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  1. Earlier
  2. Dear Anton. Great questions. I have been writing quite a long answer which may also be worth a wider readership given such interesting and relevant points, so pleaser bear with me, though anyone else is welcome to join in the response. Steve
  3. Greetings. I was just having a discussion with my brother about, whatever it makes sense to say, that the Neanderthals are extinct. So I was hoping that someone could point me to the definition of extinct used in biology. I also hope that someone could explain how or point me to an article about how hybridization is handled in phylogeny? Sincerely Anton
  4. Proceratosaurus - Was not a Ceratosaurian. It was actually a primitive Tryannosaurid, and they never bothered renaming it. Sinraptor - Means "Chinese raptor" but isn't a Dromaeosaurid (true raptor), though there are other non-dromaeosaurids with raptor in their name, but when they found an actual Dromaeosaurid in China, instead of calling it "Anything else"-Raptor, they named it Sinornithosaurus, meaning "Chinese bird lizard". They kept the "Chinese" part and ditched the "raptor" part. Saurus means lizard, which has lost absolutely all of it's meaning. I'm pretty sure there are more non-lizard Saurus's than lizards with that suffix. They've even included it in the name of at least one mammal (Basilosaurus). Not necessarily about dinosaurs per se, but the lineage of Archosaurs that led to Crocodylomorphs has been traditionally referred to as Crurotarsans and has included Phytosaurs. From my understanding, later studies determined that the crurotarsal ankle is actually an ancestral trait to all Archosaurs which was lost in the Avemetatarsalian lineage, which led to birds. The clade Crurotarsan now includes all Archosaurs and Phytosaurs which are now considered Archosauriformes. The name that is now used when referring to the croc-lineage of Archosaurs is Pseudosuchians. Please let me know if you think that I'm wrong about that.
  5. The classic model of Dinosaur evolution has two primary lineages. The Ornithischians and the Saurischians (Theropods and Sauropods). This model has been challenged by a model in which Ornithischians and Theropods fall under the clade Ornithoscelida, while Saurischia would include Sauropods and Herrerasauridae. This, would explain why feathers have been found in Ornithischian lineages as well as Theropods while no feathers have ever been discovered on any Sauropods. HOWEVER... Pterosaurs, which had diverged earlier, had feathers (I'm referring to monofilaments as feathers in this context), which might nullify that entire point, because the the potential to grow feathers is common throughout Ornithodira. Does anyone else have any thoughts on which model they prefer, or which one is more supported?
  6. Interested in helping to expand the project with my IT skills.
  7. Thank you for those links. "The Systematic Classification of Life" is my favorite youtube presentation I've seen so far. I've watched the entire series several times. As I was following the series through the PEP for the first time the other day, I got lost between Vertebrata and Gnathostomata, and fired off that inquiry. I appreciate your reply..
  8. Hi Preternat. So, I’m just trying to establish a couple of things. By being a preternaturalist, do you mean that you consider us (humans) to be outside or above nature or outside of the rest of evolution or something? I’m not aware that, ‘mother nature’ planned/plans anything and so if evolution develops intelligence enough to manipulate or alter genes, then that is an extension of the natural, isn’t it? You also mention that you are an atheist, so can you explain or reconcile these or show where I have misunderstood you? You want to communicate evolution to a wider audience. Great. There is lots of stuff available on the internet for this and that’s what the Phylogeny Explorer Project will do, too. The Phylogeny Explorer Project itself is not involved in religion or politics, but there are threads in the forums of this site that you can explore things a little more off the beaten path. Do you have any specific questions? Feel free, if you haven’t already, to join the Facebook group.
  9. Hi friend. It might be worth posting this on the Facebook group for quicker and more largely read answer. Here is one genetic comparison, but it's not my area: https://www.researchgate.net/figure/a-Cladogram-based-on-308-bp-of-gray-wolf-C-lupus-dog-C-lupus-familiaris-coyote_fig4_226328915
  10. Hi BangerDan. Please feel free to join our Facebook group if you haven’t already. Yes, AronRa has produced an excellent set of videos on the systematic classification of life along our clade line. He is also the creator of the Phylogeny Explorer Project, which aims to be the most comprehensive system, mapping the evolution of life, visually. In the Linnaean rank system (remember the DKPCOFGS), these are attempts at comparing ranks across groups – like mammals and amphibians, without regard for timeframe comparison and as though all were created at the same time. Whilst some equate to clades, the nested hierarchy (clades) of life are the true, natural order of things. The clades we tend to use and focus on, whilst naturally occurring, are man-made representative junctions to show key or notable divergences. So, whilst the point at which a notochord is first recorded is significant (for us) in ordering or explaining things, it is (in nature) of no more or less significance than any new species or divergence. Whilst having more clades than the following, (there are well over 100) the Phylogeny Explorer Project is however still in pre-production. Alternatives and recommendations in the meantime are: Open Tree of life: https://tree.opentreeoflife.org/opentree/argus/opentree12.3@ott93302 Timetree: http://www.timetree.org/ Onezoom: https://www.onezoom.org/
  11. I'd like to be able to follow the cladogram basically as presented in "The Systematic Classification of Life," and I think that would be of interest to other lay people as well. Is there a list of every clade we could use, or a cladogram with that "route" highlighted?
  12. Nuts, I'm rarely able to write, edit and re-edit enough before edit time expires. Just wanted to add, my main interest here is to find new ways to communicate evolution to people, even those people who "just don't get it" while believing in other strange things.
  13. My moniker "preternat" is not a brag about how preternatural I am (because I'm not, compared to other humans), but it's a reflection of my belief that we humans are "preternaturally" distant from our evolutionary origins. Obviously Mother Nature never planned for us to become so powerful a culture, so in a sense, imo, we're evolutionarily in uncharted and often dangerous territory... which (again imo) can probably help explain our current diseases, successes, psychology, optimistic vs dark natures, and so on. Personally, I'm in my mid-60s, keenly interested in all sciences, but especially interested in evolution. And interested in politics, as in searching for how we can improve on (e.g.) the current state of two-party power and corruption in USA, and how it distracts us from progress in scientific, social issues, and so many other positive endeavors. I'm also a mod at an atheist website, which I would mention here if it weren't for the fact that I'm still rather anonymous as an atheist. I once even considered "infiltrating" Scientology as a member, but fortunately didn't follow through. Perhaps someday I'll get over this handicap of keeping a low, personal profile. (I have kids, too. I've already admitted more than I feel totally comfortable with.)
  14. Guest

    Evolution of Canis

    I have been looking into hybridization between coyotes and red and gray wolves. It seems to my untrained eye that these three clades represent one diverse species because they have no problem reproducing with one another and producing viable fertile offspring. So whats your opinion on the idea that there all the same species and that they've been misclassified?
  15. “New study, re-writes evolution.” How (or) would YOU present a highly technical, specialist article to the general populous? Your editor (who pays you) has deadlines and targets for time, costs, readership and competing rivals’ articles. This blog is in response to (yet) another article which supposedly re-writes the theory of (in this case, shark) evolution. It tries to highlight the problem of and reasons for such article headings, looks at and compares the results of changing them from the origi8nal and asks what, if anything, can or should be done given the circumstances. I owned a shop once and one customer said that it would be nice if we had wheel chair access toilets. We had wheelchair access and wheelchair access toilets were available very close by in a larger shop. The cost of putting them in was prohibitive too, meaning no such shop to use in the first place, thus defeating the object. By trying to offer more, I (and all) would have lost all. Many of the good quality newspapers are struggling right now with such low readership. On the other hand, the British red tops (which are far more popular and reflect the greater national readership population) do pretty well. I’m sure there is a direct correlation between the quality of journalism and the survivability of the press in the UK. Too few want pure quality. Some may recall the Sunday Sport newspaper post I posted some time ago, demonstrating the level it goes to for readership. And true, those wanting it are the driving force of the editor. Spin, exaggeration, scraping the barrel, lies are things that sell. Few want straight facts. And I believe that goes for many of us, here too. In fact I have posted original research here and had little response, but when posting articles (even) from the same said report, as edited in a more popular or simplified magazine or newspaper with graphics and a fancy tag line, it gets views… It also gets read! And it also gets criticised for exaggeration or a misguided title. But it gets read as opposed to not read. If you want a technical article published in a general, miscellaneous, non-academic daily/weekly/monthly, you have to make very significant changes to attract any interest. Yes, even Time magazine, National Geographic and Nature have succumbed to targeting with overly dramatic images or titles which can play into the hands of science deniers. Look at it from the publisher’s perspective – they have to sell, compete, pay staff and survive. Where does one draw the line? It is a difficult one, when one considers all aspects or places oneself in the position of an editor. How many of us subscribe to the journals which publish original work? Would you digest it, understand the words? If competing with an edition of Punch or Private eye, which do you go for? Are you privileged or rich enough to access these journals? Does or did anyone get psychological tiredness, perhaps at university? When you want to do something you enjoy and it not taxing, you are full of energy and up for it. When it comes to study, you suddenly feel really tired. I did and still do. Youtube is a great help and bridge/gap builder! There is similar discussion in Christian and Muslim circles about Holy books. Some traditionalists argue that only the original language should be used, as it is the word of God and should not be changed. But only those few who know those languages can access it, but it is argued that all should learn it). Or should it be translated into many languages and perhaps simplified or adjusted to, ‘meaning related’ context so that more can understand and access it, at the price of some meaning, clarity or eloquence (this is an aspect of hermeneutics). Here's an article (just made up) showing 4 different views and asking which one or style would YOU read or be attracted to, if any, perhaps if the subject matter interested you (which is another trick that journalists try to widen to get readership)?
  16. @Ross Murphy Phylogeny Explorer Project facebook group can be found here https://www.facebook.com/groups/phylogenyexplorerdevelopment/
  17. Ok hi. I'm not on the Facebook group. I literally only joined Facebook during lockdown, because some friends wanted to play DnD through it. Can you link me to the group?
  18. Hi Ross. I can't seem to find you on the Facebook group and we seem to have lost contact. Apologies if this is my fault. Please do get back in touch if you can.
  19. Welcome to Phylogeny Explorer Project. Please feel free to look around and get to know the others. If you have any questions please don't hesitate to ask.

  20. Hi Jaz welcome to the project. I hope you enjoy your stay here.
  21. Well put! Just as a side note, these distinctions in all the sciences (not just bio) often seem pretty arbitrary especially in small samples or close up. For instance the difference between glass and quartz, they both have a molecular structure of one silicon and two oxygen (SiO2). In glass the molecules are all over the place and in quartz they are in nice ordered rows and if your sample is absurdly small (say two molecules) then you can't tell if they are nicely ordered or if they are amorphous/unstructured thus defining the sample as either is difficult. You see the same issue when trying to determine the boundary between our atmosphere and space, how little atmosphere is needed before it can be called space.
  22. Hi Abe. Those are good questions. We had a live book club event on youtube on Saturday with Aron Ra about his book, ‘Foundational Falsehoods of Creationism’. Not sure if you knew or were there. On the first one. I will start by an examples to set the scene. If you take a scan of a foetus in the womb, then a photo of the new born baby and on through the person’s life until s/he dies, you have very different images and stages. A baby, a child, a teenager, an adult, a middle ager and an old person. We give them man-made names that we create for identification purposes, but they are still one, single person throughout. The genetic code is the same, from where we can know this. So whilst a foetus may have little morphological resemblance to the pensioner, we KNOW (can test and prove) that they are one and the same. And a photo of two foetuses or babies or people, no matter how alike they may appear, we can know that they are not the same, by the same (and other) method(s). If we found tree-like structure on another planet that looked identical to an oak tree on earth, then it is possible that it is more similar to a rock or an elephant, because by similarity we mean relatedness. The tree from another planet would actually not even be a part of the, ‘tree of life’, because it has no place in it, just like all the aliens in film and TV, despite their humanoid appearances and they would not be able to interbreed with humans or earth life. The whole genetic (or otherwise) structure would not correspond. And we also know that a dog, a hyena, a coyote, a fox, a wolf and a thylacine are different and why and how different, by the genes, which is really helpful when they look alike. In previous centuries, we did not have genetics, so morphology and physiology were key concepts in deciding classification. So, whilst a baby is different from an adult in many ways, in terms of relatedness or ancestry, they are one and the same. And the biological parents are the last generation and so on. With genealogy, we (think we) can trace our parents back for centuries or more, but technically, we can’t, because if any mother had an affair, or secretly adopted or records got mixed up, we would not have a true ancestry and from the first erroneous parent, all previous ones would be wrong. Evolution does not operate from parent to parent – this would be impossible to keep track. It works on a species or population level. This means that if an offspring is illegitimate or a parent has multiple partners and even if there is some hybridization with a different species, it doesn’t really matter, because we are only concerned with species (or things that can viably interbreed), and that is sufficient. Due to the fossil record and many other factors, we can establish relatedness beyond the limits of genetic sampling. So, it is not really possible to take a genetic sample for things that are millions of years old due to degradation of tissue. This is when morphology, fossil order and other known or determinable factors come into play and confirm (or otherwise) one another. So, how do we know that amphibians evolved from fish and reptiles from amphibians and creatures with internal skeletons from ones that had none? The forms can be traced in the fossil record. Whilst amphibians exist now, when amphibians first emerged, there were no reptiles. We can further trace the skeletal evolution which just so happens to exactly match the geological order. And when we test living amphibian and reptile genetic markers, it matches to that ancestry. We can therefore make predictions that if true, support this concept, and this has been done many times and is counted on when searching for fossils today. Tiktaalic was such a prediction and found what (described morphology) where (geography) and when (geologically) discovered. Now, we are descended from animals that do not have backbones or internal skeletons. These have a term called, ‘invertebrates’. This is a helpful term used to describe that group of animals, but it is not a term used in cladistics because it has no place. Like saying person A is male, person B is female and person C is tall. We can describe people in terms of sex, height, race or interests etc. but you can’t mix it up. So, whilst we are descended from animals that had no backbones (invertebrates) we are not invertebrates, because that mixes terminology. When only invertebrates existed, they were never called invertebrates any more that they were in-circus actors. Invertebrate is a hindsight term used to look back and mention a unifying similarity. They lacked back bones just as much as they lacked the ability to act in a circus (which some people and other animals do today). So, to a circus performer, all other life is an incircus act (invertebrate comparable). In order to talk about ancestry, we need to stick to the correct and same terminology, like for like. So, whilst many scientist will tell you that you are a fish, they are wrong, because a fish is not an actual clade. You are (in increasingly larger key clades, simultaneously) a human (Homo sapien sapien), a hominid, an anthropoid, a prosimian, a primate, a placental, a mammal and so on. So, you can simultaneously live in your house at the same time as your street, village, town, state, country, country, region, continent etc. It’s just a matter of how specific you want to be. To your neighbour, you live at number 45. To a Japanese pen-pal, you start off by saying you live in Europe (or wherever). It’s about perspective. So, as life is all related, we have closer and further removed relatives. We are closer related to other apes than to dogs and further removed from oak trees, but at some point, we are related and shared a common ancestor with everything and with a phylogenetic tree of life, you can find the point at which any two different species split off to form new species. It can be termed the law of monophyly. A true clade is monophyletic, meaning that it is a nested hierarchy containing all and only those species within a point (clade node) of divergence. In 10 million years time, our species may still be here or have died out, but our descendants, however different, will still and always be homo, apes, mammals etc. Our cladistics lineage remains and cannot be altered or5 grown out of. In fact, we evolved from a creature that evolved an anus before it evolved a mouth (where some creatures evolved the other way round). So, it would be phylogenetically true and fair to say, once an arsehole, always an arsehole! Regarding your second point. A clade is basically a speciation event. A species is a very difficult and argued about term which is confusing to science and the world at large, because it is used differently by well informed people. This is a whole lecture on its own. If we assume for arguments’ sake, that a species is a population of related organisms that can interbreed and have departed, genetically or geographically or behaviourally from other close relatives such that they no longer interbreed (even if they are still inter-fertile), then these are examples of speciation and would justify a new species/clade. So note, speciation takes time and is a population (not an individual) event. Search, ‘ring species’ for an example of observable speciation. Note also that one species never gives birth to another species or anything that is hardly any different to itself. This is what evolution predicts (to not do so would defy evolution). Imagine a gradient from red to blue. At any point, it is identical to its neighbour. You have to zoom out and compare distant places to see or notice the difference. I hope this helps. Thanks for your interest. There are many of us who have left fundamentalism and who were conned by Creationism. Do please joint our journey into supporting or providing a visual tree of all life, demonstrating the fact of evolution. Steve
  23. Jaz


    The merging is complete!
  24. Hope everyone is doing ok in these trying pandemic times!
  25. Hi all, what a wonderful project! I am currently a cs student but I started my education first in biochemistry, then geology and finally I settled into computers! I have always been a huge fan of taxonomy and databases in general especially when it comes to the sciences. I have always found that one of the big drawbacks in science is that it is not especially accessible to most people who just want to take a look at what we know without becoming scientifically literate. Projects like this go a long way to making science approachable to many who may find it intimidating. I love to learn about what we as a species have discovered and I can't wait to help out with this explorer in any way that I can. I have applied to volunteer in the dev side of things as well as a bit of data entry but if there is anything in particular that needs doing, I am more than happy to try!
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