Loris Zamai | Urbino "Carlo Bo" (original) (raw)
Papers by Loris Zamai
Cells, 9, 2362, 2020
This article challenges the notion of the randomness of mutations in eukaryotic cells by unveilin... more This article challenges the notion of the randomness of mutations in eukaryotic cells by unveiling stress-induced human non-random genome editing mechanisms. To account for the existence of such mechanisms, I have developed molecular concepts of the cell environment and cell environmental stressors and, making use of a large quantity of published data, hypothesised the origin of some crucial biological leaps along the evolutionary path of life on Earth under the pressure of natural selection, in particular, (1) virus–cell mating as a primordial form of sexual recombination and symbiosis; (2) Lamarckian CRISPR-Cas systems; (3) eukaryotic gene development;(4) antiviral activity of retrotransposon-guided mutagenic enzymes; and finally, (5) the exaptationof antiviral mutagenic mechanisms to stress-induced genome editing mechanisms directed at“hyper-transcribed” endogenous genes. Genes transcribed at their maximum rate (hyper-transcribed), yet still unable to meet new chronic environmental demands generated by “pollution”, are inadequate and generate more and more intronic retrotransposon transcripts. In this scenario, RNA-guided mutagenic enzymes (e.g., Apolipoprotein B mRNA editing catalytic polypeptide-like enzymes, APOBECs), which have been shown to bind to retrotransposon RNA-repetitive sequences, would be surgically targeted by intronic retrotransposons on opened chromatin regions of the same “hyper-transcribed” genes. RNA-guided mutagenic enzymes may therefore “Lamarkianly” generate single nucleotide polymorphisms (SNP) and gene copy number variations (CNV), as well as transposon transposition and chromosomal translocations in the restricted areas of hyper-functional and inadequate genes, leaving intact the rest of the genome. CNV and SNP of hyper-transcribed genes may allow cells to surgically explore a new fitness scenario, which increases their adaptability to stressful environmental conditions. Like the mechanisms of immunoglobulin somatic hypermutation, non-random genome editing mechanisms may generate several cell mutants, and those codifying for the most environmentally adequate proteins would have a survival advantage and would therefore be Darwinianly selected. Non-random genome editing mechanisms represent tools of evolvability leading to organismal adaptation including transgenerational non-Mendelian gene transmission or to death of environmentally inadequate genomes. They are a link between environmental changes and biological novelty and plasticity, finally providing a molecular basis to reconcile gene-centered and“ecological” views of evolution.
Blood, 2002
To determine whether production of type 1 and type 2 cytokines defines discrete stages of natural... more To determine whether production of type 1 and type 2 cytokines defines discrete stages of natural killer (NK) cell differentiation, cytokine expression was analyzed in human NK cells generated in vitro in the presence of interleukin-15 (IL-15) and/or IL-2 from umbilical cord blood hematopoietic progenitors. Like peripheral NK cells, the CD161+/CD56+ NK cells from these cultures contained a tumor necrosis factor alpha (TNF-α)+/granulocyte macrophage–colony-stimulating factor (GM-CSF)+ subset, an interferon gamma (IFN-γ)+ subset, mostly included within the former, and very few IFN-γ−/IL-13+ cells. Instead, most immature CD161+/CD56− NK cells, detectable only in the cultures with IL-2, produced IL-13, TNF-α, and GM-CSF, but not IFN-γ, and contained an IL-5+ subset. In short-term cultures with IL-12 and feeder cells, a proportion of the immature cells acquired the ability to produce IFN-γ. Part of these produced both IFN-γ and IL-13, irrespective of induced CD56 expression. These in vit...
Drafts by Loris Zamai
Hypothesis, 2020
I am a biologist/immunologist who has recently proposed a new evolutionary theory of organisms. I... more I am a biologist/immunologist who has recently proposed a new evolutionary theory of organisms. I am looking for a "crazy/open-minded" physicist who finds some of my alternative hypotheses/proposals to some aspects of physics interesting. Hypotheses that arise to justify some "strange" behaviors in biology. I developed these ideas 6 years ago while I was writing the paper on a new evolutionary theory (attached is an excerpt of the final part with the Physics/Chemistry part). I know it is difficult to go against existing theories, especially for a .. Biologist!
Among the strange things that distinguish life is the "spontaneous" ability to produce thermal/infrared energy, the same type of low-energy radiation that Earth gives back to the extra-terrestrial environment (and of Hawkins radiation!). In this regard, it has to be noted that if you put a mouse inside an airtight container insulated from the outside, the mouse, as long as it is alive, produces heat and keeps the internal environment at 37 °C; the same mouse that dies after consuming all the oxygen loses the ability to heat the environment it is in. Note that the same mouse, whether alive or dead, produces the same calories if we "burn" it; from a thermodynamic point of view, it looks no different, alive or dead. Life is a structure specialized/organized to accelerate spontaneous biochemical reactions (usually exothermic) and to exploit chemical energy. One might say that life is functional in increasing entropy, but life is anything but entropic. The molecules of a living mouse are distributed in a highly organized manner such that the same molecules distributed in a different manner can very likely produce an agglomeration of inanimate molecules (Maxwell's devil putting them in order). Life as a whole seems incompatible with the second law of thermodynamics. How could life, a very organized system/structure, have been rewarded and expanded on Earth if it goes against the laws of thermodynamics? I propose that spontaneous chemical reactions produce compaction of matter with increased density of matter, and the electromagnetic waves that come out are a side effect of compaction. Since Life accelerates spontaneous reactions, it would promote the generation of increasingly stable structures of matter (spontaneous chemical reactions lead to products that are normally more stable than the reactants) i.e. a redistribution of atoms so that repulsions within the produced structures are reduced, and this would also spontaneously tend to reduce the volume of matter while maintaining the same mass (spontaneous increase in density as occurs when 2 H or O atoms come together to form an H2 or O2 molecules due to overlapping). I also went to look at radioactive decay, and normally, what happens is the transition from a radioactive element with a larger atomic nucleus size to an element with a smaller atomic nucleus size. The impression is that matter compacts spontaneously, but from the gas law, we know that compact matter takes work, and who does this work? This is why I hypothesized that matter spread out within an immiscible structure Space during the Big Bang and acquired a potential energy that is now expressed in gravitational attraction and .... in Life. Life in this view would behave similarly to gravitation, would be a force of matter aggregation/compaction, and would have been "rewarded" precisely because it would accelerate, like gravity, the reseparation of the two immiscible structures, transforming the potential energy acquired during the Big Bang into matter compression, releasing the Space entrapped in it. In this regard, I am attaching an excerpt from a paper published in 2020 in which, starting from the description of a new evolutionary mechanism of nonrandom gene editing induced by environmental changes, I necessarily end up also talking about Philosophy and Physics (and chemistry, "mathematics" of fractals). Here, you will find the concluding section 8.8. Conclusive Chemical and Physical Considerations on Life: The Big Bang of Life as a Gravitation-Like Force of Aggregation, a Gravitational Singularity with a Black Hole-Like Behaviour. In this paragraph, I introduce a new hypothesis of the Universe based on 2 immiscible "fluids," matter and space (a bit like oil and water), which, thanks to the Big Bang, have mixed acquiring potential energy. This potential energy would be explicated in the gravitational force that would promote the separation between the two mixed immiscible fluids. This model justifies the tendentially spherical shape/geometry of the planets/ stars (but also applies to atoms) that allows the minimum surface area containing a given volume of matter to be exposed. Stars/planets/atoms/matter would be like droplets/spheres of oil scattered after the big bang inside a "watery space" that spontaneously re-aggregates or conversely droplets/spheres of polar matter inside an apolar Space, a tridimensional inextensible/rigid immaterial net/polymer.
By putting an "immiscible Ether" that possesses specific physical properties (rigid/inextensible network/structure torn/broken by matter during the Big Bang) in place of empty space we could also justify how faster-than-light communications can take place, as happens when 2 electrons spontaneously communicate, taking opposite spins (think of the possibility of "vortexes"=moving fields/tensions in space produced by the movement/rotation of material structures that can affect other material structures that end up in the vortex).
I understand that I am a "heretic" in Physics, so I would not be surprised if you found what I propose crazy; however, I am looking for someone who finds these proposals/insights stimulating and interested in a collaboration. In this regard, I have also hypothesized that the natural movement of matter (stars, planets, objects, atoms, electrons, photons …) in Space is helicoidal with a spin that produces/justifies the duality wave-particle effect at subatomic levels. Moreover, I have developed mathematical equations (with the limitations of a biologist), reworking the equation for the law of universal gravitation and "refining" Stevin's law using spherical crowns (instead of the cylinder, given the spherical geometry of the earth/planets) that suggest a huge pressure inside planets compatible with internal atomic fusion.
Cells, 9, 2362, 2020
This article challenges the notion of the randomness of mutations in eukaryotic cells by unveilin... more This article challenges the notion of the randomness of mutations in eukaryotic cells by unveiling stress-induced human non-random genome editing mechanisms. To account for the existence of such mechanisms, I have developed molecular concepts of the cell environment and cell environmental stressors and, making use of a large quantity of published data, hypothesised the origin of some crucial biological leaps along the evolutionary path of life on Earth under the pressure of natural selection, in particular, (1) virus–cell mating as a primordial form of sexual recombination and symbiosis; (2) Lamarckian CRISPR-Cas systems; (3) eukaryotic gene development;(4) antiviral activity of retrotransposon-guided mutagenic enzymes; and finally, (5) the exaptationof antiviral mutagenic mechanisms to stress-induced genome editing mechanisms directed at“hyper-transcribed” endogenous genes. Genes transcribed at their maximum rate (hyper-transcribed), yet still unable to meet new chronic environmental demands generated by “pollution”, are inadequate and generate more and more intronic retrotransposon transcripts. In this scenario, RNA-guided mutagenic enzymes (e.g., Apolipoprotein B mRNA editing catalytic polypeptide-like enzymes, APOBECs), which have been shown to bind to retrotransposon RNA-repetitive sequences, would be surgically targeted by intronic retrotransposons on opened chromatin regions of the same “hyper-transcribed” genes. RNA-guided mutagenic enzymes may therefore “Lamarkianly” generate single nucleotide polymorphisms (SNP) and gene copy number variations (CNV), as well as transposon transposition and chromosomal translocations in the restricted areas of hyper-functional and inadequate genes, leaving intact the rest of the genome. CNV and SNP of hyper-transcribed genes may allow cells to surgically explore a new fitness scenario, which increases their adaptability to stressful environmental conditions. Like the mechanisms of immunoglobulin somatic hypermutation, non-random genome editing mechanisms may generate several cell mutants, and those codifying for the most environmentally adequate proteins would have a survival advantage and would therefore be Darwinianly selected. Non-random genome editing mechanisms represent tools of evolvability leading to organismal adaptation including transgenerational non-Mendelian gene transmission or to death of environmentally inadequate genomes. They are a link between environmental changes and biological novelty and plasticity, finally providing a molecular basis to reconcile gene-centered and“ecological” views of evolution.
Blood, 2002
To determine whether production of type 1 and type 2 cytokines defines discrete stages of natural... more To determine whether production of type 1 and type 2 cytokines defines discrete stages of natural killer (NK) cell differentiation, cytokine expression was analyzed in human NK cells generated in vitro in the presence of interleukin-15 (IL-15) and/or IL-2 from umbilical cord blood hematopoietic progenitors. Like peripheral NK cells, the CD161+/CD56+ NK cells from these cultures contained a tumor necrosis factor alpha (TNF-α)+/granulocyte macrophage–colony-stimulating factor (GM-CSF)+ subset, an interferon gamma (IFN-γ)+ subset, mostly included within the former, and very few IFN-γ−/IL-13+ cells. Instead, most immature CD161+/CD56− NK cells, detectable only in the cultures with IL-2, produced IL-13, TNF-α, and GM-CSF, but not IFN-γ, and contained an IL-5+ subset. In short-term cultures with IL-12 and feeder cells, a proportion of the immature cells acquired the ability to produce IFN-γ. Part of these produced both IFN-γ and IL-13, irrespective of induced CD56 expression. These in vit...
Hypothesis, 2020
I am a biologist/immunologist who has recently proposed a new evolutionary theory of organisms. I... more I am a biologist/immunologist who has recently proposed a new evolutionary theory of organisms. I am looking for a "crazy/open-minded" physicist who finds some of my alternative hypotheses/proposals to some aspects of physics interesting. Hypotheses that arise to justify some "strange" behaviors in biology. I developed these ideas 6 years ago while I was writing the paper on a new evolutionary theory (attached is an excerpt of the final part with the Physics/Chemistry part). I know it is difficult to go against existing theories, especially for a .. Biologist!
Among the strange things that distinguish life is the "spontaneous" ability to produce thermal/infrared energy, the same type of low-energy radiation that Earth gives back to the extra-terrestrial environment (and of Hawkins radiation!). In this regard, it has to be noted that if you put a mouse inside an airtight container insulated from the outside, the mouse, as long as it is alive, produces heat and keeps the internal environment at 37 °C; the same mouse that dies after consuming all the oxygen loses the ability to heat the environment it is in. Note that the same mouse, whether alive or dead, produces the same calories if we "burn" it; from a thermodynamic point of view, it looks no different, alive or dead. Life is a structure specialized/organized to accelerate spontaneous biochemical reactions (usually exothermic) and to exploit chemical energy. One might say that life is functional in increasing entropy, but life is anything but entropic. The molecules of a living mouse are distributed in a highly organized manner such that the same molecules distributed in a different manner can very likely produce an agglomeration of inanimate molecules (Maxwell's devil putting them in order). Life as a whole seems incompatible with the second law of thermodynamics. How could life, a very organized system/structure, have been rewarded and expanded on Earth if it goes against the laws of thermodynamics? I propose that spontaneous chemical reactions produce compaction of matter with increased density of matter, and the electromagnetic waves that come out are a side effect of compaction. Since Life accelerates spontaneous reactions, it would promote the generation of increasingly stable structures of matter (spontaneous chemical reactions lead to products that are normally more stable than the reactants) i.e. a redistribution of atoms so that repulsions within the produced structures are reduced, and this would also spontaneously tend to reduce the volume of matter while maintaining the same mass (spontaneous increase in density as occurs when 2 H or O atoms come together to form an H2 or O2 molecules due to overlapping). I also went to look at radioactive decay, and normally, what happens is the transition from a radioactive element with a larger atomic nucleus size to an element with a smaller atomic nucleus size. The impression is that matter compacts spontaneously, but from the gas law, we know that compact matter takes work, and who does this work? This is why I hypothesized that matter spread out within an immiscible structure Space during the Big Bang and acquired a potential energy that is now expressed in gravitational attraction and .... in Life. Life in this view would behave similarly to gravitation, would be a force of matter aggregation/compaction, and would have been "rewarded" precisely because it would accelerate, like gravity, the reseparation of the two immiscible structures, transforming the potential energy acquired during the Big Bang into matter compression, releasing the Space entrapped in it. In this regard, I am attaching an excerpt from a paper published in 2020 in which, starting from the description of a new evolutionary mechanism of nonrandom gene editing induced by environmental changes, I necessarily end up also talking about Philosophy and Physics (and chemistry, "mathematics" of fractals). Here, you will find the concluding section 8.8. Conclusive Chemical and Physical Considerations on Life: The Big Bang of Life as a Gravitation-Like Force of Aggregation, a Gravitational Singularity with a Black Hole-Like Behaviour. In this paragraph, I introduce a new hypothesis of the Universe based on 2 immiscible "fluids," matter and space (a bit like oil and water), which, thanks to the Big Bang, have mixed acquiring potential energy. This potential energy would be explicated in the gravitational force that would promote the separation between the two mixed immiscible fluids. This model justifies the tendentially spherical shape/geometry of the planets/ stars (but also applies to atoms) that allows the minimum surface area containing a given volume of matter to be exposed. Stars/planets/atoms/matter would be like droplets/spheres of oil scattered after the big bang inside a "watery space" that spontaneously re-aggregates or conversely droplets/spheres of polar matter inside an apolar Space, a tridimensional inextensible/rigid immaterial net/polymer.
By putting an "immiscible Ether" that possesses specific physical properties (rigid/inextensible network/structure torn/broken by matter during the Big Bang) in place of empty space we could also justify how faster-than-light communications can take place, as happens when 2 electrons spontaneously communicate, taking opposite spins (think of the possibility of "vortexes"=moving fields/tensions in space produced by the movement/rotation of material structures that can affect other material structures that end up in the vortex).
I understand that I am a "heretic" in Physics, so I would not be surprised if you found what I propose crazy; however, I am looking for someone who finds these proposals/insights stimulating and interested in a collaboration. In this regard, I have also hypothesized that the natural movement of matter (stars, planets, objects, atoms, electrons, photons …) in Space is helicoidal with a spin that produces/justifies the duality wave-particle effect at subatomic levels. Moreover, I have developed mathematical equations (with the limitations of a biologist), reworking the equation for the law of universal gravitation and "refining" Stevin's law using spherical crowns (instead of the cylinder, given the spherical geometry of the earth/planets) that suggest a huge pressure inside planets compatible with internal atomic fusion.