biotechnology


Machine Learning in Healthcare: Regulating Transparency

18 June 2020 by

Close up of Asian women with hi tech digital technology screen over the eye.

PHG, linked with Cambridge University, provides independent advice and evaluations of biomedical and digital innovations in healthcare. PHG has recently published a series of reports exploring the interpretability of machine learning in this context. The one I will focus on in this post is the report considering the requirements of the GDPR for machine learning in healthcare and medical research by way of transparency, interpretability, or explanation. Links to the other reports are given at the end of this post.

Just a brief summary of machine learning in healthcare (for the detail, go to PHG’s report Machine Learning Landscape).

Machine learning typically denotes “methods that only have task-specific intelligence and lack the broad powers of cognition feared when ‘AI’ is mentioned”. Artificial intelligence (AI) can be defined as “the science and engineering of making computers behave in ways that, until recently, we thought required human intelligence.” We are only beginning to realise the scope of intelligence that is silicone-based, rather than meat-based, in the reductionist words of neurscientist and author Sam Harris. It is important too to grasp the difference between types of programming. As this report puts it,

Machine learning as a programming paradigm differs from classical programming in that machine learning systems are trained rather than explicitly programmed. Classical programming combines rules and data to provide answers. Machine learning combines data and answers to provide the rules


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Woman’s wish to donate unwanted embryos to scientific research rejected by Strasbourg Court

8 September 2015 by

cdce0842e2fac4bcf0335ab5c367-is-embryonic-stem-cell-research-wrongParrillo v Italy (application no. 46470/11) Grand Chamber of the European Court of Human Rights, [2015] ECHR 755 (27 August 2015) – read judgment

The Grand Chamber of the Strasbourg Court has ruled that the Italian ban on the donation of embryos obtained by IVF procedures to scientific research was within Italy’s margin of appreciation and therefore not in breach of the applicant’s right of private life and autonomy, even though she was willing to give the embryos to scientific research, since she no longer wanted to proceed with pregnancy after her partner was killed covering the war in Iraq. By donating these cryopreserved embryos to research she would, she argued, make an important contribution to research into medical therapies and cures. 

A strong dissent to the majority judgment is worth pointing up at the outset. The Hungarian judge, Andras Sajó, found Italy’s general ban quite out of order. Not only did it disregard the applicant’s right to self-determination with respect to an important private decision, it did so in an absolute and unforeseeable manner.

The law contains no transitional rules which would have enabled the proper authority to take into consideration the specific situation of the applicant, whose embryos obtained from the IVF treatment were placed in cryopreservation in 2002 and whose husband passed away in 2003, three months before the law entered into force.

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EU Court gives the go ahead on certain stem cells – Olivia Hart

22 December 2014 by

parthenote-stemcellInternational Stem Cell Corporation v Comptroller General of Patents [2014] EUECJ C-364-13, 18 December 2014 – read judgment 

This was a referral to the European Court of Justice (CJEU) requesting clarification of Article 6(2) of Directive 98/44/EC protecting biotechnological inventions (“the Biotech Directive”). We posted earlier about the High Court decision leading up to the referral concerning two GB patent applications that both involve the ‘parthenogenetic activation of oocytes’. The Court asked for clarification on what exactly defines a human embryo and what precisely is the developmental potential of a parthenote

Ever since scientists came upon the idea of using embryonic stem cells for therapeutic purposes there has been a something of an ethical furore around the topic. So the pressure has been on to find alternatives. Parthenotes – products of unfertilised egg division – have been proposed as candidates. However even research using parthenotes may fall foul of the law’s protection of ‘human dignity’. 
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The patentability of living things: the latest in the BRCA gene saga

7 October 2014 by

298x232-dna_genetic_test-298x232_dna_genetic_testD’Arcy v Myriad Genetics Inc [2014] FCAFC 115 (5 September 2014) – read judgment The recent ruling from the Full Federal Court of Australia allowing the breast cancer gene isolated in the laboratory to be patented contrasts sharply with the ruling by the US Supreme Court last year that a naturally occurring DNA segment is a “product of nature” and therefore not patent eligible merely because it has been isolated. The implications of this ruling for gene testing and patenting of biological products have been eloquently discussed elsewhere and I will not attempt to cover the same ground – see for example the excellent discussion posted by the Enhanced Genetic Services Project. All I want to point up in this post – apart from the obvious need for intellectual property law to encompass the development of science and technology – is the Australian court’s focus on how easily misled one may be by semantics in this sort of dispute. This ruling upholds an earlier decision that gene patenting is permissible under Australian law, declaring that “the boundaries of the conception of patentability are not dictated only by deductive logic from the linguistic premises formulated in the scientific knowledge of a particular age”. The concept of patentability has been broadening since the first quarter of the 17th century, and there is no reason why it should reach an artificial wall erected by unfathomable and unexplained “laws of nature” (a premise much relied upon by the US Supreme Court). I posted last year on the decision of the US Supreme Court in Association for Molecular Pathology v Myriad Genetics Inc. It will be remembered that that Court held that a sequence of DNA mimicking the BRCA breast cancer mutation could not be patented because DNA’s information sequences and  all the other processes that allow the information to manufacture bodily tissues occur naturally within human cells. 
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Human genes may not be patented, but synthesised ones can, rules US Supreme Court

13 June 2013 by

298x232-dna_genetic_test-298x232_dna_genetic_testAssociation for Molecular Pathology et al v Myriad Genetics Inc, et al, United States Supreme Court 13 June 2013 – read judgment. The headlines are misleading. Myriad Genetics has lost some, but not all of its patent protection as a result of this final ruling in the long running litigation concerning the company’s BRCA 1 and BRCA 2 breast cancer gene patents.  According to the American Council on Science and Health, the Court’s decision is

a groundbreaking moment in the history of biotechnology, and a case that will surely rank among the most noteworthy biomedical decisions of our time.

I have posted here, here and here on previous stages in the Myriad patent case, in the United States and Australia, so will not set out the facts again (although for anyone who is interested, the Supreme Court judgment provides a superbly clear explanation of the molecular biology underlying the issues).
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The spanner of “human dignity” in the wheels of modern medicine

22 April 2013 by

parthenote-stemcellInternational Stem Cell Corporation v Comptroller General of Patents 17 April 2013  [2013] EWHC 807 (Ch) – read judgment

The EU bans the patenting of human embryos for commercial purposes. This ban is implemented in national law via the 1977 Patents Act. But what precisely is a “human embryo” for the purposes of the Biotech Directive? Or, put another way, must the process involving embryonic stem cells be capable of developing into a human being, before the ban can bite?

Stem cells – not just the embryonic variety – are vital to current medical research. This is because they have the capacity to differentiate into almost any type of adult cell, thus opening the door to a wide variety of new therapies and other medical applications. In theory, stem cells can be grown in the lab and developed into healthy adult cells to correct cardiovascular disorders , diabetes and a range of degenerative brain diseases and spinal cord injuries. One of the first triumphs of stem cell therapy is the ability of retinal pigment epithelium cells, cultured from embryonic stem cells (ESCs), to reverse the effects of age related macular degeneration. Other potential applications include the treatment of burns, strokes, eye disease, spinal cord injuries and certain forms of cancer.

But the concept of ESCs  is fraught with emotion and controversy and scientists have worked, with varying degrees of success, at finding stem cells elsewhere, either in adult tissue, or by creating stem cells from non-viable embryos.
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The small farmer and Goliath Monsanto

27 February 2013 by

Feb22_2013_34044559_Soybeans_MonsantoMistakeHeadline4325411721Updated: The Supreme Court has now ruled on this case, rejecting Bowman’s appeal: see judgment. On Tuesday 19 February, the US Supreme Court heard  opening arguments in the latest stage of the battle between a 75 year old farmer and the agri-giant Monsanto, over whether patents on seeds — or other things that can self-replicate — extend beyond the first generation of the products.  The dispute in  Bowman v Monsanto goes to the heart of the debate over the patenting of living organisms. This of course is also at the centre of the Myriad breast cancer gene litigation which I covered here.

The case is fascinating not just because it exposes the limits of patent law in an era of fast-growing biotechnology, but because it seems to speak to the concerns of the anti-GM lobby – the stranglehold of big corporations over farmers, the fear of transgenic organisms themselves and their consequences for agriculture. But Green woo about the dangers of genetically engineered crops will not find judicial endorsement in this litigation, despite the multiple briefs filed in support of Bowman, attacking GM technology.  This is an inquiry into the reality or otherwise of patenting nature, not the morality thereof.  As The Atlantic summarises it:

 It’s a story about technology and innovation and investment, about legal standards and appellate precedent and statutory intent, about the nature of nature and how the law ought to answer the basic question of who owns the rights to the seeds of planted seeds.
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The march of “dignity” – an anti-libertarian force?

22 October 2012 by

The recognition of a right to life, liberty, and the autonomy of the individual and the mandate of government to secure these rights is being threatened by an increasingly illiberal notion of “human dignity”, says evolutionary psychologist Stephen Pinker.

His 2008 broadside in The New Republic took to task a now defunct body, the US President’s Council on Bioethics whose publication Human Dignity and Bioethics is shot through with disquiet about advances in biotechnology. It could not be more different from the enlightened report issued earlier this year by  the Council’s successor calling on the current administration not to stifle biomedical research with over-restrictive regulation (see my post). Does the contrast between the  present advisory body’s recommendations and the report put before the previous President signal a fundamental change in the way we approach progress in this field? Probably not. Only two weeks ago, Sir John Gurdon (the Nobel physiologist whom schoolteachers had written off as a scientist) bemoaned the regulatory restrictions that make important therapies too costly to pursue. Pinker’s dismay at the “scientific illiteracy” of society rings true today:

Ever since the cloning of Dolly the sheep a decade ago, the panic sown by conservative bioethicists, amplified by a sensationalist press, has turned the public discussion of bioethics into a miasma of scientific illiteracy. Brave New World, a work of fiction, is treated as inerrant prophesy. Cloning is confused with resurrecting the dead or mass-producing babies. Longevity becomes “immortality,” improvement becomes “perfection,” the screening for disease genes becomes “designer babies” or even “reshaping the species.” The reality is that biomedical research is a Sisyphean struggle to eke small increments in health from a staggeringly complex, entropy-beset human body. It is not, and probably never will be, a runaway train. 
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Can morality be explained by science? Do human rights = echr1(hra − 1) + echr2(hra − 2)

14 September 2012 by

As scientists gather more and more information about the very large and the very small, where will they stop? Put another way, if ethics and religion can’t deliver, do we look to science for an answer?

The novelist Ian McEwan has no hesitation in incorporating the latest discoveries in physics and neuroscience in the messy psychological drama that constitutes a novel; in his latest bestseller  he investigates the possibility of embedding a mathematical problem within an ethical one which drives along the story within the story. And last week the Guardian hosted a debate between physicist Lawrence Krauss and Julian Baggini on whether science can provide better answers to the big questions of morality than any of the canons of philosophy; now we have a report from the USA in which a Georgia Tech professor has hypothesized lethal weapons systems that are ethically superior to human soldiers on the battlefield (by substituting for the unreliable human hairbreadth trigger robots that are programmed to comply with international rules of war).

 Military technology aside, the essential question asks for a bit of out of the box thinking. If we can identify specific biological answers to why we make certain decisions and judgments, then we can look to science as a basis for moral decisions, which are after all only sensible  if they are based on reason, which is itself based on empirical evidence. In Lawrence Krauss’ view, ultimately
 our understanding of neurobiology and evolutionary biology and psychology will reduce our understanding of morality to some well-defined biological constructs.
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Courts entitled to ignore European Court decision on DNA and fingerprint retention

23 July 2010 by

DNA database impact on human rightsUpdated, 1/9/10 | R (C) v Commissioner of the Police of the Metropolis [2010] WLR (D) 193 – Read judgment

When faced with conflicting authorities from the European Court of Human Rights and the House of Lords (now the Supreme Court) on the indefinite retention of DNA profiles and fingerprints by the police, the Divisional Court held that they were bound to follow the House of Lords.

This was so despite clear indications from the previous and current governments that the law would be changed to take account of the Strasbourg decision. However, as leave to appeal was granted, the Supreme Court will now have the opportunity to revisit the issue and determine the law in this controversial area.

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