Post-Genomics Blog

Forging a connection between research and clinical applications.

White Paper – “Putting Genomes in the Cloud”

Putting Genomes in the Cloud

As genomics rapidly expands the data storage needs, DDN’s Web Object Scaler (WOS) provides a cloud storage architecture that can be scaled out and rapidly accessed from around the world. This technical brief explores:

* Cloud computing benefits for genomics researchers
* Build versus rent cloud comparisons
* WOS features that make cloud storage effective and fast.

Stem Cell Research in the News Again

Recently, Michael J. Fox, a well known actor who is suffering from Parkinson’s disease, appeared in a TV ad backing a pro stem cell research candidate who is in a close race for a Senate seat.

The ad, which is both emotional and difficult to watch, shows the actor shaking uncontrollably and highlights his deteriorating health condition. Fox’s goal is to persuade the electorate in Missouri that by voting for the candidate who supports stem cell research they offer suffering people like himself a hope for recovery.

According to MSNBC, the Michael J. Fox ad stirred a strong response from voters in Missouri, where a constitutional amendment on the ballot would legalize embryonic stem cell research. The race in Missouri is very close and the incumbent republican senator is facing a tough battle mainly because his opponent, a democrat, is pro stem cell research while he is not.

Arthur Caplan, Director of the Center for Bioethics at the University of Pennsylvania, argues that stem cell research has become a focal point in heated Congressional races across the country (including New York, Florida, New Mexico and Virginia, among others) and democratic candidates are using their pro stance on this issue to gain ground against republicans, who, in general, oppose public funding for such research. What’s noteworthy is the emergence of a powerful group that is backing the pro stem cell candidates and funding these multimillion-dollar TV ad campaigns.

Caplan indicates that this is not a small interest group pushing a narrow agenda, but rather a well organized effort by lobbyists from a broad set of disease and disability organizations representing people suffering from cancer, paralysis, heart disease, and various other illnesses. These groups have pulled together and are helping pro stem cell research candidates win important votes with their significant money-raising ability.

Furthermore, by focusing their efforts on the ethical arguments in favor of public funding for embryonic stem cell research, it seems these interest groups are changing the minds of politicians on both sides of the political spectrum. To this point, Congress, which was strongly against stem cell research in 2002, recently came close to overriding President Bush’s veto, which blocked public funding for such research.

Therefore, through their access to significant funding, increasing lobbying power, and sheer control of votes (as they represent a large constituency of people suffering from a broad set of diseases), these disease advocacy groups are putting stem cell research in the spotlight. They can significantly influence the outcome of elections tomorrow and beyond.

Embryonic Stem Cell Research: New Developments and Controversies

When an embryonic stem cell research advance occurs, stories are given a superficial, brass band treatment by the media. Consequently, many people in the United States and elsewhere foster false beliefs regarding the awesome potential of embryonic stem cells for the development of new medical procedures involving regenerative medicine.

These misperceptions have societal consequences and seriously distort the bio-political debate over human cloning and embryonic stem cell research. As a result, public and private funding of embryonic and adult stem cell therapies research is detrimentally impacted.

Developing human embryonic stem cell therapy could prevent spending time and money to develop therapeutic cloning (which provides, at least in theory, perfectly immunocompatible, yet specific, tissues). People who only casually follow the research in the media are not aware of this advantage of embryonic stem cell therapy.

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Mr. Bush’s Respect for Human Embryos

On July 20th, 2006 President Bush issued the first veto of his administration, rejecting a bill that would have lightened restrictions on federal funding of embryonic stem cell research. Bush defended his veto by saying that it “would support the taking of innocent human life in the hope of finding medical benefits for others… It crosses a moral boundary that our decent society needs to respect.” According to Mr. Bush, each child created by in vitro fertilization “began his or her life as a frozen embryo that was created for in vitro fertilization but remained unused after the fertility treatments were complete. . . These boys and girls are not spare parts.” Bush characterizes embryos—including frozen ones—as human beings entitled to the same rights as other human beings.

Mr. Bush appreciates the potential benefit of embryonic stem cell research for curing various diseases and injuries. Nonetheless, he justifies his veto by his religious belief that retrieving stem cells from human embryo is destructive, resulting in the killing of a human being or, at least, a “potentialâ€? human being. Accordingly, so goes the argument, this act cannot be justified in spite of the possible therapeutic benefits. Bush’s conclusion is obviously not based on biomedical science but instead is an expression of his religious creed. Asked in March 2004 about the stem cell controversy, his science adviser, Dr. John H. Marburger III said: “I can’t tell when a fertilized egg becomes sacred,” and added, “That’s not a science issue.”

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New vaccines preventing cervical cancer and new controversies

I will focus here on cervical cancer, a disease that kills only women, for which a promising new vaccine is on the market. This disease kills perhaps 300, 000 women each year, mostly in developing countries. These deaths are unnecessary, and may now be reduced—if the vaccine is deployed and used by women, and that is where the ethical issues come in.

It is impossible to develop cervical cancer without first being infected by HPV. Thus, if a woman is not infected with HPV, she will not develop cervical cancer. Second, not all women who are infected with HPV will develop cervical cancer

The cervical cancer vaccine
A study in the US has shown that after four years a vaccine targeting HPV was still protecting women. The HPV vaccine has the potential to dramatically lower deaths from cervical cancer. Merck’s vaccine called Gardasil was already appoved by the FDA on June 8th and the other is GlaxoSmithKline’s vaccine called Cervarix which will be probably approved by next year.

Conservative objections
The vaccines are most effective when given before women are sexually active. There is opposition from some in the U.S. who think that the vaccines may encourage sexual activity in teens by promoting the view that premarital sex is safe. Others in the U.S.A. are concerned that abstinence programs may be attacked if this vaccine is promoted. The fact that Gardasil can be administered to preteens before they become sexually active is the cause of great controversy for Christian groups. They assume that this type of vaccine will promote a view—either implicitly or explicitly—that it is appropriate for children to engage in sexual activity before marriage.

This argument for rejecting the cervical cancer vaccine is equivalent to saying that seatbelts in cars are bad, because they will undoubtedly cause people to drive faster and have more wrecks. I wonder, then, how many vaccine opponents would be willing to support a law outlawing seatbelts as well?

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A New Model Microbe for Extreme Biology

Extremophiles are organisms that are adapted to environments inhospitable for conventional life forms, e.g. extremes of salinity and temperature, oxygen-starved conditions, or exposure to toxic heavy metals and intense radiation. It turns out that one extremophile, Halobacterium sp. NRC-1, is resistant to all of the above extremes, and has become a favorite subject for in-depth post-genomic studies. This is because of our ability to easily culture it in the laboratory, knock out any of its non-essential genes, and simultaneously assay gene expression for all 2500 genes using DNA microarrays. The organism is a member of the Archaeal branch of the evolutionary tree, an evolutionary relic that displays some characteristics of higher organisms and exhibits novel features that make it ideal for applications in biotechnology.

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Towards a Humanist Bioethics

Biotechnological developments raise a variety of ethical questions that compel one to reexamine one’s traditional morals and how they now apply to novel circumstances.

It was in the interest of addressing these complex questions with careful analysis and ethical considerations, devoid of dogma or oversimplification, that the IHEU-Appignani Center for Bioethics hosted its second Annual Conference on Global Bioethics this April in New York City.

The conference aimed to examine bioethical issues from a humanist perspective, basing one’s moral framework on science and rationality rather than faith, and on core values such as freedom, autonomy, responsibility and solidarity without resorting to an appeal to the supernatural.
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Molecular Biology and the New Creationism?

Molecular Biology and the New Creationism?1

The decision in the Dover creationism trial last month probably came as a relief to most biologists worried about the status of our science in the nation’s high schools. Unimpressed by the arguments of renegade biochemists such as Michael Behe, a judge ruled that “ID [Intelligent Design] is a religious view, a mere re-labeling of creationism, and not a scientific theory.�2 The judge was equally correct in holding that the ID creationists’ arguments were old, in fact going back to William Paley’s argument from design from the early nineteenth century. But one aspect of the dispute has changed, in fact changed radically from even twenty years ago, when Scientific Creationism rather than Intelligent Design was on trial.3 All of Intelligent Design’s examples and arguments are molecular. There are two questions lurking here. Why have the creationists gone molecular? And what can we expect from them in the future, given that genomics is revealing more and more complex detail about the organization and behavior of genomes? We should think about these questions seriously because, in spite of this defeat, these well-funded creationists4 are not about to go away.
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IPG (Integrative Post-Genomics) ‘05: From post-genomics to good old genes?

What is life? Answering this question is one of the ultimate goals of biologists. Since Mendel, Schrödinger, Watson, Crick, Jacob, Monod and so many others, the view has emerged that life is programmed by the DNA molecule. This view culminated during the last century through the completion of the “Human Genome Project,” the sequencing of a human genome. Simultaneously, major technical advances for counting RNAs and protein species opened the maws of the OMICS world (transcriptomics, proteomics, you-name-it-omics).

This is essentially when the smoke from our pipedream of a molecular Grail was blown away by the harsh winds of reality. If DNA is the book of life, no one has the slightest idea of how to read it. One major reason for this is that making sense of the huge amount of data is too complex—when one focuses on the small details the complete picture becomes blurred.
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Transcriptomics in Expression Profiling

The human body is made up of molecules that fit generally into the categories of DNA, RNA, proteins, sugars, salts, fats and water. These last four groups are generally governed by the proteins in the human body and become imbalanced as a result of protein dysfunction. Technological strategies, developed as a result of the Human Genome Project, can rapidly and almost comprehensively scan through the DNA, RNA and protein molecules of the human body in order to identify differences between individuals with a disorder versus those without. These strategies are collectively known as the “-omics.”

Transcriptomics refers to the comprehensive scanning of the nearly fifty thousand currently known genes that are transcribed into RNA molecules from the three-billion-letter human genome. Each cell utilizes (expresses) different genes at different times in its development and under different physiological conditions. In general, tissues express similar sets of genes that can be used to identify those tissues in the absence of any other information. For example, the brain expresses about thirty percent of all of the known genes; those specific transcripts are different from the transcribed genome in the heart. We can therefore define molecular signatures based on expression profiles, and these profiles can then be used to automatically separate normal cells or tissues into their correct category.
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