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

Hi @Sy_Garte- yes, there is no question that the origin of the code is a thorny problem, and will likely take some time to work out, if ever. I would see a “natural” explanation for it to be even more awe-inspiring than a miraculous one, though as I have said, I’m fine either way.

Hello @paulnelson, and welcome to BioLogos. I’ve read your and Meyer’s reply (some years ago) and as I recall it offers no explanation from an ID perspective for why these correspondences between amino acids and codons/anticodons exist. Certainly Meyer thought that no such correspondences existed in 2009 when he wrote Signature, and he built a significant part of his argument on that misunderstanding. Has he simply abandoned those claims, or has he worked this evidence into his approach in some way?

Dennis,

See the section of our paper headed “Statistical significance of the DRT model,” where we argue that the “correspondences” in question are artifacts of the Yarus et al. hypothesis; we write:

“The SELEX trawl captured several RNA sequences that bind tryptophan. Therefore, to avoid bias, all of these sequences should be analyzed statistically—not simply the motifs that look interesting on the stereochemical hypothesis (i.e., sequences exhibiting a disproportionate representation of code-relevant triplets). Otherwise, the screening criteria may artificially amplify the signal the investigators purport to have found—rather like catching both salmon and mackerel, throwing away the mackerel, and then claiming that the trawl caught only salmon.”

If the signal Yarus et al. claim to have detected is indeed an artifact, then there is nothing to explain from an ID perspective.

Hi Paul, (@paulnelson)

Are you claiming that all such correspondences are artifacts? I.e. the entire field?

If so, why is it that other groups are finding this evidence consistent with their new findings about the ribosome and protein/mRNA interactions (see papers linked above)?

Was Meyer aware of this evidence prior to publishing Signature in 2009? In other words, when he claimed that no evidence for binding existed, was he rejecting the results of Yarus and others, instead of (as I assumed) being unaware of it?

Edited to add: if Stephen would prefer to discuss this instead, he’d be welcome here. Thanks.

Dennis

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Dennis,

As you know, our critique of the direct templating proposal covered several aspects of the hypothesis, of which the artifactual status of the binding preferences was only the least significant. It is impossible to respond to your points on that score in your last comment, however, as our 2011 critique is quite specific on the flawed methods and results of Yarus et al., whereas you are appealing very generally to the research motives of other people (“other groups”), which I have no way to assess accurately.

In any event, your reply does not respond to the substance of our critique. I will take a look at the post-2011 cites you provided

As for what Steve knew when he was writing Signature, you’ll have to ask him.

No further comments from me. The 2011 paper speaks for itself.

Hi Paul,

FWIW, I disagree with your assessment that the observed bindings are artifacts - nor do I think you make a compelling case for that claim. The evidence for binding is good, comes from several labs (including, but not limited to Yarus’s lab), and is profitably guiding new research, as those above papers show.

If Stephen would like to dialogue on these issues here, he’s more than welcome. I am not able to comment on ID sites, so I cannot seek him out there.

All the best,

Dennis

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@paulnelson
@DennisVenema

Paul

Actually, Yarus in many of his papers, did exactly what you are asking of him here. As one example from his 2003 paper that I linked in my previous comment, he writes:

“Of the remaining isolates sequenced, only one other repetitively isolated motif was prevalent, representing 18% of clones. Although it contained a possibly interesting conserved AUAUAUA sequence, this second isolate showed little specificity, having apparently similar affinity for isoleucine, alanine, valine, and methylamine.” note this second isolate (with no useful specificity) is also based on the ILE codon.

In other words, he did look at other enriched sequences, and further evaluated them. He frequently admits that his technique isolates RNAs that are unrelated to amino acid-specific codons or anticodons. This is all germane to my comment about lack of appropriate specificity for starting a usable code, so in that I am in agreement with you and Steve.

However, Dennis point is valid - the finding of any preferential binding by codon related sequences means something since the probability of this happening by chance is very small. So there is probably something to the stereochemical idea at least as part of the code origin, even if it cannot explain very much. I also think that Yarus himself no longer is pressing for acceptance of a purely stereochemical mechanism for code origin or evolution.

Dennis, thanks for that comment. Since we share the view that God is the author of evolution, and everything else, I fully agree with your sentiment about the awe-inspiring quality of any natural explanation of the genetic code formation, and I also agree that such an explanation is likely. But, I would add that if there is any place in biology where the basis of ID makes sense, it is here (See my quote from Koonin in the previous comment, where he even uses the phrase “irreducible complexity”).

What I think might happen is that we will find that in order to make much progress in solving this thorniest of biological conundrums, we will need to somehow expand our outlook in how we view, both theoretically and methodologically, the issue of coding in biology. One would hope that ID researchers like Paul could contribute as well to this effort. I say that because even assuming that the code was designed, (which I think is entirely possible) the question still remains: how?

Ta all,

This discussion for me demonstrates the insurmountable problem of understanding evolution by only looking at only Variation or Genetics. this is the problem doth of Darwinian evolution and ID. It is like looking to understand a house by looking only at the wood and nails from which it is constructed.

Two houses are made of the same materials, but they are very different. They are different because they were built is different places by different persons with different needs. Two species of birds are made of the same chemicals, the same basic materials, but are very different.

Why? Because of Natural Selection, which determines which DNA code with survive and flourish and which will not.
The DNA of a species does not create change. DNA is the product of change. It is the result of Natural Selection.

The DNA code is a language. Whether it is natural or not depends upon whether one defines natural as not rational. Languages are rational, so the DNA code is a rational natural language.

@Relates

And fortunately, virtually all curricula in Evolutionary science treats both genetics and ecology … showing how the intersection of these two arenas produce the most amazing changes…

A) Hippo-like creatures become whales… only because ecological niches were changing at the same time as the gene pools.

B) The Hominid Bottleneck… where 15,000 or fewer individuals become a small enough African population to rapidly change in the face of climate, food supplies and predation!

C) The last remnant of reptilian monster… that would have slaughtered humanity if it had been able to reach us … the Terror Birds of South America … prospering until new competitors flooded South America from North America - - made possible by the merging of the two continental masses at future Panama!

D) Galapagos and Australia - - classic laboratories for species dispersion driven by ecology and food-chain niches… producing animals not found anywhere else in the world.

@gbrooks9

Thank you for your response.

These points remain. 1) Please provide at least one reference? It appears that you are reading material that I have not read. If this materials is as ubiquitous as you say, that should not be a problem. What is a problem is that there is so much written on evolution that it is impossible to be familiar with all of it, esp. if you are working outside the field.

  1. Sometimes those who write popular materials do not have the same perspective as those who are doing the research. Dawkins and his friends have a history of antagonism to ecology. Even Wilson does not make a clear cut connection between ecology and evolution.

  2. The debate between ID and Darwinism only makes sense when one leaves Natural Selection out of the concept of evolution.

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.

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.

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.

@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 ?

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.

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.

"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!