Sunday, December 16, 2007

El Cerrito Hillside Natural Area

American Coot
Sharp-shinned Hawk
Southern Alligator Lizard (Elgaria multicarinata)
Northern Mockingbird

Iris and I went for a very nice walk this morning. Iris found a couple of pellets (she thinks they are from an owl, I suspect they were regurgitated by a hawk) which contained the full skeleton of a pocket gopher and quite a lot of fur. We also found the partial skeleton, including the skull, of a dear. The highlight was when we came around a corner and a Red-Tailed Hawk Came running out from the bushes. It took off but circled low over us such that it was clear it did not want to leave the spot. I checked the bush it had come out from under and found a freshly killed and partly dismembered American Coot. Continuing a little way along the path we came to a swampy area and a free flowing creek that could easily be coot habitat. We left the coot for the hawk to finish off.
Iris is getting good at using binoculars, and we spent a while sitting and looking at Scrub-Jays, Spotted Towhees and hummingbirds to give her practice. Found a small (~10cm) Southern Alligator Lizard under a chunk of wood in a field. When I let it go it ran down a gopher hole. On our way back to the house, we passed a Northern Mockingbird on the edge of the park and I heard a Sharp-shinned Hawk calling.

Friday, December 14, 2007

Thursday, December 13, 2007

More on Europa's Ocean

Let's start with a simple calculation. The mean radius of Europa has been estimated at 1,560.8 km. The mean depth of the ocean has been estimated at 100km. Earth's ocean by comparison has a mean depth of 4 km, but covers a much bigger sphere. How do the volumes of these two bodies of water compare?

Volume of Europa=(4/3)*3.14*(1,560.8^3)=1.59×10^10
Volume of Europa excluding outer 100KM of water= (4/3)*3.14*(1,460.8^3)= 1.30×10^10

Volume of Europa's water=1.6×10^10- 1.3×10^10= roughly 2.8 billion cubic kilometers of water.

The volume of earth's oceans is estimated at 1.3 billion cubic kilometers.

So Europa hypothetically has about twice as much liquid water by volume as earth. So a big ocean.

Now let's think for a minute about that ocean. 100,000 meters deep. The gravity on Europa is a gentle .134g, so I'm guessing the water pressure 100K down is similar to that on earth 13,000 meters down. Deeper than the earth's ocean actually gets, but comparable to the pressure at the bottom of the Marianas Trench, something over 1000 atmospheres.

The bottom is important when thinking about life, because unlike earth, where most of the life lives on the surface, where the light is, on Europa the proposed energy source is hydrothermal vents, on the bottom. There are lots of ramifications to this. One, as I discussed before, hydrothermal vents are unlikely to produce enough usable energy to keep a whole ocean twice the size of Earth's own filled with life. Life will live where the energy is, as close to the vents as can be tolerated.
Second, unlike on Earth where there is serious stratification of the oceans because the top is warm and the bottom is cold, on Europa, the heat comes from below. Hot water rises, and cold water sinks. If you heat a pot of water from below, you quickly get powerful convection currents roiling the waters. Europa likely has powerful upwellings, downwellings, sidewellings and so on. Then, once you have all that motion on a rotating body, you get the Coriolis effect which leads to such things as cyclones, whirlpools and gyres. Add to that tides from interactions with Jupiter and the other moons, and all that water isn't just sitting still down there under the ice. It is racing too and fro and hither and yon. Which makes possible another type of energy collection on Europa; windmills (or hydro electric, or something such). Anchor yourself to ground or ice, let the water swirl by you and allow it to turn some part of you. Use that energy to fix carbon (or something) and you are an autotroph. Then other Europans can come along and eat you, and you are supporting a community, without relying on chemicals from the vents.

I admit it is a bit far fetched, but it is the only way I can think of to support life away from the hydrothermal vents in Europa's ocean. Thoughts?

Wednesday, December 12, 2007

Tuesday, December 11, 2007

El Cerrito Hillside Natural Area

Hermit Thrush
White-crowned Sparrow
Golden-crowned Sparrow
Spotted Towhee
House Finch

Monday, December 10, 2007

Musings on the Oceans of Europa

In the sequels to Arthur C. Clarke's "2001, A Space Odyssey" humans discover, and are told to not interfere with, life forms on Europa, the watery moon of Jupiter. Europa is thought to have some tens of kilometer of water ice over (potentially) 100 kilometer of liquid water, with a rocky core that is kept at least partially molten by the stretching and straining caused by the tidal pull of nearby Jupiter, around which it zips every 3.55 days.

It is thought quite possible that the ocean bottom of Europa, as the ocean bottom of earth, could have hydrothermal vents, and as on earth, these vents could potentially support life. On earth, ecosystems around the vents rely on chemosythesis (the production of energy bearing organic compounds by the oxidation of high energy chemicals, in this case hydrogen sulfide) rather than photosynthesis.

A wide range of methods have been proposed for testing the hypothesis that their are lifeforms in the waters of Europa, from biological testing of the waters to robotic submarines to a search for freeze dried lifeforms orbiting near Europa, thrown off into space by collisions with other bodies.

All of these seem like long shots to me, even assuming there is life there to find. Hydrothermal vent lifeforms on earth do not venture far from the vents. The concentration of hydrogen sulfide drops off rapidly as one moves away from the vents. It is likely that a Europan ecosystem based around hydrothermal vents would be very localized, soaking up every scrap of whatever the chemical was that fueled their physiology. Just as there is very little sunlight reaching the dirt in a mature forest, very little of the chemical energy source would likely escape beyond the immediate surroundings of the vents. The autotrophs would be in tight knots around each vent, and the heterotrophs would tend to follow. Unlike our oceans, in which the entire surface is covered with a sheen of plankton, the top of Europa's waters would likely be dead.

This line of thinking points to two other proposed methods of looking for life. One is to map out beforehand where the hydrothermal vents are, and send a probe directly there. This may be doable, if we can use magnetic and gravitational data to map the plates and faults of Europa's rocky interior's crust, and predict the mostly likely spots.

Perhaps simpler as a first step would be to look for the breakdown products of chemosynthesis in the waters. Just as the earliest sign distant aliens would have had of life on earth was the buildup of excessive oxygen in our atmosphere as a byproduct of photosynthesis, perhaps the easiest way to tell if there are Europans is to look for their waste gases.
This of course, is made more difficult that we have no idea what chemicals they would use as an energy source, or how they would process it. We would basically be looking for any sort of surprising chemical imbalance, with the assumption that we can thermodynamically predict what a balance should look like.

Of course bringing back a Europan in a jar would be much more exciting than saying, " we have a significant deviation from our predicted chemical balance." But checking the chemical balance is probably a lot more doable as a first step.

Writers' Strike

It seems to me that economists should be able to quantify the value of the work of a profession to society based on the larger societal impacts of that group temporarily ceasing their work. We'll call this variable V(s). In France, when the transit workers go on strike the nation is temporarily paralyzed. High V(s). If the New York City police department went on strike, serious trouble. They have a high V(s). I hear that the Screen Writer's Guild has been on strike for a while now. Is anyone outside of LA missing them? V(s)=?

Sunday, December 09, 2007

More Birds for the Hillside Natural Area

Iris and I went out for a walk in the EC Hillside Natural Area from 9-9:30AM. I forgot to bring my binoculars, so was mostly birding by ear. I can add the following birds to the list for the park:

Red-shafted Flicker
Red-breasted Sap-Sucker
American Robin
Black Towhee
Bush Tit
Mourning Dove

Friday, December 07, 2007

El Cerrito Hillside Natural Area

I've decided to compile a list of vertebrates occurring in El Cerrito Hillside Natural Area. More specifically, in the smaller northern section of the park that is directly behind my house.

View Larger Map

I may expand to the whole Natural Area once my mobility increases.

This afternoon, I took a short walk in the park from 1:15-1:40.

I saw or heard the following birds:
Western Scrub-Jay
Stellar's Jay
American Crow
Northern Raven
Yellow Rumped Warblers
Bewick's Wren
Chestnut-backed CHickadee
House Sparrow
Ruby-Crowned Kinglet
Anna's Hummingbird
Turkey Vulture
Red Tailed Hawk

(Added 12/9/07)
Red-shafted Flicker
Red-breasted Sap-Sucker
American Robin
Black Towhee
Bush Tit
Mourning Dove

(Added 12/11/07)
Hermit Thrush
White-crowned Sparrow
Golden-crowned Sparrow
Spotted Towhee
House Finch

(Added 12/12/07)
Red-breasted Nuthatch
Downy Woodpecker

(Added 12/14)
Dark-eyed Junco
American Goldfinch

(Added 12/16)
American Coot
Sharp-shinned Hawk
Northern Mockingbird

I saw, or sign of the following mammals:
Eastern Fox Squirrel (Sciurus niger)
Mule Dear (Odocoileus hemionus)
Voles (Microtus californicus? runways and burrows)
Pocket Gophers (burrows)
Fox (Grey fox? scat)

I didn't see any herps or fish.
(Added 12/16)
Southern Alligator Lizard (Elgaria multicarinata)

Nothing unusual so far. I will add more as I see it.

SAD, Photoinducability, Skeleton Photoperiods, and the Winter Festivals of Lights.

Seasonal Affective Disorder, generally known as SAD, or winter depression, is the most noticeable expression in humans of photoinducability, the changing of physiology or behavior by day length (or more particularly, photoperiod, the number of hours of light in a day). Sufferers of SAD, which have occasionally included myself, are generally in good mental health much of the year, but if photoperiod gets too short, they find themselves depressed. When photoperiod increases again, the depression recedes. In Alaska, where days can get very short for extended periods, about a tenth of the population suffers from clinically significant SAD.

That much is general knowledge. It is also widely known that many other species use photoperiod to time many aspects of the biology, including breeding, migration, food choice and hibernation. If the days are getting long, it is time for breeding, or whatever else one does in the spring. If they are getting very short, it is time for winter activities, such as sleeping in one's hole. Photoperiod, and the change therein, is a highly predictable indicator of what day of the year it is at any particular location.

This week, in a lecture by Dr. George Bentley, I learned a bit about how animals measure photoperiod, and this changed my thinking about SAD and the winter festival of lights that appears as so many different holidays in so many different religions.

One can imagine various methods an animal's brain could use to figure out how long the day is. An animal could have a solar powered kitchen timer in its brain. Sun comes up, timer starts. Sun goes down, timer stops. Where the timer stops is how long the day was. But there are problems with this model. For example, what if an animal goes in its burrow for much of a day? The timer would stop running. Another model, and one that seems to be what many animals do, is to have a timer that also started running at dawn, but doesn't stop every time the animal is in the dark. This timer measures the distance between dawn, the first light the animal sees that day, and dusk, or the last bright light the animals sees that day.

The ramifications of this are not immediately obvious until you hear how can be used. Animals in the lab are often kept in specific light:dark schedules (12:12 or 14:10) to see what happens to their physiology or behavior under different light regimes. In many species, when photoperiod is increased, the animal responds as though it is spring, building bigger gonads and such. But because the animal's physiology is not actually measuring the number of hours of light, but the number of hours between first light and last light, one can induce the same effect using what is called a skeleton photoperiod. A one second flash of light at 5AM and another at 7PM, with total darkness the rest of the day, is 14 hours between first light and last light. Move hamsters into these conditions, and their gonads start growing, as thought they had had 14 continuous hours of light.

After the lecture, I asked Dr. Bentley if anyone had tried a skeleton photoperiod on human volunteers, to see if it would be effective in combating SAD and similar conditions. If the human brain could be tricked into thinking the days were long by a properly timed, but short and convenient, blast of light late in the day, this would be both extremely useful and biologically fascinating. He said that while SAD was often treated with light therapy, he was not aware of any study looking at whether a short exposure to light carefully timed late in the day could have any effect. Then someone walked by, in the hallway and said to someone else, "Happy Hanukkah, are you going to light a candle tonight?"

I think you see where I am going with this. Hanukkah candles are traditionally lit an hour or two after sundown, when it has become truly dark out. In many parts of the world, Jerusalem say, this equates to 12 to 13 hours after dawn. Celebrants are directed to meditate on the candles, and the joy of Hannukah. The traditional candles burn out after about a half hour.

Festivals this time of year often involve fixating on lights in dark evenings. Hinduism, Sikhism, Jainism, Christianity, the Persians, the Chinese, the old Germanic and Norse tribes and so on all had comparable winter festivals of light. Of course it has long been thought that the winter holidays are a great way to fight the winter "blahs" with light. Cheerful light. Evening light. Photoinducing, skeleton photoperiodic light?

In clinical trials of current treatments for SAD, an hour or so of very bright light at almost any time of day has a significant ameliorative effect, among those who stick with it. But many patients drop out, citing the inconvenience and boredom of sitting and staring toward (but not directly at) a big lamp for an hour a day. I can't help but wonder if the festivals of lights point to a better way, not only making the exposure to light a celebration rather than a chore, but also giving guidance as to what time of day to observe those lights and fixate on them. Do it in the early evening, when dusk would be in the summer, and maybe, just maybe, you make some part of your brain think it is summer.

Light regime change begins at home.

Tuesday, October 23, 2007

Ecological causes and effects of SoCal fires: Initial thoughts

There are numerous wildfires currently blackening southern California. The short term response has to be to the fire itself. Save the people, save the pets, save the homes and the businesses. But what should be the response when the fires are out? Ruibiuld everything exactly as is was? That is the most likely outcome. After a disaster, people want to rebuild, regardless of how likely it is that disaster will happen again. But how likely is it these fires will return? What ecological factors played into this disaster, what ecological effects can be expected and what lessons should we draw from all of this?

I feel it is important to raise these issues before everyones attention moves on and we fail to learn from previous mistakes. I'll appreciate your input and comments.

With no further ado:

Ecological Causes:

1. Obviously the big'un is the Santa Ana Wind, the hot dry wind that blow-dries out of the Great Basin and over southern California every year. The topography and climate of coastal southern California, combined with the Santa Anas make for fires pretty much every year. It is being reported that the Santa Ana's are stronger and more persistent than usual this year. It is not yet known, so far as I know, if the Santa Ana's are expected to be stronger every year now that the Great Basin's climate is turning much hotter and drier.

2. California has had an unusually dry year this year. Unusual meaning "in comparison to the last 150 years." This year may turn out to be unusually wet as compared to the next 150 years, because, as mentioned, the climate of the southwest is drying.

3. A lot of these areas have many times the natural fuel-load. The last 150 years are important, because that is how long we have been suppressing fires in southern California. This unusually wet period allowed for a lot of biomass to build up, and not burn off, because we would not let it burn.

The natural time between fires in most of these areas is a few decades. Fires would pass through, burn off much of the fuels without destroying the local ecology because in most cases, the previous fire was recent enough to keep this fire from getting too hot. By putting out every fire we could for so long, we allowed the fuel load to build up to the point that the fires now get incredibly hot and spread incredibly fast. Some of the areas currently burning have burned recently, but the mean time since the last fire is much higher than what is natural.

4. We tend to build our settlements and structures without regard to the fact that we are building in a fire maintained ecology, and another fire will come. By failing to take that into account, we make things that much harder for firefighters and those who need to evacuate. It is like building in a floodplain and expecting your house to not get washed away every once in a while.

5. The climate is changing and the southwest is becoming more of a desert. When wet areas dry out, the vegetation eventually burns off.

Ecological Effects:

1. California is a world center of biodiversity, and quite a few of our species are found nowhere else. Many of the native plants and animals are already endangered by habitat loss, invasive species, pollution and climate change. Most of our natural areas are fragmented by human edifices. The native populations could deal with the comparatively mild natural wildfires of the past. Smaller, more fragmented and already declining native species with small ranges may well have trouble keeping a foothold in areas burning as hot and wide as the current fires.

I have a colleague who studies a species of native mouse found primarily in San Diego County. This year he could find almost none of his mice because their habitat is turning to desert. He did find them in a few places. In the last two days some of those places have gone up in smoke.

2. Fuel loads in the areas currently burning will be reduced, which is both good and bad. Good in that future fires will have less fuel. Bad in that all that fuel load was sequestered carbon, which is now in the atmosphere, and because the drier southwest won't have as much vegetation, that carbon is not going to be taken back out by the same land. My guess is, without having seen any numbers, that total carbon output from these fires will actually be quite minuscule on a global scale, and we are better off without all that tinder lying around.

3. If the rains in SoCal do get started in a month or two, we can expect some serious erosion from all the areas that have been stripped of their vegetation.

Lessons, not just for SoCal, but for the country:

1. Don't just let fuel build up until it explodes. Areas like this need to have some plan for how to get rid of fuel. My personal preference is controlled burns at times of year when the fire is easier to keep in hand. We can't keep pretending we can keep fire based ecologies from burning forever.

2. Notice that climate change is a serious problem now. Stop making the problem worse.

3. Take fire risk into consideration when deciding where and when to build. Developers should be legally responsible for planning their developments such that they are not putting residents and firefighters at risk. Planners should disallow building in areas that cannot be defended from fires.

Monday, October 22, 2007

.01% of California burned in past two days

Area of California is= 160,000 mi²

Acres per square mile= 640

Area of California in acres= 102,400,000

Acres burned in California in past two days= 100,665 (according to Bloomberg)

Portion of CA burned in past two days= 100,665/102,400,000= .0001= 0.01%

Sunday, October 14, 2007


This is a really cool invention my friend Brent brought to my attention. It would be incredibly useful in places like PNG where solar doesn't work because it is always raining.

Friday, October 12, 2007

Informed Consent Form

There are no known risks or discomforts associated with participation, other than the possibility of annoyance that it takes longer to read the informed consent form than to complete the questionnaire.

Thursday, October 11, 2007

Summary of reproductive biology, as conveyed by my four year old neighbor:

1. "I was in my mommy's belly"
2. "You was in your mommy's belly."
3. "Everything was in mommy's belly."
4. "Except fish. They don't do it."
5. "Then you crawl, crawl crawl down to, um, butt? Come out!"
6. "That cool, right?"

Tuesday, October 09, 2007

Depth vs. Depth

One of the questions on the exam I am grading asks the students to pick a physical characteristic of ocean water (pressure, density etc.) and draw a plot of that against depth into the ocean, to show how the measurement changes with depth.

One of the students decided to draw a graph of how depth changes with depth. This would technically be a good answer, except that when she plotted depth against depth she got a parabolic curve.

Friday, October 05, 2007

Sensory Bias

Last week I was trying to describe to my animal behavior students what sensory bias was. I told them that particular species, because of the particulars of their sensory organs and neurology, have a much stronger neurological response to certain shapes, patterns or colors than a member of most other species would. I told them that the sensory biases of a species affect the evolution of traits in potential prey, predators, competitors and mates.

I think this makes a fine example.

putting up with neighbors

Yesterday my friend Akaba gave a talk about her work with various rodents on the neural basis of sociality (and variation therein.) One of the interesting points that came out in the conversation that followed it that many of the researchers there had the impression that in the groups we study, the more social species are more docile when handled. I think this is cool, and makes a lot of sense. A big part of being social is just not getting pissed off too easily, or at least not responding disproportionately when you do get pissed off.

I hope she follows up on this.

Wednesday, October 03, 2007

Ladybug larva

I've mentioned in the past the usefulness of ladybug larvae in controlling aphids. A few people asked me to take a picture of one, so they would know it if they saw it. Here it is.

Tuesday, October 02, 2007

Glossary of Science

The following is the glossary I put together for my students from my lecture notes for the first section of Animal Behavior.

Adaptive- conferring a positive fitness relative to competing traits, in the current environment

Altruistic- costly to the individual behaving but beneficial to some other individual or group

Behavior- What an animal does, generally in response to an external or internal stimulus.

Behavioral Ecology- The study of behavior in relation to its adaptive value in environmental context.

Cryptic Female Choice- Female behavior, morphology, and/or physiology influencing which of the males a female has mated with end up being the genetic father of the female's eventual offspring.

Direct Fitness: The number of descendant individuals produced by an individual, times the degree of relatedness of those descendants to that individual.

Evolution: Change in the genetic makeup of a population over time.

Fitness- reproductive success

'Good Genes' Polygyny- System in which females choose among mates based on an honest signal of male quality, rather than for any resources, care or territory the male has to offer.

Hamilton's equation: rB-C>0 where r is the relatedness between the individual who acts and the individual who benefits from that action, B is the benefit in direct fitness to the recipient and C is the cost in direct fitness to the actor.

Heritable- more similar between related individuals than between unrelated individuals.

Inclusive Fitness: Direct fitness plus indirect fitness

Indirect Fitness: The number of non-descendant relatives produced by an individual, times the degree of relatedness of those relatives to that individual.

Kin Recognition: The ability to, or act of, classifying some individuals as related to oneself, and others as unrelated to oneself.

Kin Selection- non-random differential reproductive success arising from heritable variability in traits which affect the direct fitness of an individual's kin, rather than of the individual itself.

Lek Polygyny- Mating system in which males gather to display for females and females examine the males and mate with those which are most impressive.

Levels of analysis- The different ways we can attempt to explain the same behavior, including its adaptive value, it phylogeneitc background, the organismal mechanisms underlying it and the developmental and genetic factors leading to it.

Mating Strategy- everything an individual does to determine when how and with whom it mates, and to ensure that mating produces offspring.

Mating System- a description of how the species tends to mate, and which males mate with wich females under what circumstances. Female Defense Polygyny, Polyandry and Monogamy are examples of mating systems.

Monogamy: In biology, one male mating with one female. Monogamy can be social (the pair act as though they only mate with each other) and/or genetic (the pair actually parent all of each other's offspring)

Polyandry- Mating system in which one female mates with multiple males.

Polygamy- mating system in which an individual mates with multiple individuals of the opposite sex. Includes polyandry and polygyny.

Polygyny- mating system in which one male mates with multiple females.

r- stands for relatedness. Defined as the portion of two individual's genotypes which are identical because of common ancestry.

Reproductive Strategy- anything and everything an individual does that functions to allow it to reproduce. This includes its production of gametes, how and when and with whom it mates, parental care and so on.

Selection- non-random differential reproductive success arising from heritable variability

Selective Pressure- environmental factor(s) that determine adaptive value of different traits

Sexual Selection- non-random differential reproductive success arising from heritable variability in traits directly affecting sexual reproduction

Sociality- the tendency to live in groups of conspecifics

Sperm competition- "competition between sperm of two or more males for the fertilization of an ova" (Parker 1970).

Thursday, September 27, 2007

Germ-line chimerism and paternal care in marmosets (Callithrix kuhlii)

Ross, C., J. French, and G. Ortí. 2007. Germ Line Chimerism and Paternal Care in Marmosets (Callithrix kuhlii). Proc. Natl. Acad. Sci. USA, 104 (15): 6278–6282.

The formation of viable genetic chimeras in mammals through the transfer of cells between siblings in utero is rare. Using microsatellite DNA markers, we show here that chimerism in marmoset (Callithrix kuhlii) twins is not limited to blood-derived hematopoietic tissues as was previously described. All somatic tissue types sampled were found to be chimeric. Notably, chimerism was demonstrated to be present in germ-line tissues, an event never before documented as naturally occurring in a primate. In fact, we found that chimeric marmosets often transmit sibling alleles acquired in utero to their own offspring. Thus, an individual that contributes gametes to an offspring is not necessarily the genetic parent of that offspring. The presence of somatic and germ-line chimerism may have influenced the evolution of the extensive paternal and alloparental care system of this taxon. Although the exact mechanisms of sociobiological change associated with chimerism have not been fully explored, we show here that chimerism alters relatedness between twins and may alter the perceived relatedness between family members, thus influencing the allocation of parental care. Consistent with this prediction, we found a significant correlation between paternal care effort and the presence of epithelial chimerism, with males carrying chimeric infants more often than nonchimeric infants. Therefore, we propose that the presence of placental chorionic fusion and the exchange of cell lines between embryos may represent a unique adaptation affecting the evolution of cooperative care in this group of primates.

Translation: According to the seminar I went to today, what this all means is that Marmosets and their relatives almost always produce fraternal twins, and the embryos grow in close proximity, with out the usual membranes separating them. The two developing embryos can actually have blood vessels in common, meaning that blood born cells can move from one embryo to the other. And stay there. And develop. So when the little monkeys are born and grow up, they can be riddled with cells that are genetically part of their sibling. This is what we call a chimera, when one individual has cells that are of different genetic lineages.
So then one of the chimeric monkeys mates. But some of his germ line cells (the ones that make sperm) are genetically his brother. So he's doing the mating, but the young could be genetically his nephews. Weird, I know. And one outcome of all this is that marmosets put a lot more energy into taking care of their nieces and nephews than would otherwise be expected. Ain't evolution weird and wonderful.

Cartoon explanation:

Duetting Alone

I attended a seminar yesterday given by a former lab mate of mine, discussing her work to understand the duetting call of the California Towhee.

(An article in the Berkeley Alumni Magazine discusses the work and links to a sound file of the call.)

She described how this squeal-call is almost never given by just one bird, and is almost always a duet by the pairs who mate for life (and cheat on each other like mad).
It has been called the "reunion squeal" because the pair always fly towards each other while duetting, and end the duet side by side.

So this morning I was in my neighbor's backyard and noticed a pile of feathers on the ground. They have four outside cats, so I was not surprised. I bent over to examine the feathers and see who the victim was. Drab brown feathers. The wing and tail feathers were too small for a robin or a jay, but too big for most of the sparrows and finches around here. Then I noticed the clump of orange feathers, just the color of a towhee's undertail coverts. A California Towhee, one of the most common birds in the neighborhood, had bit it.
As I stood up, I heard the squeal. A rather half hearted squeal I thought. Then I looked up to see the towhee, sitting on the fence, squealing. It wasn't a half hearted squeal, it was that this bird was doing its half of the duet alone. It was initiating the reunion squeal, but couldn't reunite, because its mate wouldn't squeal back. It squealed twice more in the next several minutes, far more often than is common among pairs.
The cats sat on their lawn chairs and looked smug.

Saturday, August 18, 2007

Evolution is, in fact, a theory, not a fact.

I made my first post on Daily Kos this morning.

It was well received. Six and half hours after I posted, it, there are almost 500 comments, and more than 1400 people have voted in my poll.

Close to 1000 of those agreed with the statement, " Evolution is the only non-idiotic way to explain the data."

The text of the post was as follows:

I've decided to start my diarying with a couple of entries about evolution. I'm working on my PhD in evolutionary biology, and while I can tell most people here understand that there is no logical way to reject evolution, I thought it might be helpful to clarify a few important points about evolution. Those who reject evolution often use the inconsistencies in the understanding of those they argue with to "prove" that evolution does not make sense. So I'd like to see us all on the same page.

For those of you who reject evolution as a matter of faith, it is not my goal to convince you of anything. If you were open to being swayed by facts, reasons or logic, it would, by definition not be faith. If you like, imagine this was written in a fantasy realm in which evolution is real and your genetic code is 95% identical to that of a chimp. I don't want the comments section to turn into an argument about whether evolution is real or people on the other side are questionable. No one is going to change his mind on the topic.

With no further ado, I list insights about evolution after the jump.

I've decided to start my diarying with a couple of entries about evolution. I'm working on my PhD in evolutionary biology, and while I can tell most people here understand that there is no logical way to reject evolution, I thought it might be helpful to clarify a few important points about evolution. Those who reject evolution often use the inconsistencies in the understanding of those they argue with to "prove" that evolution does not make sense. So I'd like to see us all on the same page. For those of you who reject evolution as a matter of faith, it is not my goal to convince you of anything. If you were open to being swayed by facts, reasons or logic, it would, by definition not be faith. If you like, imagine this was written in a fantasy realm in which evolution is real and your genetic code is 95% identical to that of a chimp. I don't want the comments section to turn into an argument about whether evolution is real or people on the other side are questionable. No one is going to change his mind on the topic. With no further ado, I list insights about evolution after the jump.

1. A fact is the most trivial piece of science. A theory is the most complete.

"The average density of granite is 2.75 g·cm^-3," is a fact. Facts are important, but are the starting point, not the goal. To a scientist, theory is the entire body of understanding about a particular phenomenon, the best unifying description of all the relevant facts. Theory is the whole structure of knowledge. To say that "evolution is a fact" is like saying "the Himalayas are a stone."


Nothing in Biology Makes Sense Except in the Light of Evolution

Theodosius Dobzhansky (1900-1975)
(see for a truly classic essay.)

Evolution is the central organizing principle behind biology. Without it, biology is a list of facts and equations, a series of observations. You can study the various types and formations of igneous rock, learn that pumice is useful for this and basalt for that, but without knowing that there was molten rock involved, your understanding would be pretty limited. This is very equivalent to trying to understand biology without evolution.

3. We are all highly evolved.

Because all organisms have evolved from a common ancestor, we all have as many years of evolution behind us. Bacteria, often seen as the least evolved, actually evolve a lot faster than we do. We see the traits that are human like as being "highly evolved." Yeah us! But when we do this, it is just chauvinism.
Evolution does not push towards any kind of subjective perfection.
In order to pass on its genes, an organism needs to be as good or better than the competition. It does not need to be morally or intellectually appealing. It does not need to be perfectly efficient or maximally beautiful. It just needs to be good enough to get past the competition.
The popular view of evolution is a progression from bacteria to squiggly guys to fish to lungfish to amphibians to reptiles to mammals to primates to great apes to Neanderthals to cavemen to us us US, the pinnacle of God's design! But wait, we are talking about science here, no supernatural explanations need apply. If we overcome our religious biases and our anthropocentrism, it becomes clear that the world's organisms are not striving to be us. Some populations evolve to be bigger, others to be smaller. Brains get bigger and smaller. Number of limbs increases and decreases. There is no direction to it. Every population just drifts towards whatever happens to encourage survival and reproduction in their peculiar environment at that moment. There is no force driving things towards being human like.
Because there is no direct to evolution, the term "devolve" is not one that has a biological meaning. See for a discussion of misunderstanding and misuses of "devolution."
A trait can be highly evolved, in that it has changed a great deal from the ancestral state (e.g. frogs have a highly evolved pelvis) but after billions of years, all organisms are highly evolved.

4. Biologist don't, and will likely never, agree how to define "species."

In a creationist world view, it is easy to define a species. The decedents of each pair of organisms that lived on Noah's ark form a species. Simple process leads to easy defining.

The problem is, looking at the diversity of life, we find much more complexity, much more messiness than can be explained through static, preordained species. A single "species" can have tremendous geographic variation. Oaks hybridize like mad. Salamanders that look like the same species won't interbreed, except in particularly wet years. Salamanders that can't interbreed with each other will both interbreed with an intermediate population. Some populations, through spontaneous mutation, spawn clonal populations that don't breed with anybody. There is a tremendous diversity of process.

Pity the poor taxonomist. Everyone expects a list of species, the laws are written around endangered species and migratory species, which means we have to decide what is a species, and what is not. If two populations interbreed only once every thousand years, are they one species or two? If two groups swap nuclear DNA but not mitochondrial, can they be considered separate? Can species be delineated based on ecological traits? On behaviors? What does the word species mean when applied to organisms that reproduce asexually?

There are literally hundreds of definitions of species supported by different biologists. And there is no one right definition; the underlying process that we are trying to shoehorn is so complex that every conceivable definition simply won't work in some cases. In order to applicable in all cases a definition would have to be so broad that it was applicable in none. No matter how much data we have, there is no final answer to how many species are out there, because no single definition can be applied. Nature is messy, and doesn't read our rule books.

5. Not all evolution is because of natural selection.

Biological evolution is the heritable change in populations over time. Natural selection is one extremely important factor in driving heritable change. But it is not the only one. In small populations, there is genetic drift. A trait that is in no way advantageous can increase in frequency simply because the two guys who happen to have that trait also happen to impregnate a whole bunch of females. Mutations in and of themselves constitute evolution. Basically, in order to avoid evolving, a population would have to be infinitely large, completely homogeneous, in a completely stable environment, under no selective pressures and without either a dearth or a glut of disadvantageous mutations.

6. Evolution is an ongoing process.

I often hear people say things along the lines of, "back in evolutionary times" or "when evolution was happening." Evolution is happening now. Humanity is currently evolving. Certain populations are increasing while other with different genetic backgrounds are decreasing. Change in genetic make up of the population over time is evolution. That is how geneticists define evolution. Humans are also undergoing selective evolution, and specific genes have been identified that are currently being selected for or against. Our genes for disease resistance are under particularly strong selection.

7. Evolution can act incredibly rapidly.

Spray a field with an insecticide. There are a million crickets in the field. 9,999,998 of them keel over. The remaining two survive because they happened to have a mutation that made them resistant to the insecticide. The male calls, the female comes, candles, moonlight. 100 resistant baby crickets. The farmer comes back and sprays again. Maybe half the crickets die. The remainder all carry the resistance gene. Repeat the process and the gene that causes resistance becomes more common with each generation. Pretty soon most of the crickets have not one but two copies of the resistance gene, having gotten one from each parent. The population has evolved to be resistant. This is also why we have antibiotic resistant bacteria. And why the Cane Toad, introduced into Australia, can now survive in habitats much drier than they could have a few decades ago.

9. Almost everything you have ever read about evolution in the popular press gets it wrong.

Populations do not evolve in order to achieve a certain goal. Biologists do not disagree about evolution any more than geologists disagree about tectonics. Individuals do not act for the good of the species (present company excepted, of course). Darwin did not coin, or like, the term "survival of the fittest." Our ancestors did not look like modern day chimps. We are not descended from the lungfish. There is no such thing as "adaption." Darwin did not base his theory of evolution primarily on Darwin's Finches. Darwin did not set out to form a theory of evolution. His main interest was barnacles.

Evolution is that heritable change in populations over time. There is no way for an individual to evolve. An individual can reproduce, or die, and contribute to the evolution of her species. But there is no biological evolution of individuals.

10. Darwin got some details wrong.

Darwin had no clear concept of genetics. Mendel sent Darwin a copy of his book. Darwin never opened it. Darwin made lots of wild guesses as to the mechanisms behind heredity, and some of those guesses lead him down dead ends. Modern biologists are awed by Darwin's genius, but we are not under the delusion that he had all the answers, nor are we simply accepting him at his word. Many of Darwin's guesses have been shown to be sound. Others have been shown to be flawed.

Tell me what you think. Let me know if you disagree with something, or want a source or more information. There will be some slightly more provocative evolutionary musing tomorrow.

Monday, August 13, 2007

Professional science is hard

Late at night, with a weary brain, I attempted to document some of the process of data analysis, typesetting, and the general level of complexity involved in the production of a moderately novel physics journal article. Using direct-screen-capture video software, I just flipped through the content that I have been staring at for weeks, giving a 4 minute silent film of my work. The production of this low-res video was a greatly refreshing 6 am escape from my writing, and stands as a slightly surreal and fuzzy look at the reality of being a physicist. Do not attempt to understand any technical content, that is not the point, this is just art therapy for the sleep-deprived.

If I had to choose a sound track to this, the first thing that comes to mind is the scene at the end of 2001 where Dave has to float into the airlock, and then slowly, manually deactivate the optic circuits of Hal.

Here it is:

From Data to a Paper

- Let me know any reactions that this may incite,


Wednesday, August 08, 2007

20,000,000 years of evolution, killed as bycatch

" First human-caused extinction of a cetacean species?"

Abstract from Biology Letters:
"The Yangtze River dolphin or baiji (Lipotes vexillifer), an obligate freshwater odontocete known only from the middle-lower Yangtze River system and neighbouring Qiantang River in eastern China, has long been recognized as one of the world's rarest and most threatened mammal species. The status of the baiji has not been investigated since the late 1990s, when the surviving population was estimated to be as low as 13 individuals. An intensive six-week multi-vessel visual and acoustic survey carried out in November–December 2006, covering the entire historical range of the baiji in the main Yangtze channel, failed to find any evidence that the species survives. We are forced to conclude that the baiji is now likely to be extinct, probably due to unsustainable by-catch in local fisheries. This represents the first global extinction of a large vertebrate for over 50 years, only the fourth disappearance of an entire mammal family since AD 1500, and the first cetacean species to be driven to extinction by human activity. Immediate and extreme measures may be necessary to prevent the extinction of other endangered cetaceans, including the sympatric Yangtze finless porpoise (Neophocaena phocaenoides asiaeorientalis)." (emphasis mine)

BBC coverage

Tuesday, August 07, 2007

A Deluge of Data

The International Species Information System is an organization charged with coordinating data gathering, storage and usage among zoos and aquaria around the world. They started out keeping track of things like which zoos had which animals, how individuals were related to each other and so on. Over time they have come to have enormous demographic and physiological databases and they hold individual data on millions of captive animals.

These data were originally collected for the use of ISIS member organizations in the management of their captive populations, but as the amount and quality of data has improved, these data sets have becomeof interest to a wide range of other researchers.

In my work, I am interested to know for as many species of primates as possible, whether the males live longer, the females live longer, or the longevity of the two species is approximately the same. I am specifically interested in the capacity for longevity of each sex of each species, rather than how long they live when exposed to disease, predators and famine. And so when I heard that ISIS had longevity data on hundreds of thousands of captive primates, I was very interested.

But of course, there are problems. The data were collected by, and are owned by, ISIS's member organizations. The fact that they were collected in a decentralized way means that a chimp can be recorded as having been born in 1692 when it was probably born in 1962. Some individuals have birth dates recorded, but no death dates, and so on.
Also, the zoos consider this type of data to be potentially sensitive. No zoo wants to be known as the zoo where Gorillas have the shortest life expectancy. So the data needed to have all possible identifying information removed before ISIS could get permission from the zoos to share the data with researchers. And only someone who is really familiar with zoo data could prune the bad data, process the data into sex*species specific life tables and get approval to let me use these.

Enter Laurie Bingaman Lackey of ISIS. She agreed to get me as much of the data as she could. But she is a busy woman, and this was for her basically a side project, undertaken to help me and get her name on a paper or two. And she had to go through each species individually, look for bad data, compile a life table from what remained. So it took a little over three years to get the data to me. Sex specific life tables for all 120 species of primates that ISIS has enough data on for my purposes. A Herculean effort. Now that I have the data, I have to remember what exactly I was going to do with them.

Friday, July 13, 2007

Statement on Condors and Lead

A group of 44 scientists, including myself, have signed a statement summarizing the evidence that the use of lead ammunition leads to lead poisoning in California Condors, and that the condor population cannot be self sustaining so long as this lead poisoning continues.

The PDF can be found here.

Below is the text of the statement:

Science Links Lead Ammunition to Lead Exposure
in California Condors (Gymnogyps californianus)

Statement of Scientific Agreement
July 10, 2007

We, the undersigned, endorse the scientific chain of evidence linking lead ammunition to lead exposure in the endangered California condor as sufficiently strong to support a ban of lead ammunition in condor country. This conclusion flows from a robust chain of evidence, namely: (1) California condors are obligate scavengers on mammal carcasses, including deer and other big game; (2) large numbers of deer are killed with lead ammunition in condor country; (3) free-flying condors frequently have elevated levels of lead in their blood, and these levels peak during the fall deer hunting season; and, (4) isotopic analysis of lead in the blood of pre-release and free-flying condors in California strongly supports the link between lead ammunition and lead exposure. Lead exposure is the major obstacle to the success of condor reintroduction: condors must be captured regularly for lead testing and emergency treatment, and, for fear of lead exposure, field teams are forced to feed condors at artificial feeding stations. Untreated, lead exposure interferes with digestion, hinders normal behaviors, and can cause death. Due to the preponderance of evidence, we believe that any reduction in lead ammunition in condor country will significantly increase of the success of reintroduction efforts of California condors.

1. California condors are obligate scavengers on mammal carcasses, including deer and other big game. This foraging trait is clearly established in the scientific and popular literature (e.g., Snyder and Schmitt 2002).

2. Large numbers of deer are killed with lead ammunition in condor country. The Department of Fish and Game study by Fry (2003) indicates that 106,000 game animals are taken annually in condor range in California with an estimated 30,000 carcasses or gut piles left in field. Hunt et al. (2006) showed that hunted deer had lead ammunition fragments broadly distributed along the wounds that increase the potential for accidental ingestion by condors and humans. Ninety percent of offal piles (i.e., gut piles after field dressing deer) showed lead fragments. Of these piles, 75% contained more than 10 fragments, and 50% of the piles contained more than 100 lead ammunition fragments.

3. Free-flying condors frequently have elevated levels of lead in their blood, and these levels peak during the fall deer hunting season. Lead exposure has been recognized as a major threat to condors for several decades, and ingestion of ammunition has long been considered the primary source of this exposure. Free-flying condors have detectable blood lead levels that often require emergency veterinary intervention (Fry 20032). The vast majority of condors tested in the last ten years have blood lead levels that exceed the Centers for Disease Control (CDC) threshold for immediate clinical intervention in children of 10 µg/dL, and many condors have been observed with blood lead levels exceeding 100 µg/dL.

Sorenson and Burnett (2007) documented a sharp increase in blood lead levels in condors during the fall hunting season. Lead ammunition is the only documented source that could cause acute lead exposure at the levels seen in wild condors. Since lead is not biologically accumulated, acute levels of blood lead, as seen in the vast majority of condors in the graph below, are most reasonably derived from repeated ingestion of tiny lead fragments; condors must consume lead directly from highly concentrated sources such as lead ammunition.

4. Isotopic analysis of lead in the blood of pre-release and free-flying condors in California strongly supports the link between lead ammunition and lead exposure. Lead isotope ratios have been used for over 25 years to trace source(s) of environmental lead exposure. The use of lead isotope ratios for evaluating lead exposure is based on the natural existence of lead in four stable isotopes. The natural relative abundances of these isotopes often varies across different lead-containing industrial products (e.g., leaded paint or ammunition) because lead used in making those products came from different geological ore sources and/or from different sources of recycled lead. Lead isotopic ratios in a lead-exposed animals are like fingerprints that can be traced back to a particular source of lead exposure. Indeed, the use of lead isotopes offer the most accurate way to trace the sources of elevated lead exposures and have been used to trace the sources and pathways of lead exposure in humans, as well as in wildlife such as California condors.

Church et al. (2006) evaluated the sources of elevated lead exposure in California condors based on: (i) knowledge of the plausible sources of lead exposure to the condor, including lead concentrations; (ii) the quantified isotopic ratios of those plausible lead sources within that environment; and, (iii) information about behavioral habits, as well as an evaluation of viable pathways of exposure to the organism. This study clearly shows that pre-release condors have an isotopic signature that is significantly different from lead in free-flying condors in central California, whereas the blood lead isotopic signature of the majority of free-flying condors approached or matched the isotopic signature of lead ammunition collected from the condors’ central California range. Lead ammunition is therefore the principal and only plausible, documented source of lead exposure in condors. The Church et al. (2006) study underwent rigorous scientific peer review in the publication process for Environmental Science and Technology. This publication is an American Chemical Society journal and one of the top-ranked scientific journals in the areas of environmental chemistry and environmental toxicology.

Taken as a whole, the chain of evidence from all sources, including peer-reviewed journals, supports the conclusion that California condors are suffering lead exposure due to the ingestion of lead ammunition from game. Lead exposure is the major obstacle to the success of the condor reintroduction. Due to the preponderance of evidence, we believe that any reduction in lead ammunition in condor country will significantly improve the success of reintroduction efforts of California condors.

Tuesday, July 10, 2007

Photos of Science!

The editor would like to bring your attention to a couple of sources of science related photos on the web

1. is the home of the incomparable AKB's science and nature photographs, including an unmissable photo of the day.

2. contains many photos of my ill begotten expedition to Papua New Guinea.

That famous x-ray of a gravid brown kiwi female fill to bursting with a giant egg that weighs 1/5th what she does, like a 120 pound woman giving birth to a calcified 24 pound baby.

Thursday, June 07, 2007

A test of the idea that the voice recognition software works poorly for technical topics.

I will now train ViaVoice to understand my speech and know some of the technical words I am likely to use in my writing.

Senescence. I'm going to talk about senescence. Senescence has been defined many ways. In the biological literature definitions of senescence fall into 4 main categories. Physiological senescence, cellular and tissue senescence, actuarial senescence and reproductive senescence. These last 2 can be combined into the measure I will refer to as Hamiltonian senescence.
When most people think about senescence they think of physiological senescence. Hardening of the arteries graying of the hair gradually increasing dementia and a wide range of other traits are easily observable signs of physiological senescence. Physiological senescence can be defined as age related deleterious changes in the anatomy, biochemistry or physical functions an organism.
This is distinct from tissue senescence leaf senescence cellular senescence and other adaptive degradations of disposable subsets of an organism. In this meaning of senescence, the senescence of the whole organism is not being discussed, the breakdown, recycling or discarding of a particular piece of the organism. In a fitness context, senescence refers to the decrease in mean remaining individual fitness with age. This can be broken down into reproductive senescence, the decrease in mean reproductive output by age and actuarial senescence the decrease in mean survivorship by age. The definition of reproductive senescence can be further refined to include both direct reproduction (i.e. fertility) and indirect reduction ( i.e. aid and transfers of resources to related individuals).
as Hamilton argues, these means should be calculated across all individuals born into a particular population or cohort, rather than simply those individuals surviving to the age in question.

Much of the biological literature suffers from the conflation of these various definitions both with each other and with the observed variables used as proxies for senescence. Different authors studying the same organisms or even the same datasets have come to very different conclusion regarding the senescence those organisms because of confusion regarding the definition and measure being used.

Wednesday, June 06, 2007

Blog of Science Welcomes Stephen Howard

Our new physics and other stuff I don't get editor

Friday, June 01, 2007

Nobel Intent

I came across an interesting online journal that is worth checking out.

Most relevant to existing lines of thought that have been brought up so far:

Black holes for everyone

Could entangled particles be linked by wormholes?

Sunday, May 20, 2007

Invention I want.

I don't know if someone already builds something like this. If not, I've got dibs.

This is an idea I've had on and off for a few years. I call it the stomp charger. It is basically a wallet sized thing two plates that hinge in relation to each other, and a place for putting in a couple (maybe four?) rechargeable AA batteries. Put batteries in, bounce your foot (or anything else) up and down on it whilst you are doing other things, and, after a while, your batteries are charged. Ideally it would be waterproof, and the there would be a little door/flap that closes over the battery compartment.
I don't actually know what would work best to convert the bouncing into chemical energy in the battery, but I bet someone I know does.

I imagine this thing, if it had an efficient energy conversion ratio, would be tremendously useful to field workers, villagers and others with limited access to new batteries/wall current. The poor villagers I've met always wanted AAs.

Saturday, May 19, 2007

A note from the editor

We have received several (two) questions recently regarding commenting and posting on Blog Of Sceince.

In order to comment, simply click on the "peer reviews" link at the bottom of the post, type your comment in the comment box and click "Publish."

For those who would like to post to BoS, there are two options.
First, one can email me a piece, and if it seems apropriate for BoS, I will post it and attribute it to you.

Second, for those who might like to post more regularly, I am open to allowing other bloggers to post here. You would need to create a Blogger account (which takes maybe two minutes and is free) and then I could add you as a contributor.

I can be contacted at

Friday, May 18, 2007

Family of Science

I won't make a habit of this. But I thought posting this here would give the reader some sense of the environment that leads a young man to grow up and start Blog of Science!
For reasons unclear to me, my family has chosen to comment on my recent post "Not the end of the world" elsewhere, rather than on Blog of Science, so I have reproduced our discussion here. GML is my father, KAL my mother and JAL my brother. The following messages are in approximately chronological order:

The great physicist Enrico Fermi pointed out that interstellar travel is not very difficult for a technologically advanced and rich civilization, as long as it is designed for travel times of decades or centuries (or longer if a big colony is sent in a "generation ship". Each new colony would then grow and develop for some centuries, even a millennium, and then send out new ships (first to scout and then to colonize), and that this process would spread a civilization about our galaxy in a fairly short time, astronomically speaking, perhaps a few million years. Surely, the idea goes, at least one species somewhere would do this. This led to his famous question, "Where is everyone?" Many answers have been suggested, but the relevant one here is self-destruction, probably not by a physics experiment gone wrong, but by war within the species.
Our species has been said to need a "Moral Equivalent of War" to give us some outlet for our natural aggressive and us-them tendencies. This MEOW idea appeals to me, but I am not clear what it would be.

Dad, correct me if I'm wrong, but it was my impression that ETs wouldn't need to travel between stars for us to notice them. I thought even the level of radio noise that we currently produce would be plenty for us to notice if anyone were producing it within a few zillion light years. So the fact that we haven't heard anything (despite SETI and other projects looking for non-random radio signals) suggests not just that no one out there is traveling, but that no one out there is using radio waves, i.e., is technically advanced at all. Is that not right?

There are a lot of assumptions we are making here.
Of which these are a few:
1. We are assuming that an advanced civilization uses radio waves to
communicate. Why do we assume this? We think we are advanced, and we
use radio waves. Perhaps radio is grossly inferior to something else we
ain't thought of yet, so nobody uses it.
2. They don't care if we hear them or not. Why do we assume this? We
don't worry about ETs detecting us, so we think they don't care if they
are detectable or not. Perhaps for one reason or another, many
civilizations consider it unwise or undesirable to broadcast their
3. We assume that if they are out there broadcasting radio, we would
pick up the signal. I don't know how far off we could pick up
broadcasts from a planet transmitting like Earth, unless we
specifically targeted that point in space, but I assume it is a
relatively small section of the galaxy.
4. We assume that if we picked up their signal, we would recognize it
as nonrandom. Given that we have no idea what form life on other
planets would take, it seems hubristic to assume that we would
recognize their transmissions as a sign of intelligent life.
5. We assume that if they picked up our signals, they would then
continue behaving in a way that would allow us to detect them. Imagine
there are technologically advanced aliens 100 light years away. They
detect rapid environmental change on earth, infer a rapidly developing
early technological civilization that behaves rather voraciously. Until
they know more, do they want the aliens (us) to know they are there?
The overarching point is that we know too little to know anything
except that we don't know. If we assume we are looking for ourselves,
which is what we often assume, we are wrong. The aliens are not going
to be biologically, psychologically or technologically familiar. they
are not going to live in a niche that would be amenable to us, and they
are not going to develop all the same technologies or develop them in
the same order. They are not going to have the same weaknesses and
strengths. They are not going to be in the same phase of develoopment,
or a similar one, to where we are. They are not necessarily going to
match our current definitions of either intelligence or life. It is fun
to speculate about and make up hypotheses, but we don't know enough to
draw any conclusions or moral lessons from. We know that either there
is no one out there, or that they are undetectable given our current
technology, or for one reason or another we have failed to detect them,
or have failed to notice detecting them. Everything else is SciFi.

There is no reason why alien "life" should be carbon-based, or have discrete "bodies," or use the same senses we do (light, sound), or be on the same size scale as we - they might be miles across or microscopic or made up of filaments - or need the same amount of ambient radiation, heat, pressure, or environmental stability. There need not even be "individuals" with separate lives and separate mortalities. Probably some relatively fluid medium is needed - it would be hard to imagine solid rock being able to assume the complexity necessary for communication and reproduction. Otherwise I think that most human thought about the topic uses way too many chauvinistic assumptions. Long, thin necks and three-fingered hands, indeed!

Interesting point. There are several factors to consider. The radio-based SETI and similar programs (mostly piggy-backing onto other equipment since Senator Proxmire made fun of it and got the U.S.Gov't to make it illegal to spend gov't money for it) make various reasonable (but not necessarily correct) assumptions about what frequencies would be used, as most free of background noise, etc., but at moderate interstellar distances such signals would be very hard to sort out, anyway. Also, higher-tech systems than radio (tachyons, gravity waves, links through space warps, etc.??) could be used, so lack of radio broadcasts does not mean lack of high technology. Another thought is that any sensible advanced species would carefully refrain from broadcasting its location, for fear of hostiles killing off possible competitors. No-one really knows, but the pay-off could be so great, technically and intellectually, that it seems worthwhile to put a little money into listening for interesting patterns; even if we do not find ETs, we may hear some natural phenomena worth knowing about. This has already happened, as when the pulsars (at first jokingly termed LGM for Little Green Men) were discovered.

Dan is quite correct in all his points, except perhaps in regard to our ability to recognize non-randomness. This is based on mathematics, mainly, not on biology or (I hope) human psychology. I certainly think that mathematics is universal; though I have no non-human examples as evidence. I believe that in some sense we discover mathematics, and do not just invent it.

Once mathematics is applied to trying to recognize patterns in real data, it becomes science, and all the limitations that come with science apply. We have to look at a particular set of time scales on a particular set of frequencies for a deviation from some mathematically defined but psychologically chosen null hypothesis. And all that means we don't really know if we could detect an alien deviation from random.
Regarding mom's point, it is very true, there is no reason to assume life on other planets would be carbon based. I wouldn't dismiss some sort of solid state lifeform though. Silicon can do amazing things.

How about my idea that "life" elsewhere may accept very different conditions re solid/not solid "body" (or no actual body at all), tolerance/requirements for temperature conditions or radiation exposure, apparent passage of time per actual time passage, inevitability of mortality, use of other senses than sight/hearing, etc? Perhaps we haven't heard from anyone because we are actually very atypical in our characteristics and wouldn't think of the more common communication modalities. Or maybe no one else is out there and we are truly unique. Sometimes I think we exist only because the universe requires at least one set of observers in order for it to exist.

Very true, that any collisions that CERN will make have happened, more powerfully, many times out in space, with no-one to register and measure them.
The Big BAng, from what I read, supposedly did not create any mass-energy, hard as that is to believe. The idea is that the expansion of the universe is, in proper physical book-keeping, measured in negative units, while the mass-energy is in positive units, and that these just cancel each other out. As you note that Stephen said, "on a minute scale the universe is a froth of energymass popping in and out of existence, but that these things were usually so small and numerous they mostly canceled each other out, leaving the energymass in the universe very close to
constant." Larger sized quantum fluctuations are shorter-lived than smaller ones, and if the universe is thought of as a nearly-zero mass virtual particle, it can last a very long time. Mass-energy versus time is one of those complementary trade-offs found in quantum physics, such as (knowledge of?) a particle's momentum vs. (knowledge of?) its position.

So we can get de novo mass-energy as long as we are willing to accept an equal amount of de novo space-time with it?

Yes, in a sense, we can get more mass-energy along with more space-time, but only in a new universe, I gather. A prominent current theory is that black holes create new baby big bangs which then expand as full fledged universes; if the characteristics of a given universe leads to lots of black holes, that kind of universe will end up with lots of descendant universes with similar (but not identical) properties, leading to universes with successful characteristics (physical constants, etc.) becoming more numerous and predominating, in a Darwinian fitness paradigm. This theory is supposedly testable by figuring out what set of physical constants, etc., should be most successful in making black holes of the right sorts, and seeing how well this matches our universe.

But Darwinian evolution requires:
1. Mutations leading to variation
2. Heritability of that variation
3. Fitness differentials based on the heritable mutations
With regard to black holes as baby universes, we have no reason to assume 1 or 2, only that if 1 and 2 were to be true, that 3 could be true.
Also, your last comment implied that in order to be stable, a big bang event would have to result in something that in some strange sort of reckoning had zero mass. Black holes are not known for having zero mass.
There also seems to be the difficulty that black holes are not closed systems. Mass can go in and through quantum variation of location, evaporate off. Universes on the other hand are generally thought to be closed.

Thursday, May 17, 2007

Hurricane Season

Welcome to the 2007 Hurricane Season. Estimates I've seen predict a very active year, with 14-21 named storms including 7-9 hurricanes of which about half are expected to be category three to five, meaning winds exceeding 111 mph.

Here is a recent abstract from a paper published by a well respected lab:

Information obtained through March 2007 indicates that the 2007 Atlantic hurricane season will be much more active than the average 1950-2000 season. We estimate that 2007 will have about 9 hurricanes (average is 5.9), 17 named storms (average is 9.6), 85 named storm days (average is 49.1), 40 hurricane days (average is 24.5), 5 intense (Category 3-4-5) hurricanes (average is 2.3) and 11 intense hurricane days (average is 5.0). The probability of U.S. major hurricane landfall is estimated to be about 140 percent of the long-period average. We expect Atlantic basin Net Tropical Cyclone (NTC) activity in 2007 to be about 185 percent of the long-term average.

This early April forecast is based on a newly devised extended range statistical forecast procedure which utilizes 40 years of past global reanalysis data and is then tested on an additional 15 years of global reanalysis data. Analog predictors are also utilized. We have increased our forecast from our early December prediction due largely to the rapid dissipation of El Niño which has occurred over the past couple of months. Currently, neutral ENSO conditions are observed. We expect either neutral or weak-to-moderate La Niña conditions to be present during the upcoming hurricane season. Tropical and North Atlantic sea surface temperatures remain well above their long-period averages.

Wednesday, May 16, 2007

Not the end of the world

My friend Stephen is one of those physicists who built linear accelerators and EMP generators in his basement as a kid. And he can get all starry eyed talking about string theory and Mbrain theory and cosmic wormballs and other stuff biologists like me don't understand. But it is fun to hear him talk about it because he is so enthusiastic and brilliant.

I used to ask him physics questions that I didn't even know entirely what the question meant, just to get him started. One time, when we were in college, we were talking over nachos and tea at the Upstairs Cafe. It was a bit hard to hear him, given that the noise of the band in the Downstairs Cafe was shaking the floor. But I asked him why energymass (the two being the same) is conserved, and if there are any exceptions. Stephen thought for a while, rambled for a while, then said that they are not exactly conserved, because there is quantum variation. He talked about that for a while, and I got the impression that what he was saying was that on a minute scale the universe is a froth of energymass popping in and out of existence, but that these things were usually so small and numerous they mostly cancelled each other out, leaving the energymass in the universe very close to constant. Then he said something I didn't grok about the Big Bang being, at least in part, an example in which the scale was much larger and a whole bunch of energymass was created all at once.

So the next question I asked, having an environmental bent, was whether it was theoretically possible we could use all this in some way to make energy, and thereby end the need for fossil fuels. This started Stephen on a train of thought that he made me promise not to share with anyone, which is easy because I understood almost none of it. But it ended with me being somewhat concerned that if I understood even a little of what he was saying, he might just accidentally blow up the world. I made him promise that he wouldn't and also wouldn't teach anyone else how to. He saw why I was concerned, but said that he would make sure he fully understood the physics involved before he tried to tap into "quantum energy" whatever that is.

This all came back to me last night when my brother emailed me a NYTImes article about the Large Hadron Collider. The article claims they will recreate "conditions that last prevailed when the universe was less than a trillionth of a second old." Like the Big Bang all over again. Jason's commentary was, "I can't help but think of that theory that we don't see radio traces of other species because advanced species quickly kill themselves off, perhaps by creating huge toys that destroy their planets accidentally."

This kind of concern has been raised many times, mostly in science fiction. The basic idea is that it requires a lower level of technology to blow ourselves up than to say hi across light years. Possibly true, but I doubt this is that experiment.

I'll write later on my thoughts regarding extraterrestrial life, but sticking with the collider experiment, I think that as usual, the popular media are grossly overstating their case. The accelerator may be designed to recreate something that has certain similarities to the very early universe, but is this really the first time since the Big Bang that particles have collided at these speeds? No. They just don't usually do it in a way that we can predict, control and build giant detectors in anticipation.

Clearly the power input is not on a world destroying scale. So in order to trigger Alderaan, they would either have to set off some novel sort of mass to energy conversion chain reaction, or they would have to accidentally open the taps on quantum energy. And they would have to do this on a scale that would destroy earth, but would not be obviously detectable from the rest of the universe. If colossal amounts of energy came spilling out into the universe from nowhere every time particles collided at certain energies, wouldn't astronomers have noticed something like that?

So sleep peacefully. The Swiss are not about to blow up the world. They own too much of it.

Tuesday, May 15, 2007

DUDES (Diurnal Urban Detritus Eating Sparrows)

There are at least a dozen outdoor housecats on my block. And, as you might expect, not a whole lot of ground dwelling small wildlife. A few salamanders, the very occasional rat (the only times I've seen these there were at least two cats in purrsuit) and some squirells which can outclimb any of the cats. And there is really only one bird species that spends much time on the gound, a big drab brown sparrow called the California Towhee.

Today I saw two of them fighting. A frantic ball of beaks and feathers twisting crazily through the air. They were so intent on mauling each other, they crashed first into the neighbors' fence, then onto the driveway. The instant they touched down, still rolling and pecking, a cat appeared a few yards from them, coming for them at full speed. The cat pounced, and while it was in the air the towhees joined it, but as it began to come down, they accelerated straight upwards. The cat got nothing but the feathers they had torn from each other.

I've seen birds escape preditors before, but nothing quite that close or sudden. These birds clearly had practice. How could they not, given the feline density around here? But somehow, California Towhees seem to thrive, feeding on the ground, in exactly the kinds of neighborhoods that are full of cats.

Like most species able to exploit human created niches, they've got a bright future ahead of them. The cats could even be good for them, keeping out rodents and other birds that would compete with the Towhees for food.

And that is how we get from natural history observation to testable hypothesis.

Monday, May 14, 2007

On Natural History

Science, in the beginning, was a branch of philosophy. Natural philosophy they called it, meaning philosophy meant to explain the things we see in nature. To me though, the phrase suggests a contrast to supernatural (faith-based) philosophy. Or artificial (arbitrary) philosophy. Or unnatural (wrong) philosophy. In my mind, natural philosophy is thinking that is not faith-based and endeavors not to be arbitrary or wrong. And all the methods of asking, knowing and doing we call science, are simply the best attempts of the decedents of the natural philosophers to avoid being faith-based, arbitrary or wrong.

Science, despite what they taught you in school, is neither a collection of knowledge, nor a single method. There is plenty of very good science that skips one or more of those eight steps you memorized then forgot. I'm a scientist and I can't remember the version of the list I was taught.

Scientists don't even necessarily agree on what defines science. The foremost example of this, as far as I know, is natural history. The term is defined a huge number of ways, so I'll give a specific hypothetical. I go out in the woods, see a fly I've never seen before, record it's behavior and the specifics of it's habitat. Then I pop it in a bottle, take it back to my house, euthanize it, make careful drawings of it, submit the specimen, data and drawings to an expert in that group of flies. He says it is a new species in a known genus, and we publish a paper in some minor fly-centric journal. We didn't have a hypothesis, a priori or otherwise. We didn't even start out with a question. We had a sample size of one. There were no statistics done, or doable. I have heard professional scientists say that for all these reasons, and others, this type of thing is not science. But I know professional scientists who do little else.

In my opinion, it is science if it is an observation based method carefully designed to lead to knowledge that is not faith-based, arbitrary or wrong. (If a method is carefully designed to lead to knowledge that is not faith-based, arbitrary or wrong, but is also not in some way observation based, it is probably math. If all the observation is left to someone else, it might be engineering. These lines blur.)

The paper we write describes science, is the outcome of science, but is not science. The fly was the subject of science, but was not science. The science is in the doing. Science should be a verb. I scienced that fly. I scienced it real good.

Blog of Science

Welcome to Blog Of Science, the blog of science, for science and by science. Or at least that is my working hypothesis.