There’s no such thing as a tree (phylogenetically)
Posts tagged biology
No One Is Prepared for Hagfish Slime
Hagfish produce slime the way humans produce opinions—readily, swiftly, defensively, and prodigiously. They slime when attacked or simply when stressed. On July 14, 2017, a truck full of hagfish overturned on an Oregon highway. The animals were destined for South Korea, where they are eaten as a delicacy, but instead, they were strewn across a stretch of Highway 101, covering the road (and at least one unfortunate car) in slime. Typically, a hagfish will release less than a teaspoon of gunk from the 100 or so slime glands that line its flanks. And in less than half a second, that little amount will expand by 10,000 times—enough to fill a sizable bucket. Reach in, and every move of your hand will drag the water with it.
via https://www.theatlantic.com/science/archive/2019/01/hagfish-slime/581002/
Meet your earliest known ancestor: Saccorhytus
How is Saccorhytus related to humans? Humans are vertebrates and so are one of the major groups that collectively define the deuterostomes, a group that also includes animals that are quite different from humans, such as sea-urchins and sea-squirts, all ultimately descended from an original deuterostome. Our argument is that Saccorhytus is close to this ancestral form, and so is the most primitive known deuterostome.
via https://www.researchgate.net/blog/post/meet-your-earliest-known-ancestor-saccorhytus
Classifying Animal(s)
These names were themselves disputed and used as insults or boasts by either side, as were various taxonomic terms of art. Reading through the pages of Systematic Zoology, it is not uncommon to see authors accuse each other of redefining key terms or to see them attempt such redefinitions (usually in the name of “clarity”) themselves. Determining what a word essentially denoted was a problem not only for naming species of beetles or apes, but also for naming groups of taxonomists. As the advent of genetic sequencing shifted the central focus of biological taxonomy (Woese et al. 1977), determining which side of the debate had “won” became primarily a question of which of their features one took to be definitive. To use a term that anthropologists would later borrow from the taxonomists, the two schools were polythetic classes (Needham 1975) — identifiable through a set of shared characteristics or “family resemblances,” but not defined by any one in particular.
via https://medium.com/@npseaver/classifying-animal-s–4f86395eb801
What is the Adjacent Possible?
The “adjacent possible” is the most salient, most shared and perhaps most important of a cacophony of colorful metaphors about biology, information, and networks offered us by Stuart Kauffman in his seminal “At Home in the Universe”. Kauffman is an American theoretical biologist whose work on the mathematics of boolean networks and the biology of genomic regulatory networks in practice has defined our understanding of both the possible origins of life and of the contemporary dynamics of complex adaptive systems, such as the biosphere and the econosphere at scale. So what is the adjacent possible?
via https://medium.com/@Santafebound/what-is-the-adjacent-possible–17680e4d1198
Everything You Should Know About CRISPR — And Where to Learn More
After spending so much time researching CRISPR, I thought I’d save everyone else the time, write a summary of why I think it’s a big deal, and then curate some of the best content on the subject I found.
via https://medium.com/startup-grind/a-primer-on-crispr-and-how-to-learn-more-c1b4ca7159f6
We are the 3%
400-year-old Greenland shark is oldest vertebrate animal
Grey, plump and growing to lengths of around five metres, the Greenland shark is one of the world’s largest carnivores. With a reported growth rate of less than one centimetre a year, they were already thought to be long-lived creatures, but just how long they lived for was something of a mystery. “Fish biologists have tried to determine the age and longevity of Greenland sharks for decades, but without success.” said Steven Campana, a shark expert from the University of Iceland. “Given that this shark is the apex predator (king of the food chain) in Arctic waters, it is almost unbelievable that we didn’t know whether the shark lives for 20 years, or for 1000 years.”
Electron-Eating Microbes Found In Odd Places
The electricity-eating microbes that the researchers were hunting for belong to a larger class of organisms that scientists are only beginning to understand. They inhabit largely uncharted worlds: the bubbling cauldrons of deep sea vents; mineral-rich veins deep beneath the planet’s surface; ocean sediments just a few inches below the deep seafloor. The microbes represent a segment of life that has been largely ignored, in part because their strange habitats make them incredibly difficult to grow in the lab.
via https://www.quantamagazine.org/20160621-electron-eating-microbes-found-in-odd-places/
Wild flower blooms again after 30,000 years on ice
During the Ice Age, Earth’s northern reaches were covered by chilly, arid grasslands roamed by mammoths, woolly rhinoceros and long-horned bison. That ecosystem, known by palaeontologists as the mammoth steppe, vanished about 13,000 years ago. It has no modern counterpart. Yet one of its plants has reportedly been resurrected by a team of scientists who tapped a treasure trove of fruits and seeds, buried some 30,000 years ago by ground squirrels and preserved in the permafrost (S. Yashina et al. Proc. Natl Acad. Sci. USA http://dx.doi.org/10.1073/pnas.1118386109; 2012). The plant would be by far the most ancient ever revived; the previous record holder was a date palm grown from seeds roughly 2,000 years old.
via http://www.nature.com/news/wild-flower-blooms-again-after–30–000-years-on-ice–1.10069
Sonic hedgehog (SHH)
Sonic hedgehog is one of three proteins in the mammalian signaling pathway family called hedgehog, the others being desert hedgehog (DHH) and Indian hedgehog (IHH). SHH is the best studied ligand of the hedgehog signaling pathway. It plays a key role in regulating vertebrate organogenesis, such as in the growth of digits on limbs and organization of the brain. Sonic hedgehog is the best established example of a morphogen as defined by Lewis Wolpert’s French flag model—a molecule that diffuses to form a concentration gradient and has different effects on the cells of the developing embryo depending on its concentration.
via https://en.wikipedia.org/wiki/Sonic_hedgehog#Controversy_surrounding_name
Why Do Taxonomists Write the Meanest Obituaries?
This tension between freedom and stability was long ago formalized in two sets of official and binding rules: the International Code of Zoological Nomenclature (ICZN), which deals with animals, and the International Code of Nomenclature for algae, fungi, and plants (ICN). Periodically updated by committees of working taxonomists, these documents set out precise, legalistic frameworks for how to apply names both to species and to higher taxa. (The animal and plant codes operate independently, which means that an animal can share a scientific name with a plant, but not with another animal, and vice versa.) While this freedom opens up a valuable space for amateur contributions, it also creates a massive loophole for unscrupulous, incompetent, or fringe characters to wreak havoc. That’s because the Principle of Priority binds all taxonomists into a complicated network of interdependence; just because a species description is wrong, poorly conceived, or otherwise inadequate, doesn’t mean that it isn’t a recognized part of taxonomic history. Whereas in physics, say, “unified theories” scrawled on napkins and mailed in unmarked envelopes end up in trashcans, biologists, regardless of their own opinions, are bound to reckon with the legacy of anyone publishing a new name. Taxonomists are more than welcome to deal with (or “revise”) these incorrect names in print, but they can’t really ignore them.
via http://nautil.us/issue/35/boundaries/why-do-taxonomists-write-the-meanest-obituaries
One Fungus, One Name
The naming of organisms is an important part of how we communicate. When a fungus is found, be it a mycelium from a rotting fruit, a mushroom from the forest, or something growing on a petri dish, we have used morphological and other phenotypic characteristics to group them together and identify if it is an already known species or a new one. However, some fungi have very different shapes and forms that occur during asexual and sexual (after mating with a partner) stages, some incredible elaborate and even (to some people) beautiful. Because these stages mean that fungi can look very different, and often these fungi are not amenable to life in the laboratory (e.g. we can’t get it to complete the lifecycle in an petri dish in the lab), it was the case that observed asexual (or anamorphic) and sexual (teleomorphic) forms of a species get different names. For some species, connecting the two forms has eluded mycologists, and those which had a lack of a sexual stage were called Fungi Imperfecti. Some fungi are only thought to have an asexual stage, though that may change as more molecular and other data is developed.
Impermanence_Untitled
Impermanence_Untitled
Biologists discover electric bacteria that eat pure electrons rather than sugar
University of Southern California (USC) have discovered bacteria that survives on nothing but electricity — rather than food, they eat and excrete pure electrons. These bacteria yet again prove the almost miraculous tenacity of life — but, from a technology standpoint, they might also prove to be useful in enabling the creation of self-powered nanoscale devices that clean up pollution. Some of these bacteria also have the curious ability to form into ‘biocables,’ microbial nanowires that are centimeters long and conduct electricity as well as copper wires — a capability that might one day be tapped to build long, self-assembling subsurface networks for human use.
Turing Morphogenesis
If you want to get a rough grasp of how the leopard might get its spots, then building a CA model (or something similar) can be very illuminating. It will not tell you whether that’s actually how it works. This is an important example, because there is a classic theory of biological pattern formation, or morphogenesis, first formulated by Turing in the 1950s, which lends itself very easily to modeling in CAs, and with a little fine-tuning produces things which look like animal coats, butterfly wings, etc., etc. The problem is that there is absolutely no reason to think that’s how those patterns actually form; no one has identified even a single pair of Turing morphogens, despite decades of searching. [See “Update, 4 March 2012” below.] Indeed, the more the biologists unravel the actual mechanisms of morphogenesis, the more complicated and inelegant (but reliable) it looks. If, however, you think you have explained why leopards are spotted after coming up with a toy model that produces spots, it will not occur to you to ask why leopards have spots but polar bears do not, which is to say that you will simply be blind to the whole problem of biological adaptation.
http://vserver1.cscs.lsa.umich.edu/~crshalizi/reviews/wolfram/
Engineering the $325,000 In-Vitro Burger
The hamburger, assembled from tiny bits of beef muscle tissue grown in a laboratory and to be cooked and eaten at an event in London, perhaps in a few weeks, is meant to show the world — including potential sources of research funds — that so-called in-Vitro meat, or cultured meat, is a reality.
You’re Eye-to-Eye With a Whale in the Ocean.
In general, mammals don’t have the best color vision. In part, that’s because our ancestors developed trying to see in the dark, not out in the bright sunlight. “There was a time where to be a mammal was to be a small, nocturnal, rodent-like mammal,” said Duke’s Sonke Johnsen, author of the book, The Optics of Life. Both humans and whales retain the marks of that evolutionary path. “Our color vision is kind of a kluge,” Johnsen continued. “If you look at the color vision of birds and reptiles and fish. It’s very well put together, nicely optimized. You look at our trichromatic vision, it’s really kind of pieced together.”
Curiosities of Biological Nomenclature
Scientific names of organisms are not usually known for their entertainment value. They are indispensable for clarity in communication, but most people skip over them with barely a glance. Here I collect those names that are worth a second look.
The human microbiome: Me, myself, us
A healthy adult human harbours some 100 trillion bacteria in his gut alone. That is ten times as many bacterial cells as he has cells descended from the sperm and egg of his parents. These bugs, moreover, are diverse. Egg and sperm provide about 23,000 different genes. The microbiome, as the body’s commensal bacteria are collectively known, is reckoned to have around 3m. Admittedly, many of those millions are variations on common themes, but equally many are not, and even the number of those that are adds something to the body’s genetic mix.
Pigeons may ‘hear’ magnetic fields
Pigeons’ remarkable navigational feats have long been pegged to the birds’ ability to sense magnetic fields, but pinning down how they do so has frustrated scientists for years. Work published today in Science shows that individual cells seem to encode information on a magnetic field’s direction, intensity and polarity1. The work also suggests that these signals come from a part of the inner ear called the lagena, further complicating matters for researchers in the field.
http://www.nature.com/news/pigeons-may-hear-magnetic-fields–1.10540
Green Sea Slug Is Part Animal, Part Plant
Shaped like a leaf itself, the slug Elysia chlorotica already has a reputation for kidnapping the photosynthesizing organelles and some genes from algae. Now it turns out that the slug has acquired enough stolen goods to make an entire plant chemical-making pathway work inside an animal body, says Sidney K. Pierce of the University of South Florida in Tampa.