Biological Information and Intelligent Design: Abiogenesis and the origins of the genetic code

Faith & Science Conversation
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Sy, do we not need to distinguish how something is designed from how it is instantiated (or manufactured, if you like)? The latter is interesting, and is the substance of science, but tells us nothing about how something like the DNA code was designed.

In the context of BioLogos (where we’re allowed to talk about God rather than simply “the Designer”) classical theology would say that God “designed” the code by the intuition of creative wisdom. That would be how he designed it whether he then shoved it wholesale into a cell or designed natural processes to bring it into physical existence.

Or, pace Koonin, did it the hard way and kept making universes until the code turned up by chance.

Analogy: you have no idea (except because you have an idea of my usual slipshod habits) whether I rattled this post off in one, made endless corrections and spelling checks, dictated it to my companion Silas or what. But you know I designed it anyway.

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Good point, Jon, and speaking of slipshod, I am guilty of that in not distinguishing design properly from instantiation. So, yes, I agree with you. But that also raises the question whether ID sees design as you do. And if so, the question of translation (if I may) of a design into an actual product is what remains entirely open. I have no problem with God being the designer (using your definition) of evolution. I am not even sure that @DennisVenema would disagree. (Sorry, Dennis, if I’m wrong about that). But then what? It isnt vital, but it sure would be interesting to know which of the two processes you name was the correct one. Or maybe it doesn’t matter. I don’t know.

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Helpful, thoughtful, and imminently fair-minded post Sy!

A very small comment: while the 2007 Koonin paper does acknowledge the “thorny problem” of the translation system (they acknowledge it as “one of the hardest in evolutionary biology”), describing it as a problem for “natural explanations” may attribute to their acknowledgement a concern they would not endorse. Of course they view scientific explanation as entailing natural causes, and any challenging scientific question represents an unsolved problem for natural explanation. But the emphasis of their paper is not on the general difficulty posed to a natural account, but specifically posed to the then prevailing - primarily adaptationist - account. In proposing a multi-causal, exaptationist account it seems that they believe they’ve made significant steps toward explaining the present function of the translation system, in the face of what they recognize as apparent irreducible complexity and in spite of claims by ID that no such accounts are tenable.

In fact, they set up the paper as an affirmation of the “continuity principle” over and against the claims of what they call “the notorious Intelligent Design Movement.” Their proposal may or may not be adequate or even plausible; but their recognition of the nature and tractability of the problem is not concordant with ID. Thus it would not be the case that Koonin “has since altered his stance” to align more with naturalistic understandings and has “refuted ID”: this 2007 paper explicitly claimed to do both.

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@Relates,

Before I gather sources, I would like to make one point, and ask for one clarification.

The first: “Even Wilson does not make a clear cut connection between ecology and evolution.”

Assuming you didn’t intend to write “a clear cut distinction …”, then you are looking for a clear assertion that ecology and evolution are related. Roger, all the dramatic stories of evolution involve population responses to changes in ecology!

Do you know any story about hominids adopting a more erect stance that doesn’t include a discussion of the drying out of the African plains? … that doesn’t include a discussion of pockets of forests becoming increasingly separated from each other … with early hominids having to devise a way of surviving on the ground, instead of in the trees? … of obtaining food … while avoiding the predators of the flat lands?

Now, for my clarification … Roger, what does the reference have to say in order to satisfy you? ANY academic discussion on the evolution of whales, the evolution of hominids in the bottleneck(s), the extinction of Terror Birds, or of the divergence of Galapagos birds - - they are ALL going to include shifts in ecology - - or shifts in populations to exploit divergent ecologies !!!

If they didn’t, there wouldn’t be any story!

So what else, exactly, must my reference(s) say ?

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Thanks, Jeff, good to hear from you. And yes, you are right. I looked at the rest of the paper, (which I havent done for years) and now realize that I have over the course of time, mangled the timing of Koonin’s statements in my mind, so thanks for the correction. What happened is that Koonin has been even more outspoken against ID after that publication, and might have regretted including that paragraph in 2007, which is what prompted my comment about “refuting”.

It is also worth pointing out that Koonin’s (and also Gould’s) criticisms of the adaptationist paradigm, which you refer to, was to my mind an important step in the recognition of a much more complex mechanism for evolutionary direction. That opening has, in my opinion led to some remarkable and exciting progress in discovering some of those mechanisms.

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How about this:
Ardipithecus ramidus from Science Magazine 2 October 2009. (I couldn’t get the link to the Smithsonian Institution’s article on the critter to work, so these papers will have to do.)

There are more details here: CARTA: Early Hominids: Gen Suwa - Hominid Teeth; Significance of Ardipithecus Ramidus. It’s from the YouTube channel of University of California Television (UCTV)

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@beaglelady

Nice work! Here’s a quote from the first link… filled with references to how one link in human development fit into the hominid sequence for adapting to the environment …

“… The numerous recovered teeth and a largely complete skull show that Ar. ramidus had a small face and a reduced canine/premolar complex, indicative of minimal social aggression.”
[competition is not life-and-death like in other branches of the primate tree]

" Its hands, arms, feet, pelvis, and legs collectively reveal that it moved capably in the trees, supported on its feet and palms (palmigrade clambering), but lacked any characteristics typical of the suspension, vertical climbing, or knuckle-walking of modern gorillas and chimps."
[this primate has some skills required for arboreal living … but not the full set of skills that other primates have]

" Terrestrially, it engaged in a form of bipedality more primitive than that of Australopithecus, and it lacked adaptation to “heavy” chewing related to open environments (seen in later Australopithecus)."
[this group is not adapted to feeding on the more robust vegetations that other primates can consume…]

" Ar. ramidus thus indicates that the last common ancestors of humans and African apes were not chimpanzee-like and that both hominids and extant African apes are each highly specialized, but through very different evolutionary pathways."
[this hominid group has a very different set of specializations - - - suited to its environment, but in a different way from the other primate groups!]

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Well, if Paul Nelson is hanging around still, he can speak to this authoriitatively . As I understand IDists, though, the program is to show that undirected natural causes are insufficient to account for life, specifically focusing attention on “difficult cases” like the origin of DNA.

The fact that the tent holds special creationists both YEC and OEC, fine-tuning frontloaders like Michael Denton, theistic evolutionists like Michael Behe, Thomists like Vincent Torley etc suggests that any agreement must be over the “design” rather than the “instantiation” element.

Remember also that the first generation of TEs including Asa Gray, B B Warfield and even Alfred Russel Wallace considered evolution to be unfolding a design plan, natural selection notwithstanding. Wallace saw even the different properties of tree timber as being teleologically intended for man’s benefit, and yet was thoroughly wedded to continuous processes in nature.

The “instantiation” element must, by definition, be guided by the design (and to that extent arguably visible in the outcomes, as Asa Gray strongly affirmed against the alternative, undirectedness), but will depend on what science shows.

For example, take the “continuity principle” to which Jeff Schloss points (if, indeed, one can glean much about it from a mechanism he deems possibly “inadequate and implausible”, which was the very issue in dispute). If that principle points to lawlike chemical causes, then we’re in the realm of Denton’s fine tuning of the universe to life - and increasingly so the more contingencies have to come together to make it possible, for the alternative is that chaos leads to order without explanation.

If contingency plays a bigger part, in the sense of random mutations, statistically improbable chemical reactions and so on, one is in the realm of divine tinkering - in the crude, monergic understanding of divine action that many ideas and TEs seem to share - or of concurrence in the classical view in which God governs each and every event. To quote David Wilcox (again), chance is God’s signature.

That depends on what question you’re asking! If you’re asking “Did God design this process/eventuality or not?” it’s a foolish question, in my view - especially when the design stares you in the face.

If you’re asking, “How did God create this?” It’s also a foolish question, because creation is not a process, but a bringing into being: reproduction is a process, but the coming of a child into the world is an act of creation (final and formal causes) of which reproduction is just the tail end.

If on the other hand, you ask, “How did God instantiate this design” (which is about secondary efficient causes only, the proper business of science), then processes are of central importance. They need to be adequate and plausible, of course, or they fail the principle of “sufficient causation” for God’s purposes. But in and of themselves they say no more about design than a chisel does about Michaelangelo’s David.

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"What can we expect from a combination of genetics, genomics, biochemistry, and comparative organismal biology?"
Quote from the issue of Science

@gbrooks9 and @beaglelady

Thank you for your responses.

It appears from the quotes you have produced that the article does indicate a connection between evolution of humans and the ecology. The remarks in the bold, which I take to be from George makes this more evident.

What it does not do is connect the environment or ecology with the process of Natural Selection. The quote above is from the editor of the magazine which is a summery of all the articles. It does not mention the science of ecology and how the changing ecology may or may not influence the development of human beings.

My position is clear. Natural Selection guides evolution, which is in agreement which what Darwin said. This is an important part of the genius of his Theory, which modern science overlooks. My difference with Darwin is that he accepted Malthusian competition as the basis for Natural Selection. I understand ecological change as the basis for Natural Selection. If science has moved from Darwin’s point of view to mine, that is great, but it needs to communicate this, not just hint at it.

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Roger

Darwin came to the understanding that Natural Selection is a possible solution to the question of what could be driving evolution after reading Malthus. But it isnt accurate to say that he bases all of Natural Selection on Malthusian competition. As he studied what he had gathered from his field studies, he saw that indeed ecological factors, even in the absence of population pressure, could also result in Natural Selection.

Today, we recognize that Natural Selection can be the result of many different kinds of phenomena. Sometimes, over population leads to competition, and the most fit survive, (Malthus). Sometimes, a change in the ecological environment leads to selection of a particular variant over others. Sometimes a migration to a new environment, or a physical barrier between populations (like different islands or mountains) can lead to neutral drift followed by different variants being selected in the different environments. And sometimes (rarely) a new mutation or horizontal gene transfer or whole genome duplication or retrotransposon insertion or some other genetic change will result in a major phenotypic alteration that is much more beneficial, and natural selection will favor that in the absence of any environmental change or overpopulation related competition.

In other words, current evolutionary theory incorporates anything that increases the fitness of organisms in its view of natural selection. I think its fair to say that environmental or ecological change acting on pre existing variants, is the most common driver of them all.

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@Relates

Your position is clear. And 95% of the world’s evolutionary scientists agree with you. And they write about it.

They just don’t write about it in the way you want them to write about it. But this is to be expected … since you have a rare and special mind.

But do you think it is fair to maintain this perpetual vigil against the bulk of the world’s Evolutionists waiting for them to use the exact words you would use?

There really aren’t too many ways of understanding Natural Selection … and you and them agree on that understanding!

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@Relates

how can @Sy_Garte make it any more clear?

Without the storyline of shifting ecology pushing human evolution … and the evolutionary arc of hundreds of the greatest animal stories ever told - - there would not be a story to tell at all.

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@Sy_Garte
Thank you for your response. No doubt we do not disagree as to what happens, just how it is interpreted.

The overpopulation cause is the classical Darwinian view. The explanations I have seen usually say that this is the only cause of Natural Selection. My comment is this. This is looking at life from a human point of view. Our problem is overpopulation. Animals and plants do not have an overpopulation problem.

A tree produces thousands of seeds. Many of these seeds are used as food by animals, including humans. May are returned to the ground. Some grow to maturity to replace their parent, or to replenish an area razed by fire or humans, or to spread to areas affected by climate change. All ,of these are ecological tasks. Not everything is based on evolution.

The real question is not what caused evolutionary change, but what is the result of evolutionary change. Population pressure, which is pretty much constant, results in the fact that species a must maintain its effective adaption to the environment, or improve it if possible.

It is NOT competition as we generally use that word. Adaption is not based on competition, but on cooperation, better defined as symbiosis. Those species and individuals who work together with others of the same kind or adapt to the challenges of the environment. The dinosaurs when extinct because their ecological niches disappeared, and they were unable to adapt to new ones. Population pressure results in adaption to the environment or seeking a out new niches with less competition. It can also result in a stable population when everything is in balance.

Everything else you mention is ecological. When there is a mutation takes place, natural selection must rule it in or out. If it is negative and most mutations are, it does not survive and flourish. When it is a positive adaption to the environment, with dome luck it will survive and flourish.

There is one aspect of NS which seems not to n=be mentioned which is disease. We see today that both some bat and honey bee population have been threatened by disease, This too is ecological.

On the other hand sexual selection at least in some cases does not appe3ar on its face to be ecological. Certainly sex is ecological, but why peahens prefer the display of peacocks do not really explained.

I find that nature is organized and connected. It is not a hodgepodge or caused and events. This is far different from Dawkins anti-ecological position and belief that life has no meaning or purpose, which he appears to be passing off as based on evolutionary science.

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@gbrooks9

I would like to make it more clear that the story of evolution and life is based on Symbiosis, not by relentless competition. Also that Dawkins’ Selfish Gene and his whole worldview is not backed up by the facts.

The story is that evolution is guided by ecology, which is in turn based on the Logos, Jesus Christ. Science affirms the truth of Christianity, rather than denies it.

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@Sy_Garte My main point in making this comment is that while I do not believe that what we know about the translation system and its evolution or appearance points to a designer, I do think we need to acknowledge the very real challenge that the genetic code and the translation system present to science.

As to the ultimate origin of the genetic code and translation, I agree with you that it would be “perfectly fine with the answer being either ‘natural’ or ‘supernatural’”.

@DennisVenema

My point is that the universe was created by God, so in that sense it is supernatural. Nature created life so in that sense life is natural. Life is both “supernatural” and “natural,” but in fact that is a false dichotomy. It is Western dualism which creates this false dichotomy, not the fact themselves.

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@Relates, both positions sound fine to me.

My point is just this: virtually all the mainstream Evolutionists of the world already agree with you about changing ecologies driving evolution.

If it weren’t for changing ecological conditions, the pace of evolution would slow to a crawl - - which is already on a notoriously ponderous pace of millennia …

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@gbrooks9,

Great! Then we need to get BioLogos to endorse this approach in that:

  1. It make clear that “theistic” evolution is different from the “atheistic” evolution that Dawkins advocates, and

  2. It makes clear the way that evolution connects with Christianity through the Logos as in BioLogos.

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Please comment on this response to your BioLogos article:

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While I think that random activity coupled to a natural selection process cannot be considered a valid way that life originated, I cannot reason an argument for ID that does not include a direct act (or activities) by God to design the required components. Yet the ID argument seems to be constructed along the lines - we are not arguing for God to do this or that, simply for an intelligent cause. Am I missing something in the argument(s)?

As a comment on EC/TE, it stretches credulity to breaking point to accept our ignorance of the beginnings of life, and also the clear inability to account for anything of substance from random activity and NS, and yet insist that evolution is the way God made it all - this amounts to a contradiction and cannot be rationalised in any way.

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This area has become so speculative that I cannot see any approach that would avoid an ideological stance that harms science and its credibility. To avoid the accusation that I selectively quote to promote some specific view, I provide a lengthy extract from the Introduction to a review: From Prelife to Life: How Chemical Kinetics Become Evolutionary Dynamics” I. A. CHEN and M. A. NOWAK, Vol. 45, No. 12 ’ 2012 ’ 2088–2096 ’ ACCOUNTS OF CHEMICAL RESEARCH.

The essence, as I read it is that extremely small steps involving simple(?) molecules can explain an evolution of life from pre-life.

“Imagine an aqueous solution of small molecules on the early earth. Now try to picture how that prebiotic soup might assemble itself into even the simplest, tiniest living organism, perhaps a few hundred nanometers across. At first glance, this process may seem like an impossible leap because so many transitions must occur to transform the jittery molecules into a living structure. To understand the origin of life, one must break it down into a series of smaller transitions and look for simple ways that physical and chemical effects could accomplish each transition. One successful synthetic approach is to focus on the emergence of structures: the synthesis of monomers, polymerization ofmonomers into sequences, the formation of protocells by membrane encapsulation of sequences, and so forth. Significant experimental work has been directed at producing ribozymes and protocells and is reviewed elsewhere. Substantial theoretical work has also been particularly directed toward understanding the emergence of wellfolded RNA. But a complementary viewpoint that comes naturally from a mathematical perspective is to study the emergence of dynamics that accompany the structural transitions.

Perhaps the most well-known study of chemical evolution was introduced in the 1970s by Manfred Eigen and Peter Schuster, who described a population of sequences ……… Since then, the field has advanced considerably and now includes the aqueous synthesis of RNA nucleotides.[30] Condensation of these nucleotides can also be achieved under plausibly prebiotic conditions promoted by various means, including divalent cations, clay or lipid surfaces, and solute concentration by freezing conditions. Our model of prelife presumes the availability of activated monomers and the presence of conditions conducive to polymerization.”

I add the abstract to ref [30] to show how speculation somehow is morphed into “evidence” which then becomes “proven science”. J. Am. Chem. Soc., 2010, 132 (46), pp 16677–16688.

“The recent development of a sequential, high-yielding route to activated pyrimidine nucleotides, under conditions thought to be prebiotic, is an encouraging step toward the greater goal of a plausible prebiotic pathway to RNA and the potential for an RNA world. However, this synthesis has led to a disparity in the methodology available for stepwise construction of the canonical pyrimidine and purine nucleotides. To address this problem, and further explore prebiotically accessible chemical systems, we have developed a high-yielding, aqueous, one-pot, multicomponent reaction that tethers masked-sugar moieties to prebiotically plausible purine precursors. A pH-dependent three-component reaction system has been discovered that utilizes key nucleotide synthons 2-aminooxazole and 5-aminoimidazoles, which allows the first divergent purine/pyrimidine synthesis to be proposed. Due to regiospecific aminoimidazole tethering, the pathway allows N9 purination only, thus suggesting the first prebiotically plausible mechanism for regiospecific N9 purination.”

This highly speculative notion may be contrasted with work such as that of Douglas D. Axe and Ann K. Gauger, “Model and Laboratory Demonstrations That Evolutionary Optimization Works Well Only If Preceded by Invention—Selection Itself Is Not Inventive” Biocomplexity, Volume 2015 | Issue 2 | Page 1, who show that an incremental approach (small changes over lengthy periods that enable selection of the bio-molecules) cannot be demonstrated experimentally, and that variations in complex bio-systems such as enzymes, lead to optimisation and not invention (or formation of new) bio-entities.