Scientific facts not determined by opinion poll.

I've posted on this before but since many of you are ,ultimately, PhD bound you may as well start reading it now. PhD comics tells it like it is. Life in the lab, dealing with advisors, eating noodles and the occasional snarky comment about the media. Be aware the archive is pretty vast......

Anciently asexual

Spore-bearing fungal parasites emerge from the digested corpses of three bdelloid rotifers.

Wow, I was just looking around for something to post on and there it is right on the cover of Science this week. Great story and highly relevant to class.

Anciently Asexual Bdelloid Rotifers Escape Lethal Fungal Parasites by Drying Up and Blowing Away

Asexuality has major theoretical advantages over sexual reproduction. An important evolutionary puzzle, therefore, is why exclusively asexual metazoan lineages rarely endure. The Red Queen hypothesis posits that asexuality is rapidly extinguished by relentlessly coevolving parasites and pathogens. If so, any long-lasting asexual lineage must have unusual alternative mechanisms to deal with these biotic enemies. Bdelloid rotifers are freshwater invertebrates that abandoned sexual reproduction millions of years ago. Here, we show that cultured populations of bdelloids can rid themselves of a deadly fungal parasite through complete desiccation (anhydrobiosis) and disperse by wind to establish new populations in its absence. In Red Queen models, spatiotemporal escape can decouple and protect asexuals from coevolving enemies. Thus, our results may help to explain the persistence of the anciently asexual Bdelloidea.

Synchronicity

Cool! Listen to the end for some interesting potential applications.

You can read the paper, A synchronized quorum of genetic clocks, in this week's edition of the journal Nature.

Incidentally, although some of the YouTube comments seem to think that 'Mexican Wave' is some sort of racist comment this is the term most widely used in England for a synchronised 'wave' in a large sports stadium (usually just called 'the wave' here in the US). In England this sort of behavior was not common until it was seen on TV during the 1986 world cup in Mexico and so it became associated with Mexico even though it hardly originated there.

Snus - Smokeless Tobacco Made Easy

Now available over the internet and in stores; Snus (rhymes with loose), a smokeless tobacco product containing nicotine that originated in Sweden. Snus comes in colorful tins and is packaged in small tea bag-like packets. It’s real advantage over traditional smokeless chewing tobacco is that no spitting is necessary - the small amount of juice produced can just be swallowed. It’s likely to become popular among teens who want their tobacco use to go undetected, patrons of bars and restaurants where smoking is not permitted, and smokers who want to quit.

The tobacco companies are looking to attract a whole new generation of tobacco users and to shore up profits in the face of declining cigarette sales. R.J. Reynolds launched a nationwide marketing campaign for “Camel Snus” in 2009. As usual, the company denies that it aims its marketing campaign toward underage users.

So far there is no evidence that Snus use may be a risk factor for cancers of the mouth and throat. Nevertheless, it is a tobacco product. It’s worth remembering that there were no clear health risks associated with cigarettes, either, when they first became popular in the 1940s.

CCS, Telomeres and Gaucho fun

I guess this is more relevant to cell biology or physiology but I thought some of you may be interested in this article in the New York Times today that describes research published in the journal Circulation that demonstrates that physical exercise can actually keep your cells younger.

Cell 'age' was assessed by looking at their telomere length. Unless you've been living under a rock for the last year you are probably aware that telomeres are tiny caps on the end of DNA strands and the discovery of their function won several scientists, including CCS biology graduate, Carol Greider, the 2009 Nobel Prize in medicine.

The research looked at four groups of people: young and sedentary; middle-aged and sedentary; young professional runners in their 20s; and finally middle-aged longtime runners.

Cells in both the active and sedentary young adults had similar-size telomeres because when you are young none of your cells are old enough to have significantly shortened telomeres. But when they examined the middle aged groups they found a HUGE difference

In general, telomere loss was reduced by approximately 75 percent in the aging runners. Or, to put it more succinctly, exercise, Dr. Werner says, ‘‘at the molecular level has an anti-aging effect.’’

This study of course raises a lot of questions but it is really nice to have such a large effect and hopefully follow up studies will clarify how much exercise is required and for how long. The middle aged runners in the study were running an average of 50 miles a week and had a 35 year training history.

Anyhow if you want to stop your telomeres shortening you may need to start running now. Fortunately this Saturday sees the return of the UCSB Running Series. A good incentive to get out of bed and drag yourself around the lagoon a few times (and then eat pizza).

Living With Cystic Fibrosis

Sixty years ago, before doctors knew very much about cystic fibrosis, most children with the disease died before school age. Today people with the disorder are living well into their 30s. Today we know that cystic fibrosis is a genetic disorder and we know what causes the symptoms.

What we don’t have is a cure. Prolonging the life of cystic fibrosis patients is largely based on improvement of care, including medicines that alleviate some manifestations of the disease and physical therapy to keep the lungs clear. What works for one patient doesn’t always work as well for the next.

An effective tool in the improvement of care for cystic fibrosis patients has been the establishment of a national registry of patients. The registry, which is managed by the Cystic Fibrosis Foundation, currently collects and stores patient records from more than 100 cystic fibrosis treatment centers across the country. The pooled data has proven very useful in learning what works best for which kinds of patients, and why. It’s like having the collective experience of thousands of doctors right at your fingertips.

The concept of a using a national registry of patients to improve patient care has proven so successful that other patient groups are copying it.

Horizontal and vertical evolution

There's a great article in this week's New Scientist magazine about evolution and horizontal gene transfer. It's so relevant to class (and so interesting) you should all read this one:
Horizontal and vertical: The evolution of evolution
I thought the discussion of the evolution of the three base genetic code was fascinating. The PNAS paper that produced these results is available here.

JUST suppose that Darwin's ideas were only a part of the story of evolution. Suppose that a process he never wrote about, and never even imagined, has been controlling the evolution of life throughout most of the Earth's history. It may sound preposterous, but this is exactly what microbiologist Carl Woese and physicist Nigel Goldenfeld, both at the University of Illinois at Urbana-Champaign, believe. Darwin's explanation of evolution, they argue, even in its sophisticated modern form, applies only to a recent phase of life on Earth.

At the root of this idea is overwhelming recent evidence for horizontal gene transfer - in which organisms acquire genetic material "horizontally" from other organisms around them, rather than vertically from their parents or ancestors. The donor organisms may not even be the same species. This mechanism is already known to play a huge role in the evolution of microbial genomes, but its consequences have hardly been explored. According to Woese and Goldenfeld, they are profound, and horizontal gene transfer alters the evolutionary process itself. Since micro-organisms represented most of life on Earth for most of the time that life has existed - billions of years, in fact - the most ancient and prevalent form of evolution probably wasn't Darwinian at all, Woese and Goldenfeld say.

Populus

For this Thursday please bring your laptop (if you have one, no need to buy one specially.....) and download the Populus program onto it.

Frequency dependent cichlid

The original fequency dependent cichlid fish paper is in Science:
Frequency-Dependent Natural Selection in the Handedness of Scale-Eating Cichlid Fish.

It looks like this common text book story is true. The figure nicely illustrates that having a neat story isn't enough to get your paper into Science but having ten years of data to back it up will do the trick.

Summer Research Position

Undergraduate Summer Research Position
Evolutionary Ecology

Syracuse University
Syracuse, NY

We are seeking undergraduates interested in gaining hands-on research experience studying the interactions between plants and insects. The project will involve both field and laboratory research. Field research will be conducted at the Archbold Biological Station in Lake Placid, Florida for 4-8 weeks. Travel to and housing in Florida will be paid in addition to an hourly salary ($8-$10/hr). Laboratory research will be conducted at Syracuse University in the Department of Biology after returning from Florida. Job duration is 8-10 weeks and is full-time.

On-the-job training will be provided and no research or field experience is required. Applicants should be planning an ecology/evolutionary biology career and have taken at least one of the following courses: Evolution, Ecology, Population Biology, Field Biology, Entomology, Botany, or an OTS course. Applicants must enjoy working outside and should not have an aversion to handling insects. The start date is late April-early May (non-negotiable).

Interested applicants should send a statement of interest, résumé, transcript, one letter of recommendation, and contact information for two additional references. The statement of interest should be less than 500 words with the following information: (i) career goals, (ii) interest in position, and (iii) statement agreeing to commit to the research position
for 10 weeks without other obligations.

Send application materials in one PDF or .doc file to Dr. Kari Segraves (ksegrave@syr.edu). Letters should be e-mailed directly from the recommender with the applicants name in the subject line. Incomplete applications will not be considered. The position will be filled no later
than Mar 30, 2010.

Photosynthetic... animals?!

http://www.cbc.ca/technology/story/2010/01/22/tech-biology-solar-sea-slug.html

So... crazy creature here. Not only does this slug look like a leaf, it is able to use sunlight to produce sugars. Turns out these animals are able to uptake the chloroplasts from ingested plant matter (in this case algea) and incoperate them fuctionally and spatially into their cells!

Because the chloroplast is outside of the environment in which it evolved, it is unable to do its job without some assisting genes from its host cell , so it even transfers part of the algea's genome into its own!!! Clearly relevant to gene therapy.

Also, this animal turning into a leaf in shape and color (color reasonably being assumed to be caused by this chloroplast uptake) is a cool demonstration of structure being essential to function.

Siamese cats

The coat pattern in Siamese cats is a form of partial albinism, resulting from a mutation in tyrosinase, an enzyme involved in melanin production. The mutated enzyme is heat-sensitive; it fails to work at normal body temperatures, but becomes active in cooler areas of the skin. This results in dark colouration in the coolest parts of the cat's body, including the extremities and the face, which is cooled by the passage of air through the sinuses.

Many early Siamese were cross-eyed to compensate for the abnormal uncrossed wiring of the optic chiasm, which is produced by the same albino allele that produces coloured points. However the crossed eyes have been seen as a fault and through selective breeding, the trait is far less common today.

Details of the Tyrosinase mutation are available in this 2006 paper: Albinism in the domestic cat (Felis catus) is associated with a tyrosinase (TYR) mutation

Preservation of Traces

To continue this weekend's writing theme here's an interesting website:
The Preservation of Favored Traces.

Watch On the Origin of Species change across six editions as Darwin reconsidered his arguments and responded to criticisms.

It takes a while to load but once the screen comes up you can click on fast to speed it up. Then hold your mouse over the page to see the edits - you'll see what I mean. A very interesting way of visualizing the writing process that I haven't seen before.

I think I need a new tag for 'Well worth playing around with for a few minutes'. Done.

Writing

"He said, 'I like this song you wrote called Hallelujah. How long did that take you to write?' And I said, 'Oh, the best part of two years.' He said, 'Two years?' Kinda shocked. And then we started talking about a song of his called I And I from Infidels. I said, 'How long did you take to write that.' He said, 'Ohh, 15 minutes.' I almost fell off my chair. Bob just laughed."
Leonard Cohen talks to Bob Dylan as remembered by Cohen.

It seems that everyone struggles with writing (except maybe Bob Dylan when he's having a good day). Several people have talked to me recently about how they want to improve their writing. There's no magic trick. You work at it. You write.

Very, very, few people are gifted natural writers. Most of us labor through draft after draft. You can be a good scientist without being a naturally good writer but that means you need to work at your writing. Take it through draft after draft. You can't just throw up your hand and say you aren't a good writer.

If Leonard Cohen can labor for two years on one song then we can all go through one more draft.

Encyclopedia of Life

I encountered this website about two years ago when it was not too well developed: The Encyclopedia of Life.  Since then, a lot of information has been added, and the site just continues to grow and  become more comprehensive. You can search for an organism and find information on its evolutionary history, ecology, general biology, as well as relevant scientific papers.

Here is a link for the Koala Bear (I've no idea why I chose it for an example- it just popped into my head). As you can see, there is an image gallery, and information below the images. To the right, there is a classification index that is really fun to play around with.

Height

I'm not sure how class related this is but I was curious if the Army still had a height requirement and if and when it was abolished. I was looking specifically at the British Army simply because the history is longer.

Looking at the Army general regulations (specific regiments might have more stringent requirements) it seems there was a gradual decline in the minimum height requirement from 5'8" in the mid-1800's to 5'6" by the end of the 1800's and then a more rapid decline during the First World War - first to 5'5" then to 5'4" and finally to 5'3".

The demand for troops in the First World War ultimately led to the creation of special battalions in which the normal minimum height requirement for recruits was reduced from 5'3" to 5'.These were known as bantam battalions and recruited a large number of miners. It was the success of such battalions that probably led to the phasing out of the general height requirement.

It was around the same time (1916) that the British Army revoked the standing order that all military men were required to maintain a mustache. To be a bit more accurate the army didn't actually require a mustache it just forbade shaving of the upper lip....

There does not seem to be a height requirement these days, which makes sense now the army is less stabby and reach is less of a factor. Still, it's interesting to note that 200 years ago, when people were generally shorter, the army would have recruited largely from the upper end of the bell curve of height making a regiment of Guards (who had, and I think still have, a more stringent 6' requirement) appear massive.

Which brings us back to class and gives me the opportunity to link to this fascinating New Yorker article I mentioned: The Height Gap - Why Europeans are getting taller and taller-and Americans aren’t.

Genetics problem

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.

I'll post a comment about what the answer is not. See what answer you get first.

Peroxisome

Okay here's an interesting example of the sort of topic you could investigate for class. It only took me 15 minutes to get this far (thanks to the internets) although if I actually read the papers it would take a bit longer....

It started with a simple question - if mitochondria and chloroplasts have an endosymbiotic origin has anybody proposed an endosymbiotic origin for any other cell organelles?

Wikipedia (like I said, never a bad place to start) immediately suggests one possibility, the peroxisome 'they may have been the first endosymbionts, allowing cells to withstand growing amounts of free molecular oxygen in the Earth's atmosphere', and provides a quick review of what a peroxisome is:

Peroxisomes are organelles from the microbody family and are present in almost all eukaryotic cells. They participate in the metabolism of fatty acids and many other metabolites. Peroxisomes harbor enzymes that rid the cell of toxic peroxides.

However their article on the endosymbiotic theory gives a reference to a 2006 paper (Origin and evolution of the peroxisomal proteome) that states that
'Altogether our results indicate that the peroxisome does not have an endosymbiotic origin and that its proteins were recruited from pools existing within the primitive eukaryote.'

Time to leave Wikipedia. Is this the state of the science or have there been any recent updates? A Web of Science search for who cited the 2006 paper throws up a 2010 paper, The origin of peroxisomes: The possibility of an actinobacterial symbiosis in the journal Gene just this week, that reaches a very different conclusion:
We provide several lines of evidence supporting an actinobacteria symbiotic origin for the peroxisome.

Lifting the veil

These unassuming little brown balls, which are 5–7 micrometres in diameter, are cells of the marine alga newly described by Moore et al. In providing a connection between the apicomplexan parasites and their algal ancestors, the organism becomes a prime candidate for the complete genome analysis that should help lift more of the veil from ancient evolution.

Nature, 2008: Evolutionary biology: Bridge over troublesome plastids
Identification of a direct link between apicomplexan parasites and their algal ancestors is a development full of promise. It illuminates a dark corner in the evolution of photosynthesis, and further insights are to come.

There's also a 2004 Nature Review article on the prospect of malarial drugs targeting the apicoplast: Tropical infectious diseases: Metabolic maps and functions of the Plasmodium falciparum apicoplast.
Discovery of a relict chloroplast (the apicoplast) in malarial parasites presented new opportunities for drug development. The apicoplast – although no longer photosynthetic – is essential to parasites. Combining bioinformatics approaches with experimental validation in the laboratory, we have identified more than 500 proteins predicted to function in the apicoplast. By comparison with plant chloroplasts, we have reconstructed several anabolic pathways for the parasite plastid that are fundamentally different to the analogous pathways in the human host and are potentially good targets for drug development. Products of these pathways seem to be exported from the apicoplast and might be involved in host-cell invasion.

Bioluminescence, Bacteria, and the "Milky Sea" Phenomenon

After reading about the bacteria from the genus Vibrio in Chapter 26, I was curious to find out more about the glowing blob specified in Figure 26.8. This blob, as our book depicts, are

"...legions of Vibrio harveyi (which) form a glowing patch some thousands of square kilometers in...the Indian Ocean".

Upon some more research thanks to Wikipedia I learned that this massive glowing patch which can also be seen from space, is known as the "Milky Sea". And the bacteria that make it, Vibrio harveyi, have many characteristics that we learned about in chapter 26:they are Gram-negative (refer to page 566 in our textbooks) and also rod shaped (page 563 figure 26.2), motile (page 566), facultatively anaerobic (page 568), halophilic (page 577), and competent for both fermentative and respiratory metabolism (page 568 again, under anaerobic versus aerobic metabolisms again).

Also, through my searching, I found a neat link you guys might like about the Milky Sea phenomenon that funnily enough is part of the bioluminescence webpage by UCSB's life sciences program. Check it out!

http://www.lifesci.ucsb.edu/~biolum/organism/milkysea.html

-Ren

Panspermia

Panspermia is the idea that life on earth was 'seeded' by the arrival of organisms or compounds from space. Not necessarily little green men with a sinister plan, but maybe primitive microbes that then evolved into all life on earth. An interesting idea that is usually rarely mentioned in biology courses because, for me at least, the more interesting question is could life have once spontaneously arisen on earth? If so, under what conditions and how do these conditions relate to what we know about the early earth?

However if you want to read more about panspermia there are some fanatics on the web (just google it) or you can read this 2005 Scientific American paper - Did Life Come From Another World? for a more balanced view.

Monkey business

Like I said, Biology is full of surprises.

Contrary to a widely held scientific theory that the mammalian Y chromosome is slowly decaying or stagnating, new evidence suggests that in fact the Y is actually evolving quite rapidly through continuous, wholesale renovation. The analysis was possible because of the sequencing of the Y-chromosome from Chimpanzees.

The region of the Y that is evolving the fastest is the part that plays a role in sperm production, the rest of the Y is evolving more like the rest of the genome, only a little bit faster.

The paper is in Nature this week and there is a nice write-up at ScienceDaily.

Size

This cool tool for visualizing cell size and scale was posted on the blog for my other class this quarter (Disease Ecology). It's from the University of Utah and I just realized it's rather applicable here too. It's a nice way of visualizing size and is well worth the 2 minutes or so it takes to play around with it. Look at the footnotes to learn a couple of interesting facts.

Exploratorium Website

I found this website when I took a survey. The website goes over understanding how scientific studies are conducted and specifically looks at human evolution...but they have probably added a lot more stuff in there. Check it out and have fun!
http://www.exploratorium.edu/evidence/

Limerick 3.1

Hey everyone, this is a limerick my roommate found in her human geography book and it ties in with what we talked about today (kinda).

A eukaryote wanting to eat,
Saw bacteria as quite a nice treat.
Increasing closeness
Led to endosymbiosis,
And the modern plant cell was complete.
-Elizabeth Wenk, 1994

Hope you all enjoyed that!
-Kylie Langlois

Snowball earth and other ice ages

I've blogged on this before but Snowballearth.org is still the best site for all your Snowball Earth needs although it looks like it needs a bit of an update.
Their Questions section includes:

What caused the snowball earths?

Possibly by a lowering of atmospheric greenhouse gases to near-present levels through tectonically-mediated rock weathering, when the Sun was considerably dimmer than present.

Well, that's the short answer - here's the longer answer.

The Wikipedia article on Snowball Earth is also a really nice summary of the topic and covers the evidence for the theory, the various different controversies and, most relevant to us, a discussion of how life itself might have survived, and the implications for evolution.

We know more about what causes regular ice-ages but even then it seems that the relative contribution of different factors is much debated.

Two seminars of note

A couple of chances to see EEMB faculty presenting their research to a general audience, first Steve Gaines on Friday and then Armand next Tuesday.

Steven Gaines,
Dean Bren School of Environmental Science & Management
Friday, Jan. 15
4:00 - 5:00 p.m. Bren Hall 1414
"Seeking Ocean Solutions: Networks, Incentives, and their Interactions"
Reception in the Bren Courtyard to follow with music by Brengrass
-------------------------------------
Armand Kuris,
University of California, Santa Barbara
Marine Science Winter Colloquium
Tuesday, January
4:00 pm MSRB Auditorium 1302
"Parasites approach the Darwinian Demon: adaptations, evolutionary wormholes and their ecosystem visibility"

I found a Net. Geo article about the limbed fish Tiktaalik with some more info, including a possible explanation on its huge head. Didn't someone bring that up? Anyway, apparently the story is that it hunted like a crocodile, and so it needed large jaws. Also, becuase it had nostrils, it need to breathe through its head too. It also seemed to move like modern mudskippers in shallow flooded land. Here's the link:
http://news.nationalgeographic.com/news/2006/04/0405_060405_fish.html

Depo-Provera and Bone Loss

Around two million women use Depo-Provera as their contraceptive of choice. About 400,000 of them are teenagers. Depo-Provera is popular with teenagers because of its ease of use – just a single injection is required every three months.

However, Depo-Provera has one side effect not shared by oral contraceptives; it causes a slight but statistically significant bone loss. Researchers compared bone mineral density in young women aged 12-18 who used either Depo-Provera, oral contraceptives, or no birth control at all (the control group) for two years. Bone mineral density increased over the two-year period in the control group, as expected in young women still in their teens. It also increased in the oral contraceptives group by the same amount. However, bone mineral density decreased slightly but significantly in the Depo-Provera group.

The decrease in bone mineral density among Depo-Provera users was not sufficient to pose an immediate health risk, and any long-term risks are still unknown. Nevertheless, women’s health experts suggest that teenagers who are taking Depo-Provera should be sure to get enough calcium in their diet.

Reference: Cromer, Barbara A., et al. Bone mineral density in adolescent females using injectable or oral contraceptives; a 24-month prospective study. Fertility and Sterility 90: 2060-2067, 2008.

tau protein

here's an interesting introduction to tau protein. found in the nervous system and thought to be linked to Alzheimer's. I studied it's aggregation in a physics lab for a year, and it's amazing how much effort, and technology goes into studying it.

http://en.wikipedia.org/wiki/Tau_protein

Epigenetics

I've always tried to be fair to Lamark when I teach - after all he did get much right. It now turns out that even his mechanism may work in some situations.

In the last few years the exploding field of epigenetics has finally provided the mechanism by which acquired characteristics can be passed on to offspring. (Epigenetics is the study of how gene expression is altered by mechanisms other than changes in the underlying DNA sequence.)

Here's one very readable introduction to the topic: Two new studies show that the effects of a mother's early environment can be passed on to the next generation.
or a more in depth paper on bacterial epigenetics:
Epigenetic Gene Regulation in the Bacterial World

UCSB has a number of researchers working on epigenetics and a number of courses you can take if this is of interest to you. Professor David Low of MCDB, one of the authors of the above paper, works in this area and has just agreed to become a CCS advisor. He has had very positive interactions with CCS students in his lab and hopefully this will continue.

Chosen topics

What is this topic of which we speak? Since choosing a topic to investigate each week is an important part of the assessment for this class I thought I'd post some suggestions from the first few classes.

In no particular order here are ten topics that come to mind (this is by no means a comprehensive list):

• Giraffe neck evolution. What is the full story?
• Have recent advances in epigenetics provided a mechanism for the inheritance of acquired characteristics proposed by Lamark (see next blog post above).
• Whatever happened to that Big Bird chicken?
  
• Tiktaalik - the 'fishopod'. Is it a 'missing link'? What do we mean by that? Is there a better term?
  
• When we directly compare the DNA between species how do we do this given that there is variation within a species?
  
• How old do we now think the earth is? How do we know this? Could we be wrong?
  
• What is the likelihood we will find evidence of an alternate origin of life? Has anyone claimed we already have?
• How do you go about looking for 'weird life'?
  
• What IS life? Any interesting recent musings on this topic. If you really want to go there?
  
• Virophages. The virus parasite I briefly mentioned.
  

New techniques for sequencing

I mentioned that genetic sequencing is now one of the important tools used in systematics. However up until now this has been problematic when working with early human specimens, or close relatives. This is because the technique involved multiplying up small fragments of DNA and so even a tiny amount of contamination from a modern human (eg an archaeologist who handled the bones) could become a huge problem if this contaminant were multiplied.

'Using the remains of humans that lived in Russia about 30,000 years ago, Svante Pääbo and his colleagues now make use of the latest DNA sequencing (i.e., reading the sequence of bases that make up the DNA strands) techniques to overcome this problem. These techniques, known as "second-generation sequencing," enable the researchers to "read" directly from ancient DNA molecules, without having to use probes to multiply the DNA. Moreover, they can read from very short sequence fragments that are typical of DNA ancient remains because over time the DNA strands tend to break up. By contrast, DNA that is younger and only recently came in contact with the sample would consist of much longer fragments. This and other features, such as the chemical damage incurred by ancient as opposed to modern DNA, effectively enabled the researchers to distinguish between genuine ancient DNA molecules and modern contamination. "We can now do what I thought was impossible just a year ago -- determine reliable DNA sequences from modern humans -- but this is still possible only from very well-preserved specimens," says Pääbo.'

The paper is in the Jan 12 edition of Current Biology and there's a more popular write up on the ScienceDaily website.

What are you reading?

Here's an easy way to get posting.

What are you reading? What are your favorite science related websites? The ones that you visit on a semi-regular basis. Add a new posting or post a reply to this one. Here's a few of my favorites:

• ScienceDaily - hard to beat for keeping on top of a wide variety of biology. I wish they'd link to the actual articles they summarize, instead of giving you a few clues to track them down, but apart from that it's a great site and not a bad one to use as your homepage.
• Science of Sport -a little hard to describe but it's a bit like a Freakonomics approach to sport. For a subject that has been obsessed with statistics for many years it is surprising how rarely sport has been analyzed scientifically. They tend to focus on athletic events such as running, swimming and cycling rather than team sports but they don't seem to have any particular rules and plenty of odd subjects crop up.
  
• Pharyngula - Evolution, development, and random biological ejaculations from a godless liberal. How words not mine. The author, PZ Meyers is a biology professor at the University of Minnesota. He'll actually be speaking on campus on 'Complexity and Creationism' on January 20th if you are interested.

What do you read?

What's in a name?

I know that some of you probably live in Manzanita Village. If so, or if you have been out near a pond after dark lately, you have probably heard the deafening sound of frogs. The loudest local spots I've noticed are the pond between Manzanita Village and the lagoon and, a little later in the year, the wet area between Storke road and the golf course.

We don't have any tree frogs in England so when I came to California I was amazed to find out that all the noise is made by these little guys, Pseudacris regilla - often not much bigger than an inch.

For a little frog they also have a lot of names - at least two common names: the Pacific tree frog, and the Pacific Chorus frog and lots of people just call them Hyla because they used to be called Hyla regilla. Until 2005 Hyla was a large genus of frogs with over 300 species. However a systematic review of the genus Hyla in 2005 split the genus into three new genera: Aris, Limnaoedus, and Pseudacris (why do you think they did this?), requiring the renaming of all 300 plus species.

Although the revision better reflects our understanding of the evolution of these frogs it's unfortunate that this involves renaming all the frogs and the loss of some familiar names. The frogs haven't changed just our understanding of their evolution.

Alternative titles

It's a little fast and hard to keep up with in places, especially in the latter stages but the fast moving style, pop culture references and connections to Thursday's class make this video well worth a look. Eddie Izzard suggests some of the rejected titles for Darwin's big book....

Bypassing the constitution

You may have heard the saying 'Science progresses by the death of scientists.' Several people have said something like this, perhaps the most famous being Max Planck the German theoretical physicist and generally accepted as the founder of the quantum theory in physics.

“A new scientific truth does not triumph by convincing its opponents and making them see the light, but rather because its opponents eventually die, and a new generation grows up that is familiar with it.”

Creating a taxonomy that reflects evolutionary history is now firmly established in biology and the the techniques of cladistics are used to classify organisms into hierarchical taxonomic groups. None of this is very controversial, at least not any more.

However the question of whether we should continue with the Linnean taxonomic code or adopt something different is a very hot topic. I suspect that this is one of those changes that is going to take the death of a generation of biologists to change. There was a good article about the issue in American Scientist in 2006: Attacks on Taxonomy.

Unlike the PhyloCode, Linnean taxonomy does not formally incorporate phylogeny. However, its ranks (species within genus, genus within family, family within class and so on) imply evolutionary relationships. The main drawback of the Linnean system is that groups must be named with suffixes that denote their rank in this hierarchy. For instance, all animal families end in -ae, as in Hominidae. Reclassification of an existing species or discovery of new one can lead to changes in rank and therefore require renaming whole suites of taxonomic groups—a cascade of renaming—even without any new information on those groups. The Phylo-Code solves this problem.

Discover magazine also had a nice article that focused a little more on the people and the controversy: Pushing Phylocode.

“This would be very similar to a set of politicians who decided to bypass the Constitution to create a whole new set of laws.”

Evolutionary Trees Paper

Had to read this paper for Invertebrate Zoology- great in that it's extremely informative and clarifies many misconceptions people hold regarding evolutionary trees. Abstract is below.

Understanding Evolutionary Trees


Charles Darwin sketched his first evolutionary
tree in 1837, and trees have remained a central metaphor in
evolutionary biology up to the present. Today, phylogenetics—
the science of constructing and evaluating hypotheses
about historical patterns of descent in the form of
evolutionary trees—has become pervasive within and
increasingly outside evolutionary biology. Fostering skills
in “tree thinking” is therefore a critical component of
biological education. Conversely, misconceptions about
evolutionary trees can be very detrimental to one’s
understanding of the patterns and processes that have
occurred in the history of life. This paper provides a basic
introduction to evolutionary trees, including some guidelines
for how and how not to read them. Ten of the most
common misconceptions about evolutionary trees and their
implications for understanding evolution are addressed.

The Neuroscience of Screwing Up

I mentioned this briefly on Tuesday and I may add this as reading for the Biology Colloquium next year but I thought some of you might like to read it. A fascinating discussion of how science is done, how and why we make mistakes and how we interpret them.

Accept Defeat: the Neuroscience of Screwing Up

While the scientific process is typically seen as a lonely pursuit — researchers solve problems by themselves — Dunbar found that most new scientific ideas emerged from lab meetings, those weekly sessions in which people publicly present their data. Interestingly, the most important element of the lab meeting wasn’t the presentation — it was the debate that followed. Dunbar observed that the skeptical (and sometimes heated) questions asked during a group session frequently triggered breakthroughs, as the scientists were forced to reconsider data they’d previously ignored. The new theory was a product of spontaneous conversation, not solitude; a single bracing query was enough to turn scientists into temporary outsiders, able to look anew at their own work.

But not every lab meeting was equally effective. Dunbar tells the story of two labs that both ran into the same experimental problem: The proteins they were trying to measure were sticking to a filter, making it impossible to analyze the data. “One of the labs was full of people from different backgrounds,” Dunbar says. “They had biochemists and molecular biologists and geneticists and students in medical school.” The other lab, in contrast, was made up of E. coli experts. “They knew more about E. coli than anyone else, but that was what they knew,” he says. Dunbar watched how each of these labs dealt with their protein problem. The E. coli group took a brute-force approach, spending several weeks methodically testing various fixes. “It was extremely inefficient,” Dunbar says. “They eventually solved it, but they wasted a lot of valuable time.”

The diverse lab, in contrast, mulled the problem at a group meeting. None of the scientists were protein experts, so they began a wide-ranging discussion of possible solutions. At first, the conversation seemed rather useless. But then, as the chemists traded ideas with the biologists and the biologists bounced ideas off the med students, potential answers began to emerge. “After another 10 minutes of talking, the protein problem was solved,” Dunbar says. “They made it look easy.”

Combating Motion Sickness

What causes motion sickness? The main reason is that during certain kinds of involuntary motions the brain receives conflicting neural signals from visual receptors in the eyes, positional receptors in the inner ears and in muscles and tendons, and gravity receptors in the stomach. These conflicting signals confuse the brain, and nausea ensues.

Recently, researchers learned that the severity of motion sickness caused by a slow, cyclic motion can be reduced by deliberately breathing out of sync with the motion. Breathing either faster or slower than the cyclic motion allows the diaphragm to counteract the heaving movements of the stomach, thereby minimizing the neural disconnect between stomach gravity sensors and other motion and position receptors. The worst thing you can do is to take a breath with each heaving motion, although it’s the natural thing to do.

Reference: Denise, P. et al. Effect of temporal relationship between respiration and body motion on motion sickness. Autonomic Neuroscience 151:142-146, 2009.

Start with a bang

Okay, I'm allowed to have the odd repeat. I think I shall make it a tradition to start this course with a bang.

We didn't actually get onto abiogenesis and the very early history of the earth today (don't worry we'll get to it later). However I don't think I'll let that stop me posting this clip from the Discovery Channel. For everyone who has ever wondered what it would be like when a 500km diameter asteroid crashes into the earth. If you go to YouTube to watch it you can click a little link to watch it in high def. (highly recommended). You might also want to wait until you can crank up the speakers. The perfect soundtrack to the end of the world.

CCBER Conservation and Restoration Ecology seminar series

CCBER's Monday night seminar series will be located in room 2124 Girvetz Hall due to impacts associated with our NSF-funded renovation of our herbarium.
The topic and speakers are described below. We look forward to seeing you there. Monday nights 6-7pm.


Conservation and Restoration Ecology Seminar

Winter 2010

Conservation & Restoration Response to Global Climate Change Predictions

Lisa Stratton – stratton@lifesci.ucsb.edu

Room 2124 Girvetz

Jan. 4. – Introduction & Discussion

Jan 11. – Biodiversity Conservation in an age of climate change: the case of the Southern California Bight by: Michael V. McGinnis, PhD
Acting Director, Ocean and Coastal Policy Center, Marine Science Institute & Lecturer, Environmental Studies Program & Graduate School of Environmental Science and Management

January 18 – Holiday

January 25 – Class presentations/Discussion: Science of Global Climate Change


February 1 – Gaia theory and climate change, by: Lee Klinger – Independent Scientist

February 8 – Understanding the impacts to Global Climate Change on Plant Phenology and Pollination Patterns – Brian Haggerty, UCSB

February 15th – Holiday


February 22 – State of California and the Coastal Conservancy Policy Response to Global Climate Change Predictions – Bob Thiel, Project Manager, State Coastal Conservancy

March 1 – Global Climate Change and the Southern California Steelhead Recovery Plan – Mark Capelli, Recovery Coordinator, NOAA Fisheries Service

March 8 – Final Discussion

Quietus for Tinnitus?

Perhaps you’ve heard the ads for Quietus, an allegedly “unique homeopathic formula” containing “proven and effective ingredients” for treating tinnitus (ringing in the ears). The product’s website doesn’t list the ingredients, but I was told by a representative who answered the phone that it contains quinine sulfate, salicylates (a close relative of aspirin), and several other ingredients.

Quinine sulfate?! The FDA banned quinine sulfate in 2006 from all FDA-approved drug products except for products used in the treatment of malaria. The FDA lists a number of possible toxic effects of quinine including disorientation, cardiac arrhythmia, allergic reactions, and even death (there have been 93 deaths associated with quinine use in the past 40 years)

Why is quinine still allowed in a homeopathic remedy? Unlike pharmaceutical drugs, homeopathic remedies derived from natural products can stay on the market until they are proven to be unsafe. In other words, the makers of homeopathic remedies do not have to prove their products safe before marketing their products; they can just wait and see what happens to users. Users beware…..

Myopia is on the Rise

According to a recent report, the prevalence of myopia (nearsightedness) in persons aged 12-54 years in the U.S. has increased from 25% to 41.6% in just the past 30 years. That’s too large a change in such a short a time to be due solely to a genetic factor; there must be an environmental component. A clue is that myopia is more common in people with more than 12 years of education, suggesting that close work such as reading and computer work might be a risk factor.

The good news is that myopia is relatively easy to correct with eyeglasses, contacts, or LASIK surgery. As health problems go, myopia is not the big one. Nevertheless, scientists are curious to know what might be causing the rise in myopia so that preventive measures could be undertaken if possible. Over 40% of the population with myopia is a lot of people! If nothing else, correction of myopia represents a significant national heath care expenditure, even if it's not a big deal to any one person.