Friday, July 30, 2010


The evolution book is due in 61 days..but phyletic gradualism and parapatric speciation and cytochrome B analyses are rattling around in my brain, I need some clarity, and it's time for a break. So, off to dive. In eight hours I'll be a hundred feet down, hovering just over the sea floor in Puget Sound, illuminating the moonscape with a bright light, reathing air from a cylinder. Thank you, Jacques Cousteu and the less-well-known co-inventor of the aqualung, Emile Gagnan. The two are seen above, about to test early SCUBA devices.

Wednesday, July 28, 2010

Random Wonders of Biology

Some assorted notes taken last night. I'm not sure which, if any, will make it into the evolution book, but that doesn't matter; knowing the material conditions how I think about everything else, including things that do make it into the material. There are typos.

The main mode of corals dispersing widely is that of planula (immature coral) larvae attaching to rafts of vegetation floating in the sea. Colonies of corals may traverse 20k-40k km in their lifetime, in the Western hemisphere making several circuits of the tropical and subtropical Pacific basin. From: Helmuth, B., R.R. Veit, R. Holberton (1994). "Long-Distance Dispersal of a Subantarctic Brooding Bivalve (Gaimardia trapesina) by Kelp-Rafting." Marine Biology 120: 421-426.

Coral reef species are amongst the widest-distributed of all organisms due to dispersal of teleplanic larvae in surfae currents and transport of adults on floating rafts. Such rafts include kelp, but also the bouyant skeletons of the reef coral Symphillia agaricia measuring around 50cmx15cmx35cm, weighing about 15kg, wet. In the Great Barrier Reef area, such rafts compose ecosystems composed of filamentous algae, goose barnacles, decapod crustaceans, pearl and reef oysters, gastropods, bryozoans, and foraminaferans. These coral skeletons wash up on beaches, dry out (becoming bouyant) and then are washed to sea again, at which time they begin to accumulate the ecosysem. From: DeVantier, L. M. (1992). "Rafting of Tropical Marine Organisms on Bouyant Coralla." Marine Ecology Progress Series 86: 301-302.

A 630bp section of coral mtDNA was found to be invariant in individuals sampled from 18 populations over 3,000km from Baja California to SE Alaska. In contrast, nuclear DNA of these populations differed as expected across such a range, particularly because these species (Balanophyllia elegans) disperse only small distances, crawling briefly on the sea floor rather than, for example, riding rafts of vegetation as in some other species. The substitution rate for this species, as in others, is calculated to be about .00055 substitutions per site per year, about the same as for plants such as rice and maize. All of this supports slow mtDNA mutation rate in anthozoans; .055% per million years, or 50-100 times slower than in an array of other animals, including sharks and shrimps. From:
Hellberg, M. E. (2006). "No Variation and Low Synonymous Substitution Rates in Coral mtDNA Despite High Nuclear Variation." BMC Evolutionary Biology 6(24).

San Juan Island hermit crabs and the snails providing their shells (*most* hermits must swich out shells they normally use for protection as they grow--some species [Pagurus] occupy shells that support colonial organisms that grow continuously from the lip of the shell) were observed from 1967 to 1970. Over 4,000 snails were tagged in the 200^m study area. About half died each year, and by May 1968 the first crab using a shell was identified. Shells were 20-40mm in length. Crabs appear to select thicker shells. Most months, .5 to 1 shell became avialable per crab (crab population varied from 100-300 in the study area). Physical processes remove available but uninhabited shells. Crabs select good shells; broken or thinner shells are more suceptibel to rpedation, produce fewer eggs, and grow more slowly (p.130). More shells wer available in spring and summer than in winter. Crab population is to a degree limited by shell availability. From: Spight, T. (1977). "Availability and Use of Shells by Intertidal Hermit Crabs." Biology Bulletin 152: 120-133.

African slendter-tailed meerkats (gregarious mongooses of the species Suricata suricatta) were observed for 26 band-years over four breeding seasons. Breeding is seasonal with most births at the rainy season and females coming into new oestrus within three weeks of giving birth. Kitten mortality was largely due to cold and predation, occurring at 3-5 weeks of age. Effective foraging independence is at 12 weeks. Some instances of infanticide were inferred; they seem more to have to do with higher-ranked females killing lower-ranked offsprings' young for ranking reasons, rather than being correlated with rainfall or other environmental variables (p.316). Offspring survival can depend on many factors, including resource (vegetation and arthropod) availability due to rainfall regime, time of female investment in young (which may vary with female health at time of birthing) and climate varaition at time of gestation, lactation and the post-weaning period (p.310). Most demanding time for females is gestation and lactation, and reproduction is scheduled for this. Breeding helpers assist in rearing offspring, and can increase survival of offspring by providing food or protecting the young. In one case, an entire litter died because a tawny eagle (Aquila rapax) prevented foraging adults--and the babysitter, who had gone without food for two days and finally left the den--from returning; the kittens froze to death in the den (p.317). other birds of prey also took young. A Cape cobra (Naja nivea) entered a den once, and was repeatedly mobbed by meerkats; one male chased the snake away after it had eaten two kittens. Overall, 35% of all kittens died at den in the first 30 days after first emergence. Cold is a major killer, and kittens huddle in the den for warmth. Over 20 spp of mammals huddle for warmth (p320). When kittens were separated from babysitters, they call until they are rescued. Flooding can kill: one babysitter single-handedly moved an entire litter from a flooding den to a dry den, over 50m, while the rest of the band were away, foraging. In the first foraging behavior, when kittens leave the den at about 4 weeks, until about 3 to 6 months, predation mortality was high, but dropped significantly after this; babysitters commonly take young into the den when predators are around. Breeding was scheduled so that birth--often simultaneous among the entire band--occurs when resources are best for the period of lactation, not the period of mating. Despite work of helpers, there was no statistical effect showing more survival with more helping (p.323). It may be that helpers actually improve fitness of reproductive-age meerkats and the young-but-not-juvenile. From: Doolan, S. P., D. W. McDonald (1997). "Breeding and Juvenile Survival Among Slender-Tailed Meerkats (Suricata suricatta) in the South-Western Kalahari: Ecological and Social Influences." Journal of Zoology 242: 309-327.

Tadpoles can respond to habitat dessication (pool drying) by accelerated metamorphosis as well as cannibalism. From: Newman, R. A. (1992). "Adaptive Plasticity in Amphibian Metamorphosis." Biosciences 42: 671-678.

Roughly 2m-diameter rafts of the kelp Macrocytis pyrifera observed in the Southern Ocean between South America and South Georgia island are small ecosystems composed of 100-200 kelp plants and, attached to them, 'colonies' of the mullosc Gaimardia trapesina; not only are adults of the mullosc found on the kelp, but young are as well, indicating that kelp rafts can serve as platforms sustaining mullosc populations on long-distance voyages. up to thousands of miles in distance.

Steller sea lions (Eumetopias jubatus) observed in Alaska's Prince William Sound feed exclusively on herring (Clupea pallasi) at night; they do not eat the much more abundant walleye pollock, which are roughly five times more abundant in these waters; in winter there is particular food source stress, but even then sea lions do not eat the pollock. However, pollock live at 100m or so depth (day and night), whereas herring schools occur closer to 15-35m deep at night. Groups of up to 50 stellers were observed swimming abreast, apparently herding the herring. Stellers can dive to 250m, but it is apparenly easier for them to herd the shallower-occurring herring than dive for the pollock. From: Thomas, G. L., and R.E. Thorne (2001). "Night-Time Predation by Steller Sea Lions." Nature 411: 1013.

Viruses are the most abundant and genetically diverse 'life forms' in the ocean; typically 10^7 viruses / ml, fewer with depth and distance from shore. They are most common where bacteria and chlorophyll are most abundant. Oceans contain perhaps 4x10^40 viruses; end-to-end they would reach 10m light years and they weigh = to 75m blue whales. These have genome sizes from 997bp to 1.1mbp (p.357) and are genetically extremely diverse. At the same time, some sequences are nearly identical at the nucleotide level in environments as distant as the Southern Ocean, Antarctica, and the Gulf of Mexico. New analysis shows that HGT has occurred between cyanobacteria and their viruses (p.358) such that "viruses capture genes of host origin and exhange them among viral progeny". On a daily basis, oceanic viruses kill 20-40% of all marine bacteria, and contribute to microbial mortality at a level similar to that of grazing by zooplankton. From Suttle, C. A. (2005). "Viruses in the Sea." Nature 437: 356-361.

Romanian tadpoles were observed to cannibalize conspecifics during a period when their pond was drying and crowded with tadpoles. This is an instance verifying other such instances of adaptive behavioral placticity as noted in Newman (1992). Kovacs, E. H. a. I. S. (2009). From: "Cannibalistic Behaviour of Epidalea (Bufo) viridis Tadpoles in and Urban Breeding Habitat." North-Western Journal of Zoology 5(1): 206-208.

Monday, July 26, 2010


I was up at 4am, thinking of snow blowing across the surface of the Vatnajokull. I thought about the north face of Dead Man Peak, where Chiu and I had to rappel off a single piton in a storm one winter; that piton must still be there in the rock. On the sea floor thirty miles off Panama is a favorite rope of mine, swept off the bow of the sailing raft one night. I imagine the piton taking on a spot of rust; but no, it's chrome-molybdenum, it will survive a very long time and since nobody climbs that face I doubt the piton will ever be found. The rope is synthetic and I can only wonder how long it will skid and heave there on the sea floor with the occasional storm up above.

I though of flying my wing; I could feel it up above me, and I thought of how I will look up at it and then down past my legs again at the frozen surface of the Chukchi Sea. I'll turn easily to the right, towards land, and start setting up my landing. My flights will be short, the cliff is only a thousand feet high, so I'll only be up a few minutes at a time unless I have a bit of wind. I envisioned the terrain and the safe ways up the slope and the ones I'd have to avoid because of avalanche danger.

I thought about how I'm glad I wrapped up climbing when I did. The culture had changed and suddenly a lot more people were climbing; there were indoor gyms where people climbed plastic holds screwed into plywood. People were talking about 'play', which I never understood because I'd never thought of climbing as fun; I wanted a battle every time I went out. There was a lot of hugging going on, which was really disconcerting. I was always satisfied with shaking my partner's hand, if that, but now there was all this hugging and talk of a 'sense of community'. On a summit my partner and I usually passed the water bottle back and forth, looked at the sky, looked at our watches, and started working out the descent plan.

I didn't understand all the externalization; everyone wanted to talk about climbing. The word 'therapy' was in wide circulation. It made me want to pull my own teeth out with pliers.

Why did everyone want to talk so much?

My mind went back to that beautiful piton in the rock, and snow blowing across the ice cap.

Monday, July 19, 2010

The Temple of Nature

By Erasmus Darwin, grandfather of Charles, in his 1802 poem The Temple of Nature:

"Organic life beneath the shoreless waves
Was born and nurs'd in ocean's pearly caves;
First forms minute, unseen by spheric glass,
Move on the mud, or pierce the watery mass;
These, as successive generations bloom,
New powers acquire and larger limbs assume;
Whence countless groups of vegetation spring,
And breathing realms of fin and feet and wing."

Pressure Test Setback

Big setback in a recent pressure test. While there is only one small leak, now, and I could patch it up, I've crossed a line; I've done too many 'last little patches'. Too many pieces in the puzzle, and each is one that could fail, and failure of the pressure garment would lead to rapid decompression sickness and unconsciousness, followed of course by a trip across the Styx!

So I will completely dismantle and rebuild the helmet-pressure garment interface. That will take at least a month.

In better news, I took the wing out on Sunday, practicing a few launches and landings in a variable wind. Maintaining proficiency and automatically reacting to the wing's movements is critically important. Training sessions like this are like buying insurance!

Thursday, July 15, 2010

Wonders of the Deep

Mind-bending and beautiful video stills from exploration of the deep sea. Most of the Earth is covered with water, of course (Paul Watson thinks we should call this planet Ocean, which isn't a bad idea), and you know as well as I do, and everyone else does, because the Cousteau family have been telling us for a generation and a half, that we don't know the first thing about it!

Below, a breathless--is there any other way to be????--presentation by Bob Ballard. My favorite part comes at the end, where he talks about getting children interested (direct link in case the YouTube viewer below doesn't work:

“This is a young lady not watching a football game, not watching a basket ball game, watching exploration live from thousands of miles away, and it’s just dawning on her what she’s seeing, and when you get a jaw drop you can inform, you can put so much information into that mind, it’s in full reset mode.”


Oh! And hot off the press, from Australian scientists, a close-up photo, below of deep-sea squid skin! Has anything in your life experience prepared you for that image? I am absolutely astounded, I want to delve into the world of pigmentation, fling open the doors to a hundred special topics in dermal cells and deep-sea life. How can people watch football when things like this exist, completely new to human eyes????

Wednesday, July 14, 2010

Base Pairs

The human genome -- as well as the genomes of many species (including Neanderthals!) -- can now be browsed online. I looked for the FOXP2 gene, related to some language production and comprehension disorders in humans, and found it (image above shows it on the lower part of chromosome 7). It is mind-boggling to think that this is possible; when I was an undergraduate the study of human evolution was 99% fossils and 1% genetic: today it's 50/50. In my browsing I searched for and found that FOXP2 is 2,594 base-pairs long; I copied the list, pasted it into Word, deleted the line counters, did a character count, and wow...2,594. Below are the base pair arrangements for FOXP2, followed by a summary. Note that genes are simply arrangements of various molecules; they direct the building of the twenty proteins that make up most life forms. There are four kinds of bases; adenine (a), guanine (g), cytosine (c) and thymine (t).

LOCUS AY144615 2594 bp mRNA linear PRI 02-NOV-2002
DEFINITION Homo sapiens brain forkhead/winged helix transcription factor FOXP2
isoform mRNA, complete cds; alternatively spliced.
VERSION AY144615.1 GI:24496248
SOURCE Homo sapiens (human)
ORGANISM Homo sapiens
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
Catarrhini; Hominidae; Homo.
REFERENCE 1 (bases 1 to 2594)
AUTHORS Guo,J.H., Chen,L. and Yu,L.
TITLE Direct Submission
JOURNAL Submitted (27-AUG-2002) School of Life Sciences, Fudan University,
Institute of Genetics, Handan RD, 220, Shanghai 200433, China
FEATURES Location/Qualifiers
source 1..2594
/organism="Homo sapiens"
CDS 370..2592
/note="alternatively spliced"
/product="forkhead/winged helix transcription factor FOXP2


gcttgaacct tgtcacccct cacgtgcaca ccaaagacat accctagtga ttaaatgctg
atttgtgtac gatgtccacg gacgccaaaa caatcacaga gctgcttgat tgttttaatt
atccagcaca aaatgccatc agtctgggac gtgatcgggc agaggtgtac tcacagtagt
gtaaatactg ctgtaaatag tgtctgatgg tggcttgaca gtgagctagc ttctgagttt
tcccttcttt ttatactgtt ttctgtgctg gcttttttga atcttcctaa tttttcatct
ctttaacaaa ctcctatgaa gttgaaaccg ggaagtttgc tctaacattt ccagagaagg
tattaagtca tgatgcagga atctgcgaca gagacaataa gcaacagttc aatgaatcaa
aatggaatga gcactctaag cagccaatta gatgctggca gcagagatgg aagatcaagt
ggtgacacca gctctgaagt aagcacagta gaactgctac atctgcaaca acagcaggct
ctccaggcag caagacaact tcttttacag cagcaaacaa gtggattgaa atctcctaag
agcagtgata aacagagacc actgcaggaa ttgcttccag aaacaaaatt atgtatctgt
ggccactctt ctggtgatgg gcatcctcac aacacatttg cagtgcctgt gtcagtggcc
atgatgactc cccaggtgat cacccctcag caaatgcagc agatccttca gcaacaagtc
ctgtctcctc agcagctaca agcccttctc caacaacagc aggctgtcat gctgcagcag
caacaactac aagagtttta caagaaacag caagagcagt tacatcttca gcttttgcag
cagcagcagc aacagcagca gcagcaacaa cagcagcaac aacagcagca gcaacaacaa
caacaacagc agcaacaaca gcagcagcag cagcaacagc agcagcagca gcaacagcat
cctggaaagc aagcgaaaga gcagcagcag cagcagcagc agcaacagca attggcagcc
cagcagcttg tcttccagca gcagcttctc cagatgcaac aactccagca gcagcagcat
ctgctcagcc ttcagcgtca gggactcatc tccattccac ctggccaggc agcacttcct
gtccaatcgc tgcctcaagc tggcttaagt cctgctgaga ttcagcagtt atggaaagaa
gtgactggag ttcacagtat ggaagacaat ggcattaaac atggagggct agacctcact
actaacaatt cctcctcgac tacctcctcc aacacttcca aagcatcacc accaataact
catcattcca tagtgaatgg acagtcttca gttctaagtg caagacgaga cagctcgtca
catgaggaga ctggggcctc tcacactctc tatggccatg gagtttgcaa atggccaggc
tgtgaaagca tttgtgaaga ttttggacag tttttaaagc accttaacaa tgaacacgca
ttggatgacc gaagcactgc tcagtgtcga gtgcaaatgc aggtggtgca acagttagaa
atacagcttt ctaaagaacg cgaacgtctt caagcaatga tgacccactt gcacatgcga
ccctcagagc ccaaaccatc tcccaaacct ctaaatctgg tgtctagtgt caccatgtcg
aagaatatgt tggagacatc cccacagagc ttacctcaaa cccctaccac accaacggcc
ccagtcaccc cgattaccca gggaccctca gtaatcaccc cagccagtgt gcccaatgtg
ggagccatac gaaggcgaca ttcagacaaa tacaacattc ccatgtcatc agaaattgcc
ccaaactatg aattttataa aaatgcagat gtcagacctc catttactta tgcaactctc
ataaggcagg ctatcatgga gtcatctgac aggcagttaa cacttaatga aatttacagc
tggtttacac ggacatttgc ttacttcagg cgtaatgcag caacttggaa gaatgcagta
cgtcataatc ttagcctgca caagtgtttt gttcgagtag aaaatgttaa aggagcagta
tggactgtgg atgaagtaga ataccagaag cgaaggtcac aaaagataac aggaagtcca
accttagtaa aaaatatacc taccagttta ggctatggag cagctcttaa tgccagtttg
caggctgcct tggcagagag cagtttacct ttgctaagta atcctggact gataaataat
gcatccagtg gcctactgca ggccgtccac gaagacctca atggttctct ggatcacatt
gacagcaatg gaaacagtag tccgggctgc tcacctcagc cgcacataca ttcaatccac
gtcaaggaag agccagtgat tgcagaggat gaagactgcc caatgtcctt agtgacaaca
gctaatcaca gtccagaatt agaagacgac agagagattg aagaagagcc tttatctgaa
gatctggaat gaga


"This gene encodes a member of the forkhead/winged-helix (FOX) family of transcription factors. It is expressed in fetal and adult brain as well as in several other organs such as the lung and gut. The protein product contains a FOX DNA-binding domain and a large polyglutamine tract and is an evolutionarily conserved transcription factor, which may bind directly to approximately 300 to 400 gene promoters in the human genome to regulate the expression of a variety of genes. This gene is required for proper development of speech and language regions of the brain during embryogenesis, and may be involved in a variety of biological pathways and cascades that may ultimately influence language development. Mutations in this gene cause speech-language disorder 1 (SPCH1), also known as autosomal dominant speech and language disorder with orofacial dyspraxia. Multiple alternative transcripts encoding different isoforms have been identified in this gene."

Tuesday, July 13, 2010

A Still More Glorious Dawn Awaits

A recently-developed video: I think Carl Sagan would have approved of it:

Monday, July 12, 2010

Clear the Decks

Time to mentally clear the decks for two book projects, each due in about 90 days. The bulk of the research is done--the results of hundreds of research articles and dozens of books read in the last year, ten years of teaching and 15 years of postgraduate research and education all combining and recombining and making both old and new associations in my mind--and now the task is composing the sentences, paragraphs, pages, and chapters. I have detailed outlines and hundreds of references; now for the tone.

"Life is a constant matter of experimental centrifugal pressure outward against its environment. During the course of my life I have encountered a squirrel on a subway platform, pigeons on my book cases, and a flying squirrel who had set up housekeeping in the drawer of a kitchen cabinet. Their acts were totally exploratory."

--Loren Eisley, "Man and Novelty" p.76 in "Time and Stratigraphy in the Evolution of Man", 1967, Publication 1469 of the National Academy of Sciences, Washington, D.C.

Sunday, July 11, 2010

Pressurization Hose

A day off from field school, spent entirely on the suit project. I rebuilt (tenth time now) the oral-nasal mask (I think it's almost right now) and began work on the suit pressurization hose connection hardware. Above, working out the best place to install it; actually the best place is a few centimeters lower, to avoid complication with other systems, and to allow ease of use not when standing, but sitting. While many balloonists fly standing, I will have to fly in the seated position, for a number of reasons.

Wednesday, July 7, 2010


Above, field school student Sarah Taylor is instructed by guest instructor Kendall McDonald in the use of the cesium magnetometer, an instrument that detects very subtle variations in the Earth's magnetic field--variations that can help us find traces of ancient human activity on a landscape.