Way off topic: Disproving God with the double slit experiment?

Ok, I've been watching a lot of Hitchens and Dawkins recently on youtube, so maybe it's not a surprise that I would eventually start thinking about the age-old question"is there a god"?

After thinking about it for a while, I'm eventually left with a simple logical problem.

If you know the classical quantum physics problem, (youtube video here), you'll know that an electron can act as a wave or a particle, depending on whether or not there is anyone watching it. When no one watches it, the electron is capable of transforming itself into a wave and interfering with itself.... Yes, that sounds odd, but that is in fact the nature of the universe we inhabit. However, when someone observes it, the electron is forced to pick a single path through the two slits, and you get a different pattern emerging beyond the two slits. (The video explains it fairly well, albeit with cheesy narration by a disembodied head...)

The only thing that decides whether it passes through one or both slits is whether it is observed to do so or not. A second piece of information about the universe we live in is that observation requires that we interact in some small way with the universe. You can't observe an event or it's indirect effects if there is no information escaping the event you're observing. (think black holes...) So, if you are observing something, you are, in a small way, interacting with the event - either monitoring the change in an electric field (interacting with the event), or an escaping photon or other form of wave. No matter how you slice it, an observation is an interaction.

So one thing that puzzles me with the double slit experiment and the existence of a god (and I don't care which one), is that the electron is able to transform itself into a complex wave of all possible paths when we don't interact with it. As long us humans (or any device we can conceive of) isn't watching it, the electron will travel through all possible paths. Once we directly observe it, the electron has no choice but to follow a single path.

If observation prevents the electron from being a wave, and non-observation allows the wave, doesn't that mean that when we see the results of the electron acting as a wave, no one else is watching it either?

If you assume there is a god watching everything, how can you explain that the electron is ever able to become a wave and travel through all of the slits when there is a constant observer? The only escape is that you propose your god can observe without interacting with the universe.... and that opens the can of worms that the god must not be part of the universe. (Yes, all things in the universe interact, so not being a part of the universe necessitates non-existence... just like the Ether. If you can't ever interact with it, it doesn't exist.)

Food for thought. Clearly this argument won't convince anyone with faith, but somehow it seems to destroy the concept of an all-seeing god for me. And now, back to genetics...

Math...

I haven't opened twitter in a week and a half - I've just been too busy, but I will get back to it, starting tomorrow. So yes, I will continue the link roundups, but I just couldn't do it when I had my committee meeting, it's aftermath and a talk (which I just gave an hour ago).

Anyhow, in the meantime, I have a short video for you - and don't worry, it's short.

Juggling

Anyone who knows me knows that I juggle - not incessantly, but just as a way to pass the time or as a device for concentrating. If you sit near me at work, there's a good chance I've even got you started on juggling as well.

Although not even close to being on-topic for my blog, I figured I had to share this video. It's one of the better 3-ball juggling videos I've seen. He more or less goes through everything I can do... and then still has another 3 and a half minutes of stuff I can't do. If you've ever been curious about what you can do with three or four balls (without the usual behind the back or hacky-sac tricks), this is more or less a catalog. It's here to remind me next time I run into a problem at work and need to learn something new to get past it.

Funny Conversations, part 2

I was amused:

 -fejes-   effort is relative.
 -person2- No, it's absolute. That's why I gave a reference point.
 -person2- Sarcasm is also absolute.
 -fejes-   if it were absolute, you wouldn't need a reference point.
 -fejes-   sarcasm also lacks a good scale.
 -person2- You're somehow less funny than I am.
 -fejes-   that's relative.

Speaking English?

I have days where I wonder what language comes out of my mouth, or if I'm actually having conversations with people that make sense to anyone.

Due to unusual circumstances (Translation to English: my lunch was forcibly ejected from the fridge at work, which was incompatible with the survival of the glass-based container it was residing in at the time of the incident), I had to go out to get lunch. In the name of getting back to work quickly, as Thursdays are short days for me, I went to Wendy's. This is a reasonable approximation of the conversation I had with one of the employees.

Employee: "What kind of dressing for your salad?"

Me: "Honey-dijon, please."

Employee: "What kind of dressing do you want?"

Me: "Honey-dijon."

Employee: "dressing."

Me: "Honey-dee-john"

Employee: What kind of dressing for your salad?"

Me: "Honey-dijahn. It says honey-dijon on the board, it's a dressing, right?"

Employee: "You have the salad with your meal?"

Me: "yes.."

Employee: "You want the Honey Mustard?"

Me: "Yes."

Sometimes I just don't get fast food joints - they make me wonder if I have aspergers syndrome. After that conversation, I wasn't even going to touch the issue that my "sprite, no ice" had more ice than sprite.

Best Software Licence Ever!

I was looking for some example code of a Mahalanobis distance calculator and came across what I happen to believe is the most entertaining license I have ever seen. I had to share:

The program is free to use for non-commercial academic purposes, but for course works, you must understand what is going inside to use. The program can be used, modified, or re-distributed for any purposes if you or one of your group understand codes (the one must come to court if court cases occur.) Please contact the authors if you are interested in using the program without meeting the above conditions.

The Source.

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....

Art for sale... totally un-related to science

When I started this blog, I had planned to use it to post my photographs and other art projects. Clearly that didn't work out how I expected it to. Anyhow, I thought I'd jump back into that mode for a brief (Weekend) post, and put up a picture of a painting I did a few years ago, and am now trying to sell.


I'm reasonably sure that no one will want it, but I think it'll be an interesting experiment to post it on craigslist and see if anyone is willing to pay for it. Hey, if Genome Canada doesn't get funding for a few more years, I might have another career to fall back on. (-;

Epidemiology and next-generation(s) sequencing.

I had a very interesting conversation this morning with a co-worker, which ended up as a full fledged conversation about how next generation sequencing will end up spilling out of the research labs to the physician's office. My co-worker originally stated that it will take 20 years or so for it to happen, which seems kind of off to me. While most inventions take a lot longer to get going, I think that next-gen sequencing will cascade over more quickly to general use a lot more quickly than people appreciate. Let me explain why.

The first thing we have to acknowledge is that pharmaceutical companies have a HUGE interest in making next gen sequencing work for them. In the past, pharma companies might spend millions of dollars getting a drug candidate to phase 2 trials, and it's in their best interest to get every drug as far as they can. Thus, any drug that can be "rescued" from failing at this stage will decrease the cost of getting drugs to market, and increases revenues significantly for the company. With the price of genome sequencing falling to $5000/person, it wouldn't be unreasonable for a company to do 5-10,000 genomes for the phase 3 trial candidates, as insurance. If the drug seems to work well for a population associated with a particular set of traits, and not well for another group, it is a huge bonus for the company in getting the drug approved. If the drug causes adverse reactions in a small population of people which associate with a second set of traits, then it's even better - they'll be able to screen out adverse responders.

When it comes to getting FDA approval, any company that can clearly specify who the drug will work for - who it won't work for - and who shouldn't take it, will be miles ahead of the game, and able to fast track their application though the approval process. That's another major savings for the company.

(If you're paying attention, you'll also notice at least one new business model here: retesting old drugs that failed trials to see if you can find responsive sub-populations. Someone is going to make a fortune on this.)

Where does this meet epidemiology? Give it 5-7 years, and you'll start to see drugs appear on the shelf with warnings like "This drug is counter-indicated for patients with CYP450 variant XXXX." Once that starts to happen, physicians will really have very little choice but to start sending their patients for routine genetic testing. We already have PCR screens in the labs for some diseases and tests, but it won't be long before a whole series of drugs appear with labels like this, and insurance companies will start insisting that patients have their genomes sequenced for $5000, rather than have 40-50 individual test kits that each cost $100.

Really, though, what choice will physicians have? When drugs begin to show up that will help 99% of the patients for which they should be prescribed, but are counter indicated for genomic variations, no physician will be willing to accept the risk of prescribing without the accompanying test. (Malpractice insurance is good... but only gets you so far!) And as the tests get more complex, and our understanding of underlying cause and effect of various SNPs starts to increase, this is going to quickly go beyond the treatment of single conditions.

I can only see one conclusion: every physician will have to start working closely with a genetic councilor of some sort, who can advise on relative risk and reward of various drugs and treatment regimes. To do otherwise would be utterly reckless.

So, how long will it be until we see the effects of this transformation on our medical system? Well, give it 5 years to see the first genetic counter-indications, but it won't take long after that for our medical systems (on both sides of the border in North America) to feel the full effects of the revolution. Just wait till we start sequencing the genomes of the flu bugs we've caught to best figure out which anti-viral to use.

Gone are the days when the physician will be able to eye up his or her patient and prescribe whatever drug he or she comes up with off the top of their head. Of course, the hospitals aren't yet aware of this tsunami of information and change that's coming at them. Somehow, we need to get the message to them that they'll have to start re-thinking the way they treat people, instead of populations of people.

Oyster genome...

Note to my boss: Shenzen is sequencing the oyster genome.  See, you should have sent me back to Tahiti to work on the pearl oyster genome! (-;

Elisa for Obesity Proteins.

Ok, I can't resist. I occasionally get emails from random biotech companies promoting products that are invariably useless to me. This one amused me enough that I thought I should share it.

The title of the email is "ELISA Strip for Profiling 8 Obesity Proteins." While I'm sure there are people who have a good use for that, I have no clue why I'd want it. I'm not sure I'd want to go to a doctor who needs to use it to tell if their patients are overweight either.

What ever happened to looking at yourself in the mirror or standing on the bathroom scale and saying, "Oh man, I need to lose some weight!?" Now you're supposed to kit yourself out and do an Elisa to tell if you've got to diet?

Oh well, if you do find you have a use for it, Signosis will be more than happy to sell you one.

Howto on applying for jobs.

This post is way off topic for my usual blogging subjects, but it's something I've wanted to do for a long time. Ever since my time at the start-up company, where I read several thousand resumes, I've had the urge to write out a Howto document for job applicants. It comes out of the frustration of reading hundreds of terribly done resumes, and tens of badly written cover letters. After a while, you figure out what you don't want to see, which eventually turns into what you do want to see.

Of course, it's only in first draft mode - I haven't done much editing on it, but I figure it can only get better from here. My warning is that it's already 24 pages long without illustrations. Hopefully those will show up in later editions. Comnents and criticisms accepted. (-;

JobHowTo.pdf

Nothing like reading to stimulate ideas

Well, this week has been exciting. The house sale competed last night, with only a few hiccups. Both us and the seller of the house we were buying got low-ball offers during the week, which provided the real estate agents lots to talk about, but never really made an impact. We had a few sleepless nights waiting to find out of the seller would drop our offer and take the competing one that came in, but in the end it all worked out.

On the more science-related side, despite the fact I'm not doing any real work, I've learned a lot, and had the chance to talk about a lot of ideas.

There's been a huge ongoing discussion about the qcal values, or calibrated base call scores that are appearing in Illumina runs these days. It's my understanding that in some cases, these scores are calibrated by looking at the number of perfect alignments, 1-off alignments, and so on, and using the SNP rate to identify some sort of metric which can be applied to identify an expected rate of mismatched base calls. Now, that's fine if you're sequencing an organism that has a genome identical to, or nearly identical to the reference genome. When you're working on cancer genomes, however, that approach may seriously bias your results for very obvious reasons. I've had this debate with three people this week, and I'm sure the conversation will continue on for a few more weeks.

In terms of studying for my comprehensive exam, I'm now done the first 12 chapters of the Weinberg "Biology of Genomes" textbook, and I seem to be retaining it fairly well. My girlfriend quizzed me on a few things last night, and I did reasonably well answering the questions. 6 more days, 4 more chapters to go.

The most interesting part of the studying was Thursday's seminar day. In preparation for the Genome Sciences Centre's bi-annual retreat, there was an all-day seminar series, in which many of the PIs spoke about their research. Incidentally, 3 of my committee members were speaking, so I figured it would be a good investment of my time to attend. (Co-incidentally, the 4th committee member was also speaking that day, but on campus, so I missed his talk.)

Indeed - having read so many chapters of the textbook on cancer biology, I was FAR better equipped to understand what I was hearing - and many of the research topics presented picked up exactly where the textbook left off. I also have a pretty good idea what questions they will be asking now: I can see where the questions during my committee meetings have come from; it's never far from the research they're most interested in. Finally, the big picture is coming together!

Anyhow, two specific things this week have stood out enough that I wanted to mention them here.

The first was the keynote speaker's talk on Thursday. Dr. Morag Park spoke about the environment of tumours, and how it has a major impact on the prognosis of the cancer patient. One thing that wasn't settled was why the environment is responding to the tumour at all. Is the reaction of the environment dictated by the tumour, making this just another element of the cancer biology, or does the environment have it's own mechanism to detect growths, which is different in each person. This is definitely an area I hadn't put much thought into until seeing Dr. Park speak. (She was a very good speaker, I might add.)

The second item was something that came out of the textbook. They have a single paragraph at the end of chapter 12, which was bothering me. After discussing cancer stem cells, DNA damage and repair, and the whole works (500 pages of cancer research into the book...), they mention progeria. In progeria, children age dramatically quickly, such that a 12-14 year old has roughly the appearance of an 80-90 year old. It's a devastating disease. However, the textbook mentions it in the context of DNA damage, suggesting that the progression of this disease may be caused by general DNA damage sustained by the majority of cells in the body over the short course of the life of a progeria patient. This leaves me of two minds: 1), the DNA damage to the somatic cells of a patient would cause them to lose tissues more rapidly, which would have to be regenerated more quickly, causing more rapid degradation of tissues - shortening telomeres would take care of that. This could be cause a more rapid aging process. However, 2) the textbook just finished describing how stem cells and rapidly reproducing progenitor cells are dramatically more sensitive to DNA damage, which are the precursors involved in tissue repair. Wouldn't it be more likely then that people suffering with this disease are actually drawing down their supply of stem cells more quickly than people without DNA repair defects? All of their tissues may also suffer more rapid degradation than normal, but it's the stem cells which are clearly required for long term tissue maintenance. An interesting experiment could be done on these patients requiring no more than a few milliliters of blood - has their CD34+ ratio of cells dropped compared to non-sufferers of the disease? Alas, that's well outside of what I can do in the next couple of years, so I hope someone else gives this a whirl.

Anyhow, just some random thoughs. 6 days left till the exam!

It never rains, but it pours...

Today is a stressful day. Not only do I need to to finish my thesis proposal revisions (which are not insignificant, because my committee wants me to focus more on the biology of cancer), but we're also in the middle of real estate negotiations. Somehow, this is more than my brain can handle on the same day... At least we should know by 2pm if our counter-offer was accepted on the sales portion of the transaction, which would officially trigger the countdown on the purchase portion of the transaction. (Of course, if it's not accepted, then more rounds of offers and counter-offers will probably take place this afternoon. WHEE!)

I'm just dreading the idea of doing my comps the same week as trying to arrange moving companies and insurance - and the million other things that need to be done if the real estate deal happens.

If anyone was wondering why my blog posts have dwindled down this past couple of weeks, well, now you know! If the deal does go through, you probably won't hear much from me for the rest of this year. Some of the key dates this month:

• Dec 1st: hand in completed and reviewed Thesis Proposal
  
• Dec 5th: Sales portion of real estate deal completes.
  
• Dec 6th: remove subjects on the purchase, and begin the process of arranging the move
• Dec 7th: Significant Other goes to Hong Kong for~2 weeks!
  
• Dec 12th: Comprehensive exam (9am sharp!)
• Dec 13th: Start packing 2 houses like a madman!
  
• Dec 22nd: Hannukah
  
• Dec 24th: Christmas
• Dec 29th: Completion date on the new house
• Dec 30th: Moving day
• Dec 31st: New Years!

And now that I've procrastinated by writing this, it's time to get down to work. I seem to have stuff to do today.

Not first on the subject...

One of the challenges of writing a blog is to try and provide new content. I've always thought that there was no point in covering information that someone else has already covered - but it's hard to be the first to break every story. So, I figured I'd do something else, which is useful: provide a few links to things that someone else found first.

Today's breaking news was something I found at SeqAnswers.com, on the new relase of information on Pacific Biosystems' new SMRT technology. The open access article is here. Thanks to ECO for updating with that link! (I was trying to get it all morning, to no avail.)

For humour, I wanted to discuss the IgNobel award winning paper: You Bastard: A Narrative Exploration of the Experience of Indignation within Organizations. However, another blogger on my reading list beat me to it.

I was also going to comment on lawsuit launched by the makers of Endnote against Zotero, but the same blogger also beat me to that. (Though, there's certainly a lot to be said about that case in terms of open standards, and people with antiquated business models fighting technology advances by any means possible...) Since I'm still considering using Zotero for my own research, it's probably something I'll save for another day, when there's more information available about the progress of the case.

Otherwise, there's still the new Apple MacBook, milled out of a single piece of aluminum, and the new Dell Mini 9, which I've been debating buying. Since it now comes with Ubuntu pre-installed, maybe I can forgive Dell for not refunding me for the XP licence that they made me buy at xmas last year with my current laptop.

Oh well. Now you know what I've been looking at while I procrastinate on my thesis proposal, and the mound of code changes I need to make ASAP... and now, back to work!

Election Day in Canada

Another non-sciency post. I'll try to get back on topic later today with a few more Second Generation Sequencing posts later today. But for now, I figure a bit of politics is in order.

Us Canadians are always a step ahead of our American neighbors. We just had our thanksgiving long weekend, and today is our federal election, while Americans have to wait till November for thanksgiving and their election day. Of course, just like the American election, the Canadian election is a complete gong show. All mudslinging all the time!

Actually, for once, one party didn't bother with the attack adds, so they get my vote. They stayed on the issues, and even if I don't agree with everything they say, they seem to have a clear enough vision, and share most of my ideals. How much better can it get?

Unfortunately, unlike out American neighbours with their 2-party system, Canada has a lot of viable parties, and no clear cut winner, which means we're in for another minority government. (No one party controls the government, so power sharing becomes important.) Because the pary system in Canada is somewhat confusing and getting a lot less press time in the states than the US election, I figured I'd do my part to share a bit of Canadian culture with the world, and particularly for those Americans who are considering coming to canada if McCain wins...

Thus, I present the fejes.ca guide to Canadian political parties:

• The Conservatives: roughly analogous to the American Republicans. Basically, whatever George Bush says is good for the Statesm, they believe is also good for Canada. More oil drilling, less arts, more tax breaks for big companies, less transparency for government.
• The New Democratic Party (NDP): imagine if unions ran for office. Yep - that says it all. They have a very personable leader who makes it sound like a good idea to shift the entire tax burden of the country onto big businesses. (Won't they all leave?)
  
• The Liberals: roughly analogous to the Democrats, but without a charismatic leader. They've tired to out-bully the Conservatives (but failed), they tried to out-environmental the greens (but failed), they've tried to out baby kiss the NDP (but failed), and never once even tried to portray themselves as the most centrist party in Canada. They've come down far in the world since they last held power
  
• The Greens: a much more intelligent version of the US branch. They claim they can help reposition the ecconomy of the country to support ecologicaly sound businesses. Otherwise, their platform is relatively centrist (Education, health care, etc). On the down side, their party has a tradition of running a lot of nutjobs as candidates. Oops.
  
• The Block Quebecois: imagine if Texas wanted to separate, and elected a bunch of loudmouth cowboys to congress to sit around and heckle the other congressmen. Except, of course, they claim that only people who speak French should be allowed into their "country." (They don't seem to care if you're black, red, green or white, just that you speak french - they're generally just language snobs who believe that the French won against the British in North America.) Fortunately, you can only vote for them in Quebec.
  

Faced with that choice, Canada will have another government by tomorrow - and a long 4 years ahead of us.

How not to negotiate the price on a house.

Among all the tons of things going on in my life - as if it weren't busy enough - my girlfriend and I made an offer on a new house yesterday. With the market the way it is, houses just aren't going anywhere - and this one's been on and off the market for at least 6 months, now. The only offers they've had in that period were from us - so clearly this isn't a hot property. Even for us, it isn't a perfect place - but it fits what we're looking for. After a stunning lack of interest on the house, the developer took it off the market for August and September, and just recently re-listed it about a week ago.

Indeed, given the housing market's poor state, the developer has also been forced to drop the asking price by about 10% from their original listed price. Of course, in the way of real estate, it subsequently turned out that the developer was claiming their house was 1,500sq. ft., when it was really closer to 1366sq. ft., so I don't know that they had much choice about dropping the price - but the listing was made with the larger square footage, so I don't even think that was taken into account.

With all that going on, we made an offer about 5% below asking price - which isn't unreasonable for the price per (real) square foot in that neighborhood. (It's actually slightly higher, so it wasn't a low-ball offer by any means.)

In the game of negotiations, you'd expect the developer to counter with a price closer to what he originally had asked for. That way, both parties can converge on something agreeable to everyone. Apparently, that's not what the developer had in mind.

He counter offered at $15,000 above his listed asking price!

Needless to say, after a few rounds of discussions, this deal isn't happening. Fortunately, house prices will only continue to drop, so when we offer again in a month or two, it'll be even lower. (=

I can only shake my head and wonder what's running through the developers mind.

The best laid schemes...

"The best laid schemes o’ mice an’ men / Gang aft a-gley.” - Robert Burns

Well, ok, I don't speak 18-th century Scots, but I fully understand the sentiment. I have several major things in the works, and yet, I'm suffering from a bad cold and sore throat. So, the FindPeaks manual is going to be delayed a few days. I guess I'm not the only one working on it, but I defintely have plans for it.

Anyhow, between the FindPeaks manual, some new FindPeaks features, a poster abstract and two papers I'm working on, I have enough on my plate - but just don't have the energy to get it all done. Damn colds! They always get you just as the stress level starts to rise.

Anyhow, Thanks to tcezard (Tim), who's taking on an ever increasing role on the FindPeaks work, FindPeaks 3.2.1 was tagged today. Development is so much faster when people work together!

I thought I'd also go one further today, and add a plug in for a very cool technology that hasn't (to my knowledge) gotten much coverage - ODF@WWW. As a scientist who uses wikis and blogs, this has to be one of the best applications I've seen of extending the wiki concept. This has the ability to change the way scientists communicate data, and allow wikis to be incorporated into environments where they previously were "too complex to be useful." Of course, more people have to adopt ODF before this will really take off, but with applications like this, it's only a matter of time. (Yay open formats for making this possible!)

National Geographic prices (way off topic.)

Sometimes I have to wonder whether Americans believe that the world ends at their border. Nothing against Americans, but why discriminate against Canadians? I wanted to subscribe to the National Geographic Traveler magazine, after seeing a copy of their magazine today.

Then I came across their pricing scheme:

Subscription for anywhere in the US: $10.
Subscription for places overseas: $36

The not so smart part: Subscription for Canadians: $34

I sent them the following email.

Hi,

I'm not sure who the correct person is to contact about pricing for the national geographic traveler magazine, but I really wanted to express my displeasure at discovering the horribly skewed prices for the subscription rate for Canadians.

I came across your magazine today, and thought it had fantastic articles and photography, and was sufficiently interested that I went online to subscribe. However, once I discovered the dramatic difference between the US and the Canadian prices, I decided to send this email instead.

After all, I live within 40km of the US border and use a currency currently trading at near par with the US Dollar... and yet, I'm being asked to pay 3x the price? Hardly credible! Even worse, we're closer than either Alaska or Hawaii, and are being asked to pay more than either of those states. The Canadian postal system can't possibly cost *that* much more than the US for magazines.

I hope National Geographic seriously reconsiders it's pricing policy, and stops discriminating against a market of 36 Million people.

Signature.

8 Postdoc positions

I don't want to spam anything, but since this is my own web page, I guess I can advertise as much as I'd like. I was just passed an email from a colleague at the Plant Science department at UBC, where they're currently looking for eight post doc positions: mainly people who have or are interested in gaining Illumina sequence processing experience.

I figured this is noteworthy for several reasons:

1. There is a growing demand for next-gen trained bioinformaticians, which looks good for the future career prospects of anyone in the Next-gen Sequencing/Genomics field (though this is hardly a surprise),
2. Genomics is beginning to expand out of the narrow {yeast | human | C.elegans | etc} model organism fields into areas such as plant science, where it will have a huge impact. (going mainstream is always a good thing for a field of science, in my humble opinion.)
3. Some of the positions will put bioinformaticians into key positions where they become the cornerstone of research projects, which is a far cry from the "bioinformaticians as a service" role that's been popular in many research settings.

Anyhow, I can highly recommend at least one of these positions, having worked with the professor before, so if anyone is interested in the email, I'd be happy to forward along the advertisements.

Just overheard

Just announced at the Southwestern Florida Airport:

"Would the person who left behind a black suitcase, containing a red suitcase, containing a pair of boots.... please claim it at security."

That's some carry-on luggage.

Merry Xmas from the puppy

Normally, I'm against putting costumes on my dog, but hey, sometimes you've got to let Elaine have her way... and then this was just too cute not to post, once I'd already taken a picture.

Merry Xmas everyone!

Hawk and Handsaw

There's a line in Hamlet (Yes, the Shakespeare play) where Hamlet himself states

I am but mad north-northeast; when the wind is southerly I know a hawk from a handsaw.

I've heard all sorts of explanations for this metaphore, but I figured I'd throw out one of my own.

If Shakespeare really didn't mean to compare a hawk to a heronsaw (a bird, which seems to be the going theory) - later corrupted to handsaw - I propose instead that perhaps he really did intend Hamlet to say "a hawk from a handsaw". (Crazy, no?) Although things may have changed in the last 600 years or so, last time I checked, Hawks have always been known for their sharp eyes, while handsaws are known for their sharp teeth. Thus, I propose that Hamlet can tell those who are his friends (watching out for him), from those who are posed to do him (and his family) harm, with a sharp bite.

Proof? Actually, I have none, but I think it's an interesting alternative interpretation. Too bad we can't knock on William's door and ask what he was really thinking. There must be equally good, or likely better, explanations. Anyone care to propose any others?