These strange tales hint at what was, until quite recently, an underappreciated facet of our nature. Humans, it seems, can hibernate. 2014-03-27: Using torpor to improve ER survival odds
We’ve always assumed that you can’t bring back the dead. But it’s a matter of when you pickle the cells
For a long time, there was no evidence that primates could hibernate. A species of Madagascan lemur was shown to practise regular bouts of torpor. “If you look at the lemur and look at us, we share 98% of our genes. It would be very strange if the tools of hibernation were all packed into that 2% difference.”
2 research groups had markers in the brains of rats which they used to identify the neurons that triggered torpor. They then just activated those neurons to turn on the torpor state. Torpor is a weaker version of suspended animation. However it is 2x as efficient as sleeping or resting.
In response to a series of 3.2-megahertz pulses, the rodents’ core body temperatures dropped by about 3°C. The mice cooled off by shifting body heat into their tails—a classic sign of torpor—and their heart rates and metabolisms slowed. By automatically delivering additional pulses of ultrasound when the animals’ body temperatures began to climb back up, the researchers could keep the mice in this torpid state for up to 24 hours. When they silenced the minispeakers, the mice returned to normal, apparently with no ill consequences.
Because of the importance of beneficial / commensal microbes in human biology, there have been growing efforts to characterize the microbes in various body locations – gut, mouth, lungs, skin, etc. But the efforts so far have simply given a tantalizing taste of how interesting and important these microbes are. So here comes this meeting. Organized by NIH (specifically, Francis Collins at NHGRI), this workshop is geared to discuss the possibility that studies of the human microbiome will be included in the next list of “NIH Roadmap” programs. More on the NIH Roadmap some other time.
Basically, the general idea is – do we need an big scale, organized program to tackle the human microbiome.? To get us in the mood, we had talks by many of the pioneers/leaders in the field (e.g., David Relman, Jeff Gordon, Jim Tiedje) as well as discussion of the NIH Roadmap program. I personally did not need any convincing but it was good to hear some of the ideas presented. In the end, I think there is no doubt that a large scale Human Microbiome Program is needed and would be very beneficial.
In addition to the 10 trillion human cells, there are 100 trillion bacterial cells in a body. Our metagenome may be 100x the human genome. 2010-10-30: Space Standard Microbiome. Venter suggests NASA should replace the microbiome (bacteria species) of astronauts with a standardized, synthetic one to improve survivability of space flight. 2012-06-15: 0.3% Human
Where the human genome carries some 22K protein-coding genes, the human microbiome contributes some 8M protein-coding genes responsible for human survival: 360x more.
The microbiome is one of the most fascinating areas in biology:
in many mammals a microbial community ferments various sweats, oozes and excretions into distinctive scents that reveal age, health and much more to knowing noses in a select social circle.
That’s right, microbes are posting status updates to each other through smells, sharing with other microbes what they’ve learned about host animals. 2012-12-08: American Gut looks amazing. I will of course participate. Since you are only 10% human (the rest is bacteria), even if you do 23andme you don’t really know yourself at all. $99 for 1 bacterial DNA kit, $180 for 2. There are also higher levels, up to the $25k ultra-deep sequencing of your microbiome sample aimed at generating as many individual bacterial genomes as possible. 2015-03-03: a nice summary of The American Gut project
2016-10-01: Poop Bot. As usual, onion’s satire is leading the way:
you can tell the most about someone by sampling their microbiome, and “the sewage system is the great aggregator.” Gross, sure, but Ratti is studying waste to understand everything from heroin use to antibiotic-resistant bacteria—and all with the help of a sewer-slurping robot named Luigi.
A survey of DNA fragments circulating in the blood suggests the microbes living within us are vastly more diverse than previously known. In fact, 99% of that DNA has never been seen before. The “vast majority” of it belonged to a phylum called proteobacteria, which includes, among many other species, pathogens such as E. coli and Salmonella. Previously unidentified viruses in the torque teno family, generally not associated with disease but often found in immunocompromised patients, made up the largest group of viruses.
In 15 years, brain interfaces will be as common as the cell phone. The radical experiment that has been run over the past 100 years shifting the microbiome of infants and provoking a wide array of immune disorders (allergies, asthma, diabetes)
Now that it is clear that social behavior plays a role in shaping the gut microbiome, the next question is whether microbiomes have had a meaningful impact on our social worlds. Scientists still do not have an answer, but they are tantalized by the possibilities, which could have implications for understanding the evolution of sociality.
Humans aren’t the only organisms that we have to consider when evaluating the impacts of space travel. While we are traveling on spaceships, microbes are traveling on us. Microgravity has been shown to alter bacterial growth patterns and kinetics, and radiation increases the frequency of mutations—in both cases creating opportunities for increased antimicrobial resistance—all in an environment where astronauts immune systems are compromised. The ISS has a complex microbiome that we fundamentally alter, and that in turn alters us. It’s important to be able to understand the genetic basis of antimicrobial resistance in space. A team of researchers carried out a study with the goal of addressing this question. A considerable number of AMR genes were found in several different locations for Kalamiella piersonii—a microbe potentially involved in causing urinary tract infections. Worryingly, “the potentially very pathogenic microbe E. bugandensis was found in location 2 (forward side panel wall of the Waste and Hygiene Compartment) in flight 1, presenting more than 40 ARGs.” They were also able to detect specific types of potential drug resistance for several microbes within the Pantoea species—which provided a higher level of resolution into observations made in their past analysis.
Mother-to-infant gut microbiome transmission was considerable and stable during infancy (around 50% of the same strains among shared species (strain-sharing rate)) and remained detectable at older ages. By contrast, the transmission of the oral microbiome occurred largely horizontally and was enhanced by the duration of cohabitation. There was substantial strain sharing among cohabiting individuals, with 12% and 32% median strain-sharing rates for the gut and oral microbiomes, and time since cohabitation affected strain sharing more than age or genetics did.
2023-05-04: Using dental plaque to reconstruct the oral microbiome
Reconstructing an oral microbiome—a soup of 100s of different bacterial species, and millions of individual bacteria—from degraded ancient DNA is “like throwing together pieces of many puzzles and trying to solve them with the pieces mixed up and some pieces missing entirely”.
It took 3 years to adapt DNA sequencing tools and computer programs to work with the much shorter fragments of DNA found in ancient samples. Drawing on dental calculus from 46 ancient skeletons—including a dozen Neanderthals and modern humans who died between 30k and 150 years ago, Warinner identified DNA from 10s of extinct or previously unknown oral bacteria.
Identified as a type of bacterium called a chlorobium, its modern relatives use photosynthesis to survive on small amounts of light and live in anaerobic conditions, such as stagnant water. They aren’t found in modern mouths and appear to have vanished from ancient humans 10 ka BP. This chlorobium might have entered the mouths of ancient people because they drank water in or near caves. Or it might once have been a normal part of some people’s ancient oral microbiome, surviving on faint light penetrating the cheek.
The authors have tried all sorts of sample-handling variations, and it looks like they have had trouble finding any that don’t change the composition of the microbial samples themselves. Both papers investigated the 2 commercially available stool sample kits (OMNIgene and Zymo), and found that the latter was much more sensitive to temperature variations on storage. And both kits changed the absolute levels of various bacteria types: the OMNIgene-preserved samples had significantly higher amounts of Bacteroidetes species as compared to preservative-free controls, while the Zymo-preserved ones had significantly lower amounts. The second paper also finds that the method used for cell disruption can significantly affect the ribosomal RNA reads used to characterize the bacterial species as well.
Researchers in the field should also be measuring total bacterial load in their samples and monitoring that for signs of variability in their sample handling and people should standardize on 25 PCR cycles, because that can also change things. These effects can help explain the widely varying literature results in human microbiome studies.
Adams designed the TransHab, an inflatable housing module that connects to the International Space Station. Her work shows how architects can successfully “interface people with… interiors in space” – with strong design implications for building interiors here on Earth
If we don’t do something, sooner or later Earth will be hit by an asteroid large enough to kill all or most of us. That includes the plants and animals, not just people. Maybe this won’t happen for millions of years. Maybe in 15 minutes. We don’t know. For example, on 23 March 1989 asteroid 1989FC with the potential impact energy of over 1000 megatons missed Earth by 6 hours. We first saw this fellow after closest approach. If 1989FC had come in 6 hours later most of us would have been killed with 0 warning.
The total number of known NEAs was 2165 at the end of 2002 and 4647 in April 2007. That trend is not looking good at all.
In 2029, we have an opportunity to smash a small spacecraft into an asteroid so it misses an area of space just 600m across, and won’t come back in 2036 to unleash the energies of 65000 nuclear bombs on earth. If we succeed, we won’t have to call on bruce willis to save the day. We should totally do this: kg for kg, probably the most valuable space mission ever. even if this is a no-op, how cool is that?
Instead of worrying about nonsense like terrrrrrrists, can we start worrying about extinction risk instead? There are 1.5m civilization-ending asteroids in the solar system. Diamandis and musk are doing more for the survival of the human race than all the assholes sucking at the teat of the security theater complex combined.
Asteroid Impacts over Russia – Another Larger Rock Passing Very Close to Earth
As you may know, I’m the co-Founder and co-Chairman of an asteroid company called Planetary Resources that is backed by a group of 8 billionaires to implement the bold mission of extracting resources from near-Earth asteroids. Given my personal interest in asteroids, today is an EPIC day. If you’re interested in more info on this, I urge you to join our mission at Planetary by signing up for the regular updates on our website, PlanetaryResources.com.
In the meantime, I want to fill you in on 2 breaking stories: First: At 9:30 local time, a large meteor exploded in the skies over Chelyabinsk, a city in Russia just east of the Ural mountains, and ~1500 kilometers east of Moscow. The fireball was incredibly bright, rivaling the Sun! There was a pretty big sonic boom from the fireball, which set off car alarms and shattered windows. Reports are coming in that up to 1000 individuals have been injured (mostly by shattered glass blown out by the shock wave).
Second: This comes exactly at the same time that another asteroid — 2012-DA14, a 45 meter asteroid — is whizzing by the Earth a hair’s breadth from the surface. It’s missing us by only 22k km, well within the 36k km orbit of the geostationary satellites that orbit around the Earth’s equator. I wanted to put this in perspective for you with some of the chilling and fascinating facts:
– This asteroid 2012-DA14 is the same size as the asteroid that hit the Earth in Russia in Siberia (the “Tunguska Event”) on June 30th 1908.
– That impact was equivalent to 1000 Hiroshima nuclear bombs and knocked down 80M trees down over an area covering 2150 km2.
– Had it hit near a population center it would have killed millions of people.
Today, there are ~610k asteroids that are actively tracked in our solar system. This number represents less than 1% of the more than 60M asteroids that orbit the Sun. Of these asteroids, about 1.5M are larger than 1 kilometer in size and are what might be described as “extinction-level/dinosaur-killing asteroids.”
Scientists are closely tracking 434 asteroids that are large enough and come close enough to the Earth to be of potential future concern, and while none of these pose any significant risk today, increased surveillance is required.
While the primary business of Planetary Resources is to ultimately prospect and mine the most select of these for fuels and precious metals, the company views that this economically driven activities will assist humanity in the arena of planetary protection in 2 critical ways.
First, the Arkyd-100 Space Telescopes that the company is currently designing and building will assist in the detection and characterization of these small, potentially hazardous, yet undetected asteroids.
Second, as the company ultimately develops the capability and infrastructure for intercepting and mining asteroids, Planetary Resources expects to be able to help in the (slight) redirection of these rocks to keep the Earth safe.
Mining asteroids will ultimately benefit humanity on and off the Earth in a multitude of ways. First, by providing us access to the fuels to accelerate human exploration of space. Second, by expanding humanity’s economic access to platinum group metals important for our rapidly growing high-technology industries; and third, by giving us the infrastructure to routinely and swiftly interact with and redirect asteroids, like 2012 DA14, which could someday pose a threat to Earth.
On the production floor of Planetary Resources Inc, we also now have full-scale mechanical prototypes of the Arkyd-100 Series, which is the first line in its family of deep-space prospecting spacecraft. “The Arkyd-100 Series will be the most advanced spacecraft per kilogram that has ever been built. The system will be highly capable and cost-effective, which will allow for a constellation of them to be launched. That efficiency will not only fast-track our asteroid prospecting effort, but will also lend a hand in scientific discovery and planetary defense.”
8 hiroshima impacts since 2000. It’s amazing to watch the globe spin as 20 of the 26 hit oceans, without human witnesses. 1 hit the Australian outback, 2 hit Northwest Africa, and only 3 others hit land, including Chelyabinsk.
The conclusion of this research: “Near-Earth object impacts could be ~10x more common than we thought they were.”
The Asteroid Grand Challenge Series will be comprised of a series of topcoder challenges to get more people from around the planet involved in finding all asteroid threats to human populations and figuring out what to do about them. NASA recognizes the value of the public as a partner in addressing some of the country’s most pressing challenges.
there’s also
the 100x Declaration, urging a 100-fold increase in the detection and monitoring of asteroids. With the Sentinel Mission, you would know the trajectories 50+ years into the future, and with enough years to play with, a small delta-v imparted early on (easily achieved by just rear-ending the asteroid), alters the course of the solar system ever so slightly to preserve life on Earth.
and as of 2021, things look more promising
Over the long march of biological and now technological evolution, we have finally reached a survival gate — we have enough computational power to model the trajectory all Near-Earth Objects (NEO’s) that could threaten life on Earth. This was not possible in the year 2000, or any time over the prior millennia. We have made a million-fold improvement in computation in just the past 20 years. So, we can see the future and predict decades in advance of an impact event and then give the NEO a nudge such that it misses Earth entirely.
B612 Foundation announced the discovery of more than 100 asteroids.
That by itself is unremarkable. New asteroids are reported all the time by skywatchers around the world. That includes amateurs with backyard telescopes and robotic surveys systematically scanning the night skies.
What is remarkable is that B612 did not build a new telescope or even make new observations with existing telescopes. Instead, researchers financed by B612 applied cutting-edge computational might to 412k years-old images to sift asteroids out of the images. Of the estimated 25k near-Earth asteroids at least 140m in diameter, only 40% have been found. A single point of light that is not a star or a galaxy is a starting point for the algorithm, which they named Tracklet-less Heliocentric Orbit Recovery, or THOR. THOR constructs a test orbit that corresponds to the observed point of light, assuming a certain distance and velocity. It then calculates where the asteroid would be on subsequent and previous nights. If a point of light shows up in the data, that could be the same asteroid. If the algorithm can link together 5 observations across a few weeks, that is a promising candidate for an asteroid discovery. The NOIRLab archive contains 7 years of data, suggesting that there are 10s of 1000s of asteroids waiting to be found.
The algorithm is currently configured to only find main belt asteroids, those with orbits between Mars and Jupiter, and not near-Earth asteroids, the ones that could collide with our planet. Identifying near-Earth asteroids is more difficult because they move faster. Different observations of the same asteroid can be separated farther in time and distance, and the algorithm needs to perform more number crunching to make the connections.
“It’ll definitely work. There’s no reason why it can’t. I just really haven’t had a chance to try it.”
2023-03-06: A visualization of the NEO risk. Unclear how they know how many are left to be discovered beyond some vague orbital mechanics reason.
Although satellites have been passively relaying IP traffic since the 1970s, the use of an orbiting satellite as an active part of the Internet is a more recent development. Once you have smarter satellites, you can treat them as not completely separate but as part of your IP network and manage them as you do your IP networking assets on the ground.
Gregor J. Rothfuss 