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

Sat Dec 6 14:50:57 CET 2025

Dear Pedro and FIS, one more thought to add to the conversation..... with
regard to 'unity'/'holism' is that helium, element #2 formed from hydrogen,
element #1 through the process of 'nuclear fusion', producing enormous
amounts of energy. Given that, and the process of Stellar Nucleosynthesis
for star formation as hydrogen + helium, it is interesting (to me at least)
that *that process represents self + non-self as a distinction*. Do you
think there is merit in further considering the merits of that
interrelationship more deeply in the context of 'hidden diagonals'? Like
what I am expressing in this poem? John

*Hidden in Plain Sight*

They were there all along, the colors of the rainbow,

split by a prism into ROYGBIV, like magic, yet not.

We know that they are there, but need assistance to

‘see’ them, their angles of dispersion determining them.

The same goes for the set of Real Numbers, but now it’s

our consciousness realizing that if we diagonalize them

like Cantor did, we will witness the full complement of

 Real Numbers, which were ‘hiding’ in plain sight, like love.

The same holds true for the Periodic Table of Elements,

which when diagonalized reveals the full panoply of valences,

perhaps because the ‘Table’ is composed of horizontal and vertical

features, cartesian coordinates that expose the Elements juridical.

And then there’s “Ontogeny Recapitulates Phylogeny”, the Biologic

Law describing how and why species have evolved due to the logic

of the elements, their ‘logic’ being assimilated by living organisms,

lighter within cells, heavier in the matrix around them, resolving schisms.

So in the end, as in the beginning, it’s all one of a piece, a holism that

gives us all a sense of the “ONE”, fractals resonating together in a giant
vat,

emanating from a common source, an energy field that informs how and why

we exist, if only we would pay attention to the forces that have made us
ally.

On Thu, Dec 4, 2025 at 1:51 PM Pedro C. Marijuán <pedroc.marijuan at gmail.com>
wrote:

> Dear FIS Colleagues,
>
> Except some over-generalizations, I basically agree with John's. Gravity
> is not just a force out there, it is the fundamental fabric of the cosmos
> we live in. In our planet, all realms of life feel it and "live" it.
> Bacteria, zooplankton, phytoplankton, invertebrates, vertebrates, plants...
> It is another "water" of life-- remember "Water is life's matter and
> matrix, mother and medium. There is no life without water" by Albert
> Szent-Gyorgyi, the Nobel Prize-winning biochemist. So, gravity is not
> only within the adaptive physiology of vertebrates so well described by
> John, it is in an infinity of details in every realm of nature.
> Emphasizing the impact of this crucial field on life is really needed given
> its general neglect. Incidentally, the ongoing discussion on 31/ATLAS by
> our former FIS colleague Sungchul Ji about the radiation of this amazing
> interstellar object (a hydrogen basic frequency emitted in Fibonacci
> sequences), is a good reminder of the all-permeating cosmic fabric of
> gravity. See:
> https://urldefense.com/v3/__https://sayerji.substack.com/p/when-the-cosmos-speaks-in-fibonacci__;!!D9dNQwwGXtA!XKCI1YliRDKQLHtPL1njJxMgML-vkrasfSNMiPeGq7Ing2il00lcrgTMMhPOiQxDFNFHCYzMdO8Pe_6OBCI$ 
>
> About more mundane matters, what Eric writes on the CONTROLNOME, rather
> imaginative but a little bit outreached (perhaps one could share it
> partially), would send all the people working on paleogenomics and related
> disciplines to retirement. It is a pity because the ongoing results are
> throwing fascinating new aspects on our own evolution (self-domestication,
> sexual intercourse, language, etc.) Again I invite fis parties to that
> BioSystems issue ready to appear. Taking that view in its face value, an
> armchair experiment: if we take a vertebrate genome and substitute ALL of
> its genes, each by one, by genes of a completely different species--eg,
> human ovum changed to mouse genes and stimulate its development --  what
> would happen? There are too many details to consider, but nothing viable as
> an outcome, even the first division, I bet.
>
> I think we are not trying to "reduce" living complexity to this or to
> that, as Eric says, but emphasizing aspects not well covered in mainstream
> science, particularly on information matters. I was tempted to insist in
> the centrality of the life cycle regarding the information flow, but it
> would be too much.
>
> Regards,
> --Pedro
>
> El 03/12/2025 a las 14:54, JOHN TORDAY escribió:
>
>
> 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!XKCI1YliRDKQLHtPL1njJxMgML-vkrasfSNMiPeGq7Ing2il00lcrgTMMhPOiQxDFNFHCYzMdO8PggzfaWY$ 
>> <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!XKCI1YliRDKQLHtPL1njJxMgML-vkrasfSNMiPeGq7Ing2il00lcrgTMMhPOiQxDFNFHCYzMdO8PggzfaWY$ 
>> <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!XKCI1YliRDKQLHtPL1njJxMgML-vkrasfSNMiPeGq7Ing2il00lcrgTMMhPOiQxDFNFHCYzMdO8PAMNWsWo$ 
>>> <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!XKCI1YliRDKQLHtPL1njJxMgML-vkrasfSNMiPeGq7Ing2il00lcrgTMMhPOiQxDFNFHCYzMdO8PAMNWsWo$ 
>>>> <https://urldefense.com/v3/__https://arxiv.org/abs/1212.5439__;!!D9dNQwwGXtA!XLF-Q-SqJ-AuvQ-dic9ptw82Ooe57dI4UX6ePa7CTWADakJMPTruAnfSd0yTCHhsfb-S3Rv04mCA4h3ClsatzQ4$>
>>>>
>>>> So the sexuality of being is inherently social.
>>>>
>>>> -Eric
>>>>
>>>> https://urldefense.com/v3/__https://www.ericwerner.com/__;!!D9dNQwwGXtA!XKCI1YliRDKQLHtPL1njJxMgML-vkrasfSNMiPeGq7Ing2il00lcrgTMMhPOiQxDFNFHCYzMdO8P-ukETs0$ 
>>>> <https://urldefense.com/v3/__https://www.ericwerner.com/__;!!D9dNQwwGXtA!XLF-Q-SqJ-AuvQ-dic9ptw82Ooe57dI4UX6ePa7CTWADakJMPTruAnfSd0yTCHhsfb-S3Rv04mCA4h3CaUt82MM$>
>>>>
>>>> Sent from my iPad
>>>>
>>>>
>>>> _______________________________________________
>>>> Fis mailing list
>>>> Fis at listas.unizar.es
>>>> http://listas.unizar.es/cgi-bin/mailman/listinfo/fis 
>>>> ----------
>>>> INFORMACIÓN SOBRE PROTECCIÓN DE DATOS DE CARÁCTER PERSONAL
>>>>
>>>> Ud. recibe este correo por pertenecer a una lista de correo gestionada
>>>> por la Universidad de Zaragoza.
>>>> Puede encontrar toda la información sobre como tratamos sus datos en el
>>>> siguiente enlace:
>>>> https://sicuz.unizar.es/informacion-sobre-proteccion-de-datos-de-caracter-personal-en-listas 
>>>> Recuerde que si está suscrito a una lista voluntaria Ud. puede darse de
>>>> baja desde la propia aplicación en el momento en que lo desee.
>>>> http://listas.unizar.es 
>>>> ----------
>>>>
>>>
>>
>>
>> _______________________________________________
>> Fis mailing list
>> Fis at listas.unizar.es
>> http://listas.unizar.es/cgi-bin/mailman/listinfo/fis 
>> ----------
>> INFORMACIÓN SOBRE PROTECCIÓN DE DATOS DE CARÁCTER PERSONAL
>>
>> Ud. recibe este correo por pertenecer a una lista de correo gestionada
>> por la Universidad de Zaragoza.
>> Puede encontrar toda la información sobre como tratamos sus datos en el
>> siguiente enlace:
>> https://sicuz.unizar.es/informacion-sobre-proteccion-de-datos-de-caracter-personal-en-listas 
>> Recuerde que si está suscrito a una lista voluntaria Ud. puede darse de
>> baja desde la propia aplicación en el momento en que lo desee.
>> http://listas.unizar.es 
>> ----------
>>
>>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://listas.unizar.es/pipermail/fis/attachments/20251206/9525d6b2/attachment-0001.html>