Pitcher Plants

The usual stunning photography reveals the complex ecology of a pitcher plant.

It's not just the genes...

Increasingly we are realizing that it isn't just the genes that are important but how those genes are expressed.

This was nicely illustrated in a Science paper this week where they looked at the role of the Agouti gene in pattern development: The Developmental Role of Agouti in Color Pattern Evolution.

Agouti, ... governs color patterns in deer mice, the most widespread mammal in North America. This gene, found in all vertebrates, may establish color pattern in a wide variety of species, a process that has been poorly understood at both the molecular and the evolutionary level.

Agouti had previously been known to affect the type of pigment found in vertebrate fur, feathers, and scales: Little expression of the gene in adults results in the production of dark pigments, while robust Agouti activity generally yields light pigment production. But Manceau and Hoekstra found that subtle changes in the gene's embryonic activity can also make a profound difference in the distribution of pigments across the entire body.

"During embryogenesis, Agouti is expressed in the belly, where it delays maturation of the cells that will eventually produce pigments," says Hoekstra, John L. Loeb Associate Professor of the Natural Sciences at Harvard. "This leads to a lighter colored belly in adults, which is the most common color pattern across a wide variety of vertebrates, from fish to antelope."

Even small changes in Agouti gene expression can establish a completely new color pattern. In deer mice, natural selection drives changes in the amount and place of Agouti expression, which in turn results in new color patterns that can camouflage animals from visual predators in habitats including dark forests and light sandy beaches.

"It is hard not to speculate that Agouti plays a role in generating more complex patterns -- from stripes to spots -- in a diversity of vertebrates," Hoekstra says.
 

 Looking for a picture of a leopard to add I found this cool picture of a black panther (panthers are just black leopards). Notice how you can see the pattern of spots in the fur even though the fur is all black.

Competing sinks?

Just because two plants are sufficiently closely related to graft them together doesn't necessarily mean it's a good idea to graft them together.

I must confess that, beyond the novelty value, I don't quite get the amazing tomato-potato.

It seems more sensible from a plant physiology point of view to just plant a tomato next to a potato and have two sets of leaves each providing for one sink rather than have two large sinks competing for the same resources. I initially wondered if maybe the potatoes ripened first and then maybe the tomatoes but the inset photograph seems to show them both ripe together.

Given that tobacco is also in the Solanaceae family I wonder how long it will be before we see tomacco for real? Oh wait someone already did that.

Taxol and Repair of Spinal Cord Injuries

One of the challenges in facilitating repair of the spinal cord after spinal cord injuries has been to get axons to re-grow through the damaged area. Usually the process of axonal re-growth is inhibited by the formation of scar tissue.

But now researchers have discovered a potential new weapon in the treatment of spinal cord injuries – taxol, the same drug that is currently used to inhibit the growth of certain cancers. It turns out that taxol produces “stabilization” of microtubules in damaged areas of the spinal cord, which in turn reduces scarring and reduces the production of certain factors which normally inhibit axonal regeneration. The result is that axons tend to grow more readily through taxol-treated lesion sites.

So far, taxol has only been shown to work in rats. Nevertheless, these encouraging results could pave the way for future clinical trials in humans. Perhaps some day taxol will become part of the normal treatment regimen for spinal cord injuries.

Walking with dinosaurs

Natasha's post below, and the topic of some forthcoming lectures, reminded me of the BBC's fondness for dinosaur simulations.

I think it all started with a show called 'Walking with dinosaurs' that was , at the time, the most expensive documentary ever made. Using computer simulation and animatronics to create a 'realistic' wildlife show - but one with dinosaurs. You should check these out if you haven't seen them. I think they are available on Netflix and Veoh online.

Then there's Prehistoric Park, made by the same company, which now includes a 'time portal' and a narrator. Wikipedia calls it 'docu-fiction'. I almost posted a clip from this earlier in the quarter because they have a nice segment with one of those giant Carboniferous arthropods - Arthropleura.


Finally, keep the time portal and the dinosaurs but add in ludicrous characters, creatures from the future and the stupidest plotlines you can imagine and you have Primeval. Check out episode two of the first series for Arthropleura in the London Underground.

Choose your own level of prehistoric incredulity.

CCS Bio Sweatshirts!

Hey guys!

I was thinking it would be cool to have a CCS bio sweatshirt so I decided to create a design, but I want your input on a few things. One, do you like it? Two, do you prefer the blue or yellow? If you would prefer like a cat or something please don't message me but if you have something constructive to add to the design definitely let me know. The yellow looks brighter and more legible as a computer image but they'll both look good when printed. Also, its only going to cost $20 hooray! My email is ellabc@gmail.com or you can find me on facebook if you have a question or suggestion. I'll bring all this to class on Tuesday and we can talk more about it. Have a good weekend ; )

Ella Bendrick-Chartier

Ground sloths and mastodons

Life in prehistoric Los Angeles was more perilous than you ever thought.

Oh that's what it was...

Even though you didn't see them I added the slides from today's class so you can work out what my scribbles meant. This material is also well covered in chapters 34-36 in your textbook which has some excellent illustrations.

On an unrelated note next Monday's EEMB seminar is by Professor Mary Power of UC Berkeley. Her title is still listed as TBA but Mary works on food webs in rivers and their watersheds. She has been the president of the Ecological Society of America and usually gives a pretty enthusiastic talk.

Angel's trumpet poisoning

I looked up some information on the toxic compounds in Brugmansia. The plant contains an unhealthy brew of the alkaloids atropine, scopolamine and hyoscyamine.

Because these can cause hallucinogenic effects they are often ingested by those seeking just such an effect. When combined with alcohol the effects can be rapid. Although the plant can be eaten or smoked the most popular method of ingestion is to prepare a tea from the flowers and seeds.

Unfortunately because the levels of the alkaloids vary widely from season to season it is very easy to overdose and it is estimated that 'teas prepared from as few as 10 flowers could be extremely toxic if not fatal'. Angel's trumpet ingestion produces the classic symptoms of anticholinergic poisoning, so classic that they have their own mnemonic: 'hot as a hare, dry as a bone, blind as a bat, red as a beet and mad as a hatter.'

This paper, Ingestion of Angel's Trumpet: An increasingly Common Source of Toxicity, reports a ten fold increase in Brugmanisa poisoning in Florida in 1994. They failed to locate a particular reason for this (ie reference to Brugmania use in a movie) and suggest the idea was simply spread by word of mouth. And then the internet came along...

Night Bloomers

If anyone wants their garden to be as much of a night owl as they are, here are some amazing plants.
Night Blooming Cereus, made kind of famous in the book The Bean Trees by Barbara Kingsolver, the lovely Moon Flower, and according to this website you can watch a video of it blooming, our lovely deadly and possibly hallucinogenic flower from class, the Angel's Trumpet and for those of you who really want to plant stuff right now, The Evening Garden is a great book.
On another note, Wicked Plants is a great book on all kinds of nasty plants you don't want to run into. It's got amazing illustrations and stories for most of the plants.

Haplodiploidy

Haplodiploidy is a  mechanism of sex determination that is common in the hymenoptera but also found in some other groups. In this system sex is determined by the number of sets of chromosomes an offspring receives. Fertlized eggs develop as females, and unfertilized eggs develop as males. This means that the males have half the number of chromosomes that a female have - hence the name haplodiploidy for this system. In this system males have no father and cannot have sons, but have grandfathers and can have grandsons (think about it). Also because males are already haploid all the sperm they produce is identical.

Haplodiploidy has important consequences that seem to affect social behavior. Here's a nice description form an online Animal Behavior textbook:

1. If a queen mates only once, her daughters are highly related to each other (called supersisters), because the father's sperm are all identical.
2. A female is more related to her sisters (on average, 75% similar) than she is to her own daughters (on average 50% similar).
3. A female is more related to her son (50 % similar) than she is to a brother (on average, 25% similar).

These three factors combine to create a condition in which it may be more advantageous, evolutionarily speaking, for a female to help her mother produce sisters (to the female in question) than to produce her own daughters. Thus haplodiploidy opens the way for the evolution of a worker caste, devoted to helping their mother. If workers evolve under these conditions, then we would expect:

• That all workers will be female (males have no special pattern of relatedness in a haplodiploid system that would make working advantageous to them
• That workers will help their mother to lay and rear females, but
• That workers would prefer to lay their own male offspring, rather than rear brothers

In fact, Hymenoptera workers are uniformly female and conflict between the queen and the workers over who lays the males eggs in a nest is common. The role of haplodiploidy in the evolution of worker Hymenoptera fits into an overall theory of how genetic similarity affects social behavior called kin selection which was developed by Bill Hamilton.

Deciphering Local Diversity

Next quarter CCBER will present a series of talks on local biodiversity with a focus on developing observational and identification skills.You can take this as a class or simply attend any talks you are interested in.

CCBER Conservation and Restoration Seminar (RE 188/288) - Deciphering Local Diversity

Monday evenings, 6-7pm, Rm 1013 Harder South

• March 28th – Introduction – Lisa Stratton
• April 4th – Dan Fontaine – Interpreting animals signs
• April 11th – Mark Holmgren – Raptor ID and Behavior
• April 18th – John Bleck – Differentiating Succulents
• April 25th – Mary Carroll – Differentiating Sedges
• May 2nd – Marc Kummel – The story behind local Oak Galls
• May 9th – Mary Carroll – Learning the key to Grass Identification
• May 16th – Lisa Stratton – Local vernal pool hydrology and flora
• May 23rd – Scott Cooper – Below the surface of Vernal Pools: Invertebrate lifecycles

Contact Lisa Stratton if you have questions.

Seed Plant Phylogeny

You may be surprised to find out that the relationship between the angiosperms and the gymnosperm groups is still subject to much debate. One of the perennial questions is the position of the gnetophytes.

 One of the reasons for this debate is that the Gnetophytes (one of the gymnosperm taxa we discussed) show several features that are typically associated with the angiosperms, including double fertilisation and vessel elements in their vascular tissue. Do these indicate a close relationship and that the gnetophytes are a sister taxa to the angiosperms or are they the results of parallel evolution?

Wikipedia actually has a nice clear discussion of the alternative hypotheses or for a meatier discussion there's this paper from 2009 in the American Journal of Botany:
Phylogenetic relationships among seed plants: Persistent questions and the limits of molecular data

Lymph Node Surgery for Breast Cancer

For decades, the standard treatment for women who have been diagnosed with early-stage breast cancer has been to perform a biopsy on a nearby lymph node, called a “sentinal” lymph node, to see if the cancer has metastasized beyond the breast. If it has, then the usual recommendation is surgery to remove some or most of the thirty axillary (armpit) lymph nodes as well, to try to halt the spread of cancer. The surgery is extensive, and recovery is painful and slow.

A new study published in the Journal of the American Medical Association reports that removal of armpit lymph nodes may not be necessary any more, given the current effectiveness of post-surgical radiation therapy and chemotherapy. In the study, 891 women who had undergone a lumpectomy for early stage breast cancer were randomly assigned to just sentinal node removal, or removal of at least 10 of the axillary lymph nodes. There were no differences in survival rates or disease-free survival rates between the two groups for the entire eight years of the study.

The authors recommend that physicians consider carefully whether more radical axillary node surgery is really necessary in most patients. Some cancer centers are already starting to change their cancer treatment protocols as a result of these new findings.

The Birds and the Bees and the Flowers and the Trees

Given that about 5% of angiosperms are dioecious but only a few cases of sex chromosomes have been discovered this raises the question of how sex is determined in the rest of these species. I found this nice review in the journal Genetics last year:
The Birds and the Bees and the Flowers and the Trees: Lessons from Genetic Mapping of Sex Determination in Plants and Animals

Sex determination is an important area of study in developmental and evolutionary biology, as well as ecology. Its importance for organisms might suggest that sex determination is highly conserved. However, genetic studies have shown that sex determination mechanisms, and the genes involved, are surprisingly labile.

Trees, photosynthesis and weasels

Any questions?

The Evolution of Sex Chromosomes

Sex chromosomes have arisen independently in many taxonomic groups. It is an interesting question whether the same mechanisms were involved each time.

Sex chromosomes are an oddity in flowering plants. They are limited to dioecious species and only a few examples are known. The genus Silene, which includes the White Campion, includes both dioecious and hermaphrodite species and three of the dioecious species, Silene dioica, S. latifolia, and S. diclinis,  have an X-Y sex-determination system where Y specifies maleness.
Although the X-Y system evolved quite recently in Silene (less than 10 million years ago) compared to mammals (about 320 million years ago), our results suggest that similar processes have been at work in the evolution of sex chromosomes in plants and mammals, and shed some light on the molecular mechanisms suppressing recombination between X and Y chromosomes.

Ref:  Nicolas M, Marais G, Hykelova V, Janousek B, Laporte V, et al. (2005) A Gradual Process of Recombination Restriction in the Evolutionary History of the Sex Chromosomes in Dioecious Plants. PLoS Biol 3(1).

There's a synopsis of the article in the same issue: Evolution of Sex Chromosomes: The Case of the White Campion.

The plant in you (and vice versa)

 From: Double-fertilization, from myths to reality, a review from 2007 -

It is becoming gradually clear that although plant and animal kingdoms diverged more than 1 billion years ago, similar mechanisms govern sexual reproduction in both kingdoms. The review by Márton and Dresselhaus (2008) outlines some of these parallels. The current idiosyncratic nomenclature used to designate plant reproduction has obscured the parallels that now become apparent between plants and animals. It is likely to be the time to rethink the designation of each actor of the reproductive process such that the literature in the field becomes relevant to a broader readership working in the field of reproductive biology.
The  Márton and Dresselhauspaper referred to is A comparison of early molecular fertilization mechanisms in animals and flowering plants.

The Vaccinations-Cause-Autism Fraud

Anyone who still persists in believing that childhood vaccinations have anything to do with the development of autism should read the three well-documented articles by investigative reporter Brian Deer published recently in the prestigious British Medical Journal. The first article is presented here. For those who don’t have the time, here’s a brief synopsis:

The original research article allegedly showing a causal link between vaccinations and autism was later shown to be a deliberate fraud. The paper, published in 1998 by the Lancet, was retracted in 2010 after it was shown to contain numerous misrepresentations. The paper’s author, Dr. Andrew Wakefield, was investigated by the UK General Medical Council and ultimately lost his license to practice medicine. Records released during the investigation show that Dr. Wakefield was paid nearly $700,000 by a British lawyer who was preparing a class-action lawsuit against vaccine-makers.

Since 1998, study after study has failed to validate Dr. Wakefield’s work and failed to show any causal link between childhood vaccinations and autism. And yet, some parents of autistic children still believe in that there may be a causal link. Actress Jenny McCarthy, herself a mother of an autistic child, is one of them. Ms. McCarthy has appeared on the Oprah Winfrey show to promote the vaccination-autism “cause” and has written several books about autism. I have yet to see an admission from her that she may have been wrong about vaccines.

Sorry, Ms. McCarthy, you lose on this one. Give it up before you look even more foolish than you already do.

(Topic for debate: Why do some people continue to believe in something despite overwhelming evidence in favor of just the opposite? What does that continued belief do for them?)

Fractal ferns

Most species of ferns have pinnate fronds.  The term pinnate describes the arrangement of leaflets arising at multiple points along a common axis. A fern may be simply pinnate or may be bipinnate if the leaflets are divided again, or tripinnate or even tetrapinnate depending how many levels of division the fronds have.

Because this is a simple mathematical process, simple algorithms can make surprisingly lifelike ferns. Check out the Fractal fern page if you are interested in math.

Can you tell which of these ferns is real and which is computer generated?

Undergraduate Research Colloquium

If you have any research to present then you should present it at this year's Undergraduate Research Colloquium. This is a fantastic opportunity to practice preparing and presenting a poster. 

Every year the College of Letters and Science celebrates undergraduate research at UCSB by sponsoring a colloquium where students from all over campus may come together to showcase their research activities.  I am
writing to invite you to attend this event to be held on Thursday, May 19, 2011, in the Corwin Pavilion.  All presentations will be in poster form (poster size 2 ft by 3 ft portrait style).  The event will run from 11:30
to 2:00 p.m.

Students interested in sharing their research efforts should submit the two-part entry application (entry and abstract submission forms) found on the URCA web site, www.ltsc.ucsb.edu/urca/colloquium.php, by Wednesday, April 6.  Questions should be referred to the URCA Coordinator, urca@Ltsc.ucsb.edu.

REU

I posted about REU's before. The posting below is from just one of the dozens of opportunities available. If you want a summer research adventure then now is the time to be checking them out and applying.

Texas A&M is offering a summer Research Experiences for Undergraduates program, which will be held from June 1 to August 5 in College Station.  The theme is Interdisciplinary Research on Imaging and Biomarkers.  The application can be found at:  http://etidweb.tamu.edu/hsieh/REU and the flyer is attached.
 
Activities will include joining a research group led by a faculty mentor, completion of a 10-week research project, and participation in weekly faculty seminars, field trips, and career development workshops.  Students will write a report and present their research to their REU cohort and at an REU poster session on campus. They will also be strongly encouraged to polish their reports after completing the program, with a view toward presenting at a national conference and/or publishing in an academic journal.
 
Each participant will receive a stipend of $450/week for ten weeks. Other benefits include allowances for housing, meals and round trip travel to College Station; 1.0 credit hour of undergraduate course credit; and full access to university recreational facilities.
 
Criteria for selection include: 

• Desire to participate in research as evidenced by application responses and faculty recommendation;
• Completion of at least the sophomore year of the curriculum for an academic major in engineering, computer science, or the life sciences;
• GPA of 3.00 or above (exceptions may be made based on review of an applicant's last 60 hours of coursework);
• Citizen or permanent resident of the U.S. or its possessions;
• Plan to graduate no earlier than December 2011.

Students who have limited opportunities to participate in research on their home campuses or who are from groups traditionally underrepresented in engineering and science are highly encouraged to apply.

Manipulative microbes

In the spirit of this divisive holiday, here is an intriguing article about how bacteria in your gut may be secretively manipulating your deepest emotions. A study done in fruit flies showed that fruit flies preferred mating with other flies that had been put on the same diet (either malt sugar or starch). The intriguing part is that when the flies were treated with an antibiotic, this preference disappeared.

http://www.nature.com/news/2010/101101/full/news.2010.575.html

Who is the culprit? Lactobacillus plantarum, a Gram-positive bacterium found in dairy products and other fermented foods. It is thought - researchers are not entirely certain - that the bacteria alter the flies' pheromone levels, making them more attractive and attracted to similar members of the opposite sex. The question arises...how much of this actually applies to humans?

An important concept put forth by the researchers is the holobiont. Rather than considering just the parts directly connected to an organism, we should take into account all its "normal flora" - the diverse hordes of microbes that inhabit the body, from our skin to our gut. Although it's initially mildly disturbing to think that 90 percent of the cells in our body are not our own, we should take into account the host of tasks they perform for us. When our normal flora are destroyed - for instance, by a long-term antibiotic - we too are destroyed, unable to digest food and plagued by infections that our normal flora would have otherwise caught.

So the holobiont theory certainly applies to humans. What about the influence on mating preferences? Hard to say. But if our resident bacteria can chew our food for us and protect us from hostile (albeit microscopic) strangers, I think I'll trust their judgment in choosing a suitable mate.

Dating tips

Not only is it adorably left wing but the Guardian newspaper in England actually sometimes has some decent science reporting. I enjoyed their Valentine's Day dating tips from lovestruck scientists. It even includes a list of references at the end - a very welcome trend. Here's an example, 

Tip #4: Cross a scary bridge

Here's another very simple tip for the ladies: frighten him. No, seriously. In 1974, University of British Columbia psychologists were studying human attraction using two bridges that crossed a local river. One bridge was solid, allowed firm footing, and was made of heavy cedar. It was only ten feet above the river, and had steady handrails. The other bridge was a five-foot-wide, 450-foot-long suspension bridge made of wire cables threaded through the ends of wooden boards. It would tilt, sway, and wobble as people tried to cross, 230 feet above the river.
Men who had just crossed one of the bridges were approached by an attractive female experimenter who asked them to complete several questionnaires. The men who had crossed the anxiety-inducing suspension bridge were more likely to attempt further contact with the experimenter than were the men who had crossed the stable bridge. The researchers suggest that it's as if the men misunderstood their anxiety-induced physiological arousal – elevated heart rate, sweaty palms, and so on – interpreting it as sexual attraction and desire.
Moral of the story: scare the crap out of him and he might just make a move.

Oh and don't forget - CCBER tomorrow.

Debating Darwin

I only just heard about this conference which is going on next weekend right here ar UCSB. It's free to attend but they do request that you register: http://www.philosophy.ucsb.edu/conferences/

UC Santa Barbara Department of Philosophy Announcesa Steven Humphrey Fund for Excellence in Philosophy ConferenceDebating Darwin: Philosophical Issues in Evolution and Natural Selection
February 18-20, 2011

Friday, February 18

5:00 - 7:00 PM Peter Godfrey-Smith (Harvard), "Origin Explanations" 
7:00 - 9:00 PM Reception/Buffet, UCSB Faculty Club

Saturday, February 19

9:30 - 11:30 AM Elisabeth Lloyd (Indiana), "Adaptationism in Action"
11:30 - 1:00 PM Lunch, Graduate Student Association Lounge
1:00 - 3:00 PM Paul Griffiths (Sydney), "How Evolution Tracks Truth"
3:00 - 3:15 PM Break
3:15 - 5:15 PM Jerry Fodor (Rutgers), "From the Darwin Wars"

Sunday, February 20

9:30 - 11:30 AM Mohan Matthen (Toronto), TBA
11:30 - 1:00 PM Lunch, UCSB Faculty Club
1:00 - 3:00 PM Richard Boyd (Cornell), "Evolutionary Theory as Methodological Anesthesia: Methodological and Philosophical Lessons from Evolutionary Psychology"
3:00 - 3:15 PM Break
3:15 - 5:15 PM Alex Rosenberg (Duke), "How Jerry Fodor Slid Down the Slippery Slope to Anti-Darwinism, and How We Can Avoid the Same Fate"
Location: All talks will be in Theater & Dance 1701

Altruism for the Win!

Ants and the Buggers from Ender's Game have one important thing in common: The ability to selflessly commit their lives to the good of the colony. Social ants build nests, collect food, and defend the colony. Most ants don't reproduce, but will spend their lives helping raise non-descendant young. Their altruistic social behaviors have clearly paid off, as there are estimated to be over 20,000 species and 10,000,000,000,000,000 (that's 10 quadrillion!) individual ants in the world.

Researchers have found yet another way in which ants selflessly sacrifice their lives for the good of the colony, this time literally. Temnothorax unifasciatus ant workers infected by a fungal pathogen leave the nest hours or even days before an imminent death, to die in isolation far from the colony in order to prevent the spread of infection as well as the waste of resources. The life-span of ants who left the nest to die in isolation can be up to days shorter, further proving the altruistic nature of the worker. While some species of ants have specialized workers (evolved with special resistance to fungal disease, cool!) who dispose of sick and dying ants, T. unifasciatus ants voluntarily leave the colony.

Because of the immense (no kidding) amounts of inter-relatedness within a colony, susceptibility to disease is a very limiting factor within colonies. In order to cope with this, ants have developed a social evolution (!!!) which has allowed them to extend colony success and growth. While there are many other ways in which ants have socially evolved to compensate for this danger, T. unifasciatus ants have developed a method of altruistic sacrifice which reflects a desire for the success of a colony over the success of an individual, and... is truly inspirational.

Read more:

http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VRT-4Y89YXJ-4&_user=112642&_coverDate=02%2F09%2F2010&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000059608&_version=1&_urlVersion=0&_userid=112642&md5=34d4f862798a360a3e063acfb22b99aa&searchtype=a#sec2.2

http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VRT-4YBMJD5-J&_user=112642&_coverDate=02%2F09%2F2010&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000059608&_version=1&_urlVersion=0&_userid=112642&md5=a327743b6e416c3c35214f874ee33e73&searchtype=a

Happy Sunday:)

Analyzing and Storing Genomics Data

In just the last 10 years, the cost of sequencing a million DNA base pairs has dropped from $10,000 to just $1. A single modern DNA sequencing machine can generate more data in a single day than could once be generated in a decade. Consequently, genomics researchers now face a looming problem, according to an article in Science - the speed and efficiency with which DNA sequence data can be produced will soon outstrip the ability of most computers to analyze and store the data! That’s right; despite huge gains in computer speed and storage capacity over the years, the computers are now lagging behind.

To combat this growing problem, bioinformatics specialists are increasingly turning to “cloud computing”, whereby data are analyzed and even stored on networks of computers off-site. But cloud computing raises complex new issues of data security, particularly when that data involves human subjects.

Perhaps if the cost of sequencing DNA continues to fall it may not even be necessary to store the data long-term; it could just be regenerated as needed.

Gymnosperm Reproduction

Anything that happens in 3-d is just crying out for a video. When it comes to Gymnosperm reporoduction I rather like these videos The first one is very short and a little obvious but I liked the second and third ones a lot. I thought they really helped in visualizing what is going on.

Worster Awards

I'm copying below this year's Worster Award announcement. Note that although the graduate student must be in EEMB, the undergraduate does not and a number of CCS students have benefited from this award in the past. This is a great opportunity for Summer funding and if you are interested then you need to talk to a friendly EEMB grad student.
John



The Worster family has again graciously given EEMB a gift of $30,000. As in previous years, this award is to support the development of graduate and undergraduate research in ecology, evolution and/or marine biology through a mentoring program that pairs an undergraduate with a graduate student mentor during the summer. All graduate students that have their thesis committee chaired by an EEMB faculty member are eligible to apply for this award. We anticipate that stipends this year will be $6000 for each team ($3000 for the graduate and $3000 for the undergraduate, to be paid during the summer). We will be able to fund 5 teams this coming summer.

Applications for this award (electronic, Word or PDF files AND a printed copy delivered to my office or placed in my EEMB mailbox) are due to me by Friday, April 1st, 2011. Please be sure to send and to deliver both electronic and hard copies.

Please include:

1. Brief (2 pages, prepared by the graduate student) description of the research project and how the undergraduate student will participate in it.

2. CV of the graduate student, including progress toward his/her degree and any prior mentoring experience.

3. A brief statement from the undergraduate regarding his or her professional goals and how the research experience will prepare him/her to meet them. Undergraduates are expected to complete a senior honors thesis during the 2011-2012 or 2012-2013 academic year and express their intent to do so. In addition, undergraduate promise, experience, and GPA in their major will factor into the decision for funding.

4. Letter of support from the grad student's major professor.

Please note that recipients will be obligated to write a summary of their team's progress and accomplishments at the end of the summer. These summaries will be sent to the Worster’s in the fall as part of a package thanking them for this important gift.

Undergraduates who will graduate in June 2011 are NOT eligible for this award.

If you have any questions, please don't hesitate to contact me.

Craig Carlson

Thursday's wonder

Whoa. This is where stars are born. This is a new image of the North America Nebula from NASA's Spitzer Space Telescope. You can see the massive full size image here. Why is this important? - in all likelihood our Sun and its planets formed in a nebular cloud very much like this one.

Each little pinpoint speck of light in Spitzer's image is a young star at some particular point in its development., and haven't even become true stars yet—that only occurs when thermonuclear fusion kicks off in their cores. Others have begun their stardom, but are still sheathed in spherical cocoons of gas and dust, shells of material that will gradually grow puffy and vaporous from the inner star's light and heat, until they whisper away on stellar winds. Many of these points of light are ringed by thick accretion disks of material that formed from the angular momentum of their initial gravitational collapse. Sometimes parts of the disk get sucked too close to the star, and are shocked into plasma and spun away and out from the star's poles in powerful collimated jets that can sculpt and shape the surrounding gas and dust into abstract whorls and tendrils. And, in the background, almost unnoticed against all the stellar fireworks, in all probability planets are slowly and surely forming. Perhaps, on a few them, the seeds of life are already being sown by comets and meteorites, the infalling detritus of star formation delivering water and complex chemical compounds brewed in the stellar clouds. Some are still undergoing their initial gravitational collapse.


I tried to find a website that could explain where the  North America Nebula was in easy to understand terms and found just what I was looking for here. Unfortunately I then kept zooming out until my head exploded.

CCBER visit

With all the excitement of Valentine's Day on Monday don't forget that on Tuesday we will visit the Cheadle Center for Biodiversity and Ecological Restoration. You can find information and directions at their website. We will meet there at 11.00 am and you should allow 5 minutes to cycle or 10-15 minutes if you are walking over there - although that is naturally dependent on where you are walking from......

Here's a map showing the bike route from CCS (click for a larger version). As someone pointed out you don't have to cycle this way...

We will meet at the entrance.

Plants are scary...and fungi are amazing!

Two of my favorite plant and fungi videos... Enjoy!

http://www.nbc.com/saturday-night-live/video/googly-eyes-gardener/1119102/

Lycopodium fun

I don't have time for all the fun trivia in class but there's always the blog. Because spores are VERY fine and are very dry they can actually produce a nice explosion when they are dispersed in air. However because a mass of the spores is not flammable they make a fairly safe substance to work with. For this reason Lycopodium spores were used for many years as flash powder for photography. These days they are still apparently used in some special effect work since the explosion is very dramatic. I think the spores of any number of plants would work for this - the questions would be where can you collect them in suitably large quantities. The idea that a moss might be used is ridiculous but unfortunately since Lycopodium is a club moss it is a common misconception that these explosive spores are from mosses. Lycopodium, as I'm sure you remember, are more closely related to the ferns with large, club like structures (technically called a strobilus) producing a huge amount of spores. Perfect.

Smallpox - Gone Forever?

A deadly viral disease called smallpox killed several hundred million people in the 1800s. Thanks to the development of smallpox vaccines and a concerted effort worldwide, the disease was finally declared eradicated in 1979. To this day, smallpox is the only infectious human disease ever wiped out completely.

Nevertheless, the spectre of a return of smallpox remains. That’s because more than 500 vials containing the smallpox virus remain in tightly guarded, allegedly secure facilities in the U.S. and Russia. The question is, what to do with these vials? Some scientists and politicians (particularly in the U.S. and Russia) argue that stocks of the smallpox virus are still needed for research and for the development of new diagnostics, safer vaccines, and effective antiviral drugs. Others argue that over the past several decades we’ve learned just about all we can about the virus, and that the mere existence of these vials represents a risk that some day the disease could return, particularly if a vial were to fall into the hands of terrorists.

The World Health Organization (WHO) will decide in May whether to recommend a firm deadline for the final destruction of all remaining vials. But don’t count on the elimination of every last smallpox virus from the planet any time soon, even if a deadline is announced. An earlier deadline of 1990 was postponed indefinitely when both the U.S. and Russia argued against it. It’s more likely that a compromise will be reached to reduce stockpiles without eliminating them completely.

Forbidden experiments

 Mothra's larval form destroying the Tokyo Tower in the movie Mothra from 1961.

In the Fantastic Four comics Dr Doom was expelled from Empire State University for carrying out 'Forbidden experiments'. The experiment in question involved contacting the dead so maybe that's not that surprising, but I was always amused by the notion that a University might have a big list of 'Forbidden experiments'. Ah yes, item number 147, 'Contacting the Dead', right after number 146 'Reanimating the Dead'.

Anyway, I was reminded of that when I took a quick look for some papers on insect gigantism and came across this recent review paper Atmospheric oxygen level and the evolution of insect body size, where they mention several experiments where people have selected for insect gigantism over many generations under high oxgyen conditions in the lab.

The effects of hyperoxia on growth and body size are less consistent and often nonlinear (Harrison et al. 2009). Body size increases in the giant mealworm, Z. morio (27% O₂; Harrison et al. 2009) and in the scarabaeid beetle C. texana (40% O₂; Harrison et al. 2009).

I'm pretty sure 'Creating Giant Insects' would also have been on empire State's list. Did Mothra not teach us anything?

But the answer to our question of what other giant insect (and other arthropod) fossils have been found is:

Among insects, gigantism in the Permo-Carboniferous has also been reported for Ephemeroptera, Diplura, Thysanura and the extinct order Paleodictyoptera (Briggs 1985; Kukalova-Peck 1985). Arthropleura, a group related to modern day millipedes, reached upwards of 2 m in length, almost six times the size of any extant millipede. 

So no, no Lepidoptera, you'll just have to make do with Mothra.

Timing of Immune Response to Defend Against Disease

I thought this article from the New York Times is very relevant to what were talking about in class! The plant Arabidopsis is really intersting, it has developed the ability to express genes at specific times to make it resistant to an infectious pathogen.

Specifically, twenty-two genes were discovered in Arabidopsis that are all connected to the plant’s ability to resist infection. These genes are unique in that they are expressed only from the evening onward, peaking at dawn.

This timing corresponds with the formation of spores in a funguslike pathogen that attacks the plant and results in a condition known as downy mildew disease. The disease weakens the plant and forms an unsavory coating of fuzzy mildew.

A surprising discovery published in the Nature journal, found that these new defense genes are under circadian control by the regulator CIRCADIAN CLOCK-ASSOCIATED 1 (CCA1), allowing plants to ‘anticipate’ infection at dawn when the pathogen normally disperses the spores. Arabidopsis can then time its immune response according to the perception of different pathogenic signals upon infection. This plant then uses programmed cell death as its main contributor to resistance.

I think that the control of defensive genes by a circadian clock regulator is an amazing adaptation this plant has made to avoid being susceptible to dawn spore attacks, just like the grass in class on the copper mines flowering early to gain an advantage to remain resistant to the toxins in the soil. Hope you think this is interesting too!

http://www.nytimes.com/2011/02/08/science/08obplant.html?_r=1&scp=1&sq=defend%20against%20a%20disease&st=cse

http://www.nature.com/nature/journal/v470/n7332/full/nature09766.html

Hidden Leg of an Ancient Snake

No, not an unreleased Jim Morrison poem, but a headline on ScienceDaily today reporting on the latest imaging of a 95 million year old snake fossil published in the Feb. 8, 2011 issue of the Journal of Vertebrate Paleontology.

A novel X-ray imaging technology is helping scientists better understand how in the course of evolution snakes have lost their legs. The researchers hope the new data will help resolve a heated debate about the origin of snakes: whether they evolved from a terrestrial lizard or from one that lived in the oceans. New, detailed 3-D images reveal that the internal architecture of an ancient snake's leg bones strongly resembles that of modern terrestrial lizard legs.

Fungi not so fun: disease endangering species of bats in North America

Conservation ecologists are facing a dilemma that is slowly becoming more pressing: various species of bats across North America are being crippled by the White-Nose Syndrome (WNS), a disease named so for the spreading of a white fungus on the noses of bats. Scientists believe that it may be caused by the fungus Geomyces destructans, though other factors will have to be considered for a certain identification. The fungus, it appears, is well-adapted to the cold and damp environment that is so common to bat caves. According to a recent online article, as many as 1 million bats have been killed since 2006. If a cure or methodology for alleviating the epidemic is not invented soon, numerous bat species will be swept away by extinction. The disease is already making its way into some parts of Europe, though it currently is more prevalent in the North American region. WNS seems to be tampering with the bats' hibernation pattern, causing them to wake up and fly sporadically, thus weakening their bodies as all of the stored up fat is being burned in flight. Janet Foley from UC Davis and a team of scientists are working on diagnosis and developing a treatment.

To read more, and see a photograph of brown fluffiness, visit: http://www.sciencedaily.com/releases/2011/02/110203081451.htm

Guinness world record held by water flea

I hope you all remember how Daphnias' head shape changes with temperature leading to them having dating issues, if Dr. Latto is to be believed. Well, they get even cooler. They have been found to have the largest number of genes of any animal known, 31,000 to our 23,000. So you ask, why does something the size of half a grain of rice need all these genes? Well, the answer is we don’t know yet. 35% of their genes are new to science. Some of them allow the Daphnia to make basically armor and a spear right on the spot. Others allow it to produce hemoglobin when stressed, making the creature look red, thus giving it the name “bloodsucker”. The best part is that we know a huge amount about the Daphnia’s environment and reactions to different things. This allows us to link their genes to events nature which can tell us a huge amount about gene expression and the need for certain genes. Thank you tiny crustacean, even if some of you are pointy headed.

If you want to listen to the story click here, or read a shorter version of it on the NPR website, which is a good place to look for interesting science stories anyway.

Triffids

Last post on mobile plants, I promise.

As I mentioned in class if you remove the constraints of requiring lots of water and needing a large light capturing apparatus from photoautotrophs then we do see some mobile photoautotrophs - Euglena for example. Here they are having a party.

One way to lift this constraint for larger plants would be to be carnivorous - then they wouldn't need all that water or that light gathering apparatus. Although we colloquially call many plants 'carnivorous' they are not in fact heterotrophs because they still photosynthesize and use the animal bodies they capture for nitrogen, which is why we see the evolution of plant carnivory in nitrogen limited environments. They are still green, still need to be open to the atmosphere to take up carbon dioxide and still lose lots of water.

If a multicellular land plant did evolve towards true heterotrophy what would it look like? Thanks to the fertile imagination of British author John Wyndham we have the answer in the Triffids - and yes they would be mobile!

Although published in 1951 Wyndham's science fiction classic The Day of the Triffids is still a fantastic read. According to the director of the movie 28 days later, Danny Boyle, it was the opening sequence of The Day of the Triffids, in which a man wakes up in hospital to discover that a meteor shower has blinded his fellow countrymen, which first inspired Alex Garland to write the screenplay. As a bit of a triffid connoisseur I would rate the book and radio adaptation excellent, the BBC adaptations pretty good and the 1962 film version appallingly bad.

In England the book, and adaptations are so well known it is quite common for someone to refer to a large, somewhat creepy looking plant as 'triffid like'.