The Evolutionary Origins of Genetic Information, Part 1

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This and next week on The BioLogos Forum, join astrobiologist Stephen Freeland for a look into the nature of information and the origins of life on earth. (These posts were originally published as a paper in the ASA?s academic journal, PSCF, and are reprinted here with permission.)

Stephen was raised in a Christian family, and his father is a Methodist minister in England whose passion for natural history and science provided a rich environment in which to explore the relationship between science and faith. During Stephen'?s teenage years, he explored various denominations, from Catholic to charismatic non-denominational churches, and most recently, life in Baltimore has led Stephen to a deep and rewarding connection with St. Bartholemew's Episcopal church, where he enjoys the Christ-centered meeting point of spiritual substance, social justice, inclusive grace, and rich traditions of liturgy and music.

Because of Stephen?'s commitment to deepening his faith through conversations with other Christians, which helps to deepen our corporeal understanding of God'?s grace and processes, ?and because the nature of this material is the rather controversial subject of first life and evolution, ?Stephen will be participating in the online conversation at the bottom of each post in this series. At the end of each post, you'?ll find a few discussion questions, which we encourage you to use as starting points for commenting, (but you are of course welcome to ask him questions of your own, and add your own observations to the dialogue).

Abstract: Any living branch of science achieves progress by testing new ideas. The results of these tests determine whether each new idea is accepted as a change to what we thought we knew, dismissed as incorrect or simply stagnates owing to a lack of clear evidence. For evolutionary theory, one such proposition is that some features of genetic information cannot evolve through natural processes unless we allow a role for an intelligent designer. This proposition claims testability by defining information in a way that usually reserved for human creations, such as computer programming code. The underlying idea is that we know intelligent beings create computer-code, so if similar features occur within genetic information then perhaps genetic information derives from an intelligent agency? However, many biologists perceive that they are able to understand exactly where life’s genetic information comes from (the local environment) by thinking in terms of more fundamental and well-established definitions of information that do not involve Intelligent Design. Current science does not have a detailed, widely-accepted description for how a genetic information system evolved in the first place. Intelligent Design proponents suggest that this is a key weakness of existing evolutionary theory, consistent with the need for an intelligent designer. I describe the progress that mainstream science has made towards understandin g the origin of genetic information since the molecular basis of genetic information was first understood, encouraging readers to reach their own conclusions.


Biological evolution describes a natural process that transfers information from a local environment into the chemical known as DNA. Something similar happens when gravity causes raindrops to form a puddle, and the shape of the ground beneath becomes reflected in the underside of the water.

This unusual definition of evolution seeks to clarify an ambiguity in traditional alternatives, such as “biological evolution is a natural process of change in genetic material over time.”1 The phrase “change in genetic material” describes and confines exactly what scientists measure and test to develop their evolutionary theory, however any description of this sort omits two aspects of a living science.  One is the group of all propositions that have been revealed as incorrect through tests (such as recapitulation - the claim the embryos re-enact their evolutionary history as they develop from a single fertilized egg cell.2) Let us call these incorrect propositions Category 1 omissions. Knowing about them can help scientists avoid wasted time spent repeating previous errors.

The second element missing from a classic definition comprises all propositions for which science has yet to find clear evidence, for or against. We may refer to these as Category 2 omissions. Propositions in this second category are especially important to science because all suggestions to change existing scientific understanding start here. In other words, Category 2 propositions can gather supporting evidence until they become accepted as scientific truth. These successful challenges to established science will alter what we previously thought we understood, perhaps even requiring a change in definition of that science. (It is both humbling and inspiring to remember that scientific knowledge is incomplete in ways that are actively misleading us at present.) However, many Category 2 propositions follow a different trajectory as careful application of the scientific method reveals that they are incorrect, re-classifying these ideas as Category 1 propositions. A third fate is possible for Category 2 propositions. If they do not generate sufficient evidence to make a clear case, whether it be for or against, then they will stagnate. A proposition often ends in stagnation if it fails to generate clear, testable hypotheses that have the power to transform established theory.

Intelligent Design has already started its life in Category 2 by suggesting that current evolutionary theory cannot adequately explain the origin of new genetic information. The unusual definition of evolution written above hints why many scientists, including Christians such as myself, think this is an incorrect (Category 1) proposition. What follows seeks to explain why in greater detail – and to equip you to judge for yourself.

Evaluating suggestions for changes to evolutionary theory.

Start by imagining a line that describes every conceivable degree of genetic difference that could separate any two living organisms (Figure 1). In fact, we don’t have to rely on imagination - such differences can be measured precisely, due to life’s shared biochemistry of DNA and proteins: see Box 1. Most criticisms of evolution are, upon careful inspection, claims that evolutionary theory is incomplete. They suggest that evolutionary theory can only explain differences up to a specific point on this line. For example, older versions of creationism claim natural processes cannot change anything more than the frequency (number of copies) of genetic material already present within a species. In effect, this defines a point X on the line shown in Figure 1. To the right of Xlie larger differences in genetic material, such as those that separate different species. Under creationism, these differences are considered too large for natural processes to explain, and are therefore explained by divine intervention.  

A growing weight of detailed evidence shows that new species form by the accumulation of changing gene frequencies within a population.3,4 This evidence has led many contemporary versions of creationism to increase the acceptable limit for evolution, moving point X on the line in Figure 1 to point Y. An explanation is that God created fundamental kinds of animal and plants so that the formation of new species within these kinds are legitimate outcomes of natural processes.5 Accepting this interpretation, it is now the larger degrees of genetic difference lying to the right of Y that require supernatural explanation.

For our purposes, what matters is that different versions of creationism all accept some degree of evolution but place a cut-off on the extent of change that evolution can produce, explaining anything above that point by divine intervention. Wherever the cut-off is perceived, the same terminology is used: micro-evolution (anything to the left of the acceptable limit) is attributable to natural processes, but macro-evolution (anything to the right of this point) requires a new explanation – direct creation by God.

Figure 1:
 Any two or more organisms can be compared for genetic similarity (e.g. in terms of differences in DNA sequence), and thus plotted as a point on a line that runs from “complete genetic similarity” (clones or identical twins) to “very little genetic similarity”, such as a human and an E. coli bacterium.

The terms “micro-evolution” and “macro-evolution” come originally from similar suggestions made within secular science during the early development of evolutionary theory.6 Biologists working early in the 20th century were learning how to cause genetic mutations in a laboratory setting. These mutations could, in a single generation, produce large changes in an organism’s appearance. Some pioneers of this new science (genetics) thought their discoveries changed evolutionary theory. Darwin had previously described a process of evolution by natural selection, and this process could be observed changing the frequencies of genes within populations over one or more generations. However, subtle differences in the genetic makeup of a population seemed too small to connect with the large jumps being witnessed in laboratories, and the latter seemed more relevant to the formation of new species. A typical evolutionary debate from this time also defined a point somewhere near X on the line shown in Figure 1. Everyone agreed that Darwin’s process could explain changes to the left of this point (micro-evolution), but some now argued that a fundamentally new phenomenon called genetic mutation, ormacro-mutation, was responsible for the larger-scale differences to the right (macro-evolution.)

At first sight, both macro-mutationism and creationism seem similar. Both propose a cut-off point for the degree of genetic change that evolutionary theory can explain, and both propose a new cause must be added to explain genetic differences beyond this cut-off. Where the two propositions differ for science is in their potential for tests.  Supernatural causes (literally, those that come from beyond nature) cannot be tested directly from within the natural universe. Science can get no nearer than searching for indirect evidence, such as natural phenomena that cannot be explained by any known, natural cause. Evidence of this kind is unlikely to carry creationist propositions from Category 2 suggestions into accepted science. In part, this is because specific data used to justify un-natural causes tend to find equal or better explanation in terms of the natural causes measured by science as new data becomes available.7 Mostly, however, the problem is that un-natural phenomena can never be more than consistent with a supernatural cause. Even where specific claims for un-natural phenomena have not been refuted, it remains equally possible that science has yet to understand natural causation, and science keeps growing its understanding in ways that support evolution.8

For more views on supernatural events, divine action, and miracles, please visit BioLogos’ FAQ as well as Ard Louis’ article on the subject.

In contrast to creationism, the work of the early geneticists referred to strictly natural phenomena (i.e. those occurring within the observable, natural universe.) This focus allowed for direct evaluation by science. Through a series of hypotheses and tests, geneticists revealed that early examples of laboratory-induced macro-mutation were, in fact, large-scale genetic damage caused by powerful doses of radiation and chemicals. Meanwhile, other tests clarified that within nature, genetic mutations of far greater subtlety do indeed account for the minor differences between members of a species (micro-evolution.) Further evidence indicated that micro-evolution accumulates over time to account for all larger degrees of evolutionary diversification (macro-evolution.) In other words, science not only failed to find supporting evidence for the idea that macro-mutations are responsible for the emergence of new species, it also undermined the observation that had led to this hypothesis in the first place.  Science refuted the claim that macro-mutations filled a gap within evolutionary theory by discovering that there was no gap to fill. Macro-mutationist ideas for the origin of new species have therefore moved from Category 2 (ideas for which the evidence is unclear) to Category 1 (ideas that are incorrect), and are no longer actively researched by evolutionary biologists.9

Over the years, secular science has proposed many other novel factors that evolutionary theory should absorb to better explain biological diversity. So far, all have gone the way of macro-mutationism.10 However, cutting-edge research is, by definition, constantly probing for evidence to support new insights. For example, one recent claim is that without adding any new causal factors, enough biological evolution will ultimately produce something like our own sentient species.11 Contrary to popular belief, this outcome is not predicted by current evolutionary science.12 The new claim of inevitable outcomes has not been refuted by science, nor has the supporting evidence become overwhelming. In fact, scientists still don’t know quite how to weigh the evidence –how to measure inevitability when it comes to evolution. As a result, inevitable outcomes remains a Category 2 idea, a topic of active debate and research until scientists gather a clear majority of evidence to reject or accept it into science.13 If such evidence is not forthcoming, the idea will likely atrophy.

These three propositions, creationismmacro-mutationism and inevitable outcomes, provide context for discussing another idea that has arisen in Category 2: the idea that evolutionary theory would be improved by allowing a role for a guiding intelligence. Nothing is inherently unscientific about this suggestion so long as it can find appropriate evidence (through tests) to help scientists decide, one way or the other.  One idea for a test is to ask whether we can identify properties of genetic information that resemble human-created information. The idea is that we are intelligent, so if genetic material looks like the sort of thing we would make then it might be better explained as the product of Intelligent Design, especially if science can identify features of genetic information inexplicable by known evolutionary processes.14 Intelligent Design names one of these features Specified Complexity – a type of information content that aims to measure the semantic content of information (the amount of meaning within a piece of information.) According to the concept of Specified Complexity, natural processes that lack a guiding intelligence cannot produce new genetic information nor can they explain the origin of genetic information because this implies an increase in Specified Complexity. Each of these claims warrants careful consideration.

Box 1.    An Introduction to Biological Coding and the Central Dogma of Molecular Biology

A code is a system of rules for converting information of one representation into another. For example Morse Code describes the conversion of information represented by a simple alphabet of dots and dashes to another, more complex alphabet of letters, numbers and punctuation. The code itself is the system of rules that connects these two representations. Genetic coding involves much the same principles, and it is remarkably uniform throughout life (Figure 2): genetic information is stored in the form of nucleic acid (DNA and RNA), but organisms are built by (and to a large extent from) interacting networks of proteins. Proteins and nucleic acids are utterly different types of molecule; thus it is only by decoding genes into proteins that self-replicating organisms come into being, exposing genetic material to evolution. The decoding process occurs in two distinct stages: during transcription local portions of the DNA double-helix are unwound to expose individual genes as templates from which temporary copies are made (transcribed) in the chemical sister language RNA. These messenger RNA molecules (mRNA’s) are then translated into protein.

The language-based terminology reflects the fact that both genes and proteins are essentially 1-dimensional arrays of chemical letters. However, the nucleic acid alphabet comprises just 4 chemical letters (the 4 nucleotides are often abbreviated to ‘A’, ‘C’, ‘G’ and ‘T’ – but see footnote27), whereas proteins are built from 20 different amino acids. Clearly, no 1:1 mapping can connect nucleotides to amino acids. Instead nucleotides are translated as non-overlapping triplets known as codons. With 4 chemical letters grouped into codons of length 3, there are 4x4x4 = 64 possible codons. Each of these 64 codons is assigned to exactly one of 21 meanings (20 amino acids and a ‘stop translation’ signal found at the end of every gene.) The genetic code is quite simply the mapping of codons to amino acid meanings (Figure 2a). One consequence of this mapping is that most of the amino acids are specified by more than one codon: this is commonly referred to as the redundancy of the code. 

Although the molecular machinery that produces genetic coding is complex (and indeed, less than perfectly understood), the most essential elements for this discussion are the tRNA’s and ribosome. Each organism uses a set of slightly different tRNA’s that each bind a specific amino acid at one end, and recognize a specific codon or subset of codons at the other. As translation of a gene proceeds, appropriate tRNAs bind to successive codons, bringing the desired sequence of amino acids into close, linear proximity where they are chemically linked to form a protein translation product. In this sense, tRNA’s are adaptors and translators – between them, they represent the molecular basis of genetic coding. The ribosome is a much larger molecule, comprising both RNA and various proteins, which supervises the whole process of translation. It contains a tunnel through which the ribbon of messenger RNA feeds; somewhere near to the center of the ribosome, a window exposes just enough genetic material for tRNA’s to compete with each other to bind the exposed codons. 


Q1: “It is both humbling and inspiring to remember that scientific knowledge is incomplete in ways that are actively misleading us at present” Do you think that scientists show an appropriate awareness of this concept? Do you think that non-scientists of our scientifically dominated age show appropriate awareness? Where does this leave the concept of “scientific fact”?

Q2: Supernatural causes (literally, those that come from beyond nature) cannot be tested directly from within the natural universe. Science can get no nearer than searching for indirect evidence, such as natural phenomena that cannot be explained by any known, natural cause… The problem is that  un-natural phenomena can never be more than consistent with a supernatural cause. Even where specific claims for un-natural phenomena have not been refuted, it remains equally possible that science has yet to understand natural causation ” Is this an oversimplification? When you read this argument, does it imply to you that “supernatural phenomena” are not to be trusted, or that science is limited in what it can say about our world? Would you feel more at home in a world that can be fully described by science, or one that is larger than science can describe?

Q3: “Contrary to popular belief, [the idea that evolution leads inevitably to something like our species] is not predicted by current evolutionary science” Have you seen this idea expressed, overtly or implicitly in secular sources that assume they are reflecting evolutionary science (TV advertisements, sci-fi movies etc.?) What does this tell us about the ongoing debate about the interface of evolutionary theory and faith?


1. This definition appears, for example, within the classic text-book for undergraduates: Futuyma, D. J. Evolution. (2005, Sunderland, Massachusetts: Sinauer Associates)

2. For an accessible discussion of this topic, see Neil Shubin’s book Your Inner Fish (2009, Random House Digital)

3. For example, see the review by K. Omland and D. Funk. “Species level paraphyly and polyphyly”. Annual Reviews in Ecology, Evolution and Systematics (2003) 34: 397-423.

4. Christopher E. Bird, Brenden S. Holland, Brian W. Bowen, Robert J. Toonen. “Diversification of sympatric broadcast-spawning limpets (Cellana spp.) within the Hawaiian archipelago.” Molecular Ecology (2011) 20: 2128

5. For example, see Creation: Facts of Life. Chapter 2: Darwin and biologic change (2006, New Leaf Press, Green Forest, Arkansas). This text is freely available online at:

6. For an excellent review of the history by which evolutionary thought absorbed and dismantled these ideas to reach the “(Neo-)Darwinian Synthesis” see Chapter 9, The Eclipse of Darwinism, within P.J. Bowler’s “Evolution: The History of an Idea” (1983, University of California Press, Berkely and London)

7. P. Senter “Using creation science to demonstrate evolution: application of a creationist method for visualizing gaps in the fossil record to a phylogenetic study of coelurosaurian dinosaurs.” Journal of Evolutionary Biology (2010) 23:1732–1743. For a more accessible overview of this article, see

8. A good, recent summary is presented by Jerry Coyne’s book Why evolution is true. (2009, Viking Penguin, New York)

9. Natural mutations can sometimes have large effects, particularly in genetic regions that influence deep developmental pathways of multicellular organisms (i.e. the genes that control how other genes are switched on and off to build an adult organism from a single fertilized egg-cell.) However, these changes are generally deleterious to the organism, and are therefore unusual components of an evolutionary lineage. A deeper discussion of this type of mutation can be found in Carroll S. B. “Homeotic genes and the evolution of arthropods and chordates”. Nature (2005) 376: 479–85. I would draw the reader’s attention to the broader context: these sorts of mutations are limited to relatively few events on one small branch of the tree of life. In terms of general macro-evolution for life on our planet, biologists do not view these events as typical to the formation of new species.

10. Some of these suggestions for “skyhooks” and “cranes” that would like to lift the natural processes of evolution to produce higher levels of genetic change are discussed in Chapter 3 of Daniel Dennett’s book Darwin’s Dangerous Idea: evolution and the meaning of life (1995, Simon and Schuster, New York)

11. See for example Simon Conway Morris’ book Life’s solution: inevitable humans in a lonely universe (2003, Cambridge University Press, Cambridge). 

12. See, for example, Stephen Jay Gould’s book Wonderful Life (1989, W.W. Norton, New York). Gould is extreme in his view, but is closer to the position of mainstream evolutionary science, as can be seen from reviews of the books in which Morris (footnote 11) argues for inevitable humans (e.g. the review by the National Center for Science Education:

13. For example, see the multi-authored The Deep Structure of Biology: is convergence sufficiently ubiquitous to give a directional signal?, (2008, Templeton Foundation Press, West Conshoken PA)

14. For example, see Chapter 6 of William Dembski’s book Intelligent Design: The Bridge Between Science and Theology (1999, Inter Varsity Press)



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BioLogos Editorial Team

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