Category Archives: Earth

Aquatic Microbial Diversity

Today is a big day on Plos-Biology for the Oceanic Microbial Diversity Genomics. Last night they published not one, not two, but three big papers chockfull of data.
Accompani\ying them are not one, not two, not three, not even four, but five editorial articles about different aspects of this work.
James has already homed in on one important part of the discovery: the preponderance and diversity of proteorhodopsins – microbial photopigments that are capable of capturing solar energy in a manner different from photosynthesis. As always, light-sensitive molecules are thought to be tightly connected to the evolution of circadian clocks so I expect to see some research on this in the near future.
The biggest challenge of this kind of research is how to take gobs of goo, i.e., the collective DNA from everything collected in the samples, and figure out which sequence belongs to whom. How many microbes have really been captured in the sample? How do those microbes look like? What can we say about their biochemistry, physiology and behavior? What can we say about their ecology and their evolutionary history? What counts as a ‘species’ in the asexual world of microbes?
The methods they use to try to start answering those questions are all genomic – other bloggers may be able to better understand and explain the details which involve various sequence alignments and comparisons to known microbial genomes.
What I’d like to see is a more ecological approach: sampling at different places, at different depths and at different times.
Many aquatic organisms, both unicellular and multicellular, are vertical migrants. They may swim up to the surface during the night and sink down to a greater depth during the day (or vice versa). Sampling at two or more different depths at noon and again at midnight and comparing the sequences can separate the genomes – those sequences that always appear together in the sample will belong to the same organism, those that sequester belong to different organisms.
Likewise, some organisms swim up to the surface only once a month during the full moon. Some never do and are always found only at greater depths. There is likely a seasonal change in the community compposition as well.
Of course, it is expected that different species will be found at different parts of different oceans, in rivers and estuaries, in lakes and streams, which can tell us something about the ecology of the organisms in each of these environments.
Finally, repeated sampling over a number of years at the same place, same depth and same time of day/lunar cycle/year will allow us to track the long terms effects of climate change on the aquatic communities.

Global Warming Symposium at NCSU

Global warming change is the topic of a symposium, free and open to the public, in NC State’s Campus Cinema, located in Witherspoon Student Center, February 26-28, and featuring excellent speakers. Elizabeth Kolbert, author of FIELD NOTES FROM A CATASTROPHE, opens the meeting on Monday, Feb. 26, at 7:00 p.m.

For more information and to see who else is speaking during the three-day event, click here

When is the Biological U.N. report on Global Warming coming out?

Russ, correctly, points out that the new UN report on Climate Change says not a word about the impact global warming will have on ecosystems, plants and animals (including the human animal).

More “balanced” view on Global Warming….!

Global Warming threat may be even harsher than the latest UN report suggests, but the Wingnuts want to make sure we teach the kids quite the opposite. Yeesh!

Cloning Domesticated Animals: Pros and Cons

Food From Cloned Animals Safe? FDA Says Yes, But Asks Suppliers To Hold Off For Now:

The U.S. Food and Drug Administration (FDA) has issued three documents on the safety of animal cloning — a draft risk assessment; a proposed risk management plan; and a draft guidance for industry.
The draft risk assessment finds that meat and milk from clones of adult cattle, pigs and goats, and their offspring, are as safe to eat as food from conventionally bred animals. The assessment was peer-reviewed by a group of independent scientific experts in cloning and animal health. They agreed with the methods FDA used to evaluate the data and the conclusions set out in the document.
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The proposed plan outlines measures that FDA might take to address the risks that cloning poses to animals involved in the cloning process. These risks all have been observed in other assisted reproductive technologies currently in use in common agricultural practices.
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In the draft guidance, FDA does not recommend any special measures relating to human food use of offspring of clones of any species. Because of their cost and rarity, clones will be used as are any other elite breeding stock — to pass on naturally-occurring, desirable traits such as disease resistance and higher quality meat to production herds. Because clones will be used primarily for breeding, almost all of the food that comes from the cloning process is expected to be from sexually-reproduced offspring and descendents of clones, and not the clones themselves.

Jake already wrote what I wanted to write, but here it is in a nutshell:
Meat and Milk safety
Meat is meat. Milk is milk. Beef of any other name is still beef.
Cloned animals are not the same as genetically-modified animals. First, cloned animals are NOT identical to their parents. Second, there is no insertion of non-cow (or non-sheep, non-pig, etc) genes into these animals – no danger of aflatoxin, or peanut genes that can trigger allergies. Every protein in the steak of a cloned cow is still a typical cow protein. If you can normally eat beef, you can also eat cloned beef – there is NO chemical difference.
Ethics
Cloning animals can teach us a lot about genetics and development of animals with, probably, some practical applications down the line. I see no need – and apparently farmers don’t either – for mass production of cloned animals. Only animals targeted to be cloned will be champion breeders. And there is no way that Thorougbred racehorses will ever be cloned – even assisted fertilization (i.e., artificial insemination) is illegal (i.e, the animal will not be included in the Stud Book). So, only a few champion breeders from a couple of species (cows, I guess, perhaps sheep and pigs) will be cloned. This is good – to keep this at a minimum, at least for now – as the process of cloning produces a lot of sickly offspring, which raises ethical questions in itself.
Agricultural practice
We already have a virtual monoculture in both plant and animal production for food. Such lack of genetic variation is troublesome as a new diesase (or global warming) may quickly sweep through our herds and deplete our food supply very fast. Making the gene pool even more homogenous in order to raise the meat/milk productivity of our animals just a little bit does not, in my opinion, warrant a widespread use of cloning of domesticated animals. I’d rather support small farmers who purposefully keep rare, unusual breeds of animals like Old-Type Oldenburg horse, Curly Bashkir pony or Mangalitza pig – breeds that contain genes absent from our current gene pool of mass-produced animals and provide a reservoir of useful traits we may need in the future.
Update: On the other hand, a truly genetically modified animals mey be good: Mad Cow Breakthrough? Genetically Modified Cattle Are Prion Free!

New Cool Local Blogs

Go check out The Mill and Carrboro Commons.
The Mill Editor did some digging and found that a lot of cool scientific research on climate is being done locally.

Global Warming for Ditto-Heads

Explained patiently, with pretty pictures.

Books: Michael Pollan – The Omnivore’s Dilemma

Amanda just reviewed Michael Pollan’s book The Omnivore’s Dilemma and also recently wrote a post on the same topic while under the influence of the book. I agree with her 100%, so go and read both posts.
I have read the book a couple of months ago and never found time to write a review of my own. I also remember that I finished the book on a Thursday afternoon – an important piece of information as it is on Thursday afternoons that there is a Farmers’ Market here in Southern Village, barely a block from me. The first thing I did when I closed the book was to walk up to the Farmers’ Market, buy some locally grown food and talk to the farmers about all the issues raised in the book and, lo and behold, they all agree with Pollan on everything I asked them about.
They were also a little taken aback that I tried to talk to them. But, I grew up in the Balkans. A big part of going to the Farmer’s Market is to chat with the farmers, banter, joke, complain about the government, haggle over prices, and make sure a kilo of cheese is reserved for you for next week – it is a very friendly and talkative affair. Great fun! Here, there is much more of a class divide. The farmers set the prices. The elegantly dressed city-slickers pick and pay. And all of that is done pretty silently, with a minimal exchange of words. No eye-contact. Nobody is haggling! At the Farmers’ Market nobody is haggling!?*@#%$^&! Travesty and Heresy!
In his book, Michael Pollan initially set out to make three – industrial, organic and personal – types of meals, but once he learned more, he realized he had to do four: industrial, industrial-organic, local-sustainable, and personal.
So, although the book officially has three parts, it really has four. Each of the four parts also reads differently and has a different style and tone:
The first part (industrial) is full of facts, stats, governmental documents, etc. – it reads like Molly Ivins’ Bushwacked or Chris Mooney’s Republican War On Science, although I heard he played loose with some stuff, i.e., cited as true some studies that are very contentious within the scientific community.
While I am a biologist, focusing on animals made me “plant blind” and I learned more about biology of corn from this book than I ever knew before.
The key event, according to Pollan, is the change, during Nixon administration, in the way farmers are paid for corn – everything else flows from that single event: the monoculture, the oil, the feedlots, the fertilizers and pesticides, environmental destruction, obesity and McDonalds.
The second part (industrial organic) is a little bit less of an onslaught of information and he gets a little looser and slower, a bit more personal. He looks at the way organic food production changed since the 1960s hippy farms to today’s giant organic producers who are, more and more, playing by the rules of Big Agra.
While the food they produce is still better than the Industrial and the practices are still more energy and environmentally friendly than Industrial, it only looks good because it is compared to the Big Industrial which is totally atrocious. This part of the book resulted in a big back-and-forth debate between Pollan and John Mackey, the CEO of Whole Foods, resulting in some changes in the way Whole Foods operates. You can find the relevant links on Pollan’s website.
The third part (local-sustainable) is totally fascinating – it is a mix of a travellogue and analysis – he keeps jumping back and forth between his dialogues with his host – Joel Salatin of the Polyface Farms – and the data. This is really the most riveting part of the book and the key element of it. This is also a part of the book that covers most new ground, not stuff found in Fast Food Nation or other well-known books. It also exposes, even better than the first part, the perniciousness of the way our agricultural system is set up, the way Big Agribusiness controls legislation and regulation, and eliminates small farmers from the competition.
Joel Salatin is a Virginia farmer who has perfected amazing agricultural practices on his farm – practically nothing has to be bought by the farm and nothing gets thrown away. Everything has its use and re-use. Everything makes sense when patiently explained to the reader. I actually bought Salatin’s book Holy Cows and Hog Heaven and read it immediately after Pollan’s.
Interestingly, although the guy is a conservative, libertarian, Christian Creationist, I agree with him on almost everything. His distrust of the Government is perhaps a little bit over the top for my taste, but his Creationism is fascinating because his whole philosophy and his whole methodology of the way he runs the farm reveals a deep understanding of evolution and ecology. His farming practice is BASED on evolutionary thinking. He is, for all practical purposes, an evolutionary biologist. Yet, he says he does not believe in evolution. How is that possible? Because he has no idea what he word “evolution” means. He probably has some “chimp is your uncle” cartoon notion of evolution, while at the same time not giving his own evolutionary ideas any name at all. Someone should tell him.
The fourth part (personal) of the Pollan’s book is in a completely different mood, very introspective, sometimes even mystical. One important thing that sets this part apart is that the type of food production described in it is the only one of the four that cannot in any way be affected by legislation, politics or activism – unless one completely bans hunting, gathering, catching, picking, stealing from neighbors, planting stuff in your garden, or collecting yeast from the air!
The best part of this portion of the book is his look at animal rights and his dialogue with Peter Singer. He, being such a typical city-slicker and “Birckenstock liberal” (Come on – slaughtering a chicken, and later a pig, made him sick? Has he never watched or participated in any kind of animal slaughter in his long life yet? Never spent some time on a farm? Dissected an animal in a biology class? What a woefully unnatural and alienated existence!), started out very sympathetic to the idea, but, over a dozen pages or so, dissects the underlying logic and discovers its fatal flows and exposes it in a brilliant paragraph – the best one in the book. You’ll find it and recognize it immediately once you read it – and you will read it because Omnivore’s Dilemma is one of the most important books written in the last few years, and should be a battle cry for many political activists and a source of ideas for many candidates for political office.
In the meantime, go read Amanda’s review.

Earth Science Week

October 8-14 is Earth Science Week. This year’s theme is “Be a Citizen Scientist!” Wolverine Tom is blogging hard this week – see this, this, this and this for now. How about an Earth Science Blogroll for all of us to bookmark?

An Erratic Rock

Go see a rock with a cool story to tell.