Category Archives: Research

Arts, Research, Science, Technology, United States

DNA Phenotyping…

FORENSIC COMPUTER SCIENCE

Intro: DNA Phenotyping is the prediction of physical appearance from DNA

Until now, DNA left at the scene of a crime only proved useful if it was already stored in a database and could be matched to a suspect.

A team of forensic experts, however, have now devised a way to recreate the face of a person, including eye and skin colour, using as little as 50 picograms (0.05 nanograms) of extracted DNA.

Called DNA phenotyping, the tests also determine the person’s ancestry, if they have freckles and can be used to match with distant relatives.

DNA phenotyping is the prediction of physical appearance from DNA and is a technique being pioneered by Virginia-based Parabon Nanolabs (example pictured). The technology can be used to generate leads in cases where there are no suspects or database hits, or to help identify remains, for example.

DNA phenotyping is the prediction of physical appearance from DNA and is a technique being pioneered by Virginia-based Parabon Nanolabs (example pictured). The technology can be used to generate leads in cases where there are no suspects or database hits, or to help identify remains, for example.

DNA phenotyping is the prediction of physical appearance from DNA and is a technique being pioneered by Virginia-based Parabon Nanolabs.

The technology can be used to generate leads in criminal cases where there are no suspects or database hits, or to help identify remains, for example.

Samples can be potentially taken from as little as a fingerprint.

Parabon’s Snapshot Forensic system is said to be able to accurately predict genetic ancestry, eye colour, hair colour, skin colour, freckling, and face shape in individuals from any ethnic background.

Each prediction is presented with a ‘measure of confidence’.

As an example, the test can say a person has green eyes with 61 per cent confidence, green or blue with 79 per cent confidence, and that they definitely don’t have brown eyes, with 99 per cent confidence.

Based on ancestry, and other markers, the test also creates a likely facial shape.

From all of this information, it builds a computer generated e-fit.

And the test will predict how two people are related, as distant as third cousins, and great-great-great-great-grandparents.

‘DNA carries the genetic instruction set for an individual’s physical characteristics, producing the wide range of appearances among people,’ explained Parabon Nanolabs.

‘By determining how genetic information translates into physical appearance, it is possible to “reverse-engineer” DNA into a physical profile.

‘Snapshot reads tens of thousands of genetic variants from a DNA sample and uses this information to predict what an unknown person looks like.’

The project was supported with funding from the the US Department of Defense (DoD).

Samples can be taken from as little as a fingerprint. Parabon's Snapshot Forensic system is said to be able to accurately predict genetic ancestry, eye colour, hair colour, skin colour, freckling, and face shape in individuals from any ethnic background (example pictured).

Samples can be taken from as little as a fingerprint. Parabon’s Snapshot Forensic system is said to be able to accurately predict genetic ancestry, eye colour, hair colour, skin colour, freckling, and face shape in individuals from any ethnic background (example pictured).

Each prediction is presented with a ‘measure of confidence’. As an example, the test can say a person has green eyes with 61 per cent confidence, green or blue with 79 per cent confidence, and that they definitely don’t have brown eyes, with 99 per cent confidence. A series of example charts is pictured.

Each prediction is presented with a ‘measure of confidence’. As an example, the test can say a person has green eyes with 61 per cent confidence, green or blue with 79 per cent confidence, and that they definitely don’t have brown eyes, with 99 per cent confidence. A series of example charts is pictured.

Ellen McRae Greytak, Parabon’s director of bioinformatics told Popular Science that the system has been used in 10 cases across the US, and the first department to release a Snapshot report was the Columbia Police Department.

It produced a profile for a ‘person of interest’ in the murder of 25-year-old Candra Alston and her daughter Malaysia Boykin in 2011. (Investigators in South Carolina are hoping the DNA technique could lead to to a breakthrough in the unsolved murder case of Malaysia Boykin, three, (left) and her mother Candra Alston (right) in 2011).

The only piece of evidence left at the scene was an unspecified DNA sample.

There were no witnesses to the murder, so the local authorities turned to the forensic phenotyping and found the person was a male with dark-skinned, brown hair and brown eyes (profile pictured).

There were no witnesses to the murder, so the local authorities turned to the forensic phenotyping and found the person was a male with dark-skinned, brown hair and brown eyes (profile pictured).

There were no witnesses to the murder, so the local authorities turned to the forensic phenotyping and found the person was a male with dark-skinned, brown hair and brown eyes.

Mark Vinson, a cold case investigator with the Columbia police department, said that more than 200 people were interviewed in connection with the deaths.

Around 150 of them submitted their DNA – but none matched the sample left at the scene.

 

Ancillary:

FIND LONG-LOST RELATIVES USING YOUR DNA

Family history site Ancestry has extended its AncestryDNA service – a home testing kit that unlocks the secrets of a person’s genetic ethnicity – to the UK.

The results can be cross-checked with millions of family trees to help people discover unknown relatives.

It uses microarray-based autosomal DNA testing, which looks at person’s entire genome at more than 700,000 locations using saliva.

Since it was released in 2012, AncestryDNA has been used by around 700,000 people.

All of these results have been stored on a secure, encrypted database, and each set of results is linked to a person’s individual Ancestry account and subsequent family tree.

AncestryDNA can help people identify relationships with unknown relatives through a list of possible DNA member matches.

 

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Climate Change, Research, Science, Society

Declarations of interest…

(From the archives) Originally posted on January 25, 2013 by markdowe

ANONYMITY IS SELF-SERVING

Declarations of interest are now standard practice for scientists who publish their work in recognised peer-reviewed journals. In medical research, for instance, it is important to know not just the findings and methodology of a particular study, but who actually paid for the work. And it would be unacceptable for scientists to put their names to a study involving a certain kind of drug if they refused to say whether they were paid by the drug company.

The same is true of climate research. If an organisation such as Greenpeace commissioned a climate study that was then published in a journal, we would expect the scientists involved to make it clear who funded the work. That, indeed, is the definition of declaration of interest.

It is clear, however, that some wealthy individuals feel they can hide behind anonymity when it comes to the funding of climate “scepticism”. As an example, the curiously labyrinthine route through which American billionaire industrialist, Charles Koch, funded his climate scepticism, was documented this week in order to preserve his anonymity.

In Britain, the climate-sceptic Global Warming Policy Foundation has received as much as £1m in anonymous donations since it was set up in 2009. The organisation has repeatedly refused to name its backers, yet the foundation has pursued climate scientists relentlessly for their alleged lack of transparency over data and methodology.

The foundation, which is registered as an educational charity, could just as well be described as an attack dog of the wealthy climate sceptics who have supported it. Yet the public does not know the identity of these individuals and can only guess at their motives. Surely, if the Global Warming Policy Foundation was genuinely concerned about the transparency of climate research, it should also tell us whose money it is relying upon.

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Government, Health, Medical, Research, Science, Society

Why is a medical body giving accreditation to homeopathic medicine? It’s unscientific…

HOMEOPATHIC MEDICINE

Recently, it was announced that all homeopathic practitioners can now opt to be vetted by the Professional Standards Authority (PSA).

As a result practitioners on the Society of Homeopaths’ register will be able to display the Accredited Voluntary Register (AVR) quality mark, a sign that they belong to a register which meets the robust standards of the PSA.

The PSA is a governmental body with two main duties. The first is to oversee the nine regulators of legally-defined medical practitioners – organisations such as the General Dental Council, the General Medical Council and the Nursing and Midwifery Council. Its second duty, however, is to assess the bodies which oversee those professions which aren’t considered ‘real’ medicine such as the British Acupuncture Council, or the United Kingdom Council for Psychotherapy. The PSA’s role here is to ensure that these bodies are meeting their own standards in areas such as education, training, management and the process of how complaints are handled. These are ‘voluntary registers’, and are essentially a form of industry self-regulation.

This dual role on part of the PSA is controversial, as its stated goal is to ‘promote the health, safety and wellbeing of users of health and social care services and the public’. Critics point out that these objectives appear to be contradicted by the endorsement of medical treatments which have never been proven to be more effective than the placebo effect in a clinical trial.

Homeopaths that are registered with the Society of Homeopaths, and who meet its qualifications, are now allowed to use the AVR quality mark signifying that they meet the PSA’s ‘robust standards’. This could mean using the symbol in an advert, or it could mean displaying it on homeopathic products. But this might mean the public buying something which they believe is medicine, but which is actually just an expensive bottle of ordinary water with an AVR mark on it.

Evidence suggests that homeopathy is an ineffective treatment for all health conditions and is no better than a placebo, and is a pseudoscience. It is classified as a complementary or alternative medicine, which, unlike conventional evidence-based medicine, relies on the premises that ‘like cures like’ (one where a substance that causes a specific symptom is also meant to alleviate that symptom) and that ‘ultra-dilution’ of something in water increases its potency. Both of these claims contradict fundamental aspects of modern medical science.

Homeopathic remedies are used as ‘cures’ for a wide range of conditions – such as mental health issues, asthma, diabetes and hay fever. While many patients have reported that they work, there is no evidence to show that these treatments are effective in any way beyond the established effectiveness of the placebo effect. Indeed, the Faculty of Homeopathy website even highlights itself that, up to the end of 2013, out of 188 research studies in homeopathy, nearly 60 per cent were either found to be inconclusive or presented a negative result. The PSA’s decision to give homeopathic practitioners a stamp of approval is, therefore, potentially conveying a dangerous or misleading message.

The PSA’s own stance on the issue is that it doesn’t exist to pass judgement on the effectiveness of any kind of medical treatment, be it dentistry or Freudian psychoanalysis – it’s just there to make sure that, if someone’s practicing in one of these fields, they’re meeting the standards that the body representing that field demands.

The PSA’s own standards for accreditation states:

‘The PSA recognises that not all disciplines are underpinned by evidence of proven therapeutic value. Some disciplines are subject to controlled randomised trials, others are based on qualitative evidence. Some rely on anecdotes. Nevertheless, these disciplines are legal and the public choose to use them. The Authority requires organisations to make this clear to the public so that they may make informed decisions.’

Yet this is the problem. The PSA’s task is to make sure that people are making ‘informed decisions’ about what they’re choosing when it comes to medical treatment. But the thing that gives the work of many of the voluntary register organisations, like the Society of Homeopaths, their legitimacy is the ARV quality mark. Something’s wrong with the system if a medical regulatory body is holding neurosurgeons and homeopaths to the same standard of proof, and telling the public that they’re equally trustworthy.

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