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- The gene’s still selfish: Dawkins’ famous idea turns 40 on
- The gene’s still selfish: Dawkins’ famous idea turns 40 on
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This week was a revolutionary week in the sciences – not because we discovered a new fundamental particle or had a new breakthrough in quantum computing – but because some of the most prominent world leaders announced an initiative which asserts that European scientific papers should be made freely available to all by 2020.
This would legally only impact research supported by public and public-private funds, which are a vast portion of the papers produced annually; however, the goal is to make all science freely available.
Ultimately, the commitment rests on three main tenets: “Sharing knowledge freely”, “open access”, and “reusing research data”.
And it would totally transform the (long questioned) paid-for subscription model that is used by many scientific journals. It would also undermine the common practice of releasing reports under embargo (a method that allows scientific journals to favour certain science communicators and members of the media to the great detriment of others). Source: Europe announces that all scientific papers should be free by 2020
In 1206, Genghis Khan, a fierce tribal chieftain from northern Mongolia, began to take over the world. The khan’s ruthless tactics and loyal horde swept across Asia.
One territory after another fell under the overwhelming force of the Mongol Empire, which would eventually stretch from the eastern shores of China. A series of successful forays in Hungary and Poland made even Europe seem within reach of conquering.
But this unstoppable wave of victories in Europe suddenly ended. Almost as soon as the Mongols set their sights set on Austria, they abruptly returned to Asia.
Historians could only guess why until now, since written accounts from the point of view of Mongol military leaders are sparse. But a new study in the journal Scientific Reports looked at a different kind of record to solve the mystery of the horde’s abrupt exit from central Europe: tree rings.
This wooden chronicle revealed that a cold and wet period set in for years, leading “to reduced pastureland and decreased mobility, as well as hampering the military effectiveness of the Mongol cavalry”, according to a press release. Source: Scientists finally know what stopped Mongol hordes from conquering Europe
Turns out we know a whole lot less about Neanderthals than we thought, because our cave-painting, tool-wielding, fire-conquering cousins were sophisticated enough to build complex subterranean structures as far back as 176,500 years ago, according to new archaeological evidence.
Deep inside a dark, underground cave 50 km from the city of Toulouse, France, researchers have uncovered the remains of six ancient structures crafted from stalagmites. The find forces us to rethink our assumptions about these archaic humans, because what they appear to have built is far beyond anything we thought they were capable of.
“Neanderthals were inventive, creative, subtle and complex,” one of the team, Jacques Jaubert from France’s Bordeaux University, told AFP. “They were not mere brutes focused on chipping away at flint tools or killing bison for food.”
The ring-shaped structures were found 300 metres deep inside Bruniquel Cave in southwest France, and one is thought to have stood almost 7 metres wide. The twisted corridors of this cave are pitch black this far from the entrance, so the Neanderthals would have had to construct everything by firelight. Source: Neanderthals built complex underground structures
Quantum mechanics is difficult to understand at the best of times, but new evidence suggests that the current standard view of how particles behave on the quantum scale could be very, very wrong.
In fact, the experiment hints that an alternative view predicted almost a century ago might have been right this whole time. And before you get too bummed about that, the good news is that, if confirmed, it would actually make quantum mechanics a whole lot simpler to understand.
Read the whole artical here: New evidence could break the standard view of quantum mechanics
As The Selfish Gene notches up 40 years in print, BBC News asked Richard Dawkins whether his most famous book is relevant today (answer: yes), whether he has any regrets about public spats over religion (no), and whether he is quitting Twitter (sort of).
“I’d so much rather talk about this than about politics.”
This, from a thinker most famous as a fearless firebrand, sounds rather incongruous. But as Prof Dawkins hunches over his laptop to dig up examples of biomorphs – the computer-generated “creatures” he conceived in the 1980s to illustrate artificial selection – it is transparently, genuinely felt.
Later, we touch on the fact that he sees public debate as a scientist’s responsibility. Right now, he wants to talk about molluscs.
“I don’t know whether you know the classic book by D’Arcy Thompson, On Growth and Form? He showed that all mollusc shells are a tube, which is enlarging as it coils around. You only need three numbers to specify a mollusc shell.”
Those three numbers can be plotted inside a cube, Prof Dawkins explains. “Evolution is then just a walk through this cube of all possible shells.”
In a computerised game he wrote in 1996, people could construct their own such walk by choosing for themselves which offspring would “breed” in successive generations of shells.
This game has now been resurrected online to mark the 20th anniversary of the book it arose from, Climbing Mount Improbable. Source: The gene’s still selfish: Dawkins’ famous idea turns 40
It took nearly a half trillion tries before researchers at The University of Texas at Austin witnessed a rare event and perhaps solved an evolutionary puzzle about how introns, non-coding sequences of DNA located within genes, multiply in a genome. The results, published today in the Proceedings of the National Academy of Sciences, address fundamental questions about the evolution of new species and could expand our understanding of gene expression and the causes of diseases such as cancer.
“Until now, the only way researchers could track the evolution of introns was through phylogenetic analysis which is examining the evolutionary relationships among sets of related organisms,” says Scott Stevens, associate professor of Molecular Biosciences. “Our work is the first experimental verification that shows how introns can be transposed into an organism.”
For a long time, scientists have known that much of the DNA within any given organism’s genome does not code for functional molecules or protein. However, recent research has found that these genetic sequences, misnamed “junk” DNA in the past, often do have functional significance.
These introns are no exception. Now known to play a role in which genes are expressed, introns are the portion of gene sequences that are removed or spliced out of RNA before genes are translated into protein. When eukaryotes first diverged from bacteria, there was a massive invasion of introns into the genome. All living eukaryotes—from yeast to mammals—share this common ancestor, and while simpler organisms like yeast have eliminated most of their introns, organisms such as mammals have considerably expanded their intron inventory. Humans have over 200,000 introns which take up about 40 percent of the genome.
In the current paper, Stevens and his co-author, Sujin Lee, a former graduate student in cellular and molecular biology at UT Austin, used a new reporter assay to directly detect the loss and gain of introns in budding yeast (Saccharomyces cerevisiae). The team tested nearly a half trillion yeast and found only two instances where an intron was added to a new gene. The proposed mechanism for this addition is a reversal of a splicing reaction.
Normally, to make proteins, RNA reads instructions from DNA, skipping the code contained in the introns. But in these two instances, the cell read the DNA in reverse and allowed the introns to make it into the RNA, thus creating a permanent genetic change. These are called intron gains, and if these accumulate over time, they can contribute to the development of new species as well as human disease.”We showed in this project that introns continue to be gained, although infrequently at any point in time,” says Stevens. ”
But can introns drive evolution? If these sequences give organisms a selective advantage and become fixed in a population, others have shown that it can be a major factor in the creation of new species.”
These evolutionary advances come at a cost, however, because diseases such as cancer correlate with the improper removal of introns from RNA. Stevens adds, “We are continuing this work to further understand how this process impacts our genetic history, our future, and the prospects of curing disease.”Source: Rare evolutionary event detected in the lab
No matter how hard they try, brain scientists and cognitive psychologists will never find a copy of Beethoven’s 5th Symphony in the brain – or copies of words, pictures, grammatical rules or any other kinds of environmental stimuli. The human brain isn’t really empty, of course. But it does not contain most of the things people think it does – not even simple things such as ‘memories’.
Our shoddy thinking about the brain has deep historical roots, but the invention of computers in the 1940s got us especially confused. For more than half a century now, psychologists, linguists, neuroscientists and other experts on human behaviour have been asserting that the human brain works like a computer.
To see how vacuous this idea is, consider the brains of babies. Thanks to evolution, human neonates, like the newborns of all other mammalian species, enter the world prepared to interact with it effectively. A baby’s vision is blurry, but it pays special attention to faces, and is quickly able to identify its mother’s. It prefers the sound of voices to non-speech sounds, and can distinguish one basic speech sound from another. We are, without doubt, built to make social connections.
A healthy newborn is also equipped with more than a dozen reflexes – ready-made reactions to certain stimuli that are important for its survival. It turns its head in the direction of something that brushes its cheek and then sucks whatever enters its mouth. It holds its breath when submerged in water. It grasps things placed in its hands so strongly it can nearly support its own weight. Perhaps most important, newborns come equipped with powerful learning mechanisms that allow them to changerapidly so they can interact increasingly effectively with their world, even if that world is unlike the one their distant ancestors faced.
Senses, reflexes and learning mechanisms – this is what we start with, and it is quite a lot, when you think about it. If we lacked any of these capabilities at birth, we would probably have trouble surviving.
But here is what we are not born with: information, data, rules, software, knowledge, lexicons, representations, algorithms, programs, models, memories, images, processors, subroutines, encoders, decoders, symbols, or buffers – design elements that allow digital computers to behave somewhat intelligently. Not only are we not born with such things, we also don’t develop them – ever.
We don’t store words or the rules that tell us how to manipulate them. We don’t create representations of visual stimuli, store them in a short-term memory buffer, and then transfer the representation into a long-term memory device. We don’t retrieve information or images or words from memory registers. Computers do all of these things, but organisms do not. Source: Your brain does not process information and it is not a computer
Life was already organising itself into large communities of cells more than a billion years ago, according to evidence from China. The centimetre-scale life forms were preserved in mudstones from the Yanshan area in the country’s north and are dated to 1.56 billion years ago.
Fossils big enough to be seen by the naked eye became common between 635 and 541 million years ago. But the latest specimens are more than twice that age.
The findings by a Chinese-American team of researchers appear in the journal Nature Communications. The mysterious organisms from the Gaoyuzhuang rock formation appear to belong to the branch of life known as the eukaryotes, which today includes everything from single-celled amoebae to plants, fungi and animals.
The sea-dwelling life forms probably lived on the shelf areas of ancient oceans and bear a superficial resemblance to algae. They also appear to have used photosynthesis, the process by which plants, some bacteria and other simple organisms convert sunlight into chemical energy. Source: Life forms ‘went large’ a billion years ago
A newly discovered species of diatom, a microscopic creature that is key to the health of the planet, is named after a Lancaster professor.
Professor Philip Barker has dedicated much of his working life to the study of diatoms, exploring what these microscopic phytoplankton can tell us about climate change and water quality.
Now his efforts have have been rewarded, with a recently identified diatom species being called Afrocymbella barkeri in his honour.
Afrocymbella barkeri was identified by Belgian taxonomists Christine Cocquyt and Els Ryken in Lake Challa, a 92-metre deep crater lake at the foot of Mount Kilimanjaro on the border of Kenya and Tanzania. Phil has spent many years there doing research into long term climate change.
The paper identifying the diatom states that: “The name barkeri is in honour of Prof. Philip A. Barker (Lancaster Environment Centre, Lancaster University, United Kingdom), a diatomist with a long-term research interest in the palaeolimnology of East Africa’s lakes, including Lake Challa.”
Phil may have published more than 100 peer reviewed papers and chapters, and had many accolades for his research, but having a diatom named after him is something special. “!f something is named after you, then it is there for ever,” he said. Source: New diatom species identified
Coloured X-ray of the arteries (red) of a human neck and shoulder. The bones (purple) are also seen on the X-ray, aiding identification of the arteries. The ribs of the chest (across bottom) are seen from the front. The head (upper right) has been turned to one side to expose the right-hand side of the neck and its carotid arteries (internal and external). These bring oxygenated blood to the head. The right arm (centre left) has been raised to show how the subclavian artery passes under the collar bone (clavicle) and into the arm. The arteries carry oxygenated blood from the heart (not seen). The arteries have been highlighted by arteriography: injecting them with a radio-opaque medium to absorb the X-rays. Credits: CNRI/Science Photo Library & Daily Anatomy
Remembering Sir Harry Kroto, who was awarded the Nobel Prize for the discovery of C60…. a man with a passion for science and a mischievous streak!
A five-megabyte hard drive being shipped by IBM in 1956. Oh, how far we’ve come. Image: lord_kmz/Reddit
If you’ve ever considered getting a tattoo but have been put off by its permanence – who knows how you’ll feel about that “E = mc2” face tattoo in 10 year’s time? – then a new startup called Ephemeral has you covered. The fledgling company, run by a team of New York University graduates, is developing a special kind of tattoo ink that disappears in just one year.
Basically, after a year has passed, the tattoo starts to fade, and you have the opportunity to either adapt the original design or simply get rid of it. Oh, and current tattoo artists won’t need specialised equipment to use the new ink, so if this stuff makes it to market, it shouldn’t be too hard to find.
So here’s the science behind it: a standard tattoo remains permanent because the dye molecules are too big for your body’s immune system to clear them up, as Brian Heater explains at TechCrunch.
The ink developed by Ephemeral uses smaller molecules that can be ‘flushed out’ by a special removal solution, which is tattooed over the temporary tat after a year’s use. Before now, laser surgery was the only way to fully remove a tattoo – a process that’s expensive, lengthy, and painful. Basically, laser tattoo removal works by pulverising the ink particles trapped in your skin, allowing your body to carry them away to get pooped out. Yes, pooped out.
As ScienceAlert’s Josh Hrala explained to Modern Notion last year: “After your white blood cells obtain the ink particles, they take them to your liver, which sends it out of your body when you poop – the same way your body gets rid of all of its waste. In essence, the laser only plays a very small role in the whole ordeal because it just aids your body’s natural response to contamination.”
Silicon Valley runs on failure. Its unofficial motto, after all, is “Fail fast, fail often,” and it is the region that gave birth to FailCon, where stories of entrepreneurial failure are badges of honor.
That’s more than just cute marketing. As the New Yorker’s James Surowiecki has written, “In the delusions of entrepreneurs are the seeds of technological progress.” Failures, in other words, are not only acceptable, but beneficial.
Scientists would do well to take that message to heart. For proof, look no further than a recent study that suggests researchers, with the help of computer algorithms, can find nuggets of scientific insight in the failed experiments that gather dust in forgotten lab notebooks.
In a new article in Nature, a team of chemists at Haverford College and Purdue University described how they used a computer to outperform scientists at predicting ways to make crystals. Their algorithm considered not only previously successful experiments but those that had failed — what they call “dark reactions” because the data never become public. Not only did the software work, it worked better than chemists with years of experience in the field at coming up with likely molecules.
The Haverford/Purdue group has created a website, the Dark Reactions Project, to encourage other chemists to share their own failures. “The planning and development of such tools is essential if we are to eventually make full use of our ‘failed’ experiments,” Richard Cooper, a crystallographer at the University of Oxford, in England, tells Nature in a story accompanying the paper. Source StatNews
Mitochondria are membrane-bound components within cells that are often described as the cells’ powerhouses. They’ve long been considered as essential components for life in eukaryotes, the group including plants, fungi, animals, and unicellular protists, if for no other reason than that every known eukaryote had them. But researchers reporting in the Cell Press journal Current Biology on May 12, 2016 now challenge this notion. They’ve discovered a eukaryote that contains absolutely no trace of mitochondria at all.
“In low-oxygen environments, eukaryotes often possess a reduced form of the mitochondrion, but it was believed that some of the mitochondrial functions are so essential that these organelles are indispensable for their life,” says Anna Karnkowska, a former post-doctoral fellow at Charles University in Prague who is now at the University of British Columbia in Vancouver, Canada. “We have characterized a eukaryotic microbe which indeed possesses no mitochondrion at all.”
Organisms from the genus Monocercomonoides have been recognized for more than 80 years. They are related to the human pathogens Giardia and Trichomonas, all of which belong to a group known as Metamonada, which lives exclusively in low-oxygen environments.
In the new study, Karnkowska and Vladimir Hampl at Charles University in Prague and BIOCEV, along with colleagues from the Czech Republic and Canada, sequenced the Monocercomonoides genome. They were surprised to find that this organism lacks all mitochondrial proteins.
Monocercomonoides seems to have gotten by without mitochondria thanks to a cytosolic sulfur mobilization system (SUF) that they acquired from bacteria and that appears to substitute for essential mitochondrial functions. Through a unique combination of events including the loss of many mitochondrial functions and the acquisition of this essential machinery from prokaryotes, “this organism has evolved beyond the known limits that biologists circumscribed,” Karnkowska says. Source: Surprise! This eukaryote completely lacks mitochondria