Why OOL science needs to look past physics and chemistry.

Origin of Life and Information — Some Common Myths
Brian Miller

In previous articles (here,  here, and here) I described the thermodynamic challenges to the origin of life, and I explained the need for information in the first cell to originate from an outside source. Now, I will dispel many of the myths associated with attempts to circumvent the information challenge.

A common attempt to overcome the need for information in the first cell is to equate  information to a reduction in entropy, often referred to as the production of “negative entropy” or N-entropy. This connection is in certain contexts justified by the fact that both  entropy and the Shannon formulation for information use the same mathematics and can be related to probability and uncertainty. For instance, this approach can be used to calculate the amount of work required to  generate specific amounts of information in the amino acid sequences of proteins. However,  entropy is not equivalent to the information in cells, since the latter represents functional information To illustrate the difference, imagine entering the kitchen and seeing a bowl of alphabet soup with several letters arranged in the middle as follows:

REST TODAY AND DRINK PLENTY OF FLUIDS

I HOPE YOU FEEL BETTER SOON

You would immediately realize that some intelligence, probably your mother, arranged the letters for a purpose. Their sequence could not possibly be explained by the physics of boiling water or the chemistry of the pasta.

To continue the analogy, you mention your design inference to your friend Stanley Miller the Third who happens to be an origin-of-life chemist. Stanley believes any attribution of design to pasta sequences in soup is based on the concerned-parent-of-the-gaps fallacy, so he mocks your superstitious beliefs. He then states that the sequence could have come about as a result of the boiling soup cooling to room temperature. Since cold soup has a lower entropy than hot soup, he believes the reduction in entropy could have generated the information in the message. You would immediately recognize that a reduction in thermal entropy has no physical connection to the specific ordering of letters in a meaningful message. The same principle holds true in relation to the origin of life for the required sequencing of amino acids in proteins or nucleotides in DNA.

A related error is the claim that biological information could have come about by some  complex systems or non-linear dynamics processes. The problem is that all such processes are driven by physical laws or fixed rules. And, any medium capable of containing information (e.g., Scrabble tiles lined up on a board) cannot constrain in any way the arrangement of the associated symbols/letters. For instance, to type a message on a computer, one must be free to enter any letters in any order. If every time one typed an “a” the computer automatically generated a “b,” the computer could no longer contain the information required to create meaningful sentences. In the same way, amino acid sequences in the first cell could only form functional proteins if they were free to take on any order.

Moreover, protein chemists have determined that the vast majority of sequences in proteins today are indistinguishable from being purely random, which further confirms that those in the first cell also appeared random to first approximation. Any relevant divergence from pure randomness would have been due to  constraints associated with protein folding, such as the formation of a-helixes. To reiterate, no natural process could have directed the amino acid sequencing in the first cell without destroying the chains’ capacity to contain the required information for proper protein folding. Therefore, the sequences could never be explained by any natural process but only by the intended goal of forming the needed proteins for the cell’s operations (i.e., teleologically).

A third error relates to attempts to explain the genetic code in the first cell by a stereochemical affinity between amino acids and their corresponding codons. According to this model, naturally occurring chemical processes formed the basis for the connection between amino acids and their related codons (nucleotide triplets). Much of the key research promoting this theory  was conducted by biochemist Michael Yarus. He also devised theories on how this early stereochemical era could have evolved into the modern translation system using ribosomes, tRNAs, and supporting enzymes. His research and theories are clever, but his conclusions face numerous challenges.

For instance, Yarus’s experiments did not actually measure the direct attraction between individual amino acids and their related codons, but they tested for binding between amino acids and sets of generated nucleotide chains (aptamers). His team reported that certain amino acids bound to aptamers which contained a higher than random percentage of their corresponding codons or anticodons at the binding sites. However, other researchers were unconvinced by the findings. For instance, Andrew Ellington’s team questioned whether the correlations in these studies were statistically significant, and they argued that his theories for the development of the modern translation system were untenable. Similarly, Eugene Koonin found that the claimed affinities were weak at best and generally unconvincing. He argued instead that the code started as a  “frozen accident” undirected by any chemical properties of its physical components.

More significantly, even if such affinities existed, they would not help in any realistic origin-of-life theory. Yarus’s model centers on codons embedded in longer sequences of nucleotides folding around single amino acids. Any model for translating sequences of codons into chains of amino acids would require a much longer strand of RNA to fold around multiple amino acids and then consistently link them together in the right order. And, these RNAs would eventually have to lose the “non-coding” nucleotides surrounding the relevant codons – while somehow retaining the affinities which had previously required the removed nucleotides – in order to become modern versions of RNA and DNA. Even if such extraordinary feats could occur, the translation would take place in the wrong direction.

Within the presupposed RNA world framework, nucleotide sequences came into being which eventually evolved into RNA-based enzymes. A selective process was believed to replicate the more efficient enzyme-like sequences over others in order to eventually produce “ribozymes” which could perform all of the needed functions for some sort of protocell. However, the ribozyme sequences would have had no relationship via any code to amino acid sequences which could fold into functional proteins. Therefore, any process which could perform the translation would initially be completely useless. Instead, proteins would have needed to come into existence independently through their own selective process, and then their sequences would have needed to be encoded into new RNAs. However, Yarus’s model does not work in reverse. Another process would have been needed for the amino-acid-to-RNA encoding, but the underlying code would not have corresponded to Yarus’s affinity-based code. As a result, the decoding process would have lost the encoded information.

These problems simply highlight one of the challenges for the RNA world hypothesis and for any materialistic explanation for the genetic code. A viable theory would have to explain for both the encoding and decoding several steps:

Amino acids and nucleotides would have to be created in abundance and then brought together. They would have to originate in separate locations, since the conditions needed for their synthesis are quite different, and cross-reactions would have prevented the creation of either. (See  Shapiro’s Origins.)

A functional protein or RNA strand would have to unfold to allow for its sequence to be translated. And, such functional sequences would have to separate themselves from other useless chains. An enormous number of chains would have to exist for a useful sequence to have had any chance of forming.

Individual codons would have to be so strongly attracted to their corresponding amino acids, that they would attach to them for an extended period of time.

Some enzyme-like molecules would have to come along and then polymerize the nucleotides into strands of RNA or the amino acids into proteins.

All useful products would have to migrate to some safe location until they could be encapsulated into a cellular membrane. A viable membrane would have to be selectively semipermeable, so it would allow the right molecules to enter and waist products to leave.

Neither Yarus nor any other researcher has even come close to properly addressing any of these issues in a purely materialistic framework. Nor will they, for any realistic scenario requires intelligent agency to properly coordinate all of these fantastically improbable steps.