The Australian lungfish has the largest genome of any animal so far sequenced. Siegfried Schloissnig at the Research Institute of Molecular Pathology in Austria and his colleagues have found that the lungfish’s genome is 43 billion base pairs long, which is around 14 times larger than the human genome.

Its genome is 30 per cent larger than that of the previous record-holder: the axolotl, a Mexican amphibian that the team sequenced in 2018. The researchers used high-powered computer sequencers to piece together the lungfish genome. To account for inherent errors that the sequencers introduce, they used multiple copies of the genome, each fragmented into small pieces of DNA. After all the fragments were sequenced, the team used algorithms to reassemble the pieces into a complete genome.

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New research finds that a previously known gene variant may predispose individuals to perceive emotional events — especially negative ones — more vividly than others.

The new findings are published in Psychological Science, a journal of the Association for Psychological Science.

A high-precision, three-dimensional survey of 21 different species of trees has revealed an as-yet unknown cycle of subtle canopy movement during the night. Such ‘sleep cycles’ differed from one species to another. Detection of anomalies in overnight movement could become a future diagnostic tool to reveal stress or disease in crops.

One of the most important processes sustaining life on Earth is the transport of water from the ground and into the leaves, where photosynthesis occurs. The process has fascinated scientists for centuries, and is still debated in plant physiology. Scientists generally agree that water transport is driven by light, and consequently occurs in 24-hour cycles.

Overnight movement of leaves is well known among tree species of the legume family, but it was only recently discovered that some other trees also lower their branches by up to 10 centimeters at night and then back in the morning. These branch movements are slow and subtle, and are difficult to identify with the naked eye at night. However, terrestrial laser scanning, a 3-D surveying technique developed for precision mapping of buildings, makes it possible to measure the exact position of branches and leaves. This technique was recently used to demonstrate movements in the branches of birch trees under field conditions.

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I’ve been thinking about Petri nets a lot. Around 2010, I got excited about using them to describe chemical reactions, population dynamics and more, using ideas taken from quantum physics. Then I started working with my student Blake Pollard on ‘open’ Petri nets, which you can glue together to form larger Petri nets. Blake and I focused on their applications to chemistry, but later my student Jade Master and I applied them to computer science and brought in some new math. I was delighted when Evan Patterson and Micah Halter used all this math, along with ideas of Joachim Kock, to develop software for rapidly assembling models of COVID-19.

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The first talk I ever gave was at a conference in 1988. (This isn’t the one that went wrong.) I spoke on Constrained maximum entropy methods in an image reconstruction problem. The conference was in England, and I learned about it from a wall poster. They had travel funding for students. I sent in my abstract, and they liked it. All excited, I walked over to a travel agent office, reserved a round-trip to London, walked over to the bank, withdrew $300, and walked back to the travel agent to buy a ticket. Then I went to the Coop and spent another $100 or so on a suit. When I was preparing my talk, Hal Stern gave me some excellent advice. He said, don’t try to impress them or blow them away. Just explain what you did and say why you think it’s interesting. I flew to London and took the bus to Cambridge and went to the conference. I was the only statistician there so I ended up being the statistics expert. My talk was supposed to be 15 minutes long and was scheduled for the session before lunch on the last day. By the time my turn came up, the session was already running 20 minutes late. My talk went OK but I think that most of the audience was eager for lunch by then. (Recall this research finding.)…

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The loss of a father due to death, divorce or jail is associated with children having shorter caps on the ends of their chromosomes, according to a study that points to a possible biological explanation for health problems often encountered by kids with absent dads.

The protective caps known as telomeres shrink with age, and are also thought to erode with extreme stress.

At age 9, kids who had lost a father had 14 percent shorter telomeres than children whose dad was still involved in their lives, researchers report in Pediatrics. Death had the biggest impact, and the association was stronger for boys than for girls.

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Scientists have identified the presence of a non-tobacco plant in ancient Maya drug containers for the first time.

The Washington State University researchers detected Mexican marigold (Tagetes lucida) in residues taken from 14 miniature Maya ceramic vessels.

Originally buried more than 1,000 years ago on Mexico’s Yucatán peninsula, the vessels also contain chemical traces present in two types of dried and cured tobacco, Nicotiana tabacum and N. rustica. The research team, led by anthropology postdoc Mario Zimmermann, thinks the Mexican marigold was mixed with the tobacco to make smoking more enjoyable.

The discovery of the vessels’ contents paints a clearer picture of ancient Maya drug use practices. The research, which was published today in Scientific Reports, also paves the way for future studies investigating other types of psychoactive and non-psychoactive plants that were smoked, chewed, or snuffed among the Maya and other pre-Colombian societies.

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In previous posts I said that the extent to which “Fund people” works will depend on the distribution of scientific talent. Think about the following situation: Imagine that only a handful of scientists at every point in time are able to –if given the time and means–lead revolutions on par with the work of Darwin, Einstein, or Galileo (This is an extreme case admittedly because most of science does not look like this; most of science is more incremental and less memorable). I recently found two authors that believe something like this,

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We review the literature about reaching agreement in quantum networks, also called quantum consensus. After a brief introduction to the key feature of quantum computing, allowing the reader with no quantum theory background to have minimal tools to understand, we report a formal definition of quantum consensus and the protocols proposed. Proposals are classified according to the quantum feature used to achieve agreement.

Identical twins are not as identical as previously assumed, according to a study published today (January 7) in Nature Genetics. Rather than having exactly the same DNA sequences, twins start accumulating genetic variation from the earliest stages of development, researchers at Iceland-based company deCODE genetics found, meaning that one twin harbors variants that aren’t present in the other.

Also known as monozygotic twins because they develop from a single fertilized egg, identical twins have long been central to research on the relative effects of genes and environment—aka “nature versus nurture.” Although everyone accumulates some genetic mutations during their lifetime, the differences in identical twins were assumed to be minimal, particularly when twins are young, allowing researchers to study how different environments influence the development of people with the same genotype.

The new study focuses specifically on mutations that occur as or before embryos form from the mass of cells inside the blastocyst, a structure that implants in the uterine wall. During this stage of development, this inner cell mass can split to form two separately developing embryos.

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In this article we advance a cutting-edge methodology for the study of the dynamics of plant movements of nutation. Our approach, unlike customary kinematic analyses of shape, period, or amplitude, is based on three typical signatures of adaptively controlled processes and motions, as reported in the biological and behavioral dynamics literature: harmonicity, predictability, and complexity. We illustrate the application of a dynamical methodology to the bending movements of shoots of common beans (Phaseolus vulgaris L.) in two conditions: with and without a support to climb onto. The results herewith reported support the hypothesis that patterns of nutation are influenced by the presence of a support to climb in their vicinity. The methodology is in principle applicable to a whole range of plant movements.

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A pair of physicists from the US and Canada took a closer look at some basic assumptions in quantum theory and decided unless we discovered time necessarily ran one way, measurements made to a particle could echo back in time as well as forward.

We all know quantum mechanics is weird. And part of that weirdness comes down to the fact that at a fundamental level, particles don’t act like solid billiard balls rolling down a table, but rather like a blurry cloud of possibilities shifting around the room.

This blurry cloud comes into sharp focus when we try to measure particles, meaning we can only ever see a white ball hitting a black one into the corner pocket, and never countless white balls hitting black balls into every pocket.

There is an argument among physicists over whether that cloud of maybes represents something real, or if it’s just a convenient representation.

A physicist by the name of Huw Price claimed back in 2012 that if the strange probabilities behind quantum states reflect something real, and if nothing restricts time to one direction, the black ball in that cloud of maybes could theoretically roll out of the pocket and knock the white ball…

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It’s a persistent fallacy that glass already is a liquid, spread by misinformed high school teachers and tour guides. But that’s not technically true – glass is an amorphous solid. Normally when a substance transitions from a liquid to a solid, the formerly free-flowing atoms line up into a rigid crystal formation. That’s not the case with glass though: its atoms “freeze” in their disordered state.

Or at least, that’s how it usually goes. In the new study, the researchers discovered a form of glass where the atoms exhibit a complex behavior that’s never been seen in bulk glass before. Essentially, the atoms can move but aren’t able to rotate.

The team made this discovery in a model system of colloidal suspensions. These mixtures are made up of large solid particles suspended in a fluid, making it easier for scientists to observe the physical behavior of atoms or molecules. Normally these particles are spheres, but for this experiment the team used elliptical ones so they could tell which direction they were pointing.

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We re-examine the constraints imposed by causality and unitarity on the low-energy effective field theory expansion of four-particle scattering amplitudes, exposing a hidden “totally positive” structure strikingly similar to the positive geometries associated with grassmannians and amplituhedra. This forces the infinite tower of higher-dimension operators to lie inside a new geometry we call the “EFThedron”. We initiate a systematic investigation of the boundary structure of the EFThedron, giving infinitely many linear and non-linear inequalities that must be satisfied by the EFT expansion in any theory. We illustrate the EFThedron geometry and constraints in a wide variety of examples, including new consistency conditions on the scattering amplitudes of photons and gravitons in the real world.

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A newly-designed atomic clock uses entangled atoms to keep time even more precisely than its state-of-the-art counterparts. The design could help scientists detect dark matter and study gravity’s effect on time.

Since the dawn of communication, dreams have perplexed philosophers, priests, and poets. What do dreams mean? Do they portend the future? In recent decades, dreams have come under the gaze of neuroscientists as one of the field’s central unsolved mysteries. Do they serve a more practical, functional purpose? We suggest that dream sleep exists, at least in part, to prevent the other senses from taking over the brain’s visual cortex when it goes unused. Dreams are the counterbalance against too much flexibility. Thus, although dreams have long been the subject of song and story, they may be better understood as the strange lovechild of brain plasticity and the rotation of the planet.

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Dec 29, 2020

Almost exactly twenty years ago I started writing a short article about the problems with string theory. I had been thinking about doing this for quite a while, and the timing of entering the twenty-first century seemed appropriate for evaluating something that had long been advertised as “a piece of 21st-century physics that had fallen by accident into the 20th”. The piece was done in a week or two, after which I sent it around to a group of physicists to ask for comments. The reaction was mostly positive, although at least one well-known theorist told me that publicly challenging string theorists in this way would be counter-productive.

One person who wrote back was Phil Anderson, I’ve quoted some of what he wrote to me in this posting. He suggested I send it to Gloria Lubkin at Physics Today, and evidently talked to her about it. I did do this, and after not hearing anything back for a week or two, decided to go ahead and post the article to the arXiv, where it appeared as String Theory: An Evaluation.

Rereading that article today, there’s little I would change. Its argument is even more valid now than then. The problems of the theory and how it was pursued evolved over the next twenty years in ways far worse than what I could have imagined back then. In particular, the “multiverse” argument explaining away why string theory predicts nothing is something I could not have conceived of in 2001. The tribalistic sociology that has led to a large group of people calling themselves “string theorists” when what they do has nothing to do with string theory is also something I would have thought impossible.

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This is a community for sharing and discussing the natural sciences. Sources must be linked, or attached if possible.

Created on Jun 17, 2020
By @gurlic