CODE Marcus Sautoy / Fantastic “math in nature” for visual learners

The CODE is a three-part visual exploration of how the mathematics that are the “blueprint” for our universe are concealed in nature. My reaction: Why isn’t mathematics introduced to children using this concrete visual method? For those of us who are “math as abstract language” impaired, videos like this are essential to grasping the importance of mathematics.

There are many other videos by Sautoy available on youtube, notably the history of the development of math languages. 

Part 2 introduces geometry essential to geologic processes and structures; very familiar to anyone interested in mineralogy AND so incredibly beautiful and simple. If you don’t view anything else, at least check out the “bubble” segment starting at 10:53. 

Disappointing video quality: looking for something better! 

ASD Asperger Art Suggestion / Draw with Pastels

blue crystalwp

“Blue Crystal” 36″ x 30″

 

Pastels are manageable for anyone who has hand control problems, or ADD or ADHD tendencies. Pastels are quick and expressive and require no materials other than good paper, pastel sticks  and hands. A dust mask is a good idea. One can easily draw quickly at large scale.

img_0369-wp-1

“Running Cloud”

gourd

“Unripe Gourd”

 

What I’m reading today / Organic life on other planets

The National Academies of SCIENCES ENGINEERING MEDICINE

Book: The National Academies Press

The Limits of Organic Life in Planetary Systems, 2007

https://www.nap.edu/read/11919/chapter/3 (100 pages readable online)

1.2
DEFINING THE SCOPE OF THE PROBLEM

For generations the definition of life has eluded scientists and philosophers. (Many have come to recognize that the concept of “definition” itself is difficult to define.3) We can, however, list characteristics of the one example of life that we know—life on Earth:

  • It is chemical in essence; terran living systems contain molecular species that undergo chemical transformations (metabolism) under the direction of molecules (enzyme catalysts) whose structures are inherited, and heritable information is itself carried by molecules.

  • To have directed chemical transformations, terran living systems exploit a thermodynamic disequilibrium.

  • The biomolecules that terran life uses to support metabolism, build structures, manage energy, and transfer information take advantage of the covalent bonding properties of carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulfur and the ability of heteroatoms, primarily oxygen and nitrogen, to modulate the reactivity of hydrocarbons.

  • Terran biomolecules interact with water to be soluble (or not) or to react (or not) in a way that confers fitness on a host organism. The biomolecules found in terran life appear to have molecular structures that create properties specifically suited to the demands imposed by water.

  • Living systems that have emerged on Earth have done so by a process of random variation in the structure of inherited biomolecules, on which was superimposed natural selection to achieve fitness. These are the central elements of the Darwinian paradigm.

Various published definitions of life understandably incorporate those features, given that we are the life form defining it. Indeed, because the chemical structures of terran biomolecular systems all appear to have arisen through Darwinian processes, it is hardly surprising that some of the more thoughtful definitions of life hold that it is a “chemical system capable of Darwinian evolution.”4

1.3
IS EVOLUTION AN ESSENTIAL FEATURE OF LIFE?

Many of the definitions of life include phrases like undergoes Darwinian evolution. The implication is that phenotypic changes and adaptation are necessary to exploit unstable environmental conditions and to function optimally in the environment. Evolutionary changes have even been suggested for the hypothesized “clay crystal life” of Cairns-Smith,5 referring to randomly occurring errors in crystal structure during crystal growth as analogous to mutations. Would a self-replicating chemical system capable of chemical transformations in the environment be considered life? If self-replicating chemical compounds are not life, replication by itself is not sufficient as a defining characteristic of life. Likewise, the ability to undergo Darwinian evolution, a process that results in heritable changes in a population, is also not sufficient to define life if we consider minerals that are capable of reproducing errors in their crystal structure to be equivalent to evolution. Although that property of clays may have been vital in the origin of life and particularly in the prebiotic synthesis of organic macromolecules and as catalysts for metabolic reactions, can the perpetuation of “mistakes” in crystal structure result in the selection of a “more fit” crystal structure? It is important to emphasize that evolution is not simply reproducing mutations (mistakes in clays), but also selecting variants that are functionally more fit.

The canonical characteristics of life are an inherent capacity to adapt to changing environmental conditions and to interact with other living organisms (and, at least on Earth, also with viruses).6 Natural selection is the key to evolution and the main reason that Darwinian evolution persists as a characteristic of many definitions of life. The only alternative to evolution for producing diversity would be to have environmental conditions that continuously create different life forms or similar life forms with random and frequent “mistakes” in the synthesis of chemical templates used for replication or metabolism. Such mistakes would be equivalent to mutations and could lead to traits that gave some selective advantage in an existing community or in exploiting new habitats. That random process could lead to life forms that undergo a form of evolution without a master information macromolecule, such as DNA or RNA. It is difficult to imagine such life forms as able to “evolve” into complex structures unless other mechanisms, such as symbiosis or cell-cell fusion, are available.

Evolution is the key mechanism of heritable changes in a population. However, although mutation and natural selection are important processes, they are not the only mechanisms for acquiring new genes. It is understood that lateral gene transfer is one of the most important and one of the earliest mechanisms for creating diversity and possibly for building genomes with the requisite information to result in free-living cells.7 Lateral gene transfer is also one of the mechanisms to align genes from different sources into complex functional activities, such as magnetotaxis and dissimilatory sulfate reduction.8 It is possible that this mechanism was important in the evolution of metabolic and biosynthetic pathways and other physiological traits that may have evolved only once even though they are present in a wide variety of organisms. Coevolution of two or more species is also a hallmark of evolution manifested in many ways, from insect-plant interactions to the involvement of hundreds of species of bacteria in the nutrition of ruminant animals. Organisms and the environment also coevolve, depending on the dominant characteristics of the environment and the availability of carbon and energy sources.

If the ability to undergo Darwinian evolution is a canonical trait of life no matter how different a life form is from Earth life, are there properties of evolving extraterrestrial organisms that would be detectable as positive signs of life? Evolution provides organisms the opportunity to exploit new and changing environments, and one piece of evidence for the cosmic ubiquity of evolution is that on Earth life occupies all available habitats and even creates new ones as a consequence of metabolism. Another hallmark of evolution is the ability of organisms to coevolve with other organisms and to form permanent and obligatory associations. It is highly probable that an inevitable consequence of evolution is the elimination of radically different biochemical lineages of life that may have formed during the earliest period of the evolution of life. Extant Earth life is the result of either selection of the most fit lineage or homogenization of some or all of the different lineages into a common ancestral community that developed into the current three major lineages (domains). All have a common biochemistry based on presumably the most “fit” molecular information strategies and energy-yielding pathways among a potpourri of possibilities.

Thus, one of the apparent generalizations that can be drawn from extant Earth life, and the explanation for the development of a “unity of biochemistry” in all organisms, is that lateral gene transfer is an ancient and efficient mechanism for rapidly creating diversity and complexity. Lateral gene transfer is also an efficient mechanism for selecting the genes that are most “fit” for specific proteins and transferring them into diverse groups of organisms. The results are the addition of genes and the replacement of less-fit genes that have similar functions. Natural selection based solely on mutation is probably not an adequate mechanism for evolving complexity. More important, lateral gene transfer and endosymbiosis are probably the most obvious mechanisms for creating complex genomes that could lead to free-living cells and complex cellular communities in the short geological interval between life’s origin and the establishment of autotrophic CO2 fixation about 3.8 billion years ago and microbial sulfate reduction 3.47 billion years ago on the basis of isotope data.9 An important implication of the existence of viruses or virus-like entities during the early evolution of cellular organisms is that their genomes may have been the source of most genetic innovations because of their rapid replication, high rates of mutation due to replication errors, and gene insertions from diverse host cells.10

Is evolution an essential feature of life? Cells are more than the information encoded in their genomes; they are part of a highly integrated biological and geochemical system in whose creation and maintenance they have participated. The unity of biochemistry among all Earth’s organisms emphasizes the ability of organisms to interact with other organisms to form coevolving communities, to acquire and transmit new genes, to use old genes in new ways, to exploit new habitats, and, most important, to evolve mechanisms to help to control their own evolution. Those characteristics would probably be present in extraterrestrial life even if it had a separate origin and a unified biochemistry different from that of Earth life.

1.4
BRIEF CONSIDERATIONS OF POSSIBLE LIFE FORMS OUTSIDE THE SCOPE OF THIS REPORT

As discussed in the literature,11 chemical models of non-Earth-centric life reveal much about what the scientific community considers possible, particularly regarding ways in which systems organize matter and energy to generate life. Thus, truly “weird” life might utilize an element other than carbon for its scaffolding. Less weird, but still alien to human biological experience, would be a life form that does not exploit thermodynamic disequilibria that are largely chemical. Weirder would be a life form that does not exploit water as its liquid milieu. Still weirder would be a life form that exists in the solid or gas phase.12 In a different direction, yet also outside the scope of life that most communities think possible, would be a life form that lacks a history of Darwinian evolution.

Some features of terran life are almost certainly universal, however. In particular, the requirement for thermodynamic disequilibrium is so deeply rooted in our understanding of physics and chemistry that it is not disputable as a requirement for life. Other criteria are not absolute. Terran biology contains clear examples of the use of nonchemical energy; photosynthesis is the best known, although energy from light is soon converted to chemical energy. Silicon, in some environments, can conceivably support the scaffolding of large molecules. This report explicitly considers nonaqueous environments.

Even Darwinian evolution is presumably not an absolute. For example, depending on how human civilization applies gene therapy, our particular form of life could be able to evolve via Lamarckian,a as opposed to Darwinian, processes. Humankind will be able to perceive and solve problems in human biology without needing to select among random events, thus sparing the species the need to remove unavoidable genetic defects through the death of individuals. That will make the human biosphere no less living, even to those who make Darwinian evolution central in their concept of life.

Likewise, we can easily conceive of robots that are self-reproducing or computer-based processes that grow and replicate.13 Here, information transfer is not based on a specific molecular replication but on a replication involving information on a matrix. Whether such entities will be called life remains to be seen.

What is clear is that the scientific community does not believe that Lamarckian, robotic, or informational “life” could have arisen spontaneously from inanimate matter. At the very least, its matrix would have to be constructed initially by a chemical, Darwinian life form arising from processes similar to those seen on Earth. Again, it is not clear whether those views are constrained by our inability to conceive broadly from what we know or whether they reflect true constraints on the processes by which life might emerge in natural history.

Lamarck recognized a similar principle of evolution referred to as “inheritance of acquired characters,” stating that variations in characteristics seen in organisms were acquired in response to the environment.

Those thoughts introduce a subsidiary theme of this report. It is conceivable that chemistry, structure, or environments able to support life were not suited for the initiation of life. For example, Earth can support life today, but prevailing views hold that life could not have originated in an atmosphere that is as oxidizing as Earth’s today. If that is true, the surface of Earth would be an environment that is habitable but not able to give rise to life.

1.5

STRATEGIES TO MITIGATE ANTHROPOCENTRICITY

We have only one example of biomolecular structures that solve problems posed by requirements for life, and the human mind finds it difficult to create ideas truly different from what it already knows. It is thus difficult for us to imagine how life might look in planetary environments very different from what we find on Earth. Recognizing that difficulty, the committee chose to embrace it. The committee exploited a strategy that began with characterization of the terran life that humankind has known well, first because of its macroscopic visibility and then through microscopic observation that began in earnest 4 centuries ago. This, of course, is like life that is associated with humankind. As the next step in the strategic process, the committee assembled a set of observations about life that is considered exotic when compared with human-like life. Exploration of Earth has taken researchers to environments that human-like organisms find extreme, to the highest temperatures at which liquid water is possible, to the lowest temperatures at which water is liquid, to the depths of the ocean where pressures are high, to extremes of acidity and alkalinity, to places where the energy flux is too high for human-like life to survive, to locales where thermodynamic disequilibria are too scarce to support human-like life, and to locations where the chemical environment is toxic to human-like life.

The committee then asked, Can we identify environments on Earth where Darwinian processes that exploit human-like biochemistry cannot exploit available thermodynamic disequilibria? The answer is an only slightly qualified no. It appears that wherever the thermodynamic minimum for life is met on Earth and water is found, life is found. Furthermore, the life that is found appears to be descendant from an ancestral life form that also served as the ancestor of humankind (perhaps we would not necessarily have recognized it if its ancestry were otherwise) and exploits fundamentally human-like biochemistry.

The committee then reviewed evidence of abiotic processes that manipulate organic material in a planetary environment. It asked whether the molecules that we see in contemporary terran life might be understood as the inevitable consequences of abiotic reactivity. Although signatures of such predecessor reactivity can be adumbrated within contemporary biochemistry, they are generally faint.14 Some 4 billion years of biological evolution have attached a strong Darwinian signature to whatever went before; hypotheses regarding evidence of our inanimate ancestry within modern biostructures are the subject of intense dispute.

If life originated first on Earth, it was long ago when conditions on the surface of this planet were very different from what they are today. We do not know what those conditions were, and we may never know. Furthermore, the organisms around today are all highly evolved descendants of the first life forms and probably contributed long ago to the demise of their less fit, more primitive competitors. The historical slate has been wiped clean both geologically and biologically. Finally, because life forms replicate, singular events can have enormous impacts on future developments. Life does not have to be a probable outcome of spontaneous physicochemical processes, although it may well be. Arguments based on probability are not as powerful in this sphere as they usually are in the physical sciences.

The committee surveyed the inventory of environments in the solar system and asked which non-Earth ones might be suited to life of the terran type. Such locales are few, unless there are laws not now understood that could govern the early stages of the self-organization of biochemical structures and processes that could lead inevitably to evolving life forms.15 Subsurface Mars and the putative sub-ice oceans of the Galilean satellites are the only locales in the solar system (other than Earth itself) that are clearly compatible with terran biochemistry.

The committee’s survey made clear, however, that most locales in the solar system are at thermodynamic disequilibrium—an absolute requirement for chemical life. Furthermore, many locales that have thermodynamic disequilibrium also have solvents in liquid form and environments where the covalent bonds between carbon and other lighter elements are stable. Those are weaker requirements for life, but the three together would appear, perhaps simplistically, to be sufficient for life. The committee asked whether it could conceive of biochemistry adapted to those exotic environments, much as human-like biochemistry is adapted to terran environments. Few detailed hypotheses are available; the committee reviewed what is known, or might be speculated, and considered research directions that might expand or constrain understanding about the possibility of life in such exotic environments.

Finally, the committee considered more exotic solutions to problems that must be solved to create the emergent properties that we agree characterize life. It considered a hierarchy of “weirdness”:

  • Is the linear dimensionality of biological molecules essential? Or can a monomer collection or two-dimensional molecules support Darwinian evolution?

  • Must a standard liquid of some kind serve as the matrix for life? Can a supercritical fluid serve as well? Can life exist in the gas phase? In solid bodies, including ice?

  • Must the information content of a living system be held in a polymer? If so, must it be a standard biopolymer? Or can the information to support life be placed in a mineral form or in a matrix that is not molecularly related to Darwinian processes?

  • Are Darwinian processes and their inherent struggle to the death essential for living systems? Can altruistic processes that do not require death and extinctions and their associated molecular structures support the development of complex life?

  • Suggested Citation:“1 Introduction.” National Research Council. 2007. The Limits of Organic Life in Planetary Systems. Washington, DC: The National Academies Press. doi: 10.17226/11919.

1.6

REFERENCES

1. Sagan, C. 1973. Extraterrestrial life. Pp. 42-67 in Communication with Extraterrestrial Intelligence CETI (C. Sagan, ed.). MIT Press, Cambridge, Mass.

 

2. Ward, P. 2005. Life as We Do Not Know It. Viking, New York.

 

3. Cleland, C.E. 2001. Historical science, experimental science, and the scientific method. Geology 29:987-990.

 

4. Joyce, G.F., Young, R., Chang, S., Clark, B., Deamer, D., DeVincenzi, D., Ferris, J., Irvine, W., Kasting, J., Kerridge, J., Klein, H., Knoll, A., and Walker, J.1994. In Origins of Life: The Central Concepts (D.W. Deamer and G.R. Fleischaker, eds). Jones and Bartlett, Boston, Mass.

 

5. Cairns-Smith, A.G. 1982. Genetic Takeover and the Mineral Origins of Life. Cambridge University Press, Cambridge, U.K.

 

6. See Brown, J.R., 2003, Ancient horizontal gene transfer, Nature Rev. Genetics 4:121-132; Martin, W., Rotte, C., Hoffmeister, M., Theissen, U., Gelius-Dietrich, G., Ahr, S., and Henze, K., 2003, Early cell evolution, eukaryotes, anoxia, sulfide, oxygen, fungi first (?), and a tree of genomes revisited, IUBMB Life 55:193-204; Ochman, H., Lawrence, J.G., and Groisman, E.S., 2000, Lateral gene transfer and the nature of bacterial innovation, Nature 405:299-304; and Woese, C.R., 2002, On the evolution of cells, Proc. Natl. Acad. Sci. U.S.A. 99:8742-8747.

 

7. Martin, W., Rotte, C., Hoffmeister, M., Theissen, U., Gelius-Dietrich, G., Ahr, S., and Henze, K. 2003. Early cell evolution, eukaryotes, anoxia, sulfide, oxygen, fungi first (?), and a tree of genomes revisited. IUBMB Life 55:193-204.

 

8. See Grünberg, K., Wawer, C., Tebo, B.M., and Schüler, D., 2001, A large gene cluster encoding several magnetosome proteins is conserved in different species of magnetotactic bacteria, Appl. Environ. Microbiol. 67:4573-4582; Mazel, D., 2006, Integrons: Agents of bacterial evolution, Nature Rev. Microbiol. 4:608-620; and Mussmann, M., Richter, M., Lombardot, T., Meyerdierks, A., Kuever, J., Kube, M., Glöchner, O., and Amann, R., 2005, Clustered genes related to sulfate respiration in uncultured prokaryotes support the theory of their concomitant horizontal transfer, J. Bacteriol. 187:7126-7127.

 

9. See Rosing, M.T., 1999, 13C-depleted carbon microparticles in >3700-Ma sea-floor sedimentary rocks from West Greenland, Science 283:674-676; Shen, Y., Buick, R., and Canfield, D.E., 2001, Isotopic evidence for microbial sulphate reduction in the early Archaean era, Nature 410:77-81; and Shidlowski, M.A., 1988, A 3800-million-year isotopic record of life from carbon in sedimentary rocks, Nature 333:313-318.

 

10. Claverie, J.M., 2006, Viruses take center stage in cellular evolution, Genome Biol. 7:110; Forterre, P., 2006, The origin of viruses and their possible roles in major evolutionary transitions, Virus Res. 117:5-16; Forterre, P., 2006, Three RNA cells for ribosomal lineages and three DNA viruses to replicate their genomes: A hypothesis for the origin of cellular domain, Proc. Natl. Acad. Sci. U.S.A. 103:3669-3674; and Koonin, E.V., and Martin, W., 2005, On the origin of genomes and cells within inorganic compartments, Trends Genetics 21:647-654.

 

11. Benner, S.A., Ricardo, A., and Carrigan, M.A. 2004. Is there a common chemical model for life in the universe? Curr. Opinion Chem. Biol. 8:672-689.

 

12. Allamandola, L.J., and Hudgins, D.M. 2003. From interstellar polycyclic aromatic hydrocarbons and ice to astrobiology. In Proceedings of the NATO ASI, Solid State Astrochemistry (V. Pirronello and J. Krelowski, eds.). Kluwer, Dordrecht.

 

13. Adami, C., and Wilke, C.O., 2004, Experiments in digital life, Artificial Life 10:117-122; Rosing, M.T., 1999, 13C-depleted carbon microparticles in >3700-Ma sea-floor sedimentary rocks from West Greenland, Science 283:674-676; Shen, Y., Buick, R., and Canfield, D.E., 2001, Isotopic evidence for microbial sulphate reduction in the early Archaean era, Nature 410:77-81; and Shidlowski, M.A., 1988, A 3800-million-year isotopic record of life from carbon in sedimentary rocks, Nature 333:313-318.

 

14. Benner, S.A., Ellington, A.D., and Tauer, A. 1989. Modern metabolism as a palimpsest of the RNA world. Proc. Natl. Acad. Sci. U.S.A. 86:7054-7058.

 

15. Kauffman, S.A. 1995. At Home in the Universe: The Search for Laws of Self-organization and Complexity. Oxford University Press, New York.

Worse than Asperger’s / Other things that limit my life

I hate to fly. I really, really hate to fly. The last time I used an airplane for travel, was to return from a visit to my very ill mother. A thunderstorm struck; there was severe turbulence and the heat in the cabin failed. I hid under a blanket (too small) that only covered my head. A sixteen year-old boy in the seat next to me (and some gin) had to talk me through the flight. Combo: severe emotional stress (family) plus lightning, thunder and unstable airplane = Never fly again.

In fact, the only flight I ever enjoyed was a return trip from a business meeting in LA: the client took us to every Hell hole in Hollywood. Too much food, booze and bizarre behavior. I was so hung over that I didn’t care if the plane crashed and we all died.

People who fly all the time may not think about it, but much of modern life is unattainable if one doesn’t fly.

The childhood corollary to this handicap was a fear of heights, in particular roller coasters, Ferris wheels and amusement rides. This pretty much eliminated summer  entertainment. I stood around holding everyone’s food, drinks and jackets and purses. People made fun of me and tried to trick or shame me into “not being a party pooper” Being an Asperger child, none of this manipulation had any effect on me. I learned to take a camera with me – it was a convenient excuse to wander off by myself and avoid being harassed. And I eventually turned into a photographer, an activity that has enriched my life, whereas the lack of amusement park rides has not affected me at all.

Fortunately, I love trains and driving, although trains just aren’t what they used to be. I drove all over the U.S., but once I moved to Wyoming, I’ve stayed put. I guess all that time I spent traveling around, I was just looking for Wyoming.