Brian Miller: Thermodynamics and the Origin of Life

Design

(S. Joshua Swamidass) #117

I have. I encourage you to talk with him. I believe he would disagree with you argument. It needs to be clear that he is not an ID advocate. He disagrees with these sorts of arguments as unscientific. I agree with him.


#118

Intelligent Design is consistent with science. So is the de novo creation of Adam and Eve.


(S. Joshua Swamidass) #119

We are talking about someones career and reputation here. Let’s get protect that before going into repetitive arguments.


(Brian Miller) #120

The key issue for encoding is how amino acids interact with individual triplets, not RNA chains. And, no preference appears between amino acids and individual codons. Yarus comments:

We review the literature and find no evidence that interactions between short sequences (mono-, di- or trinucleotides) and amino acids are strong or specific enough to originate genetic coding. Instead, interactions between amino acids and longer nucleic acid sequences appear to recapture some assignments of the modern code.

The affinities are between amino acids and codons in a long chain. How exactly is a protein interacting with an RNA strand supposed to turn into the highly accurate encoding of the amino acid sequence into an RNA sequence through such correlations?


(S. Joshua Swamidass) #121

You haven’t read the proposed mechanisms on this?


(Brian Miller) #122

The proposed mechanisms I have seen are for the decoding process. Have you seen detailed mechanisms for an actual folded protein encoding into an RNA strand?


(S. Joshua Swamidass) #123

Fudge word alert. I concede upfront that we do not know the details of abiogenesis.


(T J Runyon) #124

What paper of Yarus are you referring to there? I’ve have had private discussions with him and he said you were misunderstanding his work and that Venema got it right (who you said misunderstood it). I also noticed you accused Dennis of misunderstanding his work and then you discussed another paper that Dennis wasnt even referring to. This was a while back so it’ll take me a while to track it down but I will gladly do so. I’m just very cautious when I see you bring up Yarus


(T J Runyon) #125

Here’s the context for the quote Miller uses:

“We review the literature and find no evidence that interactions between short sequences (mono-, di- or trinucleotides) and amino acids are strong or specific enough to originate genetic coding. Instead, interactions between amino acids and longer nucleic acid sequences appear to recapture some assignments of the modern code. For example, real codons are concentrated in newly selected amino acid binding sites to a greater extent than codons from similar, but randomized, codes. This implies that some initial coding assignments were made by interaction with macromolecular RNA-like molecules, and have survived. Thus, subsequent selection, such as selection to minimize coding errors, has not erased all primordial chemical relationships. Retention of initial stereochemical codon assignments for three of six amino acids (arginine, isoleucine, and tyrosine, but not glutamine, leucine or phenylalanine) is strongly supported.”

Seems like a quote mine to me… Yarus’s work shows that some amino acids do bind their respective codon or anticodon. The only way to make Miller’s quote accurate is to claim that Yarus was only interested in binding between isolated mono, di or tri-nucleotide structures. So i think it may be a little obvious why Dr. Miller cut the quote where he did.


(Arthur Hunt) #126

Quite incorrect.

Seriously, Brian. Is this what happens in living cells in the here-and-now?

I will repeat, the key issue is Brian’s assertion that “the encoding of amino acid sequences in proteins into nucleotide sequences in DNA is difficult to imagine since no chemical connection exists between an amino acid and a coding triplet.”. The research I cite refutes this categorically. It also renders pointless Brian’s attempt to belittle a vibrant and exciting field of research.

Brian, maybe you need to describe the specific, detailed model that includes the pathway or mechanism you are describing. Please include citations so that readers here can gain more insight into your statements. Because, frankly, what you are describing is quite unusual.


(T J Runyon) #127

Also, the Yarus paper Miller quotes is from 2013 I believe. Where the you one you cite is 2017. So I’m a little puzzled how someone can take a paragraph of a paper that was published four years earlier to refute an entire paper with new research by the same author.


#129

Just wondering if everyone is agreed that a code is required for life.

Was there life before coding? If so then we are not technically talking about abiogenesis.


(Neil Rickert) #130

It is not even clear what I would be agreeing with.


(Brian Miller) #131

We should let people speak for themselves. Here is how Dr. Tour wishes his position to be understood:

I have been labeled as an Intelligent Design (sometimes called “ID”) proponent. I am not. I do not know how to use science to prove intelligent design although some others might. I am sympathetic to the arguments and I find some of them intriguing, but I prefer to be free of that intelligent design label. As a modern-day scientist, I do not know how to prove intelligent design using my most sophisticated analytical tools— the canonical tools are, by their own admission, inadequate to answer the intelligent design question. I cannot lay the issue at the doorstep of a benevolent creator or even an impersonal intelligent designer. All I can presently say is that my chemical tools do not permit my assessment of intelligent design.


(Brian Miller) #132

Contrast this description with Venema’s comments:

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 difference is night and day between a statistical correlation between codons at an amino acid binding site in a mRNA chain and the direct binding of a series of individual codons with their respective amino acids with sufficient strength and consistency to allow for the assembly of a protein. Venema’s reference to encoding proteins would have implied to his readers that the binding was directly between amino acids and their respective codons, not mere correlations.

Series of neighboring codons would have to bind directly to individual amino acids or else those amino acids would not be close enough for them to chemically bind together in any realistic model. In addition, mere statistical correlations between codons and amino acids would result in such an error-prone translation that the whole process would be useless. Compounding the problem, the amino acids which demonstrate significant correlations are not those which would have been the first to participate in proteins as Koonin comments:

However, as discussed elsewhere, the stereochemical evidence does not appear to be compelling. The principal problems are two-fold. First, statistically significant affinity for cognate triplets has been demonstrated only for five amino acids, and the triplet could be either codon or anticodon. Second, and more damning, all the results of aptamer experiments that appear compatible with the physicochemical affinity between amino acids and cognate triplets pertain to complex amino acids that are unlikely to have been available at the time of the code emergence (see next Section).

Yarus’ latest paper may have found a few more amino acids with correlations, but the majority of the correlations are for amino acids which are least likely to have been part of the original code.

An additional problem is that Yarus’ model to eventually incorporate tRNAs appeals to “selection” for generating the tRNAs and other machinery needed for modern translation. However, nature cannot select for a future goal, for nature is blind. Natural selection would not even operate until accurate translation and cellular replication are already operational. Yet, they are both far downstream.

An even greater challenge is that even highly accurate translation is useless unless a mRNA strand represents the encoding of a functional protein sequence. Yarus’ identified correlations only exist between mRNA strands and amino acids. Since no connection exists between amino acids in a protein chain and individual codons, no natural process could realistically explain the encoding. All physical processes must have a causal mechanism. In the case of amino acids and their respective codons, the only plausible mechanism would be a heightened attraction between them which does not exist.

The encoding would then require the same sort of complex machinery seen in modern translation where individual codons are forced to correspond to specific amino acids and then joined together. However, even if such machinery miraculously appeared, no justification would exist for it using the same code for the encoding that would be used in the decoding.


(T J Runyon) #133

Again, Dennis was referencing a totally different paper by Yarus than the one you are referencing. The paper you are referencing is nowhere to be found in his source list.


(T J Runyon) #134

This is the paper Dennis relied on:
https://www.ncbi.nlm.nih.gov/m/pubmed/19795157/

This is the paper you are quoting:


(T J Runyon) #135

If there is no chemical affinity between amino acids and codons how did God create the code? It seems like God would have the same problem, no?


Rejecting God Sustains the ID Rhetoric
(Brian Miller) #136

Probabilities are at the foundation of quantum mechanics and statistical mechanics which form the bedrock of modern physics. And, they are also the basis for hypothesis testing in general. We cannot always calculate exact probabilities, but we can often recognize when upper bounds are so unlikely that certain events are implausible. No one has ever calculated in detail the probability for a tornado assembling a car, but we know enough about cars and tornados to say that such an event would never happen.

We also know enough about a minimally complex cell to recognize that it could not form by chance. OOL researchers have often acknowledged this fact. In fact, OOL faces greater difficulties than the car-tornado scenario:

  • The formation of life requires a system to move toward both greater energy and lower entropy for extended periods which never happens.
  • The building blocks of life would have been scattered across the planet, mostly in small quantities. The localization problem is insurmountable.
  • The constraints on self-replicating, autonomous systems are far more numerous and greater than on a simple car.

One could also calculate upper bounds for probabilities for specific steps. For instance, obtaining a single protein which could interlink two reactions would face the following probabilistic challenges:

  1. Forming Sufficiently Long Chain: The probability for forming a chain of length n in unrealistically ideal settings follows the Flory–Schulz distribution which drops off exponentially with n. The probability would be so small that an adequately long chain forming is implausible. In addition, the probabilities drop precipitously when one considers the challenge of producing the right diversity of amino acids, concentrating them, avoiding contaminants, and using only homochiral mixtures.
  2. Obtaining Useful Amino Acid Sequence: Obtaining the correct amino acid sequence to couple the correct reactions is minuscule. No random library of amino acid sequences has ever generated a protein which could couple the breakdown of an energy currency molecule with another reaction.
  3. Localization: The chances of a protein traveling from its point of origin into a viable cell membrane before it breaks apart is also minuscule by any reasonable calculation.

The probabilities multiply for all of the different required proteins for a viable metabolism which represents an incredibly small target in terms of all sets of chemical interactions. One could perform the same sort of analysis for ribozymes which present even greater difficulties. In summary, the chances of a cell forming are clearly implausible without assistance. And, natural processes will not only not assist, but they drive systems in the opposite direction. Finally, the positive evidence for design is unmistakable to those not seeing the world through a materialist lens.

I will not be able to follow the discussion for the next several weeks. However, I will have a paper coming out which will address some key issues in greater detail. I could pick it back up then. Thank you for the stimulating conversation.