Google ads

2008-08-03: Clueless Google ads on twittercounter.com: ad for granite counter tops, ad for quartz counter tops, and ad for counter-terrorism degrees.

This is an example of why humans are (so far) smarter than computers. The ads are gone now, so possibly Google tweaked its algorithms.

Haruki Murakami

2008-08-03: I recently read A Wild Sheep Chase, by Haruki Murakami. Now I want to read his new book, What I Talk About When I Talk About Running.

Geoff Dyer at the New York Times Book Review didn’t think much of What I Talk About When I Talk About Running, but I read an excerpt in the New Yorker, and that was when I decided I wanted to read the entire book. Like Murakami, I’m a marathon runner, so I’m very interested in what he has to say about running and its relation to the rest of his life.

Perl’s Weaknesses for Large Software Projects

2008-08-04: Today I read about the Ensembl core software libraries and disadvantages of using Perl.

In the paper, the authors state:

However, some aspects of Perl are not well suited for a software project of Ensembl’s size. Whereas weak typing allows for rapid program development, absence of compile time checking of function prototypes and variable types is a steady source of runtime errors. Another disadvantage of Perl is its reference-count-based garbage collector, which effectively limits the use of circular references. Variables that are part of a circular reference structure are never garbage-collected and can introduce potentially serious memory leaks. Avoidance of circular reference memory leaks has necessitated some compromises to the overall system design.

Later, the authors give this rationale for moving from Perl to Java:

Perl suffers from certain disadvantages as an implementation language for a large-scale project. Java overcomes many of these problems and has the benefits of compile time type checking, enforced interfaces, multi threading, better support for graphical user interfaces, and correct garbage collection of circularly referenced objects.

Installing Perl Modules Into a User Directory

2008-08-05: Today I installed libgd and GD, GD::Graph, and GD::Text Perl modules into a user directory; this was tricky because I didn’t have root.

I plan to write a separate post about this.

Verizon’s Slow Response to Outage

2008-08-06: Both companies in our building lost phones and Internet today, making it difficult to work. Apparently someone cut fiber on Vassar Street.

MIT and Cambridge are renovating Vassar Street from Massachusetts Avenue to Amesbury Street. A construction worker cut Verizon’s fiber, disconnecting businesses at the end of Vassar Street near Memorial Drive. It took ten hours for Verizon to identify and fix the problem. Our site manager said Verizon didn’t believe him when he first called; Verizon contented it was a problem inside our building. It wasn’t until other companies called to complain that Verizon took real action.

stackoverflow.com Beta Test

2008-08-06: I’m participating in the stackoverflow.com beta test. I’ve already learned some useful things from answers to others’ questions.

2008-08-07: I’m lonely on the stackoverflow.com beta test site. So far, there have been only six posts about Perl. The site is very Microsoft-oriented.

I have greatly enjoyed listening to Jeff Atwood and Joel Spolsky’s podcast, Stack Overflow, which is hosted by IT Conversations. Jeff is creating a web site, stackoverflow.com, that is intended to serve as a repository of knowledge for programmers. I am a participant in the private beta test.

My useful programming experience is in Perl, C, and C++, and I spend most of my time these days writing Perl. As I have commented before in this blog and on twitter, there are already substantial online resources available to Perl coders, so I think it is unlikely that the stackoverflow site will attract much Perl-related traffic. But I decided it was worth my effort to try.

In the meantime, I’m learning lots about C# and .NET. I may need to learn C# soon.

Worst Personal Genome Project Scenarios

agbiotec twittered:

reading worst Personal Genome Project scenario: someone makes synthetic DNA corresponding to the participant and plant it at a crime scene!

I responded:

2008-08-08: @agbiotec Worst Personal Genome Project scenario: Professor clones you, and the resentful clone escapes to hunt you down and kill you!

Presumably, the unnamed professor in this scenario works at a famous ivy league university and is a pioneer in personal genomes…. And I wonder: if your clone kills you and takes your place, who would know? I think I have here the makings of a biotechnology thriller.

agbiotec responded:

@conrad_halling worse, the clone being next to you constantly and saying: “Write your thesis”, “Write your paper”, “Write your thesis’…

I agree, this is the most frightening of all.

agbiotec’s blog is located at http://semanticlifescience.wordpress.com/.

New LCD Display

2008-08-08: My quest for a new display is over. Today I ordered a Dell 22-inch UltraSharp 2208WFP 1680 x 1050; with discounts and free shipping, $292.

At work I use a Dell 20-inch E207WFP display that has 1680 x 1050 resolution. Our IT group ordered this model because it was inexpensive, but I experience a lot of eye strain with this monitor because the image isn’t very sharp. My work laptop, a Dell Latitude D610, has only 1024 x 768 resolution, and this is inconveniently small when I work at home. So I decided to buy a larger and sharper monitor for use at home. I’ll report when it arrives.

Broccoli Is Good For You

2008-08-09: If broccoli is so good for you, why can’t you buy broccoli yogurt? (For me, raspberry yogurt is the most delicious.)

I eat broccoli because it is good for me, but I really dislike its flavor.

Differences in Nomenclature for Structures of GPCRs

2008-07-27: Last night I read two Nature papers about structures of GPCRs. Different nomenclature in the papers frustrates indexing and searching.

The authors of the two papers used different systems for naming the α-helices and β-strands in these homologous proteins. I hope to find the time to post about these papers soon.

Top 50 Science Fiction TV Shows

2008-07-27: The Boston Globe ranked the top 50 science fiction TV shows, but somehow omitted Star Trek Deep Space 9.

DS9 was not my favorite Star Trek series, but it was certainly better than some of the shows included in the top 50.

Photos of Jupiter

2008-07-28: There are spectacular photos of Jupiter on the Boston Globe’s web site.

Visio 2007 Training

2008-07-28: I spent yesterday and today learning Visio 2007 Professional in order to make flowcharts that map work processes. It was time well spent.

I’m still working on the computer-based training. Ultimately, I want to use Visio 2007 Pro for modeling databases.

Leo Laporte’s eBay Grudge

2008-07-29: PayPal should have refunded the $2200 Leo Laporte lost from an eBay ripoff scheme; his vocal complaints have caused them to lose business.

Leo Laporte is a podcaster, blogger, and twitterer, and I listen to many of his shows, including “This Week in Tech”, “MacBreak Weekly”, “Windows Weekly”, and “FLOSS Weekly”. Leo used PayPal instead of his credit card to pay for a $2200 purchase, but he never received his order. PayPal insurance covered only $200 of Leo’s purchase, so he was out $2000. Leo twittered about the problem (here, here, here, and here) and mentioned it on his podcasts for several weeks. I believe the end result was to increase mistrust of eBay and PayPal among Leo’s listeners, costing both companies much more than $2200 in business.

Added 2008-08-08: According to this tweet, eBay has given Leo a full refund for his camera.

cuil.com Search Engine

2008-07-29: I have tried cuil.com a few times since yesterday. It hasn’t found me or my web site; just lots of listserv posts from years ago.

The cuil search engine was released with much fanfare as an alternative to google, but so far the results are disappointing.

How Do Geeks Exercise?

2008-07-30: Slashdot thread “How do geeks exercise?” has ~1000 replies in less than 12 hours.  I walk to work (2.75 mi each way).

I found this thread very amusing. There are now over 1700 posts in the thread. I’m just a geek who happens to run marathons, so I don’t worry about exercise.

This Week in Tech Podcast: Too Much Fluff

2008-07-30: This Week in Tech podcast gets a little longer every week, but with no additional real content. This week 114 minutes; 60 would be enough.

The podcast has increasing amounts of chit-chat and fluff. I want information.

Cool Tattoos

2008-07-31: For the first time in my life, I want a tattoo. http://blogs.discovermagazine.com/loom/science-tattoo-emporium/

These tattoos are great!

Using Debian to Revive a PowerBook G4

This thread, the longest conversation I’ve had on Twitter, was prompted by a post from agbiotec, who twittered:

after getting debian with gnome in my 5-year old PowerBook I realized how lightweight and functional it is, the machine flies

I replied:

@agbiotec I’m interested in installing debian on a 3.5-yr old 1.5-GHz PowerBook G4. How’s wireless connectivity on yours?

agbiotec replied:

@conrad_halling wireless is perfect-Debian set up the card from the boot CD, and I was even able to do network install-very user friendly :-)

I responded:

@agbiotec Thanks for the PowerBook tip and the info. I will buy my wife a new MacBook Pro so I can install Debian on her old PowerBook.

agbiotec asked:

why don’t you install Debian on the new one too ? ;-)

I replied:

@agbiotec My wife is self-employed, so new laptop is deductible business expense, but she requires Word. I can recycle old laptop w/Debian.

My wife edits medical books as a freelancer. All the editing is performed using Microsoft Word, and the book publishers don’t care if she uses Word for Mac OS X or for Windows. So like all right-thinking persons, she uses Word for Mac OS X on a PowerBook. But her computer is more than three years old, so it’s time to buy her a new one, either a MacBook Pro or a MacBook Air, then recycle the PowerBook. I could use a Linux laptop, but only if the wireless works, hence my interest in agbiotec’s tweet.

Some Days, We Feel Like We Can’t Do Our Jobs

2008-08-01: Today, in my weekly meeting with my boss, he started with, “Some days, I feel like I can’t do my job.” That’s what *I* had wanted to say.

My manager is outstanding, and he does many things I could never do, so it’s discouraging that he has bad weeks, too.

Perl Threads on Stack Overflow

2008-08-02: @codinghorror Experienced Perl coders might not use Stack Overflow because we already have PerlMonks.

Stack Overflow, when it’s released, will be a web site for questions and answers about programming in various languages. I expect traffic from Perl coders will be low because we have well-established resources, including PerlMonks.

Learning Perl, 5th Edition

2008-08-02: I bought Learning Perl, 5th Edition, and I’m reading it in preparation for teaching a Perl class at work. 5th ed. covers new 5.10 features.

This is an excellent book that is completely up to date, unlike Programming Perl, 3rd Edition, which was published eight years ago. I plan to write a review when I’ve finished reading it.

• 2008-07-20:  I want what @codinghorror calls “a mobile device that replicates the desktop browser experience”, but without AT&T. I want an iPod Touch. [Long ago, I had ten cents a minute long distance service through AT&T. Except that they charged me about thirty cents a minute. They gave me the runaround when I attempted to get a refund. I have vowed never to be an AT&T customer again.]
• 2008-07-21: My latest audible.com audiobook is The Precipice, by Ben Bova. It’s entertaining and not as serious as what I’ve been reading lately.
• 2008-07-22: Today I learned how to use the Perl DBIx::Roles::Transaction module to manage database transactions.
• 2008-07-23: Last night I updated Vista on my MacBook Pro to SP1. My machine got so hot the fans were running full speed, but I’ve had no problems since. [I rarely use the Vista installation except for experimentation.]
• 2008-07-24: Twitter readjustment: My followers dropped from 33 to 22. Who was dropped? Twitter also says I’m following 59, but it shows avatars for 72.
• 2007-07-24:  OK, that was a quick fix. 5 minutes after my last tweet, Twitter now says I have 32 followers and I’m following 72. Welcome back, everyone! [This was a Twitter problem that affected all users. See http://blog.twitter.com/2008/07/where-are-my-followers.html.]
• 2008-07-25: I had to miss both ISMB 2008 and OSCON 2008, which overlapped this year. They’re scheduled on different weeks in 2009, so maybe I’ll attend both. [ISMB 2009 will be held June 27 through July 2, 2009, in Stockholm. When I posted this tweet, I thought the dates for OSCON 2009 had been set, but now I can’t find a date on O’Reilly’s Conferences site.]
• 2008-07-25: At last, it’s Friday night. That means only two more working days this week. Weekends are when I get my real work done. [Eight weekend hours equal sixteen weekday hours in terms of productivity, because there are no distractions or interruptions.]
• 2008-07-26: @starstryder sends tweets, a “silly experiment”, in five, seven, five. [Dr. Pamela Gay, astronomer, college professor, blogger, and podcaster, has been tweeting haiku. Twitter haiku has been termed twaiku. Note that this tweet is also a twaiku.]
• 2008-07-26: Today I compiled and installed EMBOSS 6.0.1 for Mac OS X, then I installed mEMBOSS for Windows under Vista. http://emboss.sourceforge.net/ [I use some of the EMBOSS programs for my work.]
  

I spent the week in St. Louis with many colleagues for five days of training. The training was excellent, but I got absolutely no exercise, and I ate way too much food.

• 2007-07-13: I flew Boston to St. Louis via Chicago today, with 2.5-hour layover. I couldn’t get an IP address from the free public wi-fi at O’Hare airport. [The “official” wi-fi, with SSID “concourse”—heavily plugged over the public announcement system—cost $7. I decided it was not worth it.]
• 2008-07-14: I pigged out today on three large St. Louis-style meals. The O’Fallon Wheat on tap was delicious. Tomorrow I need to get some exercise. [St. Louis is home to many fine breweries besides Anheuser-Busch, the maker of Budweiser and other industrial beers. AB is being purchased by InBev, the European owner of Stella Artois and other brewers.]
• 2008-07-15: I will sleep safely tonight, because Senator John McCain and the Secret Service are staying at my St. Louis hotel tonight. [Senator McCain attended a fund-raiser where the price for dinner was up to $57,000 per couple. St. Louis County is home to an extraordinary number of wealthy Republicans (whereas the city is heavily Democratic). Afterwards, Senator McCain enjoyed a concrete at Ted Drewes; maybe he didn’t get enough to eat at dinner.]
• 2008-07-17: I continue to eat St. Louis-size portions at meals. I’m getting 300 extra calories a day, which is perfect for a pregnant woman, but not me. [Restaurant meals are larger than they should be, especially when you can’t take home the leftovers.]
• 2008-07-18: Last training day in St. Louis. Last night we had a delicious dinner outside at Atlas, a restaurant near Forest Park on Pershing. [When we lived in St. Louis, my wife and I owned a condo on Pershing, but Atlas hadn’t arrived in the neighborhood before we moved.]
• 2008-07-18: My first attempt at printing boarding passes on the hotel’s printer was blanks where the bar codes should be; had to install special driver. [The printing service at the hotel was a nice feature, but it wasn’t easy to use, and it makes me uneasy when I have to install special software.]
• 2008-07-19: Last night in St. Louis, I took two colleagues to dinner at Favazza’s and then to dessert at Ted Drewes. We happily ate too much. [Favazza’s is a favorite of my running friends in St. Louis, and Ted Drewes is a favorite of everyone.]
• 2008-07-19: ISMB 2008 has begun this weekend. I can’t go this year, but colleagues are going and will report.

• 2008-07-06: Food for thought: “The Nature of Self-Improving Artificial Intelligence,” presented by Stephen M. Omohundro.
• 2008-07-07: Yesterday I made a tax-deductible contribution to the Conversations Network at the Basic Member level.
• 2008-07-08:  Implode-O-Meter, featured today in a New York Times article, has a hideously ugly 1995-style web site.
• 2008-07-09: Although I voted for Senator Clinton in the primary, I won’t give her any money to retire her campaign debt.
• 2008-07-10:  The Library of America is issuing its second volume of Philip K. Dick novels on July 31. The first volume was terrific.
• 2008-07-11: In response to @easternblot’s post, “I get it: the entire exercise of writing a PhD thesis is to learn that you don’t know anything. I keep finding new things I didn’t know.”: @easternblot Writing a paper can have the same result as writing a thesis; you find out what you don’t know, then do additional experiments.
• 2008-07-12: In response to @codinghorror’s post “A day where I have to write PHP code: not quite as bad as a day where I have to write Perl code. But on the whole, still not good.”: I’m on the other end of the spectrum from @codinghorror on using Perl. I work quickly and cleanly with Perl, but C# gives me the horrors.

• 2008-06-29: My brother couldn’t find Vista or XP drivers for his old Canon digital camera, so I used my Mac OS X laptop to download his photos.
• 2008-06-30: My next audible.com book is The Pillars of the Earth, by Ken Follett. Unfortunately, after five hours, I don’t think the book is very good.
• 2008-06-30: Lots of hysteria, ill-founded rumors, and trolls about Pfizer cutbacks on the rumor mill at biofind.com this weekend — none of them true.
• 2008-07-01: I have many friends who work at Pfizer, so I wish them the best during uncertain times. I received Pfizer paychecks until we were spun off.
• 2008-07-01: On the fluidinfo blog today: “Minor mischief: create redirect loops from predictable short URLs.”
• 2008-07-02: A demonstration of Auto-Tune, the pitch-correction software used to fix recorded music, from the New Yorker: http://tinyurl.com/5m3vcr
• 2008-07-03: I had dinner last night with a good friend who is now working for BIOBASE at their Beverly, Mass. office.
• 2008-07-03: amazon.com emptied my shopping cart, which had 52 items saved for later. That’s not good business: I really was planning to buy that stuff.
• 2008-07-04: I have to work two of three days this long weekend. And I’m having so much “fun” that I forgot to read Slashdot for three days.
• 2008-07-04: I watched the fireworks in Boston this evening. They were truly spectacular, and the view is excellent from the MIT campus.
• 2008-07-05: I’m 9 hours into the audiobook of The Pillars of the Earth, by Ken Follet, and no one has started building a cathedral yet — not good.
• 2008-07-05: This PHD Comics strip summarizes my life on three-day weekends, except it was more fun when I was in grad school.

The issue continues with a commentary about Spaceguard, a survey of near-Earth asteroids that concluded that the chance of one of these striking the Earth is extremely small. Despite this, the Los Angeles Times is running a story this week that declares that the United States is unprepared for an impact by an asteroid. This press release from the Planetary Society contains additional information. (I believe it would be a waste of money to pursue this further.)

Finally, the issue contains three papers proposing explanations for the martian hemispheric dichotomy, which is the fact that the northern lowlands, the Borealis Basin, are on average four kilometers lower than the southern highlands. Using different approaches, the three papers provide evidence that the hemispheric dichotomy was caused by the impact of a dense asteroid with a diameter 25% to 40% of the diameter of Mars. Since the basin that exists today has an elliptical shape, it is proposed that the blow was not a vertical strike.

The evidence provided by these three papers strengthens the hypothesis of an impact origin, but Walter S. Kiefer points out in a News & Views article that an alternative explanation is that the Borealis Basin was formed by convection of the mantle. It is likely that the issue will not be resolved until we can directly examine the composition of the rocks from different parts of Mars.

References:

Andrews-Hanna JC, Zuber MT, Banerdt WB. 2008. The Borealis basin and the origin of the martian crustal dichotomy. Nature 453:1212–1215. DOI: 10.1038/nature07011.

Marinova MM, Aharonson O, Asphaug E. 2008. Mega-impact formation of the Mars hemispheric dichotomy. Nature 453:1216-1219. DOI: 10.1038/nature07070.

Nimmo F, Hart SD, Korycansky DG, Agnor CB. 2008. Implications of an impact origin for the martian hemispheric dichotomy. Nature 453:1220–1223. DOI: 10.1038/nature07025.

Typical multiple sequence alignment tools, such as CLUSTAL W, MUSCLE, MAFFT, and T-COFFEE, do not handle indels accurately. The authors developed new tools, PRANK and PRANK_+F, that take into account the computed phylogeny of the sequences when placing insertions and deletions into the multiple alignment.

In this paper, the authors describe their refinements of the multiple alignment algorithm, and they provide theory and results that demonstrate that their algorithm improves the quality of multiple sequence alignments in a biologically meaningful way. The implications of their results are strongest for nucleotide sequence alignments, but the authors contend that their results are important also for peptide sequence alignments.

Source:

Löytnoja A, Goldman N. 2008. Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis. Science 320:1632-1635. DOI: 10.1126/science.1158395.

Other bloggers who have have already commented on this paper include:

• anthropology.net
• Sandwalk

The Goldman group maintains a web page listing its publications; there are many other interesting papers given there.

• 2008-06-22: Jeff’s wise words in Stack Overflow podcast #10: “Your job as a manager is to throw yourself on grenades to protect me from being interrupted.”
• 2008-06-22: The only earphones worse than the earphones Apple provides with its iPods are the free earphones you get on an airplane.
• 2008-06-22: The Talk Show podcast #22 by John Gruber and Dan Benjamin was devoid of useful content. No transcript available, but none needed.
• 2008-06-26: Yesterday I finished A Deepness in the Sky by Vernor Vinge, a flawless story that is one of the best science fiction novels I’ve read.
• 2008-06-26: Cool technology: The digEplayer you can rent for $10 on long Alaska Airlines flights.
• 2008-06-28: I don’t worry about $4/gal gas. My wife and I have not owned a car for 7 years, since moving to Boston. We use ZipCar: http://zipcar.com/
• 2008-06-28: Another reason we don’t own a car: we can walk to everything. The Walk Score for our neighborhood is 80: http://walkscore.com/

• 2008-06-17: In This Week in Tech #147, John C. Dvorak displays vast ignorance regarding investing or water supply. Can we believe anything he says?
• 2008-06-17: In my search for high-quality science fiction, I have found Vernor Vinge. I’ve started A Deepness in the Sky, which is excellent so far.
• 2008-06-17: I installed Firefox 3 on my MacBook Pro this evening (when I could finally download it). It’s a nice improvement over version 2.
• 2008-06-18: In July, the 8-GB iPhone will cost $199, whereas the 8-GB iPod Touch currently costs $299. I predict a new, lower price for the iPod Touch.
• 2008-06-18: Michael G Schwern has posted his YAPC presentation on skimmable Perl code — lots of good practices.
• 2008-06-20: I’m still reading A Deepness in the Sky by Vernor Vinge. This is a great science fiction book–I’m taking my time so it won’t end too soon.
• 2008-06-20: What I really dislike about the MacBook Pro: The lid doesn’t open as far as it did on the old PowerBook. I can’t get the screen angle right.
• 2008-06-20:  In the Firefox 3.0, 2nd bookmark in “most visited” is twitter.com, labeled as “Twitter / Over capacity”. A bug?: I can’t override the label.

• 2008-06-08: I really enjoy the Stack Overflow podcast. But I would never use the Microsoft technologies they advocate.
• 2008-06-09: I spent the day converting some old K&R-format C code to ANSI C. It’s been a long time since I worked with C, but the old skills came back!
• 2008-06-10: @easternblot When I wrote my dissertation, I wrote four hours in the morning, and one or two ours at night. It still took me six weeks.
• 2008-06-12:  I’m in Tacoma, Washington, spending the weekend with friends from the Dead Runners Society at DRSWC XVI.
• 2008-06-14:  Functional fashion in Seattle now includes the Utilikilt, a heavy kilt with pockets like cargo pants.
• 2008-06-14:  Seattle tourist tax: I bought a commuter train ticket in the a.m. to use in the p.m., but they expire after 2 hours — had to buy another.

• 2008-06-01: Bradley Headstone, the obsessed schoolmaster in Our Mutual Friend by Dickens, is one of the world’s first completely socially inept nerds.
• 2008-06-01: See Rosie Redfield’s Rrresearch blog for a great example of how profiling Perl code showed where to optimize it.
• 2008-06-02: At work, when I redock my Dell Latitude D610, it won’t recognize my new Dell E207WFP 20″ monitor, and I have to reboot. I gotta solve this.
• 2008-06-02: Get “MacOS X Security Configuration for Version 10.5 Leopard“. (Thanks to MacResearch.)
• 2008-06-03: I solved my Dell Latitude D610 vs. Dell E207WFP 20-inch monitor problem by downloading and installing latest Intel graphics video driver.
• 2008-06-03: In this week’s New Yorker, I recommend “The Running Novelist: Learning to Go the Distance”, by Haruki Murakami.
• 2008-06-04: I finished listening to “Our Mutual Friend” by Charles Dickens (40 hrs). This book, although it has its weak parts, is a great work.
• 2008-06-05: The new image of our galaxy, generated by the Spitzer Space Telescope, is now available.
• 2008-06-06: A deficiency of Twitter vs. a blog: you can’t embed URLs. When working with just 140 characters, even tiny URLs can be too long.
• 2008-06-06: My audible.com subscription provides daily news from the Wall Street Journal. Does anyone pay attention to the wrong-headed editorials?
• 2008-06-06: Mailund on the Internet writes about when scientists will want to learn how to program instead of using Excel.
• 2008-06-07: I bought a Sears Craftsman electric weed whacker for cutting my lawn. No internal combustion-created pollution, no gas cans in the cellar.

• 2008-05-25: I finished “The Mind Readers”. The mystery wasn’t mysterious, the science fiction wasn’t science, and Albert Campion wasn’t interesting.
• 2008-05-25: Like many other science geeks, I’m watching coverage of the Mars Phoenix lander…. Only 33 minutes until the first signal will be received.
• 2008-05-25: @MarsPhoenix Congratulations on a successful landing!
• 2008-05-26: On Sunday, June 1, the American Society for Microbiology annual meeting begins here in Boston. Lots of good sessions, including genomics.
• 2008-05-27: Software I use daily: Circus Ponies Notebook. http://www.circusponies.com/.
• 2008-05-28: Does anyone get excited over getting a new Dell Latitude laptop computer? The pedestrian design of Dell laptops bores me.
• 2008-05-28: Today I learned that it is impossible to do bioinformatics when the network is down. I hope the new card for our router arrives tomorrow.
• 2008-05-29: Mac OS X 10.5.3 update for my six-month old MacBook Pro: An enormous download (420 MB) and three reboots. Everything is fine so far.
• 2008-05-29: New 21st-centry prize for science: The Kavli prize (http://www.kavliprize.no/), awarded in astrophysics, nanoscience, and neuroscience.
• 2008-05-29: Congratulations, California, on legalizing same sex marriage. Signed — a proud resident of Massachusetts, where same sex marriage is legal.
• 2008-05-30: John Gruber explained Spaces in Mac OS X 10.5.3 (http://daringfireball.net/2008/05/spaces). Now I’m ready to use this feature.
• 2008-05-31: 90% of my computer activity is work-related, so I don’t take much time to have fun. But today I set up Spaces and played with Photo Booth.
• 2008-05-31: I played more on my MacBook today. GarageBand is a lot of fun. Now I want to buy a USB keyboard. But tomorrow it’s back to serious work.

Now, take a human and a yeast. Take a human gene and put it in a yeast. Does it fit? Can it be used? The answer is yes. A quick search of google.com for “human yeast complementation” results in many examples of human genes complementing yeast genes and vice versa.

How can a yeast gene work in a human? It works ecause yeasts and humans are descended from a common ancestor, through evolution, and are not designed by an intelligence.

And I hope this is all I’ll ever say about this topic.

• 2008-05-18: 14-mile long run this morning on the Minute Man Bikeway. I stupidly didn’t carry water, so I was extremely dehydrated at the end.
• 2008-05-19: The term “efficient multitasking” is an oxymoron. The human brain can’t multitask and work efficiently at the same time.
• 2008-05-20: Twice today I printed the “current page” from Microsoft Word 2007, and twice today it printed the wrong page.
• 2008-05-21: I recommend the article, “The Fall of Conservatism”, by George Packer, in this week’s New Yorker. The conservatives have no good ideas.
• 2008-05-22: I succumbed to audible.com after listening to too many TWIT podcasts. My first book is an old favorite: Our Mutual Friend, by Dickens.
• 2008-05-23: I’m shopping for a 20-inch to 24-inch LCD display. My experience with the Dell E207WFP is that it’s a low-quality monitor. I want something better.
• 2008-05-24: Thank you, Hillary, (I write sarcastically), for telling us you’re staying in the race because Barack Obama could be assassinated in June.
• 2008-05-24: I’m reading The Mind Readers, by Margery Allingham, an Albert Campion mystery (1965). It’s about ESP and a new element named nipponanium.
• 2008-05-24: Excellent advice from Bioinformatics Zen about how to organize bioinformatics experiments. See this post.