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Presto! The Origin of Life in Four Surprisingly Easy Steps


Origin-of-life theorist David Deamer's new book First Life: Discovering the Connection between Stars, Cells, and How Life Began appears intelligently designed to make students think that dramatic progress is being been made in explaining the chemical origin of life. The book is full of almost nothing but sweetness and light on this score, giving no indication that origin of life theorists are fundamentally struggling to explain key steps. Instead, we are treated to the following whitewashed summary of how life originated, all in four easy steps:

1. The sterile surface of early Earth became more complex with the addition of organic compounds by either synthesis or delivery by accretion...

2. In turn, the mixture of organic solutes became more complex over time, as organic molecules self-assembled into molecular aggregates. Examples include the chemical synthesis of random polymers from suitable monomers such as amino acids, and the assembly of membranous vesicles from amphiphilic molecules.

3. The nascent biosphere became much more complex when one or more of the self-assembled structures happened to have the properties that allowed it to use energy to accumulate simpler molecules from the environment and assemble them into reproductions of the original structure.

4. After life began, biocomplexity increased further as macromolecular structures became organized into systems within the cellular unit of life in order to catalyze metabolic pathways and to transmit information from one kind of molecule to another. Examples include the genetic code, replication, transcription, and translation.

(David Deamer, First Life: Discovering the Connection between Stars, Cells, and How Life Began, p. 148 (University of California Press, 2011).)

Could it really be that simple? Robert Shapiro's review of First Life in Nature pops Deamer's balloon and brings him back to the earth. Shapiro explains why a reality check is needed:
Because we can get reactions to work in the controlled conditions of a laboratory, he cautions, it does not follow that similar ones occurred on prebiotic Earth. We might overlook something that becomes apparent when we try to reproduce the reactions in a natural setting. This provocative insight explains why the origin-of-life field has been short on progress over the past half century, whereas molecular biology has flourished.

(Robert Shapiro, "Life's beginnings," Nature, Vol. 476:30-31 (August 4, 2011) (emphasis added).)
Deamer at least pays lip service to the importance of ensuring that an experiment mimics natural conditions:
We can get all kinds of interesting reactions to work in the controlled conditions of the laboratory and then jump to the conclusion that similar reactions must have occurred on prebiotic Earth. But what if we are overlooking something that becomes apparent only when we try to reproduce the reactions in the natural setting we are trying to simulate in the lab? (p. 25)
Yet when considering the controlled conditions laboratory experiments like the Miller-Urey experiments, Deamer fails to abide by his own principle and neglects to inform readers that geoscientists no longer believe the gasses used in the experiment were present on the early earth. Instead Deamer writes things like:
  • "The Miller-Urey experiment was designed to determine whether complex organic compounds could have been synthesized on prebiotic Earth." (p. 67)

  • Miller and Urey decided to make a chemical model of the primitive atmosphere of Earth. Urey knew that the outer planets were very high in hydrogen content, along with water, methane, and ammonia, and he reasoned that Earth would have had a similar atmosphere just after it completed the process of planet formation. Taking this to heart, Miller decided to simulate these conditions in the laboratory by enclosing a mixture of gases in a large round flask." (p. 66)

  • "Miller's paper caused a sensation when it was published in Science in 1953. It showed that the laws of chemistry allow amino acids to be synthesized under prebiotic conditions..." (p. 68)
  • Where's the disclosure in First Life that the experiment doesn't work when the actual gasses present on prebiotic Earth are used? Students will never find it because it isn't there.

    The closest Deamer gets to admitting there are problems with prebiotic synthesis comes with his acknowledgement that "amino acids and other soluble compounds required for life have finite life spans in water solutions" and "the half-time of degradation is strongly related to the temperature" and thus "the high temperatures associated with the [hydrothermal] vents (300°C and higher) would cause amino acids to break down into smaller fragments of little use for the origin of life." (p. 34)

    But then comes the sweetness and light again: he suggests that a cold origin of life could have solved many of these problems. However, Deamer never mentions that this would drastically reduce the number of chemical reactions that could otherwise increase the odds of the origin of life. Deamer instead paints a rosy picture, where Step 1 could occur under natural earth conditions.

    Regarding Step 2, the polymerization of amino acids into what Deamer calls "random polymers," he acknowledges that it requires dehydration synthesis, where water is removed to allow polymerization reactions to move forward. But dehydration synthesis won't happen in an aqueous environment like a prebiotic soup or a hydrothermal vent. As the U.S. National Academy of Sciences (NAS) observes: "In water, the assembly of nucleosides from component sugars and nucleobases, the assembly of nucleotides from nucleosides and phosphate, and the assembly of oligonucleotides from nucleotides are all thermodynamically uphill in water. Two amino acids do not spontaneously join in water. Rather, the opposite reaction is thermodynamically favored at any plausible concentrations: polypeptide chains spontaneously hydrolyze in water, yielding their constituent amino acids."

    But never fear, Deamer has an answer: polymerization could occur if "the reactants were dry so that a variety of chemical bonds could form." In this case, however, Deamer admits there's a problem: "If the temperature is high enough, the result is a brown or black substance commonly referred to as 'tar.'" (p. 169)

    Again, no worries. Deamer thinks that amino acids and proteins didn't form the first information-carrying molecules anyway. That task fell to nucleotides carrying information in the RNA world. But you won't find any mention of the NAS's observation that this problem exists equally for amino acids and nucleotides. You'll also find nothing in First Life as candid as Shapiro's critique of the RNA world hypothesis:
    Today, the simplest living cells depend on molecules that are far more intricate than those that have been isolated from sources unrelated to life (abiotic), such as meteorites. The most noteworthy chemical substances in life are functioning polymers -- large molecules made of smaller units called monomers, connected in a specific order. The nucleic acids RNA and DNA, carriers of genetic information and heredity, are made of connected nucleotide monomers. Similarly, proteins are vital polymer catalysts that are made by combining monomer amino acids. Such modern biological constructions were unlikely to have been present on the early Earth.

    Despite this, many researchers have tried to demonstrate that RNA, or something similar, turned up spontaneously between 3 billion and 4 billion years ago. Physicist and biochemist Walter Gilbert suggested in 1986 that life began with the spontaneous generation of an RNA that could copy itself: the "RNA world." The advantage of this idea is that the formation of just one polymer would be all that was needed to get life started. The disadvantage is that such an event would be staggeringly improbable.

    Nucleotides, for example, are not encountered in nature beyond organisms or laboratory synthesis. To construct RNA, high concentrations of four select nucleotides would be needed in the same location, with others being excluded. If this is the prerequisite for life, then it is an unusual phenomenon, rare in the Universe.
    Shapiro doesn't mention the biggest problem facing the RNA world hypothesis -- that of how to solve the information-sequence problem and string the nucleotides in the right order to yield a self-replicating RNA. In answer to this dilemma, Deamer cites an experiment that he claims shows information can "appear out of nowhere, by chance." I'm not kidding. That's what Deamer says. He writes:
    We can now address a simple question that is central to our understanding of the origin of life: Can non-living systems evolve? Can genetic information really appear out of nowhere, by chance? If the answer is no, then we're in trouble because those of us who work on the origin of life claim that is exactly what happened four billion years ago, when the first forms of life emerged from a sterile mixture of minerals, atmospheric gases, and dilute solutions of organic carbon compounds. To answer that question, I will describe a classic experiment by David Bartel and Jack Szostak, published in 1993. (p. 214)
    Hmmm. What's wrong with citing this experiment to explain the origin of life?

    First of all, Deamer notes that "Bartel and Szostak...began by synthesizing many trillions of different RNA molecules about 300 nucleotides long, but the nucleotides were all present as random sequences." The experiment thus assumed that there are trillions of RNA molecules lying around, a gargantuan probabilistic resource whose existence on the early earth Shapiro has already cast into doubt.

    Second, it assumes that the target function (say, self-replication) can be achieved within the probabilistic resources available. What I mean is this: If only "trillions" of RNAs were available, then far fewer than all 300 amino acids in the RNA molecules would have been required for the target function. If, say, all 300 amino acids had to be specified to perform a function, then as Deamer points out, you'd need 4300 RNAs to get the right sequence. "Trillions" of RNA is still about 10168 too few RNAs to achieve that level of specification. So it looks we might need far more probabilistic resources than even Bartel and Szostak used. How would Shapiro feel about that?

    Third, as Stephen Meyer explains in Signature in the Cell, Bartel and Szostak's experiment assumes that there is natural selection for a particular property -- an "enzyme-catalyzed process" which can amplify those molecules which meet the criteria -- which would never exist prior to the origin of replication. Meyer explains why Bartel and Szostak's experiment shows the need for intelligent guidance:
    Leading ribozyme engineers such as Jack Szostak and David Bartel have presented these results as support for an undirected process of chemical evolution starting in an RNA world. Popular scientific publications and textbooks have often heralded these experiments as models for understanding the origin of life on earth and as the leading edge of research establishing the possibility of evolving an artificial form of life in a test tube.

    Yet these claims have an obvious flaw. Ribozyme engineers tend to overlook the role that their own intelligence has played in enhancing the functional capacities of their RNA catalysts. ...

    RNA-world advocates envision ligases evolving via undirected processes into RNA polymerases that can replicate themselves from freestanding bases, thereby establishing the conditions for the beginning of natural selection. In other words, these experiments attempt to simulate a transition that, according to the RNA-world hypothesis, would have taken place before natural selection had begun to operate. Yet in order to improve the function of the ligase molecules, the experiments actually simulate what natural selection does. ... But what could have accomplished these tasks before the first replicator molecule had evolved? Szostak and his colleagues do not say. They certainly cannot say that natural selection played this role, since the origin of natural selection as a process depends on the prior origin of the self-replicating molecule that Szostak and his colleagues are working so hard to design. ... [E]ngineers perform a role in simulating natural selection that undirected natural processes cannot play prior to the commencement of natural selection.

    (Stephen C. Meyer, Signature in the Cell: DNA and the Evidence for Intelligent Design, pp. 319-321 (HarperOne, 2009).)

    The bottom line is this: Deamer's uncritical praise for the Bartel and Szostak experiment shows that he isn't applying his principle that we should reject an hypothesis when it doesn't mimic natural conditions. Rather than showing that undirected natural processes can produce new information, the experiment Deamer cites shows the need for intelligent design.

    As for an explanation of Step 4, don't even look for it in First Life because it isn't there. Instead, we're given this rosy picture:
    The history of science suggests that a continuous, focused effort to try to understand a problem, even as complex as life's beginning, leads toward increasingly complete knowledge of the factors involved and ultimately produces a satisfactory explanation. We will never know exactly how life began on early Earth, but we will know life can begin on a suitable planetary surface, because we will watch life emerge when just the right set of conditions come together. The rest of this book describes progress toward this goal. (p. 36)
    Such scientism is the theme throughout Deamer's book. First Life seeks to lead students to think that the answers to the hardest questions about the origin of life have mostly been found, and if they haven't been found then they certainly will be. More persuasive -- and more realistic -- is Robert Shapiro's understated conclusion that in the past half century, "the origin-of-life field has been short on progress."