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Did the American Journal of Physics err?
  • davidmihjn March 2012
    I got the 90% figure from a book of essays by scientists claiming to be Christians. Only about 10% of the writers expressed the belief that we can hope for salvation after we die with “fear and trembling.”

    Liberal Christians feel deeply that we should have compassion for their fellow man, and feel it is very negative to say God doesn’t exist. God exists, in their minds, because the concept of God causes people to act with more compassion. They say they believe in Jesus because they believe in Jesus’ teaching about “peace on Earth, good will towards men.” Liberal Christians think believing in life after death is irrational and detracts from self-realization and helping our fellow human beings. I wouldn’t call them “liars.”

    If I am mistaken about the 90% figure, it doesn’t mean I am delusional. The use of this word shows hostility towards me. Are you hostile because I am accusing the members of CiS of being disingenuous in signing that pledge? Or are you hostile because I am exposing the lie, perpetrated by Richard Dawkins and the American Journal of Physics, that evolution does not violate the second law of thermodynamics? Or are you hostile because you think I am wrong in saying evolution violates the second law of thermodynamic?


  • AnthonySmithAnthonySmith March 2012
    David - I have no hostility towards you
  • GavinM March 2012
    (To be clear before we start, I speak for myself here and in no way for CiS as an organisation)

    David, nobody here has shown you any hostility, even in the face of your repeated and unfounded judgementalism on the character and honesty of the membership of Christians in Science.

    What we have done is challenge you on your viewpoints both on that issue and also on your original complaint (which I add had and has nothing to do with CiS). Every time we have done so though you have simply replied with further attacks on us (and sweeping generalisations of others) based upon little more than what appears to already be a pre-existing hostility towards those who disagree with you.

    Please return to your original issue and be open to the real discussions several people have tried to have with you on it. If you don't like that we don't agree with you and want to discuss the topic further in order to perhaps convince us, then please do so without lurching off into personal attacks on people you know little about.
  • davidmihjn March 2012
    The topic of this post is the content of two articles in the American Journal of Physics that incorrectly explain why evolution does not violate the second law of thermodynamics. The articles include fake equations.

    When I point this out to the physicists responsible for correcting these lies, they respond with a shocking lack of integrity. Even scientists who are not directly involved, such as the membership of the Christians in Science and the American Scientific Affiliation, behave in a morally deficient manner.

    I consider it an example of how immoral people can be when they are members of a group. The group consists of scientists who believe human beings, not just their bodies, evolved from animals.

    No one has challenged my understanding of the relationship between evolution and the second law of thermodynamics. No one has defended the articles. Yet, nobody supports me in my efforts. Shame on you.

    My latest correspondence with the AJP and the American Association of Physics Teachers is at
    http://newevangelist.me/2012/02/23/american-association-of-physics-teachers/.

     
  • exchemist March 2012
    David, I've not read the articles and don't have the appetite for wading through a lot of maths I may (as a mere chemist) only poorly understand. But I am interested in understanding your position on whether evolution violates the 2nd Law of Thermodynamics, because this has been known to crop up in other contexts. 

    My attitude has always been that, as well as the maths, there should also be a qualitative physical picture of what is going on, that the maths serves to quantify. I do have some appetite to understand the physical picture. Up to now, my picture of evolution has been such that there is no reason to suspect any violation of the 2nd Law, because:

    a) the environment of organisms is open, not closed and, overall, takes in light energy (lower entropy) from the sun and releases low temp (higher entropy) heat from processes such as metabolism, death and decay, so there is plenty of entropy increase going on to allow for a local increase in order without violating the 2nd Law, and

    b) increase in complexity does not happen to an individual organism but occurs over aeons, during which time millions of individuals are born and die, each life involving entropy-increasing metabolism and activity by the organism and ending with its entropy-increasing death. So again, plenty of entropy increase goes on, to permit the very gradual increase in order associated with developing complexity. 

    Would you agree with these propositions or, if not, in what way do you think they are wrong? 

    (I take it for granted that you will as usual regard me as an idiot and/or morally bankrupt, so we could dispense with those preliminaries, if you agree.)     
  • davidmihjn March 2012
    Exchemist, your part a) is a good explanation of why evolution does not violate the 2nd law. However, like the articles, you imply that adding heat to a system can increase its order (decrease entropy). Suppose you have a gas with a piston under pressure because the piston is locked. If you release the lock, the gas will expand in accordance with the 2nd law (order will decrease). When you do work on the piston and compress the gas, order will increase. This does not violate the 2nd law because it is not an isolated system. However, if you add heat to the gas, the amount of order will decrease (entropy increases).

    Consider a seed in the ground, exposed to sunlight, growing into a tree. There is no violation of the 2nd law as you well know. However, the idea of using Boltzmann’s constant to calculate the entropy of the seed to prove there is no violation is absurd. This is what the two articles do.  

    Concerning your part b, I’m sorry to say you are ….. oops, I respectfully disagree.

    The molecules in a gas will fill up the entire container because that is the most probable configuration. A deck of playing cards is a model for a gas with 52 molecules. The cards are identical, non-interacting, and isolated. The advantage of the model over a real gas is that the cards come automatically labeled.

    Biologists, in their efforts to understand evolution, have a model for a protein: an English sonnet. A poem is like an isolated system of non-interacting particles. The letters represent the amino acids and the poem represents the protein. Just as every letter in the poem has to be in the right place, so every amino acid has to be in the right place. Given that there is only 3 billion years for evolution, probability calculations place a limit on the explanatory power of natural selection. My understanding is that natural selection explains only adaptation, not common descent.

    I’v had a considerable amount of correspondence with the American Journal of Physics and the American Association of Physics Teachers about these two articles. I’v posted the correspondence on my blog:

    http://newevangelist.me/2012/02/23/american-association-of-physics-teachers/

  • exchemist March 2012
    David, my dear chap, thank you so much. How nice it is to find something I've written that you can agree with. I honestly wasn't expecting it and it makes me far more inclined to continue the debate (though whether this information will elicit a smile from you or a groan I have no way of knowing - such is the internet I'm afraid.) Thanks also for your forbearance over the part you do disagree with.

    In your penultimate para, your argument looks like a quantitative rather than a qualitative one, in that (to risk attempting to paraphrase you - I live dangerously) you contend speciation by evolution requires too much increase in order for you to be convinced that this can be compensated for by the entropy increases that occur due to processes of the type I was describing. I certainly can't properly dispute your view on that, as trying to make such a calculation is certainly beyond me. (As a matter of fact I am sceptical that it can really be done, much as Schroedinger's wave equation cannot be solved for anything more complex than the hydrogen atom, and no economist has succeeded in modelling a real country's economy, but I admit this is pure instinct on my part, so not scientific.) 

    Qualitatively, it seems you and I agree that, that since each successive mutation is achieved without violating the 2nd Law, and since a development in complexity via evolution would be a sum of such changes, accumulated over a very long period of time and thousands of generations of a sub-population of organisms, then there is no reason to think the 2nd Law is violated by the accumulation of such changes. So far, so good. 

    Then, however, it is a matter of what we conclude from that. You take the view (I think?) that there is not enough time for the order we see in the biological kingdom to have arisen by this process, whereas I am content to side with informed scientific opinion, which sees no reason to doubt that there is. 

    One clue to the difference of view may be the analogies you have chosen - the deck of cards, or the gas molecules in the container, or the sonnet. I submit these analogies are defective because they take no account of natural selection or mutation mechanisms. Nobody suggests an organism waits passively for the right changes to all occur at once (like the monkeys typing the works of Shakespeare). But natural selection favours each beneficial change as it occurs and disfavours each deleterious one. So there is a filter operating. Furthermore the Shapiro article you alerted me to (in the other thread) indicates there are further processes which amplify and focus the rates of mutation in response to stress and so forth. So there is a far more active set of mechanisms at work than passive randomness. And of course the scale on which these changes can occur is almost unimaginably huge (each time a sex cell replicates, anywhere, in any creature, is it?), in addition to 3bn years or so of time. 

    This may seem a weak, hand-waving counter to your argument. But of course we do implicitly use Occam's razor a lot in science; only seeking a more complex explanation when the simpler one is shown to have failed. You I think propose a calculation that you believe might show a failure. So now, finally, I think I understand why you are so keen to pursue your dispute with the American Journal of Physics: you will only be satisfied when someone has done - properly as you see it -  the quantitative calculation that I doubt can be done at all, and which I do not think will show what you want it to. All I can do is wish you luck.   

    P.S. I've read your correspondence with the AJP reviewer and it made me chuckle. As the past responses of myself and others to you in this forum indicate, I must candidly tell you that your normal style (our present exchange being a very welcome departure) leaves a lot to be desired in terms of clarity, coherence and civility. People could be even be forgiven for dismissing you as a nutter. So I am far from surprised that you have been given a dusty answer and frankly I think the criticism of the reviewer was spot-on. If you want to be taken seriously you will have to show a lot more self-discipline, certainly in written expression and probably also in the thought processes behind it.

  • davidmihjn March 2012
    I think I am the one who knows “informed scientific opinion.” I
    offer the following quote from mainstream biologists as proof that
    natural selection only explains adaptation. It does not explain common
    descent. Biologists don’t understand evolution because of the complexity
    of life, the lack of knowledge about the innovations (genetic
    engineering, random mutations, facilitated variation), and the shortness
    of 3 billion years.

    "Facilitated variation is not like
    orthogenesis, a theory championed by the eccentric American
    paleontologist Henry Osborn (1857–1935), which imbues the organism with
    an internal preset course of evolution, a program of variations
    unfolding over time. Natural selection remains a major part of the
    explanation of how organisms have evolved characters so well adapted to
    the environment." (Marc Kirschner and John Gerhart, The Plausibility of
    Life: Resolving Darwin’s Dilemma, page 247)

    Kirschner and Gerhart
    did the probability calculations on a sonnet. They certainly did take
    into consideration natural selection. They first calculated how long it
    would take a computer to generate “to be or not to be” by the random
    variation of letters (millions of years). They then simulated natural
    selection by selecting only dictionary words and by stopping the
    computer when part of the phrase was right (short length of time).

    They
    did not say how long a computer would take to generate a 600 word
    sonnet. The reason being that nobody cares. No biologist thinks natural
    selection explains the complexity of life. The primary structure of a
    protein does not even begin to describe the complexity of life. There
    are the other three structures, the molecular machinery that uses dozens
    of proteins, genetic engineering, and instincts.

  • SimonSimon March 2012
    David, your most recent post is outrageous for a number of reasons, however whilst writing a reply it suddenly struck me that maybe your writing style and way of expressing yourself is causing the problem.

    When you say "no biologist thinks natural selection explains the complexity of life" are you meaning "explain" in terms of a step by step process of which we know precisely what each step is, or "explain" in the more general sense of understanding the mechanism but not the precise steps? If you are referring to the former you are technically correct. It is only in the latter sense that biologists claim that natural selection explains the complexity of life.
  • exchemist March 2012
    Thanks for the reply David. I'm happy to stand corrected and bow to your superior knowledge over the sonnet example, which I did not know in any detail. But not surprisingly I'm as mystified as Simon by your comment about biologists. 

    I have not read Kirschner and Gerhart's book but have found an article summarising it, here:


    From this it seems to me they think natural selection does explain the complexity we see, WHEN COMBINED with mutation mechanisms such as those now coming to light, e.g. the one they dub "facilitated variation". As they describe it, facilitated variation does not appear to me to replace natural selection but to be a mechanism by which natural selection can work on mutations to produce change more efficiently. 

    To take a related but slightly different tack from Simon (above) I am now wondering whether all of us are actually in violent agreement and are simply disputing because we are using the term "natural selection" in different senses. I can't speak for Simon I but have been using "natural selection" a bit lazily, as a broad brush term, to encompass the general body of theories (still under active elucidation and development) by which genetic variation combined with survival of the fittest leads to the complexity of life (both adaptation and speciation). This is probably slack of me. 

     If one says instead that, strictly speaking, "natural selection" is only the survival-of-the-fittest mechanism itself, then all the learned and novel stuff about the mechanisms by which mutations occur, the conditions that precipitate them, what the organism does with them and so forth, would not be termed part of "natural selection" per se, but as a separate, necessary and complementary part of the overall theory of evolution. In other words, while evolution overall does provide a satisfactory explanation, "natural selection", per se, does not. Would that be a formulation you could subscribe to?  (Maybe you or other readers will tell me that there is already terminology for the complementary part of the theory: I expect there is but it is not my speciality so I'm afraid I don't know it.)     

    But I'm rather enjoying this. It is forcing me to clarify in words a number of concepts and notions that may have lain in rather tangled form in my mind up to now. In my defence all I can say is a chemist can only think about biology in his own time...... 
  • davidmihjn March 2012
    There is nothing ambiguous about my statement, "no biologist thinks natural selection explains the complexity of life."

    The human mind is structured like the scientific method. At the level of observation, humans pay attention. At the level of inquiry, humans try to understand why things happen and the relationship between things. At the level of reflective judgment, humans marshal the evidence and decide whether or not a theory is true.

    For example, humans observed fossils and invented the theory that animals evolved over a period of 3 billion years. Rational people judge this theory to be true. Knowing this, humans want to understand how this happened. The only theory is intelligent design (ID), but there is no evidence for this. Rational people judge this theory to be false.

    The theory of innovation plus natural selection only explains the adaptation of animals to their environment. In other words, we know the steps and mechanisms that gave giraffes long necks, but we don't know the steps and mechanisms that transformed bacteria into giraffes.
  • exchemist March 2012
    David, thanks, I think I see what you are saying but I am also fairly confident you are on your own in your contention about what biologists think. I do not see how the quotation you cite in support of your views about biologists can possibly support the interpretation you place on it. From what I have read, biologists think that evolution from bacteria to giraffes is no more than a longer term effect of the same processes that gave giraffes long necks. This may be only an inference but Occam's Razor says that there is no need to invoke anything further until evidence comes along that contradicts this. There is no such evidence today. The argument you have advanced that this is not so seems to rely on your own, highly individual view of thermodynamics which nobody, other than ideologically driven IDers (who seem to be mostly engineers, mathematicians, doctors and lawyers, with a fair sprinkling of charlatans among them) would seem to support. 

    Just one other passing note. I do not think, and most certainly did not intend to imply, in my earlier posting, that "adding heat to a system can increase its order (decrease entropy)".  I am well aware that dS = dQ/T, hence my comments about the temperature at which heat passes in or out of a system. But of course most of the energy input to the biosphere is initially captured by photosynthesis, i.e. absorption of light, so Clausius' formulation does not help there. In fact, assessing the entropy changes in biochemistry is going to need concepts more along the lines of G= U+PV-TS, in which S is going to relate to the numerous energy states available to very complex molecules, in solution. So analogies with perfect gases and heat engines are not going to shed much light on the problem. As I said before, my view is this will get insolubly complicated so it is a swamp I do not propose to enter.        
       
  • davidmihjn March 2012
    I don’t understand why my quotation doesn’t prove what I am saying about natural selection. To refute what I am saying, you need to find a peer-reviewed journal or biology textbook that states, “Some people think natural selection explains only adaptation. This is wrong. Even though 3 billion years is a short amount of time and life is very complex, natural selection acting on innovation explains the complexity of life. We know enough about innovation (random mutations, genetic engineering, facilitated variation) to understand how life evolved.”

    I have two more quotes. One is from an advocate of intelligent design who is explaining why natural selection can’t explain molecular machinery in cells. The other is from a mainstream biologist refuting the advocate of intelligent design:

    “P. falciparum, HIV, and E. coli are all very, very different from each other. They range from the simple to the complex, have very different life cycles, and represent three different fundamental domains of life: eukaryote, virus, and prokaryote. Yet they all tell the same tale of Darwinian evolution. Single simple changes to old cellular machinery that can help in dire circumstances are easy to come by. This is where Darwin rules, in the land of antibiotic resistance and single tiny steps…There is no evidence tht Darwinian process can take the multiple, coherent steps needed to build new molecular machinery, the kind of machinery that fills the cell.” (Michael J. Behe, The Edge of Evolution: The Search for the Limits of Darwinism, Free Press, 2007, p. 162)

     “In Behe’s view, these are examples of nothing more than a kind of “trench warfare” in which the two species have progressively disabled or broken parts of themselves in order to survive. Nothing genuinely new, novel, or complex has resulted from this struggle, and we shouldn’t expect otherwise. The reason, according to Behe, is that the sorts of changes we see in this well-studied interaction represent the limit, the “edge” of what evolution can accomplish. They can go this far and no further. A line in the sand is drawn, and the other side of that line is intelligent design……How does Behe know where to draw that line?” (Kenneth Miller, Only a Theory: Evolution and the Battle for the American Soul, p. 67)
    ,
    Behe said that Darwinism fails on the other side of the line, not that intelligent design succeeds. There is no disagreement between Behe and Miller about natural selection.

    By the way, the articles in the American Journal of Physics say that the increase in the complexity (order) of the biosphere was due to heat energy from the sun. This is nonsense.

  • SimonSimon March 2012
    exchemist - it's probably best to leave this as I think he is trolling.
  • davidmihjn March 2012
    I wrote an essay titled, “Why Liberalism Is a Neurotic Response to Religion.” I gave four examples of where liberals are so mistaken that it is fair to say they are neurotic. The four areas are the mind-body problem, the cosmological argument for God’s existence, evolution, and the business cycle.

    In this topic, I made the very easy to understand statement that natural selection only explains adaptation, not common descent. Simon had difficulty grasping the statement and felt I was just not expressing myself accurately. Exchemist understood what I was saying, but didn’t believe me.

    I then clarified things and gave additional quotes from biologists to prove my point. Simon’s reaction is to call me a troll, whatever that means, and to tell Exchemist not to encourage me.

    This proves to me that religion causes so much anxiety that many people are inhibited from thinking intelligently.