>DTC Snps… no more risk factors!

>I’ve been reading Daniel’s blog again. Whenever I end up commenting on things I don’t understand well, that’s usually why. Still, it’s always food for thought.

First of all, has anyone quantified the actual error rate on these tests? We know they have all sorts of mistakes going on. (This one was recently in the news, and yes, unlike Wikipedia, Daniel is a valid reference source for anything genomics related.) I’ll come back to this point in a minute.

As I understand it, the risk factor is an adjustment made to the likelihood of the general population in characterizing the risk of an individual suffering from a particular disease.

So, as I interpret it, you take whatever your likelihood of having that disease was multiplied by the risk factor. For instance with a disease like Jervell and Lange-Nielsen Syndrome, 6 of every 1 Million people suffer from it’s effects (although this is a bad example since you would have discovered it in childhood, but ignoring that for the moment we can assume another rare disease with a similar rate.) If our DTC test shows we have a 1.17 risk factor because we have a SNP, we would multiply that by 1.17.

6/1,000,000 x 1.17 = 7/1,000,000

if I’ve understood it all correctly, that means you’ve gone from knowing you have a 0.000,6% chance to being certain you have a 0.000,7% chance of suffering from your selected disease. (What a great way to spend your money!)

But lets not stop there. Lets ask about the the error rate on actually calling that snp is. From my own experience in SNP validation, I’d make a guess that the validation rate is close to 80-90%. Lets even be generous and take the high end. Thus:

You’ve gone from 100% knowing you’ve got a 0.000,6% chance of having a disease to being 90% sure you have a 0.000,7% chance of having a disease and a 10% sure you’ve still got a 0.000,6% of having the disease.

Wow, I’m feeling enlightened.

Lets do the same for something like Celiacs disease, which is estimated to strike 1/250 people, but is only diagnosed 1/4,700 people in the U.S.A. – and lets be generous and assume that the SNP in your DTC test has a 1.1 risk factor. (Celiacs is far from a rare disease, I might add.)

As a member of the average U.S. population, you had a 0.4% chance of having the disease, but a 0.02% chance of being diagnosed with it. That’s a pretty big disparity, so maybe there’s a good reason to have this test done. As a Canadian it’s somewhat different odds, but lets carry on with the calculations anyhow.

lets say you do the test and find out you have a 1.1 times risk factor of having the disease. omg scary!

Wait, lets not freak out yet. That sounds bad, but we haven’t finished the calculations.

Your test has the SNP…. 1.1 x 1/250 = 0.44% likelihood you have the disease. Because Celiacs disease requires a biopsy to definitively diagnose it (and treatment does not start till you’ve done the diagnosis), would you run out and submit yourself to a biopsy on a 0.44% chance you have a disease? Probably not unless you have some other knowledge that you’re likely to have this disease already.

Then, we factor in the 90% likelyhood of getting the SNP call correct: You have a 90% likelihood of having a 0.44% chance of having the disease, and a 10% likelihood of having a 0.4% chance of having the disease.

Ok, I’d be done panic-ing about now. And we’ve only considered two simple things here. Lets add one more just for fun.

lets pretend that an unknown environmental stressor is actually involved in triggering the condition, which would explain why the odds are somewhat different in Canada. Since we know nothing about that environmental trigger, we can’t even project odds of coming in contact with it. Who knows what effect that plays with the SNP you know about.

By now, I can’t help thinking that all of this is just a wild goose chase.

So, when people start talking about how you have to take your DTC results to a Genetic Counsellor or to your MD I really have to wonder. I can’t help but to think that unless you have a very good reason to suspect a disease or if you have some form of a priori knowledge, this whole thing is generally a waste. Your Genetic Counsellor will probably just laugh at you, and your MD will order a lot of unnecessary tests – which of those sounds productive?

Let me make a proposal (and I’m happy to hear dissent): Risk factors are great – but are absolutlely useless when it comes to discussing how genetic factors affect you. Lets leave the risk factors to the people writing the studies and ask the DTC companies to make a statement: what are your odds of being affected by a given condition? And, if you can’t make a helpful prediction (aka, a diagnostic test), maybe you shouldn’t be selling it as a test.

>Networking Session – Shepa learning company

>I mentioned last week that I’d spent friday at a “howto” session on networking. The day was organized by the Mitacs group at UBC, and was run by the Shepa Learning Company, of the “Work The Pond” fame. (A book on “positive networking”.)

Overall, I was really glad I attended – The two women who ran the course did an excellent job. (One of them is the founder of the company “Cookies-by-George” which I remember from my childhood – man, I loved the chocolate cookies with cheese in them….) Anyhow, this is one of those things you really have to attend yourself to get the full value out of – however, I can pass along some of the more valuable tips.

  1. It”s not who you know well – it’s who you know vaguely. When looking for a job, it’s probably not your close contacts who will hire you, but rather it’ll be a connection through a connection – so cast your network wide, and make friends with everyone. (Corollary: if you see someone regularly, you should get to know their name – you never know who will be a good connection.)
  2. Good networking isn’t about what people can do for you, but what you can do for them. This puts things into perspective a little better than the hustling that people usually associate with networking. In fact, this is more of a western view of karma: if you do good, good will come back to you – so engage in it with the perspective that you should meet people with the aim of being a good person and helping them out. Don’t dismiss people because they can’t help you – you may be able to help them, so go for it. [Actually, this point resonated very well with me, as it’s the approach I take with my blog. Put information where it’s available in the hope that it helps people, and some of that goodwill may come back to me one day – and so far, I have no complaints! I can already vouch for this method of networking.]
  3. Networking isn’t just meeting people and exchanging cards. Always remember to follow up with the people you meet and to take the time to organize your notes/cards. I found that to be good advice – I spent a few hours organizing my card collection, making notes on where I met people, what we talked about, etc. All of this will help me next time I come across a card and want to know where it came from.
  4. Develop your brand. The way you present yourself, the way you communicate – even the way you interact distinguishes you from other people. All of that should should be reflected in your appearance, your cards, and even your “elevator pitch” when someone asks you what you do.
  5. Keep business cards everywhere – It’s always a good idea to keep a few on hand when you meet someone new. Put some into the pockets of all your coats, bags, etc. Oh, and don’t keep them in your wallet – it doesn’t look so good and the cards get mangled.
  6. When you go to an event, set a goal. For instance, set out to meet 7 new people, or to rescue one person who is too shy to get involved. Your job at events should be to make connections – not just to meet them for yourself. Try to find people that could help each other, and put them in touch.
  7. The glowing introduction. After you meet someone, you should be able to introduce them to someone else in a flattering way. learn how to do this: it’ll help you remember who they are better, and it will facilitate introductions.
  8. You have 3 seconds to make a good first impression. Make eye contact, have a firm handshake, and most importantly, decide you’re going to like someone BEFORE you meet them – you’ll have a good smile and you’ll find you tend to like more people.
  9. Use people’s name in conversation. it’s a nice touch – and it helps you remember names. Win-win.
  10. Always give people your full attention when talking with them. It’s just rude not to, and well, people don’t multi-task as well as they think they do.

The take away tasks are cool, though:

  • Stash business cards everywhere
  • Go to more events
  • work out your introduction (in response to “what do you do?”) Make sure it sells you and your desired brand”
  • meet more people (practice, practice, practice!)
  • Step out of your comfort zone
  • Connect people who could use each other’s help
  • reconnect with your old network

Finally – there were three secrets, which I’m going to paraphrase for you. (I didn’t see a trademark sign on any of them, but they’re useful.

  1. Network to figure out what you can do for other people – don’t expect a return from everyone you meet.
  2. You’ll have to meet (and help) a lot of people before you meet people who can help you, so meet everyone you can.
  3. You need to give yourself permission to engage with people you don’t know.

Was all of that useful to anyone? Probably not without the context of the course or even their book, but I found some of their points to be through provoking. As for whether I’m a better networker today than I was on thursday, I don’t know, but I’m willing to go a little further out of my shell.

>Ridiculous Bioinformatics

>I think I’ve finally figured out why bioinformatics is so ridiculous. It took me a while to figure this one out, and I’m still not sure if I believe it, but let me explain to you and see what you think.

The major problem is that bioinformatics isn’t a single field, rather, it’s the combination of (on a good day) biology and computer science. Each field on it’s own is a complete subject that can take years to master. You have to respect the biologist who can rattle off the biochemicals pathway chart and then extrapolate that to the annotations of a genome to find interesting features of a new organism. Likewise, theres some serious respect due to the programmer who can optimize code down at the assembly level to give you incredible speed while still using half the amount of memory you initially expected to use. It’s pretty rare to find someone capable of both, although I know a few who can pull it off.

Of course, each field on it’s own has some “fudge factors” working against you in your quest for simplicity.

Biologists don’t actually know the mechanisms and chemistry of all the enzymes they deal with – they are usually putting forward their best guesses, which lead them to new discoveries. Biology can effectively be summed us as “reverse engineering the living part of the universe”, and we’re far from having all the details worked out.

Computer Science, on the other hand, has an astounding amount of complexity layered over every task, with a plethora of languages and system, each with their own “gotchas” (are your arrays zero based or 1 based? how does your operating system handle wild cards at the command line? what does your text editor do to gene names like “Sep9”) leading to absolute confusion for the novice programmer.

In a similar manner, we can also think about probabilities of encountering these pitfalls. If you have two independent events, and each of which has a distinct probability attached, you can multiply the probabilities to determine the likelihood of both events occurring simultaneously.

So, after all that, I’d like to propose “Fejes’ law of interdisciplinary research

The likelihood of achieving flawless work in an interdisciplinary research project is the product of the likelihood of achieving flawless work in each independent area.

That is to say, that if your biology experiments (on average) are free of mistakes 85% of the time, and your programming is free of bugs 90% of the time. (eg, you get the right answers), your likely hood of getting the right answer in a bioinformatics project is:

Fp = Flawless work in Programming
Fb = Flawless work in Biology
Fbp = Flawless work in Bioinformatics

Thus, according to Fejes’ law:

Fb x Fp = Fbp

and the example given:

0.90 x 0.85 = 0.765

Thus, even an outstanding programmer and bioinformatician will struggle to get an extremely high rate of flawless results.

Fortunately, there’s one saving grace to all of this: The magnitude of the errors is not taken into account. If the bug in the code is tiny, and has no impact on the conclusion, then that’s hardly earth shattering, or if the biology measurements have just a small margin of error, it’s not going to change the interpretation.

So there you have it, bioinformticians. if i haven’t just scared you off of ever publishing anything again, you now know what you need to do…

Unit tests, anyone?

>I hate facebook

>I have a short rant to end the day, brought on by my ever increasing tie-in between the web and my desktop (now KDE 4.3):

I hate facebook.

It’s not that I hate it the way I hate Myspace, which I hate because it’s so easy to make horribly annoying web pages. It’s not even that I hate it the way I hate Microsoft, which I hate because their business engages in unethical practices.

I hate it because it’s a walled garden. Not that I have a problem with walled gardens in principle, but it’s just so inaccessible – which is exactly what the facebook owners want. If you can only get at facebook through the facebook interface, you have to see their adds, which makes them money, if you ever get sucked into them. (You now have to manually opt out of having your picture used in adds for your friends… its a new option for your profile in your security settings, if you don’t believe me.)

Seriously, the whole facebook wall can be recreated with twitter, the photo albums with flickr, the private messages with gmail…. and all of it can be tied together in one place. Frankly, I suspect that’s what Google’s “Wave” will be.

If I could integrate my twitter account with my wall on facebook, that would be seriously useful – but why should I invest the energy to update my status twice? Why should I have to maintain my own web page AND the profile on facebook…

Yes, it’s a minor rant, but I just wanted to put that out there. Facebook is a great idea and a leader of it’s genre, but in the end, it’s going to die if its community starts drifting towards equivalent services that are more easily integrated into the desktop. I can now update twitter using an applet on my desktop – but facebook still requires a login so that I can see their adds.

Anyhow, If you don’t believe me about where this is all going, wait to see what Google Wave and Chrome do for you. I’m willing to bet desktop publishing will have a whole new meaning, and on-line communities will be a part of your computer experience even before you open your browser window.

For a taste of what’s now on my desktop, check out the OpenDesktop, Remember the Milk and microblog ( or even Choqok) plasmoids.

>Giant Spider…

>Ok, way big diversion from my usual set of topics.

I came downstairs for a snack in the evening, slapped some cheese and tomatoes on a slice of bread, and then looked down at the floor when some movement caught my eye – and then ran for a glass. I’m not terrified of spiders, but this bugger was BIG.

After catching the spider, I looked online – I’m not used to finding spiders this size in Canada, and figured it might be something nasty. Indeed, my best classification for it is probably a Hobo Spider, which is actually a venomous spider. (So much for naively thinking there are no poisonous spiders in Canada!) It lacks the banded pattern on the legs – which I carefully investigated in the pictures I took before figuring out how to handle it.

At any rate, the spider was “ejected” from the house, and I spent some time making sure it hadn’t invited any friends over for the party. And, I’m happy to report, there were no bites at the end of the exercise.

>PHP script for latest twitter tweet in HTML

>One of my (many) projects this weekend was to sign up for twitter and then use it as a means of making micro updates to my web page. Obviously, it shouldn’t be hard, but I had a lot of details to work out, and several tickets to have my hosting service upgrade to PHP5, and install the curl library (both of which were necessary for this hack to work).

Since it’s all working now, I thought I’d share the source. This can obviously be modified, but for now, here’s the script that’s doing doing the job. Yes, bits of it were pulled from all over the web, and some of it was cobbled together by me. Obviously, you’ll need to put the correct source for the feed, which is marked below as “http://twitter.com/..####.rss”

Enjoy!



# INSTANTIATE CURL.
$curl = curl_init();

# CURL SETTINGS.
curl_setopt($curl, CURLOPT_URL, "http://twitter.com/..####.rss$
curl_setopt($curl, CURLOPT_RETURNTRANSFER, 1);
curl_setopt($curl, CURLOPT_CONNECTTIMEOUT, 0);

# GRAB THE XML FILE.
$xmlTwitter = curl_exec($curl);

#curl_close($curl);

# SET UP XML OBJECT.
$xmlObjTwitter = simplexml_load_string( $xmlTwitter );
$item = $xmlObjTwitter -> channel -> item;
$title = substr_replace($item -> title,'',0,8);
$url = $xmlObjTwitter -> channel -> link;
echo "Anthony tweets: {$title}";

>m-based heirarchy

>An IRC friend of mine proposed the following hierarchy of terms for reactiveness and I liked it so much, I figured I’d have to post it here so that I wouldn’t forget it.

minimal < minor < mild < moderate < marked < major < maximal

It’s not news worthy, but I really liked it and figured other people might get some use out of it. Thanks Jasabella!

And, in case you’re wondering, you can find me on Efnet (#chemistry) and Freenode (#bioinformatics). I don’t watch the window all the time, but if you say my name, you’ll get my attention.

>4 Freedoms of Research

>I’m going to venture off the beaten track for a few minutes. Ever since the discussion about conference blogging started to take off, I’ve been thinking about what the rights of scientists really are – and then came to the conclusion that there really aren’t any. There is no scientist’s manifesto or equivalent oath that scientists take upon receiving their degree. We don’t wear the iron ring like engineers, which signifies our commitment to integrity…

So, I figured I should do my little part to fix that. I’d like to propose the following 4 basic freedoms to research, without which science can not flourish.

  1. Freedom to explore new areas
  2. Freedom to share your results
  3. Freedom to access findings from other scientists
  4. Freedom to verify findings from other scientists

Broadly, these rights should be self evident. They are tightly intermingled, and can not be separated from each other:

  • The right to explore new ideas depends on us being able to trust and verify the results of experiments upon which our exploration is based.
  • The right to share information is contingent upon other groups being able to access those results.
  • The purpose of exploring new research opportunities is to share those results with people who can use them to build upon them
  • Being able to verify findings from other groups requires that we have access to their results.

In fact, they are so tightly mingled, that they are a direct consequence of the scientific method itself.

  1. Ask a question that explores a new area
  2. Use your prior knowledge, or access the literature to make a best guess as to what the answer is
  3. Test your result and confirm/verify if your guess matches the outcome
  4. share your results with the community.

(I liked the phrasing on this site) Of course if your question in step 1 is not new, you’re performing the verification step.

There are constraints on what we are allowed to do as scientists as well, we have to respect the ethics of the field in which we do our exploring, and we have to respect the fact that ultimately we are responsible to report to the people who fund the work.

However, that’s where we start to see problems. To the best of my knowledge, funding sources define the directions science is able to explore. We saw the U.S. restrict funding to science in order to throttle research in various fields (violating Research Freedom #1) for the past 8 years, which was effectively able to completely halt stem cell research, and suppress alternative fuel sources, etc. In the long term, this technique won’t work, because the scientists migrate to where the funding is. As the U.S. restores funding to these areas, the science is returning. Unfortunately, it’s Canada’s turn, with the conservative government (featuring a science minister who doesn’t believe in evolution) removing all funding from genomics research. The cycle of ignorance continues.

Moving along, and clearly in a related vein, Freedom #2 is also a problem of funding. Researchers who would like to verify other group’s findings (a key responsibility of the basic peer-review process) aren’t funded to do this type of work. While admitting my lack of exposure to granting committees, I’ve never heard of a grant being given to verify someone else’s findings. However, this is the basic way by which the scientists are held accountable. If no one can repeat your work, you will have many questions to answer – and yet the funding for ensuring accountability is rarely present.

The real threat to an open scientific community occurs with the last two Freedoms: sharing and access. If we’re unable to discuss the developments in our field, or are not even able to gain information on the latest work done, then science will come grinding to a major halt. We’ll waste all of our time and money exploring areas that have been exhaustively covered, or worse yet, come to the wrong conclusions about what areas are worth exploring in our ignorance of what’s really going on.

Ironically, Freedoms 3 and 4 are the most eroded in the scientific community today. Even considering only the academic world, where freedoms are taken for granted our interaction with the forums for sharing (and accessing) information are horribly stunted:

  • We do not routinely share negative results (causing unnecessary duplication and wasting resources)
  • We must pay to have our results shared in journals (limiting what can be shared)
  • We must pay to access other scientists results in journals (limiting what can be accessed)

It’s trivial to think of other examples of how these two freedoms are being eroded. Unfortunately, it’s not so easy to think of how to restore these basic rights to science, although there are a few things we can all do to encourage collaboration and sharing of information:

  • Build open source scientific software and collaborate to improve it – reducing duplication of effort
  • Publish in open access journals to help disseminate knowledge and bring down the barriers to access
  • Maintain blogs to help disseminate knowledge that is not publishable

If all scientists took advantage of these tools and opportunities to further collaborative research, I think we’d find a shift away from conferences towards online collaboration and the development of tools favoring faster and more efficient communication. This, in turn, would provide a significant speed up in the generation of ideas and technologies, leading to more efficient and productive research – something I believe all scientists would like to achieve.

To close, I’d like to propose a hypothesis of my own:

By guaranteeing the four freedoms of research, we will be able to accomplish higher quality research, more efficient use of resources and more frequent breakthroughs in science.

Now, all I need to do is to get someone to fund the research to prove this, but first, I’ll have to see what I can find in the literature…

>The Rights of Science Blogging

>An article recently appeared on scienceweb, in relation to Daniel McArthur’s blogging coverage of a conference he attended at Cold Spring Harbor, which has raised a few eyebrows (the related article is here). Cold Spring Harbor has a relatively strict policy for journalists, but it appears that Daniel wasn’t constrained by it, since he’s not a “journalist”, by the narrow definition of the word.  More than half of the advice I’ve ever received on blogging science conferences comes from Daniel, and I would consider him one of the more experienced and professional of the science bloggers – which makes this whole affair just that much more interesting.  If anyone is taking exception to blogging, Daniel’s coverage of an event is guaranteed to be the least offensive, best researched and most professional of the blogs, and hence the least likely to be the one that causes the outcry.

As far as I can tell from the articles, Cold Spring is relatively upset about this whole affair, and is going down the path that many other institutions have chosen: Trying to suppress blogging, instead of embracing it.

Unfortunately, there really very few reasons for this to be an issue – and I thought I’d put forward a few counter-points to those who think science blogging should be restrained.

1.  Public disclosure

Unless the conference organizers have explicitly asked each participant to sign a non-disclosure agreement, the conference contents are considered to be a form of public disclosure.  This is relevant, not because of the potential for people to talk about it is important, but because legally, this is when the clock starts ticking if you intend to profit from your discovery.  In most countries, the first time an invention is disclosed is when you begin to lose rights to an invention – broadly speaking, it often means that you have one year to officially file the patent, or the patent rights to it become void.  Public disclosure can be as simple as emailing your invention in an un-encrypted file, leaving a copy of a document in a public place….  the bar for public disclosure is really quite low.  More crucially, you can lose your rights to patenting things at all if they’re disclosed publicly before the patent is filed.

Closer to home, you might have to worry about academic competition.  If you stand up in front of a room and tell everyone what you’ve just discovered (before you’ve submitted it), any one can then replicate that experiment and scoop you…  The academic world works on who has published what first – so we already have the built in instinct to keep our work quiet – until we’re ready to release it.  (There’s another essay in that on open source science, but I’ll get to it another day.)  So, when academics stand up in front of an audience, it’s always something that’s ready to be broadcast to the world.  The fact that it’s then being blogged to a larger audience is generally irrelevant at that point.

2.  Content quality

An argument raised by Cold Spring suggests that they are afraid that the material being blogged may not be an accurate reflection of the content of the presentation.  I’m entirely prepared to call B*llsh!t on this point.

Given a journalist with a bachelors degree in general science, possibly a year or two of journalism school and maybe a couple years of experience writing articles and a graduate student with several years of experience tightly focussed on the subject of the conference, who is going to write the more accurate article?

I can’t seriously believe that Cold Spring or anyone else would have a quality problem with science blogging – when it’s done by scientists with an interest in the field.  More on this in the conclusion.

3. Journalistic control

This one is more iffy to begin with.  Presumably, the conference would like to have tighter control over the journalists who write articles in order to make sure that the content is presented in a manner befitting the institution at which the conference took place.  Frankly, I have a hard time separating this from the last point:  If the quality of the article is good, what right does the institution have to dictate the way it’s presented by anyone who attended.  If I sit down over beers with my colleagues and discuss what I saw at the conference, we’d all laugh if a conference organizer tried to censor my conversation.  It’s both impossible and violates a right to free speech. (Of course, if you’re in russia, or china, that argument might have a completely different meaning, but in North America or Europe, this shouldn’t be an issue.)  The fact that I record that conversation and allow free access to it in print or otherwise should not change my right to freely convey my opinions to my colleagues.

Thus, I would argue you can either have a closed conference, or an open conference – you have to pick one or the other, and not hold different attendees to different standards depending on the mode by which they converse with their colleagues.

4. Bloggers are journalists

This is a fine line.  Daniel and I have very different takes on how we interact with the blogosphere.  I tend to publish notes and essays, where Daniel focusses more on news, views and well-researched topic reviews.  (Sorry about the alliteration.)  There is no one format for bloggers, just as there isn’t one for journalists. Rather, it’s a continuous spectrum of how information is distributed and for journalists to get upset about bloggers in general makes very little sense.  Most bloggers work in the niches where journalists are sparse.  In fact, for most people, the niches are what making blogs interesting.  (I’m certainly not aware of any journalists who work on ChIP-Seq full time, and that is, I suspect the main reason why people read my feeds.)

Despite anything I might have to say on the subject, the final answer will be decided by the courts, who have been working on this particular thorny issue for years.  (Try plugging “are bloggers journalists” into google, and you’ll find more nuances to the issue than you might expect.

What it comes down to is that bloggers are generally protected by the same laws that protect journalists, such as the right to keep their sources confidential, and bound by the same limits, such as the ability to be sued for spreading false information.  Responsibility goes hand in hand with accountability.

And, of course, that should be how institutions like Cold Spring Harbor have to address the issue.

Conclusion:

Treating science bloggers the way Cold Spring Harbor treats journalists doesn’t make sense.  Specialists talking about a field in the public is something that the community has been trying to encourage for years: greater disclosure, more open dialog and sharing of ideas are the fundamental pillars of western science.  To force the bloggers into the category of the journalists in the world of print magazines is utterly ridiculous: bloggers articles can be updated to fix typos, to adjust the content and to ensure clarity.  Journalists work in a world in which a typo becomes part of the permanent record and misunderstandings can remain in the public mind for decades.   The power to reach a large audience exists – but only bloggers have the ability to go back and make corrections.    Working with bloggers is a far better strategy than working against them.

No matter how you slice it, institutions with a vested interest in a single business model always resist change – and so do those who have not yet come to terms with the advances of technology.  Unfortunately, it sounds like Cold Spring Harbor hasn’t yet adapted to the internet age and are trying to fig a square peg into a round hole.  

I’d like to go on the record in support of Daniel McArthur – blogging a conference is an important method of creating dialog in the science community.  We can’t all attend each conference, but we shouldn’t all be left out of the discussion – and blogs are one important way that that can be achieved.

If Cold Spring Harbor has a problem with Daniel’s blog, let them come forward and identify the problem.  Sure, they can ask bloggers to announce their blog urls before the conference – allowing the organizers to follow along and be aware of the reporting, I wouldn’t argue against that.  It provides accountability for those blogging the conference – which serious bloggers won’t object to – and it allows the bloggers to go forth and engage the community.  

To strangle the communication between conference attendees and their colleagues, however, is to throttle the scientific community itself.  Lets all challenge Cold Spring to do the right thing and adapt with the times, rather than to ask scientists to drop a useful tool just because it’s inconvenient and doesn’t fit in with the way the conference organizers currently interact with their audience.

>Science Nightmares

>I had friends over last week, and an interesting conversation came up where we were discussing nightmares. Apparently people who have braces have the nightmare of all their teeth falling out, undergrads have the “I missed an exam” nightmare (although I did that one in real life, so the nightmares weren’t that disturbing afterwards), and profs have the “I missed a talk” nightmare.

Well, if it’s a sign that my career is on it’s way forward, I had the “missed a talk” nightmare this morning. The ironic thing is that I’ve never been invited to give a talk a conference, so it’s a bit premature.

Anyhow, it probably has more to do with the fact that I’m somewhat freaked about the huge changes in findpeaks. We learn SO much every day about the biology behind the experiment that this is really nerve wracking to keep on top of it. The development is going well, although bug testing is always a challenge.

At any rate, we’re finally getting to the point where there are very few arbitrary decisions – the data decides how to do the analysis. Quite the contrast to 3 months ago, where we thought we’d hit the end of what new things we could pull out of the data.

Anyhow, debugging calls. Back to work….