All posts by admin

Paul Wallace: “Intelligent Design is Dead: A Christian Perspective.”

In the Huff Post Religion section dated 1/2/12, science and religion writer and teacher Paul Wallace makes a very telling set of points about Intelligent Design (ID).  He begins by reviewing a blog by Jason Rosenhouse, who, in a Science Blogs post in November 2011, argued that ID is merely recycling its scientifically weak arguments and is hence dead, while evolutionary science continues to advance.  But Wallace then goes further, and offers “another perspective from which the folly of ID is evident.”  It is his commentary on the Christian astronomer Johannes Kepler that struck me as highly original and worthy of repeating in this post.

Kepler lived in Prague, and in 1604 was working out the elliptical orbit of Mars.  But there suddenly appeared a new star a few degrees north of Scorpius.  He and the world knew nothing of supernovas in those days.  Kepler considered some possibilities, among them an act of God, “a direct and special tinkering by the divine  hand.”  But Kepler eventually discarded that option, writing that “before we come to (special) creation, which puts an end to all discussion, I think we should try everything else.”  In other words, Kepler perceived that to  fill the gap in his knowledge with a supernatural explanation would put an end to scientific inquiry.

Kepler was patient in the face of a huge explanatory gap, an event for which he had no rational explanation.  Apparently, Wallace feels, Kepler’s serenity derived from a faith that God had created a universe that was comprehensible and whose laws were discoverable.  Wallace contrasts Kepler’s attitude with that of Michael Behe’s opinion about the bacterial flagellum.  Behe could not imagine (another explanatory gap) how Life could have piecemeal constructed the flagellum, because, in Behe’s model, the flagellum would not work unless all component parts were present at the same time.  Hence, it must have been specially created.

For Kepler, then: “The universe  has been designed; therefore it must be comprehensible.”

For Behe: “The universe is incomprehensible; therefore it must have been designed.”

Wallace writes that Kepler exemplifies a spirit of humility and great faith, while ID “reduces God to a kind of holy tinkerer.  It locates the divine in places of ignorance and obscurity.  And this gives it a defensive and fearful spirit that is out of place in Christian faith and theology.”  For these reasons, Wallace concludes that ID cannot last.

I have written that tinkering is a major force in Life’s transformations to meet changing circumstances.  How it does so is a major explanatory gap.  Is God the tinkerer?  Is there random shuffling, with natural selection the sieve?  Or does living tissue have some capacity to modify itself?  It will be interesting to see what develops.

You can access Paul Wallace’s article at



Creative Reason and the Breath of Life

Pope Benedict XVI, in his Easter Vigil homily, given April 23, 2011, asserts that “Creative Reason is the Fundamental Principle of the Universe,   and Man is No Mere Late Product of Random Evolution.”  Discussing the opening words of Genesis and the Gospel of John, the Pope states that the regularly recurring phrase “And God said,” and the Logos of John indicate a creative Reason that speaks and communicates itself.  He declares “It is not the case that in the expanding universe, at a late stage, in some tiny corner of the cosmos, there evolved randomly some species of living being capable of reasoning and of trying to find rationality within creation…If man were merely a random product of evolution in some place on the margins of the universe, then his life would make no sense or might even be a chance of nature.  But no, Reason is there at the beginning: creative, divine Reason. And because it is Reason, it also created freedom, and because freedom can be abused, there also exist forces harmful to creation.”

In his new book titled “Christianity in Evolution: Discovering the Harmony of Science and Faith,” (Cathedral Center Press, Los Angeles, 2011),  author Ralph Armstrong presents a work that strongly parallels the Pope’s homily.  Armstrong, a psychiatrist and former Adjunct Professor of Pastoral Counseling at St. John’s Roman Catholic Seminary, Camarillo, California, describes, through very close readings of molecular and evolutionary biology, a creation made intelligent and agentive by the Breath of Life.  In other words, the findings of scientific research intimate that Creative Reason, intrinsic to the Breath of Life,resides in each living creature, making Life capable of modifying itself to meet the exigencies of existence. Creative Reason, the Breath of Life, lies at the heart of the intelligence of all living.

Life, made intelligent by the Breath, by Creative Reason, has in the last seconds of geologic time evolved a humankind capable of knowing and loving God and each other.  And Life is free, and this freedom allows for conflict that extends all the way back to the first virus that attacked the first bacteria, all the way across the spectrum of living things, and all the way down to the genes, where genes are capable of acting selfishly, against the broader interests of genomes. 

Armstrong melds this worldview with orthodox Christianity as he shows how the Fall of Adam and Eve in the domain of Heaven translates into an Earthly domain rife with conflict.  He then describes how God, not about to idly stand by as his creation wars with itself, intervenes in the manner described in the Old and New Testaments.  In the last three chapters of the book, Armstrong discusses prayer, offers a novel and unique theodicy, and closes with a discussion of some very new science about how we relate to each other, and how this affects the future of Christianity.

The complete article regarding the Pope’s homily can be found at





Is Life Material or of Another Order?

Is Life Material or of Another Order?

Ralph H. Armstrong

The biology professor eyed me impatiently as he mentally weighed my manuscript, a loose leaf bound 250 page draft of my book Christianity inEvolution.  “You’ve done a lot of work,” he mused, almost to himself.  I nodded, thinking to myself that the real issue was whether or not its points and conjectures were valid.  My ideas in the book were not mainstream, and biology is not my first language, so I was not sure of what I had created.  Thumbing through the draft, he whispered, “What do you want me to do with it?”  I looked him in the eye and said firmly, “I want you to shoot it down.”

From close readings of biological and evolutionary science, the Scriptures, and the tenets of Christianity, I had set out in Christianity in Evolution: Discovering the Harmony of Science and Faith to put together a rapprochement.  I sought a better understanding of the processes of the creation, as well as the whys of suffering and conflict.  I wondered how the astonishing findings of cell and molecular biology pertained to Christianity.  From my career as a physician Christian, I brought with me an assumption that Life and its animation was extraordinary, and I was aware that modern biology largely attributed Life to solely material and mechanical processes.  I have long felt that all living is animated by the breath of Life, cell respiration being a necessary but not sufficient explanation for Life’s continuous motion.

At our follow up meeting at the coffee shop in his community, the day was hot, and we sought a table in the shade to go over his critique.  The first third of the draft was liberally marked with red ink. He had very graciously noted various mistakes and areas where he disagreed with my thinking.  Then he settled back in his chair, and said that he found my idea of animation opaque.  His tempo increasing, he defended his mechanistic view of Life as he said, “What we need are more experiments, our technical capabilities are increasing, and the field of computational biology is in its infancy. ”  Then he reached into his brief case and pulled out a page he had printed out from Wikipedia.  It was an essay on Animism, and it read, in part, as follows:

Animism (from Latin anima “soullife“)[1][2] refers to the belief that non-human entities are spiritual beings, or at least embody some kind of life-principle.[3]

Animism encompasses religious beliefs that there is no separation between the spiritual and physical (or material) worlds, and souls or spirits exist, not only in humans, but also in all other animalsplantsrocks, natural phenomena such as thundergeographic features such as mountains or rivers, or other entities of the natural environment.[4] Animism may further attribute souls to abstract concepts such as words, true names, or metaphors in mythology. Animism is particularly widely found in the religions of indigenous peoples,[5] although it is also found in Shinto, and some forms of HinduismSikhismBuddhismPantheismIslamChristianity, and Neopaganism.

Throughout European history, philosophers such as Aristotle and Thomas Aquinas, among others, contemplated the possibility that souls exist in animals, plants, and people; however, the currently accepted definition of animism was only developed in the 19th century by Sir Edward Tylor, who created it as “one of anthropology‘s earliest concepts, if not the first“.[5]

Fig. 1.An example of animism in the extreme.  ‘Famous Bedik diviner just outside Iwol, southeast Senegal (West Africa). He predicted outcomes by examining the color of the organs of sacrificed chickens. The person consulting him here came all the way from Dakar — a long trip.” Courtesy Ghaku and Wikimedia Commons.

[8] According to religious scholar Robert Segal, Tylor saw all religions, “modern and primitive alike”, as forms of animism.[1] According to Tylor, animism often includes “an idea of pervading life and will in nature”;[9] i.e., a belief that natural objects other than humans have souls. As a self-described “confirmed scientific rationalist”, Tylor believed that this view was “childish” and typical of “cognitive underdevelopment”,[10] and that it was therefore common in “primitive” peoples such as those living in hunter gatherer societies.

Here then is the gulf between Christianity and “confirmed scientific rationalists” such as the professor.  The biblical idea of the Breath of Life, or Breath of God, as the animating principle in Life is dismissed as primitive, childish, and indicative of cognitive underdevelopment.  It appears that Tylor’s definition, reinforced by an emerging mechanistic Darwinism, won acceptance by most biological scientists.  Apparently, the prevailing worldview is that there is only one explanation for Life, a mechanistic one, and anyone who holds an extraordinary view is deemed infantile or at worst delusional.  The trouble is that the concept of animism, as described by Wikipedia and as intimated by the professor, though having grains of truth in it, utterly fails to do justice to the Judeo-Christian idea of God’s breath animating life on earth, or to Native American spirituality, which it condemns as infantile and primitive.

A Look at the Evidence

A drawback of animism as defined above is that it can be based on the subjective intuitions, experiences, traditions, religious practices, and worst of all, the frank superstitions of individuals, groups, and cultures.  Religions and hunter gatherer societies that endorse animism have little if any scientific, or objective, evidence with which beliefs can be tested.  My biology professor, on the other hand, drew from the rich well of cell and molecular biology and concluded that Life is material because there is no scientific evidence that it is transcendental.  But, as Huston Smith once argued, lack of evidence is not evidence of lack (italics mine). The fact is that there is at this time no direct evidence that Life is either solely material or transcendent.  It is simply an emotional and visceral assumption we make, without even realizing it.

But an abundance of evidence in the fields of cellular and molecular biology and genetics is in fact compatible with a worldview of Life as transcendent:

  1. Compared to nonliving machines, living organisms are qualitatively entirely different.  They fuel themselves, organize and regulate themselves, defend and repair themselves, reproduce, and on the molecular level, exist as layer upon layer of complex and exquisitely choreographed networks.  The central organizer is the creature itself in its totality.
  2. Living organisms are in constant motion; cell respirations— the Krebs cycle and oxidative phosphorylation— are necessary to fuel motion, but are not sufficient to explain it.  Consider the ideas of philosopher Maxine Sheets-Johnstone:  She writes that “a mechanical concept of nature is foreign to a complete understanding and explanation of emergent organization from the level of cells to the level of intact organisms-animate forms.” In this paper, she asserts that a “principle of motion or animation informs  biological nature.”  In other words,” the fundamentally dynamic character of biological form at all levels exemplifies the kinetic character of living matter.” ” She complains that our notion of matter “fails to account for the fundamental kinetics of living systems. There is a dynamic principal undergirding living matter that contradicts construing biological life as machine.” She states emphatically, “To understand living systems is to understand animation, from the level of cells and neurophysiological happenings to the level of intact organisms, that is, animate forms.  Animation-movement-is present at all levels in living systems… animation is fundamental to a veridical account of living forms, not an add on, and certainly not an incidental possibility or property.”  I would only add that all matter, not just the biological, is in motion.  Electrons whirl and strings vibrate, ceaselessly.
  3. In my book Christianity in Evolution (CIE), I cite extensive scientific evidence and commentary from scientists that Life is intelligent, learns, can modify itself, exists cooperatively in community on multiple levels, and can trade genetic information between individuals in minutes.  Life is not clay acted on by God or molded solely by natural selection; rather, Life is an agent in its adaptations.  All living creatures are sentient.
  4. Life strategizes.  Random genetic mutations leading to variations in organisms have long been touted as proof that Life is only material and ultimately meaningless.  But this worldview is only one of two ways of looking at randomness.  Random variation can alternatively be seen as a strategy for coping with changing and challenging circumstances.  Richard Colling, in his book Random Designer, presents a worldview in which God has used randomness to fashion creatures capable of connecting with him.  The bioengineering method of directed evolution generates an array of novel proteins that otherwise could not be fabricated.
  5. Furthermore, Life is intensely innovative and creative.  By molecular tinkering, Life can, by making Lego-block like rearrangements, create new and more adaptive forms in evolutionarily brief periods of time.  It is plausible that punctuated equilibrium events such as the Ediacaran and Cambrian explosions took place in such a manner. In addition, the outcomes of tinkering, much as the inventiveness of humans, are unpredictable.
  6. In cell operations such as chromosome replication and repair, molecular repair molecules move with uncanny accuracy to damaged areas to perform surgical excisions, followed by patching, almost suggesting that the molecules are flexible and capable of choice.  The whole process of DNA repair, though under tight control from higher networks, appears intelligent.  Mentioning molecular intelligence brings to mind chaperone proteins in bacteria.  Chaperonins are cup shaped proteins into which other proteins in the process of fabrication are shielded so that they can fold properly.  They even have a cap that closes over the soon-to-fold protein; it comes off to allow the now-folded protein to escape into the bacteria’s cytosol.  They are objects of intense study; little is known of their origin.  Fig. 2 illustrates it. Fig. 2. Chaperone protein, essential in protein folding.  Image from BiOpinionated.  For a beautiful animation of a chaparone protein participating in protein folding, click on the following link: or go to “Chaparonin Video” on the right margin under “Blogroll.” This will take you to “Archimedes.”  To see the link in English, click on “English” on the lower left
  7. .There is evidence that even the molecules have agency.  Small groups of DNA and RNA—specifically transposons and viruses– act autonomously to parasitize living organisms.  Viruses strategize: The human immunological deficiency virus (HIV) rapidly and randomly changes its coat with every replication, making it a particularly difficult moving target. Transposons are widespread and are thought, due to their mobility, to be important generators of evolutionary change.  These two entities have no respirations or metabolisms, yet exhibit exquisite intent.
  8. Living creatures are sentient.  Animals express sentience in their ability to move, whereas plants show through phenotypic plasticity their awareness of their environment.  Though animals do not possess the overt self-reflective consciousness of humans, they do, based on the development of their central nervous systems, exhibit varying degrees of consciousness.
  9. Life is in intense conflict, both within itself and with other creatures.    Humankind suffers grievously with conflicts within individuals.  Witness psychoanalyst Karl Menninger’s classic book, Man Against Himself. Such self-conflict, as well as the often brutal clashes between creatures, must be explained.  In Christianity in Evolution, I cite extensive evidence that conflicts extend down to the genomes of all living.

10.  In stark contrast to non-living objects, all living things die.

In summary, living creatures are clearly distinguished from non-living matter.  Given the consciousness, intelligence, agency, creativity, conflictual nature, and mortality of living creatures, it is clear that the living possess a quality that the non-living do not.

The Explanatory Gap

How do we get from organic molecules to the organized complex systems of molecules that make up living things?  Furthermore, how do we get from these systems of molecules to sentience, consciousness, agency, intelligence, creativity, and choice?  How do we go from molecules to systems to the propensity to attack the other?  Franklin Harold, emeritus Professor of Biochemistry at Colorado State University, raises this question, as he writes:

One senses that something is not accounted for very clearly in the single-minded          dissection to the molecular level.   Before cells were taken apart . . . they displayed capacities that go beyond chemistry. Homeostasis, purposeful behavior, reproduction, morphogenesis, and descent with modification are not part of the vocabulary of chemistry but point to higher levels of order . . . here we touch, if not the very secret of life, at least an essential stratum of that many-layered mystery. . . . How do millions, even billions, of molecules come to function in a collective, purposeful mode that extends over distances orders of magnitude larger? This, in essence, is the problem of biological order..

Now we see that up to now we have no way to fill this explanatory gap. At this moment, science can take us no further.  The professor holds to his implicit opinion that Life is only material, and he plans more experiments, while at the same time implying that I am delusional for thinking otherwise.   Stuart Kauffman, in his book Redefining the Sacred, (Look under “Book Reviews” elsewhere on this site for a review of Kauffman’s book), offers a gentler position.  He argues that the ten item list above constitutes a worldview that can be a meeting ground for scientists, skeptics, and people of all faiths.  Kauffman declares that Life as defined above is God enough for him, but in suggesting this middle ground he is granting to religious persons everywhere their right to interpret it otherwise.

On the other hand, I wonder if what we are seeing is matter made animate by the Ruach, the breath of God and of Life.  As I look over the ten item list above, it seems to me very  plausible that Life is transcendental. But in the end, it is a matter of assumption, though for each of us the assumption is admittedly visceral and emotional. But there is yet another possibility; could it be that what we see as matter is in essence matter and breath as a single, indivisible entity?  Think of all we see in the tangible universe as animationmatter. Is there any evidence for such radical speculation?  There is indeed very interesting evidence, in origin of Life experiments on the one hand, and Jesus in the Gospels, on the other.

Origin of Life Experiments

At first glance, it would seem that the idea of Life as transcendent can be called into question if science can create Life in the laboratory. And scientists the world over are racing to do just that. Go to the National Library of Medicine at and search for “the origins of life.” The search brings up 1,274 papers (as of September 2010) looking at various aspects of the subject, including several papers specifically addressing the question, “What is Life?” Perusal of journal publisher SpringerLink’s specialty publication Origin of Life and Evolution of Biospheres shows papers on such subjects as prebiotic chemistry, prebiotic amino acids, theoretical modeling, homochirality,[i] and defining Life. I focus below on the work of the team of Nobel laureate molecular biologist Jack W. Szotak[ii] and its efforts to create Life, particularly as set forth in the article “The Origins of Cellular Life.”[iii]

The authors, drawing on an enormous amount of research worldwide, are looking for plausible pathways for the transition from complex prebiotic chemistry to simple biological assemblies able to propagate themselves and evolve. These “protocells” require two key components—a membrane to make a compartment and a lengthy molecule able to transmit functional information to progeny. Their laboratory has focused on vesicles made up of fatty-acid membranes, by which protocells could take up nutrients, grow, and divide. They have experimented with an array of genetic polymers to understand their potential for genome replication within encapsulating membranes. Their goal is to create a laboratory model of a protocell to understand possible paths for the emergence of Life on Earth. Basically, they are investigating the advanced biochemical properties of enzymes, catalysts, and the self-assembly and self-organization inherent in some carbon-based molecules. How close are they to synthesizing life? I am convinced that it lies within the realm of the possible. What will it mean if they succeed?

If scientists can, through their sophisticated manipulations of biochemistry, coax selected molecules to assemble to create Life, I believe they will have pushed the issue of animation—- Life’s consciousness, agency, intelligence, and creativity— back from organisms to the molecules themselves. I think they will have shown that the very molecules of the Earth and the Universe have agency, confirming what I have already written above about viruses and transposons exhibiting molecular intent. This suggests to me that the Ruach is not confined to Earth and its living things. Rather, the Ruach will prove, in my opinion, to be an intrinsic property of everything that is.

I am by no means the first to consider the breath as pervading all matter and the universe. The early 20th century naturalist John Burroughs, in his 1916 book The Breath of Life, writes of Ralph Waldo Emerson, who said he would not feel threatened or insulted if a chemist should take his protoplasm, or mixes hydrogen, oxygen, and carbon, and makes an animal, swimming and jumping before his eyes.  “It would only be evidence of a new degree of power over matter which man had attained to.  It would all finally redound to the glory of matter itself, which, it appears, is impregnated with thought and heaven, and is really of God, and not of the devil, as we had too hastily believed.” (Italics mine)


Fig. 3  Ralph Waldo Emerson




With these thoughts in mind, let us take a fresh look at the miracles of Jesus, as described in the four Gospels.

The Miracles of Jesus

Substantial portions of all four Gospels document Jesus as performing an array of miraculous healings, transformations, exorcisms, and personal feats.  In our present era, we tend to focus on Jesus’ teaching, compassion, and messages of tolerance, love, forgiveness, salvation, and reconciliation with the Father, and his miracles are treated as signs pointing to the reign of God’s kingdom.  The fact remains, however, that Jesus, as portrayed in the Gospels, was the ultimate miracle worker.  Whole segments of religious commentators dismiss accounts of his miracles as fabrications, and many believers simply avoid the issue.  But the fact that so many Scripture writers attest to so many different kinds of miracles suggests that maybe there is some validity to what is written about him.  In the end, each of us chooses to either avoid the question, or believe, or disbelieve the Gospel accounts of Jesus’ miracles.

Suppose we accept at face value the accounts of Jesus’ miracles.  I then ask, “Well, how did he do these things?  What can we say about the bases of his miracles?  What do they have in common?  Would the idea put forth above—that the molecules of the universe are imbued with his breath—shed any light on his miracles?”

Let’s start by classifying the miracles; they can be grouped as follows:

  1. Miracles regarding living non-human organisms: the cursing of the fig tree, and the schooling of the fish at the calling of Peter and the other fishermen.
  2. Transformations of food matter:  water into wine, multiplication of loaves and fishes.
  3. Miracles regarding the elements:  walking on water, calming the winds, stilling the storms.
  4. Healing miracles: lepers, paralytics, withered limbs, blind persons, chronic bleeding, fevers.
  5. Casting out demons.
  6. Raising the dead

This is an utterly  astounding list of accomplishments.  There are differences between these categories: some are living, some once alive but not now living, some are inanimate, some are supernatural  (the demons).  What commonality, aside from the demons, do they share?  They are all made up of molecules.  They are part of the material world.  Let’s take these in order.

The cursing of the fig tree is described in Matthew 21:18 and Mark 11: 12-14; both accounts occur following Jesus’ triumphal entry into Jerusalem, and end with a discourse on faith and prayer.  The miracle directly supports the idea that his breath animates the fig tree; with the curse he withdraws his breath, and the tree withers .  Notice that Jesus speaks to the fig tree.   Speaking is derived from breath; for one to speak, one must breathe.  It follows then, that the Word issues from the Breath.   His action is foretold in Psalm 104 and Job 34:

If he should take back his spirit to himself, and gather to himself his breath, all flesh would perish together, and all mortals return to dust.” (Job 34:14–15)

“When you hide your face, they are dismayed; when you take away their breath, they die and return to their dust.” (Psalm 104:29)

In both Matthew and Mark, Jesus tells us that we can perform similar miracles, or even cast mountains into the sea, if we, in prayer, ask in faith.  So, how does the breath connect to faith in Jesus, on the one hand, and the efficacy of prayer, on the other?

The second miracle concerning living but non human organism is the schooling of fish at the calling of Peter (Luke 5:1-11).  Like the cursed fig tree, the fish are alive; both have the breath of life, which has been lent them.  In other words, in God they live, and move, and have their being.  When Peter and the others are fishing, but catching nothing, Jesus calls the fish to a higher purpose, to be a sign to the world, and because it is his breath that animates them, they come swimming.[1] Jesus here is a fish whisperer.

Fig. 4. “The Miraculous Draught of Fishes by Raphael, Vatican Museums”  Courtesy and Wikimedia Commons

The miracles in categories 2 and 3 above involve nonliving entities.  The water, wind, and storms are molecular, as is the water at the wedding in Cana, and as are the elements of the cooked fish and bread, at the feeding of the thousands.  Here is evidence that the Ruach is not reserved for the living, but also are intrinsic to nonliving molecules and their various networks.  Because the molecules of the universe are suffused with God’s breath, they submit to Jesus.  “Who is this that even the winds obey him?” Because he has lent his breath to the molecules of the universe, he has dominion over the elements that they make up. They hear and respond to the master from whom their breath issues.  Think here of animationmatter. What we think of as the material of the universe are molecules made animate by the breath.  Wait, one might argue that the desk upon which my computer sits is not animate.  But think again; every molecule of the wood is in constant motion.  In these examples of Jesus and the nonliving, Jesus is a whisperer of molecules!

Fig. 5. Christ in The Storm on the Sea of Galilee. Ludolf Bachhuysen 1655 

In category 4, the healing miracles, it is the diseased tissue that responds.  Diseased tissues, like the fish or the fig tree, are molecular; the networks that make up diseased organs are composed of damaged molecules.  Again, the molecules respond to his voice, or touch, even his spittle.  In some cases, but not all, the faith of the person is commended as restorative.  It would appear in these cases that the faith referred to here is the person’s openness to Jesus, leading to a wholeness, or holiness, or restoration of the whole person, not just the molecular.

In Category 5, the demons are interesting.  The Scriptures don’t tell us much about demons, where they come from, etc.  They apparently take their cues from the devil, and we know they possess people, causing maladies that today we would call psychosis or epilepsy.  But their most remarkable characteristic is that they consistently know who Jesus is!  How do they know him?  Could it be that they are elements of his breath, lent out as he has lent out his breath to all of Life and the universe, but a breath that has gone over to the other side?  Could it be that they know him because they came from him?

The second mystery is, where have all the demons gone?  There are reports that there are some still around, but they seem nowhere near as ubiquitous as in Jesus’ time.  The explanation most consistent with the gospel narratives is that in the presence of Jesus, everything moved with lightening rapidity, and he drew out the hidden powers of the world, making everything extraordinarily manifest . In my own work as a psychiatrist, I have seen several people who seemed to have an alien presence in their psyches, but in each case the alien turned out to be a rejected part of the self.  These aliens, then, needed to be invited in, not cast out. If one regards demons as elements of the breath gone to the dark side, it stands to reason that the main intent and power of demons is to induce fear, frighten, influence, tempt, or deceive.  Thus, their presence would be quite subtle and difficult to detect.  C.S. Lewis, in The Screwtape Letters, and St. Paul, in Ephesians 6:10-20, take this view.  But, beware of a “the devil made me do it” attitude.  We are responsible for our own actions, and we should not be deceived into believing that we have no power to correct them.  That said, it is not easy.  I  understand and believe in Steps 1 through 3 of Alcoholics Anonymous.

The last category is the raising of the dead.  All that is said above is true of the resurrection of Lazarus. “Lazarus, come out!”  The breath, via the Word, enlivens his molecules, and he lives.


Fig. 6.  The Resurrection of Lazarus. Vincent Van Gogh.  Courtesy Batchheizer and Wikimedia Commons.

Finally, with the idea of the molecules and elements of the universe being suffused with the Breath, a variety of Scriptural passages we take as metaphoric may be more literal than we realize.  For example, as Jesus rides the donkey into Jerusalem and the crowds sing “Hosanna,” (Lk 19:38), the Pharisees object to the shouts, and Jesus answers, “I tell you, if these keep silence the stones will cry out.” (Jerusalem Bible).  In the light of this study, Native American spirituality, with its animation of the physical  and animal world, and its plea that we are all brothers and sisters of heaven and earth, does not look primitive at all.


We have examined the question of the nature of Life:  Is Life only mechanical, or is it of another order altogether?  There is an explanatory gap between arrangements of molecules and their animation. From close readings of biology, evolutionary science, and the Scriptures, Life is, in contrast to mechanical objects, agentive, intelligent, creative, and in conflict with itself.  There is yet another explanatory gap, one between organisms and intelligence. If Life is mechanical, it possesses some distinctly non mechanical aspects.  This statement, if you look at it closely, is contradictory. Furthermore, there is evidence that some organic molecules exhibit agency and intent; I describe the actions of viruses and mobile genetic elements, or transposons.

I therefore assert that it is Life’s molecules, suffused with the Breath of Life, that generate animation, agency, intelligence, choice, and free will. Life and the molecules that compose it is made agentive and intelligent by the Ruach, the breath of the Almighty. This is a religious assertion and cannot be proven by science.  But can it be disproved?  If science can create Life in vitro, does that falsify our premise?  Or does it imply that the very molecules that science has coaxed to Life have the Ruach enlivening them?

This last idea, that the molecules of the universe are suffused with the Breath, has explanatory power.  With this idea I explore the Gospel accounts of the miracles of Jesus.  What does all this tell us about prayer, about how Jesus prayed, and about how we can pray?




[1] I thank the Very Rev. Jerome Kahler, for this idea.

[i] Homo = alike. Chirality = the handedness of an asymmetrical molecule. Life uses only left-handed amino acids and only right-handed sugars. How and why in the world did Life come up with these choices? Creationists who argue that homochirality points to a creator are posing a god-of-the-gaps argument.

[ii] Jack W. Szostak is professor of molecular biology at the Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston. His Nobel Prize was for his work on the protective function of telomeres, the tips of genes.

[iii] Schrum JP, Zhu TF, Szostak JW. “The Origins of Cellular Life.” Cold Spring Harb Perspect Biol (May 19, 2010): doi: 10.1101/cshperspect.a002212.


What is Eternal Life?

What a question!  It is certainly akin to what salvation is.  Yet Jesus explicitly defines it in John 17:1-3:

Father, the hour has come: glorify your Son so that your Son may glorify you;

and, through the power over all mankind (literally ‘all flesh’) that you have given him,

let him give eternal life to all those you have entrusted to him.

And eternal life is this; to know you, the only true God, and Jesus Christ whom you have sent.(NRSV)

Can we really know God and Jesus?  Seems like a stretch, but that’s what the passage says!

About 30 years ago I was invited to attend a Cursillo, a three day experiential retreat put on by the Episcopal Church.  It was to be held at the Mission San Miguel, a classic old Spanish mission about three hours north of my home in Ventura County, California.  I drove up on a Thursday evening with Joe Donnelly, my sponsor and a man I hardly knew.  As we drove, I lamented on a real estate loss I had incurred through a recent move to the Ventura County area.  That is where my head was as we drove north.

The retreat consisted of about 30 Cursillistas and 30 of us candidates. The clergyman leading the retreat was a protestant pastor; he immediately set the tone for the weekend by quoting John 17:1-3.  We were called on this weekend to come to know something of the mind of God, and he pointed out that “know” was the same as the word used in Genesis 4:1, translated in the NRSV to “intercourse.”   Hmmm! Intimate indeed.  We sat at tables of 12 and listened to addresses by our hosts, talks that were very frank, honest, and emotional.  Looking back on it, his challenge to come to know God and Jesus, in combination with the setting of the Cursillo, opened up an entirely new vista in my spiritual life. In essence, it introduced me to the possibility of knowing him. In this short weekend I was transported from knowing all about someone (I knew the Scriptures by heart) to the idea of actually encountering him. In retrospect, it had only dimly occurred to me before.  A world of difference!

The process made me acutely aware of all my conflicts and egocentrisms-my sins, and my guides graciously heard my confessions.  But one last obstacle remained: if I was to know him, I had to abandon those egocentrisms and risk giving myself over to him.  The solution was to say simply, “Thy will be done, one day at a time!”  I came away from that retreat with a wholly different attitude toward life. God was no longer words on a page, or rituals to be performed, or some taskmaster to be feared, or a judge weighing my actions, but my friend! My pique over my real estate loses faded to nothing.

So how do we come to know God, Father, Son, and Holy Spirit?  After all, they are spirits.  We come to know God in our hearts, through feel, through emotion, and through imagination.  It is, after all, how we ultimately come to know each other. Recall I am a psychiatrist.  The present hot topic in psychiatry and psychotherapy is mentalization, the capacity and process of tuning into another person’s mind, listening with abandon, grasping his mental states, his positions, his intents, without judgement, setting aside all the oughts and shoulds that I can think of for him, simply appreciating him as he is.  Mentalization is seeing the other person from the inside and myself from the outside.  It takes effort: the default mode of thinking and relating is egocentrism.  So here is how we can practice mentalizing the mind of the Father and Jesus, so that we can progressively come to know him:

  • We come to know him in worship, in the breaking of the bread.
  • We can hear him with the receptors of our hearts through music.
  • We can grasp his mind as we pray; prayer is definitely a mind-to-mind exercise.
  • We can encounter him as we pour over the Scriptures.
  • We can know him through service: “In as much as your have done it to the least of these my brothers, you have done it to me.”
  • We can know him through community: “When two or three are gathered in my name, I am in the midst of them.”

Ask for the ability to mentalize.  It is, after all, the essence of love.


Bibliography used for Christianity in Evolution–Discovering the Harmony of Science and Faith

*Azevedo FA et al. “Equal Numbers of Neuronal and Nonneuronal Cells Make the Human Brain an Isometrically Scaled-Up Primate Brain,” J comp Neurology 513, no. 5 (April 2009):532–37.

*Alcoholics Anonymous: The Big Book (New York: Alcoholics Anonymous World Services, 1978).

*Allen JG and Fonagy P, eds. Handbook of Mentalization-Based Treatment (Chichester, UK: John Wiley & Sons, 2006), pp. 271–88.

*Allen JG, Fonagy P, and Bateman AW. Mentalizing in Clinical Practice (Washington, DC: American Psychiatric Press, 2008), p. 9.

*Angier N. “Pursuing Synthetic Life, Dazzled by Reality,” New York Times, Feb. 5, 2008.

*Armstrong RH. Christianity and Change: Steps to Growth and Healing in Christian Counseling (Kansas City, MO: Sheed & Ward, 1990).

*Bailey CH and Kandel ER. “Synaptic Remodeling, Synaptic Growth and the Storage of Long-Term Memory in Aplysia,” Prog Brain Res 169 (2008):179–98.

*Bamford DH et al. “What does Structure Tell Us about Virus Evolution?” Curr Opin Struct Biol 15, no. 6 (Dec. 2005):655–63.

*Bassler BL and Losick R. “Bacterially Speaking,” Cell 125 (April 21, 2006):237–46.

*Bateman A and Fonagy P. Mentalization-Based Treatment for Borderline Personality Disorder (Oxford, UK: Oxford University Press, 2006).

*Behe M. Darwin’s Black Box: The Biochemical Challenge to Evolution (New York: Free Press, 1996).

*Biddle, WE. Hypnosis in the Psychoses (Springfield, IL: Charles C Thomas).

*———. “Images, the Objects Psychiatrists Treat” Archives of General Psychiatry 9, no. 5 (1963): 464–70.

*———. Integration of Religion and Psychiatry (New York: Macmillan, 1955).

*Bird CD and Emery JN. “Rooks Use Stones to Raise the Water Level to Reach a Floating Worm,” Curr Biol 19, no. 16 (Aug. 6, 2009):1410–14.

*Bloom JD and Arnold FH. “In the Light of Directed Evolution: Pathways of Adaptive Protein Evolution” PNAS 106 (June 16, 2009):9995-10000.

*Bower B. “Crows Use Sticks, Stones to Show Skills at Manipulating Tools in Lab,” Science News, Aug. 29, 2009.

*Brennan M. A Glimpse of Jesus: The Stranger to Self-Hatred (New York: HarperCollins, 2004).

*Burt A and Trivers R. Genes in Conflict (Cambridge, MA: Harvard University Press, 2006).

*Caporale L. Darwin in the Genome: Molecular Strategies in Biological Evolution (New York: McGraw-Hill, 2003).

*Collins F. The Language of God (New York: Free Press, 2006).

*Carroll SB. The Making of the Fittest: DNA and the Ultimate Forensic Record of Evolution (New York: WW Norton, 2006).

*Castelvecchi D. “Biowarfare: Engineered Virus Can Invade Bacterial Film,” Science News, June 20, 2007, p. 404.

*———. “Live Another Day: African Insect Survives Drought in Glassy State,” Science News, March 29, 2008.

*——— “Love Code: A Twist of Light Only Mantis Shrimp Can See,” Science News, March 22, 2008.

*Cavalier-Smith T. “Predation and Eukaryote Cell Origins: A Coevolutionary Perspective,” Int J Biochem Cell Biol 41, no. 2 (Feb. 2009):307–22.

*Chiou TH et al. “Circular Polarization Vision in a Stomatopod Crustacean,” Curr Biol. 18, no. 6 (March 25, 2008):429–34.

*Chivian D et al. “Environmental Genomics Reveals a Single Species Ecosystem Deep within Earth,” Science 322, no. 5899 (Oct. 10, 2008):275–78.

*Clark D and Russell L. Molecular Biology Made Simple and Fun (St. Louis, MO: Cache River Press, 2005).

*Colling RG. Random Designer: Created from Chaos to Connect with the Creator (Bourbonnnais, IL: Browning Press, 2004).

*Collins F. The Language of God (New York: Free Press, 2006).

*Coyne JA. Why Evolution Is True (New York: Penguin Books Worldwide, 2009).

*Davidov Y and Jurkevitch E. “Predation between Prokaryotes and the Origin of Eukaryotes,” Bioessays 31, no. 7 (July 2009):748–57.

*Dawkins R. The Extended Phenotype (New York: Oxford Univ. Press, 1982), pp. 156, 158.

*Denes AS et al. “Molecular Architecture of Annelid Nerve Cord Supports Common Origin of Nervous System Centralizationin Bilateria,”Cell 129 (April 20, 2007):277.

*Dere E et al. “The Case for Episodic Memory in Animals,” Neurosci Biobehav Rev 30, no. 8(2006):1206–24. Epub 2006 Oct 31.

*Dietrich LEP et al. “Redox-Active Antibiotics Control Gene Expression and Community Behavior in Divergent Bacteria,” Science 321, no. 5893 (Aug. 29, 2008):1203–06. Cited?

*Dougherty MJ and Arnold FH. “Directed Evolution: New Parts and Optimized Function,” Curr Opin Biotechnol 20, no. 4 (Aug. 2009):486–91.

*Ehrman B. God’s Problem: How the Bible Fails to Answer Our Most Important Question—Why We Suffer (New York: HarperCollins, 2008).

*Eisenberg J. A Collector’s Guide to Seashells of the World (New York: McGraw-Hill, 1981).

*Encounters at the End of the World. A Werner Herzog Film. Discovery Films. Image Entertainment, 20525 Nordhoff Street, Suite 200, Chatsworth, CA 91311.

*Evans PD et al. “Microcephalin, a Gene Regulating Brain Size, Continues to Evolve Adaptively in Humans,” Science 309, no. 5741 (Sept. 9, 2005):1717–20.

*Falk D. Coming to Peace with Science: Bridging the Worlds between Faith and Biology (Madison, WI: InterVarsity Press, 2004).

*Fernald RD. “Evolving Eyes,” Int J Dev Biol 48 (2004):701–705.

*Feschotte C. “The Contribution of Transposable Elements to the Evolution of Regulatory Networks,” Nat Rev Genet 9, no. 5 (May 2008): 397–405.

*Forterre P. “The Origin of Viruses and Their Possible Roles in Major Evolutionary Transitions,” Virus Res 117, no. 1 (April 2006):5–16.

*Fowler TB and Kuebler D. The Evolution Controversy: A Survey of Competing Theories (Grand Rapids, MI: Baker Academic, 2007).

*Freeland SJ and Hurst LD. “The Genetic Code Is One in a Million,” J Mol Evol 47, no. 3 (Sept. 1998):238–48.

*Freeland SJ, Knight RD, and Landweber LF.  “Measuring Adaptation within the Genetic Code,” Trends in Biochemical Science 25, no. 2 (Feb. 2000):44–45.

*Freeland SJ et al. “Early Fixation of an Optimal Genetic Code,” Mol Biol Evol 17, no. 4 (2000):511–18.

*Gage R. “Neuronal Plasticity and Neuronal Diversity.” Plenary address at the World Congress of Psychiatric Genetics, San Diego, November 2009.

*Gao Y et al. “Early Maternal and Paternal Bonding, Childhood Physical Abuse and Adult Psychopathic Personality,” Psychol Med. 40, no. 6 (June 2010):1007–16.

*Gehring WJ. “New Perspectives on Eye Development and the Evolution of Eyes and Photoreceptors,” J Heredity 96, no. 3 (2005):171–84.

*Gerstein M and Zheng D. “The Real Life of Pseudogenes,” Scientific American, Aug. 2006, 48–55.

*Gibbons A. “Breakthrough of the Year: Ardipithecus ramidus,” Science 326 (Dec. 18, 2009):1598.

*Girard A and Hannon GJ. “Conserved Themes in Small-RNA-Mediated Transposon Control,” Trends Cell Biol 18, no. 3 (March 2008):136–48.

*Glanzman DL. “New Tricks for an Old Slug: The Critical Role of Postsynaptic Mechanisms in Learning and Memory in Aplysia,” Prog Brain Res 169 (2008):277–92.

*Goldsmith E. “Intelligence Is Universal in Life,” Riv Bio. 93, no. 3 (Sept.–Dec. 2000):399–411.

*Gordon C and Rendsburg G. The Bible and the Ancient Near East (New York: WW Norton 1997).

*Harold F. The Way of the Cell: Molecules, Organisms, and the Order of Life (London: Oxford University Press, 2001).

*Harrison PM and Gerstein M. “Studying Genomes Through the Aeons: Protein Families, Pseudogenes and Proteomic Evolution,” J Mol Evol 318, no. 5 (May 17, 2002):1155–74.

*Hedges DJ and Deininger PL. “Inviting Instability: Transposable Elements, Double-Strand Breaks, and the Maintenance of Genome Integrity, Mutat Res 616, nos. 1–2 (March 1, 2007):46–59.

*Hesse E and Main M. “Disorganized Infant, Child, and Adult Attachment: Collapse in Behavioral and Attentional Strategies,” J Amer Psychoanalytic Assn 48, No. 4 (2000):1097–1127.

*Iturriaga G, Suárez R, and Nova-Franco B. “Trehalose Metabolism: From Osmoprotection to Signaling,” Int J Mol Sci 10 (2009):3793–3810.

*Jablonka E and Lamb M. Evolution in Four Dimensions: Genetic, Epigenetic, Behavioral, and Symbolic Variation in the History of Life (Cambridge, MA: MIT Press, 2005).

*Jablonka E and Lamb MJ. “Précis of Evolution in Four Dimensions,” Behav Brain Sci. 30, no. 4 (Aug. 2007):353–65.

*Jiang Y et al. “Epigenetics in the Nervous System,” J Neurosci 28, no. 46 (Nov. 12, 2008):11753–59.

*Johnson LT. The Apostle Paul (Chantilly, VA: The Teaching Company, 2001).

*Johnston W. Mystical Theology: The Science of Love (Maryknoll, NY: Orbis, 1995).

*Kandel E. In Search of Memory: The Emergence of a New Science of Mind (New York: WW Norton, 2006).

*Kendler KS et al. “Sexual Orientation in a U.S. National Sample of Twin and Nontwin Sibling Pairs,” Am J Psychiatry 157 (2000):1843–46.

*Kirschner MW and Gerhart JC. The Plausibility of Life (New Haven, CT: Yale University Press, 2005).

*Koch C and Greenfield S. “How Does Consciousness Happen?” Scientific American, Oct. 2007.

*Kojik, N. “Taken for a Spin” Science News, April 14, 2007, p. 231.

*Koonin EV. “The Biological Big Bang Model for the Major Transitions in Evolution,” Biol Direct 20, no. 1 (2007):21.

*Kornfield J. A Path with Heart: A Guide Through the Perils and Promises of Spiritual Life (New York: Bantam, 1993).

*Kwon DN et al. “Identification of Putative Endogenous Retroviruses Actively Transcribed in the Brain,” Virus Genes 36, no. 3 (June 2008):439–47.

*Lake JA. “Evidence for an Early Prokaryotic Endosymbiosis,” Nature 460, no. 7258 (Aug. 20, 2009):967–71.

*Lapierre D. The City of Joy (New York: Warner Books, 1985).

*Lieberman DE and Hall BK. “The Evolutionary Developmental Biology of Tinkering: An Introduction to the Challenge. Novartis Found Symp 284 (2007):1–19.

*Lobdell W. Losing My Religion: How I Lost My Faith Reporting on Religion in America and Found Unexpected Peace (New York: HarperCollins, 2009).

*Lynch M. “The Frailty of Adaptive Hypotheses for the Origins or Organismal Complexity,” PNAS 104 (May 15, 2007): 8597–8604.

*Main M. “The Organized Categories of Infant, Child, and Adult Attachment: Flexible versus Inflexible Attention under Attachment-Related Stress.” From a paper presented to the San Francisco Psychoanalytic Institute December 20, 1997.

*Margulis L. “The Conscious Cell,” Ann NY Acad Sci 929 (April 2001):55–70.

*Margulis L et al. “Community Living Long Before Man: Fossil and Living Microbial Mats and Early Life,” Sci Total Environ 56 (1986):379–97.

*Margulis L and Sagan D. What Is Life? (Berkeley and Los Angeles: Univ. of Calif. Press, 1995).

*Martinez-Romero E. “Coevolution in Rhizobium-Legume Symbiosis?” DNA Cell Biol 28, no. 8 (Aug. 2009):361–70.

*Masterson JF. The Narcissistic and Borderline Disorders: An Integrated Developmental Approach (New York: Brunner/Mazel, 1981).

*Maugh T II. “Fossils Shed Light on Human Lineage,” Los Angeles Times, Aug. 9, 2007.

*Maxmen A. “Animal Origins: Genome Reveals Early Complexity,” Science News, Feb. 16, 2008, pp. 99–100.

*McKenzie JL. Dictionary of the Bible (Milwaukee, WI: Bruce Publishing, 1965).

*Mekel-Bobrov N et al. “Ongoing Adaptive Evolution of ASPM, a Brain Size Determinant in Homo sapiens,Science 309, no. 5741 (Sept. 9, 2005):1720–22.

*Menninger K. Man against Himself (San Diego, CA: Harcourt Brace Jovanovich, 1985).

*Milius S. “Pothole Pals: Ants Pave Roads for Fellow Raiders,” Science News, June 2, 2007.

*Milius S. “Slave Ants Rebel,” Science News, Sept. 13, 2008, p. 6.

*Miller A. For Your Own Good: Hidden Cruelty in Child-Rearing and the Roots of Violence (New York: Farrar, Straus & Giroux, 1983).

*Miller KR. Only a Theory: Evolution and the Battle for America’s Soul (New York: Viking Press, 2008).

*Moltmann J. The Crucified God: The Cross of Christ as the Foundation and Criticism of Christian Theology (New York: HarperCollins, 1991).

*Morris SC. Life’s Solution: Inevitable Humans in a Lonely Universe (Cambridge, UK: Cambridge Univ. Press, 2003).

*Moyes D, Griffiths DJ, and Venables PJ. “Insertional Polymorphisms: A New Lease of Life for Endogenous Retroviruses in Human Disease,” Trends in Genetics 23, no. 7 (2007):326–33.

*Muotri AR et al. “The Necessary Junk: New Functions for Transposable Elements,” Hum Mol Gen 16 (2007):R159–R167.

*Nadell CD et al. “The Evolution of Quorum Sensing in Bacterial Biofilms,” PLoS Biol 6, no. 1 (January 2008):e14.

*“The Origins of Immunity?” Science News, August 25, 2007.

*Pallen MJ and Gophna U. “Bacterial Flagella and Type III Secretion: Case Studies in the Evolution of Complexity,” Genome Dyn 3 (2007):30–47.

*Palmer D. Prehistoric Past Revealed: The Four Billion Year History of Life on Earth (Berkeley and Los Angeles: University of California Press, 2003).

*Papachristoforou A et al. “Smothered to Death: Hornets Asphyxiated by Honeybees,” Curr Biol 17, no. 18 (Sept. 18, 2007):R795–96.

*Parker WR and St Johns E. Prayer Can Change Your Life (New York: Prentice Hall Press, 1957).

*Patton P. “One World, Many Minds,” Sci Am Mind, Dec. 2008/Jan. 2009, pp. 72–77.

*Penenberg AL. “Amazon Taps Its Inner Apple,” Fast Company, July/August 2009.

*Perkins S. “Microbes Thrive in Seafloor Rock: Diversity and Abundance Surprise Research Teams,” Science News (June 21, 2008).

*Peterson E. The Message (Colorado Springs, CO: NavPress, 2002).

*Phillips B and Shine R. “When Dinner Is Dangerous: Toxic Frogs Elicit Species-Specific Responses from a Generalist Snake Predator,” Am Nat 170, no. 6 (Dec. 2007):936–42.

*Pillard RC and Bailey JM. “Human Sexual Orientation Has a Heritable Component,” Hum Biol 70, no. 2 (April1998):347–65.

*Powell S and Franks NR. “How a Few Help All: Living Pothole Plugs Speed Prey Delivery in the Army Ant Eciton burchellii,” Animal Behavior 73, no.6 (June 2007).

*Prabhakar S et al. “Human-Specific Gain of Function in a Developmental Enhancer,” Science 321, no. 5894 (Sept. 5, 2008):1346–50.

*Prior H, Schwarz A, and Gunturkun O. “Mirror-Induced Behavior in the Magpie (Pica pica): Evidence of Self-Recognition,” PLoS Biol 6, no. 8 (Aug. 19, 2008):e202.

*Prochaska JO, Norcross J, and DiClemente C. Changing for Good (New York: Avon Books, 1994).

*Putnam NH et al. “Sea Anemone Genome Reveals Ancestral Eumetazoan Gene Repertoire and Genomic Organization,” Science 317, no. 5834 (July 6, 2007):86–94.

*Quina AS, Buschbeck M, and Di Croce L. “Chromatin Structure and Epigenetics,” Biochem Pharmacol 72, no. 11 (Nov. 30, 2006):1563–69.

*Rahman Q. “The Neurodevelopment of Human Sexual Orientation,” Neurosci Biobehav Rev 299, no. 7 (2005):1057–66.

*Reed DL et al. “Genetic Analysis of Lice Suggests Direct Contact between Modern and Archaic Humans,” PLoS Biol 2, no. 11 (Oct. 5, 2004).

*Reik T. Listening with the Third Ear (New York: Ferrar & Straus, 1949).

*Robinson D. Consciousness and Mental Life (New York: Columbia University Press, 2008).

*Roces F. “Individual Complexity and Self-Organization in Foraging by Leaf-Cutting Ants,” Biol Bull 202, no. 3 (June 2002):306–13.

*Roughgarden J. Evolution’s Rainbow (Berkeley: Univ. of Calif. Press, 2004, 2009).

*———. Evolution and Christian Faith (Washington, DC: Island Press, 2006).

*———. The Genial Gene (Berkeley: Univ. of Calif. Press, 2009).

*Roussel EG et al. “Extending the Sub-Sea-Floor Biosphere,” Science 320, no. 5870 (May 23, 2008):1046.

*Ruprecht K et al. “Endogenous Retroviruses and Cancer,” Cell Col Life Sci 65 (2008):3366–82.

*Ryan F. Darwin’s Blind Spot (Boston, New York: Houghton Mifflin, 2002).

*Saey TH. “Bacteria Make Molecular Snorkels for Surviving in Crowded Spaces,” Science News, January 17, 2009, p. 8.

*Saey TH. “Epigenetics: From Islands to the Shores: Tissue-Specific DNA Tagging Found in Unexpected Regions,” Science News, February 14, 2009.

*Saey TH. “Gold Mine Houses Community of One,” Science News, November 8, 2008, p. 20.

*Sahagun L. “Crashing Grunion’s Beach Party: Researchers Collect Eggs, Sperm in an Effort to Establish a Stable Captive Population,” Los Angeles Times, April 15, 2008, p. B. 1.

*Sakai H et al. “Frequent Emergence and Functional Resurrection of Processed Pseudogenes in the Human and Mouse Genomes,” Gene 389, no. 2 (March 15, 2007):196–203.

*Sakurai M et al. “Vitrification Is Essential for Anhydrobiosis in an African Chiromomid, Polypedilum vanderplanki,” PNAS 105 no. 13 (April 1, 2008):5093–98.

*Sanders L. “Nonstop Godwit Flights,” Science News, Nov. 22, 2008.

*Sanders L. “Slime Mold as Master Engineer,” Science News, Feb. 13, 2010.

*Santelli CM et al. “Abundance and Diversity of Microbial Life in Ocean Crust,” Nature 453, no. 7195 (May 29, 2008):653–56.

*Scheme of Influenza A Virus Replication, “Influenza A Virus,” Wikimedia Commons.

*Schrödinger E. What Is Life? The Physical Aspect of the Living Cell; with “Mind and Matter,” and “Autobiographical Sketches” (Cambridge, UK: Cambridge University Press, 1967).

*Schwartz J and Begley S. The Mind and the Brain (New York: ReganBooks, 2002).

*Shapiro, JA. “A 21st Century View of Evolution: Genome System Architecture, Repetitive DNA, and Natural Genetic Engineering,” Gene 345 (2005):91–100.

*Shapiro, JA. “Bacteria Are Small But Not Stupid: Cognition, Natural Genetic Engineering and Socio-Bacteriology,” Stud Hist Philos Biol Biomed Sci 38, no. 4 (Dec. 2007): 807–19. Epub 2007 Nov 19.

*Sheets-Johnstone M. “The Formal Nature of Emergent Biological Organization and Its Implications for Understandings of Closure,” Annals NY Acad Sci 901 (2000):320–31.

*Siepka SM et al. “Genetics and Neurobiology of Circadian Clocks in Mammals,” Cold Spring Harb Symp Quant Biol 72 (2007):251–59.

*Sompayrac L. How Pathogenic Viruses Work (Sudbury, MA: Jones & Bartlett, 2002).

*Sompayrac L. How the Immune System Works (Malden, MA: Blackwell, 2003).

*Spencer N. Darwin and God (London: Society for Promoting Christian Knowledge, 2009).

*Spitzer RL. “Can Some Gay Men and Lesbians Change Their Sexual Orientation? 200 Participants Reporting a Change from Homosexual to Heterosexual Orientation,” Arch Sex Behav 32, no. 5 (Oct. 2003):403–17.

*Sullivan JC, Reitzel, AM, and Finnerty JC. “A High Percentage of Introns in Human Genes Were Present Early in Animal Evolution: Evidence from the Basal Metazoan Nematostella vectensis,Genome Inform 17 no. 1 (2006):219–29.

*Tattersall I. “How Did Modern Human Cognition Evolve?” In H. Cohen and B. Stemmer (eds), Consciousness and Cognition: Fragments of Mind and Brain (San Diego, CA: Elsevier, 2007).

*Telford MJ. “A single origin of the central nervous system?”Cell 129, no. 2 (April 20, 2007):237–39.

*Tero A et al. “Rules for Biologically Inspired Adaptive Network Design,” Science 327, no. 5964 (Jan. 22, 2010):439–42.

*Valentine J et al. “Fossils, Molecules and Embryos: New Perspectives on the Cambrian Explosion,” Development 126 (1999):851–59.

*Van Schaik CP and Kappeler PM. “Infanticide Risk and the Evolution of Male-Female Association in Primates,” Proc R Soc Lond B 264 (1997):1687–94.

*Volff JN. “Turning Junk into Gold: Domestication of Transposable Elements and the Creation of New Genes in Eukaryotes,” Bioessays 28 (Sept. 2006):913–22.

*Wagner GP, Pavlicev M, and Cheverud JM. “The Road to Modularity” Nat Rev Genet 8, no. 12 (Dec. 2007):921–31.

*What Is Life? Retrieved January 2009, from

*Wilkins AS. “Genetic Networks as Transmitting and Amplifying Devices for Natural Genetic Tinkering,” Novartis Found Symp 284 (2007):71–86.

*Wright B. “A Biochemical Mechanism for Nonrandom Mutations and Evolution,” J. Bacteriology 182, no. 11 (June 2000):2993–3001.

*Zhu H et al. “Chasing Migration Genes: A Brain Expressed Sequence Tag Resource for Summer and Migratory Monarch Butterflies (Danaus plexippus),” PLoS ONE 3, no. 1 (Jan. 9, 2008):el345.

*Zhu H et al. “Defining Behavioral and Molecular Differences between Summer and Migratory Monarch Butterflies,” BMC Biol 7 (March 31, 2009):14.


Review of “Aspects of Plant Intelligence,” by Anthony Trewavas

Central to the uncovering of the harmony between biology, evolution, and Christianity is the idea of Life as an active agent in its adaptations to its changing circumstances.  In Chapters 2-4 in Christianity in Evolution I have presented evidence that animals are intelligent, can learn, and are able through rearrangements in their genetic and epigenetic networks to evolutionarily modify themselves.  But animals are only half of Life’s story on Earth; what of plants, the other half? I turn to plant biologist Anthony Trewavas[1] for his interpretations of the science of plants.  The following is a synopsis of his chapter in The Deep Structure of Biology (Reference below).
Plants are intelligent
It would never occur to most of us that plants are intelligent, primarily because they don’t move, as animals do.  The equation of “vegetable” with the term “brain dead” reflects our sentiments regarding intelligence in the plant world.  However, time lapse technology and striking advances in plant physiology, signal transduction (chemotaxis in E. coli is analogous), molecular biology, and cell-to-cell communication tell a strikingly different story.  In response to signals (light, heat, cold, wind, soil conditions, food sources, etc.), plants can change their various structures (leaves, shoots, roots, limbs, etc.) to individually optimize their foraging for resources.  In addition, plants are able to predict possible upcoming changes in resources (light, water, soil qualities, seasonal changes) and then alter their form, an action called phenotypic plasticity. Animals respond to such changes with movement, plants with phenotypic plasticity.
“It is in foraging for food that animal intelligence becomes a premium, and it is in plant foraging that plant intelligence comes to the fore.“ (p70)  We can perceive the processing of information by animals, but the time frames are much longer for plants, as time lapse technology makes clear. “As we acquire more knowledge about all sorts of behavioral characteristics of living organisms, not only are previous assessments of intelligence and behavior shown to be wrong, but the expanding view enlarges our perspective of life itself.”  (P. 71, emphasis mine)
Trewavas goes on to discuss the issue of intelligence, pointing out that the Latin root literally means to ‘choose between.’  He advances the idea that what we see as innate behavior of animals and plants “arose from learned, that is, intelligent, behavior in the first place, potentially by genetic assimilation.” (p72, more on genetic assimilation later)  He argues that organisms exhibit foresight “that allows organisms to come up with a behavioral solution to an environmental problem with minimal trial and error.  Improved behavioral modification enables the subsequent selection of genes and gene combinations… that allow the strategy to develop with greater rapidity, higher probability, or lower cost.  Consequently, evolution becomes much faster than mechanisms that require selection of random gene combinations, just as foresight reduces the time required for successful behavior.” (p73)  He goes on to argue for intelligence in bacteria, protists, genomes, immune systems, swarms, and metabolic networks.  He concludes that “Apart from the higher animals that use the centralized activity of the brain to process information and in which classical intelligence is located, all other biological systems possess a decentralized intelligence that is a consequence of behavior by the whole system.” (p.79, emphasis the author’s)
Plants are active, not passive
The author proposes that “Two perceptions of plant growth and behavior need to be distinguished.  A common passive view is that plants grow according to a predetermined genetic program with  rates determined merely by provided resources…The active view of plant behavior is in complete contrast.  For plants facing competition from neighbors and from other organisms in a variable abiotic environment, intelligent adaptive behavior is a necessity, not a luxury.” (p 80-81)  He documents numerous strategies , such as exploratory speculative growth of shoots and roots, variations of leaves to capture maximum light, and root strategies to maximize water and minerals in highly variable soils.  “Decision making about phenotypic change involves in some way the whole plant and is, thus, decentralized.”  (p82)  Decentralization is essential in a class of organisms constantly grazed upon by animals.
Plants are networks
Plants, being both social and modular, are interactive networks of leaves, stems, roots, flowers, and seeds.  Such networks evaluate the whole of the environment, and the whole network modifies itself to any environmental change.  As a result, there is “a very complex mixture of communicating signals moving throughout the plant individual.” (p 83)  Signal transduction is the conveying of information about the environment via complex biochemical networks.  As a result, plants “perceive their environment in considerable detail, make meaningful assessments of that information, and institute adaptive phenotypic responses designed to improve competitive ability and resource acquisition…Intelligence is an emergent property that results from complex interactions between the tissues and cells of the individual plant.” (p.93)
Plants are agentive
Throughout the article Trewavas discusses various agentive actions of plants.  For example, plants are territorial, taking over available space and denying it to others.  But plants sense their own kind and avoid competing with them.  They in addition possess complex self recognition systems.  Plants make complex decisions on how and where to vary phenotype to garner scarce resources.  Plants conduct sophisticated cost/benefit analyses in their quest for light, food, and water.  Plants are capable of foresight; they can sense the future possibility that a competitor might overshadow them, and they adapt system-wide in response.  “Foresight of future water availability also institutes characteristic morphological changes in anticipation and preparation…programs indicate an ability to anticipate environmental change, even though it may not happen during the lifetime of the individual plant.” (pp. 89-90).  The author goes on to cite extensive evidence that plants in general learn and remember.  Trewavas leaves no doubt that plants, like animals, actively contend with life’s ever changing circumstances.
Plants, Intelligence, and Evolution
Trewavas notes that intelligence is intrinsic to all biology, from bacteria to plants to animals.  Bacteria use quorum sensing, plants decentralized intelligence, and animals central nervous systems.  Bacteria learn by horizontal gene exchange, individual cells through computation, and higher animals by complex neural networks.  “Underpinning all the forms of intelligence…is a network whose connection strength can be altered, enabling control of information flow and memory to be constructed.” (p. 95)  Why, the author asks, is intelligence so widespread?  Because it is the more intelligent who will forage the most effectively and will be naturally selected.  Intelligence will beget more intelligence.
The author continues, “There are currently at least two kinds of evolutionary models relevant to this discussion. The first, the neo-Darwinian view, sees overproduction, random genetic variation, and differential survival as the basis of evolution.  The second…places behavioral changes as the first response to environmental shifts…Those that adapt most efficiently and are, thus, best able to master the current changes in the environment will experience preferential survival.” (p. 97-98)  Through inbreeding of the more intelligent, the new and more efficient behavior becomes genetically fixed, a process known as genetic assimilation.  In other words, “Whatever genes the successful organism possesses go along for the ride…The very refined and complex forms of innate behavior found in reproductive rituals in animals and birds must surely originally have been learned behavior that has now been genetically assimilated.” (pp. 98-102, emphasis mine)
The author concludes that “Genetic assimilation is initiated by changes in behavior, and, (in plants) behavior is expressed as phenotypic plasticity, which I have indicated is intelligent behavior…The evolution of intelligent behavior found in all forms of life, thus, becomes a central theme in the evolution of life itself.” (p. 102, emphasis the author’s)

[1] Trewavas A. “Aspects of Plant Intelligence,” in The Deep Structure of Biology-is Convergence Sufficiently Ubiquitous to Give a Directional Signal?” Simon Conway Morris, Ed. (2008) Templeton Press, West Conshohocken, Pa.

Anthony Trewavas is a professor at the University of Edinburgh.  He has special interests I plant-cell signal transduction and plant behavior.  He has published over 220 papers and two books.  He is a fellow in a number of professional societies.

Review of “Reinventing the Sacred,” by Stuart Kauffman

A Book Review of

Reinventing the Sacred-A New View of Science, Reason, and Religion


Stuart Kauffman

Stuart Kauffman is well known in biological circles for his theories about complex systems.  He is a prominent MetaDarwinist, and his views are not widely accepted among mainstream biologists.  He is a physician, biologist, philosopher of mind, researcher, and entrepreneur.  He was active in the thinktank Santa Fe Institute, and is now a professor at the University of Calgary.

In this book, he first systematically dismantles scientific reductionism, from the perspectives of both physics and biology.  It is from the position of NeoDarwinist reductionism that such vocal atheists as Richard Dawkins and Stephen Weinberg have declared that all life is in essence just particles slamming together and therefore ultimately meaningless.  Kauffman points out that in fact numerous features of life, including consciousness and mind, are emergent phenomena.  That is, rather than living things existing only as assemblies of particles, they function on levels and scales unimaginably  greater than the sum of their parts. Biology, he states, is not reducible to physics.

He cites what he calls Darwinian Preadaptations as illustrating his points.  (In Christianity in Evolution, I described  these preadaptations  as “Life is a tinkerer.”)  That is, life has the uncanny ability to find new and unpredictable uses for existing structures.  Thus, some of the jawbones of early reptiles  were modified to ultimately become the tiny bones in the middle ear of later vertebrates, including us.  In another example, the poison injection system in bacteria has been recruited and modified to become the base of the bacterial flagella, a propeller to swim with.  He asserts that Darwinian Preadaptations, (the tinkering of Life) “confront us with a radically new kind of unpredictable creativity in the evolution of the biosphere…Thus a radical, and, I will say, partially lawless creativity enters the universe.  The radical implication is that we live in an emergent universe in which ceaseless unforeseeable creativity arises and surrounds us.” This is the worldview I subscribe to, and around which I wrote Christianity in Evolution-Discovering the Harmony of Science and Faith.”

In Chapter 6, he illustrates how life is agent.  He states that the action of a bacterium swimming up a glucose gradient is acting teleologically.  He calls this simplest living system a “minimal molecular autonomous agent…capable of acting on its own behalf in an environment…Thus the agent must be able to detect, make a choice, and act.  Virtually all contemporary cells fulfill this expanded definition.  Such systems are emergent in (Nobel Prize winning Stanford Physics Professor) LaughIin’s sense, with novel properties, for they are agents and can act, where the action is the relevant subset of the causal evens that occur.”  It is a superb chapter that echoes my fundamental premise, the agency of life, which allows me to then make a Christian interpretation that is most plausible.  He goes on to declare that because life is agentive, meaning, values, morality, and ethics devolve.  I should note that he wrote this book in 2008.  I discovered it only a couple of months ago.  Basically, I reinvented the wheel.

In Chapter 7, The Cycle of Work, he discusses the agency of the cell as it establishes and maintains its boundaries and carries out its various metabolisms.  It is an excellent discussion of how Life recruits and utilizes biochemistry and physics. One can well see why he is unpopular among mainstream biologists.  In Chapter 8, talking about self organization, he states “It is, at a minimum, a concrete example of the possibility of emergence, non-reducibility, and, as we shall see, the powerful idea that order in biology does not come from natural selection alone but from a poorly understood marriage of self-organization and selection.  Thus, the classical belief of most biologists that the only source of order in biology is natural selection may well be wrong.”  He concludes, “We truly need a new worldview, well beyond the reductionism of Laplace and Weinberg. ..We must rethink evolution.”

In Chapter 10, “Breaking the Galilean Spell,” he is not taking aim at Jesus but at Galileo, who was the first reductionist.  He writes “We began this book by looking at reductionism, which has dominated our scientific worldview since the times of Descartes, Galileo, Newton, and Laplace.  This philosophy holds that all of reality can ultimately be understood in terms of particles in motion, and nothing else has reality, in the sense that it has the power to cause future events.  As Stephen Weinberg puts it, all the explanatory arrows point downward.  The logical conclusion is that we live in a meaningless universe of facts and happenings.”  Kauffman disagrees:  “What about all the aspects of the universe we hold sacred—agency, meaning, values, purpose, all life, and the planet?  We are neither ready to give these up nor willing to consider them mere human illusions. ..The schism between religion and science is, therefore, in part, a disagreement over the existence of meaning.” (italics mine).

I really liked his discussion of mind, in Chapter 12, as a “meaning-doing system.”  Kauffman asks, “Where then do meanings come from?…Meaning derives from agency…an increased rate of glucose molecules detected by a glucose receptor as the bacterium swims up he gradient is a sign of more glucose up the glucose gradient, and that sign was interpreted by the bacterium by its oriented motion up the gradient…the glucose is given meaning …by the bacterium’s reception of the sign, and in its doings, swimming up the gradient.He concludes, “Without agency, as far as I can tell, there can be no meaning.”

Another great chapter is #14, “Living into Mystery.”  Page 231 reinforces my idea that the Ruach is not confined to life on earth or to humankind, but rather pervades all the particles in the universe.  Perhaps this is why Jesus can stop the winds on the Sea of Galilee, why “even the winds obey him,” why he can walk on water or turn it into wine.

On page 231, he states “In the new scientific worldview I’m describing, we live in an emergent universe of ceaseless creativity in which life, in which agency, meaning, consciousness, and ethics have evolved.”  Kauffman declares this world sacred.  I totally agree.

We differ from him in one detail.  For Kauffman, the sacredness of the creation is enough God for him.  We see the universe imbued with the Ruach and made sacred and supported by the Father, Son, and Holy Spirit.


What is Life?

What can science tell us about Life?  Lots!  We learn that the oldest visible fossils date back 2.7 billion years.  Ancient bacteria supplied the earth’s atmosphere with oxygen.  Life suddenly burgeoned 575 million years ago, a phenomenon called

punctuated equilibrium. Prehuman forms appeared about 4 million years ago. An array of Genus Homos with differing DNA and biology appeared simultaneously, and some coexisted, as did humans and Neanderthals.This is a sculpture of Australopithecus africanus, an early player.


Cells, fundamental to life, come in two forms: prokaryotes (on the right) and eukaryotes. The former, usually bacteria, lack a nucleus. The latter is 10 times larger, has a nucleus, and is the building block of complex organisms. Bacteria are extremely widespread and can adapt to extreme conditions. There are many single- celled eukaryotes. There is evidence that eukaryotes resulted from the merger of differing prokaryotes.

DNA is a very long twisted molecule containing four letters, A,T, C, and G, connected in four combinations, AT, TA, GC, and CG. In groups of three, these base pairs code for 20 amino acids. The possible combinations are invariant and are collectively called the genetic code. By this code, DNA is transcribed by RNA to make multitudinous proteins.

Almost all of life is composed of 20 amino acids that are formed by strict rules called the genetic code. The code is extremely optimized and hence minimizes damage done by mutations.

DNA, copied by RNA, leads to the building of proteins via the genetic code. The body is largely composed of and supported by proteins. Receptors are lock- and- key devices made up of proteins. They are integral to self-regulation and self-organization.

For life to grow, cells must divide. DNA must be separated and meticulously copied. Mistakes must be repaired. These processes are extremely efficient, but errors are made and can add up. Bacteria divide by fission, and bodies of eukaryotes grow by mitosis. The special cell division that results in sperm or eggs is called meiosis.

File:9-Week Human Embryo from Ectopic Pregnancy.jpg

During the growth of an embryo, cells switch on and off to form tissues. It is thought that tissues are arranged in space not by the genome, but by fields in which structure begets structure. But nobody has seen a field. Could the templates have originally been an image in God’s eye?

Life, through a maze of intricate networks, is able to regulate its physical functions. Genomic restructuring, hypermutation, and induced local mutations are strategies that Life deploys. Life is an agent in its adaptations.

Life is in constant motion. All Life is animated. There is a dynamic principal undergirding living matter that contradicts construing biological life as machine.


We can with science reduce Life to its most fundamental denominators, but there is no answer to the problem of animated, organized complexity, nor to the conundrum of what animation is or where it comes from. At this point, we have to admit that our understandings of Life boil down to a matter of faith: faith that Life is only material, or faith that there is a mystical aspect to Life. Whether we consciously realize it or not, what we think Life ultimately is rests on our assumptions.