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

| By on Letters to the Duchess

Is “biological information” merely an analogy of convenience for biologists, or does the cell contain information in the sense of a language or code? In this series we explore the science behind this question and its implications for the arguments of the Intelligent Design movement. EDITOR'S NOTE: A scientific glossary is provided below the post for those who are unfamiliar with the terms used here. 

Over the last few posts in this series, we’ve explored how cells store “information” in DNA (as a sequence of DNA nucleotides), and transfer DNA information into sequences of amino acids (i.e. make proteins) that can do the day-to-day jobs needed for running a cell. As we have seen, that process is a highly intricate one, full of complex chemistry. At the heart of the system are tRNA molecules that act as a bridge between an amino acid and its corresponding codon on the mRNA (see image above).

What we see in present-day cells is a complex, integrated system for transferring “information” from DNA to RNA to proteins—using RNA as the key intermediary. Naturally, biologists are interested in the possible origins of this system: how did it come to be? In general, the success of evolution as a theory for how living things have diversified from common ancestors has led scientists to investigate if what we call “life” is the modified descendant of a previous “non-living” system. In other words, if living things are the modified descendants of other life, what happens if you work backwards to the origin of life? Might life come from non-life? Does the information processing system we observe in cells have a natural explanation, or was it created by God in a way we would describe as “supernatural”?

As an aside, as a Christian biologist I would be perfectly fine with the answer being either “natural” or “supernatural”. Both natural and supernatural means are part of the providence of God, and the distinction is not a biblical one in any case. Perhaps God set up the cosmos in a way to allow for abiogenesis to take place. Perhaps he created the first life directly—though, as we will see, there are lines of evidence that I think are suggestive of the former rather than the latter. Similarly, I would have been fine with God supernaturally sustaining the flames of the sun for our benefit, as English apologist John Edwards claimed long ago. I do happen to think that solar fusion is an elegant way to “solve” this problem, and as a person of faith I think it evinces a deeper, more satisfying design than some sort of miraculous interventionist approach for keeping the sun going. I recognize, however, that seeing design in the natural process of solar fusion—or abiogenesis—is not the sort of argument that some Christian apologists are looking for.

Information – a major ID apologetic

So, is the information storage and processing system we see in living things the result of natural processes, or God’s supernatural action? It is precisely on this question that the Intelligent Design (ID) movement has built a significant component of its apologetic. Stephen Meyer, in his book Signature in the Cell, makes two main claims with respect to biological information. The first is that scientists do not, as of yet, have a complete explanation for how biological information arose:

… no purely undirected physical or chemical process—whether those based upon chance, law-like necessity, or the combination of the two—has provided an adequate causal explanation for the ultimate origin of the functionally specified biological information.

Secondly, Meyer claims that specified information always is the result of an intelligence:

I further argue, based upon our uniform and repeated experience, we do know of a cause—a type of cause—that has demonstrated the power to produce functionally specified information from physical or chemical constituents. That cause is intelligence, or mind, or conscious activity... Indeed, whenever we find specified information—whether embedded in a radio signal, carved in a stone monument, etched on a magnetic disc, or produced by a genetic algorithm or ribozyme engineering experiment—and we trace it back to its source, invariably we come to a mind, not merely a material process.

For Meyer, then, biological information is a clear sign of a Designer who used, at least in part, a non-material process to produce it. It should come as no surprise that I do not find this approach convincing, even though I share Meyer’s Christian convictions that God is the creator of all that is, seen and unseen (to paraphrase the creeds).

On Meyer’s first point, we agree. Research on abiogenesis has not, by any stretch, provided “an adequate causal explanation for the ultimate origin of the functionally specified biological information”. Nor will it, in the foreseeable future, if ever. The second point, however, is debatable. The examples Meyer gives are all examples of human-generated information. Yes, humans can generate information. The question, however, is whether a natural system can generate information. We know by direct experience that evolution can produce new information (a topic we will explore in detail in a later post, though it is something I have written about before, several times. Meyer, as we will see, disputes this evidence). If a natural process like evolution can produce new information, then it makes sense to see if other natural processes, perhaps similar to evolution, could have produced the information we see in living systems from non-living precursors.

Is the genetic code really a “code”?

One of the key challenges for abiogenesis research is to explain the origin of the genetic code—how it came to be that certain codons specify certain amino acids. Recall that tRNA molecules recognize and bind codons on mRNA through their anticodons—and bring the correct amino acid for that codon to the ribosome in the process. One feature of the tRNA system is that there is no direct chemical or physical connection between an amino acid and its codon or anticodon. Amino acids are connected to tRNA molecules at the “acceptor stem” section (the yellow region in the above diagram). Moreover, the acceptor stem is the same sequence for every tRNA, regardless of what amino acid it carries. Connecting the proper amino acids to their tRNA molecules is the job of a set of protein enzymes called aminoacyl tRNA synthetases. These enzymes recognize free amino acids and their proper tRNA molecules and specifically connect them together. Because there is no direct interaction between an amino acid and its codon, in principle it seems that any codon could have been assigned to any amino acid. If so, how might this system have arisen without any chemical connections to guide its formation?

Significantly, the lack of a direct chemical or physical connection between amino acids and their codons or anticodons forms a critical part of the Intelligent Design (ID) argument that the “genetic code” is in fact a genuine code of the sort that is determined and manufactured by a designing intelligence, and is not the product of what scientists would call a natural origin. This argument rests on the claim that since there is no physical connection between amino acids and codons (or anticodons) in the present-day system, the “genetic code” is an arbitrary, symbolic code – that the list of codons and their corresponding amino acids are not connected through chemistry. Since there is no connecting chemistry, so the argument goes, then there is no chemical path that could bring the system into being. And if there is no material, chemical process that can bring it into being, then it must have its origin through another means—such as by a designing intelligence that produced it directly, and not through a material process.

Meyer lays out his argument for an arbitrary genetic code on pages 247-248 of Signature (emphases mine).

Self-organizational theories have failed to explain the origin of the genetic code for several reasons. First, to explain the origin of the genetic code, scientists need to explain the precise set of correspondences between specific nucleotide triplets in DNA (or codons on the messenger RNA) and specific amino acids (carried by transfer RNA). Yet molecular biologists have failed to find any significant chemical interaction between the codons on mRNA (or the anticodons on tRNA) and the amino acids on the acceptor arm of tRNA to which the codons correspond. This means that forces of chemical attraction between amino acids and these groups of bases do not explain the correspondences that constitute the genetic code…

Thus, chemical affinities between nucleotide codons and amino acids do not determine the correspondences between codons and amino acids that define the genetic code. From the standpoint of the properties of the constituents that comprise the code, the code is physically and chemically arbitrary. All possible codes are equally likely; none is favored chemically.

Here we can see Meyer’s argument clearly: in order to provide a material explanation for the origin of the genetic code, scientists need to explain how the specific correspondences between codons and amino acids came about. But, as he notes, there is no physical connection between them in the present system that can explain the correspondences. The code is arbitrary—and for Meyer, this indicates design.

Crisps or chips?

Having recently returned from a family vacation in Europe, my kids and I have a new appreciation for this line of argument. Travelling to the UK put our family into a similar, yet distinct linguistic context. Learning the words for various things in the UK was part of the fun. For example, the kids soon learned that if they wanted a bag of potato chips, they needed to ask for “crisps” instead of “chips”—“chips” being what they thought of as “French fries” (though curiously retained in the common UK/North American construction, “fish and chips”). Now, does it matter if a group settles on “chips” or “crisps”? No, not really—what matters is that people know what you are talking about. In principle, any word could be used for thinly sliced and deep-fried potatoes, as long as everyone in the group agreed on what that word meant. Languages thus have an element of arbitrariness to them, and manufactured codes even more so. In fact, a human code benefits from arbitrary associations in that it makes it much harder to crack.

I recall reading Meyer’s argument for an arbitrary code when Signature first came out in 2009, and being surprised by it. The reason for my surprise was simple: in 2009 there was already a detailed body of scientific work that demonstrated exactly what Meyer claimed had never been shown.[1] Though Meyer claimed that “molecular biologists have failed to find any significant chemical interaction between the codons on mRNA (or the anticodons on tRNA) and the amino acids on the acceptor arm of tRNA to which the codons correspond” this was simply not the case.

One hypothesis about the origin of the genetic code is that the tRNA system is a later addition to a system that originally used direct chemical interactions between amino acids and codons. In this hypothesis, amino acids would directly bind to their codons on mRNA, and then be joined together by a ribozyme (the ancestor of the present-day ribosome). This hypothesis is called “direct templating”, and it predicts that at least some amino acids will directly bind to their codons (or perhaps anticodons, since the codon/anticodon pairing could possibly flip between the mRNA and the tRNA).

So, is there evidence that amino acids can bind directly to their codons or anticodons on mRNA? Meyer’s claim notwithstanding, yes—very much so! Several amino acids do in fact directly bind to their codon (or in some cases, their anticodon), and the evidence for this has been known since the late 1980s in some cases. Our current understanding is that this applies only to a subset of the 20 amino acids found in present-day proteins. In this model, then, the original code used a subset of amino acids in the current code, and assembled proteins directly on mRNA molecules without tRNAs present. Later, tRNAs would be added to the system, allowing for other amino acids—amino acids that cannot directly bind mRNA—to be added to the code.

The fact that several amino acids do in fact bind their codons or anticodons is strong evidence that at least part of the code was formed through chemical interactions— and, contra Meyer, is not an arbitrary code. The code we have—or at least for those amino acids for which direct binding was possible—was indeed a chemically favored code. And if it was chemically favored, then it is quite likely that it had a chemical origin, even if we do not yet understand all the details of how it came to be. As such, building an apologetic on the presumed future failings of abiogenesis research, when current research already undercuts one’s thesis, seems to me as problematic for Meyer in 2009 as it did for Edwards in 1696. Do unanswered questions remain? Of course. Should we bank on them never being answered? Or would it be more wise to frame our apologetics on what we know, rather than what we don’t know?[2]

In the next post in this series, we’ll address another of Meyer’s claims: that evolution is incapable of generating significant amounts of new information.


Notes

Citations

MLA

Venema, Dennis. "Biological Information and Intelligent Design: Abiogenesis and the origins of the genetic code "
https://biologos.org/. N.p., 25 Aug. 2016. Web. 22 November 2017.

APA

Venema, D. (2016, August 25). Biological Information and Intelligent Design: Abiogenesis and the origins of the genetic code
Retrieved November 22, 2017, from /blogs/dennis-venema-letters-to-the-duchess/biological-information-and-intelligent-design-abiogenesis-and-the-origins-of-the-genetic-code

References & Credits

Glossary

DNA: deoxyribonucleic acid. Chromosomes are made of two strands of DNA, wound around each other in a double helix. The two strands are held together with weak attractions between nucleotides called hydrogen bonds. Each nucleotide bonds with a pairing partner: A with T, and C with G.

Enzyme: a molecule that acts to make a chemical reaction require less energy - and thus allow it occur. Enzymes can be made of protein or RNA. rRNA molecules that make up the ribosome are the enzymes that connect individual amino acids together to form proteins. Since rRNA molecules are both RNA and enzymes, they are called ribozymes.

Ribosome: the enzyme complex that joins amino acids together to make protein - a process called translation. The ribosome uses mRNA as a template and tRNA molecules to align the correct amino acids in sequence along it.

Ribozyme: an enzyme made up of RNA. Ribosomal RNA (rRNA) is an example of a ribozyme.

RNA:  ribonucleic acid. RNA, like DNA, is made from nucleotides strung together. RNA, however, is single stranded, and uses a nucleotide “U” instead of “T” U can bind to A with hydrogen bonds just as a T does . There are three classes of RNA: mRNA, tRNA, and rRNA:

mRNA (messenger RNA): the single-stranded, “working copy” of a gene sequence copied from the DNA sequence in a process called transcription.

tRNA (transfer RNA): tRNA molecules carry amino acids and have a section that recognizes and binds to a codon on mRNA. tRNAs bring amino acids to the ribosome, the large enzyme that connects amino acids together to form proteins - a process called translation.

rRNA (ribosomal RNA): rRNA molecules make up the enzyme portion of the ribosome. Since rRNA molecules are both RNA and enzymes, they are called ribozymes.

Notes

[1] For example, Michael Yarus, one of the leading researchers in this area, had been publishing in this area since the 1980s. Even an incomplete sampling of his articles will make the point easily. All of these papers except the last one predate the publication of Signature in 2009:

Yarus M., and Christian, E.L. (1989) Genetic code origins. Nature 342(6248):349-350.

Yarus, M. (1991). An RNA-amino acid complex and the origin of the genetic code.The New Biologist 3(2):183-189.

Yarus, M. (1998). Amino Acids as RNA Ligands: A Direct-RNA-Template Theory for the Code's Origin. Journal of Molecular Evolution 47(1): 109–117.

Yarus, M. (2000). RNA–ligand chemistry: A testable source for the genetic code. RNA 6(4):475-484.

Yarus M., and Illangasekare, M. (2002). Phenylalanine-binding RNAs and genetic code evolution. Journal of Molecular Evolution 54(3):298–311.

Majerfeld, I., Puthenvedu, D., and Yarus, M. (2005). RNA Affinity for Molecular L-Histidine; Genetic Code Origins. Journal of Molecular Evolution 61(2):226–235.

Yarus M., Widmann J., and Knight, R. (2009). RNA-amino acid binding: a stereochemical era for the genetic code. Journal of Molecular Evolution 69(5):406–429.

[2] Readers will likely know that I here I have in mind Bonhoeffer’s sage advice that I have quoted in various places before:

Weizsäcker’s book The World View of Physics is still keeping me very busy. It has again brought home to me quite clearly how wrong it is to use God as a stop-gap for the incompleteness of our knowledge. If in fact the frontiers of knowledge are being pushed back (and that is bound to be the case), then God is being pushed back with them, and is therefore continually in retreat. We are to find God in what we know, not in what we don’t know; God wants us to realize his presence, not in unsolved problems but in those that are solved.

Dietrich Bonhoeffer, Letters and Papers from Prison

For further reading

Yarus M., Widmann J., and Knight, R. (2009). RNA-amino acid binding: a stereochemical era for the genetic code. Journal of Molecular Evolution 69(5):406–429.

About the Author

Dennis Venema

Dennis Venema is professor of biology at Trinity Western University in Langley, British Columbia and Fellow of Biology for BioLogos. He holds a B.Sc. (with Honors) from the University of British Columbia (1996), and received his Ph.D. from the University of British Columbia in 2003. His research is focused on the genetics of pattern formation and signaling using the common fruit fly Drosophila melanogaster as a model organism. Dennis is a gifted thinker and writer on matters of science and faith, but also an award-winning biology teacher—he won the 2008 College Biology Teaching Award from the National Association of Biology Teachers. He and his family enjoy numerous outdoor activities that the Canadian Pacific coast region has to offer. 

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