Live blogging Dad’s update from Vista to Windows 7

After years of colorful verbal expressions regarding the quality of Microsoft Windows Vista, dad is upgrading his desktop from Vista to W7. Here is a live blog of the process.

7:15 pm: Dad has already tried upgrading once. The upgrade tool sat for about 10-15 minutes, then told him he needed to remove a bunch of software and re-run the tool. It took Vista 20 minutes to remove the software. He then started the upgrade tool again. It’s been doing its thing for the last 10-15 minutes.

7:16 pm: “I’m gonna waste three or four hours and get nothing done . . . which will make me happy.”

7:20 pm: Windows upgrader wants dad to uninstall iTunes. Screw it! He doesn’t use iTunes. Here we go!

7:24 pm: Copying over 2 GB f installation files. So far, this is like a linux upgrade!

7:31 pm: gathering files and settings…

7:39 pm: “Good God – it’s only gathered 6% of the information it needs.”

7:45 pm: 17%

8:19 pm: 77%

8:35 pm: Windows had to restart the machine. We’re not sure why.

8:37 pm: Hey! It’s the Windows 7 start logo. Yay! It now says “Upgrading Windows”

8:53 pm: Still upgrading. Dad tossed his hands into the air. “You’ve been at 21% for a long time.”

8:57 pm: Moving again!

9:10 pm: Rebooted again! Could this be the last? (At least, until the endless cycle of patches and updates)

9:22 pm: W7 has been restoring settings and files ever since the reboot. Cross your fingers…

9:37 pm: All Dad wants for Christmas is to go to bed – but W7 is still upgrading, and apparently Vista tied his sleep schedule to the operating system.

10:05 pm: Setup will continue after rebooting your computer. Linux never made me reboot this much during upgrades.

10:08 pm: It rebooted, but this marks only the 68% mark for transferring files and settings.

10:25 pm: Want to go to bed SO BAD.

10:30 pm: Rebooting AGAIN.

10:32 pm: Yes! W7 is preparing the computer for the first use!

10:33 pm: Enter the product key. It’s in such small print on the disc box, we’ve busted out the magnifying glass. Hmm. Product key. That’s a funny notion! Windows is weird.

10:46 pm: Machine is still a little pokey, but W7 is up and running. G’night!

Ethics in Research – Part III

In the last two parts of this essay, I discussed my thoughts on the veil protecting private inquiry from public scrutiny and I discussed the meaning of stolen e-mails made public. In this last part, I discuss my thoughts on the handling of conflicting data.

Quotes extracted from the stolen e-mail suggested that data which should have entered into the famous “hockey stick plot” was deliberately ignored [1].  I’ve certainly commented on the hockey stick plot before [2], and I will be the first to admit that I felt somewhat concerned when I heard that conflicting data was excluded from the plot. On the other hand, the scientist in me knows that excluding data happens all the time; when you do it, you must say so and state why.

Before going further on that specific subject, let’s take a moment to think about a situation that is quite common in science. In fact, I would say that most scientists face this problem the very first time they are asked to conduct a controlled experiment for a high school or college laboratory class.

You are asked to conduct an experiment; for instance, you are asked to attach a piece of ticker-tape paper to a weight, raise the weight to the ceiling and thread the paper between two electrodes, and then drop the weight. The electrodes fire at fast, regular intervals, marking the paper every time they fire. The spacing of the marks on the paper, and knowing the time between the sparks, tells you about the acceleration of the weight. You are asked to determine the acceleration due to gravity by doing this experiment.

You find the acceleration to be LESS than 9.8 m/s^2. You do the experiment several times, to build up a sample of repetitions. This reduces the statistical uncertainty, but each measurement confirms the original result with improved uncertainty each time. You bring your conclusions to the instructor, who then asks you to simply discuss your findings and hand in your report. What do you do?

You’ve learned in class that all objects on earth fall at 9.8 m/s^2. Yet, here is an experiment that measures something much less – let’s say (7.4 +/- 0.4) m/s^2. This is significantly different from what you learned in class. What do you do? Do you throw out the result and simply say that since you were told that acceleration on earth is 9.8 m/s^2, your result must be wrong? Do you fudge the data and try to get closer to the stated value? Do you repeat the experiment with somebody else’s sparker? Do you work to study how your own sparker functions (e.g. maybe the time between sparks is NOT what the manufacturer reported)? You have limited time – the report is due by the end of lab. What do you do?

This is the same situation that all scientists face in their work. You have a deadline – a meeting, a conference, a review, a threat of a competitor scooping you. You have a result that doesn’t agree with other measurements. It could signal something new; it could signal that other results are wrong; it could be that you didn’t understand your experiment. What do you do?

This is not an easy dilemma. The overwhelming set of measurements in climate data point to global-scale change, centered on average temperature increases that are more rapid since the mid 1800s than in any previous known period. Yet, here is data that contradicts that observation. You badly want your detractors to go away. What do you do?

There are few right answers to this question, and lots of wrong ones. Of course, few of us know enough about that climate data to make an intelligent answer to the question. The safe answer would be to report the results from the raw data, record your hypotheses about why the data do what they do, and make the result public (perhaps as a pre-print, since it’s likely such an incomplete analysis won’t withstand peer review).

I’ll close with a final thought on all of this. The veil that protects the messy process of science is important for the promotion of free thought, but cannot be relied upon to hide irresponsible action from public scrutiny. The release of electronic documents is a piercing of the veil, but unethically snapshots only a part of the overall scientific process (and, from my own experience, a part of that process where people speak all too freely and easily in ways incongruent with their final decisions). Faced with inconsistent data, the scientist faces an unpleasant set of choices where the best answer brings the least glory or recognition. But, what of the data itself? Does the public have a right to the data itself?

There is no easy answer to this as well. Many collaborations own their data, while many others are required to release the data to the public after a period of closed access. Even publicly released data has already been corrected and filtered, so public data is rarely “complete” in the sense that it’s the same data that came fresh off the instrumentation. The public is ill-equipped, either by their own dis-interest in scientific methods or by the poor quality of the educational highway for science, to deal with data. Yet the demand for the raw climate data behind the “Climate-gate” e-mails is real, and must be considered. Certainly, there can be real value in making data available to other scientists, but personally I think that the data should come with strings attached.

Here are the strings: publications on the data are not official unless they are blessed by the original person or collaboration that collected the data. Therefore, journals should not accept papers that are not affiliated with the original owners. In cases where data is old enough that it outlived the experiment or the original researchers, the journals should be required to review the paper by panel and not by just a few peer referees. They need a diversity of experts in the field, not just a few people in the field to sign-off on the analysis. The data must be released with all of the filters and calibrations that have been applied clearly documented, and the data source must also be thoroughly documented. If the original instrumentation is still available, it should be made available to the analysts. This latter issue is critical so that instrumental effects can be understood; they often shape the data in unknown or unpredictable ways.

The responsible release of data is a partnership between the original researchers, the public entity using the data, and the journals reviewing the work. Without this partnership, nobody should believe what comes from the new research.

“Climate-gate” is a window not just on the scientific process, but a means by which scientists themselves can think about the way they conduct their work. The ultimate question – does this change how we think about the climate research itself – still needs to be answered. But I won’t answer it, because I am not a climate researcher. I will say that I am taking personal responsibility for my carbon emissions, because there is no reason I need to produce as much carbon as the world has made me capable of producing. I am conserving water, I am changing my eating habits, and I am using habit and technology to throttle electrical usage.

Check out this analysis of the most held-up “conspiracy” e-mails; it’s fun, and shows what you can learn by thinking deeply about these matters and going even a little bit below the surface (thanks to Randy Scalise for bringing this to my attention):

[1] http://dotearth.blogs.nytimes.com/2009/12/01/a-climate-science-forecast-in-the-wake-of-climate-files/

[2] http://steve.cooleysekula.net/blog/2006/06/24/test-267/

The Lament of the Organist at Christmas

It was Christmas, and from many lands far away
The family convened to mark Christmas Day.
A year or more since the last time we had been
a family together, united as kin.
“Where is Sister?” asked Brother upon his arrival.
“She is busy at church; it’s her organ recital.
Each Christmas she plays for the holiday service.”
“Will we see her at all?” asked the Brother, quite nervous.
“Perhaps,” said his Mother, “but then, perhaps not,
for the organist bears a particular lot:
the children all singing must learn not to fidget –
tis the organist’s job to steady their digits!
the choir must wow during each carol singing;
tis the organist’s task to keep spirits ringing!
Add that to her day job stuck down at the mall –
It’s a miracle if we can see her at all.”

So we called her at work and we called her at church,
but her schedule left most of us stuck in the lurch;
we Facebooked and Twittered and tried her GMail –
But piles of carols walled her world like a jail.
‘Neath many a copy of old “Silent Night”
the organist toils by frail candle light;
her fingers, curled up as if by arthritis,
from practicing too much “What Child is This?”
When finally we raised her between pageant trials,
All she offered her family were frequent denials
of having no time for her kin this year –
“Let’s go out for dinner,” she said, “Never fear!”

But then when the phone rang as supper was nearing,
‘Twas the call from the Sister we all had been fearing:
In a statement that signaled a total reversal,
“I can’t go; I must schedule another rehearsal!”
The family then piled in the old minivan
And we rushed to the church (every stop light we ran!).
We burst through the doors of the church in a fury;
all the choir and the children looked on, filled with worry.
Sister, she calmed them, as organists do,
then turned to her family and tried to subdue.
“I promise, one practice, then dinner we’ll savor;
I ask of you just this, a small Christmas favor.”
The family then bristled and buzzed with commotion,
Each person still filled with a flood of emotion.
“Come now!” shouted Mother. “Yes, now!” shouted Father.
Brother thought he would add something, but then didn’t bother.
Sister blushed, clearly worried her response would bore us:
“I can’t; I must master the Hallelujah Chorus!”
So family left church for our fine Christmas homestead,
Our dreams filled with sugarplums, tucked in our warm beds,
While sister stayed late at the church with her choir.
They practiced until they came down to the wire;
The Christmas Eve service went off with no hitch
(Loved even by Ms. McGee,  that nasty old . . .)
which meant Sister could finally pack up all her things,
discard her copies of “Hark, the Herald Angels Sing”,
and go home for Christmas, away from her duty,
in the hopes of scoring some sweet Christmas booty.

Alas, as she readied, she found she was pinned
To the organ, which by stacks of sheet music, rimmed,
had been walled like a cell by the choir, for fear
that she might have tried leaving before the premier
of the Christmas-time pageant, the Christmas-time cheer;
then the choir had left and forgotten to free her!
Surrounded by music, hemmed in by the carols,
The organist wailed at the cause of her peril,
She cried and she cried, no cause to be merry,
Trapped like a rat in the dark sanctuary,

When, suddenly, light o’er the the sheet music poured,
As if someone had opened the big chapel doors.
She heard the sweet voices of her own happy kin
and the smells of a Christmas goose wafting in;
With hammers and axes they broke down the wall!
A happy Christmas was then had by all –
Father and Mother and Brother . . . and Sister –
everybody said just how much they had missed her.
She was freed from the bond to direct Christmas cheer –
at least, that is, ’til this time next year.

Steve’s Tech Picks for 2009

It’s the end of 2009, and time to have a little blog fun. Here are my tech recommendations for things I’ve discovered (or re-discovered) in the last year.

  • Ubuntu Linux 9.10 (Karmic Koala!): it seems that each time Ubuntu releases a new version of their Linux/GNU/open-source remix, they out-do themselves. Version 9.10 is no different. With an excellent desktop experience framing everything, and the latest in open-source available (from OpenOffice 3, to Firefox 3.5, to GNOME Shell), I cannot recommend more strongly that people give Ubuntu a shot. Take it for a test drive without installing it using their Live CD, or install it in a virtual machine.
  • Firefox Extensions:
    • Zotero: organize your scientific papers, search them, generate bibliographies, tag papers for use as sources in a new paper . . . in short, do it all with Zotero! No scientist should be without, and unlike programs like “Papers” for Mac, you can use it on something other than a Mac!
    • FoxTab: want a modern way to navigate your tabs? Like 3-D? You’ll love FoxTab! Key combos like CTRL+PAGE UP will now bring up a 3-D view of your tabs as thumbnails of what they currently display. You can flip through them, select the one you want, and you’re done. And don’t tell me that “Safari has had this forever,” because what matters is that now all of us can have this kind of nifty feature.
    • Total ReChrome and Chromifox Basic: like the Chrome browser but hate how it works? Like Firefox but wish it looked more like Chrome? You can be happy now. Combining the Chromifox Basic theme with the Total ReChrome addon will bring Chromey bliss to Firefox.
  • TiddlyWiki and jsMath and the jsMath Plugin: I’ve commented on this in my professional blog, but if you’re a scientist who wants a wiki experience without the need for a remote server, and who wants LaTeX in that wiki without all the headache, combining these three technologies is the way to go. TiddlyWiki gives you a go-anywhere wiki experience, jsMath gives you the javascript engine for rendering LaTeX, and the jsMath Plugin for TiddlyWiki gives you the path between them.
  • GNOME Do: here’s one for you Linux folks out there. GNOME Do is your command-line in the desktop, and so much more. A single keystroke brings up the GNOME Do window, and a few letters in the name of an application and a quick smack of the ENTER key will launch your desired program. With dozens of plugins, it can do so much more. GNOME Do is my cure for the menu/submenu/subsubmenu nightmare.