[Fis] Fwd: Contingency biological signals: Sex and Being

[JOHN TORDAY]

Dear Eric and 'All', it appears to be a 'fool's task' to debate the merits
of the role of the force of gravity in the evolution of vertebrates, given
that I have not only provided empiric evidence for it, as have others, but
have described the process in an earlier email.....John


On Wed, Dec 3, 2025 at 3:38 AM Dr. Eric Werner <evwerner at gmail.com> wrote:

> Dear Pedro, John and FIS Collegues,
>
> Fascinating points you make, Pedro.
>
> The paper by Zhizhou Zhang https://urldefense.com/v3/__https://doi.org/10.20935/AcadMolBioGen8001__;!!D9dNQwwGXtA!QKC4o_HUjQweUU_kfKB1a4NDxeK6yDwgARGIdGDS2oj73mGI5EFc5sB1Zm_Dg-1ZVmQfIlNBHFF0zme_dcQ$ 
> <https://urldefense.com/v3/__https://doi.org/10.20935/AcadMolBioGen8001__;!!D9dNQwwGXtA!UusxFDTBk3ZUgkvJ1A6efTRkbVH1ghY7Hqm_3tckntBOt0NwXJpwRR3yOZ0vQsEj9vRbkhxP9L0TnovknBDPEK5Ao7cg$> is
> provocative indeed.  The gene centric focus of the paper is foundational
> for its provocative hypothesis that we humans are mentally closer to fish
> than chimps.  While it may be genetically valid, it ignores the other 95%
> of the genome that is not genetic, and instead noncoding the so called dark
> matter of the genome.
>
> The noncoding genome is what I have argued contains the CONTROLNOME of the
> genome that actually controls and development of the morphology, the form
> and functional architecture of the multicellular species in question.   The
> complexity of form of the organism cannot be in the genes because the genes
> are shared by organisms that have overt highly complex different forms.
>  (And gravity cannot account for the difference, John, because it is
> obviously shared by all life forms on our dear planet.)
>
> The difference between the gene-coding genome and the controlnome, has
> parallels between the difference between semantics and pragmatics, between
> sentences that are true or false and those that are neither, like questions
> and commands. This parallel relationship between genome semantics and
> pragmatics and human language as well as other animal communications system
> semantics and pragmatics is no artificial construct but results from
> fundamental principles of how information works in living systems.
>
> The attempts to reduce the complexity of multicellular development to
> point mutations in shared genes, or to gravity, or to cell signaling or
> other physiological feedback mechanisms all fail the Complexity
> Conservation Principle (see my Ants paper and How central is the genome
> paper).  And then there is meta-sex complexity of meta-genome interactions
> (see my gynandromorphs paper).
>
> Best regards,
>
> Eric
>
>
>
> Sent from my iPad
>
> On Dec 2, 2025, at 8:19 PM, Pedro C. Marijuán <pedroc.marijuan at gmail.com>
> wrote:
>
> 
>
> Dear John and FIS Colleagues,
>
> Thanks for the well crafted, dense bio paragraphs. Although I agree with
> most of the comments --not with all-- the main problem I see that it is a
> really too condensed a summary. It reminds me the great little book by
> French biologist  Max Pavans de Ceccatty "La vie: de la cellule à l'homme"
> (1962), put in just half page. Given the brevity needed, I will just point
> to three extra themes that for my taste are relevant: signaling and the
> life cycle, role of the "virome" in eukaryotic complexity and multicellular
> life, and the tangled threads of Anthropogenesis.
>
> The former one, signaling and the life cycle, represents "the path not
> taken" about the deep meaning of cellular signaling. From the beginning it
> was conceived within the input-processing-output paradigm of
> techno-computer and artificial systems. It did not help the concept of
> signaling as "structural coupling" with the milieu, from the thought of
> Maturana and Varela. In any event, the information flow (signaling)
> necessary interrelationship with the energy flow (metabolism) has not been
> properly integrated with the great sink and source for both flows: the life
> cycle.  Perhaps making the cycle "modular", and susceptible to be
> maintained conveniently "frozen" along its different phases, represented
> the basis of cell differentiation & specialized tissues via signaling
> codes... Further, any complex form of life has had to maintain the same
> openness to the info flows of its niche in order to propel the advancement
> of its own life cycle. And let me stop here.
>
> About the virome, following Villareal, Witzany, and many others, the motto
> "Ex virus omnia" means that a new, forgotten realm of life has to be added
> to Margulis’ endosymbiotic theory (Margulis, 1981, 1970), so incorporating
> viruses’ essential evolutionary role within the present discussions around
> the renewal or replacement of evolutionary theory (Noble, 2016). In fact,
> one the most important genome modifications of eukaryotes has come from the
> systematic activity of components of viral provenance: mobile elements,
> transposons, retrotransposons, repetitive elements and so on. Seemingly
> (Shapiro) our species has counted with around 4 million mobile insertion
> events. As a result, ancestral viral proteins can be found in signaling
> pathways of all kind, and all across the mammalian and human proteomes.
>
> And finally about Anthropogenesis, let me copy from a recent study: "By
> employing 471 whole-genome sequence samples, including archaic humans
> (Neanderthals, Denisovans and more), modern humans, other vertebrates
> (fish, amphibians, reptiles, birds, rodents, mammals) plus four coelacanth
> and three lungfish samples, together with 18 human cognition-related genes
> and their total of 223 SNVs (Single-Nucleotide Variations),comparative
> analyses revealed that the CGPPs (cognition gene polymorphism patterns) of
> both coelacanths and lungfish are evolutionarily closer to those of archaic
> humans than those of most other animal groups. The CGPP appears to occupy
> an evolutionary inflection point, bridging diverse animal lineages to
> archaic hominoids. Our observational results suggest a hypothesis (to be
> validated in the future) that *the genetic architecture underlying human
> cognition seems to have been established during the evolutionary stage of
> fish, predating the emergence of tetrapods*..." Amazing!! (From Zhizhou
> Zhang et al., 2025, https://urldefense.com/v3/__https://doi.org/10.20935/AcadMolBioGen8001__;!!D9dNQwwGXtA!QKC4o_HUjQweUU_kfKB1a4NDxeK6yDwgARGIdGDS2oj73mGI5EFc5sB1Zm_Dg-1ZVmQfIlNBHFF0zme_dcQ$ 
> <https://urldefense.com/v3/__https://doi.org/10.20935/AcadMolBioGen8001__;!!D9dNQwwGXtA!UusxFDTBk3ZUgkvJ1A6efTRkbVH1ghY7Hqm_3tckntBOt0NwXJpwRR3yOZ0vQsEj9vRbkhxP9L0TnovknBDPEK5Ao7cg$>).
> By the way, there is a special issue on Anthropogenesis to appear soon in
> BioSystems, where brain evolution, sexual selection, social niche,
> emergence of language, cognition, etc. are updated and discussed (editors
> Marijuan, Igamberdiev, Iurato, 2025)--great job by Andrei. We will send
> soon the link.
>
> Best regards,
>
> --Pedro
>
>
>
> El 23/11/2025 a las 18:20, JOHN TORDAY escribió:
>
> Dear Eric, I am afraid you have misunderstood my allusion to the role
> gravity plays in evolution, in my opinion, based totally on experimental
> evidence. It becomes most apparent and relevant in the vertebrate
> transition from water to land, when fish adapted to land (a known fact).
> During that transition there were three hormone receptors that duplicated-
> the Parathyroid Hormone Receptor (PTHrP), the Glucocorticoid Receptor (GR)
> and the beta-adrenergic receptor (beta-AR). Which came first is the
> question I have pondered for many years, only recently coming to the
> realization that it must have been the PTHrP receptor that duplicated
> first, given that it determines bone 'stiffness', and the skeleton would
> have been under stress due to the effective force of gravity on land versus
> in water. Those members of the species that were able to 'up-regulate'
> their PTHrP receptor most readily for bone would have done so successively
> in the swim bladder to drive its evolution in becoming the lung, as
> evidenced by the fact that in the absence of PTHrP the lung does not
> alveolarize (Rubin et al, 2004), followed by the role of PTHrP in forming
> kidney glomeruli from the fish kidney glomus, and the augmentation of the
> stress signal from pituitary to adrenal cortex to produce adrenaline and
> cortisol. We know that there must have been such a scenario since fish
> attempted to breech land on at least 5 separate occasions (see Clack, J.A.,
> Gaining Ground, 2012). The relevance of these physiologic adaptations can
> be seen in astronauts who experience osteoporosis due to PTHrP deficiency
> (see Torday, 2003 for evidence of such) as well as kidney complications due
> to down-regulation of PTHrP control of salt and water balance. So in the
> aggregate, in reply to your comment that "gravity would not directly
> control the growth of a bilateral gynandromorph that is half female and
> half male down the middle", I would beg to differ based on the hormonal
> adaptations for land life, which are fundamental to land vertebrate
> physiologic adaptations for skeletal integrity, breathing, salt and water
> balance, if you get my point. And all of these physiologic traits are
> essential for the bipedalism that freed our forelimbs for tool-making,
> including speaking, and locomotion, all of which are under the control of
> the FoxP2 gene and are 'housed' within the Area of Broca (see Torday JS.
> A central theory of biology. Med Hypotheses. 2015 Jul;85(1):49-57). It is
> this transition from crawling on all fours to standing on two legs due to
> the advent of endothermy that marks the evolution of our over-seized
> central nervous system....and as a consequence, at some point in human
> evolution our heads became too large to fit in the birth canal so we are
> born prematurely, with only 25% of brain capacity, requiring decades of
> nurturing by family and society in order to effectively mature as a
> species, if ever (I note my current President).
>
> As for your glib comment about "The issue is more understanding the
> information that makes a difference (Oh dear I have slipped into Spencer
> Brown"......In this regard, I think you misunderstand Spencer-Brown too in
> that what he was telling us is that we are fractals of a 'holism' as the
> unmarked space.
>
> And as for your flippant comment about "gravity does not make the
> difference between a whale and a dog" I again beg your pardon, but gravity
> is exactly what makes the difference between a whale and a dog, referring
> again to gravity's effects on the physiologic traits of each on land (dog)
> and in water (whale) given that seals are thought to have evolved back to
> water from dogs......
>
> But you may take exception to what I am saying, so have at it. I am of the
> opinion that the way I have traced evolution from cell to our 'selves'
> accounts for the evolution of consciousness from the former to the latter
> as I have expressed in numerous peer-reviewed articles, and 14 monographs.
>
> Best, John
>
>
>
> On Sun, Nov 23, 2025 at 11:11 AM OARF <eric.werner at oarf.org> wrote:
>
>> Dear john,
>> There is a difference between necessary conditions that are just that and
>> offer no information that controls the growth of detailed structure in
>> multicellular organisms that differentiates one from another and conditions
>> like gravity that apply to all such developmental processes. Thus, for
>> example, gravity would not directly control the growth of a bilateral
>> gynandromorph that is half female and half male down the middle. See:
>> https://urldefense.com/v3/__https://arxiv.org/abs/1212.5439__;!!D9dNQwwGXtA!QKC4o_HUjQweUU_kfKB1a4NDxeK6yDwgARGIdGDS2oj73mGI5EFc5sB1Zm_Dg-1ZVmQfIlNBHFF0rLhA3mA$ 
>> <https://urldefense.com/v3/__https://arxiv.org/abs/1212.5439__;!!D9dNQwwGXtA!UusxFDTBk3ZUgkvJ1A6efTRkbVH1ghY7Hqm_3tckntBOt0NwXJpwRR3yOZ0vQsEj9vRbkhxP9L0TnovknBDPEDwcoYq4$> for
>> more details.
>>
>> But I  agree that gravity and oxygen certainly have their effects on
>> development.
>>
>> The issue is more understanding the information that makes a difference
>> (Oh dear I have slipped into Spencer Brown ;-) ).
>> and gravity does not make the difference between a whale and a dog.
>>
>> Best,
>> Eric
>>
>> Sent from my iPad
>>
>> On Nov 23, 2025, at 3:05 PM, JOHN TORDAY <jtorday at ucla.edu> wrote:
>>
>> 
>> To Eric, Gordana, Howard, regarding the role of sex in evolution, I would
>> like to point out that the role of gravity in evolution also entails sex in
>> the following way. In the study of the effect of microgravity on yeast, the
>> simplest eukaryote, they cannot 'bud' as form of asexual reproduction in
>> microgravitational conditions (Purevdorj-Gage B, Sheehan KB, Hyman LE.
>> Effects of low-shear modeled microgravity on cell function, gene
>> expression, and phenotype in Saccharomyces cerevisiae. Appl Environ
>> Microbiol. 2006 Jul;72(7):4569-75). I am of the opinion that it is only in
>> addressing the evolutionary ontology as it corresponds with the
>> epistemology that an adaptive trait can be understood, as in the case of
>> sex as a means of adapting to an ever-changing environment. In the case of
>> yeast, budding is a means of epigenetic inheritance of environmental
>> factors relevant to its adaptation, and the force of gravity affects that
>> process. These authors also observed that the yeast could not conduct a
>> calcium flux under microgravity, rendering them unconscious 'zombies'. I
>> share this information with you in an attempt to find a final common
>> pathway for the process of evolution, ultimately referring to the elements
>> in the Cosmos as the latter's 'logic', as I expressed it in an accompanying
>> email earlier today....Best, John
>>
>>
>> On Sun, Nov 23, 2025 at 8:13 AM OARF <eric.werner at oarf.org> wrote:
>>
>>> Hi Gordana,
>>>
>>> I was just responding to Howard’s more general point beyond bacteria.
>>> Eukaryotes have sex an inherently social process.  Sexuality is
>>> fundamentally a cooperative process, at many levels of organization. Even
>>> social at the level of the genome:  See my theory of meta-genome
>>> interactions between the sexes.  It is particularly clear in the case
>>> physically mixed sex organisms (this can be neurological as well).  See the
>>> theory applied to mixed sex organisms or gynandropmorphs:
>>> https://urldefense.com/v3/__https://arxiv.org/abs/1212.5439__;!!D9dNQwwGXtA!QKC4o_HUjQweUU_kfKB1a4NDxeK6yDwgARGIdGDS2oj73mGI5EFc5sB1Zm_Dg-1ZVmQfIlNBHFF0rLhA3mA$ 
>>> <https://urldefense.com/v3/__https://arxiv.org/abs/1212.5439__;!!D9dNQwwGXtA!XLF-Q-SqJ-AuvQ-dic9ptw82Ooe57dI4UX6ePa7CTWADakJMPTruAnfSd0yTCHhsfb-S3Rv04mCA4h3ClsatzQ4$>
>>>
>>> So the sexuality of being is inherently social.
>>>
>>> -Eric
>>>
>>> https://urldefense.com/v3/__https://www.ericwerner.com/__;!!D9dNQwwGXtA!QKC4o_HUjQweUU_kfKB1a4NDxeK6yDwgARGIdGDS2oj73mGI5EFc5sB1Zm_Dg-1ZVmQfIlNBHFF0_O5qpQg$ 
>>> <https://urldefense.com/v3/__https://www.ericwerner.com/__;!!D9dNQwwGXtA!XLF-Q-SqJ-AuvQ-dic9ptw82Ooe57dI4UX6ePa7CTWADakJMPTruAnfSd0yTCHhsfb-S3Rv04mCA4h3CaUt82MM$>
>>>
>>> Sent from my iPad
>>>
>>>
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>>
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