atgatg's Journal

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Jan-Feb journal
While I'm logged in, might as well dump the last month's journal entries. I keep six daily logs, as text files edited in vim. Each is very terse. At the start of each month, I start a new set from scratch. Topics of the the logs: "exercise", "work hours", "journal," "thinking," "mail notes," "to-do." Here are the entries from "journal" from Jan and the start of Feb.

Why post this? Well, since this atgatg thing is called a "journal." There's a risk of exposing too much; on the other hand, one model for this site is that it does in fact let friends and family know what I am up to. Well, here's what I've written to myself in the last month and a half. I should edit and expand, but -- but if it came to that, I probably wouldn't post at all. So here it is, unedited and unexpanded.

Feb
01 s party: Rick, Sue, Jeri, Chris, Sandy. Chris and Sandy played viols afterward.
03 s spoke at service: milestone: on gratefulness (emotionally), after 2+ years attending. Gurganuses spoke on dealing with blindness.
04 m learned that Dad received the Governor's Medal for NLVM
05 t learned that 1) mom fell and bruised her eye against the chair, and 2) basil's pelvis is broken. Everyone feels bad; but prognosis for both is OK.

14 h flight back from PAG. Such a contrast, thinking of the infrastructure in the airport, and the collapsed infrastructure in Haiti. Contribution to PiH.
15 f First day back from PAG. Bad day for E, following my inconsiderateness on the last day of PAG. Left work early and skied Carr Woods; things are much better afterwards. We're both much happier here in the clean cold air, on the snow, than under palm trees in San Diego.
16 s 2h skied Lime Creek w E & J. Outstanding. Ate afterwards at cafe in Mason City; then stopped at the Coffee Cat coffee shop.
17 s Worked inside most of the day. Evening: a walk through the park w E
18 m Worked much of the day (misc cleaning). 1.5h ski Carr Woods. Recycles; a big shop at Wheatsfield.
19 t long day, interrupted by ADA training at NAHC. Wrote T. M. re phytozome browser issue.
20 w slept badly (thinking abt moleskines vs notecards, oddly), then slept in. Significant ice storm (though warmish, so a bit slushy).

26 t Buy tickets for Italy in March
27 w Email to E. O. Signed closing docs for the land. Skate at Carr over noon (.45 h) Evening: photocopied abstract. Obama State of Union address.

30 s 1.5 h Carr area: skied on Skunk to open water across from Ada Hayden. Started assembling invite list for Mardi Gras
31 s 1.5 h Carr area: skied on Skunk to a little past bridge across from Ada Hayden. Listened to a beaver in his den; saw a bald eagle and a hawk. Evening: more work on Mardi Gras list.

Jan
01 m long work day. With e, sent invites to Mardi Gras on Feb 12th. A walk at ~9 pm through Brookside after a pretty 1" snow.
02 t to work early, and knocked off early (6:30-3:30). Then skied Squaw Creek to Onion Creek. Low 20s. 3" snow on most parts of the river. Very pretty. Home at dusk. A fair amount of open water, but the ice seems thick in most areas. Saw a herd 9-10 deer up by Onion Creek.
03 w
04 h left work at 2:30 to go to meeting on Beloit "Peoples' Garden" (Fail; was at NLAE rather than at NADC). Then to Carr to skate-ski 1 hr. *** Saw fresh otter tracks near dam.
05 f finished Chame revisions and sent to coauthors. Long day (11 h work). Went to Le's Vietnamese after work, then came home and started filling out seed orders.
06 s More seed orders. Some measuring at 1312, and experimenting with deer fence. Skate-ski and double-pole at Carr 1.2 h. Went north to the end of the bottomland fields, and a little on the river -- but warmth has softened the ice and left a lot more open water, so I spent little time on the ice. Saw a lot of fresh beaver work (from above), at the same lodge where I heard the beaver last week chewing on a branch in the lodge. Saw a "neclace" of four rounded chunks chewed from a ~8" diameter hackberry. South, another smaller lodge. In the woods, saw an owl fly above me. Also startled a herd of nearly 20 deer in the woods.

Haiti medical trip
We had a memorable last two weeks, with purchase of some land for gardening and orchard. But I'll wait to say anything about it, and point to much more important weeks for

redmed and

fdmts. I greatly admire their willingness to drop the demands of their busy lives and go to Haiti for a medical mission. More at their sites (above).

Guest essay II
Again, I am happy to post an essay of Mom's. This comes from northern Utah, where being a supporter of Obama means feeling like an embattled minority. This was written in anticipation of the State of the Union address, which will be given later today. Herewith ...

SOAPBOX II

As we approach the occasion of President Obama's State of the Nation speech marking the conclusion of his first year in office, a parable, a poem, an archetypal symbol, and a word come to mind.

( Continue ... )

soy genome
Here is a nice, accessible description of the sequencing project by the lead author, Jeremy Schmutz. He describes things pretty clearly and gives some good science in his four and a half minutes.
http://www.scivee.tv/node/15632

The genome paper
Amidst the desperate news, I will also note publication, finally, of this paper -- culmination of a project that I have put several years of work into (I, along with a lot of other people). It has some importance as the first sequenced model for several dozen domesticated species in this group of plants.

More personal connections
The posts on Haiti connections from

fdmts have been moving to me. A personal connection from a visit of his and

redmed's.

Also, photos of some of the missing, sent to the NYTimes. That is a good bit of humanizing technology. I am struck by how many of the people I could easily imagine knowing in another time and place. You can see in the faces that the snapshots are taken by friends or families of their loved-ones. Also, nice to see that a few (though only a small minority) of the people are marked "FOUND").

Haiti
I am traveling now (in the airport, returning from PAG), but am heartsick about Haiti. Making a donation was easy; I encourage anyone who stumbles across this post to do the same. The organization I chose is one that we often give to anyway; their primary bases in Haiti are two hours outside of Port-au-Prince. Word from Partners in Health today:

"We have already begun to implement a two-part strategy to address the immediate need for emergency medical care in Port-au-Prince. First, we are organizing the logistics to get the medical staff and supplies needed for setting up field hospital sites in Port-au-Prince where we can triage patients, provide emergency care, and send those who need surgery or more complex treatment to our functioning hospitals and surgical facilities. To do this, we are creating a supply chain through the Dominican Republic. Second, we are ensuring that our facilities in the Central Plateau are ready to serve the flow of patients from Port-au-Prince. Operating and procedure rooms are staffed, supplied, and equipped for surgeries and we have converted a church in Cange into a large triage area. Already our sites in Cange and Hinche are reporting a steady flow of people coming with medical needs from the capital city. In the days that come we will need to make sure our pharmacies and supplies stay stocked and our staff continue to be able to respond."

"Currently, our greatest need is financial support. Haiti is facing a crisis worse than it has seen in years, and it is a country that has faced years of crisis, both natural disaster and otherwise. The country is in need of millions of dollars right now to meet the needs of the communities hardest hit by the earthquake. Our facilities are strategically placed just two hours outside of Port-au-Prince and will inevitably absorb the flow of patients out of the city. In addition, we need cash on-hand to quickly procure emergency medical supplies, basic living necessities, as well as transportation and logistics support for the tens of thousands of people that will be seeking care at mobile field hospitals in the capital city. Any and all support that will help us respond to the immediate needs and continue our mission of strengthening the public health system in Haiti is greatly appreciated. Help us stand up for Haiti now."

Join me.

Governor's Award
I am proud to see Dad's name in this award. And to know E's significant role in the software too.

A group award in science education is also being given to the National Library of Virtual Manipulatives (NLVM) who created computer applications for use in K-12 mathematics education. At a time when mathematics and science education are being recognized as critical to the future prosperity of the country, the NLVM stands out as one of the most important contributions to K-12 mathematics education in recent years. The honorees from NLVM are, E. Robert Heal, Lawrence O. Cannon, James Dorward, and Joel W. Duffin.

Dealing with temperature
The air temperature is -4 F now. When I biked home at dusk (well-bundled, wearing some other creature's down), I saw three deer and three rabbits. Friday, we saw many fox tracks on the river; also probably mouse or vole, and deer again, and hawks and crows. By Friday, we're due for -19 again. And we're not getting above single digits any time this week.

It amazes me to think of these small animals surviving weeks at a time exposed to these temperatures. I guess some of them won't though. Saturday, there was a fresh deer carcass on the river -- picked clean, and dragged 20 feet or so. I am puzzled at what might have dragged it that far. Coyotes could easily do that, or domestic dogs; but I wasn't aware that we had coyotes here, and there shouldn't be many dogs running along that stretch of the river.

Darwin the botanist
... Unloading some more thoughts from this holiday break ...

Dec 26, I noted this quote, from Charles Darwin. This is from the close of The Origin of Species, first edition (changed in subsequent editions). "There is grandeur in this view of life .... from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved."

This points to what has struck me particularly vividly in the last several years: how strange and wonderful life is. The creation story that I believe in (and study every day) has sunk in. Why more now than earlier? I don't know. Though certainly, I have always felt this way at least in some degree. I remember the feelings from when I was a child, and wishing that I could share the feelings.

Anyway, some of the perceptions were evidently also ones that motivated Darwin, and that Oliver Sachs writes about in a lovely essay. Mom and Dad just sent a link to this essay from Sachs: Darwin and the Meaning of Flowers. That essay closes:

The notion of such vast eons of time, and the power of tiny, undirected changes which by their accumulation could generate new worlds—worlds of enormous richness and variety—was intoxicating. Evolutionary theory provided, for many of us, a sense of deep meaning and satisfaction that belief in a Divine Plan had never achieved. The world that presented itself to us became a transparent surface, through which one could see the whole history of life. The idea that it could have worked out differently, that dinosaurs might still be roaming the earth or that human beings might never have evolved, was a dizzying one. It made life seem all the more precious, and a wonderful, ongoing adventure ("a glorious accident," as Stephen Jay Gould called it)—not fixed or predetermined, but always susceptible to change and new experience.

[then a few paragraphs on one of my areas of specialization -- phylogenetic theory, which Darwin pioneered, then the close ...]

I rejoice in the knowledge of my biological uniqueness and my biological antiquity and my biological kinship with all other forms of life. This knowledge roots me, allows me to feel at home in the natural world, to feel that I have my own sense of biological meaning, whatever my role in the cultural, human world. And although animal life is far more complex than vegetable life, and human life far more complex than the life of other animals, I trace back this sense of biological meaning to Darwin's epiphany on the meaning of flowers, and to my own intimations of this in a London garden, nearly a lifetime ago.

Back from service. It was a good one. Clay and Jamie Gurganus talked about their experience, each of them, of becoming blind while in college; and about the lives they have made together since them: Jamie as a social worker, and Clay as a financial aid counselor at the university. About having a child, and then being foster parents.

I stood during the milestones part of the service. What I said, more or less: I have attended here now for a little more than two years. My first service here was the Sunday after Thanksgiving. That was a moving one for me. It simply consisted of people saying what they were grateful for. That feeling -- gratefulness -- forms the core of my spirituality. I find it so unusual to be alive, in this biosphere. I could pick out a particular joy or sorrow to share, but mostly, I will just share this feeling of gratitude; this is the ground awareness that I live with.

Other thoughts on the topic (from yesterday's ski):

- A Benedictine monk or a zen Buddhist monk (or one and the same -- thinking of Steindl-Rast): it is interesting that both seek deep quiet, and great attention to "being" and to gratitude. The former may find the concept of god important; the latter, not. The practice in either monastery may be similar now as it was in either discipline two hundred years ago. Would the practice be any different for a practitioner now who has a concept of the biological origins of life, and a neuroscientist's understanding of the biological seat of the mind? I think: no, not substantially different. The Benedictine who is grateful and humbled by our brief time in this beautiful world -- and understands this life as a gift from god -- is not so different from one who is grateful and humbled by our brief time in this beautiful world -- and understands this life as a spontaneous arising from the earth. Both may also legitimatately see an underlying connectedness among all things.

Though I will also say: personally, I find the understanding based on material origins far more profound and moving than the theologically-based one from my teens. The materially-grounded understanding has a rational basis and internal consistency, yet I think lacks none of the strangeness and mystery of the theologically-based understanding.

Yesterday:

Around 10 am, we walked to Wheatsfield to replenish groceries; then walked back along 6th and through the park. Beautiful, crisp, cold. The snow creaks loudly underfoot. We came back to a light lunch, then went out again on skis: classic, on Squaw Creek. We went quickly to stay warm. The cold snow gripped the wax well, so a couple miles upriver, I dropped the poles and just strided for the next couple miles. We went up to the entrance to Onion Creek (I stopped just short, and swung my feet to try to warm up the toes). Gorgeous trip. The water is still open a few places, where it runs quickly over shallows. Also at the low-head dam at the top of the golf course. At these places, the steam rises into the cold air and forms feathers of ice crystals on the snow nearby.

Evening: dinner with Chris & Sandy; Sue and Rick; Jeri. E and Chris played viol for a half hour or so afterward.

What I'm exploring now
http://www.gratefulness.org
... the work of a long-time Benedictine monk and zen practitioner, Br. David Steindl-Rast. I much enjoyed the three-part documentary here.
I went looking for something like this because I thought we spend so much of our lives now in front of the computer. There ought to be a quiet place on the web that could facilitate quiet meditative observances through the day. In fact, I see featured on the events page, an associated "online retreat based on the monastic tradition of marking nuances of dawn, day, dusk, and dark with prayer."
Somehow this feels appropriate to the moment. I am in the quiet upstairs bedroom, before dawn, sitting in my robe and cowl (well, electric blanket and coat and hat). The temperature outside is -15 F, and the temperature in this under-heated room is, I am guessing, around 50 F.

Update: the sun has risen; it will be a bright, clear day. But COLD. The outside air temperature has dropped to -18, and the thermometer next to me reads 51 F. I am warm enough in my coat and blanket, but the fingers are moving slowly. It is remarkable to see the little woodpecker on the big oak outside surviving the cold. We'll go check the chickens at Andy's house next. (They've got a heat lamp and a bit of an enclosure; they've done OK so far this winter, and are giving us 6 eggs a day).

Farming Detroit
For my Detroit friends.
http://money.cnn.com/2009/12/29/news/economy/farming_detroit.fortune/index.htm?cnn=yes

I would dismiss this as coming from my inner irrational hippie -- except that it is actually working in Chicago and Milwaukee:
http://www.growingpower.org/

Hopeful New Year's wishes to us all.

December letter
Written two weeks ago, mostly by Ethy (during our blizzard-enforced quiet time), is our end-of-year letter. It's a little large (4 Mb), so it is posted here.

Today, Christmas Eve, we're in the midst of another storm. Not exactly the storm we'd like: two days of light rain and freezing rain so far; but fortunately, with snow supposedly on the way this afternoon and picking up tonight and tomorrow. We'll walk downtown soon, to have a soup lunch hosted by friends Mark and Terry at their restaurant. This evening: a walk in the snow, I hope, and maybe reading or writing by the fire. Tomorrow: skiing! Then dinner at the Fellowship. We'll bring the steamed pudding that Mom sent, and rum sauce.

Wishing friends and family a peaceful holiday.

More thoughts on the campus atheist PR
I suspect there is a niche for a vibrant grassroots "spiritual atheism", mostly free of institutions. This would be distinct (though not disjoint) from most existing atheist groups and churches. Some flavors of Buddhism probably fit the bill, as do some other humanistic religions. But growing this sort of culture and belief system isn't at all trivial. Even grassroots movements require some sort of infrastructure and funding. If we're talking about a system to habituate practices, norms, and beliefs, then how are these propagated? Humans have done this through stories and rituals. But stories and rituals can lead to dogma. I have thought that the Genesis story could be interpreted as a beautiful, subtle allegory: the tree of knowledge made us mortal. (We were mortal before tasting the fruit, but what was significant was the dawning of awareness of the mortality). It is a story consistent with my science-rooted (a)theology. But instead, the story is almost universally interpreted instead as the foundation for "original sin" and creationism -- two things I adamantly disbelieve. If, in fact, an early religious genius told this allegory with profound insights in mind, they succeeded in passing the shell of the story down, but mostly failed in conveying the more profound meaning. Of course, maybe this was *only* ever a creation myth; my point is just that subtlety is easily lost in transmission; and pedantic statement of belief often falls flat. I had some hopes when I first stumbled on this web site (Iowa-grown, interestingly enough) ... but it seems to be isolated and inactive. Maybe I am looking in the wrong places though. This new grassroots movement will come in some other guise. Maybe we should instead be looking at the new environmentalism, in its many forms? Or in many, many places? Reason vs. dogma: which wins over time?

National coverage for "Ask an Atheist."
A friend from church and from work came in today and told me to type his name into Google News. That pulled up 212 fresh news articles. He and the campus student atheist group (of which Andrew was the president until he started as a postdoc with us last year) were profiled in an AP story -- which has been picked up by venues from the Washington Post to Fox and ABC.

The local UU also gets a plug, at least obliquely. "Bodnar, an ex-Catholic married to a Buddhist, recommends the local Unitarian Universalist congregation, a haven for a grab bag of religious backgrounds and a few members of the ISU Atheist and Agnostic Society." I'd like to see the intersection of the two groups grow. It was nice this year that both groups sponsored teams for Reggie's Sleepout (a fundraiser for homeless youth).

In general, I'd like to see more of this sort of intersection -- that is, spiritual atheists having more opportunity for common observance of the significant, and more time for organized "good works"; and traditional churchgoers having more space for nonbelief. For both, I would wish tolerance for differing degrees and varieties of belief. Some fraction of churchgoers (in any denomination) must be atheists or agnostics, feeling uncomfortable and "in the closet" in their church of habit. And a good fraction of those who shun church must feel some significant spirituality -- maybe also with some discomfort at having few ways to express or share or articulate the feelings. Neither group should have to be in the closet.

Guest essay
I am happy to post an essay from a special guest: Mom!

The start:
"Why," I've been asking myself lately, "do I feel as if I've been kicked hard in the solar plexus? Why do I feel sad and helpless, when my life is blessed and these autumn days have been so arrestingly beautiful?" One answer I found came by way of re-reading of Lincoln's Second Inaugural address to a war-torn nation. I found myself struck by Lincoln's closing admonition: "With malice toward none; with charity for all..." Even with brother fighting against brother, Lincoln urged healing, "binding up the nation's wounds".

"Malice," I realized, "that's it!” It's the pervasive climate of malice in our country, the malice and mean-spiritedness and vitriol in politics that so oppress me.

( Read more )

Birthday
A few noteworthy things today. (Saying nothing of the afternoon's news of "12 Dead, 31 Wounded in Base Shootings").

1. In the mail this morning: "As the manuscript '...' by Dr ... and co-authors is likely to be accepted for publication in Nature, we would like to confirm that the address details we hold on file for you and your co-authors are correct."

2. Left work early to use the unicycle on the actual Day. I strapped it to my bike (laid it flat on the rear pannier, and the seat post running horizontally along the bike's top tube), and we went up to Ada Hayden lake. I made it all the way around the short loop -- maybe a mile and a half. Also, my first un-assisted mount without a post or friend to hang on to. Thighs are burning now.

3. E made a lovely birthday cake: poppy-seed, with lots of chia seeds added at my request. They are interesting: a little like small tapioca balls, after the seed coat has imbibed.

On my birthday present!
Thank you, Mom and Dad! Makes me feel like a toddler again ...