Friday, May 29, 2009

The best stats you've ever seen


I used this video in a different class but I think everyone should see it, and it is relevant to our discussion about human population growth.

You've never seen data presented like this. With the drama and urgency of a sportscaster, statistics guru Hans Rosling debunks myths about the so-called "developing world."

And the best part about it is that the software is now available at the Gapminder website so you can play with it yourself and look at changes through time of all sorts of environmental, social and geographical parameters.

Thursday, May 28, 2009

This semesters most intriguing title

The Bren School of Environmental Science & Management at the University of California, Santa Barbara presents:
Forest Rohwer, Professor, San Diego State University
Monday, June 1, 2009, 12:30 - 1:30 p.m. Bren Hall 1414
Playing with Snot: What can corals teach us about cystic fibrosis?

Wednesday, May 27, 2009

Monkey-Man

Kathy pointed me to an interesting editorial in Nature today about the recent fossil primate discovery I mentioned here last week.

The article, entitled Media Frenzy, has the subhead:

A hyped-up fossil find highlights the potential dangers of publicity machines.

Take a look at the original paper in PLoS ONE, Nature's original report and today's editorial.

Do you agree with Nature's assertion that:
In principle, there is no reason why science should not be accompanied by highly proactive publicity machines. But in practice, such arrangements introduce conflicting incentives that can all too easily undermine the process of the assessment and communication of science.

Do you think the authors of the original paper did anything wrong?
Do you think the journalists who covered the story have been accurate in their reporting?

(The image above, which is from Nature's original report, is called 'monkey-man.jpg'. This is exactly the sort of misleading hype that Nature is railing against!)

Tuesday, May 26, 2009

Vicars and badgers

In the Church of England (which I'm not going to begin to explain), vicar is the title given to parish priests. Vicars wear a variety of different vestments but are typically seen in black and white robes like that in the picture. When you see a picture of a vicar, or any other priest type person for that matter, you have an image not only of that person's physical appearance but also of their role in the community.

In Charles Elton's 1927 book on 'Animal Ecology' he says:
"[W]hen an ecologist says 'there goes a badger,' he should include in his thoughts some definite idea of the animal's place in the community to which it belongs, just as if he had said, 'there goes the vicar.'"

This is a very evocative illustration of the 'niche' concept.

I'm sometimes a little reluctant to mention this to American students because I feel obliged to explain a little about vicars and badgers. European badgers are more distinctly black and white striped than their American equivalents so what Elton was saying was that we don't just think of a vicar as a person in black and white clothing, and we shouldn't think of a badger like that. We should try to think of the animals' place in the community.

(Contrary to the opinion of some, there is no such thing as a 'giant man-eating badger'. I almost wished I had spent my life in the British military just so I could have been the person to make the following statement:

UK military spokesman Major Mike Shearer said: "We can categorically state that we have not released man-eating badgers into the area." You can read the full story here.)

Friday, May 22, 2009

Saturdaze

Who among us has not contemplated nature and been inspired to learn about the connectedness within diversity? In this sense, natural history has attracted not only the scientist, but the artist and poet; natural history has become the romantic science. The romance of natural history stems from our desire to relate to the natural world, to regain a connectedness to it, and to preserve its diversity.

Saturdaze has partnered with the Santa Barbara Museum of Natural History and has funded a scholarship to encourage research that helps to explain one or another "entangled bank". The Saturdaze Scholarship for Natural History Research rewards exceptional students attempting to discover interactions in nature. Saturdaze and the Museum share the goal of . . .Inspiring a Passion for the Natural World


Maximum award amount: $2,000
Application Deadline: 15 June for 15 July scholarship award
Award Date: 15 July

Eligibility: (1) attended a college or university as an undergraduate in a biological sciences major in either San Luis Obispo or Santa Barbara County during the year prior to application, and (2) actively involved in research in the spirit of natural history.

To apply online visit the Saturdaze website.

Thursday, May 21, 2009

More Cohen

Joel Cohen, who wrote 'How many people can the earth support', and is different to the Joel Cohen who is half of the Cohen brothers movie directing team (Fargo, The Big Lebowski, No Country for Old Men etc) had a recent Commentary published in Nature suggesting one important step we could make in controlling world population growth: Make Secondary Education Universal. It's a short article, only a couple of pages, and well worth a quick read.

Universal, high-quality primary and secondary education is achievable within 25 years. Educating all children well is a worthwhile, affordable and achievable strategy to develop people who can cope with problems foreseen and unforeseen.

And just to follow up on class, if everyone on earth lived an American lifestyle then, under current technology at least, it seems unlikely the earth could support more than 2 billion people. As I mentioned, and you are hopefully aware, we are currently heading towards 7 billion....

Tuesday, May 19, 2009

For Thursday

For this Thursday please bring your laptop (if you have one, no need to buy one specially.....) and download the Populus program onto it if you didn't already do this last quarter.

Also, please complete the list of topics that Claudia handed out and bring that to class. If you'd rather complete this electronically the form is here.

If you look at CNN online you may have seen this report on the homepage today:
Scientists piece together human ancestry
Scientists hailed Tuesday a 47-million-year-old fossil of an ancient "small cat"-sized primate as a possible common ancestor of monkeys, primates and humans. Scientists say the fossil, dubbed "Ida," is a transitional species, living around the time the primate lineage split into two groups: A line that would eventually produce humans, primates and monkeys, and another that would give rise to lemurs and other primates.

What I noticed particularly about this report was that CNN linked directly to the original research paper in PLoS ONE: Complete Primate Skeleton from the Middle Eocene of Messel in Germany: Morphology and Paleobiology. Another victory for Open Access publishing.

Monday, May 18, 2009

25mph


Not exactly the most surprising prediction but in a blog posting last year, Most obvious nickname ever..., I wrote:
'If there was a regular 140m or 150m event I imagine the world land speed record would be set over that distance.'

Unless I'm reading the wrong news sources the news that a human has just exceeded 25mph in an athletic event for essentially the first time ever has received remarkably little attention.

On a cold and rainy Sunday in Manchester, England, on a specially laid out 150m track on the streets Usain Bolt made it look easy. His time, 14.35 works out at 10.453 m/s or 23.38mph. even more impressively the final 100m of the 150m (ie a 100m with a flying start) was timed at 8.72. This works out to be 11.468m/s or 25.65mph.

Friday, May 15, 2009

EEMB job candidate talk

Professor Edward McCauley (University of Calgary) is a candidate for Director of the National Center for Ecological Analysis and Synthesis (NCEAS) and for appointment as a Professor in EEMB. He will give a talk in EEMB on Monday 18th May.

Theory and Experiment in Ecology: A balance of forces
Monday 18 May, 12 noon, MSRB Auditorium

Ed's interests cover many areas of ecology, so this should be of broad interest.

Thursday, May 14, 2009

Talking Prairie Dogs

In this week's New Scientist magazine is a report of a paper just out in the journal 'Animal Cognition': Prairie dog alarm calls encode labels about predator colors.

Prairie dogs talk some pretty colourful talk. Not only do their alarm calls tell others about the type and size of approaching predators, but it seems they can also warn of the hue of an imminent threat.

Gunnison's prairie dogs are burrowing rodents that live in the grasslands of North America. Con Slobodchikoff of Northern Arizona University in Flagstaff and his colleagues had previously shown that they produce different alarm calls in response to humans, coyotes, domestic dogs and red-tailed hawks. For humans, the calls even vary according to the person's size. They react differently towards each call, all hiding if approached by humans, whereas only nearby animals hide if it is a hawk.

In the latest study, the team recorded the alarm calls as three similar-sized women wearing blue, yellow or green T-shirts walked past the prairie dogs 99 times. They found that the calls were similar for green and yellow T-shirts, but significantly different for blue.

Prairie dogs have dichromatic vision, a form of colour blindness where only two of the three primary colours can be discerned. As they are sensitive to blue and yellow, this explains why they cannot distinguish green. Still, the fact that they can "talk" colour "probably makes this the most sophisticated animal communication system that has been decoded so far," says Slobodchikoff.

Wednesday, May 13, 2009

How the Immune System Works

The immune system IS amazing. My ONLY goal in the brief time we have to talk about it is to make you want to learn more about it. Whilst there are several courses here that you can take there is also a book that I can highly recommend.

If you want something that falls between the single chapter in an introductory biology textbook and the hefty tome of an immunology text then I can recommend 'How the Immune System Works' by Lauren Sompayrac. If you want to learn more about the immune system, including some cutting edge stuff, but don't want to take a whole course then this impressively slim book (144 pages for $30) is the way to go.

I'm linking to Amazon so you can see the impressive reviews this book has collected: 32 of the 39 reviews are 5 star. There are several other books in the series. 'How Cancer Works' by the same author is also pretty good. These are slim books, it isn't hard to read a chapter a day and in about a week you can have a pretty good understanding of the immune system or cancer.

Tuesday, May 12, 2009

Tregs

I briefly mentioned Regulatory T cells today as a relatively newly discovered (or rediscovered depending on your viewpoint) part of our immune system. These are also known as suppressive T cells, but the cool kids just call them Tregs. (Like T. rex.....)

Here are a couple of recent papers that will give you an entry into the literature in this field.

The Journal Immunology had a series of review articles in 2007 to mark their 50th anniversary. One of these was entitled:
Special regulatory T cell review: The suppression problem!
The concept of T-cell mediated suppression evolved more than 30 years ago. At that time it spawned many claims that have not stood the test of time. The rediscovery of suppression phenomena and regulatory T cells over the past 15 years created schizophrenic responses amongst immunologists. Some claimed that the new proponents of suppression were, once again, bringing immunology into disrepute, whilst others have embraced the field with great enthusiasm and novel approaches to clarification. Without faithful repetition of the "old" experiments, it is difficult to establish what was right and what was wrong. Nevertheless, immunologists must now accept that a good number of the old claims were overstated, and reflected poor scientific discipline.

Tregs and allergic disease
Allergic diseases such as asthma, rhinitis, and eczema are increasing in prevalence and affect up to 15% of populations in Westernized countries.
........
In summary, current evidence suggests that human CD4+CD25+ T cells and IL-10–producing Tregs have the capacity to suppress Th2 responses to allergen and that this process may be defective in those who develop allergic sensitization.

Monday, May 11, 2009

Undergraduate Research Colloquium

Each year the College of Letters and Science celebrates undergraduate research at UCSB by hosting a colloquium where students from all over campus showcase their research activities. This year's Undergraduate Research Colloquium is being held, Thursday, May 14, 11:30 to 2:00 p.m. in the Corwin Pavilion.

This year's event is showcasing 175 poster presentations. Projects from all colleges, and disciplines - the arts, humanities, social sciences, sciences and engineering - will be presented.

This is a great opportunity to see some of the research undergraduates are involved in at UCSB. It's also a good chance to see how they present that research and to give you some ideas for when you come to present your own work.

Thursday, May 7, 2009

Monday Seminars

UCSB Distinguished Lecturer Series in Neuroscience:
The Brain's Mechanisms for Mapping and Remembering the Spatial Environment
Drs. Edvard & May-Britt Moser Kavli Institute for Systems Neuroscience, NTNU, Trondheim, Norway
Monday, May 11, 2009 @ 1:00pm Marine Science Institute Auditorium, Marine Science Building 1302

Cancelled

And the Monday CCBER Conservation & Restoration Seminar for May 11th will be Sarah Chaney from Channel Islands National Park who will speak on:
Islands in the Fog: The Missing Cloud Forests of Santa Rosa Island

6-7pm, Monday May 11th, Cheadle Classroom, 1013 Harder South

Science Roundup

A jawfish at Riviera Beach, Florida displaying the eggs he'll hold in his mouth till they hatch. photograph by Steven Kovacs of Clewiston, Florida, first place winner Marine Animal Portraiture in National Geographic's Annual Underwater Photos competition.

As we get towards the end of our fabulous tour of biology it's time to catch up with some advances and events that have taken place during the last few months. A brief snippet from each and a link. Enjoy.

Rise Of Oxygen Caused Earth's Earliest Ice Age
Geologists may have uncovered the answer to an age-old question - an ice-age-old question, that is. It appears that Earth's earliest ice ages may have been due to the rise of oxygen in Earth's atmosphere, which consumed atmospheric greenhouse gases and chilled the earth.

Scaling of Soaring Seabirds and Implications for Flight Abilities of Giant Pterosaurs
Giant pterosaurs, colossal winged reptiles that lived alongside the dinosaurs, have long been considered the heaviest animals ever to take to the skies. But new research suggests that the notion of giant pterosaurs soaring over Earth simply doesn't fly.

Congruence of morphologically-defined genera with molecular phylogenies
Scientists using molecular techniques assert that genetics more accurately determines evolutionary relationships than does a comparison of physical characteristics preserved in fossils. But how inaccurate, really, were the fossils? Jablonski and Finarelli compared the molecular data to data based on the kinds of features used to distinguish fossil lineages for 228 mammal and 197 mollusk lineages at the genus level.

No matter how they looked at it, the lineages defined by their fossil forms "showed an imperfect but very good fit to the molecular data," Jablonski said. The fits were generally far better than random. The few exceptions included freshwater clams, "a complete disaster," he said.

Jablonski interprets the results as good news for evolutionary studies. The work backs up a huge range of analyses among living and fossil animals, from trends in increasing body size in mammal lineages, to the dramatic ups and downs of diversity reported in the fossil record of evolutionary bursts and mass extinctions.

Bigfoot hobbit could be ancient island human
Two studies add a new twist to the plot. One claims that the skeleton's ape-like feet push back its ancestry near the dawn of Homo. Another argues that the hobbit is a later offshoot of Homo erectus, dwarfed by aeons of island isolation.

Swine Flu: the Predictable Pandemic
New Scientist has a collection of articles on Swine Flu that are really good at answering the various questions you might have

Wednesday, May 6, 2009

Multivitamins and pill wranglers

The post below reminded me about the big multivitamin study that was carried out earlier this year that I posted a blog article about last quarter: Magic pill.

(T)he study was so large and looked at so many aspects of health that it had a lot of statistical power to detect even a small effect. The study involved more than 160,000 women roughly split between those that took regular multivitamins and those that didn't. Eight years later they looked at a variety of disease incidences, including cancer (almost 10,000 cases) and cruder measures such as total mortality (again almost 10,000 deaths). Not even a hint of a difference.

This confirmed earlier studies by the NIH in 2006:"Most of the studies we examined do not provide strong evidence for beneficial health-related effects of supplements taken singly, in pairs, or in combinations of three or more." And by the United Kingdom's Food Standards Agency in 2007: "Vitamin and mineral supplements are not a replacement for good eating habits and supplements are unnecessary for healthy adults who eat a balanced diet."

For an interesting counterpoint consider this posting, Where's my pill wrangler?, from last year.

'Kurzweil does not believe in half measures. He takes 180 to 210 vitamin and mineral supplements a day, so many that he doesn't have time to organize them all himself. So he's hired a pill wrangler, who takes them out of their bottles and sorts them into daily doses, which he carries everywhere in plastic bags.'

Kurzweil believes that radical technological advances will be made throughout the 21st century, and that many of those advances will benefit the field of medicine. Kurzweil has thus focused himself towards following a maximally healthy lifestyle to heighten his odds of living to see the day when science can make him immortal. His opinion on vitamin and health supplements is to take virtually anything that MIGHT have a positive effect even if the evidence is weak PROVIDED that the evidence is strong that it does no harm.

Tuesday, May 5, 2009

Carrot power

Many people believe that carrots are good for their eyesight. There is a germ of truth in this in that carrots are indeed a good source of vitamin A, and vitamin A is required for, among other things, correct functioning of the visual system. However just because they are required for correct functioning does not necessarily mean that eating more of them will improve your vision. The origin of the myth that carrots are good for your eyesight dates back to World War II and the Battle of Britain that occurred in 1940 and marked a turning point in the war. The Battle of Britain refers to the air battle between the German and British air forces for air superiority. A German victory would have permitted a cross channel invasion of England.

Although the principles of Radar had been known for a long time it was British scientists who produced the first working system, enabling ground controllers to direct British planes to intercept German planes in poor visibility and at night. In order to maintain their advantage the British spread the rumor that their pilots were being successful because of their extraordinarily good eyesight. A feat that was achieved by the mass consumption of carrots. This rumor affected both the Germans and the British. Due to the blackout at night and the frequent requirement to move to air-raid shelters people were keen to improve their night vision and carrots were readily available from allotments and gardens.

I do not know whether the Germans fell for this story. There are a few suspicious parts to it that may not have been fully understood at the time. Or maybe this was a sneaky part of the plan, to encourage German pilots to poison themselves with large amounts of Vitamin A. As Claudia pointed out today, if you want to propose ingesting large amounts of a vitamin you might be better off picking one that is water, rather than fat, soluble. As vitamin A is fat-soluble, disposing of any excesses taken in through diet is much harder than with water-soluble vitamins B and C. As such, vitamin A toxicity can result. This can lead to nausea, jaundice, irritability, vomiting, blurry vision, headaches, muscle and abdominal pain and weakness, drowsiness and altered mental status. Too many carrots will also cause you to turn orange from the accumulating beta-carotene. Another good source, in fact a much better source, of vitamin A is liver. Too much liver is even worse and can kill you quite quickly as Arctic explorers who were reduced to eating polar bear and sled dog liver discovered. Polar bears have very high concentrations of vitamin A in their liver and the native Inuit were well aware of this fact:

After killing a bear, the Inuit ate the meat and used the fur to make warm trousers for men and kamiks for women. An average polar bear would yield three pairs of trousers and one kamik. The only part of the bear that was not used was the liver. This was immediately thrown out, as it could make even the sled dogs violently ill.
From Polar Bear International.

Monday, May 4, 2009

Seminars this week

Dr. Bill Fagan
Riverine Landscapes: Exploring Connectivity, Extinction Risk, and Biogeography in an Alternative Geometry.
Monday, 4-5pm in MSRB Auditorium

Or go crazy and go downtown,

Impacts of rising carbon dioxide and tropospheric ozone on the growth and productivity of trees
Victoria Wittig, University of Illinois at Urbana-Champaign
NCEAS Ecolunch seminar.
Thursday, May 7, 12:15 PM
GENERAL INFORMATION: Ecolunches are Thursdays, at 12:15 pm (brown bag
lunch) National Center for Ecological Analysis and Synthesis, 735 State
St., Suite 300, Santa Barbara, CA 93101 Phone: (805) 892-2500

and a big one coming up in two weeks:
Dr. Edward McCauley, candidate for the NCEAS Director position.
Seminar - Theory and Experiment in Ecology: A balance of forces
Edward McCauley, Ph.D., Department of Biological Sciences, University of Calgary
Date: Monday, May 18
Time: 12:00pm - 1:00pm
Location: MSRB Auditorium, Marine Science Institute

Friday, May 1, 2009

Fetal hemoglobin and sickle cell anemia

Speaking of hemoglobin, I find it amazing that newborn babies have a different type of hemoglobin, fetal hemoglobin, that will be completely replaced by the adult form within a few weeks of birth. The fetal hemoglobin binds oxygen more readily than the adult form, thereby allowing the developing fetus to obtain access to oxygen from the mother's bloodstream via the placenta. The reactivation of fetal hemoglobin synthesis in adults has been used to treat sickle-cell disease since 1995.

When fetal hemoglobin production is switched off after birth, normal children begin producing hemoglobin A. But children with sickle-cell disease instead begin producing a long, slender form of hemoglobin called hemoglobin S. This variety of hemoglobin causes red blood cells to change their shape from round to sickle-shaped, which have a greater tendency to stack on top of one another and crowd blood vessels causing a variety of problems. If fetal hemoglobin remains the predominant form of hemoglobin after birth, however, these problems can be reduced.

Nature Medicine covered the breakthrough discovery of fetal hemoglobin promoting drugs such as hydroxyurea in 1995: Sickle cell paths converge on hydroxyurea.