Tag: human genome project


Creative Minds: Bacteria, Gene Swaps, and Human Cancer

Julie Dunning Hotopp

When Julie Dunning Hotopp was a post-doctoral fellow in the early 2000s, bacteria were known for swapping bits of their DNA with other bacteria, a strategy known as lateral gene transfer. But the offloading of genes from bacteria into multicellular organisms was thought to be rare, with limited evidence that a bacterial genus called Wolbachia, which invades the cells of other organisms and takes up permanent residence, had passed off some of its DNA onto a species of beetle and a parasitic worm. Dunning Hotopp wondered whether lateral gene transfer might be a more common phenomenon than the evidence showed.

She and her colleagues soon discovered that Wolbachia had engaged in widespread lateral gene transfer with eight species of insects and nematode worms, possibly passing on genes and traits to their invertebrate hosts [1]. This important discovery put Dunning Hotopp on a research trail that now has taken a sharp turn toward human cancer and earned her a 2015 NIH Director’s Transformative Research Award. This NIH award supports exceptionally innovative research projects that are inherently risky and untested but have the potential to change fundamental research paradigms in areas such as cancer and throughout the biomedical sciences.

Unlike insects and worms, people don’t harbor lots of bacteria in their cells. But the human body does play host to a diverse array of microbes, collectively known as the human microbiome. Dunning Hotopp, now an associate professor of microbiology and immunology at the University of Maryland School of Medicine, Baltimore, began wondering several years ago while pursuing this new research trail whether it was possible that bacterial DNA might also make its way into the human genome—probably not into the germline (the part that gets passed to future generations), but into various cells of the body (so-called somatic cells).

The views, opinions and positions expressed by these authors and blogs are theirs and do not necessarily represent that of the Bioethics Research Library and Kennedy Institute of Ethics or Georgetown University.


Race, Genetics, Society

CGS Advisory Board member Dorothy Roberts on race and intelligence in genetic research

Important research that casts doubt on many uses of racial categories in genetic research is discussed in a recent article co-authored by CGS Advisory Board member Dorothy Roberts and published in Science.

Taking race out of human genetics, Michael Yudell, Dorothy Roberts, Rob DeSalle & Sarah Tishkoff, Science (Feb. 5, 2016), http://science.sciencemag.org/content/351/6273/564.full

The perspective piece begins by citing to scientists and historians who undermined the scientific validity of the concept of biological race—including W. E. B. DuBois some 100 years ago.  While the Human Genome Project found that humanity was 99.9% genetically the same, the authors note an uptick since 2000 in the use of race in genetics research as a data stratification factor. To avoid confusion, they helpfully define two separate but often conflated concepts: ancestry (“a very personal understanding of one’s genomic heritage” based on individual lineage) and race (“a pattern-based concept” used to “draw conclusions about hierarchical organizations of humans”).

They put forth two recommendations:

  1. “Scientific journals and professional societies should encourage use of terms like ancestry and population to describe human groupings in genetic studies … Historical racial categories that are treated as natural and infused with notions of superiority and inferiority have no place in biology.”
  2. “The U.S. National Academies of Sciences, Engineering, and Medicine should convene a panel of experts… to recommend ways for research into human biological diversity to move past the use of race as a tool for classification in both laboratory and clinical research.”

The views, opinions and positions expressed by these authors and blogs are theirs and do not necessarily represent that of the Bioethics Research Library and Kennedy Institute of Ethics or Georgetown University.


“Moonshot Medicine”: Putative Precision vs. Messy Genomes

Like so many medical terms, “precision medicine” is a combination of both wishful thinking and obfuscation.  In this case, it also carries a somewhat unsettling suggestion: if medicine has not up until now been precise, then what has it been? 

Precision medicine started being touted in the specialized journals in the late aughts as part of a “new era” being ushered in by coordinated and integrated care, fiscal transparency, and patient-centered practice.  It was one of a suite of approaches that promised to bring costs down while improving outcomes.   The idea was that by looking at drugs and other therapies according to how they succeeded (or didn’t) in people sharing particular gene variations and similar physical traits, physicians could make more intelligent choices patient-by-patient, selecting the treatment with a greater chance of working. 

Big Pharma saw promise in the approach and made strategic partnerships (Pfizer and Medco Health Solutions in 2011, for example, and Novartis and Genoptix that same year); startups and researchers rushed to secure patents; while medical groups such as the American Society of Clinical Oncology devoted sessions at their annual conferences to precision medicine’s potential benefits now that speedier gene sequencing was bringing costs down sufficiently to make it possible to contemplate tailor-making cancer drugs.

At the same time, some in the burgeoning field saw major structural hurdles.  For example, most work on biomarkers—the substances or physical signs that a disease is present or a drug is working—is done in university and government research labs, and it takes time for any given biomarker to be proven accurate, as well as to be adopted by physicians in the clinic. 

The views, opinions and positions expressed by these authors and blogs are theirs and do not necessarily represent that of the Bioethics Research Library and Kennedy Institute of Ethics or Georgetown University.


NIH throws out the bathwater, baby and all.

Yesterday, the US National Institutes of Health announced that they would “not fund any use of gene-editing technologies in human embryos.”  The announcement came in a statement from the NIH’s director and former US head of the Human Genome Project, Francis Collins.  This area is controversial, and has been the subject of a great deal of recent debate, with some scientists calling for a moratorium on human embryology research, others on the move into treatment.

This debate has, no doubt, been sharpened by the recent publication of a scientific paper reporting the – on the face of it, discouraging – results of attempts to use genome editing in non-viable, supernumerary IVF embryos to edit the HBB gene, mutations in which are responsible for the blood disorder β-thalassaemia.

The NIH statement offers no clear reason for banning federal funding of human embryo research using genome editing.  What it did was to wave casually in the general direction of the provisional conclusions in some well rehearsed debates about using genetically modified human embryos in treatment.  The argument, again only implicit, was, in effect, that ‘since we (or our colleagues in the FDA) won’t permit genome-edited embryos to be used in treatment, there is therefore no reason to fund research.  So there is really no point considering the possible benefits that we might gain from such research or reconsidering the conditions of the moral consensus, which might have changed since we last looked.’

What was rather disappointing about this statement was its apparent refusal to engage in any form of reflection or argument. 

The views, opinions and positions expressed by these authors and blogs are theirs and do not necessarily represent that of the Bioethics Research Library and Kennedy Institute of Ethics or Georgetown University.


Racial Health Disparities: It

Heart disease is the single biggest contributor to the racial mortality gap in the US, which, in case you didn’t know, is still really bad. Many hoped that advances in genetics would help explain and ultimately close that gap.

So Jay Kaufman, Professor in Epidemiology & Biostatistics at McGill, recently led a study to systematically review six years’ worth of genomic research to see if there is any evidence that genetic differences explain this major racial-health disparity.

What he found is incredibly important. He found, effectively, nothing.

A wonderful article in The Atlantic by Jason Silverstein gets right to the heart of it with its title: “Genes Don’t Cause Racial-Health Disparities, Society Does.”

Silverstein reminds us that an explicit goal of the Human Genome Project was to close health disparities, and that we’ve invested more than $1 billion in the field every year since. But given the results of efforts to understand racial health disparities by looking at our DNA, it might be argued that pretty much anything else would have done better.

You’d think that educated people knew this, right? That race is a social construct with the same scientific legitimacy as “grouping raccoons, tigers, and okapis on the basis that they are all stripey?” Some researchers seem to acknowledge this, and recommend studying “ancestry” rather than “race.”

But Silverstein points out that “ancestry” tends to be merely a proxy for race, masquerading with “a phony moustache and glasses.” Moreover, the lack of precision in the use and definition of “ancestry” has rendered it nearly meaningless scientifically.

The views, opinions and positions expressed by these authors and blogs are theirs and do not necessarily represent that of the Bioethics Research Library and Kennedy Institute of Ethics or Georgetown University.


Hallam Stevens’ Life Out of Sequence by Mads Solberg

Life Out of Sequence: A Data-driven History of Bioinformatics

by Hallam Stevens

The University of Chicago Press, 2013. 294 pages.


Life Out of Sequence is a lucid ethnographic and historical account of how computational tools changed how biologists think about and engage with living systems. In it, Hallam Stevens tells a captivating story about how genes and genomes become meaningful through the emerging field of bioinformatics. It takes the reader through a series of “data-driven” studies of key actors and locations of a new material culture where data is at the centre. Unsatisfied with simple proclamations about the digitizations of life, Stevens carefully describes how the virtualization of nucleic acids has changed epistemic practices in biology.


Chapter 1 starts with the development of digital computers originally envisioned for military applications, which later came to be trusted for bio-scientific information management and analysis. In a recent interview Stevens observes that this historical backdrop complements Joseph November’s postwar account (Biomedical Computing, 2012) by continuing the story from the 1960s until the present day. Stevens argues that while initial attempts at computerizing biology failed (because they tried to shape computers to solve biological problems), biologists eventually came to pursue the kind of questions that computers were particularly good at solving. Through narrations of bioinformatic pioneers such as Margaret Dayhoff (a physical chemist and the ‘mother’ of bioinformatics), Walter Goad (a postwar physicist who introduced computing into biology and helped found GenBank), and James Ostell (an early innovator of nucleic acid analysis software), we learn how these tools gradually become trusted, and eventually ubiquitous, in current biology.

The views, opinions and positions expressed by these authors and blogs are theirs and do not necessarily represent that of the Bioethics Research Library and Kennedy Institute of Ethics or Georgetown University.


Precision Medicine Has Imprecise Ethics

by Craig Klugman, Ph.D.

How do physicians diagnose disease? First they go through a set of symptoms and then compile a list of differential diagnoses or what the underlying disease may be. Then the doctor performs tests to rule out some diagnoses and advance others. In essence, though, diseases are classified according to their affect on the body—their symptology. What if instead of by symptoms, diseases were classified by their molecular function? Instead of being diagnosed with Type II Diabetes one might be diagnosed by whether there is a death of beta cells (i.e. production of insulin) or if the receptors do not work and cannot bind with insulin proteins (i.e. insulin resistance). This change in disease classification is part of an initiative known as “precision medicine.”

In his State of the Union Address, President Barack Obama outlined his $215 million “Precision Medicine” initiative. The idea is to use knowledge of genetics, health threats, and individual responses. For example, some people with Type II Diabetes may lose a limb and others may not. Would an examination of their DNA give a clue that would permit the development of a predictive test as to who is at risk for limg problems? People with the same disease often have it affect them in widely different ways. Precision medicine hopes to use techniques of big data and DNA analysis to discover whom and why.

This notion comes out of a 2011 Institute of Medicine Report: Toward Precision Medicine: Building A Knowledge Network for Biomedical Research and A New Taxonomy of Disease.

The views, opinions and positions expressed by these authors and blogs are theirs and do not necessarily represent that of the Bioethics Research Library and Kennedy Institute of Ethics or Georgetown University.


Obama’s BRAIN and Free Will

By Eddy Nahmias, PhD

Eddy Nahmias is professor in the Philosophy Department and the Neuroscience Institute at Georgia State University. He is also a member of the AJOB Neuroscience editorial board.

On April 2, 2013 President Barack Obama announced the BRAIN Initiative, a 10-year, $3 billion research goal to map all of the neurons and connections in the human brain. The BRAIN (Brain Research through Advancing Innovative Neurotechnologies) Initiative is modeled on the Human Genome Project, which successfully sequenced the entire DNA code of the human genome in 2003. Our brains, with 100 trillion neuronal connections, are immensely more complicated than our DNA, so the BRAIN Initiative has a much higher mountain to climb.

But let’s suppose that, finally, during the next Clinton presidency, the BRAIN Initiative is completed…. that is, the presidency of Charlotte Clinton, Bill and Hilary’s grandchild. In fact, suppose that eventually neuroimaging technology advances to the point that people’s brains can be mapped fully enough to allow real-time computations of all of their occurrent brain activity. Neuroscientists can then use this information to predict with 100% accuracy every single decision a person will make, even before the person is consciously aware of their decision. Suppose that a woman named Jill agrees to wear the lightweight BrainCapTM for a month. The neuroscientists are able to detect the activity that causes her thoughts and decisions and use it to predict all of Jill’s thoughts and decisions, even before she is aware of them. They predict, for instance, how she will vote in an election.

The views, opinions and positions expressed by these authors and blogs are theirs and do not necessarily represent that of the Bioethics Research Library and Kennedy Institute of Ethics or Georgetown University.


Why We Should Teach the History of Eugenics

Source: Miles Cole

This month, New York University and University College London have both launched initiatives to focus on the history of eugenics. Students and faculty at UCL hosted an event to encourage their institution to face up to its complicity in constructing unjust racial hierarchy through its support of Francis Galton’s research on eugenics. At NYU, a new exhibit, “Haunted Files: The Eugenics Record Office,” opened at the university’s Asian/Pacific/American Institute.   

At both universities, these initiatives acknowledge that advances in modern genetic technologies make education about the history of eugenics increasingly important.   

Galton’s legacy at UCL is extensive. It began 110 years ago this month, when he contributed funds to establish a position there for a “research fellow” in “National Eugenics,” which he defined as “the study of the agencies under social control that may improve or impair the racial qualities of future generations either physically or mentally.”   

The NYU exhibit brings to life the physical offices and paper archives of Cold Spring Harbor Laboratory on Long Island, the center of the eugenics movement in the United States between 1910 and 1939. According to The New York Times, the exhibit’s curators relied heavily on Cold Spring Harbor’s online Image Archive on the American Eugenics Movement:

David Micklos, executive director of the laboratory’s DNA Learning Center, applied for a government grant to scan files from the office and display them in an online archive, which opened in 2000. “It was a hidden part of American scientific history — people didn’t like to talk about it,” said Mr.

The views, opinions and positions expressed by these authors and blogs are theirs and do not necessarily represent that of the Bioethics Research Library and Kennedy Institute of Ethics or Georgetown University.


George Church gives good quote. He means what he says, and expresses it succinctly and vividly. The latest publication to exploit this is The Economist, which just ran a feature about him called “Welcome to my genome” that includes some of Church’s predictions for human genetic modification:

In the future Dr Church sees a world in which individuals tinker with their DNA to eliminate diseases, give their offspring extra abilities or simply to look more attractive. … To travel beyond the Earth, astronauts could also have their bodies altered to give them a better chance of surviving the journey. They could be genetically engineered to resist radiation and osteoporosis, a weakening of the bones which would result from prolonged weightlessness. Those that remain on Earth could be altered to reduce their carbon footprint [by making] people smaller.

Church also endorses the concept of “backing up my brain into another that I have in my back-pack” and (smiling) suggests that things people “think are a million years away or never, are actually four years away.”

This might be a shock to Neal Jordan, a young science-fiction author, who set his recently-published mind-uploading book Transgod 500 years in the future. Such uploading is also discussed in another new book, The Proactionary Imperative: A foundation for transhumanism, by Steve Fuller and Veronika Lipinska. Carl Elliott reviewed it in this week’s New Scientist under the descriptive online headline, “a manifesto for playing god with human evolution.” In print, the title was the catchier “More, or less, than human?” — presumably because the piece closes with the important observation that:

It is precisely because the powerless and disadvantaged have always made such tempting research subjects that strict controls on medical research are essential.

Newly published in the UK, though not due out in the United States till next February, is yet another book that considers such issues, Sapiens: A Brief History of Humankind by the Israeli historian Yuval Noah Harari. His take is darker than that of the techno-optimists. Not only does he question whether modern people are happier than our stone-age ancestors, he is deeply concerned that coming human enhancements will lead to a more unequal society than any we have seen:

“In the 20th century, the main task of medicine was to bring everybody to a certain level of health and capability. It was by definition an egalitarian aim,” Harari told the Guardian. “In the 21st century medicine is moving onwards and trying to surpass the norm, to help people live longer, to have stronger memories, to have better control of their emotions. But upgrading like that is not an egalitarian project, it’s an elitist project. No matter what norm you reach, there is always another upgrade which is possible.”

As a consequence of the efforts of Church (who is mentioned specifically) and others:

“In the 21st century, there is a real possibility of creating biological castes, with real biological differences between rich and poor,” said Harari. “The end result could be speciation. We’re used to being the only human species around, but there is no law of nature that says there can only be one species of human. With this kind of upgrading treatment we could have, in the not too distant future, more than one human species on Earth again.”

Harari is by no means the first to suggest this. Lee Silver notoriously made that prediction — which he seemed to relish — in Remaking Eden, which was first published in 1997. At that time, such expansive views of human possibilities were fueled by the approaching end of the Human Genome Project. Gene interactions turned out to be more complicated than was once hoped, and the wilder speculations died down for a bit. But now, with the advent of more precise gene-altering tools such as Crispr, ambition seems to be rising again, and the repeated warning is regrettably relevant.

The Economist is a business-focused newsmagazine, and notes that since 2007, “Dr Church has co-founded 12 biotech companies and advised many more.” His enterprises are mostly focused on genomics, diagnostics, therapeutics and synthetic biology, with a possible sideline coming in DNA-based data storage — all related to his research. They are not apparently driving his choice of projects so much as derived from what he finds and publishes. But he does have a very capitalist orientation, leading him to tell the magazine:

We’re well beyond Darwinian limitations to evolution. Evolution right now is in the marketplace.

Church is expressing here an odd combination of hubris and passivity. His ambition takes him “beyond Darwinian limitations” — he can casually discard a few billion years of evolution — and yet he is irresistibly bound to the current economic system. He has that the wrong way round.

Previously on Biopolitical Times:

Posted in Genetic Selection, Human Rights, Inheritable Genetic Modification, Media Coverage, Medical Gene Transfer, Personal genomics, Pete Shanks’s Blog Posts, Sequencing & Genomics, Synthetic Biology


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