contingo

But it's not a "hitherto conjectured form of symbiosis". It's just another example of facultative lichenization, which has already been observed in species quite widely scattered across the fungal kingdom. That to me doesn't count as a "new type of coexistence". The actual research behind the headline is valuable and entirely worthy of publication (I've made similar contributions myself), my critique relates to the headline, the angle of the reportage.

I'm skeptical that this discovery amounts to a "new type of coexistence". Fungi that are facultatively lichenized (having growth forms that include or exclude algae) have been known about for a long time, as have various stages of sophistication of the lichenized condition. I can find references dating back to at least the 1980s that describe various kinds of facultative lichenization. The authors' insistence that the symbiosis is not a lichen just because the mycobiont (fungal partner) has a free-living form is suspect: previous literature makes no such distinction. The relevant distinction here is not between lichen vs. non-lichen, but facultative vs. obligate lichenization. The observation that the mycobiont can be free-living and "does not depend on its alga for nourishment" does not imply that it doesn't derive nourishment from its algal partner once the partnership is established.

There's no major news here that I can see. The main value of this research is simply that it provides the first description of facultative lichenization occurring in a particular group of under-studied fungi (corticioid basidiomycetes).

From the article:

The donated shoes that ended up in Indonesia have added to a flood of illegal second-hand clothing pouring into that developing country, according to a senior government official there, who said such cast-offs pose a public health risk, undercut its local textile industry and often pile more waste into its already bulging landfills.

Many different groups of fish have independently evolved locomotion by "walking" on modified pectoral fins. One of my favorite examples are the bamboo sharks, among which are some pretty recently described species: https://en.wikipedia.org/wiki/Hemiscyllium_halmahera

It's woefully wrong for something in the primary literature. Yes, I understood what information they were sloppily failing to be precise about. If I were refereeing this paper I'd insist on a correction.

From the introduction, which starts by trying to give some wider taxonomic context:

The genus Ilex comprises about 450 species growing in the tropical regions of South America and Asia. Ilex trees are located exclusively in South America...

The roughly 500-600 species in the genus Ilex are commonly called hollies and include the European Christmas holly, I. aquafolium. The genus overall has a worldwide distribution over both tropical and temperate regions, there is no particular concentration of diversity in the South American tropics. Strange to get basic facts so wrong in the opening sentences.

SALT_VERSE just uses still images generated by DALL•E-2 and Midjourney. They're animated using techniques that have already been around for a long time: panning around and zooming in and out of a larger frame, fake raster-to-3d effects (auto projection mapping), typical After Effects transitions. There are some overlaid face animations done with something along the lines of NVIDIA's Audio2Face. None of it is video generated by SD, DALL•E-2 and Midjourney.

There have been some actual video explorations of SD's latent space, this example amazes me: https://twitter.com/karpathy/status/1559343616270557184

The biological term "symbiosis", by itself, in the strict sense, doesn't imply a benefit for both parties, it just describes a persistent and physically close association between two species. Hence parasitism or commensalism are also forms of symbiosis and so are associations which are not obligate, but facultative (both bionts can live without the other, however prevalent the association). "Obligate symbiotic mutualism" is the category for what you're describing. "Endosymbiosis" implies such an integrated relationship that it is at least obligate for the endosymbiont. In this human-mite case there are various claims of benefits and drawbacks to humans from the relationship, and the symbiosis is certainly already obligate for the mites.

Psilocybin-producing mushrooms are widely dispersed across the clade of all other true mushrooms and their genomes clearly show there is no great mystery about their evolutionary history or relationships to other fungi. Modern phylogenetics completely discredits panspermia as an origin for particular species or groups of fungi: they all share a single common ancestor and they are all connected to our single Tree of Life as with every other known lifeform on Earth.

Tunicates evolved long before animals that you would recognize as typical vertebrates. In their free-swimming larval state, tunicates do have a "notochord", or nerve chord, running along their head-tail axis. This structure is a kind of proto-spine. The evolution of true vertebrates proceeded from this condition by neoteny, the retention of larval traits in the adult body plan. Pyrosomes look so bizarre compared to a layman's notion of what a chordate should look like because they are colonial aggregations of lots of individual adult tunicates that have resorbed their notochords (I'm pretty sure that's the case, despite what the photo description says).

OK, I looked at some piano roll layouts in DAWs, and found examples with equal spacing between semitones, you're right.

I looked at some music mapped onto this layout. The layout allowed for speedy recognition of lone intervals and simple chords, but no more so than standard notation, and it was far worse than standard notation at showing any higher level musical content (the harmonic function of those intervals and chords in the context of the whole piece or local progression, polyphony and independent voices in general, counterpoint, organization of rhythms and cross rhythms, phrasing, larger compositional structures...). Also, because it's just a homogenous field of repeating piano octaves there is much less to positionally anchor the eye on as it reads through, like a staff with ledger and bar lines and key signature would provide to a fluent sight reader. All this musical meaning is stripped away and to reinstate it would be a case of painstakingly decoding the piano roll rather than just fluently reading the music.

I can see how this layout is really useful in a DAW for MIDI input and editing. As for learning the absolute basics of harmony, yeah it's accessible, if you can't be bothered to learn the basics of standard notation. After which point it's a dead end.

It makes sense in the context of tonal harmony. An octave is the interval between the 1st and 8th notes of a major or minor scale. I.e. a major or minor scale repeats itself (at double the frequency) every eight notes. A major third is the interval between the first and third notes of a major scale, and so on.

OK, I looked at some piano roll layouts in DAWs, and found examples with equal spacing between semitones, you're right.

I looked at some music mapped onto this layout. The layout allowed for speedy recognition of lone intervals and simple chords, but no more so than standard notation, and it was far worse than standard notation at showing any higher level musical content (the harmonic function of those intervals and chords in the context of the piece or a progression, polyphony and independent voices in general, counterpoint, organization of rhythms and cross rhythms, phrasing, larger compositional structures...). Also, because it's just a homogenous field of repeating piano octaves there is much less to positionally anchor the eye on as it reads through, like a staff with ledger and bar lines would provide to a fluent sight reader. All this musical meaning is stripped away and to reinstate it would be a case of painstakingly decoding the piano roll rather than just fluently reading the music.

I can see how this layout is really useful in a DAW for MIDI input and editing. As for learning the absolute basics of harmony, yeah it's accessible, if you can't be bothered to learn the basics of standard notation. After which point it's a dead end.

I don't trust you. You're just used to thinking in terms of the piano keyboard. As I said before, the distance between two adjacent white keys on a piano roll could be a major second, or it could be a minor second. In other words the same distance encodes different intervals. You don't know which it is until you also examine the position of the black keys. A keyboard where the twelve semitones were actually equally spaced would not have groupings of two vs. three black keys. Looking at the adjacency of the keys trivial to do, but so is reading an accidental, which gives you additional information about the functional role of the pitch it alters.

A piano roll visualization gives a somewhat more immediate depiction of intervallic information. But it isn't absolutely proportionately spaced, it's mapped to keyboard topology. Two neighboring white keys could be a major or minor second apart, etc. (And if real piano topology is shown, asymmetric positioning of black keys mean that identical intervals with one white key and one black key are different in span.)

In relation to the staff, pitches in standard notation are just as "proportionally spaced". Instead of squeezing in black keys, you have to squeeze in accidentals, but then accidentals are an extremely useful way of "showing how chords work", especially in the context of progressions in tonal harmony, which a piano roll gives you no meta-information about. It's less intuitive only in that you need some study to parse it fluently, at which point you gain the advantage of being untied to the layout of a particular physical instrument.

In any quest to "understand how music actually works", as soon as you take some baby steps beyond the basic alphabet of intervals, a piano roll visualization is going to hold you back.

Were you implying that a different kind of everyday notation exists that could be a significant improvement on the traditional system? I understand that various alternative notations can give a clearer presentation of single aspects of music, and I know of some in use for specific instruments and genres/styles, but overall, as a general purpose encoding, standard notation seems to be a well-optimized compromise arrived at by real working musicians over the centuries. Notation has to convey a lot of musical information beyond pitch specifications and relationships. Speaking as someone with good sight reading ability at the piano, and who's heard better pianists sight-reducing orchestral scores even, sheet music doesn't lack clarity, and saving just the right amount of ink also means having a readable format.

Correct, DNA is just one element of a complete organismal informatics, you need vastly more than just the genome sequence to ressurect a species. Relatively simple microbes, or recently extinct mammals where you have a semi-plausible scheme involving suitable host cells and embryo implantation technology are exceptional cases.

One thing to realize is there are significant numbers of species that have such complex ecological dependencies that we don't know how to keep them alive outside of their natural habitat anyway, even if we could manufacture them from scratch. I've worked in labs studying mycorrhizal fungi, parasitic and mycoheterotrophic plants, soil protists, rare insects... Often, even if the species is well-characterized and we have plenty of living samples, the life-cycle still cannot be completed and a viable population cannot be maintained in artificial conditions.

Environmental genomic sampling is relatively easy to do, trendy, easy to get funding for. Conservation biology produces vast amounts of this data. But it mostly serves as an "ark" in terms of individual genes, gene products, limited gene networks, not the integrated individual. We've got very good at collating and maintaining vast databases of this stuff and very bad at stopping the actual biodiversity getting destroyed. Research on "how actually do we keep more species alive in the first place" does not get enough money or attention.

In the past my research has overlapped a fair bit with alpha taxonomy. Actually, whimsically or unconventionally named species are fairly common. Here are three examples that come to mind.

[1] Forget Twitter, when it comes to species literally "discovered on the internet" I don't think you can top this one. In 2005 or so, specimens of a beautiful and striking sea urchin test, in the genus Coelopleurus, started cropping up on eBay as collectors' items. They were eventually confirmed as a new species. No, they were not named after eBay (the eventual choice of species epithet, 'exquisitus', was entirely fitting), but their status as the first new species determined directly from eBay specimens is pretty interesting, especially in bioconservation terms.

[2] Spongiforma squarepantsii is a fungus described in 2011. If you've ever eaten a bolete (a cep, or porcini, in foodie speak), then you'll know there are mushrooms where the gills are replaced with a spongey layer of tightly-packed tubes. In its extremely wet habitat, S. squarepantsii has become specialized from bolete ancestors to disperse its spores locally, by rainwater or animal transport, rather than by air, and so the entire fruiting body is reduced to a mass of convoluted sponge. From the Wiki article: "The surface of the fruit body has deep ridges and folds somewhat resembling a brain. It is sponge-like and rubbery — if water is squeezed out, it will resume its original shape... when viewed with scanning electron microscopy, [the spore producing-tissue] somewhat resembles a seafloor covered with tube sponges, reminiscent of the fictitious home of SpongeBob... Although the epithet was originally rejected by the editors of Mycologia as "frivolous", Desjardin and colleagues insisted that "we could name it whatever we liked"."

[3] In Borneo the other year I photographed a large, very hairy spider with bright red fangs that turned out to be a male color morph of a species named in 2008 as Heteropoda davidbowie. The linked Nat Geo article has more examples like that.

[1] https://www.theguardian.com/science/2006/aug/17/uknews.taxon...

[2] https://en.wikipedia.org/wiki/Spongiforma_squarepantsii

[3] https://www.nationalgeographic.com/magazine/2017/10/explore-...

Do you count orangutans as "local Malaysians"? In any case, the rainforest is certainly useful to all of the indigenous humans whose home and way of life are also being destroyed. You might find the rainforest "too dense to walk through" but unique cultures have inhabited them for millennia.

You are, by the way, more likely to contract a mosquito-bourne disease in a town than a rainforest, where much higher mosquito species diversity, plus much lower human population density, equal lower prevalence of the mosquitoes that carry human pathogens.

Also it's not "otherwise it would be all jungle". It's "otherwise more of it would be jungle, or would more resemble an intact jungle in various ways". Intelligent policy on land use and allocation is nuanced, not either/or.

Yes, the jungles are "useful for local Malaysians" in all kinds of ways. But you can find Malaysians from all backgrounds battling for the preservation of their vanishing patches of forests, against the interests of the big agribusiness and timber extraction elites. The forests are treasurehouses of biodiversity and there are powerful aguments to be made on economic, environmental, ethical and custodianship grounds.

There are many co-existing species concepts used in practice that are statistically rigorously defined, selected according to the biology of the lineage in question (e.g. it makes little sense to apply the same concept to both recombining and asexual lineages). It's an intensively researched area that becomes more refined and more explanatory with time, like any other area of science.

Delving into the recent literature might enable you to make a less clumsy critique. Independently evolving units of biological diversity exist. Any accurate knowledge about them, and about all the edge cases and fuzzinesses and genetic phenomena that make systematization complicated, comes from biology itself.

You evidently haven't encountered the biodynamic viticulture people, who are everywhere these days. They will tell you to buy a wine because its grapes were harvested when the stars were in a particular alignment and the moonlight a particular intensity.

It's a fascination problem. Everything falls into place when what genuinely deeply interests you coincides with your work, with the source of your motivation to work, and with the source of your mental fitness to do the work. When I think of long-lived scientists, mathematicians, composers, artists who produce brilliant work into old age, these are people who never lose fascination for what they do.

As the article hints, the concept of an individual is a very slippery thing in filamentous fungi. A single hyphal network can contain genetic material from more than two parental spores, and while a bi-nucleate condition is typical (in a "stable dikaryon"), genetically different nuclei can cohabit different regions of the same mycelium at different times, and even established nucleotypes can be completely displaced by newly-fusing types. This all leads to quite different genetic situations from those that delimit individuals in the usual sense.

In this study, somatic compatibility of isolates (their readiness to fuse into a single mycelium) seems to have been interpreted as an indication of clonality – that the isolates are completely genetically identical. (At least it was by the BBC; the abstract of the linked paper, which is all I read of it, is vague on this point.) That would make the determination that this is a single individual fungus rather unassailable. But it's not clear to me at all that we can assume things are so simple.

The 06-10-2010 version of this document (the linked one is 27-03-2009) is the one still bundled with the Blender source.

It just means they're headed for extinction in the wild, but that some populations are maintained in captivity. The term 'domestication' would not normally be used in this case, because it relates to the selection of improvement traits in some resource or behavior useful to humans.

It's a bit dated to characterize modern systematics as chiefly a battle between lumpers and splitters; the structures and schema being argued over are different in character from those that preoccupied Victorian naturalists.

For some groups of extant organisms, there are still competing species concepts in operation, extensive genetic sampling is not always performed (although it was in this orangutan study), and other sources of evidence are relied upon. Also, our existing Codes of Nomenclature technically permit the kind of "taxonomic vandalism" practiced by rogue taxonomists like Raymond Hoser.

In these cases (I can think of examples in many groups in all the eukaryote kingdoms) you get more lumpy and more splitty approaches (an oversimplification that pained me to type). And you certainly get that when it comes to higher-than-species-level taxa. So it's just not true to say that basically everyone is now a splitter.

In phylogenetic terms, a species concept is supposed to define an independently evolving genetic cluster. These things exist in reality - we don't observe a continuum of extant forms in nature - and the quest to delineate these clusters objectively has necessarily become a statistical quest. As much as possible we want to map classification to real units of diversity.

In the case of us mammals there's a broad consensus on long-established criteria for performing this mapping, although individual cases are not always without contention. But the idea that modern biology fails, for ideological reasons, to correctly split classification into further species in the singular case of Homo sapiens, is silly.

Read my paragraph number two?

If you have absolutely no information about what bit you, diagnostics look at habitat, bitemark characteristics, venom reaction, and of course serological tests / enzyme immunological assay can be conclusive. Taxonomy is critical generally, if the patient doesn't have an ID it's not as if taxonomy becomes irrelevant.

Compare https://www.ventusky.com/?p=19.6;-77.9;4&l=wind&w=0xIAb9A9A

It's a reach to imagine your scenario applies to snakebite emergencies generally. Copperheads are large, distinctive snakes, their nomenclature is stable and in the temperate zones where they live, there are a relatively limited number of other venomous species to distinguish, hence you being so assured of supplying remains for a nurse to casually ID. In contrast, many tropical habitats, where snakebites are much more of a problem, have a much, much higher venomous snake species diversity (particularly of those small, fast elusive ones you barely glimpse), and questions about ID and species relationships are correspondingly more confusing.

It's not so much about always turning up with a scientific name. The whole effort from doctor-patient communication, to animal control, to the production, supply and procurement of specific antivenins, needs to be conducted within as stable and precise nomenclatural framework as possible.

Snakes are just one example here, there are many examples of research programmes being derailed by faulty taxonomy, with big impacts on everything from crop production to theoretical work in ecology.

This whole discussion is somewhat moot as a real biologist would almost always write "species of octopus", singular.