Consciousness (Part 2)

Conclusion

Within the framework of a universe whose total entropy is always increasing, there is the surprising fact that the laws of physics allow for temporary decreases in entropy.  This direction of decreasing entropy is counter to the overall increase in total entropy and yet does not violate any physical law.  Processes that temporarily decrease entropy are essential to life and they are also present in such well-understood phenomenon as lasers and superconductivity where the process is traceable to quantum physics.  I think it is a reasonable position that all such processes of decreasing entropy are traceable to quantum physics and to decoherence in particular.   Quantum computation is a real process, though it is not yet practical on a large scale.  Quantum computation happens during entangled states of coherence and the results are reported by decoherence.  The most direct evidence that this is happening in biological organisms is from photosynthesis.  During photosynthesis, extended quantum coherence takes place during the transport of photons from the light-harvesting chlorophyll molecules to the reaction center where food production begins.   This results in the near 100% efficiency with which light energy is transported.

Quantum physics is the most fundamental of the physical sciences.  It accurately describes all interactions at the level of fundamental particles, whether they be matter particles such as protons, neutrons or electrons or whether they be energy particles such as photons (light).  If one takes the position that quantum states are real (though they are not directly measurable), then it is reasonable to conclude that the universe must decide where and when such states collapse into a single measurable quantity: the universe must make a decision for every single transfer of energy.  That is the fundamental decisionality underlying all physical activity.

I think it is a reasonable to extend the quantum role in photosynthesis to biology in general.  The protein folding problem in particular has significant similarities with photosynthesis in that an energy landscape must be navigated.  In photosynthesis, the energy landscape funnels a photon to the plant cell’s reaction center where food production begins.  In the protein folding problem the protein folds by navigating an energy funnel to a conformal state which has a lower overall energy level.  The shape into which proteins fold is crucial to their function in the cell and undetected misfolded proteins are implicated in some disease processes.  Recent research supports the view that quantum physics plays a role in protein folding (cf. Lou and Lu, 2011).

It is reasonable to extend the role of quantum computation to the operation of all biological molecules.  They are certainly small enough to be affected by quantum effects.  It fits the overall model that the cell is an information processing marvel.  DNA contains information about the sequence of amino acids in proteins in a coded form (three nucleotides per amino acid).  RNA and ribosomes decode the sequence to produce proteins.  Proteins work together to form complex molecular machines that assist the cell in keeping entropy low despite the constant loss of entropy to the environment.  There is an amazing real-time cooperation, an unbelievable choreography among different cell functions that would be impossible to fully explain through any other mechanism.  A reasonable position is that quantum decisionality is active throughout all biological organisms and the most basic unit of processing is the biological molecule as Professor James A. Shapiro has suggested.  Recent research supports the view that quantum entanglement is active in the DNA molecule (cf. Reiper, Anders and Vedral, 2011).

Although the exact path to creation of the earliest forms of life remains hidden from us, it is reasonable to think that the laws of physics and chemistry favored a path to life.  The alternatives to such a conclusion are either that life happened by blind chance or there was some supernatural intervention in the creation process that bypassed the laws of physics.  A reasonable thought process must rule out both of these options as highly improbable.   Since it is reasonable to think that quantum processes play a significant part in modern biological cells, it is a reasonable extension to think that quantum processes played a part in the creation of life.  It is the quantum computations that provide the necessary bias toward life.

(For those readers who have a theistic view of the universe, as I do, let me pose the question about supernatural intervention this way:  Why would the Creator of the universe put in place laws of nature that He or She would need to bypass?  I view the laws of nature as a kind of covenant with the universe.  The rules of quantum physics allow all the needed degrees of freedom for God’s intervention in history.)

Quantum computation is a real process, but is still in the research and development phase.  Some very simple calculations have been demonstrated such as factoring small numbers.  Factoring is one application that has garnered much interest because factoring can be done much faster on quantum computers than on ordinary computers.  If factoring can be done quickly on large numbers then some public key cryptographic systems would become obsolete.    For example, the RSA scheme relies on the impracticality of factoring large numbers, typically 617 digits long.  Public key cryptography is used to support the security infrastructure that enables shoppers to connect securely to a web site when they provide payment information.  The largest number factored by conventional methods during the RSA factoring challenge, which ended in 2009, was 232 digits and Microsoft has recently blocked any keys with less than 309 digits.  The largest number currently factored by quantum computer using the well-understood Shor’s algorithm is the 2 digit number 21.

However there is another quantum factoring algorithm that has demonstrated factoring of the 3 digit number 143.  Very interestingly, this algorithm finds the factors by arranging the quantum hardware (qubits) in a pattern where the answer can be read when the qubits settle in their lowest energy state, possibly using a quantum process similar to the one proposed for photosynthesis, that is, traversing an energy landscape toward the lowest overall energy level.  However, there is no reason to think this new algorithm can be scaled up for very large numbers.  (Within the past few weeks, there has been another report of quantum computation that works by traversing an energy landscape.  That claim comes from D-Wave Systems which hopes to produce the first commercial quantum computer.)

But it would be a mistake to assume that natural quantum computations of the type that take place during photosynthesis are implementations of any known mathematics.  The analysis that was done on the photosynthesis data led researchers to conclude that the quantum computation was not an ordinary search algorithm of the type that would have been implemented by a human programmer.  If quantum decisionality is the physical process underlying consciousness as Roger Penrose and Stuart Hameroff propose, then it is unlikely that the full spectrum of quantum computations could be implemented on any ordinary computer.  The quantum computations would be both non-deterministic and, ironically, non-computational in Penrose’s analysis.

In a recent paper, Physicist Roger Penrose and Anesthesiologist Stuart Hameroff have summarized their proposal and answered critics.  The paper is titled, “Consciousness in the Universe: Neuroscience, Quantum Space-Time Geometry and Orch OR Theory” (Journal of Cosmology, 2011, Vol. 14).  The Penrose-Hameroff proposal for quantum consciousness calls for quantum coherence within the very numerous microtubules that support brain cell structure.  Microtubules are very small hollow tubes in the neurons, about 25 nanometers in diameter, which would appear ideal for isolating quantum coherence from the environment.  Unlike the microtubules in other cells that form and break apart as needed, the microtubules in neurons are stabilized by another protein, called the tau protein.  Mature Nerve cells don’t divide, so microtubules do not need to become spontaneously active during nerve cell mitosis.  Neuronal microtubules will break apart if the tau protein becomes compromised, and a malfunctioning tau protein is one possible cause of Alzheimer’s disease.  Penrose and Hameroff end their summary paragraph with a surprising admission: “We conclude that consciousness plays an intrinsic role in the universe.”  That is the first time I recall hearing such a statement from Penrose and Hameroff.

While the Penrose-Hameroff hypothesis for quantum consciousness has not been experimentally verified, it does fit my overall paradigm of quantum coherence and decisionality being the primary mover of life.  I have been following the developments in quantum consciousness for over 20 years, since Roger Penrose’s first book on the subject, The Emperor’s New Mind, in 1989.  I am sufficiently comfortable with the theory to think that quantum coherence is the phenomenon behind our amazing consciousness.  The details will almost certainly be different than Penrose and Hameroff propose, but the direction is solid, and I am confident that an intelligent, decisional consciousness does indeed play an intrinsic role in the universe.

I have also emphasized that one cannot immediately conclude that such a consciousness is God.  The question of God is a theological question about oneself and one’s relationship to some power.  The power that I have elucidated over my several postings on science is the decisional, conscious ordering power of the universe.  It is a power that comes to us free of cost; it transcends time and space by its amazing non-local properties of entangled particles; it does not require any energy, and is the primary power causing a bias in the laws of physics supporting life, supporting entropy lowering processes.  I emphasize, once again, that entropy lowering processes are temporary and localized so that the total entropy in the universe increases.    For readers wanting a less theistic view, I recommend “the Information Philosopher” (Bob Doyle).  He also sees order in the universe emerging through the action of quantum physics, but he applies this concept to philosophy rather than metaphysics.  He points out that even though the total entropy in the universe is increasing, so is the available entropy: there is always more available ordering power as time increases.  His web site is http://www.informationphilosopher.com/.

Even for readers with a theistic view of the universe, I would not recommend a direct correlation between the consciousness inherent in the laws of physics and God.  It may be impossible to completely distinguish the deterministic aspects of quantum computation from its non-deterministic aspects.  Therefore, I analogize the consciousness inherent in nature as the “hand of God,” although not in any anthropomorphic sense.  It is the vehicle through which God interacts with history.

Nevertheless, these developments in physics, biology and in the very new science of consciousness have the potential of sending a shock wave through theology and religion.  Throughout history, religion has responded poorly to or reacted against the best scientific evidence.  From Galileo to Newton, religious dogma has been confronted with scientific truth and has struggled to respond appropriately.  During the enlightenment, as people of faith came to terms with Newton’s mechanistic universe, God was deemed to have withdrawn from the world and Deism was the result.  The modern secular imagination has no place for religions that demand God’s supernatural intervention in history or for a three story universe.  The scriptural worldview is woefully outdated.  Yet, theology holds that God is real and that God acts in history.  So theology must answer the question about how God acts in history if supernatural explanations are no longer appropriate.  The best answer that I know of today is something called “process theology.”

Process theology is a type of panentheism.  A panentheistic view holds that God is present in all aspects of matter and energy, but that God is not limited to or identical with all matter and energy.  Process theology is based on the process-relational philosophy of Alfred North Whitehead and Charles Hartshorne and emphasizes changeable relationships rather than permanent entities as the basis for truth.  For process theologians, God’s power is exercised through acts of consciousness, through persuasion rather than coercion, and therefore requires a robust theology of free will.  And because free will is an essential property of humankind, God is therefore not the immutable, changeless God of traditional theology.  God interacts with history and is changed by history.  Since God is in all things, process theology also reconfigures the concepts of good and evil to avoid a reductionist form of Manichaeism; that is, there is no need for a devil or Satan role to account for evil.

Process theology emphasizes God’s imminence in the world, but also acknowledges God’s transcendence of the world.  Within Process Theology, evolution is guided by God, but not in a deterministic sense.  God represents the creative aspect of evolution.  According to several sources, process theology has influenced both Christian and Jewish writers such as Harold Kushner, Abraham Joshua Heschel, William E. Kaufman, W. Norman Pittenger, John B. Cobb, Thomas Berry and Marjorie Suchocki.  Marjorie Suchocki’s pamphlet, “What is Process Theology,” is a good place to begin learning.

I found it interesting to read a review of Hartshorne’s discussion about the proof of God.  From his 1970 book, Creative Synthesis and Philosophic Method, he identifies four possible philosophical options relating to cosmic order and God:

(A1) There is no cosmic order.
(A2) There is cosmic order, but no cosmic ordering power.
(A3) There is cosmic order and ordering power, but the power is not divine.
(T)    There is cosmic order and divine power.

Hartshorne holds the fourth position identified as (T), but insists that he does not arrive there by “proof.”   I have not read Hartshorne’s book, so I don’t know to what extent he uses empirical evidence for cosmic order, but I think that empirical evidence is very helpful in giving more weight to option (A3) compared to (A1) and (A2).  In my view, reason can be very helpful in arriving at a conclusion that there is a cosmic ordering power, but that faith is necessary to conclude that such a power is an expression of divine action.   If the evidence from physics, chemistry and biology is all we have, then a “leap of faith” is required to get from position (A3) to (T).  However, there is more evidence, but exploring that evidence will require delving into the social sciences, particularly psychology, to elicit reasonable conclusions about the structure of experience and selfhood.

In this context, faith is a decision one makes when reason based on empirical evidence does not apply or cannot guide our logic.  But there are other kinds of evidence and that brings me back to consciousness and the role of empirical evidence in understanding consciousness. 

David Chalmers has probably done more than any other philosopher towards putting the science of consciousness on sound footing.  But his most contentious position is that there are two paths for making progress in consciousness studies.  One path is the traditional and reliable reductionist path where complex mental processes are explained in terms of simpler, experimentally verified biological functions.  The reductionist path can explain how the brain works and therefore what brain functions are necessary for consciousness.  Chalmers calls this the “easy” question, and it is a long way from being answered.  The second path has the very difficult problem of dealing with the experience of consciousness and why the sensation of being conscious arises from brain function.  I have phrased this second question as the question about the ontology of selfhood: why is it that we have a self with which to experience life?

Chalmers insists that the second question cannot be answered from function alone and he posits a new category to deal with the “hard” question.  Taking a clue from historical scientific efforts to subject new phenomenon to reason, he favors creating a new fundamental category for subjective experience:

I suggest that a theory of consciousness should take experience as fundamental. We know that a theory of consciousness requires the addition of something fundamental to our ontology, as everything in physical theory is compatible with the absence of consciousness. We might add some entirely new nonphysical feature, from which experience can be derived, but it is hard to see what such a feature would be like. More likely, we will take experience itself as a fundamental feature of the world, alongside mass, charge, and space-time. If we take experience as fundamental, then we can go about the business of constructing a theory of experience.

Chalmers also proposes that a bridging theory can be constructed that will correlate subjective experience with brain function and this might take 100 years for meaningful progress to occur.  Others are not so sure.  Daniel Dennett does not think the hard problem is real.  For Dennett, consciousness is an epiphenomenon; it is an illusion generated by biological function.  He thinks that consciousness is adequately explained by a reductionist approach that explains brain function biologically, neurologically or computationally.  On the other hand, both Thomas Nagel and John Searle think that the hard problem of consciousness cannot be scientifically solved at all.   For them, consciousness is real but it must be explained philosophically.

Subjective experience may be the essential evidence necessary for consciousness science, but I think that it must be organized around a concept of self in order to be coherent and have an impact on our life.  We usually are not concerned with simply reporting individual and isolated experiences; we report and attempt to make sense of what these experiences mean for ourselves.  I think the fundamental entity is a sense of self; in other words, it is human self-consciousness that is the interesting phenomenon psychologically, philosophically and theologically.  And there already exists methods for dealing with experiential self-consciousness in the only universe we know about: developmental psychology, existentialism and process theology.

Developmental psychology has shown that there is a crucial point in the development process around 18 to 36 months where self-awareness appears.  If self-awareness can be equated with self-consciousness, then the structure of self-consciousness can be described through the analysis of psychological states arising at about the same time, namely empathy, embarrassment, shame and guilt.  But such an analysis must await another series.

Thomas Nagel once wrote a paper titled, “What is it Like to Be a Bat?”  The interesting question going forward is what is it like to be a self?  H. Richard Niebuhr’s contribution to this question has been formative for me, so I expect future expositions to be based on this seminal quotation from The Meaning of Revelation: “To be a self is to have a god; to have a god is to have history, that is, events connected in a meaningful pattern”.  And, according to Niebuhr, a “god” can be any power to which we intentionally relate ourselves.

I began this series in order to examine the role of reason for a person of faith.  I believe that a mature faith must resolve certain issues with respect to science and with respect to history.  This portion has dealt only with the physical sciences, and it has confronted the question of the kind of god that is compatible with science.  I have followed the best science that I know of, but I have also woven a narrative through the scientific evidence to elucidate something of the nature of the universe and its creator.  This narrative is not meant as proof; it is an exercise in metaphysics, but it demonstrates to me that faith is compatible with science and that science informs us about how God is likely to interact with us.  Not only does science not disprove the existence of God, it provides the essential evidence for a cosmic ordering power which is, if one choses, the hand of God.  I hope my future essays will explain possible motivations for making such an affirmation.

Consciousness (Part 1)

So far, in this series on the evidence for a conscious, rational power working in and through the laws of nature, I have followed the trail of low entropy.  I have used a general notion of entropy where low entropy correlates with an increasing degree of order or where it correlates with an increasing concentration of energy.  Consequently, high entropy means a state of disorder or a state of energy dispersal, most often as wasted heat.  I began with the amazing state of low entropy (highly ordered, high energy concentration) in which the universe was created.

I followed the trail of low entropy through the complex of mathematically precise physical laws that represent the incredible ordering power of nature.  I spoke of lasers, superconductivity and photosynthesis as supreme examples of entropy lowering processes.  I looked at the incredibly diverse life processes, all based on DNA, RNA and protein synthesis, that would be impossible without the information coding capability and the molecular machines of the individual cell.  I described the computer-like processing capability of individual proteins and the inexplicable speed with which they fold into the precise shape for their purpose.

I have tried to avoid the teleological language of purposeful design, but when one looks at the trail from creation to conscious being, it is difficult to avoid the question.  Random chance cannot account for this remarkable journey.  The probabilities are just too small for undirected forces to have arrived at living beings that maintain low entropy and rely on entropy lowering processes.  This implies, to me at least, that the laws of physics are favorable to life and consciousness.  What is it that has driven evolution to the point of prizing consciousness almost above other considerations?  Consciousness requires a huge energy budget; why should our brains deserve a 20% allocation of energy if not for its powerful entropy lowering ability?

An incredible panoply of ordered life flows from the human imagination.  There is language, art, drama, literature, music and dance in addition to the social inventions of government, economic systems, justice systems, cultural institutions, family and kinship groups.  One could almost say that the creation of explicitly ordered social structures defines humanity.  And yet there is a profound puzzle in the pervasive human tendency to sow discord.  Why should that be?  Why are there wars, violence, terrorism, and dysfunctional social institutions if the human imagination can be so productive?

In discussing these and other questions of consciousness, I will attempt to follow my reductionist approach by relating emergent phenomenon to the dynamics and properties of constituent components.  However, there will come a point where this approach will fail and I will need to resort to different language to describe what I consider to be the key dynamic of consciousness: the self and its narrative.  Consciousness cannot be completely understood based on functional descriptions of biological or physical components.  But first, let me turn to the attempt to explain consciousness in term of computation.

Considering that order emerges from entropy lowering processes, it is odd that some observers think that consciousness and intelligence emerges from random, chaotic activity.  Pure randomness results in high entropy, so how can order be produced from chaos?  One such person is Ray Kurzweil, a futurist, who has written a book titled The Singularity is Near.  He states, “Intelligent behavior is an emergent property of the brain’s chaotic and complex activity.”  Neither he nor anyone else can explain how entropy lowering intelligence can emerge from random, chaotic activity.  He does, however, distinguish intelligence from consciousness.  He cites experiments by Benjamin Libet that appear to show that decisions are an illusion and that “consciousness is out of the loop.” Later, he describes a computer that could simulate intelligent behavior: “Such a machine will at least seem conscious, even if we cannot say definitely whether it is or not.  But just declaring that it is obvious that the computer . . . is not conscious is far from a compelling argument.”  Like many others, Kurzweil thinks that consciousness is present if intelligence can be successfully simulated by a machine.

Kurzweil is an optimistic supporter of the idea that the human brain will be completely mapped and understood to the point where it can be entirely simulated by computation.  He has predicted that this should occur in the fifth decade of the 21^st century: “I set the date for the Singularity – representing a profound and disruptive transformation in human capability – at 2045.  The nonbiological intelligence created in that year will be one billion times more powerful than all human intelligence today.”  Kurzweil’s prediction is based on the number of neurons in the human brain and their many interconnections, arriving at a functional memory capacity of 10¹⁸ bits of information for the human brain (10¹¹ neurons multiplied by 10³ connections for each neuron multiplied by 10⁴ bits stored in each of the synaptic contacts.)

Kurzweil welcomes this prospective technological leap as a great advancement in the intellectual potential for the world.  He writes about his vision for the world after the singularity which he names the fifth epoch: “The fifth epoch will enable our human machine civilization to transcend the human brain’s limitations of a mere hundred trillion extremely slow connections.”  He goes on to say that eventually this new paradigm for intelligence will saturate all matter and spread throughout the universe.  Kurzweil appears to have the opposite perspective from my own view which is that the universe began with consciousness and consciousness infused all matter from the beginning.

But other people look at Kurzweil’s predictions and are concerned.  I recently read an opinion piece by Huw Price in the New York Times about the dangers of artificial intelligence (AI).  Huw Price was on his way to Cambridge to take up his newly appointed position as Bertrand Russell chair in Philosophy.  He had met the AI researcher named Jaan Tallinn, one of the developers of Skype, on his way to his new job.  Tallinn was concerned that AI technology would evolve to the point where it could replace humans and through some accident the computers would take control.  So Tallinn and Price joined up with Martin Rees, a cosmologist with a strong interest in biotechnology, to form a group called the Center for Study of Existential Risk (CSER).  I suspect that the group will focus more on the risk to human life posed by biotechnology rather than from AI, but the focus of Price’s column was on the risk from artificial intelligence.

Professor Price presented the argument that, although the risk of such a computer takeover appears small, it shouldn’t be completely ignored.  Perhaps he has a valid point, but what are the empirical signs that such computer intelligence is near at hand?  Some might point to the victories in 2011 of IBM’s Watson computer over all challengers in the Jeopardy game show.  This was an impressive demonstration of computer prowess in natural language processing and in database searching, but did Watson demonstrate intelligence?  I think that Ray Kurzweil would answer yes.  To the extent that the Jeopardy game demonstrates intelligence, then, by that measure, Watson must be considered intelligent.

However, consider the following subsequent development.  In a recent news report, Watson was upgraded to use a slang dictionary called the Urban Dictionary.  As that source puts it,

“[T]he Urban Dictionary still turns out to be a rather profane place on the Web. The Urban Dictionary even defines itself as ‘a place formerly used to find out about slang, and now a place that teens with no life use as a burn book to whine about celebrities, their friends, etc., let out their sexual frustrations, show off their racist/sexist/homophobic/anti-(insert religion here) opinions, troll, and babble about things they know nothing about.’”  (From the International Business Times, January 10, 2013, “IBM’s Watson Gets A ‘Swear Filter’ After Learning The Urban Dictionary,” by Dave Smith.)

One of Watson’s developers, Eric Brown, thought that Watson would seem more human if it could incorporate slang into its vocabulary so he taught Watson to use the slang and curse words from the dictionary.  As the news report continued,

“Watson may have learned the Urban Dictionary, but it never learned the all-important axiom, ‘There’s a time and a place for everything.’ Watson simply couldn’t distinguish polite discourse from profanity.  Watson unfortunately learned all of the Urban Dictionary’s bad habits, including throwing in overly -crass language at random points in its responses; in answering one question, Watson even reportedly used the word ‘bullshit’ within an answer to one researcher’s question. Brown told Forbes that Watson picked up similarly bad habits from reading Wikipedia.”

Perhaps the news story should have given us the researcher’s question so we could make our own decision about Watson’s epithet!  Eric Brown finally removed the Urban Dictionary from Watson.

In short, Watson was very good at what it was designed to do:  win at Jeopardy.  But it lacked the kind of social intelligence needed to distinguish appropriate situations for using slang.  It also appeared to lack a mechanism for learning from experience that some situations were inappropriate for slang or how to select slang words based on the social situation.  Watson was ultimately a typical computer system that had to be modified by its developers.  I know of no theoretical framework in which a computer system could maintain and enhance itself.

Now consider another facet of Watson verses Jeopardy contestant.  Our brain requires about 20% of our energy.  For a daily energy requirement of 2000 Calories, that amounts to 400 Calories for human mental activity.  That works out to about 20 watts of power.  In terms of electricity usage, that is less than 6 cents per day in my area.  Somewhat surprisingly, the number of brain energy calories does not much depend on one’s state of alertness.  The brain uses energy at about the same rate even when you sleep.  Watson, in contrast, used 200,000 watts of power during the Jeopardy competition.  That computes to about $528 per day.  If computers are to compete with humans for evolutionary advantage, it seems to me that they will need to be much more efficient users of energy.

In fact the entire idea of comparing computers to human mental activity is absurd to many people.  Perhaps I have even encouraged this analogy by speaking of quantum computation relative to biological molecules.  But I think it will become very apparent that any putative quantum computation must be something quite unlike ordinary computer calculations.  Mathematician and physicist, Roger Penrose, thinks that the fact that human mathematicians can prove theorems is evidence for quantum computation and decisionality in human consciousness.  But he also thinks that quantum computation must have capabilities that ordinary computers do not have.

John Searle is a Philosophy Professor at UC Berkeley and thinks that the current meme that the brain is a computer is simply a fad, no more relevant than the metaphors of past ages: telephone switchboard or telegraph system.  Professor Searle supports consciousness as a real subjective experience that is not open to objective verification.  It is therefore possible to explore consciousness philosophically, but not as an objective, measurable phenomenon.  Professor Searle is known for his example of the “Chinese Room,” where Chinese is mechanically translated into English, but where Searle claims there is no real understanding of what is being translated.  Searle states, “. . . any attempt to produce a mind purely with computer programs leaves out the essential features of mind.”

Closely related to the “Chinese Room” is the Turing test which seeks to demonstrate that a computer can simulate a human being well enough to fool another person.  In the Turing test, a person, the test subject, sits at a computer terminal which is connected to either another person sitting at a keyboard or to a computer.  The task of the test subject is to determine, by conversation alone, whether he or she is dialoging with another person or a computer.  An actual test has been held each year since 1990 and prizes awarded. So far, no computer program has been able to fool the required 30 percent of test subjects.  Nevertheless, the computer program that fools the most test subjects wins a prize.  People also compete with each other because half of the test subjects are connected to other persons who must try to demonstrate some characteristic in the dialog that will convince the test subject that he or she is really talking to another person.  The person who does best at convincing test subjects that they are communicating with another person wins the “Most Human Human” award.  In 2009, Brian Christian won that prize and wrote a book about his experience: The Most Human Human: What Talking with Computers Teaches Us About What it Means to Be Alive.

One of Brian Christian’s key insights in his book is that human beings attempt to present a consistent self-image in any public or interpersonal encounter.  In a dialog with another person, there is a striving to get beyond the superficial in order to reveal something of the personality underneath.  But the revealed personality is not monolithic; there are key self-referential elements of the conversation that reveal other possibilities.  Nevertheless there is a strong commitment to an underlying self-image, even if that self-image is ambiguous:

“[The existentialist’s] answer, more or less, is that we must choose a standard to hold ourselves to. Perhaps we’re influenced to pick some particular standard; perhaps we pick it at random. Neither seems particularly ‘authentic,’ but we swerve around paradox here because it’s not clear that this matters. It’s the commitment to the choice that makes behavior authentic.”

Authentic dialog, therefore, contains elements of consistent self-image and commitment to that self-image in spite of ambiguity and paradox.  A strong sense of self-unity underlies the sometimes fragmentary nature and unpredictable direction that human discourse often takes.  This is very difficult for a computer to simulate.

I think the risk from AI is so minuscule that it doesn’t deserve the level of concern that Jaan Tallinn was portrayed as having in Huw Price’s article.  There are two main assumptions in the assessment of risk that are very unlikely to be substantiated.  One assumption is that sheer computing power will lead to a machine capable of human intelligence within any reasonable time frame.  The second assumption is that such a machine, if created, could somehow replace humans in an evolutionary sense.

There are two problems with the first assumption, one theoretical and one practical.  The theoretical problem is that there is a limit to the true, valid conclusions that any automated system can achieve.  This limitation is called “Gödel Incompleteness.”  It means that for any system powerful enough to draw useful conclusions, there will still remain true conclusions that cannot be reached by computation alone.  In computer theory, this is called the “halting problem.”  The halting problem states that it is impossible to create a computer program that can decide whether any other computer program can halt or come to completion, producing a valid result.    The practical manifestation of the halting problem is that there is no way to introduce complete self-awareness into computer systems.  One can create modules that can simulate self-awareness of other modules, but the new module would not be self-aware of itself.  This limitation implies that human intelligence will always be needed to correct and modify computer systems.

(Roger Penrose’s book, Shadows of the Mind, presents the case for quantum consciousness in detail. A key part of his argument is that computers are fundamentally limited by “Gödel Incompleteness.”  This implies, according to Penrose, that quantum coherence plays a key part in consciousness and that quantum calculations are capable of decisions exceeding the power of any ordinary computer calculation)

The second problem with the first assumption is that it is very unlikely that a unified computer system with computing power of the human brain can be developed in any reasonable time frame.   Professor Price doesn’t say what a reasonable time frame might be, but Ray Kurzweil does, placing the date for the singularity at 2045.  Kurzweil’s assumption is that the human brain contains storage for 10¹⁸ bits (about 100 petabytes) of information.

In my previous post, I reported that Professor James Shapiro at the University of Chicago thinks that biological molecules are the most basic processing unit and not the cell.  This implies that Kurzweil should be using the number of molecules in the brain rather than the number of neurons.  Assuming about 10¹³ molecules per neuron, that increases the human brain capacity to about 10³¹ (10 trillion petabytes)!  This concept of storing large volumes of data in biological molecules has been confirmed by recent research where 5.5 petabytes of data have been stored in one gram of DNA.  Keep in mind that we are speaking only of storage capacity (and only for neurons, omitting the Glial cells) and not of processing power.  If the processing power of the biological molecule is aided by a quantum computation, then we have no current method for estimating the processing power of the human neuron.

Assuming that processing power is on a par with storage capacity, and assuming that computer capacity and power can double according to Moore’s law (every two years – another questionable assumption because of quantum limits), then there would need to be 40 doublings of storage capacity or about another 80 years beyond Kurzweil’s estimate of 2045.  That places the projection for Kurzweil’s “singularity” well into the twenty-second century.

The second assumption is that sufficiently advanced machine intelligence, if it could be developed, would be able to replace humans through evolutionary competition.  I have already mentioned the energy efficiency disadvantage for current silicon-based computers:  200 kilowatts for Watson’s Jeopardy performance versus 20 watts for human intelligence.  I have also described the impossibility of computer algorithms which could in principle modify themselves in an evolutionary sense.  I can also discount approaches based on evolutionary competition in which random changes are arbitrarily made to computer code.  I have seen too many attempts to fix computer programs by guesswork that amounts to little more than random changes in the code.  It doesn’t work for computer programmers and it won’t work for competing algorithms!

My conclusion is that the main practical threat to human intellectual dominance will be biological and not computational (in addition to our own self-destructive tendencies).  That leaves open the possibility for biological computation, but that threat is subsumed by the general threat of biological genetic engineering and by the creation of biological environments that are detrimental to human health and well-being.

I have taken this lengthy excursion into the analysis of the computer / brain analogy in order to eliminate it as one path toward understanding consciousness.  The idea that computation can produce human consciousness is an example of functionalism:  the concept that a complete functional description of the brain will explain consciousness.  Human consciousness is a complex concept which resists empirical exploration.  Let’s look at the key problem.

David Chalmers is professor of philosophy at Australian National University and has clearly articulated what has become known as the hard problem of consciousness.  In his 1995 paper, “Facing up to the Problem of Consciousness,” he first describes the easy problem.  The easy problem is the explanation of how the brain accomplishes a given function such as awareness or articulation of mental states or even the difference between wakefulness and sleep.  This last category, when pushed to consider different states of awareness, previously had seemed to me to be the most promising path towards understanding consciousness.

It has been known for some time that there are different levels of consciousness that are roughly correlated to the frequency of brain waves which can be measured by electroencephalogram (EEG).  Different frequencies of brain waves have traditionally corresponded to different levels of alertness.  The frequency range that seems to hold the most promise for understanding consciousness are the gamma waves at roughly 25 to 100 cycles per second (Hz or Hertz).  40 Hz is usually cited as representative.  In 1990, Francis Crick (co-discoverer of the DNA structure) and Christof Koch proposed that the 40 Hz to 70 Hz was the key “neural correlate of consciousness.”  The neural correlate of consciousness is defined to be any measurable phenomenon which can substitute for measuring consciousness directly.

The neural correlate of consciousness is a measurable phenomenon; and measurable events are what distinguish the easy problem from the hard problem of consciousness.  The easy problem is amenable to empirical research and experiment; it explains complex function and structure in terms of simpler phenomenon.  The hard problem, by contrast, raises a new question: how is it that the functional explanation of consciousness (the easy question) produces the experience of consciousness or how is it that the experience of consciousness arises from function?  As Chalmers says, why do we experience the blue frequency of light as blue?  Implicit in this question is the idea that consciousness is unified despite different functional impact.  Color, shape, movement, odor, sound all come together to form a unified experience; we sense that there is an “I” which has the unified experience and that this “I” is the same as the self that has had a history of similar or not so similar experiences.  My rephrasing of the hard question goes like this: how is it that we have a self with which to experience life.

Chalmers thinks that a new category for subjective experience will be needed to answer the hard question.  I think that such an addition is equivalent to adding consciousness as a basic attribute of matter.  That is what panpsychism asserts, and I think that the evidence from physics, chemistry and biology supports the panpsychist view.  I think panpsychism leads directly to experiences of awareness, consciousness and self-consciousness and that the concept of a self-reflective self is the natural conclusion of such a thought process.  David Chalmers thinks that the idea has merit, but differentiates his view from panpsychism, saying “panpsychism is just one way of working out the details.”

My next post will conclude this series and will directly present the theological question.

The Evidence from Evolution and Biology (Part 3)

In part 2 of this series on evolution and biology, I presented my analysis on the origin of life and my conclusion that life could not have arisen through random chance alone.  I have concluded along with other observers that the laws of physics and chemistry must be conducive to the creation of life and that such laws are evidence for a cosmic ordering power.  The question remains, however, what part does random chance play once life was created?  In part 1 of this series, I raised the question about the role that random mutations play in natural selection.  In this part, I will present evidence that natural selection does not rely entirely on random mutation and that there is at least some portion of natural selection that relies on directed mutation.

The most likely systematic way to create random changes in DNA is through copying errors.  One of the first researchers to deal rigorously with copying errors was Manfred Eigen with his “quasi-species” model.  In this mathematical model of natural selection, survival and fitness to survive are balanced against replication errors.  Here is Freeman Dyson’s description of the problem:

The central problem for any theory of the origin of replication is that a replicative apparatus has to function almost perfectly if it is to function at all. If it does not function perfectly, it will give rise to errors in replicating itself, and the errors will accumulate from generation to generation. The accumulation of errors will result in a progressive deterioration of the system until it is totally disorganized. This deterioration of the replication apparatus is called the “error catastrophe.”

Eigen’s model sets a theoretical limit on the allowable error rate necessary to avoid the “error catastrophe.”  It turns out that the maximum error rate is approximately the inverse of the number of DNA base pairs.  So for humans with about 3.2 billion base pairs, the calculated maximum error rate is about 10^-9, or 1 error in 1 billion cell divisions.  This is consistent with the actual error rate after proofreading and repair of the copied DNA.

But some copying errors will still survive.  What becomes of them?  James A. Shapiro is professor of microbiology at the University of Chicago.  In his book, Evolution: A View from the 21^st Century, he writes, “Although our initial assumption is generally that cells die when they receive an irreparable trauma or accumulate an overwhelming burden of defects with age . . ., it turns out that a significant (perhaps overwhelming) proportion of cell deaths result from the activation of biochemical routines that bring about an orderly process of cellular disassembly known by the terms programmed cell death and apoptosis.”  In multicellular species, there is an elaborate signaling system for causing some cells to die.  This process is not necessarily disease related.  During embryonic development, some tissues grow that need to be eliminated before birth such as the webs that connect fingers and toes.  These are eliminated by apoptosis (programmed cell death).  This process also happens to embryonic neurons that do not have sufficient interconnections to be viable.  The implication of this response is that organisms have elaborate capability for determining when some cells need to be eliminated.  Some cancers are caused by problems with the apoptosis response.

Before proceeding to the evidence for directed mutation, I want to encourage an appreciation for the enormous orchestration that occurs inside the cell.  As an observer of the biological sciences, I am constantly amazed by the incredible variability and responsiveness of living cells.  If you have never watched videos or animations of cell division or other cellular processes, I would urge you to do so.   They are simply fascinating!  And part of what makes for a fascinating view is the complex orchestration that is happening inside the cell.    Here is a video dealing with mitosis, but there are many others:  http://www.youtube.com/watch?v=C6hn3sA0ip0.  A longer, more advanced animation on the cellular response to inflammation is here:  http://www.youtube.com/watch?v=GigxU1UXZXo&NR=1&feature=fvwp.

Another amazing aspect of cellular function and orchestration is protein folding.  In order for proteins to be effective, they must be folded into a three dimensional shape that is suited to their purpose.  As I explained in my previous post, the protein enzyme, sucrase, performs its function of splitting table sugar (sucrose) into the more easily metabolized glucose and fructose by “locking onto” the sucrose molecule.  Biologists have often used the analogy of a lock and key to explain the fitting of enzymes to their target molecules.

Protein misfolding plays a part in several disease processes including Alzheimer’s disease, Creutzfeldt-Jakob disease (a form of “mad cow disease”), Tay-Sachs disease and sickle cell anemia.  In sickle cell anemia the protein misfolds because of a mutation that alters the sequence of amino acids in one of the blood proteins needed to construct hemoglobin.  In the case of Creutzfeldt-Jakob disease, the cause of protein misfolding has not been conclusively identified, but may be due to an “infectious protein” called a Prion.  A Prion is a normal human protein in the cell membrane that has misfolded and that causes other normal protein to misfold which results in brain tissue degeneracy.  It would be unprecedented if it is conclusively proved that Creutzfeldt-Jakob disease is caused by Prions because all other known disease agents involve replication or modifications to DNA.

The instructions for protein folding are not contained in DNA (although the amino acid sequence is a crucial aspect), but correct folding is absolutely necessary for good health.  DNA provides the peptide sequence information and it is the task of the completed protein, after it has been manufactured by a ribosome, to fold into the correct shape.  In human cells there are regulatory mechanisms for determining whether a protein has folded into the correct shape.  If a protein has misfolded, it can be detected and the protein can be disassembled.  Some proteins have the help of chaperones as mentioned in my previous post.  Here is an animation of a short 39 residue segment of the ribosomal protein L9, identified as “NTL9”, shown folding by computer simulation:  http://www.youtube.com/watch?v=gFcp2Xpd29I.  (The full protein from Bacillus stearothermophilus is just one of many that make up a ribosome.  It contains 149 amino acids and functions as binding protein to the ribosomal RNA.)

Proteins fold at widely varying rates, from about 1 microsecond to well over 1 second with many folding in the millisecond range.  The quickness with which most proteins fold led to an observation in 1969 by Cyrus Levinthal that if nature took the time to test all the possible paths to a correct final configuration, it would take longer than the age of the universe for a protein to fold.  It is now thought that proteins fold in a hierarchical order, with segments of the protein chain folding quickly due to local forces so that the final folding process only need configure a much smaller number of segments.  Nevertheless, simulations of protein folding often require huge computational resources to recreate the folding sequence.  One source estimated that it would take about 30 CPU years to simulate one of the fastest folding proteins.  A slower protein would require 100 times the resources, or about 3000 CPU years.

So Levinthal’s question has not been completely answered.  How does nature enable proteins to fold so quickly?  The prevailing theory on folding holds that the various intermediate states are following an energy funnel from a high energy state (unfolded) to the lowest energy state (folded).  Just as water seeks its lowest level, proteins seek the conformation that has the lowest energy.  The explanation for the wide variety of folding rates then rests on the nature of the path from the unfolded energy state to the folded energy state.  If the path is straight, the folding will be fast; if the path has energy barriers that must be circumnavigated or perhaps tunneled through, the folding will be slower.  These issues are still in active research, so there is currently no clear consensus.  But in a recent paper, two researchers conclude “Our results show it is necessary to move outside the realm of classical physics when the temperature dependence of protein folding is studied quantitatively” (“Temperature dependence of protein folding deduced from quantum transition”; 2011, Liaofu Luo and Jun Lu).

I simply point out the similarity to the research on photosynthesis that showed that photons captured by photosynthesis follow a highly efficient path to the place where the photon’s energy can be turned into food production.  That research showed that quantum coherence played a significant role in the efficient transfer of energy and it was thought by analysts that a quantum computation of the energy landscape was a key part of the explanation.  It would not surprise me if quantum computation played a key role in protein folding by determining the most efficient path for navigating the energy funnel.  But without regard to whether quantum computation plays a role in protein folding, some scientists have not hesitated in applying the computer analogy to cell function.

Paul Davies is a physicist and science advocate who contrasted the vitalism of the 19^th century with our understanding of biology today by saying, “The revolution in the biological sciences, particularly in molecular biology and genetics, has revealed not only that the cell is far more complex than hitherto supposed, but that the secret of the cell lies not so much with its ingredients as with its extraordinary information storing and processing abilities. In effect, the cell is less magic matter, more supercomputer.”

James A. Shapiro continues the computer metaphor when he writes about the cognitive ability of the cell. In his book, Evolution: A View from the 21^st Century, he writes about the cell’s ability to regulate and control itself using a number of examples such as repair of damaged DNA, programmed cell death,  and regulation of the process of cell division.  He then continues to characterize the cell in computer-like terms (my emphasis):

The selected cases just described are examples where molecular biology has identified specific components of cell sensing, information transfer, and decision-making processes. In other words, we have numerous precise molecular descriptions of cell cognition, which range all the way from bacterial nutrition to mammalian cell biology and development. The cognitive, informatic view of how living cells operate and utilize their genomes is radically different from the genetic determinism perspective articulated most succinctly, in the last century, by Francis Crick’s famous “Central Dogma of Molecular Biology.“

Shapiro goes on to suggest modification to the “Central Dogma of Molecular Biology.”  The “Central Dogma” summarizes the process of protein creation from RNA which is transcribed from DNA.  Dr. Shapiro suggests that this one way summary is too simple.  There are many paths through which RNA and proteins can modify the DNA.  The primary example of RNA which can modify DNA comes from retroviruses.  The well-known HIV virus is one example.  Retroviruses contain RNA which is transcribed into proteins that can convert the RNA into DNA and then insert the viral DNA into the host DNA.  It is estimated that between 5% and 8% of the human genome is comprised of DNA that has been inserted from retroviruses.

Dr. Shapiro also uses computer programming terminology when describing detailed biological function such as E. coli’s ability to metabolize lactose when glucose is not available: “Overall computation = IF lactose present AND glucose not present AND cell can synthesize active LacZ and LacY, THEN transcribe LacZY from LacP.”  That is a statement that could be implemented in almost any standard computing system with, of course, the proper functions available for “synthesize” and “transcribe,” etc.  I would also point out that a significant portion of a cell’s “cognitive” function is concerned with self-regulation.  In other words, there is a significant amount of self-knowledge available to the cell.

Professor Shapiro itemizes five general principles of cellular automation processing:

1. There is no Cartesian dualism in the E. coli (or any other) cell. In other words, no dedicated information molecules exist separately from operation molecules. All classes of molecule (proteins, nucleic acids, small molecules) participate in sensing, information transfer, and information processing, and many of them perform other functions as well (such as transport and catalysis).
2. Information is transferred from cell surface or intracellular sensors to the genome using relays of proteins, second messengers, and DNA-binding proteins.
3. Protein-DNA recognition often occurs at special recognition sites.
4. DNA binding proteins and their cognate formatting signals operate in a combinatorial and cooperative manner.
5. Proteins operate as conditional microprocessors in regulatory circuits. They behave differently depending on their interactions with other proteins or molecules.

Regarding evolution, Dr. Shapiro advocates a concept called “natural genetic engineering” whereby the cell makes adaptive and creative changes to its own DNA.  I have used the phrase “directed mutation” to mean essentially the same thing.  These changes to a cell’s own DNA are not random: “It is difficult (if not impossible) to find a genome change operator that is truly random in its action within the DNA of the cell where it works. All careful studies of mutagenesis find statistically significant nonrandom patterns of change, and genome sequence studies confirm distinct biases in location of different mobile genetic elements. These biases can sometimes be extreme . . . “

In a recent article, Professor Shapiro further clarified his use of the phrase, “natural genetic engineering,” or NGE:

NGE is shorthand to summarize all the biochemical mechanisms cells have to cut, splice, copy, polymerize and otherwise manipulate the structure of internal DNA molecules, transport DNA from one cell to another, or acquire DNA from the environment. Totally novel sequences can result from de novo untemplated polymerization or reverse transcription of processed RNA molecules.

NGE describes a toolbox of cell processes capable of generating a virtually endless set of DNA sequence structures in a way that can be compared to erector sets, LEGOs, carpentry, architecture or computer programming.

NGE operations are not random. Each biochemical process has a set of predictable outcomes and may produce characteristic DNA sequence structures. The cases with precisely determined outcomes are rare and utilized for recurring operations, such as generating proper DNA copies for distribution to daughter cells.

It is essential to keep in mind that “non-random” does not mean “strictly deterministic.” We clearly see this distinction in the highly targeted NGE processes that generate virtually endless antibody diversity.

In summary, NGE encompasses a set of empirically demonstrated cell functions for generating novel DNA structures. These functions operate repeatedly during normal organism life cycles and also in generating evolutionary novelties, as abundantly documented in the genome sequence record.

(From What Natural Genetic Engineering Does and Does Not Mean, Huffington Post, February 28, 2013.)

Perhaps the most important evidence for natural genetic engineering is the discovery of transposable elements in the DNA.  These were first identified by Barbara McClintock in 1948 and for which she was awarded the Nobel Prize.  Transposable elements, also called transposons and retrotransposons, are segments of DNA that can move or be replicated into another part of the DNA molecule.  In general, this process can be either a “cut and paste” or a “copy and paste” operation using special proteins to operate on the DNA, sometimes with RNA as an intermediary molecule.

Retrotransposons makes up a significant portion of the human genome, about 42%.    One type of transposon, called an “Alu” sequence, is about 10% of the human genome and is one of the main markers for primates (including humans).    However, almost all transposable elements are contained within the non-coding region of DNA and therefore and not directly expressed as proteins.  This DNA has typically been called “junk DNA,” but recent research from the ENCODE project (“Encyclopedia Of DNA Elements”) has demonstrated a wide variety of function for the non-coding portions of DNA.

I have to mention that, as a computer designer and coder, this discovery of movable elements in the non-coding regions of DNA remind me of one of the most common ways we would modify computer programs.  First, we would locate an old segment of code that functioned similar to the desired new function.  Then we would copy that segment into another part of the program, but leave it unexecuted until the new segment was modified to accomplish its intended new function.  Finally we would activate the new segment and test it.  Nevertheless, DNA represents computational capabilities that I have never seen in any existing computer system.  It has now been demonstrated that the so called “junk DNA” has the ability to affect the “non-junk” portion of the genome by controlling when or whether certain proteins are expressed.

Continuing with the computer analogy, Freeman Dyson also speaks about DNA as a computer program, characterizing DNA as software and proteins as hardware.  I think that is a little too simple since individual proteins exhibit many cognitive abilities described by Dr. Shapiro.  Each separate molecule in the cell, including proteins, has its own processing capability.

One way the Professor Dyson is correct, though, is through the discovery of proteins as molecular machines. This is another fascinating area of biology.  Many of the functions of the cell are carried out by proteins that can best be described as miniature machines.  One important example is the ATP generator which is used to make ATP in the Mitochondria.  ATP, or Adenosine Triphosphate, is the main energy molecule for almost all forms of life.  This ATP generator or ATP synthase looks remarkably like a tiny motor.  This “motor” is powered by a hydrogen ion concentration differential across the mitochondria membrane.  The hydrogen ion concentration is generated by molecular pumps which push the hydrogen ions (protons) across the membrane.  An animation of ATP synthase follows:  http://www.youtube.com/watch?v=PjdPTY1wHdQ.

The implications of all the above biology for lowering entropy are enormous.  The molecular machines are themselves an example of low entropy, being a highly structured, functional set of proteins.  The pumping of protons across a membrane is using some energy to create a state of low entropy by concentrating energy at a particular location.  The ATP itself is a storehouse of energy for future use.  Protein folding is another entropy lowering process. The DNA specifying the information necessary to manufacture proteins is perhaps the supreme example of low entropy, particularly now with the discovery of purposeful “junk DNA.”  One could easily conclude that all of life is powered by of the miracle of low entropy overcoming the global tendency for entropy to increase.

Life can be viewed as a struggle to maintain low entropy.  We need sources of low entropy to live: food, shelter and energy, etc.  The ultimate source of low entropy is the sunlight used to create carbohydrates from plants.  However, once our low entropy material needs are secured, we seek an ordered personal life, family life, and social life.  Some say that old age is the result of the loss of our ability to maintain low entropy.  In other words, life is a struggle to maintain low entropy in the face of the law of increasing entropy.  As individuals, we will lose that struggle since death is certain.  As a species, however, the trend towards low entropy, towards more complex ordering, can continue.

Before life began to evolve, matter on earth was subject to laws of physics and chemistry.  One of those laws is the law of increasing entropy: low entropy sunlight is absorbed and then radiated back into space as high entropy heat.  However, the laws of nature themselves contain a provision for entropy lowering interactions.  I strongly believe that such a provision is the result of the decisionality inherent in the collapse of the quantum wave function.  My reason for such a belief lies mainly in the order that results from entropy lowering interactions, especially the order inherent in life.  All of our human experience tells us that order results from rational decisionality; it does not result from randomness.  The mathematics of random chance rules out any likelihood that life arose by chance alone.

After life began to evolve, it naturally took advantage of entropy lowering processes.  Natural selection and fitness are crucially based of efficient use of energy.  There is a recent example of a prehistoric bird that had four wings, named microraptor.   Microraptor’s four wings allowed it to make tight turns around the many forest trees in its habitat.  However, four wings caused additional drag and consequent loss of speed and energy.  It therefore took microraptor more energy to accomplish what modern birds can do. Modern birds evolved two wings with additional muscle control for improved maneuverability but without the additional drag of a second set of wings.  Efficient use of energy is crucial for survival.

It is therefore very surprising that nature and evolution would have allocated a single organ in humans that requires 20% of our energy, yet weighs only about 2% of our total weight.  That is the amazing, almost unbelievable, statistic for the brain.  If we view human life as the pinnacle of evolution, then the entire evolutionary path must proceed towards higher consciousness and higher intelligence.  Therefore, if Professor Shapiro is right about natural genetic engineering (and I am convinced he is – he draws upon a huge body of research done by others), then modification made at the cellular level must include a bias for enhanced consciousness.

In my next section, I will begin to address the evidence from consciousness.  This will be difficult because science can say very little about consciousness.  Some take the position that consciousness is an epiphenomenon; that it emerges, ex novo, from complex calculations and therefore, has no real existence.  Some take the position that mind is a separate category from matter, leading to dualism.  I take the position that consciousness is embedded in matter, a position called panpsychism.  Furthermore, I hold the position that the way that consciousness has become embedded in matter is through the inherent decisionality of quantum decoherence.  One way to view this position is that the universe performs a quantum calculation on every transfer of energy.  But it would be a mistake to think that the calculation is the same as a calculation that could performed by a computer.  Stay tuned.

The Evidence from Evolution and Biology (Part 2)

The Origin of Life

(Thanks to all who took the time to comment on my previous post.  All the comments were helpful; as one who is attempting to summarize and draw conclusions from diverse areas of science, I sometimes struggle to find the right word or right example.  The comments on entropy were particularly helpful.)

The simplest living biological organisms that we know about are bacteria. (I am omitting viruses and infectious proteins because most biologists do not classify them as living due to their dependence on living cells.)  Bacteria are one-celled organisms without a well-defined nucleus.  Cells without a well-defined nucleus are called prokaryotes.   Nucleated cells, like those found in multi-celled organisms are called eukaryotes.  Bacteria are typically one tenth the size of eukaryote cells; they are less than 10 micrometers in length.

One of the smallest and simplest bacteria is an organism called mycoplasma genitalium.  This bacterium infects the urinary tract of humans and primates.  It is less than 300 nanometers long, or about one tenth the size of typical bacteria.  It also has one of the smallest sets of genetic code.  The amount of genetic code can be measured by the number of “base pairs.”  “Base pairs” are a count of the letters of the genetic code that make up the DNA of the organism: A (adenine), C (cytosine), G (guanine) and T (thymine).  They are called “pairs” because each letter is paired with another letter in the double-stranded DNA molecule: A is paired with T and C is paired with G.  The DNA of the bacterium, mycoplasma genitalium, contains about 583,000 base pairs.  The human genome, by comparison, contains about 3.2 billion base pairs.

The DNA of mycoplasma genitalium (M. genitalium) contains code for 482 proteins.  Recall that the genetic code for proteins is a group of three base pairs that refer to a specific amino acid of the twenty amino acids that comprise all proteins.    The average length of these proteins in M. genitalium is 366 amino acid molecules with a large range from smallest (37) to largest (1805).  The amount of DNA needed to code 482 proteins with and average length of 366 is 529,236 base pairs or about 91% of the genome.  For humans, the corresponding percentage is about 1.5%.  In humans, the overwhelming majority of DNA does not directly code for proteins and its function remains somewhat uncharted. (Although recently some light has been shed on this part of our genome by the ENCODE project.)

One of the smaller proteins of M. genitalium is known as “P47633” and functions as part of a protein complex known as a protein folding chaperone or “chaperonin.” P47633 is 110 amino acids long and is the “cap” to a much larger chaperonin, P47632 (543 amino acids).  The complete chaperonin of both P47633 and P47632 provide an isolated, barrel-shaped environment in which proteins can fold properly.  (Some proteins will fold properly without chaperonin.)    Proper folding is absolutely essential to protein function and misfolded proteins in humans have been correlated with certain diseases.

If nature had attempted to form a molecule as simple as P47633 with 110 amino acids by random chance, she would have had to search for a unique combination of 110 amino acids out of approximately 20¹¹⁰ (each of 110 positions can be filled by any of 20 amino acids)!  That is a huge number: approximately 1 followed by 143 zeroes!  A more realistic calculation would take into account that some amino acids can be substituted for others, but also that amino acids in nature come in two varieties (left and right handed) and biological molecules are only formed from left handed versions.  But the number would still be huge.  If nature could search at the rate of one combination in the smallest unit of time possible (Planck time), it would take about 10¹⁰⁰ seconds to find the protein.  That is well beyond the age of the universe (about 10¹⁷ seconds).  Even if the search were taking place at multiple locations (say 10⁸⁰ different locations—the number of protons and neutrons in the universe), the length of time would still exceed the age of the universe.  And that’s just for one small protein.

This simple calculation plus the fact that life requires numerous proteins, many of them much longer than 110 amino acids, have led many questers after the origin of life to discount the role of random chance.  Some think that the laws of nature are favorable to life, as I do.  Some think that the earliest organisms must have been much simpler and that more complex organisms such as M. genitalium would have been the product of natural selection.  The natural question to ask at this point is how simple were the initial forms of life?  Or, how simple could they have been?

If we knew how complex the initial living cells were, we could then evaluate whether such cells were the likely product of random molecular encounters.  When I first heard of the Miller-Urey experiment in high school chemistry class, I had the impression that soon we would know how life began.  That was over 50 years ago and we don’t appear to be much closer to solving the mystery of the beginning of life.  The Miller-Urey experiment showed that some amino acids could be produced in an atmosphere of water vapor, ammonia, methane, and hydrogen by passing an electric spark through those chemicals.  The concept presented to me then was that life arose from a primordial chemical soup formed by such chance events.  That idea has since been discredited.  The current thinking is that life began deep underground or underwater near a thermal source of energy.  But the key question remains: did it arise by chance or do the laws of physics and chemistry favor the creation of life?

We don’t know how complex the initial forms of life were, so I am using the simplest example of life that we now have to illustrate a point about the role for random chance in the beginning of life.  M. genitalium is one of the simplest living organisms that biologists have studied.  It has the additional advantage of being the subject of the Minimal Genome Project which seeks to find the simplest possible genome.  Toward that objective, each of the 482 protein coding genes of M. genitalium was individually and systematically deleted until a viable cell with 382 proteins was created in the laboratory.   The Minimal Genome Project provides a lower bound on the complexity of a viable living organism capable of both metabolism and replication.

Metabolism is the ability of cells to produce and use energy for homeostasis, or the ability of a cell to maintain itself in its typical environment.  Replication is the ability for a cell to pass along essential information to its progeny.  Metabolism is primarily protein driven biochemistry and Replication is primarily DNA / RNA driven cell division.  Since cell division involves metabolism (energy must be expended for a cell to divide), then replication requires some minimal functioning protein based chemistry.  Conversely, metabolism in the modern cell requires DNA directed protein creation, completing what is known as the “chicken and egg” conundrum for origin of life researchers.  Physicist Paul Davies sums up the puzzle: “It is hard enough to imagine one of them forming by chance, but to suppose both nucleic acids [DNA] and proteins were happy chemical accidents occurring at the same time and place stretches credulity.”

Not all scientists agree that the simplest original living organism had both the capability for metabolism and replication.  There appear to be two camps: one favoring metabolism priority and one favoring replication priority.  For example, Freeman Dyson has put forth an abstract mathematical model for metabolism priority that requires only 8 to 10 monomers.  In Dyson’s model, monomers could be amino acid molecules, so, if the model is predictive, it would indicate that cells with a stable metabolism could be achieved from proteins built from about half the amino acids we now have.  Dyson also indicates that “a few hundred polymers [proteins]” would be sufficient.  The problem with metabolism priority is that the resulting cells have no way to reliably pass on the precise composition of its proteins to its progeny (cell division would occur through external events and splitting due to growth).  Dyson argues that imprecise replication would be sufficient and actually better than an error-prone, directed replication.

If Dyson’s model is accurate, then the earliest cells would be appreciably less complex than M. genitalium with each protein needing between 10 and 100 amino acid molecules.  And there would be only a maximum of 10 amino acids.  This would reduce the probability due to random chance to between 1 chance in 10¹⁰ and 1 chance in 10¹⁰⁰, a large range with the lower number (1 chance in 10 billion) within reach of a reasonable random search.  Still, Dyson’s model needs “a few hundred polymers [proteins],” and the combination of over 100 proteins with the simplest protein needing 10 amino acids will give a large space for random combinations.  Dyson doesn’t say how many varieties of proteins there might be.

But Dyson’s model doesn’t completely rely on random chance.  The model contains provisions for nature to favor life.  Part of his model is a table of probabilities that the correct “proteins” will be formed from monomers (amino acids).  These factors are called catalyst “discrimination factors” and Dyson characterizes them as “reasonable for the discrimination factor of primitive enzymes.”  Their values in his model range from 60 to 100.  He goes on to say:

A modern polymerase enzyme typically has a discrimination factor of 5000 or 10000. The modern enzyme is a highly specialized structure perfected by three thousand million years of fine-tuning. It is not to be expected that the original enzymes would have come close to modern standards of performance. On the other hand, simple inorganic catalysts frequently achieve discrimination factors of fifty. It is plausible that a simple peptide catalyst with an active site containing four or five amino acids would have a discrimination factor in the range preferred by the model from sixty to one hundred.

This is significant because metabolism requires enzymes (a type of protein; Dyson’s “peptide catalyst”) which act as catalysts to speed up reaction rates.  Without enzymes, reaction rates would be too slow to sustain life.  One example is the way that we metabolize sugar for energy.  Table sugar is called sucrose and is a combination of glucose and fructose, but glucose is the sugar that we best metabolize.  So sucrose is first split into glucose and fructose.   Most table sugar comes from either sugarcane or sugar beets which create the sugar through photosynthesis.

The chemical reaction to split sucrose simply requires water and can occur spontaneously, but table sugar placed in a glass of water would not dissociate fast enough to be useful.  The reason the reaction would not take place quickly is because there is a cost in energy to break the bonds between glucose and fructose so that the water can interact.  Given enough time and heat, thermal activity would eventually begin to break the bonds between glucose and fructose.  However, we have an enzyme in our small intestine named “sucrase-isomaltase” which is able to greatly speed up the reaction.

Sucrase-isomaltase is a dual enzyme with the sucrase portion able to split sucrose into glucose and fructose while the isomaltase portion breaks apart the starch from grains.  The entire enzyme is 1877 amino acids long with the sucrase portion being 820 in length.  The sucrase portion works by locking onto the dual sugar sucrose and by proximity to its own molecular structure lowers the energy cost of breaking the covalent bond between glucose and fructose.  A water molecule is then able to intervene and complete the disassociation of the two sugars.  There are thousands of enzymes needed for metabolism; life would not be possible without them, so the enzyme efficiency is a key factor in any theory about the beginning of life.  Each enzyme is incredibly specific so that, in the case of sugar metabolism, a separate enzyme is needed for sugars from grain (the isomaltase portion).  Enzyme specificity is created by the sequence of amino acids and the shape of the protein.  Protein folding is a key factor.

Freeman Dyson is a physicist who has turned his attention to the chemistry of life’s beginning.  Frank Anet, a professor of biochemistry at UCLA, has criticized Dyson’s model as too simple.  This is a charge that Dyson freely admits since his objective was to start the conversation on the metabolism first approach, which is clearly a minority position.  The main benefit of Dyson’s model is that it gives mathematical results and Dyson insists that the real proof will be in experimental results.  But I fail to see how Dyson’s model could be sufficiently convincing to generate much interest from research labs.

Professor Anet goes on to level a more serious criticism of Dyson’s model:

The range of required discrimination factors is comfortably less than the discrimination factor of several thousands in modern enzymes, as would be expected, and it is similar to the discrimination factor of simple inorganic catalyst. However, the nature of these inorganic catalysts is not given, nor are the catalysed reactions, nor is any reference to the literature provided. No reference is made to any experimental discrimination factors by oligopeptides [small protein enzymes] in catalytic reactions involving closely similar compounds, such as amino acids, which would be the appropriate reference systems. Such a large discrimination factor, it must be stressed, is far more difficult to achieve than mere catalysis. Dyson’s oligopeptides have on the order of 20 monomers, with an ‘active site’ of perhaps five monomers. However, the other fifteen monomers are important in determining the folding of the polymer and therefore also the catalytic efficiency of the active site. Additionally, with such small oligopeptides, the folding is likely to be poorly defined. Thus, it can be concluded that Dyson has no good experimental evidence for choosing high discrimination factors, which are probably too high by at least an order of magnitude. Unfortunately, this destroys his model.

I’m sure that Dyson would repeat his caveat that he is only pointing the way and that empirical results are the domain of chemists, not physicists.  Nevertheless, until there are definitive results that lend credibility to small effective organic enzymes, I think metabolism priority will continue to be ignored.  Professor Anet also reviews several other researchers who do attempt to find more specific results, but finds them all lacking.

Professor Anet is a proponent of the “RNA world” approach.  This is currently the majority position for origin of life research.  It is a form of replication priority, but has the advantage that RNA has been demonstrated to function as a catalyst in some situations.  Only 6 monomers are needed to form RNA.  There is ribose, a sugar that has been demonstrated to form from a reasonable pre-biotic environment on earth.  There is a phosphate group that combines with ribose to form the RNA backbone.  And there are the four bases for RNA, similar to the four bases for DNA: A (adenine), C (cytosine), G (guanine) and U (uracil).  The basic idea is that these 6 simple molecules were available in the pre-biotic environment and that by random movement came together to form RNA.  Further chance encounters lead to larger RNA polymers than can replicate themselves and catalyze protein formation.  Once replication begins, natural selection can operate leading to the more efficient and stable environment of protein enzymes and DNA code.

The RNA approach is an attractive picture, but strong doubts have been cast on the RNA scenario by Robert Shapiro (1935-2011; no relation to James Shapiro), previously Professor Emeritus of chemistry at NYU.   Professor Shapiro has argued that the basic components of RNA were extremely unlikely to have formed in the early earth environment.   In particular, the spontaneous formation of ribose cannot proceed in the presence of nitrogen which the four RNA bases need for their formation.   Both ribose and one of the bases (cytosine) have a relatively short half-life and it is therefore unlikely that they could be formed at separate locations and then brought together by chance.  If life began near high temperature thermal vents, then formation of RNA is even more unlikely.  Robert Shapiro became an advocate of the metabolism priority approach after criticizing the RNA world for several years.

Professor Anet was well aware of Shapiro’s criticism and commented in 2004:

From [my] analysis . . ., it does not seem that the metabolism-first theories are ‘robust’ (or to be recommended), as claimed by Shapiro. On the other hand, Shapiro has stressed some very serious weaknesses of the replication-first theories. But this does not mean that a satisfactory replication-first theory is impossible, although theories . . . that require activated nucleotide monomers to be available prebiotically are not really acceptable. The replication-first approach does not require the existence of a primitive organic soup, it should be stressed, and local conditions on Earth may have been quite varied. Shapiro admits that new discoveries or ideas could lead to more optimistic conclusions on the viability of the replication-first approaches. Some new developments that have appeared after the publication of Shapiro’s paper will now be outlined briefly.

Anet goes on to catalog several recent developments, but, in 2004, the most convincing results were not yet available.  I am speaking of the momentous 2009 experiments by Tracy Lincoln and Gerald Joyce that showed that RNA could replicate itself in the lab.  True, there were several constraints and limitations on the test, but it did show that sustained replication could take place with RNA alone, albeit under artificial conditions.  As positive as these results are, they required relatively long RNA molecules of 189 nucleotide bases.  Some researchers think this can be shortened to 100 bases, but even 100 bases gives a very large search space for assembly by random chance: 4¹⁰⁰ or 1 followed by 60 zeroes.  That is such a large space because the half-life of RNA is measured in hours; RNA degrades relatively quickly.

Professor Shapiro gets the last word on this even though he spoke in 2007, 2 years before the Lincoln-Joyce results:  Dr. Shapiro asks his audience of scientists to imagine a large pile of Scrabble letters. Then he added, “If you scooped into that heap, and you flung them on the lawn there, and the letters fell into a line which contained the words, ‘To be or not to be, that is the question,’ that is roughly the odds of an RNA molecule, given no feedback —and there would be no feedback, because it wouldn’t be functional until it attained a certain length and could copy itself—appearing on earth.”  (If you do the math, Shapiro’s odds are about 1 in 10⁵⁷!)

Given the ongoing and provisional status of research into the origin of life, what can we know with certainty?  And what does that knowledge bring to bear on the central theme of my writing: that there is a conscious, rational power at work in the universe without recourse to supernatural abilities?  Another way to frame the question is to ask: are the laws of physics and chemistry favorable to life and consciousness?  The one thing we can count on is that all of modern life is based on central dogma of molecular biology: 1) proteins, the primary workhorses of the cell, must be composed of the correct sequence of amino acids and folded into correct shape for them to be effective. 2) Proteins are created through the intermediary of RNA, acting along with other proteins.  3) The instructions for assembling proteins come from messenger RNA which is transcribed from DNA which contains both the genetic code for proteins and instructions for expressing that code.  The key point: the importance of DNA for protein assembly is its information content, not its chemical characteristics.

The modern cell is a protein manufacturing and information processing organism.  DNA contains the coded sequence of amino acids for proteins.  Information in the DNA drives the protein manufacturing work.  I worked in information processing for my entire career of more than 35 years.  There is no power in nature other than consciousness and intelligence that can create an information processing system.  A complete “artificial intelligence” solution to the software development bottleneck has been the holy grail of software management for decades.  It has not appeared nor will it appear.  There will be improvements in automated design, but there are sound mathematical reasons to think that software development cannot be totally replaced by automation.  Modern computer systems have the mathematical property of Gödel incompleteness:  they will always need an intelligent agent to make additions and improvements in them.  The bottom line is that a conscious, intelligent power that expresses itself through the laws of nature in the ultimate power behind all of life.  In other words, decisional consciousness is a property of nature.  This has been my conclusion from physics as well.  Random chance alone cannot account for the origin of life.

I think that research will eventually find smaller and possibly more primitive life forms, if not on Earth, if not in the lab, then possibly on Mars or some other nearby planet or moon.  I have taken the position that the laws of physics are favorable to life and therefore I think that life developed gradually and incrementally from ordinary matter that I think has been imbued with consciousness from the beginning.  Once life began, the power of consciousness in ordinary matter became expressed as natural selection.  Once natural selection began, something like DNA would essentially be a requirement for life so it could store the code for the wonderful protein inventions discovered through natural selection.  Once evolution became advanced, then advanced consciousness would be a natural consequence of this information-rich system.

The Evidence from Evolution and Biology (Part 1)

My previous posts have focused on the evidence for a rational agent inherent in the laws of physics.  There has been an implicit assumption that the laws of physics are rigorously deterministic.  But clearly life is not deterministic, so it was necessary for me to point to some possible feature of the laws of physics that allowed for the wild variation and unpredictability of life.  I will summarize my thought process as follows:

1. The universe is ordered by deterministic laws and forces such as the force of gravity and electromagnetism.  There are also non-deterministic laws such as quantum theory.  One of the laws that combine both features is the law of increasing entropy.  Entropy always increases throughout the universe, but it is allowed to decrease locally.  Since quantum theory ultimately controls all interactions in the universe, all forces are non-deterministic at the quantum level.  (The only possible exception is gravitation which has not yet been unified with quantum theory.)
2. The deterministic laws (electromagnetism, etc.), by themselves, cannot account for life and consciousness.  There must be another factor in the fundamental laws of physics that allows living organism to lower entropy.  The process of lowering entropy is essential to life because it concentrates energy for future use and organizes the genome for transmission to future generations.
3. That factor in the laws of physics is the collapse of the wave function in quantum physics, also called decoherence.  Decoherence is absolutely necessary for any measurable energy transfer.  In decoherence, the universe actually chooses an outcome for every transfer of energy.  This choosing, or decisionality, on the part of the universe is what I have called rational agency and it is responsible for the forward direction of time.
4. This decisionality on the part of the universe is always mixed up with randomness because we are prohibited from knowing precisely all the states of matter, particularly the states of entanglement between particles.  This is a consequence of a kind of cosmic censorship hypothesis.  The Heisenberg uncertainty principle is one such limitation on our knowledge.
5. There can be no ordering principle or lowering of entropy based on true randomness.  True randomness, by definition, is maximum entropy.  In all of physics the only candidate for non-random yet non-deterministic action is decoherence.
6. Therefore, this choice by the universe is directed choice.  It is a rational choosing based on the laws of physics and contains within it the possibility of lowering entropy.  It is the physical undergirding of all life and consciousness.  It is the physical action responsible for the forward direction of time.

Essentially, I think that the laws of physics favor life or are conducive to life.  In general, nature prefers to disperse energy; therefore there must be physical explanations for how energy gets concentrated.  Just as there is an explanation for how nature concentrates energy for lightning, there must also be an explanation for how living organisms concentrate energy and lower entropy.   These six steps summarize my explanation.  In this series on evolution and biology, I will lay out the case for the laws of physics favoring life as opposed to the case for life adapting to the laws of physics.  Both dynamics occur, but only laws conducive to life can create life from inanimate matter.

I don’t consider this logic highly dependent on particular experimental results.  Scientific theories are always provisional; they can be superseded by better theories or more accurate results.  My reasoning is broadly based on the general properties of physical laws.  A portion of the laws are rigorously deterministic and use mathematics to make predictions about future events.  A portion of the laws of physics deals with the presence of uncertainty in the universe.  I fully expect the laws of physics to be revised and improved, but I don’t expect that these general characteristics will be much altered.  If string theory is proved true, that would not change my basic logic, but my perspective might need to accommodate rational agency operating in a multiverse scenario.   String Theory, for all its promise, does not yet make any testable predictions.

Along with the laws of physics, I view the theory of evolution as a valid scientific theory.  It is a theory based on the idea that all living organisms adapt to their specific environment and pass along adaptive traits through procreation.  Darwin’s concept of “natural selection” was devised in contradistinction to “artificial selection,” whereby human breeders selected the best mates in order to raise generations of specifically adapted animals.

Biology is a complex science.  For someone like me, who has spent a major part of his life focused on math and the physical sciences, the main shock of encountering biology is the sheer astronomical diversity of life.  Last year, I took one of the online courses offered from UC Berkeley.  It was the basic undergraduate course for biology majors and it was something I needed because my previous biology class must have been in high school.  It was just as well that I didn’t have very much previous instruction because so much has changed between then and now.  The sheer volume of information is astounding.  I found myself wondering how on earth does anyone organize this much data.  In fact, it took three teachers to cover the material.  One instructor had a background in molecular biology; one was a specialist in genetics and one was from a medical background.  I had the distinct feeling that complete mastery was beyond the capability of any one individual.  But, I am still learning and I do have some observations based on my perspective from the physical sciences.

One observation concerns the principle of emergence.  Emergence is the concept that complex living organisms are able to exhibit new properties and traits by virtue of their complexity and organization.  The example from the textbook for the UC Berkeley class is one that interests me:  “For example, although photosynthesis occurs in an intact chloroplast, it will not take place in a disorganized test-tube mixture of chlorophyll and other chloroplast molecules.  Photosynthesis requires a specific organization of these molecules in the chloroplast.”  The text is saying that photosynthesis is an emergent phenomenon.  That is fine.  That helps organize knowledge, but for someone who wants to know how things work, there is a further question:  How is it that the particular organization contributes to function?  What are the properties of the constituent parts that enable the composite function to emerge?  Too often, emergence is used simply as label for a new function that can’t be explained any further.  When that happens, it becomes a kind of false knowledge: a category without explanatory power.

To take another example, water is composed of two room-temperature gases: hydrogen and oxygen.  I suppose you could say the emergent property of water is its liquidity.  But, with water, one can trace its properties to the molecular properties of hydrogen and oxygen and the strong bond between them as well as the weak bond between water molecules.  These particular molecular properties can also be used to explain surface tension, freezing and boiling.  My expectation is that biology will someday be explained in terms of molecular dynamics.  That day is a long way into the future.

Biological scientists are answering these kinds of questions and it is painstaking work.  It is slow and tedious work to demonstrate how biological molecules work, but I suppose, that is the part of biology that mainly interests me.  I have two main areas of interest in the biological sciences.  One is photosynthesis because of its use of quantum coherence for efficient transmission of sunlight energy to the “reaction center” where chemical food production begins.  The other is the biological molecule tubulin.

Tubulin is a protein molecule that assembles into microtubules.  Microtubules are long, narrow, hollow tubes that play an amazing variety of roles in living cells.  There is a natural tendency for microtubules to assemble themselves because of the positive and negative polarity on the tubulin molecule.  Once assembled, microtubules play key roles in biological cell functions.  They play an essential role during mitosis, cell division, by grabbing hold of the chromosomes and causing the genome to precisely separate toward opposite ends of the cell.  Microtubules are part of the cell’s cytoskeleton; they give shape and form to the cell.  In plants, microtubules guide the alignment of cellulose and direct plant growth at the cellular level.

Microtubules form the infrastructure that transports molecules from outside the cell to the inside and vice versa.  Motor proteins “walk” vesicles containing molecules back and forth along microtubules to their destination.  For example, pancreas cells that make insulin transport the insulin from inside the cell to the outside by this method.   In addition, microtubules are used for cell interaction with its environment.  They form some types of flagella and cilia for locomotion of the cell or movement of particles in the cell’s environment.  For example, the human sperm cell is propelled by action of a flagella made up of microtubules.

In short, microtubules are a very versatile cellular component.  Furthermore, they are an essential part of nerve cells.  Tubulin, the protein that forms microtubules, has a very high density in brain tissue.  That has led some researchers to project a key role in brain activity and consciousness for microtubules.  Microtubules are long, hollow, round tubes that might be ideal for quantum coherence.  There has been some research along these lines.

Tubulin is the protein building block of microtubules and it or similar proteins are probably very ancient, perhaps going back to the beginning of life.  One source specified that all cells had such proteins, except blue-green algae also known as cyanobacteria.  However, cyanobacteria have a tubulin-like molecule (a homologue) called “Ftsz.”  An interesting connection between my two main interests is that the cyanobacteria use photosynthesis for energy harvesting from sunlight.  It is the light harvesting complex from cyanobacteria that are used in the experiments testing quantum coherence.

Cyanobacteria are among the oldest life forms on Earth, perhaps as old as 3.5 billion years.  It would be a very interesting development if microtubules or microtubule-like structures go back to the beginning of life and if it can be demonstrated that quantum coherence played a key role in efficient energy transmission in these structures.  Those are two very big “ifs” and most researchers are very cautious about any evidence pointing towards quantum coherence in biological molecules.  But I remember some fairly incautious statements about the beginning of life from many years ago.

I think it was probably in high school chemistry class that the teacher, one day, covered the Miller-Urey experiment.  This experiment was conducted in 1952 and involved sending a spark of electricity (to simulate lightning) through a mix of chemicals assumed to represent Earth’s primitive atmosphere.  The result was a mixture of amino acids and sugars, both essential building block of life.  Stanley Miller and Harold Urey had demonstrated that organic compounds necessary for life could be easily formed from reasonable atmospheric compounds, such as water, methane, ammonia and hydrogen.  Not only that, but the teacher thought that we would soon be able to synthesize life in the test tube.  Well, that was over 50 years ago and the synthesis of life seems as elusive as ever.  Science doesn’t yet know what makes biochemicals spring to life.

The mystery of the beginning of life notwithstanding, the theory evolution brought incredible organizing power to the huge diversity of biology.  Darwin’s “natural selection” brought explanatory power to the huge diversity of species on Earth.  In the mid-twentieth century, the discovery of DNA and the genetic code brought into the evolutionary system a mechanism for adaptation.  This has led to what has been called the “central dogma” of molecular biology:  DNA makes RNA which makes proteins.  DNA contains coded information that is used to create a coded sequence of RNA which is used to create a sequence of amino acids which make up proteins.   The next step, which isn’t explicitly stated and is poorly understood, is that proteins must fold into a specific three dimensional form in order to be useful.   What is startling to me, coming from a computer programming background, is that the coded sequence of DNA contains just four characters representing four small molecules: A (adenine), C (cytosine), G (guanine) and T (thymine).

These four codes are interpreted in groups of three which gives 64 possible “words” for amino acids in the genetic code (4 X 4 X 4).  Of the 64 possible combinations of DNA code only 20 are actually needed, because there are only 20 amino acids that are needed to make all the known proteins.  Most of the 64 DNA sequences specify the same amino acid as another sequence, so there is built-in redundancy.  Only Tryptophan and Methionine rely on a single coded sequence; all the others have at least two sets of DNA codes and some (Serine, Leucine and Arginine) have six.  It seems possible to me that different evolutionary branches developed a reliance on different DNA sequences for the amino acids.  For someone with a data processing background, the DNA codes are reminiscent of a computer system that has been copied and modified to meet different objectives – even to the extent that duplicate codes are mainly sequential (e.g., Leucine: TTA, TTG, CTT, CTC, CTA, CTG).  From a “systems design” perspective it would seem that at one time there was provision for expansion with 64 codes for all 20 amino acids, but after evolutionary modifications all 64 codes are now in use.  I suppose that if there developed a need for a 21st amino acid, one of the existing redundant codes would be used.  The whole process is very complex, but the same basic DNA, RNA and amino acids are found in all life forms on Earth.  This amazing discovery of the genetic code is universal to life as we know it.  (There are some exceptions.  The Paramecium uses the “stop” codons, UAG and UAA, to code for Glutamate.)

“Natural selection” coupled with the genetic code has given enormous explanatory power to evolutionary biology.  But like all theories, it is a conceptual model of the physical processes that occur.  There remain many questions such as how did life begin.  And then there’s the question asked by Stephen Hawking, “What is it that breathes fire into the equations and makes a universe for them to govern?”  What is it that actually makes the world act in a way that is consistent with the conceptual model?  Readers of my previous posts will suspect that my answer is similar to what I’ve written before: there is a decisional power at work in the universe that breathes life into biological molecules.  It is this decisionality that insures that time flows forward and therefore gives evolution direction.

Some of the evidence for my answer resides in the evidence for directionality in evolution.  But, first of all, the evolutionary model is a rational model.  Even more amazing is that the implementation of the genetic code is an abstract, rational system!  Who would have thought that nature would have arrived at the very rational system of using a three character code to specify a sequence based on 20 amino acids that comprise the proteins for all life?   Let me be direct: The genetic code is information.  The central dogma of molecular biology is an information processing system.  The end results are proteins and decisional governance of the cell. This is exactly the type of system one might expect from a rational agent acting through nature.

As to directionality, the immediate form of the evidence is in the form of the adaptability of evolutionary change.  Evolutionary change produces living organisms that get better at adapting to their environment.  Not only are more advanced organisms better adapted, but they are better at adapting!  For higher life forms like mammals and particularly humans, this implies a higher consciousness.  Therefore, the longer range implication of evolution is higher consciousness.  I think this trend is evident from the archeological and historical record.  For almost 4 billion years, life has survived under the constant threat of a cosmic catastrophe such as the one that brought an end to the dinosaurs.  Today, we are beginning to track the asteroids and comets that have the potential to cause another life-ending cataclysm.  That would not be possible without some sort of advanced consciousness.  In a strange sort of self-reflection, adaptation has become adaptability for which is needed a higher consciousness.  This implies a robust moral development as well, but that is beyond what I can cover in these posts on science and reason.

But a rational agent is not the only explanation.  The alternative view is that evolution is the byproduct of random mutation.  First of all, I don’t think randomness is a good scientific answer.  Science succeeds when it finds and explains rational patterns.  To say that a process is random is to admit defeat from a scientific point of view.  The second thing I would say is that when someone refers to random mutation, it is unclear what type of randomness they are referring to: lack of knowledge randomness or the genuine non-determinism of quantum physics.  The common view of evolution is that it requires generations of offspring in order for nature to select the best attributes and pass those on to future generations.  Is evolution inherently random because some individuals show up at the wrong place at the wrong time or, alternatively, at the right place at the right time?  Is it random because a cosmic ray has altered the genome?  Is it random because we can’t predict how our children will turn out?  The most likely reason mutation might be random is because of a transcription or copying error.  But modern cells have evolved elaborate safeguards against such copying errors.

It turns out that when evolutionists speak of “random mutation,” they mean something specific.  My biology textbook (on Kindle!) only uses the phrase once in over 1000 pages of small font text, and that one occurrence refers to copies of genes that have lost functionality (i.e. the gene has been degraded) over time.  The textbook does not refer to new functionality as “random mutation,” but does use the phrase, “accidents during meiosis” (cell division in reproductive cells).  This phrase, too, has a specific meaning that might not be expected by normal English interpretation.  In general, the textbook prefers to state evidence positively, in terms of what we know rather than in terms of what we don’t know.  As to genetic mutation, it refers to various mechanisms for altering the genome, such as transposition of small portions of the DNA from one location to another.

One internet site was particularly helpful in tracking down the origin of the phrase “random mutation.”  This site was associated with UC Museum of Paleontology (at Berkeley).  The website is a teaching guide for evolution named “Evolution 101.”  This source was very explicit:

“Mutations are random.
Mutations can be beneficial, neutral, or harmful for the organism, but mutations do not “try” to supply what the organism “needs.” In this respect, mutations are random—whether a particular mutation happens or not is unrelated to how useful that mutation would be.”

Behind this brief description is a debate that began with Darwin.  Prior to Darwin, there was a French biologist named Jean-Baptiste Lamarck who held the view that (1) Individuals acquire traits that they need and lose traits that they don’t need and (2) Individuals inherit the traits of their ancestors.  He gave as examples the Giraffe whose neck was assumed to have stretched in order to reach higher leaves in trees and blacksmiths whose strong arms appeared to have been inherited by their sons.  But these ideas have been debunked.

When Darwin published Origin of Species in 1859, he gave some credibility to Lamarck’s view, but later evolutionists elevated Lamarck’s idea to a major theme of evolution.  By the mid-twentieth century, biologists had become adept at doing experiments with bacteria.  In 1943, two biologists, Max Delbrück and Salvador Luria, wanted to test Lamarck’s hypothesis for bacteria, which were thought to be the more likely organism to use Lamarckian adaptation.  The Luria-Delbrück experiment tested whether bacteria exposed to a lethal virus would develop any adaptive mutation and whether that mutation would be acquired prior to exposure or not.  Their experiment showed conclusively that some bacteria had acquired an adaptive mutation prior to exposure, as did subsequent experiments by others, including Esther and Joshua Lederberg who are referenced on the “Evolution 101” website.

So, based on experiments, what evolutionists mean when they say that mutations are random is that some adaptive mutations occur before any exposure to infectious agents in a test.  The mutations do not occur because of exposure.  Now this is a somewhat contentious finding because it defies the rather commonsense view that mutations happen for a reason, most likely that reason is related to some inoculation or exposure to an agent.  In other words, either the finding appears to violate causality or the explanation is an admission of ignorance about the cause of adaptation.

I take the view that the finding is an admission of ignorance.  We really don’t know what might have caused an adaptive mutation to occur before exposure.  The real scientific question is what causes the mutation and biologists prefer to focus on what we can discover.  One such biologist is James A. Shapiro, professor of microbiology at the University of Chicago.  He characterizes the association of “random mutation” with the Luria-Delbruck experiment as follows:

One has to be careful with the word “proof” in science. I always said that conventional evolutionists were hanging a very heavy coat on a very thin peg in the way they cited Luria and Delbrück. The peg broke in the first decade of this century.

Professor Shapiro goes on to write about mechanisms that bacteria have for “remembering” previous exposure to infectious agents.  Those mechanisms include modification of the bacteria DNA.  He states that Delbrück and Luria would have discovered this if they had not used a virus that was invariably lethal and if they had the tools for DNA analysis.  The announcement of the DNA structure would take place in 1953, ten years after the Luria-Delbrück experiment, and the tools for analysis are still being developed.  It should not be too big a surprise that bacteria have elaborate mechanisms for DNA sharing and modification. The human immune response to invasive agents also includes the recording of information in the DNA of certain white blood cells (lymphocytes).   You can read Shapiro’s entire article here: http://www.huffingtonpost.com/james-a-shapiro/epigenetics-ii-cellular-m_b_1668820.html.

It is no longer fashionable to speak of Lamarckian inheritance, but the field of epigenetics is devoted to adaptation by means other than DNA modification.  My own view is that the amount of debate and discussion on the issue of “soft” inheritance points to a conclusion that this is unsettled science.  Microbiologists today have many more tools and techniques for answering questions about causes for adaptive inheritance then they did sixty years ago and I suspect that they would prefer to look at changes to the DNA and other molecules rather than make statistical inferences as Luria and Delbrück did.  Current research of the type that James Shapiro is doing is demonstrating specific causes for adaptation.

The Evidence from Physics and Cosmology (Part 3)

Quantum Uncertainty

So far in my discussion of the scientific evidence for a rational power at work in the universe, I have relied heavily on the orderliness inherent in the mathematical laws of physics that model nature’s governance of the world.  I have written about the orderly application of the laws of atomic physics during the creation of the universe.  I have written about the remarkable correlation between the abstractly ordered mathematical world of theoretical physics and the empirical world of observation.  I have presented the randomness that we observe as a form of incomplete knowledge.  Though I didn’t emphasize it, that incomplete knowledge is one of the fundamental laws.  It is called the Heisenberg uncertainty principle and was itemized as Leonard Susskind’s third universal laws in my previous post.

But there was also another kind of uncertainty.  This second kind of uncertainty is based on nature’s involvement in every transfer of energy that takes place in the universe.  Quantum physics is one of Roger Penrose’s ‘SUPURB’ theories and it calls for the orderly evolution of quantum states until some final measurable state is chosen by the universe.  The mathematics is complicated, but precise.  The theory has mathematically confirmed the measured magnetic moment of the electron to about one part in one billion.  The magnetic moment measures the reaction of an electron’s magnetic field (caused by its spin) to an external magnetic field.  This effect will cause the electron’s spin to precess, like a spinning toy top.  The precision of the correspondence between theory and experiment is like measuring the distance from New York to Los Angeles to the width of a human hair!

Even though quantum theory is based on superposed quantum states (the idea that a particle can be multiple places at once, for example), we have good reason to believe that these superposed states never rise to the level of large objects (for example, Schrödinger’s cat).  This implies that some decision process is taking place in what has been traditionally called “the collapse of the wave function:” the superposed states suddenly jump to a state that conforms to the desired measurement but is based on the probabilities associated with the superposed states. And this happens even if there is no measurement being made in the scientific sense.  In the Schrödinger’s cat example, the very hypothetical superposed states of alive-cat and dead-cat carried with them each a 50% probability.  The question that I will explore in this part is to what extent that decision process can be considered random and to what extent can it be considered coherent.

First of all, we can dispense with one kind of randomness quickly.  This is the randomness due to incomplete knowledge and, as mentioned above, all of our knowledge is incomplete due to the uncertainty principle.  There will be, in any experimental situation, quantum states in the environment that the calculations cannot consider, either because they are too numerous or because we are theoretically limited in what states can be measured accurately.  I see no power in this type of randomness to create the kind of order that we observe in the universe.

One might think that this would be the end of the discussion, but there are natural quantum processes that demonstrate coherence and order.  We are aware of these powerful natural processes because of two scientific discoveries.  Let’s see if those discoveries will give us some clue as to how to proceed.

One of the surprising discoveries of the twentieth century based on quantum physics was the laser.  Today, lasers are used in many everyday applications.  They are used to record and playback compact discs of various types; they are used to read bar codes on products purchased at retail stores; they are used to measure distance and speed; they are used as pointing devices, surgical instruments and even as potential military weapons.

The surprising property of lasers on which I want to focus is that they produce coherent light; that is, light of a single color or frequency with all light particles (photons) in synchronization with each other.  This is highly ordered light, with entropy near zero.  The ability of lasers to produce highly coherent light is due to a special quantum physics property that only bosons possess.  Light particles are one of a number of elementary particles called bosons.  You may have heard of the Higgs boson for which evidence has recently been discovered at the Large Hadron Collider (LHC) near Geneva, Switzerland.  All other ordinary matter – matter that makes up virtually all of the stuff necessary for life, for example electrons, protons and neutrons – are fermions.

Aside from the major distinction between light and matter, there is another very important difference between bosons and fermions.  The distinction is related to another fundamental law of physics called the Pauli Exclusion Principle.  This principle states that two fermions cannot share the same quantum state.  Without this law, ordinary chemistry would not be possible; life would not be possible.  The Pauli Exclusion Principle is the explanation for why electrons exist in different orbits in atoms. Because electrons are in different orbits, the elements have different chemical properties, mostly due to the electrons that are in the outermost orbit.  This is why 2 atoms of hydrogen combine with one atom of oxygen to form water.  Hydrogen has one electron and one open slot in its outer orbit whereas oxygen has two open slots available in its outer orbit.  The two electrons from the two hydrogen atoms exactly satisfy the one oxygen atom’s tendency to fill up the outer orbit.  Water is highly stable with both hydrogen and oxygen sharing electrons to fill each other’s open slots for electrons.

Light particles (photons), like all bosons, do not obey the Pauli Exclusion Principle and they can share the same quantum state.  And that is why lasers are possible.  Lasers work because photons actually prefer to be in the same quantum state as other photons.  It is very important that the photons are produced synchronously. If photons are produced by heat, for example in an incandescent light bulb, they are produced at different energy levels.  Different energy levels mean different colors and different frequencies – hence incoherent light.  Lasers work because they use partially silvered mirrors to reflect light photons back and forth across a suitable material until all the emitted photons are synchronized.  The mirrors allow time for synchronization to happen.

If energy transmitted by light particles can be synchronized, what about energy transmitted through matter?  Since fermions are prohibited from being in a synchronized state, they cannot transmit coherent energy.  Or can they?  Consider the phenomenon of superconductivity.  Superconductivity does not yet have a household application, but it is very useful in certain areas where very strong and concentrated magnetic fields are needed.  Superconductivity is the free flow of electricity through a conductor which is usually cooled to a very low temperature.  Electricity flow is accomplished by electrons (fermions).  So how do low temperatures produce coherent electron flow?

The beginning of the answer is that electrons have a property called spin.  Spin is the property responsible for magnetism in permanent magnets.  Iron has three filled orbits of electrons with the outer orbit containing two electrons.  Those two electrons in the outer orbit are allowed to have the same spin.  The spin of the electrons in the inner orbits will cancel each other, leaving the total spin effect to the outer orbit electrons.  If iron is placed in a magnetic field, the spin of all the outer orbit electrons will align and the whole iron atom will have a net magnetic field.  Iron will retain the magnetism because of its crystalline structure.  Heating will generally cause iron to lose its magnetism through the strong molecular vibration caused by heat energy.

It is one of those strange quantum physics rules that measured spin has only two values.  Let’s say we want to measure electron spin in the “up” direction.  The answer will always be either yes or no.  That is, the spin will always be up or down.  This will be true no matter what actual direction we call “up.”  If we first measure spin in the up-down direction and separate all spin up electrons from all spin down electrons, we can perform another measurement on, say, the spin up electrons.  If we measure them again for spin up then the answer will always be up.  100% of the time the second measurement will agree with the first.  But if we measure the spin in the left-right direction, then we find that half will have spin left and half will have spin right.   This strange property of spin is shared by all fermions.

Bosons, on the other hand, do not share this spin property.  Fermions have what is called “half spin” and bosons have “integer spin.”  The measured spin of fermions is stated in units of one-half whereas the boson spin is stated in units of integers.  Photons, in particular, have spin one.  They do not divide into spin up and spin down.  Light can be polarized, but that is another story for another time.  So perhaps a way to cause electrons (fermions) to behave like bosons (light) is to cancel out their spin property.

That is in fact what happens in the phenomenon called superconductivity.  In the right material and at very cold temperatures, electrons can pair up so that one spin-up electron associates with a spin-down electron giving an overall spin of zero.  The electron pair can act like a boson and flow coherently and without resistance through a conductor.  The conductor must remain cold enough to prevent thermal molecular motion from splitting up the electron pair.  These pairs of electrons are called “Cooper pairs.”

As long as I’m writing about coherent light and electrons, I should mention one other interesting phenomenon: lasers can be used to cool atoms to a very low temperature.  Thus, the low entropy of the laser can be used to reduce the entropy of matter.  This does not violate any laws of thermodynamics since entropy must be increased elsewhere in order to decrease entropy in a specific location.  However, the ability for a process to decrease entropy at a particular location is very important to life.  Both the efficient concentration of energy for fuel and the remarkable ordering of the genome are key factors in the evolution of life.

Therefore, in the example of lasers, superconductivity and laser cooling, nature has given us a hint of where to look for processes that are essential for life.  The place to begin looking involves light interacting with matter.  Particularly, we should be looking for evidence that coherence in the light / living matter interaction will result in some concentration of energy or increase in order beyond what we might expect for inert matter.  Not surprisingly, that points us to photosynthesis.

For comparison, we should consider what happens when sunlight interacts with ordinary inert matter.  Consider a particle of light, a photon, traveling from the sun to earth.  That trip takes about 8 minutes.  The peak energy emission from the sun is propagated by photons in the green color range with a wavelength about .5 micrometers.  For comparison, the width of a human hair is about 25 micrometers or 50 times larger.

When the photon strikes a surface and is absorbed, it will cause the molecules to vibrate slightly faster resulting in heat.  Over the course of a day, the direct sunlight will heat up materials significantly.  But at night, the heated material will cool by emitting infrared photons.  If the heated material is about 70 degrees Fahrenheit, the emitted radiation will have a wavelength of approximately 10 micrometers.  The emitted wavelength is about 20 times longer than the sunlight arriving from the sun, so it will require about 20 times as many photons to dissipate the same energy as was absorbed.  The increased number of photons required to dissipate the sun’s energy results in an increase in entropy.

Now, what happens when a photon of sunlight is absorbed by the chlorophyll in a plant?  First of all, some of the highest energy photons are reflected because chlorophyll is green and therefore reflects green light.  Chlorophyll does not absorb green light, but strongly absorbs blue and red light.  The real surprise is that the transport of the blue or red photon through the Chlorophyll molecules is done with near 100% efficiency.  Virtually no energy is lost as heat.  I wrote about this capability in a previous post (see http://quantumveil.wordpress.com/2012/03/06/quantum-coherence-in-photosynthesis/).  I overstated the efficiency in that post since I included food production, but the essential point is that the transport of the photon’s energy from initial point of contact in the chloroplast to a molecular structure called the “reaction center” is accomplished without heat loss.  The reaction center is where the process of using sunlight energy to convert water and carbon dioxide into food begins.

The experiments that have been done to confirm this photosynthetic process also show that the efficient conduction of sunlight to the reaction center is associated with quantum coherence.  The strong implication is that quantum coherence assists the lossless transfer of energy to the right location for food production.  Without such effects, the normal expectation would be for some of the sunlight energy to escape as heat energy.  By keeping the chlorophyll as cool as possible, the chlorophyll is able to efficiently convert sun energy into food.  That keeps entropy low.  There are other processes that aid in cooling as well, but the evidence for quantum coherence in this process is a significant fact.

Because quantum coherence is involved in the transport of sunlight energy in photosynthesis, it is not out of the question that it is involved in other life processes.  All biochemical reactions involve both photons and electrons, the key components of quantum process.  The overall conversion of sunlight into food involves a local decrease of entropy.  Water is split apart to form hydrogen and oxygen and the hydrogen combines with the carbon from the carbon dioxide to make carbohydrates for food.  This is a concentration of energy and an increase in order that can be described as negative entropy.  It does not violate the law of increasing entropy because entropy rises elsewhere to compensate.  But the local decrease in entropy means a great deal to life processes.  Without the sugars and oxygen that plants produce, life on earth as we know it would not be possible.  We should all thank a plant for its miracle of negative entropy.

Analysts of the photosynthesis / quantum coherence experiments have described the phenomenon as a kind of quantum calculation.  Continuing with the computer analogy, any calculation, if it is to be useful, requires the result to be reported.  In the case of photosynthesis, the “report” is an actual decision on the path the photon should take to its destination.  I have generalized this understanding: any transfer of energy requires a decision by the universe.  That decision process is not random.  Energy must be conserved.  Momentum must be conserved.  Charge must be conserved.  Even quantum states must be preserved if the same state is measured again.  In the case of photosynthesis, there may be multiple paths to the reaction center, but it would not matter which path is chosen as long as the chosen path did not result in heat loss.  This is what I mean by “not random.”  There is uncertainty but not randomness.  Pure randomness results in increased entropy and all living organisms rely on an inherent ability to reduce or conserve entropy, or minimize entropy increase.

The best current theory is that quantum coherence enables calculations regarding the energy landscape of the molecules involved.  In photosynthesis, the thinking is that quantum coherence allows the photon to follow a “downhill” energy path to the reaction center.  This would strongly imply that quantum coherence makes calculations about the laws of physics.  We shall see more evidence of this type when we cover the phenomenon called “protein folding” where biological proteins fold into a shape that minimizes their energy.  I am using computer terminology because this is possibly the best way for people to think about the power of rational agency.  But, like any analogy, it can be stretched too far.

What kind of power could be responsible for this type of activity?  I think the evidence points to a rational power that transcends time and space.    I describe it as transcending space and time because quantum phenomenon is non-local:  it instantly affects widely disbursed particles.  The non-local properties of quantum theory have been established by several tests.  One such experiment was Alain Aspect’s 1981 test of Einstein’s EPR paradox in which Einstein attempted to show that quantum theory was incomplete.  He described the phenomenon, which he clearly thought was impossible, as “spooky action at a distance.”  Another recent test confirmed John Archibald Wheeler’s delayed choice experiment.  This 2007 test was also performed by a French team that included Alain Aspect.  The tests performed by the French teams were done using polarized light photons, but the results have been confirmed by additional experiments.

Since both the quantum phenomenon and the tests are complicated, perhaps the best way for me to describe the results is through analogy.  Let’s recall the ability of electricity to flow without resistance through a wire that has been cooled to near absolute zero.  Recall that under these special conditions, two electrons with opposite spin associate with each other and form a composite particle that has boson-like properties.  The composite particle, called a Cooper pair, can act like a boson in sense that that the pairs of electrons prefer to be in the same state as other Cooper pairs.  That means that the Cooper pair of electrons can be in a coherent state with other pairs and can move synchronously through the conductor.  The two electrons in a Cooper pair are called “entangled.”

Now, imagine that we can separate the entangled pair of electrons without disturbing their entangled state.  Progress has been made on actually performing this trick.  One of the quantum rules is that the spins must be in opposite direction, even after separation.  Suppose that a measurement of spin is done on one of the two electrons.  That measurement will cause the other electron to immediately jump to the opposite spin direction.  That will always happen, no matter what direction is chosen.  According to quantum theory, this will happen no matter how far the electrons are separated, though in the experiments with photons, the photons are generally only separated by a few meters.

This quantum trick is like a magician who puts three colored balls into one box and three balls of a different color into a second box.  Let’s say he puts a red, green and white ball into box one and he puts a blue, yellow and black ball into box two.  The boxes are separated; maybe even placed in different rooms, or even at great distance from each other.  A ball is drawn at random from box one and a ball is drawn at random from box two.  In every case, if a red ball is drawn from box one then a blue ball is drawn from box two; if a green ball is chosen from box one then the yellow ball comes out of box two; similarly for the white and black ball.  Every time the trick is performed, the ball drawn from box one appears to cause a particular ball to be drawn from box two.  Imagine the same trick with 100 balls or 1000 balls; that is the power of quantum entanglement.

Entangled particles have the power to instantly communicate a change in state to other particles.  This communication can cover great distances and occurs instantaneously.  This has led some to claim that the instantaneous communication violates the spirit of relativity.  While there is some truth to that claim, it is nevertheless impossible to use this quantum ability to instantaneously communicate to actually send a coded message.  Causality is not violated.  This appears to be another situation where the universe has an apparent ability to bypass causality, but we are prevented from using that ability to alter history.

Nor can we claim that entanglement is a rare event.  It is the norm.  This has led some to say that the entire universe is entangled.  I don’t know if that can ever be confirmed, but if entanglement can affect particles a few meters apart, then it can certainly affect biological molecules at much closer range.

This is why I think that scientific evidence supports a conclusion that a decisional, rational power is at work in the universe, a power that is conducive to life.  That power is at work in every transfer of energy because a decision must be made as to which of the quantum possibilities will be chosen.  That decision is not random; it follows certain well established rules that are the foundation of physics.  The best characterization of the decision process is that it is a quantum calculation.  It appears random to us because we do not and cannot know all the variables that affect any given particle.  In particular, we cannot know all the quantum entanglements by which any given particle is constrained.  I think this is the best explanation as to how life and consciousness can develop from ordinary matter: protons, neutrons, electrons and photons.  There is no alternative explanation as to how the forces of electromagnetism, the strong and weak forces, and gravity can accomplish the amazing reduction in entropy that exists in living organisms.

The Evidence from Physics and Cosmology (Part 2)

My previous post describes the evidence for a rational agent based on an ordered universe created by the “Big Bang”.  But if the laws of nature are so orderly, where does unpredictability come from?  Where does uncertainty come from?  We will need to know more about what we mean by “laws,” and why some of those laws might allow for some sort of non-deterministic behavior.  Might some non-deterministic activity be evidence for an ongoing role for a rational power in the universe?  But first, what are our most certain assumptions about nature?  What is it that all of physics depends on?  Leonard Susskind specifies three unconditional laws of nature (from The Black Hole War):

1. The maximum velocity of any object in the universe is the speed of light, c. This speed limit is not just a law about light but a law about everything in nature.
2. All objects in the universe attract each other with a force equal to the product of their masses and the Newton constant, G. All objects means all objects, with no exceptions.
3. For any object in the universe, the product of the mass and the uncertainties of position and velocity is never smaller than Planck’s constant, h.

Susskind emphasizes, “There is no dispute . . . .  They apply to any and all things – everything.  These three laws of nature truly deserve to be called universal.”  For the really picky reader, there are some additional qualifications that probably need to be added, but I’ll ignore those now to keep things as simple as possible.

To these three unarguably fundamental laws, Susskind would probably add the conservation of energy (energy is neither created nor destroyed; mass being a form of energy due to Einstein’s famous equation, E = MC²); the conservation of charge (charge is neither created nor destroyed; electrons and protons are examples of charged particles); and surprisingly, time reversibility or conservation of information.   Susskind maintains that it is fundamental to the laws of physics that, in addition to predicting the future, the laws do not allow for an ambiguous past.  In other words, information about the prior states of a system is never lost.  He has successfully argued this point with Steven Hawking and apparently won. Roger Penrose appears to be a lone holdout in this debate about conservation of information.   Time reversibility will prove to be a paradoxical factor in the laws of physics.

Speaking of Roger Penrose, he would probably add to this list as well.  He rates our best scientific theories as ‘SUPERB’, ‘USEFUL’, or ‘TENTATIVE’.  In the ‘SUPERB’ category, he places Einstein’s theory of relativity (both special and general relativity), quantum theory, Newton’s laws of motion and law of gravity, and Maxwell’s theory of electromagnetism.  Into the ‘USEFUL’ category go the standard model of particle physics and the Big Bang theory.

Let’s look at some of the implications of these fundamental laws of physics for an orderly, rational world.  The first fundamental law stating that the speed of light is the maximum speed for any observer is included in Einstein’s special theory of relativity.  There are some remarkable features of the special theory of relatively.  The constancy of the speed of light for all observers leads to conclusions that distances along the direction of motion must contract and time must slow down for any system that is moving with respect to another system.

This effect is symmetric with respect to two systems that are moving past each other at a uniform speed so that observers in each system will conclude that the other system is measuring shorter distances and slower times.  However, if one system reverses direction, this implication of the special theory of relativity will have permanent consequences.

For example, if identical twins are born on earth and one of them is placed on a rocket to a nearby star and that rocket is moving at a speed close to the speed of light, then the space traveler twin will return to earth younger that his or her sibling.  The effect of time slowing down is made permanent by the reversal of direction of the rocket.  The space traveler twin will experience acceleration and deceleration that will break any motion symmetry between the two twins.  This is called the twin paradox.

The surprise is that each observer in motion has his or her own time frame.  With the twin paradox, it is possible for anyone who is willing to travel fast enough to move forward in time.  The space traveler will return to earth at a time in the future compared to the traveler’s own clock or calendar. If one is willing to travel fast enough and far enough, one could actually return far into the future.

This effect has been measured in particle accelerators and in the effects of cosmic rays that strike earth’s upper atmosphere.  The high energy cosmic rays that strike high altitude molecules will create exotic particles (muons) which normally decay so quickly that few would reach the earth.  However, some of these particles are moving so fast that time is slowed down to the point where more of them can be detected at a lower altitude.

You might wonder if it’s possible to travel forward in time, is it also possible to travel back in time?  The answer is no.  Backward time travel world require traveling faster than the speed of light which is prohibited by the Einstein’s special theory of relativity, and Susskind’s first fundamental law above.  That is a good thing because if one could travel back in time, causality could be violated: it would be possible to alter history (for example, think of the movie, “Back to the Future”).  It is not even possible to send a specified signal at a speed faster than light.  If one miraculously had such a device that could send a signal at greater than light-speed, and if that signal could be relayed back to its source, then a report of a future event could be received in the past thereby providing the option of avoiding the future event!

Even though special relativity makes time relative to each moving observer, it guarantees that time will always move forward, never backward.  It thereby guarantees causality:  causes will always precede effects.  Causality is one of the fundamental guarantees of a rational universe.

From time to time, there are scientific theories or experiments that appear to show that the universe has the possibility of violating causality.  One such possible implication arises in general relativity in the theory of black holes – stars so massive that not even light can escape.  Another implication of a possible violation of causality arises in the quantum theory of entangled particles.  Both of these situations imply that the universe has capabilities that are not made available through any normal activity.  But even if the universe has the ability to violate causality, that ability is not available to its inhabitants and it is still not possible to send any message back into the past.

In fact, the mere possibility of a violation of causality in relation to black hole singularities led Roger Penrose to propose a cosmic censorship hypothesis which states that it is not possible to observe any physical process that will lead to a violation of causality.  The sort of determinism in which time always flows forward is a key property of this universe.  Yet this property is in direct conflict with Leonard Susskind’s assertion that the laws of physics must be able to be reversed.  How will this tension be resolved?

Susskind’s law concerning the conservation of information is based on a fundamental assumption that the laws of physics are unambiguous with regard to the past.  This is sometimes stated that the laws of physics are still true whether time runs forward or backward.  This feature of scientific theory is necessary if we are to project events backwards to arrive at a beginning point.  The obvious question then is why don’t we ever see time running backward?

In a previous post, I have framed my discussion of rational agency in terms of a contradiction between two concepts.  One idea is that the universe is fundamentally governed by deterministic laws which include a provision for random action. I have called this concept materialism, but its main determining factor is a randomness which accounts for any observational results that are not strictly predictable.  The other concept I have called a rational agent, but its main determining factor is directed, rational action that conforms to the deterministic laws.  I have stressed that these are two extremes and that the truth might lie somewhere in between.  So far in my discussion on science, I have described the Big Bang creation of the universe and special relativity.  Both of these narratives intimately involve matter.  Even if the rules governing matter are rational and rigorous, why does that imply a rational agent?  And how do rational laws result in uncertainty?

All of the theories listed above – from relativity to quantum theory – are models of physical reality.  That is, they describe physical reality using mathematical equations along with constraints or principles that are applied to the analysis of physical reality.  The mathematics associated with each theory is an integral part of the narrative that explains why the theory is true.  Without such a narrative, doubts would immediately set in if there were anomalous observations.  For a well-tested and mathematically consistent theory, there are strong reasons to doubt the anomalous data.

For example, not too long ago some observations suggested that neutrinos could travel faster than light.  There was an experiment associated with the Large Hadron Collider (LHC) near Geneva, Switzerland in which neutrinos were timed at about 60 nanoseconds faster than a light beam going a distance of 450 miles.  If that observation had proved true, it would have been a significant violation of special relativity.  The problem was eventually traced to a GPS synchronization issue between the two clocks used to time the trip, but resolution took several months.  This episode illustrates both the confidence generated by a mathematically consistent, well tested theory and the provisional nature of any theory.  The provisional nature of scientific evidence is one reason for looking at a gestalt of the evidence rather than relying too much on any one result.

As mentioned above, the special theory of relativity describes the way that different observers, moving at different speeds will view the same events.  Mathematical equations define how clocks and rulers change when moving at high speed.  These changes have been observed in particle accelerators:  particles accelerated to high speed flatten out, like a pancake, and particle lifetimes increase in accord with special relativity.

The naïve question won’t go away:  how is it that matter in the form of very small particles knows how to obey the laws of special relativity?  Unless one thinks that the real world is a computer simulation (and some actually do think this), how do ‘inert’ particles know how to behave under the laws of physics?  Either the particles are not so ‘inert’ or there is a rational power that enforces the laws of physics, or both.  This is part of my evidence for panpsychism.  Matter and consciousness are intimately bound together.  Matter is knowledge made manifest.  Our mathematical theories hint at the connection.

What our best theories don’t tell us is how physical reality really works, or as Stephen Hawking says (quoted by Jim Holt): “What is it that breathes fire into the equations and makes a universe for them to govern?”  Or as someone once asked, “How does the electron know to follow the rules defined by the equations of magnetic force?”  Holt adds, “How do they [the equations] reach out and make a world?  How do they force events to obey them?”  Our scientific theories are rational models of how the universe works.  As such they are evidence for a rational process at work in the universe.  But they are not the actual power that enforces the physical laws.  That power lies outside our knowledge, but our best theories are pointers or signposts that indicate that the power is real.

My answer to these questions is that it is a rational agent that breathes the fire into the laws of physics and makes out of them a coherent world in which to live.  In order to understand how that happens without recourse to any supernatural power, I will need to describe two kinds of uncertainty or unpredictability that are present in our empirical view of the universe.

The first kind is easily dispensed with.  It is what Leonard Susskind calls experimental “sloppiness.”  I think that is a bit unkind because what he means is the inability to keep track of all the minute details that are necessary for the prediction of a result.  Think of a drop of ink placed into a glass of water and how it spreads out with apparent randomness.  Theoretically, if we knew the positions and velocities of all the particles we could predict the spreading.    Not only that, but we could reverse the spreading so that the dispersed ink coalesced into a drop and popped out of the water!  This is what Susskind means by “time reversal” or conservation of information.  But before information can be conserved, we have to know what that information is, and in complex systems, it is impossible to know all the variables that we would need to know.

What is important in the conservation of information is that it be theoretically possible to reconstruct the past, not that it ever be practical to do so.  This type of unpredictability is caused by the observer’s lack of complete knowledge.  But, as far as I can tell, there is no ordering power in lack of knowledge.  So this type of uncertainty is not very interesting.  (But I don’t mean to denigrate such useful scientific tools as stochastic modeling!)

Much more interesting from the perspective of conservation of information is the uncertainty that comes from quantum physics.  This is a completely different kind of uncertainty.  It is an unpredictability caused by the universe’s direct intervention in the outcome of any transfer of energy.  If you’ve heard of Schrödinger’s cat or the “collapse of the wave function,” you already know what this is.

Schrodinger’s cat is the archetypal and somewhat hackneyed example.  A live cat is placed in a box with a poison vial which can be broken by a single well-aimed photon that passes through a half-silvered mirror.  A photon passing through a half-silvered mirror has a 50% chance of being reflected and a 50% chance of transmission.  So there is a 50% chance that the vial will be broken and the cat poisoned and a 50% chance that cat will live.  The example concludes by speculating that we won’t know if the cat is alive or dead until we look in the box.  But, more dramatically, the story raises the question of whether the cat exists in a quantum superposed state of half-dead and half-alive!  This is what distinguishes the quantum example from the first type of uncertainty which is due to lack of complete information:  Schrodinger’s cat would be both dead and alive.

We never observe half-dead cats; so most physicists believe that quantum superposition never rises to the level of cats or anything else as big as a cat.  That means that the photon wave function must collapse to a definite state before whole cats get involved.  Most people believe that the cat is either dead or alive before the box is opened.  (Lest anyone be troubled as to why the universe might get involved in choosing life or death for a cat, remember, it was the hypothetical scientist who set up the experiment!)

Oddly enough, science has not been able to resolve this deep puzzle about quantum physics.  Lee Smolin, in The Trouble with Physics, calls it one of the “five great problems in theoretical physics.”  Roger Penrose has written at least two books to put forward his theory that there must be some objective reduction in the wave function based on the laws of physics.  The main reason that this problem has resisted solution is that attempts to test when the wave function collapses typically cause the wave function to collapse.  There may be indirect evidence, however.

The indirect evidence to which I am referring is that the universe, by choosing an outcome in every transfer of energy, is actually adding knowledge to an observable process.  We shall need to look for processes at the quantum level that concentrate energy or concentrate information that would not be expected from the law of increasing entropy.  Some of this evidence will be found in my next post dealing with quantum coherence and quantum entanglement.  The remaining evidence will be described under the topic of evolution when I look at biological processes that increase order and concentrate energy.

Supplementing and partially compensating for the lack of direct evidence is the philosophical perspective of objective realism.   There are strong reasons to believe that the wave function does collapse even if there is no observer.  This is the quantum physics version of the conundrum, if a tree falls in the forest and no one hears it, did it really fall?  There are strong reasons to believe in the reality of quantum states and strong reasons to believe that the universe picks one of the possible quantum outcomes, but the evidence is circumstantial.

If one takes the point of view that the collapse of the wave function is a real event that is initiated by the universe (whether or not there are governing rules) then one has taken the position that the universe chooses one particular outcome among all the possible outcomes that are predicted by quantum theory.  That means that anytime energy is transferred, at least one choice is involved and more often many choices are required.  This is the basis for a fundamental ‘decisionality’ in the universe that underlies all activity.  It is this fundamental decision process that prohibits any backwards movement in time.  It is the reason that we only observe time moving forward.  And ‘decisionality’ is evidence for rational agency.

Leonard Susskind confirms this position by insisting that, in order for time to be reversed, the quantum state must not be disturbed:

“Take the photon. When we run the photon in reverse, does it reappear at its original location, or does the randomness of Quantum Mechanics ruin the conservation of information? The answer is weird: it all depends on whether or not we look at the photon when we intervene. By “look at the photon” I mean check where it is located or in what direction it is moving. If we do look, the final result (after running backward) will be random, and the conservation of information will fail. But if we ignore the location of the photon—do absolutely nothing to determine its position or direction of motion—and just reverse the law, the photon will magically reappear at the original location after the prescribed period of time. In other words, Quantum Mechanics, despite its unpredictability, nevertheless respects the conservation of information.”

In Susskind’s narrative about information conservation, I sense an underlying agreement with Roger Penrose.  It is the decision process associated with the collapse of the wave function that prevents time from running backwards and it is also part of the basic mystery of the law of increasing entropy.  In order for the fundamental ‘decisionality’ of the universe to lead to rational agency, it must demonstrate the ability to perform activities that minimize entropy.  We will see some of that evidence in my next post regarding lasers and superconductivity.

The inescapable conclusion is that the collapse of the wave function does indeed discard information: it concentrates information about the state of the universe; it eliminates possible energy states; it sets a limit on the increase of entropy.  Quantum physics began by solving a profound puzzle about the energy spectrum.  In the nineteenth century, the energy spectrum was considered continuous.  If the energy spectrum was continuous, then there would be an infinite number of energy states and any heated object would radiate infinite energy.  Everyone knew this wasn’t true, but it was Max Planck who postulated in 1900 that radiation energy was quantized in units that now bear his name.  This one simple change limited the number of energy states and reduced the hypothetical infinite energy to a finite energy that was confirmed by experiment.

If we are to truly understand how the universe works in all of its magnificence, how it is able to produce both deterministic order and adaptable life, then we need to understand any process that limits entropy or has the potential of reducing entropy.  That physical process is quantum physics.

These topics will be explored in my next post.