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Enlarge / Artist's conception of the early Solar System, which was at risk of a nearby supernova. (credit: NASA/JPL-Caltech)
Stars are thought to form within enormous filaments of molecular gas. Regions where one or more of these filaments meet, known as hubs, are where massive stars form.
These massive stars, located nearby, would have put the early Solar System at risk of a powerful supernova. This risk is more than just hypothetical; a research team at the National Astronomical Observatory of Japan, led by astrophysicist Doris Arzoumanian, looked at isotopes found in ancient meteorites, finding possible evidence of a massive star’s turbulent death.
So why did the Solar System survive? The gas within the filament seems to be able to protect it from the supernova and its onslaught of radioactive isotopes. “The host filament can shield the young Solar System from stellar feedback, both during the formation and evolution of stars (stellar outflow, wind, and radiation) and at the end of their lives (supernovae),” Arzoumanian and her team said in a study recently published in The Astrophysical Journal Letters.
It is currently held, not without certain uneasiness, that 90% of human DNA is ‘junk.’ The renowned Cambridge molecular biologist, Sydney Brenner, makes a helpful distinction between ‘junk’ and ‘garbage.’ Garbage is something used up and worthless which you throw away; junk is something you store for some unspecified future use. (Rabinow, 1992, 7-8)
In the bioscience lab near Tokyo where I did my ethnographic study, the researchers taught me how to do PCR experiments. This was before Covid when almost everyone came to know what PCR was, or at least, what kind of instrumental information it could be good for.[1] The lab was working with mouse models, although I never got to see them in their cages. But the researcher I was shadowing showed me how to put the mouse tail clippings she collected into small tubes. She hated cutting tails, by the way, and preferred to take ear punches when she could. She told me that she didn’t like the way the mice wiggled under her hand, as if they just knew. But at this point anyway, the mice are alive in the animal room and she is only putting small, but vital, pieces of them into a tube to dissolve them down (mice becoming means), to get to the foundation of what she really wants.
I’ve still got the protocol that I typed up from the notes I made with her in the lab. Step 1 was: “Add 75 ul of NaOH to each ear punch tube (changing tips as I go).” The changing pipette tips part was really important to avoid haphazardly spreading around DNA, I learned. I also had to make sure the clippings were at the bottom of the tube and submerged. She said I could flick the tubes with my finger to get the “material” to fall down to the bottom and she showed me how to do it. I also, she cautioned, always had to be very careful of bubbles, but more flicking could help there and by making sure I didn’t put the pipette too far down into the solution. Then we would spin the tubes in the vortex (which I always typed as VORTEX for some reason), add some other reagents, and put it all in the “PCR machine,” but that is not at all its technical name.[2] Then we would usually go with all the others to the cafeteria for lunch.
In writing this now, I couldn’t remember what “NaOH” stood for so I had to ask the internet. And as I looked back over this protocol, and these practices I was just barely learning to embody before the pandemic sent us all home, I realize that they must have settled back in my mind somewhere, just as the material-ness of the lab which anchored them for me has receded like a shrinking lake in a drought summer. But what I do hold on to is what the researcher taught me about the importance of repetition and focus, for a kind of purity of practice, and the diligence to make materials—whether of mice or of sodium hydroxide—do what they ought to do.
Because what captivated me about these initial PCR steps was what appeared to me to be the profound transformation they wrought (of course, I am not the first person to say so)—from fleshy ear punch to silt DNA multiplied in a clear plastic tube, with just a little bit of chemicals and some repetitive cycles of heat—but even more, how this transmutation had the potential to fail in one way, or for one reason, or another. How difficult it could actually be to get the materials, and even the researchers themselves, to do what they ought. Once, I used some unknown solution instead of water because it was on a shelf in an unmarked bottle close to where the water, which I later supposed had gone missing, was usually kept. Once, I didn’t remember to change pipette tips. Or the sense in my hands of precisely what to do next and properly would simply begin to unravel. When we had to throw the tubes in the trash, the researcher comforted me by telling me about a time when her mind wandered for just an instant while pipetting and she lost track of which tube she had last filled with reagent. A minor momentary mistake that grows, and can even burst, into a huge error in the downstream. She taught me that sometimes, if I lifted the tubes to the light to examine their volume of liquid, I might be able to get back on track.[3] Other times the PCR machine might not cycle its heat properly. One machine was already considered to be of questionable working order but the lab didn’t have the funding to replace it. We didn’t know about its full potential for failure until we got all the way through to the very last stage of the process and discovered we had to go back to the beginning with new clippings.
The researcher and I classified these particular (wait, was that water?) experiments-in-the-making as failures because they missed the mark of their intentions. Their purposefulness, decided in advance by the goal of genotyping these mice, was also appended to other purposes, specifically to cultivate a living gene population that the researchers needed for other more central concerns. Trashing the experiments that deviated from this intentionality, although it could be costly, was a seemingly simple decision. After the PCR melt and the second half of the experiment, the electrophoresis machine either “read” back the base pair numbers we were looking for, or those numbers were just wrong and we’d made an obvious mistake. Or worse, everything collapsed into inconclusiveness and we needed to repeat the experiment anyway.[4] In this case, deviation from expectation, and therefore from usefulness, was what pushed experiments to a kind of failure, beyond which point they could not, in this context at least, be so easily reclaimed.
But what does something like “junk” have to do with mice ear punches, chemical transmutation, and mundane laboratory failures? Garbage experiments are routine in scientific practice after all. But as any scientist might tell you, failure can be its own kind of productive; in the least, as a way to learn the value of steady hands, and how to recognize water by smell, or its necessity as a control in genotyping—to become a “capable doer,” as one scientist told me. But beyond these mundane errors, some scientists argue that failures of a particular kind can break open old ways of thinking and doing, although what that failure is, and can be, is variously classified:
Science fails. This is especially true when tackling new problems. Science is not infallible. Research activity is a desire to go outside of existing worldviews, to destroy known concepts, and to create new concepts in uncharted territories. (Iwata, 2020)
I wish “failure” were the trick to seeing and moving beyond the limits of current knowledge. Is that what Kuhn said? I think that paradigm change requires making a reproducible observation that does not fit within the existing model, then going back to the whiteboard. But I don’t think these observations are very well classified as a failure. If failure = unexpected result of a successful experiment/measurement, then I can agree. (Personal communication with laboratory supervisor, 2020)
Failure has more potential than we might often recognize, where an instinct to trash can instead push to new beginnings. Just as Rabinow described Brenner’s description (1992), failure is like junk, those materials or states that are in-the-waiting—waiting to be actualized, reordered, and reclaimed as meaningful, valid and valuable, even if we don’t yet know how or why. Junk is, in this way, more than matter “out of place,” although it may land there interstitially. If “[d]irt is the by-product of a systematic ordering and classification of matter, in so far as ordering involves rejecting inappropriate elements” (Mary Douglas, 1966, 36), then junk is garbage and failure and decay, and even breakdown, on the precipice of being made anew. After all, without intentionality or purposefulness and other values, there can be no garbage, or failed and failing experiments and paradigms, in the first place.
Consider an example that seems categorically different from scientific experiments: inventory management in role-playing videogames. In Diablo 4 (2023), any item picked up from downed enemies or collected in the environment can be marked as “junk” and then salvaged by visiting an in-game merchant. These bits of amour and other gear reappear in your inventory afterwards as junk’s constitute materials, useful again for crafting and building up new things—strips of leather and other scraps as well as blueprints for better stuff. In Fallout 4 (2015), the “Junk Jet” gun lets you repurpose your inventory instead as ammo, anything from wrenches to teddy bears, which can be shot back out into the world and at random adversaries, where you might later be able to pick them up again, if you want. Managing encumbrance in Skyrim (2011), on the other hand, is a task of drudgery and tedium. Almost every item in the game world is moveable, each with its own weight calculation, and can be picked up and stored even accidentally, until your character is weighed down to the point of being unmovable. But the game is designed to make you feel that there is always the possibility that some magical potion, random apple, or 12 candlesticks, might just come in handy for a future encounter, a book that you might really read later, leading to a hesitancy to trash anything. In turn, every item brims with, as yet undiscovered, use-value. As Caitlin DeSlivey argues: “Objects generate social effects not just in their preservation and persistence, but in their destruction and disposal” (2006, 324). And certainly this is true when, over-encumbered deep inside a dungeon, I agonize over which items to drop, in order to move again, in order to continue to collect more—or laugh as I spray the world with cigarettes and telephones.
A decaying dog, reanimated by something that is not supposed to be there. (Image by Sarah Thanner, used with permission)
For me then, junk is a way to look for when and where particular boundaries of the useful or valuable—and even the clean and functioning—are “breached” (Helmreich 2015, 187), and then reordered. Although Helmreich is speaking to scientific experimental practices and their organizing ideologies, his insight is useful for junk’s attention to those very breaches: “moments when abstractions and formalisms break, forcing reimaginations of the phenomena they would apprehend” (185). Of course, junk DNA itself has experienced this very kind of breaching—more recent scientific research demonstrating its non-coding role is actually not without usefulness (c.f. Goodier 2016)—(re)animating it for future use. And although DeSilvey is describing vibrant multispecies-animated decay within abandoned homesteads, like Helmreich, she points to junk’s transformative potential. We just have to dig through rotted wood and insect-eaten paper, or virtual backpacks and books, to find it.
Junk merges failure, trash, and decay with the processual and everyday negotiation of culturally meaningful and policed categories: garbage, scraps and waste, but also “breakdown, dissolution, and change” (Jackson 2014, 225). Although Steven J. Jackson describes the ways these last three are fundamental features of modern media and technology, an anthropology of junk collects and extends these processes into broader techniques and social practices. Junk can help us see connections criss-crossing symbolic and material breakage and disintegration. It helps us see in/visibility of the dirty and diseased, not as a property of any material or technological object alone, but as also always in coordination and collaboration with the ways they are imagined and invested—and more, always enmeshed in variously articulated forms of power.
If infrastructures like computer networks, for example, become (more) visible when broken (Star 1999), it is not their brokenness or decay in an absolute sense that reveals them, but the way their state change defies our everyday and embodied expectations—the way they push against normativity. We may be just as surprised to find things in good working order.
Metal becoming wood in “animation of other processes” (DeSilvey 2006, 324). (Image by Sarah Thanner, used with permission)
Bit rot after all, has just as much to do with the made-intentionally-inoperable systems that force the decay, or really uselessness, of data (Hayes 1998), as it does with any actual mold on CD-ROMS and other corruptions of age and wear. In fact, digital information or technological and material infrastructures don’t become broken, just as they don’t become fully ever fixed either. Breaks and breaches are hardly so linear. Instead, these are “relative, continually shifting states” (Larkin 2008: 236). This view may be in contrast to Pink et al.’s suggestion to attend “to the mundane work that precedes data breakages or follows them” (2018, 3), but not to their entreaty to follow those everyday practices of maintenance and repair, and even intentional failure and forced rot. This is not simply because data and other material practices like PCR experiments may fail under given conditions or focused intentions, perhaps as a result of a momentary distraction or a faulty machine—or in the case of programming, because debugging is actually 90% of the work, as one bioinformatician told me. Indeed, software testing in practice goes beyond merely verifying functionality or fixing bugs and broken bits of code, but helps to define and make “lively” (Lupton 2016) what that software is, and can do, and can be made to do in the first place (Carlson et al. 2023). Along the way, as a generative process, testing, tinkering, and fixing have social effects (DeSilvey 2006) which are external to, but always in extension of, broken/working materials themselves (Marres and Stark 2020).
More importantly, perhaps, broken things can be used, as Brian Larkin argued in relation to Nigerian media and infrastructures, as a “conduit” to mount critiques of the social order (2008, 239)—to call attention to inconsistency and inequality, and to demand or remodulate for change. To see this resistance at work demands a collating of junk practices. As Juris Milestone wrote in his description of a 2014 American Anthropology Association panel, “What will an anthropology of maintenance and repair look like?”:
Fixing things can be both innovation and a response to the ravages of globalization—either through reuse as a counter-narrative to disposability, or resistance to the fetish of the new, or as a search for connection to a material mechanical world that is increasingly automated and remote.
Junk’s transformative potential asks us to see removal and erasure, or in Douglas’ terms “rejection,” as always coupled to these reciprocal practices: rebirth, repair, repurpose, renewal. In this way, junk shows us the way decay, even technological corruption, is less a “death” than a “continued animation of other processes” (2006, 324).
But if junk describes a socio-cultural ordering system concerned with practices of moving materials—even ideas and people—into and out of categories of value and purposefulness, it must also contend with the vital agency of other material and microscopic worlds, which just as easily unravel out or spool up regardless of human presence, intention, and desire. Laboratory mice in fact are particularly disobedient, they hardly ever behave as they are supposed to—just as cell cultures in a lab are finicky and fail to grow to expectations, and junk ammo from the Junk Jet has a 10% chance of becoming suspended in mid-air, becoming irretrievable.[6] If we repurpose sites or moments of breakdown to resist configurations of power, then materials themselves are also always resisting what they ought to do or become.[7] This is the draw of the things in which we are enmeshed, where we are always extending, observing, destroying and deleting. If junk is the possibility, under particular cultural expectations and desires, for things to be pushed or cycled across such thresholds, and also, of making and unmaking these, it also must contend with the things themselves—with what we see in a corroded mirror, looking, or not, back at us.
A woman in a corroded mirror, disappearing and extending. (Image by Sarah Thanner, used with permission)
Although junk may be over-bursting in its use here as a metaphor, I argue it can still usefully be used to stitch growing anthropological attention to material decay, breakage, and deviation together with tinkering, maintenance, and repair—across locations, states, practices and materialities. Granted, “manifesto” is also a too decisive word to attach to this short piece. Too sure of itself. But this post is also an attempt to challenge the understanding of what it means to be (academically) polished and complete. I use manifesto here mostly tongue-in-cheek, while still holding to the idea that any argument has to begin in small seeds, and start growing from somewhere.
My thinking about junk began years ago with Brian Larkin’s attention to breakdown (2008). More recently, I found DeSilvey (2006) by way of Pink et al. (2018); and Jackson (2014) from Sachs (2020); and Hayes (1998) from Seaver (2023). This lineage is important because I am not inventing, but building. These ideas are also bits and tears of conversations with Libuše Hannah Vepřek, Sarah Thanner and Emil Rieger, and very long ago, Juris Milestone. But everything gets filtered first through Jonathan Corliss.
This research has been supported by the Japan Society for the Promotion of Science’s Grant-in-Aid for Scientific Research (C) 20K01188.
[1] PCR stands for polymerase chain reaction. It is an experimental method for duplicating selected genetic material in order to make it easier to detect in secondary experiments.
[2] Thermal cycler, for anyone interested. Also, just to note, but for the purposes of this retelling, I gloss over the most detailed part in writing so simply: “add some other reagents” and later, “after the PCR ‘melt’ and the second half of the experiment.”
[3] I wrote in my protocol notes, as an (anthropological) aside to myself: “K. stressed that the amount of liquid in this case doesn’t have to be super accurate, but that this is rare in science experiments. When I tried it for the first time, I almost knocked over all the new tips and also the NaOH solution which can cause burns! Yikes~)”
[4] Inconclusiveness includes an unclear or unaccounted for band in the electrophoresis gel, which is seen in the machine’s output as an image file.
[5] The images in this post are part of the artistic work of Sarah Thanner, a multimedia artist and anthropologist who playfully and experimentally engages with trashing and untrashing in her work.
[6] Fallout Wiki, Junk Jet (Fallout 4), https://fallout.fandom.com/wiki/Junk_Jet_(Fallout_4)
[7] Here, I also gloss over (new) materiality studies, Actor Network Theory, etc. which have linages too long to get to properly in this small piece.
Carlson, Rebecca, Gupper, Tamara, Klein, Anja, Ojala, Mace, Thanner, Sarah and Libuše Hannah Vepřek. 2023. “Testing to Circulate: Addressing the Epistemic Gaps of Software Testing.” STS-hub.de 2023: Circulations, Aachen Germany, March 2023.
DeSilvey, Caitlin. 2006. “Observed Decay: Telling Stories with Mutable Things.” Journal of Material Culture 11: 318-338.
Douglas, Mary. 1966. Purity and Danger: An Analysis of Concepts of Pollution and Taboo. London: Routledge.
Goodier, John L. “Restricting Retrotransposons: A Review.” Mobile DNA 7, 16. https://doi.org/10.1186/s13100-016-0070-z
Hayes, Brain. 1998. “Bit Rot.” American Scientist 86(5): 410–415. http://dx.doi.org/10.1511/1998.5.410.
Helmreich, Stefan. 2015. Sounding the Limits of Life: Essays in the Anthropology of Biology and Beyond. Princeton: Princeton University Press.
Iwata, Kentaro. 2020. “Infectious Diseases Do Not Exist.”「感染症は実在しない」あとがき. Retrived May 9, 2020, https://georgebest1969.typepad.jp/blog/2020/03/感染症は実在しないあとがき.html.
Jackson, Steven. J. 2014. “Rethinking Repair.” In T. Gillespie, P. J. Boczkowski, & K. A. Foot (Eds.), Media Technologies: Essays on Communication, Materiality, and Society. Cambridge: MIT Press. Pp. 221-239.
Lupton, D. 2016. The Quantified Self: A Sociology of Self Tracking. Cambridge: Polity Press.
Marres, N, Stark, D. 2020 “Put to the Test: For a New Sociology of Testing.” British Journal of Sociology 71: 423–443. https://doi.org/10.1111/1468-4446.12746.
Milestone, Juris. 2014. “What Will an Anthropology of Maintenance and Repair Look Like?” American Anthropological Association Meeting.
Pink, Sarah, Ruckenstein, Minna, Willim, Robert and Melisa Duque. 2018. “Broken Data: Conceptualising Data in an Emerging World.” Big Data & Society January–June: 1–13. https:// doi:10.1177/2053951717753228.
Rabinow, Paul. 1992. “Studies in the Anthropology of Reason.” Anthropology Today 8(5): 7-8.
Sachs, S. E. 2020. “The Algorithm at Work? Explanation and Repair in the Enactment of Similarity in Art Data.” Information, Communication & Society 23(11): 1689-1705. https://doi:10.1080/1369118X.2019.1612933.
Seaver, Nick. 2022. Computing Taste: Algorithms and the Makers of Music Recommendation. Chicago: University of Chicago Press.
Star, Susan Leigh. 1999. “The Ethnography of Infrastructure.” American Behavioral Scientist 43(3): 377–391. https://doi:10.1177/ 00027649921955326.
Enlarge (credit: D. Anschutz)
There is a reason countless songs about loneliness exist. Many are relatable, since feeling alone is often part of being human. But a particular song or experience that resonates with one lonely person may mean nothing to someone else who feels isolated and misunderstood.
Human beings are social creatures. Those who feel left out often experience loneliness. To investigate what goes on in the brains of lonely people, a team of researchers at the University of California, Los Angeles, conducted noninvasive brain scans on subjects and found something surprising. The scans revealed that non-lonely individuals were all found to have a similar way of processing the world around them. Lonely people not only interpret things differently from their non-lonely peers, but they even see them differently from each other.
“Our results suggest that lonely people process the world idiosyncratically, which may contribute to the reduced sense of being understood that often accompanies loneliness,” the research team, led by psychologist Elisa Baek, said in a study recently published in Psychological Science.
Enlarge / The Ariane 5 has been a workhorse since 1996 for the European Space Agency. (credit: ESA/Arianespace)
The Ariane 5 rocket has had a long run, with nearly three decades of service launching satellites and spacecraft. Over that time, the iconic rocket, with a liquid hydrogen-fueled core stage and solid rocket boosters, has come to symbolize Europe's guaranteed access to space.
But now, the road is ending for the Ariane 5. As soon as Tuesday evening, the final Ariane 5 rocket will lift off from Kourou, French Guiana, carrying a French military communications satellite and a German communications satellite to geostationary transfer orbit. A 90-minute launch window opens at 5:30 pm ET (21:30 UTC). The launch will be webcast on ESA TV.
And after this? Europe's space agency faces some difficult questions.
The billionaire space race is continuing to expand across the globe. Jeff Bezos-owned Blue Origin has announced plans to expand its operations to "Europe and beyond," the Financial Times reports. Part of this growth hinges on finding a site for an international launch facility — the company has already put down roots in Texas, Washington, Florida and Alabama — but the new location hasn't been chosen yet. It's also actively looking for fresh acquisitions and partnerships outside of the US in areas such as manufacturing and software.
"We're looking for anything we can do to acquire, to scale up to better serve our customers," Bob Smith, Blue Origin CEO, said. "It's not a function of size — rather how much it accelerates our road map of what we're trying to get done." Last year, Blue Origins bought New York-based Honeybee Robotics, a move that appears successful: The space-based robotics company was part of the Blue Origin team that recently received $3.4 billion to build the lunar lander for NASA's third Artemis mission. Blue Origin's biggest competitor, Elon Musk's SpaceX, is handling the first and second Artemis moon landings.
Though Blue Origin was the first to launch, land and reuse a rocket successfully, it has fallen behind its rival due to hold-ups with building its launchers. Blue Origin's plans for a more global footprint might help them catch up with SpaceX's progress. Amazon's Project Kuiper also plans to use Blue Origin's rocket New Glenn for at least 12 launches between 2024 and 2029 after a few years of delays.
This article originally appeared on Engadget at https://www.engadget.com/blue-origin-is-planning-to-open-new-launch-sites-outside-the-us-122518232.html?src=rss
Amazon Project Kuiper satellites aboard ULA, Blue Origin and Arianespace rockets
Amazon Project Kuiper satellites aboard ULA, Blue Origin and Arianespace rockets
This heron carefully places a tiny piece of bread in the water, then grabs the fish that comes to eat it.
Basically, the very human activity of Fishing.
Green heron using a piece of bread as bait to catch a fish.
Enlarge / Artist's view of what InSight looked like after landing. (credit: NASA/JPL-Caltech)
Mars appears to be a frozen expanse of red dust, gaping craters, and rocky terrain on the outside—but what lies beneath its wind-blasted surface? NASA’s InSight lander might have discovered this before it took its proverbial last breaths in a dust storm.
Whether the core of Mars is solid or liquid has been long debated. While there is no way to observe the Martian core directly, InSight tried. Its seismometer, SEIS, was the first instrument to find possible evidence of a liquid core. In the meantime, its RISE (Rotation and Interior Structure Experiment) instrument had been measuring minuscule changes in the planet’s rotation as it orbited, “wobbles” in its axis caused by the push and pull of the Sun’s gravity.
“Our analysis of InSight’s radio tracking data argues against the existence of a solid inner core and reveals the shape of the core, indicating that there are internal mass anomalies deep within the mantle,” write the researchers behind the instrument in a study recently published in Nature.
On late Saturday morning, a SpaceX Falcon 9 rocket carrying the European Space Agency’s Euclid spacecraft successfully lifted off Cape Canaveral, Florida. The near-infrared telescope, named after the ancient Greek mathematician who is widely considered the father of geometry, will study how dark matter and dark energy shape the universe.
In addition to a 600-megapixel camera astronomers will use to image a third of the night sky over the next six years, Euclid is equipped with a near-infrared spectrometer and photometer for measuring the redshift of galaxies. In conjunction with data from ground observatories, that information will assist scientists with estimating the distance between different galaxies. As The New York Times notes, one hope of physicists is that Euclid will allow them to determine whether Albert Einstein’s theory of general relativity works differently on a cosmic scale. There’s a genuine possibility the spacecraft could revolutionize our understanding of physics and even offer a glimpse of the ultimate fate of the universe.
👋 Safe travels, #ESAEuclid!
— ESA's Euclid mission (@ESA_Euclid) July 1, 2023
The #DarkUniverse 🕵️♂️ detective ventures into the unknown. pic.twitter.com/JvWBpIz4Sx
“If we want to understand the universe we live in, we need to uncover the nature of dark matter and dark energy and understand the role they played in shaping our cosmos,” said Carole Mundell, the ESA’s director of science. “To address these fundamental questions, Euclid will deliver the most detailed map of the extra-galactic sky.”
With Euclid now in space, it will travel approximately a million miles to the solar system’s second Lagrange point. That’s the same area of space where the James Webb Space Telescope has been operating for the past year. It will take Euclid about a month to travel there, and another three months for the ESA to test the spacecraft’s instruments before Euclid can begin sending data back to Earth.
This article originally appeared on Engadget at https://www.engadget.com/europes-euclid-space-telescope-launches-to-map-the-dark-universe-175331413.html?src=rss
Euclid launch
A shot of the Euclid space telescope against the dark of space.
Every person starts as just one fertilized egg. By adulthood, that single cell has turned into roughly 37 trillion cells, many of which keep dividing to create the same amount of fresh human cells every few months.
But those cells have a formidable challenge. The average dividing cell must copy—perfectly—3.2 billion base pairs of DNA, about once every 24 hours. The cell’s replication machinery does an amazing job of this, copying genetic material at a lickety-split pace of some 50 base pairs per second.
Still, that’s much too slow to duplicate the entirety of the human genome. If the cell’s copying machinery started at the tip of each of the 46 chromosomes at the same time, it would finish the longest chromosome—No. 1, at 249 million base pairs—in about two months.
“The way cells get around this, of course, is that they start replication in multiple spots,” says James Berger, a structural biologist at the Johns Hopkins University School of Medicine in Baltimore, who co-authored an article on DNA replication in eukaryotes in the 2021 Annual Review of Biochemistry. Yeast cells have hundreds of potential replication origins, as they’re called, and animals like mice and people have tens of thousands of them, sprinkled throughout their genomes.
“But that poses its own challenge,” says Berger, “which is, how do you know where to start, and how do you time everything?” Without precision control, some DNA might get copied twice, causing cellular pandemonium.
Keeping tight reins on the kickoff of DNA replication is particularly important to avoid that pandemonium. Today, researchers are making steps toward a full understanding of the molecular checks and balances that have evolved in order to ensure that each origin initiates DNA copying once and only once, to produce precisely one complete new genome.
Bad things can happen if replication doesn’t start correctly. For DNA to be copied, the DNA double helix must open up, and the resulting single strands—each of which serves as a template for building a new, second strand—are vulnerable to breakage. Or the process can get stuck. “You really want to resolve replication quickly,” says John Diffley, a biochemist at the Francis Crick Institute in London. Problems during DNA replication can cause the genome to become disorganized, which is often a key step on the route to cancer.
Some genetic diseases, too, result from problems with DNA replication. For example, Meier-Gorlin syndrome, which involves short stature, small ears, and small or no kneecaps, is caused by mutations in several genes that help to kick off the DNA replication process.
It takes a tightly coordinated dance involving dozens of proteins for the DNA-copying machinery to start replication at the right point in the cell’s life cycle. Researchers have a pretty good idea of which proteins do what, because they’ve managed to make DNA replication happen in cell-free biological mixtures in the lab. They’ve mimicked the first crucial steps in initiation of replication using proteins from yeast—the same kind used to make bread and beer—and they’ve mimicked much of the entire replication process using human versions of replication proteins, too.
The cell controls the start of DNA replication in a two-step process. The whole goal of the process is to control the actions of a crucial enzyme—called a helicase—that unwinds the DNA double helix in preparation for copying it. In the first step, inactive helicases are loaded onto the DNA at the origins, where replication starts. During the second step, the helicases are activated, to unwind the DNA.
Kicking off the process is a cluster of six proteins that sit down at the origins. Called ORC, this cluster is shaped like a double-layer ring with a handy notch that allows it to slide onto the DNA strands, Berger’s team has found.
In baker’s yeast, which is a favorite for scientists studying DNA replication, these start sites are easy to spot: They have a specific, 11- to 17-letter core DNA sequence, rich in adenine and thymine chemical bases. Scientists have watched as ORC grabs onto the DNA and then slides along, scanning for the origin sequence until it finds the right spot.
But in humans and other complex life forms, the start sites aren’t so clearly demarcated, and it’s not quite clear what makes the ORC settle down and grab on, says Alessandro Costa, a structural biologist at the Crick Institute who, with Diffley, wrote about DNA replication initiation in the 2022 Annual Review of Biochemistry. Replication seems more likely to start in places where the genome—normally tightly spooled around proteins called histones—has loosened up.
The initiation of DNA replication starts at the tail end of the previous cell division and continues through the cell cycle phase known as G1. DNA synthesis happens during the S phase. Levels of a protein called CDK are critical to ensuring that DNA is replicated once and only once. When CDK levels are low, helicases can jump onto the DNA and start to unwind it. But repeat binding does not happen because CDK levels rise, and this blocks the helicase from binding again. (credit: Knowable Magazine)
Once ORC has settled onto the DNA, it attracts a second protein complex: one that includes the helicase that will eventually unwind the DNA. Costa and colleagues used electron microscopy to work out how ORC lures in first one helicase, and then another. The helicases are also ring-shaped, and each one opens up to wrap around the double-stranded DNA. Then the two helicases close up again, facing toward each other on the DNA strands, like two beads on a string.
At first, they just sit there, like cars with no gas in the tank. They haven’t been activated yet, and for now the cell goes about its usual business.
Things kick into high gear when a crucial molecule called CDK waves the green flag, jump-starting chemical steps that lure in even more proteins. One of them is DNA polymerase—what Costa calls the “typewriter” that will build new DNA strands—which hitches onto each helicase. Others activate the helicases, which can now burn energy to chug along the DNA.
As this occurs, the helicases change shape, pushing on one DNA strand and pulling on the other. This creates strain on the weak hydrogen bonds that normally hold the two strands together by the bases—the As, Cs, Ts and Gs that make up the rungs of the DNA ladder. The two strands get ripped apart. Costa and colleagues have observed how the two helicases untwist the DNA between them, and they’ve seen how the helicases keep the unbound bases stable and out of the way.
Left: Several genes involved in the initiation of DNA replication (horizontal axis) are amplified—that is, mistakenly copied in extra numbers — to varying degrees (vertical axis) in different cancers. Right: On chromosome 8, a cluster of three genes—shown in green text—are frequently amplified together in certain cancers. (credit: Knowable Magazine)
At first, both helicases are wrapped around both strands of DNA, and they can’t get very far like this, because they are facing each other and will just run into each other. But next, they each undergo a change in position, spitting one DNA strand or the other out of the ring. Now separated, they can jostle past each other, and replication proceeds apace.
Each helicase motors along its single strand, in the opposite direction from the other. They leave the origin behind and yank apart those hydrogen-bonded base pairs as they travel. The DNA polymerase is right behind, copying the DNA letters as they’re freed from their partners.
CDK’s second job is to stop any more helicases from hopping on the origins. Thus, there is one start of replication per origin, ensuring proper copying of the genome—although copying doesn’t begin at the same time at each site. The whole process of DNA replication, in human cells, takes about eight hours.
There is still plenty to be worked out. For one thing, the DNA that’s being copied is not a naked double helix. It’s wrapped around histones and attached to lots of other proteins that are busy turning genes on or off or making RNA copies of the genes. How do those jostling proteins affect each other and avoid getting in each other’s way?
Beyond this fascinating, fundamental biology—a remarkable process essential for all life on Earth—there are implications for diseases like cancer. Scientists already know that faulty replication can destabilize DNA, and an unstable genome that’s prone to mutation may be an early hallmark of cancer development. And they are further investigating links between replication proteins and cancer.
“I think that there are opportunities for therapeutic interventions for these systems,” says Berger, “once we have enough insights about how they work and what they look like.”
Amber Dance, a science writer in the Los Angeles area, also likes to break large tasks into smaller segments: It took her five days to complete the steps to draft this article. This article originally appeared in Knowable Magazine, an independent journalistic endeavor from Annual Reviews. Sign up for the newsletter.
Enlarge / One of the medical clinics suspended by Mexican health authorities in Matamoros, Tamaulipas, Mexico, on May 19, 2023. (credit: Getty | AFP)
Three more people in the US have died from fungal meningitis in an outbreak linked to tainted surgeries in Mexico, bringing the total deaths to seven, the Centers for Disease Control and Prevention reported Thursday.
The total case count remains unchanged from an update earlier this month, with 34 cases in the US: nine confirmed, 10 probable, and 15 suspected. Health officials are investigating 161 others who may have been exposed.
The outbreak is linked to cosmetic surgeries involving epidural anesthesia at two clinics in Matamoros, Mexico, just across the border from Brownsville, Texas. Mexican and US officials suspect that a component of the anesthetic was contaminated, resulting in the pathogenic fungus Fusarium solani being injected directly into people's spinal cords. The tainted surgeries are thought to have occurred between January 1, 2023, to May 13, 2023, around when the clinics were shut down by local health officials.
On this episode of the Big Brains podcast, a scholar explains the neuroscience of how listening to and playing music builds our mind.
Music plays an important role in all of our lives. But listening to music or playing an instrument is more than just a creative outlet or hobby—it’s also scientifically good for us. Research shows that music can stimulate new connections in our brains; keeping our cognitive abilities sharp and our memories alive.
In a new book, Every Brain Needs Music: The Neuroscience of Making and Listening to Music (Columbia University Press, 2023), Larry Sherman explores why we all need music for our mental well-being—and how it can even help us later in life.
Sherman is a professor of neuroscience at Oregon Health & Science University.
Listen to the episode below:
Read the transcript to the episode. Subscribe to Big Brains on Apple Podcasts, Stitcher, and Spotify.
Source: University of Chicago
The post How music benefits your brain appeared first on Futurity.
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