Phoenix speaks to me

by NASA/JPL-Caltech/University of Arizona/Texas A&M University

I made the picture bigger so you can see. The ice is in the lower left of the trench, in shadow. The blowups make it easier to see.

Yes, there’s ice on Mars : Nature News:
[Via Nature]

“Whoohoo! Was keeping my eye on some chunks of bright stuff & they disappeared! Sublimated! So it can’t be salt, it’s ice.” That’s the triumphant verdict of the Mars lander Phoenix, which yesterday boldly declared, after 24 Martian days of scratching the planet’s surface, that yes, there is ice on Mars.

Phoenix is constantly sending back information to Earth, which is posted by the mission team using the instant messaging software Twitter (written, in touchy-feely style, in the first person as if Phoenix itself is providing its own commentary on its labours). Twitter, the ‘microblogging’ phenomenon, can thus claim to have brought the watery news to Earthlings’ attention.
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There are a lot of reasons to be happy to be alive today. The Phoenix on Mars is one of those. There are so many things we are going to learn because we were able to land this vehicle on Mars.

But OhMiGod!! I can read what Phoenix (or the humans behind it) is up to by going to its site on Twitter. If I am out and about and Phoenix discovers life on Mars, it will tell me via Twitter. I can be one of almost 25,000 followers of what Phoenix is doing now. here are the three most recent Tweets it has sent as of 12 on Friday the 20th:

• Briefing starting now at www.nasa.gov/newsaudio. It will also be avail later today on recorded line at 800-873-2093 about 2 hours ago from web
• CO2 vs. H20 ice: Temp too high and pressure too low for CO2 ice. Sci team explains at 10a PDT/1p EDT live audio here: www.nasa.gov/newsaudio. about 2 hours ago from web
• Kudos go to the science and engineering teams that sent me here. Great choice of spots. The cool news is here too at www.nasa.govphoenix/. about 18 hours ago from web

This is just too precious. Twitter rocks, even when it is not working well ;-)

Technorati Tags: Technology

Cancer cell line data

by danbuck57313
Stock market news and prices:
[Via Houston Chronicle]

Marking another positive step in the collaborative fight against cancer, GlaxoSmithKline GSK announced today the release of genomic profiling data for over 300 cancer cell lines via the National Cancer Institute’s cancer Bioinformatics Grid(TM) (caBIG(TM)). The caBIG(TM) initiative is a network of infrastructure and tools that enables the collection, analysis, and sharing of data and knowledge along the entire research pathway from laboratory bench to patient bedside. By releasing the cell line data via caBIG(TM), GSK could be enabling other cancer research institutions to save considerable drug development time and capital in their future cancer therapeutic research.
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This is a lot of information that will now be accessible to a much wider range of scientists. It can be accessed at the NCI site, caBIG. Anyone can play with the data using the available Open Source tools. I expect this will give people something to work with over the weekend.

Technorati Tags: Health, Open Access, Science

Misleading genetic screening discussions

by net_efekt
A lesson in genetic testing: the I148T mutation [Mary Meets Dolly]:
[Via The DNA Network]

In a followup to what I wrote yesterday is this nice tale of the possible pitfalls of genetic testing when we really do not know as much as we would like to.

There has been a lot in the news lately about how California Health officials have ordered 13 genetic testing companies to stop testing California residents. I think many people do not understand why public health officials are concerned about the flood of new genetic tests offered directly to the public. I think I have an example that may illustrate the problem.

Cystic Fibrosis (CF) is a devastating disease that is caused by mutations in the CFTR gene. To have CF, you must inherent one mutation from your mother and one from your father, which means that both copies of your CFTR gene do not work properly. If you only have one mutation in your CFTR gene you are called a carrier for CF, which means that while one copy of the CFTR gene isn’t up to snuff, you at least have one working copy. The one working copy is enough to prevent you from developing CF symptoms.

So having two bad copies produces the disease but even a single bad copy can have ramifications, such as being wary of marrying other carriers. (I’ll have to check on just how 23andme deals with different alleles from different chromosomes. Many genetic diseases are only a real problem there are 2 bad copies.) Anyway back to the story:

So that brings us to the I148T mutation. When researchers were studying the causes of CF, they discovered that there were a significant amount of people that had CF that also had a mutation in the CFTR gene that causes a substitution of a threonine amino acid for an isoleucine at position 148 of the CFTR protein. Hence the name I148T. Researchers made the assumption that the I148T was one of the two mutations that caused the patients’ CF.

So, anyone who was found to have the I148T mutation, but did not have CF symptoms was labeled a carrier for CF. The I148T mutation was included in the testing panel for many labs, including mine.

But as is sometimes the case, it turns out that the apparent linkage of the mutation I148T with disease was just a fluke and the mutation was not directly involved with the disease. Yet this test was included in a genetic panel run by commercial labs.

Unfortunately, that isn’t the end of the story. As more people were tested, researchers found that there were people who had the I148T mutation with another known mutation, but did not have CF. If the I148T mutation was actually was a disease causing mutation, then these people should definitely have symptoms of CF, but they did not.

What researchers eventually found was that I148T was actually what is called a benign polymorphism, which means that it is a mutation that does not cause disease. What they found was that the disease causing mutation is really a deletion of 6 base pairs at nucleotide number 3199. The mutation is called 3199del6 and just happens to be inherited in high frequency with the I148T mutation.

So, lots of people were told they were carriers when they really have nothing to worry about. And this was with validated commercial labs. This does not deal with the problem of errors that I mentioned yesterday. This is about the being able to technically do something before we actually understand the science.

It seems to me that there is a real danger of the data from genotyping labs being misleading to many people unless there is much better informing, vetting and validating, not only of the data but of the science and of the people who provide the samples. I’ll leave you with Rebecca’s words, but I expect we will have a lot more discussion about this before we reach real consensus:

So the lesson is, just because a mutation is present does not mean it causes disease. Any genetic test has to have a mound of research proving that it has any clinical relevance. A reputable genetic counselor would be able to sift through the data and give you an interpretation of your results.

Technorati Tags: Health, Science

Fun with graphs

by Fábio Pinheiro
Fishy phylogenetics figures found. [T Ryan Gregory's column]:
[Via The DNA Network]

Currently working on a paper about fishes, I came across some interesting figures. (Well, mildly interesting, as they are more of the same actually). Let me say, first of all, that much of what we have learned about genome size evolution is thanks to the work of Ralph Hinegardner in the 1970s. He did some of the most substantial investigations of DNA content diversity in groups such as molluscs, crustaceans, echinoderms, and fishes — in some cases, his work remains the main source of information. So, needless to say, I have a lot of respect for his work. Second, I want to note that I think FishBase is absolutely excellent. It is a model for how online databases should be, and I use it frequently. In fact, without it the study I am writing up could not have been accomplished.
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It is always fun to look at graphs and figure out what is wrong with them. He links to another series he has discussed. I got it right away but that is because I know what to look for. it is one of the common fallacies used when discussing evolution and something that Stephen Jay Gould discussed often.

Here is a big hint from the Boston Globe Magazine (Dec. 31, 1995):

The outstanding [misunderstanding of evolutionary theory] is clearly the equation of evolution with progress. People believe that evolution is a process that moves creatures toward greater complexity through time. This makes our very late appearance in the history of the Earth a sensible outcome. The word evolution means progress, but for Darwin, evolution is adaptation to changing local environments, which are randomly moving through time. There is no principle of general advance in that.

Complexity is an ill-defined criteria. What makes something complex? Number of genes. Size of the genome. Number of different cell types. Etc.

Anything that places us at the top or the terminus of any hierarchy is misleading and species-centric. It usually involves cherrypicking. In a scientific sense, how are we more complex than a gorilla? Exactly how are we more complex than a dog?

Attempts have been made for several hundred years now to put humans at the top of any hierarchy, using whatever means necessary. The truth is that no real measure of complexity, by any definition, puts us at the top without some sort of jury rigging of the criteria.

And, frankly, complexity has absolutely nothing to do with successful survival. If complexity is what evolution strives for, then why are the most successful species some of the simplest? Bacteria make up the largest number of organisms on Earth. They were here when life started and will be here when life ends.

There is no progress in evolution. We are not the culmination of a billion years worth of natural selection. We are one of a multitude of species trying to survive TODAY on this planet. We do alright but we will disappear much sooner than many other species will. That is how evolution works. Simple is more often a survival trait than complex.

Technorati Tags: Science

Email and time

by Darren Hester

[Crossposted at SpreadingScience]

NYT: Businesses Fight the Email Monster They Helped Create:
[Via 43 Folders -]

Lost in E-Mail, Tech Firms Face Self-Made Beast – NYTimes.com
Is Information Overload a Billion Drag on the Economy? – Bits – Technology – New York Times Blog
If you’ve seen the video of my Inbox Zero talk at Google, you may recall the moment when a few attendees start mentioning the hundreds of internal email messages they receive (and send) in a given day. I still remember, because I almost fainted.

Whenever I hear these and similar stories, the same question always comes to mind: “What does a company get out of its employees spending half their day using an email program?” Well, apparently, it’s a question a lot of people are starting to ask. Including Google.

A story in today’s New York Times covers Sili Valley’s new interest in curbing unnecessary interruptions and helping stem the flow of endless data.

Intel and other companies are already experimenting with solutions. Small units at some companies are encouraging workers to check e-mail messages less frequently, to send group messages more judiciously and to avoid letting the drumbeat of digital missives constantly shake up and reorder to-do lists.

A Google software engineer last week introduced E-Mail Addict, an experimental feature for the company’s e-mail service that lets people cut themselves off from their in-boxes for 15 minutes.

A few more stats for you:

A typical information worker who sits at a computer all day turns to his e-mail program more than 50 times and uses instant messaging 77 times…

I’d also draw your attention to this infographic illustrating data points from recent studies on “workers’ efficiency at information-intensive businesses.” 28% of a typical worker’s day is spent on:

Interruptions by things that aren’t urgent or important, like unnecessary e-mail messages — and the time it takes to get back on track.
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As with almost all new technologies, people will have to work things out. Too many people treat email as an immediate task. They will leave off of the phone call they are on to answer an email.

I’m going to talk about the supposed need to respond to relevant emails sent by colleagues. The almost spamming that can occur with email, where a tremendous amount of time is spent wading through a plethora of irrelevant emails (say 300 or more), is a discussion for another time.

My view has always been that if someone at my organization wants an answer immediately, they can track me down personally, whether I am in my office or not. The next level, a quick answer, can be gotten with a phone call. If I am out, they can leave a message. An email message is the lowest level.

This is because email is supposed to remove time and place from a response. Face-to-face is restricted in both time and space. Now and both of us in my office. Phones remove place but still determine time. Now but where we are does not matter. Email should only be for messages where the time and the place are unimportant. At a time and location of my choosing.

If someone sends me a time sensitive email, they can call me up and tell me to respond to the email <grin>

If I am involved in something, such as my own project, here is the order of priorities that will require me to break off:

1. Immediately deal with anyone entering my office that needs something done NOW
2. Let any phone call go to voicemail. I can check the voicemail when it is convenient for ME. If it is important they will leave me one or track me down personally (see 1)
3. Nothing else

When I send emails, they either are in response to a previous email, an answer or question for a colleague, an acknowledgement of some event, or some general information to spread (Hey, have you read this article in Nature?) If I need an answer now, I call.

If they are out, I leave a voicemail and may send an email just to make sure there is another route. If it needs an immediate response and I can not find them, sending an email does not absolve me of my responsibility to find an answer. “Well, I sent them an email” does not solve the problem if it needs an answer now!

I usually do check my email several times a day but only when it is convenient for me. I control when I respond. One of the benefits of Web 2.0 tools is that they remove the need for people to simultaneously occupy the same place at the same time for any information to be exchanged. Place and/or time are independent. A blog or a wiki disperses information in this way. Email should also but too many people use it for other purposes.

I need to control when my distractions distract me. Too many people let email interrupt what they are doing. They just can not seem to leave it alone if they know an unopened email is present. Heck, I’ll even sometimes let a voicemail sit there for a time before checking it. I control when I answer it and will not let that blinking red light determine my response.

I do recognize I am strange in many ways and not typical. However, at least I ‘feel’ like I have some control over these distractions.

Try this exercise once or twice a year: Go for a week without wearing or having access to a watch. Many people freak without being able to determine NOW just what time it is. But I find it very relaxing in a Zen kind of way.

Because, it turns out that you can easily stay on top of the time without a watch. Timekeepers are found throughout our culture, either wall clocks, TVs, computers or even cell phones (My son no longer wears his watch. He uses his cell phone to tell time.) In fact, cell phones and computers are much better timekeepers because they are accurately updated, usually to atomic clocks.

But this exercise really does demonstrate how few events are dependent on the exact time. Sure there are events where knowing the time is important but it is educational to find out how few these really are.

Email is like a wristwatch. Only check it when absolutely needed. Life is much easier when either time or email can be ignored. I have more important things to do with my 28%!

Technorati Tags: Knowledge Creation, Web 2.0