Sunday, February 21, 2010

Rubisco enzyme and photosynthesis and photorespireation

In studying climate and how it is intertwined with biology, plant photosynthesis, and the carbon cycle, I've read that plants, most commonly known for their photosythesis, also respire carbon dioxide. They can emit CO2 to the air and to the soil. A recent article in Nature helped me answer a few lingering questions I've had. I'm citing from Nature 14 January 2010 (News and Views by R. John Ellis and article by Liu et al).

Lingering question 1: Do plants get all their carbon from the atmosphere? If not, then the use of plants in biofuels would fail to be carbon neutral. (Note: many other factors can undermine the carbon neutrality of biofuels).
The news and views article credits "virtually all organic carbon in the biosphere" to the rubisco enzyme used in photosynthesis to capture CO2 from the atmosphere. I can't help but wonder whether in the 1/2 billion years of terrestial plants, some species may have evolved a capacity to pull carbon out of the soil, but this is just my speculation. Rubisco is present in photosynthesis, and with it, alternatively, plants may have had no incentive to get carbon from the soil.

Apparently, rubisco emerged when the Earth had little oxygen in the atmosphere and higher CO2. Thus, this choice of enzyme is not as a efficient in the higher oxygen level of the atmosphere established between 800 and 540 million years ago.

Lingering questioon 2: what enables plants to respire CO2?

Rubisco can react with either CO2 or oxygen. So, as rubisco fixes CO2, to a lesser amount, it is also reacting with oxygen and producing CO2. The News and Views author cites a loss to photorespiration of up to 25% of the CO2 captured in photosynthesis. So, I can say with confidence that plant respiration has a credible scientific basis.

The article addresses efforts to engineer a process by which the loss of photorespiration is eliminated from agriculture. I don't feel I can represent what I read on this, and so I won't.

The real interesting part, and the part that ties in with my recent effort to have more explanations of the carbon cycle and biosphere is the reviewer's mention of what happens to the ratio of rubisco's photosynthesis to photorespiration under warmer temperatures: essentially, that warmer temperatures will increase photorespiration. Thus, warmer temperatures can make plants less efficient at sequestering CO2.

So, where increased CO2 can act as a fertilization (and I've read studies making this claim), increased temperatures will take away from this benefit by making plant photosynthesis less efficient. I'm creating an ever growing list of effects and counter effects on this subject.

My remaining questions are 1) is the inefficiency accompanying warmer temperatures linked to the rise of CO2 following warmer temperatures inferred from ice cores; and 2) will plants merely get less efficient or will we see species turnover, where species  that do better at fixing CO2 under warmer temperatures replace those that don't.


Wednesday, February 17, 2010

Seasons, sinks and sources

(This topic continues the project I started with this earlier post on seasonal variation.)

Every few years, in southern California, I watch vast areas go up in flames. A small, recent, and well-contained example from August 2009 is shown here:

I make no claim to know if this is more frequent in recent years, but regardless, frequent burning is part of the ecology here. A common land cover called chaparral gets its name from the Spanish word for fire; it's dominant plant, chamise, is also called greasewood and burns easily. It's probably safe to assume that ignition sources have increased with the increased population here (as has fire suppression efforts?).

Less dramatic than the release of stored carbon by fire, is the seasonal transition from a carbon sequestering state (the spring and summer growing season) to a carbon emitting state (in autumn when carbon sequestered in new growth is less than CO2 exhaled by animals).

Chaparral, also called Elfin Forest, in July; the tallest bushes are about 12-14 ft high
Some plants in this photo are: 1) sugar bush (left foreground, low green and flowering; 2) California Everlasting dried short herbs in center--they smell like maple syrup; 3) right foreground, manzanita; 4) center background and still green, chamise; and 5) I'm looking up the tallest bushes that dominate this scene.)

Chaparral in October

I hope these photos photo shows the color and dryness of the region. Though the July photo is noticably greener, it marks the beginning of a dry season that continues through October on till when the winter rains return. (October has been quite a fire season in recent years.)

Whereas I used to watch seasons in terms of plant turnover, change in flowering and color, I now to try to imagine where my observations reside in a biome's cycle between CO2 sink (growth season) and source (decay are dormant season). Thus, I'm intrigued by efforts to quanitify the extent to which the biosphere acts as a sink or emitter of carbon and CO2. This topic has gotten quite lively with a recent paper published in Nature and discussed by RealClimate.

Two years ago I studied a review article and paper in the Jan. 3, 2008, issue of Nature that measured the sink/source effects in terms of zero crossing dates that represent the tipping point between spring-summer growth (spring zero crossing date) and between autumn-winter decay (autumn zero crossing date). I've redrawn and embellished the diagram from the original review.

The blue line shows a yearly cycle of atmospheric CO2 levels. Roughly, January would be on the far left and December on the far right. The orange line is the long term CO2 level that rises a couple parts per million each year. Warmer climate can extend spring by making it start earlier (e.g., earlier snow melt) or end later (e.g., more rainfall). Likewise, warming can make the dryness of late summer start earlier and extend longer. The illustration shows an examination of just the spring zero crossing date. A shift depending one which season (growing or decay) gets longer relative to the other can result in more or less atmospheric CO2.

 Assuming I understood the research correctly, warming (and other consequences of warming, such as changing rainfall patterns) will affect various regions differently. Some will get longer springs, thus longer growing seasons and more CO2 sequestration. Others will get longer Augusts, where growth stops, decay begins, and animal respiration dominates the CO2 cycle.

The paper I read is based on a study about a dozen locations in the northern hemisphere (update 2/21/10; added illustration):

Generally, the sites in North America were showing longer Autums (thus acting as net emitters of CO2) ; and sites in Europe were getting longer Springs (thus acting as net sinks of CO2). It is an ongoing question how regions respond globally, which will bring me to the next article I'm trying to understand, which is on the speed of climate change.
Poisen Ivy on Palomar Moutain in October

Monday, February 15, 2010

Have I learned? Has he?

Two months I ago I shared an experience from 5 years earlier about how I learned that a dedication to precision and scientific accuracy makes your writing unpublishable for local news media (Five scientific terms you can't in local news media). The columnist whom I was correcting in my unpublishable essay is back again with another letter about global warming (Wishing for some global warming). I've submitted another rebuttal (me, see 2nd comment), so this is a great opportunity to examine whether I have learned anything in the past 5.5 years. Likewise, it's an opportunity to see if he has too.

Because rebuttals I've posted online have mysteriously disappeared before, I'm posting the content below in this order:
1. The writer's 2004 column on global warming.
2. My unpublishable rebuttal submitted for their community forum column.
3. The writer's letter to the editor from 11 Feb. 2010.
4. My rebuttal. (I also sent a shorter letter to be printed, but I won't share that till it's published).

1. The column that was intrumental in my epiphany on climate propoganda:
(in progress; can't find it online and will have to transcribe a news clippin; will add soon)

2. My rebuttal (in italics)
If climate research demonstrates an unambiguous human-caused greenhouse effect, implementing appropriate corrective action will remain controversial. For example, it may be unfair and unscientific to limit fossil fuel consumption and not cement manufacture; or government regulations may be costly, too restrictive, or misguided. If mitigation solutions are market-based, objections to the unpleasant conclusions of climate scientists will decrease. But for the market to mitigate human-induced climate change, it will need better information, starting with the correction of numerous misconceptions about climate science.

One misconception is the belief that climate models are junk science: As in chemistry, physics, and weapons testing, computer models are our best chance of understanding phenomena that too complex to solve on paper and beyond controlled experimentation. Climate models merge the work of many specialties: paleoclimatology (the study of past climate inferred from coral, tree rings, gases in ice cores, and chemical isotopes in fossil-forming plankton in ocean sediments), atmospheric chemistry (how gases, aerosols, and particulates are formed, interact, and are removed), hydrology (water cycles), oceanography (currents, heat, salinity, photosynthesis). There are so many specialties, scientists, and publications involved that we must be skeptical of anyone claiming to understand these well enough to call them junk science.
Another misconception is the notion that a regional or short-term weather trend supports or discredits climate models. Climate models do not have the resolution to tell what's in store for a specific region, whether it's a good time for a drive among the vineyards, or not. They calculate general trends, such as averages of temperatures, precipitation, and wind direction, with resolutions varying between 200 km and 50 km. Finer resolutions will result as scientists continue to test their models against real phenomena. Climate researchers state their models' limitations, and the field has a well-published timeline projecting milestones for improvement.
Climate models are used in a variety of studies besides global warming. For example, in India scientists are trying to use them to predict their monsoons. Other scientists use them to examine natural effects hindering the recovery of over-exploited fisheries. Brief progress in the acceptance of climate models occurred in 2001 when the models showed that North America acts as a net carbon sink, meaning its forests, soils, and peat lands were absorbing more CO2 than North Americans were emitting. This lent support for rejecting the Kyoto protocol, which was doomed regardless, but I suspect these results-oriented skeptics failed to grasp the complete scenario described by the carbon sink modeling: the climate models showed North America to be a net carbon sink in wet and cool years; in dryer and hotter times the stored carbon gets metabolized by soil microbes and animals and North America becomes a net emitter of CO2. By 1999, the northern hemisphere went back to being a net carbon source.
Finally, changes in greenhouse gas concentrations affect more than climate. Oceanographers and ecologist are studying the effects of known increases in CO2. Rising CO2 levels may be changing species composition of pristine rainforests, preferring softwood species and vines (commercially and ecologically less valuable) over the densest understory trees. The pH of seawater is changing as the oceans absorb more CO2 from the atmosphere. Oceanographers are examining what this change portends for the ocean's food chain. Paloeoclimatologists are searching the geologic record for evidence of times when atmospheric CO2 and ocean pH reached levels similar to levels projected for the near future. Should they find these layers, they will learn whether the CO2 levels, ocean pH, and rates at which these changed, created conditions favorable to the agriculture, aquiculture, and economy needed today by six billion humans.
In 2001 president Bush exercised his right of a scientific review of the Intergovernmental Panel on Climate Change (IPCC) report. The National Academy of Sciences confirmed that the science was sound and the conclusions valid with some qualifications. Their reply was a definitive act, like the Supreme Court choosing a president, which should be cautiously accepted so we can examine the implications.

3. Wishing for some global warming
Much of the country is deluged with record snowfall, and we are supposed to believe that this is caused by global warming? Record snow packs fall onto our local mountains. A friend of mine in the D.C. area spent two hours digging his car out of the snow. He was wishing for some global warming.
So, does global warming now cause global cooling?
After the revelations of the e-mails by the Intergovernmental Panel on Climate Change showing fraud and cover-up, anybody with an sliver of common sense can conclude that global warming (and our current global cooling) are caused by, um ---- the changing of the four seasons.
Those who seek to control and regulate every aspect of our lives will utilize any moral panic available to centralize and expand government control.
Notice how they will now attempt to downplay "global warming" by substituting the term "climate change." Climate change is just the changing of the four seasons. What's the next environmental moral panic? Attacking Newton's laws of gravity?
In the meantime, I just filled up the gas tank of my Hummer. I like to think the oil comes from Iraq. Life is great.

4. my rebuttal (in italics) printed on 17 Feb 2010:
Climate change not a subject for common sense
Common sense suggests that the sun orbits the Earth; Rick Reiss (Letters, Feb. 11) asserts that common sense shows Earth is cooling. Climate change is not a subject for common sense; rather, it requires math, statistics, physics, chemistry and data collection, just as describing the solar system does. Reiss cites recent cold weather as common-sense proof that Earth is cooling. This is not common sense, but cherry picking, selecting only the information one believes. If weather observations are suitable, then you have to include killer heat waves in Europe and Australia.
Reiss says snowstorms conflict with global warming — no: Heat, then water vapor, then precipitation. Warmer climate, then more water vapor, then more snow. He claims that scientists backpedal on warming by using the phrase "climate change."
Publishing scientists have used this phrase for 20 years while showing that Earth is warming from increasing greenhouse gases. To understand the e-mails stolen from the Climate Research Center and exploited out of context by people like Reiss, you have to read science journals to know what the e-mails were talking about. One can't explain to activists the error in conclusions they've drawn from stolen information, but as long as they remain ignorant of the science, the science will remain incomprehensible to them.


Thursday, February 4, 2010

Sketch's of Grumbine's Heuristic for Stratospheric Cooling

The following illustrations are my self-inflicted homework from More Grumbine Science (heuristic for stratospheric cooling). I'm still studying his post and comments. I hope to use this exercise and the discussion for an illustration that will help me hold the basic physics in one place. Click an image to get an enlarged version. Below, you'll find blanks.

n the following blanks (templates) I added circles, in which you might want to write the amount of radiation traveling between layers; then use the boxes as sums of the incoming radiation.