Genes store INSTRUCTIONAL information

Genes store INSTRUCTIONAL information

https://reasonandscience.catsboard.com/t3097-genes-store-instructional-information

1.The information stored in DNA is a template. It is equal to a recipe or program. Nucleic acids contain information in a semantic (meaningful) sense. Instructing consists in an advance specification of the kind and order of steps yielding a certain outcome if the steps are carried out. The amino acid arrangement and sequence to make functional proteins is the product of the information stored in DNA. 
2. Recipes and programs do not just bring about a particular outcome; they are designed to do so. They are usually formulated with a purpose. The computer program output is the result of executing a pre-specified series of operations.  A purely physical description does not capture the instructional nature of the process. Instructional information is not a tangible entity, and as such, it is beyond the reach of, and cannot be created by any undirected physical process. This is not an argument about probability. Conceptual semiotic information is simply beyond the sphere of influence of any undirected physical process. To suggest that a physical process can create semiotic code is like suggesting that a rainbow can write poetry... it is never going to happen!  Physics and chemistry alone do not possess the tools to create a concept. The only cause capable of creating conceptual semiotic information is a conscious intelligent mind.
3. Therefore, the instructional information stored in DNA comes most likely from an intelligent designer. 

Genetic Information as Instructional Content July 2005. 1
Conceptualizing gene function in terms of instructions is an approach dating back to the early 1950s and taken up repeatedly ever since. For example, Francois Jacob ([1970] 1974) interpreted the genetic material as instructions. A part of the justification for his claim is the fact that the template’s linear order determines its product’s arrangement. Molecular templates share a certain way of determining outcomes with recipes and programs, and that it is this kind of determining an effect that makes them instructional.

Recipes and programs do not just bring about a particular outcome; they are designed to do so. Perhaps what makes them be about an outcome is the fact that they were designed to produce it. If so, then either templates are about their outcomes because they are biologically designed to do so, or if they are not so designed, then they cannot be about their products. In the latter case, even if templates determined their products in ways structurally similar to recipes, they would not possess semantic content. Recipes and programs are usually formulated with a purpose, and many natural templates have the biological function to contribute to causing a
certain outcome. 

Suppose the steps of the recipe or the program had been arranged randomly in advance. Then the ‘cake’ may hardly be edible, and the program may not perform anything sensible at all. Nevertheless, these outcomes would have been determined by specifying all individual steps and their order of occurrence such that the steps produce the outcome if they are carried out. I take it that we would still regard the computer output as the result of executing a pre-specified series of operations, and the inedible lump as the result of carrying out some (nasty) sort of instruction. Recipes and programs carry meaning or instructional content because they are linguistic entities, at least at some level. They are written commands and they instruct what they instruct in virtue of being meaningful sentences. Moreover, its instructional content should then be analogous to the meaning of words. A purely physical description does not capture the instructional nature of the process.

Nucleic acids contain information in a semantic (meaningful) sense. As templates for the synthesis of macromolecules, nucleic acids determine their products in a way that is constitutive for instructions in general. It is therefore legitimate to attribute instructional content to molecular templates. Recipes and programs provide specifications of the kind and order of operations, which if carried out, produce an outcome. For example, a recipe for a cake consists of a list of ingredients and a number of specifications that determine the kind and order of actions, which if carried out, produce the cake; and the recipe is provided before it is acted upon. Similarly, a computer program consists of a list of interconnected commands that specify the kind and order of operations that a computer will perform if it runs this program. Programs usually contain specifications of conditional form, and therefore, they rely on inputs to specify which operations to execute. However, the range of possible operations is specified by the program. It seems, then, that programs and recipes share a peculiar way to determine their outcomes. They specify the kind and order of operations that will result in a certain outcome. Importantly, they specify this before the operations are performed: With a certain program loaded or a particular recipe in place, it is determined which operations (among a set of alternatives defined by other programs or recipes) will occur. The idea that operations are specified before they are performed appears to be the basis for our practice to distinguish between merely specified operations and those that are, in addition, executed.

Templates, I suggest, determine their products in just the same way as do recipes and programs. For we saw that a nucleic acid serves as a template for the synthesis of a product just in case it determines the kind and order of product components in the following way: The nucleic acid is present before the start of synthesis and it determines, through the kind and linear order of its components, the kind and sequence of ‘If X, then Y*’-type reactions that will occur. The nucleic acid section reduces the number of possible pairing reactions to one at each of its sites. Thus, the section can be said to specify, before the start of synthesis, the kind and order of reactions that will result in the product if the reactions occur. Hence, templates determine their products in the same way in which recipes and programs determine their outcomes. If this mode of determination is indeed constitutive for instructional processes, then it is justified to say that molecular templates contain instructional content for the synthesis of their products. On this view, the instructional content of a molecular template consists in those of its (nonsemantic) properties that determine a product in the characterized way.

Programs and recipes are said to be about the procedures or operations yielding a specific outcome (rather than about the outcome itself). A recipe for an apple pie is about how to bake an apple pie; a program for calculating arithmetic means is about how to calculate arithmetic means. Another way to say this is that man made instructions provide the instructional content for achieving a certain outcome. Similarly, the aboutness of molecular templates can be construed as having instructional content for the synthesis of the product. Rather than saying that man made instructions like recipes and programs provide instructional content for executing particular tasks, we sometimes say that they contain the information about how to bake a pie or how to calculate arithmetic means. In these cases, the terms ‘information’ and ‘instructional content’ are synonymous. Similarly, instead of saying that a template provides the instructional content for the synthesis of its product, we may say that it carries the information for it. These formulations express the same idea. But, when expressed in terms of information, we capture what is meant by genetic information. I suggest that the genetic information of molecular templates is their instructional content. Further, a template ‘carries’ or ‘contains’
this information in the sense that the template is an instance of a certain n-tuple.

A recipe or program is carried out ‘correctly’ just in case the instantiated actions or processes are those that are specified as part of the instructional content, and they are carried out in the specified order. Conversely, the instructions are carried out ‘incorrectly’ just in case the processes and their order are not realized as specified. Similarly, it makes sense to say that molecular templates are implemented, or expressed correctly or incorrectly. The template’s information is being expressed correctly if the occurring biochemical reactions are instances of the kind of reactions specified by the template components. The result of such reactions would be the “right” or “correct” (Crick 1958) order of the product. However, the right (or wrong) order may also arise by other means. For example, molecular ‘proofreading’ mechanisms (e.g., Alberts et al. 2002) replace ‘mismatched’ nucleotides with ‘correct’ nucleotides turning a wrong order into the right one. That is, they replace tokens of one nucleotide type (any type other than the one that would result from the pairing reaction specified by the template) by tokens of another type (the type specified by the template).

Particular pieces of nucleic acids may or may not currently serve as templates for the synthesis of a product molecule. The ideas of information storage and expression can be explained in terms of this difference. If a piece of nucleic acid does not currently contribute to synthesize a product, we may say that its instructional content remains ‘unused’ or ‘stored’. By contrast, whenever a nucleic acid does serve as template, it makes sense to say that the information of the template is ‘expressed’.

The DNA’s linear order is preserved in the mRNA’s order, I conclude that the linear order of the protein is ultimately determined by the DNA’s order. That is, the DNA’s linear order is the instructional content, and hence, the genetic information that the DNA template provides for protein synthesis. Of course, DNA provides the instructional content for protein synthesis only if the RNA transcript is not altered before translation. Since the primary transcripts of eukaryotes are usually modified by RNA-splicing and RNA-editing, it may only be in organisms like bacteria where DNA actually does contain the information about the order of amino acids.

Instructing consists in an advance specification of the kind and order of steps yielding a certain outcome if the steps are carried out. It claims, further, that molecular templates determine their products in this way. For in a process like replication, one molecule specifies, prior to synthesis, the kind and order of chemical interactions that determine the kind and linear order of the product’s components. If this is accepted, then it is legitimate to describe the template’s properties, which so determine the product, as the instructional content (or information) for the synthesis of the product.

A.C. McINTOSH Information and entropy – top-down or bottom-up development in living systems? 2009 1
This paper deals with the fundamental and challenging question of the ultimate origin of genetic information from a thermodynamic perspective. The theory of evolution postulates that random mutations and natural selection can increase genetic information over successive generations. It is often argued from an evolutionary perspective that this does not violate the second law of thermodynamics because it is proposed that the entropy of a non-isolated system could reduce due to energy input from an outside source, especially the sun when considering the earth as a biotic system. By this it is proposed that a particular system can become organised at the expense of an increase in entropy elsewhere. However, whilst this argument works for structures such as snowflakes that are formed by natural forces, it does not work for genetic information because the information system is composed of machinery which requires precise and non-spontaneous raised free energy levels – and crystals like snowflakes have zero free energy as the phase transition occurs. The functional machinery of biological systems such as DNA, RNA and proteins requires that precise, non-spontaneous raised free energies be formed in the molecular bonds which are maintained in a far from equilibrium state. Furthermore, biological structures contain coded instructions which, as is shown in this paper, are not defined by the matter and energy of the molecules carrying this information. Thus, the specified complexity cannot be created by natural forces even in conditions far from equilibrium. The genetic information needed to code for complex structures like proteins actually requires information which organises the natural forces surrounding it and not the other way around – the information is crucially not defined by the material on which it sits. The information system locally requires the free energies of the molecular machinery to be raised in order for the information to be stored. Consequently, the fundamental laws of thermodynamics show that entropy reduction which can occur naturally in non-isolated systems is not a sufficient argument to explain the origin of either biological machinery or genetic information that is inextricably intertwined with it. This paper highlights the distinctive and non-material nature of information and its relationship with matter, energy and natural forces. It is proposed in conclusion that it is the non-material information (transcendent to the matter and energy) that is actually itself constraining the local thermodynamics to be in ordered disequilibrium and with specified raised free energy levels necessary for the molecular and cellular machinery to operate.

Pavel Hobza: Structure, Energetics, and Dynamics of the Nucleic Acid Base Pairs: Nonempirical Ab Initio Calculations June 29, 1999
Living organisms contain a set of instructions that specifies every step required for the organism to construct a replica of itself. This information is stored in deoxyribonucleic acid, DNA, and the respective molecule is thus one of the most important molecules in our life.
https://pubs.acs.org/doi/10.1021/cr9800255

1. Either the sequence of nucleotides in genes have their arrangement that bears instructional information defined by the material itself, through self-organization, or intrinsically, or through an extrinsic ordering principle that is not found within the material itself.
2. A thermodynamically open system is not sufficient/inadequate to explain the origin of information stored in DNA.  In other words, negative entropy cannot be the source of information.
3. Specified complex Information is not generated by matter nor energy but is repeatedly shown to be the product of a fundamentally distinct source, namely intelligence.

1. https://www.rug.nl/research/gelifes/tres/_archive/stegman2005_philoevo.pdf
2. https://www.witpress.com/elibrary/dne-volumes/4/4/420

“Instruction”, operational functional prescription on data and their behaviour by means of a language. Software consists of sets of instructions usually deployed to a target computer system (hardware) to be run. Instructions are something qualitatively different from arrangements of objects and can never be totally reduced to them.  To illustrate, let me command “put the apples on the table”. My instruction is qualitatively different from apples. Materially my command will produce the effects: (1) Moving the apples as a process and (2) An arrangement of apples as a final result. Nevertheless the instruction, as cause, is different from apples. Indeed because an instruction governs arrangements it is not simply an arrangement. This is the fundamental ontological difference between an abstract principle overarching material objects that obey it. An instruction, to be effective in an information processing system must be coded by means of a language and deployed to a target system for its execution. Language makes a material arrangement become a symbol of an abstract instruction. My put_the_apples_on_the_table instruction was coded in the English language because it was intended for humans. However it could be coded in many other ways depending on the system that must run it. For example in digital computers the programmer’s high-level instructions are coded finally in machine code, arrangements composed of 1s and 0s, represented by physical states of the hardware. Let’s continue with our apple analogy. Let’s imagine that chance and necessity could actually build an apple-dispenser system which is able to function by reading instructions. We would like it to execute the instruction put_the_apples_on_the_table. Since the Chance and Necessity system (C&N) doesn’t understand English and deals only with apples, we might codify the instruction as a binary string, e.g. according to the ASCII code or whatever, where 1 is an apple and 0 is no apple. In other words we are using arrangements of real apples to code instructions on how to distribute apples. Our message is written in “apple code”. Thus material apples symbolize an abstract instruction. Let’s input this string into the C&N system and see what happens. When this arrangement is processed, we find that the C&N system unfortunately cannot distinguish between a generic set of apples to distribute and the codified apple string to be read and executed. How could C&N be able to distinguish between them if symbols simply don’t exist for C&N? So our C&N system doesn’t work. It has an irresolvable semantic/syntactic problem for C&N. The C&N lacks the capability to chose between apples “to eat” and apples “to read”, so to speak. The machine eats the apples instead of reading them. It cannot be a software-driven machine.
https://uncommondescent.com/intelligent-design/on-the-impossibility-of-abiogenesis/

It goes through like a red line in all biology and biochemistry. There are molecules, that store and transmit information, and those that sense and react accordingly to it, and there are those that process, transcribe or translate information.  The information source generates the information to be transmitted; the encoder transforms the information into a suitable message form for transmission over the communication channel; and the decoder performs the inverse operation of the encoder, or approximately so, for the user at the other end of the channel, which then performs a certain action based on that information received. There is signal transduction and signal integration. The receivers are those that perform very specific tasks based on the information that they receive from the outside/external cells, or the inside, in various ways. Molecules, proteins, organelles, cells, and organs talk, or cross-talk to each other. Our bodies consist essentially of unimaginably sophisticated and complex landscapes of interlinked factories, where the exchange of information is performed on many different levels, through many pathways, signaling networks, cross-talk, and exchange.
Signals, for example, direct traveling white blood cells as to where they should exit blood vessels at exact locations and where they should squeeze through difficult spaces in tissues. In the plant world, trees and other plants communicate with each other through microscopic wires made of long, thin fungal cells, and this can take place through an entire forest. Signals provide mutual protection, with warnings about specific dangers, as well as a way to share nutrients. Wide-ranging conversations among various organelles respond to cell stress and provide quality control for mitochondria, membranes, and production of proteins.

I have listed so far 45 different epigenetic languages and codes. Biological information has always had a specific function. DNA for example stores information that provides instructions on how to do or create things like proteins, or regulatory micro RNAs that can either turn off or activate genes to be expressed. They are like a director of an orchestra, that signals to the player of the contrabass when to play or to stop playing.  DNA is a template with a  linear order that determines its product’s arrangement. Its information content can also be described as a recipe or program that does not just bring about a particular outcome; it's designed to do so. That's its function or job. That's why genetic information is called specified complex information. That is a nomenclature that is conveyed by the discovery institute and others. For many, it is difficult to decipher what that means unless one is already familiar with the terms, and their meaning. Specified means specification. The information specifies or instructs how things ought to be done. I prefer to use the term instructional information. The information is like a blueprint to make a house, or a car. In biology, mostly it is an instruction manual to make molecular machines, proteins, and enzymes, that speed up cellular processes, and reactions. Many claim that biology is just about chemistry and molecules interacting together in a certain way. That's far from being true. It's much more than that. A purely physical description does not capture the instructional nature of the process.

Of course, a central question is: How did all this emerge? A science paper from 2018, titled: How do complex animal signals evolve? - confessed:  A well-developed framework for the complimentary issue of signal evolution on sensory landscapes is lacking.

Our world is based on an infinite number of possible chaotic states, that are contrasted by specific arrangements that are based on informational states, and specific outcomes that depend on selective principles. Our actual world is based on a very specific set of outcomes. Biochemistry is governed by information, refined to an incredible degree. Either matter had the capacity to produce spontaneously emergent properties like information, a fundamental change in concept, or there was/is an eternal mind at the beginning. I go with the second option.