skeetersays

mosquito killing LASERS

2010-02-12T08:55:00.000-08:00

Over at nytimes.com there is a post about Nathan Myhrvold's new mosquito killing LASERs... that's right... LASERS... How Star Wars...
Check it out.

Data sharing in Ecology and Evolution

2010-01-15T15:45:00.001-08:00

Any scientist interested in analysis of genetic data knows the value of online repositories for sequence data (such as genBank). Any researcher publishing analyses of sequence data likely is required by publishers to make their sequence data publicly available in such a database. Not only does this allow for other researchers to validate one's work, it also allows for more general research that may use those sequences. In fact there is a growing number of research programs that revolve solely around mining the data stored in such repositories.

Michael Whitlock and colleagues, in the current issue of the American Naturalist, discuss the importance of data archiving in Ecology and Evolutionary Biology. There are new web-based archiving services that allow the storage of general datasets, and the authors argue that science has lost a tremendous amount of data, and there is no reason for the loss of data in an era where online data storage is so cheap and accessible.

Within the next year, several journals (American Naturalist, Molecular Ecology, etc..) will require the sharing of general data sets, similar to the genetic data sets stored at GenBank. For example, the American Naturalist's policy will read:

This journal requires, as a condition for publication, that data supporting the results in the paper should be archived in an appropriate public archive, such as GenBank, TreeBASE, Dryad, or the Knowledge Network for Biocomplexity. Data are important products of the scientific enterprise, and they should be preserved and usable for decades in the future. Authors may elect to have the data publicly available at time of publication, or, if the technology of the archive allows, may opt to embargo access to the data for a period up to a year after publication. Exceptions may be granted at the discretion of the editor, especially for sensitive information such as human subject data or the location of endangered species.

This is a fantastic idea. The open sharing of data will not only promote scientific integrity, it will also allow for expansive meta-analyses and synthesis of diverse data sets. And in the end, most work published in these journals is funded by the tax payers of various countries, and they should be allowed access to the data that they are paying for...

Whitlock, M., McPeek, M., Rausher, M., Rieseberg, L., & Moore, A. (2010). Data Archiving The American Naturalist, 175 (2), 145-146 DOI: 10.1086/650340

Pitcher-plants: Nature's toilet bowl.

2009-09-15T12:01:00.001-07:00

Pitcher plants are carnivorous plants, that unlike active traps such as the Venus Fly Trap, passively gain nutrients from animal sources. In general, the pitchers produce nectar that attract insects and other small animals (I have found frogs and salamanders in Sarracenia purpurea leaves), which then fall into the pitchers, drown, and decompose. The plant is then able to absorb nutrients from this decomposing material. Generally decomposition within the pitchers is aided by an inquiline community of microbes, rotifers, copepods and a variety of other invertebrates.

Pitcher plants usually grow in nutrient poor environments (acid bogs, tropical mountain tops etc..) and the carnivory is assumed to be an adaptation to such environments, allowing the plants to obtain the nitrogen and phosphorous necessary for growth.

The genus Nepenthes has gained attention over the last year with the recent discovery of one of the largest pitcher plants, Nepenthes attenboroughii, that can have 1.5-2 liters of water within their pitchers. A recent paper in Biology Letters (see cover image) describes another novelty within the pitcher plants. Nepenthes lowii has two types of pitchers: young plants produce ground-level pitchers which are well-suited to insect capture, whereas larger, more mature plants produce aerial pitchers which are not well-suited to insect capture, and various hypothesis have been put forth as to what these aerial pitchers were doing. In their recent paper, Clarke and colleagues show via isotope analysis that the majority of Nitrogen in the aerial pitchers was coming from the faecal matter the mountain tree shrew, Tupaia montana.

The aerial pitchers are have wide, non-slippery mouths and a large hood that folds away from the pitcher. The nectar is produced on the hood, and in order for the mountain shrew to gain access to the nectar, it much perch itself on the pitcher with its 'rump over the pot' if you will. It seems that this placement of the shrew on the pitcher is prime placement for the pitcher to collect faeces that are dropped by the shrew while it eats its dinner.

Here is an example of a plant that collects its own manure fertilizer. What a great system.

Clarke, C., Bauer, U., Lee, C., Tuen, A., Rembold, K., & Moran, J. (2009). Tree shrew lavatories: a novel nitrogen sequestration strategy in a tropical pitcher plant Biology Letters, 5 (5), 632-635 DOI: 10.1098/rsbl.2009.0311

Evolution 2009 - Highlights 1

2009-06-13T13:51:00.000-07:00

Conferences are always exciting – so much data, so many good ideas, so much to think about. A short list of highlights so far includes:

L. Morran talked about why sex was better with a partner (evolution of sex)

M. Hoso talked about asymmetry in snails and associated asymmetry in their snake predators

M. Szucs talked about the rapid evolution of diapause phenotypes in a biological control agent.

And many many more.

Conference dining and disposable one-use dishes

2009-06-13T13:11:00.000-07:00

One thing that has always bothered me about conferences is the amount of one-use dishes that are gone through every day. Here at Evolution 2009, there are ~ 1100 registrants, most of whom attend at least 2 out of three meals a day at the dining facilities. About a month ago, I accumulated several backpacker dishes that I keep in my backpack at all times to try to minimize waste. I am using a folding camp plate/bowl, a reusable spork, a steel coffee mug and a nalgene bottle for water (I am following the lead of Dave over at 365 Days of Trash - check out his awesome video).

I have been using the dishes for the last few meals and I have been pretty amazed at how it was received by most other people here, commenting on how great of an idea it was. While they are using disposable dishes, I can reuse mine the whole time. This is my own little way of protecting the planet.

I have an idea for future conferences. Generally at these things you get a bag full of sponsored 'goodies' when you register - pens, water bottles, etc... (I have only seen about 10 people here using there reusable water bottle that they got for registration...). What if the conference was to have their sponsors supply reusable plates and silverware and not offer paper plates? That might make a point. Maybe it is just wishful thinking though.

I love my reusable plates.

Evolution 2009 - Day 1

2009-06-13T09:46:00.000-07:00

After a long hiatus from posting (as I was finishing up the good ol' dissertation) and a 9.5 hour drive, I am at the Evolution 2009 meetings in Moscow, ID.

The first thing that I have learned at this meeting is that I will never again take the cheap way out and stay in a dorm room at a conference. Sure it saves some money, but is it worth it when you end up staying in a building that smells like a stale locker room? Not really. I am considering driving around the area and finding a nice campground nearby to put up my tent. Fresh Idaho air would be much nicer...

The conference started off for me with the SJ Gould Award Lecture given by Eugenie Scott of the National Center for Science Education. From the Evolution Society's website,

The Stephen Jay Gould Prize is awarded annually by the Society for the Study of Evolution to recognize individuals whose sustained and exemplary efforts have advanced public understanding of evolutionary science and its importance in biology, education, and everyday life in the spirit of Stephen Jay Gould.

Eugenie Scott definitely fits into this with her great work in advancing the public understanding of science, with particular focus paid to evolutionary biology. Her talk (which should appear at some point on the Evolution 2009 website above) focused on ways in which educators can clarify how they teach science to increase the public understanding of science. Some of her main points were:

Science has three levels: core science which are generally accepted based on a large amount of evidence (evolution, atomic theory, gravity, etc...), frontier science where most work is done to describe the core science, and the fringe science for which there is little effort expended as there is a low probability of success (esp, telekinesis, intelligent design, ID). She makes the point that it is possible to move from fringe science to core science (pointing out the example of plate techtonics), but in most cases it is unlikely. The burden of proof lies in the intelligent design community to do the research if they want to advance ID from the fringe to the frontier, and to date this has not been done.
One of the major hurdles to the public understanding evolution is that ID folks tend to point out disagreements between biologists in the realms of frontier science (this is why science works so well - we disagree), but the major point is that there is very little disagreement about the core science - that all forms of life on this planet are descended from common ancestors.
Word choice is important - we are not "darwinists" - we are evolutionary biologists. If you can attached 'ism' to a word it becomes an ideology. Evolution is not an ideology - it is science.

I will post up a link to the video as soon as I come accross it.

It was an excellent way to start the conference. The SJ Gould Award is a great thing for the Evolution Society to have started. The public pays for us to do our research, and it is our responsibility to make sure that they benefit from this work.

Full pints for Oregonians?

2009-04-04T21:11:00.000-07:00

I love Oregon - More green than you know what to do with, huge mountains, rocky beaches - and maybe soon - honest pints in the pubs.

It is astonishingly uncommon in the US to actually get a pint of beer when a 'pint' is ordered in a bar. Most places use pint sized glasses with thick bottoms that make a glass full to the brim (with no foam) as little as 12 - 13 oz, rather than the 16 for a full pint.

A bill being discussed by the Oregon House will, if approved, allow pubs that serve honest pints to display a decal displaying their full pints (Read Oregonian article here). This way, there is no cost to other places that want to keep pouring fake-pints, but will encourage true beer fans to go to those places that serve only honest pints. Oregon will survive as the best beer state in the nation... I love it here.

History of the planet in 60 sec

2009-02-12T11:47:00.001-08:00

Seed has a video posted showing the history of the planet scaled to 60 seconds. It is worth a look here.

What if you had access to unlimited DNA sequence data?

2009-02-09T13:12:00.000-08:00

As odd as it may seem to some, the possibility of having as much DNA sequence information as you want is not too far away. The human genome project , in an effort to sequence a single, full, human genome (~ 3 billion base pairs long), took 13 years and cost 2.7 billion (1991) dollars. Today, human genomes are being “resequenced” using new technologies for on the order of tens of thousands of dollars. We are not to the point where we can easily get any sequence data that we want but we are surely getting close.

Sequencing technology has come a long way in the last few years, with massively parallel sequencing becoming the norm. While you get shorter sequence reads (35 – 400 base pairs) relative to traditional sequencing technologies (700 – 900 base pairs) you get millions of reads at one time. Especially in cases where there is a good reference genome (the ones you hear about in the news – humans, drosophila, gallus etc..) you can line up your short reads to the reference genome and get a newly sequenced individual in a matter of days for a few grand.

This begs the question – In a decade or so when biologists are no longer limited by what DNA they can sequence, what questions do you ask? What does perfect DNA sequence knowledge give scientists, and what does it not give.

There are already a wealth of projects using the new sequencing technology to address fundamental questions. People are using resequencing projects to look for polymorphisms in sequences within populations (in a population of drosophila, or humans), allowing for finer resolution mapping studies to look for genes associated with a diversity of traits such as human disease. Instead of relying on culture methods, or expensive and time consuming clone libraries, microbiologists are able to metagenomics on environmental samples (water, soil etc..) to determine the diversity of microbial communities. Researchers are measuring gene expression with sequence-based technologies rather than hybridization technologies, allowing for a much higher throughput.

Imagine a time where a biologist can go out into his or her favorite field site and get complete sequence information for all individuals in the population. What are the questions to ask?

My answer would include the high resolution mapping of traits of interest to the genome. Also, you could do real-time, whole-genome assays of selection accross generations. Whole genome mapping of fitness would be phenomenal.

What other ideas are out there?

Avak Kahvejian, John Quackenbush, John F Thompson (2008). What would you do if you could sequence everything? Nature Biotechnology, 26 (10), 1125-1133 DOI: 10.1038/nbt1494

Evolution - Simpson's Style

2009-01-26T19:30:00.001-08:00

New manuscript wordle

2009-01-19T22:39:00.000-08:00

Wordle is a great tool - at least to make pretty pictures and tell you what you already know about a piece of text - the common words.

I decided to make a wordle image of the manuscript I just finished. Here it is - interesting, eh?

Darwin Celebration Feb 12

2009-01-09T09:46:00.000-08:00

If you haven't heard all about this yet, this year marks a very special year for evolutionary biology. It is the 200th birthday of Charles Darwin, as well as the 150th anniversary of the first publication of his work, The Origin of Species. There are celebrations planned at universities all over the world, and there are also several planned events happening in the blogosphere. One event is the blog for Darwin blog carnival. This will aggregate posts about evolution, Darwin, and the history of biology that were written between Feb 12 (Darwin's birthday) and Feb 15, and will serve as a reference to anyone interested in Evolution. I plan on adding a few posts during this time so keep an eye out. I am pretty sure that the posts will be about several areas of modern applications that would not exist without knowledge of evolutionary processes (medicine, wildlife management, etc..).

It's no Barry White but it works for the mosquitos

2009-01-09T09:29:00.000-08:00

Imagine you are planning for a romantic dinner with your partner and you cook up a nice dinner and light some candles - the only thing left is to choose the music. For some it is Barry White, for others it is some soft jazz, and for msoquitos it is a light buzzing at 1200 Hz.

A new article published in Science has shown that it is the buzzing at 1200 Hz that really gets the msoquito, Aedes aegypti, excited. Mosquitos buzz while flying and they have a standard fundamental frequency which is around 400 Hz in females and 600 Hz in males. It seems that female mosquitos aren't choosing their mates based on the quality of the males 600 Hz buzz, but rather the shared overtones of the two notes combined which is buzzing at around 1200 Hz. The male modifies his wing speed in order to make the overtone frequency as perfect as possible - if he does a good job, then he has found a mate.

One of the really interesting things about this study is that the two notes produced by the mating females is very close to being a "perfect fifth" - one of the most elegant and beloved intervals that has been used in music composition for centuries. Maybe there is something more fundamental about how organisms interpret sound that makes both humans and mosquitos prefer the same combinations of tones.

Now you really want to check out the mosquito love-pursuit video up at Science. The video and audio are from separate recordings and put together for your visual and auditory pleasure.

L. J. Cator, B. J. Arthur, L. C. Harrington, R. R. Hoy (2009). Harmonic Convergence in the Love Songs of the Dengue Vector Mosquito Science DOI: 10.1126/science.1166541

A new kind of campaign?

2008-11-09T16:41:00.000-08:00

President-elect Obama has just won an enormous victory as a result of a highly organized and energized core of volunteers. Most of the volunteers stood on street corners annoying us by making sure we were registered to vote. I was probably asked ~100 times if I was registered to vote. If they weren't standing on a corner registering voters, they were likely making phone calls to make sure people knew election day was coming up, where a polling location was, and that they should vote for Obama, and not that 'other guy'.

As the Onion has pointed out relentlessly over the last week, these volunteers have done what they needed to do and have helped Obama to victory. Now what?

Why not keep the energy up and focus it on things that need done. Imagine if Obama can use his amazing ability to inspire with his large army of volunteers and send them off to volunteer in their community. What if next election cycle, the Democratic party was to use their volunteer force not to annoy people relentlessly on street corners and on the phone, but rather organized major volunteer events. Maybe on a weekly schedule - week 1 of the campaign, clean up neighborhood common space - week 2, encourage children to read wtih public reading programs. What better press for a campaign to mobilize tens of thousands of volunteers to help their communities rather than to beg for votes. I think it would work better than standing on the street corner. It shows you doing something rather than talking about doing something.

I hope maybe the Obama administration will think about this for the next election in 2012. No more negative ads - just show yourself helping the world, rather than talking about it, and people will listen.

Northwest Nut Brown

2008-11-09T13:58:00.000-08:00

Well, I have finally gotten a tiny bit of time to think about and do things outside of my dissertation work, so I am putting some of that time into a few blog posts. The first will be to mention that I finally got around to bottling the Czech Pilsener that I made in May and it tastes fantastic! A few weeks to condition and it will be ready to go. I also got around to brewing a new batch (after a way-too-long hiatus). Here it is:

Northwest Nut Brown

6.5 lb Light malt extract syrup
3/4 lb Munich malt
1/2 lb British carastan malt
1/2 lb Caramel munich 120 malt
1/4 lb german curacka malt
1/4 lb british brown malt
1 oz Northern Brewer Hops (60 min)
1/2 oz Willamette Hops (30 min)
1/2 oz Willamette Hops (2 min)
4 tsp Hazlenut extract (in primary)
Pacific ale yeast (WLP041)

This is a variation on the Rogue Hazlenut brown clone recipe I have used in the past. I basically changed all of the malts to something a bit different than the clone recipe, and put in some northwest hops and yeast for a local flavor. We'll see how it goes. The pacific ale yeast works well for this recipe as my house is a bit on the cold side (we are cheap and don't like to pay much for heat) and pacific ale yeast has its optimal fermentation temperatures of 65-68. Time to drink a brew and wait for those little yeasts to do their work!

Genetic Future : African and Asian genome sequences: the last of the single human genome papers?

2008-11-05T17:33:00.001-08:00

A post over at Genetic Future discusses a new issue of nature that may include the last articles looking at single human genomes in major journals. The introduction of new sequencing technologies has paved the way to human population genomics at an unprecedented scale. The post is well worth a read.

I wish I had the time to write more on this now, but I don't - hopefully more blog posts will be showing up soon here on Skeetersays.

A single-species ecosystem?

2008-10-11T21:13:00.000-07:00

Generally speaking, most people envision an ecosystem consisting of all sorts of living beings: some trees, furry critters, flying things, maybe even a few microbes thrown in for fun. It is usually a complex web of interactions among many species that generally ends up in some stable configuration. This is what ecosystems were until a few days ago when a team of researchers reported in Science that they had found an environment where only a single species lived, 2.8 km underneath South Africa, at the bottom of a gold mine.

After extracting all of the DNA present within 5,600 liters of water from a fracture deep within the recesses of a gold mine, the authors used a combination of old and new DNA sequencing technology to sequence all of the DNA in the sample. In general, when this is done, you get pieces of DNA from a wide diversity of organisms which are then separated out after sequencing. In this case, nearly all of the sequenced DNA was assembled into one organism's genome - Candidatus Desulforudis audaxviator.

Unlike every other individual species on the planet, that rely on other species for some benefit (for example,we rely on plants to photosynthesize so that we can eat them, or to eat something that eats them), this little bacteria seems to have all of the genetic machinery in its genome to survive all on its own - the loneliest of organisms. It has also previously been reported that the cells in these samples likely only replicate themselves once every hundreds or thousands of years. Not only is it lonely in the deep, but things are also terribly slow.

Many genes that are found in this bacteria are not really bacterial genes - many come from the 'closely related' archaea. Many unicellular organisms have the ability to "swap" genes - it is in fact quite common - An archaea may have died somewhere near one of the ancestors of this bacteria that then picked up the DNA as it was floating around and incorporated it into its own genome. This is what has allowed this bacteria to have all of the biological processes necessary to sustain life. It was like a pack-rat, grabbing up all the good genes so that it could one day live on its own.

Crazy.

--------------
D. Chivian, E. L. Brodie, E. J. Alm, D. E. Culley, P. S. Dehal, T. Z. DeSantis, T. M. Gihring, A. Lapidus, L.-H. Lin, S. R. Lowry, D. P. Moser, P. M. Richardson, G. Southam, G. Wanger, L. M. Pratt, G. L. Andersen, T. C. Hazen, F. J. Brockman, A. P. Arkin, T. C. Onstott (2008). Environmental Genomics Reveals a Single-Species Ecosystem Deep Within Earth Science, 322 (5899), 275-278 DOI: 10.1126/science.1155495

Barn Raising lifestyle - you can't beat it

2008-10-06T12:07:00.000-07:00

I just wanted to write a quick post about why I really love to live where I live, Eugene, OR.

A few days back I got an email from some friends who own a small (~9 acre), local, organic farm. They mostly sell their goods to people they know and have a small booth at the summer saturday market. The email mentioned that they were having a garlic planting party this weekend. How could I pass that up? I love garlic, love gardening, love my friends. What could be better.

I think that people really long to have stronger social interactions and I think that Eugene is really a great place in which to fulfill those desires. There were ~30 people that showed up to help plant ~2 acres of garlic on grey, drizzly, day. Everyone played their part. Many of us were out in the field planting, a few were cooking (soup and bruscetta for lunch), one brought a keg (from the new local microbrewery), one brought his guitar and a PA and played for us while we worked. We all had a really great time. Helping out friends who will help you out when you need it. It is a great system.

It was one of those days that are just truly enjoyable. I can't picture this happening everywhere. I spoke with some friends on the east coast (sorry to generalize) that couldn't comprehend what a garlic planting party was, or why I was participating.

I sometimes really dread the day when I get my PhD and have to move on to a new place for a post-doc. Will I find a place like this ? I am just not sure.

Using model organisms as surrogates for your favorite organism

2008-10-06T10:00:00.001-07:00

Chance and Necessity has this post today on using drosophila to model parasite infection in mosquitos. It is an interesting post that outlines a paper that properly used the model system (drosophila) to search for candidate genes involved in some process, that they then tested in the original system (Anopheles). Check out the post and the paper.

Tell your friends to vote

2008-10-02T15:57:00.000-07:00

hat tip
hat tip's hat tip

IgNoble VP debate?

2008-10-02T11:58:00.000-07:00

Alex over at the Daily Transcript just reminded me that the 18th First Annual Ig Nobel Prize Ceremony is tonight, and the live webcast is available to watch just before the live webcast of the First National debate featuring Sarah Palin. Which will be more interesting?

Ralph Stanley for Barack Obama

2008-10-02T11:49:00.000-07:00

Well, there is now no doubt in my mind that Barack Obama should win this election (as if there were any doubt before...). Ralph Stanley, the one and only, has cut a radio ad in support of Obama being broadcast around Virginia. Listen to the ad here.

Autism revisited

2008-10-01T11:23:00.000-07:00

There is a recent post over at Sandwalk concerning another odd non-scientifically based 'cause of autism'. This time from PETA of all places. They claim that milk causes autism and have put up a billboard in NJ with the tagline "Got autism?". Check it out. It is interesting.

Sandwalk: Words That Should Not Be Used Together in the Same Sentence: PETA + Ethics

ScienceBlog's Book Club - Vaccination and Autism

2008-10-01T09:31:00.000-07:00

The ScienceBlogs Book Club is up and running again, discussing Autism's False Profits by Paul Offit, that will soon hit bookstores. I recommend heading over there over the next ten days while bloggers from around the world participate in the discussion. Right now Paul Offit has his first post there and there will soon be more I am sure.

Over the last few years there have been a few on the fringe of science (mostly lawyers and politicians, rather than scientists, it turns out) that have been pushing their belief that the MMR (Measles, Mumps, Rubella) vaccine is the cause of autism in children. Also, there are those that believe that the ethylmurcury based presevervative in the vaccines was the cause. In both of these cases, the overwhelming consensus of the scientific community is that these claims have no support. There is no evidence that vaccinated children are more likely to have autism than non vaccinated children.

The book is about the fact that even though scientific evidence overwhelmingly proves that these claims of vaccinations causing autism have no footing, the media still gives them a large amount of covereage in the name of 'balance'. This reminds of a few other things that are so commonly blogged about - Climate change and the few outsiders who claim that it is not happening and Evolution vs. Creation science. In both cases, it is common for a small minority of opinion to get equal footing in the media with the sole purpose of telling both sides of a story - Even when the story really only has one side that has empirical support.

Should the media relax its focus on minority opinions? This is a tough call. Think about the history of scientific progress. Imagine you were watching Katie Couric discussing Galileo's ideas in the early 17th century. The majority opinion, overwhelmingly accepted was that the sun revolved around the earth. It is what the media (at that time I guess Katie Couric would have been a priest, as they were the media of the time) had been saying for centuries. Along came Galileo with his novel, yet empirically based observations, claiming that, in fact, the sun was stationary and the earth rotated about the sun. Should he receive equal footing on the nightly news? My answer is yes in this case, as Galileo's observations were based on empirical data that people were able to replicate in their own laboratories (or castle towers as the case may be).

How is this different than the case with the novel (and if true, exciting) claim by the anti-vaccination crowd? Why should they not receive equal billing in the media? In this case, it has been shown time and time again, that the few empirically based, scientific studies that support vaccination as a cause of autism, have been shown to be the result of poor analysis, biased sampling, and personal belief rather than good empirical science. The more appropriate studies, that are non-biased, with large samples - these all say the same thing. Vaccinations are safe - they do not cause autism. That is what makes the anti-vaccination crowd different than Galileo. Galileo performed good science - the anti-vaccinationists do not.

Science gives a very objective means by which to look at the quality of the research. There are firm, strict, rules (non-biased sampling, adequate sample sizes etc..) that if followed give credence to the results. If these rules are not followed, then you shouldn't believe the work.

Go vaccinate your children, please.

Carnivorous plants: a model ecosystem for microbial ecology?

2008-09-30T22:23:00.000-07:00

When most people consider carnivorous plants, they probably first think of venus fly traps or Audrey from Little Shop of Horrors (5 points to those of you that knew about this before reading this post). People usually don't consider them to be model systems for studies in microbial ecology. This, though may be changing.

The majority of carnivorous plants are not active-feeders that actively catch prey (such as the fly trap, or sundew). Most carnivorous plants come in the form of pitcher plants. There are differing types of pitcher plants - some, like those in the genus Nepenthes have pitchers extending from tendrils at the end of the plant's leaves, and some like those in the genus Sarracenia have pitchers that form as the leaf folds over itself in a complicated way. In many cases there are moderately sized communities of bacteria, protists and rotifers living within the water-filled leaves of these plants and in some cases (such as the purple pitcher-plant Sarracenia purpurea), where the plants to not have digestive enzymes in the water, the pitchers can support a community of arthropods as well.

Sarracenia purpurea

[ This is where I digress for a moment to give a shout-out to my own personal model organism of choice - the pitcher-plant mosquito, Wyeomyia smithii that completes all of its pre-adult development within the leaves of the purple pitcher-plant. It is currently a great system for studying the evolution of photoperiodism and adaptive response to rapid climate change - check it out!]

A pitcher of a pitcher-plant serves as a very well-defined, naturally bounded ecosystem that contains a moderate number of taxa including microbes. For these reasons, it seems a perfect place for ecosytem level studies, such as those of food web dynamics and nutrient cycling. Each individual pitcher can be thought of as an island, each plant an archipeligo, and each bog a vast sea. They thus serve as a model system for island biogeography studies.

This concept has started to push its way into microbial ecology as there is currently a push to test general ecology theories - that were developed in macro-scale systems - at the microbial level to see if the same processes govern microbial communities. Modern techniques that allow researchers to study microbial communities without problems posed by culturing them (pcr, t-rflp, clone libraries etc...) are allowing detailed studies of microbial communities.

To this end Peterson et al. (2008) used the pitcher-plant ecosystem to test whether some general concepts in macro-scale food web ecology and basic species area relationships hold in microbial systems. They sampled the microbial communities in several pitchers from several plants at each of three locations around Massachussets. The bacterial communities were assayed using Terminal Restriction Fragment Length Polymorphism (T-RFLP) assays in which you can identify different varieties of a particular gene that are present in a sample. They are not necessarily species specific differences, but they give a general picture of the communities. For example you can identify bacteria of the genus Chloroflexi vs the genus Streptomyces. For the purposes of this study, it was not necessary (thankfully as otherwise it would have been a huge undertaking) to identify all of the microbial taxa to the species level.

Firstly, the study addressed a long-standing question of pitcher-plant biology - whether or not bacteria were vertically transmitted from the plant to the new leaves (which stay closed until they are fully developed) or whether all bacteria were transferred there from the environment (most likely from the insects that fall into the leaves). They showed relatively conclusively that the insides of unopened pitchers were sterile, so bacteria seem to be coming into the leaves from the environment rather than from the plants.

Bacterial communities followed a general island biogeographic pattern in which the communities were more similar within each of the three bogs sampled relative to among bogs. Within the bogs, there was little community variation among the various pitchers or plants sampled, suggesting that there is a large source for the microbial communities at a local (bog level) scale.

The presence of mosquito larvae (once again, my favorite dipteran, Wyeomyia smithii) was associated with an increase in microbial richness (number of taxa present) in the pitchers. This may be due to the novel nutrient sources in the pitchers (mosquito poop) or to the fact that the mosquitos enjoy eating the protists which eat the bacteria. Thus if there are more mosquitos there are fewer protists and more bacteria. The communities also fit a species-area relationship similar to macro level systems in which larger areas (in this case volumes rather than area) harbor a larger number of species.

These two results are consistent with the effects of area (volume) and keystone species (the mosquito) on communities - adding to the growing empirical evidence that ecological interactions at the microbial level seem to be governed by the same general principles as those at the marco level.

Celeste N. Peterson, Stephanie Day, Benjamin E. Wolfe, Aaron M. Ellison, Roberto Kolter, Anne Pringle (2008). A keystone predator controls bacterial diversity in the pitcher-plant (Sarracenia purpurea) microecosystem
Environmental Microbiology, 10 (9), 2257-2266 DOI: 10.1111/j.1462-2920.2008.01648.x

The best campaign ad I have seen in a long, long time

2008-09-27T21:15:00.001-07:00

Economic Bailouot?

2008-09-25T09:30:00.000-07:00

From Bill Moyers Journal on PBS (Sep 19th):

GRETCHEN MORGENSON: The ugly thing about this is this is privatizing gains and socializing losses. So when things are going well, the managements make out, the shareholders make out, the counterparties are fine. All the private sector people do well. But when something goes wrong, when decisions are made that turn out to be bad decisions, the U.S. taxpayer has to take on the problem.
And there's something very wrong about that. Because all of those people that made all that money are running off here into the distance with the money, carrying it in their bags. And the United States taxpayer is on the hook.

The locus of evolution revisited

2008-09-05T13:36:00.000-07:00

For the last several decades, evolutionary biologists have been arguing over the types of mutations that are most likely to contribute to evolutionary change. In particular, they have differentiated between mutations that affect protein structure (coding changes) or mutations that affect where and when the genes are expressed (regulatory change). The scientific debate really began in the 1970s when King and Wilson estimated that a 1% difference in the coding sequence between chimpanzees and humans was not enough to account for the myriad of phenotypic (visible) differences between the two (we will not get into the argument about whether this was a realistic claim or not, or how phenotypically different we are from chimps...).

The recent resurgence of evolutionary-developmental biology (evo-devo) has really brought this debate to the forefront of research, with Sean Carroll (University of Wisconsin) really popularizing the idea of regulatory mutations in a series of academic and popular books on the subject. The idea that regulatory mutations are the major determinants of evolutionary change has become somewhat of the mantra of the evo-devo community in the last several years. There have been many arguments made in the literature on why this was likly to be true (more later).

Last year, an article by Jerry Coyne (Chicago University) and Hopi Hoekstra (Harvard University) pushed for a more empirical approach to the question of coding vs. regulatory mutations emphasizing the fact the empirical data supporting the claim that regulatory mutations were the major players in adaptive change was weak at best. They discussed that both coding and regulatory mutations were likely to be involved in adaptive change and making generalizations about either class of mutations was unwarranted.

In the most recent issue of Evolution, David Stern (Princeton University) and Virginie Orgogozo (Universite Pierre et Marie Curie) have a follow-up article to the Coyne and Hoekstra paper. In this article they add some empirical rigor to Coyne and Hoekstra's arguments. Stern and Orgogozo pick apart the seven most widely used arguments in support of a predominant
role of regulatory changes in evolution, and really show that the empirical basis of these arguments is pretty shaky. First I will say that they distinguish between regulatory mutations and cis-regulatory mutations (regulatory mutations that are very nearby to the coding region).

Here is a rundown of the arguments and their support, I will let you read the paper for the details:

Importance of gene regulation in life: "... this argument does not explicitly provide support for the cis-regulatory hypothesis, because regulatory changes might arise through either cis-regulatory or coding mutations"
Correlation between phenotypic change and change in gene expression: "We thus consider the prevalence of evolutionary changes in gene expression as good evidence for the regulatory hypothesis, but as weak evidence for the cis-regulatory hypothesis."
Conservation of coding sequences across taxa: "...this argument does not offer compelling support for the cis-regulatory hypothesis."
Different constraints on cis-regulatory and coding regions: "There is currently insufficient data to determine whether the higher flexibility in cis-regulatory sequences evolution biases the number of mutations causing phenotypic evolution toward cis-regulatory regions."
Mutation target size: There isn't a good quote here, but the jist of the argument is even though the genome of higher eukaryotes is largely non-coding, and thus mutations are most likely in non-coding regions, that doesn't mean that they are going to fall in regulatory regions.
A population genetics argument: "we cannot find any serious difficulties with the proposal that genes with pleiotropic functions will preferentially accumulate evolutionary relevant mutations in the cis-regulatory region of the gene, especially when selection is weak and other parameter values are equal. However, in some circumstances - such as for genes without pleiotropic roles, for evolution by strong selection or in small populations, or for genes with a higher mutational target size for coding mutations than for cis-regulatory mutations - this prediction might not hold."
Experimental evidence: " We have compiled a database of published studies that provide compelling evidence for the individual genetic mutations causing evolved phenotypic variation within and between species of multicellular organisms. we found a total of 234 mutations in coding regions and 74 in cis-regulatory regions." Note though, that they then go on to argue about publication bias.

The authors go on to test 3 predictions of the cis-regulatory hypothesis given their large dataset of published results on the subject. The first prediction is that morphological evolution results more from cis-regulatory changes than physiological evolution. This prediction rests on the assumption that mutations affecting morphology are likely to be highly pleiotropic and occur relatively early in the developmental genetic network, relative to mutations affecting physiology. It turns out, that in this dataset, for mutations early and late in the developmental genetic network, ~20% of mutations are cis-regulatory. This prediction is not supported.

I will let readers refer to the article to find out the results for the tests of the other two predictions!

In general, this paper emphasizes the need for a more comprehensive approach to these problems, combining population genetics with developmental genetics. They also discuss the very important point that the question of whether regulatory or coding mutations are more important in evolution is the wrong question to ask. Rather, it mayb be "more productive to turn the question around and ask what kinds of phenotypic changes are expected from particular coding versus cis-retulatory changes in specific genes." I agree completely.

Related Posts:
Evo-Devo: The regulatory vs. coding mutation debate

You can just say what helps you in the moment

2008-09-04T14:18:00.001-07:00

Blog around the clock has a post featuring one of the best, yet disturbing (because a great number of Americans support a bunch of lying idiots) videos I have seen in quite some time.

Here it is.

Obama answers science questions

2008-08-31T18:50:00.000-07:00

Barack Obama recently answered ScienceDebate2008's 14 questions. My favorite portion is that concerning scientific integrity and the fact that our federal government's relationship with non-partisan scientists has dwindled nearly to zero over the last 8 years. Here is what B. has to say to the following question: "Scientific Integrity. Many government scientists report political interference in their job. Is it acceptable for elected officials to hold back or alter scientific reports if they conflict with their own views, and how will you balance scientific information with politics and personal beliefs in your decision-making? "

I will restore the basic principle that government decisions should be based on the best- available, scientifically-valid evidence and not on the ideological predispositions of agency officials or political appointees. More broadly, I am committed to creating a transparent and connected democracy, using cutting-edge technologies to provide a new level of transparency, accountability, and participation for America’s citizens. Policies must be determined using a process that builds on the long tradition of open debate that has characterized progress in science, including review by individuals who might bring new information or contrasting views. I have already established an impressive team of science advisors, including several Nobel Laureates, who are helping me to shape a robust science agenda for my administration.

In addition I will:

• Appoint individuals with strong science and technology backgrounds and unquestioned reputations for integrity and objectivity to the growing number of senior management positions where decisions must incorporate science and technology advice. These positions will be filled promptly with ethical, highly qualified individuals on a non-partisan basis;

• Establish the nation’s first Chief Technology Officer (CTO) to ensure that our government and all its agencies have the right infrastructure, policies and services for the 21st century. The CTO will lead an interagency effort on best-in-class technologies, sharing of best practices, and safeguarding of our networks;

• Strengthen the role of the President’s Council of Advisors on Science and Technology (PCAST) by appointing experts who are charged to provide independent advice on critical issues of science and technology. The PCAST will once again be advisory to the president; and

• Restore the science integrity of government and restore transparency of decision- making by issuing an Executive Order establishing clear guidelines for the review and release of government publications, guaranteeing that results are released in a timely manner and not distorted by the ideological biases of political appointees. I will strengthen protection for “whistle blowers” who report abuses of these processes.

Sounds good to me, at least in theory. It would be nice if the people making decisions were able to surround themselves with competent people who understand science and how it works. Unlike Arkansas senator Mark Pryor:

Making Excel Graphics Clear

2008-08-31T17:33:00.000-07:00

I think it was my undergraduate adviser who first introduced me to the work of Edward Tufte and basic concepts of the graphical display of data. He was also the first to convince me that MS Excel was just about the worst program with which to generate scientific data graphics. The noise: information ration was quite high. I learned how to change the background colors, change the axes and gridlines etc.. in compliance with good graphical design.

Recently, a discussion of excel graphics appeared on Tufte's discussion website, and there was a link to a visual basic macro to clean up bad excel graphics! In a post at Juice Analytics from April 2006, entitled "Fixing Excel charts: Or why cast stones when you can pick up a hammer" there is a link to an excel add-in that cleans up standard charts, allowing you to save a great deal of time on doing these things one at a time.

This is especially useful for older versions of excel (pre 2007) that have especially awful graphics. Excel 2007 (that I am currently using) has a standard graphic that isn't all that bad, not great yet, but much better than previous versions of excel. I was going to to do a before and after image of an excel chart using this add-on, but with 2007, they were pretty much the same. So if you use an older version of excel and want to try it out, send me a before and after shot and I will post it.

Spandrals - Read it.

2008-08-28T11:39:00.000-07:00

Over at Catalogue of Organisms, Chris Taylor put up a post on one of the classic papers in Evolutionary Biology, Gould and Lewontin's 'The spandrels of San Marco and the Panglossian paradigm: a critique of the adaptationist programme'.

He writes:

Nearly thirty years ago, a paper was published that almost every student of evolutionary science will end up reading at some point in their career. Despite being only eighteen pages long and containing no original research, many people see it as marking something of a revolution in biology. Like many a revolutionary document, it says little of substance that is not completely obvious, but entire books have been written that derive their subject matter directly from it. I speak of Gould and Lewontin's 1979 paper "The spandrels of San Marco and the Panglossian paradigm: a critique of the adaptationist programme".

I highly recommend every biologist and everyone interested in biology at any level read this paper and the post over at Catalogue of Organisms.

The text of the paper has been made freely available here.

New Book! - Analysis of Biological Data

2008-08-28T10:44:00.000-07:00

The Analysis of Biological Data by Mike Whitlock and Dolph Schluter

Getting a new statistics book in the mail can really be an exciting event ( I know, I know, I expose my true geekiness when I say things like that). I just received Whitlock and Schluter's new book that has come out of Whitlock's statistics course at UBC.

For an introductory statistics book it is pretty good, really focusing on applications rather than technical aspects of the statistics and there is a great collection of problems with real and exciting biological examples that stem from the classics to modern analysis such as QTL mapping.

One great contribution to the introductory statistics text is its inclusion of computer intensive methods, likelihood and meta-analysis which are rarely if ever featured in introductory texts. There are also several 'interleafs' - tangents making some important but tangential point. For example there is one called 'biology and the history of statistics', on on 'Pseudoreplication' and one on 'Why statistical significance is not the same as biological importance'.

Overall I have to say that this looks like it is a really nice book for an introductory biological statistics course. I do though, think it should be coupled with another more technical work such as my statistical bible Biometry by Sokal and Rohlf. One of the main problems that I see in the field of biological statistics is that it is too easy now to click on a few buttons in a computer program and have a plethora of numbers spit back at you without really understanding what you are doing or why you are doing it. I think that a more theoretical understanding of the statistics is necessary for proper analysis. Don't misunderstand me, I do not think you need to be a professional statistician in order to analyze data, but you do need to have some technical knowledge. And that is somewhat lacking in Whitlock and Schluter, but at the same time this makes it more tractible for a wider audience.

So in my opinion - This book is a hit and I look forward to seeing it used in many classrooms, but maybe with some chapters of Sokal and Rohlf as reading to hit on some of the finer points, especially on the ANOVA framework. I applaud Whitlock and Schluter, though, for including some of the commonly used statistical approaches in modern biology, such as likelihood and meta analysis in an introductory text.

Wake up America! - Kucinich at the DNC

2008-08-27T12:11:00.000-07:00

This morning I readily found a link to watch Hilary Clinton's speech at the DNC, but it took a bit of digging to find what I was more interested in- that of Dennis Kucinich (D - OH) - the extremist of the democratic party. What I saw when I finally found the video was a really spectacular speech, that was in fact quite mild compared with some of the other Kucinich speeches. This was about the economy - about corporate control of everything that Americans hold dear - health care, social security, national security.

I was quite disappointed when the camera panned back to reveal a mostly empty auditorium. Where are all the DNC delegates and other party members? Also, there were several images of normal every-day looking folks cheering and hollering in support of what Kuccinich was saying and then the camera pans to some suits not paying attention to anything that was being said. Is this the status of our democratic party? Is there no respect for Kucinich, even when he gives a mild (in terms of his sometimes-wackiness) but inspired speech. I would have to say that this is the best speech I have seen at the DNC this far. Yet it wasn't even shown on msnbc.

Wake up America!

R: no nested FOR loops

2008-08-14T15:35:00.000-07:00

I am an avid user of the R project for statistical computing and use it for much of my computational and statistical analyses. I will be posting tips, tricks and hints for using R on this blog, especially when I can't find the information elsewhere on the internet.

One of the main benefits of R is that it is vectorized, so you can simplify your code writing a great deal using vectorized functions. For example you don't have to write a loop to add 5 to every element in a vector X. You can just write "X + 5".

The R mantra is to minimize the use of loops wherever possible as they are inefficient and use a great deal of memory. I have been pretty good about this except for one situation - Running a simulation over a parameter space defined by a few vectors. For instance, anyone who is familiar with writing code in C or some other non-vectorized language will recognize the following pseudocode for running a simulation over a parameter space of 4 variables with nreps replications for each parameter set:

for (i in 1:length(m)) {
for (j in 1:length(sde)) {
for (k in 1:length(dev.coef)) {
for (l in 1:length(ttd)) {
for (rep in 1:nreps) {
Run the simulation
}
}
}
}
}

(my apologies for the bad formatting, blogger keeps taking out the spaces I put in. If anyone knows how to easily get the html version of my text to treat spaces as spaces, please, let me know).

This runs the simulation over a parameter space that is defined in a vector for each parameter. This is how I have been writing my R code for years.

I FINALLY FOUND OUT HOW TO VECTORIZE THIS PROCESS! I am not sure why it took me so long, but at long last I can do all of this in one command, using the apply and expand.grid functions. The apply command will apply a function sequentially to data taken from rows of an array and expand.grid takes factors and combines them into an array.

For example, say my parameter space is defined by:

> m <- c(1,2,3,4)
> n <- c("m","f")
> o <- c(12,45,34)

I can call expand.grid to get all of the combinations put into rows in an array:

> expand.grid(m,n,o)
Var1 Var2 Var3
1 1 m 12
2 2 m 12
3 3 m 12
4 4 m 12
5 1 f 12
6 2 f 12
7 3 f 12
8 4 f 12
9 1 m 45
10 2 m 45
11 3 m 45
12 4 m 45
13 1 f 45
14 2 f 45
15 3 f 45
16 4 f 45

then I can run my simulation command on the rows of this array by using apply() with MARGIN = 1 as a parameter telling apply to use the rows of the array:

So in my example, I have replaced the following ugly, inefficient code full of nested for loops (summarized above) with the following single command:

out <- apply(expand.grid(m,sde,dev.coef,ttd,reps), MARGIN = 1,
function(x) one.generation(N, x[1],x[2],x[3],x[4]))

Fantastic! I love it when I figure out how to do things more succinctly in R. I hopefully will regularly put in R tidbits on this blog in the hopes that some 'ignorant' R programmer like myself will find this post the first time he searches the internet for it. It may have taken me years to finally figure it out, but that doesn't mean it has to take that long for everyone else! :)

Demystifying Statistics: On the interpretation of ANOVA effects

2008-08-12T15:00:00.000-07:00

One of the statistical concepts that is very difficult for many people to grasp, yet critically important for an understanding of statistics, is the interpretation of significant effects in an Analysis of Variance (ANOVA). In this post, I will use a graphical approach to describe how to interpret effects from a two-way factorial ANOVA. I will not delve into the design, implementation, or computation involved in such ANOVAs.

Suppose we have an experiment where we are measuring a biological trait from each of two species (Sp1, Sp2) raised in each of two environments (Env1, Env2). We set up a two-way ANOVA and out pops an ANOVA table with four lines, one each for the species effect, the environment effect, the species-by-environment interaction effect, and one for the residuals (which I hope to discuss in detail in a later post, and will not talk about here.

ANOVAs are designed to look for differences in mean values accross different groupings of the data. In the case above, it is looking for a difference in mean trait values between the two species and between the two environments, while simultaneously testing for their independence (with the interaction term). So in order to look at a graph and think about ANOVAs, you have to think about mentally picturing the various means.

The first two effects are pretty straightforward to interpret. Suppose the analysis showed a significant Species effect. This means that there is a significant difference among species in the mean trait measure when pooled accross environments. Maybe that Sp1 always has a bigger eyeball width than Sp2, or something like that. Same thing with a significant environment effect; maybe both species do better in tropical vs. desert conditions.

It is the interaction term that is the hard term to understand for many people. A significant interaction term signifies a lack of independence of the other two variables, in this case species and environment. In this example, an interaction term may imply that there is environmental preference among species, with Sp1, say, preferring Env1 and Sp preferring Env2. Another way to think about significant interaction terms is in an Analysis of CoVAriance (ANCOVA) setting, where the two slopes are different (see below).

I find it easiest to think about these things graphically so below you will find the 7 different qualitative results for significant effects in a two-way ANOVA. These are the pics that always pop into my head when I think about ANOVAs. They are interaction plots of the two variables.

(Disclaimer - These graphs do not include error bars. This is purely for clarity of making my point, any time figures like these are published, they should include estimates of error - as discussed here).

Let's start with cases where there is no, or only one, significant effect:

Figure (A) - there are no significant effects. There is no difference in means either between environments or species, and there is no interaction term as the two are independent, and the slopes of the lines are the same.

Figure (B) - a significant species effect. In this case there is no difference in the mean trait value across environments (it falls between the two lines), but the mean for each species is different. The slopes are equal so there is no significant interaction.

Figure (C) - a significant environment effect. Here there is a difference among the means of the two environments, but not a difference in the means among species. Again the slopes are equal.

Figure (D) - a significant interaction effect. In this case there is a significant interaction effect as the slopes are not equal. In this case there are no other effects as the means of the environments nor species differ. This is important as many people mistakingly believe that there cannot be a significant interaction term if neither of the main effects are significant. This shows that it is possible.

Now let's move on to cases where there is more than one significant effect:

Figure (E) - a significant species effect and interaction term. In this case you can see that the slopes are unequal and thus there is an interaction term. The species means are different, but the environmental means are not.

Figure (F) - a significant environment effect and interaction term. As above, the slopes are unequal, but in this case the species means are the same while the environmental means differ.

Figure (G) - everything is significant. You can figure this one out. All the means are different, as are the slopes.

That's the basics. Now ANOVAs can get really complicated with many levels of factors and complicated designs, but this relatively simple graphical understanding of ANOVAs has greatly helped me to understand more complex designs.

Studying annoying organisms

2008-08-12T09:14:00.001-07:00

...there has been considerable interest for a long time in the temperature relationships of development time and fecundity mainly of filthy, annoying, and disease-transmitting insects in order to apply it in predicting the outbreak-time and the dynamics of pests.

From: Ratte, H. T. 1985. Temperature and insect development. Pp. 33-66 in K. H. Hoffmann, ed. Environmental physiology and biochemistry of insects. Springer, Berlin, Heidelberg, New York, Tokyo.

Influencing Darwin: Malthus

2008-08-08T19:16:00.001-07:00

This is the first in a series of posts that I am working on that concern the philosophical, theological and scientific minds that influenced Darwin in the development of his Origin of Species. I will begin with one of the most cited influences of Darwin's thoughts, Reverend Thomas Malthus. All quotes will be linked to the freely available ebooks of the texts available at Project Gutenburg.

Upcoming posts will concern Lyell and Paley who were standard reading (in geology and theology respectively) as part of Darwin's education. Other influences will follow (if you have any you would like to see, feel free to leave the suggestion in the comments).

Historical Background:

The 18^th century in Britain saw a drastic increase in poverty as the feudal system deteriorated and the large landowners became not only the wealthy, but the political class. Concurrently, Utopian writers began appearing in France (with the French Revolution) that believed that the problems in Britain were due to the political power of the wealthy classes, and that the removal of the wealthy class would create a state of the people, where hunger and poverty were no longer an issue, as commodities would be distributed as a function of need rather than wealth.

Malthus's thesis:

Thomas Malthus saw a serious flaw with logic that result from two premises that were outlined very early on in An essay on the Principle of Population.

First, that food is necessary for the existence of man.
Secondly, that the passion between the sexes is necessary and will remain nearly in its present state.

To put this bluntly, humans are always going to eat and reproduce as much as possible. He goes on with his main thesis based on the above postulates:

Assuming then my postulata as granted, I say, that the power of population is indefinitely greater than the power in the earth to produce subsistence for man.
Population, when unchecked, increases in a geometrical ratio. Subsistence increases only in an arithmetical ratio. A slight acquaintance with numbers will shew the immensity of the first power in comparison of the second.
By that law of our nature which makes food necessary to the life of man, the effects of these two unequal powers must be kept equal.
This implies a strong and constantly operating check on population from the difficulty of subsistence. This difficulty must fall somewhere and must necessarily be severely felt by a large portion of mankind.

In response to the Utopian thinkers that believed that a society could exist in which all people were well-fed and happy, Malthus made the point that Human nature (to eat and reproduce) made such a society impossible. There would always be a conflict between the desire to reproduce and the ability to remain well-fed. Malthus used the early United States census data as evidence for the geometrical growth of populations, but has very poor evidence for the arithmetical growth of subsistence; though he claims that it is a conservative estimate (this was pre-industrialization, where land was the limiting factor for productivity).

Darwin and Malthus:

In 1838, after returning home from his long voyage as a naturalist on The Beagle, Darwin 'happened to read for amusement' Malthus's essay on population.

In October 1838, that is, fifteen months after I had begun my systematic enquiry, I happened to read for amusement 'Malthus on Population,' and being well prepared to appreciate the struggle for existence which everywhere goes on from long-continued observation of the habits of animals and plants, it at once struck me that under these circumstances favourable variations would tend to be preserved, and unfavourable ones to be destroyed. The result of this would be the formation of new species. Here then I had at last got a theory by which to work… (The Autobiography of Charles Darwin)

Darwin was able to place the 18^th century view on the control of human populations into his own 19^th century view on the variation of plants and animals. This gave him context for his view that as more individuals are born than can survive, those that are the most 'fit' in a given environment will survive to reproduce, as outlined in the introduction to the Origin of Species:

In the next chapter the struggle for existence among all organic beings throughout the world, which inevitably follows from the high geometrical ratio of their increase, will be considered. This is the doctrine of Malthus, applied to the whole animal and vegetable kingdoms. As many more individuals of each species are born than can possibly survive; and as, consequently, there is a frequently recurring struggle for existence, it follows that any being, if it vary however slightly in any manner profitable to itself, under the complex and sometimes varying conditions of life, will have a better chance of surviving, and thus be NATURALLY SELECTED. From the strong principle of inheritance, any selected variety will tend to propagate its new and modified form.

EVO-DEVO: the regulatory vs. coding mutation debate

2008-08-07T20:18:00.001-07:00

In today's issue of science there is a news focus on the cis-regulatory vs. coding mutation debate (Evolutionary Biology: Deciphering the Genetics of Evolution).

The issue here concerns the kind of mutations that affect morphological evolution. For much of the history of evolutionary genetics the prominent view was that evolutionary change was the result of mutations affecting protein structure ('structural mutations'), as they were all that were really known at the time. Around 30 years or so ago, the realization was made that genes were regulated by non-coding portions of the genome and that led to the hypothesis that morphological evolution could be the result of changes in these regions affecting when, where and how the coding sequences were expressed.

Last year, Jerry Coyne (University of Chicago) and Hopi Hoekstra (Harvard University) wrote a commentary paper for Evolution, The Locus of Evolution: Evo Devo and the Genetics of Adaptation, expressing concern for the overwhelming acceptance of this regulatory mutation-centric view of the evolutionary process. They urged caution, saying that there is not enough evidence to assume that regulatory mutations are the driving forces of adaptive change, and one cannot yet exclude the possibility of coding mutations serving as the underlying force. I think that this is a reasonable statement.

The controversy quickly soared out of control with many academics misinterpreting the Evolution article, referring to it as a citation that said something along the lines of "cis-regulatory evolution is unimportant in morphological evolution" or something along those lines. Any of these particular citations of the paper show a severe misinterpretation of the article's main points. The paper mainly argued, as Jerry Coyne put it at the University of Oregon's IGERT Symposium on Evolution, Devleopment, and Genomics, "Evo-Devo needs to do a better job of policing itself," not allowing serious claims such as those concerning the 'major forces' in morphological evolution to go on without proper assessment of the evidence.

I think that most in the field tend to agree that both types of mutations are likely to play a role in morphological evolution, and personally I will add that I think we need to move on from debates about which are "more important" to address more relevant questions, such as: What are the differences in the evolutionary processes involved in one type of mutation vs the other? Are there certain types of traits that are more affected by cis vs coding mutations (Greg Wray has started approaching this question)? How many mutations are necessary for large-scale morphological evolution?

Let's move past this semantic debate and get on to some real science.

Related Links:

IGERT Symposium on Evolution, Development, and Genomics \
Live Blogging of the Symposia over at Pharyngula:

Keynote addresses (Coyne and Wray: 'The Evo-Devo Smackdown')
Session 1
Session 2
Session 3

Sparrow Quartet in Newsweek

2008-08-07T19:38:00.001-07:00

This was brought to my attention from the folks over at The Bluegrass Blog.

The Jul 12 issue of Newsweek had an article on Abigail Washburn and the Sparrow Quartet - a quartet featuring two banjos, a fiddle, a cello, and the amazing soulful vocals of Abby Washburn. The article also includes a video of the band playing their song "Captain" in a park in NY. I feel bad for all the people you see in the video walking by oblivious to what is happening right next to them. This quartet is rare in its uniqueness and is really coming into themselves. Heck, they are going to play at the ribbon-cutting ceremony for the opening of the new American embassy in Beijing.
image link

Email overload

2008-08-07T12:02:00.001-07:00

As a graduate student with a lot going on in life, both academically and personally, time management becomes a serious issue - one that I am starting to think a lot about lately. Managing several undergraduate projects, working on my own projects, making sure to keep getting out to my advisors, planning personal events including arranging gigs, spending time with friends, etc... There is a lot going on. Yesterday I decided that I would allot two hours today to try to organize and optimize one portion of my life - my email.

This was timely as I started my day reading Slate over breakfast, where an article was posted about Lifehacking the Candidates. I perused the web a bit and found a few little tricks on approaching my overloaded inbox and found InboxZero from 43folders.com. They have a lot of good suggestions, emphasizing the common sense solution of draining your inbox to zero every day by using one of five actions on every email message as soon as you read it: delete, delegate, respond, defer, do. I cleared out my inbox today with this method and it feels pretty great. Hopefully I can keep up with that.

Another thing that I found while doing my internet research on email efficiency is a discussion of how to write good emails. I think that I am going to send this link out to the people that email me the most to try to maximize email efficiency. I especially like the idea to write subject-line only emails that end with EOM (End of message) for short notes so that you don't have to spend the time opening the email. Good idea

Domestication and pleiotropy

2008-08-06T13:43:00.000-07:00

Greg Laden's Blog and then A blog around the clock posted a great video from PBS on the domestication of foxes. The blog around the clock post has a great deal of great information including some links to journal articles on the subject.

The one-liner is that artificial selection on rigidly defined 'tameness' resulted in a huge diversity of phenotypic variation in an incredibly short time period - resulting in coat color changes, behavioral changes and many more. I highly recommend the article found here and the following video (originally posted by Greg Laden and then again by many others:

Daylength affects thermal requirements for insect development

2008-08-06T10:22:00.000-07:00

An ectotherm’s rate of development is a function of its thermal environment, with warm temperatures accelerating, and cold temperatures decelerating, the developmental process. Temperatures exceeding a lower threshold (TTD – thermal threshold for development, the temperature below which no measureable development occurs) are accumulated into the sum of effective temperatures (SET), or the number of degree-days (The summation of temperature * time) above the thermal threshold needed to complete development. These two traits are estimated by a regression of developmental rate on temperature with SET being the reciprocal of the slope of the regression and TTD being the solution to the equation when developmental rate is set equal to zero. Authors may use the slope of the regression (1 / SET) rather than SET due to the ease of graphical interpretation.

Very little is known about how other environmental conditions (e.g., photoperiod, humidity, light intensity) affect the thermal requirements for development in insects as the thermal requirements are often estimated for a given population or species under a set photoperiodic environment. The paper discussed here shows that the thermal requirements for development in the linden bug Pyrrhororis apterus (see figure below) are a function of the photoperiodic environment of development.

In a straight-forward, though extensive, study, bugs from four populations spanning about 10 degrees latitude were raised at one of 5 constant temperatures (20, 22, 24, 26 and 28°C) and under either long days (Light:Dark = 20:4) or short days (Light:Dark = 14:10). One of the four populations was also raised at an intermediate daylength (Light:Dark = 17:7) which is very close to the critical photoperiod (daylength used to discriminate between long and short days) of that population.

The results are pretty clear – daylength has an effect on the thermal requirements of insect development. The data from a representative population - that grown under all three photoperiods - are shown below (error bars represent 1 standard error). Under lower temperatures, development time was increased under long-days whereas under higher temperatures development time was decreased in long days. This shows a concordance of photoperiod and temperature affecting development time as development time is minimized when environmental conditions are similar to those experienced in nature (long days with warmer temperatures, and short days with colder temperatures). The discussion in this article lacks proper treatment, though, of what daylengths correspond with these average temperatures in nature. These populations are from 45 – 55 N latitude, and so one would expect there to be a large difference (maybe more than 8°C) in temperature between when the daylengths are 14 and 20 h.

Under intermediate daylengths that are similar to the critical photoperiod for this population, development time increases. This is an interesting observation that has been shown by others as well (including Saunders and Numata). This may reflect the inability of the photoperiodic counter to ‘make decisions’ about whether the day was in fact long or short. One can make up an adaptive story about this result – A conservative counter that really needs to make sure it is responding appropriately to daylength would likely increase fitness in seasonal environments.

Shorter daylengths also reduce TTD and increase SET (see figure below) which may also have an effect on insect development.

What effect does the photoperiodic regulation of thermal requirements for insect development have on organisms living in the wild? P. apterus overwinters in a state of reproductive quiescence, and begins development in the spring as temperatures warm. Under the short photoperiods of spring, TTD is reduced allowing the individuals to begin development sooner, and as photoperiod lengthens, SET – the number of degree days to complete development decreases as well (as seen in the increased regression slopes (1 / SET) in the figure to the left). It seems that development under increasing spring photoperiod and temperatures is maximized as a result of the photoperiodic control of thermal requirements for development.

LOPATINA E.B., BALASHOV S.V. & KIPYATKOV V.E. (2007). First demonstration of the influence of photoperiod on the thermal requirements for development in insects and in particular the linden-bug, Pyrrhocoris apterus (Heteroptera: Pyrrhocoridae) European Journal of Entomology, 104 (1), 23-31

Yarrow Hefeweizen

2008-08-03T13:25:00.000-07:00

Well, I stepped out on a limb with my last brew - attempting a Hefeweizen with no hops! Instead, I used yarrow for the bittering and aroma. I opened up the first bottle today and it is fantastic! It is unlike any beer I have ever had before, a completely novel taste. I could see people having a problem with it if they went in expecting it to taste like a standard ale, but if you go in expecting something new, you will not be dissappointed. Here's the recipe (using extract for a 5 gal brew):

5 lb Wheat Dark Malt Extract
1 lb White wheat malt
1 lb Pilsner malt
0.5 lb Crystal malt (20L)
0.5 oz Dried yarrow (30 min)
1.5 oz Dried yarrow (0 min)
White labs Hefeweizen yeast (WLP380 Hefeweizen IV Ale)

Try it, its great!

The Elements of Style

2008-07-30T18:05:00.001-07:00

Vigorous writing is concise. A sentence should contain no unnecessary words, a paragraph no unnecessary sentences, for the same reason that a drawing should have no unnecessary lines and a machine no unnecessary parts. This requires not that the writer make all his sentences short, or that he avoid all detail and treat his subjects only in outline, but that every word tell.

There were two required texts for my undergraduate Evolution class: Evolutionary Analysis by Scott Freeman (link is to new edition rather thean the one I used), and The Elements of Style by William Strunk Jr and E.B. White (link to original 1918 edition). The former seemed appropriate at the time while the latter confused me greatly. The course was writing intensive and a large part of our grade was based on our writing clear, concise and substantial analyses of primary literature as well as a 30 page review paper. At the time I am sure that I looked through the style book but I can honestly say that I did not give it the consideration it deserved.

Today, in an act of procrastination, I took the 'little book' from the shelf, blew the dust off of the binding and leafed through it over a cup of coffee and realized how relevant it is, even nearly a century after its first publication. The above quote is a great summary of what my advisors have been telling me for years concerning scientific writing. In the version I have (1979) there are 11 elementary rules of usage which I mention below:

Form the possessive singular of nouns by adding 's
In a series of three or more terms with a single conjunction, use a comma after each term except the last
Enclose parenthetic expressions between commas
Place a comma before a conjunction introducing an independent clause
Do not join independent clauses by a comma
Do not break sentences in two
Use a colon after an independent clause to introduce a list of particulars, an appositive, an amplification, or an illustrative quotation
Use a dash to set off an abrupt break or interruption and to announce a long appositive or summary
The number of the subject determines the number of the verb
Use the proper case of pronoun
A participial phrase at the beginning of a sentence must refer to the grammatical object.

These are timeless rules of grammar. The book includes a few things that have not survived the ages such as the following section discriminating against the use of the suffix "-ize", that I believe only appears in the White edited version of the text (not in the original)

Do no coin verbs by adding this tempting suffix. Many good and useful verbs do end in –ize: summarize, temporize, fraternize, harmonize, fertilize. But there is a growing list of abominations: containerize, customize, prioritize, finalize, to name four. Be suspicious of –ize; let your ear and your eye guide you. Never tack –ize onto a noun to create a verb. Usually you will discover that a useful verb already exists. Why say "moisturize" when there is the simple, unpretentious word "moisten".

What a fantastic quote! Needless to say, it seems that society has not agreed with the authors, as evidenced by the inclusion of all of the 'abominations' in the MS word dictionary. Not to mention the numerous other –ize words in common usage today. I think that one of my new favorite quotes is the last sentence about the word "moisten".

Overall, this book is still as relevant and accurate as it was nearly a century ago and I will strive to make my writing follow Strunk's guidelines to the best of my ability.

On the use of error bars

2008-07-30T11:18:00.000-07:00

Dave Munger over at Cognitive Daily just wrote th is post about people's lack of understanding of error bars in the graphical representation of data. The post is very interesting and I encourage people to take the quiz that he has posted on the correct interpretation of error bars.
A particular comment on that post concerns me, and I am going to use this post to give my two cents on error bars and their importance in the understanding of data. Specifically I will try to address some misconceptions and problems with how people use and read error bars.

The comment that concerns me is:

I may, in the future, forget the exact definition of what the error bars mean, but I will still be capable of saying "Whoo, small error bar, that figure is probably pretty accurate" and "Whoa, look at that huge error bar, I'll use a bigger grain of salt to look at that figure".

This comment frightens me. I can't help but to think about the book How to Lie With Statistics (link to book at powells). The main problem with this reasoning is that there are many 'types' of error bars that are often included in scientific graphics, with most researchers choosing some multiple of either the standard error or the standard deviation. One can not just look at the length of the error bars and assume that it means accurate data (to get a bit picky on semantics - also, error bars do not reflect the accuracy of the data, rather it reflects the precision with which you can measure the data). It will all depend on which error measurement is being plotted, and it is highly variable among scientific papers. I tend to use error bars that are the length of 2 * Standard error for reasons I will get to in a bit, and thus relative to other graphics that usually plot 1 SE my data may seem 'less accurate' to the reader, and that would be a shame and completely incorrect.

The appropriate use of error bars

Data that is plotted without error bars are data that cannot be put into relevant scientific context. Are two means the same? What is the measurement error on the observations? Is there a pattern of variability among groups? These are all incredibly important scientific questions that cannot be addressed without estimates of errors of one form or another. As such, error bars should ALWAYS be included in scientific graphics. The lack of error bars in figures immediately raises suspicion in my mind as to the appropriateness of any conclusions drawn from the data. There are a few exceptions where a complex graphic would lose all meaning if the error bars were included (say there were too many points and if the error bars were included you would not be able to see any of the data), but under these conditions, the text associated with the figure should make very clear the level of error on the data.

In my publications, I tend to use error bars representing two standard errors (SE) around a mean. This is because the standard two-group t-test (or F-test) has a 95% confidence interval of ~2SE. Therefore you can use this to directly estimate the significance of a difference in means, rather than having to visually double the length of 1SE error bars that most people use (mostly because they make people like the one quoted above more trusting of their data, rather than for any worthwhile reason). With 2 SE error bars, one can look to see if the mean of one group is included in the confidence interval of the other group - if so then there is likely no difference among the groups. Note that it is not relevant whether the error bars 'overlap' but whether the mean of one group 'overlaps' with the error bars of the other.

Here is fictitious example with some randomly generated data.

In this case the two groups are significantly different using a Students t-test (t =3.59, df = 198, p = 0.0004. I have plotted the same data twice showing that the two samples are different, with the plot on the left-side having 1SE error bars and the one on the right having 2SE error bars. There is not much difference in interpretation of these graphs. In either case they look different (OK, for this example, I have two groups that are highly different to try to make this easier to visualize). The 2SE error bars do not make the data look 'less accurate' but they do make it easier to see what is going on. The mean of either sample is not included in within the error bars of the other sample - thus the two samples are different. This is easier and more appropriate to interpret than the left plot with which in order to correctly interpret the error bars, you must first visually double their length. The person quoted above may have less trust in 'accuracy' of the data on the right, even though it is the same data, just with a different choice of error bar.

The following example is again randomly generated data, but in this case there is no significant difference among the groups (t = 0.96, df = 198, p = 0.336)

In this case the difference between the left plot (with 1SE error bars) and the right plot (with 2SE error bars) is clear. The right figure yields to the most appropriate interpretation of the data. It is clear with 2SE that the mean of one group 'overlaps' with the error bars of the other group, therefore suggesting that there is no difference among groups, which is the case here. If people were incorrectly using the same reasoning in the plot with 1SE error bars, they would incorrectly conclude that the means of the two groups were different.

My main conclusions are the following:
1. Error bars should ALWAYS be included in scientific graphics or at least have associated text describing the error measurements.
2. Do not just look at the width of error bars as an estimate of 'accuracy' of the data - it is context dependent on what the data are and which type of error bars the author has decided to use.
3. I encourage the use of 2SE error bars in the majority of cases to improve the clarity of the relationships of the data and to minimize the mis-interpretation of the error bars, even though it may make your data look 'more noisy'.
4. Teach others what error bars really mean so that they can accurately read scientific figures.

PZs great desecration

2008-07-24T11:32:00.000-07:00

PZ has completed his violation of the cracker over at Pharyngula.

2008-07-23T17:24:00.000-07:00

Ahh, fond memories. This image - the cover of Nirvana's Nevermind album - has a lot of context associated with it in my past, and I am sure that it is true of millions of others that went to high school in the 90s. This baby is now 17 years old and NPR has a story and interview with him.

http://www.npr.org/templates/story/story.php?storyId=92833535

Time for some Campaigning

2008-07-17T09:11:00.001-07:00

Send a JibJab Sendables® eCard Today!

Creation Science 101

2008-07-16T14:49:00.001-07:00

Greg Laden had a link to this video on his blog and I thought it was worth reposting here. He's a bit of an oddball, but it is amusing nonetheless.

A president that doesn't use email?

2008-07-13T19:55:00.000-07:00

I have many reservations about the possibility of John McCain as a president of this country, with the most notable being his age and his inability to understand the lives of the majority of Americans (those under 50 years old - no offense to any older folks out there). This was driven home for me a bit more today when I read an interview conducted by the NY Times that ran today. Here is a bit of the article:

He said, ruefully, that he had not mastered how to use the Internet and relied on his wife and aides like Mark Salter, a senior adviser, and Brooke Buchanan, his press secretary, to get him online to read newspapers (though he prefers reading those the old-fashioned way) and political Web sites and blogs.

“They go on for me,” he said. “I am learning to get online myself, and I will have that down fairly soon, getting on myself. I don’t expect to be a great communicator, I don’t expect to set up my own blog, but I am becoming computer literate to the point where I can get the information that I need.”

Dr. Nisbit over at Framing Science brought up a really interesting point:

Should we care that McCain lacks even a basic familiarity with the online world? Consider that a President McCain would probably be the only world leader at the next G8 meetings who has never experienced first hand the world of globalized information and commerce.

Do we really think that it is a good idea to have someone running the country that is unfamiliar with basic usage of the internet - the means by which an enormous and ever growing number of Americans do everything from communicate, shop and get their news? With the increasing instantaneous nature of our global culture arising from the internet, what would happen if the 'world leader' didn't even know how to check email?

Science political Cartoon Contest

2008-07-12T14:30:00.000-07:00

The Union of Concerned Scientists is working on the Third Annual Scientific Integrity Editorial Cartoon Contest. They have narrowed it to 12 finalists and are asking for the community to vote for the winner. Vote for your favorite cartoon here.

Crazy talk

2008-07-12T12:16:00.000-07:00

I am sure by now that most readers are familiar with the Cracker fiasco invading the blogosphere centering around PZ Myers' statements concerning Webster Cook, the smuggled eucharist, the planned sacrilege, and the insane religious and political response (here here here and here). Well it has now hit the 'big time' - being picked up by the Washington Times. In the spirit of the debate, I thought I would post a picture that a colleague took and gave to me a few days ago showing the absolute ignorance of some folks to evolutionary ideas.

Really? Are you so sure about this?

Abigail Washburn and the Sparrow Quartet

2008-07-10T20:24:00.000-07:00

What do you get when you put together a amazing clawhammer banjoist, amazing soulful (and sometimes chinese) vocals, one of the world's most creative finger-style banjo players, the deep resonating sounds of a cello and the screaming melodies of a violin? You get the Sparrow Quartet, who just came out with their first full-length album.

The Sparrow Quartet (Abigail Wasburn on banjo and vocals, Bela Fleck on banjo, Casey Driessen on violin and Ben Sollee on cello) have a solid album coming after their EP released last year (EP at amazon). The album combines Wasburns soulful vocals over a combination of Appalachian and Chinese instrumentals.

There are old-time american style tunes like "Banjo-Pickin Girl" where Washburn gets to her roots and has some fast rockin' banjo licks, and there are soulful bluesy songs like "Captain" and some chinese inspired tunes like "Journey Home".

This combination of musicians is creating music as it has never been before. International, inspired, and completely unique. It is on the top of my music list and I am sure that it will be there for a long, long time.

Degenerate PCR - A guide and tutorial

2008-07-10T13:26:00.000-07:00

Finding gene sequence data in organisms for which there are no genomic resources available can be a non-trivial task. One of the most common methods for finding such sequence information is through degenerate PCR methods, either using total genomic DNA or a DNA library (genomic or cDNA library) as template. This technique is tedious and its effectiveness requires quite a bit of luck as well as skill. I have never really found a comprehensive resource for optimizing the chances of success so in this post I will outline the techniques I use and give a few tips that have really helped me in the past.

In general, polymerase chain reaction (PCR) requires two primers (short sequences of nucleotides) that specifically bind to a region of the genome that is to be amplified. This requires knowledge of at least a portion of the specific sequence to be amplified. Degenerate PCR involves using primers that allow for some 'wiggle room' in the sequence of the primers. For example the 4th nucleotide in the primer sequence may allow it to anneal to template sequence with nucleotides A, T, or G, while excluding those with C. This allows for flexibility in amplification. On the downside, it reduces specificity of the primers.

Degenerate PCR works because, in general, there is far more conservation at the amino acid (AA) level than at the nucleotide level. Conserved portions of AA sequences among organisms closely related ot the focal organisms are likely to be conserved in the focal organism as well. For example, let's say that there is a gene that has the following amino acid sequence “GCCHCDE” that is conserved among a few closely related organisms. There are 256 nucleotide sequences that will code for this specific AA sequence. It is likely that neutral changes in the nucleotide sequence of these organisms have been accumulated throughout evolutionary time, but if you design primers to take into consideration all of these possibilities, you should be able to use this sequence as a PCR primer, assuming the AA sequence is conserved in your species of interest. Aligning the nucleotide sequences of these organisms is unlikely to yield conserved primers.

I will discuss the design of degenerate primers for 'finding' a gene in an organism that has closely related organisms with gene sequences available.

Step 1 – Get the sequence data of the gene-of-interest from related organisms

I work on a mosquito, so I generally start by finding the sequence data from D. melanogaster, a fellow dipteran. I start at Flybase and look up the sequence (usually by name) that I am interested and download the protein sequence (translation) in FASTA format (you can use all of the following methods for non-coding DNA as well). The sequence should be copied into an empty text file. I usually change the beginning of the header line (the line starting with “>”) to be the species name as this is the portion of the header that will be included in the alignment files. The alignment program will read from the character after “>” until the first space, so keep that in mind when you name your sequence.

Next, it is necessary to find sequence data for other related organism (in my case other mosquitos including Culex pipiens, Aedes aegypti and Anopheles gambiae). I usually do this at NCBI using their BLAST program. I usually stick to 3 – 5 species that are closely related to the one you are after. Including more organisms make it a bit harder to work with but are more likely to give you highly conserved regions.

Once you have acquired the protein coding sequence of a variety of closely related organisms, it is time to move on to step 2!

Step 2 – Align the protein sequences

With the text file including the fasta-formatted protein sequences, the next step is to align the sequences to account for gaps. I use ClustalX, but there are web-based interfaces for Clustal available including one here. I usually just leave all of the default options and run the multiple alilgnment, which spits out an alignment file (*.aln) with the aligned protein sequences. Then I print out a copy of the alignment (working on the computer screen is difficult). This is where the tedious part begins.

Step 3 – Finding conserved sequence regions with low degeneracy

The goal here is to come up with stretches of conserved amino acid (AA) sequences that have a low degeneracy. By this I mean that the conserved AA sequence could be generated by a relatively low number of nucleotide sequences. In general the lower the degeneracy you can get (fewer possible nucleotide sequences) the better. At worst, I will use a primer that has a degeneracy of 1000 possible nucleotide sequenes, but I try to make them much smaller than that if possible.

Stare at the printout. Alignment files are nice as they put “*” under all sites that are conserved and “:” under all similar sites. Look for stretches of these symbols and that is a good place to start. Once you find conserved sequences (trying to make primers of ~17 – 24 nucleotides requires 6- 8 AAs) the degeneracy of these sequences must be determined. This can be done by taking the product of the degeneracy of each AA in the sequence. For example, Valine has four codons (GTT GTC GTA GTG) and thus has a degeneracy of 4 while Tryptophan has only one codon (TGG) and thus has a degeneracy of 1. The degeneracy of each AA, along with its codons, is included in the reference table I have linked at the end of this post.

When you find a site with low degeneracy, write out all of the possible sequences using the Degeneracy code found in the reference table and order your primers. Then you can try the PCRs and hope for the best.

Tips and Tricks that will give you the best chances of successful degenerate PCR

Keep the degeneracy of each primer low. Under 400 is great – under 1000 is ok but not good, and over 1000 isn't worth your time.
In general, larger PCR reactions work better – I tend to use 50uL reactions for degenerate PCRs
Use 3-5 times the amount of primer you would normally use to increase the chances of the appropriate primer being in the reaction at any decent concentration. I tend to use 3 uL of each primer (at 10mM) for each 50 uL reaction.
I have had the best success with nested degenerate PCR if possible. In this you have a minimum of 3, but best is at least 4 primers within the sequence. In the case of four, you will have two forward and two reverse primers. For the first PCR reaction you use the two “outer” forward and reverse primers. Then you take a portion of this first PCR and use it as template for the second reaction (I usually use 5uL of the first 50 uL reaction as template for the second reaction). This helps to reduce the number of amplicons and makes the reactions more specific to the gene you are looking for.
The more primers you can design for a given gene, the better the chances that one of the primer sets will work.
Methionine (M) and Tryptophan (W) are the only amino acids that are coded for by a unique codon. Having these in your primer sequences is great!
Try to stay away from Serine (S) Arginine (R) and Leucine (L) as they each are coded for by six codons. This said, don't let the presence of some of thes AAs keep you from using that region. But realize that a sequence of SSRLSR is not going to make a good degenerate primer.
Amplifying a 200 – 600 bp region seems to be optimal but I have done as few as 80 bp and as much as 1200 bp.

I have created a reference table that will come in very handy for any attempt to design degenerate primers. The table includes the codon list for all amino acids along with the degenerate code for the colleciton of nucleotides in both forward and reverse compliments. The degeneracy of each amino acid is also listed.

Degenerate Primer Design Reference Table

As an example, this morning, I worked up some primers for Juvenile Hormone Esterase for mosquitos. In the pdf linked below you can see the alignment file with the primer sequences highlighted along with the details of the associated primers.

JHE example

Goodnight bush

2008-07-09T14:04:00.000-07:00

Today there was an NPR story about 'Goodnight Bush' - a satirical treatment of the Bush admistration in the style of Margaret Wise Brown's children's book 'Goodnight Moon'.

The illustrations are funny, yet still disturbing - Like the painting of and oil rig with bombers flying around it over the fireplace.

Check it out at NPR

Transitional Fish

2008-07-09T12:06:00.000-07:00

Over the last few decades, a large number of fossils have been found
that fill in gaps between existing groups of organisms. One of the
coolest recent examples was published today in Nature. He describes a
fossil that he has named "Heteronectes" that is a flatfish - but not
exactly.

Flatfish are fish that live on their sides usually swimming close to the
ocean floor. The young resemble most other fish, but the amazing thing
is that as they grow, one of their eyes flips around on to the other
side of the body so that both eyes face 'up' while the fish swims along
the bottom of the ocean on its side.

M Freidman (University of Chicago) describes a fossil that has an
asymmetrical skeleton and an eye that has travelled part of the distance
to the other side of the body, but has not gone all the way. One might
argue that it was just a mutant individual or an example of development
gone awry, but in this case, there are 3 independent examples of
individual fossils with this phenotype. Cool.

Yay for transitional forms!

On vacation

2008-07-06T07:49:00.000-07:00

Well, I have been in NY visiting family for almost a week now, wondering how my dog was doing at my friends house. She sent me some pics yesterday and my little Tater seems to be doing just fine. Probably even better than if he were with me this week (the broken foot doesn't allow me to do too much with him.

today's playlist

2008-06-24T16:23:00.001-07:00

Tony Rice amazes me

2008-06-23T17:40:00.001-07:00

For the last few hours I have been working on some writing and listening to Tony Rice's Guitar and the Tony Rice Unit's Manzanita. Phenomenal. I just wanted to give the man the props he deserves. I can only wish to some day be able to pick a fraction as well as he can.

Even poor reviewers make manuscripts better

2008-06-23T17:26:00.001-07:00

Scientific literature has to pass a peer-review process before it is published (in most cases) in which two-to-three independent reviewers read the manuscript and comment on its appropriateness, completeness and relevance to the field before it is considered for publication. In my experience (limited though it is) reviewers have been insightful, honest, and most importantly careful - putting time and effort into the manuscripts so that they might have the knowledge to give it an accurate review. I have had papers returned with rejection due to very valid comments by the reviewers, and was more than happy to take their comments into consideration to rework the manuscript in the end making it orders of magnitude better. Today I received reviewer's comments that I find to be somewhat infuriating as they are obviously due to lack of care of the reviewers, and indeed, the editors.

It was obvious in reading the reviewer's comments that much of what they had to say what the direct result of the mis-interpretation (or lack of reading) what we had written in the manuscript. Several comments concern the manuscripts 'lack of explanation of X' or questions of why we did things the way we did. Most of the comments like this (not all mind you, some where decent comments) would not have been made by anyone that read the manuscript carefully. Some of the answers to the questions are given explicit explanations in the text. The reviewer's confuse words even though every word that had any possibility of mis-interpretation was defined in the text as well as in an appendix that included a glossary (as in any multidisciplinary field, word usage differs, so we are careful to make sure we clearly define our terms).

Overall these reviews were exceptionally poor and our manuscript was rejected. But all is not lost, as one can learn from all experiences. What I take out of this is the following: No matter how important, interesting, or solid one's results are, if the manuscript is not clear and simple it has the potential to be confusing to people who are not a part of your sub-discipline. Well - it is time to get back to revising this paper to get it out there for all y'all to read!

Northwest String Summit coming up!

2008-06-20T16:30:00.001-07:00

I just got my tickets for this year's Northwest String Summit. I am especially excited about the weekend because I had to miss Wintergrass because of research and Telluride (going on right now... ) because the folks organizing my high school reunion couldn't decide on a date...

I last went to the string summit in 2006 and it was one of the best weekends of my life. It is a beautiful location outside of Portland, OR, there are peacocks everywhere and some of the best music out there. There is always, of course, three full sets of music from the Yonder Mountain boys, A super jam of whoever is there led by Danny Barnes and lots of other great music. This year is going to feature Keller Williams, Strings for Industry, Bryn Davies and Sharon Gilchrist, Benny "Burle" Galloway and others (line-up here).

Looking to be a great weekend!

First Post - Where does D. melanogaster come from?

2008-06-20T10:41:00.000-07:00

For the first post, I will begin with a short statement of what I forsee for this blog. I am a graduate student in evolutionary ecology / genetics / development, and likely will have many science oriented blog posts. Though other tidbits are likely to show up here as well. I think that there are both selfish and altruistic reasons to have a blog. Selfishly, I think that writing more about science is going to help me to wrap my head around complex ideas, and really focus my thoughts. Altruistically, one of the most important, yet sadly neglected, aspects of science is communication with non-scientists. I hope that non-scientists as well as scientists will find my blog of interest.

Ok. On to the science.

I recently finished up an evolutionary physiology project using the workhorse of genetics - Drosophila melanogaster . I will begin by saying that one of the first things I told my PhD advisor when I arrived in graduate school was that there are only a few aspects of research that I did not want to pursue, and the first was that I really did not want to work with Drosophila thinking that most Drosophila research is of the type "Gene X binds with Gene Y under some highly unnatural condition". Turns out one of my projects has focused on highly adaptive traits in natural populations of melanogaster. Oh well, back to the science.

D. melanogaster is a cosmopolitan fruitfly - it is found in all biogeographic regions of the planet, and is one of only two species of the genus that has successfully colonized both tropical and temperate regions (the other speices is D. simulans - a close relative of melanogaster). D. melanogaster is highly commensal with humans, being transported all over the globe through modern commerce. Because of its relationship with humans, its likely high migration rate, and likely high rate of transient individuals, population genetic studies have been difficult. Therefore the biogeographic history of the species is not well worked out.

It is widely accepted that D. melanogaster originated in East Africa mainly due to two the fact that majority of closely related drosophilids are endemic to Africa, and most of the polymorphism in non-African populations of the species can be found in African populations. Migration patterns into Eurasia were likely ancient as the flies could move across land the whole way, whereas migration into the Americas and Australia seems to have happened with the arrival of humans with commerce in these locations on the order of several hundred years ago. Population genetic and Phylogeographic studies of non-African populations have been difficult due to the species' relationship with humans, its high level of global migration, and the recent colonization (< style="font-style: italic;">D. melanogaster into North America have been its first description on the continent in 1862 (in Cuba) and many later published reports of them throughout the Americas by the 1880s.

I am not sure if there is a better way to date the arrival of D. melanogaster into North America due to the complications of the population genetics within the species. For now we are just left with the descriptions at the end of the 19th century. Regardless, it is safe to say that D. melanogaster colonized the Americas in the recent past.

A test

2008-05-02T11:35:00.000-07:00

This is my first test post