Monday, October 09, 2006

Chimps and Humans Evolved From a Common Ancestor?

This is an excerpt from "The Wonder of the World." Also the 2% difference translates into 35 million specific genetic differences (cf. story last week on Neanderthal DNA).

Geek: I have to agree that you’ve raised inescapable issues on the mechanisms of evolutionary change. Let me take a different tack: your whole thesis of supernal interventions faces rough sailing when we get to homo sapiens. As you no doubt know, chimps and humans evolved from a common ancestor. Chimpanzees and human beings, in fact, share 98% of the same DNA. So the culmination of the evolution of life, the grand finale, is a glorified ape!

Guru: Let me first address the widely publicized 98% issue.

What conclusions do you draw from the fact that we share 98% of our DNA with chimpanzees? In his acclaimed What It Means to Be 98% Chimpanzee: Apes, People and Their Genes, the anthropologist Christopher Marks has given us a superb overview of the illicit premises and inferences that lead in general to false genetically-based explanations. The 98%statistic is just one more such red herring. “In the 1990’s,” writes Marks, “we routinely heard that we are just 1 or 2% different from chimpanzees genetically, and therefore … what? Should we accord chimpanzees human rights, as some activists have suggested? Should we acknowledge and accept as natural the promiscuity and genocidal violence that lurks just beneath the veneer of humanity and occasionally surfaces, as some biologists have implied? Or should we perhaps all simply go naked and sleep in trees as the chimpanzees do? None of these suggestions, of course, necessarily follows from the genetic similarity of humans to apes, although the first two have been proposed within the academic community and promoted in the popular media over the past few years.”

So what, he asks, “does the genetic similarity of apes to men mean? What is it based on? Does it have profound implications for our understanding of human nature? Here we will see that the universe of genetic similarities is quite different from our preconceptions of what similarities mean. For example, the very structure of DNA compels it to be no more than 75% different, no matter how diverse the species being compared are. Yet the fact that our DNA is more than 25% similar to a dandelion’s does not imply that we are over one-quarter dandelion – even if the latter were a sensible statement. This will be the primary illustration of the confrontation between scientific data and folk knowledge, and of the exploitation of the latter by the former. The extent to which our DNA resembles an ape’s predicts nothing about our general similarity to apes, much less about any moral or physical consequences arriving from it.”

We cannot draw any conclusions about the relation of anything that chimpanzees do to anything done by humans, says Marks, because we still lack the detailed physiological and genetic data and analyses required. “ Since they have been different species for several million years, anything that chimpanzees do may be either (1) an element shared with human nature; or (2) an ancient element of human nature now lost by humans; or (3) an evolved element of chimpanzee nature, never possessed by human ancestors.” In brief, as Marks said in an interview, the fact that an animal shares 98% of its DNA with humans does not mean it is 98 percent human.

Moreover, most of the DNA we share with chimpanzees is the non-coding or “junk” DNA (DNA that doesn’t code for proteins).

Elaine Morgan draws our attention to the big picture: “Considering the very close genetic relationship that has been established by comparison of biochemical properties of blood proteins, protein structure and DNA and immunological responses, the differences between a man and a chimpanzee are more astonishing than the resemblances. They include structure differences in the skeleton, the muscles, the skin, and the brain; differences in posture associated with a unique method of locomotion; differences in social organization; and finally the acquisition of speech and tool-using, together with the dramatic increase in intellectual ability which has led scientists to name their own species Homo sapiens sapiens – wise wise man. During the period when these remarkable evolutionary changes were taking place, other closely related ape-like species changed only very slowly, and with far less remarkable results. It is hard to resist the conclusion that something must have happened to the ancestors of Homo sapiens which did not happen to the ancestors of gorillas and chimpanzees.”

Monday, May 15, 2006

Evolving Evolution

Evolving Evolution

By Edward Ziff, Israel Rosenfield


Despite much recent controversy about the theory of evolution, major changes in our understanding of evolution over the past twenty years have gone virtually unnoticed.[1] At the heart of Darwin's theory of evolution is an explanation of how plants and animals evolved from earlier forms of life that have long since disappeared; but his theory says nothing about the factors that determine the shape, color, and size of a particular fish, whale, or butterfly. Darwin and his contemporaries realized that understanding the evolution of animal forms and understanding how a fertilized egg develops into a whale, cow, or human being must be deeply connected; but they didn't know how to make the connection.

Surprising discoveries in the 1980s have begun to tell us how an embryo develops into a mature animal, and these discoveries have radically altered our views of evolution and of the relation of human beings to all other animals. The new field of study in which these breakthroughs have been made is called Evo Devo, short for evolution and development, "development" referring to both how an embryo grows and how the newborn infant matures into an adult.

Sean Carroll, author of one of the books under review and a coauthor of another, has made important contributions to the understanding of evolution and development. From DNA to Diversity, written with two other scientists, is the second edition of a book that has become a classic for students of evolution. The title of Carroll's other book, Endless Forms Most Beautiful, comes from the famous final sentence of The Origin of Species: "There is a simple grandeur in this view of life... that from so simple an origin, through the process of gradual selection of infinitesimal changes, endless forms most beautiful and most wonderful have been evolved."

In 1830, nearly thirty years before Darwin published his book, two French naturalists—Georges Cuvier and Étienne Geoffroy St. Hilaire—debated the significance of the anatomical similarities between distantly related animals, such as the flippers of whales and the wings of bats. Cuvier held that form was dictated by function: the bat's wing, needed for flying, had a separate origin from the whale's flipper, needed for swimming.

Geoffroy St. Hilaire opposed this view, arguing that the underlying skeletal similarities pointed to the existence of a common archetype for both flippers and wings. While neither man claimed that animal forms could change over generations, St. Hilaire's archetypal form foreshadowed some recent discoveries about development and evolution. No doubt this debate was in the mind of Charles Darwin as he formulated his theories in an attempt to account for the origins of animal forms.

The contemporary Darwinian theory of evolution is based on three ideas: natural selection, heredity, and variation. Small random changes—variations—occur in organisms through mutations of genes, and when these changes give an organism a greater chance of survival, they persist from one generation to the next through natural selection. That is, organisms with traits that make them better adapted to the environment they inhabit will have better reproductive success than other members of the same species that do not possess the advantageous traits. In each successive generation, then, an ever-larger proportion of the species in question will possess the mutation that produces the advantageous traits. "Natural selection," Darwin wrote, "acts solely by accumulating successive, favorable variations." Evolution in the Darwinian view was gradual: "it can act only by short and slow steps." And since, in this view, all changes are random, there are no predetermined directions in which organisms evolve. All living organisms, Darwin claimed, are descended from one or a few common ancestors.

Neither Darwin nor any of his contemporaries knew about the workings of heredity—how we inherit the eye color of our father or the hair color of our mother. The work of the Czech monk Gregor Mendel, first published in 1865, had gone unnoticed in Darwin's day and was only rediscovered around 1900. Mendel had shown that specific traits, such as the color of a pea, or the smoothness or roughness of its skin, could be inherited independently of one another. The new science of "genetics," the idea that units called "genes" within each cell transmit specific traits, such as hair color, from one generation to the next, began in the first decade of the twentieth century. Studies of inherited traits in fruit flies in the following decades established convincing evidence for genes, but they remained invisible. Scientists still didn't know how the gene made it possible for information to pass from one generation to the next, and how mutations in genes could, over many generations, lead to a new species that had a form different from its distant progenitor.

By the 1940s, though the structure of the gene was still unknown, scientists had introduced the idea of the gene into Darwinian theory. They now explained evolution as the consequence of small random changes in genes. This recasting of Darwinian theory was called the Modern Synthesis, following the 1942 publication of Julian Huxley's book Evolution: The Modern Synthesis. The neo-Darwinian theory incorporated the Mendelian idea of genetics, explaining the mechanism of inheritance that was unknown to Darwin. The theory, however, did not account for how particular organisms develop from embryos in the womb to adult forms; that process, known as embryology, was not discussed.

The neo-Darwinian view was reinforced in 1953, when the double helix was discovered, showing how genes composed of the nucleic acid DNA transmitted hereditary characteristics. A molecule of DNA is made up of two long strands of chemical building blocks called nucleotides, each containing one of four bases: adenine, thymine, guanine, or cytosine, which are abbreviated A, T, G, and C. The order of the bases in each strand of DNA determines the information in the DNA molecule, information we can think of as providing an overall plan for producing enzymes and other proteins.

A gene was now understood to be a specific sequence of DNA bases. Genes vary considerably in size, most of them containing between 10,000 and 20,000 nucleotides, though they can be much longer or shorter. Each of our cells carries all our genes, although most genes remain inactive at any given moment. When a particular gene is activated it is first copied into RNA, a nucleic acid that carries instructions from DNA for assembling proteins. The RNA's instructions are then decoded in a process called "translation," and proteins, including the enzymes essential for cells to function, are produced. Proteins in turn form some 50 percent of all living cells.

How are particular genes activated? There are, according to recent research, as many as a hundred trillion cells in the human body, and each cell contains thousands of different types of molecules that vary considerably in size; many molecules move about freely inside the cell. All the cells in a given individual have the same DNA—it is contained in the largest molecules in each cell—and hence an identical set of genes. Which specific genes are activated in a particular cell depends, in part, on the cell's location in the embryo or the adult body. Moreover, the activation of one combination of genes will give rise to a liver cell, while the activation of another will produce a brain cell.

The structure of the double helix made it apparent how changes, or mutations, in the base sequence of a gene could lead to variations in the characteristics of an organism; such mutations could, if advantageous, accumulate over time. The process appeared to confirm Darwin's view that evolution is gradual. As he wrote in The Origin of Species, nature "can act only by short and slow steps. Hence, the saying Natura non facit saltum," nature doesn't make sudden jumps. The standard view, then, was that variation and selection could account for how the simple organisms of early life evolved into the complex forms of the contemporary biological world. After Mendel's discoveries had been absorbed at the beginning of the twentieth century, it was assumed that as changes accumulated between one species and another, there would be less and less similarity in the kind and number of their genes. More advanced species would have many more genes than lower forms of life; and worms, for example, would have few, if any, genes similar to those of fish, mice, or human beings.

Yet it seemed astonishing that random mutations, even over enormous periods of time, could give rise to the remarkable complexity of an organ such as the human eye. "To suppose," Darwin wrote in The Origin of Species,

that the eye with all its inimitable contrivances for adjusting the focus to different distances, for admitting different amounts of light, and for the correction of spherical and chromatic aberration, could have been formed by natural selection, seems, I freely confess, absurd in the highest degree....

Nonetheless, he continued:

Reason tells me, that if numerous gradations from a simple and imperfect eye to one complex and perfect can be shown to exist, each grade being useful to its possessor, as is certainly the case; if further, the eye ever varies and the variations be inherited, as is likewise certainly the case; and if such variations should be useful to any animal under changing conditions of life, then the difficulty of believing that a perfect and complex eye could be formed by natural selection, though insuperable by our imagination, should not be considered as subversive of the theory.

The neo-Darwinian belief in small mutational changes in DNA molecules over hundreds of millions of years made the preservation of individual genes over long periods of time highly unlikely. It was thought that the diversity of living forms was the consequence of each animal having evolved its own unique set of genes over millions of years as well. Surely human beings, for example, would not have the same genes as worms.

Those assumptions were dramatically overturned when the rough draft of the human genome—the entire set of human genes—was announced in 2001. As it turned out, human beings have far fewer genes than expected— about 25,000 rather than the 60,000 or more that had been predicted. This was about the same number as mice have, and even the tiny worms called nematodes have about 14,000 genes. The number of genes in a given species, therefore, is not a measure of its complexity. Why had biologists so overestimated the number of genes in the human genome? Why is it unnecessary for complex animals such as mammals to have ten times as many genes as worms?

The answers to these questions were already hinted at more than four decades ago. At the time it was known that the bacteria E. coli, which normally live off the sugar glucose, are also capable of producing enzymes that digest other sugars, such as lactose. But biologists noticed that the bacteria only produce the enzyme when lactose is present in their immediate environment. Scientists could not explain how the E. coli somehow "knew" when the lactose-digesting enzyme would be needed.

In 1961, Jacques Monod and François Jacob discovered that E. coli bacteria actually have a mechanism that controls the production of the enzyme for digesting lactose. As unicellular organisms, E. coli bacteria have only several thousand genes, each of which is made up of a specific sequence of DNA. A single one of these genes, present in all E. coli, carries in its DNA the genetic instructions needed to assemble the enzyme that can digest lactose; the DNA is copied into RNA, which is then "translated" to produce the enzyme itself. When there is no lactose present in the bacteria's immediate environment, the gene is switched off: its DNA is not copied into RNA and the enzyme is not produced. The reason for this, the scientists discovered, is that a protein called a repressor molecule attaches itself to the DNA site where the copying into RNA begins, thus blocking off the DNA and preventing the gene from producing the RNA responsible for the synthesis of the enzyme.

On the other hand, when the E. coli bacteria encounter lactose, the lactose binds itself to this repressor molecule, causing the repressor to be detached from the DNA site. This unblocks the DNA, allowing the gene to be copied into RNA, and produce the enzyme that can digest lactose. In other words, the repressor molecule acts as a switch that controls the gene's production of the enzyme. Since only a fraction of the total number of genes present in an organism are expressed, or turned on, at any given time, Monod and Jacob conjectured that other genes must be similarly turned on and off.

Although they had not yet found systematic evidence to support these ideas, the discovery of the repressor molecule allowed the two scientists to form a powerful new hypothesis about how genes function. As Jacob recently wrote, in a brief description of the new hypothesis:

It proposed a model to explain one of the oldest problems in biology: in organisms made up of millions, even billions of cells, every cell possesses a complete set of genes; how, then, is it that all the genes do not function in the same way in all tissues? That the nerve cells do not use the same genes as the muscle cells or the liver cells? In short, [we] presented a new view of the genetic landscape.

The deeper significance of the Monod-Jacob model of gene function, and its implications for the nature of evolution, became apparent with the new field of embryo research that arose almost twenty years later.


In 1894, the English biologist William Bateson challenged Darwin's view that evolution was gradual. He published Materials for the Study of Variation, a catalog of abnormalities he had observed in insects and animals in which one body part was replaced with another. He described, for example, a mutant fly with a leg instead of an antenna on its head, and mutant frogs and humans with extra vertebrae. The abnormalities Bateson discovered resisted explanation for much of the twentieth century. But in the late 1970s, studies by Edward Lewis at the California Institute of Technology, Christiana Nüsslein-Vollhard and Eric Wieschaus in Germany, and others began to reveal that the abnormalities were caused by mutations of a special set of genes in fruit fly embryos that controlled development of the fly's body and the distribution of its attached appendages. Very similar genes, exercising similar controls, were subsequently found in nematodes, flies, fish, mice, and human beings.

What they and others discovered were genes that regulate the development of the embryo and exert control over other genes by mechanisms analogous to that of the repressor molecule studied by Monod and Jacob. Eight of these controlling genes, called Hox genes, are found in virtually all animals —worms, mice, and human beings— and they have existed for more than half a billion years.[2] Fruit flies and worms have only one set of eight Hox genes; fish and mammals (including mice, elephants, and humans) have four sets. Each set of Hox genes in fish and mammals is remarkably similar to the eight Hox genes found in fruit flies and worms. This discovery showed that very similar genes control both embryological and later development in virtually all insects and animals. (See Figure 1.)

To understand what Hox genes do, scientists needed to observe the activity of the genes in the developing embryos of flies and mice. Using new technologies that allowed them to observe under a microscope the locations of the Hox proteins in these embryos, they were able to identify an overall pattern of how Hox genes behave. A newly fertilized fly egg looks like a tiny football: one end, or pole, will eventually become the head region; the other end will become the tail region. These and other divisions of the embryo in later development actually followed the switching on and off of the Hox genes in different parts of the embryo. (See Figure 2.)

The mechanism that causes the Hox genes to behave in this way is initiated by the release of proteins from the cells of the mother's body across the newly fertilized embryo. These proteins control the activities of the Hox genes and are released in varying concentrations, causing Hox genes to produce Hox proteins in specific places. As the embryo grows, the production of Hox proteins divides the embryo into a series of segments, or distinct regions, from which subsequent development occurs. Other genes are then activated within each segment, a finer division of the embryo is established, and wings, antennae, and other body parts are formed. In general, scientists reasoned, Hox genes establish the basic division of the embryo into distinct compartments, and each compartment, in turn, establishes the regions of the embryo where development of specific body parts and functions takes place. Still, the details of the mechanisms that a cell uses to establish its position in the embryo remain incomplete.

In fact, Nüsslein-Vollhard and Wieschaus found that within the fly's embryo there was an overall pattern in which genes were turned on or off; and they saw in this pattern the overall body plan for the full-grown fly. In other words, the activity of the Hox genes, including the formation of compartments within the embryo and the control of other genes that guide development, provided a system of organization that dictated the final adult form of the fly.

The presence of a body plan in the genome, whether of a fly, a whale, or a human, was unexpected by embryologists. Previously, most of them did not think that development of embryos was controlled by genes; they had assumed that the different parts of developing embryos were determined by physical interaction between neighboring cells and that there was no overall division of the embryo according to a genetic plan. Experiments had shown, for example, that removing developing wing tissue from one part of an embryo and implanting it elsewhere still gave rise to a wing, although an abnormal one. Scientists attributed the abnormality to the effects of the neighboring cells in the embryo. This was wrong. In fact it was caused by the disruption of the body plan.

This new understanding of Hox genes was aided by the discovery that the proteins produced by these genes function in a way that is analogous to Monod and Jacob's repressor molecule. Specifically, although they have different properties, all Hox proteins contain a molecular structure that makes them attach to DNA sites that control genes. This meant that Hox proteins, like the repressor molecule, act as switches that turn neighboring genes on and off.[3]

Hox genes, as Carroll explains, are in fact one of many kinds of genes that direct embryo development by a mechanism of switches. One example that is not a Hox gene is the gene that controls the development of the eye in fruit flies. If this gene (called Pax 6) is damaged when it mutates, the fly fails to develop eyes. We now know from the experiments described in Carroll's book that the Pax 6 gene is also found in butterflies, mice, and humans. Indeed, Pax 6 genes are interchangeable. The Pax 6 gene from a fly will turn on genes that make eyes in mice, and the Pax 6 gene from a mouse will turn on genes that make eyes in flies.

It had long been assumed that eyes had evolved independently in different species. The structures of mammalian eyes and insect eyes are very different and it would seem most unlikely that they had followed a similar evolutionary path. Mammalian eyes, for example, have a single lens that focuses an image on the retina. Insects have eyes with many tube-like structures, each tube having its own lens and retina. Yet the discovery of the Pax 6 gene gives us reason to believe that the evolution of the eye in all the animals followed related, and to some extent common, paths, though we cannot completely exclude the possibility that each kind of eye evolved following completely independent pathways. In addition to the Pax 6 gene, genes have been found that control the genes responsible for the development of the different kinds of "hearts"—or mechanisms that pump blood—whether in fruit flies or humans, again suggesting similar evolutionary pathways. Indeed the development of legs, wings, arms, fins, and other fish and marine animal appendages are all under the control of virtually identical genes and, as with the Pax genes, in many cases are interchangeable.

These findings strongly support the Darwinian view that animals descend from one or a few ancestors. However, contrary to the previously accepted neo-Darwinian view, the same findings showed that different animal forms are not primarily a function of distinct gene pools that have evolved over millions of years. How then do similar collections of genes create the enormous diversity of living forms? In Sean Carroll's view, what creates diversity is the patterns in which genes are turned "on" and "off." The different appendages found in centipedes, fruit flies, lobsters, and brine shrimp are created by varying combinations of Hox gene activity in the developing insect or crustacean embryo.

"Switches," Carroll emphasizes, "enable the same...genes to be used differently in different animals" [his italics]. In other words, a Hox gene produces a protein that binds to the DNA's sites where genes copy into RNA and can thus turn genes "on" or "off."

This has an important consequence for evolution: mutations in Hox genes will affect the ways in which they act within the embryo, thereby altering the proteins' functions as switches. When the proteins' functions are changed, in turn, this causes them to control genes that are needed for development of a specific physical trait in new ways. In this view, evolution is largely the consequence of random mutations in genetic switches. Genes remain intact, but under new patterns of control. Their function is altered. Complexity and variety are created, at least in part, by combining the activities of old genes in new ways. Carroll's view—what we might call the switches hypothesis—emphasizes the importance of changes in patterns of turning genes on and off rather than changes in the genes themselves. However, even the most ardent supporter of the switches hypothesis would admit that not only Hox genes but other genes change as well. But the contribution of these changes to evolution is far less than we had previously believed.

In fact, vertebrates—reptiles, birds, chickens, mice, pythons, and humans— do have more genes than insects, though far fewer than had been expected before the human genome was revealed. The increase in the number of genes in these animals is partly responsible for their complexity and diversity. But as Carroll notes, "frogs and snakes, dinosaurs and ostriches, giraffes and whales, have evolved around a similar set of four Hox gene clusters. So again, the mere number of Hox genes does not tell us how these forms evolved." The diversity of these animals comes from changes in the ways genes are turned on and off.

For example, though the giraffe has a long neck, it has seven cervical vertebrae, the same number as humans, whales, and all other mammals. Hox genes control this number, but they may also control cell proliferation and consequently the size of the vertebrae. The giraffe's larger vertebrae may have developed because of mutations in the Hox genes controlling the size of vertebrae. Giraffes with large vertebrae and longer necks could feed off tall trees and were consequently selected over other giraffes. Changes in gene regulation, not new genes, gave rise to the long-necked giraffe.

Evolution, then, depends on new patterns of gene regulation rather than the creation of new genes. Indeed, it is not meaningful to talk about the function of a single gene in isolation. Genes only function in the context of the organism. There is no single gene for an eye, a limb, or language, much less such tendencies as homosexuality. Genes function in relation to other genes and intercellular signals, much as words vary in meaning and function depending on the way they are used in sentences and the contexts in which they are spoken. It is the combinations of gene activity, which may be different in different species, that create the form of the organism. "We can begin to think of individual groups—insects, spiders, and centipedes, or birds, mammals, and reptiles, as well as their long extinct fossil relatives—not so much in terms of their uniqueness, but as variations on a common theme," Carroll writes. And surprising, too, is the evidence that all animals, from worms to humans, probably descend from one or a few primitive bacteria. Darwin would have been pleased to discover molecular evidence for his "common descent."


A powerful new theory adds considerable weight to this view, putting Carroll's work in a larger perspective. In The Plausibility of Life, Marc W. Kirschner and John C. Gerhart take a broader view than Carroll's on the questions of development and evolutionary biology. They agree that Hox genes make an important contribution to the mechanisms of evolution, but they argue that there are a number of other fundamental properties of organisms that give direction to evolution. The weakness of Darwinian theory—and one that has been seized upon by secular critics of evolutionary theory—is its failure to explain how the gene determines the observable traits of the organism. From an evolutionary point of view, how can complex organs such as eyes, arms, or wings evolve over long periods of time? What about the intermediary forms?

The Darwinian view was that early evolutionary forms of arms, legs, or wings might have initially served other purposes (insect legs, for example, might have evolved from gills their ancestors used for respiration). Such transformations of purpose are certainly important in evolution, Kirschner and Gerhart argue, but there must be other mechanisms at work as well. Concerning the human eye, for example: How is it possible for the different parts of an eye to evolve simultaneously—the lens, the iris, the retina, along with the blood vessels necessary for supplying the eye with oxygen and nutrition as well as the nerves that must receive signals from the retina and send signals to the muscles of the eye? Could these precise nerve and vascular networks be created by gradual random changes in genes over long periods of time, as Darwin claimed? Similarly, how can random mutations and natural selection create not only the necessary muscles and bone that make up the arm, for example, but organize the blood supply and nerves so that, after hundreds of thousands of years, an animal evolves with functioning arms, legs, and eyes? The Darwinian view that developing organs can serve different purposes at different times seems incomplete at best.

Darwin thought that at any given time variations in the forms of organisms were purely random. This is true of the neo-Darwinian view as well. However, recent research has shown that even though mutations are random, the effects of a mutation will be restricted, and may alter only one part or trait of an organism. A good example of the restricted effects of mutation is provided, as Kirschner and Gerhart point out, by the body plans created by Hox genes. Because they are contained within the different compartments of the embryo established by the body plan, individual parts of an animal can evolve independently of each other. For example, the lizard has limbs, the python has vestigial limbs, and the advanced snake has no limbs at all. These variations in limb structure have evolved without major changes in other parts of the body plan.

This independence means that mutations can occur within a single region of an embryo that may or may not be beneficial; in any case, fewer of the mutations will be lethal for the developing organism. In other words, while evolution is constrained by the body plan created by the Hox genes, this constraint gives nature a much greater freedom to experiment with variant forms through random mutations. If there were no body plans with separate parts, most variations would be lethal to the entire organism and evolution would be much, much slower. Suppose we wanted to design new windows for airplanes that would improve the visibility for passengers, resist cabin pressure, and better insulate passengers from the cold. We would test the new window designs without changing their positions on the body of the plane. If we had to redesign the entire plane every time we changed the window design, we would be much slower in developing new and more efficient planes. Similarly, Hox genes can, through mutations, shift the pattern of organization within a part of the embryo, allowing evolution to experiment with new forms, such as wings and longer necks, without affecting other parts of the embryo.

Kirschner and Gerhart thus place the activity of Hox genes inside the embryo in a broader perspective. They agree that Hox genes are important in organizing the embryo into discrete parts, a process they call the invisible anatomy (it is only visible with the aid of recent technology). But they argue that the function of Hox genes is only one of a number of "core processes" that act as constraints on evolution. The storage of genetic information in DNA and the mechanisms for translating that information in the synthesis of proteins are examples of core processes. Other kinds of core processes that are used by cells include biochemical mechanisms, such as the digestion of nutrients by enzymes. These mechanisms were established at an early stage in evolution and are still used in human cells, worms, and bacteria. Because of these core processes, natural selection is presented with a variety of forms that are more likely to succeed than if there were no constraints on variation at all. Should a new advantageous process arise by mutation, it can be incorporated into the functional repertory of the organism, and it is then inherited over generations.

Another kind of core process that can, by constraining development, create forms that are more likely to succeed is what Kirschner and Gerhart call "exploratory behavior," such as the method used by ants when foraging for food. Ants leave their nest and take random paths. As they move about they secrete a chemical substance called a pheromone that leaves a scent along the path they are following. If an ant fails to find food it will eventually return to the nest, using the pheromones it has deposited to guide it back to the nest. However, an ant that finds food will deposit more pheromones as it returns to the nest. This will reinforce the scent of the trail that led to food and other ants will now follow the reinforced trail.

Nonetheless, not all the ants will follow the successful trail. Some ants will set out on random paths in search of other sources of food and if successful they, too, will establish paths for subsequent ants. Eventually, the ants will have established a detailed map of paths to food sources. An observer might think that the ants are using a map supplied by an intelligent designer of food distribution. However, what appears to be a carefully laid out mapping of pathways to food supplies is really just a consequence of a series of random searches.

Other exploratory processes are important for the development of the vascular and nervous systems in a growing embryo. While the details of the individual processes vary considerably, the guiding principles are similar to those of ant foraging: just as the ants randomly explore the terrain around their nest, capillary vessels sprout off from the larger blood vessels and randomly explore the surrounding tissues for the signals coming from cells deprived of oxygen; they then can bring blood containing oxygen to the cells. And just as contact with food makes the ant reinforce the path that led to the food, the sprouting capillary vessels establish permanent contacts whenever they encounter tissue with oxygen-deprived cells. Similarly, fine nerve endings extend themselves randomly, establishing stable connections between nerves and muscles whenever they receive electrical and chemical signals coming from muscles.

Hence, unlike the eye or hand, whose forms follow from the body plan that is programmed by Hox genes in the developing embryo, the apparently well-designed and integrated nervous and vascular systems that serve such organs do not require predetermined paths and wirings. Darwin's view that small simultaneous changes would give rise to organs as complex as the eye is in principle true, but in need of modification. It is the very constraints created by the Hox genes and the other core processes (e.g., the exploratory behavior of capillaries and nerve endings) that permit complex designs to emerge over a relatively short period of time from a biological point of view (hundreds of thousands of years, or perhaps even less). As Carroll and Kirschner and Gerhart observe, some alteration of genes is still necessary if the changes are to be passed on from one generation to another. But the genetic alterations are considerably simpler and fewer in number than had been formerly imagined.

While Carroll argues—a claim that is at the heart of Evo Devo—that embryological development gives us the deepest clues to the mechanisms of evolution, Kirschner and Gerhart move beyond embryology to show that metabolic and physiological processes are also critical to evolutionary change. Their approach, which they call the theory of "facilitated variation," attempts to show how the regulation of genes inside the embryo, as described by Carroll, is part of a larger set of processes that allow organisms to experiment with evolution in a tightly controlled way. According to this theory, the mutations, or variations, needed to drive evolutionary change can occur with little disruption either to the basic organization of an organism or to the core processes that make its cells function.

We now have a far deeper understanding of evolution than even a decade ago.[4] And although our knowledge is still incomplete, our new understanding, as the books under review admirably show, has opened the way toward a comprehensive account of evolution and has supplied solid answers to the critics of evolutionary theory.


[1] For their critical readings and comments on this article, we would like to thank David
Botstein, Nathaniel Heintz, Luisa Hirschbein, David Ish- Horowicz, and Richard
Lewontin, none of whom should be held accountable for this text, for which we take full responsibility.

[2] No one group found all of the Hox genes. Lewis started his work in the late 1950s, earlier than Nüsslein-Vollhard and
Wieschaus, but much of the work of the two groups was contemporaneous. Both groups realized that development was under genetic control. Although Lewis focused on specific Hox genes, Nüsslein-Vollhard and Wieschaus saw the importance of identifying all of the genes that controlled the body plan, and they identified most of them.

[3] Hox proteins behave in this way because of a particular genetic feature of the Hox genes that produce them. Within their genetic composition, all eight Hox genes possess a nearly identical section of DNA, called a
homeobox. When Hox genes produce Hox proteins, the homeobox region of the Hox genes carries the genetic information to produce a specific part of these proteins called the
homeodomain. Once the protein is assembled, its homeodomain attaches to DNA sites that control genes, allowing it to function as a switch.

It is this particular characteristic that gave the Hox genes their name. In homage to Bateson, the identical sections of DNA were called "homeoboxes," since they were present in genes that, when mutated, resulted in Bateson's monsters, or "homeotic" mutants. The term "Hox gene" is a whimsical combination of "homeotic" and "homeobox."

[4] While classical genetics relies on changes in the order of the bases in the DNA strands, other heritable changes have been discovered—changes in the chemical makeup of the bases that control gene activities, for example—and are increasingly recognized as important in development and evolution. For example, the base cytosine might undergo a chemical modification involving the addition of a single carbon atom.

The New York Review of Books:
Volume 53, Number 8 · May 11, 2006

Copyright © 1963-2006 NYREV, Inc. All rights reserved. Nothing in this publication may be reproduced without the permission of the publisher. Illustrations copyright © David Levine unless otherwise noted; unauthorized use is strictly prohibited. Please contact with any questions about this site. The cover date of the next issue of The New York Review of Books will be June 8, 2006.

Saturday, February 04, 2006

Has Science Discovered God?

Famous Atheist Now Believes in God

One of World's Leading Atheists Now Believes in God, Based on Scientific Evidence

A British philosophy professor who has been a leading champion of atheism for more than a half-century has changed his mind. He now believes in God more or less based on scientific evidence, and says so on a video released Thursday.

At age 81, after decades of insisting belief is a mistake, Antony Flew has concluded that some sort of intelligence or first cause must have created the universe. A super-intelligence is the only good explanation for the origin of life and the complexity of nature, Flew said in a telephone interview from England.

Flew said he's best labeled a deist like Thomas Jefferson, whose God was not actively involved in people's lives.

"I'm thinking of a God very different from the God of the Christian and far and away from the God of Islam, because both are depicted as omnipotent Oriental despots, cosmic Saddam Husseins," he said. "It could be a person in the sense of a being that has intelligence and a purpose, I suppose."

Flew first made his mark with the 1950 article "Theology and Falsification," based on a paper for the Socratic Club, a weekly Oxford religious forum led by writer and Christian thinker C.S. Lewis.

Over the years, Flew proclaimed the lack of evidence for God while teaching at Oxford, Aberdeen, Keele, and Reading universities in Britain, in visits to numerous U.S. and Canadian campuses and in books, articles, lectures and debates.

There was no one moment of change but a gradual conclusion over recent months for Flew, a spry man who still does not believe in an afterlife.

Yet biologists' investigation of DNA "has shown, by the almost unbelievable complexity of the arrangements which are needed to produce (life), that intelligence must have been involved," Flew says in the new video, "
Has Science Discovered God?"

The video draws from a New York discussion last May organized by author Roy Abraham Varghese's Institute for Metascientific Research in Garland, Texas. Participants were Flew; Varghese; Israeli physicist Gerald Schroeder, an Orthodox Jew; and Roman Catholic philosopher John Haldane of Scotland's University of St. Andrews.

The first hint of Flew's turn was a letter to the August-September issue of Britain's Philosophy Now magazine. "It has become inordinately difficult even to begin to think about constructing a naturalistic theory of the evolution of that first reproducing organism," he wrote.
The letter commended arguments in Schroeder's "The Hidden Face of God" and "The Wonder of the World" by Varghese, an Eastern Rite Catholic layman.

This week, Flew finished writing the first formal account of his new outlook for the introduction to a new edition of his "God and Philosophy," scheduled for release next year by Prometheus Press.

Prometheus specializes in skeptical thought, but if his belief upsets people, well "that's too bad," Flew said. "My whole life has been guided by the principle of Plato's Socrates: Follow the evidence, wherever it leads."

Last week, Richard Carrier, a writer and Columbia University graduate student, posted new material based on correspondence with Flew on the atheistic Web page. Carrier assured atheists that Flew accepts only a "minimal God" and believes in no afterlife.

Flew's "name and stature are big. Whenever you hear people talk about atheists, Flew always comes up," Carrier said. Still, when it comes to Flew's reversal, "apart from curiosity, I don't think it's like a big deal."

Flew told The Associated Press his current ideas have some similarity with American "intelligent design" theorists, who see evidence for a guiding force in the construction of the universe. He accepts Darwinian evolution but doubts it can explain the ultimate origins of life.

A Methodist minister's son, Flew became an atheist at 15.

Early in his career, he argued that no conceivable events could constitute proof against God for believers, so skeptics were right to wonder whether the concept of God meant anything at all.

Another landmark was his 1984 "The Presumption of Atheism," playing off the presumption of innocence in criminal law. Flew said the debate over God must begin by presuming atheism, putting the burden of proof on those arguing that God exists.

Copyright 2005 The Associated Press. All rights reserved. This material may not be published, broadcast, rewritten, or redistributed.

NEW YORK Dec 9, 2004


Tuesday, January 10, 2006

The Fine Tuning of the Universe

An amazing array of scientists are bewildered by the design of the universe and admit a possibility of a designer.

According to growing numbers of scientists, the laws and constants of nature are so "finely-tuned," and so many "coincidences" have occurred to allow for the possibility of life, the universe must have come into existence through intentional planning and intelligence.

In fact, this "fine-tuning" is so pronounced, and the "coincidences" are so numerous, many scientists have come to espouse The Anthropic Principle, which contends that the universe was brought into existence intentionally for the sake of producing mankind.

Even those who do not accept The Anthropic Principle admit to the "fine-tuning" and conclude that the universe is "too contrived" to be a chance event.

In a BBC science documentary, "The Anthropic Principle," some of the greatest scientific minds of our day describe the recent findings which compel this conclusion.

Dr. Dennis Scania, the distinguished head of Cambridge University Observatories:

If you change a little bit the laws of nature, or you change a little bit the constants of nature -- like the charge on the electron -- then the way the universe develops is so changed, it is very likely that intelligent life would not have been able to develop.

Dr. David D. Deutsch, Institute of Mathematics, Oxford University:

If we nudge one of these constants just a few percent in one direction, stars burn out within a million years of their formation, and there is no time for evolution. If we nudge it a few percent in the other direction, then no elements heavier than helium form. No carbon, no life. Not even any chemistry. No complexity at all.

Dr. Paul Davies, noted author and professor of theoretical physics at Adelaide University:

"The really amazing thing is not that life on Earth is balanced on a knife-edge, but that the entire universe is balanced on a knife-edge, and would be total chaos if any of the natural 'constants' were off even slightly. You see," Davies adds, "even if you dismiss man as a chance happening, the fact remains that the universe seems unreasonably suited to the existence of life -- almost contrived -- you might say a 'put-up job'."

According to the latest scientific thinking, the matter of the universe originated in a huge explosion of energy called "The Big Bang." At first, the universe was only hydrogen and helium, which congealed into stars. Subsequently, all the other elements were manufactured inside the stars. The four most abundant elements in the universe are: hydrogen, helium, oxygen and carbon.

When Sir Fred Hoyle was researching how carbon came to be, in the "blast-furnaces" of the stars, his calculations indicated that it is very difficult to explain how the stars generated the necessary quantity of carbon upon which life on earth depends. Hoyle found that there were numerous "fortunate" one-time occurrences which seemed to indicate that purposeful "adjustments" had been made in the laws of physics and chemistry in order to produce the necessary carbon.

Hoyle sums up his findings as follows:

A common sense interpretation of the facts suggests that a superintendent has monkeyed with the physics, as well as chemistry and biology, and that there are no blind forces worth speaking about in nature. I do not believe that any physicist who examined the evidence could fail to draw the inference that the laws of nuclear physics have been deliberately designed with regard to the consequences they produce within stars.

Adds Dr. David D. Deutch:

If anyone claims not to be surprised by the special features that the universe has, he is hiding his head in the sand. These special features ARE surprising and unlikely.


Besides the BBC video, the scientific establishment's most prestigious journals, and its most famous physicists and cosmologists, have all gone on record as recognizing the objective truth of the fine-tuning.

The August '97 issue of "Science" (the most prestigious peer-reviewed scientific journal in the United States) featured an article entitled "Science and God: A Warming Trend?" Here is an excerpt:

The fact that the universe exhibits many features that foster organic life -- such as precisely those physical constants that result in planets and long-lived stars -- also has led some scientists to speculate that some divine influence may be present.

In his best-selling book, "A Brief History of Time", Stephen Hawking (perhaps the world's most famous cosmologist) refers to the phenomenon as "remarkable."

"The remarkable fact is that the values of these numbers (i.e. the constants of physics) seem to have been very finely adjusted to make possible the development of life". "For example," Hawking writes, "if the electric charge of the electron had been only slightly different, stars would have been unable to burn hydrogen and helium, or else they would not have exploded. It seems clear that there are relatively few ranges of values for the numbers (for the constants) that would allow for development of any form of intelligent life. Most sets of values would give rise to universes that, although they might be very beautiful, would contain no one able to wonder at that beauty."

Hawking then goes on to say that he can appreciate taking this as possible evidence of "a divine purpose in Creation and the choice of the laws of science (by God)" (ibid. p. 125). Dr. Gerald Schroeder, author of "Genesis and the Big Bang" and "The Science of Life" was formerly with the M.I.T. physics department. He adds the following examples:

1) Professor Steven Weinberg, a Nobel laureate in high energy physics (a field of science that deals with the very early universe), writing in the journal "Scientific American", reflects on

how surprising it is that the laws of nature and the initial conditions of the universe should allow for the existence of beings who could observe it. Life as we know it would be impossible if any one of several physical quantities had slightly different values.

Although Weinberg is a self-described agnostic, he cannot but be astounded by the extent of the fine-tuning. He goes on to describe how a beryllium isotope having the minuscule half life of 0.0000000000000001 seconds must find and absorb a helium nucleus in that split of time before decaying. This occurs only because of a totally unexpected, exquisitely precise, energy match between the two nuclei. If this did not occur there would be none of the heavier elements. No carbon, no nitrogen, no life. Our universe would be composed of hydrogen and helium. But this is not the end of Professor Weinberg's wonder at our well-tuned universe. He continues:

One constant does seem to require an incredible fine-tuning -- The existence of life of any kind seems to require a cancellation between different contributions to the vacuum energy, accurate to about 120 decimal places.

This means that if the energies of the Big Bang were, in arbitrary units, not:

000000000000000000000000000000000000000000000000000 000000000000000000,

but instead:

000000000000000000000000000000000000000000000000000 000000000000000001,

there would be no life of any sort in the entire universe because as Weinberg states:

the universe either would go through a complete cycle of expansion and contraction before life could arise, or would expand so rapidly that no galaxies or stars could form.

2) Michael Turner, the widely quoted astrophysicist at the University of Chicago and Fermilab, describes the fine-tuning of the universe with a simile:

The precision is as if one could throw a dart across the entire universe and hit a bulls eye one millimeter in diameter on the other side.

3) Roger Penrose, the Rouse Ball Professor of Mathematics at the University of Oxford, discovers that the likelihood of the universe having usable energy (low entropy) at the creation is even more astounding,

namely, an accuracy of one part out of ten to the power of ten to the power of 123. This is an extraordinary figure. One could not possibly even write the number down in full, in our ordinary denary (power of ten) notation: it would be one followed by ten to the power of 123 successive zeros! (That is a million billion billion billion billion billion billion billion billion billion billion billion billion billion zeros.)

Penrose continues,

Even if we were to write a zero on each separate proton and on each separate neutron in the entire universe -- and we could throw in all the other particles as well for good measure -- we should fall far short of writing down the figure needed. The precision needed to set the universe on its course is to be in no way inferior to all that extraordinary precision that we have already become accustomed to in the superb dynamical equations (Newton's, Maxwell's, Einstein's) which govern the behavior of things from moment to moment.

Cosmologists debate whether the space-time continuum is finite or infinite, bounded or unbounded. In all scenarios, the fine-tuning remains the same.

It is appropriate to complete this section on "fine tuning" with the eloquent words of Professor John Wheeler:

To my mind, there must be at the bottom of it all, not an utterly simple equation, but an utterly simple IDEA. And to me that idea, when we finally discover it, will be so compelling, and so inevitable, so beautiful, we will all say to each other, "How could it have ever been otherwise?"

See the full presentation of this and other themes on the 2001 Principle Website.
See more science quotes.

by Mordechai Steinman with Dr. Gerald Schroeder

Friday, December 09, 2005

Evolution: Rationality vs. Randomness

At the basis of the theory of neo-Darwinian evolution lie two basic assumptions: that changes in morphologies are induced by random mutations on the genome, and that these changes in the morphology of plant or animal make the life form either more or less successful in the competition to survive. With nature doing the selection, evolutionists claim to remove the theory of evolution from that of a random process. We are told that the selection is in no way random. It is a function of the environment. The randomness, however, remains as the basic driving force that produces the varied mutations from among which the selection by survival takes place.

The question is: Can random mutations produce the evolution of life?

Because evolution is primarily a study of the history of life, statistical analyses of evolution are plagued by having to assume the many conditions that were extant during those long gone eras. Rates of mutations, the contents of the "original DNA," and environmental conditions -- all these affect the rate and direction of the changes in morphology. And these are all unknowns.

From a secular view, one must never ask what the likelihood is that a specific set of mutations will occur to produce a specific animal. This would imply a direction to evolution, and basic to all Darwinian theories of evolution is the assumption that evolution has no direction. The induced changes, and hence the new morphologies, are totally random. The challenges presented by the environment determine which will survive to produce the new generations and which will perish.


With this background, let's look at the process of evolution. Life is in essence a symbiotic combination of proteins (and other structures, but here I'll discuss only the proteins). The history of life teaches us that not all combinations of proteins are viable. At an event recorded in the fossil record and known as the Cambrian explosion of animal life, some 50 phyla (basic body plans) suddenly and simultaneously appeared in the fossil record. This is the first appearance of complex animal life. Only 30 to 34 of the phyla survived. The rest perished. Since then the fossil record and modern existing biota reveal that no new phyla have evolved. At a later stage in the flow of life, a catastrophic event (possibly the collision of the earth with a massive comet or meteor) eliminated 90% of all life forms. The ecology was wide open for new phyla to develop. Again, no new phyla appear. The implication is that only a limited number of life forms (phyla) are viable.

It is no wonder that the most widely read science journal, Scientific American, asked "has the mechanism of evolution altered in ways that prevent fundamental changes in body plans of animals" (November 1992). It is not that the mechanism of evolution has changed; it is our understanding of how evolution functions that must change to fit the data presented by the fossil record and by the discoveries of molecular biology.

It is difficult and painful to discard entrenched notions of what is actually true, even when scientific data demand such an abandonment. Pure randomness as the source of the mutations that neo-Darwinian concepts demand to drive the evolution of life no longer stands against the mounting evidence of scientific data. Unfortunately, the emotional commitment to a totally materialist view of life makes discarding this notion problematic.

Let's look at the likelihood that random mutations could have produced viable forms of life. Life as we know it is built largely of combinations of proteins working in symbiotic harmony. But as we've seen, only certain combinations produce viable life. Other combinations fail.

Humans and all mammals have some 50,000 genes. That implies, as an order of magnitude estimate, some 50,000 to 100,000 proteins active in mammalian bodies. It is estimated that there are some 30 animal phyla on Earth. If the genomes of each animal phylum produced 100,000 proteins, and no proteins were common among any of the phyla (a fact we know to be false, but an assumption that makes our calculations favor the random evolutionary assumption), there would be (30 x 100,000) 3 million proteins in all life. (The actual number is vastly lower.)

Now let's consider the likelihood of these 3 million viable combinations of proteins forming by chance, recalling that the events following the Cambrian explosion of animal life and the later decimation of 90% of life taught us that only certain combinations of proteins are viable.

Proteins are complex coils of several hundred amino acids. Take a typical protein to be a chain of 200 amino acids. The observed range is from less than 100 amino acids per protein to greater than 1000. There are 20 commonly occurring amino acids that join in varying combinations to produce the proteins of life. This means that the number of possible combinations of the amino acids in our model protein of 200 amino acids is 20 to the power of 200 (i.e. 20 multiplied by itself 200 times), or in the more usual 10-based system of numbers, approximately 10 to the power of 260 (i.e. the number one, followed by 260 zeros!). Nature has the option of choosing among the 10 to power of 260 possible proteins, the 3 million proteins of which all viable life is composed. In other words, for each one correct choice, there are 10 to power of 254 wrong choices!

Simon Conway Morris, professor of evolutionary paleontology at the University of Cambridge and fellow of the Royal Society of England, is the scientist who revealed the significance of the Cambrian explosion of animal life. He refers to this vast biological waste land of failed life forms as the "multidimensional hyperspace of biological reality."

Can this have happened by random mutations of the genome? Not if our understanding of statistics is correct. It would be as if nature reached into a grab bag containing a billion billion billion billion billion billion billion billion billion billion billion billion billion billion billion billion billion billion billion billion billion billion billion billion billion billion billion billion non-viable proteins -- and pulled out the one that worked.

And then repeated this trick a million times.

With odds like that, it is amazing that nature and our bodies ever got it or get it right.

But perhaps not every amino acid can join with every other amino acid. If this is the case, then the number of possible combinations will be reduced. To get even hint for what this would do to the hyperspace of failed choices, I looked at combinations of amino acids that actually exist in just six proteins. Among the proteins I used were bovine insulin and bovine ribonuclease. The number of potential amino acid combinations just from this modest sampling of proteins was 10 to the power of 20. Again, nature would have had to select the one viable combination from among 100 billion billion wrong choices. Either our knowledge of statistical probability is skewed or something other than randomness is operating.

The late Harvard professor, Stephen Jay Gould, suggested that the flow of life is "channeled" along these basic animal phyla.

Nobel laureate, organic chemist and a leader in origin of life studies, Professor deDuve writes in his excellent book, Tour of a Living Cell, "If you equate the probability of the birth of a bacteria cell to chance assembly of its atoms, eternity will not suffice to produce one... Faced with the enormous sum of lucky draws behind the success of the evolutionary game, one may legitimately wonder to what extent this success is actually written into the fabric of the universe." Life written into the fabric of the universe sounds a bit metaphysical.

Morris, in his book Life's Solutions (Cambridge University Press, 2003), writes: "Life is simply too complex to be assembled on any believable time scale... evolution's uncanny ability to find the short cuts across the multidimensional hyperspace of biological reality. It is my suspicion that research might reveal a deeper fabric to biology..." Elsewhere Morris identifies this "deeper fabric" as having "metaphysical implications."

This impossibility of randomness producing order is not different from the attempt to produce Shakespeare or any meaningful string of letters more than a few words in length by a random letter generator. Gibberish is always the result. This is simply because the number of meaningless letter combinations vastly exceeds the number of meaningful combinations.

With life, such gibberish was and is lethal.

In brief, randomness cannot have been the driving force behind the success of life. Our understanding of statistics and molecular biology clearly supports the notion that there must have been a direction and a Director behind the success of life.

Dr. Gerald Schroeder

Monday, November 28, 2005



Science and God. Most people think the two have nothing to do with each other. Others even believe science has shown there is no God. So it comes as a shock for us to learn that pioneers and giants of modern science from Einstein to Planck to Heisenberg thought otherwise.
In the view of many of these scientists, the Mind of God was the source and ground of the cosmos. In their view, the intelligence of the universe – its laws – points to an Intelligence that has no limitation, “a superior mind” as Einstein put it. This was for them the summit of scientific discovery. In other words, of all the greatest discoveries of modern science, the greatest is God!

Modern science has shown that the Universe with its laws and fields shows a magnificent progression in degrees and kinds of intelligence. From the forces and particles of the subatomic realm that operate within a framework of precise symmetries to the inexhaustibly resourceful DNA that builds the living world, we live in a “smart” Universe. “Universe” is in fact simply our name for a network of intelligent systems operating through processes, structures and laws. At the heart of intelligence is the ability to create, process and synthesize information. The billions of galaxies that behave in accordance with the laws of cosmology and particle physics are driven by the information contained in the fields that constitute them. Living systems are independent agents that can maintain and replicate themselves and act in the world and “learn” from it.

One self-evident mark of intelligence is the very existence of the laws of nature. This mystery baffles the most skeptical scientist as much as it does anyone else. From atoms and cells to galaxies and ecosystems, we see intricately ordered activities and operations manifesting carefully defined laws; the laws that affect a quark affect a galaxy.

Every scientific discovery is a discovery of underlying intelligence and deepening mystery.

Take energy. We know that there is an electromagnetic force that holds our bodies together, a gravitational force that holds us to the earth, and a nuclear force that keeps atoms together.
We know that at every instant of our lives we’re surrounded by photons speeding by us at over 186,000 miles per second. We know that different forms of energy are converted into each other given a conversion mechanism. We know thanks to Einstein that mass is condensed energy.
But for all this, we have no idea how energy fields originated. Britain’s best-known astronomer Martin Rees acknowledges that it is basically mysterious how empty space could have energy associated with it. We do not know what is the primal nature and source of energy or the origin of the primal field.

Consider next the phenomenon of protein folding. All proteins in living beings are made from different sequences of just twenty organic molecules called amino acids. Proteins have the extraordinary ability to assemble themselves without external intervention. This self-assembly is a process called protein-folding. Every cell in the body (other than sex and blood cells) makes two thousand proteins every second from hundreds of amino acids. This process is so complex, says Scientific American, that a supercomputer, programmed with the rules for protein folding, would take 10127years to generate the final folded form of a protein with just 100 amino acids. But what takes a supercomputer trillions of years, takes seconds for real proteins.

Or take something as simple as our senses! In seeing, hearing, smelling, tasting and touching, a mechanical stimulus is transformed into a nerve signal that is sent to the brain and then converted into a conscious state. Despite decades of scientific study spent in understanding the network of proteins, ions, signals and cellular structures involved, the bridge between these two worlds, the external stimulus and the corresponding sense-perception, remains as much a mystery today as ever. On the one hand, we have an efficient chain of precise physical processes that monitor, transmit and respond to an immense variety of sensory inputs. On the other, we have a mysterious and radical conversion: the merely physical becomes something of which we are conscious, something in which we “participate”.

Now the all-pervasive intelligence of the Universe raises an obvious question: how did it come to be? This origin question divides into three: the origins of the universe, life and mind.

That there is intelligence around us here and now nobody denies. The genetic code, the periodic table, relativity and quantum physics, photosynthesis and myriad other laws and phenomena are works of genius without which the world of our experience could not exist. In other words, intelligence is a hard fact of scientific discovery.

Disagreement and polemic begin when we try to pinpoint the source and history of the intelligence of the universe. There are three popular views. According to the first view, what we conceive to be “intelligent” is simply the end-result of random processes operating on a purely material matrix over huge periods of time. At the end of the day, it all comes down to physics: material interactions and the tools that study these interactions. The second view is that an intelligent Creator brought the universe into being six thousand years ago (or several billion years ago) and the various life-forms in the world are direct results of the Creator’s interventions. Here faith is the starting-point and the physical data are shown as evidence for the truth-claims of faith. The third view is that the world as we know it is purely the result of random processes but that there is a Creator of the universe who nonetheless does not intervene in its physical history. Here the natural sciences are taken on their own terms and faith is kept entirely out of the physical realm.

Evolutionary theorists see God’s role, if any, as belonging to faith and religion. Creationists claim that divine acts of creation are a legitimate part of science. These polarizing views have spilled over into polemics over education, law and politics. Here we present a new paradigm that moves beyond polemics by changing the frameworks and categories of discussion. In short, instead of the natural sciences and religious faith, those who explore origin questions must consider a third dimension, that of ontology. When we deal with physical realities, we turn to empirical science. When we deal with ontological facts, we apply ontological methods. And when we step outside the physical and the ontological, we face the choice of faith.

The origin questions are neither scientific nor religious but ontological. Ontology concerns those essential and ultimate principles that underlie science but cannot be proved by science. Science can give us the history and structure of all that is physical. But it cannot tell us why and how the physical exists. Science operates with measurable and quantitative data. But the origins of something from absolute nothingness, of the laws of nature, of life with its inherent intelligence and of the transphysical human mind are questions that lie beyond the quantitative.

The application to the present situation is transparent. Just as there is a distinction between hardware and the instruction-sets that run hardware, namely software, so there is a distinction between matter and the various laws that organize matter. To understand the nature, source and effects of these laws is to engage in ontology. To explore the ultimate origin of the universe and life, we have to migrate from cosmology and biology to ontology. Neither test-tubes nor equations can tell us why there are laws of nature or why something exists instead of nothingness or what it means to be an intelligent agent (that is, a life-form). For this we must turn to ontological analysis. Our ontological studies tell us that the laws of nature are embodied intelligence and such intelligence can only originate from an ultimate and infinite Intelligence. Likewise, the hierarchy of intelligence in the universe can only be explained by the constant action of this infinite Intelligence.

How does this relate to the evolution-creation debate? It changes the playing field. We accept all the empirical data furnished by the physicists and cosmologists, the chemists and biologists. We then consider the data at an ontological level. The history of life on planet Earth shows a progression from primitive yet always intelligent life-forms to homo sapiens. Certainly we accept the role at a certain level of natural selection and random mutations in this progression. But at the end of the day, the existence of intelligent agents ranging from the primitive bacteria to plants to animals, the mysterious reality of their powers of replication, the marvels of consciousness and conceptual thought are new realities that cannot emerge from a purely material matrix. These can only come to be from an infinite independently existing Intelligence. Likewise the laws of nature with their mathematical precision can have no other source but an Intelligence that has no limitation, “a superior mind” as Einstein put it. And this is an ontological discovery.

Our starting-point, obviously, is the origin of the universe. As most people know, Big Bang cosmologies have made previous theories of an eternally existing universe less plausible. Our starting-point, obviously, is the origin of the universe. As most people know, Big Bang cosmologies have made previous theories of an eternally existing universe less plausible.
Forty years ago a claim that science and religion are moving closer to each other would hardly have been made let alone entertained. But the consolidation of the Big Bang theory set in motion an entirely new way of viewing the world, one in which there was a beginning of time and perhaps a beginning of the cosmos itself. “When the intellectual history of the 20th century is written,” says a Bell Labs paper, “a few achievements will tower over all. Einstein’s theory of general relativity will be one; the laws of quantum mechanics will be another. The so-called Big Bang Theory of the origin of the universe will be the third. The discovery in 1963 by Arno Penzias and Robert Wilson of the Cosmic Microwave background of the Big Bang set the seal of approval on the theory, and brought cosmology to the forefront as a scientific discipline. It was proof that the universe was born at a definite moment, some 15 billion years ago.” The implications of this discovery and related ideas like the Anthropic Principle were monumental. In a famous passage in his best-selling God and the Astronomers, the astrophysicist Robert Jastrow, himself an agnostic, noted that when the scientist who lived with faith in the power of reason scales the mountain of ignorance and clambers over the final rock "he is greeted by a band of theologians who have been sitting there for centuries." Nevertheless, any review of modern cosmological theories should be accompanied by reflection on the ontological origin question.

The origin of life is clearly the most controversial of the origin questions. Most scientists assume that life is purely physico-chemical in nature and so its origin is a result of prebiotic evolution. But this assumption ignores the ontological dimension. Consequently no attempt to replicate the origin of life in the lab has worked. And every breakthrough in the life sciences simply demonstrates the inherent ingenuity of life.

On an ontological level, life involves three things: (1) intelligent message processing; (2) autonomous agents that independently replenish and replicate themselves, a dramatically new phenomenon in the history of the universe; and (3) diversity that extends from cyanobacteria to dinosaurs.

At a fundamental biological level, life revolves around cells, proteins and the nucleic acids DNA and RNA. Each cell contains 1012 bits of information, and any one cell has the information coded within it to build a copy of the organism’s whole body. DNA is a data repository of genetic information that transmits hereditary characteristics to future generations. The interaction of DNA, RNA and proteins can only be described as the processing of intelligent messages using chemical codes. Chemical laws may explain the bases, sugars and phosphates of DNA, but not its information content or the intelligence driving it.

Secondly, each and every living being acts or is capable of action and so it can rightly be called an agent. Beyond the sum of its physics and chemistry is the “center” of all its action, the moving force, the seat of power that makes it an agent. And since these agents are capable of surviving independently, they are therefore autonomous agents. Moreover, every such agent is intelligent because all its activities depend on the intelligence of DNA.

Finally, there are many kinds of intelligent agents and it is evident that they form a hierarchy, from unicellular organisms to plants with their molecular signaling systems to animals with their own hierarchy to the human person.

When we think of the origin of life, we are really talking of the origin of living beings since there’s no abstract thing called life. A living being, be it a fern or a hippopotamus, is an autonomous agent that processes information, generates energy and reproduces using the incredibly intelligent symbol-processing system we call DNA. Such a being is not simply a configuration of matter or a life principle. It is a new kind of reality, the reality of being an agent and functioning as an intelligent system. And such a reality can only come to be if it comes from a source that is not just intelligent but also an agent.

Allied to the question of the origin of life is the origin of reproduction. Neo-Darwinists like to say that there is no purpose in nature. But neo-Darwinists themselves have to assume capabilities of self-reproduction at the earliest stages of life. Yet reproduction is an irreducibly purpose-driven act, one which can’t simply spring from matter. How is it that the first living beings had the powers of replication? How is it that life came with this fundamentally purposive capability pre-installed? John Maddox, the former editor of Nature, admits that we don’t know how sexual reproduction itself evolved despite decades of speculation. The vast variety of replicational capabilities found in material structures point again to the intelligence in nature.

Human origins are our next topic. Most discussion in this area centers on excavations in Africa and DNA similarities between chimpanzees, humans and assorted other creatures. As the ontologist sees it, this is yet another wrong turn. The relevant data are closer to home.

The greatest superstition of the last 200 years is the widespread idea that the conscious thinking experienced by all human beings at every waking moment was produced entirely from and by mindless matter and is in fact reducible purely and simply to matter. We have lost our minds in more senses than one!

We are conscious and aware of being conscious and, in addition, we are just as clearly conscious that our consciousness is dramatically different from anything material or physical. We know that thoughts and feelings do not have physical properties such as size or shape. We know that our mental activities are accompanied by physical processes and also that we cannot see a thought if we open up the brain. Consciousness, as we experience it, is irreducibly trans-physical although it interacts constantly with the physical. Most important of all, it is thoughts that drive the corresponding neural transactions and not the other way around. There is no chicken or egg question here. The thought comes first and, as a result, causes certain brain events.

Another hard fact of experience is conceptual thought. The most obvious everyday instance of conceptual thought is language. Syntactical language is unique to human beings – found even in ancient civilizations and instinctively mastered by children at a very young age. Language is built around the ability to understand. There is no organ, no part of the brain that performs “understanding.” Words are symbols or codes signifying something – and the coding and decoding activities required for using language presuppose an entity that can endow and perceive meaning in symbols. Can a material object perceive meaning? By its very nature, the act of comprehending the meaning of something is non-physical. And it’s something we do all the time. Richard Dawkins points out that (a) nobody knows how language began since there’s no syntax in non-human animals and it’s hard to imagine evolutionary forerunners of it and (b) the origin of semantics, of words and their meanings, is equally obscure.

Then there is the self. What is it that perceives and conceives, feels and thinks, judges and chooses? It is the self, the center of our consciousness, which gives us the identity of being the same person throughout our lives although the physical components of our bodies change constantly. The self is not present in any region of the brain. Nevertheless we cannot seriously deny the existence of the self that is “I”.

Once we become aware of our awareness, mindful of our minds, conscious of our consciousness, we realize that these intrinsically immaterial phenomena could not have arisen from lifeless, purposeless mass-energy given not just a few billion years but an infinite period of time. It’s simply incoherent to suppose that matter, blind, mindless matter, could ever produce consciousness or thinking. Minds can only come from an infinite Mind. Consciousness can only arise from an eternal Consciousness.

The intelligent universe revealed by modern science makes atheism an implausible option on an intellectual level. But atheism is not strictly an intellectual matter. The psychologist Paul Vitz has put many of the most famous atheists on the couch and come to the conclusion that atheism is a neurosis. Vitz contends that the major barriers to belief in God are not rational but neurotic psychological barriers of which the unbeliever may be unaware.

The world revealed by modern science is a world that (a) obeys fundamental mathematical principles, (b) resembles computational systems with their elaborate information processing and mapping of symbols, and (c) confirms our assumption that it is intelligible and rational.

The laws of nature, particularly in relativity and quantum theory, can be understood and structured in the most complex and logical thought-form known to the human mind, that of mathematics. Scientists have been stunned by the one-to-one correspondence between the “programs” of nature and the programs independently discovered and developed by the mind.

How does mind manifest itself? In the case of human beings, our minds enable us to use words. When we see a book we know it is the expression of a mind, and not just ink on paper. Likewise, all the processes in the universe bear the earmarks of mind: the mathematical codes employed everywhere in nature; the immeasurably intricate, precisely structured, comprehensively coherent patterns of interaction between energy fields and galaxies, proteins and nucleic acids; the existence of autonomous agents and purposive behavior; and the reality of conceptual thought. All of these phenomena are manifestations of mind. Scientists now take intelligence as a given, although some try to explain it away with models of self-organizing matter; this, of course, simply postpones the question one step further because we still need an explanation for the system as a whole.

Since symbolic thought and data processing are peculiar to minds as distinct from particles or force fields, it seems reasonable to assume that the laws of nature are manifestations of a sophisticated mind. The mathematician Roger Penrose dismisses the idea that the success of mathematics can be attributed to its survival value, and attributes the accord between mathematics and physics to the underlying rationality of the world. No wonder then that the Nobel-winning quantum physicist Paul Dirac said, “God is a mathematician of a very high order.”

The paradigm of infinite Intelligence expressing itself through a hierarchy of manifestations immediately makes sense of the most diverse phenomena in our experience: rationality, intention, intelligence, beauty, and love.

Roy Abraham Varghese