camwyn: Me in a bomber jacket and jeans standing next to a green two-man North Andover Flight Academy helicopter. (Default)
So, got COVID last week. Thought it was just bad cold symptoms, then I realized I was feeling my shirt against my skin the way I only do if I have a fever. Since I was supposed to go for an abdominal ultrasound (possible gallstones) last Friday I got a COVID and flu at-home test and spent fifteen minutes in the bathroom.

Fever never went above 100.6 for me, thankfully. Did not lose what little sense of smell I had to begin with. I no longer have to isolate but I am now back to my all-too-familiar state of 'sinuses full of snot, post nasal drip, HORK HORK HORK coughing'. I'm taking a store-brand severe cold and sinus pill every four hours for that and drinking so much tea I feel like the goddamn harbor. Could be worse so I am not going to bitch beyond that. I'm definitely grateful my boss's first statement to me when I logged in on Monday, after dealing with a tech support issue, was 'how're you doing? Plan on working from home this week'. I wasn't looking forward to mornings of trying to assess whether I was fit to haul my ass to the ferry terminal or not.

having said this I am trying to remember where I go to edit the quote at the top of my journal page because yesterday I found out about a species of water beetle in Japan that has been documented as surviving being eaten by frogs, but only so long as the beetle is able to keep moving. The scientists tested it by applying wax that immobilized two legs to several beetle. None of them made it out in any recognizable form, whereas the others managed to get through. Longest time documented was several hours, others made it through in 115 minutes, but one beetle managed to speedrun the frog in six, which... has to have been quite the experience for the amphibian.

Mostly I just like the sound of 'keep moving. there is light at the end of the frog'.

ETA: found the customization page.
camwyn: (I have seen the truth)
I have a new Lore: Disturbing entry!

Do you know what the term 'hypergolic' means? It's rocket chemistry. A substance is hypergolic with something, or just hypergolic, if when you mix it with another substance, you get spontaneous ignition without other intervention. Today's new chemical friend is chlorine trifluoride, which is hypergolic with literally every single known fuel substance used in rocketry, is a faster oxidizing agent than oxygen itself, and can make asbestos burst into flame on contact!

Sand Won't Save You This Time!

Science!

Aug. 4th, 2023 10:26 am
camwyn: Me in a bomber jacket and jeans standing next to a green two-man North Andover Flight Academy helicopter. (Default)
Went poking around science stuff on the Web the other day and wound up at a web site for microbiologists. Specifically, for a very particular subset of bacteriophage researchers:

"Welcome to the Actinobacteriophage Database at PhagesDB.org, an interactive site that collects and shares information related to the discovery, characterization, and genomics of phages that infect bacterial hosts within the phylum Actinobacteria."

In future I respectfully request that anyone who tries to claim that science is serious and dull and banal or anything else along those lines please go to the site in question and look up the Naming Rules For Actinobacteriophages. Rule 1 of Phage Club is "Do not name your phage after Nicolas Cage."

No, seriously.

Do not name your phage after Nicolas Cage.
Avoid words that already have specific meanings in biology, such as phage, pham, cluster, virus, capsid, or myco (or their derivatives or homophones). Please do not try to get around this rule by using words such as “fage” or “MileyVyrus.”
Similarly, avoid making your phage sound like a disease. Stay away from “Georgeitis”, “Veronicalgia”, and “Marcilepsy”.
Avoid all CAPS. In addition to making your phage name seem angry or like it forgot to turn off Caps Lock, these names often appear similar to old systematic names which we are trying to avoid.
camwyn: (if you hadn't stopped me)
https://arxiv.org/abs/2211.11970

King Ghidorah Supercluster: Mapping the light and dark matter in a new supercluster at z=0.55 using the Subaru Hyper Suprime-Cam
Rhythm Shimakawa, Nobuhiro Okabe, Masato Shirasaki, Masayuki Tanaka

This paper reports our discovery of the most massive supercluster, termed the King Ghidorah Supercluster (KGSc), at $z=0.50-0.64$ in the Third Public Data Release of the Hyper Suprime-Cam Subaru Strategic Program (HSC-SSP PDR3) over 690 deg$^2$, as well as an initial result for a galaxy and dark matter mapping. The primary structure of the KGSc comprises triple broad weak-lensing (WL) peaks over 70 comoving Mpc. Such extensive WL detection at $z>0.5$ can only currently be achieved using the wide-field high-quality images produced by the HSC-SSP. The structure is also contiguous with multiple large-scale structures across a $\sim400$ comoving Mpc scale. The entire field has a notable overdensity ($\delta=14.7\pm4.5$) of red-sequence clusters. Additionally, large-scale underdensities can be found in the foreground along the line of sight. We confirmed the overdensities in stellar mass and dark matter distributions to be tightly coupled and estimated the total mass of the main structure to be $1\times10^{16}$ solar masses, according to the mock data analyses based on large-volume cosmological simulations. Further, upcoming wide-field multi-object spectrographs such as the Subaru Prime Focus Spectrograph may aid in providing additional insights into distant superclusters beyond the 100 Mpc scale.

Comments: 5 pages, 5 figures, accepted for publication in MNRAS Letter
Subjects: Astrophysics of Galaxies (astro-ph.GA); Cosmology and Nongalactic Astrophysics (astro-ph.CO)
camwyn: A white throated sparrow perched on a fence and looking at the camera. (birding)
Don't remember if I posted it when it happened, but a while back I got an email. I've been using the eBird app to keep track of my birdwatching for years now. eBird comes from the Cornell Lab of Ornithology, and people's counts are tracked, analyzed, and used in scientific studies when they submit them. Remember that news story about how we've lost billions of birds since the 1970s? eBird reports from around the world were a sizable part of the data that allowed scientists to come to that conclusion. Old reports were done on paper; newer reports include people's app data, whether from eBird or various Audubon birding apps or other sources. It all adds up.

Anyway, the email I got was from the eBird folks, saying that my data showed I had reported shorebird sightings in the past and would I consider future participation in the International Shorebird Survey, which had a specific viewing/reporting protocol. I said sure, why not; the ISS protocol only really required a little more diligence of observation and a few extra bits of data (precipitation? tidal stage? wind levels?). I'd have to go back to the same sites at least three times, if not more, during the spring and autumn shorebird migrations. Given that this mostly means 'walk to the end of the block, turn right, then walk a block and a half', this is not a terrible hardship. I have a few other spots where I go at least three times in the course of a given season- a nearby swampy-beachy park with shoreline access, the nearest local actual beach- so yeah, okay, I figured if I spotted any of the species categorized as shorebirds at those I'd make them official ISS survey locations for my reporting and make an extra point of visiting them regularly.

Eventually went and looked up the ISS project. Turned out it wasn't just scientists doing academic processing of shorebird numbers, it's a volunteer-run thing whose data is used as one of the sources for the US Shorebird Conservation Plan and for selecting potential sites for designated reserves.

I'm good with this.

https://www.manomet.org/project/international-shorebird-survey/
https://www.manomet.org/iss-map/


(Side note: I'm not entirely sure what the specific species that constitute shorebirds as opposed to other categories of water-intensive birds are, but fortunately I don't have to make the distinction, I just have to submit appropriately formatted surveys and the people on the other end sort out the data. But my beloved weirdoes the oystercatchers definitely qualify. So do the piping plovers I saw at the beach the other day, and the killdeer I spotted yesterday as I was getting ready to leave the swampy-beachy park.)

(Another side note: unless shorebirds practice the same kind of dominance displays as dogs, it's oystercatcher mating season.)
camwyn: Me in a bomber jacket and jeans standing next to a green two-man North Andover Flight Academy helicopter. (Default)
From the news section at CERN's website:

"MADMAX is preparing for a stopover at CERN from 2022. Mel Gibson, his artillery and quest for revenge will not be there, but instead a handful of physicists armed with an aged magnet will be searching for dark matter in CERN’s North Area (not to be confused with a post-apocalyptic wasteland).

"Indeed, the MADMAX collaboration (MAgnetized Disks and Mirror Axion eXperiment, external to CERN), humbly proposes to identify the nature of dark matter and to solve the enigma of the absence of so-called charge-parity (CP) symmetry violation in the strong sector, while detecting a particle that has eluded physicists for decades: axions."

https://home.cern/news/news/experiments/madmax-and-cerns-morpurgo-magnet
camwyn: (if you hadn't stopped me)
Turning space images into music makes astronomy more accessible

Put into music, telescope observations of the center of the Milky Way create a tranquil tune, glittering with xylophone and piano notes. The iconic Pillars of Creation in the Eagle Nebula, meanwhile, sound like an eerie sci-fi score. And the supernova remnant Cassiopeia A is a sweeping symphony.

These musical renditions, or sonifications, were released on September 22 by NASA’s Chandra X-ray Center. “Listening to the data gives [people] another dimension to experience the universe,” says Matt Russo, an astrophysicist and musician at the astronomy outreach project SYSTEM Sounds in Toronto.

Sonification can make cosmic wonders more accessible to people with blindness or visual impairments, and complement images for sighted learners. SYSTEM Sounds teamed up with Kimberly Arcand, a visualization scientist at the Harvard-Smithsonian Center for Astrophysics in Cambridge, Mass., to create the new pieces.

Christine Malec, a musician and astronomy enthusiast who is blind, vividly recalls the first sonification she ever heard — a rendering of the TRAPPIST-1 planetary system that Russo played during a planetarium show in Toronto (SN: 2/22/17). “I had goosebumps, because I felt like I was getting a faint impression of what it’s like to perceive the night sky, or a cosmological phenomenon,” she says. Music affords data “a spatial quality that astronomical phenomena have, but that words can’t quite convey.”

The new renditions combine data from multiple telescopes tuned to different types of light. The sonification of an image of the Milky Way’s center, for instance, includes observations from the Chandra X-ray Observatory, optical images from the Hubble Space Telescope and infrared observations from the Spitzer Space Telescope. Users can listen to data from each telescope alone or the trio in harmony.

As a cursor pans from left to right across the image of the galactic center, showing a 400-light-year expanse, Chandra X-ray observations, played on the xylophone, trace filaments of superhot gas. Hubble observations on the violin highlight pockets of star formation, and Spitzer’s piano notes illuminate infrared clouds of gas and dust. Light sources near the top of the image play at higher pitches, and brighter objects play louder. The song crescendos around a luminous region in the lower-right corner of the image, where glowing gas and dust shroud the galaxy’s supermassive black hole.

Layering the instruments on top of each other gives the observations an element of texture, Malec says. “It appealed to my musical sense, because it was done in a harmonious way — it was not discordant.”

That was on purpose. “We wanted to create an output that was not just scientifically accurate, but also hopefully nice to listen to,” Arcand says. “It was a matter of making sure that the instruments played together in symphony.”

But discordant sounds can also can be educational, Malec says. She points to the new sonification of supernova remnant Cassiopeia A: The sonification traces chemical elements throughout this great plume of celestial debris using notes played on stringed instruments (SN: 2/19/14). Those notes make a pretty harmony, but they can be difficult to tell apart, Malec says. “I would have picked very different instruments” to make it easier for the ear to follow — perhaps a violin paired with a trumpet or an organ.

While sonification is a valuable tool to get the public interested in astronomy, it also has untapped potential to help professional astronomers analyze data, says Wanda Díaz-Merced, an astronomer who is also at the Harvard-Smithsonian Center for Astrophysics but was not involved in the project (SN: 10/22/14).

Astronomers including Díaz-Merced, who is blind, have used sonifications to study stars, solar wind and cosmic rays. And in experiments, Díaz-Merced has demonstrated that sighted astronomers can better pick out signals in datasets by analyzing audio and visual information together rather than relying on vision alone.

Still, efforts to sonify astronomy datasets for research have been rare. Making data sonification a mainstream research method would not only break down barriers to pursuing astronomy research, but may also lead to many new discoveries, she says.
camwyn: Me in a bomber jacket and jeans standing next to a green two-man North Andover Flight Academy helicopter. (Default)
https://www.birdwatchingdaily.com/news/science/magpies-share-food-less-fortunate/

"...Dutch biologist Jorg Massen found that Azure-winged Magpies of eastern Asia will share food with other birds of their species that do not have enough to eat. “They seem to take each other’s perspective into account in their decision and thus seem to show sympathy,” says Massen, of Utrecht University in the Netherlands.

"Helping others has long been regarded as typical human behavior. Nowadays we know that primates and some other social mammals also show so-called prosocial behavior. “My earlier research has shown that birds, too, sometimes do something for someone else,” Massen explains. “The question was, however, whether this is ‘instinctive’ behavior that is ingrained, or whether this behavior is flexible, and whether these birds might also take into account how great the need of the other animal is.”

"To investigate prosociality in birds, Massen subjected Azure-winged Magpies to an experiment. He gave one bird an abundance of mealworms while other magpies also had access to the highly desired food or were given nothing at all. The magpie then had the opportunity to share the portion of mealworms with conspecifics through a wire-mesh screen.

"Massen and his co-authors discovered that the magpies are inclined to share food with their peers. They differentiate, however, between whether others have food or do not have food, and subsequently cater to that lack. “Females mainly shared with the others if they had nothing. The males always shared. We think the latter has to do with ‘advertisement;’ look at me being generous. With the females it’s mainly to help the other if they have nothing.”..."
camwyn: A white KitchenAid stand mixer with flame decals on it. FOR GREAT AWESOME. (kitchenaid)
Also, recently started reading Kitchen Mysteries: Revealing The Science of Cooking, by Hervé This, who is basically the god of molecular gastronomy. It's a little startling; the style of the text is like reading a book by and intended for very educated people of the late 19th century, with ornate little turns of phrase that put one in mind of old school writers, vocabulary words that of course people reading the book might logically have been expected to know but which you yourself did not, and footnotes referencing Giants In Their Field Who Have Been Dead Longer Than My Family Has Been In The Americas... and then whammo, molecular diagrams and cheerful discussion of carbon groupings and chemical reactions in ornately intricate detail.

I feel a bit as if I'm reading Jules Verne's Little Yellow Book of Cookery.
camwyn: Me in a bomber jacket and jeans standing next to a green two-man North Andover Flight Academy helicopter. (Default)
https://en.wikipedia.org/wiki/Tapputi

"Tapputi, also referred to as Tapputi-Belatekallim ("Belatekallim" refers to female overseer of a palace), is considered to be the world’s first recorded chemist, a perfume-maker mentioned in a cuneiform tablet dated around 1200 BC in Babylonian Mesopotamia. She used flowers, oil, and calamus along with cyperus, myrrh, and balsam. She added water or other solvents then distilled and filtered several times. This is also the oldest referenced still.

"She also was an overseer at the Royal Palace, and worked with a researcher named (—)-ninu (the first part of her name has been lost)."



... man, suddenly the fact that I learned more about how organic chemistry actually works and what all the individual components of complex compounds actually do from soap-making than I ever did from my high school AP and college chemistry teachers (no offense, Sister Marybeth who taught the introductory high school chemistry class, you were actually pretty good at it) just seems... kinda historically appropriate.
camwyn: Me in a bomber jacket and jeans standing next to a green two-man North Andover Flight Academy helicopter. (Default)
one of the experiments I'm backing at experiment.com is about forty-eight hours away from the end of its initial campaign. It's on developing accurate, useful ways to study the migration of big damn fish in and around the Amazon basin.

https://experiment.com/projects/could-teeth-and-scale-chemistry-reveal-threatened-amazonian-mega-fish-movements

I've backed this guy's research before. He's got some neat science going. Check it out, if you like.
camwyn: Me in a bomber jacket and jeans standing next to a green two-man North Andover Flight Academy helicopter. (Default)
https://phys.org/news/2018-12-life-deep-earth-totals-billion.html

December 10, 2018, Deep Carbon Observatory

Barely living "zombie" bacteria and other forms of life constitute an immense amount of carbon deep within Earth's subsurface—245 to 385 times greater than the carbon mass of all humans on the surface, according to scientists nearing the end of a 10-year international collaboration to reveal Earth's innermost secrets.

On the eve of the American Geophysical Union's annual meeting, scientists with the Deep Carbon Observatory today reported several transformational discoveries, including how much and what kinds of life exist in the deep subsurface under the greatest extremes of pressure, temperature, and low nutrient availability.

Drilling 2.5 kilometers into the seafloor, and sampling microbes from continental mines and boreholes more than 5 km deep, scientists have used the results to construct models of the ecosystem deep within the planet.

With insights from now hundreds of sites under the continents and seas, they have approximated the size of the deep biosphere—2 to 2.3 billion cubic km (almost twice the volume of all oceans) - as well as the carbon mass of deep life: 15 to 23 billion tonnes (an average of at least 7.5 tonnes of carbon per cu km subsurface).

The work also helps determine types of extraterrestrial environments that could support life.

Among many key discoveries and insights:

The deep biosphere constitutes a world that can be viewed as a sort of "subterranean Galapagos" and includes members of all three domains of life: bacteria and archaea (microbes with no membrane-bound nucleus), and eukarya (microbes or multicellular organisms with cells that contain a nucleus as well as membrane-bound organelles)
Two types of microbes—bacteria and archaea—dominate Deep Earth. Among them are millions of distinct types, most yet to be discovered or characterized. This so-called microbial "dark matter" dramatically expands our perspective on the tree of life. Deep Life scientists say about 70% of Earth's bacteria and archaea live in the subsurface
Deep microbes are often very different from their surface cousins, with life cycles on near-geologic timescales, dining in some cases on nothing more than energy from rocks
The genetic diversity of life below the surface is comparable to or exceeds that above the surface
While subsurface microbial communities differ greatly between environments, certain genera and higher taxonomic groups are ubiquitous—they appear planet-wide
Microbial community richness relates to the age of marine sediments where cells are found—suggesting that in older sediments, food energy has declined over time, reducing the microbial community
The absolute limits of life on Earth in terms of temperature, pressure, and energy availability have yet to be found. The records continually get broken. A frontrunner for Earth's hottest organism in the natural world is Geogemma barossii, a single-celled organism thriving in hydrothermal vents on the seafloor. Its cells, tiny microscopic spheres, grow and replicate at 121 degrees Celsius (21 degrees hotter than the boiling point of water). Microbial life can survive up to 122°C, the record achieved in a lab culture (by comparison, the record-holding hottest place on Earth's surface, in an uninhabited Iranian desert, is about 71°C—the temperature of well-done steak)
The record depth at which life has been found in the continental subsurface is approximately 5 km; the record in marine waters is 10.5 km from the ocean surface, a depth of extreme pressure; at 4000 meters depth, for example, the pressure is approximately 400 times greater than at sea level
Scientists have a better understanding of the impact on life in subsurface locations manipulated by humans (e.g., fracked shales, carbon capture and storage)

Ever-increasing accuracy and the declining cost of DNA sequencing, coupled with breakthroughs in deep ocean drilling technologies (pioneered on the Japanese scientific vessel Chikyu, designed to ultimately drill far beneath the seabed in some of the planet's most seismically-active regions) made it possible for researchers to take their first detailed look at the composition of the deep biosphere.

There are comparable efforts to drill ever deeper beneath continental environments, using sampling devices that maintain pressure to preserve microbial life (none thought to pose any threat or benefit to human health).

To estimate the total mass of Earth's subcontinental deep life, for example, scientists compiled data on cell concentration and microbial diversity from locations around the globe.

Led by Cara Magnabosco of the Flatiron Institute Center for Computational Biology, New York, and an international team of researchers, subsurface scientists factored in a suite of considerations, including global heat flow, surface temperature, depth and lithology—the physical characteristics of rocks in each location—to estimate that the continental subsurface hosts 2 to 6 × 10^29 cells.

Combined with estimates of subsurface life under the oceans, total global Deep Earth biomass is approximately 15 to 23 petagrams (15 to 23 billion tonnes) of carbon.

Says Mitch Sogin of the Marine Biological Laboratory Woods Hole, USA, co-chair of DCO's Deep Life community of more than 300 researchers in 34 countries: "Exploring the deep subsurface is akin to exploring the Amazon rainforest. There is life everywhere, and everywhere there's an awe-inspiring abundance of unexpected and unusual organisms.

"Molecular studies raise the likelihood that microbial dark matter is much more diverse than what we currently know it to be, and the deepest branching lineages challenge the three-domain concept introduced by Carl Woese in 1977. Perhaps we are approaching a nexus where the earliest possible branching patterns might be accessible through deep life investigation.

"Ten years ago, we knew far less about the physiologies of the bacteria and microbes that dominate the subsurface biosphere," says Karen Lloyd, University of Tennessee at Knoxville, USA. "Today, we know that, in many places, they invest most of their energy to simply maintaining their existence and little into growth, which is a fascinating way to live.

"Today too, we know that subsurface life is common. Ten years ago, we had sampled only a few sites—the kinds of places we'd expect to find life. Now, thanks to ultra-deep sampling, we know we can find them pretty much everywhere, albeit the sampling has obviously reached only an infinitesimally tiny part of the deep biosphere."

"Our studies of deep biosphere microbes have produced much new knowledge, but also a realization and far greater appreciation of how much we have yet to learn about subsurface life," says Rick Colwell, Oregon State University, USA. "For example, scientists do not yet know all the ways in which deep subsurface life affects surface life and vice versa. And, for now, we can only marvel at the nature of the metabolisms that allow life to survive under the extremely impoverished and forbidding conditions for life in deep Earth."

Among the many remaining enigmas of deep life on Earth:

Movement: How does deep life spread—laterally through cracks in rocks? Up, down? How can deep life be so similar in South Africa and Seattle, Washington? Did they have similar origins and were separated by plate tectonics, for example? Or do the communities themselves move? What roles do big geological events (such as plate tectonics, earthquakes; creation of large igneous provinces; meteoritic bombardments) play in deep life movements?

Origins: Did life start deep in Earth (either within the crust, near hydrothermal vents, or in subduction zones) then migrate up, toward the sun? Or did life start in a warm little surface pond and migrate down? How do subsurface microbial zombies reproduce, or live without dividing for millions to tens of millions of years?

Energy: Is methane, hydrogen, or natural radiation (from uranium and other elements) the most important energy source for deep life? Which sources of deep energy are most important in different settings? How do the absence of nutrients, and extreme temperatures and pressure, impact microbial distribution and diversity in the subsurface?

"Discoveries regarding the nature and extent of the deep microbial biosphere are among the crowning achievements of the Deep Carbon Observatory. Deep life researchers have opened our eyes to remarkable vistas—emerging views of life that we never knew existed."says Robert Hazen, senior staff scientist, Geophysical Laboratory, Carnegie Institution for Science, and DCO Executive Director.

"They are not Christmas ornaments, but the tiny balls and tinsel of deep life look they could decorate a tree as well as Swarovski glass. Why would nature make deep life beautiful when there is no light, no mirrors?" says Jesse Ausubel of the Rockefeller University, a founder of the DCO.

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