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The Evolutionary Origins of Genetic Information, Part 1

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July 29, 2013 Tags: Genetics, History of Life

Today's entry was written by Stephen Freeland. Please note the views expressed here are those of the author, not necessarily of The BioLogos Foundation. You can read more about what we believe here.

The Evolutionary Origins of Genetic Information, Part 1

Note: 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.

Introduction

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 X lie 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, or macro-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, creationism, macro-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. 

DISCUSSION QUESTIONS

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?

Notes

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: http://www.answersingenesis.org/articles/cfl/

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 http://www.bbc.co.uk/blogs/wondermonkey/2011/07/faith-versus-science-does-crea.shtml

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: http://ncse.com/rncse/30/review-deep-structure-biology )

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)

 


Stephen Freeland is currently project manager for the NASA Astrobiology Institute research team based at the University of Hawaii. His academic background (a bachelor’s degree in zoology from Oxford, a master’s in biological computation from York University, and a doctorate in genetics from Cambridge) has led him to spend the past twelve years researching the evolution of genetic coding. Steve’s current research explores the evolution of the amino acid “alphabet”—the set of twenty building blocks with which life has been making the proteins of metabolism for more than three billion years. Underlying this research is a growing interest in the cosmological question, “To what degree is life on Earth (or elsewhere) a result of chance?” As the son of a biology teacher who retrained as a Methodist minister, Steve has been blessed with an encouraging environment with which to explore the interface of science and faith since childhood.

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Roger A. Sawtelle - #82171

July 29th 2013

Stephen,

It appears to me by what you have written that this process does not involve natural selection.  I think that this is a mistake.  As far as I can tell nom genetic changes takes placew without natural selection.

Darwinism has been trying to eliminate natural selection for a while, which would make things much easier for it.  It would also be wrong.  I think that Denis Noble is on the right track, while Dawkins and his Selfish Gene are wrong.  


evolving man - #82178

July 29th 2013

Hi Roger,

I apologize, but I am a little confused as to what process you are focusing upon with this question?

I very much agree that natural selection is important to evolution in general! The way we usually teach this in class to identify that evolution is an outcome, natural selection is one of the mechanisms that produce this outcome (the other one is genetic drift - and some people make finer distinctions beyond this). Studying what balance of these two are responsible for producing a specific evolutionary outcome is very much the sort of thing that evolutionary researchers spend their time studying.

I hope that helps get us on the same page?

Best wishes,

Stephen


Merv - #82176

July 29th 2013

Thanks for this educational essay, Dr. Freeland.  The line diagram with its points of varied difference was a great way to illustrate the macro-micro issue.

Would you call the notion of “convergence” in evolution an active “category 2” pursuit?  If it could be shown that known laws contribute to convergence on, say, hominids, or on intelligence in a species, how would such a demonstration interact with your faith?  (I realize that such demonstration has not happened, but to deny the possibility seems theologically ‘gappish’).  


evolving man - #82180

July 29th 2013

Hi Merv,

(And please do call me Stephen or Steve)

Thank you for a great question that cuts to the heart of this first installment – Sorry this answer is long, but I couldn’t find a way to say anything of substance in fewer words!

I would alter slightly your wording to identify something that something that I feel comfortable identifying in category 2. Convergence is well known in specific instances - so for me, the big (category 2) question is what all this convergence adds up to ... is it a general theme? an occasional curiosity? or something in between? (and perhaps more importantly, what sort of research can answer that for us?) For me that is still an open question. I know others who are confident it has already been answered - but, interestingly, some think it’s answered in each of two ways (convergence is a rare curiosity vs convergence is a general theme) - so I conclude that it has yet to be answered satisfactorily!

This of course cuts to the second part of your question. To me, a first reaction to discovering “inevitable” convergence of evolution towards self-aware hominids is a great hint (to those who choose to see the world in terms of theistic evolution) that God is working through evolution, more or less linearly, to bring about the world we live in. It certainly carries very interesting implications for a universe that seems ever more likely (from secular science) to contain more than one example of life. Over recent years, though, I have found myself questioning this. Atheistic writing about 20th century science seized upon our low-probability existence to emphasize a Godless universe. That connection is not at all clear to me. I think it makes me feel equally (more?) special to think that God’s infinitely delicate management of creation brought about my existence in ways that science cannot detect.

So there’s an Episcopalean answer for you! I am happy with either one. I’d love to see BioLogos encourage this particular debate somewhere in the future, since I think a lot more could usefully be said (and by people more skillful in these ways of thinking!)

Best wishes,

Stephen


Jon Garvey - #82184

July 30th 2013

Stephen

As I understand the penultimate paragraph of your reply to Merv, you’re distinguishing evolution as (at heart) a lawlike process that shows (to the theist) God’s orderliness, from the possibility that it’s a very highly contingent process (“low-probability existence”). It seems you’ve been drifting towards the latter scenario in your thinking - so that, for example, it might be less surprising to you if “Rare Earth” scenarios turned out to be the case, and life uncommon or unique in the Universe.

As you know much of the discussion over Intelligent Design has been about the nature of just those probabilities - which are notoriously hard to assess given our great ignorance of whether the huge “search spaces” involved are actually limited in some way that would render them less problematic and more lawlike - the quest for scientific skyhooks, if you like.

But if one grants, at any point or many in evolution, very low probabilities (such as, for example, near-neutral mutations happening to turn up useful new protein folds from open frames as ORFans on a regular basis), then is there actually any way of distinguishing “chance” from “divine action” at all? It becomes a question of choosing, non-scientifically, between “I believe there is a divine cause for this creative chance event” and “I believe there is no cause for this creative chance event.” There could never be a testable hypothesis to distinguish them, because they’re alternative faith positions.

Or to put it another way, is it not fair to suggest that “very low contingency” leading to order is, in itself, a sign of divine action unless one is prejudiced against it? Theistic Evolutionist (and population geneticist) David L Wilcox actually writes, in God and Evolution, “Chance is, in fact, the hand of God.” Is there anything in science to refute that statement?


evolving man - #82196

July 31st 2013

Dear Jon,

Yes exactly - and very nicely fleshed out in your comment! My (very personal) growth here is to see that neither inevitability nor unlikeliness is a better clue to God’s involvement in creation - unless one has already chosen how one expects to find God working through natural laws.

For what it is worth, I am not so much leaning towards unlikeliness as noting that I remain unconvinced, as yet, that science can distinguish between the two…yet. I think (and hope, and pray!) that I have an open mind here - helped by the conviction that neither one is more surprising to me from a spiritual perspective,

Thanks for writing!

Steve

 


Jon Garvey - #82203

July 31st 2013

“Unconvinced… that science can distinguish between the two”.

Stephen, I take it that you mean here distinguishing between “chance” and “divine guidance” (rather than between “law” and “chance”). I would venture to suggest that science normally uses “chance” (in the sense we’re using it of “extremely low probability”) as shorthand for “lack of any material causation that is accessible to analysis.”

So in my old field (medicine) drugs were said to be inactive when their “successes” strayed outside standard deviations. In other words, it wasn’t a fluke they made a person better, but the recovery was due to some other cause altogether and the drug was a non-cause.

Similarly, in the solar system, computer simulations predict there is something like a 2% possibility that Newton will turn out right and the inner planets will eventually become unstable. Should that happen, there would be no scientific explanation except that it wasn’t too low a possibility and stuff happens. But if the odds had actually been estimated at 1:10^50, and Mercury still became unstable, it would be humanly, if not scientifically, perverse not to consider some other explanation (such as divine judgement, maybe?). So as I hinted above, under those odds science’s “failure to distinguish” would actually be based on (a) excluding God as a cause a priori and (b) instead accepting a lack of any cause as “science”, when it is actually a capitulation to ignorance.

But when such low probabilities are under consideration the distinction between “natural” and “supernatural” becomes completely meaningless - and especially so if like you, me and the classical theist tradition, we are committed to saying that God is working both through law and chance in all things. There is no conceptual difference, that I can see, between God’s “working through” a probability of 1:10^50 (say), and God doing miraculously what would otherwise only happen 1:10^50 times. In either case, something completely beyond the ordinary occurs because God wills it.

The real theological issue, it seems to me, is the suggestion by some theists that God doesn’t actually “work through” either law or chance: ie in the first case his hands are tied by “natural law” and he has to accept whatever “happens” to emerge as the clock unwinds; and in the second case he tosses the dice but spits on his hands first - or maybe makes 10^50 universes to he gets lucky in at least one. To me that is not even theism, let alone Christian (ie Christological) creation doctrine.


Roger A. Sawtelle - #82191

July 30th 2013

Stephen,

Thank you very much for your reply and welcome to BioLogos.

evolution is an outcome, natural selection is one of the mechanisms that produce this outcome (the other one is genetic drift

However forgive my temerity for disgreeing with you as you have expressed yourself above.  As I understand Darwin and here I agree with him there are two distinct aspects of evolution, two distinct processes which act together to produce evolutionary change. 

The first is Variation, which is the process of producing differing alleles, and the second is Natural Selection which determines which of these alleles or characteristics will survive and flourish and which will not.  Most do not.  Most are selected out so genetics or Variation itself does not produce evolution, nor does Natural Selection. 

Much confusion occurs when people confuse Variation and Natural Selection which appears to be the case today.  Genetic drift is a form of Variation.  It causes the genome to change.  Apparently it is different from other kinds of Variation because, as I understand it, it is not caused by mutation, but some sort of housekeeping (stabilization and purification) done by the genome itself. 

People claim that genetic drift does not involve Natural Selection, but my understanding of this is that genetic drift is neutral in terms of Natural Selection, and if not precisely neutral, close enough that the new allele is selected in, rather than selected out.  Would a drifted gene survive if it were not fit?   

Thus it is my understanding (please correct me if I am wrong) that there is only one way to understand how evolution works and that is Variation proposes new life forms, and Natural Selection disposes, it determines which new life forms will be selected in and which will not. 

A more serious problem is that Darwinism does not know how natural selection works.  Yes, they know it works, but you can use the internet without the slightest ideas how the internet works.  Yes, the can measure fitness and model how Natural Selection works, but reading a textbook on this it cautioned students not to confuse the mechanism with the measurement of the results. 

To say Natural Selection is determined by relative fitness and relative fitness is determined by measuring relative fitness is a circular statement. 

I hope that I have made myself clear.  Please correct me if my use of scientific terms is not the best.  

The structure of Natural Selection is one of the most important scientific questions of our time.  I have tried to elucidate it in my book Darwin’s MYTH.   

I awat your response.  Thank you for your time and patience.


evolving man - #82197

July 31st 2013

Dear Roger,

Thank you for the welcome!

Just one small point of discrepancy here: both natural selection AND genetic drift are “sorting” mechanisms that sift through genetic variation (reducing it in the process)...so when I leave out variation from my previous desciption above - and thank you for a very important correction, to specify where the “raw material” of variation comes from - it is indeed because I am careless in forgetting that saide of the equation. Mutation feeds variation into the gene pool - then either selection or drift (or normally some combination of both) reduce this variation. Selection “chooses” variation according to the environment; drift “chooses” variation at random.

I would go further and say that we think we do understand exactly how selection works - we just lack the sophistication to predict, for the most part, ahead of time (because the environment is a complicated place!)

 

Steve


GJDS - #82192

July 30th 2013

Stephen,

I want to begin by agreeing with you in the way you categorise scientific endeavour as some knowledge and insights that we may regard with confidence, and another that we may regard in need of clarification or ends up being rejected.

“Most criticisms of evolution are, upon careful inspection, claims that evolutionary theory is incomplete.”

I think the term ‘inadequate’ instead ‘incomplete’ may be closer to the mark. By this I mean the theory does not take into account a number of factors, including mechanistic constraints. For example, your example of genetic coding appears more as an exercise in probabilities and yet the descriptive nature you provide seems to me to be that of mechanism(s) involving complex bio-molecules. If it is the latter, these molecular mechanisms need to be understood to a far greater extent scientifically – until a mechanism can be provided in clear steps with the understanding of any intermediates and possible outcomes, it cannot be regarded as anything but a semantic description. I suggest that your treatment is an oversimplification of a complex and elegant mechanism that we have yet to adequately understand. I offer this example to illustrate my meaning of inadequate within your discussion.

While I agree with your comment, “Although the molecular machinery that produces genetic coding is complex (and indeed, less than perfectly understood), the most essential elements for this discussion....”, I suggest that the most essential element is an understanding of this machinery. Until an adequate understanding is achieved, we are left with astronomical possibilities coupled to extraordinary speculation that ‘begs the question’ .. perhaps you may need a third category, although I cannot offer a suggestion besides ‘wildly speculative and unpersuasive’.

I find your alternatives of the way evolution may be regarded to include ‘creationism’ inappropriate. It is generally accepted that the physical sciences are not able to address non-physical aspects of the cosmos; we may discuss such things within metaphysics and theology, but not within the physical sciences. Since this is the case, it seems odd that an appeal to an external agency would be discussed as one of a number of alternatives to evolution. 

Allow me to suggest that there are often instances in the progress of science that are termed ‘serendipity’, or ‘unexpected outcomes’ ; I think such an occurrence is needed to progress Darwinian thinking. In any event, your description, such as  “The ribosome is a much larger molecule, comprising both RNA and various proteins, which supervises the whole process of translation.”..... can just easily be interpreted as the language of intent. If we invoke causes, these need not be identified as supernatural – science may view a chain of causality in a similar manner to mechanism(s), as both would fit within a ‘law-like’ structure that the sciences are understood. This imo is what Darwinism needs (or better still a complete change in thinking), and not the constant modification that we have seen for so long.


evolving man - #82198

July 31st 2013

Hi! (Sorry, I don’t know who I am writing to?)

The four parts of this essay seek to add up to pose question(s) at the big focal point you address - I’d be happy to revisit this with you towards the end of the posts when I think we might have the most productive discussion… So with respect, I’d be delighted if we can rejoin this line of discussion after part 4 - is that OK?

Best wishes,

Steve

http://finewoodworking.assets.tauntonnet.com/assets/uploads/posts/38623/teacup_shelf.jpg


GJDS - #82201

July 31st 2013

Thanks Steve, I look forward to reading the rest of your discussion and to look at any questions we may jointly consider. I use GJDS and am happy with whatever manner you wish to reply to me. 


Roger A. Sawtelle - #82202

July 31st 2013

Stephan,

Thank you for your helpful comments.

Selection “chooses” variation according to the environment; drift “chooses” variation at random.

Your statement that Natural Selection determines relative fitness according to how a allele sucessfully adapts to its environmental niche in my opinion is very obvious, but is not accepted by NeoDarwinists like Dawkins who seem to dominate the scientific scene.

His Selfish Gene places the gene in an ecological vacuum. The only real aspect of NS he tries to discuss is competition between carnivores and herbivores, which is about the balance of nature, not natural selection.

NeoDarwinists fail to understand that Symbiosis is the real driving force of evolution and ecology, not competition, so they attack E. O. Wilson for his new group selection view. I think that Darwin, Dawkins, and Dennett are wed to this unproven conflict based atomistic understanding of Natural Selection because it supports their view that the universe is chaos without God and meaning.

Those who support this view seem to agree with this understanding of the universe. Christians need a viable scientific alternative.

I do not know if you saw the video of a lecture by Denis Noble on YouTube, which has since been taken down for copyright reasons. He is very clear in his criticism of Dawkins for scientific and philosophical reasons. He specifically puts ecology into his tricorner, nonlinear model of evolution as opposed Dawkins’ linear, gene-centered model.

I question as to whether drift chooses variation at random. As I tried to indicate my understanding of genetic drift was the genome doing some genetic houskeeping to wrap up some loose ends to make sure the genome was fuctioning properly.

It does not effect the outward aspect of the life form, but it does makes some changes in the genome and could possibily lead to other changes. Since I am trying to understand the reports of others, my understanding could be flawed.

However if this understanding is correct, if genetic drift is the result of the genome puting its house in better order, it does not seem that it is a random process. Indeed “Monod’s Law” that nature works without meaning and purpose is not true, particulary for organic nature.

Animals and plants are clearly able to seek food, to avoid danger, and to repair injury. We even know that laboratory mice can learn from experience as I expect most animals do.

Where evolution is indeterminate in that it cannot be predicted in advance, this does not mean that it is without cause and direction. We know that our climate is changing and we know that this will have significant impact on all life forms including us.

We also know that this change is not natural but human caused, the the normal mechanisms of nature may well not be able to keep these changes in acceptable limits. I read a troubling article in a recent issue of Scientific American on this issue.

 

 


Jon Garvey - #82275

August 1st 2013

Can’t somebody shoot the spammer?


Jon Garvey - #82285

August 2nd 2013

Thankyou, Mr Mod.


Roger A. Sawtelle - #82276

August 1st 2013

Merv, Stephen, and Jon,

I must say that I find this kind of discussion not to be fruitful. 

The Bible says that the person who believes that there is no God is a fool.  They understood that God the Father created the universe, so if there is a universe then there is a God.  This left them free to try to distinguish the workings of the real God, YHWH, from the false gods. 

Now there are some who claim that the universe in effect created itself, which means that they believe in pantheism, that is the universe is God, rather than atheism.  If humans and their world were created by Nature, then Nature is their God. 

The Greeks and many others believed that the universe is eternal and thus uncreated, but this more difficult since most Westerners accept the Big Bag theory.  This is probably the basis of our dualistic worldview, but it is no longer valid scientifically or philosophically.

Thus it seems that the question is not the existence of God, but the character of God as revealed in God’s Creation.  Is God good?  To which Nick says No.  Does the universe have rational structure, meaning, and purpose?  To which Monod and New Atheists say No.   

The fact is there is no way that the universe and humanity could have been created by pure chance.  Even Dawkins admits that.  The only alternative to that is divine Intelligence and Will.  And there is no way that a good world could be created by any One other than a Loving God. 

Let others attack the character of the universe and God if they will.  Christians know the Truth about Life, Jesus Christ the Logos, and the Truth sets us free.    

 


Merv - #82278

August 1st 2013

Roger, reading through some of your posts (like this last one) felt to me like a trip with Alice down the rabbit hole.  But you always swing around to proper conclusions by the end of it all.

Just to pick out a point:   pointing out to atheists that God must exist because the universe is here is like claiming that goblins create mushrooms, and then while displaying some actual mushrooms you proclaim:  “See?  I told you goblins are real!”  Our existence is evidence of something ... don’t get me wrong.  But I only enlist it as evidence of God because I’ve already grounded my convictions in other more revelatory foundations.

By the way—you may have opened up another avenue of scientific investigation:  the big bag theory.  I like it already.  In the beginning was the big bag.  The bag opened…

 


Roger A. Sawtelle - #82283

August 2nd 2013

Merv,

The difference is that goblins even if they did exist could not make mushrooms. 

YHWH and only YHWH has the power, wisdom, and the love needed to create the universe.  Thus YHWH is the necessary Reality.  There is no viable alternative.

 


RBH - #82355

August 5th 2013

Stephen, you wrote<blockquote>Biological evolution describes a natural process that transfers information from a local environment into the chemical known as DNA.</blockquote>I quite like that formulation. <a href=“http://pandasthumb.org/archives/2009/08/a-peer-reviewed-1.html#comment-192704”>This is how I put it</a> several years ago:<blockquote>In a real sense, evolution by natural selection is [a process] for transferring ‘information’ from an environment to the genome of a species. The distribution of alleles in a population changes as a function of changes in the environment. Someone – Dawkins, maybe? – suggested that the genome of a species is a palimpsest recording the prior selective environments that species’ ancestors lived in.</blockquote>I use the inverted commas on “information” to indicate that it is the vernacular—ordinary language—sense, not Shannon information or K-C-S (algorithmic) information that’s intended: I doubt that either could be measured in that situation.


RBH - #82356

August 5th 2013

So much for formatting.


Jon Garvey - #82357

August 5th 2013

RBH

I see the point of  what you’re saying, but wonder if “information” is a good term to use, given the very specific semantic-type information systems within living things, eg the genome and the DNA code.

Analogy - if you find a submarine, you can deduce that there was deep water and it was designed to travel in it, but the transfer of information from the mind of the engineers to the artifact is of a different order altogether from the “transfer of information” from the ocean to the designer’s mind.

If, as many modern scenarios (ehg J Shapiro) suggest, organisms are active in moulding themselves to the environment, viewing genes as a passive recipient of environmental situations  viewed as “information” could be greatly misleading.

Is my wearing a coat best seen as an information transfer from a cold environment?


RBH - #82376

August 6th 2013

I’m not sure about “best,” but it’s surely a valid way of concpetualizing it. One way to get information about one’s own wardrobe choices in the morning is to peek outside to see what others are wearing—shorts, parkas, or whatever.


RBH - #82377

August 6th 2013

Ugh. “One way to get information to inform one’s own wardrobe choices ...”.


Jon Garvey - #82387

August 7th 2013

Mmm - unconvinced. If everything is information, nothing is.

Scenario 1:

My friend shouts through the door that it’s cold and I should wear a coat.

Scenario 2:

I look out the window as you suggest and interpret the visual cues as implying cold weather.

Scenario 3:

I step outside and my nose and fingers drop off.

One surely needs to distinguish “information” in those three cases: the first case is semantic information, the second is intelligent interpretation of circumstance, and the third is just cause and effect.

Your match of environment to genome seems most like the third: we see certain genes and deduce clues about the environment in which they arose. Or we see a guy trying to hold a knife and fork with no fingers and deduce he went outside in the cold. Frostbite is only “information” by a severe stretch of the term. most importantly it forecloses seeing any actual informational process at work, such as as active response to environmental conditions.

Sulphuric acid informs your fingers of the need to dissolve. Asteroids inform most species to go extinct. The wind is the information in a boat’s sails. Just like a Shakespeare sonnet really - not.


Roger A. Sawtelle - #82366

August 6th 2013

Is my wearing a coat best seen as an information transfer from a cold environment?

Jon,

Very good question.

I would say that it the result of reacting to a cold environment and thus is information about that environment.

I would also acknowledge that some people see all of reality as information and there is some validity to this.

For instance the Bible is information about how humans related to God.  We can learn from the Bible about God by putting ourselves into the Biblical environment and see how we relate to God similarly or differently from the way Moses, Peter, and other people reacted.  We can learn from their experiences as it illuminates our lives.

Evolution is where history and science meet.  A problem with Scientism is that it tries to make evolution ahistorical, because science has been seen as ahistorical, but it is not.  The problem with Creationism is that it tries to make life and the Bible ahistorical, which of course it isn’t. 

Evolution, Life, and the Bible are all historical and we see them in this way, God’s way, then most of the problems concerning them are solved.  This does not make life a subjective or relative, but it puts life in context of God’s Salvation History as God intends it.

 


Jon Garvey - #82388

August 7th 2013

Good to pin this down Roger. My wearing a coat is only information (type 2 in my response to RBH above) to you as an intelligent human capable of weighing evidence about what coats are for, why people usually put them on, whether I’m the usual kind of person or an eccentric recluse, etc. My dog interprets my wearing a coat purely in terms of “going out now” - there’s no information to him about the ambient temperature.

The Bible narratives, too, are highly directive in their information, like any story and all history. We might, or might well not, learn the same lessons from the Bible as from spending a month in Abraham’s entourage. If he prayed privately, we might notice more about his clothes and his management of animals: but the Bible tells us where to look. Similarly one can live through important historical times and miss what historians come to see as the Big Historical Movements, because history is, intrinsically, the intelligent selection and interpretation of events, not just the whole sum of all that happens. Information reduces uncertainty be reducing choice.

That’s why if I want information about the world, I buy a book rather than shrug and say, “I’m in the world, so it’s giving me all the information I need already.”

So I say that information has, at least, to obey Shannon’s law - as DNA and numbers of other codes in living things clearly do. To respond to an environment means making some organised changes after sensing its salient features - it’s not simply to live or die.


Roger A. Sawtelle - #82392

August 7th 2013

Jon,

I think that information is information.  Information assumes a knower, which means the fact that “natural” information exists indicates that Nature is designed by a Rational Intelligence.  We know that DNA is a very complex form of information which is read every life form even though they cannot think in the same way humans do.

Putting on a warm coat sends a message that most people understand.  I expect that many dogs also would understand that putting on a coat is usually is a sign that you are going outside and thus will be taking them for a walk.  Do not estimate the power of communication and the ability of non-humans to “read” our actions which is consistent with our discussion.

Now the problem appears to be, How does DNA communicate or how is information communicated from outside of the life form to the genes?  First let us be clear that outside of the life form is the environment or the ecology.  Second this is the reverse of the Darwinist scientific view that changes in genes power evolutionary change.

Now my understanding of evolution is that a species uses Variation, genetic changes, which provides multiple alternative combination of alleles, which are accepted or rejected by Natural Selection according to how well these alleles adapt to the ecological niche.  Thus these alleles provide for the needs of the life form based on its ecological requirements, which are often changing and thus bring the DNA into harmony with the ecology. 

I see evolution is like echolocation used by bats to feel out their environment so to speak.  Life forms generate many Variations, from small to large, and they flourish or not according in how they match up with the environment, thus providing the ability to adapt to it, as do bats. 

If the climate is growing colder, then it is likely that those alleles which provide warmer fur or feathers will do better.  Other adaptations are migration (seasonal or permanent,) hibernation, building warm dwellings, and use of clothing. 

We see that life forms learn from experiece.  That seems to apply to genes also as we see from the changes in the pocket mouse and the stickle fish.  The world is not about things, Life is about history.  Philosophy and science tend to be about things.  Christianity is basically about God’s Salvation History.  That is why they are out of sync.                        


Backcreek - #82420

August 12th 2013

“Further evidence indicated that micro-evolution accumulates over time to account for all larger degrees of evolutionary diversification (macro-evolution.)”. 

This would appear to be one of the major bones of contention with the Intelligent Design movement.  Behe, for example, would want to see the “chain of custody” from the point of micro-evolution until it results in macro-evolution.  Is there a book written for scientific layman that would provide further detail on this “further evidence”?


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