[{"id":558,"title":"Toward Developing a Comprehensive Theory of Immunology for Guiding Future Immunological Research","sha":"03111b36267c547db30e1cc76aa625cb","user_id":null,"state":"published","body":"Concluding my research in plant and comparative immunology, I theorized that immunity is fundamentally the genetic program’s ability to resist change and maintain homeostasis. All immunological phenomena are governed not by molecular discontinuities mediated by receptor-ligand interactions—known as Continuity Theory—but more specifically by discontinuities that ultimately disrupt the program’s stability. Immunity is the program’s ability to stabilize—to resist natural selection—as replication perpetuates existence. Perceived this way, immunity may be considered the program’s intrinsic predisposition toward adaptation, with evolution originating as the interplay between immunity and natural selection.\r\n\r\nRequisite for biological life is the genetic program’s abilities of replication and stability under environmental forces. Polymerization/replication coexists with the reverse reaction of depolymerization/de-replication. Genetic code strand variants formed through imperfect replication might interfere with the parent molecule’s stability; therefore, parent molecules may—as a form of resistance—catalyze the depolymerization of interfering progeny. Progeny resistant to this degradation could persist and outcompete inferior, less stable replicants. To test this hypothesis and support the aforementioned theory, we must conduct experiments involving competition among identical self-replicating ribozymes occupying finite space and resources, and analyze the resultant spectrum, respective concentration, 3D structure, and catalytic capabilities of ribozyme variants formed over time.","created_at":"2019-01-26T22:43:45.875Z","updated_at":"2019-06-02T06:01:15.447Z","zenodo_id":3236946,"doi":"https://doi.org/10.5281/zenodo.3236946","subject":null,"tags":["evolution","immunity","immunology","adaptation","genetics","homeostasis","natural selection","replication","resistance"],"vote_count":0,"view_count":1,"score":0.1,"deleted":false,"muted":false,"tweeted":false,"attachment_file_name":null,"attachment_content_type":null,"attachment_file_size":null,"attachment_updated_at":null},{"id":205,"title":"Large scale species hybridization as a new tool for brain mapping ","sha":"a6ed57daffad7d0b94e0241f4d58d2de","user_id":null,"state":"published","body":"Cichlid fishes have undergone massive speciation in [recent years] (http://www.nature.com/nrg/journal/v5/n4/full/nrg1316.html). The species number of Cichlid fishes in [African lakes are in hundreds] (http://onlinelibrary.wiley.com/doi/10.1046/j.1365-294x.2001.01200.x/abstract;jsessionid=58D9FA770C91788F7EFC99DE6DF65156.f01t01) . The ecological niche and behavioral repertoire of each species can be vastly different, yet due to recent divergence, several retain the ability to produce viable and fertile offspring in forced [settings] (http://www.nature.com/nrg/journal/v5/n4/full/nrg1316.html). While comparative brain anatomy of few cichlids has provided some limited insights into brain evolution, the potential of Cichlids for detailed neuronal mapping has been completely unexplored. We propose a simple scheme for the exploration of macroscopic brain anatomy, neuronal network architecture and single neuron computation using crossing of cichlids with vastly different behavioral responses, for example a bottom feeder and a top carnivore or solitary species and a more social species. The progeny of such scheme of crosses would exhibit certain behavioral traits of one or the other parent or an average and correspondingly have underlying neuronal changes. A large scale systematic crossing, behavioral, genomic, and neuronal mapping of hybrid progenies would enable nuanced brain mapping. This approach can open an entirely new direction of brain mapping, as compared to the single gene mutation approach of neurogenetics. ","created_at":"2015-08-18T10:44:16.471Z","updated_at":"2015-08-19T06:00:40.683Z","zenodo_id":54644,"doi":"http://dx.doi.org/10.5281/zenodo.28319","subject":null,"tags":["african cichlid fishes","species complex","brain mapping","neuronal mapping","neurophysiology","evolution","circuits","hybridization","neurogenetics","crosses","behavior","ecological niche","species","computational neuroscience"],"vote_count":0,"view_count":1,"score":0.1,"deleted":false,"muted":false,"tweeted":true,"attachment_file_name":null,"attachment_content_type":null,"attachment_file_size":null,"attachment_updated_at":null},{"id":773,"title":"Explanation for spheno-ethmoid contact on the organ-crowded hominoid anterior cranial floor","sha":"9fe380f137306382cc7e2798f6960c26","user_id":null,"state":"published","body":"The anterior cranial floor is variably configured in primates. The [sphenoid and ethmoid bones contact each other](https://www.worldcat.org/title/mans-place-among-the-mammals/oclc/1463021) in strepsirrhines, orangutans, and modern humans, whereas a [horizontal plate of frontal bone](https://www.jstor.org/stable/3031137?seq=1) interrupts spheno-ethmoid contact in Old World monkeys, lesser apes, and, more variably, in New World monkeys and African great apes. Frontal contribution to the midline anterior cranial floor has been tied to [differential growth of the brain and orbits](https://www.worldcat.org/title/mans-place-among-the-mammals/oclc/1463021), [developmental competition for space](https://books.google.com/books/about/Trait%C3%A9_d_anatomie_humaine_Nouvelle_%C3%A9di.html?id=GiLocQAACAAJ), [upper facial prognathism](https://onlinelibrary.wiley.com/doi/abs/10.1002/ajpa.1330010208), and [size of the supraorbital ridges](https://openlibrary.org/books/OL6093349M/Evolution_emerging). In anthropoids, the jugum sphenoidale and cribriform plate scale isometrically with brain size but total anterior cranial floor length scales with negative allometry, leaving [insufficient room for frontal contribution to the midline at larger brain sizes](https://www.sciencedirect.com/science/article/abs/pii/S0047248400904469). These allometric “spatial packing” limitations may explain secondarily-derived spheno-ethmoid contact in large-brained African apes, but the underlying scaling relationships need to be tested intraspecifically. Spheno-ethmoid contact in orangutans, on the other hand, may be the byproduct of crowding a [large](https://www.sciencedirect.com/science/article/abs/pii/S0047248401905378?via%3Dihub), [projecting](https://www.sciencedirect.com/science/article/abs/pii/S0047248410002034?via%3Dihub) temporal lobe and [dorsally-rotated cribriform plate](https://onlinelibrary.wiley.com/doi/abs/10.1002/ajpa.1330010208) onto the endocranial surface. These ideas are consistent with the hypothesis that spheno-ethmoid contact at the level of the anterior cranial floor is not developmentally homologous in small- and large- brained primates.","created_at":"2020-07-21T03:24:19.447Z","updated_at":"2020-07-21T06:01:44.399Z","zenodo_id":3953298,"doi":"https://doi.org/10.5281/zenodo.3953298","subject":null,"tags":["basicranium","anterior cranial fossa","primate","anthropoid","hominin","evolution","brain","cranial architecture","human evolution"],"vote_count":0,"view_count":1,"score":0.1,"deleted":false,"muted":false,"tweeted":false,"attachment_file_name":null,"attachment_content_type":null,"attachment_file_size":null,"attachment_updated_at":null},{"id":140,"title":"Naturalness of Atheism and Unnaturalnes of Religion","sha":"4ed82f88af3d32867a5489847a4fb334","user_id":257,"state":"published","body":"The standard model of Cognitive Science of Religion (CSR) explains religion as some kind of natural phenomenon. Religious ideas and beliefs are considered as natural not only in the sense of their foundation on cognitive processes and mechanisms, but also as obvious, intuitive, and in some sense inevitable. What is more CSR suggests that religious ideas and beliefs are more natural and evident than atheism. In consequence atheism is considered as unnatural cultural phenomenon which requires special conditions, first of all high development of education and science, in the modern times associated with the Enlightenment. However, biological and evolutionary approaches show that the human being is a species which focuses on natural, sensual information and behaviors which are strategic for survival. Therefore, how can we connect natural selection with religious beliefs which are counter-intuitive and unnatural? Here I would like to show that naturalness of religion hypothesis is not compatible with biological long-orientation perspective. Religion was useful tool after agricultural revolution – however, not for transmission of good moral behavioral patterns. Its main aim was consolidation and strengthening in-group trust and internal network for the purpose of inter-group conflicts and aggression at the level of large groups.   ","created_at":"2015-04-05T16:35:41.347Z","updated_at":"2015-04-10T19:22:24.186Z","zenodo_id":26413,"doi":"http://dx.doi.org/10.5281/zenodo.16628","subject":null,"tags":["atheism","religion","evolution","biology","morality"],"vote_count":2,"view_count":1,"score":2.1,"deleted":false,"muted":false,"tweeted":false,"attachment_file_name":null,"attachment_content_type":null,"attachment_file_size":null,"attachment_updated_at":null},{"id":79,"title":"Endurance Hunting aa a Driver for Sexual Dimorphism and Role Differentiation","sha":"120b1f47e6890550933c0958d25e7f1c","user_id":325,"state":"published","body":"Early humans were endurance hunters. They were successful in long distance pursuit of prey. This behavioral strategy is believed to be at least 2MM years old, predating h. sapiens, and persists in Kalahari bushmen and the Tarahumara, amongst others. However, long distance running reduces body fat to \u003c10%, which in females is inadequate for fertility. Thus endurance hunting may have been an early driver of role differentiation (male hunters vs. female gatherers) with female gathering allowing a maintained \u003e20% body fat composition, and maintained fertility.\r\nInsofar as any female runners  would be at a fertility disadvantage it is possible that gatherer females, with dimorphically distinct evolutionary modern body habitus would have been regarded positively in comparison. \r\n","created_at":"2015-02-20T23:36:39.889Z","updated_at":"2023-06-28T17:39:34.552Z","zenodo_id":23230,"doi":"http://dx.doi.org/10.5281/zenodo.15563","subject":null,"tags":["endurance","dimorphism","running","evolution","gender","prehistory"],"vote_count":3,"view_count":1,"score":3.1,"deleted":false,"muted":false,"tweeted":false,"attachment_file_name":null,"attachment_content_type":null,"attachment_file_size":null,"attachment_updated_at":null},{"id":225,"title":"Evolution in genetic terms – Is it RNA world or DNA world or is it anything else?","sha":"69b03c4db6269df0798781ef07244e59","user_id":null,"state":"published","body":"\r\nThe RNA world concept that self-replicating ribonucleic acid (RNA) molecules are keys to all current forms of life on Earth and geticists could not go further down might have missed out on how evolution has actually happened in real genetic terms. \r\n\r\nOut of all hypothesis and proposals, one that stands strong in the debate of “RNA before DNA” is \u003cb\u003e “protein synthesis can occur in the absence of DNA but not in the absence of RNA” \u003c/b\u003e. To contest this hypothesis, one should take a close look on life of an RNA molecule and their early degeneration process. \r\n\r\nEarlier RNA-protein interaction systems are highly doubtful because RNA is never a long-time informational molecule and even if they are or they used to be, many such information might got lost. Assuming this kind of unstable molecule being the early days primary replication machinery, information contents might have significantly lost and this will again raise a question on how similar or same species maintains identity?\r\n\r\nTransferring information outside of the nucleus is only required when there is a nucleus.\r\n\r\nTaken together these concepts, \u003cb\u003ewe need to revisit the origin of life in newer genetic terms.\u003c/b\u003e\r\n","created_at":"2015-09-16T17:43:27.824Z","updated_at":"2015-09-18T06:00:54.818Z","zenodo_id":61235,"doi":"http://dx.doi.org/10.5281/zenodo.31054","subject":null,"tags":["evolution","rna","dna","rna world","dna world","genetics"],"vote_count":1,"view_count":1,"score":1.1,"deleted":false,"muted":false,"tweeted":false,"attachment_file_name":null,"attachment_content_type":null,"attachment_file_size":null,"attachment_updated_at":null},{"id":131,"title":"The evolution of smaller arms in theropod dinosaurs","sha":"29ffd9fa11e898da1905098178e8c5c6","user_id":510,"state":"published","body":"Carnivorous theropod dinosaurs may have had brilliant breast displays that were better shown off with less distracting arm size.  At mating time female theropods selected males with smaller arms, for it was in the display that male potency was better measured.  Arms blocked and confused the message.\r\n   Today many dull, dark, and drab colored birds have complex breast displays with bright colors, bold spots, streaks, and bands.  Birds evolved arms that were held at their sides to maximize their displays since they had to maintain certain wing size for flight.  Large theropod dinosaurs didn't have such needs, so arms simply aimed at getting less obvious by getting smaller.\r\n  Carnivorous theropods that hunted live prey would also do well to reduce ostentation to the breast where it could be directed or hidden at will.  Loud fluorescent patterns and colors wouldn't much help a large stalking predator.\r\n  Breast displays could be accomplished via skin pigmentation or short feathers.  Feathers would be additionally useful by providing iridescence.  Feathers could be made erect; and with head shaking, strengthen the display. It would also be a protecting layer where the body made contact with the ground. ","created_at":"2015-03-26T08:45:08.018Z","updated_at":"2023-02-07T09:02:47.124Z","zenodo_id":25717,"doi":"http://dx.doi.org/10.5281/zenodo.16374","subject":null,"tags":["evolution","dinosaurs","theropod","breast display"],"vote_count":1,"view_count":1,"score":1.1,"deleted":false,"muted":false,"tweeted":false,"attachment_file_name":null,"attachment_content_type":null,"attachment_file_size":null,"attachment_updated_at":null},{"id":72,"title":"Complexity spaces will capture more a more nuanced understanding of technological evolution in the Pleistocene","sha":"c1ed1c7574111dd65a413b3b28d11519","user_id":290,"state":"published","body":"In Paleolithic archaeology, we are interested in changes in complexity in technology, social networks, and communication over time. However, little research has been done to specify and quantify what is meant by ‘complexity.’ Recently that has begun to change.\r\n\r\nAll of these contributions seem promising, but they focus on different conceptualizations of complexity. Perault et al. [(2013)](http://www.jstor.org/stable/10.1086/673264) develop the concept of techno-units. Mahaney ([2013](https://www.researchgate.net/publication/263465321_Measuring_the_Evolution_of_Toolmaking_Complexity_Indices_of_Operational_Complexity), [2014](http://www.paleoanthro.org/media/journal/content/PA20140586.pdf), In progress) has focused on individual action sequences, using complexity indices from information theory ([Gabadnho et al. 2011](http://www.researchgate.net/profile/Gilbert_Ritschard/publication/220786242_Indice_de_complexit_pour_le_tri_et_la_comparaison_de_squences_catgorielles/links/53edabdb0cf26b9b7dc5f259.pdf)) and graph theory. Rugg [(2011)] (http://www.paleoanthro.org/media/journal/content/PA20110154.pdf) focuses on the organization of the foraging economy.   Instead of attempting to develop a single complexity metric, perhaps archaeologists should attempt to situate lithic technologies in a complexity space comprise of multiple measures each capturing different aspects complexity. Elaboration may take place at different levels at different times. For instance, it may be the case that the transition from Oldowan to Acheulean technologies after 1.8 ma involved changes at the level of the individual action, techno-units or cultural recipes. However, the emergence of the Levallois and Mousterian technologies after 250 ka may represent increased economic complexity. \r\n\r\n[Robert Mahaney Researchgate](https://www.researchgate.net/profile/Robert_Mahaney)\r\n","created_at":"2015-02-19T21:33:56.695Z","updated_at":"2019-02-04T21:53:37.221Z","zenodo_id":23170,"doi":"http://dx.doi.org/10.5281/zenodo.15538","subject":null,"tags":["archaeology","paleolithic","achelean","lithics","technology","evolution","paleoanthropology","oldowan"],"vote_count":2,"view_count":1,"score":2.1,"deleted":false,"muted":false,"tweeted":false,"attachment_file_name":null,"attachment_content_type":null,"attachment_file_size":null,"attachment_updated_at":null},{"id":158,"title":"What’s black and white and eating stuff all over? Hypotheses for the evolution of killer whale coloration and similar coloration patterns in prey species","sha":"70f5d0970e8f60a595f62f31a34701a0","user_id":562,"state":"published","body":"The greatest diversity of killer whale forms–or possible (sub)species – is in the Antarctic. One reason may be because killer whales originated in, or near, the Antarctic, which would also explain their large size - an example of Bergmann’s rule [http://en.wikipedia.org/wiki/Bergmann%27s_rule], i.e. species that evolve in higher latitudes are larger. \r\nIf killer whales did evolve in the Southern Ocean, penguins would have been an abundant prey source. There was a great diversity of penguin species when toothed whales arose [http://rsbl.royalsocietypublishing.org/content/9/6/20130748]. The distinctive black and white coloration of killer whales could have been aggressive mimicry [http://en.wikipedia.org/wiki/Aggressive_mimicry], allowing them to approach penguins - Gerlache killer whales (small type B) appear feed preferentially on penguins today [https://swfsc.noaa.gov/uploadedFiles/2010_Pitman%20and%20Durban_Polar%20Biology_Penguin%20predation.pdf]. Killer whales may then have diversified to fill other niches and eat other prey beyond the Southern Ocean. Many species of porpoises/ delphinids upon which killer whales prey also share their predators’ black and white coloration. This may again be mimicry, but defensive mimicry [http://en.wikipedia.org/wiki/Mimicry] – prey species resembling their chief predator gain a few precious seconds of confusion when they approach. These hypotheses might explain the ubiquitous and convergent black and white coloration in the cetacean prey of killer whales, and their unusual black and white color pattern.\r\n","created_at":"2015-04-30T17:49:49.056Z","updated_at":"2024-07-18T08:53:15.089Z","zenodo_id":28316,"doi":"http://dx.doi.org/10.5281/zenodo.17281","subject":null,"tags":["killer whale","orcinus orca","mimicry","penguins","evolution"],"vote_count":3,"view_count":1,"score":3.1,"deleted":false,"muted":false,"tweeted":true,"attachment_file_name":null,"attachment_content_type":null,"attachment_file_size":null,"attachment_updated_at":null},{"id":143,"title":"Naturalness of Atheism and Supernaturalness of Religion - A Role for Theological Science","sha":"c4fcf79b9c0be4b2b24ee2baa941a221","user_id":540,"state":"published","body":"Scientific approaches (\"science\" narrowly defined as the \"sciences of nature\") metaphysically exclude divine effects as appropriate--in other words, science itself is structured to exclude divine action (pragmatically). The problem with the \"natural\" study of religion is that religion cannot be reduced to its natural causes and effects. This is precisely because divine causes and effects are the source and telos of religious life, with natural causes being more appropriately \"effects which follow from divine causes\". Science can contribute, because of its structure, studying natural phenomena associated with religion understood as natural phenomena and not as divine phenomena. Therefore, the word \"natural\" must be defined here as \"strictly scientifically natural\", suggesting that atheism is a strictly scientifically natural belief (excluding divinity not only pragmatically but substantially), whereas religion, limited to strictly scientific investigation, is \"natural\" because of its natural effects, but points to something outside of strictly natural explanations. The word \"unnaturalness\" applied to religion by [konrad szocik](/users/76d3c51025e2ea94f969165c2ad98be7) signified the opposite of only a strictly scientific \"naturalness\". A more appropriate word than \"unnaturalness\" would be \"supernaturalness\". This word is more proper to the object of study (religion) and is not contradictory to \"natural\" but suggests explanatory plausibility \"outside\" or beyond the structure of nature, suggesting reality beyond nature. Here is where theology might begin to have significant input.","created_at":"2015-04-10T18:35:46.345Z","updated_at":"2015-04-12T06:01:06.958Z","zenodo_id":26806,"doi":"http://dx.doi.org/10.5281/zenodo.16762","subject":null,"tags":["religion","atheism","science","philosophy","evolution","biology","morality"],"vote_count":0,"view_count":1,"score":0.1,"deleted":false,"muted":false,"tweeted":false,"attachment_file_name":null,"attachment_content_type":null,"attachment_file_size":null,"attachment_updated_at":null}]