Today’s New Reason To Believe

Keith McPherson

Keith McPherson received his Master of Science in Electrical Engineering from Georgia Institute of Technology in 1993, and currently works as an electrical engineer in Melbourne, FL, in the fields of communications and signal processing.

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In part 1 of this series we learned how the genetic system is an information-processing system, and outlined several reasons why we could expect to find coding techniques in play to protect the genetic data. Such coding techniques are known and used by engineers to protect the data processed by many modern digital communications systems.

We now turn our attention to a few analogies of such coding techniques.

Analogy: Optimality of the Genetic Code and Gray Mapping

The first analogy will show from a qualitative and quantitative perspective that the genetic code is in fact an optimal (or near optimal) mapping from codons to amino acids. (See here for a table describing the genetic code.)

The genetic code seems optimized to the specific nucleotide error probabilities quite well, as is the case for a good code from an engineering perspective. For example, the first and third nucleotides of a codon (see here) are more likely to be misread during translation, and this error appears to be taken into account in the genetic code mapping. These most common errors, or mutations, translate the desired codon into a codon that codes either for the same amino acid, or for an amino acid that has very similar physicochemical properties, thus minimizing function loss. This is similar to Gray codes used in digital communications.

More specifically, the genetic code seems to be specifically designed to code for the same or very similar amino acids for the most common types of substitution mutations (errors), thereby minimizing protein function loss. In like fashion, Gray codes used in engineering are specifically designed to code for the most similar bit patterns for the most common types of symbol errors, thereby minimizing information loss.

I noticed the similarity to Gray coding after reading a paper by Dr. Fazale Rana in 2002. The Gray code interpretation was highlighted by Manish Gupta in a paper published in 2006. Gupta plotted the 64 codons used in the genetic code in terms of nucleotide distance (see Figure 3 here), and remarked on the correspondence to Gray codes used in engineering. The concept of nucleotide distance and the illustrated plot establishes the validity of the Gray map interpretation.

Recall from part 1 that many genetic code mappings are possible due to the high level of redundancy. Therefore, from a qualitative perspective, and from an engineering perspective, the genetic code is superb, perhaps much better than one may expect from a naturalistic perspective.

Recent work shows just how remarkable the natural code is. (See here and here.) Researchers studying the error-minimizing properties of the genetic code noticed that prior work concluded that the natural code ranked in the top 0.02 percent for efficiency, but that the prior work overlooked bias in mutations.¹ When this bias is taken into account, the natural code makes a radical leap forward from the top 0.02 percent to literally one in a million.

Dr. Fazale Rana comments further on the error-minimizing properties of the genetic code:

The genetic code’s error-minimization properties are actually more dramatic than these results indicate. When researchers calculated the error-minimization capacity of one million randomly generated genetic codes, they discovered that the error-minimization values formed a distribution where the naturally occurring genetic code’s capacity occurred outside the distribution. Researchers estimate the existence of 10¹⁸ possible genetic codes possessing the same type and degree of redundancy as the universal genetic code. All of these codes fall within the error-minimization distribution. This finding means that of 10¹⁸ possible genetic codes, few, if any, have an error-minimization capacity that approaches the code found universally in nature. ²

In summary, qualitative and quantitative evidence suggests that the natural genetic code is highly optimized and, in fact, tuned to the most common type of errors (mutations). In addition, this work highlights an underlying analogy between the genetic system and modern communications systems—the so-called Gray code.

The next article in this series will look at another coding analogy between modern digital communications systems and the genetic information-processing system.

Notes/References:

1. Bias includes the fact that not all codons are equally mistranslated to other codons, and that certain nucleotide positions within the codon are more prone to error. Purine/purine and pyrimidine/pyrimidine errors (transition mutations) are more common than purine/pyrimidine errors (transversion mutations), and the ranking of the positions is 3rd, 1st, and 2nd in terms of being more error prone.

2. Fazale Rana, “FYI: I.D. in DNA; Deciphering Design in the Genetic Code,” Facts for Faith, Quarter 1, 2002, 14-23.

Posted by Fazale ‘Fuz’ Rana, Ph.D.

Discovery of Old Lab Vials Erupts New Interest in a Famous Origin-of-Life Experiment

It never ceases to amaze me what turns up when I clean out our garage: forgotten stuff that brings back memories, and occasionally, old things that still have value.

And this is exactly what some former students and associates of the late origin-of-life researcher Stanley Miller discovered when they cleaned out his lab after his death. Old vials from leftover experiments that bring back memories of his famous spark-discharge experiment may shed valuable new light on how prebiotic materials could have formed on the early Earth.

The Miller-Urey Experiment

Miller’s work, conducted in the early 1950s, was the first experimental validation of the Oparin-Haldane hypothesis. Based on the principles of chemical evolution, this model was one of the first scientific theories to describe a mechanistic pathway between simple chemical compounds and life.

To test this hypothesis Miller filled the confines of a carefully assembled glass apparatus with methane, ammonia, and hydrogen after diligently excluding oxygen from the system. At that time, scientists thought the gases Miller used in his experiment existed in early Earth’s atmosphere. A boiling flask of water connected to the glassware introduced water vapor into the headspace and simulated early Earth’s oceans. Miller passed a continuous electric discharge through the gas mix to simulate lightning. The results showed that the primitive atmosphere of the early Earth could, in principle, generate amino acids, one of the key building blocks of life.

Status of the Miller-Urey Experiment

Today, the Miller-Urey experiment is generally considered to be irrelevant to the origin-of-life question. Current understanding of the composition of early Earth’s atmosphere differs significantly from the thinking of the 1950s. Most planetary scientists now believe the Earth’s primeval atmosphere consisted of carbon dioxide, nitrogen, and water vapor. Laboratory experiments indicate that this gas mixture is incapable of yielding organic materials in Miller-Urey-type experiments.

In May 2003 origin-of-life researchers Jeffrey Bada and Antonio Lazcano, long-time associates of Miller, wrote an essay for Science commemorating the 50th anniversary of the publication of Miller’s initial results. They pointed out that the Miller-Urey experiment has historical significance, but not scientific importance in contemporary origin-of-life thought. Bada and Lazcano wrote:

Is the “prebiotic soup” theory a reasonable explanation for the emergence of life? Contemporary geoscientists tend to doubt that the primitive atmosphere had the highly reducing composition used by Miller in 1953.

In his book Biogenesis, origin-of-life researcher Noam Lahav passes similar judgment:

The prebiotic conditions assumed by Miller and Urey were essentially those of a reducing atmosphere. Under slightly reducing conditions, the Miller-Urey reaction does not produce amino acids, nor does it produce the chemicals that may serve as the predecessors of other important biopolymer building blocks. Thus, by challenging the assumption of a reducing atmosphere, we challenge the very existence of the “prebiotic soup,” with its richness of biologically important organic compounds.

Revived Interest in Miller’s Experiment

By sifting through the items left behind in Stanley Miller’s laboratory, his former students and associates uncovered vials of material from his original experiments that they think gives new importance to the Miller-Urey experiment.

Miller actually performed three versions of the spark-discharge experiment. All three permutations yielded amino acids and other organic compounds. Miller decided to focus his efforts, however, on the version that now appears in biology textbooks because he thought that it most closely modeled the atmosphere of early Earth.

Still, Miller held on to cartons of vials containing materials from the other two variations of the spark-discharge experiment along with notebooks that carefully documented the experimental work he performed.

After stumbling upon the vials and corresponding notebooks, Miller’s colleagues decided to re-analyze their contents using state-of-the-art analytical methods not available to Miller fifty years ago.

To their surprise, Miller’s associates discovered that the “textbook” version of the Miller-Urey experiment wasn’t the most successful. The most productive synthesis was one that introduced water into the headspace as a fine mist using an aspirator. This particular experimental rig produced more amino acids with a greater chemical diversity than the textbook experiment.

The design of this forgotten experiment intrigued Miller’s collaborators because it models volcanic emissions that could have occurred on early Earth. Accordingly, volcanic lightning would have served as the energy source that generated prebiotic compounds as it passed through volcanic gases and steam—assuming that the volcanic emissions on early Earth consisted of reducing gases.

Miller’s cohorts now argue that this re-discovery gives new relevance to Miller’s old experiment. Perhaps the sources of prebiotic materials on early Earth were volcanic emissions, not chemical reactions taking place in the atmosphere.

Were Volcanoes the Source of Prebiotic Compounds?

The proposal by Miller’s former associates is not the first time that origin-of-life researchers have appealed to volcanoes as the source of prebiotic compounds. As Hugh Ross and I describe in our book Origins of Life, other scientists have suggested this possibility.

Based on the chemical composition of volcanic emissions today, there doesn’t seem to be much hope that prebiotic materials could form in this environment. The gases spewing from volcanoes today consist primarily of water, carbon dioxide, and sulfur dioxide. This is a highly oxidizing mixture of gases that will not generate prebiotic materials in laboratory simulation experiments like the ones that Miller performed.

But were the gaseous emissions of volcanoes on early Earth different? Did they consist of gases like the ones used by Miller in his spark-discharge experiments? Research conducted a few years ago indicates the opposite. It appears as if the gaseous emissions of volcanoes 3.9 billion years ago were identical to the emissions today. This result means that the conditions of Miller’s experiment were not relevant for either the atmosphere of the early Earth or volcanic environments at that time.

Miller’s work and his status as a scientist remain fixed in a prominent place in the history of science. However, perhaps it’s best that Miller’s vials are removed from the lab once and for all, and sent to a museum for posterity.

by Jeff Zweerink

History disfavors any theory placing Earth in a geometrically special location. Early scientists, such as Ptolemy of ancient Greece, thought Earth resided at the center of the solar system. However, geocentric cosmology eventually gave way to heliocentrism most notably associated with Nicolas Copernicus. Since Copernicus’s time extensive observations have demonstrated that the Sun does not reside at the center of the Milky Way Galaxy (MWG). Nor does the MWG reside at the center of the Local Group of galaxies or the universe. Scientists refer to the fact that Earth is not in a central, specially favored position as the Copernican Principle.

Although this view provides a foundation of cosmological research, scientists don’t simply accept the Copernican Principle. They continue to test it.

One area of research particularly suited to testing is the universe’s mysterious dark energy. The first need to invoke dark energy to explain features of the universe arose as astronomers tried to understand observations of distant Type Ia supernovae. The supernovae appeared dimmer than expected and the simplest explanation was that dark energy was causing the expansion of the universe to accelerate. However, dark energy is not the only explanation.

The same supernovae data would arise if the MWG resides at the center of a large region (something similar in size to the observable universe) with a lower density than that of the surrounding regions. However, placing the solar system (located within the MWG) at the center of such a special region clearly violates the Copernican Principle. Nevertheless, scientists do not simply reject the low density region, also called the void model. They seek to test its validity.

In a previous TNRTB I highlighted one test of the void model that used the cosmic microwave background. Now scientists have developed another test using supernovae data. Reseachers started by characterizing void density profiles that could explain the supernovae data. Then they modeled in detail how the supernovae data would appear with a much larger sample than currently exists. They found that with a sufficient sample of supernovae data from a specified distance, the void model produced different results when compared to dark energy models. Observations over the next few years should definitively tell which model is correct.

If dark energy models prevail, cosmologists will continue to face the great challenge of trying to understand what it is and why it exhibits such extraordinary fine-tuning in order for this universe to support life. If the void models prevail, a guiding scientific principle will need revision. Either way, exciting times lay ahead.

If you would like to see a question about the multiverse addressed in this forum, send it to multiverse@reasons.org.