November 19, 2017

A Review of “A World From Dust- How the Periodic Table Shaped Life” by Ben McFarland

A Review of A World From Dust: How the Periodic Table Shaped Life by Ben McFarland

I originally bought this book on a recommendation from RJS over at Jesus Creed .  RJS is the science blogger at Scot McKnight’s blog who is a PhD professor of chemistry.  Ben McFarland teaches biochemistry and chemistry at Seattle Pacific University in Seattle WA. He grew up near Kennedy Space Center and wanted to be a paleontologist in the second grade. He received a dual B.S. in Chemistry and Technical Writing from the University of Florida and a Ph.D. in Biomolecular Structure and Design from the University of Washington. His research uses the rules of chemistry to redesign immune system proteins. He lives near Seattle with his wife Laurie and his four boys.

Here is a video trailer for the book here .  I bought the book a year ago and was going to do a chapter by chapter review.  But as I got into it, I realized that, despite McFarland’s best effort to write down for the layman, it was just too technical for a casual blog post.  I had just finished Adam and the Genome, and the eyes-glazing-over reaction was fresh in my mind.  To understand a chapter by chapter detail for McFarland’s book would necessitate a college-level understanding of chemistry or would require a lot of digressive explanation which I was afraid would detract from the review.

The book is an examination of the history of life from the perspective of chemistry, specifically the periodic table of the elements.  McFarland’s main point is that chemistry constrains evolution and guides it to certain predictable ends.    In popular imagination, evolution is a messy, chaotic, highly contingent and random process.   This image of randomness in evolution was emphatically insisted on by Stephen Jay Gould. Run the tape over and something entirely different will emerge.  Gould said in his famous 1994 Scientific American article:

History includes too much chaos, or extremely sensitive dependence on minute and unmeasurable differences in initial conditions, leading to massively divergent outcomes based on tiny and unknowable disparities in starting points. And history includes too much contingency, or shaping of present results by long chains of unpredictable antecedent states, rather than immediate determination by timeless laws of nature.

Homo sapiens did not appear on the earth, just a geologic second ago, because evolutionary theory predicts such an outcome based on themes of progress and increasing neural complexity. Humans arose, rather, as a fortuitous and contingent outcome of thousands of linked events, any one of which could have occurred differently and sent history on an alternative pathway that would not have led to consciousness.

Ben McFarland respectfully disagrees, and the book builds a case by case empirical basis by examining those chemical factors that constrain the biology.  Ben is a Christian and freely admits this shapes his viewpoint.  But this is no god-of-the-gaps discourse.  As RJS says about Ben :

McFarland is a Christian, and this, of course, shapes his views as my Christian faith shapes mine. But I will also point out that I have colleagues who are not at all religious and are investigating the essence of the chemical toolbox in a manner consistent with McFarland’s approach. I have sat through a number of talks at scientific meetings on this very subject in one fashion or another. As a chemist myself (Ph.D. 1986 UC Berkeley) I find McFarland’s approach compelling and fascinating.

McFarland himself says this:

As Darwin said of natural selection, “I believe in the truth of the theory, because it collects under one point of view, and gives rational explanation of, many apparently independent classes of facts (p. 16).” What natural selection did for Darwin, chemistry does for me. In my view, a chemical sequence and chemical order shape the chaos of biology and history in surprising, yet rational ways, explaining many facts. It is a long story, but it coheres with chemical logic, and it shows that the nature of history is ordered by chemistry. That has reshaped the way I look at every blade of grass and every rock on the beach. I hope you enjoy thinking about this old subject in this new way. (p. xiv)

Ben begins his history with the periodic table.  The periodic table is a tabular arrangement of the chemical elements, ordered by their atomic number (the number of protons in the nucleus), electron configurations, and recurring chemical properties. This ordering shows periodic trends, such as elements with similar behavior in the same column. In general, within one row (period) the elements are metals on the left, and non-metals on the right.  The rows of the table are called periods; the columns are called groups. Six groups have generally accepted names as well as numbers: for example, group 17 elements are the halogens; and group 18, the noble gases.  Note that Ben shows some elements as necessary for biochemical balance, some for biochemical building, some for both building and balance, and some for catalysis or facilitating the chemical reactions.  The periodic table then is a map that will guide us through the history of chemistry on this planet.

Ben begins by discussing the basic building blocks of organic molecules and how they plausibly could have combined to make a cell.  Discussing the three categories of Building, Balance, and Catalysis, he says:

  1. Building. Most of the cell is built from the big six elements for life used as building blocks: the CHON elements (carbon, hydrogen, oxygen, nitrogen), phosphorus and sulfur.

  2. Balance. A second group of seven elements floats around in the water, unattached, like tiny glinting snowflakes.  These are used because they don’t form long-lived bonds, so they can be pumped in or out to balance (or unbalance) the cell’s overall charge.  This group includes sodium, potassium, calcium, magnesium, chloride, and the oxidized elements phosphate and sulfate.  The singly charged metal ions of sodium and potassium and the doubly charged ions of calcium and magnesium are therefore used in large quantities.

  3. Chemistry. The rest of the elements found in the cell are present in smaller amounts and follow the constant concentrations dictated by the Irving Williams series .  These are the metals located in the middle of the periodic table, the region of transition metals.  Most of these have two positive charges, but they have slightly different shapes, sizes, and relativities, and some have special abilities, which can end up making them useful for very different things.  Each of these has the ability to catalyze different reactions and must be kept around like ingredients in a pantry for when the cell needs to cook something up.

The key philosophical elements that he returns to again and again are flow and consistency.  Life, like a river, flows between boundaries.  The boundaries that constrain the river in a consistent manner are the chemical laws of the universe.  Although life is a seeming flow of random contingencies, those contingencies still obey the chemical laws that constrain them.

Mars, Earth, and Venus

As the earth’s chemistry, through the geologic and cosmologic processes acting on it, changed, they reached a point habitable to life.  Of the whole solar system, Mars and Venus are most like the Earth.  At first they looked the same, colored with black mafic basalt and glowing red magma.  The original planets were all so hot their atmospheres were driven off into space.  The oceans and the air came from within.  Oceans changed the planet.  Water is a transformative chemical, small yet highly charged, seeping into the smallest cracks, dissolving what it can and carrying those things long distances.  Venus, Earth, and Mars don’t look like the moon because they have been washed in water.  Mars is dry now, although the Curiosity rover left no doubt that the red planet was first blue with water.  Venus, too close to the sun, had its oceans turned to steam.  The steamy atmosphere locked in more heat and so on until the oceans of Venus became the hot clouds of Venus; hot enough to melt lead, and probably sterilize the planet.

On Earth, the river of life was able to flow on from organic molecules to cells to proteins to RNA and DNA to complex cells to complex plants and animals with complex brains, all the while obeying and being constrained by the properties of the periodic table (the chemical “banks” of the river).

Ben makes the final point that convergence in evolution supports the thesis of A World From Dust.  Evolutionary convergence is probably best known from the writings of British paleontologist Simon Conway Morris.  Convergent evolution is the independent evolution of similar features in species of different lineages.  The recurrent evolution of flight is a classic example, as flying insects, birds, pterosaurs, and bats have independently evolved the useful capacity of flight.  As RJS says :

The idea that we are products of random chance and historic contingency seems at odds with any reasonable Christian theology. But evolution is not a random process where just anything can happen. Evolution is constrained by chemistry and physics. Historical contingency may well play a much smaller role in the diversity of life we see around us than suggested by Gould. Simon Conway Morris and Ard Louis, professors at the University of Cambridge and the University of Oxford respectively discuss randomness and convergence in this video .

The point being made in this clip is that the scientific definition of randomness does not imply that something is open-ended and purposeless. The evolutionary process is an efficient search algorithm optimizing for specific functions. In fact, the evolutionary process follows well defined roads and paths constrained by the nature of chemistry and physics. Not everything is possible, there are a limited number of possible solutions, stable points in biological space. There is no reason to conclude that evolution demonstrates that we are accidents of nature.

Is this a slam dunk argument?  Well, of course not, and Ben McFarland isn’t presenting it as one.  But it is surely a reasonable counter-argument to the typical evolution-is-random-therefore-unplanned-therefore-there-is-no-creator schtick.  Perhaps you don’t find it persuasive?  I, however, like RJS, find it compelling and fascinating.

Comments

  1. Burro [Mule] says:

    Water is a transformative chemical, small yet highly charged, seeping into the smallest cracks, dissolving what it can and carrying those things long distances.

    Did anyone else immediately think of baptism? Our planet’s first baptism made all the others possible.

    • Stimulating thought, Mule

    • Mule, I love that!

    • Christiane says:

      Great comment, Mule!

      I think about the blessing of the waters as the Holy Spirit passed over them.
      And your concept of ‘baptism’ fits when you think of the symbolism to going down into the water symbolizes dying to self and coming up out of the waters symbolizes rising in Christ
      And in the Book of Revalation, we learn that ‘the sea shall give up its dead’.

      Yes. I have thought about it a lot.
      I had a problem with my husband (retired USN) being buried at sea, until I read Rev. 20:13 “And the sea gave up the dead who were in it”. . . . .

      then I put the pieces together:
      Alpha and Omega, the first blessings of the water, the stormy waters calm at the command of Christ, Our Lord calls the dead forth from their graves, and even the sea responds to His voice and ‘gives up the dead that were in it’

      Yes. Good call, Mule

  2. But in scientific thinking, doesn’t randomness essentially mean that all observed phenomenon can be explained without reference to a conscious or intelligent agent causing or directing them?

    • That is, randomness has to do with being undirected by any intelligent intention, not uncaused, or unconstrained by physical cause and effect. Thus, God is an unnecessary and superfluous hypothesis in scientific thinking. Everything can, and should, be explained in science without talking about God.

      • But here’s the thing Robert, the process is not wholly unconstrained. The laws of physics constrain the universe so that stars would form, that elements would be created in those stars (like carbon), and that the end life of those stars would spread those elements throughout the universe. The laws of chemistry constrain the randomness of the evolutionary process so that life can form. As RJS said, the evolutionary process is an efficient search algorithm optimizing for specific functions. And as I said in a previous post, if you make God a hypothesis of nature you can only end up making that god into a demiurge. Therefore, empirically, God does not exist, as we have no need of that hypothesis.

        But as I said in the Finding God in the Waves post: In the end, one is, of course perfectly free to believe in the “just-there-ness” of the cosmos. But that naturalist view of things is just a picture of the world, not a truth about it that we can know, or even a conviction that rests upon a secure rational foundation. If the naturalist is perfectly consistent then we must see that such a view is utterly deterministic. On the other hand, this deterministic machine floats upon a quantum flux of ceaseless spontaneity and infinite indeterminacy. Neither level of reality explains the existence of the other. So nothing we know obliges us to find this picture more convincing that one in which higher causes (among which we might, for instance, include free will) operate upon lower, or in which all physical reality is open to a transcendent order that reveals itself in the very existence of nature. To my mind, “chaos” could not produce laws unless it were already governed by laws, and the question of being cannot be answered by a theory that applies only to physical realities. I think you intuitively grasp this, Robert, because you do believe in a certain level of free will (not absolute, of course). So we see these laws in operation and they have produced thinking, reasoning, worshipping creatures such as ourselves. Creatures who can ask the question, “To what end?” Do you think there is an answer to that question, Robert? I know, I know, sometimes you do and sometimes you don’t. But I’m satisfied that the love of God is the reason for life.

        • Dana Ames says:

          Whether one posits a divine being or not, I think the point is that chemistry and biology can’t be totally random, or else very little – or nothing at all – would happen. If you’re going to try to answer the question “Why is there something, rather than nothing?” with scientific investigation, it seems logical to me that, in light of at least these observations about chemistry, total randomness has to be set aside.

          If a divine being exists but is not a hypothesis of nature, then that being must be beyond nature – that is, uncreated, transcendent. That’s about all we can say, unless that being should disclose itself to us. So it seems to me.

          Dana

        • It’s science’s job to explain as many phenomena as it can without reference to God, or any other intelligence that might direct natural processes, other than the intelligent direction that human’s, and to a lesser degree other animals, wield from within the framework of preexisting natural processes. When science asserts that phenomena are random, it is saying that they can be explained without reference to any intelligent designer, and without reference any teleology. A designer with teleological intentions would actually make scientific explanations impossible, beyond a certain point.

    • That’s always been my thought, too. Atheistic scientists see God as a magic wand, not realizing their “over a bazillion years” is a magic wand, also.

      Although I guess you could claim that if you roll six million dice enough times it’s bound to come up all sixes at some point.

      (I rather like the idea that God helped all sixes come up. If he used physics and chemistry to do it, more power to Him!”

    • Klasie Kraalogies says:

      Not at all. See my mathematical answer to Mike below.

  3. In the beginning………not trying to figure out the progression from basic building blocks, the balance needed, and the catalysis of it all…….in the very beginning it is posited that there was a bang, because in red shift we know that it is all expanding. The very first heavenly element was hydrogen. So simple a building block. And then some or even just two fused and there was a bang and light. And that has continued. 99.99% of it all is still hydrogen and helium, the simplest, the building blocks of every star.
    Take it either as those first two hydrogen were natural or spirit formed. 99.99% of those who are inclined to the spiritual aspects have also gone from basic to modified revelations. And the catalyst is and still remains unchanged in that realm. There is evolution in the natural and spiritual realms of this existence. Neither of the those of either persuasion have exhausted the implications of their research. I still maintain that belief in divine( of, from God) is by direct perception. I’ve heard metaphysical, logical, empirical arguments from both sides from “God,no” to “Hell, yes”. Both sides making arguments leave me as cold as the vacuum that is between the hydrogen and helium building blocks out there. Listening to people who share direct perception does not. Actually, neither do people who
    who talk about value formation from a natural perspective. I don’t believe talking about basics is off the topic of chemical catalysis and the topic of its being constrained. And those edges of the river, as it were, have implications in the way the spirituals and naturals should constrain. Both RJS and Mike the Geologist are good at it.

  4. I guess I don’t understand the argument.

    A coin toss is “constrained” to two outcomes. How do I get to an argument for a coin creator?

    • Three outcomes. Don’t forget the edge.

    • Mike the Geologist says:

      I am Anton Chigurh. I am are going to toss the coin 10 times. If the coin doesn’t come up heads all 10 times, I’m going to shoot you dead. I toss the coin 10 times and lo and behold it comes up heads all 10 times. There are basically 3 competing explanations (I think):

      1. All though the probability of the any coin toss is 0.50, it is possible that 10 heads could come up in a row. So you, my friend, are very, very lucky.

      2. There are an infinite number of universes, in most of them you died, but there is an infinitely large subset in which you lived.

      3. I cheated because it was my will that you live.

      • “Do you know what date is on this coin?”
        “No.”
        “1958. It’s been traveling twenty-two years to get here. And now it’s here. And it’s either heads or tails. And you have to say. Call it.”
        “Look, I need to know what I stand to win.”
        “Everything.”
        “How’s that?”
        “You stand to win everything. Call it.”
        “Alright. Heads then.”
        “Well done…Don’t put it in your pocket, sir. Don’t put it in your pocket. It’s your lucky quarter.”
        “Where do you want me to put it?”
        “Anywhere not in your pocket. Where it’ll get mixed in with the others and become just a coin. Which it is.”

        Creepiest villain of all time.

        • Writing is talking to people in the future.

          Reading is listening to people from the past.

          Your future self is looking at you right now through memory.

        • I need to see that movie again. Probably didn’t appreciate it at all when it came out. I was in college.

    • Michael Bell says:

      Unless you are tossing a Canadian Nickel manufactured between 1942 and 1962. They had 12 edges.

  5. Dana Ames says:

    A couple of years ago, I saw the short PBS series, “The Mystery of Matter: Search for the Elements”. Fascinating! All about how the periodic table came to be, through the stories of those who contributed the most to its development. Very well done for the non-specialist. You can find the episodes on YouTube:

    1. Out of Thin Air
    2. Unruly Elements
    3. Into the Atom

    Dana

  6. Klasie Kraalogies says:

    Fundamental problem here from my perspective is the use of the words “chaos”, “random” etc.

    Any system that is self-interacting, and not perfectly uniformly distributed, cannot be perfectly random. Therefore, it becomes causative, and although apparently chaotic, will necessarily contain structure, thus a dynamical system. And dynamical systems can “evolve”, and produce incredibly complex, ordered outcomes (think Mandelbrot sets, for instance).

    In essence, we can, even in terms of numbers, create “random enough” sets, but not truly ransom sets. For instance, creating random numbers by computer is still caused, by programming, electronic parameters etc.

    Just as the original argument is not one positively proving a Causative Intelligence, neither are my remarks a disproof. It is just reality as is, and as understood.

    • Mike the Geologist says:

      A fair point, Klasie. But you have to admit it is still pretty amazing that a group of conscious beings is having this conversation 🙂

      • Mike the Geologist says:

        Also Klasie, your remarks come under point number one of my Anton Chigurh analogy 🙂

        • Klasie Kraalogies says:

          Increase your number of throws: The growth of the number of universes in which you die is significantly less than the ones where you live. Both are still infinite.

      • Klasie Kraalogies says:

        Of course it is amazing.

        I don’t know if you saw Neil de Grasse Tyson’s appearance on The Daily Show this week. If not, watch it. He mentions the concept of “The Cosmic Perspective”. Hard to go around fighting people over politics and nonsense when you have that perspective.

        • Clay Crouch says:

          Have you looked into biocentrism? Listened to a podcast on the CBC entitled Biocentrism: Rethinking Time, Space, Consciousness, and the Illusion of Death.

  7. Christiane says:

    I remember a film called ‘The Cardinal’ which had this scene:
    a large group of parishioners had gathered weeping and praying in front of a statue of Mary in the Church that had ‘blood’ dripping from her heart which was painted red

    so the priests come in to examine the situation, and one says, ‘oh look, there’s a rusted water pipe that is slowly leaking drops down onto the statue, and it is causing the red paint to appear to ‘bleed’ . . . .

    end of ‘miracle’? not quite, not in the film’s scene

    the other priest pointed to the pipe and said, but what are the chances that the pipe would rust exactly where it did to release the drops directly and slowly down on to the statue’s ‘heart’?

    If it’s all about ‘chance’, we do have an awful lot of ‘order’ and ‘sequence’ and ‘cycles’ . . . . . just ENOUGH not to force us to ‘accept God’s existence’, no . . . . . but enough to give hope, the hope seen universally among mankind, that we are here for some ‘reason’ on this planet where just by chance, a pipe might rust in just the right place above a statue and result in a recognition that ‘maybe’, just ‘maybe’ there was more to it than ‘chance’ 🙂

  8. “But this is no god-of-the-gaps discourse.”
    +1000. Nice nod to Einstein.