Sterilization

Boiled Dirty Water under the Microscope
Sci- Inspi

Just a little biology refresher.

Parasites

Reverie, 1872, Edward Radford

Biological, not political. Petr Frost's Newsletter has a very weird tale:

Are tiny parasites messing with our brains?

They might be causing changes in behavior, but the changes might be subtle, and only to a small portion of the population. Still, pretty weird.

P. S. Looking for information about Edward (the artist), I found lots of sites selling his pictures, but Wikipedia has no page about him. Google tells us he lived from 1831 to 1920.

Digital DNA Sequencing

DNA Sequencing chip
EvilmonkeyzDesignz

I guess we should have seen this coming. Silicon chip technology is down to 2 nanometers. Amino acids measure between 0.4 and 1 nanometers in length. Some people like to measure these things using Ångströms, which are one-tenth of a nanometer. That is, there are ten Ångströms in a nanometer.

This Discovery Just Won the Nobel Prize in Chemistry

This Discovery Just Won the Nobel Prize in Chemistry
Cleo Abram

Machine Learning sounds a lot like Artificial Intelligence, so maybe AI does have some uses.

Jump Spider, Jump

What Jumping Spiders Teach Us About Color
Veritasium

The techniques they are using in microbiology these days are out of this world.

Brains

Downloading nematode brains from Github
Dungeonman from youtube

Nematodes are very small, slender worms: typically about 5 to 100 µm thick, and 0.1 to 2.5 mm long.

Nematodes are pervasive:

Nematodes have successfully adapted to nearly every ecosystem: from marine (salt) to fresh water, soils, from the polar regions to the tropics, as well as the highest to the lowest of elevations. They are ubiquitous in freshwater, marine, and terrestrial environments, where they often outnumber other animals in both individual and species counts, and are found in locations as diverse as mountains, deserts, and oceanic trenches. They are found in every part of the Earth's lithosphere, even at great depths below the surface of the Earth. They represent 90% of all animals on the ocean floor.

Story I heard was that they are so pervasive that if you took away all grass and trees and dirt but left the nematodes, everything would still look the same.

Worm simulation in your browser

CElegans Neurorobotics
Timothy Busbice

Toy robot running a nematode brain simulation to control its actions.

GoPiGo Programmable Robot Kit

More technical stuff:

• Heyseth github
• connectomeengine. Note: that is connectome engine, not connect to me engine.

What's a connectome?

A connectome is a map of the brain's neural connections, also known as the brain's wiring diagram. It's made up of neurons that communicate through synapses, and each connection is made up of the presynaptic axon, the postsynaptic dendrites, and synapses between the neurons. Connectomes can be represented in graph or matrix form, and are used to analyze network organization. 

Nematodes brains aren't the only microscopic brains the whiz-kids are studying - some people are studying fruit fly brains.

The Making of a Fly

Thanks to Matt Parker, we have this book about fruit fly genetics.

Salt River - Randy Wayne White

Picked up a Doc Ford novel, Salt River by Randy Wayne White, at Powell's this afternoon. Waiting for my wife, I open the book and start reading the Author's Note and I am just entranced. What he is describing here sounds just like the political arguments we hear about on social media. Shoot, sounds like any controversy. It's so great I've copied the bulk of it here:

Organisms that contribute to destructive algae blooms are found in most water environs, salt and fresh, throughout the world, year around. "Pollutants" they are not. Indeed, the global food chain would collapse without these microorganisms and macro algae. Keep this in mind the next time you read about small quantities of "red tide organisms" found at your local beach. This is not news. The micro flora are always present-and, sadly, so is the hysteria associated with the word "algae."

There isn't much that biologists agree upon regarding harmful algae blooms (HABs) save for a worldwide consensus that the phenomenon, while naturally occurring and massively destructive, can be enhanced by human activities. The degree to which humans cause, or contribute, to these events is at the historic epicenter of disagreements SO passionate that opinions too often have more in common with theology than science.

In this book, the fictional Doc Ford attempts to provide readers with an overview of the subject that is dispassionate and, above all, factual. This was a challenge. As I explained in an editorial I wrote for the Sunday New York Times (September 29, 2018): “During my 50 years on this coast, I've experienced four killer algae blooms as a fishing guide (1974, '82, '96 and 2004). As a novelist, I've researched the subject, yet my understanding lacks the certainty or rage of those newly acquainted with these blooms." [https://www.nytimes.com/2018/09/29/opinion/sunday/red-tide-florida-tourism.html] (paywall)

In other words, the more I learn, the less likely I am to be persuaded by those whose convictions are unshakable, for they invariably have a financial stake in whatever "solution" they advocate. This includes organized camps representing the phosphate, sugarcane, and agriculture industries as well as low-profile developers who view agriculture as a waste of acreage that would become a goldmine if bulldozed and transformed into golf courses and gated communities.

This is another element to keep in mind when ferreting through arguments regarding the solutions to red tides.

The newer, booming "environmental industry" also has a stake in the controversy. According to Environmental Business International Inc., a publishing and research firm, the industry grew by 4.8 percent in 2017 and produced $370 billion in annual revenue. This amount dwarfs the $10.1 million collected in 2016 by the Everglades Foundation, one of fourteen Florida-based nonprofit organizations that have a vested interest in the causes and effects of harmful algae blooms. I do not doubt the altruistic motives of these groups, nor do I think it unfair to acknowledge a simple fiduciary fact: to survive, to continue their good work, each must motivate the public sector to provide funding.

In this novel, you will meet Mack, the owner of Dinkin's Bay Marina. Mack has strong opinions on this subject. Even the unflappable Marion Ford cannot convince Mack that hysteria mongering has become a dangerously misleading fundraising tool.

For decades, I've collected newspaper accounts and research on algae blooms that date back to the 1800s. My file contains hundreds of clippings, many acquired at Florida libraries, after scanning through reels of microfiche. The historic overview they provide suggests a predictable cycle, and that cycle has not changed much. When acres of dead fish begin to wash ashore, there is a sustained, communal panic. Civic leaders demand action - and an explanation.

A few examples: According to a study issued by the University of Miami in 1955, a series of lethal red tides between 1844 and 1878 were, according to local fishermen, caused by a "poisonous" flow of freshwater from the Everglades into Florida Bay. A December 1918 headline in the Punta Gorda Herald asserted "Seismic Explosion Under Gulf Kills Many Fish Between Boca Grande and Marco." In July 1937, the St. Pete Times suggested that "the discharge of chemicals from freighters at Port Tampa" was to blame for the sudden death of "fish and eels rarely caught." An article in a November 1940 edition of the Fort Myers New-Press claimed that a massive fish kill was the result of a mysterious "subterranean disturbance." A Miami Herald article, dated February 1954, referenced the devastating red tides of 1947-50, and reported that scientists had traced the cause to excessive amounts of phosphorus found in the Peace River. A year later, in February 1955, the News-Press, under the optimistic headline "Red Tide Seen Under Control in Three Years," cited a study that concluded that phosphate had nothing to do with red tide, then reassured readers that "government scientists" had discovered that dusting algae blooms with copper sulphate (sic) was an 1 inexpensive and effective solution. 

Problem solved? Of course not, and it is ironic to note that, as recently as 1989, the idea of dusting algae outbreaks was revisited - but with phosphatic clay, a residue produced by Florida's controversial phosphate industry. 

I posted a couple of pages about another of White's books: Cuba Straits. Page 1 here. Page 2 here.

Flagella

This MOTOR Lives INSIDE YOU!
Tech Planet

Atomic scale motors propelling bacteria on their journey into the unknown.

Via Dennis

Retrotransposons

R2 Retrotransposons 1
From a Max Wilkinson post on Twitter

I don't understand exactly what is going on here, but it's very cool that molecular biologists have been able to sort this out. I have made a playlist of all four of the videos, you can find it here.

Via Ross and Harvard

Black Crab Movie

BLACK CRAB Trailer (2022) Noomi Rapace, Thriller Movie
Movie Coverage
War movie between unidentified parties, fought in the mostly frozen north, on ice skates. Looks like it could be Ukraine or Eastern Europe, but it's probably Scandinavia. All them countries have beaucoup d'islands in waters that freeze in the winter. In any case, the war is brutal and vicious. 

Roger Ebert has a decent review, though he somehow confuses a capsized lifeboat with global warming. I mean, how many middle eastern refugees have drowned in the mediterranean, and I'm pretty sure global warming doesn't have anything to do with that.

Then there is the bit about the two packets our crew is carrying that could end the war. Turns out they each contain a vial of deadly pathogens. At one point our hero (Noomi) tapes these two packets to a grenade and then pulls the pin. Would the fireball destroy the pathogens, or would the blast just disperse them? Either option would fit the story.

Then there's the moral dilemma of what do you do with a couple of vials of deadly pathogens? Do you turn them over to the authorities, who are almost certainly going to unleash them on someone? Will they just kill the enemy, or will they kill everyone? Or do you destroy them?

And what's going on in those biological research laboratories in Ukraine? Are they just doing research on microbes and virii, or are they trying to make nastier diseases that can be used as a weapon? Even it we knew exactly what they were doing it might be hard to tell. Whether you are trying to find a way to combat a disease or a way to make the disease more deadly, you are going to want to learn more about the pathogen that causes it, i.e. research. About the only way to judge these things is to see if they are trying to keep it secret and who is running the show. Since everyone who is denying that these facilities exist is a fully paid up member of wolf pack that is running our Empire of Lies [tm], I suspect the worst.

I've seen a couple other movies starring Noomi Rapace. Black Crab is the best of the lot.

This was directed by Adam Berg. He hasn't directed many movies, but he has directed a bunch of music videos. I guess that's one way to get into the movie business. I checked out a few of them but the most of the tunes didn't do anything for me, but there were a couple that I have posted.

Venom and Anti-Venom

How Horses Save Humans From Snake Bites
Veritasium
Some people are terrified by snakes, some people enjoy killing them, others are enthralled by them. I think they are kind of cool, but not cool enough that I would have one in my house. There are a couple other posts about snakes and venom here.

Time flies like an arrow,

Fly Brain Imaged at Nanoscale Resolution
HHMI Howard Hughes Medical Institute

fruit flies like bananas. Talking to a neurobiology student last night. They're studying fruit fly brains. These brains have 100,000 neurons and it's pretty well understood how they work. That's for some value of 'pretty well'. This video is an easy introduction.

Gain-Of-Function

Artist's Conception of a Virion

There are scientists studying the microbes and virions that cause disease. This research is essential if we want to learn more about these disease causing agents, and there is much more to learn because they are very complex and we really don't know very much about them now.

But there are also people / scientists studying these disease causing agents to see if they can find ways to make them more deadly. This is bio-weapons research and is essentially a criminal activity.

However, what can be learned in one area can be applied in the other, mostly because we don't know very much so any knowledge gained is a step towards our ultimate goal of understanding how everything in the universe works.

I say we don't know very much, but that's not really true. We know a great deal, but compared to how much we still need to learn in order to completely understand these things, it is not very much.

A post by David Warren got me started. Pages on the National Institute of Health (NIH) and Frontiers in Bioengineering and Biotechnology didn't make me feel any better.

It probably didn't help my state of mind that I have been reading The Demon in the Freezer by Richard Preston, which is all about recent smallpox and anthrax research / disasters.

Links

• What Assange was indicted for. Good explanation of password cracking. Via Borepatch
• Berlin Wall Escape that was financed by an American News Agency. 1962. My Daily Kona
• How a Few Lucky Civil War Soldiers Started Glowing and Healed Faster. Bio-luminescent bacteria. Knuckle Draggin My Life Away

Twisting DNA

Why Women Are Stripey
They (women) aren't actually stripey, at least they don't look that way because we don't have chromosome vision.  I liked the animation, and the bit about the cellualar level fight between the two X-chromosomes was interesting. Makes me wonder if the same thing is going with all the other normally paired chromosomes.

The part that isn't explained here, and which I haven't seen anywhere, is how DNA gets untwisted enough that it can be read. Because DNA isn't just twisted like a rope, it's curled up, and then recurled, and then curled some more, as this video shows.


✔ DNA Replication Animation - Super EASY
(www.freesciencelectures.com, shown on the bottom of the video doesn't exist, though there is a YouTube channel with that name.)

It might be that the DNA does get completely untwisted when only a short segment needs to get copied. In that case perhaps only a short segment gets untwisted, kind of like when you are trying to splice a rope or cable.


Fastest loadsling splicer...1 1/8" X 28' .in 3min 20sec (greasy rope).DCR (www.chainandrigging.com)

Prickly

A very large organ pipe cactus in Baja California, photo by Leon Diguet (1895).

Special techniques are needed to survive in hostile environments:

A symbiotic relationship with bacterial and fungal colonies on its roots allows P. pringlei to grow on bare rock even where no soil is available at all, as the bacteria can fix nitrogen from the air and break down the rock to produce nutrients. The cactus even packages symbiotic bacteria in with its seeds.

Bird Brain

Ramón y Cajal’s drawing of the neurons in a bird’s cerebellum.
Early 20th Century.

The Nobel Prize committee decided that Ramón y Cajal and [Camillo] Golgi should share the 1906 Nobel Prize for Medicine/Physiology, even though the two scientists held absolutely opposite views about how the nervous system worked. If one of them was right, the other one must certainly be wrong. - Santiago Ramón y Cajal

Small songbirds, which weigh as little as 4.5g, really do have small brains. Their brains can weigh as little as a third of a gram and only contain about 100 million neurons. But the heavier birds can have brains that weigh more than a dozen grams and pack in more than 2 billion neurons. On average, birds have twice as many neurons per unit mass as mammals do. So a bird called the goldcrest, which Wikipedia introduces as "a very small passerine bird," weighs a bit more than 10 percent of your average mouse but has more than double the neurons. - Bird brains are dense—with neurons by John Timmer - June 17, 2016

Via Detroit Steve

Tree of Life, Revised, Redux

Tree of Life

In my previous post about this, I complained about that the legend was uninformative. Carl Zimmer corrects that failing with this cogent explanation:

The red dots represent species only known from DNA gathered from the environment. “Isolated” means that someone was able to actually observe the whole organism, typically by culturing it in a lab.

Tree of Life, Revised

Tree of Life

Not too long ago, there were three branches to the tree of life:

• Eukaryotes, which are all the things that have a macroscopic existence,
• Bacteria, which are everywhere but too small to see without a microscope, and
• Archaea, which are bacteria which live in places were no normal kind of life can live.

There were three branches and all was well. But then some wise guys started poking around, stirring up shit, and found that there were a hell of lot more bacteria than they had realized. Now someone has condensed all this new data into this drawing and we find the part that we consider important, the part that contains us and all our animal friends, is just this one branch growing off to the side. Just goes to show that if you make enough microbes eventually one of them will grow up to be somebody. Story in The New York Times. Via Detroit Steve.

Meanwhile, back at the ranch, I don't understand the key on this drawing, to wit:

Major lineages with isolated representative - italics
Major lineage lacking isolated representative - (red dot)

I can understand having an isolated representative of a particular thing, and I can understand having a representative of a group or class of things, but having an isolated representative of a big group doesn't make any sense to me. Does this mean you have a single representative of a large group, but it is isolated so we don't know if it is really representative or not?

And if we are lacking an isolated representative, does that mean we have no representatives at all? Or we have a whole bunch, but they are so different we can't call them representative?

I know microbiology has their own lingo, but these two lines need translating.

People are complicated, right down to the cellular level

Sex Is a Coping Mechanism

Did sexual reproduction evolve to keep up with mitochondrial mutation?

BY JILL NEIMARKILLUSTRATION BY FRANCESCO IZZO

Excerpt:

That link lies in the fact that mitochondria are not just cellular batteries. Billions of years ago they were actually independent organisms. They are an example of how the human body is not entirely “human.” Our guts are full of trillions of foreign bacterial cells; our DNA is riddled with shards of old viruses; and even our cells are dollops of primordial soup. Scientists are increasingly realizing that many diseases are not external assaults, but imbalances of our inner ecosystem. In the case of mitochondria, conflicts can arise because these organelles contain their own unique and separate DNA. “Until recently, science has basically ignored the fact that we are all walking around with two genomes in every cell,” Dowling says, “that of our own nuclear genome, and that of the mitochondria.”

Via Detroit Steve