Say Hello to Dickinsonia, the Animal Kingdom’s Newest (and Oldest) Member


Half-billion-year-old fossils reveal new details about one of the most mysterious chapters in Earth’s history.

Say Hello to Dickinsonia, the Animal Kingdom's Newest (and Oldest) Member
A fossilized imprint of Dickinsonia, mysterious organisms that may have been Earth’s earliest animals.

Nearly 600 million years ago Earth’s continents were lifeless lands—but the oceans were teeming. Below the white-capped waves a dizzying variety of life-forms grazed blindly on gooey mats of microbes that covered the seafloor.

Thought to represent the earliest flowering of complex multicellular life on our planet, these creatures arose in a world devoid of predators, and had no need for hard protective carapaces or skeletons. Their soft, squishy bodies resembled, tubes, fronds or even thin, quilted pillows; they bore scant similarity to the anatomy of animals today. This ancient biosphere seems quite alien—and yet these organisms must be our early ancestors.

At least that is the story according to a new paper published today in Science, where researchers argue an iconic fossil from this time period is the oldest known animal that would have been visible without the help of a microscope. If correct, the finding settles a 70-year-old debate and could help explain the emergence of more advanced life-forms on our once-barren planet.

The fossils from some 575 to 541 million years ago, from a time known as the Ediacaran period, represent the earliest known complex life on Earth—meaning these creatures were neither microscopic single-celled organisms nor simple multicellular colonies of unicellular microbes. Yet because of their remoteness from us in planetary and evolutionary time—and the fact flesh fossilizes far less readily than shell or bone does—their true nature has mostly remained unknown. In 1947, for example, when scientists in Australia first discovered the segmented, pancake-shaped fossils of Ediacaran creatures dubbed Dickinsonia that can run up to one meter in length, they thought the strange organisms were an early form of jellyfish. And yet fossilized Dickinsonia and other Ediacarans exhibit no obvious characteristics such as appendages, a mouth or a gut that would link them to anything in the animal kingdom. As such, their place on the family tree of life has been quite contentious: If Dickinsonia were not jellyfish, perhaps they were instead annelid worms or mushrooms, or enormously oversize lichens or single-celled organisms.

The problem is that although Dickinsonia fossils have now been spotted at dozens of sites across the globe, they are typically found solely as two-dimensional imprints in sandstone. “It would be like trying to judge the structure of our modern world if all you had was footprints,” says Guy Narbonne, a paleontologist at Queen’s University in Ontario who was not involved in the study. Then in 2016, Ilya Bobrovskiy, a graduate student at Australian National University, made a startling discovery, stumbling upon Dickinsonia fossils in Russia that were essentially mummified in a mixture of clay and sandstone. “Just imagine finding a T. rex that is so well preserved you still have the hard-tissue, the skin, maybe even a mummified eye,” says Bobrovskiy’s PhD Advisor Jochen Brocks, a biogeochemist at the Australian National University. “Think about how much we would learn about dinosaurs! That’s in principle what my student found.”

The potential was enormous. “I’m in awe of this study because it’s a spectacular opportunity to get molecular information about a fossil that has been so enigmatic,” says Roger Summons, a geobiologist at Massachusetts Institute of Technology who was not part of the work. Indeed, when Brocks and his colleagues analyzed the samples, they uncovered cholesteroids: the molecular fossils of cholesterol, a distinctive signature of animal life. Whether animal, vegetable or otherwise, every Earthly organism is composed of cells bounded by layers of lipid molecules; only animals, however, have cholesterol in their cell membranes. So spotting cholesteroid meant Dickinsonia were in fact animals. Still, the detection could have been due to contamination—a careless brush of a finger against a fossil, for instance, could immediately transfer cholesterol-containing cells and produce an artificial signal of ancient animal life. So, Brocks and his colleagues carefully scrutinized the rocks surrounding the mummified Dickinsonia as well. There, rather than cholesteroids they found stigmasteroids, a molecular fossil commonly associated with green algae. That difference, they say, all but confirms the cholesteroid came from the fossils themselves and not from contamination, cementing Dickinsonia’s foundational status in the animal kingdom.

“I think the paper puts to bed any suggestion that they were otherwise,” Summons says. “To me, chemistry doesn’t lie.” Not only does it prove that Dickinsonia was an animal—it also now holds the record as the oldest macroscopic creature in the fossil record. And that is a crucial finding. At the end of the Ediacaran (which marks the beginning of the next period, the Cambrian), an evolutionary uprising overturned the simple and peaceful ecosystems that had reigned for 30 million years, setting the stage for our modern world. The Cambrian explosion, as it is called, produced animals with far more familiar anatomies and behaviors, such as creatures with shells, spines, thrashing limbs and tooth-rimmed jaws that could trap and devour prey. But scientists still do not know what sparked this eruption of life-forms.

Based on his team’s latest findings, Brocks argues the answer must lie somewhere within the evolutionary vagaries of Ediacaran biota. That is different from previous notions that suggested the Ediacarans were not animals at all, causing some scientists to argue the creatures were evolutionary dead ends wholly distinct from their Cambrian successors. For Dickinsonia, at least, scientists can now argue these strange soft-bodied beings were the progenitors of the Cambrian animals that swept over the planet, and thus were our ancestors.

Ultimately, this finding could help scientists better understand the complicated interplay of geology and biology that triggered the evolution of complex life on Earth—and perhaps on other worlds as well. Douglas Erwin, a paleobiologist at the Smithsonian National Museum of Natural History who did not take part in the study, is hopeful it will bolster the search for life elsewhere in the solar system because it demonstrates how faint chemical traces—rather than the more obvious analysis of fossil morphology—can uncover new, previously overlooked biological details. That is crucial because beyond Earth, he says, “we’re more likely to find fossils of something than we are to find something sticking its head up and waving.”

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Exploring the Mysterious Life of One of Earth’s First Giant Organisms


Strange creatures known as “rangeomorphs” could help paleontologists understand the origins of animal life

Exploring the Mysterious Life of One of Earth's First Giant Organisms
An artist’s depiction of the extinct giant, frondshaped
organisms known as rangeomorphs. 

Paleontologists unearthed a strange sight in Newfoundland in the early 2000s: an ancient fossil bed of giant, frond-shaped marine organisms. Researchers had discovered these mysterious extinct creatures—called rangeomorphs—before, but they continue to defy categorization. Now scientists believe the Newfoundland fossils and their brethren could help answer key questions about life on Earth.

Rangeomorphs date back to the Ediacaran period, which lasted from about 635 million to 541 million years ago. They had stemlike bodies that sprouted fractal-like branches and were soft like jellyfish. Scientists think these creatures grew to sizes until then unseen among animals—up to two meters long. After they went extinct, the planet saw an explosion of diverse large animal life during the Cambrian. “Rangeomorphs are part of the broader context of what was going on at this time in Earth’s history,” says study co-author Jennifer Hoyal Cuthill, a paleobiology research fellow at the Tokyo Institute of Technology. Figuring out how rangeomorphs grew to such great sizes could help provide context for understanding how big, diverse animals originated and how conditions on Earth—which were shifting around this time—may have affected the evolution of life.

To better understand these connections, Hoyal Cuthill and University of Cambridge paleontologist Simon Conway Morris analyzed several rangeomorph fossils. The pair performed a micro CT scan on one well-preserved fossil of a species called Avalofractus abaculus, found in Newfoundland, to examine its 3-D structure in fine detail. They also took photographic measurements of two other specimens for comparison.

The researchers examined various aspects of the rangeomorphs’ stems and branches, then used mathematical models to investigate the relation between the fossils’ surface areas and volumes. Their models, combined with the fossil observations, revealed that the organisms’ size and shape appeared to be governed by the amount of available nutrients, according to the study, published recently in Nature Ecology & Evolution. This may explain why they could reach such large sizes during a period when Earth’s geochemistry was changing.

But other experts are hesitant to generalize in this way. “This is an interesting finding that supports the growing consensus among researchers that rangeomorphs had the potential to grow differently in response to their environment,” says Jack Matthews, a research fellow at the Oxford University Museum of Natural History, who was not involved in the work. But “it is perhaps premature for this study to apply its finding to all rangeomorphs.”

If the explanation turns out to be correct, though, Hoyal Cuthill says, it could provide an answer for “what links this amazing appearance of larger organisms in the fossil record with [what was] happening on Earth.”

A Nerve Pathway Links the Gut to the Brain’s Pleasure Centers


A newly discovered neural circuit in mice may one day help modify food preferences and eating behavior.
A Nerve Pathway Links the Gut to the Brain's Pleasure Centers
Credit: Getty Images

How do we decide what we like to eat? Although tasty foods typically top the list, a number of studies suggest preferences about consumption go beyond palatability. Scientists have found both humans and animals can form choices about what to consume based on the caloric content of food, independent of taste.

Research spanning many decades has shown nutrients in the gastrointestinal tract can shape animals’ flavor preferences. One of the earliest findings of this effect dates back to the 1960s, when Garvin Holman of the University of Washington reported hungry rats preferred consuming a liquid paired with food injected into the stomach rather than a solution coupled with a gastric infusion of water.

More recently Ivan de Araujo, a neuroscientist at the Icahn School of Medicine at Mount Sinai, and his colleagues have shown calories can trump palatability: Their work has demonstrated mice prefer consuming bitter solutions paired with a sugar infusion injected in the gut rather than a calorie-free sweet solution.

For years De Araujo and his group have been working to tease apart how the contents of the gut produce pleasure in the brain. In mice they have found sugar in the digestive tract can activate the brain’s reward centers. In animals bred without the ability to taste sweetness, sugary snacks still triggered activity in the ventral striatum, a brain region involved in reward processing. But according to De Araujo, the specific pathway that relayed signals between the gut and the brain remained a mystery.

Now, De Araujo and his colleagues have identified the vagus nerve, a bundle of fibers that connects the brain stem to the intestines and other major organs in the body, as a potential conduit of these gut-borne pleasure-related signals to the brain—at least in mice. Using optogenetics, a technique that involves genetically engineering animals so that flashes of light can activate specific cells, the researchers discovered stimulating neurons in the gut-innervating branches of the vagus nerve can induce the release of the neurotransmitter dopamine from the substantia nigra, a brain region involved in movement and reward.

The findings, which were recently published in Cell, also reveal animals would repeatedly poke their noses into holes in order to self-stimulate these cells—and that they preferred flavors paired with the activation of this circuit. “[Our study] provides a mechanism via which we understand why the presence of calories or nutrients in the gut changes our behavior,” De Araujo says.

Future studies will need to tease apart what types of gut stimuli, such as the presence of specific foods or the stomach stretch that occurs after a meal, will activate this pathway, notes Gary Schwartz, a neuroscientist at the Albert Einstein College of Medicine who was not involved with the work. “If one knew what kinds of stimuli we should give the gut to make [food] rewarding or not rewarding, maybe we can help control overeating or make people who don’t want to eat, eat more.”

Scientists have long known the gut–vagus–brain pathway is responsible for producing feelings of fullness, but this new study—and other recent research—has started to uncover new roles for this system in higher-order brain functions, says Scott Kanoski, a neuroscientist at the University of Southern California who was not part of the research. Earlier this year, his team found this circuit also controls some memory functions. Selectively cutting the branches of the vagus that were connected to the gut, they discovered, impaired the animals’ ability to form memories about new objects or locations.

Of course, additional research is necessary to confirm this type of circuit exerts the same behavioral effects in humans. In the meantime vagal stimulation is already used to treat emotional and eating disorders such as depression and obesity. And there is a growing interest in using this technique as a therapy for anxiety disorders and a variety of additional conditions—even Alzheimer’s and related memory disorders, Kanoski says. “Understanding more about the biology of the system could have implications for future applications.”

A key question that remains about these gut–vagus–brain pathways is: How is information about gut contents relayed to the sensory branches of the vagus nerve? One possibility is the vagus senses hormones within the gut, De Araujo says. Another was outlined in a recent Science study in which Diego Bohórquez, a neuroscientist at Duke University, and his colleagues discovered that some enteroendocrine cells, which are found in the walls of the gastrointestinal tract, directly form synapses with the vagus nerves of mice. Introducing an environmental stimulus—in this case, sugar—into the gut could activate this circuit. Bohórquez—who was also a co-author in De Aruajo’s study—dubbed these synapse-forming gut cells “neuropods.”

In addition to transmitting information about nutrients in the gastrointestinal tract, these newly identified vagal circuits may also be involved in bacterial signaling from the gut to the brain, says John Cryan, a neuroscientist at University College Cork in Ireland who was not involved in either study.

A large body of research now provides support for findings that the microscopic organisms in our intestines can influence behavior and mental health—and some evidence already suggests the vagus is a possible route via which these effects occur. In a 2011 study Cryan and his colleagues demonstrated that severing the vagus nerves of mice blocked the anxiety-reducing effects of the probiotic bacterium Lactobacillus rhamnosus. This study showed the vagus is critical for signaling to the brain by certain strains of bacteria. But how microbes send signals to the vagus remains an open question.

“It would be interesting to see if metabolites from the microbiome could activate these neuropod cells [or the] reward pathway,” Cryan says. “I think this is really exciting for the microbiome field.”

Form A Daily Writing Habit—It Will Improve Your Life


One of the most important habits that I’ve formed in my life is daily writing.

Without question, writing every day has brought me many great things: A better career, fulfillment, self-improvement, and most importantly, the ability to share my ideas with you, the reader.

I wanted to be a writer for a decade before I became one. All it took was a decision. At some point, you have to look at yourself and say, “I’m a writer.” And then, start doing your job by writing every day.

I recommend that to everyone because of these 5 reasons:

  1. Better self-discipline
    Living a life of pleasure is simple. Everyone can “Netflix and chill.” It’s easy to “hang out” all the time. But those easy things will not give you inner satisfaction. The reason that we don’t do anything useful with our precious time is that we lack self-discipline. But when you write every day, you strengthen your discipline. You can use that better self-discipline to achieve virtually anything in life.
  2. Improving you persuasion skills
    Writing is nothing more than persuading the reader with words. But your tools are limited—you can only use words to tell a story. And when you write for yourself, you’re trying to convince yourself of your own thoughts. So the more you write, the better you become at persuasion.
  3. Cultivating self-awareness
    Nothing will help you to get to know yourself more than translating your thoughts into words. When you force yourself to write every day, you automatically become more aware of your thoughts. And self-awareness is one of the most important skills that predict career success.
  4. Better decision making
    Too often, we do something without fully understanding why we do it. Think about it. How often do you answer “I don’t know” when someone asks you “Why did you do that?” That’s the sign of weak thinking. Sure, we don’t know everything. But we must aware of that too. And when you write about your decision-making process, you will automatically become more aware of the “why.”
  5. Seeing the power of compounding in action
    When you do something every day, you don’t notice any difference at that moment. You think, “Where are the benefits?” But when you keep doing it for a long time, the positive effects compound. Writing every day will demonstrate the power of compounding like very few other things can.

To be honest, there are many other benefits to writing every day. It’s great for reflection, dealing with anxiety, coming up with new ideas. On top of that, you can use writing to inspire others or achieve your goals.

“That’s great and all. But how do you even form a daily writing habit?”

Here are 4 tips that can help you with that:

  1. Read & study
    Start by stealing other people’s writing styles. It’s a strategy I learned from Austin Kleon. Stealing is an effective way to develop your own style. Plus, when you can steal ideas, you can never use the excuse of: “I don’t have any inspiration.” But take the craft of writing seriously. Study it as much as you can by reading books and taking courses/workshops.
  2. Set a daily reminder to write
    Nothing is more important to a writer than having a routine. First, think about what time is the best for you to write. In the morning or evening? Before/after the kids are awake? Then, set a daily reminder on your phone—when it goes off, sit down and write.
  3. Set the bar low
    Your goal is to write only one true sentence. Just one. The beauty of that goal is that the first sentence that comes up in your mind is always the truest of them all. So never say that your writing sucks. Avoid aiming for setting goals like, “I want to write 1000 words a day.” That’s too absolute. Instead, strive for writing one sentence. Then, keep going.
  4. Remove distractions
    Tell the people in your life about your daily writing habit. Ask them to not disturb you during the time you’re writing. I block 3 hours every morning. During that time, I put my phone in do not disturb mode, don’t take calls, and don’t answer to messages—I write. I’ve told my family and girl about this too so they don’t disturb me during that time.

Often, people give advice like, “just get started!” And there’s truth in that. Starting is important.

But here’s the thing: Everyone can write for a day—or two, or three. But there are very few people who write consistently for years. But you need to write for a long time to see the actual benefits.

So don’t just get started. Keep going.

Everything Is Weird Right Now, But Here Are Some Really Good Things Happening on The Planet


main article image

Help! We all need some good news.

We don’t need to tell you world news is pretty grim right now – if you use social media, it’s nigh on impossible to avoid articles about bubbling permafrost, drug-resistant gonorrhoea, and deadly obesity treatments. And that’s just the science headlines.

But despite all the doom and gloom, in reality there are a whole bunch of incredible people doing really good things around the world right now. Sometimes they just don’t get as much press as they deserve.

So as a much-needed reminder that not everything is ruined, here are some of the awesome things happening in the world right now that you can talk about over dinner tonight (instead of global tension and nuclear weapons). You’re welcome.

1. Young gorillas have learned to dismantle poachers traps

Days after a poacher’s trap killed a young mountain gorilla in Rwanda’s Volcanoes National Park in 2012, researchers spotted something remarkable: two four-year old gorillas working together to dismantle similar snares in the area. It’s the ultimate feel-good story.

mountain gorillasbody(Dian Fossey Gorilla Fund)

“This is absolutely the first time that we’ve seen juveniles doing that … I don’t know of any other reports in the world of juveniles destroying snares,” Veronica Vecellio from the Dian Fossey Gorilla Fund’s Karisoke Research Centre in Rwanda told National Geographic at the time.

2. We’re finally getting close to achieving sustainable nuclear fusion

Nuclear fusion could be the key to producing almost-unlimited energy with few byproducts other than saltwater, but researchers have long struggled to create a machine that could sustainably control such a powerful reaction.

But that’s changing. At the end of 2015, Germany switched on a massive nuclear fusion reactor that’s since successfully been able to contain a scorching hot blob of hydrogen plasma.

They’re not the only ones, either, with South Korea and China both achieving record-breaking reactions in their own fusion machines. The UK has also switched on a revolutionary type of reactor that is now sustainably generating plasma within its core.

In fact, MIT scientists predict that thanks to all these new advances, we should be able to get fusion energy on the grid by 2030.

3. We can now ‘listen in’ to the Universe 

By now you’re probably very familiar with the huge gravitational wave breakthrough that happened in 2015. But what you might not know is that we’ve continued to detect at least two more gravitational waves since then.

And with a new space-based series of detectors known as LISA coming online by 2034, we’re going to soon be able to use them to test all kinds of crazy hypotheses – including the idea of multiple dimensions within our Universe.

4. We’re getting really close to eradicating the second disease from the planet

First, humans got rid of smallpox. Now we’re on the verge of wiping out the Guinea Worm parasite, which is a living nightmare that painfully erupts from people’s skin.

At the start of 2015 there were just 126 cases of Guinea Worm left on Earth, mostly thanks to an ingenious and cheap drinking straw filter that stops people from being contaminated via water. As of May this year, there were only five recorded cases.

5. And Australia is on track to become the first country to wipe out one type of cancer

According to a new study, Australia will become the first country in the world to eliminate cervical cancer by 2028, with a predicted rate of just four new cases per 100,000 people.

And in just two years it will be considered a rare cancer.

This is thanks to a comprehensive prevention strategy that started back in 1991, involving regular pap smears and since 2007, free HPV vaccines for girls (and boys since 2013). Last year Australia also replaced pap smears with HPV cervical screening tests, which are predicted to reduce cancer rates by up to 30 percent in combination with the vaccine.

6. We’re closer than ever before to having a drug that can treat autism symptoms

A small, but promising clinical trial in the US showed this year that a 100-year-old drug called suramin can measurably improve the symptoms of autism spectrum disorder (ASD) in children.

There’s a lot more work to be done, but it’s the first time we’ve been so close to having a drug that can potentially treat ASD symptoms.

7. Scientists are working on a graphene-based sieve that turns seawater into drinking water

As if graphene wasn’t awesome enough, back in April researchers achieved a major turning point in the quest for efficient desalination by announcing the invention of a graphene-oxide membrane that sieves salt right out of seawater.

At this stage, the technique is still limited to the lab, but it’s a demonstration of how we could one day quickly and easily turn one of our most abundant resources, seawater, into one of our most scarce – clean drinking water.

8. You no longer need to pay ridiculous amounts to access peer-reviewed science research

The scientific community is fighting back against crazy paywalls, with a new study showing that more than a quarter of all scientific papers are now available free online thanks to the Unpaywall app.

9. We just discovered a vitamin that could reduce the incidence of birth defects and miscarriages worldwide 

In what scientists are calling “the most important discovery for pregnant women since folate“, a 12-year study has revealed that women could avoid miscarriages and birth defects by simply taking vitamin B3 during pregnancy.

10. Researchers are finally beginning to understand how we can repair spinal cord injuries

There’s nothing simple about repairing spinal cord injuries. But new research has pinned down how one of the most cutting edge techniques works, and in particular how the body can repair itself with a little prompting from surgeons.

By finally understanding how spinal cord injuries can heal, researchers will eventually be able to develop even more effective treatments that could potentially go as far as reversing paralysis and other nervous system damage.

11. Hyperloops are coming!!

The hyperloop transport system is a brain child of Elon Musk that promises to shuttle people in tube-contained pods between cities at crazy speeds of roughly 1,126 km/h (700 mph). That’s New York to Washington DC in around 29 minutes.

So far test hyperloops are being built in the US, the Netherlands, Slovakia, and the Czech Republic. The goal is to have a Hyperloop system between Amsterdam and Paris by 2021.

There’s even a (slightly crazy) proposal to turn the US/Mexico border wall into a giant hyperloop.

12. African wild dogs communicate with each other in the most adorable way ever: sneezes

Scientists have observed African wild dogs in Botswana sneezing at each other in order to cast their vote on whether it’s time to get up and go hunting. And, yes, we have video footage:

13. Scientists are fighting back against antibiotic resistance

The United Nations has declared antibiotic resistance a ‘fundamental threat‘ to global health, which some scientists predict could kill 10 million people annually by 2050. But we haven’t lost the battle yet.

At the start of this year, scientists announced the development of a molecule that reverses antibiotic resistance in multiple strains of bacteria at once, making it one of the most promising advances we’ve had to date in the fight against superbugs.

And Australian PhD student Shu Lam has the research community freaking out over a way to actually kill bacteria in the first place… without antibiotics. She’s developed a star-shaped polymer that can kill six different superbug strains without antibiotics, simply by ripping apart their cell walls.

14. NASA has released all its research to the public for free

Last year, NASA announced that any published research funded by the space agency will now be available at no cost, launching a new public web portal that anybody can access.

The free online archive comes in response to a new NASA policy, which requires that any NASA-funded research articles in peer-reviewed journals be publicly accessible within one year of publication.

And last but definitely not least…

15. Scientists have classified a brand new type of celestial phenomenon… and they named it Steve.

Steve the ‘aurora’ was the feel-good story of 2017.

But this year, scientists found out that Steve isn’t actually an aurora at all – even cooler, it’s an entirely new type of celestial phenomenon we hadn’t seen before and are still learning more about.

The new astronomical phenomenon looks like a ribbon of flickering light, and has been spotted in the high latitudes of the northern hemisphere.

Check out below how awesome Steve looks in all his glory. See? Life isn’t all bad.

large aurora steve

I, holobiont. Are you and your microbes a community or a single entity?


<p>Cicada, North Carolina, May 2011. <em>Photo courtesy Wikimedia.</em></p>

Cicada, North Carolina, May 2011.

 

Cicadas might be a pest, but they’re special in a few respects. For one, these droning insects have a habit of emerging after a prime number of years (7, 13, or 17). They also feed exclusively on plant sap, which is strikingly low in nutrients. To make up for this deficiency, cicadas depend on two different strains of bacteria that they keep cloistered within special cells, and that provide them with additional amino acids. All three partners – the cicadas and the two types of microbes – have evolved in concert, and none could survive on its own.

These organisms together make up what’s known as a holobiont: a combination of a host, plus all of the resident microbes that live in it and on it. The concept has taken off within biology in the past 10 years, as we’ve discovered more and more plants and animals that are accompanied by a jostling menagerie of internal and external fellow-travellers. Some of the microorganisms kill each other with toxins, while others leak or release enzymes and nutrients to the benefit of their neighbours. As they compete for space and food, cohabiting microbes have been found to affect the nutrition, development, immune system and behaviour of their hosts. The hosts, for their part, can often manipulate their resident microbiota in many ways, usually via the immune system.

You yourself are swarming with bacteria, archaea, protists and viruses, and might even be carrying larger organisms such as worms and fungi as well. So are you a holobiont, or are you just part of one? Are you a multispecies entity, made up of some human bits and some microbial bits – or are you just the human bits, with an admittedly fuzzy boundary between yourself and your tiny companions? The future direction of medical science could very well hinge on the answer.

The American evolutionary theorist Lynn Margulis, who popularised the theory of symbiosis, first coined the term ‘holobiont’ in 1991. She was interested in long-term, tightly integrated associations such as those evident in lichens – the crusty-looking growths found on rocks and trees, made up of fungus conjoined with algae. Margulis thought that there was a tight analogy between an egg and a sperm coming together to form a new organism, and the coming together of two species to form a new symbiotic consortium, which she called a holobiont.

Margulis argued that the interactions within a holobiont aren’t too different from the life cycle of sexually reproducing organisms. The partners are integrated wholes that die and reproduce as one. But instead of sending out tiny cells to reproduce, holobionts send out individual organisms of different species.

With this framing in mind, when biologists began to use the term in the 1990s, they applied it to a few (usually two) organisms. But the word took on a very different cast in the hands of the American coral reef biologist Forest Rohwer and his colleagues, who defined a holobiont as a host and all of its associated microorganisms.

Two protagonists just aren’t enough when it comes to explaining the evolutionary success of corals. They are made up of clusters of polyps, tiny wiggling things that get by with just a few tentacles and a toothless maw. Coral polyps reproduce by cloning themselves, and then sticking together to form large colonies, supported by a jointly fashioned skeleton. The most spectacular corals work hand-in-hand with photosynthetic algae that they host within their own cells. The algae provide nutrients via photosynthesis, while the coral gives the algae both food and protection. And those simple little polyps don’t end their symbiotic relationships there. Corals don’t possess a complicated immune system to fend off pathogens; instead, they seem to selectively cultivate helpful or benign bacteria, which crowd out the harmful microbes. Corals also produce mucus that appears to be able to trap phages, viruses that infect and kill only bacteria. An enemy of an enemy is a friend, after all.

Rohwer and colleagues, unaware of Margulis’s idea, introduced the term holobiont to capture the dynamics of coral physiology. As a result, by the early 2000s, the scientific literature contained two contrasting definitions. One picked out an organism-like symbiotic pair that reproduced, while the other identified an ecological community of microbes indexed to a host.

For a time, the ecological account prevailed. But Margulis’s physiological conception of holobionts was revitalised in the late 2000s as part of a new theory: what’s known as the hologenome theory of evolution. Advocates merged both versions of holobiont into something a bit more conceptually loaded. On this view, the ecological notion of holobiont (the host and all its resident microbes) is given additional properties. It’s an entity that’s coherent enough to have its own hologenome, made up of the host genome plus all the microbial genomes. A major implication of this theory is that natural selection doesn’t just act on the genome of individual organisms: it acts on the hologenome of holobionts, which are seen as single units that can evolve at the level of the holobiont.

Today, researchers engage in fierce debate over which forces shape holobionts and host-microbiome systems. They can be roughly split into two factions, the ecological and the evolutionary. On the ecological side, holobionts are seen as complex and dynamic ecosystems, in constant flux shaped by individual interactions from the bottom up. So you are part of a holobiont. But this stands in opposition to the evolutionary account, which casts holobionts as higher-level entities akin to organisms or units of selection, and believes that they are shaped as a whole from the top down. On this view, you are a holobiont.

The ecological and evolutionary views make for very different predictions about how a holobiont will change over time. Evolutionary theory predicts that the parts of a unit of selection will tend to cooperate: to sacrifice their own interests for the good of the whole. Ecological theory, by contrast, predicts competition and exploitation: parts will cooperate only insofar as it benefits them. Think of the differences between an ant colony and a motley assortment of insects fighting over scarce resources.

A dominant view in medicine treats the body as a battleground where any invaders are bad and must be exterminated. But in an ecosystem, there are no bad guys, just species playing different roles. If the ecological account of holobionts is true, a human host is more like a habitat to be managed, with the right balance and competition between different kinds of microbes being an important consideration. What counts as healthy can depend on what kinds of services we want out of our attendant ecosystem. If the microbes in a holobiont are more like ants in a colony, or genes in a genome, they are parts of a larger integrated whole. So we might expect stable co-adapted partners living in concert across holobiont generations.

However, the evolutionary version of holobionts gives us reason to stick to an expanded version of the ‘us versus them’ picture of medicine. It’s just that now we have a few more allies on our side that we need to take care of. The evolutionary framework might also provide some justification for the calls for a return to a palaeomicrobiome that existed before the modern diet – for that would literally help to return a missing part of ourselves.

As things stand, the evidence leans heavily towards a more ecological interpretation of holobionts. Most of the partners come together anew each generation, and don’t interact in the ways that are necessary for higher-level integration into organismic wholes. The theoretical bar for making that transition is high, and getting over it is going to be rare. But it potentially varies from holobiont to holobiont. There is still a long and exciting scientific road ahead, as researchers begin to unravel the secret lives and complex effects of microbes on the development, behaviour and evolution of their hosts.

Something Unexpected Has Been Happening to Plants in The Arctic as It Gets Warmer


This delicate ecosystem is changing way too fast.

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The plants of the Arctic, typically very low-lying shrubs, are getting taller as the region warms up because of climate change, new research has revealed. Existing plant species are growing in height and taller plants are moving into the neighbourhood too.

How that affects the delicate ecosystems and carbon cycles of the Arctic is yet to be confirmed, scientists say, though these changes are going to have to be closely watched. The shifts in the ecosystem have happened rapidly over the past 30 years.

Taller plants tend to trap more snow, which is one of the ways they could have an impact: the extra snow insulates the soil underneath, which then takes longer to freeze in winter, and could ultimately end up releasing more carbon. And these shifts in vegetation height aren’t just happening in pockets.

arctic plants 2Measurements being taken on Ellesmere Island, Canada (Anne D. Bjorkman)

“We found that the increase in height didn’t happen in just a few sites, it was nearly everywhere across the tundra,” says one of the researchers, Anne Bjorkman from the Senckenberg Biodiversity and Climate Research Centre (BiK-F) in Germany.

“If taller plants continue to increase at the current rate, the plant community height could increase by 20 to 60 percent by the end of the century.”

While taller plants in the Arctic might not seem like much of an immediate concern, remember that 30-50 percent of the world’s soil carbon is trapped in the permafrost of the Northern Hemisphere. Anything that shifts the ecological balance could release a serious amount of carbon dioxide and methane into the atmosphere.

The team studied the tundra across 117 different sites in the Arctic, taking more than 60,000 different data readings in total. Data from the European Alps and Colorado Rockies was also included in the final report.

Various plant traits were logged, including height, leaf area, nitrogen content, woodiness and evergreenness. Only height was observed to have changed significantly over the last three decades, with both moisture levels and temperature both appearing to have an impact on the speedy growth.

arctic plants 3Dryas integrifolia, or Mountain Avens. (Anne D. Bjorkman)

Shrubs are apparently taking advantage of a growing season that’s no longer as cold or as short as it was in the past.

The researchers noted increased height in the Arctic’s native plants, as well as the spreading of other taller plants, like vernal sweet grass – which has sneaked up from lowland Europe to parts of Iceland and Sweden.

And as well as trapping more snow, plants that poke their heads above the snow line darken the overall landscape of the Arctic, which in turn traps more of the Sun’s heat.

“Although there are still many uncertainties, taller tundra plants could fuel climate change, both in the Arctic and for the planet as a whole,” Bjorkman told the BBC.

As other studies have shown, as the permafrost in the northern reaches of the planet starts to thaw out, we could be looking at a serious shift in the release of greenhouse gasses. As the planet warms, it creates more warning – a feedback effect.

More research is going to be needed to figure out exactly how these taller plants will contribute to a change in the climate, but it’s another factor to plug into our prediction models – and it should give us a more accurate idea of just how severely we’re altering the planet’s ecosystems.

You can read more about the researchers’ work and see some dramatic shots of the Arctic tundra at the Team Shrub website.

“Quantifying the link between environment and plant traits is critical to understanding the consequences of climate change, but such research has rarely extended into the Northern hemisphere, home to the planet’s coldest tundra ecosystems,” says one of the team, geoscientist Isla Myers-Smith from the University of Edinburgh in the UK.

“This is the first time that a biome-scale study has been carried out to get to the root of the critical role that plants play in this rapidly warming part of the planet.”

The research has been published in Nature.

It’s Official, Australia Has Had Its First Recorded Marine Animal Extinction


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We barely knew you.

We see the surface of the sea: the rock pools, the waves, the horizon. But there is so much more going on underneath, hidden from view.

The sea’s surface conceals human impact as well.

Today, I am writing a eulogy to the Derwent River Seastar (or starfish), that formerly inhabited the shores near the Tasman Bridge in Hobart, Tasmania.

https://giphy.com/embed/TgFkyRxbZCTLx8OEqF

(Christy Hipsley, Museums Victoria/University of Melbourne)

It is Australia’s first documented marine animal extinction and one of the few recorded anywhere in the world.

Scientists only knew the Derwent River Seastar for about 25 years. It was first described in 1969 by Alan Dartnall, a former curator of the Tasmanian Museum and Art Gallery.

It was found on and off until the early 1990s but scientists noted a decline in numbers. Targeted surveys in 1993 and 2010 failed to find a single individual.

file 20180918 158240 1ix0smp(Blair Patulo, Museums Victoria)

It was listed as critically endangered by the Tasmanian and Australian governments. But now, like a long-lost missing person, it is time to call it: the Derwent River Seastar appears extinct.

It is actually quite hard to document the extinction of marine animals.

There is always hope that it will turn up in some unusual spot, somewhere in that hidden world. Australia has an ambitious plan to create high-resolution maps of 50 percent of our marine environment by 2025.

This is a formidable task. But it is a reflection of our lack of knowledge about the oceans that, 20 years after the launch of Google Maps and despite an enormous effort in the interim, much of Australia’s seafloor in 2025 will be still largely known from the occasional 19th-century depth sounding, or imprecise gravity measurements from satellites.

We do notice when big animals go. There used to be a gigantic dugong-like creature called Steller’s Sea Cow, which lived in the North Pacific Ocean until it was hunted to oblivion by 1768. There is no mistaking that loss.

file 20180918 158234 sqfldo

But the vast majority of the estimated 1 million to 2 million marine animals are invertebrates, animals without backbones such as shells, crabs, corals and seastars. We just don’t monitor those enough to observe their decline.

We noticed the Derwent River Seastar because it was only found at a few sites near a major city. Its story is intertwined with the usual developments that happen near many large ports.

The Derwent River became silty and was at times heavily polluted by industrial and residential waste. The construction of the Tasman Bridge in the early 1960s cannot have helped.

From the 1920s a series of marine pests were accidentally introduced by live oysters imported from New Zealand, or by hitching a ride on ships. Some of these pests are now abundant in southeast Tasmanian waters and eat or compete with local species.

The Derwent River Seastar has been a bit of an enigma. From the start, it was mistakenly classified as belonging to group of seastars (poranids) otherwise known from deep or polar habitats.

Some people wondered whether it was an introduced species as well, one that couldn’t cope with the Derwent environment.

However, we used a CT scanner at the School of Earth Sciences, University of Melbourne, to look at the internal skeleton of one of the few museum specimens.

Sure enough, it has internal struts to strengthen the body, which are characteristic of a different group of seastars (asterinids) that have adapted to coastal environments and are sometimes restricted to very small areas.

Below is a CT scan showing the internal structure of the seastar.

https://giphy.com/embed/3ksOMV7xcoVKhOXVE2

(Christy Hipsley, Museums Victoria/University of Melbourne)

Is this seastar like a canary in a coal mine, a warning of a wave of marine extinctions? Sea levels are rising with global warming, and that is going to be a big problem for life adapted to living along the shoreline.

Mangroves, salt marsh, seagrass beds, mud flats, beaches and rock platforms only form at specific water depths. They are going to need to follow rising sea levels and reform higher up the shoreline.

Coastal life can take hundreds to thousands of years to adjust to these sorts of changes. But in many places we don’t have a natural environment anymore.

Humans will increasingly protect coastal property by building seawalls and other infrastructure, especially around towns and bays. This will mean far less space for marine animals and plants.

We need to start planning new places for our shore life to go – areas they can migrate to with rising sea levels. Otherwise, the Derwent River Seastar won’t be the last human-induced extinction from these environments.

Scientists Want to Align Your Internal Clock Because Timing Is Everything


internal clock

In life, timing is everything.

Your body’s internal clock — the circadian rhythm — regulates an enormous variety of processes: when you sleep and wake, when you’re hungry, when you’re most productive. Given its palpable effect on so much of our lives, it’s not surprising that it has an enormous impact on our health as well. Researchers have linked circadian health to the risk of diabetes, cardiovascular disease, and neurodegeneration. It’s also known that the timing of meals and medicines can influence how they’re metabolized.

The ability to measure one’s internal clock is vital to improving health and personalizing medicine. It could be used to predict who is at risk for disease and track recovery from injuries. It can also be used to time the delivery of chemotherapy and blood pressure and other drugs so that they have the optimum effect at lower doses, minimizing the risk of side effects.

However, reading one’s internal clock precisely enough remains a major challenge in sleep and circadian health. The current approach requires taking hourly samples of blood melatonin — the hormone that controls sleep — during day and night, which is expensive and extremely burdensome for the patient. This makes it impossible to incorporate into routine clinical evaluations.

My colleagues and I wanted to obtain precise measurements of internal time without the need for burdensome serial sampling. I’m a computational biologist with a passion for using mathematical and computational algorithms to make sense of complex data. My collaborators, Phyllis Zee and Ravi Allada, are world-renowned experts in sleep medicine and circadian biology. Working together, we designed a simple blood test to read a person’s internal clock.

Listening to the Music of Cells

The circadian rhythm is present in every single cell of your body, guided by the central clock that resides in the suprachiasmatic nucleus region of the brain. Like the secondary clocks in an old factory, these so-called “peripheral” clocks are synchronized to the master clock in your brain, but also tick forward on their owneven in petri dishes!

Your cells keep time through a network of core clock genes that interact in a feedback loop: When one gene turns on, its activity causes another molecule to turn it back down, and this competition results in an ebb and flow of gene activation within a 24-hour cycle. These genes in turn regulate the activity of other genes, which also oscillate over the course of the day. This mechanism of periodic gene activation orchestrates biological processes across cells and tissues, allowing them to take place in synchrony at specific times of day.

The circadian rhythm orchestrates many biological processes, including digestion, immune function, and blood pressure, all of which rise and fall at specific times of the day. Misregulation of the circadian rhythm can have adverse effects on metabolism, cognitive function, and cardiovascular health.
The circadian rhythm orchestrates many biological processes, including digestion, immune function, and blood pressure, all of which rise and fall at specific times of the day. Misregulation of the circadian rhythm can have adverse effects on metabolism, cognitive function, and cardiovascular health.

The discovery of the core clock genes is so fundamental to our understanding of how biological functions are orchestrated that it was recognized by the Nobel Committee last year. Jeffrey C. Hall, Michael Rosbash, and Michael W. Young together won the 2017 Nobel Prize in Physiology or Medicine “for their discoveries of molecular mechanisms controlling the circadian rhythm.” Other researchers have noted that as many as 40 percent of all other genes respond to the circadian rhythm, changing their activity over the course of the day as well.

This gave us an idea: Perhaps we could use the activity levels of a set of genes in the blood to deduce a person’s internal time — the time your body thinks it is, regardless of what the clock on the wall says. Many of us have had the experience of feeling “out of sync” with our environments — of feeling like it’s 5:00 a.m. even though our alarm insists it’s already 7:00 a.m. That can be a result of our activities being out of sync with our internal clock — the clock on the wall isn’t always a good indication of what time it is for you personally. Knowing what a profound impact one’s internal clock can have on biology and health, we were inspired to try to gauge gene activity to measure the precise internal time in an individual’s body. We developed TimeSignature: a sophisticated computational algorithm that could measure a person’s internal clock from gene expression using two simple blood draws.

Designing a Robust Test

To achieve our goals, TimeSignature had to be easy (measuring a minimal number of genes in just a couple blood draws), highly accurate, and — most importantly — robust. That is, it should provide just as accurate a measure of your intrinsic physiological time regardless of whether you’d gotten a good night’s sleep, recently returned from an overseas vacation, or were up all night with a new baby. And it needed to work not just in our labs but in labs across the country and around the world.

A mismatch between our internal time and our daily activities may raise the risk of disease.
A mismatch between our internal time and our daily activities may raise the risk of disease.

To develop the gene signature biomarker, we collected tens of thousands of measurements every two hours from a group of healthy adult volunteers. These measurements indicated how active each gene was in the blood of each person during the course of the day. We also used published data from three other studies that had collected similar measurements. We then developed a new machine learning algorithm, called TimeSignature, that could computationally search through this data to pull out a small set of biomarkers that would reveal the time of day. A set of 41 genes was identified as being the best markers.

Surprisingly, not all the TimeSignature genes are part of the known “core clock” circuit — many of them are genes for other biological functions, such as your immune system, that are driven by the clock to fluctuate over the day. This underscores how important circadian control is — its effect on other biological processes is so strong that we can use those processes to monitor the clock!

Using data from a small subset of the patients from one of the public studies, we trained the TimeSignature machine to predict the time of day based on the activity of those 41 genes. (Data from the other patients was kept separate for testing our method.) Based on the training data, TimeSignature was able to “learn” how different patterns of gene activity correlate with different times of day. Having learned those patterns, TimeSignature can then analyze the activity of these genes in combination to work out the time that your body thinks it is. For example, although it might be 7 a.m. outside, the gene activity in your blood might correspond to the 5 a.m. pattern, indicating that it’s still 5 a.m. in your body.

Many genes peak in activity at different times of day. This set of 41 genes, each shown as a different color, shows a robust wave of circadian expression. By monitoring the level of each gene relative to the others, the TimeSignature algorithm learns to ‘read’ your body’s internal clock.
Many genes peak in activity at different times of day. This set of 41 genes, each shown as a different color, shows a robust wave of circadian expression. By monitoring the level of each gene relative to the others, the TimeSignature algorithm learns to ‘read’ your body’s internal clock. 

We then tested our TimeSignature algorithm by applying it to the remaining data, and demonstrated that it was highly accurate: We were able to deduce a person’s internal time to within 1.5 hours. We also demonstrated our algorithm works on data collected in different labs around the world, suggesting it could be easily adopted. We were also able to demonstrate that our TimeSignature test could detect a person’s intrinsic circadian rhythm with high accuracy, even if they were sleep-deprived or jet-lagged.

Harmonizing Health With TimeSignature

By making circadian rhythms easy to measure, TimeSignature opens up a wide range of possibilities for integrating time into personalized medicine. Although the importance of circadian rhythms to health has been noted, we have really only scratched the surface when it comes to understanding how they work. With TimeSignature, researchers can now easily include highly accurate measures of internal time in their studies, incorporating this vital measurement using just two simple blood draws. TimeSignature enables scientists to investigate how the physiological clock impacts the risk of various diseases, the efficacy of new drugs, the best times to study or exercise, and more.

Of course, there’s still a lot of work to be done. While we know that circadian misalignment is a risk factor for disease, we don’t yet know how much misalignment is bad for you. TimeSignature enables further research to quantify the precise relationships between circadian rhythms and disease. By comparing the TimeSignatures of people with and without disease, we can investigate how a disrupted clock correlates with disease and predict who is at risk.

Down the road, we envision that TimeSignature will make its way into your doctor’s office, where your circadian health could be monitored just as quickly, easily, and accurately as a cholesterol test. Many drugs, for example, have optimal times for dosing, but the best time for you to take your blood pressure medicine or chemotherapy may differ from somebody else.

Previously, there was no clinically feasible way to measure this, but TimeSignature makes it possible for your doctor to do a simple blood test, analyze the activity of 41 genes, and recommend the time that would give you the most effective benefits. We also know that circadian misalignment — when your body’s clock is out of sync with the external time — is a treatable risk factor for cognitive decline; with TimeSignature, we could predict who is at risk, and potentially intervene to align their clocks.

Sharks love jazz but are stumped by classical, say scientists


A study at Macquarie University in Sydney found that sharks could recognise jazz – if there was food on offer

A Port Jackson shark, the kind used in the jazz study.
Fluke Ellington … a Port Jackson shark, the kind used in the jazz study.

Researchers at Sydney’s Macquarie University have discovered that sharks can recognise jazz music.

In a paper published in Animal Cognition, the researchers, led by Catarina Vila Pouca, trained juvenile Port Jackson sharks to swim over to where jazz was playing, to receive food. It has been thought that sharks have learned to associate the sound of a boat engine with food, because food is often thrown from tourist boats to attract sharks to cage-diving expeditions – the study shows that they can learn these associations quickly.

The test was made more complex with the addition of classical music – this confused the sharks, who couldn’t differentiate between jazz and classical. “It was obvious that the sharks knew that they had to do something when the classical music was played, but they couldn’t figure out that they had to go to a different location,” said researcher Culum Brown. “The task is harder than it sounds, because the sharks had to learn that different locations were associated with a particular genre of music, which was then paired with a food reward. Perhaps with more training, they would have figured it out.”

Vila Pouca added: “Sharks are generally underestimated when it comes to learning abilities – most people see them as mindless, instinctive animals. However, they have really big brains and are obviously much smarter than we give them credit for.” She said that the evidence would hopefully prompt more conservation work.

 

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