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Tuesday, February 4, 2014

A Beautiful Map of Global Ocean Currents

A Beautiful Map of Global Ocean Currents
A fitting addition to his interactive global windmap, Cameron Beccario's interactive map of Earth's ocean currents takes near-realtime data-mapping to the seas – and the results are mesmerizing.
If the previous incarnation of Beccario's weather-modeling applet bore a passing similarity to NASA's spellbinding Perpetual Ocean video, this newest version resembles it even more. As with the Agency's visualization, Beccario's earth portrays the surface currents that flow and twist their way across Earth's surface. The key difference between earth and Perpetual Ocean, however, is that the latter depicts currents between June 2005 and December 2007, whereas the former depicts them in near real-time. As with similar weather-maps, earth relies on data compiled by NOAA's Global Forecast System to update its global wind patterns every three hours, and OSCAR Earth & Space Research to update its ocean surface current patterns every five days.
A Beautiful Map of Global Ocean Currents
The ability to select from eight different map projections when visualizing the data adds an extra layer to the experience. Go try it out for yourself!

Why Bill Nye the Science Guy is trying to reason with America's creationists

Tonight's debate between Nye and the head of the Creation Museum is yet another effort to ensure US children learn science
 
theguardian.com,
 
Bill Nye Sciene Guy
Bill Nye, aka the 'Science Guy', will debate Ken Ham, head of the Creation Museum, on 4 February 2014. Photograph: Guardian

Tonight Bill Nye the Science Guy will debate Ken Ham, president of the Creation Museum. Ham believes the earth was created 6,000 years ago and fossils were formed in Noah's flood. Nye accepts the mountains of evidence which support the theory of evolution, the best explanation scientists have for the diversity of life on the planet. It's a debate between reality and someone who is completely detached from reality.

Nye has been criticized for agreeing to this debate. What Nye is doing gives creationists "the oxygen of respectability in the world of real science", according to Richard Dawkins. Ham is relishing the opportunity to misinform the public and pretend that real scientists take his work seriously.
In science, debates aren't what decide which explanations best describe natural phenomena. Instead, scientists set up controlled experiments and test and retest hypotheses. As we've continued to conduct experiments about evolution, the evidence has mounted to unquestionable levels. Creationism doesn't meet basic standards in the "world of real science" and a debate will give it false legitimacy in the eyes of the public.

Unfortunately, with or without the Nye debate, much of the American population already sees creationism as a scientifically valid alternative to evolution. There isn't a single legitimate research lab in the country studying biblical creation or Noah's flood, but creationism is still influencing public policy and is still being taught in public school science classes.

According to Gallup, nearly half of the country rejects evolution. Forty-Six percent of Americans believe humans were created in their present form, by God, in the last 10,000 years. Over the past 30 years, belief in creationism has remained relatively stable, despite creationism's repeated court losses.

That's why Nye agreed to this debate, he wants to raise awareness that "this belief [in creationism] is still among us" and it is a political issue that cannot be ignored. Creationism still "finds its way onto school boards in the United States".

This debate isn't about the world of real science. In the scientific community, the support for the theory of evolution is unquestionable. Instead, this is about alerting the whole population that creationism is still an issue and that teaching it to students is a moral wrong.

In September, I heard Nye speak and he explained that he had spoken out because he had a moral responsibility to oppose the teaching of creationism. He's said creationism is "completely inconsistent with everything we observe in the universe" and miseducating a generation of students by teaching creationism will harm our country because "we need scientifically literate voters and tax payers for the future".

Nye is doing his part by raising awareness of the issue, but as citizens, we all have a moral responsibility to speak out and make sure the next generation of students is scientifically literate. We can do that by fighting back against policy that would allow creationism into public school science classes.

My home state of Louisiana has a creationism law, the misnamed and misguided Louisiana Science Education Act. This law allows creationism to be snuck into public school science classrooms through a loophole: teachers can bring in unregulated supplemental materials to "critique" evolution and, according to state Senator Ben Nevers, who sponsored the law, it was meant to allow the "scientific data related to creationism should be discussed when dealing with Darwin's theory".
This legislation that allows "critiques" to be snuck into public school classes is the modern day strategy of creationists. Federal courts, including the Supreme Court in Edwards v Aguillard, and Judge John Jones III in Kitzmiller v Dover, have invalidated the teaching of creationism or if its offshoot, intelligent design creationism in public schools. Creationists are now resorting to stealth and this type of stealth legislation is what we must fight against today.

Tennessee has a law based off Louisiana's that allows creationism to be snuck into the classroom, and each year we see dozens of copycat bills introduced across the country to attack the teaching of evolution. Already in 2014, there have been five bills that promote creationism or attack evolution in four different states (Virginia, Oklahoma, Missouri, and South Dakota). Some bills aren't even as clever as Louisiana's; In South Dakota, 13 legislators signed onto a flagrantly unconstitutional bill to "prohibit schools from preventing the instruction of intelligent design".

Texas also has problems with creationism. The largest charter program in the state, Responsive Education Solutions, is teaching creationism. They describe evolution as "dogma", call the fossil record "sketchy", and explain that supernatural creation is an equally valid explanation of life on earth and a competing theory among scientists. Facing challenges by watchdog organizations, the CEO of Responsive Education Solutions, Chuck Cook, explained that he wasn't violating any laws, because Texas science standards call for teaching "all sides" of evolution. The Texas Education Agency appears to agree with him, although it is "voluntarily" doing a review now.

In schools across America, creationism remains a problem. According to a report in Science magazine (pdf), 13% of public school biology teachers are teaching creationism instead of evolution and another 60% are avoiding endorsing either.

This harms our students and our country. We need our kids educated about evolution and the scientific method, so that they can be scientifically literate citizens and make the discoveries that will fuel our economy in the years to come. That's why I'm with Bill Nye. Let's raise awareness that there is a real issue with teaching creationism in American schools. Let's fight back.

Monday, February 3, 2014

A nested phylogenetic reconstruction approach provides scalable resolution in the eukaryotic Tree Of Life

 

Author and article information

Abstract

 
Assembling the Tree Of Life (TOL) faces the pressing challenge of incorporating a rapidly growing number of sequenced genomes. This problem is exacerbated by the fact that different sets of genes are informative at different evolutionary scales. Here, we present a novel phylogenetic approach ( N ested P hylogenetic R econstruction) in which each tree node is optimized based on the genes shared at that taxonomic level. We apply such procedure to reconstruct a 216-species eukaryotic TOL and compare it with a standard concatenation-based approach. The resulting topology is highly accurate, and reveals general trends such as the relationship between branch lengths and genome content in eukaryotes. The approach lends itself to continuous update, and we show this by adding 29 and 173 newly-sequenced species in two consecutive steps. The proposed approach, which has been implemented in a fully-automated pipeline, enables the reconstruction and continuous update of highly-resolved phylogenies of sequenced organisms.
Cite this as
Huerta-Cepas J, Marcet-Houben M, Gabaldón T. (2014) A nested phylogenetic reconstruction approach provides scalable resolution in the eukaryotic Tree Of Life. PeerJ PrePrints 2:e223v1
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Sections

 

Supplemental Information

Schematic representation of the nested phylogenetic reconstruction approach.

Schematic representation of the nested phylogenetic reconstruction approach. First, a starting unrooted tree is reconstructed including all species (iteration 0, red node in panel A) and using a Gene Concatenation Methodology (GCM, panel C). GCM includes: C1) searching for groups of one-to-one orthologs (Ortholog Groups, OGs), C2) reconstruction of multiple sequence alignments of each OG, C3) phylogenetic reconstruction for each single OG, C4) concatenation of OG alignments, C5) species tree reconstruction based on the concatenated alignment. Secondly, the first resulting tree is split into two well supported clades, each of them defining a subset of species. GCM is then applied to each of the new sets of organisms, including four extra species as rooting anchors. As a result, two new trees are obtained (iteration 1, blue nodes in panel A). Subsequently, each of the new sub-trees is rooted using their anchor species (C6) and split into its two major clades (C7). The four resulting partitions (iteration 2, green nodes in panel A) are used to continue the same procedure until reaching a given limit for the size (number of species) in the recomputed partitions (panel B). An animation showing how the tree is re-shaped at each iteration can be seen at http://tol.cgenomics.org/TOL_animation.gif .
DOI: 10.7287/peerj.preprints.223v1/supp-1

TOL analyses I

TOL analyses I: A-B) Grey lines represent topological distance between reference trees and the TOL (A-Chordates, B-Fungi, see Figure S5). Black line represents the number of protein families used at each iteration. C) Number of NCBI taxonomic groups not recovered at each iteration.
DOI: 10.7287/peerj.preprints.223v1/supp-2

Supplementary data

Supplementary methods, figures and tables
DOI: 10.7287/peerj.preprints.223v1/supp-5

Additional Information

Competing Interests

The authors declare they have no competing interests.

Author Contributions

Jaime Huerta-Cepas conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.
Marina Marcet-Houben conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.
Toni Gabaldón conceived and designed the experiments, analyzed the data, wrote the paper, reviewed drafts of the paper.

Grant Disclosures

The following grant information was disclosed by the authors:
Spanish Ministry of Economy and Competitiveness (BIO2012-37161) and (JCI2010-07614)
The European Research Council under the European Union’s Seventh Framework Programme (FP/2007-2013)/ERC Grant agreement n. 310325.

Funding

We acknowledge funding from the Spanish Ministry of Economy and Competitiveness to TG (BIO2012-37161) and to JHC (Subprograma Juan de la Cierva: JCI2010-07614), and the European Research Council under the European Union’s Seventh Framework Programme (FP/2007-2013)/ERC Grant agreement n. 310325. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Sunday, February 2, 2014

Starving hives: Pesticides cause bees to collect 57 percent less pollen, study says

Published time: February 02, 2014 21:15                         
 
Reuters / Leonhard Foeger
Reuters / Leonhard Foeger
 

In a spin-off of their earlier study, a team of British scientists have revealed how the neurotoxic chemicals contained in agricultural neonicotinoids affect the very basic function of the honeybees – the gathering of pollen, or flower nectar.

“Pollen is the only source of protein that bees have, and it is vital for rearing their young. Collecting it is fiddly, slow work for the bees and intoxicated bees become much worse at it. Without much pollen, nests will inevitably struggle,” explained University of Sussex professor Dave Goulson, who has led the study. His comments were made in a statement released alongside the research.
Goulson’s latest paper called “Field realistic doses of pesticide imidacloprid reduce bumblebee pollen foraging efficiency” was published at the end of January in peer-reviewed journal Ecotoxicology.

The scientists exposed some of the studied bees to low doses of imidacloprid and tracked their movement with the help of electronic tags. Unexposed bees were also tracked, and each insect flying out and returning to a hive was weighed to find out the amount of pollen it gathered.

It turned out that bees exposed to the neonicotinoid brought back pollen from only 40 percent of their trips asopposed to 63 percent of useful trips which their “healthy” counterparts undertook.
Intoxicated bees cut the amount of pollen gathered by nearly a third - overall, the comparative study showed that the hives exposed to the pesticide received 57 percent less pollen.

“Even near-infinitesimal doses of these neurotoxins seem to be enough to mess up the ability of bees to gather food. Given the vital importance of bumblebees as pollinators, this is surely a cause for concern,” Hannah Feltham of the University of Stirling, another member of the research team, stated.

For bees themselves, the cut appeared to represent a sharp decline in the amount of food that the hive’s population received.

Feltham believed the study adds “another piece to the jigsaw” of why the bees have been in sharp decline lately.

Three types of controversial neonicotinoids have been temporarily banned in the European Union after the European Food Safety Authority carried out peer review of several studies showing that widely-used pesticides could harm the bees’ populations.

“It is unclear what will happen when the [EU ban] expires, as the agrochemical companies that produce them are in a legal dispute with the EU over their decision. Our new study adds to the weight of evidence for making the ban permanent,” Goulson said.

But the dispute over the role of pesticides in the so-called Colony Collapse Disorder (CCD), or mass extinction of bees, is far from being over, the reaction to the study has shown.

“This is a very important study, because it provides further detail on how bumblebee foraging is made less efficient by exposure to imidacloprid at these levels,” said Lynn Dicks, an ecologist at the University of Cambridge.

However, she then questioned the “field-realistic” dose of chemical used by the UK scientists in their study.

“The [levels in this study], particularly the pollen level, are at the upper end of what is found in the field, and likely to be higher than what bumblebee colonies are actually exposed to, because they don’t feed exclusively on oilseed rape,” Dicks argued.

Pesticide manufacturers appeared to be even more dismissive of the study’s results, comparing it to a practice of force-feeding in laboratory conditions.

“It would appear the bumble bees are essentially force-fed relatively high levels of the pesticide in sugar solutions, rather than allowing them to forage on plants treated with a seed treatment. Real field studies, such as those being initiated this autumn in the UK will give more realistic data on this subject,” Julian Little, a spokesman for major German imidacloprid producer Bayer AG has said.

Whether such open-field tests could provide a more balanced data is another issue the researchers have been arguing over. Some say that properly controlled field trials are difficult to conduct, as neonicotinoids have been widely used and bees range over wide areas to gather pollen.

Obama's Great Conflation and What it Means for You

| February 2, 2014

If there’s one dead-of-winter public spectacle even more soul-sapping and self-congratulatory than the Grammys —now taking its cues, however well-intentioned, from the late Rev. Sun Myung Moon by staging mass weddings —it’s the annual State of the Union address (due to be delivered tonight at 9 p.m. ET).

Like high school graduation speeches, State of the Union addresses are typically forgotten in real time, even as they are being delivered. Perhaps realizing his time in office is dwindling down with little to show for it, Obama will take a page from Lady Gaga at the 2011 Grammys and emerge from a translucent egg.

Alas, that’s as unlikely as his declaring an end to the federal war on pot. By all accounts, Obama will instead talk a lot about economic inequality, the increasing spread in income and wealth between the richest and poorest Americans that he calls the “defining challenge of our time” and that has only gotten worse on his watch.

If past pronouncements are any indication, the president will immediately—and erroneously—conflate growing income inequality with reduced economic mobility. As he said in a speech last December, “The problem is that alongside increased inequality, we’ve seen diminished levels of upward mobility in recent years.”

This is flatly wrong. Research published last week by economists at Harvard (Raj Chetty, Nathaniel Hendren) and Berkeley (Patrick Kline, Emmanuel Saez) concludes that rates of mobility among income quintiles have not in fact changed in decades. As the Washington Post summarized it,
“Children growing up in America today are just as likely—no more, no less—to climb the economic ladder as children born more than a half-century ago, a team of economists reported Thursday.”

While noting large variations in mobility based on geographic location and other factors (the biggest being “the fraction of single parents in the area”), Chetty, et al. conclude “a child born in the bottom fifth of the income distribution has a 7.8% chance of reaching the top fifth in the U.S. as a whole.”

That chance at going from bottom to top may strike you as unacceptably low—it does me, for sure—but the larger point is that it hasn’t changed over time. Elsewhere, the researchers show similarly constant rates of mobility for people born into middle and higher-income quintiles. Growing inequality doesn’t mean that mobility has declined, much less stopped altogether, and policies designed to level or redistribute income won’t increase mobility (if they even succeed at actually squeezing income disparities).

It’s important to stress that the new study by Chetty et al. simply confirms what other researchers have been finding for years. For instance, Scott Winship, who has worked at Pew and Brookings and now is a scholar at the Manhattan Institute, compared mobility for Americans born in the early 1960s and early 1980s. He found “that upward mobility from poverty to the middle class rose from 51 percent to 57 percent between the early-'60s cohorts and the early-'80s ones. Rather than assert that mobility has increased, I want to simply say—at this stage of my research (which is ongoing)—that it has not declined.”

As Winship told me in a 2012 interview, “You can be concerned that there’s not enough [economic] mobility or enough opportunity, but you don’t have to also believe that things are getting worse.” Winship also underscored what is clear from the past 50 years or more: It’s actually incredibly hard to figure out exactly how to increase mobility rates.

Tonight, don’t expect President Obama to cite any research showing that mobility has remained constant. Instead, expect him to echo his December speech, which was filled with lines about “a dangerous and growing inequality and lack of upward mobility that has jeopardized middle-class America’s basic bargain—that if you work hard, you have a chance to get ahead.”

From a political perspective, the erroneous but strategic conflation of inequality and mobility makes obvious sense. After all, if mobility is as alive and well as it has been in the post-war era, then the sense of urgency the president needs to sell any legislation is largely undercut. As important, constant mobility rates also make a mockery of the president’s long-preferred strategy of redistributing income from the top of the income ladder down to the lower rungs. Whether he’s talking to Joe the Plumber (god, that seems like a different planet, doesn’t it?) or addressing Congress, Obama rarely misses an opportunity to ask richer Americans to “do a little bit more.”

But as it stands, the United States already has one of the very most progressive tax systems in the world. Even the liberals at Wonkblog grant that much. The real problem, they and others note, is that rather than give direct cash payments to the less well-off, the U.S. prefers to dole out favors via tax breaks that are far more likely to benefit the wealthy and not the middle or lower classes (think mortgage-interest deductions on not just one but two homes).

Don’t expect Obama to talk seriously about reining in tax breaks or reforming entitlements that benefit the wealthy even as he says they must pay “a bit more.” In fact, don’t expect anything new from tonight’s speech. This is a president who is long on revealed truth and exceptionally short of wisdom borne out of his experience in office.

Instead, get ready for a long list of calls to maintain and increase many programs that have been in place since before Obama took office: extending unemployment benefits (without paying for them by, say, cutting defense spending), making it easier for people to buy or stay in homes whose prices are inflated by government policies, and increasing access to higher education in ways that continue to increase prices far higher than the rate of inflation. Pump more money into a broken K-12 education system whose per-pupils costs rise as results stay flat (certainly the president won’t call for giving parents and children the right to choose their own schools).

In short, expect Obama to invoke income inequality and supposed declines in upward mobility as a way of maintaining a status quo that has managed to increase inequality without affecting mobility rates.

The upside to tonight’s speech? We all will have forgotten it by the weekend, when we still might be talking about the Grammys’ mass weddings.

Nick Gillespie is the editor in chief of Reason.com and Reason TV and the co-author of The Declaration of Independents: How Libertarian Politics Can Fix What's Wrong With America, just out in paperback.

George Lakoff on Communication: "Liberals Do Everything Wrong"

Progressives have got it wrong — and if they don't start to get it right, the conservatives will maintain the upperhand.
Photo Credit: By Pop!Tech (Flickr: Pop!Tech 2008 - George Lakoff) [CC-BY-2.0 (http://creativecommons.org/licenses/by/2.0)], via Wikimedia Commons
 
"The progressive mindset is screwing up the world. The progressive mindset is guaranteeing no progress on global warming. The progressive mindset is saying, 'Yes, fracking is fine.' The progressive mindset is saying, 'Yes, genetically modified organisms are OK', when, in fact, they're horrible, and the progressive mindset doesn't know how to describe how horrible they are. There's a difference between progressive morality, which is great, and the progressive mindset, which is half OK and half awful."

George Lakoff, professor of cognitive science at the University of California, Berkeley, has been working on moral frames for 50 years. In  Communicating Our American Values and Vision, he gives this precis: "Framing is not primarily about politics or political messaging or communication. It is far more fundamental than that: frames are the mental structures that allow human beings to understand reality – and sometimes to create what we take to be reality. But frames do have an enormous bearing on politics … they structure our ideas and concepts, they shape the way we reason … For the most part, our use of frames is unconscious and automatic."

Lakoff is affable and generous. In public meetings he greets every question with: "That is an extremely good question." But he cannot keep the frustration out of his voice: the left, he argues, is losing the political argument – every year, it cedes more ground to the right, under the mistaken impression that this will bring everything closer to the centre. In fact, there is no centre: the more progressives capitulate, the more boldly the conservatives express their vision, and the further to the right the mainstream moves. The reason is that conservatives speak from an authentic moral position, and appeal to voters' values. Liberals try to argue against them using evidence; they are embarrassed by emotionality. They think that if you can just demonstrate to voters how their self-interest is served by a socially egalitarian position, that will work, and everyone will vote for them and the debate will be over. In fact, Lakoff asserts, voters don't vote for bald self-interest; self-interest fails to ignite, it inspires nothing – progressives, of all people, ought to understand this.

When he talks about the collapse of the left, he clearly doesn't mean that those parties have disintegrated: they could be in government, as the Democrats are in the US. But their vision of progressive politics is compromised and weak. So in the UK there have been racist "Go home" vans and there is an immigration bill going through parliament, unopposed, that mandates doctors, the DVLA, banks and landlords to interrogate the immigration status of us all; Hungary has vigilante groups attacking Roma, and its government recently tried to criminalise homelessness; the leaders of the Golden Dawn in Greece have only just been arrested, having been flirting with fascism since the collapse of the eurozone. We see, time and again, people in need being dehumanised, in a way that seems like a throwback to 60 or 70 years ago. Nobody could say the left was winning.

Lakoff predicted all this in Moral Politics, first published in 1996. In it, he warned that "if liberals do not concern themselves very seriously and very quickly with the unity of their own  philosophy and with morality and the family, they will not merely continue to lose elections but will as well bear responsibility for the success of conservatives in turning back the clock of progress in America."
Since then, the left has cleaved moderately well to established principles around the politics of the individual – women are equal, racism is wrong, homophobia is wrong. But everything else: a fair day's work for a fair day's pay, the essential dignity of all humans, even if they're foreign people or young people, education as a public good, the natural world as a treasure rather than an instrument of our convenience, the existence of motives besides profit, the pointlessness and poison of privatisation, the profundity, worth and purpose of pooling resources … this stuff is an embarrassment to centre-left parties, even when they're in government, let alone when they're in opposition. When unions reference these ideas, they are dismissed as dinosaurs.

This is just page one.

Breastfeeding Is Now Required By Law In The United Arab Emirates

Posted:   |  Updated: 01/30/2014 11:59 pm EST 
                                                                                                                                                                                                                                         
The Emirates' Federal National Council has passed a clause, part of their new Child Rights Law, requiring new moms to breastfeed their babies for two full years, The National reports. Now, men can sue their wives if they don't breastfeed.

According to the National, there was a "marathon debate" over the legislation, but it was ultimately decided that it is every child's right to be breastfed.
Research has found many benefits of breastfeeding for baby, from reducing the risk of obesity to better language and motor development.

However, not all new moms are able to nurse. In those instances, if a woman is prohibited by health reasons, the council will provide a wet nurse to her. It's unclear exactly how a mother's ability to breastfeed will be determined though. Carrie Murphy at Mommyish raises some additional questions about those exceptions:
Where do the wet nurses come from? Do they live with UAE women and their families? How and who determines if you need one? Who pays their salary? .... And what about formula? Will it be sold in the country? Will it be contraband? Will you need a prescription for it? Some babies actually need formula rather breast milk and some babies can’t digest anything with milk at all, either formula OR breast milk.
Council members are trying to improve rights for working moms to make the legislation more practical. But, unsurprisingly, mothers' support groups have raised issues that go beyond logistics.

Because breastfeeding is universally accepted as the healthiest option for moms and babies, new mothers already face great pressure to nurse, a Dubai-based group, Out of the Blues explains. Their purpose is to help women suffering from postnatal illness, many who have trouble breastfeeding.
In an article, also on the National, Out of the Blues writes:
New mothers are extremely vulnerable and need more support, encouragement and education. It is our opinion that, while encouraging women to breastfeed is a laudable aim, it is by supporting those who can and want to breastfeed, and not by punishing those who can’t, that we will reap the benefits we all want to see in our society.
                    
Here in the U.S., breastfeeding has never been legally required, but politicians have intervened to increase the number of babies being breastfed. In 2012, former NYC Mayor Bloomberg introduced "Latch On NYC," a program that encouraged hospitals to make it difficult for new moms to obtain formula "goody bags." Instead of traditional take-home bottles being handed out, mothers have to request it like medication, and listen to a lecture from hospital staff discouraging formula feeding, unless absolutely necessary.

At the time, the initiative faced its own backlash. Many argued that Bloomberg's tactics would make mothers feel guilty, and as blogger Lenore Skenazy put it, "suck the choice out of parenting."

Marie-Claire Bakker, a member of U.S.-based breastfeeding support group, La Leche League, has echoed those sentiments in response to the Emirates' new legislation. “At this vulnerable time, to think of criminalising a new mother who, for whatever reason, is struggling with breastfeeding is not helpful ... She needs informed support, not threats," she told the National.

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