The DNA Network

Monogamy and Eusociality [Yann Klimentidis' Weblog]

Posted: 31 May 2008 12:58 PM CDT

Is high relatedness a cause or effect of eusociality? In this paper that just came out in Science, they find through some phylogenetic analyses and mating data among social insects that monogamy (which maximizes relatedness) is ancestral for all lineages, meaning that kin selection is likely a cause of eusociality (I have no idea of the details of how they did this). It's somewhat disappointing and surprising that they make no mention of humans or the paper by Bowles which hints at the relationship between monogamy (reproductive leveling), relatedness and kin selection and group selection, although in a different way.

Ancestral Monogamy Shows Kin Selection Is Key to the Evolution of Eusociality
William O. H. Hughes, Benjamin P. Oldroyd, Madeleine Beekman, Francis L. W. Ratnieks
Science 30 May 2008: Vol. 320. no. 5880, pp. 1213 - 1216

Abstract: Close relatedness has long been considered crucial to the evolution of eusociality. However, it has recently been suggested that close relatedness may be a consequence, rather than a cause, of eusociality. We tested this idea with a comparative analysis of female mating frequencies in 267 species of eusocial bees, wasps, and ants. We found that mating with a single male, which maximizes relatedness, is ancestral for all eight independent eusocial lineages that we investigated. Mating with multiple males is always derived. Furthermore, we found that high polyandry (>2 effective mates) occurs only in lineages whose workers have lost reproductive totipotency. These results provide the first evidence that monogamy was critical in the evolution of eusociality, strongly supporting the prediction of inclusive fitness theory.

The Best Predictive Health Ethics Blogs - May 2008 [PredictER Blog]

Posted: 31 May 2008 10:36 AM CDT

It was a busy month for predictive health news: the president signed GINA, Francis Collins announced his eminent retirement, bloggers reported from important conferences at Case Western and Cold Spring Harbor, and Google announced the debut of Google Health. These events, and others, are reflected in this month's edition of the best blogs on the ethical issues of predictive health.

Are you diseased? Pre-diseased? Potentially diseased? Greg Dahlmann, blog.bioethics.net. 6 May 2008.
In this insightful post, Dahlmann examines how predictive health is changing our concept of disease. When, exactly, does increased risk = illness? Dahlmann writes:

So we're moving from the concept of disease as a state of impaired function to it representing particular sets of probabilities. In the past you were sick when you had a heart attack. Today, you're sick -- or pre-sick, perhaps -- when you have high cholesterol. What about when it's possible to identify constellations of genes that significantly increase your chances of having high cholesterol, or a heart attack. Would that be considered a disease?

Also see Dahlmann's follow up post on "previvors": Blood Matters. Greg Dahlmann, blog.bioethics.net. 11 May 2008.

NHGRI Director Francis Collins to Step Down on August 1. Hsien-Hsien Lei, Eye on DNA. 28 May 2008.
Lei shares the news the Francis Collins will retire from his post this summer and that Alan E. Guttmacher will become acting director. Lei also some thoughts on Collins' book The Language of God.

In All Fairness. Fred Trotter, Fred Trotter: My life and thoughts, often about FOSS in medicine. 23 May 2008.
Following the news coverage on the release of Google Health, Fred Trotter weighs in on the privacy questions. Trotter argues that Google is not a health care provider and is, therefore, not covered by HIPAA. He writes:

Both Google Health and HealthVault are designed to make the process of dissemination of your health information to people you want them to be disseminated to easier. Are they doing that in a secure, privacy respecting way? Excellent question; fodder for further posts. Should they be covered by the same laws that cover your healthcare providers? No.

Workman's Compensation, Stereotypes and GATTACA. Steve Murphy, Gene Sherpas: Personalized Medicine and You. 10 May 2008.
Murphy addresses a few of the potential social consequences of predictive medicine, by examining the following scenario:

Young person goes to 23andME/Navigenics/ETC (They just may add this immediately)....gets predictive testing indicating that he is at a 300 fold increased risk of herniating a disc in his back. Avoids manual labor (plays video games all day) never herniates the disc. Did we do society a service?

23andMe, deCODEme and Navigenics at Cold Spring Harbor. Daniel MacArthur, Genetic Future. 9 May 2008.
MacArthur reports, first hand, from the "Biology of Genomes" meeting at Cold Spring Harbor. In addition to the big players in the consumer genomics movement, the speakers at the event included some ethics and policy experts, like Kathy Hudson from Johns Hopkins. Hudson, MacArthur notes, "responded to the problem of patients being given data of very limited predictive value with a very sensible solution: 'In the absence of demonstrable harm, the default should be to provide the information.'"

Genetic testing ethics - consent forms becoming incomprehensible. Elaine Warburton, Genetics and Health. 7 May 2008.
Warburton covers the Translating ELSI, Ethical Legal Social Implications of Human Genetics Research conference at Case Western University in Cleveland. In this entry she reports on Laura Beskow's comments regarding informed consent and the attitudes and concerns of research participants. Also see Warburton's related coverage of pediatric research ethics discussions at the conference in her post: Genetic Ethics - testing and storing our kids' DNA. Genetics and Health. 7 May 2008.

The FDA ditches the Declaration of Helsinki. Stuart Rennie, Global Bioethics Blog. 6 May 2008.
Stuart Rennie of Global Bioethics Blog examines the implications of the FDA's decision to abandon the Declaration of Helsinki. While Rennie focuses on the potential impact of this decision on US research overseas, and not specifically on predictive health research, this decision may have far reaching consequences on clinical trials of any sort. Rennie concludes with the following verdict: "the decision would seem to encourage pharmaceutical companies to cut ethical corners when working abroad".

GINA Series: Irrational Bureaucratic Risk Abhorrence [Page 1]. Andrew Yates, Think Gene. 24 May 2008.
This is the first post of a (thus far) four part series on GINA. Each post begins with the introduction:

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 it's wrong that employers and services review objective facts to make decisions. … "It's not fair…" but why?

The Puzzling Consensus in Favor of the Genetic Information Nondiscrimination Act. Eric Posner, The University of Chicago Law School Faculty Blog. 6 May 2008.
In what may be the most influential post covered in this addition of the best predictive health ethics blogs, Chicago Law professor Eric Posner examines the GINA and asks some compelling questions:

Should the insurance company be permitted to offer the cheap insurance policy only to people who obtain a doctor's certification that a genetic test shows that they belong to the low-risk group? If you think that insurers should be able to discriminate on the basis of visible markers and on the basis of simple doctors' tests for the presence of dangerous diseases, then you should think they should be able to discriminate on the basis of genetic tests. There is no morally relevant distinction between looking at a person's blood for the evidence of infection and looking at his DNA for evidence of susceptibility to a disease. ... The only explanation for the enthusiasm for GINA is that there is an inchoate feeling among people that there is something wrong with the way the insurance market operates.

Medical Genetics Is Not Eugenics. Gabriella Coleman ("biella"), What Sorts of People. 16 May 2008.
Coleman responds to Ruth Cowan's article in The Chronicle of Higher Education, "Medical Genetics Is Not Eugenics". Although Cowan sees little value in thinking about the similarities of modern medical genetics and the mid-century eugenics movement, Coleman cautions:

Even if, as [Cowan] rightly states that genetic testing is oriented primarily toward easing human suffering, genetic testing is still entangled with fraught ethical questions about what types of life we value, what is acceptable human life, and what is not—the very sorts of questions central to eugenics.

Starting to add up to some real money [Omics! Omics!]

Posted: 31 May 2008 09:56 AM CDT

Last week's Globe carried an item that a real estate firm is planning a 5-year, $1 billion dollar, 1.5M square foot biotech complex in Cambridge. Given all the recent news about Gov. Patrick's $1 billion biotech initiative, perhaps Sen Dirksen was right. Predictably, one letter to the editor proposed that the private money obviates the need for the public mone.

Of course, they're addressing two different things, well, mostly. The original biotech proposal was going to be heavily research oriented, but now there is the earmarks for education & earmarks for local infrastructure. The real estate development is going to provide space for future growth, space that the company is hoping will exist.

Real estate in general & biotech specifically are a boom-and-bust phenomenon in Cambridge, though the trend is clearly weighted a bit towards boom. Even before the genomics boom there was a shortage of space & all sorts of old factory space was converted -- one MLNM site was known as the "Box Factory", as it had previously manufactured heart-shaped candy boxes for Valentine's Day. New buildings went up, such as the cluster of current & former MLNM buildings and the Cambridge beachhead for Partners Healthcare's research empire. The really big daddy's were the conversion of a candy factory to the Novartis site & Genzyme's beautiful building. When the tech boom crashed, space intended for companies such as Akamai was hastily converted.

Then the genomics era came crashing down, and suddenly MLNM wasn't gobbling up space but instead dumping it. Sites such as 640 Memorial Drive sat largely vacant, along with many smaller ones. Signs for 'Biotech Space Available'.

The pendulum is apparently closer to boom again, and several biotechs are heading to the suburbs for cheaper rents or more space. Cambridge will never be cheap, that's for sure.

A billion dollars is no pocket change. One unintentionally humorous element in the story was that no clients had been lined up yet -- like anybody in this business can plan 5 years ahead! MLNM got burnt multiple times on shorter term planning -- stuck in a long lease at 640, buildings configured for the wrong mix of chemistry & biology labs, etc.

Biotech buildings have all sorts of additional requirements, many of which I've only recently become aware of. Heavy-duty floors are needed to support equipment. Complicated ventilation infrastructure. Systems to pH neutralize waste water. Some companies have systems to move waste solvents downstairs; Cambridge's fire department has strict limits which grow tighter the higher the floor. Trying to get leeway there is a non-starter; a year and a half ago a non-biotech solvent explosion blew apart a neighborhood in a town north of Boston.

The location is very good; close to a lot of existing biotech, major road routes, and two mass transit lines -- one of which will probably be extended by the middle of the next decade. The area is already congested, but where isn't?

In the image, the Charles River is the dark slash in the lower right corner, and the Genzyme building anchors the lower left corner.
View Larger Map The big parking lot in the center would be a key site, and has begged for redevelopment for a while. The parking lot above it and to the right would also be included -- but also the low rise buildings going diagonally up to the upper left. These are apparently currently low-rent startup space, a useful commodity, but the new buildings will be much taller -- critical in the increasingly crowded biotech zone. A little bit of the space will be restaurant/retail, but with Kendall Square & the Cambridge Galleria nearby, it won't be lacking for eating & errands.

DNA Video: History of the Species [Eye on DNA]

Posted: 31 May 2008 03:06 AM CDT

Work by the MRG at Goldsmiths.
Including: William Latham, Stephen Todd, Frederic Fol Leymarie, Miki Shaw, Ben Jefferys, Lawrence Kelley.

At the core of this work is the idea of feeding DNA data sequences into a rich 3D form generator called FormGrow, to generate organic-looking 3D growth structures, creating an equivalence of the DNA mapped into an alternative multi-dimensional space.

via Kevin Kelly

Simpsons Evolution Video [The Tree of Life]

Posted: 31 May 2008 02:13 AM CDT

Just a little post showing this Simpsons Evolution Video from YouTube

Around the Blogs [Bitesize Bio]

Posted: 31 May 2008 12:11 AM CDT

While I generally am a lurker on other people’s blogs (I admit it), I have a long list of blogs that I subscribe to in my Google Reader feed. And since it’s Friday, I thought it time again to share some of the postings from around the blogs that caught my eye.

On the Five Stages of Proposal Writing - Professors, for the most part, are writers. Grant proposal writers, especially. One prof describes the stages behind her writing.

Life Science Ph.D.s as Industrial Strength Technicians? - Sandra discusses some of the issues for PhDs trying to find jobs, and the biotech companies who find them overqualified.

Walking the Line Between Grades and Experience: My Life as an Undergraduate Researcher (Part 2) - Continued from Part 1, Tim discusses the struggles between getting laboratory experience and earning high marks in his coursework.

The Future of Cell Biology: Organellar Shape - Alex shares some insights regarding what we don’t (yet) fully comprehend, with commentary.

Bacteria on Rocks - A recent paper in Nature reveals that microbes have been found thriving on fresh volcanic basalt on the ocean seafloor, implying that our understanding of carbon cycling and deep-sea systems is missing an entire food source and web.

And from last month:

Serial Endosymbiosis and Intelligent Design - Allen makes an excellent case how science progresses and that while science may resist change, the only way to change science is to do hard work, research and show how your ideas form scientifically relevant contributions.

Avoding the Lure of The Internet [Bitesize Bio]

Posted: 31 May 2008 12:10 AM CDT

There is no doubt that the internet has revolutionised science by making information freely available. But when it comes to actually getting work done, the internet can be a problem.

With all of that lovely information available right at your fingertips it’s easy to get sucked into surfing when you are trying to work.

Here are 5 ways to avoid the lure of the internet and stay efficient

1. Leechblock is a Firefox extension that will block access to any website for any period you specify. So you can block all of those sites that suck up your time, or schedule a set time each day where you can view them. You could allow access to your favorite news sites only during your lunch hour, for example.

2. Temptation blocker is a bit more of a blunt instrument than Leechblock. It allows you to lock yourself out of applications for a set amount of time - so you could use it to block your browser, games, email or whatever is distracting you. If you need to get back into the application before the time is up you can, but the program makes you type in a 32-digit alphanumeric code as a disincentive before unblocking the program.

3. Deleting all bookmarks to websites that eat up your time is a simple way to make it more difficult to navigate to your favorite time-consuming site. But that can be a bit drastic as sometimes you might just want to surf. Alternatively you could use Firefox’s multiple profile capabilities to create one profile for work and one for play.

4. Mozilla’s Prism, is an intriguing piece of software that allows you to run web applications you use/need often as if they were on your desktop. So there is no need to actually open a browser, meaning less opportunity for distractions.

5. Lo-tech options include unplugging/switching your wireless off while working, using pen and paper instead of a computer and exercising some sell control!

How do you avoid online distractions? Let us know in the comments.

Feynman Shows Us How To Be A Scientist [adaptivecomplexity's column]

Posted: 30 May 2008 11:17 PM CDT

Can one ever hear too many stories about Richard Feynman? Cosmic Variance brought my attention to a great piece from Physics Today by Daniel Hillis (who worked with Feynman in the 80's to build a pioneering computer) that shows us how a great scientist continued to tackle interesting problems well into his 60's. How did Feynman do it - how did he keep finding interesting problems to work on?

A global informatics collaboratory [business|bytes|genes|molecules]

Posted: 30 May 2008 09:36 PM CDT

Thinking about BioBarCamp, listening to Chris Messina talking about DiSo, Barcamp and open projects in general and all consumed by the cloud and web services. Over the past year, we’ve built a fairly cool group of bio and data geeks distributed all over the world. We have different skills, different backgrounds and different knowledge bases. Question is, are there enough of us to achieve the kind of bursty success that has driven efforts like OpenID, OAuth, DiSo, Wordpress, etc in the tech/web world? Can we come up with simple tools and protocols that have the same impact on bioinformatics, cheminformatics, molecular modeling and perhaps life science discovery in general?

It is Friday evening, and I am allowed to dream!!!

Technorati Tags: Collaboration, Bursty Work, Life Sciences, Bioinformatics, Cheminformatics