Sunday, January 31, 2010
Saturday, January 30, 2010
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.
Friday, January 29, 2010
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.
Thursday, January 28, 2010
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).
Wednesday, January 27, 2010
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.
Tuesday, January 26, 2010
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.
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 (firstname.lastname@example.org). 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.
Monday, January 25, 2010
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.
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
Sunday, January 24, 2010
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.
Saturday, January 23, 2010
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.
Friday, January 22, 2010
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.
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.
Thursday, January 21, 2010
I'll post a comment about what the answer is not. See what answer you get first.
Wednesday, January 20, 2010
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.
Tuesday, January 19, 2010
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.
Monday, January 18, 2010
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
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.
Sunday, January 17, 2010
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.
Friday, January 15, 2010
Thursday, January 14, 2010
A eukaryote wanting to eat,
Saw bacteria as quite a nice treat.
Led to endosymbiosis,
And the modern plant cell was complete.
-Elizabeth Wenk, 1994
Hope you all enjoyed that!
Their Questions section includes:
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.
Wednesday, January 13, 2010
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
University of California, Santa Barbara
Marine Science Winter Colloquium
4:00 pm MSRB Auditorium 1302
"Parasites approach the Darwinian Demon: adaptations, evolutionary wormholes and their ecosystem visibility"
Tuesday, January 12, 2010
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.
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.
Monday, January 11, 2010
'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.
Sunday, January 10, 2010
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.
Saturday, January 9, 2010
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.
Friday, January 8, 2010
Thursday, January 7, 2010
“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.”
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.
Wednesday, January 6, 2010
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.”
Tuesday, January 5, 2010
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.
Monday, January 4, 2010
The topic and speakers are described below. We look forward to seeing you there. Monday nights 6-7pm.
Conservation and Restoration Ecology Seminar
Conservation & Restoration Response to Global Climate Change Predictions
Lisa Stratton – email@example.com
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