He Thinks What?

Michigan State University professor Richard Lenski recently published one of the more exciting papers in biology to come out recently. It's the outcome of a 20-year experiment in e. coli evolution. In a nutshell, Lenski started with a single e. coli bacterium. From this he created 12 identical bacterial colonies. Each colony was grown in a citrate-heavy, glucose-poor medium. For twenty years, the colonies have been re-inoculated into fresh medium each morning(the old medium having exhausted all it's glucose by about halfway through the day), and a sample frozen. Lenski has been watching for genetic divergence among the twelve colonies.

The bacteria responded with the expected genetic divergence - developing more efficent ways to metabolize glucose, for example. Then something less expected happened. One of those colonies evolved the capacity to metabolize citrate. Based on Lenksi's work looking back through the samples, the ability seems to have required three separate mutations, the first one providing no apparent advantage to the bacterium posessing it.

While this is really cool, and why I started reading this article about the whole thing, it's not what this post is about. The discussion after the article is interesting, at least partially because one of the co-authors (Lenski's student Zachary Blount) pops in about halfway through and offers to answer questions as he can. A fairly hostile questioner immediately pops in and starts peppering him with questions (most of which could have been easily answered by simply reading the initial paper, many of which could be answered by a serious look at the review papers). Being unsatisfied with the answers he got (some of which were "go read this paper" with a link), he became even more hostile. Eventually he lets loose with this whopper.

"Zachary and his paper have no credibility because he won't answer some simple, basic, objective questions about it. Zachary and his supporters have long ago passed the final point where they could redeem themselves by giving straight, consistent answers to my questions.

This paper has attracted a tremendous amount of reviews and comments. I hope that a lot of people will see this thread so that Zachary and his paper will be thoroughly discredited."

Wait. What? What kind of doofus thinks that a comment thread on a blog involving a bunch of people who are merely interested non-scientists (and certainly mostly non-biologists), has any power whatsoever to discredit a reviewed, published and ground-breaking paper?

The web sure gives some people delusions of grandeur.

Home Again

Actually, we've been home for a few days now (since Wed.). But by now we're unpacked and I've caught up on my sleep.

The trip was great. We spent the first week up at L's house, where there was much book reading, knitting and some writing. We had a low-key party for L's oldest son (whose actual birthday is later this month) so that he could celebrate while we were there. Ice cream, chocolate cake (the kind made with boiling water over cocoa), and fresh strawberries. We only actually talked S into having a cake at all by telling him we needed something to put the candles into. Given his own way it would have been strawberries, whipped cream and ice cream.

Because S's birthday celebration was the day before A's graduation party we ended up making four homemade cakes in 24 hours. For the graduation party it was lemon/white chocolate cake, chocolate angel food cake, and an apple-spice ring (vegan). Those were carted into Boston for the party, but held up well and were duly demolished by the guests.

A's place was next. As usual that was a whirlwind of visits to everywhere in creation. On the plus side, she now has a high-end GPS, which means that for the first time ever I spent a week driving around downtown Boston without getting lost. For those who haven't been there, Boston streets are supposed to be paved over cow paths. This is supposed to explain why they are so twisted. Given the sheer number of one-way streets, five and six-way intersections, roundabouts that aren't round and other bizarre features my contention is that the cows of early Boston were ingesting some kind of hallucinagen. If you miss your turn it is impossible to simply go around the block and try again - even attempting such a thing is likely to land you across the harbor. This is complicated by Boston not posting street names for most of its major streets apparently under the impression that everyone knows what they are anyway, so why bother? The GPS was a godsend. It even got me to my clinic appointment at Mass General on time and on the first try with only one wrong turn. (Even a GPS isn't a miracle worker. "Turn left in 50' " isn't always going to work in a town with five, six and more way intersections. "WHICH LEFT!!!")

The neuroendocrinologist visit was all good. Dr. Utz was lovely, spending a good 90 minutes with me answering every question under the sun. I have a couple of blood-test results waiting to come in, but the upshot so far is that the adenoma appears to be doing no harm and is unlikely to ever do any harm. She feels that if the next MRI (in August) shows no growth, then I can drop back to having an MRI every second or third year just for safety's sake. As much as I like Dr. Utz though, I'm very glad MGH isn't my regular hospital. It's hellish to get around in - lots of traffic, weird street patterns, and a huge campus that isn't particularly well labeled.

While we were at A's, I got to leave the boys behind for a day and jaunt down to NYC for a day with Beth and Becky. B&B are friends from college. I've seen each of them several times since then, but have not in the last 15 years had a chance to just spend a day hanging around as a trio. It was wonderful. We had lunch at Alice's Tea Cup, and Alice in Wonderland themed restaurant with out-of-this-world food. For a random note, BLT's with dark bread and bleu cheese spread are marvelous. We also sampled frozen hot chocolate (fabulous), went to a good yarn store (where I got materials to knit Beth a beaded stole for weddings), went shoe shopping (successfully), and hit a Tibetan store where I finally got a pouch for my MP3 player and a leather case for my PDA.

Then it was back to Boston, where we spent the day at the New England Aquarium. We went with one of A's friends from work and her two girls. All four kids had a grand time. Aaron (with A's encouragement) is now talking about spending a summer volunteering there when he's old enough at fourteen. Robbie would rather volunteer at the Science Museum.

The last day of the trip was Beth's ordination. We left A's early, went to Connecticut to meet up with Becky, and then all crammed into her and her husband's Civic to go down to Manhattan. The 4th Universalist Society is a beautiful old stone church - with air-conditioning, thank goodness. Beth and her mother had already hung up yards of rainbow organza and yellow satin. I got to help with setting out candles. Lots and lots of candles. Judging by the number we had to choose from, the UU's really, really like their candles.

The service itself was beautiful. UU congregations ordain the ministers, so there were a number of welcoming speeches by various communities, readings selected by Beth, a couple of beautiful songs, and then Beth and the congregation read vows and charges to each other. This was followed by a laying on of hands by everybody in the room in a sort of giant human web. Followed by more welcoming speeches, a gift of her robe by her parents and of a stole by the congregation. For me it was a wonderful chance to see Beth in her element (she's going to make an awesome chaplain), and to meet many of the other important people in her life.

After that it was the drive home, losing one of the DS's (after we got home, no less), and flopping out to recover for a couple of days. Normal life to resume tomorrow.

Sundays in the Park with Sensei

We knew it was coming, though I wasn't sure it would happen this quickly. We have split away from the TKD dojo. There were a lot of issues involved, which I'm not likely to discuss in detail, since it would be very easy to slide into badmouthing, but suffice it to say that practically none of our students were very happy with how things were going, and we were getting more unhappy with time.

Sensei tried to find us a new place to go. In fact we very nearly ended up at a Shrine Club literally around the corner from me (less than 200 yards from my house), but negotiating fell through over whether and when we could use our padded flooring. So far that's the closest he's been able to come to finding us a new place.

So for now, we are practicing in the local park. There are a few disadvantages, the biggest being the unpredictability of class (Sensei checks the weather report each weekend and calls us Sundays to tell us which days we'll have class.). Allergies are also a problem for at least one student. On the other hand, the outdoor practices are quite fun. The uneveness of the ground isn't extreme, but it's enough to provide more challenge than a level indoor surface. Plus we've been generating a lot of interest from new students. Pretty much every class, three or four people will wander by, sit down for a while, and watch us. Others watch more distantly. About once a class somebody will wander up and talk to one of us about what we're doing. We've already had one new student join, and at least two others have expressed interest.

It would be nice to have an indoor place so we could have regular class hours, and access to things like heavy bags and makiwaras - but you know, for a complete improvisation, this isn't doing too bad. I think it might even be worth holding summer classes in the park again next year, even if we are in a more permanent spot. It seems to be really good advertising.

In other news, Lance - Sensei's first black belt, has opened his own class at the YMCA in Frankfort, KY. (That's the capitol of Kentucky.) Four of us went down for his opening day. So far he has two students, but they've been back for repeat classes, so he's off to a good start. He has a pretty good space - a basketball court, complete with some padded walls that would make pretty good punching practice.

More personally, I've finally made it through Kusanku. Just in time, too, since I'm hitting the road for Boston day after tomorrow. I really wanted to have it complete. It's much easier (to me anyway) to practice and retain a kata once I have the whole thing in there, then while I'm still learning it piecemeal. Sensei has loaned me his DVD of tonfa basics to practice with also while I'm gone, so I can keep working on those.

Rob has made me a perfectly beautiful pair of tonfas. He checked the general proportions from the commercial set I had, plus descriptions from other places. Then he made me a pair of pine blanks to check proportions - I actually used these in class for several weeks, because even out of pine and held together with screws, they already fit and moved much better than the commerical set. Once I was sure of exactly what I wanted based on the blanks, he went ahead and made the final set. They're gorgeous. Osage Orange (to match my bo staff), in a block-style tonfa (see here). The handle is exactly my hand-width, which improved my accuracy about 100% almost immediately. This is good, because these things are heavy. If I miss with the commerical tonfas and whack myself in the shoulder or back of the head, I get a bruise. With these suckers I'm likely to do real damage. They spin like a dream though, and the handles are perfect. Sensei has asked Rob to make a custom pair for him.

I may or may not get another post in before Boston. Tomorrow is packing, rental car pick-up, and the arrival of my FIL (aka Nicky's personal door-opener). I found both of the boys' DS's, so the actual traveling should be minimally boring for them. Plus, since I'm getting the car a day early I can stick some holes in an old sheet and make a cover for the back seat of the car - thus permitting minor eating back there, which should also help. This coming week is at L's for writing, baking, trivia contests (last time we won L a pizza parlor gift certificate), and present-hunting (what do you get someone for an ordination?). Then it's A's for our usual whirlwind of running madly- plus a neuroendocrinologist visit for a second opinion as to whether my little tumor is actually doing anything or not. Then we spend the last three days at Beth's for her ordination and general fun and hanging out. I will post as people allow me computer time, but since I don't have a laptop to bring, I'm dependant on charity for computer access.

Child Takeover

Robbie and Aaron have discovered our computers big-time in the last few days. Mind you, they were both pretty computer literate before - but they also had a limited number of things they wanted to do on the computer. Generally the TV and video games (or even sometimes books) looked more exciting than the computers most of the time.

That has changed. Aaron has discovered his first dungeon-crawl game, Dungeon Seige II. (For the unenlightened, a dungeon-crawl is a role-playing game of greater or lesser complexity, wherein the basic form is find a dungeon, wander around the dungeon killing monsters until the monsters are all killed, find new dungeon, repeat.) He is now spending every allowed waking minute on Rob's computer playing his character - Mommy is fairly pleased that his chosen character is a female mage and dryad, both because so many boys won't have anything to do with female roles, and because it's a nice change from a Paladin (what he's wanted to play in boardgame versions), where the stick-up-the-rear is a character attribute. Seriously, try playing a thief in a game where your co-gamer walks into every town and immediately seeks out the local gendarmes and announces your character status. It's enough to drive a poor thief to drink.

Robbie, on the other hand, has discovered YouTube and related sites, and more importantly, that many of these sites keep video archives of various shows that he loves, but that Cartoon Network doesn't show enough, or any more, or shows too late, etc. etc.. Right now he's working his way through Zatch Bell on my computer, probably to be followed by One Piece. I'm thinking I'm going to put my foot down if he tries for Bobobo-Bo-Bo-Bobo (yes, that's actually the name of the show). It's simply too silly.

If they don't ease up on the enamourment soon, we're going to have to institute strict hours because right now we're barely getting e-mail checking time in on our own computers.

In other news, Rob starts his new position officially on June 1. Except for shutdown in early July, which is still all his. I don't expect to see him, other than nose-down on the bed for about two weeks.

Monday starts the last week of school, and then we're off to the northeast! Boston-Ho!

Oh - and we (the Isshin-ryu people) split off from the larger dojo this last week. More on that later.

The Name Game

I have a few upcoming posts in mind, so there shouldn't be another hiatus on here (more than a day or so, anyway) until the boys and I head up to Massachusetts in two weeks. I will try to post at least a few times during our trip, but no guarantees, we're going to be very busy.

In the meanwhile, for today, Createcraft is having a contest, wherein we are supposed to explain where our blog name came from. Best story gets some nice prizes, and I don't think I've ever explained my thinking, so what the hey!

Back when I first wanted to start this blog, I wasn't at all sure that I wanted to hook my blog (which mostly contains personal meanderings) with my other on-line commentary. So I didn't want to use my usual on-line handle for commenting (I post many places as Tapetum.). So as much as I like that name (from the Latin Tapetum Lucidum, tapestry of light, meaning the iridescent layer that makes cats' eyes glow), I needed to find something else to call the blog. Blogging was a new thing for me - yet trying new things is hardly a new thing at all for me. I have more hobbies than you can shake a stick at. Over the years I've tried writing, knitting. crocheting, drawing, weaving, spinning, counted cross-stitch, latch-hooking, karate, beading, woodworking, piano, organ, biking, triathlon, and a fair few other things as well. One of my cousins calls me a skills collector with good reason. Most of these things I've pursued at least long enough to gain a reasonable level of competency, which I then try to maintain. Some I actively maintain indefinitely - karate, knitting, piano and writing are the major parts of that set. So blogging seemed to be one more hobby to begin - as I am perpetually doing.

In addition, I was reading a couple of books on Zen. (Zen Mind, Beginner's Mind was one.) The concept of a beginner's mind is important in Zen - to remember that the full mind cannot gain more knowledge because there is no room - it's like trying to pour tea into a full teacup. As many things as I keep trying to stuff into my head it's difficult to maintain the beginner's mindset, but it seems ever more important.

So I decided to name my blog The Perpetual Beginner - both in recognition of my beginning over and over again in different places, and to remind myself of the importance of being that beginner, no matter how long I've been doing something. It's been a good name for me. It seems to suit me more the longer I use it, and I've never really had a desire to change it.

Well, That's Different

Something new happened - something that has never, ever happened to us before. Not in sixteen years of marriage and five jobs.

Rob got promoted.

For the first time in our lives so far, he's got a new job and a pay raise without us having to move cross-country, rack up new debt, and otherwise upend our lives. He not only doesn't have to move to a new city, he doesn't even have to move offices - though they did try to make him.

Of course until he can get a replacement controls engineer hired and up to speed he'll be doing both jobs, but since his new position is a new one he can ease into it somewhat. Which is good, because shut-down (the annual closing of the plant, where most of the people go home and Rob lives at the plant for two weeks installing new systems) is the beginning of July, and there's no way he could get someone going fast enough to take that over.

His new title is (I believe) North American Controls Development Manager. It's a heck of a lot more responsibility, but it also looks to be right up his alley, with more real engineering than administrative work, and likely a good deal of troubleshooting.

And we didn't have to move!!!

Body Talk

The Turbokick class at the Y has developed a small group of women who all hang together at the back left. It's my preferred spot, but I've never really made friends with anybody in the class until now. (Yoga and Core, being quieter classes, have more comraderie) However, about a month ago, a group of newbies clustered back by me, and when I took some time to walk them through the more complicated moves (Turbokick moves fast), they sort of adopted me in. They're a nice group of ladies.

Anyway, today after class we hung out for a little while in the sauna (which turned out to be a mistake, but more on that later), and after two of the group had left, the last two women started talking bodies. The smaller (a tiny woman) started complaining that she had gained some weight while the taller was reassuring her that she was still skinny. She then appealed to me for backup - we will note that both of these women are far thinner than I am (or would be even if I became anorexic), and when I said so, then both of them started telling me all the things that they envied about my body. Which is when I realized that among the three of us, none of us could see anything good about our own bodies, but had no trouble at all seeing the good points of the others. The tall drink of water feels like a rake, the little, petite one, hates her curvy hips and butt. I, of course, am not fond of my top-heavy figure. It was a rather new experience for me to have anyone envying any parts of my body, but these women who have lovely figures (that they can't see) do. It felt very strange.

In other news, I finally got tired of having my back hurt every night, which it has ever since December when I took a kick in the low ribs, so I wandered off to a chiropractor. The news is all good. Apparently I've got some residual (and now habitual) irritation and spasming around the site (I probably had a mild sprain). So a week or so of icing and some other therapy, and not staying long in the positions that irritate it (like sitting at the computer), and it should be good to go. However, I'm to avoid heat (even long, hot showers). Of course I found this out about 90 minutes after the stint in the sauna - oops!

School is winding down for the year - about three weeks left to go. I will try to do a little better about keeping things updated here. Ernie, I haven't forgotten your meme - I'll get to it, I promise!