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.

57 thoughts on “The Evidence from Evolution and Biology (Part 1)

  1. The existence of the SOUL of man is plain evidence that there is a God. People only want to consider the body, and do not want to admit that man has an eternal soul. To do so would force them to admit the accountability of the soul to a greater, higher, moral, spiritual Being….the Creator of both body and soul, Jesus Christ. Read John 1:1-5 Thanks, Connie
    http://kingjesusblog.wordpress.com/

    • This is a discussion about science. Please cite scientific evidence that a soul exists, and then we can take your presumption seriously. I’m of course speaking rhetorically, because there is absolutely no evidence that a soul exists. It was an idea thought up by people who lived before anyone knew anything about the functions or mechanisms of the human brain, and today aspects of man’s perception, thinking patterns, and psychology can be explained in the context of biology. Your theory is outdated, and is no more relevant to a discussion about evolution than astrology to astrophysics.

      • You are speaking for the owner of this blog when you should let him speak for himself. I am a scientist and former atheist who is now a confirmed believer. I’m equally at home in a scientific laboratory or in the “laboratory of faith”. Each has it’s own immutable truths, laws, principles, and language. People who only operate in one lab cannot possibly understand the other. I personally believe in the science of evolution AND in the living God who is the creator of all. I am no accidental bioform, but a purposely, intentionally created person in a body, soul, and spirit made in His image. Those are some of the basic facts that I KNOW to be true with every fiber of my existence; facts which anyone who does not work in the lab of faith can never accept, unfortunately. Yet, to people who work and live daily in the lab of faith, the proof is self-evident. What does God have to say about evidence and proof? Consider this, His direct word: “Faith is the substance of things hoped for, the evidence of things not seen.” To me and my fellow workers, that truth is as solidly real as anything we have discovered in the science lab, for we have a second set of instruments, apparatus, observations,
        and truths to work from, and they don’t ever vacillate as do the scientific ones, not that there is anything wrong with science, it is what it is, but it is not the be-all-end-all; it is not God.

    • Man’s eternal soul is the mind of man through which we receive messages directly from God when we believe so.

      • There is no evidence of a soul. No one receives messages from a supernatural source as far as we know. If you hear voices in your head, other than your own… Get checked out, please.

    • In the “freshly pressed” section I came across this entry: https://quantumveil.wordpress.com/2013/01/31/the-evidence-from-evolution-and-biology-part-1/

      The first commenter wrote:
      “The existence of the SOUL of man is plain evidence that (sic) there is a God.”
      She posits we have a soul but provides no evidence for such. Without evidence, her conclusion, “there is a God” is unsubstantiated.
      Her second statement restates her position: “man has an eternal soul.” Where is the evidence for this eternal soul? Again she provides no evidence for her position.
      Her follow-up statement is twisted logic about denying we have a soul is to deny our creator, someone named Jesus Christ.
      I deny I have a “soul”, in her language, and deny I have a creator that doesn’t include my parents. How can I do otherwise?
      Well, I personally don’t think JC was a god, nor an original thinker, nor a moral thinker. How can someone who endorses the Old Testament be considered moral? I don’t think so.

  2. “The genetic code is information.” That there is a rational agency operating in the universe, conceiving and organizing this information, implies intelligence, yes?
    Very well written. Thank you for sharing. JML

  3. There are so many theories, so many studies, so much speculation on God’s inexistence. No one, however, can prove anything. Despite the scientific breakthroughs of our times, life and the universe remain a great mystery to everyone.

    • Emergence is a fascinating phenomenon and, as a phenomenon, it is evidence for order through the laws of physics. I am a reductionist at heart and that reductionist streak won’t let me stop at the appreciation of order. The snowflake is a good example. I think that it should be possible in principle to explain the order of the snowflake through the molecular interactions of freezing water. As a practical matter, that may be impossible due to the limitations placed on our knowledge through the Heisenberg Uncertainty Principle.

  4. “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.”

    A little independent research suggests to me that the Luria-Delbruck experiment was specifically designed to show that mutations are not driven by environmental factors, that with or without the virus, some bacteria will randomly develop resistance. The developers of the experiment concluded that mutations are random and not directed. You have interpreted their findings to mean the opposite. While it may be common-sense to you, I don’t believe that any biologist would claim that mutations happen for a reason and this experiment proves that.

  5. I enjoyed reading this post. The implication of a part 2 seems daunting. The broader concepts of reason and logic applied or slantedly observed in science and religion are always thrilling. The idea that nature can favour order certainly does not rule out the roll of randomness when a biological process can be observed over a very long period of time. Randomness has a musty temporay odour to it. Still just as we can infer what gives an organism life we must deduce what keeps mathematics inorganic. What happens when I try to divine a behavioral pattern in Pi? So far I keep running out of time Looking forward to part two.

  6. Eminently readable and some and a nice summary of some intriguing ideas here! Lenski’s longitudinal multiplication of E Coli is a fascinating piece of work. After 40 000+ generations to date, over 600 genetic variants have been found under the constant pressure of glucose stress. What is fascinating is that whilst coping with the change, the rate of mutation was not linear with the rate of efficiency in the organisms. Mutations finally exploded but the organisms were not conferred with greater metabolic efficiency. Tellingly also, the net amount of genetically coded information has not expanded yet. Molecular Biochemistry is no doubt the key to either understanding possibly evolutionary mechanisms or, conversely putting the proverbial nail in the coffin once and for all. These are exciting times in science and faith! :)

  7. Extremely coherent article providing food for thought on many levels and therein I applaud this article unreservedly.

    As a former man of science myself I smile much more now especially when fellow mortals get hot under the collar postulating; what is, what can’t be and why they’re so sure.

    If only they knew how much they didn’t know about what is or what can be, perhaps they’d see the funny side of all our mortal preoccupation’s too.

    But then again and as some of us understand that as mortals; “we don’t need eyes to see we need vision” where as the rest unfortunately spend far to much of their mortality looking in the wrong direction and all because of a glaring lack of vision.

    Extending my warmest regards, for a fine article, Barry

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  10. You should read Schrodinger’s essay “What is Life?” I think you would find it interesting for its take on entropy and its implications for life.

    Also, you might want to look into “quantum Darwinism.” It explains, from one perspective, how the classical laws of electromagnetism and mechanics arise from the quantum world as a result of selecting the most stable “reality.”

    Finally, a good literature read: “The Gods Themselves,” by Isaac Asimov. It does a great job of discussing the very fabric of reality in larger terms than localized phenomena.

    As for my thoughts, addressing the “decisionality” of the universe is ambitious and I respect the hell out of you for it. Looking at the big picture, how the entire universe, as it steps from the now into the next moment, and collapses into a single reality, is admirable, and most scientists disregard it for the sake of dealing with the easier questions of local phenomena.

    However, I stray from seeing in it an overseeing “rational agent.” First, I dislike the qualifier of “rational.” Strategies are only reasonable insofar as the achieve a set of goals. Based on your analysis, this would tautologically define life as the goal, as if the vastness of our universe was implemented solely to create life on earth, a planet “far out in the uncharted backwaters of the unfashionable end of the western spiral arm of the galaxy.” If we are to address the universe in its grand and all-encompassing scope, eschewing the study of local phenomena, it seems contradictory to then make its purpose no more than one of its MANY local phenomena (i.e. ourselves).

    I prefer to see the universe as a set of various local phenomena, all working and pressing against each other within the fabric of time, thus forming the perception of an evolution: meaningless, directionless, and each moment no more than the byproduct of accident. In that manner, the universe could be seen as a single “life” itself, because what is life other than a set of subsystems working and pressing against each other, discharging entropy into other subsystems, until it finally leaves our body as waste, thus maintaining a low entropy for the system as a whole.

    Anywho, great post. It got me thinking and I like that.

    Sincerely,
    Julien Haller

  11. Hi,

    I think you would be interested in reading “The Red Queen” by Matt Ridley. I am a keen believer in evolution, and I have been studying different perspectives held by evolutionary biologists. Here’s my 2 cents worth of contribute with regards to your post, and you might find criticism in the following, but I hope it to be constructive.

    First, it is quite erroneous to imply that evolution has a direction. Maybe you have a different interpretation, but most evolution biologists are averse to saying so. Nature doesn’t intend humans to have five fingers, or intellect – it just happens to be. It happened via natural selection. At one point of time, one pre-homo is smarter than the other, and he had a higher chance of survival and reproduction. Over many generations, we have intellect. The end-product wasn’t intended for, but it isn’t random; it was due to differential reproductive capacity. “Evolutionary change produces living organisms that get better at adapting to their environment” – It would be better if you say “Evolutionary change results in living organisms that are better adapted to their environment.” They do not get better at adapting; they are better adapted. For humans, there are arguments that we are evolved to be good at adapting. But this is not necessarily true for all other organisms. A bacteria today and a bacteria 100,000 years ago may have the same adaptive capability – both are better adapted for their environment. Because of changes in the environment, they are different. Stephen Jay Gould’s book “The Blind Watchmaker” has a much more detailed explanation, you can take a look.

    The “rational agent” argument is tenuous, in my humble opinion. The genetic code isn’t a product of a rational agent, nor is it a rational system. It is a system, that this codon correspond to that genetic code, but it isn’t designed by any agent, in any direction. If there was a rational agent, I would prefer to design only 3 different nucleotides. If the codon consists of three nucleotides, I would have enough, 3x3x3=27 codons to correspond to 20 amino acids, and a few for terminating the translation. Alternatively, I can have only 2 different nucleotides (just like in computers, 1 and 0), but I would need 5 nucleotides to make a codon to have enough for 20 amino acids. But having only 3 or 2 different types of nucleotides mean that any organism can save its resources for synthesizing the extra type of nucleotides. In one sense, perhaps you meant it this way, that there is a direction. Nature at this point of time cannot revert to simplicity to design the 3-nucleotide organism. But that ‘direction’ refers to the near impossibility of reversion, and not the direction of design from simplicity.

    As for randomness, biologists are divided. In classical Darwinism, evolution is the result of natural selection. But for natural selection to occur, there must be differences between organisms, especially of the same species, or as Darwin has put it, “inherent variation”. Without variation, selection is meaningless. But is the variation random? Of course there is the nature vs nurture debate. Put it this way – If another Earth was created again, with the exact same conditions, down to every molecule, will evolution progress in the same direction? Will there still be humans? In my opinion, only with absolute determinism will we get the same earth, all the same species as we have today, and I do not stand with absolute determinism.

    It is interesting, because if we stand for absolute determinism, it is akin to saying that we have no free will. We have the illusion of free will, but if everything has been pre-determined, how every single molecule, electron in our neurons and in the environment, where does free will come in?

    A very detailed exposition on evolution you have, so I hope my opinions and the books I’ve recommended will be of great help to you. I’m only slightly acquainted with formal logic, physics and all that, so I might have misunderstood you. Perhaps physicists and biologists use different words to mean the same thing.

  12. as yer no doubt aware, “they” have started using DNA to store written stuff. at present such a procedure is XXXpensive, etc. but heck, we all could “go sumwear” from here/there! my spouse is a distant relative of Dr. Luria, always enjoy seeing him furthurly promulgated.
    your essay is definitely worth a reread. thanx,

  13. a brilliant read, reminds me of some bbc4 programs, one was showing how motor proteins work, and another was showing how life (seems) to work (evolution of the eye, etc).
    It is fascinating and i don’t doubt most of it but i can’t help asking,
    if we know so much about life, why can’t we take a dead creature and give it the right mix of science to re-animate it?
    Sorry for my poor fund of word knowledge, i never got beyond electrical engineering in college.
    Isaac Asimov was apparently fond of the Bhagavad Gita, what are your thoughts on this?

  14. Well written and you did your homework to a good extent. I am an aquatic biologist studying physiology and biochemistry of aquatic organisms. It’s good to read interpretation of biology from someone with a physical sciences background.
    I would like to comment on two points that I could take from your post: You mentioned an example of energy concentration in clouds and disperse as lightening. I appreciate you think life as entropy limiting entity but that’s not so. Every organism has a role to play in food chain and while it draws energy from an earlier trophic zone, 90% of energy is lost. Therefore, higher the population, higher the feeding and greater the energy loss. Glycolysis (glucose catabolism reaction) has two phases; 1st is energy concentrating where two ATP molecules are utilised to form high energy bonds so that they can result in formation of 6 ATP molecules later. Now, glycolysis is seen in all organisms. Hence energy is concentrated only to be lost later when those 6 ATP molecules would be utilised – adding to increasing entropy.
    Another point is when you say that natural selection is antagonistic to artificial selection. I differ on this too. Evolution is simply selecting the best kind. The selection is done by some agents like disease, natural calamity or some other kind of challenge. Now, if we think human being as a selecting agent, we are unknowingly being used by animals for survival just because they have traits that are required by us. It wouldn’t have been possible for rice (a kind of grass) to spread the way it has had it not been food for the most dominant species on Earth.
    Nature works in mysterious ways and I love studying them. Nothing is random but biological machinery has been deliberately designed to have flaws; that is why sexual reproduction is favoured over asexual propagation (simple cloning) so that crossing over creates new combinations and nature gets chance to ask its agents of selection to work on them.
    Sorry for a long comment, just got washed in the flow of emotions. :-)
    Congrats for your lovely post hope you would like to read this one http://wp.me/p1spkl-1R

    Ankur

  15. There is sometimes as much or more revealed in what is missing from our view, than what is there. One of the commonly obvious neglects in discussing these things, at least from my perspective, has been the following: If we are “chunks of reality” and we are intentional beings capable of planning and decision making, then this is consciousness thing part of reality, since nothing unreal can exist. Although to channel this empirical information into some Abrahamic god model, or an idea of god at, all seems like it is detached from empirical grounds – but to assume that we understand the breadth and scope of consciousness in all its scope and form seems to me to be an unfounded possibility crushing hubris as well.

    The very fact that somehow oxygen and 2 hydrogen atoms recognize and relate to each other as water in certain circumstances is perhaps an expression of some form of awareness. This it seems unsettles the scientific mind which is content to assert that explaining a process defines its full breadth and depth. If we as humans deal in meaning in order to assert that fact then we must also acknowledge the presence of meaning in reality as well. While it appears meaning from our perspective emerges out of a confluence of relationships for which we can identify processes, it also appears that both process and meaning exist. The full scope of meaning that might exist when viewing with a lens that encompasses the whole of reality seems like something we cannot lay claim to a full grasp of as yet, but we have a necessary and sufficient vision to assert that we are living proof that both process and meaning exist.

    The point I am making here is that we have much to discover and I think we have to be careful. We can easily craft abstractions that can limit our view as much as we can craft them to deepen it. 1500 years of medical science was stalled because we mistakenly looked through an abstract lens of humors largely crafted by Galen. We have to be careful about what we allow, but equally we have to be careful about what we disallow because that can be just as unfounded and just as crippling to our vision. I appreciate what you wrote here and your willingness to entertain the notion of an anthropic principle without asserting it as an axiom-neither denying it as a proven exclusion either. We simply do not have enough information to know yet.

    I explored this a little lens crafting idea a little deeper here.if anyone is interested.
    http://thewisdomoflife.wordpress.com/2012/12/03/lost-in-our-own-little-words/ Thanks for the great post!

    • Interesting ideas there. I too suspect that both process and meaning exist. I believe all of this might exist simultaneously: process, meaning, randomness, etc. I’ve been working a very similar theme on my blog, from an earth scientist’s perspective. The latest installment: http://bit.ly/XFVKRC

  16. Nothing in Science points to a creator. To imply a cause is overzealous at the least. I have never understood this sect of scientists. we are still in the very early stages of understanding the Universe. Why jump to the conclusion that it was created, (directed), rather than holding out for further evidence? People used to think the Earth was flat, and they assumed they would fall of the face of the Earth if they ventured too far. Without sufficient evidence, we should err on the side of cation, because it is the very act of jumping to a conclusion that causes humanity to back-step.

  17. Entropy is tangible and to the eye would seem to be an iron law–things decline into disorder, often rapidly. One might say that the fact that there is evidently a force holding things together at all is evidence of the effect of God’s Word at work. I leave it to science to assume that this is intelligible and to figure out how He’s doing that :).

  18. Pingback: Evolution « The Tormented Mind

  19. The evidence for the soul/mind(same thing) is your personal experiences (all of them) the senses are the proof of the mind. Sensation is not material or objective, nothing we experience is. This is not proof of ‘god’ if by god you mean an exterior soul which created your soul. This is proof only of your own soul.

    • What a confining feeling it must be to limit your world to what is provable by science in February of 2013. Please prove love, beauty, peace, art. Please explain what preceded the big bang. Science relies on the fact that there is an order, an intelligibility to the universe, something outside of time and space that could create both. In short, science relies on God, without whom science has nothing to say. I invite you to try to experience more than you can prove for a few days. You might enjoy it :).

      • “Please explain what preceded the big bang.”
        As far as I’m aware, there’s no definitive answer to this important question. It means therefore the best we can say is we don’t have an answer, not insert god as the answer.

        “Science relies on God”
        Science relies on facts and observations of the natural world and says nothing about the supernatural such as the various gods put forth by humans.

        “I invite you to try to experience more than you can prove for a few days.”
        If you are asking me to believe in imaginary gods, I say no thanks. I have no interest in being a slave to the vengeful, vain god of the bible. He is no worthy of worship.

  20. Two thoughts from a layman:

    I think you make a leap of faith between point 5. and point 6.

    A short summary of what you are saying would be invaluable.

    • Here is my ‘short’ summary:

      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. I call it ‘directed’ because it runs counter to the general overall direction of increasing entropy. 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 phenomenon of decreasing entropy are traceable to quantum physics and to decoherence in particular. Quantum computation is a real phenomenon, 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 the phenomenon of 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.

  21. Hi! I really enjoyed reading your post, especially the part about random mutations. Have you read about Richard Lenski’s experiments with e. coli? He placed e. coli in twelve petri dishes, each filled with a solution of glucose and citric acid. Each day, he would transfer a drop of the e. coli population from each of the twelve groups into a new petri dish (filled with the solution). So basically, he managed to cultivate twelve generation lines of e. coli bacteria, each of which were kept entirely separate from the others. I think the experiment is still ongoing, and it started in 1988, so it’s been running for a while now. In some of the populations, random mutations did occur. In one of the groups, the e. coli mutation allowed the bacteria to use the citric acid as a food source, which meant that their population greatly increased. This is an excellent example of a random – though advantageous – mutation. (If it were non-random, surely all of the groups would have developed the advantageous capability to metabolise citric acid.)

  22. I’m glad you’re getting into biology and using some great resources like the UC Berkeley webcasts and UCMP Evolution website. I’d urge you to continue, moving on to resources beyond the intro level. Much of what you discuss here is problematic and will be addressed as you get farther into the discipline; for example, biologists are not conflicted about what a “random mutation” means (it means that it occurs due to random processes, and is not directed; whether it is adaptive later is a matter of chance), and we certainly are not conflicted over whether evolution is directed (it is not). Also, more complex organisms are not “better at adapting,” as you say – many incredibly simple, “primitive” organisms have been massively successful. (I’d wager good money that nematodes will be along long after humans have gone extinct.) Evolution is not a process intended to produce humans (or any other organism) – it is not directed.

    I’m glad you’re thinking and writing about this, but maybe try to understand the discipline better before announcing that it is conflicted over these matters. You know physics is complex and requires a lot of study before the real issues can be fully grasped; well, evolutionary biology is no different. Those of us who spend our lives studying this stuff would love to have more people fully understanding it!

    • I’m glad somebody said this, but I do have to give the author credit for acknowledging the complexity of biology before he discussed his ideas based on his learning thus far. Seems he was honest about his ignorance.

  23. Pingback: Re-Blogged: The Evidence from Evolution and Biology (Part 1) | Lifeinpawprints’s Weblog

  24. I was searching for exactly what this article held. Thank you! I think I may have come across one of yours before. I found the 6 step break down of your thoughts really helpful!

  25. Pingback: Why Life Is Physics, Not Chemistry | b.Logictive

  26. Great post. I’ve been working a theme very much like this on my blog, so I was naturally drawn to reading all of this. I have three parts so far, all with a lot of imagery. The third is at http://bit.ly/XFVKRC. Sorry for the plug (don’t usually do that), but we are both so parallel right now!

    My perspective is an earth scientist’s, but I’ve done plenty of reading in cosmology and have gotten pretty far along in biology. You are versed in the science that I’m weakest in, so I’ll keep a lookout on your blog. I agree with much of what you say. Of course I like others take issue with things like organisms are getting better at adapting through time. On the whole this is arguable, and in detail just false.

    I thought about polar bears while reading part of your post. What a bummer! They split off from brown bears to inhabit a very rich ecological niche, the glacial age showing no signs of slowing down (in fact ice was on the increase). What a brilliant move! Now of course the tables have turned on them. Their formerly superb adaptations have become maladaptive because of another organism’s activities in places to the south, beings in places they have no experience with. The promise of a long existence on this planet has become a nightmarish struggle for survival. Will they adapt in time? Do they have in their genetics the ability to move back to their brown bear roots? There are so many factors all working together in these processes, so many examples of false starts and unexpected (lucky?) species survival stories that directionality is not exactly the word that I would use to describe it. That said, the functioning and development of this living Earth, as viewed in the broadest way possible, do not preclude the existence of some over-arching consciousness.

    The random nature of life’s development on earth through the ages is obvious to me, but I agree that the way the universe operates on the whole in no way precludes some intelligence behind it all, God if you wish. Of course there is the very real probability that ultimately we’ll discover that there is no designer, that it came to be from nothingness, just as virtual particles do. Even then, if multiple universe’s exist we will need to suspend judgement until everything is uncovered.

    I think your admission that gravity is still unexplained says a lot about our ignorance. That’s a huge missing piece, isn’t it? I’m glad this was the first of your posts I have read. Although there is definitely a hint of your belief that there must be some design to this universe (and thus perhaps a bias), I glean from this that you are open-minded and not pushing some creationist agenda. Thanks.

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