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 The site is no longer maintained, but the language persists.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.
Well, there you are! An OP could be a first draft of that chapter and the feedback from our erudite clientele could be useful input. Anyway, I’ll buy the book! 😉
Is that a threat or a promise? I’m sorry if this seems harsh but the more you post the less I feel you have any real grasp on biology.
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’.
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
The Role of Methylation in Gene Expression by Theresa Phillips, Ph.D.
New way cells turn off genes, July 19, 2017, Howard Hughes Medical Institute
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.
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.
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.
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.“).
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?
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.
So looking at human genomes today, what would you say has remained intact compared with the genome of our last common vertebrate ancestor?
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.
No. It’s just that I appreciate the vital role genes play in the process.
No, I do not believe in tornado-in-a-junkyard scenario’s. Try harder, Charlie.
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?
Yeah well, I don’t blame her.
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.
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.
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 clear message here is that it’s not so much the genes but the in the way that they are used.
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.
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.
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.
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.
Evidence from personal experience. Been there, done that.
It’s not my belief, either.
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.
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.
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.
I’d see mine as more the product of education than belief, but what the hey!
CharlieM,
Ach, Talbott, Noble, Jablonka … should I just dump the collected works of Richard Dawkins on you; save either of us having to type anything?
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.
Genomes have evolved wonderful ways of preserving their sequence through indefinite copying cycles.
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! 🤣).
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.
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:
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.
.
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.
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.
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.
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 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?
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.
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?
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.
Now you are happy to call a sperm cell a phenotype! Aren’t you being a bit loose with the term ‘phenotype’? 🙂
The sperm carries protein complexes which are vital to reproduction.
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.
Yes. Who can say? Whatever the case it’s the action of the whole organism which leads to its further development.
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.
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.
But my form is a copy of the form of my parents.
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.
So can you give me an example of a form of life that does not begin from a minimum of a single cell?
See my previous chicken and egg post.
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?
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?
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.
If everybody created the same building, in the same way that birds create the same nests you’d have a point.
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.
Oh, riheally?
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.
Yes. Phenotype is everything about an organism beyond its raw genetic sequence (genotype).
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.
No. Whatever gives you that idea?
You don’t say.
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.
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.
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.
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.
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.
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.
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.
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.
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.
CharlieM,
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.
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.
The most abundant material in a cell is water. Is this derived from the genome?
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.
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?
It’s not forgotten, not even for a moment, except by a gene centrist of your imagination.
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.
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.
Guffaw! “There was this mind, see, and it just ..”