Monday, April 25, 2005


Yes, I know this silly graphic has been here forever without any text... blogging is not everything, I was out living and working.

What is the point of the graphic? I thought today's forecast showed nicely that you can live only a few hundred kilometers from the equator and still be comfortable. Those of you who know me or pay attention to my postings will be able to easily guess the city this is from. And the time of year does not matter - the temperatures would always be similar, just the cloud cover would change.

Sigh. Life near the Equator is so boring. Posted by Hello

 Tuesday, April 19, 2005

Archie returns:

Spotted the first hummingbird of the season today. Adult male, from his red gorget. Right on schedule, same week as the last two years.

Here's a photo I took during a previous season:

Archilocus colubris Posted by Hello

Note the absence of a red gorget, which means that this is either a female or a subadult male. No way of telling them apart.

 Friday, April 15, 2005

Rocket fuel:

On a recent trip to Brazil's Space Research Institute (INPE), I spotted this official car making the rounds, replenishing coffee throughout the campus.

"Executive power" Posted by Hello

You can get your coffee sugared, or without sugar, but never, never, ever decaf.

As you can see, it has serious racks of java.

caffeine jackpot Posted by Hello

This is one reason why Brazil is capable of building its own satellites, and why they are very close to being able to launch them with their very own launch system. Coffee delivery infrastructure is critical for engineering and science.

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 Tuesday, April 12, 2005

Return to Flight:

On this anniversary of the first shuttle flight, and the forty-fifth of Gagarin's flight as first man, I decided to focus on one aspect of the upcoming STS-114 mission to which I have a (tenuous) link.

I have posted previously about another workhorse in the U.S. research aircraft fleet, the WB-57. For some time now, the two NASA birds have been used to photograph shuttle launches. For the upcoming launch they were tasked with acquiring high-quality video from lift-off to just past the solid rocket booster (SRB) separation.

926 and 928... Posted by Hello

These are the two NASA WBs - known from their fleet numbers as simply 926 and 928. They are modified B-57 Canberras, made by Martin based on the original English Electric design. Both were originally made in 1963, and their wings were modified in 1967 by General Dynamics for high-altitude reconnaisance missions. 926 was RB-57D 53-3974 while in the USAF, and 928 was RB-57B 52-1536, and they most probably did high altitude sampling over US and Chinese nuclear tests. Lately they have flown through the exhaust plumes left by the shuttle's SRBs and main engines.

HDTV! Posted by Hello

To provide high-quality imaging of the shuttle, SRBs and the external tank (ET) during ascent, both 926 and 928 will be carrying specially manufactured imaging systems. NASA contracted the Aerospace Corporation and the Southern Research Institute to put together the equipment and plan the mission for the WBs. This is a shot of the imaging package - a Celestron telescope lens provides an aperture for near infra-red (NIR) and HDTV imaging, and an NTSC system provides the initial sighting for the tracking software.

nose job Posted by Hello

In order to track the shuttle's ascent, a turret and gimbal system will be attached to the nose of the aircraft. This is the hangar at JSC where they are doing the first mods to attach the turret.

flankers Posted by Hello

During the actual launch, the WBs will fly at 60,000 feet along tracks on either side of the ascent path, giving views of the orbiter, ET and SRBs through SRB separation+10. The technical constraint areas for the position of the WBs during a particular ascent moment are the blue boxes.

RTF! Posted by Hello

These are simulations done by the Aerospace Corp. for what the HDTV FOV should be from both aircraft, at different times during the ascent. WAVE stands for WB-57 Ascent Video Experiment.

Of course, since the data will be in HDTV, I am sure that NASA's PR Office is already salivating. But no, it will not be shown live - the data is being recorded on board, and will have to be downloaded at Patrick AFB when the birds return. Time to release, probably about launch + 30 hours. I can't wait. I hope to be in Orlando during the launch window, and will keep my eyes glued to the East.

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 Friday, April 08, 2005

Non habemus Papam:

Sede vacante Posted by Hello

As I suspected it would, the death of Pope John Paul II hit me hard. I'm not sure why, since I am an errant Catholic, but he seems to have attracted many in that way. I dug out a set of rosaries he blessed while I was at the Vatican in December of 1993, and I have been carrying them around in my pocket. And no, I didn't get an audience with His Holiness - he blessed the rosaries as I held them out above my head among the large crowd in St. Peter's Square (Catholics count such things as legitimate blessings), and then took them back to my mother, who was dying at the time.

In creating the following table, I was trying to figure out how long conclaves have lasted, what the lengths of the interregnums between Popes have been, and what the lengths of papal reigns have been. Well, of course, it wasn't that simple.

First was finding a listing of Popes - since the Papacy extends back nearly 2000 years, there are several different lists, and they differ in agreeing who was and was not a Pope. The two 'best' lists I found were at and in the wikipedia papal list (I suspect the wiki author(s) used as a source, which yields the good agreement - I have posted discussions of this dangerous sampling tactic before). The Vatican website, surprisingly, has very little covering this set of basic facts (in any language - I looked, they all go back only to Leo XIII).

The second issue was that the listing did not have dates, and the article under each of the links for the Popes did not consistently give dates for birth, death, election or the beginning dates of the electing or following conclaves, even for recent Popes. The first of my questions, "what have lengths of conclaves been?" had to be abandoned due to lack of (quickly available) data. There is a good set of articles on the more recent conclaves at wikipedia, and a listing of conclaves at Salvador Miranda's site.

The other questions, the length of interregnums and reigns, quickly ran into problems for several reasons. Although the Wiki site has dates listed by each Pope's name, I was not sure of several things: was the start date the election or the coronation? (the definition of when the elected person becomes Pope has changed with time). There are also some overlapping dates - the death of a Pope post-dates the election/corontaion of the next. Are these abdications and/or resignations? I did not go back to check these cases.

The most fundamental question revolved around the dates themselves: for dates before 1752, I was not sure whether the stated dates were using the Gregorian, proleptic Gregorian, or Julian calendars. Also, since 1752 was the year the U.K. and its colonies adopted the Gregorian calendar, and the events were occurring in Rome, which had dropped the Julian calendar during Gregory XIII's reign in 1572, what about the dates between 1572 and 1752? Under which calendar were they stated? And of course, the exact dates get very hazy as one goes further back, and there are cases of second or even third terms after depositions/revolutions. etc. I decided only to take this list back to Popes since the year 1000.

To top it all off, Excel cannot handle dates before 1900 (1903 on a Mac) without special add-in functions, so calculations for these pre-1900 dates were impossible until I hunted down free extended date add-in functions (which, incidentally, do not properly account for the fact that 14 September 1752 was the day after 2 September 1752, in the U.K. at least).

So, with the above caveats, here is the table:

PopeLength of ReignDate of DeathLength of FOLLOWING interregnumDate of Election
John Paul II (the Great)9,6652-Apr-200516-Oct-1978
John Paul I3328-Sep-19781826-Aug-1978
Paul VI5,5256-Aug-19782021-Jun-1963
John XXIII1,6793-Jun-19631828-Oct-1958
Pius XII7,1619-Oct-1958192-Mar-1939
Pius XI6,21310-Feb-1939206-Feb-1922
Benedict XV2,69822-Jan-1922153-Sep-1914
Pius X4,03420-Aug-1914144-Aug-1903
Leo XIII9,28020-Jul-19031520-Feb-1878
Pius IX11,5597-Feb-18781316-Jun-1846
Gregory XVI5,6069-Jun-184672-Feb-1831
Pius VIII6101-Dec-18306331-Mar-1829
Leo XII1,96210-Feb-18294928-Sep-1823
Pius VII8,55920-Aug-18233914-Mar-1800
Pius VI8,96129-Aug-179919715-Feb-1775
Clement XIV1,95322-Sep-177414618-May-1769
Clement XIII3,8642-Feb-17691056-Jul-1758
Benedict XIV6,4683-May-17586417-Aug-1740
Adoption of Gregorian calendar in the U.K. and its colonies
Clement XII3,4966-Feb-174019312-Jul-1730
Benedict XIII2,09621-Feb-173014127-May-1724
Innocent XIII1,0347-Mar-1724818-May-1721
Clement XI7,42119-Mar-17215023-Nov-1700
Innocent XII3,36427-Sep-17005712-July-1691
Alexander VIII4831-Feb-16911616-Oct-1689
Innocent XI4,70711-aug-16895621-Sep-1676
Clement X2,27622-jul-16766129-Apr-1670
Clement IX9039-dec-166914120-Jun-1667
Alexander VII4,42822-may-1667297-apr-1655
Innocent X3,7657-jan-16559016-sep-1644
Urban VIII7,66329-jul-1644496-aug-1623
Gregory XV8743-jul-1623349-feb-1621
Paul V5,73628-jan-16211216-may-1605
Leo XI1112-apr-1605341-apr-1605
Clement VIII4,7813-mar-16052930-jan-1592
Innocent IX6230-dec-15913129-oct-1591
Gregory XIV31415-oct-1591145-dec-1590
Urban VII1227-sep-15906915-sep-1590
Sixtus V1,95127-aug-15901924-apr-1585
Gregory XIII4,71510-apr-15851413-may-1572
Julian calendar dropped by the church
St. Pius V2,3061-may-1572127-jan-1566
Pius IV2,1769-dec-15652925-dec-1559
Paul IV1,54818-aug-155912923-may-1555
Marcellus II221-may-1555229-apr-1555
Julius III1,87023-mar-1555177-feb-1550
Paul III5,50710-nov-15498913-oct-1534
Clement VII3,95625-sep-15341826-nov-1523
Adrian VI40114-feb-15232859-jan-1522
Leo X3,1891-dec-1521399-mar-1513
Julius II3,40121-feb-15131631-oct-1503
Pius III2618-oct-15031322-sep-1503
Alexander VI4,02318-aug-15033511-aug-1492
Innocent VIII2,88725-jul-14921729-aug-1484
Sixtus IV4,75212-aug-1484179-aug-1471
Paul II2,52126-jul-14711430-aug-1464
Pius II2,18815-aug-14641519-aug-1458
Callistus III1,2166-aug-1458138-apr-1455
Nicholas V2,94024-mar-1455156-mar-1447
Eugene IV5,83623-feb-1447113-mar-1431
Martin V4,84920-feb-14311111-nov-1417
Gregory XII3,1384-jul-141586130-nov-1406
Innocent VII7506-nov-14062417-oct-1404
Boniface IX5,4461-oct-1404162-nov-1389
Urban VI4,20815-oct-1389188-apr-1378
Gregory XI2,64326-mar-13781330-dec-1370
Blessed Urban V3,00419-dec-13701128-sep-1362
Innocent VI3,55512-sep-13621618-dec-1352
Clement VI3,8666-dec-1352127-may-1342
Benedict XII2,68325-apr-13421220-dec-1334
John XXII6,6934-dec-1334167-aug-1316
Clement V3,21120-apr-13148405-jul-1305
Blessed Benedict XI2597-jul-130436322-oct-1303
Boniface VIII3,21211-oct-13031124-dec-1294
St. Celestine V16113-dec-1294115-jul-1294
Nicholas IV1,5034-apr-129282222-feb-1288
Honorius IV7313-apr-12873252-apr-1285
Martin IV1,49528-mar-1285522-feb-1281
Nicholas III1,00122-aug-128018425-nov-1277
John XXI25420-may-12771898-sep-1276
Adrian V3818-aug-12762111-jul-1276
Blessed Innocent V15322-jun-12761921-jan-1276
Blessed Gregory X1,59210-jan-1276111-sep-1271
Clement IV1,39329-nov-12681,0065-feb-1265
Urban IV1,1302-oct-126412629-aug-1261
Alexander IV2,35625-may-12619612-dec-1254
Innocent IV4,20327-dec-1254-15 (?)25-jun-1243
Celestine IV1610-nov-124159225-oct-1241
Gregory IX5,27022-aug-12416419-mar-1227
Honorius III3,89518-mar-1227118-jul-1216
Innocent III6,76416-jul-121628-jan-1198
Celestine III2,4768-jan-11980 (?)30-mar-1191
Clement III1,19427-mar-1191319-dec-1187
Gregory VIII5717-dec-1187221-oct-1187
Urban III69319-oct-1187225-nov-1185
Lucius III1,48525-sep-1185611-sep-1181
Alexander III8,02830-aug-118127-sep-1159
Adrian IV1,7321-sep-115964-dec-1154
Anastasius IV21815-feb-115429212-jul-1153
Blessed Eugene III3,0658-jul-1153415-feb-1145
Lucius II36815-mar-1145-28 (?)12-mar-1144
Celestine II1648-mar-1144426-sep-1143
Innocent II4,97024-sep-1143214-feb-1130
Honorius II1,88613-feb-1130115-dec-1124
Callistus II2,14113-dec-112422-feb-1119
Gelasius II36928-jan-1119524-jan-1118
Paschal II6,73521-jan-1118313-aug-1099
Blessed Urban II4,15629-jul-10991512-mar-1088
Blessed Victor III47616-sep-108717828-may-1086
St. Gregory VII4,42029-may-108536422-apr-1073
Alexander II4,22121-apr-1073130-sep-1061
Nicholas II96427-jul-1061656-dec-1058
Stephen X23929-mar-10582522-aug-1057
Victor II83728-jul-1057513-apr-1055
St. Leo IX1,89219-apr-105435912-feb-1049
Damasus II239-aug-104818717-jul-1048

The average papal reign over the last 1,000 years: 2,973 days.

The average interregnum: 93 days.

 Tuesday, April 05, 2005

Schweitzer, Weiner, Lowenstam, and a T-rex named Sue:

You have probably heard about the recent discovery that scientist Mary Schweitzer made: soft tissue preserved inside a dinosaur bone. It was interesting to see the media frenzy that occurred - just about every major source carried the story. The trigger, of course, being the Jurassic Park aspects of it all: after de-mineralizing a 68 million year old T. rex bone, Dr. Schweitzer found pliable material, some tubular, with dark red to brown spheres enclosed. Both the pliable tube walls and the spheres had smaller, darker central portions. The immediate interpretation by the media was veins and red blood cells with nuclei, and of course from there it was a quick jump to dino-DNA.

There are some parts to the March 25 Science article ("Soft-Tissue Vessels and Cellular Preservation in Tyrannosaurus rex," Mary H. Schweitzer, Jennifer L. Wittmeyer, John R. Horner, and Jan K. Toporski Science 307: 1952-1955; doi 10.1126/science.1108397; abstract) that the media did not choose to follow, but which I found interesting. Perhaps you will too.

My first question was 'what did her team de-mineralize the fossils with?' It turns out they used 0.5 M ethylenediaminetetraacetic acid, more commonly known as EDTA. I laughed, since EDTA is used as a food preservative, metal sequestrant and stabilizer in a lot of things we eat - check out the ingredients for many MacDonald's items (and since EDTA is used to chelate metals, it is often used in canning, as well as a poisoning antidote, and there is active debate about EDTA chelation therapy - but that's a whole 'nother subject...). In any case, it's currently thought to be safe to eat, and at the concentrations used in foods, it will not de-mineralize your bones and turn you into a quivering blob of collagen.

The next piece that the media did not pursue was the link to the T. rex nicknamed "Sue," the most complete T. rex ever found (~90% complete). Dr. Schweitzer's team used the same technique on specimens from several dinosaur fossils, including pieces of "Sue," to try and duplicate their results from the T. rex dug up in 2003 (and lo and behold, pliable material was found in the others, too! There were some really nasty lawsuits over the ownership of "Sue," and the fossil ended up on the auction block. The science of paleontology was at risk of losing this valuable find to a private collector, but luckily McDonald's, Disney, the Cal State system and several private individuals put up over 7 million dollars, and "Sue" ended up at the Field Museum of Natural History in Chicago as specimen FMNH-PR-2081).

I thought the pictures that the media chose to use were odd, because they didn't show off the part of the story that they emphasized in their text. Here is the picture I saw used in almost all of the media (used w/ permission of Science):

MOR-1125 endosteal tissue (c) 2005 Science

Here the arrows indicate the flexible, fibrous, even 'stretchy' material left after de-mineralization - sure, it looks like a piece of meat with gristle, but the media's main focus was the blood cells and the nuclei, and these photos certainly don't show those.

So here is a set of four pictures, also used with permission from Science, that illustrate how startlingly good the preservation is in these samples, and that you probably did not see in the paper or on TV. Schweitzer was particularly careful to avoid calling these things 'capillaries,' 'nuclei,' 'organelles,' or even 'cells.' And I will be too. More on that later.

1) This is a shot of an area about 2 mm across, showing the structure of the interior of the femur on the T. rex MOR-555, from the Museum of the Rockies, also known as the "Wankel rex" after its discoverer. I don't know how often you dine on meat with the bone in it, and if you ever pick at marrow within that, but this texture is absolutely identifiable as bone interior:

Wankel endosteal bone surface (c) 2005 Science

2) This is a photomicrograph of the Wankel rex again, showing tubular structures about 50 micrometers across, with the enclosed darker spheres. I'd love to have a medical student look at this without knowing what it was, just to hear what they said:

Wankel vessel (c) 2005 Science

3) This is a shot of a piece from "Sue," showing the same type of micro-structures:

FMNH-PR-2081 (c) 2005 Science

Note that you can see darker centres to some of the red spheres in both of the above photomicrographs.

4) Here is a shot of a microstructure from the 2003 juvenile T. rex, MOR-1125, which shows internal structure, as well as thin extensions protruding from the main body:

MOR-1125 (c) 2005 Science

This looks very much like an osteoblast or osteocyte, or a bone-producing cell, from any modern animal. The extensions are known as filipodia and they fit into thin channels called canaliculi that allow the cells to pass information and nutrients through the dense calcium phosphate (apatite) bone matrix (here is a slide showing osteocytes in place from a fossil theropod's toe!). While osteocytes have been seen before in fossils, we had never seen internal structure. The microstructures inside the 'osteocyte' in the picture above are interpreted as the remnants of cellular organelles. Schweitzer's team also found microstructures in the other two T. rexes and the hadrosaur Brachylophosaurus MOR-794 that looked very much like osteocytes. Immunoassay tests done against the materials from the first T. rex, MOR-1125, indicate that proteins from the original bone are highly likely to be present.

We do not know as much about what fossilization does and does not destroy as we thought we did. What Schweitzer's current work shows is that there are certain levels of physical microstructure that are preserved that we did not think were possible. Not much has yet been published about the possible preservation of the biochemical microstructure inside these things, which is where the holy grail of dino-DNA lies (but more on that later). It is slowly becoming clear that fossilization can preserve some very odd things - shapes of things certainly, like bones (even delicate ones in embryos), but also the overall shapes of soft tissues, like feathers, bananas, dinosaur heart, and even jellyfish. There are cases where fossil beetle casings and dinosaur feathers/hair (?) preserve their pigmentation, or colour.

But until now, no one had thought that cellular-level physical structures might be preserved. We knew that some of the original chemicals could be preserved - I worked with Heinz Lowenstam and Joe Kirschvink while I was at Caltech, and collected 63 million year-old Cretaceous ammonites (Baculites inornatus) from Baja California that still had mother of pearl lustre in them, in the unstable aragonite form (here are examples from Japan and from South Dakota). Based on ion exchange chromatography, Weiner, Lowenstam, Taborek and Hood found that the organic matrix in the shells of 80 million year old molluscs from Tennessee (Scabrotrigonia thoracica) probably had the primary, secondary and possibly even tertiary conformations of their proteins preserved. Weiner and Lowenstam also found that the isoleucine in fossil shells was sometimes not racemized - that is, it was still all of the same chirality (handedness), when most materials will naturally devolve into a 50-50 mix of epimers. The lack of epimerization for the shell in the intervening 63 million years, when the characteristic epimerization time is about 10^5 years, is thought to be due to the stabilization of the amino acids by the bioinorganic phase of the shell matrix. Whereas dinsoaur blood had never been found, traces of hemoglobin had been seen, by Schweitzer and others.

It exactly is this 'protection' afforded by the surrounding minerals in the dense bone that contributed to the preservation in the dinosaur soft tissues - as well as the burial under anoxic conditions in sediments that apparently did not allow bacterial action, or later flow of fluids that so often severely alter biological materials. The study of all this, how living materials become fossils, is called 'taphonomy,' and obviously these latest results will have a large impact on this field. One large point in the Schweitzer article is that these types of microstructures have never been found before not because they are rare, but because we had never thought them possible, and so had never even looked.

So the question really comes down to 'exactly what level of detail is preserved in these specimens, and can we expect even better examples?'

We can probably expect to learn a good deal about cellular structure, since the morphology seems to be well preserved, whether with the original biomolecules, or with substituted materials. If original biomolecules are present, or even their degradation products, then a lot can be learned - consider that the presence of certain proteins is in fact a flag for certain DNA sequences and metabolic pathways, so there can be a lot of work done on dino-DNA by inference. And this of course will be very closely watched by folks looking at the phylogeny of the dinosaurs - are modern birds really descendants of the theropods? Were the dinosaurs warm-blooded? Proteins will play a very large part in decyphering those stories.

It turns out I have an inside track on this one, since Mary Schweitzer, the scientist who found the soft tissue in the Tyrannosaurus rex bones, is working with funding from a paleontology program I co-direct. So I picked up the phone and called her - to congratulate her, and also to get an idea of what was ahead, now that the media was paying attention. She was also amazed at the media response, and had been on the telephone pretty much continuously for the whole week.

She is working on another publication, this time looking more closely at bone sub-types and physiological function as well as chemistry - 'nuff said. I had asked her for permission to use a particularly spectacular picture that was not in the Science article for this posting, but it is being used in the new article, so I will leave it for a later date. Although we did not speak about it, I can only assume that future work by Mary and others will explore whether dinosaur fossils have the types of cells associated with bone formation and maintenance (osteoblasts and osteocytes), as well as the cells that break down bone to supply calcium when needed (osteoclasts, for making egg shells, or bones in embryos).

In an interesting aside to all this, I saw that the discovery of well-preserved materials like this is always picked up by short-time creationists (1, 2, 3), as evidence that the Earth cannot be millions of years old. It's an interesting exercise to try and refute this argument, because both sides of Occam's razor are being used: it's a simple explanation (dino bones are only thousands of years old, not millions) and yet you would have to throw away a lot of other work to accept it (all the stratigraphy and geochronology). Here's one refutation. Then again, there are also long-time creationists in the fray...

Of course when I told my nine year old son about the dinosaur marrow, he came right back with: "Did you see the special the other night on Discovery Channel where they had found a real dragon?" After probing a bit, I think he knew the dragon was not real, but the fact that dragons had been mixed with dinosaurs on the TV show made him less apt to believe in the dinosaurs themselves - an interesting effect.

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