The Message in the Microcosm: DNA and the Death of Materialism

Stephen C. Meyer

Traditional approaches that fail to take account of new findings in molecular cell biology cannot survive the present day. Materialistic explanations for the origin of information have been systematically eliminated over the past forty years. Has origin-of-life research brought us to the brink of a new scientific revolution?

Despite the now well-documented influence of Christian thinking on the rise of modern science from the time of Ockham to Newton, much of science during the 19th century took a decidedly materialistic turn. From cosmology to geology to biology, science seemed to support the rise of materialistic thought. In field after field, new scientific theories implied the complete autonomy of nature from God. Materialism denied evidence of any intelligent design in nature and any ultimate purpose to human existence.

Darwin's evolutionary theory, in particular, seemed to show that the blind process of natural selection acting on random variations could, and did, account for the origin of new forms of life from simpler forms without any divine intervention or guidance. According to Darwin, living organisms only appeared to be designed by an intelligent creator; nature itself was the real creator of new species. By the late 19th century only the origin of the first life-something Darwin's theory did not address-lacked a detailed materialistic explanation.

Explaining Life's Origin in Materialistic Terms

Nevertheless, in the 1870s and 1880s scientists assumed that devising an explanation for the origin of life would be fairly easy. For one thing, they assumed that life was essentially a rather simple substance called protoplasm that could be easily constructed by combining and recombining simple chemicals such as carbon dioxide, oxygen, and nitrogen. Thus, the German evolutionary biologist Ernst Haeckel would refer to cells as simple "homogeneous globules of plasm."

To Haeckel, a living cell seemed no more complex than a blob of jello. His theory of how life first came into existence reflected this view. His method likened cell "autogeny," as he called it, to the process of inorganic crystallization. Haeckel's English counterpart, T.H. Huxley, proposed a simple two-step method of chemical recombination to explain the origin of the first cell. Just as salt could be produced spontaneously by adding sodium to chloride, so thought Haeckel and Huxley, could a living cell be produced by adding several chemical constituents together and then allowing spontaneous chemical reactions to produce the simple protoplasmic substance that they assumed to be the essence of life.

During the 1920s and 1930s a more sophisticated version of this so-called "chemical evolutionary theory" was proposed by a Russian biochemist named Alexander I. Oparin. Oparin had a much more accurate understanding of the complexity of cellular metabolism, but neither he, nor any one else in the 1930s, fully appreciated the complexity of the molecules such as protein and DNA that make life possible. Oparin, like his 19th-century predecessors, suggested that life could have first evolved as the result of a series of chemical reactions. Unlike his predecessors, however, he envisioned that this process of chemical evolution would involve many more chemical transformations and reactions and many hundreds of millions (or even billions) of years.

The first experimental support for Oparin's hypothesis came in December of 1952. While doing graduate work under Harold Urey at the University of Chicago, Stanley Miller conducted the first experimental test of the Oparin chemical evolutionary model. Miller circulated a gaseous mixture of methane, ammonia, water vapor, and hydrogen through a glass vessel containing an electrical discharge chamber. Miller sent a high voltage charge of electricity into the chamber via tungsten filaments in an attempt to simulate the effects of ultraviolet light on prebiotic atmospheric gases. After two days, Miller found a small (2%) yield of amino acids in the U-shaped water trap he used to collect reaction products at the bottom of the vessel.

Miller's success in producing biologically relevant "building blocks" under ostensibly prebiotic conditions was heralded as a great breakthrough. His experiment seemed to provide experimental support for Oparin's chemical evolutionary theory by showing that an important step in Oparin's scenario-the production of biological building blocks from simpler atmospheric gases-was possible on the early earth.

Miller's experimental results also received widespread press coverage in popular publications such as Time magazine and gave Oparin's model the status of textbook orthodoxy almost overnight. Thanks largely to Miller's experimental work, chemical evolution is now routinely presented in both high school and college biology textbooks as the accepted scientific explanation for the origin of life.

Yet as we shall see, chemical evolutionary theory is now known to be riddled with difficulties; and Miller's work is understood by the origin-of-life research community itself to have little if any relevance to explaining how amino acids-let alone proteins or living cells-actually could have arisen on the early earth.

To understand today's growing crisis in chemical evolutionary theory, this article will focus on the two most severe difficulties confronting it: the problem of hostile pre-biotic conditions and the problem posed by the complexity of the cell and its components.

The Problem of Hostile Pre-biotic Conditions

When Stanley Miller conducted his experiment simulating the production of amino acids on the early earth, he presupposed that the earth's atmosphere was composed of a mixture of what chemists call reducing gases such as methane, ammonia, and hydrogen. He also assumed that the earth's atmosphere contained virtually no free oxygen. In the years following Miller's experiment, however, new geochemical evidence made it clear that the assumptions that Oparin and Miller had made about the early atmosphere could not be justified.

Instead, evidence strongly suggested that neutral gases-not methane, ammonia, and hydrogen-predominated in the early atmosphere. Moreover, a number of geochemical studies showed that significant amounts of free oxygen were also present even before the advent of plant life, probably as the result of volcanic outgassing and the photodissociation of water vapor.

In a chemically neutral atmosphere, reactions among atmospheric gases will not take place readily. Moreover, even a small amount of atmospheric oxygen will quench the production of biological building blocks and cause any biomolecules otherwise present to degrade rapidly.

As had been well known even before Miller's experiment, amino acids will form readily in an appropriate mixture of reducing gases. What made Miller's experiment significant was not the production of amino acids per se, but the production of amino acids from presumably plausible prebiotic conditions. As Miller himself stated, "In this apparatus an attempt was made to duplicate a primitive atmosphere of the earth, and not to obtain the optimum conditions for the formation of amino acids." Now, however, the situation has changed. The only reason to continue assuming the existence of a chemically-reducing, prebiotic atmosphere is that chemical evolutionary theory requires it.

Ironically, even if we assume for the moment that the reducing gases used by Stanley Miller do actually simulate conditions on the early Earth, his experiments inadvertently demonstrated the necessity of intelligent agency. Even successful simulation experiments require the intervention of the experimenters to prevent what are known as "interfering cross reactions" and other chemically destructive processes. Without human intervention, Miller-type experiments invariably produce non-biological substances that degrade amino acids into non-biologically relevant compounds.

Experimenters prevent this by removing chemical products that induce undesirable cross reactions. They employ other "unnatural" interventions as well. Simulation experimenters have typically used only short wavelength light, rather than both short and long wavelength ultraviolet light, which would be present in any realistic atmosphere. Why? The presence of the long wavelength UV light quickly degrades amino acids.

Such manipulations constitute what chemist Michael Polanyi called a "profoundly informative intervention." They seem to "simulate," if anything, the need for an intelligent agent to overcome the randomizing influences of natural chemical processes.

The Problem of Specific Sequencing

Yet a more fundamental problem remains for all chemical evolutionary scenarios. Even if it could be demonstrated that the building blocks of essential molecules could arise in realistic prebiotic conditions, the problem of assembling those building blocks into functioning proteins or DNA chains would remain. This problem of explaining the specific sequencing and thus, the information within biopolymers, lies at the heart of the current crisis in materialistic evolutionary thinking.

During the 1950s and 60s, at roughly the same time molecular biologists found that protein molecules were composed of long and definitely arranged sequences of amino acids, scientists also learned the structure and function of DNA, the molecule of heredity. Molecular biologists discovered that the specificity of amino acids in proteins derives from a prior specificity within the DNA molecule-from information on the DNA molecule stored as millions of specifically arranged chemicals called nucleotides or bases along the spine of DNA's helical strands. So the sequence specificity of proteins depends upon another sequence specificity-upon information-encoded in DNA.

The elucidation of this system by molecular biologists has raised the question of the ultimate origin of the specificity-the information-in both DNA and proteins. Indeed, many scientists now refer to the information problem as the "Holy Grail" of origin-of-life biology. As Bernd-Olaf Kuppers recently stated, "the problem of the origin of life is clearly basically equivalent to the problem of the origin of biological information."

Explaining the Origin of Information

While many outside origin-of-life biology may still invoke "chance" as a causal explanation for the origin of biological information, few serious researchers still do. Since molecular biologists began to appreciate the sequence specificity of proteins and nucleic acids in the 1950s and 60s, many calculations have been made to determine the probability of formulating functional proteins and nucleic acids at random. Even assuming extremely favorable prebiotic conditions (whether realistic or not) and theoretically maximal reaction rates, such calculations have invariably shown that the probability of obtaining functionally sequenced biomacromolecules at random is, in Prigogine's words, "vanishingly small ... even on the scale of ... billions of years." As Cairns-Smith wrote:

Blind chance ... is very limited. Low-levels of cooperation he [blind chance] can produce exceedingly easily (the equivalent of letters and small words), but he becomes very quickly incompetent as the amount of organization increases. Very soon indeed long waiting periods and massive material resources become irrelevant.

Consider the probabilistic hurdles that must be overcome to construct even one short protein molecule of about one hundred amino acids in length. First, all amino acids must form a chemical bond known as a peptide bond so as to join with other amino acids in the protein chain. Yet in nature many other types of chemical bonds are possible between amino acids. The probability of building a chain of 100 amino acids in which all linkages involve peptide bonds is roughly 1 chance in 1030. Second, functioning proteins tolerate only left-handed amino acids.

Third and most important of all: functioning proteins must have amino acids that link up in a specific sequential arrangement, just as the letters in a meaningful sentence. Because there are twenty biologically occurring amino acids the probability of getting a specific amino acid at a given site is 1/20. Actually the probability is even lower because there are many non-proteinous amino acids in nature. Even if we assume that some sites along the chain will tolerate several amino acids (using the variances determined by biochemist Robert Sauer of M.I.T.), we find that the probability of achieving a functional sequence of amino acids in several functioning proteins at random is still "vanishingly small," roughly 1 chance in 1065-an astronomically large number.

Moreover, if one also factors in the probability of attaining proper bonding and optical isomers, the probability of constructing a rather short, functional protein at random becomes so small as to be effectively zero (1 chance in 10125) even given our multi-billion-year-old universe. Such calculations, thus, simply reinforce the opinion that has prevailed since the mid-1960s within origin-of-life biology: chance is not an adequate explanation for the origin of biological complexity and specificity.

Natural Selection as an Explanation

At nearly the same time that many researchers became disenchanted with "chance" explanations, theories of pre-biotic natural selection also fell out of favor. Such theories allegedly overcome the difficulties of pure chance by providing a mechanism by which complexity-increasing events in the cell might be preserved and selected. Yet these theories share many of the difficulties that afflict purely chance-based theories.

Oparin's revised theory, for example, seemed to presuppose a pre-existing mechanism of self-replication. Self-replication in all extant cells depends upon functional (and, therefore, to a high degree sequence-specific) proteins and nucleic acids. Yet the origin of these molecules is precisely what Oparin needed to explain. Thus, many rejected the postulation of pre-biotic natural selection as question begging.

Further, natural selection can only select what chance has first produced, and chance, at least in a prebiotic setting, seems an implausible agent for producing the information present in even a single functioning protein or DNA molecule. For this reason, most scientists now dismiss appeals to prebiotic natural selection as essentially indistinguishable from appeals to chance.

Self-Organization as an Explanation

Because of these difficulties, many origin-of-life theorists after the mid-1960s attempted to address the problem of the origin of biological information in a completely new way. Rather than invoking prebiotic natural selection or "frozen accidents," many theorists suggested that the laws of nature and chemical attraction may themselves be responsible for the information in DNA and proteins. Some have suggested that simple chemicals might possess "self-ordering properties" capable of organizing the constituent parts of proteins, DNA and RNA into the specific arrangements they now possess.

In 1977, Prigogine and Nicolis proposed a theory of self-organization based on their observation that open systems driven far from equilibrium often display self-ordering tendencies. For example, gravitational energy will produce highly ordered vortices in a draining bathtub; and thermal energy flowing through a heat sink will generate distinctive convection currents or "spiral wave activity."

For many current origin-of-life scientists, self-organizational models now seem to offer the most promising approach to explaining the origin of biological information. Nevertheless, critics have called into question both the plausibility and the relevance of self-organizational models. Ironically, perhaps the most prominent early advocate of self-organization, Professor Dean Kenyon, has now explicitly repudiated such theories as both incompatible with empirical findings and theoretically incoherent.

The empirical difficulties attendant self-organizational scenarios can be illustrated by examining a DNA molecule. The diagram here shows that the structure of DNA depends upon several chemical bonds. There are bonds, for example, between the sugar and the phosphate molecules that form the two twisting backbones of the DNA molecule. There are bonds fixing individual (nucleotide) bases to the sugar-phosphate backbones on each side of the molecule. Yet notice that there are no chemical bonds between the bases that run along the spine of the helix. Yet it is precisely along this axis of the molecule that the genetic instructions in DNA are encoded.

Further, just as magnetic letters can be combined and recombined in any way to form various sequences on a metal surface, so too can each of the four bases A, T, G, and C attach to any site on the DNA backbone with equal facility, making all sequences equally probably (or improbable). The same type of chemical bond occurs between the bases and the backbone regardless of which base attaches. All four bases are acceptable; none is preferred. In other words, differential bonding affinities do not account for the sequencing of the bases. Because these same facts hold for RNA molecules, researchers who speculate that life began in an "RNA world" have also failed to solve the sequencing problem-i.e., the problem of explaining how information present in all functioning RNA molecules could have arisen in the first place.

For those who want to explain the origin of life as the result of self-organizing properties intrinsic to the material constituents of living systems, these rather elementary facts of molecular biology have devastating implications. The most logical place to look for self-organizing properties to explain the origin of genetic information is in the constituent parts of the molecules carrying that information. But biochemistry and molecular biology make clear that the forces of attraction between the constituents in DNA, RNA, and protein do not explain the sequence specificity of these large information-bearing biomolecules.

Significantly, information theorists insist that there is a good reason for this. If chemical affinities between the constituents in the DNA message text determined the arrangement of the text, such affinities would dramatically diminish the capacity of DNA to carry information. To illustrate, consider what would happen if the individual nucleotide "letters" (A,T,G,C) in a DNA molecule did interact by chemical necessity with each other. Every time adenine (A) occurred in a growing genetic sequence, it would likely drag thymine (T) along with it. Every time cytosine (C) found a slot, guanine (G) would follow. As a result, the DNA message text would be peppered with repeating sequences of A's followed by T's and C's followed by G's.

Rather than having a genetic molecule capable of unlimited novelty, with all the unpredictable and aperiodic sequences that characterize informative texts, we would have a highly repetitive text awash in redundant sequences-much as happens in crystals. Indeed, in a crystal the forces of mutual chemical attraction do completely explain the sequential ordering of the constituent parts, and consequently crystals cannot convey novel information. Sequencing in crystals is repetitive and highly ordered, but not informative. Once one has seen "Na" followed by "Cl" in a crystal of salt, for example, one has seen the extent of the sequencing possible.

Bonding affinities, to the extent they exist, mitigate against the maximization of information. They cannot, therefore, be used to explain the origin of information. Affinities create mantras, not messages.

The tendency to confuse the qualitative distinction between "order" and "information" has characterized self-organizational research efforts and calls into question the relevance of such work to the origin of life. Self-organizational theorists explain well what doesn't need explaining. What needs explaining is not the origin of order (whether in the form of crystals, swirling tornadoes or the "eyes" of hurricanes), but the origin of information-the highly improbable, aperiodic, and yet specified sequences that make biological function possible.

For Help, Call Information

To see the distinction between order and information compare the sequence "ABABABABABABAB" to the sequence "Help! Our neighbor's house is on fire!" The first sequence is repetitive and ordered, but not complex or informative. Systems that are characterized by both specificity and complexity (what information theorists call "specified complexity") have "information content." Since such systems have the qualitative feature of aperiodicity or complexity, they are qualitatively distinguishable from systems characterized by simple periodic order. Thus, attempts to explain the origin of order have no relevance to discussions of the origin of information content. Significantly, the nucleotide sequences in the coding regions of DNA have, by all accounts, a high information content-that is, they are both highly specified and complex, just like meaningful English sentences.

Yet the information contained in an English sentence-in a newspaper, for example-does not derive from the chemistry of the ink or paper, but from a source extrinsic to physics and chemistry altogether. Indeed the message transcends the properties of the medium.

The information in DNA also transcends the properties of its material medium. Because chemical bonds do not determine the arrangement of nucleotide bases, the nucleotides can assume a vast array of possible sequences and thereby express many different messages.

If the properties of matter (i.e., the medium) do not suffice to explain the origin of information, what does? Our experience with information-intensive systems (especially codes and languages) indicates that such systems always come from an intelligent source-i.e., from mental or personal agents, not chance or material necessity.

Our generalization about the cause of information has, ironically, also received confirmation from origin-of-life research itself. During the last forty years, every naturalistic model proposed has failed to explain the origin of information-the great stumbling block for materialistic scenarios. Thus, mind or intelligence or what philosophers call "agent causation," now stands as the only cause known to be capable of creating an information-rich system, including the coding regions of DNA, functional proteins, and the cell as a whole.

The Design Inference

Because mind or intelligent design is a necessary cause of an informative system, one can detect the past action of an intelligent cause from the presence of an information-intensive effect, even if the cause itself cannot be directly observed. Since information requires an intelligent source, the flowers spelling "Welcome to Victoria" in the gardens of Victoria harbor lead visitors to infer the activity of intelligent agents even if they did not see the flowers planted and arranged.

Scientists in many fields now recognize the connection between intelligence and information and make inferences accordingly. Archaeologists assume a mind produced the inscriptions on the Rosetta Stone. SETI's search for extraterrestrial intelligence presupposes that the presence of information imbedded in electromagnetic signals from space would indicate an intelligent source. As yet, radio astronomers have not found information-bearing signals coming from space. But molecular biologists, looking closer to home, have identified encoded information in the cell. Consequently, a growing number of scientists now suggest that the information in DNA justifies making what probability theorist William Dembski and biochemist Michael Behe call "the design inference."

The materialistic science we have inherited from the late 19th century, with its exclusive conceptual reliance on matter and energy, could neither envision nor can it now account for today's biology. As Norbert Weiner puts it, "Information is information, neither energy nor matter. No materialism that fails to take account of this can survive the present day."

The molecular biology of the cell raises the possibility that "no materialism" will survive the revolution beginning to take root in science. While established journals and institutions continue to propagate the orthodoxies of a generation ago, many scientists, philosophers of science, and mathematicians have begun to challenge these views and to formulate alternative approaches.

If the simplest life owes its origin to an intelligent Creator, then perhaps man is not the "cosmic orphan" that 20th-century scientific materialism has suggested. Perhaps then, during the 21st century, the traditional moral and spiritual foundations of the West will find support from the very sciences that once seemed to undermine them.