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


(system) #1
Christian apologists are often too quick to use fields of emerging scientific research as arguments for supernatural intervention in nature.
This is a companion discussion topic for the original entry at https://biologos.org/blogs/dennis-venema-letters-to-the-duchess/biological-information-and-intelligent-design-abiogenesis-and-the-origins-of-the-genetic-code

(George Brooks) #2

To distinguish BioLogos from those who craft “arguments for supernatural intervention in nature” … we pretty much have to adopt a “Front-Loaded” approach, apparently described here and there by Collins himself (but not using the phrase Front-Loaded).

Then the intersection of “supernatural” and “nature” is the way God has configured his creation perfectly (and in the light of knowledge of the future) … where naturally lawful events are harnessed to accomplish God’s ends!

What are the negative repercussions of such a view?

[edited for caps]


(Richard Wright) #3

@DennisVenema

Dennis,

Thanks for posting such a beautifully written and easy to understand blog. And you always leave us wanting more. Keep up the good work.


(Doug B) #4

When folks talk about “life” what are the criteria: replication, spatial separation (a lipid bilayer), enzymatic activity, something else?


(sy_garte) #5

@DennisVenema

It has been a while since I read Yarus. Do you know if anyone has managed to reproduce his work, and if he continues to publish his aptamer work? Also, I had been under the impression that the binding was quite limited and not very specific. This doesnt rule out a strongly error prone original code, but the problem has always been, how do such codes evolve when the inheritibility of more effective codes is weakened by a high rate of transcriptional errors putting the system on the wrong side of an error catastrophe?


(Dennis Venema) #6

Hi Sy,

There is a number of groups working on this topic - one way to see it would be to look at the papers that cite Yarus. I believe Yarus has now retired, but I am not certain.

One example paper from the field, after Yarus’s 2009 paper:

Edited to add another, showing how the field is progressing:

(see also this review article from the same issue:)

I’m not sure where your impression comes from that the binding is not overly specific. You can see the Yarus papers for the details (or the other papers in the field).

Yes, the question of how the whole thing evolved is still very much up for discussion. The main observation - that some amino acids preferentially bind their codons or anticodons - strongly suggests that the code does have a stereochemical basis.

Thanks for the comment,

Dennis


(Dennis Venema) #7

Hi Doug -

There are generally thought to be seven defining features of “life” - but don’t forget that we define life by observing present-day stuff.

The popular Campbell Biology text defines life this way:

"Order. Organisms are highly ordered, and other characteristics of life emerge from this complex organization.

Reproduction. Organisms reproduce; life comes only from life (biogenesis).

Growth and Development. Heritable programs stored in DNA direct the species-specific pattern of growth and development.

Energy Utilization. Organisms take in and transform energy to do work, including the maintenance of their ordered state.

Response to Environment. Organisms respond to stimuli from their environment.

Homeostasis. Organisms regulate their internal environment to maintain a steady-state, even in the face of a fluctuating external environment.

Evolutionary Adaptation. Life evolves in response to interactions between organisms and their environment."


(Dennis Venema) #8

Hello Richard - thank you for the encouragement! I’m always glad to hear that folks find this useful.


(Doug B) #9

Dennis,
Thanks for the rely and the interesting article series.
-Doug


(sy_garte) #10

@DennisVenema

Dennis

Thanks for the references and comment. I certainly agree that it appears likely that some form of rudimentary code could be constructed based on stereochemistry. Clearly the code is not totally random, or the results that Yarus has on specific affinity between some amino acids and their codons or anti-codons would not be possible.

However, my comment on lack of specificity is I believe accurate, as can be seen by looking at the data in Yarus’ work. For example in one paper

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1287053/

on isoleucine and binding to its anti-codon UAU (actually, they found the simplest binding sequence to be UAUU, but close enough) says in the abstract “This UAUU motif (16 highly conserved positions; 27 total), is also the most abundant site in successful selections on short random tracts.” The key phrase is “most abundant”. This allows us to conclude a nonrandom association, but leaves open the question “how abundant?”

That is answered in the body of the paper. The authors report that in previous work looking for larger sequences they found that “These original UAUU-containing RNAs comprised 14% of 50 sequenced isolates after 13 rounds of selection-amplification and were derived independently from five parental randomized RNAs.”

What this means is that after running through the selection column 13 times, they isolated 50 binding sequences of which 7 (14%) contained the anticodon.

In further work in the paper using newer techniques, they found that “The UAUU motif accounted for 26 of 41, or 61%, of the sequences from the 22-random RNAs after 10 rounds of selection.”

This is good evidence for a non-random association, but very far from the kind of specificity needed for even an error prone code. I think Yarus agrees. He says “There is strong experimental evidence for one stereochemical hypothesis, that some coding sequences are abstracted from amino acid binding sites.”

He goes on to say the following (and he has not significantly deviated from this view since the date of this publication):

“Nevertheless, RNA is versatile; often many small RNAs bind the same amino acid. Binding sites can be so diverse that multiple selections fail to reisolate the same sites, as for arginine (Yarus 1998). This makes it difficult to know how sites would be chosen when the genetic code was composed.

However, from this work it appears that that choice of amino acid binding sites may sometimes be strongly constrained. The UAUU motif seems to be uniquely the simplest and the most frequent isoleucine binding structure.”

So, in summary, I think it is fair to say that some stereochemical effects were part of the origin of some rudimentary code, but the data show a lack of binding specificity. This is what leads me to question how subsequent evolution to the canonical code occurred.

I am not suggesting that this is impossible. A paper by Copley et al, presents a plausible hypothesis for how a highly error-prone translation system might evolve, which also includes amino acid/codon interaction.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC555468/

Furthermore, Stephen Freeland showed some time ago (Freeland SJ, Hurst LD. The genetic code is one in a million. J Mol Evol. 1998 Sep;47(3):238-48).

that the canonical code is quite special in terms of its resistance to errors, something we would expect from an evolved, selected code, rather than from a “frozen accident”,

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’”. While you see more evidence toward the natural, Meyer and other IDers see it more the other way, and I think we simply cannot say which is correct, and cannot rule out either .

Let’s also remember that it isn’t only ID that raises the question of the thorny problem that natural explanations have for addressing this question. Eugene Koonin, an atheist pioneer in code evolution, said in 2007:

“the translation system might appear to be the epitome of irreducible complexity because, although some elaborations of this machinery could be readily explainable by incremental evolution, the emergence of the basic principle of translation is not. Indeed, we are unaware of translation being possible without the involvement of ribosomes, the complete sets of tRNA and aminoacyl-tRNA synthetases (aaRS), and (at least, for translation to occur at a reasonable rate and accuracy) several translation factors. In other words, staggering complexity is inherent even in the minimally functional translation system.”

(Wolf, Yuri I., and Eugene V. Koonin. 2007. “On the origin of the translation system and the genetic code in the RNA world by means of natural selection, exaptation, and subfunctionalization.” Biology Direct 2:14)

I do know that Koonin has since altered this stance to be more in line with a naturalist understanding of code evolution and has refuted ID as an answer. But the fact remains that as scientists, and certainly as Christians, his points in the above quote allow us to approach the issue of how the modern translation system got here with a good deal of wonder and awe.


(Paul Nelson) #11

Readers may be interested to know that, in 2011, Steve Meyer and I responded to the Yarus direct templating hypothesis. Our article, “Can the Origin of the Genetic Code Be Explaining By Direct Templating?” is open access and available as a pdf here:

http://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2011.2

Here’s the abstract:

Motivated by the RNA world hypothesis, Michael Yarus and colleagues have proposed a model for the origin of the ‘universal’ genetic code, in which RNA aptamers directly template amino acids for protein assembly. Yarus et al. claim that this “direct RNA templating” (DRT) model provides a stereochemical basis for the origin of the code, as shown by the higher-than-expected frequency of cognate coding triplets in aptamer amino acid-binding sites. However, the DRT model suffers from several defects. These include the selective use of data, incorrect null models, a weak signal even from positive results, an implausible geometry for the primordial RNA template (in relation to the universally-conserved structures of modern ribosomes), and unsupported assumptions about the pre-biotic availability of amino acids. Although Yarus et al. claim that the DRT model undermines an intelligent design explanation for the origin of the genetic code, the model’s many shortcomings in fact illustrate the insufficiency of undirected chemistry to construct the semantic system represented by the code we see today.


(Dennis Venema) #12

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?


(Paul Nelson) #13

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.


(Dennis Venema) #14

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


(Paul Nelson) #15

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.


(Dennis Venema) #16

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


(sy_garte) #17

@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?


(Roger A. Sawtelle) #18

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.


(George Brooks) #19

@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.


(Roger A. Sawtelle) #20

@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.