Category: Living World

To Avoid Humans, More Wildlife Now Work the Night Shift

fox-london-night

An urban fox scavenges on the edge of a park. (Credit: Shutterstock)

For their first 100 million years on planet Earth, our mammal ancestors relied on the cover of darkness to escape their dinosaur predators and competitors. Only after the meteor-induced mass extinction of dinosaurs 66 million years ago could these nocturnal mammals explore the many wondrous opportunities available in the light of day.

Fast forward to the present, and the honeymoon in the sun may be over for mammals. They’re increasingly returning to the protection of night to avoid the Earth’s current terrifying super-predator: Homo sapiens. Read More

CATEGORIZED UNDER: Living World, Top Posts
MORE ABOUT: animals

How Can a Baby Have 3 Parents?

By Jennifer Barfield, Colorado State University | June 15, 2018 11:21 am
baby-3-parents

(Credit: Shutterstock)

It seems impossible, right? We have been taught from the time we were young that babies are made when a sperm and an egg come together, and the DNA from these two cells combine to make a unique individual with half the DNA from the mother and half from the father. So how can there be a third person involved in this process? Read More

When Did Humans First Learn to Count?

By Peter Schumer, Middlebury College | June 8, 2018 4:55 pm
Where did our written numbers come from? (Credit: Nikita Rogul/Shutterstock)

Where did our written numbers come from? (Credit: Nikita Rogul/Shutterstock)

The history of math is murky, predating any written records. When did humans first grasp the basic concept of a number? What about size and magnitude, or form and shape?

In my math history courses and my research travels in Guatemala, Egypt and Japan, I’ve been especially interested in the commonality and differences of mathematics from various cultures.

Although no one knows math’s exact origins, modern mathematicians like myself know that spoken language precedes written language by scores of millennia. Linguistic clues show how people around the world must have first developed mathematical thought.

Early Clues

Differences are easier to comprehend than similarities. The ability to distinguish more versus less, male versus female or short versus tall must be very ancient concepts. But the concept of different objects sharing a common attribute – such as being green or round or the idea that a single rabbit, a solitary bird and one moon all share the attribute of uniqueness – is far subtler.

In English, there are many different words for two, like “duo,” “pair” and “couple,” as well as very particular phrases such as “team of horses” or “brace of partridge.” This suggests that the mathematical concept of twoness developed well after humans had a highly developed and rich language.

By the way, the word “two” probably was once pronounced closer to the way it’s spelled, based on the modern pronunciation of twin, between, twain (two fathoms), twilight (where day meets night), twine (the twisting of two strands) and twig (where a tree branch splits in two).

Written language developed much later than spoken language. Unfortunately, much was recorded on perishable media, which have long since decayed. But some ancient artifacts that have survived do exhibit some mathematical sophistication.

For example, prehistoric tally sticks – notches incised on animal bones – are found in many locations around the world. Though these might not be proof of actual counting, they do suggest some sense of numerical record keeping. Certainly people were making one-to-one comparisons between the notches and external collections of objects – perhaps stones, fruits or animals.

A tally stick found in Scandinavia. (Credit: The British Museum, CC BY-NC-SA)

A tally stick found in Scandinavia. (Credit: The British Museum, CC BY-NC-SA)

Counting Objects

The study of modern “primitive” cultures offers another window into human mathematical development. By “primitive,” I mean cultures that lack a written language or the use of modern tools and technology. Many “primitive” societies have well-developed arts and a deep sense of ethics and morals, and they live within sophisticated societies with complex rules and expectations.

In these cultures, counting is often done silently by bending down fingers or pointing to specific parts of the body. A Papuan tribe of New Guinea can count from 1 to 22 by pointing to various fingers as well as to their elbows, shoulders, mouth and nose.

Most primitive cultures use object-specific counting, depending on what’s prevalent in their environment. For example, the Aztecs would count one stone, two stone, three stone and so on. Five fish would be “five stone fish.” Counting by a native tribe in Java begins with one grain. The Nicie tribe of the South Pacific counts by fruit.

English number words were probably object-specific as well, but their meanings have long been lost. The word “five” probably has something to do with “hand.” Eleven and 12 meant something akin to “one over” and “two over” – over a full count of 10 fingers.

The math Americans use today is a decimal, or base 10, system. We inherited it from the ancient Greeks. However, other cultures show a great deal of variety. Some ancient Chinese, as well as a tribe in South Africa, used a base 2 system. Base 3 is rare, but not unheard of among Native American tribes.

The ancient Babylonians used a sexagesimal, or base 60, system. Many vestiges of that system remain today. That’s why we have 60 minutes in an hour and 360 degrees in a circle.

Written Numbers

What about written numbers?

Plimpton 322: The world’s first trigonometric table. (Courtesy of the Rare Book and Manuscript Library, Columbia University. Historia Mathematica, CC BY-NC-ND)

Plimpton 322: The world’s first trigonometric table. (Courtesy of the Rare Book and Manuscript Library, Columbia University. Historia Mathematica, CC BY-NC-ND)

Ancient Mesopotamia had a very simple numerical system. It used just two symbols: a vertical wedge (v) to represent 1 and a horizontal wedge (<) to represent 10. So <<vvv could represent 23.

But the Mesopotamians had no concept of zero either as a number or as a place holder. By way of analogy, it would be as if a modern person were unable to distinguish between 5.03, 53 and 503. Context was essential.

The ancient Egyptians used different hieroglyphs for each power of 10. The number one was a vertical stroke, just as we currently use. But 10 was a heel bone, 100 a scroll or coiled rope, 1000 a lotus flower, 10,000 a pointed finger, 100,000 a tadpole and 1,000,000 the god Heh holding up the universe.

The numerals most of us know today developed over time in India, where computation and algebra were of utmost importance. It was also here that many modern rules for multiplication, division, square roots and the like were first born. These ideas were further developed and gradually transmitted to the Western world via Islamic scholars. That’s why we now refer to our numerals as the Hindu-Arabic numeral system.

The ConversationIt’s good for a young struggling math student to realize that it took thousands of years to progress from counting “one, two, many” to our modern mathematical world.

 

[This article was originally published on The Conversation. Read the original article.]

CATEGORIZED UNDER: Living World
MORE ABOUT: anthropology

A Master Teller of Fish Stories

By Bob Holmes | May 21, 2018 8:00 am
A school of blue-striped grunt (Haemulon sciurus). As the name implies, this subtropical species makes a grunting sound that's generated when it grinds its teeth together. (Credit: Peter Leahy/Shutterstock)

A school of blue-striped grunt (Haemulon sciurus). As the name implies, this subtropical species makes a grunting sound that’s generated when it grinds its teeth together. (Credit: Peter Leahy/Shutterstock)

It has been called “the world’s most dangerous meal,” a fish whose internal organs are laced with one of the deadliest toxins on Earth. Specialized restaurants in Japan and a few other places serve carefully prepared fugu flesh as an expensive delicacy, in part because of this risky thrill.

But Byrappa Venkatesh was drawn to the fugu for an entirely different reason: It has the smallest genome of any vertebrate. That quality was gold back in the 1990s, when geneticists were still racing to sequence the human genome or that of any other vertebrate: Fugu offered a shortcut to the finish line. The puffer was still a slog, though. It cost Venkatesh and his colleagues nine years of hard work and about $10 million, and, in the end, the human genome project nosed them out, just barely, as the first vertebrate genome ever completed.

The puffer fish Fugu rubripes has the smallest genome of any vertebrate. It was the first fish species selected for genome sequencing. (Credit: javarman/Shutterstock)

The puffer fish Fugu rubripes has the smallest genome of any vertebrate. It was the first fish species selected for genome sequencing. (Credit: javarman/Shutterstock)

The project kindled a passion for fish genomics that has propelled Venkatesh ever since. With good reason: Fish are the most diverse group of vertebrates on the planet. They live in deep ocean, in acid waters and in Antarctic seas below the freezing point of blood. Their bodies range from eely, jawless lampreys to flattened flounders to huge, lumpish ocean sunfish. Some lay eggs, some bear live young, and in seahorses, it is the males that become pregnant. In short, fish are a geneticist’s dream. “They show so many variations,” says Venkatesh. “If there is any adaptation in any vertebrate, it should be there in fish.”

In the years since completing the fugu genome in 2002, Venkatesh — known universally as Venki — has sequenced the genomes of more than a dozen fishes, from sharks to the living-fossil coelacanth to his personal favorite, the seahorse. “He’s been a champion, in a very mild-mannered but persistent way, for a long time,” says Richard Durbin, a genomicist at the University of Cambridge. “He’s one of the focal persons for evolutionary fish genomics.”

Venkatesh has seen an enormous growth in sequencing power and technology since the early days of fugu. Today, generating a high-quality genome sequence from scratch takes just two months’ work and about $30,000. “Nobody predicted it would happen so fast,” he says. “You can sequence any genome now.”

And you can sequence lots of them. Venkatesh, based at Singapore’s Institute of Molecular and Cell Biology, helps lead a consortium with big ambitions to sequence hundreds of vertebrate genomes by the end of this decade, nearly half of them fish, en route to eventually completing sequences of every living vertebrate, and more.

A Student Takes the Bait

Despite his current prominence in genomics, Venkatesh came to the field almost by accident. Born in Bangalore, India, to a scientific family — his father was a veterinarian — he chose to study fisheries in university because it sounded like fun. “I thought I could go diving and have a great time,” he recalls.

He never did learn to dive. Instead, after a few years as a fisheries biologist in India, he headed off to Singapore for graduate school, where he studied the hormonal regulation of pregnancy in guppies.

(Credit: feathercollector/Shutterstock)

The ocean sunfish (Mola mola) has a strange, truncated back end. It also is the largest bony fish species in the world, with some adults weighing in at more than 2,000 pounds. Analysis of the sunfish genome reveals features that may explain its rapid growth rate and impressive size. (Credit: feathercollector/Shutterstock)

While there, he met Sydney Brenner of the University of Cambridge, one of the founders of molecular biology. Brenner wanted to be first to sequence a complete vertebrate genome and selected fugu for its tiny genome. He was looking for scientists to work with him on the project and saw something special in Venkatesh. “He said I should go join him in Cambridge,” says Venkatesh. “I had very little molecular biology background at that time, but he said it would be good for me.” Off he went to Cambridge, as the only fish expert on Brenner’s team.

In 1992, after Brenner left Cambridge for California, Venkatesh returned to Singapore to take up a job at the institute, bringing the fugu genome project with him. (Eventually Brenner, too, moved to Singapore, where he established his own lab next door to his protege’s. Now age 91, he still lives in Singapore and the two meet weekly for a drink or dinner.)

The fugu genome gave geneticists a valuable point of comparison to the human genome. They found that, despite its small size — just one-eighth the size of the human genome — the fugu has roughly the same complement of genes, and the on-off switches that control them, as humans do. To reach its slimline state, fugu seems to have lost many of the long, baffling stretches of DNA of unknown function — often called junk DNA — that litter most genomes. That made the fugu genome a helpful tool for separating the human genomic wheat from the chaff and especially for identifying the crucial regulatory switches, says Venkatesh. He later showed that the fugu’s regulatory switches are so similar to their mammalian counterparts that they can sometimes be swapped without loss of function.

Dipping Into the Shark Tank

Fresh from that success, Venkatesh turned his attention to other fish genomes. His first goal was to sequence a shark. Sharks lack bony skeletons, which indicates that they are an early branch in the evolutionary tree of vertebrates. Comparing their genes with those of bony fishes can thus shed new light on the evolution of higher fishes and their descendants, including humans.

But Venkatesh faced a big problem. Most sharks have huge genomes, far larger than those of humans, so they were difficult to sequence with the technology of the day. After two years of rummaging through the genomes of various shark species, he stumbled on the solution: the elephant shark, whose genome is only about a third the size of our own. “It’s the fugu among the sharks,” he says. That one, he could handle.

The elephant shark, Callorhinchus milii, is a genetic standout in two ways: Its genome is far smaller than that of most sharks and has changed far less over time than those of other vertebrates. (Credit: Fir0002/Flagstaffotos)

The elephant shark, Callorhinchus milii, is a genetic standout in two ways: Its genome is far smaller than that of most sharks and has changed far less over time than those of other vertebrates. (Credit: Fir0002/Flagstaffotos)

The sequencing, completed in 2007, revealed that the elephant shark is a living genomic fossil — it has changed less from its ancestral state than any other vertebrate known. “It’s like a screen shot of the past, how our ancestors looked,” says Venkatesh. “That makes it a very useful model for examining what changes have occurred.”

More genomes followed quickly, including those of the deep-sea coelacanth (one of the closest living relatives of terrestrial vertebrates) in 2013, the spotted gar (a primitive bony fish) in 2015, and the gigantic ocean sunfish and the distinctively shaped seahorse in 2016. Other research groups joined the hunt, so that by early 2018, Venkatesh could list 60 bony fish genomes completed by various labs around the world.

The genome of the spotted gar (Lepisosteus oculatus), a primitive bony fish, offers insights into the evolution of vertebrate development, gene control, immunity and tissue mineralization. (Credit: Sergey Lavrentev/Shutterstock)

The genome of the spotted gar (Lepisosteus oculatus), a primitive bony fish, offers insights into the evolution of vertebrate development, gene control, immunity and tissue mineralization. (Credit: Sergey Lavrentev/Shutterstock)

At the molecular level, fish turn out to be much more diverse than land vertebrates. Some time early in their evolution, bony fishes underwent a duplication of their entire genome. This freed up “spare” copies of genes for evolutionary tinkering without risking loss of the original gene function. This may explain why bony fish genomes have evolved more rapidly than those of their terrestrial cousins.

The Big Catch

Though Venkatesh finds fish fascinating in their own right, there is a larger prize in play as well. Humans and fish share most of the same molecular building blocks — their complement of genes — but deploy them in different ways. “You can take a pile of bricks and make a cathedral, you can make a bridge, you can make a villa, or you can make a road. The question is, what are the controlling mechanisms that take those bricks and make them into what you can see? That’s the big question,” says Edward Wiley, an ichthyologist at the University of Kansas. Because fish vary so much in body form, they make an ideal test bed to work out many of those controls, with big potential payoffs for our understanding of all vertebrates, including humans.

These and other genome studies are now coalescing into a systematic effort to sequence the greatest possible diversity of vertebrate life. Venkatesh is one of the leaders of this consortium, known as Genome 10K, and is playing a key role in identifying which fish to include. “Venki has been in on fish genomics since the beginning. When G10K was formed, it was natural that they would ask him to be responsible for the fishes,” says Wiley who, with Venkatesh, cochairs the effort’s fish section.

As its name suggests, G10K began with the goal of sequencing 10,000 vertebrate genomes, mostly in a rudimentary fashion. Since then, though, the group has refocused on quality over quantity: sequencing at least one genome from every major group, or order, of vertebrates — some 260 in all — using the newest, high-precision sequencing technology. The first hundred genomes should roll off the line within the next year, and the full set of 260 should be done by 2020, says Erich Jarvis, a genomic neurobiologist at Rockefeller University in New York City, who chairs the project. After that, the group has an even more ambitious goal: to sequence the genomes of every one of the 60,000-plus vertebrate species.

(Credit: Catmando/Shutterstock)

A coelacanth. The fish are from a lineage that was thought to have gone extinct 70 million years ago until a living specimen was discovered in the 1930s. The lineage is closely related to ancestral fish that gave rise to four-legged vertebrates. (Credit: Catmando/Shutterstock)

The technology is advancing so fast that a few genome biologists are talking of the ultimate goal: sequencing the genome of every species on Earth. The plan is not as far-fetched as it sounds. “There are something on the order of a million-and-a-half named species,” says Durbin. “We’ve probably sequenced on the order of a thousand. So there’s a thousandfold improvement to make. Typically, sequencing technologies are improving twofold a year. On that scale, in the next decade we’re going to be able to find the genomes of everything.”

If geneticists get anywhere close to that goal, current methods of sorting, comparing and understanding genomes will not cope with the enormous mass of data, says Gene Myers, a bioinformatician at the Max Planck Institute for Molecular Cell Biology and Genetics in Dresden, Germany. But Myers is optimistic that researchers, in time, will solve that problem, just as they learned to handle the once-daunting data management challenge posed by the human genome. “Meeting these challenges is the fun part,” he says. “I want to be overwhelmed and figure it out.”

Working Away on DNA

Genome researchers will need help on another front, too, Venkatesh notes. Spelling out the genome of a species and picking out the genes it contains is relatively easy. Working out exactly what each gene actually does — and how variations in DNA sequence within the gene alter that — can be a much bigger challenge that involves a lot of detailed lab work. “You can sequence a genome in two months, but understanding the functional aspect of even one variant takes two years. We need to catch up on the functional study.”

Seahorses, such as the tiger tail seahorse Hippocampus comes, have a wealth of distinctive features; one of them, in males, is a specialized brood pouch where the embryos develop. (Credit: By Ekkapan Poddamrong.Shutterstock)

Seahorses, such as the tiger tail seahorse Hippocampus comes, have a wealth of distinctive features; one of them, in males, is a specialized brood pouch where the embryos develop. (Credit: Ekkapan Poddamrong/Shutterstock)

If geneticists can clear these hurdles — and if the consortium can find the funding to do the work — having a complete set of genomes could open whole new avenues of research. “Once you have the blueprints of all vertebrates on the planet, you’re going to be able to address questions that you could never address,” says Jarvis. Evolutionary biologists could track the genetic changes that underpin speciation — how a single cichlid species evolved into hundreds in Africa’s Lake Malawi, for example. Conservation biologists could more easily identify genetically distinct populations of threatened species or nonintrusively monitor their distribution from traces of DNA left in the environment. Someday, they may be able to understand the genetic reasons why some species are rare, and perhaps even resurrect extinct species from their genome sequences.

Human geneticists will get their payoff, too. With a complete set of genomes, they could reconstruct the evolutionary history of our own genome and trace the origin and function of each and every gene and on-off switch. “Once we have the complete sequences, we can start asking the question of how they’re regulated, and how that regulation or misregulation affects human health,” says Venkatesh, who has already begun exploring the genomic basis of some rare human diseases. “This is what I’d like to do in ten years, if I’m still around.”

CATEGORIZED UNDER: Living World, Top Posts
MORE ABOUT: animals, evolution, genetics

What Makes A Tree A Tree?

By Rachel Ehrenberg, Knowable Magazine | April 16, 2018 3:06 pm
(Credit: Cristina Gottardi/Unsplash)

(Credit: Cristina Gottardi/Unsplash)

Several years ago, after Thanksgiving dinner at my parents’ house in Vermont, lightning struck a backyard maple tree. There was a ferocious crack and the darkness outside the kitchen windows briefly turned day-bright. It wasn’t until spring that we knew for certain the tree was dead.

This maple was a youngster, its trunk the diameter of a salad plate. Were its life not cut short by catastrophe, the tree might have lived 300 years. But death by disaster is surprisingly common in trees. Sometimes it results from a tragic human blunder, as with the 3,500-year-old Florida bald cypress that was killed in 2012 by an intentionally lit fire. More often, calamity strikes via extreme weather — drought, wind, fire or ice. Of course, trees also are susceptible to pests and disease; adversaries like wood-decaying fungi can significantly shorten a tree’s life. But the ones that manage to evade such foes can live for an incredibly long time. Read More

CATEGORIZED UNDER: Living World
MORE ABOUT: plants

Let’s Journey Through the Mind of a Dog

By Erica Tennenhouse | March 22, 2018 12:55 pm
an adorable dog looking at the camera

(Credit: Shutterstock)

Inside a dog’s furry head are millions of neurons firing away, passing chemicals to one another and generating thoughts. We may guess at what our canine pals are thinking about: food, a walk, their loving owners.

But for all the time humans spend interacting with dogs, their thoughts largely elude us, and it’s easy to see why: dogs can’t speak their minds (at least in any language we know). But we still are curious about our best bud’s mindset, and scientists have devised creative methods to get into their heads. While our grasp of canine cognition may never approach what we know of the human psyche, the latest research has yielded tantalizing nuggets about the inner lives of dogs. Read More

CATEGORIZED UNDER: Living World, Mind & Brain, Top Posts

Beneath an Outhouse, a 19th Century Brothel’s Secrets Are Revealed

By Anna Goldfield | March 7, 2018 3:48 pm
brothel-1800s

Life in an 19th century Boston brothel. (Credit: Boston University/YouTube)

For Jade Luiz, a graduate student in archaeology at Boston University, historical archaeology is all about detective work. Through piecing together historical documents and archaeological finds from the outdoor toilet, or privy, of a former brothel near Boston’s North End, she’s been reconstructing the lives of women who participated in sex work in the mid-1800s.

Louisa Cowen, for example, who in 1856 took over as the madam of 27–29 Endicott Street—the brothel behind which stood the privy—typically presented herself as a respectable widow, according to historical mentions of the brothel and census records. Given her status, she likely wore black clothing and adorned herself in somber black jewelry. Her tombstone names her as the wife of Henry Cowen, a Boston house painter who predeceased her. Whether or not the two had been officially married remains unknown. What Luiz does know is that Louisa Cowen became very successful. Read More

CATEGORIZED UNDER: Living World, Top Posts
MORE ABOUT: archaeology

What a Fossil Revolution Reveals About the History of ‘Big Data’

By David Sepkoski | February 16, 2018 8:57 am

stenopterygius

In 1981, when I was nine years old, my father took me to see Raiders of the Lost Ark. Although I had to squint my eyes during some of the scary scenes, I loved it – in particular because I was fairly sure that Harrison Ford’s character was based on my dad. My father was a paleontologist at the University of Chicago, and I’d gone on several field trips with him to the Rocky Mountains, where he seemed to transform into a rock-hammer-wielding superhero.

That illusion was shattered some years later when I figured out what he actually did: far from spending his time climbing dangerous cliffs and digging up dinosaurs, Jack Sepkoski spent most of his career in front of a computer, building what would become the first comprehensive database on the fossil record of life. The analysis that he and his colleagues performed revealed new understandings of phenomena such as diversification and extinction, and changed the way that paleontologists work. But he was about as different from Indiana Jones as you can get. The intertwining tales of my father and his discipline contain lessons for the current era of algorithmic analysis and artificial intelligence (AI), and points to the value-laden way in which we ‘see’ data. Read More

CATEGORIZED UNDER: Living World, Top Posts

Astonishing Ways Animals Ensure Their Sperm Win

By Louise Gentle, Nottingham Trent University | February 14, 2018 9:43 am
Echidnas sport for penises (only two ejaculate). (Credit: Shutterstock)

Echidnas sport four penises (only two ejaculate). (Credit: Shutterstock)

We all know that individuals fight over potential love interests. Just think of Daniel Cleaver (Hugh Grant) and Mark Darcy (Colin Firth) scuffling, rather impotently, over Bridget Jones in a fountain. But you might be surprised to hear that the fierce rivalry continues behind the scenes — in the form of sperm competition. This is when the sperm of two or more males compete inside the reproductive tract of a female, to fertilize the eggs, something that is widespread in the animal kingdom.

It is generally assumed that the sperm in a female’s reproductive tract around the time of fertilization will belong to one male. But DNA fingerprinting has revealed that even “monogamous” bird species that form exclusive pair bonds are not as exclusive as was once thought. Read More

CATEGORIZED UNDER: Living World, Top Posts
MORE ABOUT: sex & reproduction

Peek Inside a Meerkat’s Mazelike Manor

By Adam Booth, University of Leeds | February 6, 2018 11:47 am
File 20180131 131730 1h78wpf.jpg?ixlib=rb 1.1

(Credit: anetapics / Shutterstock)

I’m a scientist and my job is to look below the surface of the earth. One of the questions often asked of people working with what we call geophysical imaging is, “How deep can you see?” It’s a difficult question to answer of course, since one person’s “deep” is another person’s “shallow”, and what is deep to the archaeologist will barely scratch the surface for the planetary seismologist.

For my own part, I’m a “near-surface geophysicist”, interested in the physical properties of material within the upper 100 meters of the ground – the rock, soil and (occasionally) ice located directly in the zone of human interaction – and I’ll often apply ground-penetrating radar to these targets. But there is still a lot that can happen in 100 meters: indeed, go to the right place, and even the top meter of the ground is a bustling metropolis of mammals. And that’s how I ended up investigating an underground meerkat maze for the new BBC series Animals with Cameras. Read More

CATEGORIZED UNDER: Living World, Top Posts
MORE ABOUT: animals
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