Biology
Health and Nutrition
Did A Melatonin Patent Inspire Current Dose Confusion?: This is a kind of follow-up to the article about Melatonin dosages that I linked to a few days ago.
Kitchen sponges are festering germ dens—and sanitizing them doesn’t help: I knew they were bad news.
When We Eat, or Don’t Eat, May Be Critical for Health: “Eat breakfast like a king, lunch like a prince and dinner like a pauper.”
One Minute of All-Out Exercise May Have Benefits of 45 Minutes of Moderate Exertion: The first careful study of the phenomenon shows surprising results.
Melatonin: Much More Than You Wanted To Know: Are you taking melatonin to help you with sleep? If your pill supplies more than 0.3 mg, you should read this.
Is Your Workout Not Working? Maybe You’re a Non-Responder: Exercise is complicated.
Hey Parents, Surprise, Fruit Juice Is Not Fruit: The American Academy of Pediatrics is asking pediatricians to advise against fruit juice for children. I’ll add my voice: fellow parents, lay off the juice boxes.
Book Review: The Hungry Brain: Recent research on appetite and diet is fascinating, and the subject is complex. Scott Alexander’s reviews are so exhaustive that they make me feel as if I’ve learned a significant amount about the subject without having read the book.
Chemicals That Pushed Man’s Ancestors To Run Down Wild Boar Flare At Sight Of White Cheddar Popcorn Bag: A decent summary of recent research in diet and obesity.
Dust Mites are not Impressed by Your Fancy Vacuum: These tiny creatures, that live in our beds, stuffed tigers, and pillows, cause asthma and other allergic reactions in many of us humans. So there has recently arisen an industry of expensive vacuum cleaners, mattress covers, and other gadgets designed to reduce their numbers and help us. None of these things work. The only effective control is to wash your bedding in hot water and keep soft toys out of the bed.
“What if It’s All Been a Big Fat Lie?”: Gary Taubes’ interesting and controversial NY Times article on diet; strongly challenged here and defended by Taubes here. Also see this.
Resources
Cornell University’s bird resource.
Curiosities of Biological Nomenclature
AntWeb: An amazing catalog of the ants of California and Madagascar.
“This website grew out of the activities of Sylvia and Stephen Sharnoff, who did the photographic fieldwork for the book Lichens of North America, by Irwin M.Brodo and the Sharnoffs, published in November, 2001 by Yale University Press.”
MIT Biology Hypertextbook: “A website which contains the basic molecular biology that is the basis of MIT’s core Biology course, ‘Introductory Biology’”
Ivory-Billed Woodpecker
NYTimes on Ivory-Billed Woodpecker discovery: April 28, 2005:
“The ivory-billed woodpecker, a bird long thought extinct, has been sighted in the swamp forests of eastern Arkansas for the first time in more than 60 years, Cornell University scientists said today.”
Ivory-Billed Woodpecker Rediscovered in Arkansas: A National Public Radio “Radio Expeditions” story.
Listening for the Call of a Vanished Bird - By James Gorman (With audio recordings):
“It was early afternoon in the swamp. We had spent the morning hiking through Louisiana bottomland forest and the early afternoon slogging through bayous in search of the ivory-billed woodpecker”
More Biology Links
Flowers can hear buzzing bees—and it makes their nectar sweeter: A nice experiment that demonstrates how a plant uses acoustic information to increase pollination activity. This is the first evidence for plants actively responding to sound.
Nearly perfectly preserved puppy was frozen for 12,400 years: “As a warming climate melts some of the permafrost that covers much of Siberia, ancient treasures are emerging.”
Once again, Scientific American distorts biology, and now history, to buttress its ideology: The biologist Jerry Coyne explains why there are exactly two sexes in humans, and exposes Scientific American’s continuing devolution into a dishonest exponent of a political ideology.
Multipole Methods for the Masses: Excellent introduction to the fast multipole method, with illuminating animations. The author, Andy Jones, applies the algorithm, commonly used in physics for such things as calculating the gravitational interactions among a bunch of masses, to the spread of an infection.
Big Pharma, Big Tech, and Synthetic Sex Identities: Following the money yields crucial insights.
Abigail Shrier on Joe Rogan: A surprisingly intelligent and reasonable conversation about the issues raised in the guest’s book Irreversible Damage: The Transgender Craze Seducing Our Daughters.
Biologists Home In on Turing Patterns: “For the work that led to his 1952 paper, Turing wanted to understand the underlying mechanism that produces natural patterns. He proposed that patterns such as spots form as a result of the interactions between two chemicals”.
Butterfly wing patterns emerge from ancient “junk” DNA: “Butterfly wing patterns have a basic plan to them, which is manipulated by non-coding regulatory DNA to create the diversity of wings seen in different species, according to new [fascinating] research.”
Learning from the past to develop data analysis curricula for the future: “Half of psychology papers that perform null hypothesis significance testing include at least 1 misreported p-value”. A more fundamental problem is that they are performing null hypothesis significance testing.
The Missing Link Fallacy: “In a nutshell: I like fossils. But even more than than that, I like arguments about fossils.”
Life’s First Handshake: Chiral Molecule Detected in Interstellar Space
Why flying insects gather at artificial light: Finally, a convincing explanation for a commonly observed phenomenon.
Fern leaves and cauliflower curds are not fractals: “The popular demonstration of drawing a mature fern leaf as expressed by Barnsley’s fractal method is mathematically and visually very attractive but anatomically and developmentally misleading, and thus has limited, if any, biological significance.”
Revised Estimates for the Number of Human and Bacteria Cells in the Body: A new urban myth is born: there are roughly the same number of bacterial cells living within us as human cells.
Adaptation of sperm whales to open-boat whalers: rapid social learning on a large scale?: “It appears that whales swiftly learned effective defensive behaviour.”
Agents.jl: A Julia package for agent-based modeling. Very easy to set up simulations on a variety of spaces, including Open Street Map.
The Meaning of Human Existence: Edward O. Wilson’s 2015 book.
The demise of Scientific American: Guest post by Ashutosh Jogalekar: “One week ago, E. O. Wilson […] passed away at age 92. A mere three days later, Scientific American—or more precisely, the zombie clickbait rag that now flaunts that name—published a shameful hit-piece”.
How Do Octopuses Experience the World?: Fascinating creatures, mulled over in a well-linked article.
Random Search Wired Into Animals May Help Them Hunt: “The nervous systems of foraging and predatory animals may prompt them to move along a special kind of random path called a Lévy walk to find food efficiently when no clues are available.”
Visualize Squirmers: ‘The visualization shown here is based on simulation data generated as part of the work “Modeling a spheroidal microswimmer and cooperative swimming in a narrow slit”.’
Defining vs Determining Sex: “Many often conflate two concepts in biology: how sex is defined versus how sex is determined. Conflating these two things, as we will see, can create absurd conclusions, so it is important we separate them out to accurately understand what male and female are and how they develop in the womb.”
Foes of genetically modified foods know less than they think, study finds: “The surveys asked respondents how well they thought they understood genetically modified foods, then tested how much they actually knew with a battery of true-false questions on general science and genetics.”
Brown Bear Moms Use “Human Shields” To Protect Their Cubs: The bears, and several other species, have been observed seeking proximity to humans in an apparent attempt to protect their young from predators.
Julia for Biologists: “Major computational challenges exist in relation to the collection, curation, processing and analysis of large genomic and imaging datasets, as well as the simulation of larger and more realistic models in systems biology. Here we discuss how a relative newcomer among programming languages—Julia—is poised to meet the current and emerging demands in the computational biosciences and beyond. Speed, flexibility, a thriving package ecosystem and readability are major factors that make high-performance computing and data analysis available to an unprecedented degree. We highlight how Julia’s design is already enabling new ways of analyzing biological data and systems, and we provide a list of resources that can facilitate the transition into Julian computing.”
Corpse Flower in DC: This is featured, it seems, at least once a year at the US Botanical Gardens. If you’re in DC at the right time to catch it (especially at peak stink) it’s definitely worth a visit.
Why biological sex matters: Richard Dawkins stating the obvious about biology, language, and politics, at a time when stating the obvious has become a courageous stand.
Dolphins have a language that helps them solve problems together: “they have a type of vocalisation dedicated to cooperating on problem solving.”
A Quick Climb Up Mount Olympus: The Double Helix. A Personal Account of the Discovery of the Structure of DNA.: A scathing review of the disastrous book by James Watson.
Microstructure.jl: “Microstructure.jl is a Julia package for fast and probabilistic microstructure imaging… under active development…ocuses on tissue microstructure estimation.”
Evolution designed by parasites: As parasites manipulate the nervous and endocrine systems of their hosts, they encourage the evolution of countermeasures.
Letter from Francis Crick to James D. Watson: See the reviewchargaff1968? of the book that this letter is about.
500px: Amazing photography of deep-sea creatures by Yung-sen Wu.
Turkey arrests spider smuggler said to be American Museum of Natural History curator: The article doesn’t refer to any specific law, but the officials object to the potential financial value of medicine that might potentially be synthesized from venom. The article misuses “poisonous”. Update: smuggler may not have been smuggling at all.
Peacock Crests Are Vibration Sensors, Tuned to Shaking Tail-Feathers: Report of a beautiful piece of biophysics research.
Nocebo effects with antidepressant clinical drug trial placebos.: A man became severely ill after overdosing on what he believed to be antidepressants. After he was informed that the pills were placebos, he recovered.
No Meaningful Differences in Male and Female Brains, Study Finds: There are no girl brains or boy brains. You were not “born in the wrong body”.
Musical components important for the Mozart K448 effect in epilepsy: “There is growing evidence for the efficacy of music, specifically Mozart’s Sonata for Two Pianos in D Major (K448), at reducing ictal and interictal epileptiform activity. Nonetheless, little is known about the mechanism underlying this beneficial ‘Mozart K448 effect’ for persons with epilepsy. Here, we measured the influence that K448 had on intracranial interictal epileptiform discharges (IEDs) in sixteen subjects undergoing intracranial monitoring for refractory focal epilepsy.”
Collective memory in bacteria: “Individual bacterial cells have short memories. But groups of bacteria can develop a collective memory that can increase their tolerance to stress.”
BioJulia: The bioinformatics infrastructure for the Julia language.
Corona virus transmission simulation: A simple model of the progression of a pandemic, written using sveltesvelte?.
Scientists find new bird species at South America’s edge: “In the Diego Ramirez Islands, 100 kilometers (62 miles) from southern Chile’s Cape Horn, scientists have identified the Subantarctic rayadito, a 0.035 pound (16 gram) brown bird with black and yellow bands, and a large beak that is confounding biologists.”
Six Scientists, 1,000 Miles, One Prize: The Arctic Bumblebee: Another beautifully designed, engaging story from The New York Times
Dolphins may speak in words and sentences, say researchers: Apparently, they are also polite, avoiding interruption.
A wonderful life by leaps and bounds: Sort-of review of Stephen Jay Gould: Reflections on His View of Life.
First Carnivorous Plant Identified In 20 Years Grows Near Vancouver, B.C.: And it looks so sweet and innocent.
A unicellular walker controlled by a microtubule-based finite-state machine: A fascinating collaboration among biologists and computer scientists.
Minimizing the Elastic Energy of Growing Leaves by Conformal Mapping: I learned to love conformal mapping while studying fluid dynamics. This is a fascinating application.
Stunning Videos of Evolution in Action - The Atlantic: On a giant petri dish. Shows mutations leading to antibiotic resistance.
Your Cortex Contains 17 Billion Computers: Each neuron can compute a nonlinear function of its inputs.
Sea Dragon Images: Beautiful pictures and movies of these cousins to the seahorse.
Images of bioluminescence: from the Harbor Branch Oceanographic Image Library.
“The wasp slips her stinger through the roach’s exoskeleton and directly into its brain. She apparently uses sensors along the sides of the stinger to guide it through the brain […]. She continues to probe the roach’s brain until she reaches one particular spot that appears to control the escape reflex. She injects a second venom that influences these neurons in such a way that the escape reflex disappears. […] now it cannot move of its own accord. The wasp takes hold of one of the roach’s antennae and leads it […] like a dog on a leash.”
There is a grisly movie of the process.
“Semmelweis ordered all of the medical students to wash their hands[…]”
Calorie Restricted Diets in Humans:
“Severely restricting calories has been shown to slow aging and prolong life in mice and rats. Now early research hints that the same just might be true in humans.”
Scientists develop “brain chip”:
“US scientists say a silicon chip could be used to replace the hippocampus, where the storage of memories is co-ordinated.”
From the BBC science news website:
“Owls have been observed using dung as bait to trap beetles for food, the journal Nature has reported. Scientists have likened the behavior to ‘tool use’, something that is rarely seen amongst wild animals.”
“Scientists say they have identified an ocean sponge living in the darkness of the deep sea that grows thin glass fibers capable of transmitting light at least as well as industrial fiber optic cables used for telecommunication. The natural glass fibers also are much more flexible than manufactured fiber optic cable that can crack if bent too far.”
Rats Can Smell In Stereo: Rats can home in on smells using a method similar to the stereo processing of sounds, according to researchers at the University of Agricultural Science, Bangalore, India. The rats needed only one or two sniffs and sometimes as little as 50 milliseconds to accurately determine the source of an odour. For rats, “each sniff is a perceptually complete snapshot of the olfactory world, including both odour identity and stereo-based location.”
The mangrove rivulus: It can become a hermaphrodite and produce clones of itself; it has been found living inside coconuts and in beer cans; it can breath and eliminate waste through its skin, and can do so for months inside hollow logs, a behavior that biologists unfortunately term “logpacking”.
Kha-Nyou: A new rodent species, Laonastes aenigmamus, has been discovered in Laos: “To find something so distinct in this day and age is just extraordinary. For all we know, this could be the last remaining mammal family left to be discovered.”
