Senin, 31 Januari 2011

EEMB grad student symposium

Much as I would like to continue posting cute animal videos I shall reluctantly move on. (Oh okay, check out this picture if you want one more invertebrate smile).

Several of the departments on campus now organize mini-conferences around presentations by the grad students and/or faculty. EEMB has a faculty symposium in the Fall and a Grad student symposium in the Winter. This is coming up soon, Saturday Feb 12, and although it is free they do ask for people to register so they know how much coffee etc. to get (and you have to pay for dinner if you want feeding). Since I'm very keen that they have sufficient coffee I encourage you to register if you intend going.

This can be a great way to find out a lot about the research going on in a department. You really get a good sense of what graduate students do and you get to watch, and critique, a lot of talks in a short time. The agenda and abstracts are on the website but note that they do ask for you to sign up by the 1st Feb, Tuesday, tomorrow. It is certainly appropriate for undergraduates to go to this and there's usually a few CCS students there.

I see your cute vertebrates...

...and bid a ladybug.


Minggu, 30 Januari 2011

Cute overload

Ha, I see your cute rabbits and raise you an otter. If you need more cute animals to relax from the stress of upcoming midterms then Cute Overload or Zooborn should give you everything you need.

Cute rabbits

Who cares if they grow up to be the rabbit from Monty Python...

Sabtu, 29 Januari 2011

Every second breath...

Well I could make fun of some parts of it but I won't because it's actually a pretty nice video. They get a lot across in 3 minutes and hopefully leave you more interested in the Census on Marine Life than you were when you started. Can we ask any more than that?

Jumat, 28 Januari 2011

Summer opportunities

Hopefully you all got the SURF announcement from CCS. SURF (Summer Undergraduate Research Fellowship) provides a stipend to support CCS students in summer research projects working in a faculty-led research group at UCSB.

If you are a CCS student and did not get this e-maik then CCS does not have your correct e-mail address and you shoudl rectify this since you are missing important e-mails (like the SURF announcement).

On the subject of summer a great source of opportunities is the NSF REU program (National Science Foundation's Research Experience for Undergraduates).

NSF funds a large number of research opportunities for undergraduate students through its REU Sites program. An REU Site consists of a group of ten or so undergraduates who work in the research programs of the host institution. Each student is associated with a specific research project, where he/she works closely with the faculty and other researchers. Students are granted stipends and, in many cases, assistance with housing and travel.

CCS students have been very successful in obtaining these and we hope that some of you continue this tradition. NSF maintains a website that can help you find these opportunities - you can search for REU sites by topic, keyword or geographic location. Applications are all made through the individual sites.

Kamis, 27 Januari 2011


Today's featured picture of the day on the Wikipedia home page is this splendid picture of a flesh-fly:

Flesh fly, from the Sarcophagidae family "blowing a bubble". One explanation for this behaviour is that it concentrates the fly's meal by evaporation. The diet of the flesh fly is very high in water content. The fly regurgitates the liquid portion of the food, holds it whilst evaporation reduces the water content and the fly then swallows a much more concentrated food meal without the water content. This continues until sufficient amount of liquid is left for the fly.

Reducing Test Anxiety

Some students get so anxious before tests that their test performance falls well below their abilities. The effect is usually greatest on high-stakes tests such as finals and standardized entrance exams. Why do such students “choke under pressure”?

According to current learning theory, anxious thoughts compete for space in the short-term working memory system. If the short-term memory system is concentrating on anxious thoughts, so the theory goes, it can’t focus as well on the information that might be most useful for the test.

If the current learning theory is true, then getting anxious thoughts out of one’s head before the exam might result in improved exam scores. Indeed, in a recent study, students who suffered from test anxiety had better final exam scores in high school biology when they sat down before the exam and wrote their anxious thoughts down, compared to students who didn’t write.

Just 10 minutes of writing was enough to raise the students’ final exam grades from a B- to a B+.

Rabu, 26 Januari 2011

Heterozygote advantage

At this point it's fairly clear that heterozygote advantage is not going to be a major force in the maintenance of genetic diversity simply because we've found so few examples. Perhaps not surprisingly with our rapidly expanding knowledge of genetics and gene function someone has now found some examples of heterozygote advantage that don't involve partial resistance to a disease. I missed this paper in PLoS ONE a few years ago:

Heterozygote Advantage for Fecundity
Heterozygote advantage, or overdominance, remains a popular and persuasive explanation for the maintenance of genetic variation in natural populations in the face of selection. However, despite being first proposed more than 80 years ago, there remain few examples that fit the criteria for heterozygote advantage, all of which are associated with disease resistance and are maintained only in the presence of disease or other gene-by-environment interaction. Here we report five new examples of heterozygote advantage, based around polymorphisms in the BMP15 and GDF9 genes that affect female fecundity in domesticated sheep and are not reliant on disease for their maintenance.

Selasa, 25 Januari 2011

Genetically modified - Good? Or very, very bad?

Intense but very good article.


.... and one more story - just for the heck of it, totally fascinating (swine flu = super immunity):

The real reason...

Are blondes/redheads dying out?

In 2002 there was a series of stories in the press announcing that blondes were dying out. A typical story from the BBC:
Blondes 'to die out in 200 years'.
The proposed mechanism for this loss of blondes was simply that the gene was recessive

..too few people now carry the gene for blondes to last beyond the next two centuries.   The problem is that blonde hair is caused by a recessive gene.

But, as we saw today, Hardy and Weinberg cleared that up for us over 100 years ago. An allele will not decline in frequency simply because it is recessive.

The story appeared to originate with the World Health Organization, although suspiciously, no scientists were named. It subsequently turned out the whole story was dubious if not fake. The WHO eventually issued a press release: 

''W.H.O. has no knowledge of how these news reports originated,'' said the organization, an agency of the United Nations based in Geneva, ''but would like to stress that we have no opinion of the future existence of blonds.''

Because news stories tend to have a cyclical life of their own this story has resurfaced a number of times since 2002.

Skip forward a few years  to 2005 and a series of press reports on a similar fate for redheads:
Gingers extinct in 100 years, say scientists
This time the story can be chased back to a misreporting of a story in National Geographic and the 'Oxford Hair Foundation' - funded by a manufacturer of hair dye.

Senin, 24 Januari 2011

Two forms of world's 'newest' cat, the Sunda leopard

The "newest" cat species described to science, the Sunda clouded leopard, actually exists in two distinct forms, scientists have confirmed.

Monday funnies

I don't know what made me think of Tim Minchin, I must have seen a reference to him somewhere, but I thought you might enjoy these. Phrases like 'I don't think you're special, I mean you're special but you fall within a bell-curve' probably explain why so many scientists marry other scientists.

Minggu, 23 Januari 2011

Fascinating Amoeba Farm Bacteria

Farming is often thought of as a completely human idea, though many animals actually engage in "farming behavior", however none of these species has been as tiny as the Dictyostelium discoideum slime mold.
As an example of animal farming behavior: some Damselfish actually farm their own algae and are surprisingly protective of it. They will often attempt to attack humans that disrupt their algae farms!
D. discoideum farms bacteria is a very interesting little oragnism according to BBC News:
"More than just a snack for the journey of dispersal, the idea is that the bacteria that travel with the spores can 'seed' a new bacterial colony, and thus a food source in case the new locale should be lacking in bacteria.
D. discoideum is already something of a famous creature, having proven its 'social' nature as it gathers together into a mobile, multicellular structure in which a fifth of the individuals die, to the benefit of the ones that make it into the fruiting body.
'Bacteria generally provide huge resources that are really untapped,' Ms Brock said.
'These amoebas carry bacteria that aren't just used for food, so that's what I'm looking into now.'"

The untapped power of bacteria is certainly an interesting topic, as is the unique symbiosis and initial possible evolutionary cost of farming behavior.

Read the article here: BBC New- Amoebas show primitive farming behaviour as they travel



Fluorescence micrographs of rappemonads in the North Pacific. The nucleus (blue) was often slightly elongated with a tapering end. Two to four plastids (green) appeared to be present per cell.

Like I said, the use of modern molecular methodology is allowing us to look at microbes within the oceans in ways never before possible and this is leading to some amazing discoveries - not just new twigs on the tree of life but major new branches we did not even know existed. This paper, in PNAS, last week has a fairly self-descriptive title:
Newly identified and diverse plastid-bearing branch on the eukaryotic tree of life

Here, we report a newly discovered uncultured plastid-bearing eukaryotic lineage named the rappemonads. 

Environmental DNA sequencing revealed extensive diversity at North Atlantic, North Pacific, and European freshwater sites, suggesting a broad ecophysiology and wide habitat distribution. 

The rappemonads are unique, widespread, putatively photosynthetic algae that are absent from present-day ecosystem models and current versions of the tree of life. 

Greenhouses in the Desert

The very real possibility of shortages of energy and freshwater some day are prompting the development of all sorts of innovative technologies, especially in the hottest, driest regions of the world. How about this - greenhouses in the desert that produce freshwater, powered only by the sun and using only saltwater drawn from the sea?

Here’s how it would work. Concentrated solar power would produce steam to drive turbines, producing electricity for power. Evaporation of saltwater would produce cool, moist air for the greenhouse. Hotter, more humid air leaving the greenhouse would be further heated and humidified using solar energy, then cooled (by cool seawater), producing freshwater by condensation. The freshwater would be used to irrigate crops both within and outside the greenhouse, and would support a local settlement. Presumably most of the saltwater (now saltier than before) would be returned to the sea.

An 8-acre pilot project is expected to begin operations in Jordan within five years. If it works, other larger projects may follow.

Sabtu, 22 Januari 2011


I hope that some of you got to attend Carol Greider's talks on Friday, or the meet and greet on Saturday. I went to the talk on Friday afternoon and was very impressed, not only was the science very impressive (well duh) but she also gave a great talk that I thought was pitched just right for the audience.

She also used a word that I immediately realized I should know and, fortunately, was fairly self explanatory - haploinsufficiency -

Haploinsufficiency occurs when a diploid organism only has a single functional copy of a gene (with the other copy inactivated by mutation) and the single functional copy of the gene does not produce enough of a gene product to bring about a wild-type condition. Haploinsufficiency is therefore an example of incomplete or partial dominance.
Production of telomerase within a cell appears to be an example of haploinsufficiency.

The most interesting part of the talk was at the end when the link between the evolution of insufficient production of telomerase (and therefore diseases of aging) and the dangers of too much telomerase and cancer became clear.

Jumat, 21 Januari 2011

Polar bears

This is not my topic post, I just thought it was absolutely hilarious. Apparently the BBC is making a documentary about polar bears and has designed a series of spy cameras with which to observe the polar bears unnoticed. The cameras were engineered to be cold- and weather-resistant, but unfortunately not bear-resistant...

Mendelian inheritance

It is known that Mendel ordered 40 reprints of the paper that described the results of his now classic experiments, "Experiments on plant hybrids" published in the transactions of the Natural History Society of Brünn in 1866.

He sent these out to scientists he thought would be interested (possibly including Darwin). Only a single scientist responded and, unfortunately he steered Mendel completely wrong.

Karl (or Carl) von Nägeli, of the University of Munich, had previously experimented with hawkweed, a plant that follows an obscure asexual reproductive method. Mendel started experimenting with hawkweed, and began to question his findings from studying peas. He finally gave up all experimentation when he became abbot of the monastery, though he continued to dabble in ornamental horticulture.

Although very few of these 40 reprints survive, in a strange story last year Mendel's original manuscript has surfaced and has become the subject of an inheritance dispute (seriously): A Family Feud Over Mendel’s Manuscript on the Laws of Heredity

Kamis, 20 Januari 2011

How to Learn Stuff

Bruce sent me a cool link on 'How to learn stuff'. Scroll down the page and you'll find some priceless advice.

Tricky question

This is a question from one of the major biology textbooks. I've always felt questions like this one to be right on the borderline between being a trick question and not. What do you think? Fair question? I'll post a comment on what the answer is NOT.

Karen and Steve each have a sibling with sickle-cell disease. Neither Karen nor Steve nor any of their parents have the disease, and none of them have been tested to reveal the sickle-cell trait. Based on this incomplete information, calculate the probability that if this couple has a child, the child will have sickle-cell disease.

Rabu, 19 Januari 2011

Ecology Seminars

I'm not posting as many seminar announcements this quarter but you should still keep an eye on them and try to attend one or two a quarter that look particularly interesting to you. I tend to notice the more ecology oriented ones (that's my background) and there are a couple from fairly distinguished mid-career ecologists coming up that should be well worth attending.

The first is the EEMB seminar this coming Monday 1/24/2011 @ 4pm in the MSRB auditorium (the MSI building)
Gary Mittelbach, Michigan State University
Biodiversity gradients from the small to the large

Fascinating Survival Principle

To survive brutal winters, inhabitants of Siberia and the Far East as recently as the late 19th century raided food stores—of rodents.

According to a new study, records by 18th-century Russian, Swedish, and German explorers describe people using sticks, hoes, or hooks to dig up caches of food gathered by voles and other small mammals.

See more HERE......

National Geographic Photos

Cool pictures of weird things that live in the ocean!
(Just for fun) :)

Transgenic Chickens Resist Bird Flu

By inserting a small piece of DNA into chickens that interferes with bird flu viral replication, scientists have developed transgenic chickens that are genetically resistant to infection by the bird flu virus. The inserted DNA fragment blocks a key enzyme required by the bird flu virus for replication of its RNA. Transgenic chickens exposed directly to the deadly H5N1 bird flu virus still get the flu and die, but they don’t pass it on to other birds in the flock. From an economic point of view, losing a few chickens is a lot less damaging than having to destroy a whole flock to try to prevent the spread of the disease. Flu-resistant transgenic chickens might also reduce the risk of a bird flu pandemic among humans some day.

Flocks of transgenic flu-resistant chickens could be widely available within a couple of years. That’s IF regulators decide that they and their eggs are safe to eat, and IF the public accepts them. Both are big “IF”s.

Selasa, 18 Januari 2011

Viral Eukaryogenesis

One of the things I love about biology is how quickly you can fall down the rabbit hole. One minute you are checking something in a textbook, it raises a question, you search for an answer and suddenly you are in a strange and less certain world that makes you go whoa. Case in point - which other organelles might have an endosymbiotic origin? Last year I blogged about the peroxisome. This year it's the turn of the nucleus. Yes, the nucleus itself.

Viral Eukaryogenesis: Was the Ancestor of the Nucleus a Complex DNA Virus?

This paper, from 2001, has been cited 60 times since then (thank you Web of Science), so it has attracted some attention but not a huge amount. Looking at the titles of some of the citing papers it is clear that this whole question is now wrapped up in the question of viral origins and our friend the mimivirus again.


Just about everyone will agree that trees are made from sunlight, water, and soil the trees sucks up from their roots. But the surprising truth is that trees are made from air! Trees are solar-powered machines that convert air into wood. Why is it that, despite the fact that photosynthesis is one of the most widely taught subjects in science, so few people really understand the central idea underlying this system?

Watch the video here.

I've posted this to the blog before but I think it is worth another bump. I've thought about this video a lot and I think the point it makes is spot on. Somewhere in all the teaching, especially in big intro classes, we forget to include the wonder. Sometimes you really do need to stop and see the wood in the trees.

Senin, 17 Januari 2011

Putting the dead to work

There's an interesting article in TREE (Trends in Ecology and Evolution) this month about the emerging science of conservation paleobiology.

There's a report at ScienceDaily: Putting the Dead to Work: Conservation Paleobiologists Dig Deep to Solve Today's Ecological, Evolutionary Questions, and the actual paper: Conservation paleobiology: putting the dead to work.

A new review of the research in this emerging field provides examples of how the fossil record can help assess environmental impacts, predict which species will be most vulnerable to environmental changes, and provide guidelines for restoration.

ScienceDaily is a good source for science news although it is almost always worth tracking down the original papers. They have got a lot better lately at including the full references at the end of their articles.

Climate Change Casualties

The evidence keeps getting stronger that climate change brought about by global warming is likely to cause disruptions in food production and mass migrations of some people from their homes and homelands within the next century. The latest article, in the January issue of Scientific American, describes three critical “hot spots” to watch – Mozambique, already experiencing more frequent droughts and floods; the Mekong Delta region of Vietnam, a rich farming area that is likely to face severe floods and loss of food production as the sea level rises; and Mexico and Central America, likely to be hit with increased numbers of tropical storms and crippling droughts.

Do we have the will to do something about climate change? Frankly, I’m not sure we do – the problem of global warming is still seen by many nations as either not severe enough, slow to develop, or not their fault (or at least not sufficiently their fault). Most nations have other more urgent issues to worry about first.

My prediction is that nations will spend more money over the next century dealing with the disastrous effects of climate change than they will in joining together to prevent the problems from ever happening in the first place. I sincerely hope I’m wrong.

But then, I won’t be here to see it, will I?

Minggu, 16 Januari 2011

Loss of trust

I've tended to post MMR vaccine related stuff to my Disease Ecology blog (look here if you are interested) but Bruce suggested I post here about this week's news that Andrew Wakefield and his colleagues had faked some of the data behind their 1998 Lancet article that suggested a link between the MMR vaccine (for Measles, Mumps and Rubella) and a type of autism. To its credit the LA Times has always been on top of this story. Their latest story, from Thursday,  is, Autism-vaccine link debunked — too little, too late, a CNN story from Friday: Vaccine-autism researcher should be prosecuted

If you are not familiar with the case then it might sound like something of interest only to the medical community but nothing could be further from the truth.

By falsely discrediting a widely used vaccine Wakefield's work has led to a decreased vaccine uptake and a loss of herd immunity. This has led to disease outbreaks and actual deaths. The deaths are directly attributable to the actions of this man. There is a reason that Dante Alighieri reserved one of the deepest circles of hell for those that destroyed the trust that allows a society to function. (If you read Dante it seems odd to our modern sensibilities that forgers end up worse off than murderers but the argument is sound - a murderer kills one person, by destroying trust in society a forger or perjurer undermines society itself).

Bruce suggested I post this news here both as a commentary on honesty in science, and  also so that you are well pepared when someone tries to tell you  that vaccinations have been demonstrated to cause autism (which, trust me, they will). I'd add a third reason and that is that California, sadly, is ground zero for the anti-vaccine movement.

California is currently seeing a big increase in whooping cough cases - most likely the largest number of cases since 1955. Whooping cough is a nasty disease in children and the only good news is that it isn't measles which can be a real killer.

Many parents forgo vaccines for their children because of concerns about autism, typically fueled by misinformation on the Internet, said Dr. Mark Sawyer, a University of California-San Diego professor and fellow of the American Academy of Pediatrics.

"We need to remember that vaccines are probably the biggest reason that so few of us lose our children when they are young," said Dr. Patricia Samuelson, speaking on behalf of the California Academy of Family Physicians. "They used to say in this country, 'Don't count your children until after they've had measles' because so many would die."

And that's my weekend rant. This whole topic makes me so mad that I can barely write about it. It isn't just the crimes of ex-Dr Wakefield that get to me but the complicity of much of the press. In an earlier blog post I commented on some of the newspaper headlines on an article that essentially was discrediting ex-Dr Wakefields work (ie showing NO link between the MMR vaccine and autism - New research further debunks any link between measles vaccine and autism, work that comes as the nation is experiencing a surge in measles cases fueled by children left unvaccinated.):

This science story was picked up by most news outlets as an item that would be of interest to their readership. A quick google news search suggests over 300 articles in the first few days alone. But, bearing in mind that many more people scan the headline than will read the article, let's look at some of the headlines.

In relation to Chapter 27 the marine world and its species

This is a link to a site that I had to use in Honors Biology in high school. It contains extensive field guides of the greatly diverse life at Zuma Beach in Malibu California. If you are interested you should check out the Field Guides and the pictures from the beach it has a lot of info. It has guides on the birds, plankton, mamals, macrophyte wrack and macrofauna of the beach. It also has a beaufort sea state chart and a temperature-Density-Salinity Conversion Chart. There is a lot of stuff there so feel free to explore. anyway here is the link to the main site:

you can check out the Honors Biology and Marine Bio they are to the left of the main photo. If you click on those you will get to the guides.

Sabtu, 15 Januari 2011

Overlooking the obvious

Weekend wildcard again.

Until now, the wing colors of many flies and wasps were dismissed as random iridescence. But they may be as distinctive and marvelous as the much-studied, much-celebrated wings of butterflies and beetles.

“Given favorable light conditions, they display a world of brightly patterned wings that are apparently unnoticed by contemporary biologists,” wrote researchers led by University of Lund entomologists Ekaterina Shevtsova and Christer Hansson in a December 3 Proceedings of the National Academy of Sciences paper: Stable structural color patterns displayed on transparent insect wings

Generations of biologists seem to have missed this partly because they didn’t look for it, and partly because the colors are most evident against a dark background. Against a white background, they’re invisible — which is exactly how most entomologists study transparent wings.


Yay people started posting. Well, Olivia and Bettina did and don't think that I didn't notice. Join the fun, there's room for everybody.

Although spontaneous generation does not occur and we now believe evolution of species is generally a gradual evolutionary process it is important to note that many superheroes are created much more quickly. Usually a one step process and often involving radiation.

For the punchline see the latest Super-Fun-Pak Comix by Tom the Dancing Bug (Ruben Bolling). This strip, especially the occasional Super-Fun-Pak Comix, often has some good biology and science jokes - Selfish Gene, Chaos butterfly, 10,000 years between panels, and the splendidly juvenile Science Facts for the Immature.

Redwoods are simply fascinating...

Here is an excerpt from a paper I was reading today.....

But on a glorious May day, nearly three-quarters of the way into the transect, they arrived at the southern end of Humboldt Redwoods State Park, home to the largest contiguous block of old-growth redwood forest left on the planet--some 10,000 acres. The alluvial flats along its creeks and rivers are prime redwood habitat, where the mix of rich soils, water, and fog rolling in from the ocean have produced the planet's tallest forest. Of the 180 knownredwoods greater than 350 feet, more than 130 grow right here.

Fording a vein of emerald water known as the South Fork of the Eel, they climbed the far bank and entered the translucent shade of the most magnificent grove they'd seen yet. Redwoods the size of Saturn rockets sprouted from the ground like giant beanstalks, their butts blackened by fire. Some bore thick, ropy bark that spiraled skyward in candy-cane swirls. Others had huge cavities known as goose pens--after the use early pioneers put them to--big enough to hold 20 people. Treetops the size of VW buses lay half-buried among the sorrel and sword ferns, where they'd plummeted from 30 stories up--the casualties of titanic wars with the wind, which even now coursed through the tops with panpipe-like creaks and groans. It's no wonder Steven Spielberg and George Lucas filmed scenes for the Jurassic Park sequel and Return of the Jedi among the redwood giants: It felt as if a T. rex or a furry Ewok could poke its head out at any minute.

Redwoods are no less magical for foresters. Because their bark and heartwood are rich in compounds called polyphenols, bugs and decay-causing fungi don't like them. And since there's not a lot of resin in their stringy bark, larger redwoods are highly resistant to fire.

Question: It's known that older trees are more resistant to fire. But is this b/c they have more sap? Size? Does the resin, bark and sap structure change in an older tree? why...?


REDWOODS The Super Trees.
Bourne Jr., Joel K.
National Geographic, Oct2009, Vol. 216 Issue 4, p28-59, 32p, 21 Color Photographs, 1 Diagram, 1 Map

34,000-Year-Old Life Found Still Alive...

I was searching for a topic to research for this week, and found this article which I thought might interest some of you and relates to our last lecture.  A 34,000 year old bacteria

was found alive in Death Valley

These bacteria are not doing anything other than maintaining themselves: "They're alive, but they're not using any energy to swim around, they're not reproducing".  Depending on algae for food these bacteria have managed to survive for 34,000 years and are one of the oldest life forms found on Earth. Sweet!

This discovery was published in the January 2011 issues of Geological Society Today, and the paper can be found here.
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