Search This Blog

Thursday, February 6, 2014

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

by
   

Farm statistics: usually illuminating ... occasionally misleading.
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.
Herbicide use data from Food and Water Watch
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.
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.
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.)
The soil erosion situation looked pretty bad in 1982.
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.
Fast-forward almost 30 years, and soil erosion suddenly looks much better. But that's not the whole story.
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.

Tuesday, February 4, 2014

How Prohibition Makes Heroin More Dangerous

|

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.
 

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
View PrePrint PDF

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.

Cryogenics

From Wikipedia, the free encyclopedia https://en.wikipedia.org/wiki/Cryogenics...