Body: <p>I have been thinking about to what extent a biological entity’s characteristics can be decomposed into discrete sections of the genome that are parsed and mapped one-to-one to a physical structure. It is fascinating in this regard how indistinguishable biology is from computational linguistics and formal systems theory in general - DNA is a formal language; and we are still trying to unravel the grammar. Right?</p>
  <p>I think the following question depends on what type of “grammar” DNA has. I don’t know the term in the field, but I have been using the term “holographic” in my own thinking, when a sequence in a code is interpreted twice - by two different grammars, or two different parts or stages of a grammar, contributing meaning to multiple realizations in the output. (“Holographic”, as in, a 2D surface appears to be 3D so long as the information is encoded on it in such a way to be parsible / reconstructible - the information is not lost, in the mix, but is able to be separated and mathematically resolved (some sort of non-associativity under some function, is what I suspect).</p>
  <p>My question is about to what extent “kinship” is indicated by “having similar genes”.</p>
  <p>Genes are <em>virtual</em> (I think) - pure information. It seems like the same genes can come into being without them having replicated from the same ancestor (convergent evolution). The presence of the same gene in two biological entities does not strictly imply closer “kinship” when compared to two biological entities without that shared gene. Conversely, we need not expect entities of close kinship to share the same genes (a sibling can inherit one allele of some gene, another sibling the other one, dominant or recessive, etc.)</p>
  <p>Perhaps there is an analogy between language and biology, that I haven’t clearly spelled out, yet.</p>
  <p>-&gt; Organisms are to DNA what sentences are to “logical form” (in linguistics).</p>
  <p>-&gt; DNA is to mechanisms that build DNA (RNA transcription, protein synthesis, etc.) what logical form is to “universal grammar” (or, the actual system cradling the human aptitude for languages, itself).</p>
  <p>-&gt; (The odd part): Biological reproduction is when a “sentence” of language directly, physically transforms (or, contributes a part of itself) into an instance of a “grammar” (a valid grammar, as specified by the parameters/constraints/dictates of “universal grammar”). It is intriguing how the analogy gets challenged here, perhaps to be probed further. For now, it could be seen to stretch to how human language can <em>express</em> grammars (like humans can define grammars - constructed languages, as one example - mathematics - or any formal system at all.)</p>
  <p>-&gt; Lastly, biological evolution has some analogy to language evolution (perhaps, a fourth “layer” or “grammar” (a specification of means by which something can change - rules, constraints) of the system), in that there is some stochastic generation which gets selected for some (chaotically changing, varying) context (ie, natural selection; as for humans and language, it might be hard to specify the various reasons, including highly social ones, why language features, or cultural features, are either retained or dissipate (Dawkins’s concept of “memes”)).</p>
  <p>I think there are two competing dynamics.</p>
  <p>One says that similar genes are not “informationally significant” because the “universal grammar” <em>and</em> the transformation rules/rounds/generations on universal grammars themselves (the ways the system can vary from generation to generation, in the space of possible evolutionary trajectories) can easily generate the same structure with multiplicity, independently.</p>
  <p>Another competing force says that presence of similar genes indicates a likelihood of kinship because it is improbable that two people who collectively have a high degree of similarity between their total collection of genes, perhaps (this is how ethnicities arise - a group exchanging genes internally, within a single evolutionary path, pass the same genes around amongst each other; the same with human languages).</p>
  <p>I wonder if there is any “equilibrium” theory, where the extent to which a system’s propensity to permit random duplicates of a form, is somehow balanced with the (evolutionary) dynamic where memes (genes, language features) cluster with regards to proximity of interaction.</p>
  <p>So we at the end of the day have a situation where similar overall gene profiles is actually a probable indicator of “poly”-kinship (a kinship vector where any two entities have some last common ancestor for each of their genes, not just their last common “parent” - and those kinship vectors can have unique distributions, from homogeneous to with wide range - but the same average).</p>
  <p>But, there are still outliers where a person is able to have a similar phenotype because of sufficient randomness in the way genes work, without it indicating a high-value (normed) kinship-vector.</p>
  <p>(This could apply to linguistics where it would be fallacious to assume Japanese and Turkish must be related to each other just because they share strikingly agglutinative morphology features.)</p>
  <p>How is this modeled mathematically, in bioinformatics?</p>
  <p>Thank you.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-06-13T20:58:36.020Z
Comments.Text: Please edit the question to limit it to a specific problem with enough detail to identify an adequate answer.
Comments.UserDisplayName: Community
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Comments.Text: The question is too broad and needs to be focussed. Game theory has been applied to population dynamics to explain diverse behaviours of "fitness". Phylogenetics is the tool to answer to your question and has been applied to linguistics.
Comments.UserDisplayName: M__
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Comments.CreationDate: 2023-06-13T21:07:14.517Z
Comments.Text: By game theory I mean understanding equilibrium selection.
Comments.UserDisplayName: M__
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Comments.CreationDate: 2023-06-14T08:01:02.773Z
Comments.Text: Could you please suggest good sub-questions the post could be broken down into? Experienced people in a field often are able to ask better questions because they have more meta-knowledge, but a beginner has many strands of interconnected thought they can’t organize enough yet to separate. I guess my question is about the “formal grammar” of biology (to what extent is it known). It is quite broad. I guess I’ll polish off new sub-questions, one at a time. Yes, that could be a good approach.
Comments.UserDisplayName: Julius Hamilton
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Comments.Text: Do you have a specific project or analysis goal in mind? Because bioinformatics is such a broad area of study, It's usually better to start off with your actual problem, and find tools or solutions to fix that.
Comments.UserDisplayName: gringer
Tags: <r>
Title: The mathematics of kinship (degrees and distributions of relatedness on individual and group levels)
ThreadText: # The mathematics of kinship (degrees and distributions of relatedness on individual and group levels)
  
  (Asked by: username_0 on 2023-06-13)
  
  I have been thinking about to what extent a biological entity’s characteristics can be decomposed into discrete sections of the genome that are parsed and mapped one-to-one to a physical structure. It is fascinating in this regard how indistinguishable biology is from computational linguistics and formal systems theory in general - DNA is a formal language; and we are still trying to unravel the grammar. Right?
  
  I think the following question depends on what type of “grammar” DNA has. I don’t know the term in the field, but I have been using the term “holographic” in my own thinking, when a sequence in a code is interpreted twice - by two different grammars, or two different parts or stages of a grammar, contributing meaning to multiple realizations in the output. (“Holographic”, as in, a 2D surface appears to be 3D so long as the information is encoded on it in such a way to be parsible / reconstructible - the information is not lost, in the mix, but is able to be separated and mathematically resolved (some sort of non-associativity under some function, is what I suspect).
  
  My question is about to what extent “kinship” is indicated by “having similar genes”.
  
  Genes are *virtual* (I think) - pure information. It seems like the same genes can come into being without them having replicated from the same ancestor (convergent evolution). The presence of the same gene in two biological entities does not strictly imply closer “kinship” when compared to two biological entities without that shared gene. Conversely, we need not expect entities of close kinship to share the same genes (a sibling can inherit one allele of some gene, another sibling the other one, dominant or recessive, etc.)
  
  Perhaps there is an analogy between language and biology, that I haven’t clearly spelled out, yet.
  
  -> Organisms are to DNA what sentences are to “logical form” (in linguistics).
  
  -> DNA is to mechanisms that build DNA (RNA transcription, protein synthesis, etc.) what logical form is to “universal grammar” (or, the actual system cradling the human aptitude for languages, itself).
  
  -> (The odd part): Biological reproduction is when a “sentence” of language directly, physically transforms (or, contributes a part of itself) into an instance of a “grammar” (a valid grammar, as specified by the parameters/constraints/dictates of “universal grammar”). It is intriguing how the analogy gets challenged here, perhaps to be probed further. For now, it could be seen to stretch to how human language can *express* grammars (like humans can define grammars - constructed languages, as one example - mathematics - or any formal system at all.)
  
  -> Lastly, biological evolution has some analogy to language evolution (perhaps, a fourth “layer” or “grammar” (a specification of means by which something can change - rules, constraints) of the system), in that there is some stochastic generation which gets selected for some (chaotically changing, varying) context (ie, natural selection; as for humans and language, it might be hard to specify the various reasons, including highly social ones, why language features, or cultural features, are either retained or dissipate (Dawkins’s concept of “memes”)).
  
  I think there are two competing dynamics.
  
  One says that similar genes are not “informationally significant” because the “universal grammar” *and* the transformation rules/rounds/generations on universal grammars themselves (the ways the system can vary from generation to generation, in the space of possible evolutionary trajectories) can easily generate the same structure with multiplicity, independently.
  
  Another competing force says that presence of similar genes indicates a likelihood of kinship because it is improbable that two people who collectively have a high degree of similarity between their total collection of genes, perhaps (this is how ethnicities arise - a group exchanging genes internally, within a single evolutionary path, pass the same genes around amongst each other; the same with human languages).
  
  I wonder if there is any “equilibrium” theory, where the extent to which a system’s propensity to permit random duplicates of a form, is somehow balanced with the (evolutionary) dynamic where memes (genes, language features) cluster with regards to proximity of interaction.
  
  So we at the end of the day have a situation where similar overall gene profiles is actually a probable indicator of “poly”-kinship (a kinship vector where any two entities have some last common ancestor for each of their genes, not just their last common “parent” - and those kinship vectors can have unique distributions, from homogeneous to with wide range - but the same average).
  
  But, there are still outliers where a person is able to have a similar phenotype because of sufficient randomness in the way genes work, without it indicating a high-value (normed) kinship-vector.
  
  (This could apply to linguistics where it would be fallacious to assume Japanese and Turkish must be related to each other just because they share strikingly agglutinative morphology features.)
  
  How is this modeled mathematically, in bioinformatics?
  
  Thank you.
  
  **Tags:** r
  
  > **Comments:**
  > **username_1**: Please edit the question to limit it to a specific problem with enough detail to identify an adequate answer.  
  > **username_2**: The question is too broad and needs to be focussed. Game theory has been applied to population dynamics to explain diverse behaviours of "fitness". Phylogenetics is the tool to answer to your question and has been applied to linguistics.  
  > **username_2**: By game theory I mean understanding equilibrium selection.  
  > **username_0**: Could you please suggest good sub-questions the post could be broken down into? Experienced people in a field often are able to ask better questions because they have more meta-knowledge, but a beginner has many strands of interconnected thought they can’t organize enough yet to separate. I guess my question is about the “formal grammar” of biology (to what extent is it known). It is quite broad. I guess I’ll polish off new sub-questions, one at a time. Yes, that could be a good approach.  
  > **username_3**: Do you have a specific project or analysis goal in mind? Because bioinformatics is such a broad area of study, It's usually better to start off with your actual problem, and find tools or solutions to fix that.  
  
  ---
  
  ## 0 answers
  
  