Did the American Journal of Physics err?
  • davidmihjn January 2012
    On the website of the Skeptics Society, in a moderated blog topic (“Evolution and Religion”), I said Richard Dawkins was wrong when he said this:

    “When creationists say, as they frequently do, that the theory of evolution contradicts the Second Law of Thermodynamics, they are telling us no more than that they don’t understand the Second Law (we already knew that they don’t understand evolution). There is no contraction, because of the sun!” (Richard Dawkins, The Greatest Show on Earth: The Evidence for Evolution, p. 415)

    The Deputy Director of the National Center for Science Education, Glenn Branch, said that I was wrong and cited an article by Emory F. Bunn titled, “Evolution and the second law of thermodynamics,” published in American Journal of Physics [(2009) 77(10):922-925]. This article does indeed present calculations involving the sun showing that evolution does not violate the second law.

    I think the American Journal of Physics erred in publishing this article it for two reasons.The first reason is that the insight evolution violates this law comes from biologists, and only biologists are qualified to discuss it competently. The second reason is that the author has an understanding of the second law that is different from my understanding of it. One of us must be wrong.

    If a gas in a container is connected with a valve to a vacuum and the valve is opened, the gas will flow into the empty container. There is more knowledge of the location of the gas molecules in the small volume than in the large volume. There is an increase in disorder or a decrease in complexity. Entropy is another word for order. Entropy always decreases in nature, according to the second law.

    If a gas in a container has a piston that can compress the gas, an animal can increase the complexity of the gas by pushing the piston. This does not violate the second law because the gas is not an isolated system. The idea that the complexity of the gas increases because the complexity of the animal decreases by a greater amount strikes me as being flat out wrong. The idea of calculating the decrease of the entropy of the animal and showing it is greater than the increase of the entropy of the gas strikes me as absurd. I don’t see any difference between such a calculation and the calculation offered by Emory F. Bunn.

    Statistical mechanics explains why a gas will fill up a container. If a gas consists of N molecules, there are N! = N x (N - 1) x (N - 2)…  possible ways the molecules can be distributed in the container. The chance of getting any particular distribution is 1 in N!. I don’t know how to complete the proof. But I know Maxwell’s distribution of velocities in a gas and the bell-shaped curve are derived using Stirling’s approximation: log N! = Nlog N.

    The primary structure of a large protein can have 600 amino acids. There are 20 different kinds of amino acids. Biologists imagine that the 600 amino acids are non-interacting particles, just like in a gas. Just as in statistical mechanics, biologists ask how many different ways there are of arranging 600 amino acids? The answer is 600 to the 20th power instead of N!. Thus, it is impossible to get a protein by random chance since there is only 3 billion years available for the protein to evolve. This is why biologists say evolution violates the second law. It is the same kind of reasoning that explains why a gas will fill up the entire container.

  • SimonSimon January 2012
    I'm a biologist (handily a protein X-ray crystallographer) and I say evolution DOESN'T violate the second law of thermodynamics.

    The best way to combat entropy is with a bit of enthalpy however this takes energy. Handily for us we have a nearby star that pumps huge amounts of energy into the earth. Handily for evolution this energy gets collected by biology and used to combat entropy, hence complex organisms can exist without violating any law of thermodynamics.

    It is a complete misunderstanding to think that proteins need to "randomly" explore all arrangements of amino acids before a functional protein can exist. The reason why evolution through natural selection is a compelling theory is precisely because it DOES explain a mechanism that selects for functional proteins despite the huge amount of sequence space. 

    An analogy - the probability of flipping 600 coins and getting a "heads" for each one is rather small. HOWEVER if we keep flipping a coin until we get a "head" before moving on to the next coin we can quite easily get 600 in a row. Not an exact analogy but it is in the right ballpark of how to think about these things.
  • davidmihjn January 2012
    A better way is to read The Plausibility of Life: Resolving Darwin’s Dilemma, a book written by two mainstream biologists from Harvard and Berkeley (Mark Kirschner and John Gerhart).

    An English sonnet is like a large protein because it has 600 letters and 27 different kinds of letters. Saying that the primary structure of a protein evolved by natural selection is like saying a computer randomly selecting 600 letters can produce a sonnet in 3 billion years.

    Gehart and Kirschner report a calculation for the phase “to be or not to be” using two models. The first model ignores natural selection and assumes individual letters are randomly selection. The second model simulates natural selection by keeping “to” when that pops up, and generating the rest of the phrase. The second model also does not randomly select letters but only dictionary words. This corresponds to the fact that clumps of amino acids are subject to random mutations, not just individual amino acids. The second model produces the phrase in a short amount of time. The first model takes millions of years.

    Gerhart and Kirschner do not say how long it will take for a computer to produce a sonnet. The reason they don’t say is that nobody cares. The primary structure of a protein doesn’t even begin to describe the complexity of life. No biologist thinks that natural selection explains the complexity of life. Natural selection only explains adaptation.

  • SimonSimon January 2012
    There's so many problems with what you have written that I am not sure where to start! I fear that the main problem is that you are using language in a way that is highly misleading. For instance when you say:

    No biologist thinks that natural selection explains the complexity of life

    there are at least two cases of equivocation that I can see. Firstly natural selection only works if there is something to be selected. This is why we normally use the phrase "evolution through natural selection". It is therefore rather difficult to work out what you are meaning by your use of the words "natural selection". Secondly (and assuming you mean to say evolution through natural selection) it is also difficult to work out what you mean by complexity. If you are referring to biological complexity your statement is blatantly false. If you are referring to the existence of complex life as a whole your statement is still mostly false as there are many atheist biologists who do think evolution through natural selection is largely sufficient to explain complexity. I (on the other hand as a Christian) do happen to think that God is needed to explain the existence of complex life such as us, however only in the sense of God being imminent in his creation using evolution through natural selection. The "God-of-the-gaps" required by Behe, Meyer et al. for their "Intelligent Design Creationism" is not a place that I think makes sense theologically, philosophically or biologically.
  • davidmihjn January 2012
    To me, an atheist is someone who thinks belief in an afterlife is irrational. Liberal Christians, like Karen Armstrong and Marcus Borg, think that life ends in the grave. My suspicion is that most of the members of Christians in Science think the same way. They say that God exists because they have compassion for their fellow human beings and believe in being good. They think God is real because the idea of God causes people to behave better.

    I think the following quote proves that natural selection only explains adaptation, not the increase in the complexity of life. One of the most complex biological processes is the growth of a single cell into full-grown mammal in a year’s time. Biological machinery involves dozens of proteins and is also very complex. This is the quote:

    “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)

    Advocates of intelligent design and creationism tend to be Protestants. Protestants don’t understand why the human soul is spiritual and don’t understand the cosmological argument for God’s existence. Protestants consider the Big Bang, the origin of life, and evolution as evidence for God’s existence.

    Catholics prove that humans are embodied spirits. The Big Bang is evidence that God inspired the human authors of the Bible. According to the Bible, God created the universe from nothing.  Most of the creation myths at Biblical times involved pre-existing matter. See especially John's Gospel: In the beginning was the Word, and the Word was with God.... The "Word" is the concept of the universe in God's mind.

  • GavinM January 2012
    I can't help but feel this thread has changed topics rather quickly and multiple times (often within a single posting) which leaves me a little confused as to what you are wanting to discuss?

    You seem to have gone from making us aware of a disagreement you have with a journal paper on entropy in evolution, to the use of probability in determining whether some things in genetics are possible or not to general stereotyping (and bashing) of groups on all sides.

    If you have a problem with the journals definition of the 2nd Law of Thermodynamics I suggest you take it up with them through the appropriate channels (letters of correspondence, writing your own counter paper, etc) or be open to the possibility that you have been honestly mistaken.

    If you are wanting to understanding the current scientific understanding of how genetic structures can come about through natural means and how the calculation you provide for a protein forming at random is not how it works in the real biological world Simon makes many good points to start with. The book 'Life's Solution' by Simon Conway Morris also has a few opening few chapters highlighting how such formations are not simply down to one simple calculation and how the assumptions that back up that way of looking at protein or DNA formation don't stack up.

    Either way please refrain from bashing people and groups you clearly don't know much about. Your conclusions on CiS members and their belief in an afterlife are particularly unfounded and frustrating.
  • davidmihjn January 2012
    My original post said nothing about philosophical or religious ideas. Simon responded with a little lesson on probability theory. I responded with the statement that no biologists think natural selection explains the complexity of life. I backed this statement up with a quote from a book written by professors of biology from Harvard and Berkeley.

    Simon then quoted my statement and contradicted it. But he did not back up his contradiction with quotes from biology textbooks or peer-reviewed articles. In his response, he mentioned intelligent design. It was Simon who changed the topic by bringing up intelligent design. Intelligent design is a religious or philosophical idea, not a scientific one.

    I have re-worded my original post on CiS, and emailed it:

    Robert L. Crowther, II
    Director of Communications
    Discovery Institute

    Glenn Branch
    Deputy Director
    National Center for Science Education

    I am planning to write a letter of complaint to the editor of the American Journal of Physics for publishing an article by a physics professor, Emory F. Bunn, titled “Evolution and the second law of thermodynamics,” in 2009 [77(10):922-925]. As your organizations claim to be dedicated to truth in science, I am asking for your support.

    The article reports calculations purporting to show that evolution does not violate the second law of thermodynamics. This is true, but it can’t be proven the way the author says.

    What is inconsistent with the second law of thermodynamics is the false idea that natural selection explains the increase in the complexity of life as it evolved. Biologists think of a protein as being a system of non-interacting amino acids and perform probability calculations similar to those performed by physicists. Such calculations and a knowledge of the complexity of living organisms is why natural selection only explains the adaptation of living organisms to the environment.

    The fake calculations in the article imply that natural selection does indeed explain the complexity of living organisms. The author or the American Journal of Physics should take whatever steps are necessary to undo their mistake.

    I made a YouTube video titled, “The Truth About Evolution and Religion,” with references to peer-reviewed articles, biology textbooks, and scholarly works.

    Very truly yours,
    David Roemer

  • SimonSimon February 2012
    Hi David - could I just make sure that you have read the yellow box that appears at the top of every page of this forum? Neither I nor anyone else who responds to your posts here have the power to "represent CiS". Likewise any critique of your thinking is only the opinion of the person who writes the post, not CiS as an organisation. If you want the support of CiS for anything you need to interact directly with the chairman NOT through this forum.
  • davidmihjn February 2012
    Dear Simon,
    Instead of worrying about the reputation of the CiS, you should worry about your own conscience.

    I am criticizing the American Journal of Physics and its publisher, the American Society of Physics Teachers, for publishing misinformation about evolution.

    I am perfectly entitled from the responses to my postings to draw conclusions about the integrity and character of the leadership and membership of the CiS. I already have a low opinion of the integrity of the CiS. I doubt if more than 10 percent of its members believe in its “Statement of Faith.”

    If the chairman of the CiS doesn’t like it, tell him to contact me.
  • SimonSimon February 2012
    "Entitlement to an opinion" and "validity of an opinion" are two different things.
  • davidmihjn February 2012
    My experience with atheists and liberals is that they are dishonest about evolution. PhDs in biology deceive others about evolution, and non-PhDs allow themselves to be deceived.

    On November 24, 2009, I attended an event held at the New York Academy of Science honoring Charles Darwin. The program included a question and answer period with three prominent evolutionary biologists: Gerald M. Edelman (1972 Nobel Prize in Medicine or Physiology), Paul Ekman (1971 Research Scientist Award from the National Institute of Mental Health), and Terrence Deacon (Professor of Biological Anthropology and Linguistics at University of California-Berkeley). (http://www.nyas.org/Publications/Media/PodcastDetail.aspx?cid=7a339444-fa29-42a0-b3a9-dc0cde6103c2)

    After telling the panel of experts I made a video on YouTube titled “The Truth About Evolution and Religion”, I said:

    1. Evolution applies only to the bodies of humans, not their souls.
    2. Natural selection only explains the adaptation of organisms to their environment, not the increase in the complexity of organisms as they evolved from bacteria to mammals (common descent).

    The panel did not respond to the first point. The panel’s answer to the second point gave the many school children in the audience and web conferences the impression that natural selection was indeed a scientific explanation for both adaptation and common decent. My question is 2 hours, 21 minutes, and 43 seconds into the podcast.

    The article in the American Journal of Physics about evolution and the second law of thermodynamics is pseudoscience. The CiS is either unable to grasp this or is unwilling to criticize fellow atheists.

  • davidmihjn February 2012
    I just submitted an article to the American Journal of Physics explaining why the two articles about evolution and the second law of thermodynamics were shockingly false and unconscionable. The temporary submission ID is 7032.
  • AndyR March 2012

    Just read through these posts.

    Would like to correct false sweeping statements made by 'davidmihjn' on Jan 28

    I am a protestant. I believe in God, Father , Son and Holy Spirit.

    I DO NOT believe in the big bang, origin of life or evolution as being proof of God's existence. 6 day creation proves it for me

    I DO believe that man has a soul and has a spiritual existence.


    The 'Word' actually refers to the Lord Jesus Christ.

  • AndyR March 2012
  • davidmihjn March 2012
    I am under the impression that 90% of the members of Christians in Science are not orthodox Christians, who believe in the trinity, but liberal Christians, who think believing in life after death is irrational. One reason for this is that no one on this website or that of your sister organization, the American Scientific Affiliation, are supporting my efforts to get the American Journal of Physics to put an end to the damage being done by the two articles criticizing creationism and promoting Darwinism.

    In the light of Christian doctrine, “the Word” in John’s gospel can be a reference to Jesus and the doctrine of the trinity. However, talking about the trinity in front of atheists is like speculating about the number of angels that can dance on the head of a pin.

    The interpretation that gives atheists a reason to believe in God is that the “Word” is the concept of the universe in God’s mind before God created the universe. The discovery of the Big Bang in the 1960s is a sign that God was the primary author of the Bible.

  • AnthonySmithAnthonySmith March 2012
    David - http://www.cis.org.uk/about-cis/ says CiS has 1000+ members.

    There are definitely no more than 71 participants in this forum. Excluding those that are not human beings and those that do not participate in discussions, that's much less than 71. And many of those are not CiS members.

    71 / 1000 = 7.1%.

    7.1% is less than 90%.

    Also, CiS members have to sign up to http://www.cis.org.uk/about-cis/statement-of-faith/ which says "I declare my belief in the triune God...". So you are also under the impression that 90% of CiS members are liars or deluded.

    But then maybe everyone in the world is deluded, except for yourself?