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CRISPR and editing the germline in the US (part 3 of 3): public discussions and pop culture

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After giving a basic explanation of the technology and some of the controversies in part 1 and offering more detail about the technology and about the possibility of designer babies in part 2; this part covers public discussion, a call for one and the suggestion that one is taking place in popular culture.

But a discussion does need to happen

In a move that is either an exquisite coincidence or has been carefully orchestrated (I vote for the latter), researchers from the University of Wisconsin-Madison have released a study about attitudes in the US to human genome editing. From an Aug. 11, 2017 University of Wisconsin-Madison news release (also on EurekAllert),

In early August 2017, an international team of scientists announced they had successfully edited the DNA of human embryos. As people process the political, moral and regulatory issues of the technology — which nudges us closer to nonfiction than science fiction — researchers at the University of Wisconsin-Madison and Temple University show the time is now to involve the American public in discussions about human genome editing.

In a study published Aug. 11 in the journal Science, the researchers assessed what people in the United States think about the uses of human genome editing and how their attitudes may drive public discussion. They found a public divided on its uses but united in the importance of moving conversations forward.

“There are several pathways we can go down with gene editing,” says UW-Madison’s Dietram Scheufele, lead author of the study and member of a National Academy of Sciences committee that compiled a report focused on human gene editing earlier this year. “Our study takes an exhaustive look at all of those possible pathways forward and asks where the public stands on each one of them.”

Compared to previous studies on public attitudes about the technology, the new study takes a more nuanced approach, examining public opinion about the use of gene editing for disease therapy versus for human enhancement, and about editing that becomes hereditary versus editing that does not.

The research team, which included Scheufele and Dominique Brossard — both professors of life sciences communication — along with Michael Xenos, professor of communication arts, first surveyed study participants about the use of editing to treat disease (therapy) versus for enhancement (creating so-called “designer babies”). While about two-thirds of respondents expressed at least some support for therapeutic editing, only one-third expressed support for using the technology for enhancement.

Diving even deeper, researchers looked into public attitudes about gene editing on specific cell types — somatic or germline — either for therapy or enhancement. Somatic cells are non-reproductive, so edits made in those cells do not affect future generations. Germline cells, however, are heritable, and changes made in these cells would be passed on to children.

Public support of therapeutic editing was high both in cells that would be inherited and those that would not, with 65 percent of respondents supporting therapy in germline cells and 64 percent supporting therapy in somatic cells. When considering enhancement editing, however, support depended more upon whether the changes would affect future generations. Only 26 percent of people surveyed supported enhancement editing in heritable germline cells and 39 percent supported enhancement of somatic cells that would not be passed on to children.

“A majority of people are saying that germline enhancement is where the technology crosses that invisible line and becomes unacceptable,” says Scheufele. “When it comes to therapy, the public is more open, and that may partly be reflective of how severe some of those genetically inherited diseases are. The potential treatments for those diseases are something the public at least is willing to consider.”

Beyond questions of support, researchers also wanted to understand what was driving public opinions. They found that two factors were related to respondents’ attitudes toward gene editing as well as their attitudes toward the public’s role in its emergence: the level of religious guidance in their lives, and factual knowledge about the technology.

Those with a high level of religious guidance in their daily lives had lower support for human genome editing than those with low religious guidance. Additionally, those with high knowledge of the technology were more supportive of it than those with less knowledge.

While respondents with high religious guidance and those with high knowledge differed on their support for the technology, both groups highly supported public engagement in its development and use. These results suggest broad agreement that the public should be involved in questions of political, regulatory and moral aspects of human genome editing.

“The public may be split along lines of religiosity or knowledge with regard to what they think about the technology and scientific community, but they are united in the idea that this is an issue that requires public involvement,” says Scheufele. “Our findings show very nicely that the public is ready for these discussions and that the time to have the discussions is now, before the science is fully ready and while we have time to carefully think through different options regarding how we want to move forward.”

Here’s a  link to and a citation for the paper,

U.S. attitudes on human genome editing by Dietram A. Scheufele, Michael A. Xenos, Emily L. Howell, Kathleen M. Rose, Dominique Brossard1, and Bruce W. Hardy. Science 11 Aug 2017: Vol. 357, Issue 6351, pp. 553-554 DOI: 10.1126/science.aan3708

This paper is behind a paywall.

A couple of final comments

Briefly, I notice that there’s no mention of the ethics of patenting this technology in the news release about the study.

Moving on, it seems surprising that the first team to engage in germline editing in the US is in Oregon; I would have expected the work to come from Massachusetts, California, or Illinois where a lot of bleeding edge medical research is performed. However, given the dearth of financial support from federal funding institutions, it seems likely that only an outsider would dare to engage i the research. Given the timing, Mitalipov’s work was already well underway before the recent about-face from the US National Academy of Sciences (Note: Kaiser’s Feb. 14, 2017 article does note that for some the recent recommendations do not represent any change).

As for discussion on issues such as editing of the germline, I’ve often noted here that popular culture (including advertising with the science fiction and other dramas laid in various media) often provides an informal forum for discussion. Joelle Renstrom in an Aug. 13, 2017 article for slate.com writes that Orphan Black (a BBC America series featuring clones) opened up a series of questions about science and ethics in the guise of a thriller about clones. She offers a précis of the first four seasons (Note: A link has been removed),

If you stopped watching a few seasons back, here’s a brief synopsis of how the mysteries wrap up. Neolution, an organization that seeks to control human evolution through genetic modification, began Project Leda, the cloning program, for two primary reasons: to see whether they could and to experiment with mutations that might allow people (i.e., themselves) to live longer. Neolution partnered with biotech companies such as Dyad, using its big pharma reach and deep pockets to harvest people’s genetic information and to conduct individual and germline (that is, genetic alterations passed down through generations) experiments, including infertility treatments that result in horrifying birth defects and body modification, such as tail-growing.

She then provides the article’s thesis (Note: Links have been removed),

Orphan Black demonstrates Carl Sagan’s warning of a time when “awesome technological powers are in the hands of a very few.” Neolutionists do whatever they want, pausing only to consider whether they’re missing an opportunity to exploit. Their hubris is straight out of Victor Frankenstein’s playbook. Frankenstein wonders whether he ought to first reanimate something “of simpler organisation” than a human, but starting small means waiting for glory. Orphan Black’s evil scientists embody this belief: if they’re going to play God, then they’ll control not just their own destinies, but the clones’ and, ultimately, all of humanity’s. Any sacrifices along the way are for the greater good—reasoning that culminates in Westmoreland’s eugenics fantasy to genetically sterilize 99 percent of the population he doesn’t enhance.

Orphan Black uses sci-fi tropes to explore real-world plausibility. Neolution shares similarities with transhumanism, the belief that humans should use science and technology to take control of their own evolution. While some transhumanists dabble in body modifications, such as microchip implants or night-vision eye drops, others seek to end suffering by curing human illness and aging. But even these goals can be seen as selfish, as access to disease-eradicating or life-extending technologies would be limited to the wealthy. Westmoreland’s goal to “sell Neolution to the 1 percent” seems frighteningly plausible—transhumanists, who statistically tend to be white, well-educated, and male, and their associated organizations raise and spend massive sums of money to help fulfill their goals. …

…

On Orphan Black, denial of choice is tantamount to imprisonment. That the clones have to earn autonomy underscores the need for ethics in science, especially when it comes to genetics. The show’s message here is timely given the rise of gene-editing techniques such as CRISPR. Recently, the National Academy of Sciences gave germline gene editing the green light, just one year after academy scientists from around the world argued it would be “irresponsible to proceed” without further exploring the implications. Scientists in the United Kingdom and China have already begun human genetic engineering and American scientists recently genetically engineered a human embryo for the first time. The possibility of Project Leda isn’t farfetched. Orphan Black warns us that money, power, and fear of death can corrupt both people and science. Once that happens, loss of humanity—of both the scientists and the subjects—is inevitable.

In Carl Sagan’s dark vision of the future, “people have lost the ability to set their own agendas or knowledgeably question those in authority.” This describes the plight of the clones at the outset of Orphan Black, but as the series continues, they challenge this paradigm by approaching science and scientists with skepticism, ingenuity, and grit. …

I hope there are discussions such as those Scheufele and Brossard are advocating but it might be worth considering that there is already some discussion underway, as informal as it is.

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Part 1: CRISPR and editing the germline in the US (part 1 of 3): In the beginning

Part 2: CRISPR and editing the germline in the US (part 2 of 3): ‘designer babies’?

CRISPR and editing the germline in the US (part 2 of 3): ‘designer babies’?

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Having included an explanation of CRISPR-CAS9 technology along with the news about the first US team to edit the germline and bits and pieces about ethics and a patent fight (part 1), this part hones in on the details of the work and worries about ‘designer babies’.

The interest flurry

I found three articles addressing the research and all three concur that despite some of the early reporting, this is not the beginning of a ‘designer baby’ generation.

First up was Nick Thieme in a July 28, 2017 article for Slate,

MIT Technology Review reported Thursday that a team of researchers from Portland, Oregon were the first team of U.S.-based scientists to successfully create a genetically modified human embryo. The researchers, led by Shoukhrat Mitalipov of Oregon Health and Science University, changed the DNA of—in MIT Technology Review’s words—“many tens” of genetically-diseased embryos by injecting the host egg with CRISPR, a DNA-based gene editing tool first discovered in bacteria, at the time of fertilization. CRISPR-Cas9, as the full editing system is called, allows scientists to change genes accurately and efficiently. As has happened with research elsewhere, the CRISPR-edited embryos weren’t implanted—they were kept sustained for only a couple of days.

In addition to being the first American team to complete this feat, the researchers also improved upon the work of the three Chinese research teams that beat them to editing embryos with CRISPR: Mitalipov’s team increased the proportion of embryonic cells that received the intended genetic changes, addressing an issue called “mosaicism,” which is when an embryo is comprised of cells with different genetic makeups. Increasing that proportion is essential to CRISPR work in eliminating inherited diseases, to ensure that the CRISPR therapy has the intended result. The Oregon team also reduced the number of genetic errors introduced by CRISPR, reducing the likelihood that a patient would develop cancer elsewhere in the body.

Separate from the scientific advancements, it’s a big deal that this work happened in a country with such intense politicization of embryo research. …

But there are a great number of obstacles between the current research and the future of genetically editing all children to be 12-foot-tall Einsteins.

…

Ed Yong in an Aug. 2, 2017 article for The Atlantic offered a comprehensive overview of the research and its implications (unusually for Yong, there seems to be mildly condescending note but it’s worth ignoring for the wealth of information in the article; Note: Links have been removed),

… the full details of the experiment, which are released today, show that the study is scientifically important but much less of a social inflection point than has been suggested. “This has been widely reported as the dawn of the era of the designer baby, making it probably the fifth or sixth time people have reported that dawn,” says Alta Charo, an expert on law and bioethics at the University of Wisconsin-Madison. “And it’s not.”

Given the persistent confusion around CRISPR and its implications, I’ve laid out exactly what the team did, and what it means.

Who did the experiments?

Shoukhrat Mitalipov is a Kazakhstani-born cell biologist with a history of breakthroughs—and controversy—in the stem cell field. He was the scientist to clone monkeys. He was the first to create human embryos by cloning adult cells—a move that could provide patients with an easy supply of personalized stem cells. He also pioneered a technique for creating embryos with genetic material from three biological parents, as a way of preventing a group of debilitating inherited diseases.

Although MIT Tech Review name-checked Mitalipov alone, the paper splits credit for the research between five collaborating teams—four based in the United States, and one in South Korea.

What did they actually do?

The project effectively began with an elevator conversation between Mitalipov and his colleague Sanjiv Kaul. Mitalipov explained that he wanted to use CRISPR to correct a disease-causing gene in human embryos, and was trying to figure out which disease to focus on. Kaul, a cardiologist, told him about hypertrophic cardiomyopathy (HCM)—an inherited heart disease that’s commonly caused by mutations in a gene called MYBPC3. HCM is surprisingly common, affecting 1 in 500 adults. Many of them lead normal lives, but in some, the walls of their hearts can thicken and suddenly fail. For that reason, HCM is the commonest cause of sudden death in athletes. “There really is no treatment,” says Kaul. “A number of drugs are being evaluated but they are all experimental,” and they merely treat the symptoms. The team wanted to prevent HCM entirely by removing the underlying mutation.

They collected sperm from a man with HCM and used CRISPR to change his mutant gene into its normal healthy version, while simultaneously using the sperm to fertilize eggs that had been donated by female volunteers. In this way, they created embryos that were completely free of the mutation. The procedure was effective, and avoided some of the critical problems that have plagued past attempts to use CRISPR in human embryos.

Wait, other human embryos have been edited before?

There have been three attempts in China. The first two—in 2015 and 2016—used non-viable embryos that could never have resulted in a live birth. The third—announced this March—was the first to use viable embryos that could theoretically have been implanted in a womb. All of these studies showed that CRISPR gene-editing, for all its hype, is still in its infancy.

The editing was imprecise. CRISPR is heralded for its precision, allowing scientists to edit particular genes of choice. But in practice, some of the Chinese researchers found worrying levels of off-target mutations, where CRISPR mistakenly cut other parts of the genome.

The editing was inefficient. The first Chinese team only managed to successfully edit a disease gene in 4 out of 86 embryos, and the second team fared even worse.

The editing was incomplete. Even in the successful cases, each embryo had a mix of modified and unmodified cells. This pattern, known as mosaicism, poses serious safety problems if gene-editing were ever to be used in practice. Doctors could end up implanting women with embryos that they thought were free of a disease-causing mutation, but were only partially free. The resulting person would still have many tissues and organs that carry those mutations, and might go on to develop symptoms.

What did the American team do differently?

The Chinese teams all used CRISPR to edit embryos at early stages of their development. By contrast, the Oregon researchers delivered the CRISPR components at the earliest possible point—minutes before fertilization. That neatly avoids the problem of mosaicism by ensuring that an embryo is edited from the very moment it is created. The team did this with 54 embryos and successfully edited the mutant MYBPC3 gene in 72 percent of them. In the other 28 percent, the editing didn’t work—a high failure rate, but far lower than in previous attempts. Better still, the team found no evidence of off-target mutations.

This is a big deal. Many scientists assumed that they’d have to do something more convoluted to avoid mosaicism. They’d have to collect a patient’s cells, which they’d revert into stem cells, which they’d use to make sperm or eggs, which they’d edit using CRISPR. “That’s a lot of extra steps, with more risks,” says Alta Charo. “If it’s possible to edit the embryo itself, that’s a real advance.” Perhaps for that reason, this is the first study to edit human embryos that was published in a top-tier scientific journal—Nature, which rejected some of the earlier Chinese papers.

Is this kind of research even legal?

Yes. In Western Europe, 15 countries out of 22 ban any attempts to change the human germ line—a term referring to sperm, eggs, and other cells that can transmit genetic information to future generations. No such stance exists in the United States but Congress has banned the Food and Drug Administration from considering research applications that make such modifications. Separately, federal agencies like the National Institutes of Health are banned from funding research that ultimately destroys human embryos. But the Oregon team used non-federal money from their institutions, and donations from several small non-profits. No taxpayer money went into their work. [emphasis mine]

Why would you want to edit embryos at all?

Partly to learn more about ourselves. By using CRISPR to manipulate the genes of embryos, scientists can learn more about the earliest stages of human development, and about problems like infertility and miscarriages. That’s why biologist Kathy Niakan from the Crick Institute in London recently secured a license from a British regulator to use CRISPR on human embryos.

…

Isn’t this a slippery slope toward making designer babies?

In terms of avoiding genetic diseases, it’s not conceptually different from PGD, which is already widely used. The bigger worry is that gene-editing could be used to make people stronger, smarter, or taller, paving the way for a new eugenics, and widening the already substantial gaps between the wealthy and poor. But many geneticists believe that such a future is fundamentally unlikely because complex traits like height and intelligence are the work of hundreds or thousands of genes, each of which have a tiny effect. The prospect of editing them all is implausible. And since genes are so thoroughly interconnected, it may be impossible to edit one particular trait without also affecting many others.

“There’s the worry that this could be used for enhancement, so society has to draw a line,” says Mitalipov. “But this is pretty complex technology and it wouldn’t be hard to regulate it.”

…

Does this discovery have any social importance at all?

“It’s not so much about designer babies as it is about geographical location,” says Charo. “It’s happening in the United States, and everything here around embryo research has high sensitivity.” She and others worry that the early report about the study, before the actual details were available for scrutiny, could lead to unnecessary panic. “Panic reactions often lead to panic-driven policy … which is usually bad policy,” wrote Greely [bioethicist Hank Greely].

…

As I understand it, despite the change in stance, there is no federal funding available for the research performed by Mitalipov and his team.

Finally, University College London (UCL) scientists Joyce Harper and Helen O’Neill wrote about CRISPR, the Oregon team’s work, and the possibilities in an Aug. 3, 2017 essay for The Conversation (Note: Links have been removed),

…

The genome editing tool used, CRISPR-Cas9, has transformed the field of biology in the short time since its discovery in that it not only promises, but delivers. CRISPR has surpassed all previous efforts to engineer cells and alter genomes at a fraction of the time and cost.

The technology, which works like molecular scissors to cut and paste DNA, is a natural defence system that bacteria use to fend off harmful infections. This system has the ability to recognise invading virus DNA, cut it and integrate this cut sequence into its own genome – allowing the bacterium to render itself immune to future infections of viruses with similar DNA. It is this ability to recognise and cut DNA that has allowed scientists to use it to target and edit specific DNA regions.

When this technology is applied to “germ cells” – the sperm and eggs – or embryos, it changes the germline. That means that any alterations made would be permanent and passed down to future generations. This makes it more ethically complex, but there are strict regulations around human germline genome editing, which is predominantly illegal. The UK received a licence in 2016 to carry out CRISPR on human embryos for research into early development. But edited embryos are not allowed to be inserted into the uterus and develop into a fetus in any country.

Germline genome editing came into the global spotlight when Chinese scientists announced in 2015 that they had used CRISPR to edit non-viable human embryos – cells that could never result in a live birth. They did this to modify the gene responsible for the blood disorder β-thalassaemia. While it was met with some success, it received a lot of criticism because of the premature use of this technology in human embryos. The results showed a high number of potentially dangerous, off-target mutations created in the procedure.

Impressive results

The new study, published in Nature, is different because it deals with viable human embryos and shows that the genome editing can be carried out safely – without creating harmful mutations. The team used CRISPR to correct a mutation in the gene MYBPC3, which accounts for approximately 40% of the myocardial disease hypertrophic cardiomyopathy. This is a dominant disease, so an affected individual only needs one abnormal copy of the gene to be affected.

The researchers used sperm from a patient carrying one copy of the MYBPC3 mutation to create 54 embryos. They edited them using CRISPR-Cas9 to correct the mutation. Without genome editing, approximately 50% of the embryos would carry the patients’ normal gene and 50% would carry his abnormal gene.

After genome editing, the aim would be for 100% of embryos to be normal. In the first round of the experiments, they found that 66.7% of embryos – 36 out of 54 – were normal after being injected with CRIPSR. Of the remaining 18 embryos, five had remained unchanged, suggesting editing had not worked. In 13 embryos, only a portion of cells had been edited.

The level of efficiency is affected by the type of CRISPR machinery used and, critically, the timing in which it is put into the embryo. The researchers therefore also tried injecting the sperm and the CRISPR-Cas9 complex into the egg at the same time, which resulted in more promising results. This was done for 75 mature donated human eggs using a common IVF technique called intracytoplasmic sperm injection. This time, impressively, 72.4% of embryos were normal as a result. The approach also lowered the number of embryos containing a mixture of edited and unedited cells (these embryos are called mosaics).

Finally, the team injected a further 22 embryos which were grown into blastocyst – a later stage of embryo development. These were sequenced and the researchers found that the editing had indeed worked. Importantly, they could show that the level of off-target mutations was low.

A brave new world?

So does this mean we finally have a cure for debilitating, heritable diseases? It’s important to remember that the study did not achieve a 100% success rate. Even the researchers themselves stress that further research is needed in order to fully understand the potential and limitations of the technique.

In our view, it is unlikely that genome editing would be used to treat the majority of inherited conditions anytime soon. We still can’t be sure how a child with a genetically altered genome will develop over a lifetime, so it seems unlikely that couples carrying a genetic disease would embark on gene editing rather than undergoing already available tests – such as preimplantation genetic diagnosis or prenatal diagnosis – where the embryos or fetus are tested for genetic faults.

…

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As might be expected there is now a call for public discussion about the ethics about this kind of work. See Part 3.

For anyone who started in the middle of this series, here’s Part 1 featuring an introduction to the technology and some of the issues.

CRISPR and editing the germline in the US (part 1 of 3): In the beginning

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There’s been a minor flurry of interest in CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats; also known as CRISPR-CAS9), a gene-editing technique, since a team in Oregon announced a paper describing their work editing the germline. Since I’ve been following the CRISPR-CAS9 story for a while this seems like a good juncture for a more in-depth look at the topic. In this first part I’m including an introduction to CRISPR, some information about the latest US work, and some previous writing about ethics issues raised when Chinese scientists first announced their work editing germlines in 2015 and during the patent dispute between the University of California at Berkeley and Harvard University’s Broad Institute.

Introduction to CRISPR

I’ve been searching for a good description of CRISPR and this helped to clear up some questions for me (Thank you to MIT Review),

For anyone who’s been reading about science for a while, this upbeat approach to explaining how a particular technology will solve all sorts of problems will seem quite familiar. It’s not the most hyperbolic piece I’ve seen but it barely mentions any problems associated with research (for some of the problems see: ‘The interest flurry’ later in part 2).

Oregon team

Steve Connor’s July 26, 2017 article for the MIT (Massachusetts Institute of Technology) Technology Review breaks the news (Note: Links have been removed),

The first known attempt at creating genetically modified human embryos in the United States has been carried out by a team of researchers in Portland, Oregon, MIT Technology Review has learned.

The effort, led by Shoukhrat Mitalipov of Oregon Health and Science University, involved changing the DNA of a large number of one-cell embryos with the gene-editing technique CRISPR, according to people familiar with the scientific results.

Until now, American scientists have watched with a combination of awe, envy, and some alarm as scientists elsewhere were first to explore the controversial practice. To date, three previous reports of editing human embryos were all published by scientists in China.

Now Mitalipov is believed to have broken new ground both in the number of embryos experimented upon and by demonstrating that it is possible to safely and efficiently correct defective genes that cause inherited diseases.

Although none of the embryos were allowed to develop for more than a few days—and there was never any intention of implanting them into a womb—the experiments are a milestone on what may prove to be an inevitable journey toward the birth of the first genetically modified humans.

In altering the DNA code of human embryos, the objective of scientists is to show that they can eradicate or correct genes that cause inherited disease, like the blood condition beta-thalassemia. The process is termed “germline engineering” because any genetically modified child would then pass the changes on to subsequent generations via their own germ cells—the egg and sperm.

Some critics say germline experiments could open the floodgates to a brave new world of “designer babies” engineered with genetic enhancements—a prospect bitterly opposed by a range of religious organizations, civil society groups, and biotech companies.

The U.S. intelligence community last year called CRISPR a potential “weapon of mass destruction.”

Here’s a link to a citation for the groundbreaking paper,

Correction of a pathogenic gene mutation in human embryos by Hong Ma, Nuria Marti-Gutierrez, Sang-Wook Park, Jun Wu, Yeonmi Lee, Keiichiro Suzuki, Amy Koski, Dongmei Ji, Tomonari Hayama, Riffat Ahmed, Hayley Darby, Crystal Van Dyken, Ying Li, Eunju Kang, A.-Reum Park, Daesik Kim, Sang-Tae Kim, Jianhui Gong, Ying Gu, Xun Xu, David Battaglia, Sacha A. Krieg, David M. Lee, Diana H. Wu, Don P. Wolf, Stephen B. Heitner, Juan Carlos Izpisua Belmonte, Paula Amato, Jin-Soo Kim, Sanjiv Kaul, & Shoukhrat Mitalipov. Nature (2017) doi:10.1038/nature23305 Published online 02 August 2017

This paper appears to be open access.

CRISPR Issues: ethics and patents

In my May 14, 2015 posting I mentioned a ‘moratorium’ on germline research, the Chinese research paper, and the stance taken by the US National Institutes of Health (NIH),

The CRISPR technology has reignited a discussion about ethical and moral issues of human genetic engineering some of which is reviewed in an April 7, 2015 posting about a moratorium by Sheila Jasanoff, J. Benjamin Hurlbut and Krishanu Saha for the Guardian science blogs (Note: A link has been removed),

On April 3, 2015, a group of prominent biologists and ethicists writing in Science called for a moratorium on germline gene engineering; modifications to the human genome that will be passed on to future generations. The moratorium would apply to a technology called CRISPR/Cas9, which enables the removal of undesirable genes, insertion of desirable ones, and the broad recoding of nearly any DNA sequence.

Such modifications could affect every cell in an adult human being, including germ cells, and therefore be passed down through the generations. Many organisms across the range of biological complexity have already been edited in this way to generate designer bacteria, plants and primates. There is little reason to believe the same could not be done with human eggs, sperm and embryos. Now that the technology to engineer human germlines is here, the advocates for a moratorium declared, it is time to chart a prudent path forward. They recommend four actions: a hold on clinical applications; creation of expert forums; transparent research; and a globally representative group to recommend policy approaches.

…

The authors go on to review precedents and reasons for the moratorium while suggesting we need better ways for citizens to engage with and debate these issues,

An effective moratorium must be grounded in the principle that the power to modify the human genome demands serious engagement not only from scientists and ethicists but from all citizens. We need a more complex architecture for public deliberation, built on the recognition that we, as citizens, have a duty to participate in shaping our biotechnological futures, just as governments have a duty to empower us to participate in that process. Decisions such as whether or not to edit human genes should not be left to elite and invisible experts, whether in universities, ad hoc commissions, or parliamentary advisory committees. Nor should public deliberation be temporally limited by the span of a moratorium or narrowed to topics that experts deem reasonable to debate.

I recommend reading the post in its entirety as there are nuances that are best appreciated in the entirety of the piece.

Shortly after this essay was published, Chinese scientists announced they had genetically modified (nonviable) human embryos. From an April 22, 2015 article by David Cyranoski and Sara Reardon in Nature where the research and some of the ethical issues discussed,

In a world first, Chinese scientists have reported editing the genomes of human embryos. The results are published1 in the online journal Protein & Cell and confirm widespread rumours that such experiments had been conducted — rumours that sparked a high-profile debate last month2, 3 about the ethical implications of such work.

In the paper, researchers led by Junjiu Huang, a gene-function researcher at Sun Yat-sen University in Guangzhou, tried to head off such concerns by using ‘non-viable’ embryos, which cannot result in a live birth, that were obtained from local fertility clinics. The team attempted to modify the gene responsible for β-thalassaemia, a potentially fatal blood disorder, using a gene-editing technique known as CRISPR/Cas9. The researchers say that their results reveal serious obstacles to using the method in medical applications.

“I believe this is the first report of CRISPR/Cas9 applied to human pre-implantation embryos and as such the study is a landmark, as well as a cautionary tale,” says George Daley, a stem-cell biologist at Harvard Medical School in Boston, Massachusetts. “Their study should be a stern warning to any practitioner who thinks the technology is ready for testing to eradicate disease genes.”

….

Huang says that the paper was rejected by Nature and Science, in part because of ethical objections; both journals declined to comment on the claim. (Nature’s news team is editorially independent of its research editorial team.)

He adds that critics of the paper have noted that the low efficiencies and high number of off-target mutations could be specific to the abnormal embryos used in the study. Huang acknowledges the critique, but because there are no examples of gene editing in normal embryos he says that there is no way to know if the technique operates differently in them.

Still, he maintains that the embryos allow for a more meaningful model — and one closer to a normal human embryo — than an animal model or one using adult human cells. “We wanted to show our data to the world so people know what really happened with this model, rather than just talking about what would happen without data,” he says.

This, too, is a good and thoughtful read.

There was an official response in the US to the publication of this research, from an April 29, 2015 post by David Bruggeman on his Pasco Phronesis blog (Note: Links have been removed),

In light of Chinese researchers reporting their efforts to edit the genes of ‘non-viable’ human embryos, the National Institutes of Health (NIH) Director Francis Collins issued a statement (H/T Carl Zimmer).

…

“NIH will not fund any use of gene-editing technologies in human embryos. The concept of altering the human germline in embryos for clinical purposes has been debated over many years from many different perspectives, and has been viewed almost universally as a line that should not be crossed. Advances in technology have given us an elegant new way of carrying out genome editing, but the strong arguments against engaging in this activity remain. These include the serious and unquantifiable safety issues, ethical issues presented by altering the germline in a way that affects the next generation without their consent, and a current lack of compelling medical applications justifying the use of CRISPR/Cas9 in embryos.” …

The US has modified its stance according to a February 14, 2017 article by Jocelyn Kaiser for Science Magazine (Note: Links have been removed),

Editing the DNA of a human embryo to prevent a disease in a baby could be ethically allowable one day—but only in rare circumstances and with safeguards in place, says a widely anticipated report released today.

The report from an international committee convened by the U.S. National Academy of Sciences (NAS) and the National Academy of Medicine in Washington, D.C., concludes that such a clinical trial “might be permitted, but only following much more research” on risks and benefits, and “only for compelling reasons and under strict oversight.” Those situations could be limited to couples who both have a serious genetic disease and for whom embryo editing is “really the last reasonable option” if they want to have a healthy biological child, says committee co-chair Alta Charo, a bioethicist at the University of Wisconsin in Madison.

Some researchers are pleased with the report, saying it is consistent with previous conclusions that safely altering the DNA of human eggs, sperm, or early embryos—known as germline editing—to create a baby could be possible eventually. “They have closed the door to the vast majority of germline applications and left it open for a very small, well-defined subset. That’s not unreasonable in my opinion,” says genome researcher Eric Lander of the Broad Institute in Cambridge, Massachusetts. Lander was among the organizers of an international summit at NAS in December 2015 who called for more discussion before proceeding with embryo editing.

But others see the report as lowering the bar for such experiments because it does not explicitly say they should be prohibited for now. “It changes the tone to an affirmative position in the absence of the broad public debate this report calls for,” says Edward Lanphier, chairman of the DNA editing company Sangamo Therapeutics in Richmond, California. Two years ago, he co-authored a Nature commentary calling for a moratorium on clinical embryo editing.

One advocacy group opposed to embryo editing goes further. “We’re very disappointed with the report. It’s really a pretty dramatic shift from the existing and widespread agreement globally that human germline editing should be prohibited,” says Marcy Darnovsky, executive director of the Center for Genetics and Society in Berkeley, California.

Interestingly, this change of stance occurred just prior to a CRISPR patent decision (from my March 15, 2017 posting),

I have written about the CRISPR patent tussle (Harvard & MIT’s [Massachusetts Institute of Technology] Broad Institute vs the University of California at Berkeley) previously in a Jan. 6, 2015 posting and in a more detailed May 14, 2015 posting. I also mentioned (in a Jan. 17, 2017 posting) CRISPR and its patent issues in the context of a posting about a Slate.com series on Frankenstein and the novel’s applicability to our own time. This patent fight is being bitterly fought as fortunes are at stake.

It seems a decision has been made regarding the CRISPR patent claims. From a Feb. 17, 2017 article by Charmaine Distor for The Science Times,

After an intense court battle, the US Patent and Trademark Office (USPTO) released its ruling on February 15 [2017]. The rights for the CRISPR-Cas9 gene editing technology was handed over to the Broad Institute of Harvard University and the Massachusetts Institute of Technology (MIT).

According to an article in Nature, the said court battle was between the Broad Institute and the University of California. The two institutions are fighting over the intellectual property right for the CRISPR patent. The case between the two started when the patent was first awarded to the Broad Institute despite having the University of California apply first for the CRISPR patent.

…

Heidi Ledford’s Feb. 17, 2017 article for Nature provides more insight into the situation (Note: Links have been removed),

It [USPTO] ruled that the Broad Institute of Harvard and MIT in Cambridge could keep its patents on using CRISPR–Cas9 in eukaryotic cells. That was a blow to the University of California in Berkeley, which had filed its own patents and had hoped to have the Broad’s thrown out.

The fight goes back to 2012, when Jennifer Doudna at Berkeley, Emmanuelle Charpentier, then at the University of Vienna, and their colleagues outlined how CRISPR–Cas9 could be used to precisely cut isolated DNA1. In 2013, Feng Zhang at the Broad and his colleagues — and other teams — showed2 how it could be adapted to edit DNA in eukaryotic cells such as plants, livestock and humans.

Berkeley filed for a patent earlier, but the USPTO granted the Broad’s patents first — and this week upheld them. There are high stakes involved in the ruling. The holder of key patents could make millions of dollars from CRISPR–Cas9’s applications in industry: already, the technique has sped up genetic research, and scientists are using it to develop disease-resistant livestock and treatments for human diseases.

….

I also noted this eyebrow-lifting statistic,  “As for Ledford’s 3rd point, there are an estimated 763 patent families (groups of related patents) claiming CAS9 leading to the distinct possibility that the Broad Institute will be fighting many patent claims in the future.)

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Part 2 covers three critical responses to the reporting and between them describe the technology in more detail and the possibility of ‘designer babies’.  CRISPR and editing the germline in the US (part 2 of 3): ‘designer babies’?

Part 3 is all about public discussion or, rather, the lack of and need for according to a couple of social scientists. Informally, there is some discussion via pop culture and Joelle Renstrom notes although she is focused on the larger issues touched on by the television series, Orphan Black and as I touch on in my final comments. CRISPR and editing the germline in the US (part 3 of 3): public discussions and pop culture

Communicating science effectively—a December 2016 book from the US National Academy of Sciences

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I stumbled across this Dec. 13, 2016  essay/book announcement by Dr. Andrew Maynard and Dr. Dietram A. Scheufele on The Conversation,

Many scientists and science communicators have grappled with disregard for, or inappropriate use of, scientific evidence for years – especially around contentious issues like the causes of global warming, or the benefits of vaccinating children. A long debunked study on links between vaccinations and autism, for instance, cost the researcher his medical license but continues to keep vaccination rates lower than they should be.

Only recently, however, have people begun to think systematically about what actually works to promote better public discourse and decision-making around what is sometimes controversial science. Of course scientists would like to rely on evidence, generated by research, to gain insights into how to most effectively convey to others what they know and do.

As it turns out, the science on how to best communicate science across different issues, social settings and audiences has not led to easy-to-follow, concrete recommendations.

About a year ago, the National Academies of Sciences, Engineering and Medicine brought together a diverse group of experts and practitioners to address this gap between research and practice. The goal was to apply scientific thinking to the process of how we go about communicating science effectively. Both of us were a part of this group (with Dietram as the vice chair).

The public draft of the group’s findings – “Communicating Science Effectively: A Research Agenda” – has just been published. In it, we take a hard look at what effective science communication means and why it’s important; what makes it so challenging – especially where the science is uncertain or contested; and how researchers and science communicators can increase our knowledge of what works, and under what conditions.

…

At some level, all science communication has embedded values. Information always comes wrapped in a complex skein of purpose and intent – even when presented as impartial scientific facts. Despite, or maybe because of, this complexity, there remains a need to develop a stronger empirical foundation for effective communication of and about science.

Addressing this, the National Academies draft report makes an extensive number of recommendations. A few in particular stand out:

  • Use a systems approach to guide science communication. In other words, recognize that science communication is part of a larger network of information and influences that affect what people and organizations think and do.
  • Assess the effectiveness of science communication. Yes, researchers try, but often we still engage in communication first and evaluate later. Better to design the best approach to communication based on empirical insights about both audiences and contexts. Very often, the technical risk that scientists think must be communicated have nothing to do with the hopes or concerns public audiences have.
  • Get better at meaningful engagement between scientists and others to enable that “honest, bidirectional dialogue” about the promises and pitfalls of science that our committee chair Alan Leshner and others have called for.
  • Consider social media’s impact – positive and negative.
  • Work toward better understanding when and how to communicate science around issues that are contentious, or potentially so.

The paper version of the book has a cost but you can get a free online version.  Unfortunately,  I cannot copy and paste the book’s table of contents here and was not able to find a book index although there is a handy list of reference texts.

I have taken a very quick look at the book. If you’re in the field, it’s definitely worth a look. It is, however, written for and by academics. If you look at the list of writers and reviewers, you will find over 90% are professors at one university or another. That said, I was happy to see references to Dan Kahan’s work at the Yale Law School’s Culture Cognition Project cited. As happens they weren’t able to cite his latest work [***see my xxx, 2017 curiosity post***], released about a month after “Communicating Science Effectively: A Research Agenda.”

I was unable to find any reference to science communication via popular culture. I’m a little dismayed as I feel that this is a seriously ignored source of information by science communication specialists and academicians but not by the folks at MIT (Massachusetts Institute of Technology) who announced a wireless app in the same week as it was featured in an episode of the US television comedy, The Big Bang Theory. Here’s more from MIT’s emotion detection wireless app in a Feb. 1, 2017 news release (also on EurekAlert),

It’s a fact of nature that a single conversation can be interpreted in very different ways. For people with anxiety or conditions such as Asperger’s, this can make social situations extremely stressful. But what if there was a more objective way to measure and understand our interactions?

Researchers from MIT’s Computer Science and Artificial Intelligence Laboratory (CSAIL) and Institute of Medical Engineering and Science (IMES) say that they’ve gotten closer to a potential solution: an artificially intelligent, wearable system that can predict if a conversation is happy, sad, or neutral based on a person’s speech patterns and vitals.

“Imagine if, at the end of a conversation, you could rewind it and see the moments when the people around you felt the most anxious,” says graduate student Tuka Alhanai, who co-authored a related paper with PhD candidate Mohammad Ghassemi that they will present at next week’s Association for the Advancement of Artificial Intelligence (AAAI) conference in San Francisco. “Our work is a step in this direction, suggesting that we may not be that far away from a world where people can have an AI social coach right in their pocket.”

As a participant tells a story, the system can analyze audio, text transcriptions, and physiological signals to determine the overall tone of the story with 83 percent accuracy. Using deep-learning techniques, the system can also provide a “sentiment score” for specific five-second intervals within a conversation.

“As far as we know, this is the first experiment that collects both physical data and speech data in a passive but robust way, even while subjects are having natural, unstructured interactions,” says Ghassemi. “Our results show that it’s possible to classify the emotional tone of conversations in real-time.”

The researchers say that the system’s performance would be further improved by having multiple people in a conversation use it on their smartwatches, creating more data to be analyzed by their algorithms. The team is keen to point out that they developed the system with privacy strongly in mind: The algorithm runs locally on a user’s device as a way of protecting personal information. (Alhanai says that a consumer version would obviously need clear protocols for getting consent from the people involved in the conversations.)

How it works

Many emotion-detection studies show participants “happy” and “sad” videos, or ask them to artificially act out specific emotive states. But in an effort to elicit more organic emotions, the team instead asked subjects to tell a happy or sad story of their own choosing.

Subjects wore a Samsung Simband, a research device that captures high-resolution physiological waveforms to measure features such as movement, heart rate, blood pressure, blood flow, and skin temperature. The system also captured audio data and text transcripts to analyze the speaker’s tone, pitch, energy, and vocabulary.

“The team’s usage of consumer market devices for collecting physiological data and speech data shows how close we are to having such tools in everyday devices,” says Björn Schuller, professor and chair of Complex and Intelligent Systems at the University of Passau in Germany, who was not involved in the research. “Technology could soon feel much more emotionally intelligent, or even ‘emotional’ itself.”

After capturing 31 different conversations of several minutes each, the team trained two algorithms on the data: One classified the overall nature of a conversation as either happy or sad, while the second classified each five-second block of every conversation as positive, negative, or neutral.

Alhanai notes that, in traditional neural networks, all features about the data are provided to the algorithm at the base of the network. In contrast, her team found that they could improve performance by organizing different features at the various layers of the network.

“The system picks up on how, for example, the sentiment in the text transcription was more abstract than the raw accelerometer data,” says Alhanai. “It’s quite remarkable that a machine could approximate how we humans perceive these interactions, without significant input from us as researchers.”

Results

Indeed, the algorithm’s findings align well with what we humans might expect to observe. For instance, long pauses and monotonous vocal tones were associated with sadder stories, while more energetic, varied speech patterns were associated with happier ones. In terms of body language, sadder stories were also strongly associated with increased fidgeting and cardiovascular activity, as well as certain postures like putting one’s hands on one’s face.

On average, the model could classify the mood of each five-second interval with an accuracy that was approximately 18 percent above chance, and a full 7.5 percent better than existing approaches.

The algorithm is not yet reliable enough to be deployed for social coaching, but Alhanai says that they are actively working toward that goal. For future work the team plans to collect data on a much larger scale, potentially using commercial devices such as the Apple Watch that would allow them to more easily implement the system out in the world.

“Our next step is to improve the algorithm’s emotional granularity so that it is more accurate at calling out boring, tense, and excited moments, rather than just labeling interactions as ‘positive’ or ‘negative,’” says Alhanai. “Developing technology that can take the pulse of human emotions has the potential to dramatically improve how we communicate with each other.”

This research was made possible in part by the Samsung Strategy and Innovation Center.

Episode 14 of season 10 of The Big Bang Theory was titled “The Emotion Detection Automation”  (full episode can be found on this webpage) and broadcast on Feb. 2, 2017. There’s also a Feb. 2, 2017 recap (recapitulation) by Lincee Ray for EW.com (it seems Ray is unaware that there really is such a machine),

Who knew we would see the day when Sheldon and Raj figured out solutions for their social ineptitudes? Only The Big Bang Theory writers would think to tackle our favorite physicists’ lack of social skills with an emotion detector and an ex-girlfriend focus group. It’s been a while since I enjoyed both storylines as much as I did in this episode. That’s no bazinga.

When Raj tells the guys that he is back on the market, he wonders out loud what is wrong with his game. Why do women reject him? Sheldon receives the information like a scientist and runs through many possible answers. Raj shuts him down with a simple, “I’m fine.”

Sheldon is irritated when he learns that this obligatory remark is a mask for what Raj is really feeling. It turns out, Raj is not fine. Sheldon whines, wondering why no one just says exactly what’s on their mind. It’s quite annoying for those who struggle with recognizing emotional cues.

Lo and behold, Bernadette recently read about a gizmo that was created for people who have this exact same anxiety. MIT has a prototype, and because Howard is an alum, he can probably submit Sheldon’s name as a beta tester.

Of course this is a real thing. If anyone can build an emotion detector, it’s a bunch of awkward scientists with zero social skills.

This is the first time I’ve noticed an academic institution’s news release to be almost simultaneous with mention of its research in a popular culture television program, which suggests things have come a long way since I featured news about a webinar by the National Academies ‘ Science and Entertainment Exchange for film and television productions collaborating with scientists in an Aug. 28, 2012 post.

One last science/popular culture moment: Hidden Figures, a movie about African American women who were human computers supporting NASA (US National Aeronautics and Space Agency) efforts during the 1960s space race and getting a man on the moon was (shockingly) no. 1 in the US box office for a few weeks (there’s more about the movie here in my Sept. 2, 2016 post covering then upcoming movies featuring science).  After the movie was released, Mary Elizabeth Williams wrote up a Jan. 23, 2017 interview with the ‘Hidden Figures’ scriptwriter for Salon.com

…

I [Allison Schroeder] got on the phone with her [co-producer Renee Witt] and Donna  [co-producer Donna Gigliotti] and I said, “You have to hire me for this; I was born to write this.” Donna sort of rolled her eyes and was like, “God, these Hollywood types would say anything.” I said, “No, no, I grew up at Cape Canaveral. My grandmother was a computer programmer at NASA, my grandfather worked on the Mercury prototype, and I interned there all through high school and then the summer after my freshman year at Stanford I interned. I worked at a missile launch company.”

She was like, “OK that’s impressive.” And I said, “No, I literally grew up climbing on the Mercury capsule — hitting all the buttons, trying to launch myself into space.”

She said, “Well do you think you can handle the math?” I said that I had to study a certain amount of math at Stanford for economics degree. She said, “Oh, all right, that sounds pretty good.”

I pitched her a few scenes. I pitched her the end of the movie that you saw with Katherine running the numbers as John Glenn is trying to get up in space. I pitched her the idea of one of the women as a mechanic and to see her legs underneath the engine. You’re used to seeing a guy like that, but what would it be like to see heels and pantyhose and a skirt and she’s a mechanic and fixing something? Those are some of the scenes that I pitched them, and I got the job.

I love that the film begins with setting up their mechanical aptitude. You set up these are women; you set up these women of color. You set up exactly what that means in this moment in history. It’s like you just go from there.

I was on a really tight timeline because this started as an indie film. It was just Donna Gigliotti, Renee Witt, me and the author Margot Lee Shetterly for about a year working on it. I was only given four weeks for research and 12 weeks for writing the first draft. I’m not sure if I hadn’t known NASA and known the culture and just knew what the machines would look like, knew what the prototypes looked like, if I could have done it that quickly. I turned in that draft and Donna was like, “OK you’ve got the math and the science; it’s all here. Now go have fun.” Then I did a few more drafts and that was really enjoyable because I could let go of the fact I did it and make sure that the characters and the drive of the story and everything just fit what needed to happen.

For anyone interested in the science/popular culture connection, David Bruggeman of the Pasco Phronesis blog does a better job than I do of keeping up with the latest doings.

Getting back to ‘Communicating Science Effectively: A Research Agenda’, even with a mention of popular culture, it is a thoughtful book on the topic.

2016 thoughts and 2017 hopes from FrogHeart

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This is the 4900th post on this blog and as FrogHeart moves forward to 5000, I’m thinking there will be some changes although I’m not sure what they’ll be. In the meantime, here are some random thoughts on the year that was in Canadian science and on the FrogHeart blog.

Changeover to Liberal government: year one

Hopes were high after the Trudeau government was elected. Certainly, there seems to have been a loosening where science communication policies have been concerned although it may not have been quite the open and transparent process people dreamed of. On the plus side, it’s been easier to participate in public consultations but there has been no move (perceptible to me) towards open government science or better access to government-funded science papers.

Open Science in Québec

As far as I know, la crème de la crème of open science (internationally) is the Montreal Neurological Institute (Montreal Neuro; affiliated with McGill University. They bookended the year with two announcements. In January 2016, Montreal Neuro announced it was going to be an “Open Science institution (my Jan. 22, 2016 posting),

The Montreal Neurological Institute (MNI) in Québec, Canada, known informally and widely as Montreal Neuro, has ‘opened’ its science research to the world. David Bruggeman tells the story in a Jan. 21, 2016 posting on his Pasco Phronesis blog (Note: Links have been removed),

The Montreal Neurological Institute (MNI) at McGill University announced that it will be the first academic research institute to become what it calls ‘Open Science.’  As Science is reporting, the MNI will make available all research results and research data at the time of publication.  Additionally it will not seek patents on any of the discoveries made on research at the Institute.

…

Will this catch on?  I have no idea if this particular combination of open access research data and results with no patents will spread to other university research institutes.  But I do believe that those elements will continue to spread.  More universities and federal agencies are pursuing open access options for research they support.  Elon Musk has opted to not pursue patent litigation for any of Tesla Motors’ patents, and has not pursued patents for SpaceX technology (though it has pursued litigation over patents in rocket technology). …

Then, there’s my Dec. 19, 2016 posting about this Montreal Neuro announcement,

It’s one heck of a Christmas present. Canadian businessmen Larry Tannenbaum and his wife Judy have given the Montreal Neurological Institute (Montreal Neuro), which is affiliated with McGill University, a $20M donation. From a Dec. 16, 2016 McGill University news release,

The Prime Minister of Canada, Justin Trudeau, was present today at the Montreal Neurological Institute and Hospital (MNI) for the announcement of an important donation of $20 million by the Larry and Judy Tanenbaum family. This transformative gift will help to establish the Tanenbaum Open Science Institute, a bold initiative that will facilitate the sharing of neuroscience findings worldwide to accelerate the discovery of leading edge therapeutics to treat patients suffering from neurological diseases.

‟Today, we take an important step forward in opening up new horizons in neuroscience research and discovery,” said Mr. Larry Tanenbaum. ‟Our digital world provides for unprecedented opportunities to leverage advances in technology to the benefit of science.  That is what we are celebrating here today: the transformation of research, the removal of barriers, the breaking of silos and, most of all, the courage of researchers to put patients and progress ahead of all other considerations.”

Neuroscience has reached a new frontier, and advances in technology now allow scientists to better understand the brain and all its complexities in ways that were previously deemed impossible. The sharing of research findings amongst scientists is critical, not only due to the sheer scale of data involved, but also because diseases of the brain and the nervous system are amongst the most compelling unmet medical needs of our time.

Neurological diseases, mental illnesses, addictions, and brain and spinal cord injuries directly impact 1 in 3 Canadians, representing approximately 11 million people across the country.

“As internationally-recognized leaders in the field of brain research, we are uniquely placed to deliver on this ambitious initiative and reinforce our reputation as an institution that drives innovation, discovery and advanced patient care,” said Dr. Guy Rouleau, Director of the Montreal Neurological Institute and Hospital and Chair of McGill University’s Department of Neurology and Neurosurgery. “Part of the Tanenbaum family’s donation will be used to incentivize other Canadian researchers and institutions to adopt an Open Science model, thus strengthening the network of like-minded institutes working in this field.”

Chief Science Advisor

Getting back to the federal government, we’re still waiting for a Chief Science Advisor. Should you be interested in the job, apply here. The job search was launched in early Dec. 2016 (see my Dec. 7, 2016 posting for details) a little over a year after the Liberal government was elected. I’m not sure why the process is taking so long. It’s not like the Canadian government is inventing a position or trailblazing in this regard. Many, many countries and jurisdictions have chief science advisors. Heck the European Union managed to find their first chief science advisor in considerably less time than we’ve spent on the project. My guess, it just wasn’t a priority.

Prime Minister Trudeau, quantum, nano, and Canada’s 150th birthday

In April 2016, Prime Minister Justin Trudeau stunned many when he was able to answer, in an articulate and informed manner, a question about quantum physics during a press conference at the Perimeter Institute in Waterloo, Ontario (my April 18, 2016 post discussing that incident and the so called ‘quantum valley’ in Ontario).

In Sept. 2016, the University of Waterloo publicized the world’s smallest Canadian flag to celebrate the country’s upcoming 150th birthday and to announce its presence in QUANTUM: The Exhibition (a show which will tour across Canada). Here’s more from my Sept. 20, 2016 posting,

The record-setting flag was unveiled at IQC’s [Institute of Quantum Computing at the University of Waterloo] open house on September 17 [2016], which attracted nearly 1,000 visitors. It will also be on display in QUANTUM: The Exhibition, a Canada 150 Fund Signature Initiative, and part of Innovation150, a consortium of five leading Canadian science-outreach organizations. QUANTUM: The Exhibition is a 4,000-square-foot, interactive, travelling exhibit IQC developed highlighting Canada’s leadership in quantum information science and technology.

“I’m delighted that IQC is celebrating Canadian innovation through QUANTUM: The Exhibition and Innovation150,” said Raymond Laflamme, executive director of IQC. “It’s an opportunity to share the transformative technologies resulting from Canadian research and bring quantum computing to fellow Canadians from coast to coast to coast.”

The first of its kind, the exhibition will open at THEMUSEUM in downtown Kitchener on October 14 [2016], and then travel to science centres across the country throughout 2017.

You can find the English language version of QUANTUM: The Exhibition website here and the French language version of QUANTUM: The Exhibition website here.

There are currently four other venues for the show once finishes its run in Waterloo. From QUANTUM’S Join the Celebration webpage,

2017

  • Science World at TELUS World of Science, Vancouver
  • TELUS Spark, Calgary
  • Discovery Centre, Halifax
  • Canada Science and Technology Museum, Ottawa

I gather they’re still looking for other venues to host the exhibition. If interested, there’s this: Contact us.

Other than the flag which is both nanoscale and microscale, they haven’t revealed what else will be included in their 4000 square foot exhibit but it will be “bilingual, accessible, and interactive.” Also, there will be stories.

Hmm. The exhibition is opening in roughly three weeks and they have no details. Strategy or disorganization? Only time will tell.

Calgary and quantum teleportation

This is one of my favourite stories of the year. Scientists at the University of Calgary teleported photons six kilometers from the university to city hall breaking the teleportation record. What I found particularly interesting was the support for science from Calgary City Hall. Here’s more from my Sept. 21, 2016 post,

Through a collaboration between the University of Calgary, The City of Calgary and researchers in the United States, a group of physicists led by Wolfgang Tittel, professor in the Department of Physics and Astronomy at the University of Calgary have successfully demonstrated teleportation of a photon (an elementary particle of light) over a straight-line distance of six kilometres using The City of Calgary’s fibre optic cable infrastructure. The project began with an Urban Alliance seed grant in 2014.

This accomplishment, which set a new record for distance of transferring a quantum state by teleportation, has landed the researchers a spot in the prestigious Nature Photonics scientific journal. The finding was published back-to-back with a similar demonstration by a group of Chinese researchers.

…

The research could not be possible without access to the proper technology. One of the critical pieces of infrastructure that support quantum networking is accessible dark fibre. Dark fibre, so named because of its composition — a single optical cable with no electronics or network equipment on the alignment — doesn’t interfere with quantum technology.

The City of Calgary is building and provisioning dark fibre to enable next-generation municipal services today and for the future.

“By opening The City’s dark fibre infrastructure to the private and public sector, non-profit companies, and academia, we help enable the development of projects like quantum encryption and create opportunities for further research, innovation and economic growth in Calgary,” said Tyler Andruschak, project manager with Innovation and Collaboration at The City of Calgary.

As for the science of it (also from my post),

A Sept. 20, 2016 article by Robson Fletcher for CBC (Canadian Broadcasting News) online provides a bit more insight from the lead researcher (Note: A link has been removed),

“What is remarkable about this is that this information transfer happens in what we call a disembodied manner,” said physics professor Wolfgang Tittel, whose team’s work was published this week in the journal Nature Photonics.

“Our transfer happens without any need for an object to move between these two particles.”

A Sept. 20, 2016 University of Calgary news release by Drew Scherban, which originated the news item, provides more insight into the research,

“Such a network will enable secure communication without having to worry about eavesdropping, and allow distant quantum computers to connect,” says Tittel.

Experiment draws on ‘spooky action at a distance’

The experiment is based on the entanglement property of quantum mechanics, also known as “spooky action at a distance” — a property so mysterious that not even Einstein could come to terms with it.

“Being entangled means that the two photons that form an entangled pair have properties that are linked regardless of how far the two are separated,” explains Tittel. “When one of the photons was sent over to City Hall, it remained entangled with the photon that stayed at the University of Calgary.”

Next, the photon whose state was teleported to the university was generated in a third location in Calgary and then also travelled to City Hall where it met the photon that was part of the entangled pair.

“What happened is the instantaneous and disembodied transfer of the photon’s quantum state onto the remaining photon of the entangled pair, which is the one that remained six kilometres away at the university,” says Tittel.

Council of Canadian Academies and The State of Science and Technology and Industrial Research and Development in Canada

Preliminary data was released by the CCA’s expert panel in mid-December 2016. I reviewed that material briefly in my Dec. 15, 2016 post but am eagerly awaiting the full report due late 2017 when, hopefully, I’ll have the time to critique the material, and which I hope will have more surprises and offer greater insights than the preliminary report did.

Colleagues

Thank you to my online colleagues. While we don’t interact much it’s impossible to estimate how encouraging it is to know that these people continually participate and help create the nano and/or science blogosphere.

David Bruggeman at his Pasco Phronesis blog keeps me up-to-date on science policy both in the US, Canada, and internationally, as well as, keeping me abreast of the performing arts/science scene. Also, kudos to David for raising my (and his audience’s) awareness of just how much science is discussed on late night US television. Also, I don’t know how he does it but he keeps scooping me on Canadian science policy matters. Thankfully, I’m not bitter and hope he continues to scoop me which will mean that I will get the information from somewhere since it won’t be from the Canadian government.

Tim Harper of Cientifica Research keeps me on my toes as he keeps shifting his focus. Most lately, it’s been on smart textiles and wearables. You can download his latest White Paper titled, Fashion, Smart Textiles, Wearables and Disappearables, from his website. Tim consults on nanotechnology and other emerging technologies at the international level.

Dexter Johnson of the Nanoclast blog on the IEEE (Institute of Electrical and Electronics Engineers) website consistently provides informed insight into how a particular piece of research fits into the nano scene and often provides historical details that you’re not likely to get from anyone else.

Dr. Andrew Maynard is currently the founding Director of the Risk Innovation Lab at the University of Arizona. I know him through his 2020 Science blog where he posts text and videos on many topics including emerging technologies, nanotechnologies, risk, science communication, and much more. Do check out 2020 Science as it is a treasure trove.

2017 hopes and dreams

I hope Canada’s Chief Science Advisor brings some fresh thinking to science in government and that the Council of Canadian Academies’ upcoming assessment on The State of Science and Technology and Industrial Research and Development in Canada is visionary. Also, let’s send up some collective prayers for the Canada Science and Technology Museum which has been closed since 2014 (?) due to black mold (?). It would be lovely to see it open in time for Canada’s 150th anniversary.

I’d like to see the nanotechnology promise come closer to a reality, which benefits as many people as possible.

As for me and FrogHeart, I’m not sure about the future. I do know there’s one more Steep project (I’m working with Raewyn Turner on a multiple project endeavour known as Steep; this project will involve sound and gold nanoparticles).

Should anything sparkling occur to me, I will add it at a future date.

In the meantime, Happy New Year and thank you from the bottom of my heart for reading this blog!

Westworld: a US television programme investigating AI (artificial intelligence) and consciousness

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The US television network, Home Box Office (HBO) is getting ready to première Westworld, a new series based on a movie first released in 1973. Here’s more about the movie from its Wikipedia entry (Note: Links have been removed),

Westworld is a 1973 science fiction Western thriller film written and directed by novelist Michael Crichton and produced by Paul Lazarus III about amusement park robots that malfunction and begin killing visitors. It stars Yul Brynner as an android in a futuristic Western-themed amusement park, and Richard Benjamin and James Brolin as guests of the park.

Westworld was the first theatrical feature directed by Michael Crichton.[3] It was also the first feature film to use digital image processing, to pixellate photography to simulate an android point of view.[4] The film was nominated for Hugo, Nebula and Saturn awards, and was followed by a sequel film, Futureworld, and a short-lived television series, Beyond Westworld. In August 2013, HBO announced plans for a television series based on the original film.

The latest version is due to start broadcasting in the US on Sunday, Oct. 2, 2016 and as part of the publicity effort the producers are profiled by Sean Captain for Fast Company in a Sept. 30, 2016 article,

As Game of Thrones marches into its final seasons, HBO is debuting this Sunday what it hopes—and is betting millions of dollars on—will be its new blockbuster series: Westworld, a thorough reimagining of Michael Crichton’s 1973 cult classic film about a Western theme park populated by lifelike robot hosts. A philosophical prelude to Jurassic Park, Crichton’s Westworld is a cautionary tale about technology gone very wrong: the classic tale of robots that rise up and kill the humans. HBO’s new series, starring Evan Rachel Wood, Anthony Hopkins, and Ed Harris, is subtler and also darker: The humans are the scary ones.

“We subverted the entire premise of Westworld in that our sympathies are meant to be with the robots, the hosts,” says series co-creator Lisa Joy. She’s sitting on a couch in her Burbank office next to her partner in life and on the show—writer, director, producer, and husband Jonathan Nolan—who goes by Jonah. …

Their Westworld, which runs in the revered Sunday-night 9 p.m. time slot, combines present-day production values and futuristic technological visions—thoroughly revamping Crichton’s story with hybrid mechanical-biological robots [emphasis mine] fumbling along the blurry line between simulated and actual consciousness.

Captain never does explain the “hybrid mechanical-biological robots.” For example, do they have human skin or other organs grown for use in a robot? In other words, how are they hybrid?

That nitpick aside, the article provides some interesting nuggets of information and insight into the themes and ideas 2016 Westworld’s creators are exploring (Note: A link has been removed),

… Based on the four episodes I previewed (which get progressively more interesting), Westworld does a good job with the trope—which focused especially on the awakening of Dolores, an old soul of a robot played by Evan Rachel Wood. Dolores is also the catchall Spanish word for suffering, pain, grief, and other displeasures. “There are no coincidences in Westworld,” says Joy, noting that the name is also a play on Dolly, the first cloned mammal.

The show operates on a deeper, though hard-to-define level, that runs beneath the shoot-em and screw-em frontier adventure and robotic enlightenment narratives. It’s an allegory of how even today’s artificial intelligence is already taking over, by cataloging and monetizing our lives and identities. “Google and Facebook, their business is reading your mind in order to advertise shit to you,” says Jonah Nolan. …

…

“Exist free of rules, laws or judgment. No impulse is taboo,” reads a spoof home page for the resort that HBO launched a few weeks ago. That’s lived to the fullest by the park’s utterly sadistic loyal guest, played by Ed Harris and known only as the Man in Black.

The article also features some quotes from scientists on the topic of artificial intelligence (Note: Links have been removed),

“In some sense, being human, but less than human, it’s a good thing,” says Jon Gratch, professor of computer science and psychology at the University of Southern California [USC]. Gratch directs research at the university’s Institute for Creative Technologies on “virtual humans,” AI-driven onscreen avatars used in military-funded training programs. One of the projects, SimSensei, features an avatar of a sympathetic female therapist, Ellie. It uses AI and sensors to interpret facial expressions, posture, tension in the voice, and word choices by users in order to direct a conversation with them.

“One of the things that we’ve found is that people don’t feel like they’re being judged by this character,” says Gratch. In work with a National Guard unit, Ellie elicited more honest responses about their psychological stresses than a web form did, he says. Other data show that people are more honest when they know the avatar is controlled by an AI versus being told that it was controlled remotely by a human mental health clinician.

…

“If you build it like a human, and it can interact like a human. That solves a lot of the human-computer or human-robot interaction issues,” says professor Paul Rosenbloom, also with USC’s Institute for Creative Technologies. He works on artificial general intelligence, or AGI—the effort to create a human-like or human level of intellect.

Rosenbloom is building an AGI platform called Sigma that models human cognition, including emotions. These could make a more effective robotic tutor, for instance, “There are times you want the person to know you are unhappy with them, times you want them to know that you think they’re doing great,” he says, where “you” is the AI programmer. “And there’s an emotional component as well as the content.”

Achieving full AGI could take a long time, says Rosenbloom, perhaps a century. Bernie Meyerson, IBM’s chief innovation officer, is also circumspect in predicting if or when Watson could evolve into something like HAL or Her. “Boy, we are so far from that reality, or even that possibility, that it becomes ludicrous trying to get hung up there, when we’re trying to get something to reasonably deal with fact-based data,” he says.

Gratch, Rosenbloom, and Meyerson are talking about screen-based entities and concepts of consciousness and emotions. Then, there’s a scientist who’s talking about the difficulties with robots,

…

… Ken Goldberg, an artist and professor of engineering at UC [University of California] Berkeley, calls the notion of cyborg robots in Westworld “a pretty common trope in science fiction.” (Joy will take up the theme again, as the screenwriter for a new Battlestar Galactica movie.) Goldberg’s lab is struggling just to build and program a robotic hand that can reliably pick things up. But a sympathetic, somewhat believable Dolores in a virtual setting is not so farfetched.

Captain delves further into a thorny issue,

“Can simulations, at some point, become the real thing?” asks Patrick Lin, director of the Ethics + Emerging Sciences Group at California Polytechnic State University. “If we perfectly simulate a rainstorm on a computer, it’s still not a rainstorm. We won’t get wet. But is the mind or consciousness different? The jury is still out.”

…

While artificial consciousness is still in the dreamy phase, today’s level of AI is serious business. “What was sort of a highfalutin philosophical question a few years ago has become an urgent industrial need,” says Jonah Nolan. It’s not clear yet how the Delos management intends, beyond entrance fees, to monetize Westworld, although you get a hint when Ford tells Theresa Cullen “We know everything about our guests, don’t we? As we know everything about our employees.”

AI has a clear moneymaking model in this world, according to Nolan. “Facebook is monetizing your social graph, and Google is advertising to you.” Both companies (and others) are investing in AI to better understand users and find ways to make money off this knowledge. …

As my colleague David Bruggeman has often noted on his Pasco Phronesis blog, there’s a lot of science on television.

For anyone who’s interested in artificial intelligence and the effects it may have on urban life, see my Sept. 27, 2016 posting featuring the ‘One Hundred Year Study on Artificial Intelligence (AI100)’, hosted by Stanford University.

Points to anyone who recognized Jonah (Jonathan) Nolan as the producer for the US television series, Person of Interest, a programme based on the concept of a supercomputer with intelligence and personality and the ability to continuously monitor the population 24/7.

Doctor Strange contest for girls in the US aged 15 – 18

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The deadline is Oct. 5, 2016 so if you do qualify for entry, you’d best be quick.

David Bruggeman in his Sept. 25, 2016 posting provides more information,

… the latest contest is called The Magic of STEM Challenge and is tied to the November [2016] release of the film Doctor Strange.

The name highlights part of the dramatic arc of the film – a neurosurgeon engaging with magic as he seeks to recover from an accident.  I have not seen the film, but it may bear some resemblance to how the Thor films have tried to explain the fantastical actions of those characters with some basis in science.  But don’t look too close (as you shouldn’t in any superhero film) or the gloss of scientific realism will disappear.

But I’m writing about the contest.  There’s a short window for entries, because the contest is open until October 5th.  Entrants are girls in the U.S. from 15-18 years old (grades 10-12), and must submit a video blog (vlog) on a scientific or technological questions. …

As some may know, Canadian actress Rachel McAdams is one of the leads in the film so she’s introducing the contest and the winner of the previous STEM Marvel contest (Captain America: Civil War),

You can find out more about the contest and the rules here.

One final thing about the movie, there has been a bit of a controversy with regard to the casting of Brit actress Tilda Swinton. From an April 28, 2016 posting by Kaiser on the Celebitchy blog,

… now C. Robert Cargill, the Strange screenwriter, has come out to try to explain it.

Tilda Swinton was cast as a Tibetan monk in the Marvel movie Doctor Strange so the comic book character could be changed to a ‘Celtic’ to avoid upsetting China, a screenwriter has claimed. One of the film’s screenwriters has suggested that the casting of the British actress as sorcerer the Ancient One was partly done to avoid offending China’s government. Moviegoers in China now represent the world’s second-largest annual box office after North America but the film’s backers apparently did not want to risk losing out on the Chinese market by introducing the highly politically charged subject of Tibet.

“He originates from Tibet, so if you acknowledge that Tibet is a place and that he’s Tibetan, you risk alienating one billion people who think that that’s bullsh*t and risk the Chinese government going, ‘Hey, you know one of the biggest film-watching countries in the world? We’re not going to show your movie because you decided to get political,” screenwriter C. Robert Cargill said in a podcast interview with the Texas-based DoubleToasted.com.

Cargill, who wasn’t involved in the casting of Swinton, said the comic book character of the Ancient One was ‘a racist stereotype.’

‘There is no other character in Marvel history that is such a cultural landmine, that is absolutely unwinnable,’ he said, adding: ‘It all comes down on to which way you are willing to lose.’

…

After the controversy over the 2016 Academy Awards regarding the paucity of minority nominees which  extended into a conversation about the lack of opportunity for minorities, it seems Hollywood is being held to closer account on topics of race.

As for the science end of things, I guess we can expect a light sprinkling of relatively accurate information mixed in with fantasy science.

Good luck to everyone who enters the contest and may your science be as accurate as possible.

‘Fill in the Planck’ with Tom McFadden

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A science rhyming quiz set to music? Here’s more from David Bruggeman’s Aug. 30, 2016 posting (on his Pasco Phronesis blog; Note: Links have been removed),

Tom McFadden, fresh off of his featured appearance as Joseph-Louis Lagrange in William Rowan Hamilton [a science-oriented production by Tim Blais featuring music from the Broadway musical, Hamilton], has a rhyming quiz going on at his YouTube channel.  That’s right, a rhyming quiz, and it’s called Fill in the Planck.

There are two quizzes so far, one on the JUNO spacecraft and the most recent on water.  The idea is to complete each rhyme in the verse. …

McFadden includes instructions in his into. to the quiz. Here’s the second in the series, Hot Water – Fill in the Planck #2,

The ‘Fill in the Planck’ video series can be found here.

You can find out more about McFadden and his work here and there was this: vote for his panel ‘Hip Hop in the Science Classroom’ (voting ended Sept. 2, 2016) to be presented at the 2017 SXSWedu (South by Southwest education). There is no word yet as to whether or not McFadden’s presentation will be seen at the 2017 SXSWedu.

Movies and science, science, science (Part 2 of 2)

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Part 1 concerned the soon-to-be-released movie, Hidden Figures and a film which has yet to start production, Photograph 51 (about Rosalind Franklin and the discovery of the double helix structure DNA [deoxyribonucleic acid]). Now for Part 2:

A matter of blood, Theranos, and Elizabeth Holmes

A few months ago, a friend asked me if I’d heard of Theranos. Given that I have featured various kinds of cutting edge diagnostic tests here, it was a fair enough question. Some  of my first questions to her were about the science. My friend had read about the situation in The Economist where the focus of the story (which I later read) was about venture capital. I got back to my friend and said that if they hadn’t published any scientific papers, I most likely would not have stumbled across them. Since then I’ve heard much more about Theranos but it seems there’s not much scientific information to be had from the company.

Reportedly, US film star Jennifer Lawrence is set to star, from a June 10, 2016 posting by Lainey (at Lainey Gossip; Note: A link has been removed),

Deadline reported yesterday [June 9, 2016] that Jennifer Lawrence will star in Adam McKay’s upcoming film about Elizabeth Holmes and Theranos. Elizabeth Holmes was basically the Jennifer Lawrence of Silicon Valley after inventing what she claimed to be a revolutionary blood testing system. Instead of submitting full vials of blood for limited testing, her product promised more efficiency and quicker results with just a pinprick. You can imagine how that would change the health care industry.

Last year, The Wall Street Journal investigated the viability of Theranos’s business plan, exposing major problems in the company’s infrastructure. Elizabeth Holmes went from being called the world’s youngest self-made female billionaire, the millennial in a turtleneck, to a possible fraud. It’s a fascinating story. …

In a July 16, 2016 article The Economist provides an update to the evolving Theranos/Holmes story,

FIRST they think you’re crazy, then they fight you, and then all of the sudden you change the world,” said Elizabeth Holmes as troubles mounted for her blood-testing startup, Theranos, last year. Things look ever less likely to go beyond the fighting stage.

On July 7th [2016] a government regulator, the Centres for Medicare and Medicaid Services, said Ms Holmes would be barred from owning or running a laboratory for two years. It will also revoke her company’s licence to operate one of two laboratories where it conducts tests. As The Economist went to press the firm was due to reply to a letter from Congress, which asked how, exactly, Theranos is going to handle the tens of thousands of patients who were given incorrect test results. Even so, Ms Holmes looks set to remain in position even as the situation deteriorates around a firm that once commanded a multi-billion-dollar valuation.

These may be some of the last twists in a story which will be turned into a Hollywood film by the director of “The Big Short”.

For anyone wondering how a movie could be made when the story has come to any kind of resolution, there’s this from a June 24, 2016 posting by David Bruggeman for his Pasco Phronesis blog (Note: Links have been removed),

Since last I wrote about a possible film about the medical device/testing company Theranos, a studio has successfully bid on the project.  Legendary Studios won an auction on the film rights, beating out 9 other offers on the project, which has Jennifer Lawrence attached to star as Theranos CEO Elizabeth Holmes.  Adam McKay would write the script and direct the project, duplicating his roles on the Oscar-nominated film The Big Short.  The film now has a preliminary title of Bad Blood.  It is certainly too early to tell if the Taylor Swift song of the same name will be used in the movie.

While getting a studio offer is important to the film getting produced, what is perhaps as interesting to our readers is that a book is connected to the film deal.  Two-time Pulitzer-prize winning writer John Carreyrou, who has written extensively on Theranos in The Wall Street Journal, will be writing a book that (presumably) serves as the basis for the script.  This follows the development arc for The Big Short, for which McKay shares an Adapted Screenplay Oscar (in addition to his nomination for directing the film)

So, are they going to wait until Holmes is either finally vindicated or vilified before going to film? Meanwhile, Holmes continues in a quest to save her company (from an Aug. 1, 2016 article for Fast Company by Christina Farr titled: Scientists Wanted Transparency From Theranos, But Got A Product Launch Instead (Note: A link has been removed),

Theranos once promised to revolutionize the blood testing industry. But its methodology remains secretive, despite calls for transparency from the scientific community. Now, it is facing federal investigations, private litigation, voided tests, and its CEO, Elizabeth Holmes, is banned from operating a lab for two years.

But all that was entirely glossed over today at the company’s much-awaited first presentation to the scientific community at the American Association for Clinical Chemistry’s conference in Philadelphia.

In an hour-long presentation (you can review the slides here), Holmes failed to discuss the fate of the company’s proprietary blood-testing technology, Edison, or address any of the controversy. Instead, she skipped right to pitching a new product, dubbed the MiniLab.

In fairness to Theranos, this was a positive step as the company did provide some internal data to show that the company could perform a small number of tests. But despite that, many took to social media to protest its failure to address and acknowledge its shortcomings before moving on to a new product.

“Clearly, the scientific and medical community was hoping for a data-driven discussion today, and instead got a new product announcement,” says John Torous, a psychiatrist and clinical informatics fellow at Harvard Medical School.

In an emailed response to Fast Company, a Theranos company spokesperson did not say whether components of Edison would be used in the miniLAB, but instead stressed that it’s one early iteration of the technology. “The miniLab is the latest iteration of the company’s testing platform and an evolution of Theranos’ technology,” they said.

Farr describes the MiniLab and notes that it is entering a competitive market,

The new product, the MiniLab, essentially takes equipment used in a standard lab and puts it in a single box. Holmes refers to this technique as “decentralizing the lab,” as in theory, clinicians could use this as an alternative to sending samples to a centralized facility and awaiting results. “Think of it as being a huge diagnostics lab that has been condensed down to the size of a microwave,” the company’s website explains.

..

But scientists are questioning whether the MiniLab technology is a breakthrough. The current market is already fairly saturated: Abbott’s iStat system, for instance, is a handheld device for clinicians to test patients for a plethora of common tests. Roche just received FDA [US Food and Drug Administration] clearance for its Cobas device, which can test for ailments like the flu and some strep infections in under 20 minutes. And Theranos competitors Quest and Labcorp already operate versions of this type of equipment in their own labs.

“I can’t imagine why they’re wasting their time,” says MIT-trained material scientist and biotech entrepreneur Kaveh Milaninia by phone. …

I recommend reading Farr’s article in its entirety as she provides more detail and analysis as to just how competitive the market Theranos proposes entering with its MiniLab actually is.

An Aug. 31, 2016 article by Lydia Ramsey for Slate.com the most recent update on the Theranos situation,

Theranos is withdrawing its bid for FDA approval of a diagnostic test for Zika that they announced earlier in August, according to a story in the Wall Street Journal.

Theranos confirmed to Business Insider that the test has been withdrawn, but said the company has plans to resubmit it.

John Carreyrou and Christopher Weaver report that an FDA inspection found that, as part of a study to validate the new test, the company had collected some data without a patient safety plan in place that was approved by an institutional review board.

…

“We hope that our decision to withdraw the Zika submission voluntarily is further evidence of our commitment to engage positively with the agency. We are confident in the Zika tests and will resubmit it,” Theranos vice president of regulatory and quality Dave Wurtz said in a statement emailed to Business Insider. Wurtz joined the company in July [2016].

Getting back to the point of my story at the beginning of this piece, it seems that Theranos and Elizabeth Holmes have not been as forthcoming with scientific data as is common in the biotech field. Interestingly, I read somewhere that the top 10 venture capitalists in the biotech field had not invested a penny in Theranos. The money had come from venture capitalists expert in other fields. (If you can confirm or know differently, please let me know in the comments section.)

In its favour, the company does appear to be attempting to address its shortcomings.

*ETA Oct. 6, 2016: Theranos is closing down some of its labs according to an Oct. 6, 2016 news item on phys.org,

Theranos, a onetime star Silicon Valley startup focused on health technology, is closing its consumer blood-testing facilities amid its struggles with US regulators.

The company, which has been seeking to disrupt the medical testing sector with new technology, said the closings will mean cutting some 340 jobs.

“After many months spent assessing our strengths and addressing our weaknesses, we have moved to structure our company around the model best aligned with our core values and mission,” company founder Elizabeth Holmes said in an open letter.

Theranos, which touts a new way of testing that uses far less blood and delivers faster results at much lower cost than traditional methods in US labs, has been under civil and criminal investigation over its claims.

Holmes said the company would focus on a so-called miniLab which can be commercialized with partners.

Things don’t look good.*

In any event, all these goings on should make for an interesting script writing challenge.

Bits and bobs of science and movies (The Man Who Knew Infinity, Ghostbusters, and Imagine Science Films)

The Man Who Knew Infinity had its debut at the 2015 Toronto International Film Festival. I haven’t seen it at any movie houses here (Vancouver, Canada) yet but a film trailer featuring its star, Dev Patel, was released in Feb. 2016,

Ramanujan must have been quite the mathematician, given the tenor of the times. Here’s more about the movie from its Wikipedia entry (Note: Links have been removed),

The Man Who Knew Infinity is a 2015 British biographical drama film based on the 1991 book of the same name by Robert Kanigel. The film stars Dev Patel as the real-life Srinivasa Ramanujan, a mathematician who after growing up poor in Madras, India, earns admittance to Cambridge University during World War I, where he becomes a pioneer in mathematical theories with the guidance of his professor, G. H. Hardy (played by Jeremy Irons despite Hardy being only 10 years older than Ramanujan).

Filming began in August 2014 at Trinity College, Cambridge.[4] The film had its world premiere as a gala presentation at the 2015 Toronto International Film Festival,[1][5] and was selected as the opening gala of the 2015 Zurich Film Festival.[6] It also played other film festivals including Singapore International Film Festival[7] and Dubai International Film Festival.[8]

Distinguished mathematicians Manjul Bhargava and Ken Ono are Associate Producers of the film.[9] Ono, the mathematics consultant, is a Guggenheim Fellow, and Bhargava is a winner of the Fields Medal.

Next up, Ghostbusters, the all woman edition. While it hasn’t become the blockbuster some were hoping for, I have some hope that it will become a quiet blockbuster over time. As I wait there is this information about how Ghostbuster: The All Woman Edition was grounded in real science. From a July 18, 2016 news item on phys.org,

Janet Conrad and Lindley Winslow, colleagues in the MIT [Massachusetts Institute of Technology] Department of Physics and researchers in MIT’s Lab for Nuclear Science, were key consultants for the all-female reboot of the classic 1984 supernatural comedy that is opening in theaters today. And the creative side of the STEM fields—science, technology, engineering, and mathematics—will be on full display.

A July 16, 2016 MIT news release, which originated the news item expands on the theme (Note: Links have been removed),

Kristin Wiig’s character, Erin Gilbert, a no-nonsense physicist at Columbia University, is all the more convincing because of Conrad’s toys. Her office features demos and other actual trappings from Conrad’s workspace: books, posters, and scientific models. She even created detailed academic papers and grant applications for use as desk props.

“I loved the original ‘Ghostbusters,’” says Conrad. “And I thought the switch to four women, the girl-power concept, was a great way to change it up for the reboot. Plus I love all of the stuff in my office. I was happy to have my books become stars.”

Conrad developed an affection for MIT while absorbing another piece of pop culture: “Doonesbury.” She remembers one cartoon strip featuring a girl doing Psets. She is discouraged until a robot comes to her door and beeps. All is right with the world again. The exchange made an impression. “Only at MIT do robots come by your door to cheer you up,” she thought.

Like her colleague, Winslow describes mainstream role models as powerful, particularly when fantasy elements in film and television enhance their childhood appeal. She, too, loved “Ghostbusters” as a kid. “I watched the original many times,” she recalls. “And my sister had a stuffed Slimer.”

Winslow jokes that she “probably put in too much time” helping with the remake. Indeed, Wired magazine recently detailed that: “In one scene in the movie, Wiig’s Gilbert stands in front of a lecture hall, speaking on challenges of reconciling quantum mechanics with Einstein’s gravity. On the whiteboards, behind her, a series of equations tells the same story: a self-contained narrative, written by Winslow and later transcribed on set, illustrating the failure of a once-promising physics theory called SU(5).”

Movie reviewers have been floored by the level of set detail. Also deserving of serious credit is James Maxwell, a postdoc at the Lab for Nuclear Science during the period he worked on “Ghostbusters.” He is now a staff scientist at Thomas Jefferson National Accelerator Facility in Newport News, Virginia.

Maxwell crafted realistic schematics of how proton packs, ghost traps, and other paranormal equipment might work. “I recalled myself as a kid, poring over the technical schematics of X-wings and Star Destroyers. I wanted to be sure that boys and especially girls of today could pore over my schematics, plug the components into Wikipedia, and find out about real tools that experimental physicists use to study the workings of the universe.”

He too hopes this behind-the-scenes MIT link with a Hollywood blockbuster will get people thinking. “I hope that it shows a little bit of the giddy side of science and of MIT; the laughs that can come with a spectacular experimental failure or an unexpected break-through.”

The movie depicts the worlds of science and engineering, as drawn from MIT, with remarkable conviction, says Maxwell. “So much of the feel of the movie, and to a great degree the personalities of the characters, is conveyed by the props,” he says.

Kate McKinnon’s character, Jillian Holtzmann, an eccentric engineer, is nearly inseparable from, as Maxwell says, “a mess of wires and magnets and lasers” — a pile of equipment replicated from his MIT lab. When she talks proton packs, her lines are drawn from his work.

Keep an eye out for treasures hidden in the props. For instance, Wiig’s character is the recipient of the Maria Goeppert Mayer “MGM Award” from the American Physical Society, which hangs on her office wall. Conrad and Winslow say the honor holds a special place in their hearts.

“We both think MGM was inspirational. She did amazing things at a time when it was tough for women to do anything in physics,” says Conrad. “She is one of our favorite women in physics,” adds Winslow. Clearly, some of the film’s props and scientific details reflect their personal predilections but Hollywood — and the nation — is also getting a real taste of MIT.

Finally and strictly speaking not a movie but it is an online magazine about science-based movies according to David Bruggeman’s Aug. 6, 2016 posting on his Pasco Phronesis blog (Note: Links have been removed),

LaboCine is an online film magazine from the people behind Imagine Science Films.  The films in each issue come from artists and scientists from around the world.  They are not restricted to documentary films, and mix live-action, animated and computer film styles.

The first issue of LaboCine is now online, so you can view the short films, which are organized around a common theme.  For August the theme is Model Organisms. …

You find the LaboCine magazine here and Imagine Science Films here. Btw, Raewyn Turner (NZ artist) has submitted our filmpoem, Steep (1) : A digital poetry of gold nanoparticles to the 9th Imagine Science Festival to be held Oct. 14-21, 2016 in New York City.

And that is it!

Here’s Part 1 for those who missed it.

Movies and science, science, science (Part 1 of 2)

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In the last few years, there’s been a veritable plethora of movies (and television shows in Canada and the US) that are about science and technology or have a significant  component or investigate the social impact. The trend does not seem to be slowing.

This first of two parts features the film, *Hidden* Figures, and a play being turned into a film, Photograph 51. The second part features the evolving Theranos story and plans to turn it into a film, The Man Who Knew Infinity, a film about an Indian mathematician, the science of the recent all woman Ghostbusters, and an ezine devoted to science films.

For the following movie tidbits, I have David Bruggeman to thank.

Hidden Figures

From David’s June 21, 2016 post on his Pasco Phronesis blog (Note: A link has been removed),

Hidden Figures is a fictionalized treatment of the book of the same name written by Margot Lee Shetterly (and underwritten by the Sloan Foundation).  Neither the book nor the film are released yet.  The book is scheduled for a September release, and the film currently has a January release date in the U.S.

Both the film and the book focus on the story of African American women who worked as computers for the government at the Langley National Aeronautic Laboratory in Hampton, Virginia.  The women served as human computers, making the calculations NASA needed during the Space Race.  While the book features four women, the film is focused on three: Katherine Johnson (recipient of the Presidential Medal of Freedom), Dorothy Vaughan, and Mary Jackson.  They are played by, respectively, Taraji P. Henson, Octavia Spencer, and Janelle Monae.  Other actors in the film include Kevin Costner, Kirsten Dunst, Aldis Hodge, and Jim Parsons.  The film is directed by Theodore Melfi, and the script is by Allison Schroeder.

*ETA Oct. 6, 2016: The book ‘Hidden Figures’ is nonfiction while the movie is a fictionalized adaptation  based on a true story.*

According to imdb.com, the movie’s release date is Dec. 25, 2016 (this could change again).

The history for ‘human computers’ stretches back to the 17th century, at least. From the Human Computer entry in Wikipedia (Note: Links have been removed),

The term “computer”, in use from the early 17th century (the first known written reference dates from 1613),[1] meant “one who computes”: a person performing mathematical calculations, before electronic computers became commercially available. “The human computer is supposed to be following fixed rules; he has no authority to deviate from them in any detail.” (Turing, 1950) Teams of people were frequently used to undertake long and often tedious calculations; the work was divided so that this could be done in parallel.

Prior to NASA, a team of women in the 19th century in the US were known as Harvard Computers (from the Wikipedia entry; Note: Links have been removed),

Edward Charles Pickering (director of the Harvard Observatory from 1877 to 1919) decided to hire women as skilled workers to process astronomical data. Among these women were Williamina Fleming, Annie Jump Cannon, Henrietta Swan Leavitt and Antonia Maury. This staff came to be known as “Pickering’s Harem” or, more respectfully, as the Harvard Computers.[1] This was an example of what has been identified as the “harem effect” in the history and sociology of science.

It seems that several factors contributed to Pickering’s decision to hire women instead of men. Among them was the fact that men were paid much more than women, so he could employ more staff with the same budget. This was relevant in a time when the amount of astronomical data was surpassing the capacity of the Observatories to process it.[2]

The first woman hired was Williamina Fleming, who was working as a maid for Pickering. It seems that Pickering was increasingly frustrated with his male assistants and declared that even his maid could do a better job. Apparently he was not mistaken, as Fleming undertook her assigned chores efficiently. When the Harvard Observatory received in 1886 a generous donation from the widow of Henry Draper, Pickering decided to hire more female staff and put Fleming in charge of them.[3]

While it’s not thrilling to find out that Pickering was content to exploit the women he was hiring, he deserves kudos for recognizing that women could do excellent work and acting on that recognition. When you consider the times, Pickering’s was an extraordinary act.

Getting back to Hidden Figures, an Aug.15, 2016 posting by Kathleen for Lainey Gossip celebrates the then newly released trailer for the movie,

If you’ve been watching the Olympics [Rio 2016], you know how much the past 10 days have been an epic display of #BlackGirlMagic. Fittingly, the trailer for Hidden Figures was released last night during Sunday’s Olympic coverage. It’s the story of three brilliant African American women, played by Taraji P Henson, Octavia Spencer and Janelle Monae, who made history by serving as the brains behind the NASA launch of astronaut John Glenn into orbit in 1962.

Three black women helped launch a dude into space in the 60s. AT NASA. Think about how America treated black women in the 60s. As Katherine Johnson, played by Taraji P Henson, jokes in the trailer, they were still sitting at the back of the bus. In 1962 Malcolm X said, “The most disrespected person in America is the Black woman, the most unprotected person in America is the Black woman. The most neglected person in America is the Black woman.” These women had to face that truth every day and they still rose to greatness. I’m obsessed with this story.

Overall, the trailer is good. I like the pace and the performances look strong. …

…

I’m most excited for Hidden Figures (as Lainey pointed out, this title is THE WORST) because black girls are being celebrated for their brains on screen. That is rare. When the trailer aired, my brother Sam texted me, “WHOA, a smart black girl movie!”

*ETA Sept. 5, 2016: Aran Shetterly contacted me to say this:

What you may not know is that the term “Hidden Figures” is a specific reference to flight science. It tested a pilot’s ability to pick out a simple figure from a set of more complex, difficult to see images. http://www.militaryaptitudetests.com/afoqt/

Thank you Mr. Shetterly!

Photograph 51 (the Rosalind Franklin story)

Also in David’s June 21, 2016 post is a mention of Photograph 51, a play and soon-to-be film about Rosalind Franklin, the discovery of the double helix, and a science controversy. I first wrote about Photograph 51 in a Jan. 16, 2012 posting (scroll down about 50% of the way) regarding an international script writing competition being held in Dublin, Ireland. At the time, I noted that Anna Ziegler’s play, Photograph 51 had won a previous competition cycle of the screenwriting competition. I wrote again about the play in a Sept. 2, 2015 posting about its London production (Sept. 5 – Nov. 21, 2015) featuring actress Nicole Kidman.

The versions of the Franklin story with which I’m familiar paint her as the wronged party, ignored and unacknowledged by the scientists (Francis, Crick, James Watson, and Maurice Wilkins) who got all the glory and the Nobel Prize. Stephen Curry in a Sept. 16, 2015 posting on the Guardian science blogs suggests the story may not be quite as simple as that (Note: A link has been removed),

Ziegler [Anna Ziegler, playwright] is up front in admitting that she has rearranged facts to suit the drama. This creates some oddities of chronology and motive for those familiar with the history. I know of no suggestion of romantic interest in Franklin from Wilkins, or of a separation of Crick from his wife in the aftermath of his triumph with Watson in solving the DNA structure. There is no mention in the play of the fact that Franklin published her work (and the famous photograph 51) in the journal Nature alongside Watson and Crick’s paper and one by Wilkins. Nor does the audience hear of the international recognition that Franklin enjoyed in her own right between 1953 and her untimely death in 1958, not just for her involvement in DNA, but also for her work on the structure of coal and of viruses.

Published long after her death, The Double Helix is widely thought to treat Franklin unfairly. In the minds of many she remains the wronged woman whose pioneering results were taken by others to solve DNA and win the Nobel prize. But the real story – many elements of which come across strongly in the play – is more complex*.

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Franklin is a gifted experimentalist. Her key contributions to the discovery were in improving methods for taking X-ray pictures of and discovering the distinct A and B conformations of DNA. But it becomes clear that her methodical, meticulous approach to data analysis – much to Wilkins’ impotent frustration – eventually allows the Kings ‘team’ to be overtaken by the bolder, intuitive stratagem of Watson and Crick.

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Curry’s piece is a good read and provides insight into the ways temperament affects how science is practiced.

Interestingly, there was a 1987 dramatization of the ‘double helix or life story’ (from the Life Story entry on Wikipedia; Note: Links have been removed),

The film tells the story of the rivalries of the two teams of scientists attempting to discover the structure of DNA. Francis Crick and James D. Watson at Cambridge University and Maurice Wilkins and Rosalind Franklin at King’s College London.

The film manages to convey the loneliness and competitiveness of scientific research but also educates the viewer as to how the structure of DNA was discovered. In particular, it explores the tension between the patient, dedicated laboratory work of Franklin and the sometimes uninformed intuitive leaps of Watson and Crick, all played against a background of institutional turf wars, personality conflicts and sexism. In the film Watson jokes, plugging the path of intuition: “Blessed are they who believed before there was any evidence.” The film also shows why Watson and Crick made their discovery, overtaking their competitors in part by reasoning from genetic function to predict chemical structure, thus helping to establish the then still-nascent field of molecular biology.

You can find out more about the stars, crew, and cast here on imdb.com

In addition to Life Story, the dramatization is also sometimes titled as ‘The Race for the Double Helix’ or the ‘Double Helix’.

Getting back to Photograph 51 (the film), Michael Grandage who directed the stage play will also direct the film. Grandage just made his debut as a film director with ‘Genius’ starring Colin Firth and Jude Law. According to this June 23, 2016 review by Sarah on Laineygossip.com, he stumbled a bit by casting British and Australian actors as Americans,

The first hurdle to clear with Genius, the feature film debut of English theater director Michael Grandage, is that everyone is played by Brits and Aussies, and by “everyone” I mean some of the most towering figures of American literature. You cast the best actor for the role and a good actor can convince you they’re anyone, so it shouldn’t really matter, but there is something profoundly odd about watching a parade of Lit 101 All Stars appear on screen and struggle with American accents. …

That kind of casting should not be a problem with Photograph 51 where the action takes place with British personalities.

Part 2 is here.

*’Human’ corrected to ‘Hidden’ on Sept. 5, 2016.