Ethical issues in bioinformatics: some recent cases

A list of recent cases that illustrate the ethical issues confronting bioinformatics. These cases are taken from the news items at

Open Source, Open Science

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.
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."

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.   

Molecular Terrorism

The DNA Bomb. How to target individuals or ethnic groups with engineered pathogens. From the Village Voice (seen on

Open source biology may well cook up a generation of molecular hackers.

The 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.

The hacker magazine 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.

Science, Celera, and the Human Genome

Subject: [bioinformatics] New York Times: Celera to Charge Other
Companies to Use Its Genome Data


"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

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

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):"

Science Announces Plan for Ensuring Access to Celera Human Genome
Sequence Data:

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Subject: [bioinformatics] An Open Letter to Bioinformatics Researchers

[ 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:

``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 -
- 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-, the Editor-in-Chief of
Science, and/or to Barbara Jasny (bjasny -at-, the managing
editor in charge of genomics papers at Science.''

Full Text of message can be found here:

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Subject: [bioinformatics] GenomeWeb: Bioinformaticists Debate
Science-Celera Agreement


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

"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:

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Gene Patents

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."


This is a copy of a message posted on the Bioinformatics.Org website.

Subject: [bioinformatics] ColorMax Buys Patent for Human Colorblindness Genes

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:

Most people don't even realize that this sort of thing is happening.
Tell a colleague.

Reference by

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Subject: [bioinformatics] Scientific American: Who Owns Your Body?

``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:

Reference by

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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

Full story (free subscription required):

Reference by 

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:

Reference by

Subject: [BiO News] Farmer Pirates Genetically Modified Seeds

``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:

It'd be interesting to see if Monsanto's ``seed license'' resembles a
software EULA.  Otherwise, the parallels are striking.

Reference by

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Free Access to Scientific Literature

Subject: [bioinformatics] PubMed Central and the Public Library of Science

``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''

``PubMed Central: The GenBank of the Published Literature'' at PNAS

`` 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:

Open letter:

Thanks to Holly Miller for these references.

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Subject: [BiO News] Science: Building A "GenBank" of the Published Literature

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."


JWB: The Public Library of Science was mentioned here before, but the Science article is new...and free!

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Subject: [BiO News] Nature: Future E-Access to the Primary Literature

``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!):

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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.

Troglodita approved!

Humberto Ortiz Zuazaga

Most recent change: 2012/12/3 at 08:48
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