Monday, August 28, 2006

Human Evolution - Instant Expert

New Scientist have just done one of their Instant Expert guides to Human Evolution. There is also a useful timeline, a nice set of recent articles on human evolution and even 'infrequently asked questions' (in this case: Over the past few hundred thousand years, humans have greatly increased in intelligence and in the size of their brains. As intelligence appears to produce an advantage to survival, I wonder if all animals show a tendency to evolve greater intelligence over time. Or is the value of intelligence overrated?).


Extreme seabed-survival boosts hope of aliens

Microbes discovered by a lake of liquid carbon dioxide under the sea off Taiwan could help us locate life on Mars, researchers say.
Japanese and German researchers have found billions of bacteria and other tiny organisms living in a layer of sediment which traps the CO2 under the seabed. Their survival in such a hostile natural environment suggests that something similar could be happening on other planets.

New Scientist, 28 August 2006


Fast evolution in mussels

Invasive crab species in New England have influenced blue mussels in the area to exhibit evolutionary change in as little as 15 years, report U.S. scientists in the journal Science. The change gives the mussels better advantage against the predator crabs.

Reported by the Discovery Channel, NPR and Fox News amongst many others.

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Thursday, August 17, 2006

Midterm 3 etc.

Here are the results of the third midterm. Please don't e-mail me for your individual scores, I don't have them!

The overall mean was 81% and the median was 82%.

Nobody managed to get all fifty questions correct this time but four students, in three different sections, got all but one question correct.

Section means were very similar and, yet again, no section mean was more then 3% away from the overall mean of 82%

The histogram of scores is above and the breakdown by grade is below.

A (ie >=90%) - 31%
B - 37%
C - 18%
D - 8%
F - 6%

I have looked closely at all the questions where either less than two thirds of you got the correct answer (I only have this data by section, but it looks like maybe 4 questions) or more than 20% of you picked a particular incorrect answer (again, maybe 4 questions) and don't see any serious problems.

Well it's been fun. I hope some of you have enjoyed reading the blog. Google's blogger is certainly convenient but I have to say it has the most bizarre spell checker. It's not surprising it doesn't have technical terms in its database but it tries to replace them with amusingly inappropriate terms. Here's a couple I particularly enjoyed:

one of a whole family of defoliants used during the Vietnam war.
is much improved as:
one of a whole family of diplomats used during the Vietnam war.

and humongous fungus.
is alliterative but, again, is much improved as
unionized fungus



Wednesday, August 16, 2006

We beat Turkey!

The chart shows the proportion of people in numerous countries that answered true (blue), false (red) or unsure (yellow) to the statement:

"Human beings, as we know them, developed from earlier species of animals."

The report was published in Science last week and the full paper is available online. Note that for the precise methodology and questions asked you need to click on the link at the end that takes you to the supplementary material. I mention it because there is some interesting stuff there.

It was widely discussed on the internet, and I'll use this chance to recommend two evolution related blogs, Pharyngula and the Panda's Thumb, both of which reported on it - direct links here and here. It was not widely reported in the mainstream media - although Fox did have an article.


Tuesday, August 15, 2006

Humongous Fungus

If you'd like to read a little more about the original humongous fungus there's a really interesting article by Tom Volk, first published in Inoculum in 2002, a decade after the discovery of the fungus. You can read the article online here. The fungus they discovered, an individual Armillaria bulbosa, aka the honey mushroom, was conservatively estimated to be at least 1500 years old and weigh around 100 tons - making it one of the largest and oldest living organisms.

I learned lots of fascinating trivia from this article:

The project was actually an offshoot of a grant from the Department of Defense, which funded a project to study the possible biological effects of ELF (Extra Low Frequency) stations in the Upper Peninsula of Michigan. These ELF stations were built to communicate underground with ocean-going submarines in time of war.

They sampled for the fungus by 'baiting' with tongue depressors. The fungal mycelium quickly colonized the wood sticks.

They were not looking for a large fungus, or even trying to measure the size of any fungus. The project was originally to look at how mitochondrial DNA was inherited in fungi in nature.

When news of the 'giant fungus' broke in the press CNN wanted someone to go out into the woods and wave from the fungus so they could get an aerial picture of the humongous fungus.

Even better, a Japanese businessman called and wanted to build a boardwalk around the humongous fungus and charge people to view the 'pulsating mass of fungus'.


Monday, August 14, 2006

Campbell 7th

It was brought to my attention that there is a fairly serious error in some copies of the Campbell 7th edition. It doesn't appear to be present in the 6th edition.

In figure 38.4 (The development of Angiosperm Gametophytes), earlier copies of the 7th edition have the haploid and diploid labels reversed. It SHOULD be labeled so that the microsporocyte, megasporangium, megasporocyte and integuments are DIPLOID, and all the other structures are HAPLOID (except the micropyle, which is a gap and so is neither haploid nor diploid!)

As an aside, it can be tricky in the US to tell what printing a book is. However for many books there is a simple code on the rear of the title page that gives you the necessary info. In Campbell you'll find this on page ii just above the Benjamin Cummings logo. You are looking for a string of numbers like:
1 2 3 4 5 6 7 8 9 10 -VHC - 08 07 06 05 04
By taking the lowest numbers you get the printing and year (for some odd reason these numbers are not always in order). So the book I'm looking at was the first printing in 2004. Another copy I looked at in the Bio1B office did not have this mistake and was labeled:
4 5 6 7 8 9 10 - VHC - 08 07 06 05
or the 4th printing from 2005.

So now you know. I suppose if you wanted to get maximum value for your dollar in a used textbook store you would look for later printings hoping that mistakes had been corrected.


As requested

I do not make my powerpoint slides available to you for one very simple reason - I have not obtained permission to use all the images. To try to make the lectures interesting I pull up all sorts of images from the web and numerous other sources. As long as they don't explicitly request that the image not be copied I don't worry too much for a single in lecture use. However I would not feel comfortable making all these images available to the whole class by putting the powerpoint slides online.

The legally correct solution would be to just use images I have taken myself (the only pictures I take are of Scooter, my dog) or to use those from Campbell (which would make for a fairly dull lecture since you've seen all these images) or to get permission to use all the images I want to use (which would take forever).

So instead I use what I want but don't make the slides available. That is why I have copied much of the text on the slides in the form of the lecture outlines and indicate, wherever possible, equivalent figures in Campbell.

But someone did point out that I could go one step further and make available all the text slides I use and those very few images I make myself. I'm not sure it provides much more than you already have but here are the text slides from the Plant Section powerpoints. (There is also one other image snuck in there that someone requested so I hope you are reading this).


Only You Can Prevent Forests

Agent Orange was but one of a whole family of defoliants used during the Vietnam war. There were so many in fact that they are known collectively as the "rainbow herbicides": Agent Orange; Agent Purple; Agent Pink; Agent Blue; Agent White; and Agent Green. (Reservoir Dogs enter the Matrix.) They are named, incidentally, not for the color of the chemical but for the color coded stripe on the barrels they came in.

We now know that although the synthetic auxins might have been highly effective they came contaminated with dioxins - causing cancers and horrendous birth defects (deformities so extreme that photographs of affected individuals are often assumed to be faked). Whilst the action of destroying the environment as an act of war is not without ethical issues itself the more pressing matter is the fate of US soldiers, South Koreans (present as US allies in the Vietnam War) and Vietnamese citizens who suffered from the effects of these chemicals.

Thirty years after the end of the war and thirty five years since the widespread use of defoliants, a number of court cases are still pending. Most recently (end of 2005) a suit by a victim's rights group, the Vietnam Association for Victims of Agent Orange/Dioxin (VAVA) had their lawsuit dismissed because Agent Orange was not considered a poison under international law at the time of its use by the US. This, despite accumulating evidence that the companies new about, and kept quiet about, the dioxin impurities:

In March 1965, Dow official V.K. Rowe convened a meeting of executives of Monsanto, Hooker Chemical and others. According to documents uncovered only years later, the purpose of this meeting was "to discuss the toxicological problems caused by the presence of certain highly toxic impurities" in samples of 2,4,5-T. The primary "highly toxic impurity" was 2,3,7,8 TCDD, one of 75 dioxin compounds.

From 'The Story of Agent Orange, from the November 1990 issue of the US Veteran Dispatch Staff Report.'

There is much more about the ongoing Agent Orange issue at numerous websites. As usual Wikipedia is a good entry point.

The US government, is not a party in any of the lawsuits claiming sovereign immunity.

(The title of this entry comes from a sign over the door to the ready room for pilots involved in the defoliation operations at Tan Son Nhut Airport near Saigon. For those of you who are not US residents, it is a play on the words of the famous slogan: Only you can prevent forest fires)


Sunday, August 13, 2006

Life in a seed

Some species of insects complete their entire development in seeds. Protected by the seed coat and nourished by the seed's food supply a developing insect has everything it needs. However these reserves only normally accumulate in fertilized ovules - requiring female insects that wish to lay eggs inside the seeds to either wait until ovules are fertilized (and be able to discriminate), or to lay their eggs earlier and risk many being laid in unfertilized seed. A paper in the Proceedings of the Royal Society last year describes how a host-specific insect, the chalcid Megastigmus spermotrophus that lays its eggs in ovules of Douglas fir has managed to evolve a solution to this problem. This insect lays its eggs before fertilization has taken place in the plant and ovipoisiton of eggs not only prevents the expected degeneration and death of unfertilized ovules, but it induces energy reserve accumulation. Ovules that would otherwise develop as empty seed are redirected in their development by the insect to provide food for the developing larvae. This is the first report of this type of insect-host relationship.


Saturday, August 12, 2006

Eastern Garbage Patch

Just under 100 years ago, in 1909, Leo Hendrik Baekeland invented the first plastic based on a synthetic polymer - Bakelite. Since then plastics have changed our world in a great many ways. The problem is that practically all the plastics we have made in the last 100 years are still with us, particularly those that end up in the ocean where biodegradation, which is slow to begin with, is even slower.

If you've been to a beach in your life you will have seen how much plastic waste washes up. But it turns out this isn't the worst of it. Ocean currents, caused by winds and the earth's rotation, create large circular systems, or gyres. The center of these gyres, thousands of miles from continental land, contain vast accumulations of floating garbage. An accumulation in the large gyre in the pacific is known as the Eastern Garbage Patch. Situated about halfway between California and Hawaii this floating garbage dump is about twice the size of Texas. To save you reading that again I'll just type it again - a floating patch of garbage in the Pacific that is twice the size of Texas. The amounts of plastic involved are staggering, using trawl samples it is estimated that there is already six kilos of plastic for every kilo of naturally occurring plankton.

This plastic is proving disastrous for oceanic islands. For example Midway atoll is littered with decomposing bird remains, piles of feathers and bone surrounding colorful piles of bottle caps, plastic dinosaurs, checkers, highlighter pens, perfume bottles, fishing line and small Styrofoam balls. It is estimated that albatross feed their chicks about 5 tons of plastic a year on Midway alone. Albatross fly hundreds of miles in their search for food for their young and their flight paths from Midway take them directly over the Eastern Garbage Patch. A piece of plastic found in an albatross stomach last year bore a serial number that was traced to a World War II seaplane shot down in 1944.

I find the idea of this vast patch of slowly circling garbage out there in the middle of nowhere to be profoundly depressing.


Friday, August 11, 2006

GM plant escapes into wild

For the first time in the US a genetically modified plant has escaped into the wild. Even worse it has done it before securing USDA approval. The plant, creeping bentgrass, Agrostis stolonifera, had been modified to make it impervious to the herbicide glysophate and was designed for golf courses and homeowners. Lawn owners would be able to spray lawns to kill off weeds without damaging the grass.

As far as I can tell not a single US media source has picked up on this story. You can read about it in an Australian newspaper and a British Science magazine and, well, that's it.

Although only nine escaped plants have been identified (out of 20,400 plants of various grass varieties sampled) one of the escapees was found over 3.5 kilometers away from where the grass was being grown.

In this case the weedkiller-resistance gene is unlikely to be a particular advantage for this plant in the wild but this discovery doesn't bode well for our ability to contain other genetically moderated crops.

On the more worrying side bentgrass has many close relatives with which it can potentially hybridize. This could add glyphosate-resistance genes to other grass species, some of which are noxious weeds.


Thursday, August 10, 2006

Some like it hot.

From a paper in last week's edition of the journal 'Nature' comes news that some bees may be looking for more than nectar when they visit flowers - they are also looking for warmth. Insects use large amounts of energy maintaining their body temperature and some flowers offer warmth, using color to advertise its presence.

The paper by Adrian Dyer and colleagues describes a controlled experiment that showed that bumblebees preferred to visit warmer flowers, and they learnt to use color to predict floral temperature before landing.

You can access the editorial summary at the Nature site, a news report at the New Scientist website and, if you have a UC Berkeley IP address or a proxy server you should be able to access the article from the nature link.


Wednesday, August 09, 2006

Final Jeopardy

When I was younger I was fascinated about how other people's minds worked. I was intensely curious about whether other people had a mind full of junk all the time and whether they were constantly making the same sort of apparently random links and jumps.

I was recently reassured to see this animated cartoon by Scott Bateman which illustrates what happened inside Bob Harris's head when faced with a Final Jeopardy question. (Bob Harris is an American radio commentator, writer, stand-up comedian, Jeopardy contestant and blogger.)

I'm always reminded of this when I try to write exams. It is so difficult to try and step back and see questions as others might see them. I've also been talking with Mike Moser and some others about ways to help people who learn the material, feel they understand it, and yet are disappointed by their midterm results. (There was an earlier blog posting on this if you missed it, and a list of advice is on the Bio1b website.)

Speaking with a couple of separate people this week I realized I need to add a section here on time management. I'll illustrate this for a Bio1B midterm but the principal applies to lots of other exams.

Let's assume that you find 35 of the 50 questions straightforward, they only take you a minute or so, let's say 40 minutes total.

There are another 10 questions that you find harder, maybe they are problems, or take extra reading or calculation. You take two minutes over each of these for a total of 20 minutes.

You now have 20 minutes left for the last 5 questions which you are really puzzling over. It is pretty easy to spend most of this time puzzling over these questions and only leave a few minutes for a cursory check of your answers to the earlier questions. You become obsessed by the harder questions at the expense of checking for errors on the easier questions.

However, if you are anything like me, you have probably made at least half a dozen mistakes on those 35 'easy' questions because you misread the question, filled in the wrong entry on the scantron, failed to notice a negative qualifier etc. etc. Fifteen minutes spent checking your answers will probably bring you much better returns than agonizing over the questions you find hardest.

A better strategy, in this example, would be to allot about 1 minute per question to work through the entire 50 questions. Some questions may take less time but try not to go beyond 1 minute on any question. Cross out answers you know to be wrong as you go along. If you run out of time then put a question mark by your best guess and move on. You should finish this in under 50 minutes. Now split the remaining time in two parts. Spend half the time (15 mins) checking your answers. Make sure you read the question correctly. Look for negatives and qualifiers. In doing this you can take another look at the questions you didn't complete the first time. Something new might come to you. Finally, divide the last 15 minutes between the questions that remain.


Tuesday, August 08, 2006

Songs of Science

If you like your education in rhyming form (and who doesn't?) then you'll want to check out the Singing Science Records website. Dozens and dozens of priceless gems from the late '50's and early '60's. Now available in mp3 form.

The one I played at the start of lecture today is near the end of the page ' What Are The Parts Of A Flower?' (links to mp3 file).

'It's time we were explainin' the purpose of the stamen.'

Let me know if you find any more real gems here. I haven't listened to them all. Another of my favorites is How Does A Frog Become A Frog? Although a little skimpy on the details of how a frog actually becomes a frog it makes up for it with a great tune. It reminds me of the 'insane circus' style of music favored by Tom Waits. Come to think of it I bet Tom Waits could do a great version of this.


Monday, August 07, 2006

CNR smorgasbord

A selection of items gleaned from the CNR website. The first concerns some of the long lived gymnosperms I mentioned today.

From an article in the SF Chronicle last week entitled Performing high-altitude research on global warming:

The famous bristlecones have endured countless challenges over the millennia, yet always seem to muster one more burst of life when spring warms the rocky dolomitic soil. Growing seasons may expand and shrink, but the trees carry on, their growth rings faithfully recording the bad years alongside the good.

From the CNR Breakthroughs magazine is a nice description of an ambitious program to catalogue the DNA of all the species on an entire island - the South Pacific island of Moorea, home to UC Berkeley's Richard B. Gump South Pacific Research station.

Also in the magazine is an article about the Exploring California Biodiversity program which sends Berkeley graduate students to teach in four Bay Area schools. I mention it here because they also involve undergraduates in the program. If you think you might be interested in teaching, or just want to gain some practical experience it is a tremendous opportunity. Check out their website and contact Betsy Mitchell if you are interested (it may be too late for the coming year, but it never hurts to ask).

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Sunday, August 06, 2006

Dead Zone

No, not the David Cronenberg movie with Martin Sheen foreshadowing his West Wing presidential role. The dead zone in question is a 70-mile-long zone of oxygen-depleted water, along the Continental Shelf between Florence and Lincoln City in Oregon. It has reappeared each year since scientists first noticed it in 2002. The zone is caused by the action of photosynthetic algae in the water. Explosive blooms of algae eventually die and sink to the bottom, they are then eaten by bacteria which use up the oxygen in the water. This leaves a zone of very low oxygen levels, a so called 'dead zone'. Although these are not toxic algal blooms they are having dramatic effects on the ecosystem causing a massive die-off of fish and invertebrate marine species.

The key question of course is what causes the algae to bloom. In contrast to other dead zones (eg in the Gulf of Mexico) the dead zone on the Oregon coast is not thought to be due to agricultural run off. Attention is now turning to whether it could be climate change related. This combination of catchy name ('dead zone'), dead fish and crabs, financial implications for fishing communities and a global warming tie-in makes for good headlines.

The San Francisco Chronicle today had a report and the story has also been covered by ABC, CBS, the New York Times, National Geographic and many others.


Saturday, August 05, 2006

Deep Green

There are a number of useful resources on the web to help you understand the relationship between the different plant groups and explore their diversity.

The Tree of Life is a collaborative project that provides information about the diversity of organisms on Earth, their evolutionary history and their characteristics. The link above takes you to the main page or you can skip directly to the green plants.

The Green Plant Phylogeny Research Group (Deep Green) is a group that coordinates research into the phylogeny of the green plants. Their website contains a useful hyperbolic tree. Hyperbolic trees are one way to display complex trees clearly.

The Green Tree of Life aims to resolve the primary pattern of evolutionary diversification among green plants. An overview of the results to date can be seen in this poster.

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Friday, August 04, 2006

Beatrix versus the Botanists

When I was a sophomore at college in England I spent a summer working at the Freshwater Biological Association in the English Lake District. The cottage I stayed in was in a tiny village called Far Sawrey. Just down the road is the village of Near Sawrey which contains a small 17th century farm house where Beatrix Potter spent most of her later years, and where she wrote and set her many Peter Rabbit books.

Having mentioned it in class I thought I'd see if I could find out whether Beatrix Potter was happy in her later life or whether she resented being excluded from the male dominated scientific community. Thanks to the wonders of the internet I found a highly relevant book and, even better, the relevant chapter is available online as a sample chapter.

Chapter 1 of Liaisons of Life, Beatrix versus the Botanists, by Tom Wakeford describes Beatrix Potter's encounters with the scientific establishment. Fascinating reading and a picture of science at the turn of the century. Beatrix Potter was facing an uphill battle, not just as a woman in science but also in proposing lichens as a symbiotic and mutualistic association. James Crombie, a prominent English naturalist said:

"A useful and invigorating parasitism —who ever before heard of such a thing?"

and he described the relationship as:

"an unnatural union between a captive algal damsel and a tyrant fungal master."

After her aborted scientific career and her successful career as a children's author Beatrix Potter went on to a third, and equally successful career as a sheep breeder and conservationist in the English Lake District.


Thursday, August 03, 2006

Lichens in Space

During the European Space agency's 2005 Foton mission lichens were exposed to space for 15 days. They had to endure a wide range of harsh conditions: a vacuum; wide fluctuations of temperature; the complete spectrum of solar UV light; and bombarded with cosmic radiation. If we were living in a comic book then the lichens would have returned with super powers but here in the real world most people were surprised to find the lichens merely survived. They appeared totally dormant whilst in space but soon revived back on earth.

One conclusion of this experiment is that it appears likely that lichens may be able to survive on the surface of Mars.
Although the Martian atmosphere is very thin, it is filled with carbon dioxide, which is necessary for Â’photosynthesis. However, long term survival and growth may be prevented by the low oxygen levels in the Martian atmosphere.


Midterm 2 results

Here are the results of the second midterm. Again, I can't post your individual results but here is an analysis of the complete data set.

The overall mean was 84% and the median was 86%.

The highest score was 100%, and, again, two students in different sections managed to achieve this.

Section means were very similar and no section mean was more then 3% away from the overall mean of 82%

The histogram of scores is above and the breakdown by grade is below.

A (ie >=90%) - 38%
B - 37%
C - 17%
D - 6%
F - 2%

There are two issues with individual questions. These changes will be made by your gsi and will not show up on your scantron reports.

Due to the conflicting information presented in Campbell 7th I will accept A or B as answers to question 27 (the island biogeography question).

There was an error on the answer key (my fault, it was due to a last minute change in a question). The correct answer for question 15 (inefficiency of food chain transfer) was B (productivity). Answer C (endotherm/ectotherm) is incorrect. For 152 of you this means your score will go up. My apologies for this mistake.

I have looked closely at all the rest of the questions where either less than two thirds of you got the correct answer (4 questions) or more than 20% of you picked a particular incorrect answer (5 questions) and don't see any other problems.



Wednesday, August 02, 2006

Diatom art

I love this stuff! If you want to see more then check out Klaus Kemp's work. He has singlehandedly reinvented the 'lost art' of diatom arrangement and taken it to new heights.

There are some beautiful photographs of his work here, that show, at different magnifications, the beautiful structure of the diatom shells.

Definitely a hobby for the patient. Traditionally pig eyelashes were used to collect and place the diatoms because the shells will stick to their oily tips (who knew there was a use for pig eyelashes beyond the obvious pig related one?). The diatom shell is then placed into the mounting material on the microscope slide. Once placed it is hard to make changes........


Fertilizing the Oceans

The image to the left shows a satellite image of a 150km long phytoplankton bloom created during the 2002 Southern Ocean Iron (Fe) Experiment (SOFex). The arced distribution is due to oceanic currents and the bloom appeared only six weeks after the initial fertilization.

The fertilization involved adding iron to surface waters in two patches, each 15 kilometers on a side, so that the concentration of this micronutrient reached about 50 parts per trillion, increasing the natural level by about two orders of magnitude.

Each of these blooms consumed over 30,000 tons of carbon dioxide, but the crucial question is whether this carbon dioxide would be returned to the atmosphere, or would sink into deep waters as the phytoplankton died. One of the factors that determines which will occur is what type of organisms form the bloom. Diatoms, for example, are relatively heavy and sink easily. But the abundance of diatoms may be limited by silica as well as iron.

The results were published in the journal Science in 2004 and were reported on quite widely by the press. Here is a nice report by the Sciencedaily website.

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Tuesday, August 01, 2006

Pathogens Determined to Attack Inside the United States.

In June 1996, President Clinton issued a Presidential Decision Directive calling for a more focused US policy on infectious diseases. The intelligence community of the United States is responsible for assessing threats to the United States and in 1999, as part of the US Government's effort in response to the Presidential Directive, produced a report entitled 'The Global Infectious Disease Threat and its Implications for the United States.'

It examines the most lethal diseases globally and by region; develops alternative scenarios about their future course; examines national and international capacities to deal with them; and assesses their national and global social, economic, political, and security impact. It then assesses the infectious disease threat from international sources to the United States; to US military personnel overseas; and to regions in which the United States has or may develop significant equities.

The report was produced by members of the Armed Forces Medical Intelligence Center, the National Intelligence Council and included conclusions from a conference on infectious diseases held jointly with the State Department's Bureau of Intelligence and Research.

You can find it at the CIA webpage as a pdf file but more easily accessible html versions are available.

The conclusions are not optimistic.

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Bug soup

Looking for information to post here has encouraged me to look at Science, Nature, PNAS and several other Journals more frequently than normal. It has surprised me just how many papers are being published that are directly relevant to this course. In PNAS (Proceedings of the National Academy 0f Sciences) next week will be a paper by Mitchell Sogin and others describing a new estimate of the microbial diversity in the deep sea. Only 5,000 marine microbes have currently been named but Sogin's study estimates that the true number of bacterial species living in the ocean could be between five and ten million. You can read the original paper in pdf form or check this link to google news as various newspapers and magazines pick up on the story.

Favorite headlines so far:
Enough to make you swim with your mouth closed
Marine census blows researchers out of the water
Oceans a complex, diverse bug soup

and my vote for least inspired headline:
Scientists` view of oceans might be wrong

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