The National Human Genome Research Institute (NHGRI), the branch of the NIH which funds the majority of academic genome research in the US, is trying to lay out its next big road map, and personalized medicine looms large. The NHGRI wants to use its hefty funding power to ensure that personalized medicine is based on solid research as it become more commercially available.

The institute has offered several white papers, including one on "Applying Genomics to Clinical Problems-Diagnostics, Preventative Medicine, Pharmacogenomics".

Some of the key questions are:

1. "What do new genetically-based diagnostic or risk assessment strategies add to the existing medical armamentarium?"

John Hawks discusses how messy the abuse of genetic testing results could get:

Imagine a custody battle, in which the father hires a private investigator to get a mother's genome. With two variants that yield a 15 percent higher risk of schizophrenia, will the mother's genetic risk be held against her? Or think of corporate boards, looking for a way to dismiss a CEO without paying that golden parachute. Could a genetic test result showing a higher risk for early Alzheimer's give them a reason to invoke a "health" clause in the contract?

Sound familiar?

If you find yourself saying, "No matter how hard I try and try, I can't make my kid do X ..." or "No matter how hard I try, I can't make my kid understand Y ..." it's usually a clear sign that expectation and enforcing that expectation are a significant part of the problem. Your expectation may in fact accurately address the mean—that is, you may expect a behavior of your 9-year-old that most 9-year-olds can do—but remember the range of human variability and try to structure antecedents (the things you do to encourage a behavior to occur) with room for that variability.

This is of course harder to do when you're surrounded by parents whose kids nicely hit or exceed that behavioral mean.

Salon has an interview with Stuart Kauffman, a biologist who has written multiple fascinating books about complex systems. Kauffman has a new book, Reinventing the Sacred, in which he argues that we need to toss out scientific reductionism and take a new, holistic approach to science and rename it God. But how bad is the problem really?

Laplace famously claimed that if we knew the initial position and momentum of all the particles in the universe, we could confidently predict the future of the universe - that is, the universe is completely deterministic. Quantum mechanics seems to indicate that it is not - there is a graininess to the universe at a fundamental level (unless there are so-called 'hidden variables' determining the quantum behavior of particles).

The combination of a very pleasant but busy holiday visit with my In-laws and feeling a bit under the weather has caused my blogging to drop precipitously this past week. I'm back, ready to start off the New Year on the right foot with some free, meaty, internet science reading. (No, I'm not talking about my writing!)

Is there something missing at the heart of quantum mechanics? Einstein and Bohr, like King Kong vs. Godzilla, famously battled over the possible incompleteness of quantum mechanics.

A "new respect for science" in the Obama administration?

The dissonance is jarring:
Obama says:

I am confident that if we recommit ourselves to discovery, if we support science education to create the next generation of scientists and engineers right here in America; if we have the vision to believe and invest in things unseen, then we can lead the world into a new future of peace and prosperity.

And then he passes the megaphone to Rick Warren:

To be honest, I don't really care about the answer to this question. But read this Kristof NY Times column, and see if you're convinced of the answer. It's time to practice your critical thinking skills - questions you should ask about the claims presented in this column are exactly the sorts of questions you should ask when you read a press report about any statistics-based study, especially medical research.

Here is the basic result Kristof is talking about:

Arthur Brooks, the author of a book on donors to charity, “Who Really Cares,” cites data that households headed by conservatives give 30 percent more to charity than households headed by liberals. A study by Google found an even greater disproportion: average annual contributions reported by conservatives were almost double those of liberals.

A friend was telling me the other day about a class he plans on taking on the philosophy of science. When I hear philosophy of science, I immediately think Richard Feynman. Feynman was, of course, not a philosopher, but a scientist par excellence. His lectures are filled with insights like these:

There is always the possibility of proving any definite [well-defined] theory wrong; but notice that we can never proce it right. Suppose that you invent a good guess, calculate the consequences, and discover every time that the consequences you have calculated agree with experiment. The theory is then right? No, it is simple not proved wrong. In the future you could compute a wider range of consequences, there could be a wider range of experiments, and you might then discover that the thing is wrong... We never are definitely right, we can only be sure we are wrong.

Continuing today's theme of science and the Obama administration...

Physicist John Holdren will be Obama's science advisor. I was hoping we'd finally get a biologist in that position, but his expertise on energy and climate issues will be timely.

A marine biologist at Oregon State University, Jane Lubchenco has been tapped to head the National Oceanic and Atmospheric Administration.

Both of these people are past AAAS presidents.

Larry Summers says that R&D spending should not be part of an economic stimulus package, contrary to what many scientists were probably hoping for.

Summers actually has a good point. The rationale for current ideas about a fiscal stimulus package is that government deficit spending is helpful during times when monetary policy isn't getting traction, but such spending has to be followed by a commitment to deficit reduction during better times. So now we spend like it's 1943, but when things pick up we need to cut back.

Can science journalism get any more embarrassingly bad?

"Real-time gene monitoring developed" says a headline over at physorg.com. The piece starts off with an insane hook that makes no sense whatsoever:

With GeneVision, military commanders could compare gene expression in victorious and defeated troops. Retailers could track genes related to craving as shoppers moved about a store. "The Bachelor" would enjoy yet one more secret advantage over his love-struck dates.

I can relate to Olivia Judson's experience with the digitization of science journals:

On the good side, instead of hauling dusty volumes off shelves and standing over the photocopier, I sit comfortably in my office, downloading papers from journal Web sites.

On the bad side, this has produced informational bedlam.

The journal articles arrive with file names like 456330a.pdf or sd-article121.pdf. Keeping track of what these are, what I have, where I’ve put them, which other papers are related to them — hopeless...

Ivory towers are replacing smoke stacks in Alabama and all over the US.

This can be a good thing, but there is a core problem:

Until relatively recently, most universities and the cities surrounding them went about their business without taking full stock of what each meant to the other. Many local and state government leaders, notes Temple University political scientist Carolyn Adams, "don't see these institutions as having an economic development function much beyond employment and land development." For their part, hospitals and academic institutions aren't accustomed to thinking of themselves as de facto economic bigwigs or pondering the responsibilities that go along with that status; for many, the prevailing attitude toward the communities that host them has essentially been, "You should just thank your lucky stars we're here."

Anyone surprised?

The inspector general of the Interior Department has found that agency officials often interfered with scientific work in order to limit protections for species at risk of becoming extinct, reviving attention to years of disputes overthe Bush administration’s science policies.

In a report delivered to Congress on Monday, the inspector general, Earl E. Devaney, found serious flaws in the process that led to 15 decisions related to policies on endangered species.

An editor at Nature discusses the internet and the ethics of science communication (PDF). The paper doesn't turn out to be much of a discussion of science communication on the web - the piece ends up being more of a dig at open-access publishing advocates. On top of that, the discussion of science on the internet is rather banal, making a few fairly obvious points without offering any new solutions.

The Journey of Man: A Genetic Odyssey, Spencer Wells
Random House, 2002

Spencer Wells, in his short, accessible book designed to accompany a similarly titled documentary film, describes the deep history of humans as it has been inscribed in Y chromosomes. This history has only recently become decipherable through modern genetic tools, and the results have settled some centuries-old controversies about how humans in different parts of the world have become so diverse. The biggest surprise is that our differences are recent: the dramatic differences that distinguish Kenyans, Swedes, Han Chinese, and Polynesians all arose less than 50,000 years ago.

Obama is going to appoint a Nobel-prize winning physicist to be his Energy Secretary. I don't know anything about the physicist, Steven Chu (except that he's director of the Lawrence Berkely National Lab), but I can't complain anymore that scientists never make it into influential positions in the Executive Branch.

Like I said, I don't know anything about Chu, but with his technical background, he ought to be comfortable dealing with issues the Energy Secretary must face, from climate change to biofuels to nuclear power and weapons.

How can we share 98% of our DNA with a chimpanzee and still be so different? One of the biggest biological surprises found in our genomes is that chimps, mice, and even flies don't differ very much from us in either number or types of genes. What makes the many diverse animal groups different is not what genes they have; the secret is in how those genes are used.

Something similar takes place inside ourselves: nearly every one of our cells carries the exact same DNA, and yet some cells transmit electrical signals in the brain, while others break down toxic compounds in the liver. How do you get such different cells from the same DNA? Again, the secret lies in how genes are regulated.

It should be no surprise then that gene regulation has been the subject of intense study. Most of these studies have focused on taking known genes and describing how they are regulated, but what biologists would really like to do is predict how an unfamiliar gene is controlled, simply by analyzing that gene's regulatory DNA. Once we can predict how genes are regulated, we're not far away from being able to design new regulatory DNA, which we can use to control the fate of stem cells, manipulate dosing in gene therapy, and design microbes that make better biofuels or degrade toxic waste.  A new report in Nature describes an innovative new way to learn the logic of gene regulation.

Via Larry at Sandwalk, the Howard Hughes Medical Institute is excited about Facebook, YouTube, and Blogs.

What does this have to do with science? Like Larry, I'm still skeptical of what impact this has on what I do in the lab:

...the result is never pretty. I made this point in a comment, but I've hoisted it up here because this issue deserves more visibility.

Physics professor Steve Hsu makes this argument: