SAN FRANCISCO An Alabama man was charged this month with the 1980 murder of an Oxnard teen. A Placerville man was arrested last month for a 1986 rape and murder of a San Mateo teen. A San Francisco man is currently on trial for the murder and robbery of a tourist two decades ago.

Technological advances in genetic research and computers in recent years have turned solving "cold cases" into near-routine police work. The California Attorney General reports that the state's DNA database of close to 2 million samples spits outs more than 425 "hits" a month, more than double the average monthly rate of 183 in 2008. More than 10,000 suspects have been identified in the last five years.

But on Wednesday, the American Civil Liberties Union will argue before a federal appellate court in San Francisco that California's DNA collection efforts have become unconstitutionally aggressive and that the spike in hits comes at the expense of civil liberties.

The ACLU is asking the 9th U.S. Circuit Court of Appeals to strike down California's Proposition 69, which authorized police to obtain a genetic sample from every person arrested on felony charges, not just those convicted. Some 25 other states have enacted similar laws since 62 percent of the California electorate passed the measure in 2004.

The issue of the warrantless swabbing of the cheek with a Q-tip of everyone arrested for a felony has sparked one of the hottest "search and seizure" debates in state and federal courts in decades.

The U.S. Supreme Court has already signaled its willingness to review Maryland's DNA collection law after a federal appeals court there ruled it unconstitutional in April. The California Supreme Court has agreed to review a lower court's overturning of the California law. Several other state and federal courts have already ruled or are weighing the issue throughout the country.

While the courts are sorting out the issue, California law enforcement officials are collecting more than 11,000 samples a month.

"Cold hit DNA is integral to bringing criminals to justice," said San Francisco District Attorney George Gascon, whose office is prosecuting William Payne for the 1983 strangulation murder of Nikolaus Crumbley. Crumbley's body was found in the city's McLaren Park along with DNA that was finally matched to Payne earlier this year. Payne denies killing Crumbley, saying his DNA was found at the scene because the two had had consensual sex. The match was made after Payne submitted a DNA sample after an unrelated assault conviction.

"Almost three decades later, we have charged the person responsible for this horrific murder," Gascon said.

The 9th Circuit itself has previously upheld the California law, which went into full effect in 2009. But underscoring the importance of the debate, a majority of the court's 24 judges voted to reconsider that divided ruling of three-judge panel. The matter now goes before a special "en banc" court of 11 judges.

Continued here:
ACLU challenges California DNA collection practice

A week ago, a huge, painstakingly orchestrated PR campaign was timed to coincide with multiple publications of a long-term study by the ENCODE consortium in top-ranking journals. The ENCODE project (EP) is essentially the next stage after the Human Genome Project (HGP). The HGP sequenced all our DNA (actually a mixture of individual genomes); the EP is an attempt to define what all our DNA does by several circumstantial-evidence gathering and analysis techniques.

The EP results purportedly revolutionize our understanding of the genome by proving that DNA hitherto labeled junk is in fact functional and this knowledge will enable us to maintain individual wellbeing but also miraculously cure intractable diseases like cancer and diabetes.

Unlike the arsenic bacteria fiasco, the EP experiments were done carefully and thoroughly. The information unearthed and collated with this research is very useful, if only a foundation; as with the HGP, this cataloguing quest also contributed to development of techniques. What is way off are the claims, both proximal and distal.

A similar kind of theory of everything hype surrounded the HGP but in the case of the EP the hype has been ratcheted several fold, partly due to the increased capacity for rapid, saturating online dissemination. And science journalists who should know better (in Science, BBC, NY Times, The Guardian, Discover Magazine) made things worse by conflating junk, non-protein-coding and regulatory DNA.

Biologists particularly those of us involved in dissecting RNA regulation have known since the eighties that much of junk DNA has functions (to paraphrase Sydney Brenner, junk is not garbage). The EP results dont alter the current view of the genome, they just provide a basis for further investigation; their definition of functional is biochemically active two very different beasts; the functions (let alone any disease cures) will require exhaustive independent authentication of the EP batch results.

Additionally, the findings were embargoed for years to enable the PR blitz at minimum unseemly when public funds are involved. On the larger canvas, EP signals the increased siphoning of ever-scarcer funds into mega-projects that preempt imaginative, risky work. Last but not least, the PR phrasing choices put wind in the sails of creationists and intelligent design (ID) adherents, by implying that everything in the genome has a purpose under heaven.

What did the study actually do? The EP consortium labs systematically catalogued such things as DNAase I hypersensitive and methylated sites, transcription factor (TF) binding sites and transcribed regions in many cell types. Unmethylated nuclease-sensitive DNA is in the open configuration aka euchromatin, a state in which DNA can discharge its various roles. The TF sites mean little by themselves: to give you a sense of their predictive power, any synthetically made DNA stretch will contain several such sites. Whether they have a function depends on a whole slew of prerequisites. Ditto the transcripts, of which more anon.

Lets tackle junk DNA first, a term I find as ugly and misleading as the word slush for responses to open submission calls. Semantic baggage aside, the label junk was traditionally given to DNA segments with no apparent function. Back in the depths of time (well, circa 1970), all DNA that did not code for proteins or proximal regulatory elements (promoters and terminators) was tossed on the junk pile.

However, in the eighties the definition of functional DNA started shifting rapidly, though I suspect it will never reach the 80% used by the EP PR juggernaut. To show you how the definition has drifted, expanded, and had its meaning muddied as a term of art that is useful for everyone besides the workaday splicers et al who are abreast of trendy interpretations that may elude the laity, lets meander down the genome buffet table.

Protein-coding segments in the genome (called exons, which are interrupted by non-protein-coding segments called introns) account for about 2% of the total. That percentage increases a bit if non-protein-coding but clearly functional RNAs are factored in (structural RNAs: the U family, r- and tRNAs; regulatory miRNAs and their cousins).

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Junk DNA, Junky PR

An Alabama man was charged this month with the 1980 murder of an Oxnard teen. A Placerville man was arrested last month for a 1986 rape and murder of a San Mateo teen. A San Francisco man is currently on trial for the murder and robbery of a tourist two decades ago.

Technological advances in genetic research and computers in recent years have turned solving "cold cases" into near-routine police work. The California Attorney General reports that the state's DNA database of close to 2 million samples spits outs more than 425 "hits" a month, more than double the average monthly rate of 183 in 2008. More than 10,000 suspects have been identified in the last five years.

But on Wednesday, the American Civil Liberties Union will argue before a federal appellate court in San Francisco that California's DNA collection efforts have become unconstitutionally aggressive and that the spike in hits comes at the expense of civil liberties.

The ACLU is asking the 9th U.S. Circuit Court of Appeals to strike down California's Proposition 69, which authorized police to obtain a genetic sample from every person arrested on felony charges, not just those convicted. Some 25 other states have enacted similar laws since 62 percent of the California electorate passed the measure in 2004.

The issue of the warrantless swabbing of the cheek with a Q-tip of everyone arrested for a felony has sparked one of the hottest "search and seizure" debates in state and federal courts in decades.

The U.S. Supreme Court has already signaled its willingness to review Maryland's DNA collection law after a federal appeals court there ruled it unconstitutional in April. The California Supreme Court has agreed to review a lower court's overturning of the California law. Several other state and federal courts have already ruled or are weighing the issue throughout the country.

While the courts are sorting out the issue, California law enforcement officials are collecting more than 11,000 samples a month.

"Cold hit DNA is integral to bringing criminals to justice," said San Francisco District Attorney George Gascon, whose office is prosecuting William Payne for the 1983 strangulation murder of Nikolaus Crumbley. Crumbley's body was found in the city's McLaren Park along with DNA that was finally matched to Payne earlier this year. Payne denies killing Crumbley, saying his DNA was found at the scene because the two had had consensual sex. The match was made after Payne submitted a DNA sample after an unrelated assault conviction.

"Almost three decades later, we have charged the person responsible for this horrific murder," Gascon said.

The 9th Circuit itself has previously upheld the California law, which went into full effect in 2009. But underscoring the importance of the debate, a majority of the court's 24 judges voted to reconsider that divided ruling of three-judge panel. The matter now goes before a special "en banc" court of 11 judges.

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Calif. DNA Collection From Arrestees Challenged

STONY BROOK, NY--(Marketwire - Sep 17, 2012) - The Textile Center of Excellence at Huddersfield, United Kingdom (TCOE), and Applied DNA Sciences, Inc. ( OTCBB : APDN ) (Twitter: @APDN), a provider of DNA-based anti-counterfeiting technology and product authentication solutions, announced today the roll out of a new platform for protecting textile brands, under the SigNature DNA brand. The services, which the two organizations call "revolutionary," aim to protect textiles from a wave of counterfeiting which has struck the industry.

The platform includes applications which protect a wide range of textile, apparel and accessory products, including impregnation and authentication of DNA-marked:

The platform will be unveiled at the world-famous Premire Vision Pluriel, opening at Paris Nord Villepinte Parc d'Expositions (exhibition center) at Booth #5C18, from September 19-21, 2012. At the show, APDN and TCOE will feature demonstrations, samples, and technical experts, all showing the "unique, uncopyable, and uncompromising" abilities of the technology in protecting brands from counterfeiting.

In a joint statement, the two organizations said that their technology "offers our industry a unique and powerful means to mark and authenticate original items marked with DNA."

The two organizations described SigNature DNA as "a leading anti-counterfeiting technology that can be incorporated at any point in the textile supply chain as a means to link a genuine product to its original source of manufacture." Botanical SigNature DNA markers are authenticated in a laboratory and help to provide forensic evidence that can be used in a court of law.

The Textile Centre of Excellence has partnered with some of the most prestigious mills in the United Kingdom, including Bower Roebuck, Dormeuil, Holland and Sherry, Taylor and Lodge, and John Foster. Collectively, these fabric designers and weavers supply fabric to many of the most famous designer lines of Europe and America. Its botanical SigNature DNA-based technology protects historic and high-value Yorkshire Wool. APDN has separately partnered with Supima, a promotional organization of American growers of American Pima cotton.

Bill Macbeth, Managing Director of the Textile Centre of Excellence, commented: "SigNature DNA technology offers textile and clothing manufacturers a fool-proof and affordable solution to the growing menace of product counterfeiting. We are ready and willing to help brand owners and manufacturers to boost their brand values and revenues by incorporating this unique protection into their products."

Said Dr. James A Hayward, President and CEO, Applied DNA Sciences: "We believe that the Textile Centre's new platform is a powerful demonstration of the versatility and effectiveness of our SigNature DNA product. We urge visitors to Premiere Vision to visit the TCOE booth and see for themselves how DNA marking and authentication can add great value to their product lines."

About The Textile Centre of Excellence, and the Huddersfield and District Textile Training Company

The Huddersfield and District Textile Training Company was established in 1976 to unite the local textile industry in a shared approach to professional, equitable and high-quality training. In 1999 the company established the Textile Centre of Excellence, a 2 million development located in Leeds Road Huddersfield, providing a wide range of 'state of the art' textile and clothing research and development, training and production facilities including:

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Applied DNA Sciences, Textile Centre of Excellence Unveil Textiles Anti-Counterfeiting Platform

SAN FRANCISCO -- On a March day three years ago in San Francisco's Civic Center Plaza, Elizabeth "Lily" Haskell was arrested during a rally against the Iraq war, cuffed on a felony allegation that she tried to spring another protester who had been taken into custody.

But once hauled off to jail, Haskell found herself in the legal crosshairs for more than just civic rabble-rousing. Sheriff's deputies ordered her to submit to DNA testing under a then-new provision of California law, giving her the choice of letting them swab the inside of her cheek or face an additional misdemeanor charge and sit in a jail cell for two days.

Haskell relented and took the DNA test. But now the Oakland woman is at the center of an American Civil Liberties Union legal challenge to a state law that allows law enforcement to collect DNA samples from anyone arrested for a felony, regardless of whether they are later charged or convicted. In Haskell's case, prosecutors never followed up the 2009 arrest with a criminal charge.

"My DNA was taken without any kind of due process," Haskell said last week. "I believe people should have the right to refuse to give their DNA."

On Wednesday, a special 11-judge panel of the 9th U.S. Circuit Court of Appeals will hear arguments in the latest round in the case, which has highlighted a legal issue that appears bound for the U.S. Supreme Court. In fact, in a brief order earlier this year, Chief Justice John Roberts said

At the request of civil liberties lawyers, the 9th Circuit agreed to take a second look at the Haskell case after a three-judge panel, in a 2-1 ruling, earlier this year upheld a voter-approved 2004 California law allowing DNA collection. The 9th Circuit rejected arguments that the law, which went into effect in 2009, tramples on the constitutional rights of those arrested for felonies, saying "government's compelling interests far outweigh arrestees' privacy concerns."

In court papers, lawyers for Haskell and others arrested but never charged with felonies argue that the California law "is an unprecedented expansion of the government's power to collect DNA evidence and to DNA profile individuals who have never been convicted of any crime."

To the ACLU, there is no reason someone's DNA should wind up in the state's DNA database if the person has never appeared in court, much less in front of a jury.

"People who haven't been convicted of anything shouldn't be treated like criminals," ACLU attorney Michael Risher said.

Law enforcement officials argue that the DNA collection law is a crucial tool in solving crimes. They liken taking a DNA swab at the time of arrest to fingerprinting.

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Federal appeals court to hear challenge to California DNA collection law

The Irish Times - Monday, September 17, 2012

MATTHEW HOLMES

LEGAL OPINION: This legislation will strengthen the ability of the Garda to detect and prevent crime and, in particular, to snare repeat offenders

A DNA DATABASE is one of the most effective crime-fighting tools ever devised. Thanks to DNA databases, crimes that were previously unsolvable are now being solved and miscarriages of justice are being corrected.

Such databases save valuable time in investigations by quickly eliminating suspects or pinning them to a crime scene. They are particularly effective in sex crimes and in catching repeat offenders such as burglars. They also have uses beyond the criminal sphere in terms of identifying bodies and helping to locate missing persons. In February 2000, the then government announced a plan to establish a DNA database in Ireland. More than a decade has passed and this has still not been done. The lack of relevant legislation is hampering criminal investigations.

To date, three Bills have been drafted which seek to establish a DNA database in Ireland the Criminal Justice (Forensic Sampling and Evidence) Bill 2007, the Criminal Justice (Forensic Evidence and DNA Database System) Bill 2010 and the Criminal Justice (Forensic Evidence and DNA Database System) Bill, currently before the Dil.

The first had to be dropped after the decision of the European Court of Human Rights in Marper v the United Kingdom, which led to European-level change in the law on DNA databases; the second lapsed following the change of government last year. In April 2011, Minister for Justice Alan Shatter told a conference of Garda sergeants and inspectors he hoped to publish a new Bill before the end of that year and to progress its speedy enactment. This was postponed to the middle of this year and it has been pushed back again to the end of the year.

There is currently an ad-hoc Irish DNA database which contains a representative sample of DNA profiles from 300 Irish citizens. To put this in context, the British database contained the profiles of 3.1 million people at the end of 2005. Clearly the scope for accuracy and effectiveness of results is exponentially higher in their system than in ours. In the UK, using the database has resulted in a 50 per cent hit rate. One in two samples on the databanks result in information regarding suspects being provided to the police. At one stage the hit rate was 74 per cent.

When he was in opposition, Mr Shatter said it was almost beyond belief that more than a decade had passed and this important legislation had still not been passed. Speaking in January 2011, he said: It is completely outrageous important issue hasnt been prioritised, and extraordinary lethargy has been displayed; the legislation is on the back burner. If there was any sense of urgency about it, this legislation would have been implemented last Easter considering it was published last January.

Over a year has passed since Mr Shatter became Minister for Justice, and legislation has yet to be enacted.

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Lack of DNA database is a national disgrace

Forensic experts have failed to find crucial DNA evidence in the sexual assault case against Julian Assange, a British newspaper reports.

In a 100-page document shown to lawyers for the Australian WikiLeaks founder, Swedish police outlined their basis for seeking the 41-year-old's extradition to Stockholm to face questioning.

The report said staff at two forensic laboratories were unable to find conclusive evidence of Mr Assange's DNA on a torn condom provided by one of two women who claim to have been assaulted in August 2010.

However, the same analysts have found DNA believed to belong to Mr Assange on a condom provided by a second woman, The Mail on Sunday reported.

Mr Assange denies any wrongdoing and says sex with the two women was consensual.

He remains holed up in London's Ecuadorian embassy in a bid to avoid Swedish extradition, which he insists would lead to him being handed to authorities in the United States, where the actions of his secret-leaking website are under investigation.

The Swedish police report said that one woman, now aged 33, claims she was repeatedly molested by Mr Assange at her flat in Stockholm, adding on one occasion he deliberately broke a condom before wearing it to have unprotected sex with her against her will.

Scientists were unable to find traces of Mr Assange's DNA on the condom and his lawyers suggest that is because a fake one may have been submitted, the tabloid reports.

Mr Assange, who has been granted asylum by Ecuador, is yet to be formally charged with any offence by Swedish authorities.

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Missing DNA evidence in Assange case

Forensic experts have failed to find crucial DNA evidence in the sexual assault case against Julian Assange, a British newspaper reports.

In a 100-page document shown to lawyers for the Australian WikiLeaks founder, Swedish police outlined their basis for seeking the 41-year-old's extradition to Stockholm to face questioning.

The report said staff at two forensic laboratories were unable to find conclusive evidence of Mr Assange's DNA on a torn condom provided by one of two women who claim to have been assaulted in August 2010.

However, the same analysts have found DNA believed to belong to Mr Assange on a condom provided by a second woman, The Mail on Sunday reported.

Mr Assange denies any wrongdoing and says sex with the two women was consensual.

He remains holed up in London's Ecuadorian embassy in a bid to avoid Swedish extradition, which he insists would lead to him being handed to authorities in the United States, where the actions of his secret-leaking website are under investigation.

The Swedish police report said that one woman, now aged 33, claims she was repeatedly molested by Mr Assange at her flat in Stockholm, adding on one occasion he deliberately broke a condom before wearing it to have unprotected sex with her against her will.

Scientists were unable to find traces of Mr Assange's DNA on the condom and his lawyers suggest that is because a fake one may have been submitted, the tabloid reports.

Mr Assange, who has been granted asylum by Ecuador, is yet to be formally charged with any offence by Swedish authorities.

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DNA evidence missing in Assange case

The Irish Times - Monday, September 17, 2012

INNOVATION PROFILE:Teagascs Animal Bioscience facility, Grange, Co Meath

TEAGASCS NEWLY opened Animal Bioscience Facility in Grange, Co Meath, will use the latest DNA-based approaches to assist Irish farmers produce better quality and healthier livestock and ultimately improve Irish food production.

The publication of the genome sequence for cattle in 2009 has opened up the possibility to use these approaches to study commercially important traits. These include milk and meat production, immunity and disease, nutrition and reproduction, explains Teagasc director Prof Gerry Boyle.

The new facility was developed as part of the Teagasc vision programme which was initiated in 2006 with the objective of establishing centres of excellence in the key sciences that underpin Irish agriculture. Animal bioscience is a key component of the organisations Animal and Grassland, Research and Innovation Programme which integrates applied and strategic research across the main livestock species in Ireland namely dairy cattle, beef cattle and sheep.

The Animal and Bioscience Department carries out research in the areas of animal breeding and genomics, animal health and welfare, infection and disease, computational and systems biology, fertility and reproduction, feed efficiency and product quality. The new technologies being developed have the potential to accelerate the rate of gain in efficiency and quality.

Using the new areas of science such as genomics, proteomics, and systems biology, we are seeking to develop tools to more accurately identify the most profitable animals for current and future production systems, says Dr Richard Dewhurst, head of the Teagasc animal and bioscience department.

We are developing the optimal breeding programmes to maximise genetic gain in the long term. Our main research activities include the development of multi-breed genetic and genomic evaluations, breeding objectives and breeding programmes for dairy cattle, beef cattle and sheep. We also aim to identify genes, pathways and biological processes mediating resistance to infectious diseases in cattle and sheep and how these genes interact with pathogens and the environment.

While we are not quite at the stage of designer animals the use of these new DNA techniques could have a dramatic impact on Irish agriculture. If we take the DNA sequence of a bull, for example, we can use that to more accurately predict the characteristics that will be passed on to his progeny, Dewhurst explains. And the rate at which we can get the information is accelerating so we will soon be able to get the DNA sequence for individual animals. Its all about analysing the data and relating it to the traits we want to predict.

This highly scientific data led approach is a revolution in terms of the practices which obtained just 25 years ago. Over the past 25 years genetics has become much more statistics-based, before that it was an art, says Dewhurst. We have been using statistical models to predict traits in animals for the past while but now with the genome we will be able to identify good quality animals with the desired traits even before they reach maturity.

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DNA research key for Irish agriculture