A list of recent cases that illustrate the ethical issues confronting bioinformatics. These cases are taken from the news items at http://bioinformatics.org/.
Open source advocates ask people "Would you buy a car with the hood welded shut?" when describing the differences between open source and closed source programs. A more appropriate analogy for scientists may be "Would you accept for publication a manuscript with no methods section?".
Closed source software prevents scrutiny of the exact methodology used in a computational analysis. For this reason, there is a growing movement to promote the use of open source software in science.
http://www.openscience.org/From: "J.W. Bizzaro" Subject: [bioinformatics] Chronicle: The 'Open-Source Movement' Turns Its Eye to Science Excerpt: "Scientists in academe, who already share research materials and papers freely with each other, should take a further step toward openness by releasing the full texts of computer programs that they use to reach conclusions in their work." http://chronicle.com/free/v46/i11/11a05101.htm The article mentions The Open Lab's Loci Project as well as AMMP by Robert Harrison, advisor to the Lab. It appears the article stems from the Open Source/Open Science conference held at Brookhaven National Laboratory in October.
The DNA Bomb. How to target individuals or ethnic groups with engineered pathogens. From the Village Voice (seen on http://slashdot.org/).
http://www.villagevoice.com/issues/0120/baard.shtmlOpen source biology may well cook up a generation of molecular hackers.
http://bioinformatics.org/forum/forum.php?forum_id=466The Pace and Proliferation of Biological Technologies: argues that soon an individual could design and produce pathogenic organismns from scratch in their garage, argues against regulation and advocates creating Open Source like communities for biology.
http://www.molsci.org/~rcarlson/Carlson_Pace_and_Prolif.pdfThe hacker magazine 2600.org published an article in Volume 20 Number 4 (Winter 2003-2004) titled "Hacking the Genome" by Professor L that describes how to create glow-in-the-dark E. Coli, complete with links to a $73.52 kit and a free detailed protocol.
The most horrifying detail is that man-made viruses that are pathogenic have already been synthesized, using similar techniques. Quoting from this BBC Story:
To construct the virus, the researchers say they followed a recipe they downloaded from the internet and used gene sequences from a mail-order supplier.
Having constructed the virus, which appears to be identical to its natural counterpart, the researchers, from the University of New York at Stony Brook, injected it into mice to demonstrate that it was active.
The animals were paralysed and then died.
Subject: [bioinformatics] New York Times: Celera to Charge Other
Companies to Use Its Genome Data
From: News@bioinformatics.org
"A company that deciphered the human genome has just submitted a paper
for publication. But, in a highly unusual move, the company will not
be adhering to the customary practice of simultaneously depositing its
gene sequence data in a public repository freely available to all.
Instead, the company, Celera Genomics, will put the data on its Web
site, making them available to researchers free and to companies for a
fee.
The arrangement, announced by Celera and the editor of the journal
Science, who said the paper would be published early next year,
highlights the tricky financial issues that accompany the new era of
genome research. Celera wants to sell its data. But scientific
journals are committed to making all data related to its papers
public.
So how, Science's editors had asked, could they satisfy these
conflicting goals? And did they want to set a precedent?"
Full Story (Requires Free Registration):
http://www.nytimes.com/2000/12/08/science/08GENO.html"
Science Announces Plan for Ensuring Access to Celera Human Genome
Sequence Data:
http://www.sciencemag.org/feature/data/announcement/genomesequenceplan.shl
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Comments? Post your replies to http://bioinformatics.org/forum/forum.php?forum_id=321
Subject: [bioinformatics] An Open Letter to Bioinformatics Researchers From: News@bioinformatics.org [ This message was sent to the Bio* lists by Sean Eddy and Ewan Birney. ] ``By now you have probably heard that Celera Genomics has submitted their human genome paper to the journal Science. Science and Celera have agreed to special terms for the release of the human genome sequence data. It will be made available through the Celera website, and will not be submitted to the international DNA database consortium (GenBank, EMBL and DDBJ). Science's statement regarding the agreement is at: http://www.sciencemag.org/feature/data/announcement/genomesequenceplan.shl ``All major journals, including Science, have a policy of deposition of sequence data with the `appropriate data bank'. The accepted community standard is submission to GenBank/EMBL/DDBJ. The reason for this deposition is to make the results of the work openly available for future research. This principle was specifically mentioned in the Clinton/Blair statement on human genome sequencing - http://www.usinfo.state.gov/topical/global/biotech/00031401.htm - who strongly upheld the view that `unencumbered access' to genome data was critical. ``The terms of the Celera/Science agreement will give us access to the genome sequence, but not unencumbered access. Celera is suggesting publishing their data under a MTA (Material Transfer Agreement) which would prevent large scale downloads and incorporation of this data into GenBank/EMBL/DDBJ. In order to download the data, you and your institution will have to sign a contract guaranteeing that you will not `redistribute' the Celera data. ``Science believes that the deal is an adequate compromise because it provides us the right to download the data and publish our results. We believe Science is thinking in terms of single gene biology, not large scale bioinformatics. It is probably not hard for you to imagine scenarios in bioinformatics in which `publication' and `redistribution' are virtually the same thing; we cannot imagine Celera allowing us to incorporate data into Pfam, for example, nor into Ensembl. ``We are asking for your support in writing to Science to politely insist that genome sequence papers should be accompanied by unencumbered deposition to GenBank/EMBL/DDBJ. Please note that we have no issue with Celera either keeping this data unpublished for commercial reasons, nor with them combining their data with freely available data from the public genome projects. We would defend their right to do either. Our view is simply that the genome community has established a clear principle that published genome data must be deposited in the international databases, that bioinformatics is fueled by this principle, and that Science therefore threatens to set a precedent that undermines our research. ``We encourage you to express your views on this matter to Donald Kennedy (kennedyd -at- kennedyd.pobox.stanford.edu), the Editor-in-Chief of Science, and/or to Barbara Jasny (bjasny -at- aaas.org), the managing editor in charge of genomics papers at Science.'' Full Text of message can be found here: http://bioperl.org/pipermail/bioperl-l/2000-December/001826.html -- Comments? Post your replies to http://bioinformatics.org/forum/forum.php?forum_id=322
Subject: [bioinformatics] GenomeWeb: Bioinformaticists Debate Science-Celera Agreement From: News@bioinformatics.org Written By: Marian Moser Jones and Bernadette Toner NEW YORK, Dec 11 - Two leading bioinformaticists have issued a call to arms to their colleagues in response to Science's decision to allow Celera to submit its genome data under special circumstances. "Agitate. Let Science know you care," write the letter?s authors, Ewan Birney of the European Bioinformatics Institute and Sean Eddy of the Howard Hughes Medical Institute and Washington University. "Even if we can?t change the deal with Celera, we can try to make sure it's a one-time only deal that's viewed as a Big Mistake." Under the terms of the agreement, which the parties announced Thursday, Science has agreed to allow Celera to submit its human genome sequence data to the journal while making the data available only on its website, not through a public international database such as Genbank, EMBL, or DDBJ. Previously, researchers have had to submit gene data to a public database before publication in Science. Celera has agreed to make the published sequence data available free to academic users, but stipulated that researchers will have to agree in writing not to redistribute the data if they wish to download over one megabase. Commercial users also will be able to access this data, as long as they sign a material transfer agreement not to commercialize the results or redistribute the sequence. Birney and Eddy decided to write the letter, "because it's a huge issue in bioinformatics, and from talking to [supervisory senior editor] Barbara Jasny at Science lastweek, I got the impression that Science had overlooked some serious problems with the deal they were proposing to Science ," Eddy told GenomeWeb. In their letter, Birney and Eddy said these restrictions on redistribution would present a significant obstacle to bioinformatics research. "Bioinformatics research relies on open data with minimal legal encumbrances submitted to public databases," wrote Birney and Eddy. "Without these databases there is no real substrate for bioinformatics research." Celera and Science have not yet hammered out the details for how the sequence data could be retrieved and used with minimal obstacles. Full Story: http://genomeweb.com/articles/view-article.asp?Article=20001211131433 -- Comments? Post your replies to http://bioinformatics.org/forum/forum.php?forum_id=323
Bioinformatics.Org News & Commentary --------------------------------------------------------------------- [BiO News] Reuters: US Supreme Court to decide if human genes patentable Submitted by J.W. Bizzaro; posted on Saturday, December 01, 2012 --------------------------------------------------------------------- Jonathan Stempel writes: "The nation's highest court in a brief order agreed to review a case over whether Myriad Genetics Inc may patent two genes linked to hereditary breast and ovarian cancer. "In a 2-1 ruling on August 16, a panel of the U.S. Federal Circuit Court of Appeals in Washington, D.C., upheld the biotechnology company's right to patent 'isolated' genes that account for most inherited forms of the two cancers. "That ruling also denied Myriad's effort to patent methods of 'comparing' or 'analyzing' DNA sequences." FULL STORY: http://www.reuters.com/article/2012/11/30/us-usa-court-genes-idUSBRE8AT19620121130 --------------------------------------------------------------------- This is a copy of a message posted on the Bioinformatics.Org website.
Subject: [bioinformatics] ColorMax Buys Patent for Human Colorblindness Genes From: News@bioinformatics.org From the press release: ``Tustin, CA (Nov 14, 2000) ColorMax Technologies, Inc. (OTC:BB) has acquired exclusive rights to the, patent for the human genes responsible for common, hereditary, red-green colorblindness. The Tustin, CA-based company is currently marketing the first legally-approved prescription lenses designed to aid persons with this vision disorder. ColorMax acquired a broad patent license covering the human genes for color vision from the Medical College of Wisconsin in Milwaukee.'' Full press release: http://www.colormaxtech.com/newsroom/pr111400.htm Most people don't even realize that this sort of thing is happening. Tell a colleague. Reference by Slashdot.org. -- Comments? Post your replies to http://bioinformatics.org/forum/forum.php?forum_id=343
Subject: [bioinformatics] Scientific American: Who Owns Your Body? From: News@bioinformatics.org ``Meet Daniel and Debbie Greenberg, who transformed the deaths of their son and daughter from Canavan disease into a biomedical blessing. They initiated a research program that led to the discovery of that disease's causative gene--only to learn that the university that co-sponsored the research had quickly patented the gene and made it unavailable or unaffordable to researchers who wanted to use it to help parents and patients.'' Full story: http://www.scientificamerican.com/2001/0301issue/0301reviews1.html Reference by Slashdot.org. -- Comments? Post your replies to http://bioinformatics.org/forum/forum.php?forum_id=388
From: "J.W. Bizzaro" Subject: [bioinformatics] NY Times: The 'Slippery Slope' of Patenting Farmers' Crops "For more than 40 years, plant breeders from around the world have freely used genetic material from one of the world's great collections of wheat seeds -- 150,000 varieties stored in a concrete bunker here built to last 100 years. A twin repository holds 20,000 kinds of corn, sometimes called maize. Wheat and corn are the world's most important food crops, and researchers use basic crossbreeding techniques to improve them, developing, for example, wheat better suited to drought in Africa, or corn more resistant to Latin American insects. Now, what some see as a new threat that could be far more dangerous than any pest has emerged. Private companies and universities are busy patenting plant genes and claiming intellectual property rights to biotechnology advances. Suddenly, the free exchange of plant resources is in question as discoveries representing millions of dollars in profits are patented, potentially keeping poor farmers from using them." Full story (free subscription required): http://www.nytimes.com/library/world/americas/052400mexico-crops-gm.html Reference by Slashdot.com.
Subject: [bioinformatics] Information as a Global Public Good: A Right to Knowledge and Communication "The Green Revolution clearly demonstrated the hazards of allowing agribusiness to dictate development policy and control agriculture. Like the Green Revolution, biotechnology promises great benefits at nearly no cost, but threatens to increase inequalities and reduce the autonomy of farmers. Biotech firms and pharmaceutical companies are identifying and then patenting indigenous knowledge and Southern biodata: this `ownership' of information appropriates what was previously common knowledge and turns it the private property of an elite. Particularly preposterous is ownership of genetic code and the uncompensated appropriation of seed varieties from the locals who have developed them over generations." Proposal to Oxfam International by Ronni Martin et al: http://danny.oz.au/free-software/advocacy/oicampaign.html Reference by Slashdot.com.
Subject: [BiO News] Farmer Pirates Genetically Modified Seeds From: News@bioinformatics.org ``A multinational biotech company has successfully sued a Saskatchewan [Canada] farmer for growing its special canola without a licence. The case raised debate over new food technology. ``Monsanto took Percy Schmeiser of Bruno, Sask. to court for illegally using the company's genetically modified and pesticide-resistant canola seeds.... ``Alan McHughen, an author and plant geneticist, says the ruling clarifies that farmers can't grow genetically modified seed they haven't paid for, and if they find it growing on their land, they must destroy it.'' Full story at CBC News: http://cbc.ca/cgi-bin/templates/view.cgi?/news/2001/03/29/monsanto_schmeiser010329 It'd be interesting to see if Monsanto's ``seed license'' resembles a software EULA. Otherwise, the parallels are striking. Reference by Slashdot.org. -- Comments? Post your replies to http://bioinformatics.org/forum/forum.php?forum_id=436
Subject: [bioinformatics] PubMed Central and the Public Library of Science From: News@bioinformatics.org ``In 1999, Harold Varmus, then Director of the National Institutes of Health, proposed a bold new initiative called PubMed Central (PMC) designed to provide a central repository for literature in the life sciences [see Marshall, E. (1999) Science 284, 718]. Following an initial period of confusion, PMC now exists. It has a clear mission, a stable home, and a nucleus of papers. Its mission is to provide a comprehensive electronic archive of the peer-reviewed literature relevant to the biological sciences. Its home is the National Center for Biotechnology Information (NCBI), whose director is David Lipman. NCBI is also home to GenBank, the public archive of DNA sequences. The publications already present in PMC and freely accessible to the world's scientific community include all articles published in PNAS that are more than 1 month old and that were in a suitable electronic format, as well as articles from a number of other journals such as Molecular Biology of the Cell, Arthri! tis Research, and Breast Cancer Research. Several other journals, including The British Medical Journal (BMJ) and Nucleic Acids Research (NAR), are committed to join. A full list is available at http://www.pubmedcentral.nih.gov.'' ``PubMed Central: The GenBank of the Published Literature'' at PNAS Online: http://www.pnas.org/cgi/content/full/041601398v1 ``publiclibraryofscience.org was established to organize support within the scientific community for online public libraries of science, providing unrestricted free access to the archival record of scientific research. ``Scientists can express their support for this effort by signing an open letter. 1177 scientists from 49 countries have already signed. Your support will help us to persuade the publishers of scientific journals to commit to giving their archival material to the public domain for distribution through online public libraries.'' Public Library of Science: http://www.publiclibraryofscience.org/ Open letter: http://www.publiclibraryofscience.org/plosLetter.htm Thanks to Holly Miller for these references. -- Comments? Post your replies to http://bioinformatics.org/forum/forum.php?forum_id=348
Subject: [BiO News] Science: Building A "GenBank" of the Published Literature From: News@bioinformatics.org This article [1] describes the effort to "create public, electronic archives of the scientific literature, containing complete copies of all published scientific papers." It shows how bringing this data together in an electronic archive will "encourage the development of new, more sophisticated, and valuable ways of using this information, much as GenBank has done for DNA sequences." Growing support is being demonstrated "by the growing list of scientists who have signed an open letter [2] advocating free and unrestricted distribution of scientific literature 6 months after publication." References: 1. http://www.sciencemag.org/cgi/content/full/291/5512/2318a 2. http://www.publiclibraryofscience.org JWB: The Public Library of Science was mentioned here before, but the Science article is new...and free! -- Comments? Post your replies to http://bioinformatics.org/forum/forum.php?forum_id=433
Subject: [BiO News] Nature: Future E-Access to the Primary Literature From: News@bioinformatics.org ``The communication of research results impacts on everyone involved in science. Today, Nature launches an online debate on the most crucial and talked-about aspect of scientific publishing -- the impact of the web on the publication of original research.'' From the article: ``The issue is, to say the least, multifactorial. At one level, there is the economics. It is hardly a state secret that some commercial publishers have charged high prices for low-circulation journals, and enjoyed very high profit margins while contributing to the so-called serials crisis. Few if any libraries can afford subscriptions to even a significant fraction of the literature (see Nature 397, 195-200; 1999). The most recent and prominent manifestation of the debates surrounding this topic is an initiative by researchers -- `The Public Library of Science'. (PLS) who, by threatening a boycott, are trying to force publishers to release archive reports of original research into centralized, (as opposed to dispersed) databases that are freely available and to which there is unrestricted access.'' Full story (free!): http://www.nature.com/nature/debates/e-access/ -- Comments? Post your replies to http://bioinformatics.org/forum/forum.php?forum_id=442
The following is a press release issued today.
The movement to provide free online access to results of scientific and medical research took an important step forward today with the launch of PLoS Biology - the first open access journal from the Public Library of Science (PLoS) publishers.
The inaugural issue, available online and in print today, features peer-reviewed research articles on diverse topics---ranging from malaria genetics to elephant evolution---authored by prominent scientists from around the world.
PLoS Biology is an open access publication - all of these articles are freely available via the Internet to anyone, anywhere to read, download, print, distribute and reuse, so long as proper attribution of authorship is maintained. http://www.plos.org
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