tag:blogger.com,1999:blog-1592175903857348966.comments2024-03-29T08:29:23.265+01:00Res.I.P. – an unprofessional science (and other things) blogDas Grimmhttp://www.blogger.com/profile/13213125622809796109noreply@blogger.comBlogger83125tag:blogger.com,1999:blog-1592175903857348966.post-90961373125409675492023-12-19T09:11:38.642+01:002023-12-19T09:11:38.642+01:00Posted by crapcyclelanes, 19 Dec 2023:
"Immen...Posted by crapcyclelanes, 19 Dec 2023:<br />"Immensely frustrating system. Dealing with adding accents or special characters? Cutting and pasting a complex bit of text or sentence, including moving a sentence within the text? Seems impossible. Even, adding a completely new reference - where does that happen?"<br />[I accidently flagged and deleted the original comment as spam, apologies for that]Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-1592175903857348966.post-77142905550726910322022-09-06T08:53:30.819+02:002022-09-06T08:53:30.819+02:00Paleontology and Evolutionary Science is the topic...Paleontology and Evolutionary Science is the topic section within the journal <i>PeerJ</i>. <i>PeerJ</i> is, to my opinion, currently one of the best journals (if not the best) and honest publisher on the market (reasonably low APC, highly professional paper handling and proofing) because they have a very strict open data policy, and actively promote peer review transparence. If the authors opt for it. So, it's very easy to see how good a paper is. If an established veteran author doesn't opt to publish the peers' reports on the articles page, it's a sign it was pal-reviewed or included some unpleasant (to the veteran author) reviewer comments. Note that pal-review is pretty common, and including flagship journals such as <i>Science</i> or <i>Nature</i> (a <a href="https://researchinpeace.blogspot.com/2020/02/surviving-parsimonists-just-tree-naive.html" rel="nofollow">recent example</a>). Review transparency (see <a href="https://researchinpeace.blogspot.com/2017/09/the-review-process-should-be.html" rel="nofollow">my second Res.I.P post</a>) is the only counter-measure against (inevitably) compromised peer review.<br /><br />Furthermore it promotes post-publication discussion by its (starting to be used) Q&A option. Which is a good thing to do. We cannot expect anymore that a single reviewer knows all there is to know about a study, and being an handling editor, having to find people willing to do proper reviews, is the worst possible job in all of science.<br /><br />We hence explicitly chose <i>PeerJ</i> as venue for all our research including the Osmundaceae systematics, where we could expect hostile fire from the Mighty (incl. cladistic) Beasts of the Forest of Reviews. Because they don't like to see their profoundly destructive otherwise "anonymous" and "confidential" reviews out in the open. <br />For more on the topic, see my <a href="https://researchinpeace.blogspot.com/search/label/%23FightTheFog" rel="nofollow">#FightTheFog</a> posts.<br /><br />With <i>PeerJ</i> we still got critical but profoundly constructive reviews, much in contrast to most reviews for studies we published with Holtzbrinck's (SpringerNature) or RELX's (Elsevier) cashcows. Because, cladism is the Holy Truth in palaeo- and neobotany, too, and, very obviously, most fields of palaeozoology. I have not yet crossed any palaeoverterbrate study that would fulfil my minimum standards for phylogenetic analyses. Those dealing with groups that still live today (bears, wolves, hominids) are much better in all methodological aspects (probably because any gene sequence kills the finely tuned morpho-cladogram, so you have to be a bit more open-minded rather than keep spinning the rat-wheel).<br /><br />Really can recommend publishing there.Das Grimmhttps://www.blogger.com/profile/13213125622809796109noreply@blogger.comtag:blogger.com,1999:blog-1592175903857348966.post-85705564326684169962022-09-05T21:58:22.774+02:002022-09-05T21:58:22.774+02:00Just a quick question for now: what do you know ab...Just a quick question for now: what do you know about PeerJ.com? I only came across it last month, through an article in one of its many journals, PALEONTOLOGY AND EVOLUTIONARY SCIENCE (yup, it's in all caps). The 2019 article I skimmed included the cladism zealot Mickey Mortimer as one of its co-authors, and so far I am unimpressed by it. Do you happen to know anything about its reputation among evolutionary biologists, and of PeerJ.com among scientists in general? <br />pnyikoshttps://www.blogger.com/profile/00945669460553697323noreply@blogger.comtag:blogger.com,1999:blog-1592175903857348966.post-86013911358274963512022-09-05T12:09:20.940+02:002022-09-05T12:09:20.940+02:00For extinct-extant groups it's very straightfo...For extinct-extant groups it's very straightforward to assess the <i>phylogenetic distance</i>, i.e. the distance between two tips over the tree (or all possible trees, i.e. the species network) or all members of a subtree/ putative taxonomic group to each other, in relation to their absolute distance. And use this as guideline for erecting taxa (holophyletic and paraphyletic ones) because we can use the molecular data (supposedly neutrally evolved) to correct inherent bias in the morphological data (e.g. due to positively selected traits, homoiologies, symplesiomorphies misinferred as synapomorphies (and v.v.; clades easily become grades and v.v. in phylogenetic trees in any part comprising short internodes). And the morphological (dis-)similarity to decide which of the 2n+2 clades in the rooted tree should be named. This is now pretty much the standard when neosystematicists talk about “monophyletic” groups (genera, tribes, families, orders), you may read “cladistic classification” but in strictly speaking it's a clado-phenetic or pheno-cladistic classification.<br /><br />For extinct groups, it's much more difficult, since we lack the much needed comparative data. It's obvious morphological evolution was not parsimonious and that similarity can be severely misleading, too. So, one really needs to assess the stability of the background tree and explore the signal in the matrix. And keep an critical eye on one's “synapomorphies” or unique character suites characterising a holophylum. <br /><br />As exemplarily seen in king fern rhizomes, for (palaeo-)systematics fusing “cladistics” (in the traditional sense, i.e. pre-Farris) with phylo-phenetics (viewing distance distributions in an explicit phylogenetic context) is a viable way to do it (open access paper): <br /><a href="https://peerj.com/articles/3433/" rel="nofollow">Bomfleur et al. (2017), <i>The fossil Osmundales (Royal Ferns)—a phylogenetic network analysis, revised taxonomy, and evolutionary classification of anatomically preserved trunks and rhizomes</i></a><br /><br />The same procedure and logic could be applied to all purely or mostly extinct<br />groups, and I've no doubt it would lead to much more stable <i>phylogenetic</i> classifications: having names and explicit thresholds for when we should give a clade a name, and where we have to do with (potential) paraphyla to keep things simple and applicable (the number of unranked "Clades" between the MRCA of today's Aves and the MRCA of all related dinosaurs is simply ridiculous and pointless).<br />Das Grimmhttps://www.blogger.com/profile/13213125622809796109noreply@blogger.comtag:blogger.com,1999:blog-1592175903857348966.post-44496373173696850092022-09-04T23:20:52.247+02:002022-09-04T23:20:52.247+02:00Thank you for letting me know of an ongoing effort...Thank you for letting me know of an ongoing effort to combine tree inferences and disparity; I didn't know such an effort existed on such a scale. <br /><br />I've been reviewing discussions in sci.bio.paleontology back in 2016, and it impressed on me the way doctrinaire cladists are still stuck in the false dichotomy between cladistics and phenetics. This also seems to have been the blind spot of both sides in the "cladist wars". In both cases, the paleontological point of view of Romer was missing, because the majority of systematists deal in extant taxa.<br /><br />In our 2016 discussion/debate, the cladist side could see no use for tools from graph theory such as finding the length of the path from one species to another, given that the graph was a tree. That is, of course, because they were thinking purely in terms of the number of nodes separating the two species in the tree.<br /><br />But here is exactly where disparity between two successive nodes comes in. The line segment joining them is given a number estimating degree of disparity, and the numbers are added together to compute the length of the path.<br /><br />The concept of "more closely related" then could be given a whole new meaning -- or, rather an old meaning but now quantified. We would be able to say that vertebrate A is more closely related to B than it is to C even when the LCA of A and B is strictly ancestral to the LCA of B and C. <br /><br />Example: A = Panderichthys, B = Tiktaalik, C = Homo. A cladist would say B and C are equally distant from A because they are in a clade that excludes A. <br /><br />A pheneticist would agree with the disparity measurer in this example, but I think it is not hard to cook up an example where evolutionary convergence could make the pheneticist disagree with the disparity measurer, because the latter takes a plunge down the tree and back up to do the measuring, but the pheneticist hops across the tree in a beeline from one species to another.pnyikoshttps://www.blogger.com/profile/00945669460553697323noreply@blogger.comtag:blogger.com,1999:blog-1592175903857348966.post-36549225532490306092022-08-29T09:04:14.163+02:002022-08-29T09:04:14.163+02:00Regarding the rejection of paraphyletic taxa, it&#...Regarding the rejection of paraphyletic taxa, it's important to realise that this the official scientific standard, also among neontologists. I very early stopped discussing this with those you called “cladophiles”. It's really just the people who work at the coalface of evolution (within generic lineages, above and below species, where all the fun stuff happens) and at the intersection of neo- and palaeontology who beg to differ—we like to give fossils Linnéan binominals, and this is simply impossible in the presence of potential ancestors/ ancestral forms without either collapsing well-circumscribed, coherent holophyletic modern-day taxa or introducing paraphyletic genera (see my posts on “What is an angiosperm?” for a prominant case). Professional (i.e. being paid to do science), ex (i.e. not being paid anymore) or amateur (i.e. never been paid to do research): anyone really dealing with the data we handled, simply cannot adhere to the theory of cladistic systematics. Which, by the way, much differs from the practise: we have numerous “non-monophyletic” accepted genera and modern-day species; and for a vast number of fossil genera/species, it has never been tested, or cannot be e.g. for any fossil-species (and extinct genus) based on a single skeleton. <br /><br />From a purely professional point of view, speaking a formely tax-paid scientist dealing with evolution and biodiversity, it's utterly instable and pointless to define all biological taxa, including genus-species pairs – the biological units we ultimately name (and count for biodiversity) – merely on their position in an inferred phylogenetic tree. <br /><br />But terminology is always something a scientific community should be able to discuss and adapt, where needed, and even on a case-by-case basis. There is no ultimate model or truth. Mother Nature is simply too complex, no matter how fancy the (thought) model, it will always beg to differ in not few cases.Das Grimmhttps://www.blogger.com/profile/13213125622809796109noreply@blogger.comtag:blogger.com,1999:blog-1592175903857348966.post-90207432277898434022022-08-28T23:11:09.599+02:002022-08-28T23:11:09.599+02:00Glad to hear from you, Das Grimm. I've posted ...Glad to hear from you, Das Grimm. I've posted to forums of your caliber from time to time, but one or two years "too late" and almost never got a response.<br /><br />Let me tell you a little bit more about the cladophile [1] whom I told you about. His name is John Harshman, and we have regularly crossed swords in the Usenet newsgroups talk.origins and sci.bio.paleontology since December 2010. We tolerate each other because we are the two best paleontology and evolution and systematics "experts" [2] in these newsgroups and we convey enough scientific information on our posts to keep each other reasonably content. I have learned a great deal in this way. <br /><br />[1] My term for those who will not countenance paraphyletic taxa nor any offshoot like trees showing direct ancestry, such as Richard Zander's, in peer reviewed papers in leading journals. Harshman is such a fanatical cladophile, he has complained about this term even though it does not have any negative connotations, probably because he knows how much I dislike that attitude.<br /><br />[2] Right now, there is an ongoing discussion about the proper use of the terms "paleontologist," "amateur paleontologist," and "real paleontologist." My stance is that neither of us qualifies as any of the above: to be amateur paleontologist, I would have to participate in at least one fossil hunt in each of ten years, and so far I'm only up to three. To be a "real paleontologist" I would also have to contribute significantly to a research article in a respected peer-reviewed journal. And to be a "paleontologist" without qualification I would have to be paid for this kind of work on a regular basis.<br /><br />This discussion is important because there is no such thing as a licensed paleontologist. This is in contrast to the existence of licensed geologists. <br />pnyikoshttps://www.blogger.com/profile/00945669460553697323noreply@blogger.comtag:blogger.com,1999:blog-1592175903857348966.post-57552891164577701592022-08-16T10:16:24.379+02:002022-08-16T10:16:24.379+02:00PS Regarding the lack of comments. This is not sur...PS Regarding the lack of comments. This is not surprising. First, my Res.I.P blog is not really trending: right now, this particular post has accumulated 666 "views" (quite fittingly...) <br /><br />A rule-of-thumb is that 25%-50% of Blogger-views are bots. Plus, there are probably multiple views by the same recipient (only Google will know).<br /><br />Let's say this post has been viewed by a 100– 200 different humans.<br /><br />My posts are generally long, too long for most blogpost consumers: the number of actual readers will hence be even lower. Maybe ~50.<br /><br />Given the provenance of my post's views, I suppose most of the &plusm; regular human viewers are people familiar with my work, inevitably sharing my philosophies (stemming from dealing with real-world data not coming from a philosophical viewpoint). They have no reason to comment; they simply enjoy reading and maybe pick up the one or other idea. <br /><br />That leaves maybe a dozen or two new ones accidently crossing this when browsing for a definition. Most will be freshlings (an establish researchers knows the truth, doesn't have to look anything up, right?) They may find it very interesting but wouldn't feel confident to comment. At best they discuss it, try to apply it in their own research. At worst, they discuss with their cladist supervisor and are informed how wrong they are.<br /><br />Now, there are a lot of established researchers strongly opposing the content of this (or any other my posts, and our peer-reviewed papers). They wouldn't have any reason to comment either, because any faith thrives on the simple ignorance of facts contradicting one's believes. Let's say such a person would read beyond the first line through the entire text: such a person's could only be profoundly negative. <br /><br />So, it's actually a good sign to have no comments. It shows, in the optimal case, that the faithful, if any of them has read this, can't think of an argument against it :)Das Grimmhttps://www.blogger.com/profile/13213125622809796109noreply@blogger.comtag:blogger.com,1999:blog-1592175903857348966.post-70008616295708553612022-08-16T09:28:47.791+02:002022-08-16T09:28:47.791+02:00I enjoyed his papers, too, having crossed them whe...I enjoyed his papers, too, having crossed them when I was just a fledgling. His paper on branch support is one of <a href="https://researchinpeace.blogspot.com/2017/09/two-papers-you-may-want-to-read-before.html" rel="nofollow">“two papers you may want to read before inferring trees from morphological (or other) data”</a>. If more people would have read his papers, more reviewers acknowledged the issues in them, a lot of pointless and inherently instable re-classifications could have been avoided.<br /><br />We also used "evolutionary tree" often in contrast of "phylogenetic tree" because reviewers made us believe and misconceived that the latter is a propriatory trade mark of cladistics. And we never just wanted to infer phyl(ogen)y, we wanted to reconstruct the evolution of our study objects.<br /><br />But of course, since phylogenetics are (substantially older) than cladistics, such a distinction may not be really necessary. We just need to correct any cladist telling us otherwise, with the very concrete example at hand: the paper just reviewed by the cladist peer. (It was tough at the start, after a decade of battling the Mighty Beasts in the Forest of Reviews, we faced little to no resistance.)<br /><br />David Morrison has pondered such terminology issues in various posts on the Genealogical World of Phylogenetic Networks.<br /><br />A nice early collection of very evolutionary trees are in his 2012 post <a href="https://phylonetworks.blogspot.com/2012/07/evolutionary-trees-old-wine-in-new.html" rel="nofollow">Evolutionary trees: old wine in new bottles?</a><br /><br />While originally (before Hennig, Farris, etc.) phylogenetic and evolutionary graphs (trees or networks) where and still usually are synonymous, it could make sense to discern between them because phylogenetic methods can be handy to classify, categorise, sort or just visulise non-biological data including data sets that are not the product of evolutionary processes, i.e. not depicting ancestor-descendant relationships (such as <a href="https://phylonetworks.blogspot.com/2018/01/false-reports-of-us-womens-breast-sizes.html" rel="nofollow">U.S. breast sizes</a>, <a href="https://phylonetworks.blogspot.com/2018/07/a-network-of-world-happiness.html" rel="nofollow">world happiness</a>, <a href="https://phylonetworks.blogspot.com/2018/06/to-boldy-go-where-no-one-has-gone.html" rel="nofollow">Jovian and Saturnian moons</a>)<br /><br />If I use a phylogenetic method like Maximum likelihood or Neighbour-Net, I infer a phylogenetic tree or (meta-)phylogenetic network.<br />But only if this phylogentic graph depicts an evolution of some sort (biological or a-biological, e.g. the <a href="https://phylonetworks.blogspot.com/2019/06/a-phylogenetic-network-outside-science.html" rel="nofollow">evolution of Linux systems</a>), it is an evolutionary tree or network.<br />Personally, to depict the inferred evolutionary pathways, I do prefer other <a href="https://phylonetworks.blogspot.com/2018/02/tree-metaphors-and-mathematical-trees.html" rel="nofollow">metaphors: cactusses and corals</a>. But since they are interpretations of algorithm-based inferences, not computer-generated graphs, reviewers usually refuse them as "Results", one has to move them to "Discussion" or the supplementary information.Das Grimmhttps://www.blogger.com/profile/13213125622809796109noreply@blogger.comtag:blogger.com,1999:blog-1592175903857348966.post-48039212320878317912022-08-16T08:35:57.427+02:002022-08-16T08:35:57.427+02:00I wouldn't say it made little progress because...I wouldn't say it made little progress because there are whole groups of organisms (such as bacteria, single-cell metazoans like foraminifera, invertebrates at various levels, fungi, primitive plants, any research close to the speciation horizont, any research involving fossils, ancestors, and their modern counterparts, descendants, like everything I was involved in) still or just now classified dominately using combination of tree inferences and absolute disparity. <br /><br />It's just not so visible, not promoted so fiercely that it sipped into the mainstream of the great classifications: vertebrates and angiosperms.<br />But it may be just a matter of time: the more dense our phylogenomic datasets become, the more difficult it will be to infer that single-best tree cladistics needs to classify. The only reason, cladistics have become mainstream for classification is its simplicity: one doesn't need <i>any</i> prior knowledge to define groups based on a tree.<br /><br />I guess, in the long run, defining "valid" taxa solely based on high-supported clades in inferred trees (inferred clade = holophyly, an equation that too often just doesn't hold) will only survive at mid-/high-hierachical levels in <i>(i)</i> angiosperms because the big lineages are data-wise trivial to discern having high coherence: their members are much more similiar within than with anyone outside the tribe, family, order) and <i>(ii)</i> extinct groups of vertebrates, where one has a huge amount of morphological-anatomical characters to code but runs no risk that molecular data reveals the character suites behind clades or detected synapomorphies are at worst composed entirely of convergences, at best homoiologies and/or (ironically enough) Hennig's symplesiomorphies.Das Grimmhttps://www.blogger.com/profile/13213125622809796109noreply@blogger.comtag:blogger.com,1999:blog-1592175903857348966.post-88611106830895494802022-08-14T00:40:35.824+02:002022-08-14T00:40:35.824+02:00It's sad that no one has commented on this pag...It's sad that no one has commented on this page since it was set up. Someone could have mentioned the work that Richard Zander was doing in producing trees that show direct ancestry. One can read about it here:<br /><br />https://en.wikipedia.org/wiki/Evolutionary_taxonomy<br /><br />A note on terminology: cladists would have you think that "phylogenetic trees," by definition, means trees with all organisms at branch tips. Zander accordingly calls his trees "evolutionary trees." When I mentioned this to a zealous cladist, he called this move "unfair!" and thus displayed his use of double standards.pnyikoshttps://www.blogger.com/profile/00945669460553697323noreply@blogger.comtag:blogger.com,1999:blog-1592175903857348966.post-61424801188724039502022-08-13T23:21:44.894+02:002022-08-13T23:21:44.894+02:00I've been trying to find out about the "c...I've been trying to find out about the "cladist wars," which produced a revolution in biology, whose fallout you, Das Grimm, are ably dealing with. The essays I've read so far are (1) long on generalities and short on details and (2) have little to do with the issue of which I am most concerned: the demise of the Linnean system of classification, including the banishment of paraphyletic taxa and the resulting forcing of all organisms to the branch tips of phylogenetic trees.<br /><br />The only specific event of those wars that I have ever read about (from two different sources, one of which I own: Kenneth S. Thompson's LIVING FOSSIL: The Story of the Coelacanth) is the 1978 event "the lungfish, the salmon, and the cow". It had to do with a corollary of item (2) above, the radical redefinement by cladists of the word "related". The anti-cladist side claimed that it was absurd to regard a lungfish to be more closely related to a cow than to a salmon, but that was a naive choice of taxa, and the outcome was an undeserved victory for the cladist side.<br /><br />Had a competent vertebrate paleontologist been involved, the choice of taxa could have been very different. One choice readily available at that time was "Bos, Ichthyostega, Elpistostege." [Nowadays, the third is better replaced by the more familiar Tiktaalik.]<br />It does violence to our ordinary idea of human relationships to claim that Ichthyostega is more closely related to us human beings than it is to Elpistostege. It's almost as bad as saying that Mitochondrial Eve is more closely related to everyone alive today than she was to anyone in her family at the time she was born.<br /><br />Had the victory gone the other way, we might be far advanced in a definition of "more related" that combines phylogeny with measures of disparity. As it is, the theory of macroevolution, to which disparity is an indispensable tool, has made comparatively little progress to date.pnyikoshttps://www.blogger.com/profile/00945669460553697323noreply@blogger.comtag:blogger.com,1999:blog-1592175903857348966.post-33804383223467360952022-04-19T06:26:24.696+02:002022-04-19T06:26:24.696+02:00This is a masterpiece. thanks for sharing the know...This is a masterpiece. thanks for sharing the knowledge.Anonymoushttps://www.blogger.com/profile/03589059762571291817noreply@blogger.comtag:blogger.com,1999:blog-1592175903857348966.post-4662632185883160772022-01-10T16:06:28.093+01:002022-01-10T16:06:28.093+01:00Thanks.
It's not that difficult. A proper edu...Thanks.<br /><br />It's not that difficult. A proper education (state-guaranteed and -funded), an open eye, a basic curiosity for the world, and common sense is all that's needed.<br /><br />And free time: There's a lot of useful free-to-access data out there and well-done websites. They are only not as much visited as the crab ones. <br /><br />Most people use the internet to find filth. If not porn, it's right-wing "alternative media" providing a safe bank for utter dirt (pretty main-stream given their access numbers and followers).<br /><br />There's also the monetary aspects. To start earning money with blogs, you need at least 10,000 visitors a month (rule-of-thumb), activating Google's AdServ. That's a number, you don't get without serving the demand of the many. Lies and superficial hypes sell not only better but are also much quicker to produce. That's a constant in human society.<br /><br />I can spend days drafting a post, look in things that interest me, because I don't need to (or intend to) earn a cent with this blog.Das Grimmhttps://www.blogger.com/profile/13213125622809796109noreply@blogger.comtag:blogger.com,1999:blog-1592175903857348966.post-91562029218703126852022-01-08T12:33:20.598+01:002022-01-08T12:33:20.598+01:00Can I just say what a relief to discover somebody ...Can I just say what a relief to discover somebody who genuinely understands what they are talking about on the net? You actually know how to bring a problem to light and make it important.<br />imrankhttps://gntme.com/ws-c3560cx-12pc-s/noreply@blogger.comtag:blogger.com,1999:blog-1592175903857348966.post-53465823334783710132021-11-02T09:54:19.154+01:002021-11-02T09:54:19.154+01:00I got the same mail. It was a quick research about...I got the same mail. It was a quick research about the mail that made me to read this. I will say it is a very useful tool to use for anyone so contacted. I was alarmed when I was told I would have to pay £1400 for me to be able to contribute a chapter. Thanks for taking your time to write this.Maclawrence Famuyiwahttps://www.blogger.com/profile/16378781334533763112noreply@blogger.comtag:blogger.com,1999:blog-1592175903857348966.post-30125933535033162752021-09-30T12:10:19.998+02:002021-09-30T12:10:19.998+02:00All non-profit sciences still have a generally hig...All non-profit sciences still have a generally high level of integrity. It's far from cloud-cuckoo land and there are very foul apples, but it's typically (getting fewer and fewer) old white males forcing their young researchers to follow their faulty ways. And there are of course self-interest groups, that purposely ride dead horses to keep the rubels rollings (German saying). I covered examples of this in my <a href="https://researchinpeace.blogspot.com/search/label/bad%20science" rel="nofollow">bad science</a> category.<br /><br />The first major problem is the confidential peer review process. The Jiang et al. paper is not "bad science": the authors did, compared to many other papers in the field, a very good job—but only to an unwitting researcher's eye, who has no idea about the data and organism. We cannot tell how rigorous the review was, because there's no <a href="https://researchinpeace.blogspot.com/2017/09/the-review-process-should-be.html" rel="nofollow">transparency in the review process</a>. I didn't get this paper to review, neither my beech-knowing colleagues. Giving the spectacularity of the data, one may wonder why this paper has been published in Chinese journal with domestically inflated impact factor and not some fancier journal such as e.g. <i>J Biogeogr</i>. Maybe they tried, and got rejected. But <i>JSE</i> is a natural choice: even if there was a challenging review, the prominence of the last author would have assured, it can be largely ignored. <a href="https://researchinpeace.blogspot.com/2019/02/peer-review-transparency-reveals.html" rel="nofollow">Provincialism is a increasing problem in peer review</a>, gradually replacing classic peer review imperalism, e.g. retired U.S.-based "experts" rejecting research just because of "poor English".<br /><br />Second problem is fragmentation of science. How to find equally competent as unbiased reviewers? Being an editor of a (classic) journal is the worst job you can have.<br /><br />The third major problem is publish-or-perish. I probably spend more time looking at the data than the many authors spend analysing it. Feeding data into a black box is a no-brainer and self-seller; understanding the result, finding the pitfalls, requires a lot of background and experience (not just "expertise"). Which the authors cannot have. Plus, the more complex your data, the more complex the paper, the less the chance you get it published. Editors prefer easy food for their readers, need impact, and impact comes with big names and simple, shiny stories. With beech, you open the evolutionary Pandora's Box <i>and</i> you go down the darkest fox-hole. Now, far the most phylogeneticists are tree-thinkers. It's trivial to read a tree and sell it to the audience. If the authors would have analysed their data properly, having very few templates to follow, they would have run into problems and possibly erred as well; there would have been very few positive-constructive reviewers available making such a paper publishable.<br /><br />Which is, by the way, also the reason that I will hide away this analysis in a supplement to a paper and not waste time trying to publish a formal, confidentially peer-reviewed comment :) The only possibly competent reviewers of such a comment would be my (former) co-authors.Das Grimmhttps://www.blogger.com/profile/13213125622809796109noreply@blogger.comtag:blogger.com,1999:blog-1592175903857348966.post-76002617918361428142021-09-30T10:57:15.926+02:002021-09-30T10:57:15.926+02:00Just went through the whole post and I could tell ...Just went through the whole post and I could tell how science is a rigged game. I am confused about what is considered to be integrity in science. as a new scientist I wonder what is going on.Anonymoushttps://www.blogger.com/profile/03589059762571291817noreply@blogger.comtag:blogger.com,1999:blog-1592175903857348966.post-72201559161108541742021-06-07T18:58:57.894+02:002021-06-07T18:58:57.894+02:00Moin moin, super Idee!Moin moin, super Idee!Guyhttps://www.blogger.com/profile/11806715906915755139noreply@blogger.comtag:blogger.com,1999:blog-1592175903857348966.post-51672029792300861882021-03-10T17:15:35.863+01:002021-03-10T17:15:35.863+01:00Sorry, not for most of the state election posts (t...Sorry, not for most of the state election posts (time-constraints). I just tried to look what Google-Translator does but I don't get English to choose right now. It will loose a lot in translation (I used some German linguistic creativity) but the basic content should be transported.<br /><br />But there is an English version for the last federal German elections and some state elections on <i>Genealogical World of Phylogenetic Networks</i> which explains the data sources and basic methodology.<br />— <a href="https://phylonetworks.blogspot.com/2017/09/a-network-of-political-parties.html" rel="nofollow">A network of political parties competing for the 2017 Bundestag</a><br />— <a href="https://phylonetworks.blogspot.com/2018/10/jumping-political-parties-in-germanys.html" rel="nofollow">Jumping political parties in Germany's state elections</a><br /><br />There are also a few similar posts in English here on Res.I.P., keywords <a href="https://researchinpeace.blogspot.com/search/label/politics" rel="nofollow">politics</a> and <a href="https://researchinpeace.blogspot.com/search/label/Wahl-O-Mat" rel="nofollow">Wahl-O-Mat</a>Das Grimmhttps://www.blogger.com/profile/13213125622809796109noreply@blogger.comtag:blogger.com,1999:blog-1592175903857348966.post-80329901863392822592021-03-10T15:26:34.215+01:002021-03-10T15:26:34.215+01:00English version?
English version?<br />Odagohttps://www.blogger.com/profile/13601370605947856637noreply@blogger.comtag:blogger.com,1999:blog-1592175903857348966.post-13792153137084680782021-02-12T17:06:53.027+01:002021-02-12T17:06:53.027+01:00Postscriptum and epilogue
Absolutely not sorry f...<b>Postscriptum and epilogue</b> <br /><br />Absolutely not sorry for myself; I'm very happy in my early retirement because I don't have to fight anymore utterly useless fights with anonymous shadows shooting from the dark, who occassionaly demonstrated to even know less about their own data/papers (<a href="https://researchinpeace.blogspot.com/2018/05/trivial-but-illogical-reconstructing.html" rel="nofollow">one example</a>) than they had about ours. But, and apparently in contrast to you, I met many people who suffered during peer-review without really knowing why having been indoctrinated by cladists. That's why I have such an illustrious collection of co-authors ranging from micropalaeontologists to bioinformaticians: people came to me with data that was <i>not</i> trivial to analyse, and required some open-minded creativity. In my early retirement, I can afford to give all those victims of doctrines a voice, and a helping hand, pointing them to solutions that worked for us. And call-out challenging hindering doctrines, such as cladistic classification (be it Hennig, Nelson or Farris-style).Das Grimmhttps://www.blogger.com/profile/13213125622809796109noreply@blogger.comtag:blogger.com,1999:blog-1592175903857348966.post-6794315291390096032021-02-12T17:02:09.760+01:002021-02-12T17:02:09.760+01:00Re: Paraphyly; not "just lack of signal"...Re: <b>Paraphyly; not "just lack of signal"</b><br /><br />Paraphyly is the lack of lineage-conserved, uniquely derived character suites—<a href="https://phylonetworks.blogspot.com/2019/03/has-homoiology-been-neglected-in.html" rel="nofollow">homoiologies</a> and Hennig's rare synapomorphies. What makes paraphyletic groups useful in classification is exactly what you point out: we can define them via (nested) monophyla. <br /><br />Paraphyly is furthermore also a common consequence of population dynamics (<a href="https://researchinpeace.blogspot.com/2018/04/digging-deeper-population-dynamics-and.html" rel="nofollow">interesting case: individual-based fossil phylogenies</a>), and, subsequently, genetic drift, active population sizes, and effect and frequence of bottleneck situations, in short: asymmetric speciation processes. If I remove one population (or species) from a master population (source species), it may become quickly different but the master population doesn't change. As soon as I give the isolate a name (being beyond doubt monophyletic and <i>visibly</i>different), the still-unchanged remainder becomes a paraphylum and becomes invalid. Fast ancient radiations popping up easy-to-diagnose, highly-supported clades with prominent roots, i.e. easy-to-argue monophyla, quite often keep leftovers that are genetically ambiguous and morphologically poorly differentiated. Which we, using cladistic classifications, solve by erecting monotypic genera of little diagnostic value, or simply not recognising the easy-to-diagnose monophyla within the larger group (see e.g. certain much-inflated angiosperm families).<br /><br />I guess, in most aspects, we are not that far apart. It's only (pretty dogmatic, sorry) statements like "paraphyly is lack of evidence" that distinguish your (in principle, good-)cladistic (in contrast to Farrisian naive-cladistic) doctrine ("Only monophyla must be named!") from my real-world inspired (as in this post), utterly doctrine-free solutions to complex (non-trivial) cases, hence, different solutions for different sets of data and data situations.<br /><br />If you have time to waste: Just try one of the many freely accessible datasets I covered in my papers and posts, following the suggestions in your own book to demonstrate that (the original, pre-Farris) cladistics are still the only possible classification system and are applicable also to non-trivial situations (rather to those where Mayr's overall similarity would suffice, see example in the response above). <b>Proof</b> me wrong, there are many examples to choose from.Das Grimmhttps://www.blogger.com/profile/13213125622809796109noreply@blogger.comtag:blogger.com,1999:blog-1592175903857348966.post-53202807479940114732021-02-12T16:52:58.535+01:002021-02-12T16:52:58.535+01:00Re: Overall similarity
I don't want to "r...Re: <b>Overall similarity</b><br />I don't want to "resurrect" overall similarity (Mayr's 2002 paper was convolute and a bit pointless); but one should not ignoring lineage coherence when doing classification. Especially not in an era, where species are erected based on 3% rules and environmental bulk DNA samples in order to replace good alpha-taxonomy. <br /><br />Just to give a concrete example: To classify the angiosperms cladistically sensu Hennig (Nelson?), I don't need to infer any tree at all. It's obvious from a heat-map of genetic distances: members of likely monophyla (holophyla) are much more similar to each other than to any other taxon in the data set. That's why they give us highly-supported (and model-independent) clades. Morphologically, we have such trivial situations, too (<a href="https://phylonetworks.blogspot.com/2020/02/large-morphomatrices-trivial-signal.html" rel="nofollow">an example from the dinosaurs</a>), but often we face much more complex data situations, e.g. when putting up a <a href="https://phylonetworks.blogspot.com/2017/07/should-we-try-to-infer-trees-on.html" rel="nofollow">matrix for extant and extinct angiosperms</a>. <br />Das Grimmhttps://www.blogger.com/profile/13213125622809796109noreply@blogger.comtag:blogger.com,1999:blog-1592175903857348966.post-38185823354609642832021-02-12T16:51:34.783+01:002021-02-12T16:51:34.783+01:00Regarding no ancestors in the fossil record: Since...Regarding <b>no ancestors in the fossil record</b>: Since I worked at evolution's coalface (mostly plants but including foraminifers), I know, it's nonsense. I actually posted on it, too, in response to an according comment.<br /><br /><a href="https://researchinpeace.blogspot.com/2018/04/where-have-all-ancestors-gone.html" rel="nofollow">Where have all the ancestors gone</a>Das Grimmhttps://www.blogger.com/profile/13213125622809796109noreply@blogger.com