Category: Genetics

Microflaccid Office Fail

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It turns out that one of the major data exchange formats for genetics is Microsoft Excel, and we have now discovered that the Redmond company’s flagship spreadsheet program has been autocorrecting the data into oblivion:

For many people, working with error-ridden spreadsheets is a way of life. This takes on added meaning for genomics researchers, who study the building blocks of life. It turns out that their work, too, is rife with dodgy spreadsheets.

A new paper has revealed the vast extent of errors in published genomics research, which is down to an unfortunate quirk of Microsoft Excel. A trio of scientists in Australia scanned 7,500 Excel files with gene lists accompanying 3,600 papers in 18 journals over a 10-year period. One-fifth of the files had easily identified errors, which is “quite striking and a little bit embarrassing,” says Mark Ziemann of the Baker IDI medical research institute in Melbourne, one of the paper’s co-authors.

What happened? By default, Excel and other popular spreadsheet applications convert some gene symbols to dates and numbers. For example, instead of writing out “Membrane-Associated Ring Finger (C3HC4) 1, E3 Ubiquitin Protein Ligase,” researchers have dubbed the gene MARCH1. Excel converts this into a date—03/01/2016, say—because that’s probably what the majority of spreadsheet users mean when they type it into a cell. Similarly, gene identifiers like “2310009E13” are converted to exponential numbers (2.31E+19). In both cases, the conversions strip out valuable information about the genes in question.

What on earth inspired all these researchers to use what can only be described as the greasy kid stuff of analysis and data storage for this purpose?

It’s nucking futz.

Peter Parker, Eat Your Heart Out

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The US army is looking at using spider silk generated from genetically modified silkworms:

Spider silk is one of nature’s toughest substances, similar in strength to the Kevlar plastic found in bulletproof vests but much more flexible. Kraig Biocraft, a company out of Ann Arbor, Michigan, genetically altered silkworms to produce a fiber that’s similar to pure spider silk. Today, they announced an Army contract to test this so-called Dragon Silk for possible use in body armor.

 There’s a reason that silk from worms is cheap but you can’t buy pajamas made from spider fabric: spiders are territorial and cannibalistic, which makes farming them for fabric production almost exorbitant.

 ………

 The technology behind Dragon Silk is based in part on the work of Malcolm J. Fraser, Donald L. Jarvis, and their colleagues. As they explain in this paper, they introduce specific pieces of spider DNA into silkworm eggs, creating an entirely new type of silkworm that can spin spider silk.

 ………

 Rice doesn’t anticipate that Dragon Silk will be a direct replacement for Kevlar, which has a strength of 3 gigapascals. [425,000 psi] Spider silk has a strength of 2 gigapascals, [290,000 psi] only about two-thirds as strong.

 “But Kevlar has an elasticity of 3 percent,” says Rice. “If you have a Kevlar fiber, it’s not going to move at all. Our fibers have a 30 to 40 percent elasticity before they break.”


FWIW, the additional deformation that spider silk can take means that it is absorbing a lot more energy than the Kevlar.  (The very crude sketch depicts energy as the area under the various curves)

I am not sure of how spider silk could be used in a structural context, but given my experience with the material, it’s relatively low modulus would indicate that any design would be driven by stiffness issues rather than strength issues, which would make it rather similar to handle to fiberglass.

Return of the Mad Sh%$ter

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The funniest thing ever posted to the internet is an essay, “The Attack of the Mad Sh%$ter” a hilarious essay on an instance of fecal sabotage at what was then Texas Instruments.

Well, it appears that literal poo flinging in the workplace is far more common that I had anticipated, and now we have a lawsuit challenging an employer demanding DNA samples in order to identify a dung defiler:

Who was the “devious defecator” leaving their “offending fecal matter” across an Atlanta-area warehouse that stored and delivered products for grocery stores?

That’s how US District Judge Amy Totenberg described the issue as she ruled (PDF) in favor of two employees who were forced to give a buccal cheek swab to determine if their DNA was a match. But a match was not to be had. The two sued, claiming that the Genetic Information Nondiscrimination Act (GINA) prohibited their 2012 tests by a forensics lab hired by their employer, Atlas Logistics Group Retail Services.

Employees Jack Lowe and Dennis Reynolds are expected to go to trial against their employer on June 17 in what could be the first damages trial resulting from the 2008 civil rights legislation, which generally bars employers from using individuals’ genetic information when making hiring, firing, job placement, or promotion decisions. The Office of Management and Budget has said the “potential misuse of this information raises moral and legal issues.”

Ahead of trial, Judge Totenberg set aside Atlas Logistics’ claims that the “genetic information” at issue wasn’t covered by the law. Atlas Logistics asserted that GINA excludes analyses of DNA, RNA, chromosomes, proteins, or metabolites if such analyses do not reveal an individual’s propensity for disease. The judge ruled that the “plain meaning of the statute’s text” is satisfactory for the case to go forward despite the tests at issue not revealing disease propensities.

But how much is a breach of this act worth to the warehouse workers Lowe and Reynolds? Phrased differently, what’s the monetary value of falsely being fingered as the “devious defecator”?

According to Atlas Logistics, the answer is a combined $200,000 for both plaintiffs. Days ago, the company offered that deal (PDF) without admitting wrongdoing. “This Offer includes any and all damages sought by Plaintiffs in this matter and is inclusive of attorneys’ fees and taxable costs,” Atlas Logistics attorney Dion Kohler wrote.

The plaintiffs, however, said the offer was a load of doo doo. “We are not taking the offer,” Amanda Farahany, the plaintiffs’ attorney, told Ars in an e-mail.

When asked how much damages they were seeking, Farahany replied, “We are asking that a jury determine the value of this important right.”

I have to agree with the plaintiffs:  Employers are not entitled to the genetic information of their employees.

It’s also funny as hell.

Dodged a Bullet Yet Again

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No hang over.

I’ve never had a hangover.

I know of 4 people, including myself, who have never had a hangover as a result of being drunk.

It’s genetics, I think.

3 of the 4 people who appear to be hangover proof are Eastern European Jews.  (The 4th might be, I’m not sure)

If you possess this mutant power, I would add a warning:  2 of the 4 people who do not get hangovers are alcoholics.

Just a Reminder: Big Ag is Evil, Not Just Monsanto, and it is US Policy to Subsidize them Through International Agreements

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You really need to read this account of a systematic program of harassment and libel against Tyrone Hayes for his research showing that Syngenta’s herbicide atrazine was dangerous:

In 2001, seven years after joining the biology faculty of the University of California, Berkeley, Tyrone Hayes stopped talking about his research with people he didn’t trust. He instructed the students in his lab, where he was raising three thousand frogs, to hang up the phone if they heard a click, a signal that a third party might be on the line. Other scientists seemed to remember events differently, he noticed, so he started carrying an audio recorder to meetings. “The secret to a happy, successful life of paranoia,” he liked to say, “is to keep careful track of your persecutors.”

Three years earlier, Syngenta, one of the largest agribusinesses in the world, had asked Hayes to conduct experiments on the herbicide atrazine, which is applied to more than half the corn in the United States. Hayes was thirty-one, and he had already published twenty papers on the endocrinology of amphibians. David Wake, a professor in Hayes’s department, said that Hayes “may have had the greatest potential of anyone in the field.” But, when Hayes discovered that atrazine might impede the sexual development of frogs, his dealings with Syngenta became strained, and, in November, 2000, he ended his relationship with the company.

………

[Former student Roger] Liu and several other former students said that they had remained skeptical of Hayes’s accusations until last summer, when an article appeared in Environmental Health News (in partnership with 100Reporters)* that drew on Syngenta’s internal records. Hundreds of Syngenta’s memos, notes, and e-mails have been unsealed following the settlement, in 2012, of two class-action suits brought by twenty-three Midwestern cities and towns that accused Syngenta of “concealing atrazine’s true dangerous nature” and contaminating their drinking water. Stephen Tillery, the lawyer who argued the cases, said, “Tyrone’s work gave us the scientific basis for the lawsuit.”

Hayes has devoted the past fifteen years to studying atrazine, and during that time scientists around the world have expanded on his findings, suggesting that the herbicide is associated with birth defects in humans as well as in animals. The company documents show that, while Hayes was studying atrazine, Syngenta was studying him, as he had long suspected. Syngenta’s public-relations team had drafted a list of four goals. The first was “discredit Hayes.” In a spiral-bound notebook, Syngenta’s communications manager, Sherry Ford, who referred to Hayes by his initials, wrote that the company could “prevent citing of TH data by revealing him as noncredible.” He was a frequent topic of conversation at company meetings. Syngenta looked for ways to “exploit Hayes’ faults/problems.” “If TH involved in scandal, enviros will drop him,” Ford wrote. She observed that Hayes “grew up in world (S.C.) that wouldn’t accept him,” “needs adulation,” “doesn’t sleep,” was “scarred for life.” She wrote, “What’s motivating Hayes?—basic question.”

………

In January, 2001, Syngenta employees and members of the EcoRisk panel travelled to Berkeley to discuss Hayes’s new findings. Syngenta asked to meet with him privately, but Hayes insisted on the presence of his students, a few colleagues, and his wife. He had previously had an amiable relationship with the panel—he had enjoyed taking long runs with the scientist who supervised it—and he began the meeting, in a large room at Berkeley’s Museum of Vertebrate Zoology, as if he were hosting an academic conference. He wore a new suit and brought in catered meals.

After lunch, Syngenta introduced a guest speaker, a statistical consultant, who listed numerous errors in Hayes’s report and concluded that the results were not statistically significant. Hayes’s wife, Katherine Kim, said that the consultant seemed to be trying to “make Tyrone look as foolish as possible.” Wake, the biology professor, said that the men on the EcoRisk panel looked increasingly uncomfortable. “They were experienced enough to know that the issues the statistical consultant was raising were routine and ridiculous,” he said. “A couple of glitches were presented as if they were the end of the world. I’ve been a scientist in academic settings for forty years, and I’ve never experienced anything like that. They were after Tyrone.”

………

Michelle Boone, a professor of aquatic ecology at Miami University, who served on the E.P.A.’s scientific advisory panel, said, “We all follow the Tyrone Hayes drama, and some people will say, ‘He should just do the science.’ But the science doesn’t speak for itself. Industry has unlimited resources and bully power. Tyrone is the only one calling them out on what they’re doing.………

The Supreme Court has said that corporations are people in the Citizens United case.

Why isn’t Syngenta being criminally prosecuted for stalking?

H/t The Washington Monthly.

Most Amazing Medical Development Ever Happened Wednesday

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This guy turned 70 on Wednesday.

Considering the level of abuse that he has voluntarily inflicted on himself, he should have been found dead in his swimming pool about 40 years ago.

Somewhere in his genes is the making of an absolutely indestructible superhero, as well as a kick ass rhythm guitarist.

You can hover over the image with your cursor to get the answer if you do not recognize the guy.

I Hope So

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Ars Technica asks, “Will the Supreme Court end human gene patents after three decades?“

I think that it likely that they role back patent protections.

These days, they only seem to take patent cases when the United States Court of Customs and Patent Appeals goes too far with patents.  (Which it does with mind-numbing regularity):

Since the 1980s, patent lawyers have been claiming pieces of humanity’s genetic code. The United States Patent and Trademark Office has granted thousands of gene patents. The Federal Circuit, the court that hears all patent appeals, has consistently ruled such patents are legal.

But the judicial winds have been shifting. The Supreme Court has never ruled on the legality of gene patents. And recently, the Supreme Court has grown increasingly skeptical of the Federal Circuit’s patent-friendly jurisprudence.

Meanwhile, a growing number of researchers, health care providers, and public interest groups have raised concerns about the harms of gene patents. The American Civil Liberties Union estimates that more than 40 percent of genes are now patented. Those patents have created “patent thickets” that make it difficult for scientists to do genetic research and commercialize their results. Monopolies on genetic testing have raised prices and reduced patient options.

On Monday, the high court will hear arguments about whether to invalidate a Utah company’s patents on two genes associated with breast cancer. But the legal challenge, spearheaded by the American Civil Liberties Union and the Public Patent Foundation, could have much broader implications. A decision could invalidate thousands of patents and free medical researchers and clinicians to practice medicine without interference from the patent system.

It’s very clear that a gene is a discovery, not an invention, but the patent court believes that you can patent a rainy day (I mean this literally: They approved a patent on weather derivatives in Bilski v. Kappos, which was later overturned by the Supreme Court. This court also allowed for patenting of tax deductions)

Hoocoodanode? Monsanto Edition

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It turns out that what Montsanto thought was a win-win, it use of genes to create Roundup resistant crops, allowing it to make money on both the crops, and on the increased sales of its popular herbicide has had a not-unexpected side effect.

It seems that with Roundup Ready® ready crops, farmers soak their fields in the herbicide, and so now we are seeing an explosion of herbicide resistant weeds:“Superweeds” are plaguing high-tech Monsanto crops in southern US states, driving farmers to use more herbicides, return to conventional crops or even abandon their farms.

How has this happened? Farmers over-relied on Monsanto’s revolutionary and controversial combination of a single “round up” herbicide and a high-tech seed with a built-in resistance to glyphosate, scientists say.

Today, 100,000 acres in Georgia are severely infested with pigweed and 29 counties have now confirmed resistance to glyphosate, according to weed specialist Stanley Culpepper from the University of Georgia.

“Farmers are taking this threat very seriously. It took us two years to make them understand how serious it was. But once they understood, they started taking a very aggressive approach to the weed,” Culpepper told FRANCE 24.

“Just to illustrate how aggressive we are, last year we hand-weeded 45% of our severely infested fields,” said Culpepper, adding that the fight involved “spending a lot of money.”

In 2007, 10,000 acres of land were abandoned in Macon country, the epicentre of the superweed explosion, North Carolina State University’s Alan York told local media.

Imagine that.  It’s so bad, that farmers are abandoning land.

The problem here is that the rulings changing the patent laws over the past few decades, which allow the patenting of genes and species, have made the seed business so lucrative that companies like Monsanto are inclined to skip appropriate testing in the rush to market.

The solution is, in addition to stricter regulation, is to remove the IP protections to genes and species, which will remove much of the incentive to cheat.

Crap

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A federal appeals court has overturned a lower court ruling and ruled that patents of genes are legal:

A federal appeals court affirmed the right of Myriad Genetics to patent two genes linked to breast cancer, overturning a lower court ruling that threatened a key element of the biotech business.

The U.S. Court of Appeals for the Federal Circuit in a ruling on Friday backed Myriad’s right to patent two “isolated” human genes — BRCA1 and BRCA2 — that account for most inherited forms of breast and ovarian cancers.

………

The appeals court said the genes isolated by the company can be patented because Myriad is testing for distinctive chemical forms of the genes, and not as they appear naturally in the body.

One member of the three-judge appellate panel dissented, saying that despite Myriad’s process of isolating a human gene it still could not be patented.

………

The appeals court also said that Myriad’s method for screening potential therapies was patentable.

The judges did, however, agree with the district court that Myriad’s method of analyzing DNA sequences did not involve sufficient transformation, and thus could not be patented

I’m not surprised. This is the Court of Appeals for the Federal Circuit, a body that was created specifically to rule on patents, and they, under the “when all you have is a hammer, everything looks like a nail” theory, are insanely pro patent.

How insanely pro patent? They are assuming patently false facts to justify their ruling:

Bruce Wexler, a patent expert at the law firm Paul Hastings, said the ruling means the appeals court has recognized that DNA takes on a different molecular structure when it is isolated and removed from the body.

“That is a very significant result that is very important to the biotech industry,” Wexler said.

This is scientific bullsh%$. DNA is DNA is DNA is DNA, whether in vivo or in vitro.

Here’s hoping that the Supreme Court or the full appeals court (unlikely, see my hammer nail argument), and it gets slapped down.

SCOTUS has issued a number of “what are you smoking?” rebukes of the Court of Appeals for the Federal Circuit regarding patents over the past few years, so there is some hope, but such a ruling would be highly disruptive to the industry, and the Roberts court has been very pro-industry, so I think that it is a small one.

Background here.

US Comes Out Against Patenting Genes

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This is a big deal, and a case where a very bad actor forced their hand:

Reversing a longstanding policy, the federal government said on Friday that human and other genes should not be eligible for patents because they are part of nature. The new position could have a huge impact on medicine and on the biotechnology industry.

The new position was declared in a friend-of-the-court brief filed by the Department of Justice late Friday in a case involving two human genes linked to breast and ovarian cancer.

“We acknowledge that this conclusion is contrary to the longstanding practice of the Patent and Trademark Office, as well as the practice of the National Institutes of Health and other government agencies that have in the past sought and obtained patents for isolated genomic DNA,” the brief said.

Basically, a company, Myriad Genetics, got a patent on breast cancer genes, it licenses government funded research which found the BRCA1 and BRCA2 genes, and has used this patent to prevent the development of better and cheaper tests, and their behavior was so egregious that the government felt compelled to act.

It’s still up to the judge, but this is a good first step.

Genes have never been an invention, they have been a discovery, and discoveries are not supposed to be patentable.

Here’s a Shocker

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Monsanto’s genetically modified corn has been linked to organ damage:

In a study released by the International Journal of Biological Sciences, analyzing the effects of genetically modified foods on mammalian health, researchers found that agricultural giant Monsanto’s GM corn is linked to organ damage in rats.

When you give enormous guaranteed monopoly profits by allowing the patenting of genes and species, those profits guarantee that safety is a secondary concern.

10……9……8……7……6……5………

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Happy new year.

I actually posted it some hours before, and set this to post just before midnight, as I am by this point 3 sheets to the wind courtesy of the products of Rudolph Jelníek, specifically Slivovitz.

It’s highly unlikely that I will be hungover tomorrow, as I have a trick that prevents this: my genetics.

Something about my Eastern European Jewish heritage prevents this.

I’ve never been hung over.

Ummmm….I Got Nothing Here.

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This is too weird for me to comment on. I’m left speechless.

Chinese women crave Bill Gates’ spermGive me a baby, big fella
By Lester Haines → More by this author
Published Wednesday 4th July 2007 08:50 GMT
Mobile computing: Opportunities and risk – Free whitepaper

There’s some good news this morning for Bill Gates: if he ever finds himself fallen on hard times he can always make a few quid offloading his sperm on eager Chinese female recipients.

That’s if China’s Self magazine is to be believed, because the IT potentate secured second spot in a poll which asked 1,000 women from 15 cities whose precious bodily fluid they’d most like to accommodate for some hot baby-making action.

Indeed, so sought-after is Bill’s magic water that he beat Becks and Brad Pitt into fifth and tenth places, respectively. The ideal sperm donor was not, however, George Clooney or Larry Ellison, but Hong Kong entertainer Andy Lau.

…

TheStar.com – News – DNA `junk’ appears to have uses

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I’ve always wondered if DNA outside the nucleus, like the malformed DNA that causes Creuzfelt-Jakov (mad cow) disease might have other, more basic, effects on how creatures develop.

Then again, I’m an Engineer, Not a Doctor, Dammit!!!!!!

I Love it When I can Mangle a “Dr. McCoy” line.

DNA `junk’ appears to have uses

Jun 14, 2007 04:30 AM
Joseph Hall
health reporter

A groundbreaking study says scientists may have to substantially alter their long-held conception of life’s basic blueprint, DNA.

In a departure from traditional thinking, the four-year study says that genes can no longer be considered the only active parts of DNA and that huge segments thought to be ‘junk’ may play a significant role in such individual traits as susceptibility to diseases.

‘A lot of these regions that previously we were thinking were junk DNA, or vast deserts of non-functionality, have been found to be a lot more active,’ says Steven Jones, associate director of the British Columbia Cancer Agency’s Genome Sciences Centre, and one of numerous authors of the scientific paper published today in the journal Nature.

‘This was the surprise … they seem to be doing things from a biological level.’

…