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Gender: Female
Current location: India
Member since: Thu Jun 18, 2020, 11:40 AM
Number of posts: 497

About Me

I am an old-timer. I posted here as nam78_two for 4-5 years (2004 or 5 to 2009-10) in the Bush, Obama years.

Journal Archives

I know - the cruelty is horrific and saddening

Actually this is why I am vegetarian..I cannot endorse cruelty on this scale. It has less to do with climate change than the horrific cruelty of the animal industry.

Scientists Use Machine Learning to Listen to Nature

This is very cool:


The United Nations has called on the world to protect 30 percent of the planet from human activity to help protect ecosystems and slow down climate change. But conservation areas are often vulnerable to illegal logging, poaching, mining, and other activities that threaten biodiversity. How can land managers detect these kinds of human impacts on protected ecosystems? Scientists are applying machine learning to identify human influence on the environment by literally listening to the environment — that is, by monitoring forest “soundscapes.”

Every ecosystem has its own distinctive collection of sounds that change with the season and even the time of day. According to Bryan Pijanowski, soundscape ecologist and director of Purdue University’s Center for Global Soundscapes, “Sounds are part of the ecosystem, and they are signatures of that ecosystem.” The unique sound environment of an ecosystem is known as a soundscape, the aggregate of all the sounds — biological, geophysical, and anthropogenic — that make up a place.

Sound has long been used by soundscape ecologists to assess biodiversity and other metrics of ecosystem health. Pijanowski has his own, informal rule of thumb: “If I can tap my foot to a soundscape, I know it’s fairly healthy,” he says, because it means “the rhythmic animals — the frogs and the insects, the base of the food chain — are there.”

Detecting human activity that impacts ecosystem health, like illegal logging and poaching, has long been a challenge for land managers and scientists, often requiring expensive and time-consuming surveys in which specialists manually identify species. But this new method requires only basic audio equipment that allows for remote monitoring of the soundscape, which can be done in real time, and a machine learning algorithm that listens for sounds that aren’t typical in a forest environment. “Say that there’s weird things going on or illegal activity, like guns being shot, or chainsaws from illegal logging,” explained Sarab Sethi, a mathematician at Imperial College London and the lead author of the new paper. “We work under the assumption that illegal activity contains a lot of anomalous sounds that are different from whatever usual sounds are in the ecosystem.”

How does the computer identify strange sounds? The key is unsupervised machine learning, meaning machine learning that doesn’t require human input to “train” the model on pre-identified data. “The way that we measure similarities and differences in sound is really the technical advance from our work,” Sethi told Grist. This new method uses a neural network to compare the “fingerprints” of sounds — not only their frequencies, but the structure of how their frequencies change over time — to one another other. “Once we’ve got a fingerprint, like a bird calling — a bird calling is more similar to a different species of bird calling, in this fingerprint, than it is to, say, a gunshot,” says Sethi. The neural network learns which sounds are typical of a healthy forest environment, and which ones are out of the ordinary.

The unsupervised technique requires less work from humans to identify sound; it’s also more robust than so-called supervised machine learning.

Paper abstract
Human pressures are causing natural ecosystems to change at an unprecedented rate. Understanding these changes is important (e.g., to inform policy decisions), but we are hampered by the slow, labor-intensive nature of traditional ecological surveys. In this study, we show that automated analysis of the sounds of an ecosystem—its soundscape—enables rapid and scalable ecological monitoring. We used a neural network to calculate fingerprints of soundscapes from a variety of ecosystems. From these acoustic fingerprints we could accurately predict habitat quality and biodiversity across multiple scales and automatically identify anomalous sounds such as gunshots and chainsaws. Crucially, our approach generalized well across ecosystems, offering promise as a backbone technology for global monitoring efforts.

Artificial (Abiotic) Energy Source for Molecular Motors

I posted a thread yesterday about molecular motors:

Molecular motors are nanomachines inside the cell that use the chemical energy (in the form of ATP) produced by food (1 molecule of glucose produces some 30 odd molecules of ATP) to generate force and movement. They carry out a variety of functions ranging from vesicle transport to muscle contraction.

That was a motor molecule called Kinesin.

This is a different one called Myosin which is found in muscle cells and powers muscle contraction.

(Image credit: https://bau.seas.upenn.edu/. The Bau lab at UPenn. The Myosin isoform involved in muscle contraction is Myosin II.The Myosins shown there however, are Myosins V and VI, which are involved in vesicle/organelle transport).

Scientists have characterized various Myosins (there is a whole family of them) at the molecular level pretty thoroughly - its step-size (which is on the scale of nanometers. For comparison a single hair strand is about 17000-181000 nanometers in diameter), the energy consumed per step (about 1 ATP I think but I am not sure), force produced (which is on the scale of pico Newtons - for comparison the force needed to pick up a weight of 1g against gravity is 10^10 times that).

In the latest edition of the Biophysical Journal there is an article about an artificial energy source for muscle, which will help us advance our understanding of myosin further.


Muscle physiologists sought an alternative energy source to replace the body's usual one, adenosine triphosphate (ATP). Such a source could control muscle activity, and might lead to new muscle spasm-calming treatments in cerebral palsy, for example, or activate or enhance skeletal muscle function in MS, ALS and chronic heart failure. They report this month that they have made a series of synthetic compounds to serve as alternative energy sources for the muscle protein myosin.

This month, the researchers report in the Biophysical Journal that they have made a series of synthetic compounds to serve as alternative energy sources for the muscle protein myosin, and that myosin can use this new energy source to generate force and velocity. Mike Woodward from the Debold lab is the first author of their paper and Xiaorong Liu from the Chen lab performed the computer simulation.

By using different isomers -- molecules with atoms in different arrangements -- they were able to "effectively modulate, and even inhibit, the activity of myosin," suggesting that changing the isomer may offer a simple yet powerful approach to control molecular motor function. With three isomers of the new ATP substitute, they show that myosin's force- and motion-generating capacity can be dramatically altered. "By correlating our experimental results with computation, we show that each isomer exerts intrinsic control by affecting distinct steps in myosin's mechano-chemical cycle."

DV recalls, "My lab had never made such types of compounds before, we had to learn a new chemistry; my student Eric Ostrander worked on the synthesis." The new chemistry involves sticking three phosphate groups onto a light-sensitive molecule, azobenzene, making what the researchers now call Azobenzene triphosphate, he adds.

The next stage for the trio will be to map the process at various points in myosin's biochemical cycle, Debold says. "In the muscle research field, we still don't fully understand how myosin converts energy gain from the food we eat into mechanical work. It's a question that lies at the heart of understanding how muscles contract. By feeding myosin carefully designed alternative energy sources, we can understand how this complex molecular motor works. And along the way we are likely to reveal novel targets and approaches to address a host of muscle related diseases."

This is the original article:

Edit: Thanks are owed to eppur_se_muova for catching an error in the original message.

Crowding Stalls Traffic in Cells Too!

Though apparently only for teams of motors and not individual motors.

A Kinesin Motor Stepping Along a Microtuble. Image credit: Tom Snelling, UK. An earlier version of this post did not credit the source. It was an oversight.


As many diseases, including neurodegenerative diseases such as Alzheimer's, have been linked to the defective functioning of motor proteins in cell transport systems, understanding the intricacies of how motor proteins work in their native crowded cell environments is essential to understanding what goes wrong when they function incorrectly. Molecular motors are specialized proteins that bind to a variety of organelles, referred to as cell cargo, and transport them along microtubule filaments (structural proteins commonly referred to as the highway of the cell). Motor proteins often work in groups, binding to one cargo and inching together along the filament's path in the cell.

In the recent study Macromolecular crowding acts as a physical regular of intracellular transport, published in the journal Nature Physics, lead researcher and Assistant Professor of Physics at NYU Abu Dhabi George Shubeita and his team present the findings that in a native cell environment, which is crowded with a high concentration of macromolecules, the crowding significantly impacts the speed of groups of motor proteins, but not singular motor proteins. Motor proteins have been isolated from cells and studied in a laboratory setting, but this is the first time that cargo carried by motor proteins have been studied both in their native cell and in a setting that imitates the crowded cellular environment.

To simulate the crowded nature of cells, bovine serum albumin (a serum concentrated with proteins) was applied to glass slides, in addition to the kinesin motor proteins and microtubule filaments. Utilizing the laser light of optical tweezers to probe the movement of single motors and groups of motors, it was found that in more crowded environments, motors were more likely to fall off the filament when opposed. A group of motors would therefore be set-back each time a singular motor fell from the guideway. Even though groups of motors are shown to slow down in native cell environments, they are commonly used to carry cargo over long distances and overcome hindrances they face in a crowded cell by sharing the load, which singular motors cannot do.

For some background, motor proteins are molecular motors which use chemical energy (derived by hydrolysing ATP) to produce force and movement:



This is the original article in Nature Physics:
Macromolecular crowding acts as a physical regulator of intracellular transport

Am concerned at not seeing factory farms on that list

That is where large scale cruelty at the most horrific levels occurs.

It is very worrying if they are not even monitored.


You do have a gift with words Sir. I am normally not enamored of that which in common parlance is referred to as snark. But when it is this Jeevesian I have to raise my hat to it! I enjoy your posts.

It tickles me no end to picture Jeeves logging on to DemocraticUnderground and going about administering various smackdowns .....

Interestingly Jeeves himself (unlike Stephen Fry) was probably a Tory while Bertie was probably apolitical.

At any rate our late friend GriffenRamsay answered my question re: what the current incarnation of the Tombstone is....

Love Far Side


This is why I stopped following environmental news

I know one has an obligation to because if environmentalists and animal activists stop following this stuff who will?
But there is never any good news. It is like tilting at windmills......Of course this one is less clear. But it is probably tied to humans - most of it is.


I suppose they will go extinct then

Getting harder to be an environmental optimist...But maybe we can pull them back from the brink. One should hope so.
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