This photomicrograph shows Cyanobacteria (green) found
in a common pond. Image source: Wayne LanierLast blog I talked about mitochondria. These are the parts of a cell that ultimately turn our food into energy. They also have a very interesting past.

A billion years ago or so, mitochondria were free living bacteria. Then our ancestors hijacked them and now they do our bidding. And mitochondria aren't the only cells that got hijacked. So did the chloroplast’s ancestors.

Chloroplasts are the part of a plant cell that turns sunshine into sugar. Every green plant that we’ve looked at has them. And chloroplasts were almost certainly once free living cyanobacteria.

Both mitochondria and chloroplasts still have many bacterial qualities including having their own DNA. But they don't have a lot of their old DNA left. Most of it has migrated to where the rest of our DNA is kept—the nucleus. Or at least that's the theory.

Do scientists have any proof that DNA can move in a cell from compartment to compartment? As a matter of fact they do. At least with the chloroplast.

Scientists used their ability to put DNA specifically into a chloroplast or mitochondrion to design an experiment to look for cells where DNA had migrated. What they did was put some DNA into a chloroplast that could only be read in the nucleus. (Remember, chloroplasts and mitochondria are different enough that nuclear DNA doesn't work there and vice versa.)

The DNA they put in made the plant resistant to a poison IF the DNA could be read. One way the plant could survive was if the DNA they put in the chloroplast ended up moving from there to the nucleus. And it did.

In fact, it was pretty common in their experiment. The DNA moved in something like 1 in 16,000 pollen cells. A rate like this suggests that, for example, different cells on the same leaf might have different amounts of chloroplast DNA in their nuclei.

So DNA can move from the chloroplast to the nucleus. And probably from the mitochondrion to the nucleus too. The evidence is less direct for this but there is plenty of DNA in the nuclei of lots of different plants and animals that looks very mitochondrion-like.

This all fits in with our understanding that DNA is not as stable as a lot of people think. DNA changes between generations and within an organism. Chromosomes can get rearranged, genes copied or deleted, small DNA changes can happen and who knows what else. And these changes are a big part of the motor that drives evolution.

Sea anemone and clownfish, ants and the acacia tree; in the natural world, there are many symbiotic relationships, those in which two species benefit from each other. Humans, it seems, are rarely part of such a partnership, so it was all the sweeter to believe I had discovered one.

I knew that my fall journey to Uganda and Rwanda would include a grand finale of hiking into the Virungas Mountains and encountering the rare (only 700 left) Mountain Gorilla. I knew it was going to be incredible to see such endangered and magnificent creatures close up. I knew the hike through mud and thistles would be challenging. I knew what to wear. I thought I knew it all, but was quite unprepared for what I witnessed.

Entering the Virungas Park headquarters after a hectic boarder crossing and rain threatening to dampen our experience, our group of 20 felt incredible relief to arrive in the care of our guides, who greeted us with smiles and hot coffee.

As the men spoke of Group 22, the gorillas we were to visit, it was clear this was more than a job to them and that these gorillas were not simply their livelihood. One of the guides had known a particular gorilla for over 10 years. They worried about their well being, about the poaching and human born disease (www.mgvp.org) that threatened them, and about how they were doing within their group. They were their family.

After a rather magical three hour journey through bamboo and mud, we met up with the trackers and left everything besides ourselves and our cameras in a pile.

"Let us meet our cousins," the guides said.

We climbed over a ridge… and there they were.

Now for the part I was unprepared for: the gorillas were willing to let us into their bamboo forest homes, willing to let us to gaze at their long-eyelashed females and infants with tiny human-like feet, willing to hear us giggle at the antics of their juveniles and quietly gasp at the sheer size and gentle power of their silverback. It was astounding what they allowed, and it seemed their allowance was part of a contract agreed upon long ago, to be part of a mutually beneficial partnership.

Upon first seeing the silverback, the guides gave a greeting: a long grunting huff-growl which seemed to say, "Hello. It is us. You know us and trust us. We are here for our one-hour allotted visit with 8 friends. They mean you no harm. You are the boss." The silverback made a small grunt at them that seemed to say, "Fine. Just be cool." Each time any gorilla in the group got too close to us, the grunting huff-growl was given to the silverback. They were communicating.

As we began our blissed-out descent, one more grunt from the silverback seemed to say, "Thank you for protecting us and our habitat. Now your time is up. We will see you tomorrow, if that is what it takes. Good Day, Sirs."

A symbiotic relationship? Let's just say yes.

On the public floor of the California Academy of Sciences is a direct tie into research and resources of many a variety and color. The Naturalist Center is located on the third floor adjacent to the exit from the planetarium. It is an often overlooked treasure. The Center offers a wide range of resources and services to individuals interested in learning more about the natural world. Academy visitors can walk in during open hours, explore the library, conduct research, and connect with staff members as well as other visitors.

Academy visitors can also ask questions about Academy exhibits or natural history. One day, when I was working in the Naturalist Center, a woman asked if squirrels eat bark and if so are they particularly fond of citrus bark? With a bit of research, we found out that some California-native squirrels indeed do eat bark and are fond of citrus trees. Below are some of the questions asked recently in the naturalist center, their corresponding answers as well as links to relevant fact sheets.

Q: Why is the green iguana orange? What do you feed it? (Visitor)

A: According to an Academy aquarium biologists, when males reach sexual maturity their coloring will turn orange. It's more hormonal than dietary, however diet can slightly influence color. The Academy has a male that is roughly three years old. He was rescued from a flea market as a baby in very poor condition. He is fed primarily greens (dandelion, collard, arugula) and small amounts of green beans, sweet potato, yellow squash, mango, berries, banana, papaya, cactus, and flowers along with a vitamin/calcium supplement.

Q: What is a hyrax?

A: A hyrax is related to the manatee and dugong and is the closest living relative of the elephant. More information is given on hyraxes in this fact sheet: www.awf.org/content/wildlife/detail/hyrax

Q: What is the wattage of the lights that are above the rainforest dome?

A: The electrician in the Academy noted that they are 1000 and 2000 watt bulbs.

Q: How much does the roof weigh?

A: It weighs between 2.7 and 2.8 million pounds not including the steel and concrete. More specific information is given on the Living Roof Fact Sheet: http://www.calacademy.org/newsroom/releases/2007/living_roof_fact_sheet.php

Q: How many African Penguins are in an average colony?

A: The number varies greatly and there is no true average. There are colonies with as few as 240 breeding pairs and one that was as high as 55,000 at one time. African penguin numbers have declined worldwide at an alarming rate in recent years. Decline in numbers is due to threats that range from oil spills to feral cats. Food availability and prime breeding territory are major factors in colony size as well. Today, there are an estimated 50,000 total breeding pairs worldwide. More information is given on African penguins in this fact sheet: http://combine.cs.bris.ac.uk/opencms/opencms/Richards_Homepage/My_Research/AfricanPenguin.html

23 hours 59 minutes 60 seconds—this is what a leap second
looks likeDid you make good use of the extra second you received in 2008? A little extra sleep perhaps? Did you notice the extra time?

Probably not, but there it was:  a leap second was added to the end of 2008, such that the world's precision timekeeping system held its breath for a second at 11:59:60 PM, December 31st before declaring 12:00:00 AM January 1st, 2009….

So why all the fuss about adjusting clocks by a second? As accurate as I try to keep my own clocks, they're never better than plus or minus a minute or so anyway.  For most of us, this level of nit-pickery is unnecessary– but there are many functions in our modern digital, computerized society that rely on extremely accurate timekeeping and coordination.

Ever used a Global Positioning System (GPS) device to locate your dog or stolen car or help guide you to a desired destination? The GPS satellite system requires hyper-accurate timekeeping to do its job.

Computer networks are coordinated with precise standard time.

Some cutting-edge scientific research depends on accurate time, sometimes to millisecond.  The observatory I worked at in Flagstaff, Arizona– the Naval Prototype Optical Interferometer– was so dependent on accurate time that one night our interferometric observations could not be made because there had been a leap second no one had taken into account!

So why do we have leap seconds? When it is explained that leap seconds have something to do with the fact that the Earth's rotation slowly changes over time, people often make the assumption that the Earth's rotation has slowed down by a second since the last leap second (and leap seconds occur roughly every 20 months).  But if this were so, then in a mere 144,000 years the Earth's spinning would grind to a complete stop! In reality, at present, the Earth's rotation slows by about 1.7 milliseconds per century (a millisecond is one thousandth of a second).

With leap seconds, it's important to understand that the adjustment doesn't reflect how much the Earth's rotation has changed since the last leap second, but rather the difference in the length of a day between two different time systems that have gradually drifted apart over a century or so:  mean solar time and coordinated universal time (UTC).

For a long time, the second was defined as 1/86,400th of a mean solar day.  But around the middle of the 20th Century it was realized that a mean solar day, based on Earth's rotation, slows over time through tidal friction, and also varies due to mass shifts, such as glacial rebound.

In 1956, the second was redefined to be based on the Earth's revolution around the Sun:  one second was set to be 1/31,556,925.9747th of the mean solar year of 1900.  But even this was decided to be too variable over time to be the basis for a uniform time system.

So, in 1967, another, far more uniform natural rhythm was used to again redefine the second:  oscillations of the atom Cesium-133, which can be measured with an atomic clock.  One second in the new time system (UTC) was equal to 9,192,631,770 oscillations of a particular ground state of Cesium-133.  As it was contrived, the length of one second of mean solar time and UTC time were exactly equal in 1820…

…but since 1820, the Earth's rotation has slowed so that now, the mean solar day is about 86,400.002 seconds long as measured by the UTC system—2 milliseconds longer than in 1820.  So every 500 days that difference grows to 500 x 0.002 = 1 second.  A leap second is born.

That makes 2008 an exceptionally long year, since it was also a leap year:  366 days, 1 second.  I hope you enjoyed it!

The Bush Administration has recently passed dozens of so-called "midnight regulations" - last-minute rules and amendments. Many of those new laws affect the environment, including a change to the Endangered Species Act that has California environmentalists deeply worried.

Listen to the Last Minute Rules radio report online.

Bad for the Lab, Good for the Country

Staff at Building Solutions, a home performance
company, install PV on a roof in Oakland. Next year, the renewable
and energy efficiency business will be even better.
Credit: Kate KenkeDr. Steven Chu, Noble-prize-winning physicist, and director of Lawrence Berkeley National Laboratory, was named as President-elect Barack Obama’s nominee for Secretary of Energy. Home Energy is a nonprofit magazine, but our offices are at Lawrence Berkeley Lab and the magazine was founded by Alan Meier, a lab scientist. People around here are saddened by the loss of Dr. Chu as director of the lab, but extremely excited about his nomination as Secretary of Energy. Dr. Chu believes in science and the important place of technology in helping us meet our energy goals and fight global warming—think cellulosic bio-fuels, nanotechnology, and yet undreamed of solutions to the present energy and environmental crisis.

Weatherization Works!

Word in energy efficiency circles is that the funding for Department of Energy (DOE’s) Weatherization Program will increase several-fold with President Obama’s proposed economic stimulus package. The Weatherization Program is managed state by state from money provided by DOE, and the funds pay to retrofit the homes of low-income families. Homes become healthier to live in, more energy efficient, and more comfortable for the occupants. For every one dollar the Weatherization Program spends, almost two dollars in energy savings results. Hundreds of thousands of homes have been retrofit so far, leaving about 99.5% of existing homes. Talk about green jobs potential! Many nonprofit and for profit organizations do weatherization work, and, basically, you retrofit the home of a low-income family the same way you retrofit a mansion. Lots more skilled people will be needed to do the work, and the jobs will provide a good income, benefits, and the possibility of future advancement. Community colleges, unions, professional training organizations, online trainers, and other players are gearing up to train the new green workforce.

How Many Btu Do You Do?

I promised in my last blog entry to explain the concept of heating-degree day and cooling-degree day. Sometimes you will hear that a home uses so many Btu or kWh per heating- or cooling-degree day, per square foot, per year. The degree days indicate the heating or cooling load on a building’s HVAC systems. A degree day is the rise or fall of one degree Fahrenheit for 24 hours. The rise or fall in temperature is measured from a baseline of 65F°. For example, if the average temperature tomorrow is 45F°, than the heating load on your heating system is 20 heating-degree days. If on a hot summer day the average temperature over a 24-hour period is 85F°, than the load on your air conditioner is 20 cooling-degree days. The number of heating-degree days for a winter in New York is around 5,000. Barrow, Alaska has about 20,000.

You can figure out how much energy you use to heat or cool your home by subtracting the baseline energy use. During a month when you are using neither your air conditioner or heater, such as in October or March (called the “shoulder” months), your gas and electric use represent your baseline. The baseline covers energy for lighting, appliances, hot water, and plug loads. Subtract out the baseline from your winter or summer energy use and you have the amount of energy to heat or cool your house. If you know the square footage of your home, and you have weather data for your area (go to www.degreeday.net to find out heating-degree days and cooling-degree days for your area), you are in a position to brag to your neighbors (or not) about your energy use.

At our house we used about 90 therms of natural gas from September 7 through December 7, 2008. There were about 480 heating-degree days (HDD) in our area during that time. Our baseline use of natural gas is about 10 therms per month, for heating water and cooking, leaving 60 therms for heating over the three-month period. Our house is about 1,200 square feet (ft²). Therefore, we used 60 therms/(480 HDD x 1,200 ft²), or about 0.0001 therms/HDD·ft². Since one therm of natural gas contains about 100,000 Btu of energy, that equals about 10 Btu/HDD·ft². That’s not bad, but not great either. How about you?

This former free living bacterium now supplies our cells
their energy.Current theories hold that life began on Earth around 3.5 billion years ago. About a billion years ago, a single celled beast engulfed and absorbed another single celled creature. We are all descended from that hijacking.

The hijacked cell has over time become the mitochondrion. This organelle is responsible for making our energy. But it still has the marks of having once been a free living bacterium.

First off, mitochondria still have remnants of their old DNA. There isn’t much there in human mitochondria but there is enough to still get us into trouble. A big part of aging might be due to damage to this mitochondrial DNA (mtDNA). Some genetic diseases are also caused by mutations in mtDNA.

The DNA in mitochondria is also much more like bacterial DNA compared to the rest of our DNA. In fact, the mitochondrion has its own bacteria-like machinery for reading its DNA. This means that mitochondria can’t read the genes in our nucleus and vice versa. Mitochondria are so similar to bacteria that some antibiotics can damage them too.

Even though it was once free living, the mitochondrion doesn’t have a lot of its original DNA left. Over time, most of our mitochondrion’s original genes have traveled to the nucleus. These genes now work in the nucleus to make most of a mitochondrion’s proteins which are then transported back to the mitochondrion.

After all these years, human mtDNA is now only around 16,000 bases long and has only 37 genes left. This is a far cry from even the simplest of bacteria, Mycoplasma genitalium, with its 582,970 bases and 521 genes.

Humans are not unique in having mitochondria. Every plant, animal, and fungus cell in the world that has been looked at has mitochondria. But the DNA in these mitochondria is all wildly different.

The size of mtDNA can range from just 6000 base pairs all the way up to 2 million base pairs. Sometimes the mtDNA is a circle like ours. Sometimes it is spread out over lots of little circles. Sometimes it is one long, linear piece of DNA. Sometimes it is lots and lots of little pieces of linear DNA. And sometimes it is too weird to describe in a short blog like this.

Mitochondria from different species also have different numbers of genes. Some species have mitochondria with nearly 100 genes. While others have as few as 5.

With up to 2000 mitochondria/cell, evolution has had a free hand in tinkering with mtDNA. If a mutation or change in mtDNA causes a problem, that mitochondrion simply goes away. If there is some advantage to the new DNA structure, it is free to sweep through and take over. It is amazing what evolution has done to this bacterium!

Of course, evolution has made the mitochondrion a shell of what it once was. But we could argue that it is one of the most successful beasts ever.

It has gone from humble bacterium to being part of every eukaryote in the world. If humans die out, mitochondria will still be around somewhere else. Mitochondria will outlive us all.

More information on mitochondrial genomes: http://dx.doi.org/10.1016/j.tig.2003.10.012

Terrestrial snow at Chabot on December 16, 2008
Photo by Craig CoryellDriving to work today, I was amused to notice that the raindrops falling on my windshield were a bit grainy–and getting more so the higher up the hill I drove. I starting to think, is it starting to sleet? By the time I reached Chabot–at 1500 feet elevation–the precipitation had turned to bona fide snow!

This is quite unusual for the Oakland Hills, of course. In the ten years I've worked here, this is the second, maybe third, dusting I've witnessed. I recall the great freeze of '74, when it actually snowed in Oakland close to sea level—that's the year all the eucalyptus in the hills froze and died.

My mind wandered—pretty far out in space (an occupational hazard at Chabot). I started thinking about all the recent news and discoveries from around the Solar System, my thoughts guided by the fat white flakes drifting down all around the observatory domes.

Last September, NASA's Mars Phoenix Lander detected snow falling high in the atmosphere–about 4 kilometers high. This Martian snow, however, quickly evaporated in Mars' thin, dry air, never reaching the ground. Phoenix used a laser probe to make the detection–so we don't actually have picture to look at!

Snows of the Solar System may also fall out of the plumes of "cryovolcanoes"–the frigid outer Solar System's version of volcanism (may it live long and prosper). On moons such as Saturn's Enceladus and Neptune's Triton, plumes of material have been detected spouting from fissures and cracks–probably fueled by heat generated by tidal forces from their parent planets.

On Enceladus, the geyser plumes contain water vapor and ice crystals, and are believed to come from subsurface lakes of "warm" water (32 degrees Fahrenheit–in other words, ice water… but that's a veritable hot spring, or magma chamber, on a cold moon like Enceladus!).

The ice crystals in the geysers' plumes mostly fall back to Enceladus–maybe in a diffuse fall of "snow" across the globe? I'm waiting for those pictures…

Saturn's large moon Titan is speculated to possibly have a form of cryvolcanism, though no direct detection has yet been made. Still, any water vapor that might erupt from a Titanian cryovolcano might be expected to fall in a form of snow….

Triton, much farther from the Sun than Saturn, is even colder than Enceladus. In fact, it's been called the coldest measured surface in the Solar System, at -391 degrees Fahrenheit. Here, nitrogen freezes solid. Triton cryovolcanoes, or geysers, may be partially solar-heated, but tidal heating within Triton is probably dominant. Triton's geysers spout nitrogen gas and dark material, which falls across the landscape in dark streaks and lighter deposits of frozen nitrogen–a form of extreme cryo-snow, to my imagination!

Now, are you as cold as I am just thinking about it? Time for a cup of cocoa…

By reporter Marjorie Sun.

I got interested in this story after hearing Silicon Valley venture capitalist Vinod Khosla speak at a conference this fall in Sausalito. He explained how he decides where to invest in green tech and it was fascinating. He and other top venture capitalists think they can help stop global warming and make a ton of money at the same time. You can listen to Khosla's talk on a webcast and listen to all sorts of entrepreneurs and v.c.'s talk about the latest renewable energy projects.

Khosla says to achieve a huge reduction in greenhouse gas emissions fast, we have to think about solutions that make big cuts in emissions and will be widely adopted. Buying a Prius is fine, he says, but it's really just "fashion." We need solutions that people in India and China will buy, Khosla says. To him, the key issues that guide his investments are cost, scale, and adoption. If a renewable solution isn't cheaper than coal, forget it, he says. Geothermal "is nice, but it doesn't scale."

Same with wind. It's "a great technology, but it's a toy." As for hydrogen fuel, the adoption risk is too high. Again, forget it, he says. The focus should be a war on coal, oil, and the manufacturing of cement and steel, which are huge emitters of carbon dioxide. (He's a major investor in Calera, an alternative cement maker in Silicon Valley.)

One more area for potentially huge gains is to improve energy efficiency, such as lighting. Another legendary venture capital company, Kleiner Perkins, is also racing to develop renewable energy solutions and make a fortune. (Khosla is a former partner there.) Kleiner's efforts were profiled in a cover story in The New York Times Sunday Magazine recently

With the Obama administration, it will be interesting to see what new federal policies– tax, economic and regulatory– will be adopted to accelerate solutions and spur more investment during a double whammy of crises: the economic meltdown and climate change.

Listen to the Building Blocks Go Green radio report online.

On the surface, geoengineering almost seems like science fiction. Could humans engineer a way to compensate for global warming by changing dynamics in the Earth's atmosphere? But it's one of the ideas being discussing at the American Geophysical Union conference in San Francisco. Each year, thousands of scientists descend on downtown San Francisco to hold a week of meetings and discussions.

Here's how the idea would work: Using planes or other high-altitude transport, we'd disburse millions of tons of sulfur dioxide (or hydrogen sulfide) into the stratosphere, 13 miles above the Earth. Those gases would create tiny particles, which would reflect sunlight. This process already goes on in the stratosphere - about a third of the energy from the sun is reflected back into space thanks to this dynamic. But by adding more reflecting particles, scientists think it might be possible to cool the planet - and compensate for human-induced warming.

No one has tried this idea yet - but it's something scientists have already observed — through volcanoes. In 1991, Mount Pinatubo erupted in the Philippines, spewing 20 million tons of sulfur dioxide into the atmosphere. As a result, global temperatures temporarily dropped about one degree Fahrenheit.

That doesn't necessarily mean a scheme like this would work. As UCLA Scientist Richard Turco said, it's not easy to predict how the particles would react and disburse. "If the particles are too large, that would actually create a warming effect, a greenhouse warming. Small particles are not useful because they don't reflect much radiation."

This plan isn't just a one time deal. As Turco continued, "we would need a huge monitoring system and can't afford to make any mistakes. Once you start this process, you have to maintain it for two to three centuries."

And then there's the "get out of jail free" aspect. If the focus of climate change policy becomes geoengineering, what happens to simply cutting emissions? As Professor Alan Robock of Rutgers University acknowledged, the costs and technology of geoengineering are uncertain — and it wouldn't curb other climate change impacts, like ocean acidification. "We have to focus on mitigation and keep this in our back pocket for emergencies."

According to Professor David Keith of the University of Calagry, it's worth studying geoengineering — just in case. Our greenhouse gas emissions will continue to grow. "We're not going to stop today, and even if we stopped today, there's enormous inertia," Keith said. In the event that climate change becomes catastrophic, Keith says we may need a last resort. "Whether you like or don't like this, it can be done quickly."

For more on what's new at the AGU, check out KQED's Climate Watch blog.