6. The Field of Chemistry

 

Kathleen has talked with her obstetrician and is now certain she pregnant, admitting her condition to friends, struggling with her religious beliefs, but all alone with her thoughts about what to do.  She is opposed to abortion but realizes that she cannot support herself, a baby, and continue with her college education. Her parents are working hard just to pay for her tuition while she has been working for board and room on campus. She is filled with faith that God will provide the answer that is right for her. She reads the Psalms while facing her reality of becoming a single mother — having to raise a child alone.

 

Dean Barth: Welcome. It is a beautiful day, and another opportunity to learn from great scientists (smiles to guests). We have with us Professor Linus Kornberg and his colleague Roger Adams from the chemistry department. And colleagues join us today who were with us for our last class: Professors Benedict in anthropology, Parsons in sociology, and Wilson in biology. (He is beaming now.)

We all had dinner together last night, spent the evening talking about our fields of knowledge. The six of us each have a different angle on evolution. You will hear our views as we speak about them in class.

Professor Kornberg, you have agreed to begin telling us something about the history of chemistry; and then Professor Benedict will make her contribution on the early stages of human evolution. Then, it’s a free-for-all, but we did agree to cover certain points together. There are key words in chemistry, such as self-organization and auto-evolution, which we want to discuss. We know where we are going, generally speaking, but (gesturing to students) your participation will influence our ultimate direction. Oh, and Mary, you are writing a paper on reflectaphors. Are you  prepared to report on something for us here? (Mary nods.)

Let’s begin. Prof. Kornberg, introduce us, if you would, to the history of chemistry.

Prof. Kornberg: Thank you for inviting me. Well, yes. We did talk at dinner, and we discussed our thoughts on the origin of chemistry, on where its origin might lie. Our discussion led me to think about tracing chemistry back to when it was discovered that fire could be started by combustion. The ability to create fire was a revolutionary step for humankind, as great in its day as any of our discoveries. It introduced groundbreaking technology. Let me see. …

Creating fire is a process by which a substance combines and reacts vigorously with oxygen to produce heat and light; I think it was the first chemical experiment. It led to a leap into civilization: the purification of metals and the beginning of metallurgy. 

Margaret, Professor Benedict, you take it from here. (Prof. Kornberg met Professor Margaret Benedict for the first time the evening before at the faculty dinner and was captivated by her exceptional knowledge of prehistoric times. He immediately became interested in anthropology, and is looking forward to reading any ethnographic reports that she may recommend to him. He defers to her authority as they report jointly on the beginnings of what came to be called  “chemistry.”)

Prof. Benedict: People who had fire did not have to use stone—which was the substance commonly used for many centuries—in order to slice and tip their arrows. They could create metal and its alloys with the heat of fire. So these early people were experimental chemists.

 Copper was discovered about 8000 B.C. near the Tigris and Euphrates Rivers in what is now Iraq, and in Egypt; and independently among the Chinese and the Incas in Peru about 5000 BC. This was about the time when fire could be contained, which meant that pottery could also be invented. (Pottery was clay vessels that held their shape after being baked in ovens.)

An open fire is not hot enough to heat copper ore —where the metal runs free, but in an enclosed space, fire does reach that temperature. Around 3500 B.C., people were synthesizing copper with tin, to make bronze. And this new substance had other uses than either substance alone could have because it was harder.

By 1700 B.C., during King Hammurabi’s reign over Babylon, metals were listed in conjunction with heavenly bodies  (looks toward Linus Kornberg).

Prof. Kornberg: Last night we talked about these primitive chemists. About 1500 B.C., people invented iron, because it was more abundant and cheap. We discussed how metallurgy began by combination and synthesis – principles that the Dean has set forth as an explanation for evolution. (He looks toward Margaret Benedict, fondly.)

 Prof. Benedict: To derive iron from ore, people had to heat the ore to high temperatures in combination with charcoal. Iron had to be freed of its brittle impurities by heating, pounding, and reheating. Heating alone would not enough; the removal of oxygen from the ore was an essential step....[i]

Dean: So you see these principles of evolution –the synthesizing of differences – at work right from the beginning. And the language we use to explain and understand these as general principles goes right with them.

Prof. Benedict: Yes, and we talked about how early languages evolved by combination and synthesis. People were beginning to combine different words to create new images and ideas. New words were being coined and combined at the time that people coined and combined new metals, so to speak. Words that were new at the time—such as the words for fire, heating, and handicrafts—matched people’s new experience. (Class members look a little puzzled.)

The invention of copper and iron, for example, required that new names be thought up for these metals. . The new metals, in other words, required more “thought,” which broadens human consciousness.  People started to classify the things they were inventing. They classified their seeds, instruments, and metals by inventing words for them . . . as over-arching concepts.

Out of these developments in more abstract ways of thinking, science and philosophy begin. We might call it induction, the form of reasoning from the particular to the general.

Prof. Kornberg: Yes, we talked about how the word “matter” had to be induced from specific terms for inanimate things. (He has never thought about this before meeting Margaret Benedict, and looking her way, he now concedes to her.)

Prof. Benedict: As was said in an earlier class, human thought evolved by symbolizing. So the word “matter” was created as people compared dead things with living things. People compare, contrast, and generalize by symbolizing.

The symbol-word “matter” involves people looking at one inanimate object after another and abstracting a word about all of them as being different from what is animate. Democritus theorized on “matter” in 465 B.C. He said that it is composed of “atoms” but he was not talking about what we think of as atoms today, rather about “indestructible things” (Looking to Kornberg).[ii]

Prof. Kornberg: Fire, on the other hand, was destructible. We talked about how fire developed as a mystical force in the primitive mind, because it could “transform” one substance into another. (looking to Margaret Benedict.)

Prof. Benedict: People began to talk about the magical power of fire and the idea of transforming things. Fire allowed people to cook food, make pottery, and make tools for utensils. The enchantment became a mode of thought called “alchemy.” And . . .

the primary dictum of alchemy in its common Latin expression is Solve et Coagula, which means “to separate and join together”:  the same principle that you (looking to the Dean) propose applies to evolution.

At this point, I want to defer to Prof. Kornberg (addressing him warmly), who will bring us into the history of chemistry as a modern field of study. And that is all beyond my ken.

Prof. Kornberg: (Delighted, he takes over the conversation.) The alchemists wanted to transmute base metals into gold and silver and hoped to create a substance that would cure diseases and prolong life.  Alchemists talked about a “philosopher's stone,” which they thought would have a number of properties enabling them to realize their goal of converting inexpensive metals into costly ones, and also to heal all diseases and extend life.[iii]

Dean: (Interrupts.) At some point, science differentiates itself from alchemy, which had a connection with spirituality and religion. Tell us about that.

Prof. Kornberg: Yes, there was a big separation. We see science splitting from alchemy. The event brought a whole new transformation in thought.

Dean: When did that split take place?

Prof. Kornberg: With Sir Isaac Newton. He was an alchemist who turned alchemical work into a science.

Dean: But people tend to forget that chemistry evolved from alchemy. Did they not see the “continuity” between them in this evolution?

Prof. Kornberg: Many of the men at the time of Newton who we now regard as having great minds were into alchemy—such as John Locke, Robert Boyle, Leibnitz, and others—but few today recognize that alchemy was the womb from which science could be born. Newton learned how to do experiments in the practice of alchemy, and for thirty years was seriously involved in a study of the subject, but after his death in 1727, England’s Royal Society said his alchemical writings were "not fit to be printed" and suppressed them. That was unfortunate. (Margaret Benedict nods a quick agreement.) The inspiration for his laws of light and theory of gravity were formed from his alchemical studies. Science became a new species so to speak now separate from religion and theology. [iv] 

Prof. Benedict: Not everybody was happy about this separation. Carl Jung, the psychoanalyst, looked at Newton’s break with religion and felt that science had forgotten its original values and ethics. Science was no longer designed to work for the common good. Newton’s effort to create a science -- stripped from any spiritual or humanistic purpose – could be dangerous. Science, Jung said, could not – nor should it -- define the whole nature of things.[v]

Prof. Kornberg: Newton was a genius. He described the principles of conservation of momentum and angular momentum; he invented the reflecting telescope; he developed a theory of color by seeing a prism decompose white light into a spectrum. He formulated a law of cooling and studied the speed of sound. He demonstrated the binomial theorem; he developed a “method” for approximating the zeroes of a function, and so much more.

Prof. Benedict: Newton’s break with alchemy was hard on him personally; historians say he had a nervous breakdown. He had created a science in the context of the ancient Hermetic tradition, born from ideas in the “Emerald Tablet,” which was written around 3000 B.C. But he left that presumed wisdom all behind for a secular field of thought.[vi] 

Dean: In principle, in our discussions we have said that evolution seems to conserve key elements of the past. Are you saying that ancient thinkers laid the groundwork for principles that Newton discovered? What was lost in the transition to the new science?

Prof. Benedict: How much Newton and his other experimenters knew at the time may never be known. Newton wrote a letter to his fellow alchemist Sir Robert Boyle in the late 1600s urging him to keep "high silence" in discussing the principles of alchemy. He said that there are “other things besides the transmutation of metals” that only “they” could understand. He felt that they shared a secret. If so, it was a secret that died with them. [vii] 

Prof. Kornberg: But Boyle stayed with the new science and wrote about how small particles could combine to form molecules. He formulated the fundamental laws of gas. Hmm…(Pauses.)

The details of how chemistry evolved are too complex to cover here. I cannot tell you all the particulars because of our time limit, but I can say that each chemist learned from others. They developed a common stock of knowledge from which they drew their ideas and conducted experiments. They compared their findings and synthesized their work.[viii]

I am passing out this sheet for you to read. It offers you an idea of how each chemist took small steps to help in the building of chemistry as a science. They were all experimenting and inventing, declaring facts, integrating ideas. (He passes out the following sheet of information.)

Chemists’ Combinations of  Ideas and Facts.

Evangelista Torricelli (1643) invented the mercury barometer. Otto von Guericke 1645) constructed the first vacuum pump. James Bradley (1728) began to use the aberration of starlight to determine the speed of light. Joseph Priestley (1733-1804) discovered oxygen, carbon monoxide, and nitrous oxide and, in 1767, proposed the electrical inverse-square law. C. W. Scheele (1742–1786) discovered chlorine, tartaric acid, metal oxidation, and the sensitivity of silver compounds to light (photochemistry). Nicholas Le Blanc, (1742–1806)  invented the process for making soda ash from sodium sulfate, limestone, and coal. A. L. Lavoisier (1743-1794) discovered nitrogen and described the composition of different organic compounds.  A. Volta (1745-1827) invented the electric battery. C. L. Berthollet, (1748-1822) corrected Lavoiser’s theory of acids and discovered the bleaching ability of chlorine, analyzed the weights of atoms (stoichiometry). Edward Jenner (1749-1823) developed a smallpox vaccine (1776). Ben Franklin (1752) demonstrated that lightning is electricity. John Dalton (1766-1844) proposed an atomic theory based upon measurable masses (1807) and stated the law of the partial pressure of gases. Amedeo Avogadro (1776-1856) proposed a principle that equal volumes of gases contain the same number of molecules. Sir Humphry Davy (1778-1829) laid the foundation of electrochemistry, studying the electroysis of salts in water and isolated sodium and potassium. J. L. Gay-Lussac (1778-1850) discovered boron and iodine and acid-based indicators (litmus). J. J. Berzelius (1779-1850) classified minerals according to their chemical composition and isolated different elements. Charles Coulomb (1795) introduced the inverse-square law of electrostatics. Michael Faraday (1791-1867) coined the term 'electrolysis' and developed theories of electrical and mechanical energy, corrosion, batteries, and electrometallurgy. Rumford Count (1798) thought about how heat was a form of energy. F. Wohler  (1800-1882) created the first synthesis of an organic compound (urea in 1828). Charles Goodyear (1800-1860) discovered vulcanization of rubber (1844).  Thomas Young (1801) demonstrated the wave nature of light and the principle of interference. J. von Liebig (1803-1873) investigated photosynthesis reaction and soil chemistry and proposed the use of fertilizers as well as chloroform and cyanogen compounds. Hans Oersted (1820) observed that a current in a wire can deflect a compass needle - providing the first concrete evidence of the connection between electricity and magnetism. Thomas Graham (1822-1869) studied the diffusion of solutions through membranes and established colloid chemistry. Louis Pasteur (1822-1895) recognized bacteria as a disease-causing agent and developed immunochemistry and introduced heat-sterilization of wine and milk (pasteurization). William Sturgeon (1823) invented the electromagnet. Sadi Carnot (1824) analyzed heat engines. Simon Ohm (1826) stated the law of electrical resistance. Robert Brown (1827) discovered Brownian motion. Joseph Lister, Joseph (1827-1912) initiated use of antiseptics in surgery, e.g., phenols, carbolic acid, cresols.[ix]

The scientists (on this sheet) include some who are into electricity but they all exemplify how—gradually, over time—chemistry came to be the way that we know it today.

Dean: Hmm. Chemistry was growing from ideas in the way that plants grow from seeds, setting roots in the ground and adjusting to others in this garden of thought, so to speak. Could you talk to us about chemistry today? (Prof. Kornberg goes to the blackboard and writes:)

Chemistry Today

Chemistry is the study of the properties and composition of matter; it is about how types of matter interact with other types of matter. Chemists test the ground for all sorts of relationships between atoms and molecules.

Look. Almost every topic in chemistry is about bonding, breaking, and re-joining. Everything that evolved from the Big Bang includes these processes of “binding and separating,” and the properties of matter keep coming together at ever more complex levels of organization.

Dean: Uniting, dividing, synthesizing. Why do these terms we use in human relations also apply to chemistry?  I wonder whether in using these terms we are misappropriating them, whether they are just our projections? I am also guilty. (Professor Kornberg looks puzzled as the Dean thinks about how to explain what he means.) We say that a newborn infant is bonding with its mother; we say that married people getting a divorce are separating. We say that nations sometimes break their treaties and that conflicts are resolved by a new bonding. Why do chemists use these same words that are used for human relations?

Prof. Kornberg: (Looks toward Margaret Benedict) I think the words are the same because Nature is inside us. We are part of Nature. All things have a tendency to bond, divide, and come back together in new forms. Your course on evolution is an example.

Dean: What do you mean? I believe I understand you, but I would like to hear your explanation as part of our discussion.

Prof. Kornberg: University faculties are so divided and specialized in their terminologies that they cannot talk to one another. The work that you are doing suggests how we might “gravitate” back toward an ability to converse among each other as a single community. (He smiles and looks to both Margaret Kornberg and the Dean.)

Dean: (The Dean nods gravely.) Thank you. Now, if you would, tell us about chemistry in the 20th century.

Prof. Kornberg: After the discoveries by Ernest Rutherford and Niels Bohr on the atomic structure, and by Marie and Pierre Curie on radioactivity, almost all scientists had developed a common view. Chemists were going to explain only specific aspects of nature.

Dean: What happened?

Prof. Kornberg: By the mid 20th century, physics and chemistry were united in explaining chemical properties. These properties were the result of the electronic structure of the atom. Linus Paulings’ book on The Nature of the Chemical Bond used the principles of quantum mechanics to deduce bond angles in more complicated molecules.

Dean: So a close connection existed between the two fields?

Prof. Kornberg: The connections were thick in 1953 when James Watson and Francis Crick deduced the double helical structure of DNA. The models were informed by their knowledge of chemistry and X-ray diffraction patterns. This led researchers toward biochemistry, basically the chemistry of life.

Dean: The “chemistry of life?”

Prof. Kornberg: Well, the idea was popularized in the 1950s when scientists began to study the origin of life. They wanted to know what kind of environment would encourage the beginnings of biological life on earth.

In 1953, Stanley L. Miller and Harold C. Urey at the University of Chicago conducted an experiment that shocked everybody. Miller took molecules believed to represent the components of the early Earth's atmosphere and put them into a closed system. They used methane (CH4), ammonia (NH3), hydrogen (H2), and water (H2O) and ran an electric current through the system, to simulate lightning storms common on earth. (He writes the terms on the blackboard.)

Dean: What happened?

Prof. Kornberg: At the end of one week, Miller found that as much as 10-15% of the carbon was now in the form of organic compounds. Two percent of the carbon had formed some of the amino acids used to make proteins. He showed that organic compounds such as amino acids -- essential to cellular life -- could be synthesized easily under the conditions that scientists believed to be present early on during earth’s formation. A lot of experiments followed.

Dean: Interesting. Did chemists ever create biological life?

Prof. Kornberg: No. The debate continues. [x]  

Dean: Okay. We’ll wait for that to happen. (Jokingly he looks toward the ceiling in a “waiting” posture. The class howls: it may be a “long wait.” This is uncharacteristic of the Dean, who is always respectful of all disciplines. With a smile, he adds:)

We won’t wait too long. Let’s see, we agreed to talk about self-organization as an idea in chemistry.

Prof. Kornberg: (a cloud crossing his face: he believes that chemists will create biological life someday) My colleague Roger Adams has offered to talk about this. (Professor Adams goes to the blackboard and writes:)

Self-Organization

Prof. Adams: Ilya Prigogine was a Nobel Laureate chemist working on dissipative structures and complex systems when he conceived of the idea of “self-organization.” He shared this idea with Erich Jantsch, who was an associate working with him.[xi]

They both saw self-organization in chemicals as a process of increasing complexity. Jantsch wrote in detail about how it operates, from the creation of atoms to the construction of social life and knowledge (looking to the Dean). This work is very close to your idea.[xii]

They describe an “emerging hierarchy of structures,” as they say, leading to the “evolution of knowledge” by a “symbiosis of information.” 

Dean: This idea would be interdisciplinary. Prof. Parsons, what do you think about it. We need a sociological perspective. (Parsons had been asked to speak at their after-dinner conversation on the subject of self-organization in society.)

Prof. Parsons: Just for fun, I made a list this morning of self-organizing chemical associations. Chemistry associations have evolved together in the last fifty years. We call this self-organizing in civil society. I study how nations have constructed millions of self-organizing associations.  

In the field of chemistry I see associations differentiating -- like molecules . . . no, maybe more like rabbits ( laughing.) Look at this. (He takes a note out of his shirt pocket). Hundreds of them -- the American Chemical Society, American Peptide Society, Applied Molecular Science, Australian Chemicals Resources, Canadian Society for Chemistry Organic Chemistry, Canadian Society for Chemistry Surface Science Division, Danish Chemical Society, Electrochemical Society, Inc., European Chemical Society, European Photochemistry Association, European Federation for Medicinal Chemistry (EFMC). And the list goes on.[xiii]

Dean: All these associations are just in chemistry! So you are saying that Jantsch’s principle on the self-organization of atoms applies to the evolution of society, and that chemistry associations are self-organizing, like chemicals in a laboratory.

And yet these associations are not subject to natural laws. They are subject to the laws of society.

Prof. Parsons: Well, in its evolutionary development, perhaps society has conserved the principles of nature. Chemists are social – just as amoebas are social; they’re just more complex. Chemists transmit information through hundreds of subfields in journals, each with its own argot. They are in networks in which they share very specialized information.

Dean: Okay. These early creatures were the beginning of symbiotic life, and they have shaped the way we organize today. Right?

Prof. Adams: Right. Bonding and separating, attraction and repulsion, and self-organizing: these are actions that commonly manifest in both humans and chemicals.

Dean: I think at this point it would help many of us if you would say something more about what self-organizing is, in general.

Prof. Adams: Self-organization is a process of attraction and repulsion in which the internal organization of a system increases in complexity without being guided or managed by an outside source.

Self-organizing systems typically display emergent properties, on their own: a new system appears without pressure from the outside. In other words, the drive to overcome stress or solve problems comes within the system itself. The system works through interactions among its components. Resources flow into or out of the system, but they are not critical to the changes that occur inside.

In physical chemistry we see this in “phase transitions,” spontaneous magnetization, crystallization, superconductivity and Bose-Einstein condensation. (Members of the class look puzzled.) These are just some examples.

Put simply, self-organization is a process in which a system increases its organization without this increase being controlled by its environment or any external system. (Kathleen is thinking: “My body is feeding and influencing this baby but not determining the baby’s direction. It is self-organizing.”)

 Dean: In other words, the key changes happen from within a system itself.

Prof. Adams: Yes.

Dean: Professor Wilson, what happened to Natural Selection? How does this theory apply to chemistry? (The Dean’s eyes glance between Wilson and Adams.)

Prof. Wilson: Natural Selection is a choice between competing options for organisms. One arrangement works better than another. In self-organization there is only one system that shapes itself internally in the space it occupies.[xiv]

Living organisms have been called autopoietic systems. Autopoiesis, you remember, refers to a self-creating system, that is, a system of self-constructing, self-maintaining, energy-transducing autocatalytic entities.[xv] 

Dean: Hmm (wondering if he has understood that long sentence). Is this true of all living things?

Prof. Wilson: Yes. We talked about bees, ants, and termites; but it is also found in the unfolding of proteins, in the self-inventing cell, in the behavior of flocks of birds and schools of fish.

Prof. Kornberg: It’s in the creation of DNA. It is in hypercycles, in the organization of Earth's biosphere conducive to life, as you discussed last time in the Gaia hypothesis.[xvi]

Dean: Prof. Parsons, tell us more about “self-organization” as it relates to society, and to social theory.

Prof. Parsons: “Self-organization” is documented in all systems of human communication. Loet Leydesdorff studied the case in communication systems.[xvii] Charles Cooley wrote about it in his research on the “self and social organization.”[xviii] Anthony Giddens wrote about self-organizing activity in his work on “structuration”[xix] (Dean winces at this word.) . . . none of which we need to go into in detail now.

You find it in social economics. A market economy is self-organizing, relatively speaking. Friedrich Hayek coined the term catallaxy to describe a "self-organizing system of voluntary co-operation in capitalism.”

And this word is catching on. The economist Paul Krugman -- who writes columns for the New York Times -- claims that, “the link between the study of embryos and hurricanes, magnetic materials and collections of neurons, is their self-organizing capacity. [xx]

Economic sociologists all have different angles on this matter, but they insist that it is not just individuals who are self-organizing in the economy but, more significantly, “associations.” Associations are the “ground” for advancing a self-regulating economy. Associations make market freedom possible.[xxi] (Kathleen has pondered the meaning of “freedom to choose” but has not thought of it as pertaining to associations in terms of the market.)

Dean: I want to bring some of these ideas together with ones that we have been discussing as a class. In our first discussion, I talked about Aristotle and his idea of potentiality. Does this resonate with you?

Prof. Wilson: I struggle with this idea. What does it mean? Is each stage of evolution marked by a greater potential for freedom? Does each stage show a greater capacity to move into new directions? 

Here is a word in biochemistry that is close to it. (He goes to the blackboard and writes:)

Evolvability.

In 1987, Richard Dawkins presented a paper at the First Artificial Life Workshop entitled "The Evolution of Evolvability." He proposed that evolution is based not only on survivability, but also on evolvability.

Dean: What did he mean?

Prof. Wilson: Evolvability refers to the ability to evolve, and it does not rest in a single trait or function. It does not just depend on a mutation rate. In this proposition, Dawkins was beginning to see a larger system of forces operating here. All systems play a role in evolution.[xxii]

Dean: It sounds like Dawkins has been broadening his outlook from his early book on the “selfish gene.” (Smiles). But I’m not sure just how much he is getting of that larger picture.[xxiii]

Prof. Wilson: Let me pick up on that. Dawkins is an expert in molecular biology, but that field has limits. I think you’ve done this before at some point in this class, but let’s look again at the social organization of ants.

The monarch ant, the queen, does not direct an army of drones. Drones take their direction from a small set of signals released by other drones. A drone collecting food emits a scent, and other drones that pick it up will follow that path to the food source. No single drone knows where the food is, or has a map of the terrain. Nor does the queen have a map.

The system is smarter than all of the individual members of the colony. It acts as the decision-maker in this process of change. Changes emerge from within the system itself. So Prof. Parsons is right. The system is social and self-directing. It is in the larger community -- where the action is.

Prof. Parsons: (impressed by the kind reference to him.) Well. The stock market is a system more complex than its individual players. It is a group of associations in which no one person has the whole answer to where it is going. Even the queen bee – the Securities and Exchange Commission – does not have the answer.

Here is a system in which millions of investors are acting on their own as they all converge at one point in the exchange market. They look for money in the way that ants look for food. The results do not always come out the way they want. (He has in mind how crashes in the stock market lead to self-corrections and more transparent systems of exchange.)

Prof. Wilson: An individual ant alters its behavior based on the behavior of other ants that it happens to encounter. So out of all those chance encounters, a social order emerges.

Dean: Could these “interacting systems” be the key to evolution?

Prof. Wilson: I think so. A neuron in the human brain decides to fire (or not to fire) based on the input from other neurons to which it is connected. All of these neurons (like ants and investors) follow simple rules, but they are all “interacting agents,” with billions of other agents in the brain. Given enough interactions, something new will happen. It is all internally determined.

Dean: The ants in the colony, the neurons in the brain, and the investors in a market are all self-organizing systems, all self-directing, relatively speaking.[xxiv]

(There is a moment of silence as everybody pauses, thinking about this very broad idea.) Are other concepts similar to this notion of self-organization? (Kathleen is still thinking about ways in which her child is “self-organizing,” but does not speak.)  Prof. Adams?

Prof. Adams: (goes to the blackboard and writes:)

Autoevolution.

Antonio Lima-de-Faria is Professor Emeritus of Molecular Cytogenetics at Lund University in Sweden. He claims that Natural Selection cannot explain evolution. Evolution is an abstract idea and cannot be measured scientifically in well-defined units, such as millimeters. But he can explain evolution with the hard facts of chemistry.

Dean: Professor Lima-de-Faria prefers “scientific precision,” not the generality of the theory of Natural Selection?

Prof. Adams: He wants to be accurate. He has coined this concept: “autoevolution.” 

Dean: Well, that sounds “general” to me. What does it mean?

Prof. Adams: In his book Evolution without Selection, he claims that life can be explained by the “form and function” of minerals. Chemical elements are in the structures of animals and are the basis for explaining evolution, not the process of Natural Selection.[xxv] 

Prof. Kornberg: Erwin Schrödinger said the genetic material -- whatever its chemical structure -- must be a crystal. That was back in 1944.[xxvi]  Then in the 1980s, Lima-de-Faria argues that the chemistry preceding life “canalized” into biological life. Chemicals are the basis of evolution. You (looking at the Dean with a grin) would put it this way: chemicals transformed and then transcended into biological life.

Dean: Well, yes. In his day, Darwin did not know about the independent evolution of atoms and minerals.

Prof. Kornberg: Chemistry created the foundation for plants and animals. Now we can see all of those mineral patterns embedded in biological life forms.

Dean: So, atoms and molecules each had “autonomous evolutions.” Their “forms” show up later in the bodies of plants.

Prof. Adams:  Lima-de-Faria’s research shows that the rules created in these prior evolutions became the frame for building biological life. Biological life could not depart from those chemical patterns, as he puts it. 

Dean: So, Antonio Lima-de-Faria says life does not begin in biological forms? It begins in chemistry?

Prof. Adams: Yes, life is inherent to the structure of the universe. (The Dean’s eyebrows rise in astonishment.) But Antonio is not a creationist. He is a scientist speaking from his observations.

Dean: Interesting!

Prof. Adams: You can see for yourself what he is talking about. Look at the swirls of frost on a windowpane and compare them with a fern with all its swirls and curled shoots. They look alike because of the forms of chemistry in the fern.

Ask why a particular insect is leaf-shaped. It is not just to protect it from predators. It’s shaped by its chemistry. Ask why brain coral and the human brain look alike. Lima-de-Faria’s research shows the mineral foundations of organic life. You should buy his book, and study those illustrations. And then students should study fractals.[xxvii]

Dean: I will consider those books for the class.

Prof. Adams: Well, they are written for professionals and cost well over a hundred dollars each. They illustrate how chemical patterns shape living organisms. Living organisms have the same atoms that are in minerals, with the same symmetries. Chemical patterns are transferred intact to the cell and organism level. So forget about Natural Selection.

Dean: He looks at everything from the standpoint of chemistry!

Prof. Adams: Yes, but—or, I should say, and—his information is accurate. The human body is built on the atomic plan of a twin crystal. It has the symmetry of the crystal, shaped by the electronic properties of the atoms within it. 

Dean: Is this Lima-de-Faria a respected scientist?

Prof. Adams: He’s been a Fellow of The Rockefeller Foundation, International Atomic Energy Agency, and the Institute for Cancer Research in Philadelphia, a Visiting Scientist to half a dozen research institutes and universities, including Duke and Cornell in the U.S., the Max Planck Institut für Meeresbiologie in Germany, the National Institute of Genetics in Japan, and more.

He has now collected enough data to construct a “preliminary periodic table” in biology like that in chemistry; it accounts for the form and function of organisms evolving chemically at regular intervals over time.[xxviii]

Dean: It’s hard for me to see how he could reject Natural Selection.

Prof. Adams: He says “flight” emerged in insects but in none of the other invertebrate groups. It appeared suddenly in pterosaurs, which were flying reptiles not directly related to insects. So it is not Natural Selection; it is autoevolution. (Pause, as Adams is thinking.)  

Mammals radiated into many families, but Lima-de-Faria says that only mammal bats were able to fly. They had no immediate affiliation with birds. No organic growth here, no continuity, no sequence between creatures in their capacity to take flight. 

Dean: Other examples?

Prof. Adams: Lots. Another is the formation of the penis, which does not occur in most fish, amphibians, or birds. Lower invertebrates—such as flatworms—have developed almost as complex an organ as that of the human male penis, with a seminal vesicle, a prostate gland, and an ejaculatory duct. The penis structure has appeared at different times in evolution, not sequentially. It is well developed in snails, barnacles, and mammals. 

Dean: So the recurrence of similar structures and functions is not due to forces in the environment or the stage of complexity of the organism. It is autonomously created.

Prof. Adams: At the base of biological life, he says, is mimicry. It occurs at the molecular and atomic level; it has been established in minerals and proteins.

Darwinism starts from the wrong end of evolution. The Origin of Species is about the end process of a transformation that begins in chemistry.

Dean: So biology cannot explain what happened before life began? Why didn’t chemists complain?

Prof. Adams: There was insufficient evidence on the self-assembly of molecules and cells, and on molecular mechanisms.

 

Dean: Would you explain this in more detail: self-assembly.

Prof. Adams: Of course. Lima-de-Faria’s way of thinking is close to your own. He says that the origin of “form and function” exists in self-assembly, which is demonstrated at the level of elementary particles, atoms, macromolecules, and cells.

Dean: Okay, but what is it?

Prof. Adams: Self-assembly is the “spontaneous aggregation of biological structures that involves the formation of weak chemical bonds between surfaces with complementary shapes.” Isolated subunits can spontaneously assemble in a test tube into a final structure. (The Dean starts shaking his head at all of this scientific formality.) The process is inevitable and automatic.[xxix]

Dean: (eyes lowering) That means nothing to me.

Prof. Adams: Self-assembly fits into your theory of synthesis and self-development. Your idea works at the chemical level.

Dean: How?

Prof. Wilson: At the first stage, quarks and anti-quarks united into mesons and other particles. Then these protons, neutrons, and electrons grew—we say “self-assembled”—into atoms. Then atoms “self-assembled” into crystals. At the protein level, the different units of aspartase transcarbamoylase assemble and reconstitute the active enzyme. [xxx]

Dean: Wait (holding up his hand). Some terms are over my head.

Prof. Adams: You have to take chemistry!

Dean: (The class laughs, and the dean asks, “Who has taken chemistry?” One half of the class members raise their hands.) Okay, go ahead. (Smiles, humbly.)

Prof. Adams:  In his book Evolution without Selection, Lima-de-Faria says that the nuclear envelope has no clear ancestor.[xxxi]

Dean: Okay, what’s a nuclear envelope? (Tosses his hands up in surrender.)

Prof. Adams:  The nuclear envelope is a double lipid that encloses the genetic material in eukaryotic cells. It serves as a physical barrier, separating the contents of the nucleus, or DNA, from the cytoplasm. (The Dean continues to look puzzled.)

The envelope is an example of the power of self-assembly. (Adams looks toward the class). At every cell division, the nuclear envelope has “self-assembled” with a tremendous precision, which is decided by collections of RNA. (The Dean glances out the window.) Small and large RNAs—that is, pure atomic processes, which possess the “road map”—decide the cellular pathways in the pattern of an embryo.

Dean: Do I understand this correctly? Is this a movement of atoms that keeps producing the alternatives that biologists call “errors”?

Prof. Adams: Yes. I would say the change is based on an agreement of vibrations. Only those molecules or atoms that partly agree with the original pattern are incorporated into each novel construction.[xxxii]

Dean: (afraid that Professor Adams is talking over all their heads, not just his own, and wanting to involve students more.) It is as if there are “reflectaphors” at work. Mary, you have been studying reflectaphors since our class on physics. What do you think about this?

Mary: Yes, I’ve been reading about them. I could say a few words.

 (The Dean goes to the blackboard and writes:)

Reflectaphors

Dean: Professor Adams, we talked in an earlier class period about how metaphors bounce off one another, so to speak, in the creation of a whole work of art. We can see how this happens in a poem or novel. 

So Mary, tell us. You are writing a paper on reflectaphors. Are they like this self-assembling of atoms?

Mary: Reflectaphors refer to interactions among elements in the field of art. In chemistry, the “elements” are atoms, but in portrait painting the elements are shape, line, color, and negative space. It is in the interplay of these elements that real art happens. (Jane, who majors in portrait painting, is nodding her head in agreement.) In chemistry, the interplay is in and among molecules, but in literature the interplay is with its own elements: images, irony, synecdoche, motifs, symbols, and different types of rhetorical figures. In a work of art, a new creation happens at the intersection between parts in relation to the whole. (Prof. Adam’s left eyebrow goes up quizzically, as he puzzles what this means.)

Dean: Reflectaphors are mirrors of likeness in a work of art. But you may not always see them. You have to have the skill or capacity to see them. In other words, some people may not be able to see them even though they are there.

Prof. Adams: Could you illustrate that for me?

Mary: Yes. I read Joseph Conrad's novel Typhoon and saw them. Slowly, I came to see how reflectaphors were working in the interaction of the characters in their setting, the environment, and the plot.

Prof. Adams: Okay, but how does it happen? 

Mary: The novel is about a sea captain who guides his ship through a tropical typhoon. The story is full of reflecting metaphors—mirrors, we might say. I was constantly comparing the elements that made the story so creative and powerful.

Dean: In what way?

Mary: The ship’s captain is named MacWhirr. He is a simple, easygoing guy, but he has “fiery gleams” on his cheeks. You know that, intuitively, he possesses some hidden power. Reading on, you soon you realize that those “fiery gleams” are, metaphorically speaking, a reflection of the fire in the ship’s boilers. The boilers keep the ship heading steadily into the wind, as steady and powerful as the Captain shows himself to be.

The ship carries Chinese coolies, who seem to be pretty easygoing like MacWhirr, but during a storm their footlockers are battered open by the pitching of the ship, and the silver dollars they have saved start flying around everywhere. Inside, the ship becomes as wild and confusing as the typhoon outside. (Mary is speaking excitedly now.)

The coolies begin thrashing each other in frenzy. Their circular dollars roll with the ship and the rolling sea. The Chinese chase them, all reflecting the “spiraling storm” in the sea.

Dean: Interesting: the storm on board the ship and the internal emotions of the sailors reflect the storm outside.

Mary: Yes. Conrad creates interlocking images. One image or event reflects with another.

I saw mirroring metaphors that went back and forth between the Chinese and the storm: the dollars to the storm; the ship boilers to the captain; the storm to the rolling ship, and so on.

Dean: Hmm. The novelist Thomas Mann said that the only way to write a story is with mirrors.  But how does that connect with what we are saying?

 Mary: The novel assembles these parts together as it goes along. It is like a chemical solution assembling a final mix of elements. I think it is a self-reflexive action.[xxxiii]

Prof. Kornberg: (Interrupts.) Sorry. I don’t understand the connection between literature—a novel, in this case—and chemistry.

Dean: Mary, give us another example. 

Mary: Hmmm. Richard Hugo is my favorite poet. I cite him in my term paper. Listen to this line:

 “The sun bruises the oats gold.”

I applied the formula we learned in the last class. . . . Remember, we talked about it in physics? The poetry is formed from three combinations that are compressed together.

Dean: Compressed? Can you write them on the blackboard? (Mary goes to the blackboard and writes)

Mary: First, (X) the sun = (Y) something capable of bruising;

Second, (X) the act of bruising = (Y) natural processes that involve photosynthesis;

Third, this “bruising,” as action (X) is equated in the metaphor with (Y) making the oats valuable, like gold. It is all compressed into this one line.

Dean: Compression. So we see a compression of different elements in metaphors that follow this interlocking X/Y tension. Prof. Perry in physics said this is typical of an artistic structure.

Prof. Adams: Sorry, I don’t get the connection.

Mary: In poetry, reflectaphors could represent at the level of human feeling and language what happens among those elements in auto-evolution. The connection between X and Y images generates a new image, while the connection between X and Y atoms generates a new atom.  (Professor Adams Iooksamazed at the astuteness of this senior undergraduate.)

Dean: Interesting. The recombination of elements in a novel or a poem increases our insight into the nature of things. 

Prof. Adams: Oh. I know nothing about this. (He is at once puzzled and sardonic, but friendly.)

Dean: The word “evolution” refers to “long-term changes” that increase in complexity, subtleness, and intricacy. Look at how far we have come with the interaction of all these chemical elements, in the universe over billions of years …. Then we see millions of years of animal populations, and finally thousands of years of civilizations.

But we do not think of this natural process as related to our inner life. To me, it all looks like a movement from the outer to the inner, increasingly transcendent mirrors …

Prof. Parsons: (with good humor) Do you mean that we are developing better telescopes to see into the sky and a greater interior life to see what lies inside the Big Bang?

Dean: (He is not sure what Parsons means or where his thought may be heading.) Let’s go back to chemistry. Professor Adams, for those of us hearing about these matters for the first time: What does Lima-de-Faria say about self-assembly?

Prof. Adams: (consulting his notes.) He says that, “Self-assembly is the spontaneous organization of molecular units into ordered structures by non-covalent interactions.”[xxxiv]

 Dean: “Non-covalent.” I don’t know what that means.

Prof. Adams: “Covalence” refers to the fact that a chemical bond has an attractive force between atoms created by the sharing of electrons. It does not happen in this case. (The Dean looks puzzled.)

Well, here’s another definition from the realm of nanotechnology that may help to clarify things for the class. At this micro-level, scientists understand “self-assembly” in this way: First, they see spontaneity in the assembly of elements. They say that a nanostructure builds itself. Second, the self-assembled structure creates a higher order than the isolated components, which does not happen in normal chemical reactions.[xxxv]

Dean: A higher order!

Mary: The novel Typhoon, like other novels, has a higher order than any of its parts.

Prof. Adams: (He does not hear her.) At the University of California at Berkeley, researchers found how to make a nanostructure by a “self-assembly synthesis method” and could lead to (quotes) “intricate nanomaterials for more-efficient solar cells and less expensive devices for directly converting heat into electricity.” They are synthesizing different orders of atoms at the nanoscale. [xxxvi]

Dean: That’s too complex for me.

Prof. Adams: But scientists are generalizing around this concept now. Chemists at Harvard University say: (reading) “Self-assembly is the autonomous organization of components into patterns or structures without human intervention.” And,

listen to George Whitesides in this generalization:  “Self-assembling processes involve components from the molecular crystals to the planetary level in weather systems.”[xxxvii] 

Dean: Interesting! Look at how the word “self” is used in all those instances!

Prof. Adams: Yes. Biochemists at Tel Aviv University talk about self-regulating processes. “Self- regulation” is different from “self-assembly,” but you can see how scientists are looking at nature, generally speaking, as though it has its own potentiality to change, from within itself.[xxxviii]

Dean: Could this be a constant cycle of self-change toward a higher order? (The Dean does not necessarily know what he means by “self-change.” The term just comes to him.)

Prof. Kornberg: We do not say “higher order.” We talk about a more “complex order.”

Dean: Class, any questions?  (Looks toward this class, whose members have been more silent than usual in this discussion.)

Barbara: (Looks embarrassed.) I hate to ask but – what are molecules? I’ve forgotten, or never really understood.

Prof. Kornberg: (Friendly smile.) Molecules are small units of energy that make up everything. They are created from more than 100 different types of atoms known to exist in the universe. A molecule may contain a few atoms or hundreds of millions of them. (Barbara looks puzzled.)  Oh! If you have not had chemistry, I should tell you that there are more molecules in your body than there are stars in the universe!

Barbara: Ooo. That’s a lot. 

Prof. Kornberg: Yes, and each molecule has a unique shape. This allows it to interact with other molecules. This also makes it possible for all living things to move, experience sensations, reproduce, and stay alive.

Barbara: What’s an example of a molecule?

Prof. Kornberg: You probably are familiar with Tylenol or Aspirin-- the painkillers. Chemists made aspirin by studying a pain-killing molecule in willow trees. It has 9 black carbon atoms, 8 white hydrogen atoms, and 4 red oxygen atoms.[xxxix]

 Barbara: (Barbara took an aspirin for a headache she had this morning.  Her curiosity heightens.) Are there any other molecules I would know about?

Prof. Kornberg: Carbon Dioxide. It has 1 black carbon atom and 2 red oxygen atoms. Less than 1% of the air is carbon dioxide, but it’s essential for life. Plants use carbon dioxide to build energy-rich molecules.[xl]

Barbara: So a molecule is what you get when you synthesize atoms. Is this how evolution happens –

synthesis, all the way? (Kathleen is thinking about her baby: ”The synthesis of sperm and ovum.”)

Prof. Kornberg: Yes. Oxygen is a molecule because it is made from two atoms of oxygen. It’s not a compound because it is made from atoms of only one element - oxygen. A compound is what you get when atoms of two or more different elements join together. Atoms attract, combine, and grow in complexity.

Barbara: Now we’re really getting to the nitty-gritty, and so I need to ask: What are atoms?

Prof. Kornberg: Atoms are made from particles called protons, neutrons, and electrons. Protons carry a positive electrical charge; neutrons carry no electrical charge; and electrons carry a negative electrical charge. The protons and neutrons come together in the central part of the atom called the nucleus, and the electrons 'orbit' that nucleus. 

Barbara: I’m trying to figure out what causes the synthesis. What’s behind this process of evolution?

Prof. Kornberg: Oh. That question is too big. But look, atoms and molecules all have a frequency. And if you want to know more about them, you might want to look into spectroscopy.

Barbara: What’s that?

Prof. Kornberg: Spectroscopy is the study of spectra, which are seen in the distribution of light, like in a prism. It is about the radiation of frequencies that have a specific property. Spectroscopy helps us determine the chemical composition of substances and the physical properties of all molecules, ions, and atoms. [xli]

Dean: It might be interesting to calculate those resonance frequencies. They could tell us more about the sequence of evolution. How – and why -- do these frequencies keep becoming more complex?

Prof. Kornberg: Mutations take place in the germ cells, not in the somatic cells, except for plants where the mutations can occur in them. Somatic cells are the cells involved in growth and repair and maintenance of the organism…

Dean: I think that Barbara is reaching for a way to know how it all happens. The process of evolution looks like it has a purpose. How does all this increased complexity keep happening? How did chemicals keep evolving into more complex orders? What’s the sequence?

Prof. Kornberg: The sequence goes something like this: (writing on the blackboard)

1. Monatomic (metals);

2. Ionic compounds (salts, most acids, and bases);

3. Nonfunctional compounds (the paraffin series);

4. Functional compounds (compounds of compounds);

5. Nonfunctional polymers (chains 100,000 units long);

6. Functional polymers (proteins);

7. DNA and viruses (Double helix, self replicating).[xlii]

Our department does not study this sequence. We focus on the usefulness of molecules. 

(The Dean goes to the blackboard and writes.)

 Directionality

Dean: You do research on what is useful?

Prof: Kornberg: Yes.

Dean: That’s a particular direction. It’s called utilitarianism.

Prof. Kornberg: Utility guides much of our research.

Dean: So you make molecules that will sell on the market? 

Prof. Kornberg: Well, in the public interest.

Dean:  Drug companies have made a lot of money by inventing molecules. Perfume makers spend billions on research to find new “smell molecules.” They patent and sell a lot of them.

Prof. Kornberg: (a little upset.) You must not oversimplify the work we do; we also do pure research. Not all that we do is just “applied” to the market.

Dean: What about toxicity in chemicals?

Prof. Kroneberg: We need a better assessment of risk.[xliii]

Dean: (The Dean’s energy heightens along with his critique.) I’ve heard about Green Chemistry.

Prof. Kroneberg: Yes. It’s less expensive to manufacture benign materials that do not have regulatory and disposal costs. That’s green chemistry.

Dean: I believe that scientists are influencing the direction of evolution in this market. (No answer. Silence. Prof. Kroneberg is miffed; he does not like the suggestion that chemistry is not morally responsible.)  Prof. Benedict, you look across the cultures among different departments. What are the major themes of science? Is there a culture of science here?

Prof. Benedict: Science has key themes in its framework. Let’s see if I can think of them: control… predictability… objectivity… causation… rationality… impersonality …manipulation… exteriority.

Prof. Kornberg: So? What does these mean?

Prof. Benedict: Science is not the whole story of nature. 

Dean: What’s missing?  (He senses a debate.)

Prof. Benedict: Freedomsubjectivity… purpose… tendernesssurrender

Prof. Kornberg: (He has been feeling attracted to Margaret Benedict as a woman, but now he is befuddled. He does not like what her statement about the framework of science implies. Hairs rise on his head, and fire gleams in his cheeks. The Dean wonders whether this “ship” might be heading into a “storm.”) What do you mean by this?

Prof. Benedict: In the framework of science there are themes of causation but no telos, no direction toward an end, no overall purpose. There are objects but no subjects. There is reason, but no feeling for nature in a scientific framework, no compassion 

Prof. Kornberg: (Kornberg has been “down in the boiler room,” but cools now as he “climbs on deck.”) Well put. But you must admit: science gives us a slice of nature; no other field can provide that. (Margaret Benedict looks at him with shining blue eyes. Linus Kornberg sees them twinkling like the sun on a quiet sea. She is about to speak, but the Dean interrupts.)

Dean: We need to be objective. And we need to be indifferent to scientific findings. We are in the pursuit of truth.

Prof. Benedict: But what if the universe is a theater of all our differences? What if there is some great tenderness behind the toughness we see in nature? (She is thinking of a question that William James asked: is nature tough or tender in its basic force?)

Prof. Kornberg: (focusing on the issue of causation as a dominant theme of science) Let me take up one of your points, the one about causation being a consistent theme in science. All things are caused by something. We scientists look for what causes things. This is not a religious question for me, arguing toward some general purpose. (His cheeks start to glow again; then) But we need to be rational about this.

Dean: (noticing some “whirling turbulence” and looking for a solid and stable way to “steer his ship”) I recall how Professor Albert Hawking spoke about the mountain he climbed. The mountain was indifferent to his purposes and all of his feelings. A mountain does not care about human feelings, he said. A sudden freezing storm could kill him. Nature can be tough … even cruel. A bolt of lightning will murder you -- without any reason. There is no rationality in that killing.

Prof. Adams: I agree. A mountain can teach us many things.  (Linus and Margaret look at one another.  Each of them, unmarried, feels an attraction to the other. High intelligence and reason prevail for the moment. They are calm; but they both want to come back to this point, talk about it further.)

Dean: (glancing at both of them, then at the notes he has been taking) Oh! We have come a long way. (to the class) Look at how far we have come. (Students squirm into position, anticipating a synthesis of the professors’ discussion,  but the Dean continues, in good humor) We began over 13 billion years ago when the Big Bang exploded; 4.5 billion years ago, our Sun and Earth appeared; 3.4 billion years ago, life appeared; 450 million years ago, there were the first Fishes; 300 million years ago, the first Reptiles; 200 million years ago, the first mammals; 120 thousand years ago, Homo Sapiens appeared. So, can you students tell us: What’s next? After all this, what possibly could happen next? Does anybody want to hazard a guess? (The class enjoys his humor.)

 Well, I would like to propose that “synthesis” is our key principle. It is key. And look: Interiority. Evolution is something that keeps happening from the inside; it’s not just imposed at the macro level, from without. (Kathleen knows that something from outside joined something within, to produce what is now growing inside her.) So evolution began with a fusion, a concentration of all the energy we know today…

Prof. Kornberg: (not yet finished promoting science with his energy and expertise: this is his day.) You know that the Big Bang might have been a Big Bounce. The Big Bang does not carry the fine quantum structure of spacetime. There is a limit to how tightly matter can be concentrated and how strong gravity can become.

Dean: Whaddyamean? Is there an alternative to the Big Bang?

Prof. Kornberg: Yes, as I said, the Big Bounce. In Loop Quantum Gravity, space is divided into “atoms” of volume and has a finite capacity to store matter and energy. This prevents true singularities from existing.

Dean: Does that mean that something might have existed before the Big Bang?

Prof. Kornberg: It could be. (He signs the quotation mark:) “Physicists must transcend relativity.” Under such concentration of energy the attraction of gravity reverses into repulsion. The Big Bang could be just a Bounce from a previous universe.[xliv]

Dean: My God. (shaking his head, incredulous) There is no beginning or end to things!

Prof. Kornberg: This could be true. So, what’s the purpose to it all?

Dean: So far, we don’t know. But we do know something. This universe is a process of constant invention. Forces of attraction and repulsion keep reappearing, and things keep transcending through hierarchies in all these stages.

Prof. Kornberg: I don’t know what you mean by the term “transcending.”

Dean: Notice how just one force, “attraction,” transforms and transcends through evolution. It becomes so much more complex and multifaceted. (Kornberg looks puzzled.)

Physicists study the forces of attraction in gravity; chemists study the forces of attraction in bonding; biologists study the animal forces of attraction in the act of mating; psychologists study the forces of human attraction in love – with all its varieties. Sociologists study the collective forces of attraction in the quest for community. This “force” is the same in kind but becomes so much subtler, finer, and more intricate and sensitive over this period of time. (Looking at Kornberg.)

Prof. Kornberg: Well. I can see the greater complexity over time. 

Dean: Yes, but where was this attraction headed in the course of history? It began in the stars, and then what? The force of attraction is headed somewhere; this does not look like random occurrences.

Prof. Kornberg: Right. Well, most stars are made of hydrogen and helium; they turn hydrogen into helium. (He is refusing to look at the question.)

Dean: Then what?

Prof. Kornberg: And fusion produces a huge amount of energy that makes a star hot. The energy then radiates away, becoming electromagnetic radiation and visible light. (He looks at Margaret and pauses.)

Dean: (The Dean notices. He is familiar with some of the aspects of this science and says) Fusion happens when atomic nuclei combine to form those new elements. All stars are nuclear furnaces, fueled by fusion. (Mary thinks these stars are like boilers with fiery gleams shooting out from them). Then there are periods of equilibrium. (“These are the calms between the storms,” Mary thinks.)

Prof. Kornberg: During the first second after the Big Bang, the temperature was so high that protons and neutrons were in equilibrium.

Dean: But after that…

Prof. Kornberg: Soon the temperature dropped, and neutrons started to decay — producing protons, an electron, and an anti-neutrino. 

Dean: Aaah. This was the beginning of polarity, which brought about a continuous process of invention from within the interior of all things. This process has kept preserving its past. (Kornberg has now redirected the Dean’s question on directionality.)

Prof. Kornberg: Preserving. Yes. Conserving. The Universe would have lost neutrons had it not been for that reaction that “preserved” them. A neutron and a proton combined into a deuteron, the nucleus of deuterium.

Dean: Deuterium? (The Dean notices the clock — ten minutes before the end of the class. He knows they must reach a stopping point soon, but hates to break their momentum.)

Prof. Kornberg: Deuterium is famous for its use in the production of nuclear bombs. The Germans tried to make them during World War II. We finished the job here in America.

Dean: Whooo. (Whooping: The Dean is disturbed by the abruptness of Kornberg’s interjecting this idea of “finishing the job.” Does this point to insensitivity in him?) The bomb was useful at the time. Now many more nations can make them. (The Dean’s response signals his irony again.) Is science based on the needs of each nation?

Prof. Kornberg: Yes.

Dean: And nations may collide -- like deutrons. Right?

Prof. Kornberg: Yes, but you’re stretching the analogy. When deuterons collide, they produce a neutron and a helium nucleus, consisting of a neutron and two protons.

Dean: It’s just like soup, a little bit of this and a little bit of that; then you get something new and powerful. (More irony bordering on sarcasm, but Kornberg ignores this.)

Prof. Kornberg: Right. Three parts hydrogen, one part helium-4, a little deuterium and helium-3, and a pinch of lithium. After the Big Bang, a great cosmic soup was created, the basis of all the other ingredients yet to come in the stars, planets, and…

Dean: And now, voilà . . .: life! Okay. (Kornberg nods, acknowledging the whole evolutionary process implied in the Dean’s statement.) It’s amazing. Preparing soup is so simple, you know. (The Dean is again ironic, teasing, but  Kornberg continues to ignore his tone. And the Dean does not want to end the class with an argument.)

Prof. Kornberg: Yes. And the balance of ingredients depends on a single parameter, in fact: the initial density of protons and neutrons.

Dean: And all those other elements then “self-assembled,” as you say. So, where and how were they created?

Prof. Kornberg: We say: “inside the stars.”

Dean: An inside job, right from the beginning. (He is pleased to be able to advance his theory of Interiority again in this context of Kornberg’s explanation of origins, but not everyone is aware of his implicit point.)

Prof.  Kornberg: Yes. Inside, the temperature and density are high enough to overcome the forces that cause atomic nuclei to repel each other. This allows them to fuse. The Sun comes from hydrogen nuclei that fuse to form helium at its inner core. The same happens in all stars that are in a similar stage, at which they burn hydrogen. (Kornberg  is in his element.)

Dean: Now let me go back to what we were saying about physics. Evolution displays cycles that move upward, reflecting ever more complex spiraling paths of planets and stars and galaxies.  Each cycle experiences some unity that divides into diversity, leading it back into conflict, which then moves into resolutions at a higher level of unity. 

Prof. Kornberg: That’s an over-simplification.

Dean: But what causes evolution to happen?

Prof. Adams: I have to stay at my level if a question like that comes up.

Dean: Okay. What happens at your level? What level is that?

Prof. Adams: (Adams is a biochemist, but he looks toward professor Wilson as though checking on Wilson’s response.) When organisms are “environmentally stressed,” the DNA reorganizes and redirects itself. It seems to obey the transfer of information in the form of non-locality, rather than through chemical or electromagnetic transmission.

Errors known to occur in DNA during reproduction and by cosmic radiation or other accidents are recognized at the molecular level and fixed by “repair genes.” 

Dean: Could we say that some inner intelligence is at work in animal brains, as well as in bacteria and cells? That in biochemistry, we are in a post-Darwinian era?

Prof. Adams: (He does not want to get into religious issues.) Barbara McClintock pioneered this work on DNA sequences. She used plants in her experiments and showed that their DNA sequences move about to new locations, and that this genetic activity increases when the plants are stressed.  She also found closed-loop molecular bits of self-reproducing DNA called plasmids moving about among the normal DNA and exchanged from cell to cell. 

Dean: Plasmids? Could you help all of us by explaining that a bit?

Prof. Adams: A plasmid is a small circle of DNA that replicates itself independently of chromosomal DNA, especially in the cells of bacteria. Plasmids were invented by ancient bacteria and persist in multi-celled creatures. They are used in genetic engineering and can be inserted into new genomes.[xlv]

Dean: So, is evolution is caused by stress?

Prof. Adams: Well, yes, maybe, in part; but it’s caused by more than that. Creatures in stress depend on trading genes to survive. We are still learning the extent to which DNA is freely traded among microbes to benefit the survival of their communities. 

Dean: Could you say that what they are doing manifests some proto-form of  “intelligence”?

Prof. Adams: We think of genetic alteration at cellular levels as “intelligent responses” -- to the changing environments of these creatures. We know that viruses and plasmids carry bits of DNA from whales to seagulls, from monkeys to cats, and so on; but it remains to be understood how all of this transfer takes place. It looks random. So, in response to your question about whether there could there be some purpose to all of this: I dunno.

Dean: Could the instinct to survival itself be an overall purpose? 

Prof. Adams: Remember. Most research in the area I’ve been talking about is confined to microbes. We do not know how this DNA trading occurs in larger creatures. We do not know to what extent it facilitates specific responses to environmental conditions.

One thing does seem reasonable to speculate: Nature would not have evolved a strategy as sophisticated as gene trading in order to facilitate evolution billions of years ago -- only to then abandon it in larger creatures.

Dean: So genetic activity increases when the plants are stressed? Can we also say, then, that stress promotes invention?

Prof. Adams: A growing body of evidence suggests that evolution proceeds much faster under stress than was once thought possible.  It also reveals how DNA information exchange -- invented by those ancient bacteria -- still functions today. It occurs not only among bacteria, but also within multi-celled creatures and among species.

Lynn Margulis says that evolution is no linear family tree. It is “change in the single multi-dimensional being” that has grown “to cover the entire surface of Earth," as she puts it.[xlvi]

Dean: So the causes of evolution could still be in those bacteria! Hmm. This is too big for us to go into in more detail in a single class discussion. But what about the electromagnetic field? What influence do you think it has on this process?

Prof. Adams: Any influence of electromagnetic fields on us starts at the cellular level. A single living human cell performs over 50,000 different biochemical reactions. The DNA molecule alone carries billions of bits of data linked to survival.

Dean: That’s all microcosmic, below the level of anything we can see. [xlvii]

Prof. Adams: Yes. In every living cell there is a process of electromagnetic vibrations going on when all those biochemical molecules and proteins are being created. This DNA molecule contains around a 100,000 genes, with 5,000 producing just as many different proteins each. One cell carries within it all our organs, the nerve system, brains, and everything that makes up our body.[xlviii]

Dean: (Happy.) Yes, indeed. Each cell is a seed, like the Big Bang. It contains the entire potential for the future of our body. It carries all those vibrations.  

Prof. Adams: Everything in nature vibrates. The smaller the entity -- the faster it vibrates. The frequencies of the vibrations in a living cell depend on the size of its components.  

Dean: Tell us about these frequencies. They may be one of our clues to what is happening here.

Prof. Adams: The cell, as a whole, vibrates with lower frequencies than its individual molecules or atoms do. To get an idea about these “frequencies,” look at the division of a cell, in which a DNA molecule -- an extremely long string of coded material -- divides itself into two exact copies.

The molecule is folded into a tiny ball, but when it divides itself, it has to unroll at speeds between 10,000 and 20,000 revolutions per minute, that is, about 200 to 300 Hertz. The 50,000 different biochemical reactions and the creation of 5,000 different proteins is a continuous bio-electro- chemical game. There are electrical vibrations occurring all over the place.

Dean: Amazing! I’m starting to think I should have taken chemistry.

Prof. Adams: Every single biochemical reaction is an electronic process in itself. These reactions are a matter of reduction and oxidation processes. Reduction removes electrons and oxidation adds them. And that’s what chemistry is all about.

Dean: It is a dance of electrons.

Prof. Adams: Oh, well. I wouldn’t want to go too far. (He does not want to get corralled into the Dean’s idealism.) The electrical frequencies of these processes vary with the size of the molecules. So, I’d say you’re partly right. Life within a single cell could be imagined, artistically speaking, like a “dance of electrons” – that is, it uses an enormous range of electromagnetic frequencies.[xlix]

Dean: So this “dance” is the basis of life!

 (Prof. Adams rolls his eyes upward like he used to do when, as a kid playing on the street at night, his mother told him he’d have to come in before eight o’clock. The Dean notices Adams’s frustration and shifts to accommodate him.) I am amazed at how bacteria communicate with one another in this movement.

Prof. Adams: Biochemist Eshel Ben-Jacob finds bacteria trading genes, with interactions between each individual and their communities. 

The genomes of individuals – I mean, their set of structural and regulatory genes -- alter their patterns in the interests of the whole, bacterial, community.  Bacteria signal each other chemically, calculate their own numbers in relation to food supplies, and make decisions on how to maximize community wellbeing. They change their environments to their communal benefit.[l]

Dean: It looks like they have a higher purpose, and this is it:  “Work for the larger community!”

Prof. Adams: Well. (unwilling to generalize) Bacterial communities create genetic patterns, specific to different environmental conditions.  The genomes of individual bacteria alter their composition and the pattern by which genes are turned on -- in response to changes in the environment or their communal circumstances.[li] 

Dean: Direction. Community. Interesting. …

Oh dear! We are overtime. We must stop.

So much has happened, I cannot begin to summarize it all. But I’m pleased, I am. I believe we are definitely making progress. But we have more questions to answer. There are more pieces to this puzzle.

(The puzzle for the Dean right now has to do with that high moment in the conversation between Linus Kornberg and Margaret Benedict. It was about themes that characterize the framework of chemistry. It was a point of stress, he is thinking, between them. The Dean hopes that they will have a chance to revisit the subject. He also is sensitive enough to see that there is more than an academic argument going on here between them. Something is happening at the personal level.) We have an unfinished symphony. (He says, sadly, and feeling rushed.) Time is up! See you at our next class.

 

The eyes of Linus and Margaret flash toward one another, as though drawn by some magnetic field. Their eyes meet electrically and then automatically move away. It is as though a sun has beamed from behind clouds, and then, disappeared, a sun we know will strengthen.

Kathleen thinks about how her baby is organizing itself. That little baby, she believes, should keep “self-organizing” long after its birth. And then . . .?  Will it take its own direction more and more from within itself, not just from her? Will it grow into its own authority?

 



[i] During the Iron Age, the best tools and weapons were made from steel, which is an alloy consisting mostly of iron, with a carbon content between 0.02% and 1.7% by weight. Steel weapons and tools were superior to bronze weapons, but steel was difficult to produce with the methods available at the time, and so most of the metal produced in the Iron Age was wrought iron. Wrought iron is weaker than bronze, but iron is much cheaper because it is much more common than copper and tin, the ingredients of bronze.

 

[ii] Democritus proclaimed that matter was composed of indestructible particles. These particles he described by using the Greek word atomos, which means “indestructible things.” The first use of the word “matter” is not known, but it developed in modern times from the Anglo term matere, and from Latin materia, a substance from which something is made (attested from c.1340). See Chaucer, c.1395. Oxford English Dictionary.

 

[iii] Starting with the Middle Ages, European alchemists were on a quest for the "philosopher's stone." The Stone was believed to amplify the user's knowledge of alchemy so much that anything was attainable. Alchemists enjoyed prestige for their contributions to the "chemical" industries of the day—the invention of gunpowder, ore testing and refining, metalworking, production of ink, dyes, paints, and cosmetics, leather tanning, ceramics and glass manufacture, preparation of extracts and liquors, and so on.

 

[iv] In 1936, the auction house of Sotheby's released a catalogue describing three hundred twenty-nine lots of Newton's manuscripts, of which over a third were alchemical. Newton broke from alchemy and created a “science of matter.” In texts that are written according to alchemy, the cryptic symbols, diagrams, and imagery contain multiple layers of meanings, allegories, and references to other equally cryptic works. They must be "decoded" in order to discover their true meaning.

 

[v] Carl Jung was fascinated by alchemy. He believed that alchemists were invoking images coming to them from the unconscious. In 1926 Jung had a dream in which he found himself in the 17th century as an alchemist doing important work. This impressed on him the connection between the ancient gnostics and the modern era. Jung saw alchemy as a hidden quest of the soul on its path to perfection. In 1944 he published Psychology and Alchemy, in which he asks for a reevaluation of the symbolism of Alchemy. In this book, Jung argues for a deeper understanding of the Western spiritual traditions alongside Eastern ones, such as Buddhism, Hinduism, etc. Just as in the alchemist's furnace the impurities are burned away, so too in psychoanalysis, disharmonious personality traits are burned away.

 

[vi] Michael White, Isaac Newton: The Last Sorcerer (Addison Wesley, 1997). The Emerald Tablet refers to the One Mind and the One Thing, as well as to the correspondences between what is described as “Above and Below.” It was discovered among Egyptian papyri, the Book of the Dead (1500 BC), the Berlin Papyrus (2000 BC), and other scrolls dating from between 1000 and 300 BC.

 

[vii] According to B. J. T. Dobbs in The Foundations of Newton's Alchemy (Cambridge University Press, 1984), the fact that Newton never published a work on alchemy cannot be taken to mean that he knew he had failed. Rather it could mean that he had had enough success to think that he might be on the track of something of fundamental importance; he may have had religious reasons for keeping his 'high silence.' But the full story of his motives has never been told.

 

[viii] The development of chemistry was long and laborious. An early scientific method began emerging among early Muslim chemists. One of the most influential was the 9th century chemist Geber (c. 721–c. 815). He was a Muslim philosopher-scientist, an alchemist, astronomer and astrologer, engineer, geologist, physicist, pharmacist and physician. Other influential Muslim chemists included Al-Razi, Abu-Rayhan Biruni and Al-Kindi. Alexander von Humboldt regarded the Muslim chemists as the founders of chemistry. Will Durant, The Age of Faith (The Story of Civilization, Volume 4, 1980), 162-186.

 

[ix] The names and dates on this collation are drawn from scientific history and chemistry texts.

 

[x] This follow-up on what happened is a story in itself. In 1961, Juan Oro found that amino acids could be made from hydrogen cyanide (HCN) and ammonia in an aqueous solution. He also found that his experiment produced an amazing amount of the nucleotide base, adenine. Adenine is one of the four bases in RNA and DNA. It is also a component of adenosine triphosphate, or ATP, which is a major energy-releasing molecule in cells. But there are objections to his discovery.

One objection is that the Miller experiment required a tremendous amount of energy. While it is believed that lightning storms were common on primitive Earth, they were not as continuous as the Miller/Urey experiment portrayed. And many of the compounds made in the Miller/Urey experiment are known to exist in outer space. Biological life could have come from outside the Earth.

 

[xi] Ilya Prigogini, “Mind and Matter: Beyond the Cartesian Dualism," Origins: Brain and Self Organization, ed. Karl Pribram (Lawrence Erlbaum Associates, New Jersey, 1994).

[xii] Erich Jantsch, The Self-Organizing Universe: Scientific and Human Implications of the Emerging Paradigm of Evolution (Oxford, 1979).

George Kampis, Self-modifying systems in biology and cognitive science: A new framework for dynamics, information, and complexity (Pergamon, 1991).

    Stuart Kauffman, At Home in the Universe - The Search for the Laws of Self-Organisation and Complexity (OUP, 1995). 

 

[xiii] There are many more examples, such as North American Catalysis Society, Polish Chemical Society, Royal Society of Chemistry, and the World Association of Theoretical Organic Chemists. The Internet provides a detailed survey of them. See http://www.dmoz.org/Science/Chemistry/Associations. 

 

[xiv] There are many books along this line, such as Ross Ashby, Design for a Brain - The Origin of Adaptive Behaviour (NY: Chapman & Hall, 1960).

Per Bak, How Nature Works - The Science of Self-Organised Criticality (Copernicus books, 1996).

Cameron and Yovits (Eds.), Self-Organizing Systems (1960 Pergamon Press).Nicolis and Prigogine, Self-Organization in Non-Equilibrium Systems (1977 Wiley); Nicolis and Prigogine, Exploring Complexity (1989 Freeman). K. H. Pribram (ed), Origins: Brain and Self-organization (Lawrence Ealbaum, 1994)

 

[xv] Humberto Maturana, and Francisco Varela([1st edition 1973] 1980), Autopoiesis and Cognition: the Realization of the Living. Robert S. Cohen and Marx W. Wartofsky (Eds.), Boston Studies in the Philosophy of Science, 42. Dordecht: D. Reidel Harold, F.M. 2001. The Way of the Cell: Molecules, Organisms and the Order of Life. (New York: Oxford University Press). S. A. Kauffman, The Origins of Order: Self-Organization and Selection in Evolution. (New York: Oxford University Press, 1993).

[xvi] E. Bonabeau, M. Dorigo, G. Théraulaz,  Swarm Intelligence. From Natural to Artificial Systems, (Oxford University Press, 1999) p. 8-14.

F. Moyson and B. Manderick, The Collective Behaviour of Ants: an Example of Self-Organisation in Massive Parallelism”, Proceedings of the AAAI Spring Symposium on Parallel Models of Intelligence. Stanford, California. 1988.

M. Dorigo, L.M. Gambardella, Ant Colonies for the Traveling Salesman problem, BioSystems, 43, 1997.

 

[xvii] Loet Leydesdorff, A sociological theory of communication: the self-organization of the knowledge-based society. (Parkland, FL: Universal Publishers, 2001). Leydesdorff’s concept of “interaction” constitutes a system for events different from social action or its aggregates. (Talcott Parsons and Anthony Giddens attributed actions to human actors and aggregates of people living roles in institutions.) When action is attributed to communication as a “system” at the network level, it has its own dynamics. The dynamics are assumed to "self-organize” the roles that are attributed to the actors. This “architecture of relations” carries the information for the network's development.

[xviii] Charles Horton Cooley, On Self and Social Organization, (Chicago: University Of Chicago Press,1998).

[xix] Giddens argues that “structures” both enable and constrain social actions. Social systems are re-creative, i.e., self-organizing social systems. All self-organizing systems are information-generating systems. Anthony Giddens, Beyond Left and Right — (Stanford University Press, 1994); The Third Way. The Renewal of Social Democracy. (Cambridge : Polity, 1999).  

 

[xx] Paul Krugman, The Self-Organizing Economy (NY: Wiley-Blackwell, 1996), 3-4. Krugman talks about how the size of cities obeys a power known as “Zipf's Law,” which is usually stated as: the size of a city is inversely proportional to its rank order, so that, for example, the 100th largest city is a tenth the size of the tenth largest city. Prof. Per Bak also suggests that everything obeys a power law distribution for "self-organized criticality." But Krugman works at the level of a “model.”

[xxi]  My own books focus on self-governance, self-regulation, and self-development in the economy.  Severyn T. Bruyn, The Social Economy (NY: John Wiley, 1977). Also: The Field of Social Investment, Beyond the Market and the State, A Civil Economy, A Civil Republic, and A Future for the American Economy. I use these terms (“self-regulation,” “self-direction,” “self-organization,” and “self-development”) to describe changes in the economy. But this outlook has two sides: “general” and “specific.” I treat a term like “self-regulation” first as a general principle; it operates in the market and in corporations, generally speaking, in its relative sense. It thus remains a theory for testing the degree to which it operates. I also treat it operationally to study specific firms and markets to assess its evidence of operation in quantitative terms. It is thus similar to the “theory” of biological evolution. Biological evolution has much evidence at the general level, but it also must be tested as a “scientific fact” through empirical research.

[xxii] Christopher Wills wrote simultaneously in Wisdom of the Genes about how genes might control their own evolvability. Christopher Wills, Wisdom of the Genes (NY: Basic Books, 1989)

[xxiii] Andreas Wagner, Robustness and Evolvability in Living Systems (Princeton University Press, 2007). Wagner is a biochemist who develops this idea of evolvability. He argues that evolution by natural selection preferentially finds and favors robust solutions to the problems organisms face in surviving. This “robustness” enhances the potential for future evolutionary innovation. 

 

[xxiv] Steven Johnson, Emergence: The Connected Lives of Ants, Brains, Cities, and Software. (New York: Touchstone, 2002).  M. Annett, Left, Right, Hand and Brain: The Right Shift Theory (Lawrence Erlbaum, London, 1985);  J. H. Barkow, L. Cosmides and J. Tooby, The Adapted Mind (Oxford Univ. Press, New York, 1992). D. M. Buss, “Sex differences in human mate selection: Evolutionary hypotheses tested in 37 cultures.” Behavioral Brain Sciences 12 (1), 1-49 

 

[xxv]  Lima-de-Faria says he has worked at his laboratory bench and at his light and electron microscopes for 13 hours a day, without weekends and vacations, for 30 years. Sweden's king decorated him "Knight of the Order of the North Star" for his outstanding experimental work, elaborating the molecular organization of the chromosome and its evolutionary path. A. Lima-de-Faria, “The atomic basis of biological symmetry and periodicity,” Biosystems  43: 1997. 115—135. A. Lima-de-Faria, Biological Periodicity: Its Molecular Mechanism and Evolutionary Implications: JAI Press, 1995.

 

[xxvi] Schrödinger was sympathetic to the view of Indian mysticism, that each individual's consciousness is only a manifestation of a unitary consciousness pervading the universe. "The genetic material must resemble a crystal in being stable and relatively inert, but it must also be 'a-periodic,' in the sense of being composed of several different kinds of units and not just of one kind of unit like a crystal of salt. The reason is that a string of identical units cannot convey information, whereas a string of dissimilar units can." Erwin Schrödinger, What is Life? (NY: Macmillan, 1946).

 

[xxvii] Today the study of fractals is popular. They are found in nature and artists have created some astonishing renderings. Fractals are too irregular for Euclidean geometry; iterative and recursive and seemingly infinite. They turn up in food and germs, plants and animals, mountains and water and sky. The nautilus is one of the most common examples of a fractal in nature. The perfect pattern is called a Fibonacci spiral. Lightning reveals fractals created as arbitrary and irregular. Walter G. Rothschild, Fractals in Chemistry, (NY: John Wiley, 1998).

 

[xxviii] Lima-de-Faria first presented a working biological periodicity table in his book Biological Periodicity (JAI Press, U.S.A. 1995), 283. He also discussed various molecular functions and structures, such as the re-occurrence of the placenta, flight, vision, penis, and bioluminescence.

 

[xxix] In structural biology, a protein subunit is a single protein molecule that "coassembles" with other protein molecules to form a multimeric or oligomeric protein. M. Kreiner, Z. Li, J. Beattie, S.M. Kelly, H.J. Mardon, and C.F. van der Walle, “Self-assembling multimeric integrin 5β1 ligands for cell attachment and spreading Protein,” Eng. Des. Sel., September 2008; 21: 553 - 560.

 

[xxx] Lima-De-Faria examines self-assembly at different levels of organic evolution. For example, he says that “the self-assembly of the dispersed amoeboid cells of Dictyostelium results in a complete slime mold. The animal Hydra can self-assemble from its dispersed cells, which are highly complex. At the level of the organs of mammals, dispersed liver cells, kept in culture, can self-assemble into a functional liver, and dispersed cells from human organs, like those of skin and capillaries, are also able to self-assemble into these tissues and organs.” He says there is no need for any theory of “vitalism” or any spiritual interpretation of these facts. His scientific experiments have demonstrated that the evolving cellular order is due to the production of specific molecules that are recognized by the cell's surface proteins. This evidence was critical in allowing him to propose a mechanism of evolution based on an internal atomic organization. A. Lima-De-Faria, Biological Periodicity. Its Molecular Mechanism and Evolutionary Implications, (Jai, 1995).

 

[xxxi] Nucleosomes are the essential components of chromosomes. When their purified DNA and histones are isolated, they rebuild the chromosome thread spontaneously. As one reaches the level of viruses, their RNA and proteins, as is the case in tobacco mosaic virus, will spontaneously reassemble, producing infectious particles. Living organisms do same thing. Antonio Lima-De-Faria, Evolution without Selection, (Elsevier, 1989)

 

[xxxii]  This explanation is based on an interview made with Lima-De-Faria on Tuesday, 17 June 2008, 4:50 pm by Suzan Mazur, “A. Lima-De-Faria: Autoevolution, Atoms To Humans” Scoop.co.nz is New Zealand's leading news resource. See .http://www.scoop.co.nz/about/about.html

 

[xxxiii]  John Briggs, Quantum Implications, Essays in Honor of David Bohm, Routledge & Kegan Paul, Ltd., 1987.

[xxxiv] Ozin and Arsenault, Nanochemistry: a chemical approach to nanomaterials (Cambridge: Royal Society of Chemistry, 2005)

 

[xxxv]  Science 21 April 2006: Vol. 312. no. 5772, pp. 420 – 424 DOI: 10.1126/science.1125124

Electrostatic Self-Assembly of Binary Nanoparticle Crystals with a Diamond-Like Lattice, Alexander M. Kalsin, Marcin Fialkowski, Maciej Paszewski, Stoyan K. Smoukov, Kyle J. M. Bishop, Bartosz A. Grzybowski. In this article, the authors describe how the self-assembly of charged, equally sized metal nanoparticles of two types (gold and silver) leads to the formation of large, sphalerite (diamond-like) crystals, in which each nanoparticle has four oppositely charged neighbors. In their words, the formation of these non-close-packed structures is a consequence of electrostatic effects specific to the nanoscale, where the thickness of the screening layer is commensurate with the dimensions of the assembling objects. Because of electrostatic stabilization of larger crystallizing particles by smaller ones, better quality crystals can be obtained from more polydisperse nanoparticle solutions.

 

[xxxvi] Kevin Bullis, “Self-Assembling Nanostructures:

Researchers find an easy route to complex nanomaterials,” MIT  Technology Review July 27, 2007. Researchers at the University of California, Berkeley, make a nanostructure that consists of tiny rods studded with nanocrystals. The new self-assembly synthesis method could lead to intricate nanomaterials for more-efficient solar cells and less expensive devices for directly converting heat into electricity. See also George M. Whitesides, Bartosz Grzybowski, “Self-Assembling Nanostructures: Self-Assembly at All Scales,” MIT Technology Review, Friday, July 27, 2007

 

[xxxvii] George M. Whitesides, Bartosz Grzybowski. “Self-Assembly at All Scales,” Science March 29, 2002. These writers, in the Department of Chemistry at Harvard University, go on to say: “In the structures, the quantum dots are all about the same size and are spaced evenly along the rods--a feat that in the past required special conditions such as a vacuum, with researchers carefully controlling the size and spacing of different materials… The concept of self-assembly is used increasingly in many disciplines, with a different flavor and emphasis in each.”  Vol. 295. no. 5564, pp. 2418 - 2421

DOI: 10.1126/science.1070821

Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA. E-mail: gwhitesides@gmwgroup.harvard.edu .

Michael L. Klein and Wataru Shinoda,

“Large-Scale Molecular Dynamics Simulations of Self-Assembling Systems”

Science 8 August 2008:Vol. 321. no. 5890, pp. 798 – 800.

 

 

[xxxviii] Faculty members at Tel-Aviv University in Israel have recorded the spontaneous activity in vitro neuronal networks on different time scales. These include synchronized firing of neurons, bursting events of firing on both cell and network levels, hierarchies of bursting events, etc. Their findings suggest that the networks’ natural dynamics are self-regulated to facilitate different processes on intervals in orders of magnitude ranging from fractions of seconds to hours. Observing these unique structures of recorded time-series gives rise to questions regarding the diversity of the basic elements of the sequences, the information storage capacity of a network, and the means of implementing calculations. Eyal Hulata, Vladislav Volman, and Eshel Ben-Jacob, “Self-regulated complexity in neural networks,” 2005.  Natural Computing, V.4 no. 4http://star.tau.ac.il/~eshel/listall.html

 

[xxxix] The key compound in the synthesis of aspirin, salicylic acid, is prepared from phenols by a process discovered over 100 years ago by the German chemist Hermann Kolbe. In the Kolbe synthesis sodium phenoxide is heated with CO2 under pressure and the reaction mixture is subsequently acidified to yield salicylic acid. F. A. Carey, Organic Chemistry (NY: McGraw-Hill, 1987).

[xl] Joseph Black, a Scottish chemist and physician, identified carbon dioxide in the 1750s. At room temperatures (20-25 degrees centigrade), carbon dioxide is an odorless, colorless gas, which is faintly acidic and non-flammable, a molecule with the formula CO2. It is water-soluble when pressure is maintained. After pressure drops, it tries to escape to air, leaving a mass of air-bubbles in the water.

[xli] Linus Pauling speaks of a resonance in which they all oscillate. The Nature of the Chemical Bond; 3rd ed. (Cornell University Press: Ithaca, 1960).

 

[xlii]  Arthur Young, The Geometry of Meaning (Anodos Foundation, 1976).

[xliii] John Warner, Professor of Chemistry, Guest editorial: “Asking the right questions,” Green Chemistry, 2004, 6, G27-G28. DOI: 10.1039/b400793.

[xliv]  Martin Bojowald, “Following the Bouncing Universe,” Scientific American, October 2008, p. 45ff.

[xlv] Barbara McClintock, “The significance of responses of the genome to challenge,” Science, 1984, p. 792-801

[xlvi] Lynn Margulis, Symbiosis in Cell Evolution: Microbial Communities in the Archean and Proterozoic Eons. 2nd edn. (W.H. Freeman, New York, 1993).

[xlvii]  The DNA molecule is threaded so fine that it is possible to see it only under high-powered electron microscopes. To get a sense of exactly how long an uncoiled DNA molecule is compared to a typical cell, a cell is magnified 1000 times. At this scale, the total length of the DNA in the cell's nucleus would be 3 km -- the equivalent distance from the Lincoln Memorial to the Capitol building in Washington, DC.

[xlviii] The human genome is estimated to comprise at least 100,000 genes. All living organisms are composed largely of proteins; humans can synthesize at least 100, 000 different kinds. Proteins are large molecules made up of long chains of subunits called amino acids. Twenty different kinds of amino acids are usually found in proteins. Within the gene, each specific sequence of three DNA bases (codons) directs the cells protein-synthesizing machinery to add specific amino acids.

[xlix] Gerrit Teule, “The Swedish Association for the ElectroSensitive International UNSAFE AT ANY FREQUENCY” 1997.

http://www.feb.se/ARTICLES/unsafhttp://www.feb.se/ARTICLES/unsafe.htmle.html

[l] Eshel Ben Jacob, Israela Becker, Yoash Shapira, and Herbert Levine, “Bacterial linguistic communication and social intelligence,” Faculty of Exact Sciences, Tel-Aviv University, Tel-Aviv 69978, Israel. The authors find that bacteria have developed intricate capabilities of communication to “cooperatively self-organize” into highly structured colonies with elevated environmental adaptability. They propose that bacteria use their intracellular flexibility, involving signal transduction networks and genomic plasticity, to maintain communication collectively.

[li] This outlook comes from different research laboratories including that of Ben-Jacob, who sees individual bacteria “gaining the benefits of group living by putting group interests ahead of their own.”  Ben-Jacob concludes that colonies form a kind of super-mind genomic web of intelligent, individual genomes.  Such webs “are capable of creative responses to the environment,” which bring about "cooperative self-improvement or cooperative evolution."