High Octane Fuels and the Use of Ethanol in Engine Fuels

You've seen and heard the word octane with relation to cars and gasoline all your life.  Well, unless you never pumped gasoline into your car.  Ever wonder what it means?  Well, the basic answer is, the higher the octane number the more smoothly the gasoline will burn in you engine, reducing any "knocking" and increasing efficiency and mpg.

But that still doesn't tell us much.  Where does this number come from, how is it determined, and what chemical and physical properties of the fuel control the final rating?

 

A little chemistry is needed to explain this.

 

Octane rating is measured relative to a mixture of 2,2,4-trimethylpentane, CH3-C(CH3)2-CH2-CH(CH3)-CH3(an isomer of octane; it has eight carbons) and n-heptane (7 carbons in a straight line).

Arbitrarily but unsurprisingly, the octane is given an octane number of 100, while the heptane is assigned 0.  Mixtures of the two are then used in engine to access their different octane numbers.  Incidentally, there are hydrocarbons with octane numbers (not to be confused with octane numbers compounds!) higher than 100, for jet and rocket fuels (which of course cannot be allowed to knock or fail).

 

You're probably asking at this point:  why not just give me pure 2,2,4-trimethylpentane at the gas pump and "put a tiger in my tank?"  Well, they could, but there'll be another tiger in your bank account as it would be horribly expensive.  Why?  Now, finally, we get to petroleum, oil, that is pumped out of the ground.  Petroleum is not one compound; it is instead a mixture of many, many different chemicals.  The cheapest way to separate them is by "fractional" distillation, which is rather like a much more complicated and expensive kind of distillation than used to turn wine into cognac, or mash into beer or whiskey, or just to extract straight ethanol.

 

So, trying to fractionate pure 2,2,4-trimethylpentane, or any pure chemical, out of crude petroleum is so expensive that only a professional race driver could afford it, if they wanted to -- they actually use other, better, fuels.  It is far easier and cheaper to just take an entire fraction of the distillation process and use that as gasoline.  Now we come to problem two, the big problem.  This fraction, untreated, will not perform well in gasoline engines because its octane number is simply not up there enough; certainly not the 86 of the standard gasoline you buy at the pump.  So -- what might we add to the fraction to get its octane number up to 86, or 89, or 91-93 (pump standards)?

The standard method for boosting octane is to add an additive.  The first additive (that I know of) was tetraethyl lead.  Because of its spherical shape, this compound was very effect.  It did have a serious downside however.  Burning it in a car engine spewed lead and lead compounds into the atmosphere, where it could be inhaled/absorbed into bodies and do real damage there -- rather like mercuric compounds.  Thus, tetraethyl lead was gradually phased out, and the search for a safer additive was undertaken.  The first(?) of these was methyl tert-ethyl ether, or methyl - O - C(Me)3.  Like tetraethyl lead it also it is also highly spherical, making it an excellent octane booster.  Unfortunately, it ran into another problem.  It tended to seep into groundwater from tanks, poisoning water supplies.  So it too, in the end was phased out.

Nowadays we mix up to 10% corn-ethanol (drinking alcohol) into gasoline to improve its anti-knock properties.  A second reason is that, ethanol being derived from atmospheric carbon dioxide, doesn't increase the level of this important greenhouse gas, thus helping to fight anthropogenic climate warming.  Many environmentalists was to increase it to 15% -- but there are negatives to it to that cause others to rid it altogether is gasoline.  The problem is gasoline containing ethanol is especially subject to absorbing atmospheric moisture, then forming gums, solids, or two phases (a hydrocarbon phase floating on top of a water-alcohol phase), all of which shorten the lives of engines.  This is why ethanol is still not the perfect additive.  It also takes a great quantity of land to grow a sufficient quantity of corn, which drives it and other vegetables up in price.

I claim no knowledge of what a perfect additive would be.  Perhaps we will have migrated from natural gasoline to syn-fuel mixtures derived from algae/plants first, via genetic engineering (as we already are), if that is, electricity and hydrogen/LNG don't get there first.

Soil, Weedkillers And GMOs: When Numbers Don't Tell The Whole Story

by Dan Charles

January 27, 201412:08 PM   

Farm statistics: usually illuminating ... occasionally misleading.
Seth Perlman/AP

I love numbers. A picture may be worth a thousand words, but I think a good bar graph can be worth a thousand pictures.

But three times in the past few days, I've come across statistics in reputable-looking publications that made me stop and say, "Huh?"

I did some investigating so you don't have to. And indeed, the numbers don't quite tell the story that they purport to tell.

So here goes: My skeptical inquiry into statistics on herbicide use, soil erosion, and the production of fruits and nuts.

First, weedkillers (and GMOs). I was struck by this graph, which appeared in a report issued by Food and Water Watch, an environmentalist group.

Food and Water Watch

The report was published a while ago, but Tom Philpott reused it recently in a post for the website of Mother Jones magazine. The point of the chart is to show how increases in herbicide use on soybeans, corn, and cotton have gone hand-in-hand with the rise of genetically modified, herbicide-tolerant, versions of those crops.

That link seems logical, but still, farmers have been planting more corn and soybeans in recent years. How much of this soaring curve is simply because farmers have more acres to cover?

I dived into the USDA numbers, and discovered, first of all, that they're fragmentary. In recent years, the USDA didn't collect such numbers for all three crops in all years. The curve, in this case, is based on just two data points.

No matter. I took the numbers that were available and divided them by the number of acres planted. (I'm using a column chart to make clear for which years we have data.) Suddenly, the trend doesn't seem quite so dramatic.

Herbicide use on corn, soybeans and cotton — break it down per acre and it's not so dramatic.
NPR using USDA data

And how do we know if herbicide-tolerant GMOs are driving this increase? What if it's something else entirely? For comparison, I decided to look at herbicide use in wheat, since no GMO wheat is being planted. Here's a graph of herbicide use in wheat, per acre, over the same period of time.

Whoa. No GMOs here, and herbicide use went up at a faster rate. (In absolute amounts, farmers still use much less herbicide on wheat than on soybeans or corn.)

Herbicide use per acre on wheat has been going up a lot in recent years.
NPR using USDA data
 

What could be driving this increase, if not herbicide-tolerant GMOs? I called a few wheat experts in Kansas and Oregon, who mentioned some possibilities.

First, farmers are reducing their use of tillage to control weeds, in part to conserve their soil. Many are relying more on chemical weedkillers instead. Second, with grain prices high, farmers are more inclined to spend more money on anything that will boost yields.

Both of these factors are probably influencing herbicide use in corn and soybeans, too. They may be more important than the popularity of GMOs.

One thing, though, is perfectly clear. The rise of glyphosate-tolerant GMOs did persuade farmers to use much more of that particular chemical. Some argue that a new generation of GMOs that are tolerant to other weedkillers will drive further increases in herbicide use.

Maybe they will. I'll wait for the numbers.

Next up, soil erosion. Here are two maps that caught my attention. They're published in a report called the National Resources Inventory, released last week by the USDA's Natural Resources Conservation Service. (I should also tell you that the NRCS is one of my very favorite federal agencies; please don't hold this post against it.)

U.S. Dept. of Agriculture/NRCS

The dramatic shrinkage of those red and orange blotches along America's major rivers is terrific news. It shows that less topsoil is washing away today, compared with 1982.

U.S. Dept. of Agriculture/NRCS

 

Intrigued by this apparent good-news story, I called Craig Cox, in the Iowa office of the Environmental Working Group.

Cox already knew about this map. He wasn't happy about it. In his view, it obscures more than it reveals.

According to Cox, the good news is old news. Practically all of the dramatic progress in fighting soil erosion occurred 15 years ago, between 1982 and 1997. At that time, "we were on a really solid pathway to finally getting on top of this ancient enemy," he says.

Since 1997, however, progress has stalled, so the map paints an overly cheerful picture. (In fairness to NRCS, there is another, less prominent, graph in the report that does show this stagnation in anti-erosion efforts.)

In addition, there's a basic problem with these data, Cox says: "They only capture one kind of erosion," called sheet and rill erosion. This is the erosion that happens evenly across a field, and can be predicted from the amount of rain, the field's slope, its soil type and whether it is bare or covered by grass. The NRCS data are based on such predictions, and the estimated improvements since 1982 happened mainly because farmers are tilling less, and protecting more of their land with vegetation.

By contrast, no models can predict when something more catastrophic will occur; when small rivulets of water combine into larger, fast-moving streams that cut deep ditches, or gullies, into a field. According to Cox, those gullies actually carry off more soil than the predictable kinds of erosion, and they were especially bad during the storms that hit the Midwest last spring and summer.

So my straightforward good-news story about soil erosion evaporated.

Finally, there was a second surprising statistic buried deep inside that NRCS report, and I noticed it only because of a press release that the USDA put out. According to that release, the NRCS's National Resources Inventory detected "a boom in land dedicated to growing fruits, nuts and flowers, increasing from 124,800 acres in 2007 to 273,800 in 2010."

Wow! I looked at the numbers again. In fact, the boom was only in a category of production called "cultivated" fruit and nut production. Turns out, that's a tiny category, barely worth counting. It apparently refers to orchards in which there's also some tillage going on to grow a second crop.

"Uncultivated" fruit, nut, and flower production, by contrast, went from 4.7 million acres in 2007 to 4.4 million acres in 2010.

Sorry. No boom.

Has anyone noticed the biggest (I think) problem with the Biblical Ark that makes the whole story utterly impossible?  It's staring you in the face.

The ark was built on land.  Therefor, as the picture shows, it has no keel -- it's flat-bottomed.  Look at serious ocean going ships and they are all built largely in water because they have a keel:

 

The keel converts sideways force into a forward force.  This is absolutely essential for ocean going vessels, both to propel them and to keep them from floundering in rough seas.  On rivers, inland bays, along coasts -- the only types of sea going known when the ark was allegedly built -- flat bottoms were sufficient.  It was only the invention of keels, both in Europe and China, that truly allowed for ships that could traverse thousands of miles of open ocean reasonably safely.

 

So a unkeeled-vessel simply could not stay afloat on the worldwide ocean the Flood would have caused; the entire planet would essentially be one gigantic ocean.  Of course Noah nor his followers could have known that, but that doesn't matter because Yahweh gave the instructions -- wait a minute; why doesn't Yahweh know?  And how can we be here to discuss it when the ark certaintly sank with all hands (including the animals), unless by miracle the ark survives anyway, something Yahweh could have pulled off -- but then, why have the ark built in the first place?

 

Praise be until His wisdom and power.

How Prohibition Makes Heroin More Dangerous

Jacob Sullum|Feb. 4, 2014 11:21 am

Because someone famous died in Manhattan from an apparent heroin overdose on Sunday, The New York Times has a front-page story today about "a city that is awash in cheap heroin." How cheap? The Times says a bag of heroin, which typically contains about 100 milligrams, "can sell for as little as $6 on the street." Yet it also reports that the Drug Enforcement Administration's New York office last year "seized 144 kilograms of heroin...valued at roughly $43 million." Do the math ($43 million divided by 144,000 grams), and that comes out to about $300 per gram, or $30 for a 100-milligram bag—six times the retail price mentioned higher in the same story. So how did the DEA come up with that $43 million estimate? Apparently by assuming that all of the heroin it seized would have ended up in New England, where a "$6 bag in the city could fetch as much as $30 or $40."

In addition to illustrating the creative calculations behind drug warriors' "street value" estimates, the story shows how prohibition magnifies drug hazards by creating a black market where quality and purity are unpredictable:

Recently, 22 people died in and around Pittsburgh after overdosing from a batch of heroin mixed with fentanyl, a powerful opiate usually found in patches given to cancer patients. Heroin containing fentanyl, which gives a more intense but potentially more dangerous high, has begun to appear in New York City, said Kati Cornell, a spokeswoman for Bridget G. Brennan, the special narcotics prosecutor for the city. An undercover officer bought fentanyl-laced heroin on Jan. 14 from a dealer in the Bronx, she said. The dealer did not warn of the mixture, which is not apparent to the user; subsequent testing revealed it. (The patches themselves had turned up in drug seizures in the city before, she said.) 

Ultimately, users have no way to be sure what they're buying. "There's no F.D.A. approval; it's made however they decide to make it that day," Ms. Brennan said.

According to the Substance Abuse and Mental Health Services Administration, fentanyl is "roughly 50-80 times more potent than morphine," so it's the sort of ingredient you'd want to know about before snorting or injecting that white powder you just bought. This kind of thing—passing one drug off as another, delivering something much more (or less) potent than the customer expects—almost never happens in a legal market. When was the last time you bought a bottle of 80-proof whiskey that turned out to be 160 proof? The main reason liquor buyers do not have to worry about such a switcheroo is not that distillers are regulated, or even that their customers, unlike consumers in a black market, have legal recourse in case of fraud. The main reason is that legitimate businesses need to worry about their reputations if they want to keep customers coming back. It is hard to build and maintain a reputation in a black market, where brands do not mean much:

The same shipment of heroin may be packaged under several different labels, she said. "At the big mills, we'll seize 20 stamps. It's all the same."...
The Police Department on Monday said detectives were working to track down the origin of the substances Mr. Hoffman used, though a police official conceded it could be difficult to determine. "Just because it's a name brand doesn't mean that anyone has an exclusive on that name," the official said. "Ace of Spades; I would venture to say that someone else has used that name."

The takeaway: After a century of attempts to stamp out the heroin trade, the drug is cheap, plentiful, and much more dangerous than it would otherwise be.

Jacob Sullum is a senior editor at Reason magazine and a nationally syndicated columnist.

Finally, a Confession ABout Global Warming and the Turn it Has Been Taking for a While Now.

Will Sidelining Science Help Advance the Climate Debate?

By Keith Kloor | February 4, 2014 3:17 pm

From the Department of Counterintuitive Thinking:

"The debate about climate change needs to become more political, and less scientific."

That is from climate researcher Mike Hulme, in a provocative essay at The Conversation. The above quote makes more sense when you read the sentence that follows:

"Articulating radically different policy options in response to the risks posed by climate change is a good way of reinvigorating democratic politics."

I’m all for this, but you can only have a robust debate about potential solutions if enough people feel strongly that there is a globally significant threat worth discussing and acting on. But the nature of the climate problem–its complexity and timescale–make it hard for us to wrap our minds around. For a recent explanation on why that is, read this piece by Bryan Walsh in Time, headlined:

Why we don’t care about saving our grandchildren from climate change

The biggest stumbling block, as Walsh notes, is that “climate policy asks the present to sacrifice for the future.” Even western Europe, which has perhaps the most climate-concerned citizenry, is now less inclined to do this.

So context is everything in the climate debate. Hulme argues that we should proceed from this framework:

What matters is not whether the climate is changing (it is); nor whether human actions are to blame (they are, at the very least partly and, quite likely, largely); nor whether future climate change brings additional risks to human or non-human interests (it does)…in the end, the only question that matters is, what are we going to do about it?

No, what matters equally is just how much we feel threatened (right now) by the risks of climate change. This is what David Ropeik gets into when he talks about our “risk perception gap.” (See here and here.) Several years ago, Andy Revkin helpfully summarized a body of behavioral research:

a large part of the climate challenge is not out in the world of eroding glaciers and limited energy choices, but inside the human mind.
There’s the “finite pool of worry” (Did we pay the rent this month?). There’s “single action bias” (I changed bulbs; all set.) There are powerful internal filters (dare I say blinders?) that shape how different people see the same body of information.
And of course there’s the hard reality that the risks posed by an unabated rise in greenhouse-gas emissions are still mainly somewhere and someday while our attention, as individuals and communities, is mostly on the here and now.

I agree with Hulme when he says that debates about climate change “will not be settled by scientific facts,” but rather will turn on “debates about values and about the forms of political organisation and representation that people believe are desirable.”

This is why I’ve said numerous times that the symbolic importance of the Keystone pipeline is under-appreciated by many commentators. In of itself this one pipeline isn’t going to affect the trajectory of climate change, but climate activists have effectively used it as a means to build a larger movement that is very much values-oriented, as in: Should we continue supporting an energy infrastructure that reinforces societal dependence on fossil fuels ?

That is an important question to take up in the context of climate change. And it’s likely more productive to engage it from a values–rather than a risk–perspective.

CATEGORIZED UNDER: climate change, climate policy, climate politics, climate science, global warming

 

MORE ABOUT: climate change, climate policy, global warming, Keystone pipeline

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.

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, Tuesday 4 February 2014 10.45 EST

 

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.

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

 

Jaime Huerta-Cepas^1,2, Marina Marcet-Houben^1,3, Toni Gabaldón​^1,3,4

Author and article information

 

1 Bioinformatics and Genomics, Centre for Genomic Regulation, Barcelona, Spain

2 Structural and Computational Biology Unit, EMBL, Heidelberg, Germany

3 Universitat Pompeu Fabra, Barcelona, Spain

4 Inctitució Catalana d'Estudis Avançats (ICREA), Barcelona, Spain

DOI

10.7287/peerj.preprints.223v1

Published

2014-01-28

Accepted

2014-01-28

Subject Areas

Bioinformatics, Computational Biology, Evolutionary Studies, Genomics

Keywords

Tree of life, Genomics, Phylogeny, Species tree, Phylogenomics

Copyright

© 2014 Huerta-Cepas et al.

Licence

This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ PrePrints) and either DOI or URL of the article must be cited.

Cite this article

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 http://dx.doi.org/10.7287/peerj.preprints.223v1

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 http://dx.doi.org/10.7287/peerj.preprints.223v1

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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

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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

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TOL analyses II

DOI: 10.7287/peerj.preprints.223v1/supp-3

  Download

216-species TOL

DOI: 10.7287/peerj.preprints.223v1/supp-4

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Supplementary data

Supplementary methods, figures and tables

DOI: 10.7287/peerj.preprints.223v1/supp-5

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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.

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

Published time: February 02, 2014 21:15                         

 

Reuters / Leonhard Foeger

 

 

Bees exposed to "field-realistic" doses of insecticides gather less than a half the pollen that they normally do, dooming their young to starvation, UK researches have said. While some scientists hailed the findings, pesticide makers remained unimpressed

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

Nick Gillespie | 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.

Follow Nick Gillespie on Twitter

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.

http://www.alternet.org/culture/george-lakoff-communication-liberals-do-everything-wrong?akid=11469.1151017.sQqXuS&rd=1&src=newsletter953817&t=9

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

February 1, 2014  |  

 

 

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"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: 01/30/2014 3:59 pm EST  |  Updated: 01/30/2014 11:59 pm EST 

                                                                                                                                                                                                                                         

       

Shalom Ormsby via Getty Images

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.

We Need To Regulate Guns, Not Women's Bodies

This past week marked the forty-first anniversary of Roe v. Wade, the Supreme Court decision that expanded the right to privacy to include a woman’s right to an abortion. It also marked yet another tragic shooting, this one at a mall in Columbia, Md., that left three dead, including the gunman who committed suicide. On the surface, it may seem like abortion and gun violence don’t have anything in common but the way these issues have historically been framed — abortion as murder and the right to bear arms as essential — reflects how tightly we clutch our guns and Bibles in an effort to maintain founding principles, ones whose merit should be challenged based on our ever-evolving society.
If there’s anything that needs comprehensive reform, it’s current gun laws — not abortion rights.
Our nation is no stranger to gun violence — in fact, it’s often our bedfellow, and the facts are startling. In the first nine months of 2013, there were six mass shootings in the United States with at least 20 of those having occurred since President Obama was elected. What’s even more startling is that half of the deadliest shootings in our nation have occurred since 2007.

After 26 people — including 20 children — were slaughtered at Sandy Hook Elementary School in Newtown, Connecticut in December 2012, the media, public and to a degree, political response had the same message: it’s time for comprehensive gun control laws to be enacted. But, we hear the same message after every mass shooting — we heard it after the shootings at Columbine, Virginia Tech, Aurora, Tuscon, the Washington Navy Yard, the Sikh Temple, the Seattle Coffee Shop, Fort Hood and more. While mass shootings are the form of gun violence that most frequently dominates the media, it’s important to note that a plethora of U.S. cities having higher rates of gun violence than entire nations.

Given the consistent gun violence in our country, it’s getting harder and harder to support the Second Amendment without recognizing that it badly needs to be reevaluted. As Harvey Wasserman wrote for The Huffington Post in 2011 after attempted assassination of Rep. Gabbie Giffords (D-AZ), the Second Amendment “is granted only in the context of a well-regulated militia and thus the security of a free state.” He uses the National Guard as an example of this kind of organization, not armed individuals seeking personal retribution. Wasserman argues that this kind of “murder and mayhem” that has escalated “has been made possible by the claim to a Constitutional right that is not there,” meaning that outside the ‘well-regulated militia,’ the Second Amendment holds little relevancy, especially in our current society.

If you take all this into consideration, paired with the fact that nine in 10 Americans support expanded background checks on guns, it’s logical to assume something is being done to curb gun violence, right?

Wrong. Just over a month ago, The Huffington Post reported that despite legislation being proposed, including one that would have enacted comprehensive background checks, Congress has not passed any gun control laws since the Sandy Hook shooting in 2012.

 

In a stark paradox, the Guttmacher Institute reported that in the first half of 2013, 43 state provisions were enacted that restrict access to abortion. By the end of 2013, NARAL Pro-Choice America reports that a total of 53 anti-choice measures were enacted across 24 states despite a recent poll that found Americans support Roe’s landmark decision. You can’t debate the facts and if these numbers are any indication of our legislator’s priorities, it’s saying that they’re more afraid of women with reproductive rights than a nation with lax gun control laws.

Since Roe was decided, the anti-choice movement has been carefully executing a plan to turn back the clock on women’s reproductive rights. This effort can best be described as an assault on women’s bodies but is often presented by the anti-choice community as a “safety concern.” It’s a known fact that abortion is one of thesafest medical procedures but opponents have created myths to drum up support for their restrictions, like abortion being linked to breast cancer (it isn’t), a fetus being able to feel pain at 20 weeks (it can’t), in an all-out attempt to frame abortions as unsafe, murderous and morally negligent. Statistics prove that restricting abortion is what makes it unsafe, but facts, shmacts — who needs them when we’ve got all-male Congressional panels debating women’s health care (hint: not this guy)?

It seems pretty asinine that we live in a country whose state legislators are more likely to restrict abortion than enact comprehensive gun control laws (I’m looking at you, Rick Perry). Take Texas, for example. Last summer, the state imposed catastrophic abortion restrictions under the omnibus anti-choice bill HB 2 that have closed clinics and left patients to travel hundreds of miles to get an abortion. Texas is currently in a reproductive state of emergency but gun rights advocates fear not, because it’s easier to get a gun than an abortion.

How’s that for warped logic, especially when you consider that family planning and women’s reproductive services are good for the economy. Restricting access to reproductive health care can force women to carry unwanted or intended pregnancies to term, thus limiting her ability to fully participate in the workforce and contribute to the economy. A woman’s right to bodily autonomy and agency surrounding her decisions about pregnancy isn’t just good economics, it’s necessary as we build a more gender equal society. Viewing women as primarily baby-making receptacles does nothing for equality. If anything, it promotes the idea that a woman’s place is in the kitchen, not the workforce.

Efforts that restrict access to abortion and reproductive rights but uphold dangerous gun laws magnifies the disconnect between public opinion and actual representation and reflects the desperation of status quo stakeholders to maintain the three Ps: power, privilege and the patriarchy.
There’s no bigger threat to these structures than disrupting their history of power but our current social, political and economic environment calls for change. If we want to save more American lives, it’s not women’s bodies that need regulation — it’s gun laws.