Scientists Probe Differences Between Living and Nonliving Chemicals

“All life forms are composed of molecules that are not themselves alive.  But in what ways do living and nonliving matter differ?  How could a primitive life form arise from a collection of nonliving molecules?”  Any article beginning with questions like that is bound to be interesting.  That’s how Rasmussen et al. tantalized readers of Science¹ on Feb. 13 as they described two recent international workshops discussing the origin of life and artificial life.
    The workshops, one at Los Alamos and one in Germany, focused on two overlapping questions: (1) How did life originate? and (2) Will scientists ever be able to create life?  Regarding the latter, some are taking the “top-down” approach, taking the smallest known living organism and trying to tweak it, and others are taking a “bottom-up approach,” trying to build a self-replicating cell from scratch.  The bottom-up approach is “general and more challenging,” but holds more promise, they think, for understanding ways in which life might have originated on its own.
    Recognizing that “the definition of life is notoriously controversial,” the authors sought middle ground in their definition: “there is general agreement that a localized molecular assemblage should be considered alive if it continually regenerates itself, replicates itself, and is capable of evolving.”  (For another view, see 12/30/2002.)
    Those seeking to produce a cell matching those criteria have generally recognized three requirements that would have had to be met: genetic information, metabolism, and containment:

Regeneration and replication involve transforming molecules and energy from the environment into cellular aggregations, and evolution requires heritable variation in cellular processes.  The current consensus is that the simplest way to achieve these characteristics is to house informational polymers (such as DNA and RNA) and a metabolic system that chemically regulates and regenerates cellular components within a physical container (such as a lipid vesicle).

The scientists have developed models of how these three requirements might be met, and have partially achieved some of them separately  One proposal would make use of a simpler polymer than DNA/RNA, called PNA.  According to the model, light energy might synthesize lipids (for the container) and PNA, with the PNA…

…acting as both an information molecule and as an electron-relay chain.  This is the first explicit proposal that integrates genetics, metabolism, and containment in one chemical system.  Metabolism in this system has been shown to produce lipids, but experimental realization of the rest of the integrated system has not yet been achieved.

Harold Morowitz (George Mason Univ.), long interested in the requirements for a minimal living system (see online reference at this site), helped clarify the divide between living and nonliving matter.  Morowitz and three colleagues gave presentations at the workshops:

They described how nonliving chemical reactions, driven by thermodynamics, explore the state of space in an ergodical fashion, and thus tend to conduct a random exhaustive search of all possibilities; in contrast, living systems explore a combinatorially large space of possibilities through an evolutionary process.  This echoed a central workshop theme: how and when information becomes a dominant factor in the evolution of life, that is, how and when selection plays a greater role than thermodynamics in the observed distribution of phenotypes.

This opened up a number of proposals by Morowitz and others:

• “Peter Stadler (Univ. Leipzig) reviewed selection using replicator network dynamics, a theoretical framework describing population growth produced by different kinetic conditions.”
• “Smith and Morowitz further described how the citric acid cycle of living cells might be a thermodynamic attractor for all possible metabolic networks, thus explaining its appearance at the core of all living systems.”
• “Universal scaling in biological systems was discussed by Geoff West (SFI) and Woody Woodruff (LANL), who explained why regular patterns can be found, for example, between an organism’s weight and metabolic rate, regardless of whether the organism is a bacterium or an elephant.”
• “Shelly Copley (Univ. of Colorado, Boulder) explained how catalysts operate in living systems today and how these were likely to have evolved from less efficient precursors.”
• “Andrew Shreve (LANL) presented a rich variety of self-assembled nanomaterials that display specific emergent properties of a mechanical, photonic, or fluidic nature.”
• “Yi Jiang (LANL) reviewed the state of the art for molecular multiscale simulations in which the challenge is to connect realistic but slow molecular dynamic simulations with less accurate but fast higher level simulations.”
• “Andy Pohorille (NASA Ames Research Center, California) used simulations to argue that nongenomic early organisms could undergo evolution before the origin of organisms with genes.”
• “Takashi Ikegami (Univ. of Tokyo) presented simulations of a simple and abstract model of metabolic chemistry that demonstrates the spontaneous formation and reproduction of cell-like structures.”

Not everyone agreed with every proposal, but all agreed on the road map ahead.  Four main questions need to be answered.  Their answers will shed light, hopefully, on the biggest questions of all:

(i) What is the boundary between physical and biological phenomena?  (ii) What are key hurdles to integrating genes and energetics within a container?  (iii) How can theory and simulation better inform artificial cell experiment?  (iv) What are the most likely early technological applications of artificial cell research?
    In time, research on these forms of artificial life will illuminate the perennial questions “What is life?” and “Where do we come from?”

In addition, work on artificially-created nanobots, including some that could repair and replicate themselves, require “cautious courage,” because creating such entities “would literally form the basis of a living technology possessing powerful capabilities and raising important social and ethical implications.”  The authors noted that everyone at the workshops was confident that “useful artificial cells will eventually be created, but there was no consensus about when.”

¹Rasmussen, Chen, Deamer, Krakauer, Packard, Stadler, and Bedau, “EVOLUTION: Transitions from Nonliving to Living Matter,” Science Volume 303, Number 5660, Issue of 13 Feb 2004, pp. 963-965, 10.1126/science.1093669.

We almost titled this entry “Mad Scientists Threaten World With Destruction!” but didn’t want to scare the adults.  Here you have it, folks: Frankenscience alive and well in the labs that gave us atomic bombs.  Our next fear may be artificial cells too small to see that will wreak havoc on us, brought about by some out-of-control prize seeker with courage but not enough caution.
    Actually, that is not the intriguing thing about this story.  It is that evolutionary biologists have no sense of smell.  We quoted extensively from this article to give readers the chance to sharpen their noses and do some serious baloney detecting, because this article stinks of rotten baloney left and right, up and down, through and through.  If you need practice in thinking straight, this article is a good one to practice on.
    It’s not that the questions are bad: they are vital: What is life?  Where do we come from?  People have asked these questions since antiquity, and are not human if they don’t wonder about them.  The baloney begins with the assumption that evolution permeates all of reality, even defines life, and emerges as a victor over thermodynamics – all by itself.  That is the pervasive myth in this story.  They don’t phrase their questions the way most people do: Is there a God? a Designer? an all-wise, all-knowing Creator? (i.e., a source of information).  No!  Every scientist at these conferences assumed from the get-go that elephants and bacteria and human beings “emerged” out of some unknown, fortuitous concourse of atoms that crossed that divide between nonlife and life without help.  That is the only approach permitted under their Darwinian “rules of science.”  It leaves them in a hopeless muddle that becomes almost comic, like a group of blindfolded cave explorers, stumbling around because their rules forbid flashlights and require the wearing of blindfolds.
    Let’s start by unraveling the distinction made by Morowitz between living and nonliving chemistry.  He characterized nonliving chemical reactions as being “driven by thermodynamics.”  This means that nonliving chemicals follow the laws of nature obediently.  The first law of TD says that no new matter and energy will emerge out of nothing.  The second law of TD, more important for our analysis, dictates that chemicals will seek equilibrium and gravitate toward a state of maximum disorder (notice that information is the polar opposite of disorder).  Scientists like to use big words, not just to show off, but in an attempt to be precise.  But here, Morowitz confused the issue by subtly personifying nonliving chemicals, claiming that they “explore the state of space in an ergodical fashion.”  (Ergodic means each member is representative of the whole; for instance, the way one sodium chloride molecule reacts can be considered the way all do; the word also is used in statistics regarding the probability a state will recur.)  Thus, as he describes them, nonliving chemicals “tend to conduct a random, exhaustive search of all possibilities.”  Can a nonliving entity search?  Obviously not.
    Surely what he intended to say is that nonliving chemicals, merely bouncing around at random, will eventually hit on any possible interactions.  Depending on the energy states between them, some interactions will be endothermic, using energy; others will be exothermic, releasing energy.  But whatever is possible, nonliving chemicals will randomly “explore” that space and then do what comes naturally.  Water trickling down a rocky slope appears to be searching for a way down, but is really just responding to the laws of thermodynamics.  Sometimes water will jet up into the air, as in a seaside blowhole or Yellowstone geyser, but only with the input of energy, and even then, not because of a code or special combination of molecules.  Any and all water molecules will react the same under the circumstances, because each is a representative of the set of all water molecules.
    What about life?  “In contrast,” he points out, “living systems explore a combinatorially large space of possibilities through an evolutionary process.”  The key word here is combinatorially.  DNA combines bases into a genetic code, and proteins combine amino acids into functional machines.  The combinations, when meaningful and useful, open up seemingly limitless possibilities that (when energized by metabolism in a container), can allow an organism to beat thermodynamics in the short term.  Locally and temporarily, it can achieve a state of low entropy.  A seed can grow into a gravity-defying plant, and an egg can grow into a bird, flying through the air, with feathers, bones, lungs and a host of richly functional parts.  Eventually, of course, TD wins; the plant withers, and the bird weakens and dies.  Both decay into particles with high entropy.
    This distinction cannot be overemphasized.  Nonliving chemicals do not “explore” combination space because they lack a genetic code to do so: i.e., they lack information.  You will notice that this article tosses around the word information as if it will just magically appear if an appropriate “informational polymer” can be found, whether DNA, RNA or PNA.  Stop right there.  That is equivalent to claiming that the availability of ink, paper and type will form books without an author.  Foul; out; game over.  It is not even worth considering this argument further, but we shall, just for the fun of it.
    Morowitz sneaks in a Darwinian assumption into the second half of his description of living chemicals: he claims that living systems explore a combinatorially large space of possibilities through an evolutionary process.  If we can ever get a Darwinian to prove this instead of assuming it, the intellectual debate over origins will come out of a dense fog.  Yes, organisms can vary through mutation, and yes, traits from pre-existing information can sort into distinct populations, but can a Darwinist name one instance of new information for a new function coming out of an evolutionary process?  Richard Dawkins, the king of Darwin dogmatists, was stumped on this question, and in 3.5 years of reporting from the premiere Darwinist journals, we have yet to run across a clear example.  We can, however, provide many cases of Darwinians moaning about the lack of examples (see 11/01/2002, for instance).
    Evolutionists are sneaky at embedding their philosophy into their terms.  They define life as something that evolves, and they define science as materialism.  It’s impossible to carry on a rational discussion with someone who controls the dictionary.
    In past commentaries, we characterized the gap between life and nonlife as a canyon, and described the ways evolutionists try to imagine nonliving chemicals spontaneously bridging the canyon.  This would be good time to review the 05/22/2002 entry about the ways evolutionists try to help life bridge the gap from both sides.  The important thing to remember is that the top-down approach and the bottom-up approach both cheat by using information from the evolutionist’s brain.  If you keep the cheater out of the process, the chemicals are simply not going to do what the evolutionist wants without his help.
    All the talk about “artificial life,” furthermore, is intelligent design, not evolution, so it is irrelevant to the question of the origin of life.  With these principles in mind, it is easy to detect the baloney in the various proposals in the article:

• So-called self-organizing nanostructures require intelligent design of the components and the environment.  Mass-produced, magnetized Lego blocks might be coaxed to link up, for example, but only in an ergodic fashion and only if they are put into a conducive container.  Even so, the structures contain no real information in the sense of coding; they consist of repetitive patterns.
• The word selection is often misused as a personification; who is doing the selecting?  Remember, chemicals don’t care.  Example: “how and when selection plays a greater role than thermodynamics in the observed distribution of phenotypes.”  Subtle, isn’t it?  Only actors play roles.  He embeds Darwinian assumptions into the sentence.  It suggests a goddess called Evolution that is like a stage director, gradually promoting the actor “selection” over the actor “thermodynamics.”  Sorry.  Thermodynamics always gets “lead role” unless information is directing metabolism within a container to locally and temporarily counteract it.  This requires preprogrammed instructions.  Those are the rules in the theater of physics.
• Theoretical frameworks are intelligently designed, so they have no relevance to a materialistic origin of life.  No theory or model can trump a realistic lab experiment.  So PNA might hold information, huh?  And lipids might form a container, huh?  And the PNA might double as a metabolic engine, huh?  OK: put the raw ingredients into a realistic environment, keep your informational hands off, don’t prevent the harmful cross-reactions, wait a few million years, and watch what happens.  Entropy.
• What life already does is irrelevant to what nonliving chemicals might do.  If metabolism scales with body size between bacteria and elephants, that’s nice.  What does that have to do with the origin of life?
• A container without active transport is a death trap (see 01/17/2002), or would leak out the vital ingredients just as readily as the toxins.  Now analyze the article’s bluffing, overconfident caption to a picture of one of these death traps: “Short RNA oligonucleotides (red) are adsorbed to a particle of montmorillonite (clay) and encapsulated within a fatty acid vesicle (green).  The assembly of RNA within the vesicle is coordinated by the clay particle.”  Come on, now.  You can’t get information out of clay.  You can’t concentrate metabolic ingredients into the vesicle or expel wastes out of it except by diffusion, in which the action will be opposite what is needed.  You can’t have natural selection without replication (see online book).  Thus, the picture and the caption and the big words are utterly irrelevant to the origin of life.
      A thing that looks like a cell is no more a cell than a bronze statue of Teddy Roosevelt is the living man.  This should be obvious.  The normally good-natured organic chemist, Dr. A. E. Wilder-Smith, used to get pretty heated up about similar claims by Sidney Fox years ago.  Fox gained fame by showcasing his contrived “cell-like proteinoid microspheres.”  Wilder-Smith called the claim “rubbish.”  Nothing has changed in 2004; the rubbish has just been reshuffled.
• The current consensus smokescreen fails on two points.  If it’s consensus, it isn’t science (see 12/23/2003).  And how could it be a consensus anyway, when the opposition has been denied a hearing?  Claiming a consensus with only Darwin Party members participating is like claiming the opinion of a majority of Senate Democrats represents American opinion.  (This is not just to pick on Democrats.  Charlie Darwin described his political persuasion as “liberal or radical” [Browne, p. 399], as did most of his ardent disciples.)
• State of the art and simulation: here are two more terms that imply intelligent design, not evolution.
• Debug this code: “the challenge is to connect realistic but slow molecular dynamic simulations with less accurate but fast higher level simulations.”  Pick your disappointment: slow realism or fast fantasy?  (See 02/10/2004 entry on misuse of mathematics in biology.)
• Saying something doesn’t make it so: Copley “explained how catalysts operate in living systems today and how these were likely to have evolved from less efficient precursors.”  Instead of the cute just-so story, can you please perform a stage demonstration of less-efficient precursors evolving into a highly-efficient enzyme?  If not, don’t call it science (see 01/12/2004).
• Debug another line of code: “the citric acid cycle of living cells might be a thermodynamic attractor for all possible metabolic networks, thus explaining its appearance at the core of all living systems.”  Ever heard of the post-hoc fallacy? 

Charles Darwin was privately interested in the origin of life, but publicly reticent to make statements about it.  Out of a desire not to appear impious, he had inserted into the ending of The Origin of Species a suggestion that a Creator might have breathed life into a few forms, or into one, which since had evolved.  His real agenda, however, was all-encompassing: he wanted a materialistic universe with God out of the picture.  But he was cautious.  Charlie was keenly aware of the trap Pouchet had fallen into with Pasteur over spontaneous generation.  He watched cautiously from a distance as Huxley and Haeckel made fools of themselves claiming to have found primordial protoplasm in the seabed.  He dreamed about a “warm little pond” in a letter to his friend Joseph Hooker, but “he remained silent” publicly, writes Janet Browne in Charles Darwin: The Power of Place (Princeton, 2002).  His caution was admirable, but inwardly, he desired this philosopher’s stone, because it would make his denial of God complete:

His own theory of evolution would stand to gain if spontaneous generation was shown to be possible—it would acquire its necessary starting point.  Yet it was easy to make rash mistakes….
    To onlookers, the interconnections between these ideas and the people who proposed them appeared close—evolutionary theory and the physical basis of life seemed part and parcel of the same sprawling intellectual enigma of scepticism, agnosticism, and materialism. …it looked as if naturalists were asserting the sole sufficiency of science [i.e., materialism] as a means of comprehending the entire universe….
    …. Wallace suggested that these rapid transformations of simple matter could quicken evolution to the point where Thomson’s warnings about the shortened age of the earth could safely be ignored.  Darwin saw the value in this.  He would like to see spontaneous generation proved true, he told Wallace, “for it would be a discovery of transcendent importance.”  For the rest of his life he watched and pondered.
(Browne, pp. 394-395.)

It could hardly be denied that the same “enigma of skepticism, agnosticism and materialism” permeated the thoughts of most participants at these two international workshops.  What would really have been interesting at the proceedings, more than the self-absorbed fluff about theoretical frameworks and models, would have been a lively debate about the film Unlocking the Mystery of Life.  If you haven’t seen it yet, by all means do.  And for additional humor, follow the chain links below on Origin of Life.  They might be termed the comic section of Creation-Evolution Headlines.  If you enjoy the just-so storytelling ability of the Darwinians, you might also enjoy the Meatball Theory for the Origin of Music (08/26/2003).