[Sadhu Sanga] Chance and Necessity do not explain the origin of life - Part 4
Bhakti Madhava Puri
© 2004 International Federation for Cell Biology. Published by Elsevier Ltd. All rights reserved.
[abridged version - continued]
7. The nature of prescriptive information
All of the above problems pale in comparison to the difficulty of explaining the origin of
(1) an operating system,
(2) genetic programming, and
(3) encryption/decryption coding.
Natural processes, mechanisms, and chemical catalyses do not explain any of these emergent conceptual phenomena. There is an immense paucity of information/knowledge that we do not have. For example, transcription and translation can only function if there is a predetermined shared meaning as to what required proteins are synthesized at translation. How was this shared meaning between source and destination pre-established? Each specific genetic message from DNA to RNA to protein can only be decoded if the coding/decoding apparatus and operating system preexist the message. The message received by the ribosome must be decrypted and translated into particular proteins needed for certain tasks. These proteins in turn must be transported to the correct binding site, the true destination of the source's original message. Even "meaningful" RNA or DNA inserted into a lifeless physical world such as the ancient Earth, would not be "readable". It could not communicate its coded message for protein synthesis unless a language (operating system) context already existed. Programs must be executable. This requires the equivalent of a hardware and an operating system context. All necessary structures/functions for protein synthesis would have had to be in place, and a predetermined specific correspondence between codon sequence and amino acid sequence had to have predated translation.
8. The RNA world
It is not surprising that the RNA world model is so appealing despite its many biochemical problems. The RNA world conveniently bypasses translative coding issues. The same molecule acts as a catalyst and physical information matrix. Ribonucleotides do not have to be grouped into triplet "block codes" such that each symbolize a different amino acid letter in a protein sentence. No plausible natural-process mechanism for development of such an ingenious noise-reducing, redundancy-based coding scheme is needed for RNA world theory.
RNA may have been copied to DNA (as by current retroviruses). This would have allowed DNA to take over as the more stable, double-stranded, genetic instruction set. DNA has many other advantages such as the capability of exact replication and partitioning between offspring cells, and transcription to mRNA (Line, 2002). But retroviruses depend upon reverse transcriptase, a complex protein enzyme not available in the RNA world. Most metabolic functions require highly tailored protein enzymes that not only act to regulate DNA, but do most of the work of the cell. The "Which came first, DNA or proteins?" question, otherwise known as the "chicken and the egg problem", is a real enigma and not easily solved despite a century of life-origin research. In addition, the conversion from RNA to DNA worlds does not explain the origin of initial RNA genetic programming. How did covalently-bound nucleotide sequencing anticipate what amino acid sequences would be needed? Moreover, the instruction code for the enzymes needed to make all this function are contained in the genetic instruction set. The instruction set needs protein synthesis to replicate the instruction set and regulate cell division (Trevors, 2004).
9. Did genetic instruction arise by "necessity"?
We keep intuiting, "there must be some natural mechanism that we are overlooking which will explain the origin of genetic instruction". By this we mean some cause-and-effect "necessity" rather than "chance" (Monod, 1972). But is such a natural mechanism a plausible scenario for the origin of genetic instructions?
Natural mechanisms are all highly self-ordering. Reams of data can be reduced to very simple compression algorithms called the laws of physics and chemistry. No natural mechanism of nature reducible to law can explain the high information content of genomes. This is a mathematical truism, not a matter subject to overturning by future empirical data. The cause-and-effect necessity described by natural law manifests a probability approaching 1.0. Shannon uncertainty is a probability function ( - log2 p). When the probability of natural law events approaches 1.0, the Shannon uncertainty content becomes miniscule ( - log2 p = - log2 1.0 = 0 uncertainty). There is simply not enough Shannon uncertainty in cause-and-effect determinism and its reductionistic laws to retain instructions for life. Prescriptive information (instruction) can only be explained algorithmic programming. Such DNA programming requires extraordinary bit measurements often extending into megabytes and even gigabytes. That kind of uncertainty reflects freedom from law-like constraints. This is exactly what we find at each decision-node selection of an additional untemplated nucleotide.
Living cells are capable of replication, error correction, and sufficient mutation for diversity; yet sufficient accuracy of replication is maintained to preserve the relative constancy of any species. The DNA template can be transcribed to mRNA which is then translated into predetermined, useful, necessary, proteins. This is an immense instructional complexity and prone to errors at several steps and at every base. However, within the confines of a cell, the entire process functions at a high level of fidelity. Exceptions include the effects of mutagen(s), cell stress, injury, and death. Under appropriate environmental conditions, minimal errors are made. This means that the genetic communication system is functionally.
The sequence of nucleotides in DNA determines the coded instruction set. A predetermined knowledge of the decryption cipher and the cellular enzymes and organelles is needed to translate the coded information. Specific sequences of deoxyribonucleotides are essential to communicate each biomessage. The correct protein must be synthesized in the correct amounts and at the correct time. Without a coding/decoding system, message sequences in the first mRNA and DNA molecules would have been meaningless (nonfunctional metabolically). Communication within the protocell could not have been established. The nucleotide sequence is also meaningless without a conceptual translative scheme and physical "hardware" capabilities. Ribosomes, tRNAs, aminoacyl tRNA synthetases, and amino acids are all hardware components of the Shannon message "receiver". But the instructions for this machinery is itself coded in DNA and executed by protein "workers" produced by that machinery. Without the machinery and protein workers, the message cannot be received and understood. And without genetic instruction, the machinery cannot be assembled.
10. Did the genetic code arise by "chance"?
It is not reasonable to expect hundreds to thousands of random sequence polymers to all cooperatively self-organize into an amazingly efficient holistic metabolic network. The spontaneous generation of long sequences of DNA out of sequence space (U) does have the potential to include the same sequences as genetic information. But there is no reason to suspect that any instructive biopolymer would isolate itself out of U and present itself at the right place and time. Eigen and Schuster, along with others, have pointed out repeatedly that a competition for resources would have existed in any prebiotic environment. This would have greatly limited both sequence space and hypercyclic advance. The latter is especially true of a theoretical RNA world where the number and length of RNA strands is greatly limited. In aqueous solution, a maximum of 8e10 RNA mers can polymerize (Ferris et al., 1996; Joyce and Orgel, 1999). Up to 55 mers can polymerize on montmorillonite (Ferris et al., 1996), but only at the expense of information content. The polyadenines and polyuracils contain essentially no Shannon uncertainty. They could not have contributed to algorithmic programming of genes.
Even if all the right primary structures (digital messages) mysteriously emerged at the same time from U, "a cell is not a bag of enzymes". And, as we have pointed out several times, there would be no operating system to read these messages.
Without selection of functional base sequencing at the covalent level, no biopolymer would be expected to meet the needs of an organizing metabolic network. There is no prescriptive information in random sequence nucleic acid. Even if there were, unless a system for interpreting and translating those messages existed, the digital sequence would be unintelligible at the receiver and destination. The letters of any alphabet used in words have no prescriptive function unless the destination reading those words first knows the language convention.
11. The role of biological editing functions
No new information can be inserted into existing DNA without sophisticated restriction and ligase enzymes. The editing function of these enzymes, including that of the far less sophisticated ribozymes, must be itself algorithmically instructed. All in vitro ribozymic editing requires extensive artificial selection by humans (e.g., SELEX) (Ellington and Szostak, 1990; Robertson and Joyce, 1990; Tuerk and Gold, 1990). Nucleotide sequence is deliberately manipulated and steered through many iterations to achieve the experimenter's goal. SELEX experiments demonstrate the extraordinary inventive prowess of some excellent RNA chemists. But the fine work of these biopolymer engineers has little or nothing to do with natural selection. In addition, "directed evolution" is a self-contradictory nonsense phrase that has no place in the literature. If an experiment is directed, it is not evolutionary. Evolution has no goal.
Whatever prescriptive information DNA contains has to be instantiated into its physical matrix as the strand forms with covalent bonds. Conformation and function are ultimately determined by primary structure. The linear digital sequence of nucleotide selections constitutes the message of "messenger molecules". A genetic information system or convention must have been devised prior to ribonucleotide sequencing. Only then could message source and destination (binding sites) "be on the same page".
Random sequences are the antithesis of prescribed genetic information. There is no empirical or rational justification for theorizing that the random shuffling of nucleotides could generate instructions for a metabolic network. Progress has been made, however, on the evolution of already existing genetic. But none of these papers provide mechanisms whereby stochastic ensembles in prebiotic environments acquire algorithmic programming prowess. Even the earliest protometabolism would have needed integrative management.
12. Conclusions
New approaches to investigating the origin of the genetic code are required. The constraints of historical science are such that the origin of life may never be understood. Selection pressure cannot select nucleotides at the digital programming level where primary structures form. Genomes predetermine the phenotypes which natural selection only secondarily favors. Contentions that offer nothing more than long periods of time offer no mechanism of explanation for the derivation of genetic programming. No new information is provided by such tautologies. The argument simply says it happened. As such, it is nothing more than blind belief. Science must provide rational theoretical mechanism, empirical support, prediction fulfillment, or some combination of these three. If none of these three are available, science should reconsider that molecular evolution of genetic cybernetics is a proven fact and press forward with new research approaches which are not obvious at this time.
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Surendra Pokharna
Respected Shri Bhakti Madhvan Puri
Thanks a lot for very illuminating views. There is a paper by one German Scientist M. Eigen which was published in 1972 in one German Science Journal Natureweiss.. This is called fundamental mathematical model which explains the process of generation of DNA from amino acids. This was treated as most important work in science after Relativiy and Quantum Mechanics.
Kindly have a look at it. It may be of some interest to you.
Regards
Dr. Surendra Singh Pokharna (Former Scientist, ISRO) --- On Tue, 20/4/10, Bhakti Madhava Puri <bmp...@binstitute.net> wrote: |
Bhakti Madhava Puri
Respected Dr Pokharna,
There are several problems with Eigen's seminal theoretical paper, actually published in 1971, on the self organization of matter. The practical problems of the RNA world have already been mentioned several times on this forum. Freeman Dyson explains, "for the Eigen theory to work, four "catastrophes" need to be avoided. First is the "error catastrophe," where there are simply too many errors in replication of long RNA molecules. Second is the "selfish RNA catastrophe," where an RNA molecule mutates and dominates the scene, but the mutation takes away its critical role as a catalyst. Third is the "short-circuit catastrophe," where a mutated RNA molecule catalyzes the wrong reaction (a later one in a chain than the proper one). Fourth is the "population collapse catastrophe," where one simply runs out of a critical component."
Manfred Eigen himself noted that this mutation process places a limit on the number of digits a molecule may have. If a molecule exceeds this critical size, the effect of the mutations become overwhelming and a runaway mutation process will destroy the information in subsequent generations of the molecule. This critical mutation rate, or "error threshold" is crucial to understanding "Eigen's paradox."
Eigen's paradox is one of the most intractable puzzles in the study of the origins of life. It is thought that the error threshold concept described above limits the size of self replicating molecules to perhaps a few hundred digits, yet almost all life on earth requires much longer molecules to encode their genetic information. This problem is handled in living cells by the presence of enzymes which repair mutations, allowing the encoding molecules to reach sizes on the order of millions of base pairs. These large molecules must, of course, encode the very enzymes that repair them, and herein lies Eigen's paradox:
1. Without error correction enzymes, the maximum size of a replicating molecule is about 100 base pairs.
2, In order for a replicating molecule to encode error correction enzymes, it must be substantially larger than 100 bases.
There is the further problem that self-organization relates to organized matter, but not to information. As Paul Davies states: "Life is actually not an example of self-organization. Life is in fact specified--i.e., genetically directed--organization." In other words, the sequence specific order of large DNA molecules is not explained on the basis of physical and chemical laws, and yet this "information" is critical in determining the function of the DNA "code." Eigen, himself, realizes this in his 1992 paper where he states: "Our task is to find an algorithm, a natural law that leads to the origin of [this] information."
From: Surendra Pokharna <sspokh...@yahoo.com>
To: online_sa...@googlegroups.com
Sent: Tue, April 20, 2010 5:33:32 AM
Subject: Re: [Sadhu Sanga] Chance and Necessity do not explain the origin of life - Part 4