[Fis] Fwd: Contingency biological signals: Sex and Being
Pedro C. Marijuán
pedroc.marijuan at gmail.com
Thu Dec 4 19:51:16 CET 2025
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!UN5Qkr4MMHvVFgjxrE8GKOUT__SCPVApKzSiss-NOjGyuklM4kUiq2rVFM3p-XKxI27KcpMhBaLbJuUWfT2Ftv37jbkQ$
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!UN5Qkr4MMHvVFgjxrE8GKOUT__SCPVApKzSiss-NOjGyuklM4kUiq2rVFM3p-XKxI27KcpMhBaLbJuUWfT2Ftm4bQLAR$
> <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!UN5Qkr4MMHvVFgjxrE8GKOUT__SCPVApKzSiss-NOjGyuklM4kUiq2rVFM3p-XKxI27KcpMhBaLbJuUWfT2Ftm4bQLAR$
>> <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!UN5Qkr4MMHvVFgjxrE8GKOUT__SCPVApKzSiss-NOjGyuklM4kUiq2rVFM3p-XKxI27KcpMhBaLbJuUWfT2FtvEAYh1f$
>>>> <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!UN5Qkr4MMHvVFgjxrE8GKOUT__SCPVApKzSiss-NOjGyuklM4kUiq2rVFM3p-XKxI27KcpMhBaLbJuUWfT2FtvEAYh1f$
>>>>> <https://urldefense.com/v3/__https://arxiv.org/abs/1212.5439__;!!D9dNQwwGXtA!XLF-Q-SqJ-AuvQ-dic9ptw82Ooe57dI4UX6ePa7CTWADakJMPTruAnfSd0yTCHhsfb-S3Rv04mCA4h3ClsatzQ4$>
>>>>> So the sexuality of being is inherently social.
>>>>>
>>>>> -Eric
>>>>>
>>>>> https://urldefense.com/v3/__https://www.ericwerner.com/__;!!D9dNQwwGXtA!UN5Qkr4MMHvVFgjxrE8GKOUT__SCPVApKzSiss-NOjGyuklM4kUiq2rVFM3p-XKxI27KcpMhBaLbJuUWfT2FtpYJq5jg$
>>>>> <https://urldefense.com/v3/__https://www.ericwerner.com/__;!!D9dNQwwGXtA!XLF-Q-SqJ-AuvQ-dic9ptw82Ooe57dI4UX6ePa7CTWADakJMPTruAnfSd0yTCHhsfb-S3Rv04mCA4h3CaUt82MM$>
>>>>>
>>>>> Sent from my iPad
>>>>>
>>>>>
>>>>> _______________________________________________
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