Tetrapod Evolution and the Evolution of Consciousness

It is here proposed that the evolution of life was destined to produce self consciousness out of physical matter just as surely as self-consciousness is destined to be produced by the build up of matter from the human zygote.

Our external vantage point allows us to see the process whereby an individual human matures from the point of conception  We are in a position to witness all the stages in the life of individual humans. Activities such as birth, death, growth and decay go on all around us. Conversely on the grand scale of things, taking life as a whole, we are in the middle of evolving life and so we don’t have an overall, clear picture of the process.

In this video Sean B. Carroll states that:
…living things are occupying a planet whose surface is always changing. Hurricanes, earthquakes, volcanoes, tectonic movement, ice ages, climate changes whether local or global, all of these keep changing the environments that species are in, they are running to keep up and most of the time they fail. So we have to think about earth’s history to understand life’s history. We have to understand what’s going on at any particular place to appreciate what’s going on with any particular species.

The same could be said for the cells in your body. Their environment is always changing and most of them do not survive as you change from embryo to adult. From an individual cell’s point of view there may not seem to be any direction.Some live some die, some change slowly, others change dramatically. But from the higher perspective of the whole body there certainly is direction.

It must be acknowledged that vertebrates evolve at the different rates. Coelacanths have been around for hundreds of millions of years. When animals within a group are compared, the ones that are deemed to be the most primitive are those that retain characteristics from the node of the group’s branch. So among vertebrates coelacanths are considered more primitive than humans even taking into account that they have had the same amount of time for their evolution.

Rational Wiki explains that:
Biologists have evidence that all life developed from a common ancestor that lived just under 4 billion years ago, and the concept is accepted by virtually all scientists working in the field.

If that is true then every single tetrapod alive today has an unbroken ancestry dating  back to this common ancestor. Every amniote can trace their ancestry from a water existence to organisms that first set foot on the land, to fully air breathing, but still exothermic, organisms, and finally on to endothermic mammals and birds. At each stage these animals have become more detached from the external environment. I hope the following points will make this clear.

If we follow tetrapod evolution there is a progression from external to internal fertilisation, from eggs deposited in the environment to eggs protected from the environment by an outer shell and then on to gestation within the mother. Even after birth mammals do not take their sustenance directly from the environment but from the mammary glands of the mother.

And humans generally are not content to eat food taken directly from nature. It is altered by extracting, mixing, cooking and preparing so that much of the time the consumer does not even know where it originated.

We aim to nullify the effects of weather and seasons by the use of suitable clothing, We are able to eat food that is out of season by having it transported round the world or by preserving it, or dehydrating it or freezing it. We do not depend on the seasons for procreation and we are able assist conception when it doesn’t occur naturally. All of this serves to detach us more and more from our surrounding environment. Some people are not happy about this detachment and so they call for us to “get back to nature”.

But this separation is necessary for self consciousness to develop. An organism that does not feel itself to be outside of nature cannot have self consciousness.

There must be a feeling of “me in here against nature out there”. We humans are unique in considering our activities as contrasting with the natural world. We contrast natural with artificial. No other animal has separated itself from nature to the extent that humans have.
Humans can trace their ancestry back through reptile-like, amphibian-like and fish-like conditions, the latter three have obviously remained at an earlier condition than humans. This does not mean that they haven’t evolved since the split with the ancestors of humans. After all there are a multitude of ways of being a reptile, an amphibian or a fish. It just means that they haven’t grown out of the environment they find themselves in to the extent that humans have.

This separation from the environment can even be observed in each individual human looking from toe to top. We can be said to have our feet planted firmly on the earth. Gravity holds us to the earth and our legs support our weight and allow us to move about. Our arms are freed from this task and using the marvelous structures at the ends of them we can create out of the substances of the earth. Gravity plays a lesser part in their activities.  Moving on up our brains, being suspended in cerebrospinal fluid, are even more free from earths gravity. Using our brains we create, not from the substances of the earth but out of our inner selves. Being encased in the skull separates our brains even more from the external environment.

Using our hands we mould earthly substance, using our brains we mould thoughts.

Evolution is a creative process and it has turned creatures into creators.

216 thoughts on “Tetrapod Evolution and the Evolution of Consciousness

  1. John Harshman:
    Frankie,

    Do you know what any of that meant, and if so can you explain it? Certainly almost every developmental geneticist would disagree strongly with both those claims, assuming I know what they mean. Development is indeed a complex interaction among DNA, proteins, RNAs, a few other signaling molecules (e.g. cAMP), and environmental factors. But all except the last two arise from DNA and almost all of them arise from DNA during development, so DNA is central. And the differences between species are clear enough: they’re differences in DNA. Do you know of any evidence to refute any of my claims? No fair just saying that Denton must know, or so you assume.

    Yes, the differences between say two species of vole is due to differences in DNA. The differences between humans and chimps isn’t- or if it is no one has been able to make the connection.

    And yes DNA is central. It just isn’t the determining factor. Assembly lines are central but they do not determine what they are assembling.

    Do you realize that developmental biologists have switched DNA and either nothing fully develops or it resembles the egg donor.

  2. Frankie: Yes, the differences between say two species of vole is due to differences in DNA. The differences between humans and chimps isn’t- or if it is no one has been able to make the connection.

    Nonsense. There’s quite a literature on the connection.

    And yes DNA is central. It just isn’t the determining factor. Assembly lines are central but they do not determine what they are assembling.

    What is it with creationists and analogies? The point is that changes in development during evolution result from changes in DNA. That’s the only thing we have any evidence for. Everything else comes from changes in DNA.

    Do you realize that developmental biologists have switched DNA and either nothing fully develops or it resembles the egg donor.

    Can you cite some evidence that this is true?

  3. CharlieM: The sentience-to-sapience trajectory happens during the normal development of each human individual. Life has a fractal property, We see patterns within patterns.

    Yes, but that’s a teleological process of individual human maturation. The fact that individual human maturation is teleological doesn’t support your claim that the evolution of sentience and the evolution of sapience from sentience is also a teleological process.

    And as above, teleology is a feature of the natural world. Organs and structures are formed in the embryo and only later are put to their intended use.

    I don’t deny that teleology is a real feature of the natural world. My point is simply that the teleological structure of embryonic development doesn’t show us that evolution is also teleological. And it seems to me as if you want to claim that evolution is teleological, or at least that the evolution of consciousness is.

    I think that today we are in a good position to revisit the question of teleology as most thinking people already believe that the various examples of this limb are modifications of a general plan.

    But the adaptive radiation of tetrapod limbs into wings (three different kinds), fins, and flukes as well as arms and feet doesn’t seem like a teleological progression. It’s far too “bushy”.

    Comparison between species of the uses to which the tetrapod limb is put is very informative. From amphibians to humans we can see a progress from a very restricted use of this limb to the human. Amphibians use their limbs for locomotion, support and scratching at most, whereas we could go on and on listing its uses in humans. We see a movement from the particular to the general.

    But there you’re already focusing on that particular trajectory. Are human hands less restricted and more generic because we cannot burrow with them (as moles do), or swim with them as cetaceans do, or fly (as pterosaurs, bats, and birds do), or effortlessly brachiate as the apes do? It seems like there’s just as much loss of function as there is gain.

    “Space and time” are concepts arrived at through thinking no less than archetypes are.

    “Space” is a concept, but the structure of space — spatiality, if you like — is (arguably) non-conceptual. Likewise for temporality.

    If we are to have a consistent epistemology we need to begin at the right place. IMO we begin with the given and add to it our thinking. We never really experience the given because by the time it enters our consciousness it has already had our thinking applied to it. The given is a chaos of unconnected entities. By using our thinking we gradually connect these entities. There is only one given that, in its final form is no different to the form in which we first apprehend it, and that is thinking itself. It is not due to reality itself that the given is an unconnected chaos, it is due to the human makeup that it first appears that way to us. But through thinking we have been given the ability to reconnect the given to its real state which we had torn apart in the first place. By the use of thinking we are moving from the particulars to a unified whole. It is this whole which is the reality, not the particulars.

    I am not entirely opposed to this view.

    In my estimation the best articulation and defense of this view is C. I. Lewis’s Mind and the World Order (1929). Lewis argues that experience consists of two distinct elements, concepts and the given. All concepts, he argues, are guides to acting in some definite way. Different conceptual systems — including different logics — allow for different interpretations of the given. The given itself is the ‘bloom’, buzzin’ confusion’ of the consciousness of the infant — a completely unstructured, undifferentiated awareness. (It is not even awareness of anything, since to introduce the of-structure of intentionality is already to introduce concepts.)

    Perhaps the more advanced stages of meditation allow the adult to experience the given as such, though Lewis never makes that claim.

    The problem with the given is this: since we cannot conceptualize the given as such — since to apply concepts is to interpret it — the question arises as to how we know what the given is, or even how we know that there is any given at all. There’s also a question here of what exact role the given serves within our epistemology. Since it is wholly nonconceptual, it cannot play any justificatory role. Justification involves reasons, and it is hard to see how there could be reasons that lack all conceptual structure.

    In short, the given cannot play the role of a foundation for knowledge, or even meaning.

  4. John Harshman,

    The Evolutionary Landscape of Alternative Splicing in Vertebrate Species
    Nuno L. Barbosa-Morais1,2, Manuel Irimia1,*, Qun Pan1,*, Hui Y. Xiong3,*, Serge Gueroussov1,4,*,
    Leo J. Lee3, Valentina Slobodeniuc1, Claudia Kutter5, Stephen Watt5, Recep Çolak1,6, TaeHyung Kim1,7, Christine M. Misquitta-Ali1, Michael D. Wilson4,5,7, Philip M. Kim1,4,6, Duncan T. Odom5,8,
    Brendan J. Frey1,3, Benjamin J. Blencowe1,4,†
    Author Affiliations
    ↵†To whom correspondence should be addressed. E-mail: b.blencowe@utoronto.ca ↵* These authors contributed equally to this work.
    +
    
    ABSTRACT
    How species with similar repertoires of protein-coding genes differ so markedly at the phenotypic level is poorly understood. By comparing organ transcriptomes from vertebrate species spanning ~350 million years of evolution, we observed significant differences in alternative splicing complexity between vertebrate lineages, with the highest complexity in primates. Within 6 million years, the splicing profiles of physiologically equivalent organs diverged such that they are more strongly related to the identity of a species than they are to organ type. Most vertebrate species- specific splicing patterns are cis-directed. However, a subset of pronounced splicing changes are predicted to remodel protein interactions involving trans-acting regulators. These events likely further contributed to the diversification of splicing and other transcriptomic changes that underlie phenotypic differences among vertebrate species.

  5. John Harshman,

    Nonsense. There’s quite a literature on the connection.

    Nonsense as no one knows what makes a human a human nor a chimp a chimp.

    What is it with creationists and analogies?

    At least ID has them and you don’t

    The point is that changes in development during evolution result from changes in DNA. That’s the only thing we have any evidence for. Everything else comes from changes in DNA.

    There isn’t any evidence tat DNA determines the archetype. And obviously you cannot find any.

    Can you cite some evidence that this is true?

    When I have time to look it up, again. Or you could do your own research

  6. Kantian Naturalist,

    I don’t deny that teleology is a real feature of the natural world. My point is simply that the teleological structure of embryonic development doesn’t show us that evolution is also teleological. And it seems to me as if you want to claim that evolution is teleological, or at least that the evolution of consciousness is.

    First: I have very little education in philosophy so I have enjoyed reading your posts. The question I would propose to your above point is if there is teleological structure in embryonic development how would that teleology emerge from undirected processes?

  7. colewd:

    Thanks, but what was that intended to support? I see nothing in that abstract, even if we believe it reports a real phenomenon (which is not generally accepted), that’s relevant to anything I have said.

  8. Frankie:
    John Harshman,
    Nonsense as no one knows what makes a human a human nor a chimp a chimp.

    A link or three: http://www.nature.com/nature/journal/v443/n7108/abs/nature05113.html
    http://www.sciencedirect.com/science/article/pii/S0092867404011432
    http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.0030245

    The first two are papers specifically on the effects of particular genetic differences between the two species, and the last is a very nice review on how developmental differences in general evolve. True, we don’t know everything; but neither do we know nothing, as you claim.

    At least ID has them and you don’t

    This is only an advantage if pointless analogies are a good thing.

    There isn’t any evidence tat DNA determines the archetype. And obviously you cannot find any.

    I don’t think there’s any such thing as an archetype to determine. DNA determines the differences among species. This should be obvious, as it’s the only thing that’s stably inherited, a prerequisite for any such determination.

    When I have time to look it up, again. Or you could do your own research

    Not enough information to go on. I’ll wait here.

  9. John Harshman,

    Not one of those links says it knows what makes a human a human and a chimp a chimp. What’s wrong with you? And I never claimed that we know nothing. But it is true that we don’t know what makes a human a human or a chimp a chimp.

    The analogy provided wasn’t pointless. Just because you didn’t understand it doesn’t make it pointless.

    I don’t think there’s any such thing as an archetype to determine.

    That’s one way to ignore the problem.

    DNA determines the differences among species

    That is your opinion. But you cannot support it.

    This should be obvious, as it’s the only thing that’s stably inherited, a prerequisite for any such determination.

    Nonsense. There is plenty in the egg that is also stably inherited

  10. John Harshman,
    You said the differences in species was based on DNA. This shows difference based on splicing sequences and shows that splicing sequences are dramatically different in vertebrae. So the spliceosome and alternative splicing codes are added differentiation to the specie biochemistry beyond the DNA codes. There is another paper I can send you on DNA expression differences between vertebrae but it is pay walled. I will print the abstract below.

  11. John Harshman
    Evolutionary dynamics of coding and non-coding transcriptomes.

    Necsulea A1, Kaessmann H2.
    Author information

    Abstract

    Gene expression changes may underlie much of phenotypic evolution. The development of high-throughput RNA sequencing protocols has opened the door to unprecedented large-scale and cross-species transcriptome comparisons by allowing accurate and sensitive assessments of transcript sequences and expression levels. Here, we review the initial wave of the new generation of comparative transcriptomic studies in mammals and vertebrate outgroup species in the context of earlier work. Together with various large-scale genomic and epigenomic data, these studies have unveiled commonalities and differences in the dynamics of gene expression evolution for various types of coding and non-coding genes across mammalian lineages, organs, developmental stages, chromosomes and sexes. They have also provided intriguing new clues to the regulatory basis and phenotypic implications of evolutionary gene expression changes.

  12. colewd,

    Yes, that is their only hope but one they cannot test. Heck they can’t even account for gene expression and regulatory networks.

  13. Frankie,

    The reality here is the biochemistry differences, it you count splicing and gene expression are the very large. The evidence here shows the biggest evolutionary leap in splicing and gene expression among all the vertebrate is the change from chimps to humans. Also splicing and gene expression appear to be much more relevant to specie change then DNA.

  14. colewd:
    Frankie,

    The reality here is the biochemistry differences, it you count splicing and gene expression are the very large.The evidence here shows the biggest evolutionary leap in splicing and gene expression among all the vertebrate is the change from chimps to humans.Also splicing and gene expression appear to be much more relevant to specie change then DNA.

    Good stuff. Thank you. However I have heard the “it isn’t new genes it is the same genes used differently” shtick from reading Shubin’s “Your Inner Fish” and Carroll’s books “Making of the fittest” and “Endless forms…”. It hasn’t panned out but it is their last hope

  15. Frankie:
    John Harshman,
    Not one of those links says it knows what makes a human a human and a chimp a chimp.

    The links say some of what makes a human a human and a chimp a chimp.

    The analogy provided wasn’t pointless. Just because you didn’t understand it doesn’t make it pointless.

    So go on. How is DNA like an assembly line, other than being long and narrow?

    That’s one way to ignore the problem.

    What problem? And what do you think an archetype is?

    That is your opinion. But you cannot support it.

    I support it by pointing out that there is nothing else that can account for the differences. If you disagree, what else do you have in mind?

    Nonsense. There is plenty in the egg that is also stably inherited

    Name one. Everything except the genome is produced anew each generation (using instructions in the genome), not copied.

  16. colewd:
    John Harshman,
    You said thedifferences in species was based on DNA.This shows difference based on splicing sequences and shows that splicing sequences are dramatically different in vertebrae.So the spliceosome and alternative splicing codes are added differentiation to the specie biochemistry beyond the DNA codes.There is another paper I can send you on DNA expression differences between vertebrae but it is pay walled.I will print the abstract below.

    First off, the actual existence of these differences is dubious, except as errors in translation. Second, where there is known alternative splicing, its occurrence is controlled by proteins whose sequence and expression can be traced back to the genome. That is, differences in expression and splicing result from differences in DNA sequence somewhere in the genome (though not necessarily in the gene being expressed or spliced).

  17. colewd:
    Frankie,
    The evidence here shows the biggest evolutionary leap in splicing and gene expression among all the vertebrate is the change from chimps to humans.Also splicing and gene expression appear to be much more relevant to specie change then DNA.

    I don’t think you can support any of that, and I will remind you that differences in expression and splicing result from differences in genome sequences.

    Have you ever thought about how differences in splicing and expression are inherited?

  18. John Harshman,

    The links say some of what makes a human a human and a chimp a chimp.

    It just shows the differences

    Development is like an assembly line. The assembly line does not determine what will be manufactured.

    I support it by pointing out that there is nothing else that can account for the differences.

    And yet you have no idea if DNA can

    Name one

    microtubule arrays and membrane patterns. Then there are mitochondria and all of the other organelles

  19. John Harshman: I don’t think you can support any of that, and I will remind you that differences in expression and splicing result from differences in genome sequences.

    Have you ever thought about how differences in splicing and expression are inherited?

    Epigenetic factors change gene expression and splicing

  20. John Harshman,

    I don’t think you can support any of that, and I will remind you that differences in expression and splicing result from differences in genome sequences.

    Small molecules like vitamin d can control gene expression. Vitamin d is synthesized from the Sun and modified in the liver and kidney. The splicing codes are not well understood at this point.

  21. Frankie:
    John Harshman,
    It just shows the differences

    It shows differences in sequences that have known effects on development.

    Development is like an assembly line. The assembly line does not determine what will be manufactured.

    Development is very little like an assembly line. It’s a process that involves all sorts of interactions. But the point is that changes in the interactions result from changes in the genome.

    And yet you have no idea if DNA can

    Of course I do. Again, we know quite a lot about what some changes in sequence can do, just not everything.

    Cytoskeleton and membrane. Then there are mitochondria and all of the other organelles

    Nope, not inherited. The mitochondrial genome is inherited, but everything else is reconstructed each generation. The zygote begins with the egg’s cell membrane, but that cell membrane isn’t descended from the mother’s egg’s cell membrane, and differences among species in cell membranes are determined by differences in genomes. And so on.

    Frankie: Epigenetic factors change gene expression and splicing

    Indeed they do. And those epigenetic factors can be traced back to the genome.

  22. colewd:
    John Harshman,

    Small molecules like vitamin d can control gene expression.Vitamin d is synthesized from the Sun and modified in the liver and kidney.The splicing codes are not well understood at this point.

    But do changes in vitamin D cause differences in species? No. Vitamin D is synthesized by a metabolism that results from enzymes coded by the genome. Response to vitamin D depends on the genome. This is all confusion about different levels of causation. When we’re talking about differences among species you have to look at what causes those differences to be there.

  23. John Harshman,

    It shows differences in sequences that have known effects on development.

    I have already said they do.

    Of course I do

    No, you don’t. What changes to the chimp genome were responsible for our upright bipedal structure?

    Nope, not inherited.

    Nonsense. The egg’s microtubule array and membrane pattern is inherited. As are all of the organelles.

    The zygote begins with the egg’s cell membrane, but that cell membrane isn’t descended from the mother’s egg’s cell membrane,

    It is the mother’s egg cell membrane.

    and differences among species in cell membranes are determined by differences in genomes. And so on.

    Bacteria refute your claim. Did DNA produce the first membrane? How and when did it gain control over it?

    And those epigenetic factors can be traced back to the genome.

    Epigenetic factors are outside of the genome, by definition.

    Look John, I quoted a geneticist who actually did the work. He has this new book out that destroys your claims.

  24. John Harshman,

    No one knows what caused the differences between fish and amphibians, for example. You may think it is all DNA but you cannot test that claim. All you have is a desperate hope and you are clinging on to it as if your life depends on it.

  25. John Harshman:

    And those epigenetic factors can be traced back to the genome.

    Uknown claim at best, likely false at worst. As usual, a claim made in the absence of actual knowledge. We know very little of how biological systems work. It’s premature to be making such claims.

    The cytoplasm may contain a lot of heritable information that we are unaware of. Put human DNA in a bacterium, does the bacterium start becoming a human? No. That’s because the DNA doesn’t have all the information! Plain as day to see.

    DNA may give instructions how to make parts, but that’s not the same thing as instructions as how to put parts together.

    A cytoplasm loaded with mRNA can reproduce without DNA. Enucleated zygotes without DNA can multiply up to the blasula stage. In contrast, one can’t just have DNA without a cytpolasm and expect the DNA to duplicate. This tells me the cytoplasm has more priority in terms of critical information.

    Put a frog in a blender (OUCH). It will have lots of the proteins coded by DNA in the right proportion. Having expressed proteins from DNA in the right proportion does not an organism make!

    This diagram shows some of the epigenetic differences between vertebrates and invertebrates. We don’t know how epigenetic marks are managed:

    http://www.nature.com/nature/journal/v517/n7534/fig_tab/nature14192_F1.html

    The representative genomic region includes an example of an active and an inactive gene with proximal (promoter) and distal (enhancer) regulatory regions. The height of the bar indicates the relative proportion of DNA methylation (5-methylcytosine, 5mC) that is observed in each region. CpG islands (CGIs), which often overlap with promoter regions, generally remain unmethylated, whereas CG-poor promoters are methylated when not active.

  26. John Harshman: That implies that you have at least some of the answers. Can you in fact answer any of the questions I asked? Your pointless analogy suggests not. I will salvage the only bit that seem to be attempting, unsuccessfully, to explain something.

    What formative force? What, stripped of the silly analogy, is this “periphery”? You can’t imagine that you have achieved anything with that “reply”, can you?

    To give you some idea of what I mean by periphery and formative forces, here is a quote from “Space and Counterspace” by George Adams:

    Balanced between the non-Euclidian spaces there is, therefore, not only the Euclidian but its precise opposite-“a negative-Euclidian” type of space determined not by an infinite plane from without but by an infinite point from within. In its relation to ordinary space we may describe it as “counter-Euclidian” or more simply as “counter-space”. And as the former is related to the physical forces and substances-being their natural field of action and container-so is the latter to the etherial. I have therefore presupposed to call these types of space “physical” and “etherial space” respectively. The great difference is that while “physical space-in our universe at least-is single and permanent or of cosmic duration, “ethereal spaces” are legion; moreover they come into being and pass away with the birth and decay of living creatures.

    When people think of non-Euclidian spaces they generally have in mind a slight-though in quality essential-modification of the Euclidian. The absolute is then imagined as a very large and distant though not infinite surface, making but a slight difference to the practical relationships of measure. Moreover, the space thus determines is nearly always thought of in its pointwise aspect. But the “counter-space”, determined by a point functioning as infinitude within, is radically different from the Euclidean, for by its very nature it is predominantly planewise. To speak pictorially, it is to the physical space of Euclid as the mould is to the cast. In it there tend to arise what we, from our earthly-spacial point of view, should experience as hollow spaces. In more imaginative and realistic language we might even call them “holes-in-space”-a concept which comes near again to ancient eastern cosmological traditions.

    Once more the functional polarities of projective space are interlaced. The plane serves the point and the point the plane. Paradoxical though it may seem at first, it comes about that the space of Euclid-the space determined by an absolute, once-given plane-is predominately pointwise. And the reverse is also true: the negative-Euclidian type of space-determined by an absolute, once-given point-is predominantly planewise. Its planar forms-polyhedral or continuously plastic-tend to fold inward from the vast periphery, enveloping the infinite point within,just as the forms we build in earthly space reach out as they increase towards the infinite all-embracing plane. Such forms are clearly recognisable once the idea is awakened in the mind. We see them in the flowers, in the unfolding leaves, in many other forms of the living world. This other principle of construction-planewise instead of pointwise, from without inward instead of from without inward-this too, is inherent in the very nature of the spacial world, and living nature everywhere bears witness to its reality.

    As a formal possibility, mathematicians have of course from time to time conceived the other type of space which I have here called “negative-Euclidian”, but they did not take it seriously in relation to the real world; moreover, from a purely formal as distinct from an imaginative and realistic aspect it seemed to offer nothing new. It was, so to speak, the Euclidean game all over again, only with heads and tails interchanged. Yet I believe in this direction the all-important key is to be found, differentiating the living from the seemingly lifeless world. The unfruitful controversy between vague phylosophic vitalism and a strictly physical if not mechanistic outlook in biology will be transcended when the specific nature of the life-sustaining and morphogenetic forces is apprehended in a mathematically recognisable form. The following should therefore be examined, at least as a working hypothesis.

    My apologies for the length of it but I don’t feel I could have left any of that excerpt out. He goes on to explain his point in more detail.

    To give an example of the two ways of thinking about these spaces, a straight line can be thought of as an infinite number of points, but it can also be thought of as the intersection of an infinite number of planes.

  27. colewd: First: I have very little education in philosophy so I have enjoyed reading your posts. The question I would propose to your above point is if there is teleological structure in embryonic development how would that teleology emerge from undirected processes?

    Thank you!

    I do think that teleology is real, but I do not think of it as a kind of cause that is distinct from mechanistic causation. Rather, I think of teleology as a distinct kind of organization or structure, such that there can be true (or false) teleological explanations.

    A dynamical system is teleological if characterizing that system in terms of “goals” and “purposes” is an indispensable vocabulary for successfully explaining the behavior of that structure.

    The question then is, what kind of structure must a system have to be characterizable in that way?

    The answer there, I think, is that the structure must involve self-constraint: the dynamics of the system over time tends to generate the parameters of the system itself. This sustains a degree of organizational closure: the system can be understood as a sub-system that is relatively or partially decoupled from the larger systems in which it is embedded. (I say relatively or partially because the sub-system must still be thermodynamically open to the larger system.) The sub-system, in other words, behaves so as to continually generate the boundary conditions of its own relative decoupling from the system. A sub-system with that kind of structure is then usefully characterized in terms of goals.

    On this approach, the sub-system here is any organism and the systems in which it is embedded is the environment of that organism.

    The question of abiogenesis is the question of how subsystems can emerge which display both organizational closure and thermodynamic openness with the systems in which they are embedded. This is an interesting question but I do not think it conceptually intractable. All that is required, at an absolute bare minimum, is an autocatalytic network of molecules (to continually generate the parameters of the system) and a semipermeable membrane (to sustain both organizational closure and thermodynamic openness).

    As I see it, to say that abiogenesis cannot be naturalistically explained is to say one of the following:

    (1) Naturalistic explanations cannot account for how an autocatalytic network emerged and/or became enclosed in a semipermeable membrane;

    (2) An autocatalytic network enclosed in a semipermeable membrane may be necessary for life (i.e. teleological unities) but it is not sufficient.

    I think that (1) and (2) are difficult (if not impossible) claims to sustain.

  28. Kantian Naturalist

    On this approach, the sub-system here is any organism and the systems in which it is embedded is the environment of that organism.

    I understand from this analysis of teleology that you are considering subsystems from a philosophical viewpoint, rather than a scientific one.

    A question that interests me is whether and how this subsystem understanding can be applied to other topics in the the philosophical discussion of mind.

    In particular:
    – if meaning is individuated externally, how can we understand the interaction of mental causation and meaning?
    – are qualia best understood as part of a subsystem which is causally realized solely in the body?
    – how rich are internal mental representations; how much of the subsystem which supports them can be separated from the world?
    – are philosophical understandings of perception amenable to a subsystem analysis?

    There is a philosophy of mind called “long-arm functionalism” (see last paragraph of this section ) which Putnam ended up with, I believe. I think the above issues could all be subsumed in a question of whether the causal network underlying that functionalism can be useful split up into interacting subsystems.

    A couple of links that may interest you:
    A conference on Mechanistic Integration and the Unity of Science. What caught my eye was this sentence in the conference description:

    “There is a growing consensus that cognitive science and cognitive neuroscience explain their phenomena of interest mechanistically”.

    I have no idea if that is true. How does one measure a growing consensus? Anyway, if you are planning to be in Warsaw in June, you might want to check it out.

    Brains blog is hosting Jaworski to discuss his book on How Hylomorphism Solves the Mind-Body Problem in May. I recall Hylomorphism interested you at one point. I think it may even be on topic for some of the discussion about teleological causation in this thread.

  29. CharlieM,

    Charlie, once again you present a useless analogy that has nothing to do with biology. This is not helping. Please just start answering some of the questions I have actually asked. I already know the difference between peripheries and centers as abstract concepts. What I don’t know is what you think those correspond to in biology.

  30. stcordova,

    Sal, we may not know exactly how epigenetic marks are managed, but we do know that the only thing stably inherited over many generations is the genome. Everything else is made anew rather than copied. Epigenetic inheritance decays over at most a few generations. This cannot account for the differences between species, including the differences in epigenetic marking.

    Of course the genome doesn’t do everything on its own. It needs a working metabolism of the proper sort surrounding it. But that’s irrelevant to my point. That working metabolism is inherited over the short term, but over the long term its nature is determined by the genome contained within it. Nothing else is stable.

  31. John Harshman:
    What is this archetype? Is there more than one? If so, how many, what are they, and how do you know that? How is the archetype accessed by organisms? What causes them to express it? Are they approaching closer to it? And what does “archetype” have to do with your notions of progress in evolution?

    The archetype should not be thought of as anything existing in space and time as we experience it, but it works into space and time, The life of each individual organism can be thought of as the archetype concenrated in space and made manifest. Asking how it is accessed is to misunderstand what it is. Organisms don’t access it, they (organisms) are that facet of it available to our perception. Turn a cube in a certain way and it will appear to be a two dimensional hexagon. We don’t ask, “how is the cube accessed by the hexagon?” The hexagon is the cube, but a being which peceives in just two dimensions will not experience the higher dimensional quality of the cube, they will only see the hexagon.

  32. CharlieM: The archetype should not be thought of as anything existing in space and time as we experience it, . . .

    That sounds very like the definition of non-existence.

    but it works into space and time

    How, exactly? And how do you know this? What evidence supports your claim?

    I’ve been reading through the comments on this thread and I see nothing more than baseless assertions about this vaguely described “archetype”. Let’s see the hard evidence for it.

  33. CharlieM: The archetype should not be thought of as anything existing in space and time as we experience it, but it works into space and time, The life of each individual organism can be thought of as the archetype concenrated in space and made manifest. Asking how it is accessed is to misunderstand what it is. Organisms don’t access it, they (organisms) are that facet of it available to our perception. Turn a cube in a certain way and it will appear to be a two dimensional hexagon. We don’t ask, “how is the cube accessed by the hexagon?” The hexagon is the cube, but a being which peceives in just two dimensions will not experience the higher dimensional quality of the cube, they will only see the hexagon.

    I ask again, what is this archetype? Etcetera. You respond with what it isn’t and a lame analogy, neither of which answers any of the questions I asked. If “access” is the wrong word, then how does an organism express the archetype? What archetype does it express, assuming there’s more than one, which you have never answered? In what way is an organism a facet; in other words, what in your analogy corresponds to anything in biology and how does that work? Please don’t explain your analogy by posting another analogy.

  34. John Harshman,

    From what I can find out archetype has always pertained to body plans. And the different archetypes are depicted by Linnaean classification. For example there is a basic animal archetype. And each Phyla represents another basic archetype that also includes the animal archetype. And so on down to Genus, with species being a variation on that. However some say it stops at the family level.

  35. Frankie:
    John Harshman,

    From what I can find out archetype has always pertained to body plans. And the different archetypes are depicted by Linnaean classification. For example there is a basic animal archetype. And each Phyla represents another basic archetype that also includes the animal archetype. And so on down to Genus, with species being a variation on that. However some say it stops at the family level.

    So there are archetypes within archetypes, and all “archetype” means is “what the organism looks like”. If some say it goes to genus level and others only to family, how would either side justify their claim?

  36. John Harshman: So there are archetypes within archetypes, and all “archetype” means is “what the organism looks like”. If some say it goes to genus level and others only to family, how would either side justify their claim?

    Science presses on, John. Just because all of the answers are not at hand now doesn’t mean that will never be. The Creationist has to find out what the originally Created kinds were and you and yours have more difficulty with the alleged common ancestors, LUCA and before. Do you guys have all of your leaves, branches and trunks thoroughly filled in?

    I was just telling you what I found out by searching and asking. Creationist orgs are helpful if you are friendly.

  37. Frankie: Science presses on, John. Just because all of the answers are not at hand now doesn’t mean that will never be. The Creationist has to find out what the originally Created kinds were and you and yours have more difficulty with the alleged common ancestors, LUCA and before. Do you guys have all of your leaves, branches and trunks thoroughly filled in?

    I was just telling you what I found out by searching and asking. Creationist orgs are helpful if you are friendly.

    You have found nothing by searching and asking, apparently, other than contradictions with no means of choosing among them. Contrast creationism with mainstream biology: creationists have no means of discovering created kinds (and I see you have abandoned the fig leaf of “archetype”), while biologists have good methods for discovering the tree of life. (I’ve made a considerable study of baraminology, certainly much more than you have, and it’s clear to me that there is no there there.)

    Yes, we do know most of the leaves, branches, and trunks. You make a big deal about the fact that we don’t know quite all of them and ignore the majority. The parts we do know transgress across anyone’s idea of “kind”, which is inconvenient for you. And of course no creationist has been able to delimit “kinds” at all, except that you all know humans are a separate kind. What a pity that the primates are a part of the tree that’s especially well “filled in”.

  38. Frankie: The Creationist has to find out what the originally Created kinds were

    What do you mean “find out”? You already know, it’s in the Bible?

    Are you a creationist Frankie?

  39. John Harshman,

    You have found nothing by searching and asking, apparently, other than contradictions with no means of choosing among them.

    What contradictions? And who says there isn’t any way to choose?

    Contrast creationism with mainstream biology: creationists have no means of discovering created kinds (and I see you have abandoned the fig leaf of “archetype”)

    The created kind is the archetype- well the final form given all of the higher levels

    while biologists have good methods for discovering the tree of life.

    Opinion is neither evidence nor an argument

    Yes, we do know most of the leaves, branches, and trunks.

    Yet you don’t have a testable mechanism and your “knowledge” is merely opinion based on the assumption there is a tree. It is all question-begging

    What a pity that the primates are a part of the tree that’s especially well “filled in”.

    What a pity that you don’t have a mechanism capable of producing primates

  40. Frankie,

    Might I suggest that you know absolutely nothing about phylogenetics and little more about baraminology?

    Anyway, the particular contradiction that I’m talking about right at the moment is that some say the created kind is the genus, others the family. Would you agree that was a contradiction? As for there being no way to choose, you can show me wrong by telling me how one would go about deciding. How do you determine what species belong to the same kind or different kinds? (I ask this in the full knowledge that you have no idea and will evade the question.)

  41. John Harshman,

    Might I suggest that you know absolutely nothing about phylogenetics and little more about baraminology?

    Laughable

    Anyway, the particular contradiction that I’m talking about right at the moment is that some say the created kind is the genus, others the family.

    1- It all depends on which Genera and Families

    2- It is just a matter of degree

    As for there being no way to choose, you can show me wrong by telling me how one would go about deciding.

    Probably very similar to the way you decide, John. Creating clades and finding the CK seem to be very, very similar. But anyway and AGAIN, science marches on. No one has all of the answers at this time. The same goes for you

  42. Frankie:
    Probably very similar to the way you decide, John. Creating clades and finding the CK seem to be very, very similar. But anyway and AGAIN, science marches on. No one has all of the answers at this time. The same goes for you

    And so you show the truth of two of my assertions simultaneously. 1) “Might I suggest that you know absolutely nothing about phylogenetics and little more about baraminology?” and 2) “I ask this in the full knowledge that you have no idea and will evade the question.”

  43. John Harshman: And so you show the truth of two of my assertions simultaneously. 1) “Might I suggest that you know absolutely nothing about phylogenetics and little more about baraminology?” and 2) “I ask this in the full knowledge that you have no idea and will evade the question.”

    like shooting fish in a barrel

  44. John Harshman: And so you show the truth of two of my assertions simultaneously. 1) “Might I suggest that you know absolutely nothing about phylogenetics and little more about baraminology?” and 2) “I ask this in the full knowledge that you have no idea and will evade the question.”

    And thank you for proving that all you can do is BS your way through a discussion. So sorry that I gave you an honest answer and it is very telling that you couldn’t grasp it.

    And unfortunately you still don’t have a mechanism capable of producing a tree of life starting from some much simpler biological replicator

  45. John Harshman,

    Seeing that you failed to grasp the implications the first time:

    “One would expect a priori that such a complete change of the philosophical bias of classification would result in a radical change of classification, but this was by no means the case. There was hardly and change in method before and after Darwin, except that “archetype” was replaced by the common ancestor.”– Ernst Mayr

    G. Simpson echoed those comments:

    “From their classifications alone, it is practically impossible to tell whether zoologists of the middle decades of the nineteenth century were evolutionists or not. The common ancestor was at first, and in most cases, just as hypothetical as the archetype, and the methods of inference were much the same for both, so that classification continued to develop with no immediate evidence of the revolution in principles….the hierarchy looked the same as before even if it meant something totally different.”

    “Hardly any change in method” pretty much supports my answer, John

  46. Frankie:
    John Harshman,
    “Hardly any change in method” pretty much supports my answer, John

    You have two major problems in that assertion. First, pre-evolutionary classifications are not attempts to discern “kinds”, which is what we’re supposedly talking about. The fact that groups are nested within groups should have given you a clue to that. “Kinds” by definition are not nested within other “kinds”. Second, methods in systematics have changed radically since the period Mayr and Simpson are talking about there. Quote-mining will not help you.

  47. newton: like shooting fish in a barrel

    Except that the fish refuses to admit it’s been shot. More like fighting the Black Knight, really.

  48. BruceS,

    I like the connections you’re drawing between my attempt to think about the organism/environment relation as a subsystem/system distinction.

    I suppose I think that everything is a subsystem of the total system, the Cosmos (Deus sive Natura). But more Deleuze than Whitehead. I prefer nested subsystems as a metaphor for understanding the relation of the quantum to the cosmic. But we lack a comprehensive fundamental physical theory, so my Deleuzean process ontology must remain a bit of speculative metascience (for the time being. I live in hope).

    One nice objection that Wheeler raises against radical, anti-representationalist enactivism is that if the cognitive system is not functionally decomposable into components, the cognitive system would be too closely coupled to its environment to respond adaptively and creatively. I would even go a bit further and say that it is not clear how, under enactivism, a cognitive system could solve problems. Problem-solving seems to require representations.

    Unfortunately, I don’t plan to be in Warsaw in June. I plan to be in my cabin in the mountains, unless I’m invited to a conference.

    I did find hylomorphism intriguing, at least descriptively or phenomenologically. There seems to be something very helpful about the form/matter distinction. (It just now occurs to me that Ryle is probably much closer to hylomorphism than he is behaviorism.) But I don’t think that forms are fundamentally real — rather, I am of the intuition that the form/matter relation emerges from a local configuration of forces.

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