What mixture of “design” and “evolution” is possible as the IDM collapses?

This offers the simplest “neutral” colloquial mixture of “design” and “evolution” that I’ve seen in a long time. The site is no longer maintained, but the language persists.

“As a designer it is important to understand where design came from, how it developed, and who shaped its evolution. The more exposure you have to past, current and future design trends, styles and designers, the larger your problem-solving toolkit. The larger your toolkit, the more effective of a designer you can be.” http://www.designishistory.com/this-site/

Here, the term “evolution” as used just meant “history”. The author was not indicating “design theory evolution”, but rather instead the “history of designs” themselves, which have been already instantiated.

The topic “design is history” nevertheless enables an obvious point of contact between “evolution” and “design”. They both have histories that can be studied. Present in the above meaning of “design” are the origin, processes and agent(s) involved in the “designing”. This differs significantly from the Discovery Institute’s version of “design theory”, when it comes to history, aim, structure and agency, since the DI’s version flat out avoids discussion of design processes and agent(s). The primary purpose of the DI’s “design theory”, meanwhile, is USAmerican religious apologetics and “theistic science”.

The quotation above likely didn’t come from an IDist, and it isn’t referencing “Intelligent Design” theory as a supposed “scientific theory”. The “designer” in the quotation above is a (more or less intelligent) human designer, not a Divine Designer. This fact distinguishes it “in principle” from the Discovery Institute’s ID theory, which is supposed to be (depends on who you’re speaking with in the IDM) about first biology, then informatics, and statistics. The DI’s ID theory is not actually focused on “designing by real designers”, but rather on apologetics using “design” and informational probabilism.

The Discovery Institute’s failure to distinguish or even highlight the differences and similarities between human design and Divine Design, and instead their engagement in active distortion, equivocation, double-talking, and obfuscation between them, are marks of its eventual downward trend to collapse.

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885 thoughts on “What mixture of “design” and “evolution” is possible as the IDM collapses?

  1. CharlieM,

    Centrioles are made of tubulin which is made by enzymes whose sequence is contained within the genome acting on tubulin sequences. The organising principles are likewise enzyme-directed.

    I will, if you prefer, retreat from my ‘trivial’ assertion. There is a significant amount of phenotype contained in an egg. But none of that persists beyond a few divisions of the blastocyst – new copies are made from the genotype of the zygote, and the parental copies turn over and dilute. And in that process, new levels of phenotype emerge, from cellular replication. Blastula phenotype gives way to gastrula phenotype, then embryo, foetus, infant, junior, adult.

    You seem to be mashing this nest of phenotypes into one. Because an egg contains a bit of phenotype, necessary to get the ball rolling, in some vague manner then it also contains the phenotype of the adult. But that phenotype actually arises by genomic repetition, with epigenetics – enzymes are extracted differentially under chemical influence depending on location. Those chemical influences themselves are genetically sourced.

    But deep inside this growing soma, lie new eggs – their haploid composition is already set while she is a foetus, and they lie suspended in meiosis for 20 years or so, before maturing and releasing. The whirr of organismal development takes place largely above their heads, and is not passed on. All that is passed on is in the genome of the egg, with its starter pack of components derived from the mother’s genotype. The capacity of these quiescent genes to be passed on depends largely on the success of their identical copies engaged in the ‘whirr of development’.

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  2. Allan Miller: Where resides the detailed control in a gamete in your version of events? You’ve got this massive genome sat there, just the one copy, all ready and willing to provide a fundamental explanation of the repetitious production of broadly similar organisms, but you reject it in favour of ‘the system’. Where in ‘the system’, in its minimal gametic form, resides the informatic capacity to build a heart, from replication of a cell line (and its genes), if not in the genes?

    The cell controls the activity within it. A very quick scan of the literature shows us that there’s no getting round this fact. Here are one or two examples with the relevant phrases in bold:


    Mechanisms of Genomic Imprinting by Karl Pfeifer

    Taken together, these studies indicate that mechanisms for parent-of-origin–specific gene expression are likely to vary from gene to gene, since the cell exploits cis-acting sequences and transcription factors already involved in determining the cell type–specific patterns of expression. Thus, dissection of imprinting pathways contributes to a general understanding of mechanisms for controlling the expression of nonimprinted genes in the mammalian cell…

    These examples of imprinting effects on promoter activation, insulator function, and long-range chromatin structure suggest that imprinting has evolved in the mammal by using conventional mechanisms of transcriptional regulation. Thus, through clever engineering, the cell is able to use methylation imprints as both positive and negative signals. Dissecting monoallelic expression pathways will therefore contribute toward an understanding of normal gene regulation and of the molecular basis for diseases associated with disregulation at imprinted loci.

    The Role of Methylation in Gene Expression by Theresa Phillips, Ph.D.

    Not all genes are active at all times. DNA methylation is one of several epigenetic mechanisms that cells use to control gene expression.


    New way cells turn off genes, July 19, 2017, Howard Hughes Medical Institute

    Cells have more than one trick up their sleeve for controlling certain genes that regulate fetal growth and development.
    It’s crucial for one copy of these genes, called imprinted genes, to be turned off in either the sperm or egg. If one copy isn’t turned off, developmental and neurological disorders can occur, or cancer may strike later in life. Now, scientists have discovered a new way that cells keep these genes quiet: by chemically tagging histones — proteins that help keep DNA tightly coiled in the nucleus…

    Zhang and colleagues have discovered a new way that cells can silence some imprinted genes: by adding methyl groups to histones.

    This sort of language is used for a reason. Control comes from the higher level.

    Just as the flow of nutrients through your body is highly dependent on the genetic activity within your cells but it is you and your body that have overall control over what passes through it.

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  3. Corneel:

    CharlieM: I’m not arguing that genetic variation is an important indicator of evolution. I am questioning how this genetic variation comes about.

    Genetic variation ultimately is the result of mutation. Period. If you want to hop on the epigenetics bandwagon, you should argue that a lot of the evolutionary differentiation between lineages is due to non-genetic sources of variation.

    I’m sure we can both agree that mutations are a fact of life. That chance mutations bring about all life forms is your belief not mine. I look at life and see inner organisational forces fighting to alleviate disruptive external influences such as cause mutations.

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  4. Corneel:

    CharlieM: I do not believe in the power of accidents to achieve the creativity of life.

    What is “the creativity of life”? The ability to create something new perchance? Please define.

    Yes. Novelty within limits. Such as the ability to take and use the archetypal form in an individual way. The archetypal form is all encompassing and constant although not static. It is the essential form. The vertebrate form is used in countless individual ways to suit the desires and needs of the creature.

    For example an anteater has a passion for social insects and it has adapted its form to suit those needs while retaining the general form of the vertebrate.

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  5. CharlieM,

    You’re just picking random examples of a particular linguistic stance. People hardly ever talk of ‘genes doing things’ when there is another stance available. Birds make nests, couples have intercourse, hearts beat, cells replicate, enzymes methylate. You’ll find Dawkins***, or any less self-publicising gene-centrist, doing much the same thing, and they aren’t contradicting themselves.

    Your examples do nothing to address nor undermine any of the points I have repeatedly made.

    (ETA, I knew I’d seen Dawkins comment on this, so had a quick look. Given your penchant for arguing with the words of others: “At times gene language gets a bit tedious, and for brevity and vividness we shall lapse into metaphor.“).

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  6. Corneel:

    CharlieM: Genes are vital in the production of proteins. But in order for these proteins to be produced in the right amounts, in the right place, at the right time, to use mechanistic similes, the genome needs to be played like a musical instrument, it cannot be wound up like a clock.

    These are both awful analogies, as neither captures the two functions of genomes: they get replicated and are expressed. The significance of the replication part is what you appear to be perpetually struggling with.

    Genomes get replicated with variation but so do cells and so do organisms. The whole reflected in the parts. I am a physical replication with variation of my father and likewise my son is of me.

    Someone works out at the gym. Cells work overtime to express the specific genes needed in the process of muscle forming. What would you say instigated this expression activity?

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  7. Gregory:
    If “design” just counts as a banned metaphor to the skeptics here, so be it. While I reject Dembski’s “design revolution!” social propaganda, I still actually designed something yesterday, but not (yet) today. Aside from the labels, in my heart I also believe in a Divine Creator, which is actually a commonly held belief across @85 % of human beings around the world today. Skepticism isn’t a functional living worldview itself as it is just doubtful. Otoh, theism lived and applied is what most people believe in one form or another, specifically in the religious theology or worldview of their ancestors. There is much lost memory to be accounted for, the absence of which harms this conversation space. On ID theory’s limits, however, there seems to be broad agreement across the spectrum, of course, outside of a small (largely fanatical) community of IDists themselves.

    This evening I’ll be watching a presentation about a very interesting new dynamic design system that was imagined and built by designers and software engineers who can all be accounted for (time sheets, pay stubs, etc.). One of the designers of the “technology” (cf. “applied science”) itself will be presenting about the design. She’s a world leader in the field. I’m excited to listen & learn since the previous one last year this time!

    Being a “world leader” immediately distinguishes her from anyone in the ID movement, which has no one fitting that category working on “ID theory” (there’s Schaefer III, who wasn’t awarded or promoted for anything to do with “ID theory”; Tour is pro-IDM as an evangelical USAmerican Christian, but can’t vouch for “ID theory as science”).

    The IDM also has very, very few women, and none among the leadership. Ann Gauger and Nancy Pearcey as scholars, Denyse O’Leary as propaganda journalist, plus staff & secretaries at the DI. Check the website: 65/67 Fellows at the DI are men. In “design thinking”, there is much more gender parity, and not such gender imbalance as in professional ID advocates at the DI. Why is that?

    The world is full of designed objects, both ‘natural’ and created by humans. They can be admired and studied from an engineering perspective without any further thoughts about the designer. If the actual designer is to be brought into consideration then I suppose the first step is to ask, who was the builder? And from there to ask, is the builder the same being as the designer?

    When I compare say the eyes of any creature compared with the early attempt by humans at designing cameras I am aware of which are exquisitely designed and which are cobbled together.

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  8. Allan Miller:

    CharlieM:
    Yet it is in the somatic cells of individuals where we find the greatest stability of the genome.

    I don’t think that’s true, but it doesn’t matter anyway: somatic cell lines die with the individual.

    So looking at human genomes today, what would you say has remained intact compared with the genome of our last common vertebrate ancestor?

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  9. Allan Miller:

    Over evolutionary succession genomes change markedly. Our genomes are vastly different from any prokaryote.

    I don’t think, per replication, that there is much difference between the error rate of somatic and germline replication, if we could just stick with one end of the evolutionary series rather than leaping madly about.

    If we want to understand evolution then we need to think in these time scales. We think about individual development in terms of the lifetime of the organism and we think of evolution in terms of the timescale of life on earth.

    We contain the genes that are required for the function of a single celled organism. a multicellular organism, a motile organism and a conscious organism.

    Sure. Sounds like you’re coming round to gene centrism … 🤣

    No. It’s just that I appreciate the vital role genes play in the process.

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  10. CharlieM: That chance mutations bring about all life forms is your belief not mine.

    No, I do not believe in tornado-in-a-junkyard scenario’s. Try harder, Charlie.

    CharlieM: Me: What is “the creativity of life”? The ability to create something new perchance? Please define.

    Charlie: Yes. Novelty within limits. Such as the ability to take and use the archetypal form in an individual way.

    So the “creativity of life” is the ability to use the archetypal form in an individual way? Could you suggest another slightly less presupposing definition please?

    CharlieM: an anteater has a passion for social insects

    Yeah well, I don’t blame her.

    CharlieM: Genomes get replicated with variation but so do cells and so do organisms.

    Again: phenotypic variation needs to be heritable and stable in order to be evolutionary relevant. Modifications of cells and organisms typically do not get propagated to future generations.

    I don’t see what’s so hard about this.

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  11. Allan Miller:

    CharlieM: Me: Must? Whence comes this dogmatism?

    Charlie: I say ‘must’ because an isolated genome is an abstraction. Put a e-coli in a petri dish with nutrients and it will thrive, but as Denis Noble said above, put its genome in a petri dish with nutrients and it will do nothing.

    I can only urge you to re-read this comment in which I address the vital distinction between the conditions for individual lives (complex phenotype extracted from genotype), and what persists through the generations (genotype). Recognising the second case – the evolutionary series – doesn’t stop Noble the physiologist from doing physiology however he pleases.

    Nor does recognising that a gamete is furnished with a few molecules of prior phenotype (extracted from a prior copy of current genotype) mean that genes are not at the centre – precisely because of the statement in italics.

    You believe that the phenotype is extracted from the genotype (what is doing the extracting?) and I believe the genotype contains the instructions for producing the various complex materials that are necessary in the building up of the phenotype, but the construction of form requires more than the genome provides.

    And we are both stubbornly sticking to our beliefs.

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  12. Allan Miller:

    Take the seed of a plant sitting in a packet in a garden centre it is inert. It needs to be surrounded by the right environmental conditions to become active. You cannot isolate the genome from the context in which it exists. And of course the seed is not just a bare genome, but it is the minimum level of existence of the plant. It never is or was just a genome, and that is the reality.

    There you go. Repeat ad nauseam, ‘naked genomes don’t exist’, and you will not find me disagreeing with you. As I’ve said before, I’ve got a degree and everything; I did not just get off the boat. I’m probably more aware than you of the complex mechanisms of gene expression. But still I insist that genes lie at the head of the causal chain. And, when it comes to evolution, genes are all that persist. They recreate organismal instances pretty much from scratch.

    It simply doesn’t matter that one can trot out example after example of living states that aren’t naked genomes: that is not what gene-centrism is arguing.

    I won’t disagree that you probably know more than me about these processes. That is why I don’t just rely on my own knowledge but I like to quote from the experts.

    Stephen Talbott, who also probably knows more than me, has done the same thing much more thoroughly than I have and supplies a multitude of references here below:
    Steve Talbott: How the Organism Decides What to Make of Its Genes

    He ends with this observation:

    The organism is an activity, not a collection of things
    This truth is emerging on all fronts. An illustration: researchers looked at a “spectacular example of convergent evolution and phenotypic plasticity” — namely the independent arising of queen and worker castes in bees, ants, and wasps. The common notion that such cases must involve deeply conserved genes was not supported by this work. Rather, “Overall, we found few shared caste differentially expressed transcripts across the three social lineages. However, there is substantially more overlap at the levels of pathways and biological functions. Thus, there are shared elements but not on the level of specific genes. Instead, the toolkit appears to be relatively “loose,” that is, different lineages show convergent molecular evolution involving similar metabolic pathways and molecular functions but not the exact same genes. Additionally, our paper wasp data do not support a complementary hypothesis that “novel” taxonomically restricted genes are related to caste differences” (Berens, Hunt and Toth 2015, doi:10.1093/molbev/msu330).
    Genes, in other words, are not master controllers or bearers of controlling instructions, but rather represent resources that evolving organisms can employ in their own ways. The same genes can be put to very different uses, and different genes can be caught up in the service of similar ends. The determination of a gene’s meaning is made by the organism as a whole, based on its patterns of activity.

    The clear message here is that it’s not so much the genes but the in the way that they are used.

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  13. CharlieM,

    Please go back to snoozing with Steiner, CharlieM, & don’t pretend to know anything about “ID theory” with me as you just did. You’re not a voice that has offered anything that isn’t said better about ID theory by others. What you wrote shows you don’t understand and I will not spend time with a Steiner-Goethe fox to explain.

    “The world is full of designed objects, both ‘natural’ and created by humans.”

    So, you either agree with atheist Adrian Bejan’s “design in nature” or with the DI’s “Design in nature” that can be inferred “strictly scientifically”. Which is it? Please don’t duck, as it exposes the silly in what you wrote. It would appear you support the “theistic science” of the DI, except from the marginal, very tiny echo chamber that is Goethean foxiness.

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  14. Allan Miller:

    CharlieM:
    The is a process in which the genome is manipulated. It sits within the cellular processes and so is not isolated.

    Over multiple generations, it is indeed isolated, even though it never appears naked at any moment. Given a replicative process, the things replicated increase or decrease in the population, and because of recombination they increase or decrease at a subgenome level. This is what I mean by ‘isolation’. You don’t need to study ‘the system’ – you can just look at the genes. They travel through the generations independently – granted that they never do so unlinked for more than a moment.

    Whether they are male or female sex genomes, they are never separate or isolated from the cell that contains them. Cells have wonderful ways of transferring materials without compromising their outer barriers and fertilisation is no different.

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  15. Corneel:

    CharlieM: They can take measures to try to ensure they get the outcome they desire. Deciding the direction of further evolution is slowly being passed into the hands of the creatures that are evolving.

    How are creatures that decide not to reproduce going to carry their lineage into the future? All further evolution exclusively belongs to the offspring of those organisms that procreate, consciously or not.

    I’m not talking about individual reproduction. I’m talking about the evolution of life in general and the ways in which we are becoming aware of how we are affecting earthly life in general.

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  16. Alan Fox:

    CharlieM: In fact, to be serious, each night when we enter dreamless sleep, every one of us has a mind that is little different from that of a new born baby.

    Evidence? What do we know of the minds of new born babies? Come to that, what do we know about adult minds?

    Evidence from personal experience. Been there, done that.

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  17. CharlieM: That chance mutations bring about all life forms is your belief not mine.

    It’s not my belief, either.

    I look at life and see inner organisational forces fighting to alleviate disruptive external influences such as cause mutations.

    If one of those mutations turns out to be useful to those inner organizational forces, then shouldn’t those forces go ahead and use that mutation?

    Don’t forget that those inner organizational forces are also a result of earlier evolution.

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  18. CharlieM: When I compare say the eyes of any creature compared with the early attempt by humans at designing cameras I am aware of which are exquisitely designed and which are cobbled together.

    Indeed. The camera is exquisitely designed, while the eyes are cobbled together. The eyes work pretty well, but mostly because the neurons in the visual cortex are able to compensate for the crudeness of the “cobbled together” apparatus.

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  19. CharlieM:
    You believe that the phenotype is extracted from the genotype (what is doing the extracting?)

    The genotype. RNA polymerase, the ribosome, tRNA – all extracted from genotype (by RNA polymerase, the ribosome, tRNA…). The latter two, indeed, are direct template-copies of genotype.

    And we are both stubbornly sticking to our beliefs.

    I’d see mine as more the product of education than belief, but what the hey!

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  20. CharlieM,

    Stephen Talbott, …

    Ach, Talbott, Noble, Jablonka … should I just dump the collected works of Richard Dawkins on you; save either of us having to type anything?

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  21. CharlieM
    Whether they are male or female sex genomes, they are never separate or isolated from the cell that contains them.

    Over multiple generations, cells fall by the wayside. Especially somatic ones, and sperm. Indeed, with crossover, most of any given gene instance’s genome-fellows are lost too. What remains, like a Cheshire-cat smile, is the genotype, biased towards those fragments from ‘the best’ ancestors.

    Cells have wonderful ways of transferring materials without compromising their outer barriers and fertilisation is no different.

    Genomes have evolved wonderful ways of preserving their sequence through indefinite copying cycles.

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  22. CharlieM,

    Against my better judgement, I read the Talbott text-dump, and it’s just a non-sequitur. After a discussion of whether a particular state is convergent or synapomorphic (commonly descended), his ‘genes, in other words…’ paragraph does not flow as a conclusion from either possibility.

    (ETA -Talbott’s background is computing, which, as it happens, is how I make my crust. So he’s no more expert than I! 🤣).

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  23. CharlieM: Evidence from personal experience. Been there, done that.

    You’re up against Fox’s conjecture. No intelligent entity can understand, in the sense of deconstruct, anything as complex than itself. Your first person experience is very misleading and it shows.

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  24. CharlieM,

    I also like Talbott’s stuff, though I think he’s sloppy in ways that make it easy to caricature. But if you agree with Talbott’s view about organisms as centers of their own activity & exhibiting what Kant calls ‘intrinsic teleology’ (the link from Kant to Talbott is a straight line that runs through Coleridge), then one should not say that:

    CharlieM: When I compare say the eyes of any creature compared with the early attempt by humans at designing cameras I am aware of which are exquisitely designed and which are cobbled together.

    if the ones that are “exquisitely designed” are “the eyes of any creature” and those that are “cobbled together” are “the early attempt by humans at designing cameras”

    The reason why is that the design argument depends upon conceptualizing living things as devoid of their own intrinsic purposiveness, which is why it must be imposed on matter from outside. In this regard the whole “design argument” or “design inference” depends upon a mechanistic ontology of matter, and that is not compatible with the vitalism that Talbott is drawing upon.

    It is because matter is construed as passive and inert that something essentially non-material must be added to it in order to get life and mind. But if matter is not construed as passive and inert to begin with, then there is no need for design.

    Talbott’s remarks on the Intelligent Design reasoning — a response to Klinghoffer — give a pretty good idea of where the line is drawn.

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  25. Allan Miller:

    Charlie: We are discussing consciousness with respect to cause and effect.

    And your “I create consciousness” response was just waffle: the cause is “I”

    .

    Let me try to flesh out my waffle with some further thoughts.

    We are constituted in such a way as to allow for self-consciousness. The process of building up our physical bodies allows this consciousness to emerge. Something that is repeated at a lower level every time we emerge from sleep. The whole reflected in the parts.

    Our senses are a mirror by which we can experience ourselves in relation to the external world and so they are a necessary, but not the sole, attribute in the process of becoming self-conscious human beings.

    Imagining ourselves to be stood apart from the world around us is bound up with our ego consciousness.

    You look for cause and effects as if everything is just the result of physical interactions. When life, minds and consciousness are involved cause and effect take on a different relationship.

    Think of some newly invented machine. Even before it is built, the end result can be imagined in the mind of the inventor. The mind can look into the future and imagine the effect. It can picture the whole and build the parts from there. A machine can be constructed and the physical processes of this construction can be mapped out in terms of cause and effect. But the understanding of these physical interactions will never get to the mind behind the invention.

    If you are determined to reduce all of this activity to a natural starting point from which it all began then the furthest you can take it is to the zygote that instigated my development.

    And the zygote contains no ‘consciousness’. That emerges, in certain species, from a developmental process of multicellular repetition, with epigenetic variation, that, in other species, produces trees, or beehives with their sundry bees.

    The zygote does not have anything like the wide awake consciousness of the adult human. As I said above this requires more than is contained in the zygote. It has no notion of self, but then again, neither does the new born baby. The sense of self emerges slowly through the experience which the body can provide.

    But within the zygote, as within the adult body, there is plenty of purposeful activity. Combined activities that are aimed at some end or other.

    Individuals of other species stop short of developing the balanced combination of senses and nerves which allow for self-consciousness. That does not mean they are not conscious at all. All we can say is that they do not share human type self-consciousness.

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  26. Allan Miller:

    The zygote contained not just my genome but all the cellular material that was transferred with it; the plasma membranes, the cytoplasm, the proteins, the microRNAs and every other organelle and complex required for the further development of the body which I now find myself in. I inherited a complete system, not just a genome.

    There you go again. I KNOW. Can we just take it as read that I know a little about biology? Nonetheless, all of this content is simply parental phenotype extracted from parental genotype. That starts the ball rolling. Phenotype from then on is extracted from current genotype.

    And there needs to be processes in place to build the products by way of the parental genotype. And so the chicken and egg cycle rolls on. The only way out of this impasse is if a mind is involved. Then there is no need to look for causes and effect between the parts. The whole appears as a unit, condensed out of a mind in a similar way to which a physical invention can be seen as a condensation from mind to matter. The cause is not in the material.

    What it doesn’t contain is a shred of ‘consciousness’, or any genome-independent means to make a heart or a hair follicle.

    Of course hearts and hair follicles cannot be realised independently of the genome. We all know that proteins cannot be produced without the relevant gene expressions.

    You are treating phenotype in a very slack, imprecise way. Because a zygote contains a bit of phenotype, and sometimes phenotype has a nucleic acid substrate, and multicellular bodies are also a phenotype, suddenly, by sleight of hand, “phenotype uses genotype”. But whence comes that phenotype? Genotype. In every case.

    You are treating phenotype in a very rigid way. Phenotypes come in all shapes and sizes and they are whole. A bit of a phenotype is something which is within the whole organism. Do you not think that prokaryotes have phenotypes? Our phenotype is in a constant state of change. The phenotype consists of the whole body of the organism at any and every stage of its development. Is a tadpole a phenotype? Do you think that only the adult form of an organism is entitled to be called its phenotype? Why?

    The proteins and RNAs that extract proteins and RNAs from genotype, the ones upon which genotype now depend, have a sequence that is specified by genotype. Inter alia, they extract themselves. Likewise the proteins that replicate the genome. Self-replicating systems are unique, in that regard.

    Self replicating systems are just that: systems. They are coordinated networks in which individual causes and effects are forever working back on each other. The organisational activity involved protein complexes, RNA and DNA and other associated elements. All of these are vital components of cellular activity.

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  27. Allan Miller:

    CharlieM: I don’t think any other animal has the forethought to link the sexual urge with the production of offspring. I don’t believe that animals engage in such teleological thinking.

    Indeed. This is why it is rather unhelpful to slip from my general talk of the universality of reproductive mechanism in biology to the lack of parental desire among certain of your mates.

    Their thinking might not be teleological but their activities certainly are. There is a purpose to animal reproduction even if they are unaware of it. Why should it be necessary for animals to have the incentive of the feeling of pleasure in order to produce the next generation?

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  28. Allan Miller:

    CharlieM: Do you believe that plants have urges?

    What do you think? 🤣 Nonetheless, they are as doggedly engaged in gamete generation as I am. They use different mechanisms to get them out …

    They might have urges, but how would we tell. It isn’t obvious in the way that is is in the case of higher animals. Put a bull in a field next to a herd of cows that are ready to mate and it will soon make its urges known.

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  29. Allan Miller:

    CharlieM:
    A zygote is much more than a genome.

    I was actually referring to gametes. In the male, gametes are little more than genome injection vehicles. Their phenotype remains outside the egg.

    Now you are happy to call a sperm cell a phenotype! Aren’t you being a bit loose with the term ‘phenotype’? 🙂

    One might plead that the egg is ‘so much more’, but still, in any sexual species, the extreme reduction to male gametes occurs every second generation, on the average, for any set of autosomal or X genes. Throughout the natural world. This is only rendered possible by the existence of female gametes, but these are not part of ‘the system’ at the moment of male-gamete expulsion. A new ‘system’ forms on fertilisation.

    The sperm carries protein complexes which are vital to reproduction.

    Even the egg’s initial phenotype rapidly disappears. At the 4 cell stage, the mother’s ‘starter’ phenotype has been diluted by a factor of 4 by zygote-sourced phenotype, even without turnover. Cell replication and gene expression – and everything else – are soon the sole result of phenotype extracted from the zygote’s genome.

    At the point of fertilisation the cell becomes an organism in its own right and it uses its inner materials to suit its needs. The nutrients required for further development still come from the mother. Even after birth mammals still generally get their nutrients directly from the mother. It is not the source of the material which makes them an individual, it is the inner processes of the phenotype.

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  30. OMagain:

    CharlieM: Do you believe that plants have urges?

    If you look at a video of plants speeded up it’s hard not to come to that conclusion, in some cases.

    Yes. Who can say? Whatever the case it’s the action of the whole organism which leads to its further development.

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  31. Allan Miller: CharlieM,

    But you miss the point. Sperm squeeze the entire ‘system’ into something that is not even a ‘system’ at all, in the sense you are trying to advocate. This is true of eggs as well, in relation to the body from which they came, but is particularly laid bare in sperm, pollen and haploid spores. They are simply mobile haploid genomes. And this reduction takes place every other generation, on average. The fact that, in an egg, they may land on metaphorical fertile ground is neither here nor there in terms of evading this extreme reduction to a genome. “Half the time, they don’t” still means that half the time, they do

    You may marginalise everything but the genome but nothing you say alters the fact that new life begins with a complete cell and all its inner processes of which genomes are a vital part.

    The same activities are in operation in all eukaryote cells in all creatures and have necessarily been taking place since the beginning of their evolution. Genomes change throughout the species but the basic processes remain the same. It is these processes that are the constant feature of living systems.

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  32. CharlieM: I’m not talking about individual reproduction. I’m talking about the evolution of life in general and the ways in which we are becoming aware of how we are affecting earthly life in general.

    Life in general is becoming aware of their urges? Life in general is starting to make conscious decisions? Life in general starts wearing condoms and taking contraceptives?

    Hogwash. You were talking about particular human individuals that decided to “not get their genomes replicated” and now try to generalize to all of life from that.

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  33. Allan Miller:

    CharlieM: Life is a process whereby like produces like.

    Genomes replicate, you mean? 🤣. And from them, a new instance of a cell, or an organism made of cells, emerges. The ‘like’ is produced by the near-perfect replication of genomes, not the copying of systems. You don’t copy yourself into your sperm. And certainly not into your wife’s eggs.

    But my form is a copy of the form of my parents.

    New life begins with the zygote not the gamete.

    That’s a little arbitrary, and diplocentric. Haploid cells have rights too. Indeed, multicellular haploid forms exist, as do isogamous organisms where the haploid state has some independence.

    Even haploid organisms begin from a single cell. I was using zygotes as an example. I didn’t say that they were exclusive in this respect.

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  34. Allan Miller:

    Feel free to distribute your gametes wherever you wish, new life will not spring from it unless it unites with the egg of a woman. There is a good reason why the process of IVF must begin with an egg.

    Sure, in obligately sexual anisogamous forms. Your familiarity with a particularly asymmetric organism blinds you to the fundamentals.

    So can you give me an example of a form of life that does not begin from a minimum of a single cell?

    It is not just the physical substance that gets passed on from generation to generation, it is also the activities and processes that are required for its continuation that are passed on.

    All of which – I may have mentioned this once or twice – are derived from the genome; some initially from the parental copies, later all from the new ‘individual’. But since, in either case, it is often an identical sequence either way, that distinction is not vital.

    See my previous chicken and egg post.

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  35. Allan Miller:

    CharlieM: Analogies are never perfect and should not be taken too far.

    You are a prime example of someone taking them too far. They illustrate little more than your own misunderstanding. Why not talk about the actual phenomena? Why muddy the waters with bad analogies?

    I didn’t misunderstand. I was just making the point that the activity of organisms involves using material from many sources.

    Compounding the misunderstanding. What’s important about nests for birds is not that they ‘utilise materials’ – everything about the bird utilises materials. It is that their construction is every bit as much a part of the phenotype of genes as any more directly organismal feature, and hence, a strong candidate for a genetic basis. Better and worse nests have a clear capacity to impact fecundity, and hence be under Natural Selection

    You imply that I should stick to the actual phenomena and then you tell me that nest building activity has its source in the genome. You don’t give any details as to how specific genes translate into nest building activity. We don’t witness genes building nests, we witness birds building nests. To take this to the extreme when an architect creates a magnificent building do we heap our admiration on the person or on their genes?

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  36. Allan Miller:

    In order for them to use their own genomes they must supply the cells with nutrients and a means of disposing of waste products. You say the source of their behaviour in doing this is in the genes.

    Name a part of metabolism that is not genetically derived or controlled.

    I have never denied that metabolism involves and requires genetic activity.

    The other day I went to the local shop. I considered whether to take the car or to cycle. I decided to cycle. In doing this I had effectively increased my metabolic activity. I would say that the source of this metabolic change was a conscious decision. Or do you think that my genes made me do it?

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  37. CharlieM: The other day I went to the local shop. I considered whether to take the car or to cycle. I decided to cycle. In doing this I had effectively increased my metabolic activity. I would say that the source of this metabolic change was a conscious decision. Or do you think that my genes made me do it?

    Yes, it was your decision, but that decision is not heritable. It doesn’t get transmitted to your children in any way whatsoever. That decision did not make you the founder of a stable lineage of proud cyclists with high metabolic demands.

    Encore: phenotypic variation needs to be heritable and stable in order to be evolutionary relevant. The rest is completely irrelevant in this particular context.

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  38. CharlieM: To take this to the extreme when an architect creates a magnificent building do we heap our admiration on the person or on their genes?

    If everybody created the same building, in the same way that birds create the same nests you’d have a point.

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  39. CharlieM:And so the chicken and egg cycle rolls on.

    It’s not chicken and egg. The sequence of all enzymes is in the genotype. It’s not the other way round. If (say) our RNA polymerase is required before an enzyme can be made, then clearly the sequence of this RNApol enzyme cannot temporally precede the sequence of this RNApol gene.

    Nonetheless it is perfectly possible that this particular activity was performed by RNA formerly, being subsequently replaced by a protein enzyme. It is noteworthy that several parts of translation are still performed by RNA, including the formation of the peptide bond, a vital step in formation of protein enzymes.

    The only way out of this impasse is ifa mind is involved.

    Oh, riheally?

    Then there is no need to look for causes and effect between the parts. The whole appears as a unit, condensed out of a mind in a similar way to which a physical invention can be seen as a condensation from mind to matter. The cause is not in the material.

    If you are insisting that this specific mechanism of RNA polymerisation is the only one that works, how does a mind cause the contemporary occurrence of a genetic sequence whose translated sequence allows translation and a ‘starter’ protein with the same sequence? Where does the mind come from, given the apparent restriction of minds to physical substrates subject to your paradox? Your answer to the chicken and egg paradox is another chicken and egg paradox, or the invocation of a special case: a nonphysical mind.

    You are treating phenotype in a very rigid way. Phenotypes come in all shapes and sizes and they are whole. A bit of a phenotype is something which is within the whole organism. Do you not think that prokaryotes have phenotypes?

    Yes. Phenotype is everything about an organism beyond its raw genetic sequence (genotype).

    Our phenotype is in a constant state of change. The phenotype consists of the whole body of the organism at any and every stage of its development.

    No it doesn’t. A phenotype is any observable characteristic. This could include an enzyme, or a subcellular structure, a cell, a tissue, an organ, a whole organism, a behaviour, a product.

    Do you think that only the adult form of an organism is entitled to be called its phenotype? Why?

    No. Whatever gives you that idea?

    The organisational activity involved protein complexes, RNA and DNA and other associated elements. All of these are vital components of cellular activity.

    You don’t say.

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  40. CharlieM:
    Their thinking might not be teleological but their activities certainly are. There is a purpose to animal reproduction even if they are unaware of it. Why should it be necessary for animals to have the incentive of the feeling of pleasure in order to produce the next generation?

    Why indeed? Why do I experience a curious tendency to gawp, possibly a stirring in my loins, when a pretty girl walks by? What strange magic is this, when it’s all about me deciding if I want kids or not?

    I suspect it’s because my male ancestors had similar urges, passed genetically through both sperm and eggs, rather than because my zygote was a cell with some ‘processes’ in it.

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  41. CharlieM:
    Now you are happy to call a sperm cell a phenotype! Aren’t you being a bit loose with the term ‘phenotype’?

    Yes, a sperm is a phenotype. If I called a nest a phenotype, I’d hardly be jibbing at sperm. As stated above, phenotype is any ‘feature’ of an organism.

    The sperm carries protein complexes which are vital to reproduction.

    Mostly, it contains genome. It is an example of extreme reduction. Despite the massive asymmetry, though, the zygote develops with a roughly 50/50 contribution from each parent. This alone is evidence that the ‘phenotype’ present in gametes is not part of development, but is there for gene expression, and it is the latter which determines form etc.

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  42. CharlieM: You may marginalise everything but the genome but nothing you say alters the fact that new life begins with a complete cell and all its inner processes of which genomes are a vital part.

    Marginalise everything but the genome? How so? It doesn’t marginalise the downstream consequences of gene expression to call them downstream consequences. It just recognises the advances made in understanding the structure of process over the last 70 years or so.

    Genomes change throughout the species but the basic processes remain the same. It is these processes that are the constant feature of living systems.

    Sure, there are some fundamental processes, recognised by the constancy of their genetic sequences across the surviving eukaryote clade. This does not necessarily indicate that the early eukaryotes had these, of course – they may well be extinct, so we can’t tell.

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  43. CharlieM: You imply that I should stick to the actual phenomena and then you tell me that nest building activity has its source in the genome.

    No, be fair, I hedged somewhat. The presence of a particular feature common to a clade is a strong indicator of an ultimate genetic basis, not proof. If the colouration of a bird is genetic, or the shape of its beak or whatever, then the consistent shape of its nest – or the fact it builds a nest at all – are equally legitimately assumed to have a genetic basis. Birds of a nest-building species that don’t build nests don’t pass on their genes. If nest-building relied on repeat ‘creativity’, I’d say genetic nest-builders would probably come to dominate the population.

    You don’t give any details as to how specific genes translate into nest building activity.

    Which would be a better criticism if your counterargument didn’t involve wafting your hands and saying “it’s something else in the zygote … or the intelligence of nature … or summink”. If you’re all about the detail, give me some detail.

    We don’t witness genes building nests, we witness birds building nests. To take this to the extreme when an architect creates a magnificent building do we heap our admiration on the person or on their genes?

    Ah, the return of the bad analogy. If we all built buildings to house our young, and they tended to adopt a consistent form that distinguished our buildings from those of – say – chimps, I would not be giving prizes to anyone claiming originality and creativity.

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  44. CharlieM: The other day I went to the local shop. I considered whether to take the car or to cycle. I decided to cycle. In doing this I had effectively increased my metabolic activity. I would say that the source of this metabolic change was a conscious decision. Or do you think that my genes made me do it?

    What the genes indirectly ‘made you do’ is breathe faster in response to stimulus – CO2 concentration increasing in response to breakdown of carbohydrates in generating ATP*** to supply energy to muscles. You do all this instinctively, thanks to genes shared widely among animals.

    ***ATP is particularly interesting. Not only is it a standard means of energy transfer, it’s an RNA monomer – as is GTP, performing the same role in protein synthesis. Their energetic and informatic roles are not obviously linked.

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  45. CharlieM,

    So can you give me an example of a form of life that does not begin from a minimum of a single cell?

    Do I need to? Gene centrism does not require that genes ever appear without any phenotype around them. Their generation of this phenotype is, indeed, a reason for their persistence.

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  46. Allan Miller:

    Isolated genes are an abstraction.

    Oh, for goodness’ sake! I know! I’ve said “I know” several dozen times. You seem to think the architects of gene centrism – amateurish punters like Crick, Maynard Smith, Williams, Hamilton, Trivers – know no biology. You only have to say ‘there are no naked genes’ or something similar and they are supposed to slap their heads: “Of course! How could we be so foolish! Turns out genomes don’t just replicate without making products. To the library!.”.

    It can happen that component parts are isolated for the sake of analysis and then occasionally it is forgotten that these component parts are meaningless outwith the whole to which they belong.

    Me: Good job I am advocating nothing of the sort

    Charlie: Good! Life is distinguished from non-life through its inherent activity. Activity does not happen without the interaction of the necessary components which include genomes, protein complexes, a suitable medium, some form of containment, etc.

    All of which derive from the genome. All of it. How many times do we need to spin this record?

    The most abundant material in a cell is water. Is this derived from the genome?

    ife cannot begin without these features. And this is why the origin of life is so difficult to fathom from the perspective of the chance coming together of the necessary components.

    Ah, the origin. We always end up there. You are making a bold statement that, because modern replication is wrapped in complexity, it must always have been thus. This is not necessarily so. Modern replicators have wrapped complex shells around themselves – made of or from their own productions – but 3.8 billion years of evolution have rather helped there. You can’t declare this the minimal possible system.

    And the modern replicator is the whole cell. Relatively simple life forms still exists. Prokaryotes are thought to have replicated the same way for the billions of years in which they are supposed to have existed. To imagine that there were any more basic replicators prior to prokaryotes is just speculation.

    The only replicators we know of that do not comprise a complete cell are viruses, but even these require active cellular processes in order to replicate.

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  47. Allan Miller:

    CharlieM: Can you pick one specific example of an epigenetic marker being set by a gene from start to finish? Or pick any other process you mention and sketch the details for us.

    Genomic imprinting

    I rushed that post without realising that I’d left out the most important part of the question. I had meant to ask if you could give an account of the process from start to finish. So from your example, what steps are involved in an example of genome imprinting?

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  48. CharlieM:
    It can happen that component parts are isolated for the sake of analysis and then occasionally it is forgotten that these component parts are meaningless outwith the whole to which they belong.

    It’s not forgotten, not even for a moment, except by a gene centrist of your imagination.

    Me: All of which derive from the genome. All of it. How many times do we need to spin this record?

    Charlie: The most abundant material in a cell is water. Is this derived from the genome?

    I frequently exclude ‘small molecules’ specifically to head off this dodge, but may occasionally forget to do so. No, water isn’t derived from the genome. Although control of its ingress and egress are.

    And the modern replicator is the whole cell. Relatively simple life forms still exists. Prokaryotes are thought to have replicated the same way for the billions of years in which they are supposed to have existed.

    That doesn’t preclude the possibility that they outcompeted yet more primitive forms. Sweeping up after itself is the very essence of an evolutionary process, so the present absence of ancestral forms is no strike against it.

    To imagine that there were any more basic replicators prior to prokaryotes is just speculation.

    Guffaw! “There was this mind, see, and it just ..”

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  49. CharlieM:
    I rushed that post without realising that I’d left out the most important part of the question. I had meant to ask if you could give an account of the process from start to finish. So from your example, what steps are involved in an example of genome imprinting?

    To what end? It’s certainly noteworthy that this form of imprinting is consistent across species, and between genders. Methylation and demethylation are basic biochemical tasks, achieved by enzymes, not ‘systems’. But as to a detailed account of all the genes involved: despite appearances, I’m a busy man! Heading off backpacking for the next few days.

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  50. Allan Miller:

    CharlieM: And there you have it. Whether it is regarded as upstream, downstream or midstream it is but a component.

    It is a fundamental principle of biology – a dogma, almost! – that the sequence information for phenotype resides in genotype. You seek to obscure this by vague terms such as ‘component’.

    What is vague about ‘component’ Components are parts nested within wholes.

    The sequence information for producing proteins resides in the genome, I’m sure we all agree on that. A stretch of DNA selected for expression is a component of the whole genome. And even at the more basic level of the protein the same sequence of the genome can be used to produce different proteins depending on how it is manipulated. Multiple outcomes depending on the way the DNA products are dealt with.

    eg: Sequence cannot be extracted without RNA polymerase, that is a given. But the sequence of RNA polymerase itself is in the genome, therefore the genome is definitively upstream: a source. Better and worse variants of that genetic sequence are marked by the production of better and worse RNA polymerases. The polymerase enzyme is not passed on. The gene is.

    RNA polymerase was already present in the cell at your conception and so to trace its origin we must step back a generation to your parents.

    And it’s not just derived from the egg. Even the sperm contains

    modified histones that may poise downstream epigenetic effects. This notion is supported by increasing evidence that the embryo inherits these differing levels of chromatin organization. In concert with the suite of RNAs retained in the mature sperm they may synergistically interact to direct early embryonic gene expression.

    And this is why I brought up the origin of life. Because even recognising that the genome contains the sequences necessary for the production of complexes such as RNA polymerase, these genes can only be expressed by already present active molecules passed on through the generations. We can speculate about how, where and when this ball started rolling, but it has been rolling on ever since. Life did not begin with molecules, it began with the process of replication. And the reason they prefer to speculate about RNA, in preference to DNA, being involved in this beginning is that it is a much more active molecule. Life is not a bag of molecules, it is an inner activity.

    Now, you can add any ‘component’ you like, you will find that exactly the same relationship holds. The sequence is in the genome, never the other way around. And because only genes are passed on, over the longer term (‘the system’ is not passed on, but is continually refreshed from genotype), then those, subsections of genotype, are the ultimate beneficiaries of the differentiating process of Natural Selection. It is they that increase or decrease in the population, even though their products inevitably do as well.

    Replicating activities are passed on.

    But living entities are whole. They are the whole stream. They always were and they will always be that way.

    Separating living beings into their components involves killing them.

    Indeed. Many organisms have died during the elucidation of the funmdamental structure of living things. Have they died in vain, that you endlessly insist that Holism is the Only Way To Comprehend?

    No they haven’t dies in vain because life can only progress through the continuous replacement and renewal of its component parts. Individual feathers grow, wear down through use and are then discarded as new ones grow. This life and death process of its component parts ensures the continued existence of the whole that is a bird. It is the same with life as a whole. The parts reflected in the whole.

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