Dave Angelini

16 April 2008 - The Strange New World of Bioengineering
For a while now I've been listening to the RadioLab podcast. This is a program on the public radio station WNYC in New York. It takes a humorous look at different science topics and typically uses that as a starting point to delve into societal and artistic ideas that relate. The latest episode is about bioengineering, transgenesis, chimerism and what it means in an evolutionary sense to be human. They get a little silly at times, but this struck me as a great way to engage the general public with this issue. It avoids the usual controversial pitfalls without ignoring the ethical issues, and it still keeps the sense of wonder that I think drives so many biologists. It reminded me of the first time I heard about experiments that produced chimeric mice... "You can do that?!", I thought. Give a listen...

1 January 2008 - New Year's Snowed In
Back during Y2K, Serena and I, Beth and Frank, as well as a number of other friends and acquaintances rented a house in Bass Harbor Maine, on Mount Desert Island for New Year's eve. We had semi-serious worries about the collapse of modern technology, but really we never needed much of an excuse to get away from civilization. We hung out with our friends, danced around, talked into the wee hours, and made the long distance phone calls the authorities advised everyone against at 12:01am. The big event was a hike up Mount Cadillac to watch the sun rise on the new millennium. Local folklore says that because of its easterly location and height, this rocky peak overlooking the Gulf of Maine is the first place in the US to see the sun. - But again - We never needed much excuse to climb a mountain. Despite the cold, this was great fun. The hike was easy along a service road, and we could look down on the lights of Bar Harbor and see the stars peak between clouds. The actually dawn was obscured by clouds, but the scene was wonderful despite the weather, as a sizable crowd of like-minded hikers waited for the New Age to begin.

In the years since then, we have remembered that night well. And while we have often thought about replicating it, we've had never gotten back up to Maine. This year, however, our regular companions for New Year's, Beth and Frank, booked us into a B&B in Bass Harbor again. We drove up late on the 31st in snowy weather. We let ourselves into our rooms and slipped into the hot tub to welcome 2008. I got up early the next day and took a walk. The view was a snow-blasted trees and rocky tidal inlets, but it was a beautiful sunny morning for the new year. The innkeeper's dog joined me for a bit of exploring. After a breakfast and some talking with our innkeeper we headed across the island for some hiking. We knew we were due for more snow, and during lunch in Bar Harbor it started in. This turned into a major blizzard. We listened to the wind while we had a great time by the fire. We were just settling in for a movie when the power went out. So another few more hours of ghost stories while we blew out the candles and retired. If this is any indication of 2008, it should to low-tech...

7 December 2007 - Cave Creatures of Jordan Hall
The world is indeed a small place! I recently met an invertebrate zoologist, who after learning that I'd done my graduate work at Indiana University told me an interesting story. Southern Indiana and Bloomington sit on limestone that is riddled with caves and home to a number of strange cave creatures. In the late 1940's it came time for IU to build a new biology building which was to become Jordan Hall, where much of bio dept still works. During excavation for the foundation, a system of caves was actually exposed and this included some small subterranean streams. Years later these subterranean waterways found there way back into the subbasement of Jordan Hall, which might amuse some of the current residents. But wait-it gets better. Someone noticed that there were some critters living in these basement/cave streams that he didn't recognize. As it turned out it was an unidentified species of troglobitc isopod, similar to woodlice or sowbugs, which eventually got the name Asellus jordani. Two other undescribed species, sometime seen running across the basement floors weren't so lucky, as I'm told that they perished during a treatment for termites. People might joke about the strange endemic fauna of their workplace, but I guess in some cases it's really true!

8 November 2007 - Attack of the Flies!
I need to express the extent of my joy as nerd... The Drosophila 12 Genomes Consortium has just published the complete genome sequences of... big surprise... twelve fruitfly species. I expect this annoucemnet in this week's Nature won't cause too much of a stir in the mainstream media since by now people are used to seeing announcements of genome sequencing from humans, individual humans, dogs, cats, bees, every farm animal you can think of, even one extinct species (the Neanderthal). The average news reader has probably reached genomics saturation. Some biologists might even dismiss this as a project aimed only at the fruitfly genetics community.

I think this is actually very big, and a sign of things to come... This puts genomic technology squarely in an evolutionary context. The way genome projects have been going, the sequenceing of all the major research organisms, then organisms of agricultural or medical importance, has been a necessary first step. But it has meant that many evolutionary questions have not benefited from genomic resources except at the very largest scales. (Which admittedly has had great usefulness.) I expect that being able to examine the detail of sequences from closely related species will allow these flies to become case studies for a miriade of questions in genetics, molecular evolution, population biology, phylogenetics, bioinformatics, biochemistry, and cell biology- pretty much every science concerned with genes. What really has me excited is that I predict this marriage of genomics and evolution will produce all sorts of applications we can only guess at now. I'll rein in my hyperbole here since much of this issue of Nature is dedicated to speculation on the applications of all this data.

Still, I've been asking around for a copy of this week's issue, and so far no one wants to part with it...

10 September 2007
We just set up a new web site for Serena at She has been steadily producing a wide range of amazing artwork over the years. Painting, stained glass, scientific illustrations, as well as eccentric projects such as her rendition of the Korean Hanafuda deck of playing cards. I've have come to realize that this is something she does mostly for her own sake. Although friends and family have snatched up some pieces here and there. It's very satisfying for me that her work can be viewed by a wider range of people now. And potential buyers are quite welcome...

15 March 2007
Cleaning out old directories I found an interesting file collecting quotes. I had kept these in part because some of the lines struck me as poetic or insightful. Many of them come from important old books on biology, but just as many are from random sources. I was also looking for quotes to introduce chapters of dissertation. In that regard I was particularly pleased with myself for using some lines from Tom Waits' song Cold Water at the beginning of an appendix dealing with methods...

What price freedom
Dirt is my rug
Well I sleep like a baby
With the snakes and the bugs

Around this time I was also listening to alt-folk group The Mammals. They used a poem by William James in one particularly erie song, and it seemed an interesting way of putting things in perspective. It headed up my appendix of DNA sequences.

I am done with great things and big things:
Great institutions and big success.
And I am for those tiny invisible, molecular moral forces
That work from individual to individual
Through the crannies of the world
Like so many rootlets
Or like the capillary oozing of water
Yet which, if you give them time,
Will rend the hardest monuments of man's pride.

30 January 2007
The complete text of Charles Darwin's Origin of Species is now available in mp3 audio format. This project got its start last summer, when I was listening to a number of biology and science related podcasts. Sometimes just listening to relatively non-technical stories on science is a very convenient way of assimilating the information. Darwin's classic text works surprisingly well in this way. The book is organized basically in a series of examples which Darwin uses to bolster or challenge the concepts of inheritance and selection. Many of the key issues presented in Origin remain major fields in modern evolutionary biology. For the general public, I highly recommend listening to the introduction, in which the major arguments are summarized. Also, for a prespective on the importance of evolution, I've included Dobzhansky's classic essay "Nothing in Biology Makes Sense Except in the Light of Evolution". Just import these files into your favorite mp3 player and listen in the car or at work!

14 January 2007
Much has happened in recent months. Those of you who received our holiday card this year may be interested to know that at least two of our chickens have started laying eggs. I know it's the middle of winter, but evidently they're not aware of the fact that chickens usually don't lay many eggs when the days are short. So we've been keeping them well fed and watered, and we're enjoying more eggs than we know what to do with!

28 October 2005
From: "Tebo, Kathleen"
To: "EEB Department"
Subject: cockroach
Date: Fri, 28 Oct 2005 11:43:33 -0400

The staff in BCS caught a large roach downstairs - they have it in a box and didn't kill it because it has the number 7 on it - does it belong to anyone in EEB?
From: "Les, Donald"
To: "Tebo, Kathleen", "EEB Department"
Subject: RE: cockroach
Date: Fri, 28 Oct 2005 12:07:12 -0400

More importantly, does ANYBODY know what happened to the other six????
From: "Turchin, Peter"
To: "EEB Department"
Subject: cockroach #7
Date: Fri, 28 Oct 2005 13:20:16 -0400

I just realized it must be my fault, alhtough I am unsure about the exact mechanism. Here is a question that I asked in EEB 244 Exam I on Sept. 29:

25. (6 points) In a study designed to estimate the cockroach population in the TLS building, Prof. Turchin placed 200 nonlethal traps on all floors of the building which caught 60 cockroaches. Professor marked these cockroaches and released them in the building. Two days later, he put traps out again and captured 100 cockroaches, 6 of which were marked. How many cockroaches are there in the building? Show your work.

    Copyright 2007 David R. Angelini