The DNA Network

Festivus for the rest of us [genomeboy.com]

Posted: 28 May 2008 06:12 PM CDT

A programming note: On Saturday afternoon I will be at the World Science Festival, which looks like more fun than people should be allowed to have. There I will ~~infiltrate~~…~~pretend I belong on~~…~~annoy~~…er, appear on an otherwise esteemed panel, including Nobel laureate Paul Nurse, NHGRI Director Francis Collins (what the…?), computer scientist Latanya Sweeney, sociologist Nikolas Rose and geneticist Jim Evans. We will be talking about how personal genomics affects/will affect our lives; my genome and phenome (yawn) and, I expect, the PGP will be topics for discussion. Please stop by and say hello if you’re so inclined. (Thanks to the indefatigable Alison Snyder for making this panel happen.)

And even if genes and identity aren’t your thing, I encourage those in the NYC area to check out the rest of the Festival. Brian Greene, Tracy Day and company have done a masterful job in putting together an amazing program. It’s dork heaven. baby!

Good-bye Frank! [evolgen]

Posted: 28 May 2008 05:00 PM CDT

Francis Collins, head of the National Human Genome Research Institute (NHGRI), will be stepping down from that position in August. Collins has overseen the sequencing of the human genome, the HapMap project, the ENCODE project, and many other large advances in genomics. The NHGRI has had a major impact in the field of genetics while Collins was at its helm.

Collins also has a history of putting his foot in his mouth -- not that it's a bad thing to do so (lord knows my foot's spent more time lodged in my face than on the ground). He's been incorrect about morality and human evolution, to name two of the more noticeable faux pas. I hope the next head of the NHGRI has more solid grasp of evolutionary genetics than Collins does. Modern genomics requires it.

So, who should take over as head of the NHGRI in August? I have some ideas.

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Physician digital marketing & sales trends webcast [Microarray and bioinformatics]

Posted: 28 May 2008 03:43 PM CDT

Taking the Pulse® U.S. — Physicians and Emerging Information Technologies, is a syndicated multi-client physician research study and advisory service focused on understanding technology adoption and integration trends among U.S. practicing physicians. Now in its seventh year, the primary objective of the research study is to track which technologies physicians have adopted, how they are currently using them, and how they plan to use them in the future.

Taking the Pulse® v8.0 was fielded in Q1 2008 among 1,832 practicing U.S. physicians. Covering subjects that ranges from

General Access and Technology Profile: Practice technology profile, frequency of Internet use, frequency of professional activities online
Online and Offline Professional Information Sources: Online and offline information sources used, including textbooks, journals, CME, reps, search engines, sites visited, conditions researched
Detailing and Pharma Services: eDetailing participation and future interest, use and interest in full-service portals, product and corporate site visitation, rep technology usage
Web 2.0 Technologies: Awareness and use of streaming video, blogs, podcasting and social networking, including use of sites such as Sermo
Email Use and Opportunity: Email newsletters, email with patients, colleagues, and pharmaceutical, biotech or device companies
Patient Interaction and Education: Patients bringing information into office, sites recommended to patients, types of patient education sources of interest
Digital Health Infrastructure: ePrescribing, EMR, Practice Management, Speed of Access
Mobile Technology Profile: PDA, Mobile Phone, Internet, Mobile Integration, iPods, MP3 players and tablet PCs

The Webinar is on June 5 2008, by Manhattan Research about physician digital marketing & sales trends webcast –register at manhattanresearch.webex.com

Note: as is from manhattanresearch website

So long Francis! [Discovering Biology in a Digital World]

Posted: 28 May 2008 03:31 PM CDT

After leading the Human Genome Project and the National Human Genome Research Institute at the NIH for many years, Francis Collins is retiring.

No matter what you think of Francis Collins, he's been successful in getting the genome project done and he's done some amazing things during the 15 years that he's headed NHGRI.

My friend, Dr. Joan Messer, told me many times about the hours he spent talking with students at one of the AAAS meetings. I will always remember him from the NWABR fund-raising dinner where he pulled out his guitar and had the entire audience singing about DNA.

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Francis Collins SteepingStepping Down from NHGRI [The Tree of Life]

Posted: 28 May 2008 03:27 PM CDT

Just got forwarded this email from Francis Collins to multiple people. Collins is stepping down. I wonder what specifically triggered this ... my guess is he is being recruited by one of the presidential candidates to be some sort of advisor. Nothing like having a prominent scientist who also is born again being on your team ....

From: FSCollins (NIH/NHGRI)
Date: Wed, May 28, 2008 at 11:58 AM
Subject: News

Dear friends and colleagues in the many wonderful team projects that I have had the privilege of being part of,

I am writing to let you know of my plans to step down August 1, 2008 as Director of the National Human Genome Research Institute, a position that has been both a joy and privilege to hold for the past 15 years.

The key to success is having wonderful scientific opportunities and stellar colleagues with whom to work. Many challenges lie ahead as genomics increasingly becomes a leading force in medicine, and I leave my position supremely confident that NHGRI and NIH will continue to achieve notable success in meeting them.

Looking back, I'm tremendously proud of our collective work in leading the Human Genome Project (HGP) to its successful conclusion in 2003, and of our wide range of large-scale projects that built upon the foundation laid by the HGP. Collectively, these projects and the priceless data they generated have transformed biomedical research and empowered researchers all around the world. I'm also proud of these projects' commitments to protecting the privacy of genetic information and addressing the ethical, legal and social implications of genome research.

My decision to step down as NHGRI Director came only after much personal deliberation and was driven by a desire for an interval of time dedicated to writing, reflection and exploration of other professional opportunities in the public or private sectors. Rest assured that NHGRI's leadership will be in good hands. Alan E. Guttmacher, M.D., the current deputy director of NHGRI, will become acting director of NHGRI on August 1, and Mark Guyer, Ph.D., the long-time director of the Division of Extramural Research will continue his able leadership. A formal search process for a permanent NHGRI director will get underway shortly.

Finally, I'd like to let each of you know that while I may be leaving the NHGRI Director's office in search of other challenges, I will be cheering for the success of your dedicated and creative scientific achievements over the coming weeks, months, and years.

Keep up the good work!

Francis

NHGRI Director Francis Collins to Step Down on August 1 [Eye on DNA]

Posted: 28 May 2008 02:52 PM CDT

Last year I wondered why Dr. Francis Collins, director of the National Human Genome Research Institute (NHGRI), seemed to be keeping a low profile. Maybe he was already plotting his exit then.

About an hour ago, I received an email from the man himself announcing his plans to resign from the NHGRI starting August 1, 2008. (For a second I thought I was on some personal mailing list of his until I realized it was distributed via the Genetic Alliance Announcements List. D’oh. Delusions of grandeur….) He is leaving to devote time to “writing, reflection and exploration of other professional opportunities in the public or private sectors.” Alan E. Guttmacher, M.D., will become acting director.

Here’s an excerpt from his email:

Looking back, I'm tremendously proud of our collective work in leading the Human Genome Project (HGP) to its successful conclusion in 2003, and of our wide range of large-scale projects that built upon the foundation laid by the HGP. Collectively, these projects and the priceless data they generated have transformed biomedical research and empowered researchers all around the world. I'm also proud of these projects' commitments to protecting the privacy of genetic information and addressing the ethical, legal and social implications of genome research.

In addition to his work on the human genome, Dr. Collins has also been known for his controversial religious beliefs. In a 2006 interview I conducted with Dr. PZ Myers of Pharyngula, he said the following of Francis Collins’ book - The Language of God.

Once upon a time, I would have said that my view of genetics/genomics wouldn't be much different from those who profess a faith — good scientists can sequester their religious beliefs from the practice of science. Unfortunately, I've since read Francis Collins' new book, and that incoherent spewage of irrational lunacy is swaying me the other way, to regard religion as a toxin that corrupts good minds. The Language of God is precisely the kind of example that convinces me of the destructive failures of religious belief.

What memories do you have of Francis Collins?

More: Francis S. Collins to Step Down as Director of National Human Genome Research Institute, NIH News

Teaching in the digital world, part I: technology is not always your friend [Discovering Biology in a Digital World]

Posted: 28 May 2008 02:00 PM CDT

On-line courses were a still a new phenomenon when I was teaching full-time. Our school was pretty gung-ho about on-line education but many instructors were skeptical, some were still lamenting having to learn how to use a computer and losing the services that used to be provided by departmental secretaries. Other instructors simply distrusted the entire idea, seeing distance learning as the equivalent of an educational scam, a kind of "get rich quick scheme" that would allow the school to collect more tuition dollars without paying instructors.

I never did teach an on-line course during my years as a tenured faculty member but I did take an on-line class in on-line teaching.

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A Physicist, a Marine Biologist, and a Geneticist Walk into a Bar... [evolgen]

Posted: 28 May 2008 01:00 PM CDT

Chad's in town for the DAMOP meeting. What that means isn't all that important in the grand scheme of things. But it did give us a chance to have a blogger meet-up. So, I grabbed Professor Steve Steve and Kevin (of Deep Sea Nudes and the Unimportant 95%), and we met Chad for some dinner and beers.

Kevin's posted another version of the picture.

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Quick Entry [The Daily Transcript]

Posted: 28 May 2008 11:46 AM CDT

No I'm not dead. I have been performing some tricky bucket biochemistry, traveling to Montreal every second weekend, taking care of the upcoming season of NERD talks, dealing with job applications, supervising a rotation student and will soon be supervising an undergrad. How do young PIs have time to blog????

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is moderate Islam a lie? (part I) [the skeptical alchemist]

Posted: 28 May 2008 10:50 AM CDT

I have not written about religion for a while. Some of you might be happy about that, some of you might be wondering why I have not touched the topic. The truth is that I am confused. I really am!

We are told basically every day, that this or that religion encourages love, tolerance and strengthens us as human beings - whether this is Christianity, Islam, or Judaism. I hardly hear about the polytheistic religions anymore, even if I know that there is probably more than a billion people who does not only believe in God, but in Gods. But forget that. The main point is that I am being fed this notion that the true meaning of all these religions, and their true aims, are peaceful and bent on tolerance and love.

However, I keep seeing the opposite. I keep seeing people dying and being killed in the name of God (or Gods) all over the world, and freedom of speech being attacked, together with many other human rights, always in the name of God and Paradise. Then one skeptical like me would start asking him/herself a simple question: if this is not the true meaning and aim of religion, then why are all these people perverting the real aim? How can I tell who is the real Muslim, the real Christian, and who is not? Are the fundamentalists of any religion perverting the meaning of their religious scriptures?

Because the Western world is basically split between people who hate Muslims, people who tolerate them, people who love anything to do with Islam, and people who, like me, don't really know what to think anymore, and I find myself stranded without a position. I know plenty of Muslim people. I do not have any close Muslim friend, but I see, work, and talk to Muslims often. They are people like anybody else, not worse not better. But things are being done, in the name of their religion and their God, that have not been done in "Christendom" for a long time. So I need to make up my mind to whether Muslims are stuck in a pre-illuministic age just like Christians used to be at the time of the Crusades (not likely) or whether there is something fundamentally different between the preachings of Christianity and those of Islam. Or, as well, if this mess is to be tributed to hotheads and despots, rather than to Islam itself.

So I am going to embark in this journey. It is going to be a reflection about the main monotheistic religions, what they mean, what their objectives are, and what they mean to me - in terms of how I see them affecting world history and order. You might agree or disagree along the way - great, we can discuss about that. But seeing as I am basically an atheist, this is sure going to look like an interesting journey. I am not going to diminish religious people, religion, and their books. I am not going to be talking about delusions. But I am going to be looking at the facts, and trying to understand what they mean - at least, for me.

I will start with looking at Islam. Why? Because at this moment in history, Islam and the way it is affecting world order can possibly help me better answer those questions for myself: how can I tell who is the real Muslim, the real Christian, and who is not? Are the fundamentalists of any religion perverting the meaning of their religious scriptures?

I am going to start looking at what Islam says the role of the woman should be. According to moderate Muslims and to sympathetic Westerners, the true Islam defends the woman, and gives her rights that previous religions had never accorded her. What I see in most countries where Islam is the official religion is that women are bereft of most rights accorded to them in the West, abused, and treated as mentally inferior beings. So I am going to try and reconcile these two things, while trying to address the issue of whether true Islam is being subverted in these countries, or whether the true Islam is actually at the basis for this discrimination.

As a prelude, I would like you to know that I am not a scholar versed in reading the Quran and that I do not have a strong background in religious studies/theology. So forgive me if I have to cite what other people have said, and limit myself to judge, using my logic only, whether what they say potentially makes sense or not.

First of all, I should explain what the position of moderate Muslims is. Since I am not one of them, I am going to have to use their own words to describe it. I think to find a simple explanation of this position you need go no further than here or here. Basically, the main argument used by moderate Muslims to explain this is that abusive practices do not have a basis in true Islam - the Quran and the Hadiths. Instead, these abusive and/or discriminatory practices are rooted in the pre-Islamic culture of the places where they are carried out. These moderates then go on to cite the Quran and the Hadiths to show that Islamic scriptures protect women and consider them to be individuals with the same rights as men. With the exception, of course, for prescription that relate to topics such as pregnancy, menstruation, and other issues only pertaining to women.

Anyone wishing to understand Islam must first separate the religion from the cultural norms and style of a society. Female genital mutilation is still practised in certain pockets of Africa and Egypt, but viewed as an inconceivable horror by the vast majority of Muslims. Forced marriages may still take place in certain Indian, Pakistani and Bangladeshi communities, but would be anathema to Muslim women from other backgrounds.

This argument can be made to address basically all human rights violations related to women in countries where Islam is the prevalent, or official religion. There is then, of course, the topic of the veil, which is strongly linked to this discussion. But the veil is dismissed as a personal choice, not an obligation - again, the obligation can be linked to cultural, rather than strictly religious, practices.

If you ask a group of Muslim women why they wear the headscarf, you will definitely get diverse answers since it is a very personal issue. Islamically, it is believed that in matters of religion and faith, no one can simply force an ideal on you; for, as it says in the Quran, "there is no compulsion in religion."

When accepting the choice to embrace the veil, then, a Muslim woman becomes the epitome of good character. She is not only modest in her dress, but in her actions and manners as well.

For those who say she's oppressed, let me ask you this: Is it not also a form of oppression to set extremely high standards for the "acceptable" look, weight, and style for a woman in a capitalist society, and to end up with some women spending hours perfecting themselves in order to become an acceptable member of that society? Alternately, is it not a type of freedom and honour when a woman, any woman - Muslim or not - believes her attractiveness comes from her personality and intelligence (along with having a decent, good-looking style that is not set back in the '50s), rather than how low her "low rise" pants go?

But we know that women in countries where Islam is the prevalent, or official religion, simply do not have the same status as men - often by law. And even where the law consents that they are equal under the law, they are still often the victims of honor killings, rapes, and disfiguration. Of course, Muslim countries are not the only ones where this happens - but that is another story. Now, is there any evidence, in the Quran, the Hadith, or the writing of Muslim scholars, against the argument brought forth by the moderate Muslims? That is, is there any evidence that discrimination against women is actually enshrined in the sacred texts of Islam, and in the works of revered Muslim scholars?

I am afraid there is. So I guess I will follow the same line of argument, and let this evidence speak for itself.

The best way to subjugate women is to make them financially dependent on males. This usually implies an inequality enshrined in law, and the lack of access to family wealth (inheritance). This is what the Quran says regards to inheritance:

4.11-12. A male shall inherit twice as much as a female. If there be more than two girls, they shall have two thirds of the inheritance, but if there be one only, she shall inherit the half. Parents shall inherit a sixth each, if the deceased have a child; but if he leave no child and his parents be his heirs, his mother shall have a third. If he have brothers, his mother shall have one sixth after payment of any legacy he may have bequeathed or any debt he may have owed.

Of course, there is more. Remember what moderate Muslims said about the veil: it is supposed to be up to the woman. But if a state considers the Quran to be law, then using a veil is not a personal choice but a legal obligation for women. In fact, the Quran says:

24.30-31. Enjoin believing women to turn their eyes away from temptation and to preserve their chastity: to cover their adornments - except such as are normally displayed; - to draw their veils over their bosoms, and not to reveal their finery, except to their husbands.

There is more, of course, but I am not going to mention it all at this point. However, it comes to mind that if women and men really are equal, then they should at least get equal treatment in Paradise. What is a man that fought for Allah supposed to get as a reward in the afterlife? The Quran puts quite a bit of emphasis on sexual compensation. But this compensation is notably skewed - because only men are entitled to it. The Islamic Paradise has a serious "glass ceiling" issue when it comes to sexual empowerment...

46.10-22. They shall recline on jeweled couches face to face, and there shall wait on them immortal youths with bowls and ewers and a cup of purest wine (that will neither pain their heads nor take away their reason); with fruits of their own choice and flesh of fowls that they relish. And theirs shall be the dark-eyed houris, chaste as hidden pearls: guerdon for their deeds.

44.51-55. The pious will be in a peaceful abode among, gardens and fountains; clothed in satin and brocade, face to face. We shall marry them to wide-eyed houris. In utter tranquility, they will demand all kinds of fruit.

Of course, the pious would be getting houris in addition to their wives. Mohamed said that "there will be no bachelors in Paradise". Alas, it also sounds like there will be no blondes, and no gigolos for the ladies...

At this point, I somehow feel that I have not really convinced you that it is considered acceptable, from an Islamic point of view, to consider women inferior to men. Again, I will let the Quran convince you:

4.34. Men are in charge of women, because Allah hath made the one of them to excel the other, and because they spend of their property (for the support of women). So good women are the obedient, guarding in secret that which Allah hath guarded. As for those from whom ye fear rebellion, admonish them and banish them to beds apart; and scourge (beat) them. Then if they obey you, seek not a way against them Lo! Allah is ever High Exalted, Great.

If you are a Muslim, and you believe, as any good Muslim should, that the Quran is the word of God, and that the word of God must be obeyed, than you are obliged to consider women inferior: they are worth about half a man when it comes to giving testimony, they should cover themselves while men are not obliged to do that, they get no reward in Paradise that is comparable to a man's, and they should be subordinate to men, as men are in charge of women - financially in charge too, as women are not entitled to family property, or to the full inheritance from their dead husband.

All of this is sanctioned by the Quran, and those moderate Muslims who deny it are either ignorant or worse, blasphemous, and they will probably be punished for it.

If you, of course, believe that there is a Hell...

Source: the websites linked from this post, and the book by Ibn Warraq, "Why I am not a Muslim", published by Prometheus Books.

P.S. The latest edition of Gene Genie is out! So if you are tired of reading about women and the Quran, I suggest you get over there to get a science injection.

Disclaimer: this post is not intended to offend, nor is it intended to incite to hate and harm other people. You are free to disagree with what I say, of course, but that's how free speech works. If you disagree with me, you are free to express your opinion in the comments...as long as you do not break any US laws, as this is where this blog is hosted. Cheers.

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It’s all fun until someone gets hurt [genomeboy.com]

Posted: 28 May 2008 10:47 AM CDT

Comic lives here. Hat tip.

More on Digital Clubbing... [DNA and You]

Posted: 28 May 2008 10:18 AM CDT

I just noticed that there is a pretty good wikipedia article related to my earlier post on digital clubbing.

The web as platform: WikiProteins [business|bytes|genes|molecules]

Posted: 28 May 2008 10:00 AM CDT

WikiProteins is all over the web, including BoingBoing and Ars Technica (and of course all over my FriendFeed). This is the first project by WikiProfessional, essentially a Wikipedia for specific content (not unlike the idea of Wikipedia focussing on scientific topics at a high level and pointing to other sites for more technical, domain-specific detail). Sound familiar? WikiProfessional has some of the same ideas as Google’s Knol project (where is that?). The idea is to build a concept web of knowlets. In order to achieve that, MediaWiki has been extended to help some of those underlying relationships to be captured. What I think is missing (and I am not a 100% sure about this) is a true RDF backend, which would really make this phenomenal. The cool part, the current Concept Web as they call it, is all about the life sciences.

To a great degree, this is what the web and science should be all about; Pulling in data from different sources to build a new resource. WikiProteins pulls in data from other sources, e.g. Pubmed. This is why, IMO, every biological content site should have a RESTful API. Let me go one step further and say that every biological content site should provide access to the data in RDF, then we can truly say we have a linked data web.

WikiProteins comes from some heavyweights. Anytime your PI is Amos Bairoch, and Jimmy Wales is a co-author, you know this is serious stuff, and I really like what they’ve done. In some ways, this is better than the Encyclopedia of Life, at least when it comes to making things accessible and available. Here is the abstract for the paper in Genome Biology

WikiProteins enables community annotation in a Wiki-based system. Extracts of major data sources have been fused into an editable environment that links out to the original sources. Data from community edits create automatic copies of the original data. Semantic technology captures concepts co-occurring in one sentence and thus potential factual statements. In addition, indirect associations between concepts have been calculated. We call on a ‘million minds’ to annotate a ‘million concepts’ and to collect facts from the literature with the reward of collaborative knowledge discovery. The system is available for beta testing at http://www.wikiprofessional.org.

Sounds just like what the doctor ordered in some ways, especially for a protein person like yours truly. A search from one of my favorite proteins, bacteriorhodosin, yields a knowlet, already populated with a ton of info (note that the information has not been added manually, but automatically, but once there, “experts” can edit the information). The knowlet is information rich, although it is sorely missing structural information. The publications chosen are also not necessarily the first ones that come to mind. I wonder how they select relevancy? There is a nice visual histogram which allows you to select various pieces of information extracted from the underlying data, concepts, and classifying them as well (whether they are predictive, factural or a co-occurence)

This is probably a good time to describe knowlets and concepts. From the paper

In WikiProteins each concept can be edited by the community. Each concept page is hyperlinked to the Knowlets of all concepts mentioned in that page. A Knowlet stores relationships between a given source concept and individual target concepts. The various relationships (F, C and A) between two concepts are computed into a single composite value, named the ’semantic association’. The technology allows the coupling of all Knowlets into a larger, dynamic ontology called the ‘concept space’

The paper has a nice figure showing how they arrive at these concepts. The next section though is what really gets me excited (emphasis mine)

Knowlets and their connections can be exported into standard ontology and web languages such as the Resource Description Framework (RDF) and the Web Ontology Language (OWL). Therefore, any application using these languages will enable the use of Knowlet output for reasoning and querying with programmes such as the SPARQL Protocol and RDF Query Language. The concept space is provided in open access. The system performs a recalculation of the semantic relationships in the entire biomedical concept space at regular intervals.

Also take a look at the linker, which adds concept web capabilities to a number of resources, including PubMed

That’s all I have time for right now. More later, after I’ve had a chance to play.

Technorati Tags: WikiProteins, WikiProfessional, Semantic Web, Proteins, Ontologies

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Genetic Susceptibility to Cancer [The Gene Sherpa: Personalized Medicine and You]

Posted: 28 May 2008 09:10 AM CDT

I love the pen. It has the ability to befuddle, convince, coerce, and give false or true hope. This is the case with journal articles. I am always amazed by what is reported and what is real. You...

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More workforce issues in science: where have all the grad students gone? [Discovering Biology in a Digital World]

Posted: 28 May 2008 08:49 AM CDT

Where have all the flowers gone?
Long time passing
Where do all the flowers gone?
Long time ago
Where do all the flowers gone?
Young girls picked them everyone,
When will they ever learn? When will they ever learn?
- Pete Seeger

Where do graduate students and post-docs go when they decide it's time to leave the pipeline? And, if they're thinking about going, how do they find a path into something new?

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Sex and Sin and Some Science [Sciencebase Science Blog]

Posted: 28 May 2008 07:00 AM CDT

Lingerie shopping Porn star names originally posted in August 2005, this was something of a joke post about how porn star names have become almost the post-modern equivalent of a person’s astrological star sign, and a whole lot more scientifically valid, if you ask me, with names like Lucky Cocker and Goldie Black common. That’s despite first appearing almost three years ago, this post has had almost 14,000 readers so far in 2008 alone and that figure does not include anyone who read the post on any of the hundreds of sites that syndicate (legit) or scrape (exploitative) Sciencebase content.

Seven deadly sins With this year’s pronouncements from a certain central office in Rome, was it, this post about the so-called seven deadly sins, originally posted in February 2007 has garnered renewed interest from more than 8000 readers in 2008, not counting those who read it purely in the fulltext RSS newsfeed rather than visiting the site. A follow-up post entitled Seven Deadly Sins for Scientists also did very well at the time with a burst of 2000+ readers.

Anandamide cannabinoid This post has had more than 7000 readers this year. I cannot imagine what they’re hoping to find, but given it’s a spoof Beavis and Butthead style script together with a great cartoon about dope, cannabis, weed, skunk, call it what you will, I guess that might have something to do with its popularity.

Viagra sildenafil citrate They do say that almost every pub conversation will eventually boil down to talk of sh*t or sex, well the same goes for blogs, I guess and this post is no exception grabbing the attention of almost 4000 of you so far this year.

Obesity gene A perennial discussion topic on any sci-tech-med-health blog is inevitably going to be the issue of overweight and obesity, especially if scientists have brought up the subject of a genetic excuse, and this post from April 2007, with its Barbie girl photo has caught the eye of about 3500 readers from jan to May 2008

A billion light years from home Finally, another blockbuster this one with 10,000 readers since its ascendance on New Year’s Day 2008 (no, I wasn’t blogging then, it was a post scheduled prior to the break) does rather suggest that Sciencebase readers are not only interested in sex, obesity, pornstar names, sins, and cannabis, but also quite like a bit of astronomy too.

A post from David Bradley Science Writer

Sex and Sin and Some Science

Genomics By Press Release Award #2: Lieden Leiden University and the First "Female" Genome [The Tree of Life]

Posted: 28 May 2008 04:43 AM CDT

Ooh. Ahh. That is what we should all be saying as it has been announced that the first "female" genome has been sequenced. The press has eaten this up a bit, because of course, the other human genomes that have been sequenced have been from males.

Sure, in terms of public perception, it will be good to have a woman's genome sequenced. And in terms of science, there could be some major uses (e.g., if phenotypes such as health status are made available along with the genome one could try to use the genome to dissect female specific health issues). But as far as I can tell, this whole story is about perception with no reality involved.

The problem is that ~~the~~there is no there there yet. The data is not released. There is no paper (e.g., MSNBC reports ""No other scientists have yet verified the Dutch data, but some experts said they were eager to see the sequence.") This is just some group wanting to stake out some territory in an area that certainly others are working on at the same time. Their press release, by the way, has some icky stuff in it. Most annoying is that they make a point to emphasize that the woman whose genome was sequences is a clinical geneticist. And then they say

"If anyone could properly consider the ramifications of knowing his or her sequence, it is a clinical geneticist," says professor Gert-Jan B van Ommen, leader of the LUMC team and director of the 'Center for Medical Systems Biology' (CMSB), a center of the Netherlands Genomics Initiative.

I do not even know what to say to this. What exactly makes a clinical geneticist better able to think about these issues than say, a genetic counselor, or a ethicist or a priest, or a bioinformatician?

Anyway, they also say

Following in-depth analysis, the sequence will be made public, except incidental privacy-sensitive findings

And for this, Lieden University is becoming the recipient of my second "Genomics By Press Release Award." (see my first one here, where interestingly, the discussion of sequencing a woman's genome came up when I announced I was going to sequence a genome on my new Excercycler machine).

What does DNA mean to you? #7 [Eye on DNA]

Posted: 28 May 2008 03:24 AM CDT

What does DNA mean to you?

Reader and frequent commenter NA says:

DNA, to me, means everything. It’s who I am. DNA is what separates the haves and the have-nots for pure atheletic talent.

I think he’s joking, but I’m not too sure. You can never really tell with NA.

Interview Series I - Bennett Greenspan of Family Tree DNA [The Genetic Genealogist]

Posted: 28 May 2008 02:00 AM CDT

Genetic genealogy has been commercially available since 2000, and in the last 8 years many genealogists have used this new tool to learn about their ancestry. Over the course of the next two weeks, I will be sharing interviews I recently conducted with 9 individuals who have had a huge impact on the field of genetic genealogy. The list includes - in the random order that their interview will appear - Bennett Greenspan, Megan Smolenyak Smolenyak, Terry Barton, Alastair Greenshields, Whit Athey, Ann Turner, Katherine Hope Borges, Max Blankfeld, and Ana Oquendo Pabón.

Just a quick disclaimer about the list of interviewed individuals before I begin this series. Genetic genealogy has become the valuable tool that it is due to the efforts of many people, but I was not able to interview everyone (and some were unable to commit the time to do an interview). I apologize to anyone that should be on the list but isn’t.

Now, without further ado, I present the first interview in this exciting series. Bennett Greenspan is the President and CEO of Family Tree DNA, as well as a Founding Partner of the new start-up DNATraits. In the following interview, I ask Mr. Greenspan about the founding of the two companies, and about his thoughts regarding the future of genetic genealogy.

TGG: How long have you been actively involved in genetic genealogy, and how did you become interested in the field?

Bennett Greenspan: I started Family Tree DNA in early 2000 because I had hit a brick wall and needed a new tool to determine if my cousin was related to a person I founding Argentina with the same name. Once I saw how effective using DNA for genealogy were I knew that every genealogist would need to avail themselves of this wonderful confirmation tool.

TGG: You founded Family Tree DNA in 1999, one of the first companies to offer genetic genealogy testing. What led you to create FTDNA?

BG: I got the idea in 1999 but before the proof of concept was completed it was march of 2000…we began to accept orders at that time and formally launched the service, for Y DNA, in May of 2000…3 days after Oxford Ancestors launched their mtDNA testing service…As we all know Y-DNA is much more genealogical then the female inherited mitochondria because of the much faster mutation rates for the STR's that we test in male genetic genealogy, as well as the fact that in the Western world surnames go down the line along with the Y-DNA, which is not the case with the mtDNA.

TGG: Genetic genealogy, unfortunately, has received some bad press lately, largely through the misconceptions of journalists or confusion between genetic genealogy and other types of personal genomic services. What can amateur genetic genealogists do to counteract this bad press?

BG: I'd say be aggressive in writing letters to the editor and making your positive feelings known. I have received scores of support letters since that silly article came out in the English press last week, even thought we were not among the companies that they used…It's clear that the amateur genealogist who uses our services knows much better then the reporter who, in many cases, seem to have an agenda of fear uncertainly and doubt (FUD) because FUD sells newspapers.

TGG: You recently launched DNATraits. What led you to explore this area of genetic testing?

BG: After being reluctant for some time to offer these tests I thought that it was time to launch them for 2 reasons. 1. We saw the demand starting from our own community 2. Mendelian disorders ARE genealogy…we either have had a disaster in our families and therefore we know that someone carries the mutation, or they are hidden and depending upon whom we marry they might create a personal disaster for the family who is a carrier. 2. Because Mendelian diseases are testable and predictable along the lines of 1-2-1 (presuming both parents are carriers for the same recessive mutation) we can actually prevent the birth of sick children by education and screening pre-conception or pre-marriage. This seems to us a noble if not earnest task. It's quite different form the associated gene tests by 23&Me, et. al. since they tell you that you have a greater risk but the SNP's are incomplete and therefore, IMHO, not ready for prime time.

TGG: What do you think the future holds for genetic genealogy?

BG: Will we have high double digit growth rates like in the past? I don’t know. But, as our database grows the likelihood of everyone finding matches with their surname (and prior to surname adoption) is growing exponentially. Today we are beginning to find that most people from a western European background find a strong match…quite often with the same surname. The matches are also beginning to get exciting in the group of adoptees who number in the 1-2,000,000 in the US alone. As the database grows and as this gets mapped out the concept of anonymous sperm donor will become like Jumbo Shrimp…an oxymoron. At least when it comes to adoptees intend to help in that regard more so then we can do today (and we already have a pretty good number of adoptees that found through us their biological surname).

Ogoglio Project: Open virtual collaborative [business|bytes|genes|molecules]

Posted: 28 May 2008 12:56 AM CDT

Uber-geek alert!!!

I believe the following was a tweet by Trevor Smith, whom I met at Startup Weekend last year this year and recall as one sharp cookie (that he has spent time at PARC does not come as a surprise once you spend some time with him)

Imagine a city the size and detail of Liberty City, but dedicated to professional collaboration and culture.

Out of curiousity, I had to ask what this was all about. The answer; Ogoglio. At one level Ogoglio is a virtual world, not unlike Second Life, but if you take a deeper look, there is much more there. Just take a look at the goal: Creat an online city for work. The goal is to build a world, Ogoglio City, which mirrors the network effects and structures of the real world. While obviously there is technology involved, the end goal is to make this about collaboration, not a technology project, almost detaching the concept from the technology.

We’ve all, well some of us, have spent considerable time in Second Life, using it for scientific communication. What if we have a true virtual world, one where we could actually work together and do our tasks? Is this futuristic? Perhaps, but instead of being some kind of distinct application, the goal of the Ogoglio project is to function as part of the existing fabric of the web. I quote

Information that sits on the shelf is wasted. Ogoglio spaces connect to your existing databases, documents, and web services to become a nexus of information for your project. They provide a persistent working environment which is shared between offices and continents. Whether you need to set up a Big Board to simultaneously display all of the text, video, and news feeds relevant to your project or you just need a quiet place to go over your notes with a coworker, Ogoglio spaces gather everything together for your team.

The architecture is the part I really dig. It emphasizes the goals of the Ogoglio project to be part of the web, to use existing protocols and rendering technologies to build a metaverse that spans the world. Of course, the software is all open source.

The project is still young, and little known, but I dig what it stands for, and the possibilities. In fact, of all the virtual worlds out there, this is what comes closest to how I’ve always envisioned a metaverse, much like the concept of the holodeck, providing us with a world to actually get work done, without necessarily making it feel like a computer game.

There is a video on the homepage for the project, and a set of screencasts. Screencast #1 is embedded below.

WDYT? Do you think that some day there will be a metaverse embedded onto the web (or multiple metaverses), which will allow us to do real, useful collaboration, perhaps this amalgamation of todays virtual worlds, irc and FriendFeed? I don’t think such a world is realistic for at least a couple of decades, but the idea is still appealing.

Technorati Tags: Ogoglio, Trever Smith, Metaverse, Collaboration, Virtual Worlds

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Digital Clubbing and Your Genes: Prostaglandin E2 in the Pathogenesis of Finger Clubbing (aka Hypertrophic Osteoarthropathy) [DNA and You]

Posted: 28 May 2008 12:36 AM CDT

A new paper (abstract available here) published online in the journal Nature Genetics demonstrates the power of traditional Mendelian genetics to reveal clues to the underlying mechanisms of more common diseases. Finger or digital clubbing, which is also known as hypertrophic osteoarthropathy, is one of the classic physical signs taught to medical students. Hippocrates is commonly thought to have been the first to recognize digital clubbing in the fifth century BC. The clubbing depicted in the figure below (from www.nail-disorders.com) is the hallmark of so-called pulmonary hypertrophic osteoarthropathy, a clinical sign that can develop in the context of a number of clinical conditions including intrathoracic neoplasms (i.e., cancers within the chest):

Some Clinical Conditions Associated with Digital Clubbing

Lung Cancer
Congenital Heart Disease
Inflammatory Bowel Disease

032708-0308-clbbinghipp1 from www.nail-disorders

Figure: Digital clubbing (aka hypertrophic osteoarthropathy). From www.nail-disorders.com.

Despite the fact that the form of hypertrophic osteoarthropathy secondary to lung cancer and other disorders has been recognized for many centuries, its actual cause has remained remarkably enigmatic. However, the new study in Nature Genetics breaks important new ground.

The authors, led by Dr. David Bonthron of the Leeds Institute of Molecular Medicine and Yorkshire Regional Genetics Service, studied several families with a rare inherited form of digital clubbing, known as "primary (idiopathic) hypertrophic osteoarthropathy (PHO)." They localized the gene responsible for PHO to the long arm of chromosome 4 and demonstrated that the responsible gene is HPGD, which provides the coding information to produce a protein called "15-hydroxyprostaglandin dehydrogenase." The affected individuals in these families had mutations in both of their copies of HPGD, suggesting that the inheritance pattern is autosomal recessive (i.e., similar to cystic fibrosis in that a mutation in both copies of the gene are necessary to get the clinical condition).

Importantly, 15-hydroxyprostaglandin dehydrogenase is the main enzyme responsible for breaking down prostaglandin E2 (PGE2, a lipid compound which has a number of functions in the lung, the GI tract, and in the uterus during pregnancy) and other prostaglandins and related compounds.

The authors measured PGE2 levels in the urine of the study subjects and showed that they were elevated in the individuals from the families with mutations in both copies of HPGD. Interestingly, intermediate elevations of urinary PGE2 levels were seen in some of the family members with one normal copy and one mutated copy of HPGD. Some of these individuals had mild, late-onset digital clubbing, which is consistent with the degree of elevation of prostaglandin levels within the body determining the severity and age of onset of the digital clubbing.

In hindsight, the identification of HPGD, the key enzyme in prostaglandin degradation, as a disease gene for PHO makes a great deal of sense. PGE2 is known to have a number of effects upon bone. The demonstration, in this rare disorder, that mutations in the key enzyme of prostaglandin degradation lead to PHO suggests that elevated prostaglandin levels are critical in causing the much more common clubbing seen in pulmonary hypertrophic osteoarthropathy (the clubbing seen in association with lung cancer and other disorders). As the lung is known to be a site of PGE2 clearance by HPGD, perhaps the lung diseases associated with pulmonary hypertrophic osteoarthropathy lead to decreased clearance and degradation of PGE2.

PGE2 is also known to be important in the context of a type of congenital heart disease known as "patent ductus arteriosus" (PDA). Normally, the ductus arteriosus is closed after birth when circulating PGE2 levels fall significantly (due to exposure of the blood to HPGD in the newborn's lung). One might expect that PGE2 levels would not drop as rapidly in individuals with mutations in HPGD, and, indeed, 4 of the 13 HPGD-deficient individuals in this study had patent ductus arteriosus. Although, this association was previously recognized, it now makes much more sense given the association with a disruption in the capacity to metabolize PGE2. It will be interesting to see if significant numbers of individuals with PDA have mutations in one or both copies of HPGD.

The authors point out that there were some previous clues to the involvement of prostaglandins in clubbing. For example, liver transplant patients who received prostaglandin E therapy developed clubbing. Nevertheless, this novel result suggests that PHO and the more common secondary pulmonary hypertrophic osteoarthropathy have a common cause: elevated prostaglandin levels.

There are two important clinical implications for the future:

Strategies aimed at decreasing prostaglandin levels might be helpful in individuals with PHO.
For middle-aged or elderly individuals presenting to a physician with clubbing in the future, it may be worthwhile considering whether there are HPGD mutations, as their presence could help the patient avoid an extensive work-up looking for other underlying causes including malignancy.

The illusive high impact paper [Mailund on the Internet]

Posted: 28 May 2008 12:11 AM CDT

Sciencewomen describes a problem I know very well:

On a day when I am feeling increasingly dismal about the publication prospects of my current project, my mood was not lightened with the arrival of the table of contents for the current issue of a very high impact journal (say, cell/nature/science). One of the papers was right up my research alley and the lead author is someone junior to me. Why is it that the other guy is getting a very high profile paper and I’m struggling to get results that will merit publication at all?

I did my PhD in theoretical computer science, where high impact papers (high impact outside your own field, that is) are few and far between, and I didn’t really expect to write high impact papers then.

Now I’m doing bioinformatics, and that is a hot field, so now I do want to, but I am not particularly successful. There’s a few that have received some interest, in particularly this one about the speciation of humans, but I wasn’t the first author on that.

Lately, I do not seem to manage to be first author on any paper…

I’m in the weird situation where I am not senior enough to be last author on any paper, but I am spending too much time on too many different projects that I can focus enough on a single project to expect to be first author on a paper.

I feel like I’ve substituted quantity of publications for quality. Of course, I have no one to blame but myself, so I just need to change my working habits, I guess. Spending too much time blogging probably doesn’t help either.

Great, now I’m depressed. What a way to start the day… Oh well, I’ll head to the office to get some work done, that should cheer me up!

A critical look at islam [Mailund on the Internet]

Posted: 27 May 2008 11:53 PM CDT

I don’t want to turn this into a religion blog — I would be ranting about cartoons all the time (I am Danish, after all) — but just after I posted the atheism talk by Dawkins, I saw this post at the skeptical alchemist: Is moderate Islam a lie? (part I)

Now, before you start threatening my life for insulting the religion of peace (and by the way, Islam does not mean “peace” but “submission”, just thought I’d clear that up for you) let me make it clear that Islam is not being picked on in particular here. It is just the religion discussed in the post I spotted.

I would like all religions to get out of my face. Islam annoys me a lot these days, because a lot of muslims refuse to make religion a private matter. I don’t care what you believe. Go ahead and worship Jehova, Allah, Santa or Zeus, but stop trying to force your beliefs on me! Freedom of religion also means freedom from religion, damn it!

I’ll stop my ranting now. I’ve already spent more time on religion than it really deserves…

GINA Series: When Employer Genetic Testing is Appropriate [Page 3] [Think Gene]

Posted: 27 May 2008 11:00 PM CDT

Recently, President Bush signed GINA, the Genetic Information Nondiscrimination Act, into law. GINA makes it illegal for employers or health insurers to discriminate based on genetics. Virtually the entire genetics community has lauds this legislation, yet few have written why its wrong that employers and services review objective facts to make decisions.

“It’s not fair…” but why?

Under what conditions would an employee benefit from a genetic test mandated by an employer? If an employee had a risk of illness, would the employer be obligated to provide preventive medicine? Would the employer be obligated to better fit employment to people based on tests?

Unfortunately, most employment doesn’t work this way. Our modern economy trains and treats our working and middle classes to be interchangeable automatons. Why invest in a disposable, mass-produced part?

“All people equal” —perhaps the most revered human curse in modern history.

So until we all work at Google, employers who proactively and responsibly invest in preventive medicine for their employees through genetic testing is not likely for the average person.

However, voluntary employee genetic testing can entirely appropriate for some specialized jobs. For example, when you are an astronaut assigned to critical mission in space, you had better not have a 90% chance of dying of a heart attack during the mission. Oh… I guess the scene where Vincent dies in space and the mission is aborted at the cost of decades and trillions… was cut.

Maybe if society impressed into Vincent’s mother that creating a life is subject to enormous social responsibility and is not a whimsical selfish accident, Vincent wouldn’t have suffered.

Notes: Gattaca.

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TED talks: Atheism [Mailund on the Internet]

Posted: 27 May 2008 11:00 PM CDT

Ok, it is only a single talk, but I’ve had to defend my atheism recently, so I feel like sharing Dawkins’ talk with you. After seeing it, go buy his God Delusion!

Table of contents for TED Talks

Previous in series

What to do when a billionaire loves your brother ... [The Tree of Life]

Posted: 27 May 2008 10:05 PM CDT

Well, many people confuse me with my brother, Michael. I guess, if they do not know us, it is understandable. He is at Berkeley. I am at Davis. He works on genomics related things. So do I. We both are passionate about PLoS and Open Access publishing. We both went to Harvard. We both spent time at Stanford. I could go on (we used to look a bit alike ... see the lovely family portrait). Sure, sometimes I get sick of people asking me questions about microarray clustering software and Drosophila.

But most of the time, it only is good for me. Like today. If people want to confuse me with my brother today, fine by me. That is because today, HHMI announced the selection of their new "Investigators". Becoming an HHMI Investigator is the scientific equivalent of getting a sugar daddy. They give you money to do whatever research you want to do. They call it "People, not Projects." or something like that.

So - I saw some of the press on this and mostly it was very general - just talking about how HHMI is really important when NIH budgets are flat and all. But then this afternoon, I was listening to NPRs "Marketplace" when they do a story on the HHMI announcement. And I am thinking - wouldn't it be cool if they mention my brother? And so my ears perked up. And they discussed some background a bit and then Tom Cech, the head of HHMI, was explaining why they want to give money to people with no restrictions and he said

TOM CECH: Often in the course of research, you stumble upon leads to your question that were different from what you originally proposed and by funding the person, not the project, we are freeing people up to follow those leads.

For example, he says, one investigator started out studying retroviruses, but he switched gears and started building miniature arrays to look at the expression of genes in an organism -- don't worry, I have no idea what that means either.

CECH: But before long, he was looking at typing various sorts of leukemias and lymphomas and breast cancers. So he moved into the cancer area with tremendous results.

Certainly sounds like he was talking about my brother, who worked on flu viruses for part of his PhD (ok, they are not retroviruses, but they are RNA viruses), and did a post doc working on arrays (with Pat Brown and David Botstein) and also then used arrays to do cancer classification studies. Sure, he could also be talking about Pat Brown but hey, I am going to pretend he was talking about my brother since it is pretty close.

So, sure, I am a bit peeved they did not select me (thankfully, it seems on first glance that they people they did pick all pretty much rock in terms of science so it is not like I lost out to a bunch of dolts). But I am not jealous. Proud would be more accurate.

Sexually Ambiguous Flies and the Evolution of A Courtship Gene [adaptivecomplexity's column]

Posted: 27 May 2008 10:00 PM CDT

How do you distinguish a male fly from a female fly? Apparently even flies have problems with this one sometimes, and an interesting paper in PNAS describes a recently evolved gene in fruit flies that reduces the amount of male-male courtship they engage in. A research group based at the University of Chicago found that when you knock out the fly gene sphinix, the flies engaged more frequently in male-male courtship rituals. Flies with their sphinx gene intact will engage in male-male courtship about 1% of the time. But when both copies of the sphinx gene are knocked out, male-male courtship increases in frequency to nearly 8%.

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Wednesday, May 28, 2008

The DNA Network

The DNA Network

Table of contents for TED Talks

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