p241
Life and flame
To maintain the system in nonequilibrium, and to preserve its fundamental conditions for a complex system within the world filled with noise, it is necessary for life to exchange things with its external world as an open system. However, this ‘insight’ must have been realized consciously or unconsciously for a very long time.
This insight must have existed almost since we have started to use fire (i.e., since Homo erectus , more than 500 kaBP). The author thought that the synapomorphy of genus Homo is the use of fire; Homo habilis is better excluded from Homo , because use (and production of tools) is not confined to us. [This was written in 2009 for the Japanese version. Soon after this was written the following reviews by A Keller of books asserting that fire molded human beings appeared in Science 325 , 394 (2009) [A. Keller, The Cooking Ape]:
Richard Wrangham, Catching Fire How Cooking Made Us Human
Basic Books, New York, 2009. 315 pp.
Frances D. Burton, Fire The Spark That Ignited Human Evolution
University of New Mexico Press, Albuquerque, 2009. 245 pp.]
The following is a relevant review article:
Importance of fire in paleontology and neontology
Pausas A, Burning Story: The Role of Fire in the History of Life
BioScience 59 593 (2009)
*Wildfire appeared concomitant with the origin of terrestrial plants and played an important role throughout the history of life.
The prehuman era :
*The origin of fire is tied to the origin of plants. Before the appearance of photosynthetic organisms, the atmosphere lacked sufficient oxygen, and before the appearance of terrestrial plants, it lacked fuels; thus, fire did not exist on our planet. With the earliest Silurian origins of land plants, there is evidence of fire. Glasspool and colleagues (2004) reported charred remains of low-growing vegetation of the earliest stomata-bearing plants (440 mya), plus charred coprolites, indicating a low-temperature surface fire.
*The subsequent fire history seems to be tied to atmospheric oxygen levels (Scott and Glasspool 2006). There is clear evidence of charcoal in the Devonian deposits (400 mya; Scott 2000, Glasspool et al. 2006), although extensive charcoal deposits do not appear until the late Paleozoic Era (345 mya; Falcon-Lang 2000, Scott 2000), concomitant with a rapid rise in atmospheric oxygen from the late Devonian to the late Carboniferous (figure 3). The peak of approximately 31\% atmospheric oxygen during the Carboniferous (Berner 2006), compared with the current 21\%, would have greatly facilitated combustion.
*The major fall in atmospheric oxygen levels during the Permian and the Triassic may explain the scant evidence for fires, as inferred from the few charcoal deposits found for this period. Nevertheless, during the remainder of the Mesozoic (Jurassic and Cretaceous periods), fires were increasingly important (Scott 2000).
*Evidence that fire has actually altered the biogeography of landscapes and had major impacts on ecosystem function may be tied to the late Tertiary. The dramatic rise in charcoal deposition in marine sediments (Herring 1985, Jia et al. 2003) is often cited as evidence of the first rise in fire as an important ecosystem process. It has been postulated that the spread of C4 grasses during the more seasonal climate of the late Tertiary was due to this increase in fire activity, which opened up woodlands and created environments favorable to C4 grasslands (Keeley and Rundel 2005). Although other factors, such as increasing aridity, have been invoked to explain this expansion of C4 grasslands, only fire can account for the fact that expansion was possible because these grasses shifted their distribution to more mesic environments. The high flammability of C4 grasses would have produced a feedback process that further increased fire activity, thus maintaining the grassland dominated landscape, a process similar to the one currently maintaining many of our savannas.
*Fire has most likely played a selective role in the evolution of sprouting in Northern Hemisphere gymnosperms; most lack any capacity for resprouting, as would be predicted judging from their occurrence in forests typically subjected to low-intensity surface fires, which most mature trees survive. However, of the few gymnosperms that do resprout, all are components of crown-fire regimes, in which aboveground mortality is nearly certain (Keeley and Zedler 1998).
*The genus Pinus is an outstanding example in which fire clearly is the driving force for thick bark (Keeley and Zedler 1998). This radiation very likely began in the Cretaceous and continued through the Tertiary (Millar 1998), suggesting fire was an important ecosystem process throughout these periods.
The human era : Fire in the preindustrial world
*Early hominids (genus Homo) appeared in eastern Africa about 2.5 mya, and fire has been closely integrated into many stages of their evolution. It is believed that the rise of Homo erectus from its more primitive ancestors was fueled by the ability to cook―that is, to use fire (Wrangham et al. 1999). Recent studies demonstrate a preference by nonhuman primates for cooked food (Wobber et al. 2008). The higher food energy that cooking supplies, as well as the detoxifying effects of heating (which increased the diversity of available food), contributed to a fitness advantage in these early humans.
*Furthermore, cooking implied a delay in food consumption, which required the development of social abilities for the distribution of tasks within the group (e.g., collection, accumulation, cooking, defense, even stealing), as well as the socializing effect of gathering around nighttime campfires (Pyne 1995).
*There is evidence of the controlled use of fire by Homo erectus in Africa (clusters of ancient hearths) during the Lower Pleistocene (James 1989), about 1.5 MaBP.
*The earliest noncontroversial evidence out of Africa is from the Near East during the Early-Middle Pleistocene (0.79 mya; Goren-Inbar et al. 2004).
During the Paleolithic and Mesolithic ages, fire was used extensively for what has been termed `fire-stick farming' (Bird et al. 2008). This term implies using fire for a variety of activities to change human habitats and environments. For instance, fire-stick farming by Australian Aborigines created fine-grained landscape mosaics with greater small-animal diversity and increased hunting productivity (Bird et al. 2008).
*Fire-stick farming was probably necessary after the megafauna extinction, not only to open up closed-canopy woodlands to create habitable environments but also to reduce catastrophic fires that would pose a risk to humans (Burney and Flannery 2005), and to increase seed resources needed as humans were forced to switch to a less meat-dependent diet.
*The Neolithic agricultural revolution required fire to alter the natural vegetation from perennial-dominated to annual dominated landscapes. It has been postulated that people preferred to live in fire-prone places because the burning provided them advantages for hunting, foraging, cultivating, and livestock herding (Pyne 1995).
*Charcoal evidence suggests monotonic increases of biomass burning from the last glacial maximum (about 21,000 years BP) up to the start of the agricultural stage (about 10,000 year BP; figure 3), and this trend is linked to climatic warming and the expansion of terrestrial vegetation as a result of the waning of ice sheets (Power et al. 2008).
*This upward tendency in global fire activity was halted with the rise of agriculture, although a marked regional variation in charcoal accumulation has been observed for this period.
Then came the following paper denying the author’s guess:
Was there fire use associated with H erectus? Doubtful
Wil Roebroeks and Paola Villa
On the earliest evidence for habitual use of fire in Europe
Proc Nat Acad Sci 108 5209-5214 (2001).
Wrangham recently hypothesized that fire was a central evolutionary force toward larger human brains: Wrangham situates these developments around the time of the emergence
of Homo erectus, approximately 2MaBP.
However, the authors of this paper wrote that European evidence suggests that early hominins moved into northern latitudes without the habitual use of fire. Itwas only much later, from 300,000 to 400,000 y ago onward, that fire became a significant part of the hominin technological repertoire.
African record: oxidized remains of 1.5- to 1.6-million-y-old hominin fires: These sites do demonstrate that fire altered materials are associated with early hominin activity areas
but not that hominins were involved in the production and/or the use of such fires.
It is also from the second half of the Middle Pleistocene onward that we can observe spectacular cases of Neandertal pyrotechnological knowledge in the production of hafting materials.'
Then came a paper demonstrating at least 1 MaBP
Berna, F. et al. Proc. Natl Acad. Sci. USA 109, E1215–E1220 (2011).
The paper shows, using micromorphological and Fourier transform infrared microspectroscopy analyses of intact sediments (the most conclusive evidence for
fire was visible only through the use of soil micromorphology), Wonderwerk Cave, Northern Cape province, South Africa, provide unambiguous evidence — in the form of burned bone and ashed plant remains — that burning took place in the cave during the early Acheulean occupation, approximately 1.0 MaBP.
Thus, the author’s opinion at present (July, 2012) is that to assert the use of fire as a synapomorphy of Homo is incorrect, because even language does not characterize Homo sapiens ; the use of fire is NOT a characteristic feature of Homo erectus , but during this stage the use of fire was firmly incorporated in their ecology.
Incidentally, three interesting topics related to fire will be mentioned [Is there any occasion to enjoy intellectual conversations unfolding like a chain reaction in these days?]
(1) P opulation size and maintaining culture (the loss of technology to generate fire in Tasmania): The reader must have felt that this book occasionally express increasing awareness of cultural crisis. It is an interesting fact that a small isolated population can lose even the technology of making fire [However, the author has not seen any original paper on this topic; only a description in T. Flannery, The Future Eaters: an Ecological History of the Australasia Lands and People (Grove Press, New York, 2002)].
One might assert that in the future our population grows, so we need not worry about loss of culture, but this is an overly simple-minded opinion. To maintain highly developed technology and culture inevitably we need people who undergo a long period of training. Thus, the number of qualified people can easily go below the threshold. For example, Chinese mathematics illustrates the point:
The traditional mathematics of China was basically the most advanced in the world in the era of the Southern Sung Dynasty (南宋) and the Yuan Dynasty (元) especially in algebra (Tian Yuan Shu 天元術), but it was totally forgotten in the Min Dynasty (明) [K Ueno and N Kurokawa, “Accomplishments of mathematicians from Japanese mathematics (和算) to the modern mathematics,” Genndaishiso 2009/12 p68]
(2) There must have been a large change in our gut microbiome before and after the use of fire, but the author has not seen any paper discussing this point. However, as to the Neolithic Revolution, see
Mira et al., The Neolithic revolution of bacterial genomes
Trends Microbiol. 14 200 (2006)
Dramatic genomic changes have been identified in bacteria that are associated with large and stable human communities, agriculture and animal domestication: three features unequivocally linked to the Neolithic revolution.
(3) Extensive fire occurred only after the collapse of indigenous populations in Amazonian savannas. Now, it is well recognized that there was a large agriculturally sustained population in Amazonia. Their agriculture was not ‘fire-stick farming.’
J Iriarte et al., Fire-free land use in pre-1492 Amazonian savannas
Proc Nat Acad Sci 109 , 6473-6478 (2012)
Unexpectedly low levels of biomass burning associated with pre-A.D. 1492 savanna raised-field agriculture and a sharp increase in fires following the arrival of Europeans are reported.
The charcoal record indicates that extensive fires in the seasonally flooded savannas of French Guiana are a post-Columbian phenomenon, postdating the collapse of indigenous populations.
It is sure that the importance of environmental fire in the global warming tendency, but the effect is not yet very clear. This is one of the uncertainty elements of the large scale earth model:
B owman et al., Fire in the Earth System
Science 324 481 (2009)
To manage fire may become more difficult in the future as climate change alters fire regimes. This risk is difficult to assess, however, because fires are still poorly represented in global models.
The number of related papers is increasing. For example,
Invading grass -> fire -> erosion
Ravi et al., Can biological invasions induce desertification?
New Phytologists 181 512 (2009)
Two major drivers of global environmental change, namely biological invasions and climate change, may act in concert and amplify each other's effect on land cover and soil resources.
In years of high precipitation, invasive grasses can spread into the interspaces, thereby establishing connectivity either between shrub islands or between shrubs and the sparse cover of native perennial grasses in the interspaces. Grass connectivity provides conditions favorable for the spread of fires, which result in the enhancement of soil erodibility.
Garbage In, Gospel Out
W Willinger, D Alderson, and J C. Doyle
Mathematics and the Internet: A Source of Enormous Confusion and Great Potential
Notices AMS 56, 586 (2009).
Measurement based Internet research (phenomenology!)
“we illustrate why and how in the case of the Internet, scale-free network models of the preferential attachment type have become a classic lesson in how errors of various forms occur and can add up to produce results and claims that create excitement among non-networking researchers, but quickly collapse under scrutiny with real data or when examined by domain experts.” “ we motivate here the development of a novel modeling approach for Internet-like systems that
(1) respects the highly designed nature of the network;
(2) reflects the engineering intuition that exists about a great many of its parts;
(3) is fully consistent with a wide range of measurements; and
(4) outlines a mathematical agenda that is more challenging, more relevant, and ultimately more rewarding than the type of mathematics motivated by an alluring but largely misguided approach to Internet modeling based on scale-free graphs of the preferential attachment type.”
“Ask not what mathematics can do for [the Internet]; ask what [the Internet] can do for mathematics.” (Ulam)
Foremost among these issues are the dangers of taking available data “at face value” without a deeper understanding of the idiosyncracies and ambiguities resulting from domain-specific collection and measurement techniques.
*No amount of number crunching or mathematical sophistication can extract knowledge we can trust from low-quality data sets, whether they are of petabyte scale or not.
Can we trust networks? Mostly not very much.
The data so far obtained for food chains are gross oversimplification. See, for example, I. D. Hodkinson and S. J. Coulson, “Are high Arctic terrestrial food chains really that simple? ―The Bear Island food web revisited,” Oikos 106 , 427 (2004)．
Crudeness, if not incorrectness, of self similarity in omic networks
See, for example, R. May, ``Subnets of scale-free networks are not scale-free: Sampling properties of networks,'' Proc Natl Acad Sci 102, 4221 (2005) as to omic networks; R. May, “Network structure and the biology of populations,” Trends Eco. Evo. 21 , 394-399 (2006) as to ecology. May writes, “ many of the observed degree distributions for intracellular signaling, although roughly linear on a log-log plot (i.e. a power law), are in fact better fit with an exponential or other degree distribution .''
As to protein-protein interaction network, N. Przlj, D. G. Corneil and Jurisica, “Modeling interactome: scale-free or geometric?” Bioinformatics 20 , 3508 (2005) demonstrates that high precision interaction network for yeast is definitely not scale-free as will be discussed later.
Is physiological 3/4-power law meaningful?
For physiology, see Glazier, “The 3/4-Power law is not universal: evolution of isometric, ontogenetic metabolic scaling in pelagic animals,” BioScience 56 , 325 (2006): For pelagic life style the linear law holds robustly. Several models have been proposed that appear to provide a strong theoretical basis for the law (due to West et al. or Banavar et al.). However, empirical work suggests that the 3/4-power law is not universal, and should at most be regarded as a statistical rule or a trend, rather than as an inviolable law. A metaanalysis result is in WHITE, “ALLOMETRIC EXPONENTS DO NOT SUPPORT A UNIVERSAL METABOLIC ALLOMETRY,” Ecology, 88 , 315 (2007):
The debate about the value of the allometric scaling often revolves around a dichotomous distinction between the 3/4-power exponent predicted by recent models. Such an approach does not allow for the possibility that there is no single `true' exponent. Significant differences between scaling exponents were also identified between ectotherms and endotherms, as well as between metabolic states (e.g., rest, field, and exercise). That is, there is no universal metab olic allometry.
The nongenericity of this scaling is confirmed in the following paper, which tried to correct the power law taking the finite size effect into account: Savage et al., “Sizing Up Allometric Scaling Theory,” PLoS Comp. Biol. 4 , e1000171 (2008). The WBE model result only holds in the limit of infinite network size (body mass) and that the actual exponent predicted by the model depends on the sizes of the organisms being studied. When accounting for corrections over a size range spanning the eight orders of magnitude observed in mammals, the WBE model predicts a scaling exponent of 0.81, seemingly at odds with data. The current canonical model may need amendments. This paper frankly admits the data Glazier compiled cannot be explained by the scaling idea.
Failure of 3/4-power law has a reason
Glazier, “Effects of metabolic level on the body size scaling of metabolic rate in birds and mammals,” Proc. Roy. Soc. 275 , 1405 (2008). Significant deviations from the ‘3/4-power lawﾕ have been observed. Therefore, the author proposed a new model, the metabolic-level boundaries (MLB) hypothesis. According to the MLB hypothesis, the scaling slope b should vary between two extreme boundary limits: 2/3 as a result of surface-related constraints on fluxes of resources, wastes and heat, and 1 as a result of mass (volume) constraints on energy use or power production.
*As predicted, in both of these independently evolved endothermic taxa, the scaling slope approaches 1 at the lowest and highest metabolic levels (as observed during torpor and strenuous exercise, respectively), whereas it is near 2/3 at intermediate resting andcold-inducedmetabolic levels. Remarkably, both taxa show similar, approximately U-shaped relationships between the scaling slope and the metabolic (activity) level.
*Variation of the scaling slope is not merely noise obscuring the signal of a universal scaling law, but rather is the result of multiple physical constraints whose relative influence depends on the metabolic state of the organisms beinganalyzed.
Food web’s incompleteness must be the rule
I. D. Hodkinson and S. J. Coulson, “Are high Arctic terrestrial food chains really that simple? ---The Bear Island food web revisited,'” Oikos 106 , 427 (2004):
The work supports the increasingly accepted view that many food webs presented in the literature are gross oversimplifications and that analysis of their structure can produce misleading conclu sions.
Parasites are really significant in ecosystems
Kuris et al., “Ecosystem energetic implications of parasite and free-living biomass in three estuaries,” Nature 454 , 515 (2008). The biomass is estimated for free-living and parasitic species in three estuaries on the Pacific coast of California and Baja California. Parasites have substantial biomass, which exceeded that of top predators. The biomass of trematodes was particularly high, being comparable to that of the abundant birds, fishes, burrowing shrimps and polychaetes.
May said networks with scaling laws may be useful to engineering systems, but even that does not seem to hold. As already quoted:
Garbage In, Gospel Out
W Willinger, D Alderson, and J C. Doyle, “Mathematics and the Internet: A Source of Enormous Confusion and Great Potential,” Notices AMS {¥bf 56}, 586 (2009) advocates measurement based internet research (i.e., phenomenology).
“We illustrate why and how in the case of the Internet, scale-free network models of the preferential attachment type have become a classic lesson in how errors of various forms occur and can add up to produce results and claims that create excitement among non-networking researchers, but quickly collapse under scrutiny with real data or when examined by domain experts.”
“We motivate here the development of a novel modeling approach for Internet-like systems that (1) respects the highly designed nature of the network; (2) reflects the engineering intuition that exists about a great many of its parts; (3) is fully consistent with a wide range of measurements; and (4) outlines a mathematical agenda that is more challenging, more relevant, and ultimately more rewarding than the type of mathematics motivated by an alluring but largely misguided approach to Internet modeling based on scale-free graphs of the preferential attachment type.”
“ Ask not what mathematics can do for [the Internet]; ask what [the Internet] can do for mathematics. ” (Ulam)
Foremost among these issues are the dangers of taking available data “at face value” without a deeper understanding of the idiosyncrasies and ambiguities resulting from domain-specific collection and measurement techniques. No amount of number crunching or mathematical sophistication can extract knowledge we can trust from low-quality data sets, whether they are of petabyte scale or not.
Michael P. H. Stumpf an Mason A. Porter
Critical Truths About Power Laws
Science 335 665 (2012)
Most reported power laws lack statistical support and mechanistic backing. However, this article regard size-metabolism allometric scaling good and empirically supported, perhaps because it appeared in Science.
For scale free network: formal statistical tools have been applied to network data, evidence favoring power-law relationships has almost always been negligible
df. W. Willinger, D. Alderson, J. C. Doyle, L. Li, in Proceedings of the 2004 Winter Simulation Conference, R. G. Ingalls, M. D. Rossetti, J. S. Smith, B. A. Peters, Eds.
(Institute for Operations Research and the Management Sciences, Hanover, MD, 2004), pp. 130-141; paper available at www.informs-sim.org/wsc04papers/016.pdf .
*Two orders of magnitude in both the x and y axes. This criterion rules out many data sets,
including just about all biological networks.
* Indeed, the same power law (that is, with the same value of λ3).[ 3. J. P. Sethna, Entropy, Order Parameters, and Complexity (Oxford Univ. Press, Oxford, 2010).]
A critical question remains: What genuinely new insights have been gained by having found a robust, mechanistically supported, and in-all-other-ways superb power law? We believe that such insights are very rare.
Turing pattern
As we have already seen, since Turing was interested in our brains, naturally he was also interested in living systems, and their developments. A Turing pattern is a pattern produced by a reaction-diffusion system (= a system in which chemical reactions occur among chemical species that can diffuse) due to the destabilization of spatial uniformity caused by diffusion. Suppose there are chemical species A and B. A is self-reproducing and increases more if its density is higher, and B multiplies consuming A (as can be seen from this explanation, we may consider the model as an ecological system). If there is no diffusion, the density of A would be uniformly bounded by B everywhere. Assume that the diffusion rate of $B$ is larger than that of A. If there is more A locally, then near the place B also multiplies, but since B diffuses away quickly, B cannot exhaust locally increased A. Consequently, the local concentration of A runs away unchecked (until some other nonlinear effects intervene), and its distribution become spatially nonuniform. This is the fundamental idea; since chemical reaction must happen, free energy must be consumed, so this can never happen near equilibrium.
Benard pattern
Place a thermally expanding liquid in a horizontal tray to the depth of about 1-2 cm, and then heat the tray from below. The bottom layer of the liquid become warmer and less dense, so a top heavy situation is produced (a metastable state). If the temperature gradient becomes large than some threshold value, the quiescent state become unstable and convection starts. If the tray is observed from above, various convection cell patterns can be observed. These patterns are called Benard patterns. See, for example, http://www.sciencephoto.com/media/92423/enlarge