#PhyloCode

[molusca]

phylocode is kinda... based tbh

#oliver.txt

[gravesenmahmood84]

Will Dupracetam Before long Be Part of Main and also Extra Aerobic Elimination?

Main towards the setup of the general way of the discovery involving DNA presenting small molecule inhibitors of gene transcription has been (1) utilizing a officially nondemanding phosphorescent intercalator displacement (FID) analysis regarding initial examination from the DNA joining affinity as well as selectivity of the library associated with substances for virtually any series appealing, and (A couple of) we've got the technology employed to create a big enough collection of Genetic make-up binding materials.Within this cardstock, we all develop a cross-layer logical construction pertaining to studying the functionality regarding reliable sending plans throughout multihop supportive selection methods. Any Dupracetam generalized signaling model over independent nonidentical Nakagami-m removal channels is presumed, and mathematical expression pertaining to end-to-end throughput price, spectral effectiveness, as well as latency submission are usually extracted. The particular offered platform can easily get the effect involving correlated packet errors brought on by helpful retransmission makes an attempt and, hence, properly appraise the network functionality. While using the framework, the actual functionality associated with automatic-repeat-request-based sending strategies this website is shown over the variety of circle circumstances and also technique details. It's demonstrated that will tradeoffs are necessary amid community sturdiness, throughput rate, spectral productivity, and also latency variation.Taxa along with homologues can easily in our opinion be viewed equally since types and as men and women. Nonetheless, the conceptualization regarding taxa because organic sorts meaning involving homeostatic residence cluster kinds has become belittled by some systematists, because it appears as if also this sort of varieties can not progress this can getting homeostatic. All of us respond by fighting how the management of life changing and find more taxic homologies, correspondingly, as vibrant along with static facets of the identical homeostatic residence group kind symbolizes a fantastic viewpoint for promoting the conceptualization regarding taxa while types. The main objective on a trend of homology depending on causal processes (at the.grams., connectivity, activity-function, genes, gift of money, as well as modularity) along with suggesting connection along with changes yields a notion regarding natural kinds contouring for the phylogenetic-evolutionary framework. Even so, homeostatic property group kinds within taxonomic and also major apply must be seated within the primacy associated with epistemological classification (homology while observational properties) around metaphysical generalization (compilation of change and customary ancestry since unobservational functions). The attitude associated with individuating heroes specifically simply by historical-transformational independence rather than their educational, structural, and useful self-reliance fails to generate an acceptable useful interplay between idea and statement. Solely ontological along with ostensional perspectives within progression as well as phylogeny (at the.g., an ideographic personality idea and also PhyloCode's 'individualism' regarding clades) might be pragmatically competitive when it comes to immediate issues inside biodiversity investigation, preservation, as well as systematics.

#Linsitinib #Afatinib #Dupracetam

[incidentsandreflections]

Incidents and Reflections Episode 67 - 06/21/2020

For anyone who missed or wants to re-experience the Dino Nerds for Black Lives stream back in June, you can now watch a recorded version of our one-time revival, as well as almost 40 hours’ worth of other paleo presentations! Article links

Prehistoric Road Trip [02:26]

Ensonglopedia of the Human (recorded stream of WIP performance) [05:13]

Life Through the Ages II [08:31]

PhyloCode, Phylonyms, and RegNum [11:33]

Ontogenetic dietary shifts in Deinonychus [18:21]

Thermal comfort of Triassic dinosaurs [27:51]

Aquatic stem myriapods [36:27]

Peopling of the Caribbean [44:22]

#Palaeoblr #Paleontology #Dino Nerds for Black Lives #Podcast #Science #Dinosaurs #Deinonychus #Metabolism #Physiology #Euthycarcinoids #Myriapods #Arthropods #Evolution #Anthropology #Humans #Prehistoric Road Trip #Ensonglopedia #PhyloCode #Nomenclature #Incidents and Reflections

[albertonykus]

I have a new paper out with my supervisor, Daniel Field, on the nomenclature of caprimulgimorph birds (nightjars, potoos, hummingbirds. etc.). (You might recall that we previously co-authored a study on the phylogeny of these birds.) This new paper is something of a bookkeeping article, primarily aimed at formalizing definitions for clade names within this group following the recent release of the International Code of Phylogenetic Nomenclature (PhyloCode). However, we also took the opportunity to review the fossil record and diagnostic anatomical features of these clades.

We coin two new names. The first is Sedentaves for the clade uniting the oilbird and potoos. This name translates to "sitting birds", after the very short foot found in these species. The other new name is Letornithes. In Greek mythology, Leto was the mother of Artemis (goddess of the moon and the hunt) and Apollo (god of the sun and the arts), and this clade unites the nocturnal, carnivorous frogmouths and the diurnal swifts and hummingbirds, which often have very elaborate visual displays! Additionally, in one legend, Leto turned some peasants into frogs, hearkening to the name "frogmouth".

For more details, the paper is open access and available here.

#Palaeoblr #Birblr #Birds #Dinosaurs #Strisoreans

[jurassicsunsets]

What does a "crown" group mean, exactly? Is it just things that are still alive, or is it the latest surviving members of a lineage? Would dodos or passenger pigeons count as crown birds?

So, the “crown” is defined as the group that consists of the most recent common ancestor of all modern* members of the lineage, and all of that ancestor’s descendants. That’s a little confusing, so let’s have a diagram to clarify:

*Modern is defined as “not extinct by 1500 AD”, per phylocode

Here’s (a simplified view of) how modern elephants are related to some extinct elephant groups. 

To find the crown group, we look at what groups are still around, and then we follow the family tree back to the point where these lineages all diverged. This is the most recent common ancestor (sometimes called the concestor or MRCA) of all living elephants.

To find what’s in the crown group, then, we go the other way - we look at the most recent common ancestor, and then take every branch that diverged from it. These are all in the “crown”, while the others are in the “stem”.

Note, however, that the “stem” only includes extinct species that are more closely related to elephants than to any other living things - in fact, that’s more or less the definition of a “stem” (though obviously for any group, not just specifically elephants”. 

If we zoom out a bit on the elephant family tree, we see that their closest relatives are thought to be manatees and kin (which I’ll just call “manatees” now for ease of understanding), as well as their extinct relatives. Manatees aren’t stem-elephants, and neither are their extinct relatives.

So, what’s the point of this whole “stem and crown” thing? Well, if you’re trying to learn about the biology of extinct creatures, it can make it a lot easier. The “crown” represents the clade (branch) that we have definite knowledge of based on living species. All living elephant species have trunks, thick skin, and are very intelligent - we can pretty confidently say this about all crown elephants.

This isn’t to say that it’s infallible - for example, we might conclude - inaccurately - that, because living elephants don’t have thick, shaggy hair, that all crown elephants lacked this feature. But on a broader level, we can say some more definite things about their biology.

The answer to the second part of your question, then, is yes. Crown birds refers to the MRCA of all birds as well as its descendants, and both Passenger Pigeons and Dodos are members of that lineage.

[synapsid-taxonomy]

Can we talk about Pantodonta being a mammal clade even though Pantodon is a fish?

At least it’s not a “ranked clade” so the ICZN doesn’t care. The Phylocode might, though…

[ricardo12us-blog]

Taxonomía

La Taxonomía (del griego ταξις, taxis, ‘ordenamiento’, y νομος, nomos, ‘norma’ o ‘regla’) es, en su sentido más general, la ciencia de la clasificación. Habitualmente se emplea el término para designar a la Taxonomía Biológica, la "teoría y práctica de clasificar organismos"15​16​cita 4​ Como se la entiende en la actualidad, la clasificación biológica tiene que ser congruente con las hipótesis de árbol filogenético disponibles, en ella, los organismos se agrupan en taxones mutuamente excluyentes a su vez agrupados en taxones de rango más alto también mutuamente excluyentes, de forma que cada organismo pertenece a uno y sólo un taxón en cada rango o "categoría taxonómica". En cada taxón, los organismos poseen caracteres (singular carácter) cuyos estados del carácter los diferencian de los organismos fuera del taxón, y son los que en conjunto se utilizan para delimitar los taxones. La mayoríacita 5​ de los especialistas ve a las especies, a las que ubican en taxones en la categoría taxonómica del mismo nombre, como una realidad objetiva, y a los diferentes conceptos de especie como diferentes aproximaciones para reconocer esos linajes que evolucionan independientemente, por lo que a pesar de las discrepancias entre autores en su concepto taxonómico y por lo tanto en general en los límites taxonómicos de cada una, suele ser considerada la categoría taxonómica más importantecita 6​cita 7​ en la clasificación. Los taxones supraespecíficos son los que agrupan especies y se jerarquizan en categorías taxonómicas de rango cada vez más alto: género (grupo de especies), familia, etc. hasta el reino. En esta área también está debatido el concepto de taxón a utilizar. Muchos especialistas afirman que sólo la "filosofía taxonómica" para agrupar los organismos en taxones de la escuela cladista logra que la clasificación ofrezca el servicio que se espera de ella al resto de las ramas de la biología, pero la escuela evolucionista tiene razones para delimitar con otros conceptos los taxones, también congruentes con las hipótesis de árbol filogenético, y las dos escuelas se atribuyen la creación de sistemas de clasificación que cumplen en mayor medida sus funciones de sistemas de almacenamiento y recuperación de datos, y de predictores del estado de los caracteres y las direcciones de la evolución que no se han medido.

La Taxonomía actual también se ocupa de debatir y actualizar los Códigos Internacionales de Nomenclatura, cuyo uso para crear y reutilizar nombres "formales" está consensuado desde hace unos 100 años. En ellos se define el sistema taxonómico a utilizar -el recién descripto es el "sistema lineano"-, deciden la formación de nombres y cuál es el "tipo" que decide cómo se heredan los nombres de taxón en taxón, y cuidan que todos los nombres se atengan a los Principios de Nomenclatura, explicitados con el objetivo de proveer la máxima estabilidad en la nomenclatura. Los Códigos en uso no evitan las "diferencias filosóficas" entre taxónomos en los conceptos taxonómicos a utilizar ni en la categoría especie ni en las categorías supraespecíficas que son una fuente de inestabilidad frecuente en los nombres de los taxones.

La Taxonomía Biológica es aquí tratada como una subdisciplina de la Biología Sistemática, que además tiene como objetivo la reconstrucción de la filogenia, o historia evolutiva, de la vida.cita 3​ Como aquí comprendida la Taxonomía abarca la decisión de qué sistema taxonómico utilizar, la de qué conceptos taxonómicos asociar a esos taxones, la delimitación de esos taxones dejando explícitos los métodos que fueron utilizados para alcanzarla, la formalización de sus nombres en la subdisciplina de la Nomenclatura, y también las herramientas para la Determinación o identificación de especímenes.cita 3​cita 6​ Como se calcula que sólo un 10% de las especies está descripto, esas descripciones tienen diferentes grados de resolución,cita 8​ y las especies evolucionan (cambian con el tiempo en términos de sus caracteres) y cambia su distribución, la determinación funciona recursivamente con la descripción, delimitación y distribución de especies en el área llamada alfa-Taxonomía o Taxonomía Descriptiva, o, deslindándola de la definición minimalista de Taxonomía que se maneja desde hace décadas y debido a que se intergradan en esa categoría taxonómica, el área de la Sistemática Descriptiva22​ o Ciencia de la Biodiversidadcita 6​, la que se ocupa del descubrimiento, la identificación, la descripción, la clasificación y la catalogacióncita 6​ de la biodiversidad del planeta, utilizando el organismo como unidad de trabajo y cuya prioridad23​ es la descripción de todas las especies dentro de un contexto evolutivo.cita 6​

La Historia de la Taxonomía ha sido largamente recorrida por éstos y otros interrogantes y a lo largo de ella fueron formándose el sistema de clasificación y las reglas que nos han quedado como legado.

La crisis de biodiversidad que es foco de atención desde mediados de 1990, la cantidad de datos acumulados con los análisis de ADN, y la posibilidad de intercambiar información a través de internet, han revitalizado a esta ciencia en el ambiente científico desde las décadas de 1990-2000, y han generado un debate acerca de la necesidad de hacer reformas sustanciales a los Códigos, algunas de las cuales aún se están debatiendo y otras ya se han incorporado. Algunas de estas propuestas son el BioCode, el PhyloCode, el agregado de atributos al tipo nomenclatural como podrían ser los nuevos "marcadores de ADN" (ADN barcodes), y las relacionadas con la informatización de los datos y la utilización formal de Internet.

[rcraft404]

A Dictionary of Science (Oxford Quick Reference)

A Dictionary of Science (Oxford Quick Reference)

This bestselling dictionary contains more than 9,500 entries on all aspects of chemistry, physics, biology (including human biology), earth sciences, computer science, and astronomy. This fully revised edition includes hundreds of new entries, such as bone morphogenetic protein, Convention on Biological Diversity, genome editing, Ice Cube experiment, multi-core processor, PhyloCode, quarkonium,…

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#Dictionary #Oxford #Quick #Reference #Science

[mrvaidya]

Discussions like this are one reason I can't take the phylocode seriously. Of all the things we should be doing, renaming perfectly usable names connected to lots of existing data is not one of them. We have enough problems in retrieving biological data without introducing new ones.

@rdmpage on a proposal changing how species names work under the PhyloCode.

#taxonomy #phylocode

[albertonykus]

Every time I say that birds are reptiles on Reddit, I get people telling me that tetrapods should be considered fish, amniotes should be considered amphibians, and mammals should be considered reptiles. How do I respond to these people?

More seriously: it’s true that the terms “fish”, “amphibians”, and “reptiles” all traditionally referred to paraphyletic groups. If and how these names should be modified such that they refer to clades is subjective, so one certainly could make an argument in favor of extending “fish” to include all tetrapods. It wouldn’t be how the term “fish” is widely or traditionally used, but there wouldn’t be anything inherently wrong with it. Conversely, one could also make the argument that “reptile” should be abandoned as a formal classification and retain its traditional, paraphyletic meaning excluding birds (and mammals), even though many biologists now use it to refer to a clade.

So there’s no “objectively right” way of defining these names in a phylogenetic context. However, we can gauge whether a proposed usage of a name is consistent with how evolutionary biologists have used it in recent years. After all, if we’re discussing the scientific use of these names, one could certainly do worse than following scientific consensus.

For a long time, there was no formal regulation of phylogenetic nomenclature, so assessing this would have been largely limited to surveying how the names have been used in recent scientific literature. With the publication of the PhyloCode though, there is now a formal set of rules for establishing phylogenetic definitions for taxon names. All names that have been established under the PhyloCode can be searched up in the RegNum database. This is probably the closest we’ll get to there being an “official” source for how taxon names should be applied in a phylogenetic context.

The PhyloCode was only published earlier this year, so there are still numerous taxon names that have not yet been defined following its rules. However, many of the relevant names brought up here have been. Reptilia, for example, is formally defined as the last common ancestor of Testudo graeca (the Greek tortoise), Iguana iguana (the green iguana), and Crocodylus niloticus (the Nile crocodile), and all of that ancestor’s descendants. Birds are descendants of that ancestor, so they would be considered reptiles under that definition, but mammals are not and would not. In this case, this definition is similar to how many evolutionary biologists had already been using the term “reptile” prior to the publication of the PhyloCode.

The formal definition of Amphibia under the PhyloCode is anything more closely related to Caecilia tentaculata, Siren lacertina (the greater siren), Andrias japonicus (the Japanese giant salamander), Proteus anguinus (the olm), and Rana temporaria (the common frog) than to Homo sapiens (the human). Given that humans are amniotes, all other amniotes are more closely related to humans than to the other taxa in the definition, so amniotes are explicitly excluded from being amphibians.

No formal phylogenetic definition has yet been established for “fish” (technically Pisces), so we’re back to qualitatively surveying scientific literature for this one. In my experience, very few biologists use the term “fish” for a clade, and this seems to be backed up by a quick search on Google Scholar. (There are only a handful of papers that use the phrase “non-tetrapod fish” or similar.) This is most likely because there is already a well-known name for the clade uniting all fish and tetrapods, that being Vertebrata. So unless they’re trying to be cheeky, most biologists use the term “fish” as excluding tetrapods.

[albertonykus]

Does the PhyloCode have any official standing? (Your Caprimulgimorphae paper makes it sound like it does.) Do all clade names have to follow it? What about genus and species names?

The PhyloCode is at least intended to govern phylogenetic nomenclature, and all of the auxiliary publications required for it to take effect (Phylonyms and RegNum) have been released. There is no higher power forcing us to follow it, but there also isn’t one forcing us to follow the ICZN or any of the other codes of biological nomenclature. We follow the ICZN and other such codes because taxonomists implicitly agree that it’s useful to have rules for how to coin and use scientific names. So the answer to whether the PhyloCode has “any official standing” is that it does if the community agrees it does.

As of now, I think it is too early to say whether the community has come to a consensus on that. I admit, part of me is not optimistic about PhyloCode’s chances, simply because phylogenetic nomenclature has already been practiced for a long time without any formal governance. The way I see it, however, it’s useful to have rules to follow in applying phylogenetic nomenclature (for the same reasons that it’s useful to have rules for applying binomial nomenclature), in which case there is no other authority attempting to establish such rules other than the PhyloCode. And though we can quibble about the decisions taken in the Phylonyms volume that is intended to set an example for following the PhyloCode, I don’t find the rules outlined by the PhyloCode to be unreasonable or objectionable in themselves. Consider my caprimulgimorph nomenclature paper a way of hedging my bets: in the event that PhyloCode does take off, we at least have an existing framework of PhyloCode-compliant phylogenetic nomenclature for my main group of interest.

As for whether all clade names are required to follow the PhyloCode: for now, it’s certainly possible to publish proposed definitions for clades without following the PhyloCode, but such definitions wouldn’t have any formal standing under any nomenclatural code, in much the same way that proposed genus and species names that don’t follow the appropriate code aren’t considered valid. Genus names can be given phylogenetic definitions following the PhyloCode (I defined a few in my paper), but they don’t need one to be valid genus names. The validity of genus names instead falls under the jurisdiction of one of the other nomenclatural codes (depending on the type of organism). As for species names, PhyloCode doesn’t govern those at all, per Article 21.1.

[albertonykus]

Do you agree with Gauthier, Padian, etc. that priority applies to names not covered by the ICZN (so that e.g. Ornithosuchia takes precedence over Avemetatarsalia despite excluding ornithosuchids)?

Whether or not priority does apply to such names is simply a question of whether any formal rules have been established that regulate their usage based on priority, and the answer to that is simple: there haven’t, therefore it doesn’t. The ICZN doesn’t cover them, whereas priority for preexisting names under the PhyloCode is determined by when the names were converted following PhyloCode requirements, and neither Ornithosuchia nor Avemetatarsalia have been converted yet.

As for whether priority based on date of naming should apply to these names, there’s more room for debate. I’m inclined to say that the date of naming is worth considering as a factor in deciding which names to convert under the PhyloCode. However, given that these names have generally been used without much regard to date of naming in the past, mandating it as a requirement for usage would likely work against taxonomic stability more than promoting it. In fact, PhyloCode Recommendation 10.1A encourages conversion of the most widely and consistently used (not the earliest coined) name for a given clade, under which Avemetatarsalia is undoubtedly better qualified than Ornithosuchia.

In any case, I’m under the impression that Ornithosuchia was originally coined to include Ornithosuchus, in which case Ornithosuchus would be required as an internal specifier under PhyloCode Rule 11.10 if Ornithosuchia were to be converted, and it thus wouldn’t be a synonym of Avemetatarsalia under our current understanding of archosaur phylogeny.

[albertonykus]

Re priority & Ornithosuchia: my understanding is that priority can also apply to which name was defined first, in which case Ornithosuchia would indeed supersede Avemetatarsalia.

The only formal set of rules that would be potentially applicable to this case is the PhyloCode, which is very clear that precedence is determined by the date of establishment. Establishment of names under the PhyloCode requires more than just a phylogenetic definition, and neither Avemetatarsalia nor Ornithosuchia have fulfilled those requirements yet. Thus, as far as PhyloCode is concerned, it’s a level playing field for these names at the moment, and neither takes precedence over the other.

And as I mentioned in my answer to the previous ask, it wouldn’t be possible to establish Ornithosuchia with a definition synonymous to our current concept of Avemetatarsalia under the PhyloCode anyway.

[jurassicsunsets]

Where are you getting your clade definitions from? I haven't seen any official list, since the PhyloCode isn't in force yet.

I generally use the ones that are most recently used in scientific papers, although I will admit to sometimes cheating and choosing two taxa that form an equivalent stem or node when I don’t know the exact taxa.

[albertonykus]

Is Jura's stance on phylogenetic taxonomy (as seen in his recent Ornithoscelida post) at all reasonable?

He is free to dislike phylogenetic taxonomy. That’s a question of opinion, not of science.

With that in mind, the reason phylogenetic taxonomy is currently “unstable” as he claims is that the PhyloCode has not yet been implemented. Once that happens, it will be more difficult to redefine clades at will. In fairness, the fact that the PhyloCode has not come to fruition after a ridiculous amount of time does not inspire confidence, but that’s a feature of human foibles, not of phylogenetic taxonomy itself. (Though it should be said that not all phylogenetic taxonomists like the idea of PhyloCode; ask @fezraptor about that some time.)

I also contest the notion that phylogenetic taxonomy inherently “waters down” meaning compared to traditional classification. Though some grades (such as “fish”) may be convenient concepts to have, I would be hard pressed to come up with an instance where talking about dromaeosaurids and sauropods at the same time but actively excluding Archaeopteryx is biologically meaningful.