Two administrative notes

Two administrative items:

First, sometimes comments are getting moderated very late.  I do pledge this is not an attempt on my part to bury negative commentary.  Rather, it appears that sometimes when I thought I had moderated comments via my Android phone it hasn't succeeded.   

Second, I am trying out the new smartphone-friendly layout option for Blogger.  Please let me know if you are reading this on a smartphone and hate the new layout.

Blogger glitch

Blogger experienced an outage which I found out about today.  This caused my last post to disappear; any posts or comments in a certain time period were lost.

Thanks go out to the anonymous reader who posted a comment wondering where my last post went.  Blogger (Google) did not notify me of the issue.  The really disconcerting part is the Google cached version of the post was missing as well -- this suggested something very odd going on.

I often write posts directly in Blogger, so I don't have a backup.  This was an exception & I did actually have the rough draft, which I would have posted if the old one wasn't restored.

Bad blog! Bad, bad, bad blog!

Thanks to Dan Koboldt from Mass Genomics, I've discovered that another blog (the Oregon Personal Injury Law Blog had copied my breast cancer genome piece. Actually, it appears that since it started this summer it may have copied every one of my posts here at Omics! Omics! without any attribution or apparent linking back. I've left a comment (which is moderated) protesting this.

curiously, the author of this blog (I assume it has one) doesn't seem to have left any identifying information or contact info, so for the moment the comments section is my only way of communicating. Perhaps this is some sort of wierd RSS-driven bug; that's the only charitable explanation I can contemplate. But it is strange -- most of these have no possible link to personal injury -- or can PNAS sue me for complaining about their RSS feed?

We'll see if the author fixes this, or at least replies with something along the lines of "head down, ears flat & tail between the legs".

Just to double-check the RSS hypothesis, I'm actually going to explicitly sign this one -- Keith Robison from Omics! Omics!.

One lap around

Officially, I started this blog a year ago yesterday, with the first post about science coming the next day.

At times, I wonder what possessed me to assign myself a regular writing assignment. But, it's definitely been rewarding. I've learned from comments & emails, made a lot of new connections, and maintained an incentive to read a lot of papers that aren't directly connected to my current professional duties. I've also gotten to indulge my fondness for wordplay and pun-filled headlines.

I thought I knew what I'd write about, and in general I've stuck to it, though I've certainly strayed periodically a bit outside of biotech & bioinformatics (or figured out tenuous links to them). I've also covered some topics more than I ever would have guessed: I had no idea when I started I'd write so much about dogs!

What might I change for the next year? I really should be more active in blog carnivals -- I miss the deadlines far more than I hit them, and have probably shown up in as many from editors being kind as those I've submitted. I really should take some turns at editing a carnival edition. I also plan to try to join the Blogging on Peer-Reviewed Research bandwagon, though with diligence to only claim that icon when I have actually fully read the article (which dings all the papers I have access to only the abstracts!).

Keeping posts on a regular schedule has been challenging, which makes me appreciate all the more folks like Derek Lowe who post intelligent writing like clockwork. Sometimes there are good excuses (internet-free vacations), but too often the writing gets put off until too late at night. I've also noticed a tendency to follow-up flurries of writing with droughts -- the week long marathon in February, for example, followed by a weak March. Need to work on that. 182 posts over a year's time -- averaging to one every other day. I thought I'd be higher than that, but maybe that really is the comfortable hobby level.

While the writing is a solo effort, getting readership has been helped by an army of others. GenomeWeb is nice enough to feature me regularly in their blog, and a number of individual bloggers have helped through blogrolls, carnival invites & cross-links. The DNA Network is now my primary blog read each day (plus Dr. Lowe).

I'm also surprised at the number of article ideas I've let sit on the shelf -- some dating back to near the beginning. Either post them or kill them!

Thanks to all for reading this. I hope I'll continue to earn your eyes for another year.

Tagging Along on Grand Rounds

It is an honor that my piece on genome sequencing to explore rare genetic diseases was accepted into Tuesday's Grand Rounds, a venerable (for blogging!) blog carnival covering medicine. This week's was hosted at Dr. Val & the Voice of Reason, part of Revolution Health.

Blog Carnivals & such

Blog carnivals are a wonderful thing: a bunch of bloggers with related topics take turns writing capsule summaries of other blog entries, forming a sort of meta-blog on a topic. I've stumbled across a number in biology, and there are three which I contribute to somewhat erratically (I really need to put the deadlines on my calendar!), Gene Genie, Mendel's Garden and Bio::Blogs. Each of these have new editions out, with Eye on DNA hosting the latest Gene Genie, The Daily Transcript hosting Mendel's Garden and Pedro Beltrao editing Bio::Blogs

A related concept is a shared feed, and I belong to The DNA Network. Indeed, this is my main blog feed now which gets checked regularly -- a nice bit of one-stop-shopping.

How do you sharpen a keyboard?

I've signed up for the Just Science 2007 blogging effort. The idea is for a bunch of science blogs to each post at least once a day for a week on purely scientific topics -- no bashing on pseudoscience/anti-science, no movie reviews, etc.

It's an interesting idea & of course a bit of promotion of this site. But it is also a bit of an obligation -- my pattern has been to post 4-5 times during the workweek, occasionally giving myself the night off if too many other things intrude (and indeed, I'm scheduled to give a seminar next week & I'm overdue on an academic collaboration & etc). No bailing this time: seven days, seven posts -- balanced against the day job & a normal family life.

Back in my student days, also known as 60% of my existence so far, there were ways to prepare for a big scholastic event. I never sharpened quills or picked out fresh nibs, but sharpening pencils was a time-honored tradition to prepare for critical tests. No electric for me -- only a hand-cranked model has the proper tactile & auditory bouquet to satisfy! For a brief while, a big writing assignment might mean finding our freshest typewriter ribbon & a nice stack of clean paper. Later this morphed into a good dot matrix ribbon & microperf paper. High school & college meant a return to pencil sharpening, so those #2's would be in top shape for the PSAT, SAT or GREs. Not only were the rituals practical (a dull #2 does NOT work on those #$#$$ circles as well), but they were a way to burn off a little nervous energy.

But for this, what do I do? Buy some high-end (Martha Stewart?) packets for my router? Break out a box of high energy electrons? Get a reserve bottle of ether for my Ethernet? Modern technology has ruined all the old rituals!

Well, there's always Mom's old standby -- get a good night's sleep. Perhaps that's just what I'll start on now...

Nose to the Grindstone, Shoulder to the Wheel

One impetus for starting this blog was the end of my career at a biotech company -- I thought I might have a lot of time on my hands, which represented both an opportunity to do something new and a threat to my professional sanity. That hiatus ended up being significantly compressed due to an extension of my term of service, but the blog was out there and required feeding.

Because my former employer, Millennium Pharmaceuticals, had grown so huge and shrunk so much, plus with my lengthy service there, I know a lot of alumni and a large number of them are still in the Boston area. Thanks to many of them, I had rapid success with obtaining screening interviews & as a result tomorrow I get to embark on the next stage of my career as I begin a new position. I will be joining the startup synthetic biology company Codon Devices, one of whose founders is my graduate advisor George Church. It's an unbelievable opportunity to try to explore amazing technologies & apply them to interesting biological problems.

So what to do about the blog? I hope to continue it, but we'll see what the reality is. Time, particularly mental cycle time, may become a rare commodity -- one of the first blogs I got hooked on dried up when the author joined a startup. Some distillations of topics of interest may need to be reserved for my new organization. But, there's still plenty out there. I also don't intend for this to become some sort of propaganda site for Codon; I may comment on synthetic biology sometimes, but perhaps this will largely be an outlet for my musings on topics at best only distantly connected to their business plans.

In any case, I do thank all of you who have read this pages & commented or emailed me or otherwise noted this daily attempt to go beyond PowerPoint bullets (it was gratifying, but novel, to have my blog cited in the intro at one job talk!). It is gratifying, and I hope you will continue to find reading these blurbs worth your while.

Perverse Milestone

Well, this blog hit a dubious milestone today -- my first comment spam! Unsurprisingly, given my topic choice, it was for an online "pharmacy.

On the other hand, it is wonderful to see helpful & friendly comments -- people actually are reading this! Thank you thank you thank you!

Administrative note: RSS Feed

In my usual fashion, I plunged into this after doing all of 1 minute of homework. So I really didn't know what I was doing. Several people have suggested I needed RSS feed, but I couldn't find that at the pet store :-) Seriously, here it is (I assumed RSS came with things -- I have some learnin' to do!)

http://feeds.feedburner.com/OmicsOmics

If anyone is willing to comment, how gauche is it to host Google AdSense ads on a blog? With a little luck, I could use the proceeds to park a Solexa 1G in my garage, right? :-)

Starting out

Okay, here goes nothing. Millennium Pharmaceuticals just sloughed off its genomics assets, which included me. So I have some time on my hands to try something new.

I've spent 10 years with Millennium, and prior to that I was trained in the labs of two pioneers in genomics, Wally Gilbert & George Church. I'm a biologist by training, a computational biologist by preference, and an omics-fan by heart. At Millennium I played with or thought about about every omics technology there is, from DNA sequencing to expression profiling to proteomics. I won't claim I am an expert on all of them; just that I have ideas (perhaps deluded) about how they might be used.

I'll try to make a few initial promises & a few requests of you, the readers I haven't found yet. First, I will try to make my biases clear. For example, I have a hard time being objective about stuff coming from the Church lab -- my heart will long be there.

Second, I won't be a touter or a trasher. I'll try to be fair. Other than my former employer, I don't have a financial stake in anything; all other investments are in broad index funds. If my next job or some consulting gig is at a technology company, then I'll try to be open about that or avoid subjects that present a conflict-of-interest. Please don't use this blog to invest or ask me for stock tips -- I confidently predicted the Tigers would sweep this year's World Series.

Third, I'll try to stay somewhat within my expertise. If you catch me saying something dumb, please point it out. But most of the interesting stuff requires a stretch, and I strongly believe that the best results come from vigorously hashing lots of half-baked ideas -- eventually you find the ones worth sticking back in the oven.

Fourth, I'll try to keep this focused. Minimal straying off into politics or beating up on pseudoscience. It's not that I don't care about these things, it's just I need the practice keeping something focused.

Fifth, this won't be a blow-by-blow of my job search. I'd love to get leads on compuational biology positions in Boston/Cambridge or the burbs (particularly north/west of the city), but I'm not going to go blow-by-blow on my interviews. That's not what this is for.

Sixth, this won't be a place to routinely trash or praise my former employer. Millennium was an exciting place where I learned a lot, but we made plenty of mistakes too. I'll be referring to my time there frequently, but I'll try to keep some balance.

The name? Well, I played with several. I have a fondness for silliness, and the Little Caesars ads fit that. It fit the subject matter & didn't seem to be taken already. Now all I need is a picture of a little DNA helix with a laurel wreath & a spear...