procedure of constructing a map from 242 coarse-grained data in a system without boundary. Incomplete 243 identication connected with uncertainty in measurement process 244 is read and interpreted as a cause for new realizations. Biological 245 systems are adapting to the environment that is changing in the 246
202

course of adaptation. A possibility of such mode of adaptation is reected in genome structure. Genome is a system which possesses an internal complementarity between linear texts and their superposition. Relevantly to this, complementarity means that text and hypertext cannot be viewed at the same moment: they should be separated by time interval. It is an example of uncertainty between the system and its embedding. Overlapping genes, alternatively splicing sequences, RNA and DNA editing, introns, and recombination according to molecular addresses are the features of this hypertext generating potentially innite number of language games. Genome as a complete language exists as a complementary set of its alternative combinations resulting in logical paradoxes which determine its temporal dynamics (Isalan, 2009). This superposition is a basis for ontogenesis, adaptation and evolution. Thus, the total true genome is a superposition of contradictory arrangements, which generate one single arrangement at concrete moment of time. The combinatorial capacity of genome increases by many times through the pool of mobile genetic elements. An ambiguity in meaning is analogous to the quantum uncertainty principle in which it is impossible to strictly dene the position and impulse of particle simultaneously, or to x certain energy in a very short period of time necessary for its registration. The problem of a minimum size of the autocatalytic selfreproducing system and its composition has been discussed in several works (Sharov, 1991, 2009; Steel et al., 2013). Selfreproduction itself is a creative process of placing text in text following by self-growth of this joint structure. Any evolutionary change also begins from placing text in text. This is possible because most of genome serves for realization of such non-trivial function. Moreover, even point mutations or deletions can be considered as generative if they are placed in the repeated (e.g. diploid) structure. Doubling is a premise of metasystem transition, which includes duplication of the original system and establishment of the control over multiple copies (Turchin, 1977). The evolutionary signicance of gene duplication was considered by Ohno (1970) as leading to neofunctionalization. The advantage of sexual reproduction is in casual combinatorial generation of new statements from two separate texts that can acquire meanings, thus it resists evolutionary degradation. It becomes a prerequisite for growing of complexity and further evolution. The combinatorial interaction of heterochronic texts generates a new system in which the internal time is rescaled in a new way that generally cannot be forecasted. The heterochronic duplication occurring via hybridization of temporally different organisms generates more possibilities for metasystem transition. Thus, the incompleteness of embedded set of symbols is the formal cause of evolution (Igamberdiev, 1986). Quantum uncertainty in the course of measurement is the physical representation of this incompleteness (Matsuno, 1992). It spans from the level of elementary particles to biological evolution and to the phenomenon of free will and consciousness (Conway and Kochen, 2006). Incomplete identication within a larger system becomes the initial challenge for systems evolution. Fig. 1 shows the parallel representation of physical and logical events underlying biological evolution.

3. Nomothetic constraints of the evolutionary process Change of organisms in their individual life or in evolution can be described in terms of alteration of the composition of parts or relations between parts. The morphological and evolutionary variability follows certain rules that can be called nomothetical laws and analyzed as symmetrical transformations (Meyen, 1974). Q7 E.g. in leaf evolution some transitions are possible, other transitions are less probable and some are prohibited. The probability of

302

303 304 305 306 307 308 309

Please cite this article in press as: Igamberdiev, A.U., Time rescaling and pattern formation in biological evolution. BioSystems (2014), http://dx.doi.org/10.1016/j.biosystems.2014.03.002

G Model
BIO 3469 18 4
310 311

ARTICLE IN PRESS
A.U. Igamberdiev / BioSystems xxx (2014) xxxxxx

transition depends on stage of development, on evolutionary position of species and on their geographical location. The sequence of evolutionary transitions of a certain structure can be viewed 312 as a recursion process called refrain by Meyen (1974). This type 313 of recursion follows the principle of self-similarity in which the 314 quantitative invariants may not conserve but the qualitative (e.g. 315 topological) characteristics will be preserved. This means that a 316 pre-fractal structure is generated, in which we cannot trace its 317 unfolding up to innity thus deviating it from classical fractals. The 318 book of DArcy Thompson (1917) remains the most comprehen319 sive compendium of nomothetical laws operating in the course of 320 biological transformations. 321 Actually fractal is an iteration arising from the set of com322 plex numbers by squaring them, i.e. by reecting them to the 323 2D space. We discussed earlier that in course of quantum mea324 surement, the simplest and most general way of transformation 325 occurs when a new domain is composed of two previous domains 326 (Igamberdiev, 2004). In this process, the evolving state is deter327 mined by the two contradictory values of the system separated by 328 time interval, and the value in time future is acquired after address329 ing them. Two contradictory statements taken as sequential values 330 separated by time interval are composed to obtain the third state331 ment. Thus the next statement (quantitatively modeled as having 332 correspondent value) is composed from the two previous state333 ments when they are memorized as real numbers in the course 334 of recursive process: Fn+2 = Fn + Fn+1 . In this case, certain recursive 335 limits will appear as fundamental canons of perfection formed as 336 memorization within reective loops. The notion of golden section 337 ( = lim Fn+1 /Fn ), which commonly appears in biological pattern 338 formation, follows from this type of memorization (Igamberdiev, 339 2004). 340 The patterns based on the golden rectangle and golden ratio, are 341 self-similar, and each part of the structure is similar to smaller parts 342 and larger parts, which makes it a pre-fractal. In modern mathe343 matics, the golden ratio occurs in fractal geometry due to its own 344 iterative nature (Gulick and Scott, 2010). The fractal property of the 345 proper Fibonacci system is proven in mathematics, and the golden 346 ratio and the specic inversion property intrinsic to the Fibonacci 347 system underlie the Fibonacci fractal (Yudin and Startzev, 2012). 348 Thus the continuous quantum measurement has a property of the 349 Fibonacci generator. The golden section in the course of evolu350 tionary unfolding implicates the principle of optimal construction 351 based on maximal simplicity, which is characterized by minimum 352 of numerical relations between integer and its parts, that indicate 353 the fractal character of recursive processes (Radyuk, 2001). Fractal 354 spatiotemporal patterns and rhythms can originate in hypercycles 355 from the auto-regulatory feedback loops. Maps and clocks based 356 on metabolic hypercycles are used by living organisms to main357 tain their homeodynamic equilibrium and biodiversity at different 358 levels (Damiani, 2002). 359 The evolutionary process takes place via resetting the values of 360 systems organizational invariance. Such resetting cannot be pre361 dicted with certainty and can be evaluated in the newly evolved 362 system, which is embedded in a new environment modied by 363 it. On the other hand, many traits are independent on the values 364 Q8 of organizational invariance forming homology series of variation 365 according to Vavilovs law. Vavilov (1922) formulated the law of 366 homology series as a rule claiming that different taxa (species, gen367 era and up) are distinguished by their radicals (Ln ) representing 368 organizational invariance while the changes in traits (a, b, c. . .) are 369 370 parallel and can be predicted:
371

generally reduced to spatial archetype but has a temporal constituent expressed in certain transformation principles. In the law of homological series, a new statement corresponds to the radical, while the one-level (intraspecies, intragenus, etc.) variability picks up changes from already established sets. In the process of evolution, nomothetic and selection-based decisions can work together. The meaning of newly generated anticipatory models can be tested via the selection process. Interpretation of new statements has a high degree of exibility, however beyond this exibility the rules of selection of the actual forms apply. This process can be called rather episelective (Cherdantsev et al., 1996) because it operates on a countable number of spatially ordered structures capable of self-reproduction. In this process, the appearance of new correlations is expressed in reorganization of the phenotypic variation pattern, and the directional transformations of the phenotype occur on the basis of nonspecic and randomly directed effects of selection. Although the selection process does not add to explanation of nomothetic unfolding of patterns during the evolutionary process, it restricts the number of possibilities that can be realized in such unfolding. Thus biological evolution appears as partially directed, and a prior information about the tness space determines the unfolding process (Melkikh, 2014). Understanding of evolution as partially directed suggests consideration of the genotypephenotype interaction as not that of determination but as interpretation (Kull, 1998). In these interpretation patterns, the closed loops of causation are mapped into a single coherent spacetime frame (Rosen, 1993). Certain optimal values that can be redundantly repeated in any reective loop correspond to the topological inevitability of certain developmental and evolutionary processes. These topological singularities inevitably emerge during epigenetic realization, and are retained and transformed in pattern formation. These patterns are not encoded but unfolded within the whole organization, which is in line with the basic idea that the whole system cannot be reduced to its internal description. To understand a relation of pattern formation to underlying phenomena, we need to go beyond the concept of genetic determination and analyze fundamental principles of biological organization based on percolation between different levels spanning from basic quantum phenomena to life and consciousness (Conrad, 1996).

374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415

4. Rescaling of internal time and epigenetic evolution The growth of complexity is particularly evident upon formation of eukaryotic cells and then of multicellular organisms. These organisms have complex programs of temporal development, which work over their whole life but most drastic spatiotemporal changes take place at early stages in embryogenesis. In multicellular organisms, all cells possess the same genetic text, which is interpreted in different ways. In evolution, changes are introduced in genomes, but still changes in interpretation remain more meaningful than changes in genetic information itself. The discovery of homeotic genes causing the development of specic morphological structures (Lewis, 1994) rooted the emerging discipline of evo-devo in molecular genetics. Genome is a dynamic open system with different possibilities of its reading. The relationship of ontogeny and phylogeny in this context can be represented as follows. Ontogeny is characterized by reproduction of structures of truth values of the internal logical calculus of biosystems and the evolutionary process corresponds to assigning truth values at the external level. Thus, in biology, we are dealing with the two levels of algebraic logic, and their relationship can be found in a non-trivial indeterminist interpretation.

416

417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436

Ln (a + b + c + d + e + f + g + h + i + k ) A difculty to dene radicals can be related to the problem of formulating organizational invariance because it is not

372 373

Please cite this article in press as: Igamberdiev, A.U., Time rescaling and pattern formation in biological evolution. BioSystems (2014), http://dx.doi.org/10.1016/j.biosystems.2014.03.002

G Model
BIO 3469 18

ARTICLE IN PRESS
A.U. Igamberdiev / BioSystems xxx (2014) xxxxxx 5

tienne Geoffroy Saint-Hilaire for the rst time considered transformations of species as a consequence of inherited changes in embryos caused by changes in the environment and assumed 439 that early stages of ontogenesis are most important for transfor440 mation of living organisms (Geoffroy Saint-Hilaire, 1838; reviewed 441 in Le Guyader, 2004). Karl Ernst von Baer dened the mechanism 442 of epigenetic evolution in more detail by explaining change as 443 organisms interpretation of itself in changing environment and 444 persistence of this interpretation over generations which can be 445 further inherited (Baer, 1828). DArcy Thompson (1917) in his 446 book On Growth and Form postulated that differential growth 447 rates could produce variations in form. He showed the underly448 ing similarities in body plans and how geometric transformations 449 could be used to explain the variations. The locally measurable 450 spacetime of biological organisms is transformed through time 451 rescaling. In agreement with these ideas, Waddington (1959) intro452 duced the concept of canalization, which refers to the ability of 453 an organism to produce the same phenotype despite variations 454 in genotype or environment, and identied a mechanism called 455 genetic assimilation which would allow organisms response to 456 environmental stress to become a xed part of its developmental 457 repertoire. 458 From the framework of quantum measurement, a local increase 459 of energy dissipation can result in a shorter time of holding the 460 coherent state (IQS) of a subsystem according to the energy-time 461 Heisenbergs uncertainty ratio and consequently to changes in 462 the conformational dynamics of cytoskeleton and in the scales of 463 hyper-restoration processes (Igamberdiev, 2012). These processes 464 are essential in morphogenetic events and provide a possibility 465 of accumulation of additional energy and making an extra-work 466 which can be used for building-up of new morphological structures 467 (Beloussov, 2012). This leads to rescaling of the individual time of 468 this subsystem and to a possibility of inclusion of additional subsys469 tems that would support holding the IQS of the whole system with 470 a higher precision and for a more prolonged time. The most radical 471 case is decreasing the internal time of a subsystem to zero by the 472 apoptosis. This process plays an important role in morphogenesis 473 of all multicellular organisms and provides a powerful mechanism 474 of time rescaling and pattern formation. 475 The reduction of individual time of a subsystem is one of con476 ditions of further complication of organization and of addition 477 of new structural and dynamical levels to it. Stephen Jay Gould 478 suggested the approach to explaining evolution called terminal 479 addition; according to it every evolutionary advance was added 480 as new stage by reducing the duration of the older stages, the 481 idea based on observations of neoteny (Gould, 2010). This was 482 extended by more general ideas of heterochrony (changes in tim483 ing of development) as a mechanism for evolutionary change. It 484 was suggested that a new feature may appear as exaptation, which 485 is not adaptation but its anticipation, i.e. a feature that is avail486 able for useful cooptation by descendants (Gould and Vrba, 1982; 487 Kirby, 1998). These features enhance tness but do not have current 488 Q9 role; they are empowered by meaning in the course of evolu489 tion. Berg (1922) called them anticipations of phylogenesis by 490 ontogenesis and suggested that they play a role in phylogenetic 491 acceleration, i.e. in time rescaling. There are various examples 492 of exaptations that play role as pre-adaptations, e.g. many cyclic 493 processes appeared rst as casual constructs and then acquired 494 functional roles. 495 The mechanisms of epigenetic inheritance were studied in 496 ciliates. These unicellular organisms represent a unique group 497 containing two nuclei: a small diploid micronucleus and a large 498 polyploid macronucleus. The latter is generated from the micronu499 cleus by amplication of the genome and heavy editing. The 500 micronucleus serves as the germ line nucleus but does not express 501 its genes, while the macronucleus provides the nuclear RNA for 502
437 438

vegetative growth. It was shown that maternal RNA templates provide both an organizing guide for DNA rearrangements and a template that can transmit spontaneous mutations that may arise during somatic growth to the next generation (Nowacki and Landweber, 2009). This suggests that the somatic ciliate genome is really an epigenome, formed through templates and signals arising from previous generations. In ciliates we have a spatial separation between the edited and non-edited genome, while in the multicellular organisms it refers more to the temporal separation. Therefore ciliates represent a unique object to study the mechanism of evolutionary exibility (Landweber and Kari, 1999). Parental noncoding RNA molecules instruct whole-genome reorganization. This includes removal of nearly all noncoding DNA and sorting the remaining fragments, producing extremely generich somatic genomes (Nowacki et al., 2010). Nowacki et al. (2011) describe how the RNA templates provide both an organizing guide for DNA rearrangements and a template that can transport somatic mutations to the next generation. They dene this biological role for RNA as to sculpt genomic information in cells. Thus the most general role of RNA consists in generation of possibility of new Gdel statements, which can be memorized in genome. In fact, there is no denition for the general function of all various forms of RNA in the trinitary structure of the central dogma (DNARNAprotein). It consists in implementation of the dynamic exibility in the system, providing mechanisms of generation of Gdel statements. Recursion is not possible in the dual system gene-protein, in the best way it can generate only a strict evolution by mutations followed by selection. In the system with the intermediate component (RNA) the exibility arises and evolution appears as a sophisticated language game in which RNA becomes a part of the temporal component moderating incomplete identication and increasing plasticity between genes and their realized functions. Shapiro (2013) suggests changing our understanding of genome as a Read-Only Memory subject to change by copying errors and accidents, to an intricately formatted Read-Write (RW) data storage system constantly subject to cellular modications and inscriptions. These inscriptions occur over three distinct time-scales (cell reproduction, multicellular development and evolutionary change) and involve a variety of different processes at each time scale (forming nucleoprotein complexes, epigenetic formatting and changes in DNA sequence structure). The writing capacity of the genome directly depends on generating new statements and empowering them by meanings. Therefore it is not a direct writing but the process mediated logically by a generative capacity of the formal system and physically by a reduction of uncertainty. There is always a way for a new interpretation to be memorized and for heredity to be a memory. The epigenetic approach to understanding evolution is based on the integrity of living organization, and according to it, heredity expresses canalization of development toward a stable nal state (Shishkin, 2006). Canalization can be considered as a typical selforganization process leading to complementarity between parts and the whole (Gunji and Ono, 2012). It is generally impossible to describe normal genotype in terms of xed allelic states. Deviations from normal phenotype characterize a space of possibilities of biosystems responses, and every evolutionary shift stabilizes one of the alternative ontogenetic pathways within the system. Thus evolution is a process of continuous reparation of the ontogenetic stability at the cost of increasing complication of the integral organization and its each step is a compelled reorganization of the ontogenetic system toward a new ultimate systems stable nonequilibrium state. Increase in stability of realization of the latter results in progressive remodeling of the earlier stages of ontogeny. The changes caused by these stabilizing processes result in a number of manifestations, such as initially labile expression of new acquisitions, the remodeling of their morphogenesis with time and

503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568

Please cite this article in press as: Igamberdiev, A.U., Time rescaling and pattern formation in biological evolution. BioSystems (2014), http://dx.doi.org/10.1016/j.biosystems.2014.03.002

G Model
BIO 3469 18 6
569 570

ARTICLE IN PRESS
A.U. Igamberdiev / BioSystems xxx (2014) xxxxxx

the predominant maintenance of ancestral traits in late ontogeny of the closest descendants (Shishkin, 2012). The consistent patterns of heterochrony in relation to plant 571 evolution were outlined by Takhtajan (1946). He noted that the 572 phenomena of heterochrony are expressed in the highest degree in 573 most primitive groups of a given taxon. In the course of progres574 sive idioadaptive specialization of the phylogenetic branches, the 575 evolutionary heterochrony of characters gradually comes to equal576 ity, and the characters of organisms become more and more coeval. 577 In case of narrow one-sided specialization the strengthening of the 578 difference of expression levels of separate characters occurs. Despe579 cialization opens possibilities of further evolution by increasing 580 evolutionary plasticity. Large systematic units emerged by means 581 of general degeneration and following progressive evolution. The 582 organism is subjected to profound reconstruction, which however 583 touches not all parts. In case of stronger correlation of characters, 584 the systematic group gets more advanced on the way of idioadap585 tive evolution but the phenomenon of evolutionary heterochrony 586 comes to be weaker. The profound evolutionary changes based on 587 time rescaling we can nd in gametophyte reduction and special588 ization and prolongation of the sporophyte phase. This trend is an 589 example of neoteny, i.e. of the change in time of individual devel590 opment leading to acquisition of the ability to sexual reproduction 591 at the earlier than adult stage and resulting in a higher evolutionary 592 plasticity. 593 Q10 Kauffman (1993) claimed that the occurrence of positional 594 maps and ordered spatial heterogeneities can be understood 595 as generic self-organized properties in biological systems: thus, 596 morphogenesis includes complementary interaction of the digital 597 information (encoding) with the non-digital information (tem598 plating) which reads (decodes) the code (i.e. realizes reective 599 action). The interaction between these two types of information 600 non-recursively forms an interpretant for the semiotic system of 601 living being. The information based on specic recognitions trig602 gering dynamical energy-driven processes appears as non-digital; 603 the transfer of digital information is realized within hypercycles 604 and corresponds to operation of the genetic code (Igamberdiev, 605 1998). 606 The main material of evolution is the intraindividual variation, 607 the only source of which is the mechanics of morphogenesis itself, 608 and the morphological evolution can take place at an initially zero 609 heritability and zero adaptive value of morphological differences 610 (Cherdantsev and Grigorieva, 2010). In the studies of pattern for611 mation, it was shown that morphogenesis becomes a driving force 612 of the adaptively silent, but directional evolution of the developing 613 systems, which seems to be the only possible way of originating of 614 the evolutionary novelties, both in evolution and ontogeny of bio615 logical structures (Cherdantsev and Scobeyeva, 2012). The linear 616 ontogeny (succession of the developmental stages) is a secondary 617 evolutionary phenomenon originating from cyclic self-organizing 618 algorithms of the active shell shaping (Cherdantsev and Grigorieva, 619 2012). Changes in cyclic processes result in rescaling of the linear 620 time of individual development. 621

622

5. Biospheric factors of time rescaling In the course of evolution, biological systems recognize external gradients and acquire a capacity of rescaling according to them. This represents a continuous global adaptation process based on the dynamic negotiation between the global and local information (Nizato and Gunji, 2013). In this process, evolution is realized via coupling a part of environment recognized by the system (the Umwelt) to the system itself with the following transformation of the combined system. The global tness landscape for all living organisms is biosphere. While major evolutionary changes proceed

623 624 625 626 627 628 629 630 631

via empowering by meaning of new statements followed by rescal632 ing of internal time, it is worth to explore if the temporal changes 633 in biological processes during individual development are linked to 634 biospheric factors that directly affect temporal processes in biosys635 tems and participate in setting biological time clock. Time rescaling 636 can involve changes in the rates at one or more of systems levels, i.e. 637 the rates of metabolism, of protein turnover and of gene expression. 638 Biosphere involves oscillatory processes of different scales based 639 on the geological (plate tectonics) and astronomical (precession of 640 Earths orbit) phenomena that can directly affect time rescaling of 641 biosystems and determine evolutionary changes. It was shown by Q11642 Meyen (1987, 1992) that almost all taxa higher than genus have 643 the equatorial (tropical) origin. The average ages of taxa increase 644 with latitude with the tropics harboring both old and young taxa 645 and higher latitudes progressively lacking in younger taxa. During 646 periods of warming they migrate to higher latitudes (equatorial 647 pump). This process Meyen called phytospreading for plants and 648 it can be dened as biospreading in general. At higher latitudes, 649 the macroevolution rate decreases and evolutionary changes occur 650 mostly within genera. The macroevolutionary changes in tropics 651 are connected, according to Meyen, with selective neutral salta652 tion in conditions of low pressure of natural selection or at least of 653 its abiotic constituent. In other words, in tropical areas there is a 654 higher possibility of generation of uncertainties and formation of 655 new genetic combinations that can be empowered by meaning. 656 Several possible mechanisms of generation of heterochrony in 657 these conditions can be considered. The species migrated to higher 658 latitudes (during the periods of climate warming) evolve to new 659 species and genera and only very rarely to higher taxa (families). 660 The reverse process (in the periods of climate cooling) results in 661 shifting of migrated species back to lower latitudes. The alteration 662 in time of developmental processes and turnover of living cycles 663 of migrated organisms may be achieved by variability in the bal664 ance between the anabolic and catabolic processes, in particular by 665 greater involvement of the pathways of respiration non-coupled to 666 ATP synthesis at higher latitudes. Futile recycling processes result 667 in faster living cycles and lower biomass accumulations, leading to 668 simpler morphology and smaller size (McNulty et al., 1988). Thus 669 the migration of organisms to higher latitudes results in internal 670 time rescaling: the duration of internal processes and morpho671 logical proportions of these organisms will change. Time rescaling 672 (heterochrony), in particular, refers to the changes in duration of 673 embryogenesis of different organs, leading to alterations of the 674 site of embryonic initiation of a particular organ (heterotopy). 675 These changes may be initially epigenetic. The migration back from 676 tropics during the next colder period can result in coexistence of 677 organisms with different internal times but not signicantly differ678 ent genetically and potentially keeping a possibility of crossing and 679 getting fertile progeny, in particular if this is followed by genome 680 duplication. As a result, the advanced forms emerge possessing 681 altered spatiotemporal characteristics (archetypes) and constitut682 ing new progressive taxa. 683 The uctuations of Earths climate forming evolution-driving 684 gradients were particularly evident during icehouse epochs of the 685 Earth when the oscillations between glacial and interglacial peri686 ods occurred with the periods of tens or hundreds of thousand 687 years. These oscillations were observed in the Pleistocene and 688 likely in the preceding epoch (late Pliocene) (De Schepper et al., 689 2013) and accompanied the origin and evolution of genus Homo. 690 It is very likely that similar oscillations occurred during the earlier 691 major peak of icehouse climate 300 million years before present, 692 at the Permo-Carboniferous boundary (Algeo et al., 2008). By tak693 ing bivalves as an example, Jablonski et al. (2006) suggested that 694 most clades tend to originate in tropics and then expand out 695 to higher latitudes while retaining their tropical presence. The 696 steepest latitudinal gradients occur in the geologically youngest 697

Please cite this article in press as: Igamberdiev, A.U., Time rescaling and pattern formation in biological evolution. BioSystems (2014), http://dx.doi.org/10.1016/j.biosystems.2014.03.002

G Model
BIO 3469 18

ARTICLE IN PRESS
A.U. Igamberdiev / BioSystems xxx (2014) xxxxxx 7
735 736 737 738 739 740 741 742 743 744 745

698 699 700 701 702 703 704 705 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720 721 722 723 724 725 726 727 728 729 730 731 732 733 734

clades and are consistent with dynamic processes involving preferential origination at low latitudes and poleward expansion over time. The expansion of taxa correspond to expansion of niches, and during this expansion, the areas of refugia are formed in which, under a relative isolation, a secondary evolutionary process takes place increasing lower scale diversity of communities of these refugia. Range expansion of clades may occur via bridge species, which violate climate-niche conservatism to bridge the tropical-temperate boundary. Substantial time lags (5 million years) between the origins of tropical clades and their entry into the temperate zone suggest that out of tropics events are rare on a per-clade basis. Clades with higher diversication rates within the tropics are likely to produce multiple bridge species, suggesting that high speciation rates promote the out of tropics dynamics (Jablonski et al., 2013). Svenning et al. (2008), by investigating palm species, conrmed the basic phytospreading tendencies for this plant group. Dowle et al. (2013) further developed the concept of geographical pattern in evolution. They showed that species density is higher in the tropics (low latitude) than in temperate regions (high latitude) resulting in a latitudinal biodiversity gradient. This gradient is supported by differences in latitude-dependent rates in molecular evolution. Investigations of the metabolic background of phytospreading (Allen et al., 2002; Brown et al., 2004) were intended to provide a thermodynamic basis for the regulation of species diversity and the organization of ecological communities. The main idea here is that the increased energy ow results in generation of metabolic bifurcations in major pathways. If the additional energy, needed for closure of newly formed pathways and thus for formation of a new stable non-equilibrium state shielding the coherent quantum, does not strictly constrain the survival, this results in formation of more complicated evolutionary organization (Igamberdiev, 1999; Igamberdiev and Lea, 2002, 2006). The reversible and oscillating biospreading represents a powerful engine for evolution. Besides the equatorial pump, other similar mechanisms exploiting the existent natural gradients may play important role, in particular in early evolution of multicellular organisms, including oscillations in the level of ocean or ebbs

and ows, accompanied by exchange of water between the ocean and the atmosphere, so the driving factor will be in switching between hydrolysis and dehydration. Changes in salinity and salt content, temperature, electrochemical and optical characteristics of water, pH in closed water reservoirs will be among other factors that determine generation of heterochronic and heterotopic events. Fig. 2 schematically shows the sequence of events in the biospheric causation of evolution when changes in energy ows in the biosphere cause biospreading, leading to time rescaling and to merging (e.g. via hybridization) of biological units having different times, thus triggering the macroevolutionary process. 6. Conclusion The systems having embedded internal description are, according to Rosen, anticipatory in the sense that the embedded description generates a model of their behavior. If the model does not provide a correct result, they can evolve due to acquisition of new statements inside the embedded description that overcome limitations of the existing model. Generation of new statements has its logical precondition in the incompleteness of internal formal system of biosystem and its physical precondition is quantum uncertainty in the course of internal measurement. The newly generated statements are empowered by meanings in the changing environment. The internal time emerges in the hypercyclic structure when irreversible quantum measurements are used for building clocks with repeatable temporal patterns. The growth of complexity is a consequence of internal quantum measurements performed by the systems having embedded description. It increases the amount of external work and generates nomothetic patterns of spatiotemporal structures of evolving systems. These patterns unfold in a fractal-like manner and reproduce certain optimal proportions during their realizations such as the golden ratio. Thus living systems have their internal times, and in the course of evolution, time rescaling takes place. The processes of time rescaling are triggered in epigenetic evolution by the biospheric parameters causing time shift in metabolic processes and in genome mobility. Uncited references Goldschmidt (1940), Gunji et al. (2006), Rojdestvenski and Igamberdiev (2007) and Rosen (1978a, 1978b). References
Algeo, T., Rowe, H., Hower, J.C., Schwark, L., Herrmann, A., Heckel, P., 2008. Changes in ocean denitrication during Late Carboniferous glacial-interglacial cycles. Nat. Geosci. 1, 709714. Allen, A.P., Brown, J.H., Gillooly, J.F., 2002. Global biodiversity, biochemical kinetics, and the energetic-equivalence rule. Science 297, 15451548. Baer, K.E.v., 1828. Ueber Entwicklungsgeschichte der Thiere. In: Beobachtung und Reexion. Gebrder Borntrger, Knigsberg. Beloussov, L.V., 2012. Morphogenesis as a macroscopic self-organizing process. Biosystems 109, 262279. Briegel, H.J., Browne, D.E., Dur, W., Raussendorf, R., Van den Nest, M., 2009. Measurement-based quantum computation. Nat. Phys. 5, 1926. Brown, J., Gillooly, J., Allen, A., Savage, V., West, G., 2004. Toward a metabolic theory of ecology. Ecology 85, 17711789. Cherdantsev, V.G., Kreslavsky, A.G., Severtsov, A.S., 1996. Episelective evolution. Evol. Theor. Rev. 11, 6987. Cherdantsev, V.G., Grigorieva, O.G., 2010. Morphogenetic bases and parametric system of trichome evolution in plants of the genus Draba L. Russ. J. Dev. Biol. 41, 227239. Cherdantsev, V.G., Grigorieva, O.V., 2012. Morphogenesis of active shells. Biosystems 109, 314328. Cherdantsev, V.G., Scobeyeva, V.A., 2012. Morphogenetic origin of natural variation. Biosystems 109, 299313. Christiansen, P.V., 1985. The semiotics of quantum non-locality. IMFUFA, Roskilde University, pp. 60.

746

747 748 749 750 751 752 753 754 755 756 757 758 759 760 761 762 763 764 765 766 767 768 769 770

Q12 771
772 773

774

775 776 777 778 779 780 781 782 783 784 785 786 787 788 789 790 791 792 793 794 795 796 797 798

Fig. 2. Biospheric triggering of the macroevolutionary process via time rescaling.

Please cite this article in press as: Igamberdiev, A.U., Time rescaling and pattern formation in biological evolution. BioSystems (2014), http://dx.doi.org/10.1016/j.biosystems.2014.03.002

G Model
BIO 3469 18 8
799 800 801 802 803 804 805 806 807 808 809 810 811 812 813 814 815 816 817 818 819 820 821 822 823 824 825 826 827 828 829 830 831 832 833 834 835 836 837 838 839 840 841 842 843 844 845 846 847 848 849 850 851 852 853 854 855 856 857 858 859 860 861 862 863 864 865 866 867 868 869 870 871 872 873

ARTICLE IN PRESS
A.U. Igamberdiev / BioSystems xxx (2014) xxxxxx Lewis, E.B., 1994. Homeosis the rst 100 years. Trends Genet. 10, 341343. Libet, B., 1985. Unconscious cerebral initiative and the role of conscious will in voluntary action. Behav. Brain Sci. 8, 529566. Magdalef, R., 1996. Information and uncertainty in living systems, a view from ecology. Biosystems 38, 141146. Matsuno, K., 1992. The uncertainty principle as an evolutionary engine. Biosystems 27, 6376. Matsuno, K., 1995. Quantum and biological computation. Biosystems 35, 209212. McNulty, A.K., Cummins, W.R., Pellizzari, A., 1988. A eld study of respiration rates in leaves of arctic plants. Arctic 41, 15. Melkikh, A.V., 2014. Quantum information and the problem of mechanisms of biological evolution. Biosystems 115, 3345. Migita, M., Mizukami, E., Gunji, Y.P., 2005. Flexibility in starsh behavior by multilayered mechanism of self-organization. Biosystems 82, 107115. Nizato, T., Gunji, Y.P., 2013. Interactions between species and environments from incomplete information. Biosystems 111, 145155. Nowacki, M., Landweber, L.F., 2009. Epigenetic inheritance in ciliates. Curr. Opin. Microbiol. 12, 638643. Nowacki, M., Haye, J.E., Fang, W.W., Vijayan, V., Landweber, L.F., 2010. RNA-mediated epigenetic regulation of DNA copy number. Proc. Natl. Acad. Sci. U. S. A. 107, 2214022144. Nowacki, M., Shetty, K., Landweber, L.F., 2011. RNA-mediated epigenetic programming of genome rearrangements. Annu. Rev. Genomics Hum. Genet. 12, 367389. Ohno, S., 1970. Evolution by Gene Duplication. Springer-Verlag, New York. Pattee, H.H., 1989. The measurement problem in articial world models. Biosystems 23, 281290. Radyuk, M.S., 2001. On biological essence of golden section. Zhurnal Obshchei Biologii (J. Gen. Biol.) 62, 403409 (in Russian). Rojdestvenski, I., Cottam, M.G., 2000. Time rescaling and generalized entropy in relation to the internal measurement concept. Physica A 278, 150160. Rojdestvenski, I., Igamberdiev, A.U., 1999. Recursive embedding, quantum measurement and uncertainty principle. In: Hall, M.L.W., Wolby, J. (Eds.), Humanity, Science, Technology: The Systemic Foundations of the Information Age. International Society for System Studies, Asilomar, pp. 347348. Rojdestvenski, I.V., Igamberdiev, A.U., 2007. Recursive embedding, quantum measurement, uncertainty principle, and evolution of biological systems. In: Shilkov, Yu.M. (Ed.), Viktor Alexandrovich Shtoff and Modern Philosophy of Science. St. Petersburg State University Publishers, pp. 190204 (in Russian). Rosen, R., 1978a. On anticipatory systems. I. When can a system contain a predictive model of another? J. Soc. Biol. Struct. 1, 155162. Rosen, R., 1978b. Feedforwards and global system failure general mechanism for senescence. J. Theor. Biol. 74, 579590. Rosen, R., 1985. Anticipatory Systems. Philosophical, Mathematical and Methodological Foundations. Pergamon Press, New York. Rosen, R., 1991. Beyond dynamical systems. J. Soc. Biol. Struct. 14, 217220. Rosen, R., 1993. Drawing the boundary between subject and object comments on the mind-brain problem. Theor. Med. 14, 89100. Shapiro, J.A., 2013. How life changes itself: the Read-Write (RW) genome. Phys. Life Rev. 10, 287323. Sharov, A.A., 1991. Self-reproducing systems structure, niche relations and evolution. Biosystems 25, 237249. Sharov, A.A., 2009. Coenzyme autocatalytic network on the surface of oil microspheres as a model for the origin of life. Int. J. Mol. Sci. 10, 18381852. Shiokawa, K., Hu, B.L., 1995. Decoherence, delocalization, and irreversibility in quantum chaotic systems. Phys. Rev. E 52, 24972509. Shishkin, M.A., 2006. Development and lessons of evolutionism. Russ. J. Dev. Biol. 37, 146162. Shishkin, M.A., 2012. Systemic grounds of morphogenesis and their manifestation in the fossil record. Paleontol. J. 46, 331342. Steel, M., Hordijk, W., Smith, J., 2013. Minimal autocatalytic networks. J. Theor. Biol. 332, 96107. Svenning, J.C., Borchsenius, F., Bjorholm, S., Balslev, H., 2008. High tropical net diversication drives the New World latitudinal gradient in palm (Arecaceae) species richness. J. Biogeogr. 35, 394406. Takhtajan, A.L., 1946. On the evolutionary heterochrony of characters. Proc. Acad. Sci. Armenian SSR 5, 7986. Turchin, V., 1977. Phenomenon of Science. Columbia University Press, New York. Van den Nest, M., Briegel, H.J., 2008. Measurement-based quantum computation and undecidable logic. Found. Phys. 38, 448457. Waddington, C.H., 1959. Canalization of development and genetic assimilation of acquired characters. Nature 183, 16541655. Wootters, W., Zurek, W., 1982. A single quantum cannot be cloned. Nature 299, 802803. Yudin, V.V., Startzev, E.S., 2012. The Fibonacci fractal is a new fractal type. Theor. Math. Phys. 173, 13871402.
874 875 876 877 878 879 880 881 882 883 884 885 886 887 888 889 890 891 892 893 894 895 896 897 898 899 900 901 902 903 904 905 906 907 908 909 910 911 912 913 914 915 916 917 918 919 920 921 922 923 924 925 926 927 928 929 930 931 932 933 934 935 936 937 938 939 940 941 942 943 944 945 946 947 948 949

Conrad, M., 1996. Cross-scale information processing in evolution, development and intelligence. Biosystems 38, 97109. Conway, J., Kochen, S., 2006. The free will theorem. Found. Phys. 36, 14411473. DArcy Thompson, W., 1917. On Growth and Form. Cambridge University Press, London. Damiani, G., 2002. Metabolic hypercycles, universality and fractals in biological evolution. In: Losa, G.A., Merlini, D., Nonnenmacher, T.F., Weibel, E.R. (Eds.), Fractals in Biology and Medicine. Book Series: Mathematics and Biosciences in interaction, vol. III. Birkhauser, Basel, pp. 259269. De Schepper, S., Groeneveld, J., Naafs, B.D., Van Renterghem, C., Hennissen, J., Head, M.J., Louwye, S., Fabian, K., 2013. Northern hemisphere glaciation during the globally warm early late Pliocene. PLoS ONE 8, e81508. Dieks, D., 1982. Communication by EPR devices. Phys. Lett. A 92, 271272. Dowle, E.J., Morgan-Richards, M., Trewick, S.A., 2013. Molecular evolution and the latitudinal biodiversity gradient. Heredity 110, 501510. Eigen, M., Schuster, P., 1979. The Hypercycle: A Principle of Natural SelfOrganization. Springer-Verlag, Berlin. Fukano, T., Hamanishi, Y., Gunji, Y.P., 2004. Event detection by forward- and backward-prediction, illustrating the analysis for behaviors of black larder beetle Dermestes haemorrhoidalis Kster. Biosystems 78, 8191. Geoffroy Saint-Hilaire, E., 1838. Notions Synthtiques, Historiques et Physiologiques de Philosophie Naturelle. Dnain, Paris, pp. 138. Goldschmidt, R., 1940. The Material Basis of Evolution. Yale Univ. Press, New Haven. Gould, S.J., 2010. Of coiled oysters and big brains: how to rescue the terminology of heterochrony, now gone astray. Evol. Dev. 2, 241248. Gould, S.J., Vrba, E.S., 1982. Exaptation a missing term in the science of form. Paleobiology 8, 415. Gulick, D., Scott, J. (Eds.), 2010. The Beauty of Fractals: Six Different Views. Mathematical Association of America, Washington. Gunji, Y.-P., 1994. Autonomic life as the proof of incompleteness and Lawveres theorem of a xed point. Appl. Math. Comput. 61, 231267. Gunji, Y.-P., Haruna, T., Sawa, K., 2006. Principles of biological organization: localglobal negotiation based on material cause. Phys. D: Nonlinear Phenomena 219, 152167. Gunji, Y.P., Ono, R., 2012. Sociality of an agent during morphogenetic canalization: asynchronous updating with potential resonance. Biosystems 109, 420429. Igamberdiev, A.U., 1985. Time in biological systems. Zhurnal Obshchei Biologii (J. Gen. Biol.) 46, 471482 (in Russian). Igamberdiev, A.U., 1986. Problems of description of epigenetic systems. Zhurnal Obshchei Biologii (J. Gen. Biol.) 47, 592600 (in Russian). Igamberdiev, A.U., 1993. Quantum mechanical properties of biosystems: a framework for complexity, structural stability and transformations. Biosystems 31, 6573. Igamberdiev, A.U., 1998. Time, reectivity and information processing in living systems. A sketch for the unied information paradigm in biology. Biosystems 46, 95101. Igamberdiev, A.U., 1999. Foundations of metabolic organization: coherence as a basis of computational properties in metabolic networks. Biosystems 50, 116. Igamberdiev, A.U., 2004. Quantum computation, non-demolition measurements, and reective control in living systems. Biosystems 77, 4756. Igamberdiev, A.U., 2007. Physical limits of computation and emergence of life. Biosystems 90, 340349. Igamberdiev, A.U., 2012. Biomechanical and coherent phenomena in morphogenetic relaxation processes. Biosystems 109, 336345. Igamberdiev, A.U., Lea, P.J., 2002. The role of peroxisomes in the integration of metabolism and evolution of land plants. Phytochemistry 60, 651674. Igamberdiev, A.U., Lea, P.J., 2006. Land plants equilibrate O2 and CO2 concentrations in the atmosphere. Photosynth. Res. 87, 177194. Isalan, M., 2009. Gene networks and liar paradoxes. Bioessays 31, 11101115. Jablonski, D., Roy, K., Valentine, J.W., 2006. Out of the tropics: evolutionary dynamics of the latitudinal diversity gradient. Science 314, 102106. Jablonski, D., Belanger, C.L., Berke, S.K., Huang, S., Krug, A.Z., Roy, K., Tomasovych, A., Valentine, J.W., 2013. Out of the tropics, but how? Fossils, bridge species, and thermal ranges in the dynamics of the marine latitudinal diversity gradient. Proc. Natl. Acad. Sci. U. S. A. 110, 1048710494. Kirby, K.G., 1998. Exaptation and torsion: toward a theory of natural information processing. Biosystems 46, 8188. Kull, K., 1998. Baerian biology: evolution by means of organisms interpretation. In: Farr, G.L., Oksala, T. (Eds.), Emergence, Complexity, Hierarchy, Organization. Finnish Academy of Technology, Espoo, pp. 197200. Landweber, L.F., Kari, L., 1999. The evolution of cellular computing: natures solution to a computational problem. Biosystems 52, 313. Le Guyader, H., 2004. Geoffroy Saint-Hilaire: A Visionary Naturalist. University of Chicago Press, Chicago. Letelier, J.C., Crdenas, M.L., Cornish-Bowden, A., 2011. From LHomme Machine to metabolic closure: steps towards understanding life. J. Theor. Biol. 286, 100113.

Please cite this article in press as: Igamberdiev, A.U., Time rescaling and pattern formation in biological evolution. BioSystems (2014), http://dx.doi.org/10.1016/j.biosystems.2014.03.002