Falling in love

I'm a sap, what can i say. I love adorable falling in love videos (and love that this one includes some of the frustrating times that make the love all the more worth it).

This is my life

Phil Collins for your morning enjoyment (?).

Congratulations to NSF Graduate Research Fellows!

I am so very happy for the awardees of the NSF Graduate Research Fellowship Program.

I was a NSF graduate research fellow at Penn State, working with Kateryna Makova, and have gladly taken opportunities to participate in panel discussions, and assisting individuals with their applications.

The credit certainly goes to these outstanding graduate students, but I am very happy to say that I contributed in a very small way to proof-reading and giving some tips to two recent NSF grfp awardees:











Melinda Yang was awarded the NSF grf last year,


and

Ruowang Li was warded the NSF grf this year!


Congratulations to both of them, and all of the other NSF grfp awardees!!

Culture Wars: What I'm taking home with me

What I'm taking home from the Catalysis meeting.

I recently attended a Catalysis meeting at the National Evolutionary Synthesis Center (NESCent) on Communicating Across the Culture Wars: Engaging Media on Evolution. The meeting consisted of people with very diverse perspectives on communicating science. In fact, as I think about it now, nearly everyone had a different niche, so I'll say that there were two board categories of journalists and scientists, with many overlapping shades in between including: academics, science writers, bloggers, science educators, political scientists, education researchers, public relations specialists, and more! I cannot express how much I appreciate the opportunity to interact with this outstanding group of people.

We were asked at the end of the three days to share what we had learned, and I found it an overwhelming task. I am still absorbing, sorting through, and integrating what I learned. But, I'd like to share my initial reactions, many of which I could not have ever predicted. I'll note that these are quite personal and unique to me, and cover much more than the conference intended.

1. I have a lot of interesting stories to tell. As a scientist, I find myself surrounded by very smart people, and focusing on the small corner of research that I have the time and interest to conduct. I go to conferences and learn about all of the wonderful research going on. I am constantly challenged to learn new things, and confronted by the wealth of information that I don't know of. But this conference reminded me of all that I do have to share. Holly Dunsworth said something very profound (that I'll mess up here) to the effect that scientists should realize how much we have to say that will be new (whether it is ground-breaking to scientists or not), and thus news, to the public.

2. Communicating science is an art. Literally. We should think in pictures, and analogies, and metaphors. Cara Santa Maria said, "never underestimate the intelligence of your audience, but underestimate their vocabulary". As difficult as it may be, finding visual or accessible references can dramatically improve communication about science. Ken Miller gave an amazingly simple analogy to explain the hubbub about the ENCODE project (which I'll share soon). I am inspired to develop analogies and find simple language for explaining my own science.

3. Opportunities to communicate science are waiting. I plan to seek out opportunities to share my research, and even to simply discuss science with journalists, from our Public Relations office, fostering relationships with journalists, and reaching out to our local communities. I plan to reach out to my home town newspaper (the Syracuse Journal Democrat... yes there is a Syracuse, Nebraska). Local papers are, as pointed out by Lou Dubose, starving for content. There was some debate about whether communicating science through a newspaper is a wasted effort because most people get their news via television and the internet. But, my anecdotal experience is that while people may not read the local town newspaper for the news, they do read it to find out gossip to share, and to stay in touch with one another. I would love it for science to become part of the small town discussion. Further, even local newspapers are now being published online, increasing their visibility and reach.

4. Blogging science isn't a science. To be an effective blogger of science, I need to let go (just a little) of my science-side. As a scientist, I never want to say something that is incorrect, or misleading. Nor do I want to be misinterpreted, or appear sloppy. But, I think blogging is about getting interesting material out, about starting a conversation (either on the blog, or by the reader sharing the information), and, indeed, entertainment. So, first, as Bora Zivkovic alluded to, blogs do not need to be painstakingly edited - this takes up time and results in fewer posts, and thus, fewer readers. Second, certainly the science should be accurate, but it doesn't need to be described in painful detail. Too much detail is distracting and turnoff many readers. The published manuscripts (which we can and should link to) are available for all the nitty gritty detail. 

As Brian Switek points out, not everyone should blog science, but everyone should try.

I'm so tired of hearing that all scientists should blog or use social media. NO THEY SHOULDN'T! Good for some, not for others #evocomm
— Brian Switek (@Laelaps) March 24, 2013

Holly Dunsworth goes into more detail about the role of social media in science today:  "This is where and what science is now".

5. I am critical, and opinionated, and stubborn. Okay, I guess I already knew that. But, I am uncomfortable interrupting other people, or speaking over them. One of the biggest divides I noticed between the participants was not between the journalists and the scientists. It was between those who dominated the spoken conversations, and those who communicated mainly through social media. Curiously, this  allowed two narratives to occur simultaneously, sometimes in parallel, and sometimes intersecting. Not only does social media offer new outlets for communicating, it simply opens the channels for communication. 

And, a couple very tangential points:

6. Work-life balance. I'm not sure the organizers could have planned it, but, for me, it was so... empowering, inspiring, comforting, to see the other active science moms and dads. I loved seeing adorable toothy grins during the break, and hearing stories about breastfeeding and college applications when walking to dinner. Even more, I appreciated that it wasn't the dominant part of the conversation, but it was just acknowledged as a part of who we are. All of the participants have their own extracurricular activities, and it was great to not feel singled-out that one of mine happens to have an opinion of her own and call me "mommy".

7. The internet can be a mean place for all. The parallel experiences shared by scientists who are Atheists and scientists who are Christians in a side conversation during one of the breaks was so refreshing. There was no yelling, no name-calling, no blaming. It was a very honest discussion of the very hurtful things that are spewed at people with both perspectives. I was surprised by how very sad I felt listening to (and feel now remembering) the terrible, unfounded, and inflammatory things that are said about scientists because of their world-views. But also impressed, and hopeful, with the respectful discussion.

--

I made connections at this meeting that I hope to maintain long after the meeting. I look forward to continuing discussions, and to working on the actionable items we discussed.  I will work on improving my own communications about science, and fostering relationships with the media. Oh, and getting back to research!

Science Writing Internships

I was talking to a colleague at lunch about the recent NESCent Catalysis meeting I attended on communicating science. He mentioned that his daughter is an undergraduate studying both Chemistry and English, and asked if there were any opportunities for science writing internships.

Well, yes there are! Here are a few I was able to collect.


Tips and suggestions from Nature on Science Writing internships:
http://blogs.nature.com/naturejobs/2013/01/28/getting-an-internship-in-science-journalism

Washington and Jefferson College lists several:
http://www.washjeff.edu/biology-department/search-internships/science-writingjournalism-internships

Here is one at Earth Magazine:
http://www.earthmagazine.org/article/earth-internship-opportunity

Here is one at Argonne National Lab:
http://www.anl.gov/news-room/2013-summer-science-writing-internship-undergraduates

And, not specific to science writing, but the Office of Biology Undergraduate Affairs at Brown has Summer Internship Database (external to Brown):
http://biology.brown.edu/bug/summer-internship-database

Happy Science Writing!

Communicating across the culture wars: Storified

Many thanks to Brian Switek for Storifying the tweets and electronic communications from the NESCent Catalysis meeting:

Reporting Across the Culture Wars: Engaging Media on Evolution

From March 22nd to March 24th, 2013, a working group of scientists, science writers, and other experts met at the National Evolutionary Synthesis Center in Raleigh, North Carolina to discuss the state of science in the media and how to improve communication between scientists and journalists.

The experts that assembled at NESCent this past week were a motley science communication crew .

 My thoughts will be coming soon.

Thoughts on an extremely ancient root of the human Y tree

I was recently interviewed by Alan Boyle at NBC to comment on: 

 An African American Paternal Lineage Adds an Extremely Ancient Root to the Human Y Chromosome Phylogenetic Tree 

Fernando L. Mendez, Thomas Krahn, Bonnie Schrack, Astrid-Maria Krahn, Krishna R. Veeramah, August E. Woerner, Forka Leypey Mathew Fomine, Neil Bradman, Mark G. Thomas, Tatiana M. Karafet and Michael F. Hammer

The American Journal of Human Genetics, 28 February 2013

doi:10.1016/j.ajhg.2013.02.002

I do think the paper is very exciting. The identification of a new Y lineage is always interesting, and this one appears to be very long-lived. However, after a more careful reading, and some thought, I am not sure I agree with the way the TMRCA (Time to the Most Recent Common Ancestor) of the Y chromosomes was computed. And the ancient TMRCA depends quite a bit on the TMRCA. I have written up my thoughts and submitted them to the American Journal of Human Genetics, AJHG. The AJHG has a pretty strict pre-print policy (emphasis is mine):

"Work intended for submission to AJHG, currently under consideration at AJHG, or in press at AJHG may not be discussed with the media before publication. Providing preprints, granting interviews, discussing data with members of the media, or participating in press conferences in advance of publication without prior approval from the AJHG editorial office may be grounds for rejection."

But, I have gotten permission from the editor to discuss my thoughts about the submitted manuscript with colleagues (and in blog form). I am sharing the full AJHG manuscript with Mendez, but want to summarize here: 

Mendez et al. identify a Y chromosome haplotype that has not been characterized before and, with more work, they determine that it is nearly identical to a small group of Y chromosomes from Cameroon. They also estimate the TMRCA for the Y haplotype phylogeny, including this new Y chromosome and find it to be at least twice as large as anyone else, and as noted by the authors themselves, this TMRCA is inconsistent with what is known in the human fossil record.  While the new Y haplotype does increase the diversity, and thus the TMRCA, the TMRCA calculation is extremely sensitive to the mutation rate used. Mendez et al. advocate for using a mutation rate from human pedigree data instead of from comparative genomics. They then derive a mutation for the human Y chromosome from the mutation rate estimated from autosomal pedigree data. The equation they use assumes a linear correlation between the mutation rate on the autosomes, and the mutation rate on the Y chromosome. 

The authors themselves note that the TMRCA they suggest is incompatible with the known human fossil record. I present a case in my response that: 1) it is not appropriate to assume a linear correlation between the mutation rate on the autosomes and the mutation rate on the Y chromosome; 2) the mutation rate Mendez et al. computed for the Y from autosomal data is an order of magnitude lower than the mutation rate that was measured for the Y chromosome from a pedigree analysis in 2009; 3) the resulting TMRCA is inconsistent with what is known about diversity on the mtDNA, autosomes and X chromosome. Further, our own research suggests that selection is acting to reduce diversity on the Y chromosome relative to the autosomes, X, and mtDNA, which would make an extremely high TMRCA on the Y even more incompatible with observed data. 

As such, I am curious why the mutation rate measured from Y chromosomes in a pedigree analysis was not used. I think the results would still be quite exciting and novel. Given what we expect to be strong purifying selection acting to reduce diversity on the Y, the same arguments, of ancient population structure or even archaic introgression may still apply to this unique Y haplotype. 

Cross-posted at the Neilsen Lab. Please direct your comments on this article there.

Natural selection reduced diversity on human Y chromosomes

We are officially in the ArXiv! Many thanks to Graham Coop for highlighting our paper over at Haldane's Sieve. 

Title:
Natural selection reduced diversity on human Y chromosomes

Authors:

Melissa A. Wilson Sayres, Kirk E. Lohmueller, and Rasmus Nielsen

Abstract:

The human Y chromosome exhibits surprisingly low levels of genetic diversity. This could result from neutral processes if the effective population size of males is reduced relative to females due to a higher variance in the number of offspring from males than from females. Alternatively, selection acting on new mutations, and affecting linked neutral sites, could reduce variability on the Y chromosome. Here, using genome-wide analyses of X, Y, autosomal and mitochondrial DNA, in combination with extensive population genetic simulations, we show that low observed Y chromosome variability is not consistent with a purely neutral model. Instead, we show that models of purifying selection are consistent with observed Y diversity. Further, the number of sites estimated to be under purifying selection greatly exceeds the number of Y-linked coding sites, suggesting the importance of the highly repetitive ampliconic regions. Because the functional significance of the ampliconic regions is poorly understood, our findings should motivate future research in this area.

We have submitted to PLoS Genetics, and I plan to present (as a talk or a poster) at SMBE 2013.

Cross-posted at the Nielsen Lab Blog.

Dinosaur alphabet

I was away this weekend at the NESCent Catalysis meeting: Reporting Across the Culture Wars Engaging Media on Evolution. I had the good fortune of meeting an amazing group of people, but was so very happy last night to come back to my sweet Little Bear (2 years, 3months), Little Brown Dog, and my husband.

Well, Little Bear decided while I was gone to tear down her alphabet (letters and pictures of animals) that hung on the back of our front door. It was perfect timing however, because Brian Switek is working his way through the #DinosaurAlphabet!

This week's article is: V is for Velafrons.

I wonder if Brian has thought about making a Dinosaur Alphabet poster for kids? I would definitely buy one (and might even volunteer to help put it together).

---------

As soon as I posted this, I switched back to twitter to see that, "yes!" the poster has definitely been thought about. 

Non-selective evolution activity by Holly Dunsworth

Speaking of the power of genetic drift, and the importance of teaching it:

This is a wonderful activity for teaching non-selective evolution, developed by Holly Dunsworth. The activity is hands-on (love!), visual, and engages the students to develop the content, then interpret it at the end.

Holly has a wonderful description about how "A strict selection perspective creates potential for societal harm". You should go read it, but I'd like to highlight:

"From this perspective it is all too easy to assign differential value, worth, or beauty to variation within and between species under the backing assumption that “Mother Nature” has “favored” one trait over another."

This articulates my concerns with a "selection" view of evolution.

I am excited to try this activity (hopefully soon).

Challenge: research in the 1000 most common words

Here is a list of the 1000 most commonly used words in the English language.

Check it out. See if you can explain your research in these 1000 words.

My try:

I study how things that are different between men and women change over time.

If you want to share, I'll add your descriptions here, so comment, or email me!

So, what do you think?

Should I devote this blog to science, science policy and teaching, and make a separate blog for nonscience/musings? Or keep them together?

Thoughts?

Chirp... chirp...

Teaching evolution: what should the focus be

Last week I went with a group of postdocs and grad students to teach a lesson on Phylogenetics to local high school freshman. I had the foresight to do a pre-assessment and post-assessment (those results will be coming soon), but I wanted to start by sharing how this experience made me think about how we introduce the concept of evolution.

During one of the breaks, I spoke with the students' teacher. I told him how, to me, one of the neatest things about studying evolution is understanding the tremendous effects of genetic drift. It amazes me that so much of the natural variation we observe within and across species is due simply to stochastic processes in the population. Selection doesn't need to enter the picture. It does, of course, most popularly through positive selection acting to increase the frequency of beneficial alleles, and also (and perhaps more often) through purifying selection acting to remove deleterious alleles, or through balancing selection to maintain a balance of alleles that might be harmful under some conditions and helpful under others. And, all of this natural selection can affect the frequency of linked neutral alleles.

But, a large proportion of natural variation doesn't result from natural selection. It can just accumulate and drift to high frequency or fixation through neutral processes. This could be as populations separate geographically from each other, or if one population experiences a severe reduction in size, or any number of scenarios that change the history of the population. How cool is that?!

Later the teacher went through their evolution lesson. I am, first of all, very excited that they have a whole unit on evolution. They spend several classes introducing the concept of natural selection, giving examples of different island populations of lizards adapting to their new environments, and learn to build phylogenetic trees using the physical features of the lizards, and then analyze DNA sequences from the lizards. Cool!

But, the whole lesson focused on the small part of evolution that is positive natural selection. Sure, positive selection is the cool kid on the block, but I think it would be very instructive, and perhaps even more convincing to also introduce purifying selection (because, hey, there are a lot of sequence/functions/features conserved across any chosen clade), and the awesomeness that is neutral evolution (because otherwise we're training students to look for zebras see function everywhere they look).

I guess I shouldn't be surprised by this when, at the NESCent Catalysis meeting today, very qualified evolutionary biologists suggested that one of the primary topics journalists should know about science is natural selection, and then gave a detailed example of positive selection acting on a population.

Maybe natural selection is a good place to start to introduce evolution. It is tangible, easy to understand, and, there are very accessible examples of positive selection.  But, there is so much more to evolution that positive selection. I hope educators can see the importance of reaching beyond positive selection.

tweet tweet: Reporting Across the Culture Wars

I'm live tweeting (@mwilsonsayres) today through Sunday from NESCent:

Reporting Across the Culture Wars: http://www.nescent.org/cal/calendar_detail.php?id=935

hashtag: #evocomm

A healthier whole.

In an opinion piece on CNN, Dean Ornis advocates for focusing on the prevention of diseases (and even reversal) through lifestyle choices rather than treatment.

First, I want to acknowledge that, yes, some healthy people do get sick, and we should also be concerned with the quality of our environment. And I think Ornis goes a *little* too far in saying that heart disease and Type II diabetes "are completely preventable", which can turn some people off. But, it still stands that the majority of medical maladies can be reversed by taking care of ourselves:

"What we eat, how we respond to stress, whether or not we smoke, how much we exercise, and how much love, intimacy and social support we have in our lives."

I would be thrilled to let scientists focus on finding the causes, and developing treatments for conditions that afflict relatively healthy people, instead of spending a disproportionately large amount of time and resources figuring out how to treat the symptoms of (largely) preventable ailments. 

I was struck by the statement that it isn't just our own habits, but also the "love, intimacy, and social support we have in our lives". Bad habits are easy to make, and hard to break. But it's so much easier to make a change when you know you are not alone. So, thank-you to everyone who has been my support. You are too numerous to list, but I'd like to recognize everyone who has ever shared about taking their first steps (quitting smoking, starting to get out and walk, avoiding that sweet/salty temptation), or about their big accomplishments (recuperating after an injury/surgery, finishing the race, reaching your own health goals), who have reminded me to bring my stress down with laughter (reveling in your indulgence of that donut, sharing the precious moments with your family, as well as your embarrassingly human moments),  and who have shared your love and kindness, physically, and digitally.  

You inspire me to be a healthier whole. 

Interviewed about the new Y lineage

It is going to take me a bit longer to finish my write-up, with some thoughtful comments on the manuscript, so I'll just say for now:
I was interviewed by NBC this afternoon, and the article is up already!

http://cosmiclog.nbcnews.com/_news/2013/03/05/17199580-african-americans-y-chromosome-sparks-shift-in-evolutionary-timetable

Scientists: changing the view

I recently attended a talk by a world-class male Scientist. He routinely publishes wonderful work in high quality journals, is excellent at communicating science to the public, and has won several awards for his research.

He began his talk by apologizing for not being able to participate more in a particular invited fellowship because he and his partner just had a baby (just a few months old, in addition to an older child), so he, understandably, is limiting his travel. He then proceeded to give an excellent talk.

I thoroughly enjoyed his presentation (did I mention he is phenomenal at communicating science?). I was also immensely impressed by the very tiny act of publicly recognizing his life outside of research. In the work-life balance, sometimes "life" comes before "work". In one sentence, he humanized himself, crushed conjectures that people who choose to have children are somehow not as dedicated to research, and highlighted the challenge of balancing one's family with taking advantage of all that a scientific career may offer.

Further, it was once and done. Unlike spending an hour on the subject, this was short and to the point, then got on with it. We all make sacrifices in our lives (both personal and professional). Let's acknowledge it (yes!) and move on.

Accomplishment

Today marks the first time I submitted a paper with a student! One of the students I am working with will be graduating at the end of the semester, so I asked her to write up a summary of her work, to submit to an undergraduate journal. Well, as of 2:57pm, it is submitted for consideration at the Berkeley Scientific Journal!

I am not familiar with the process of submitting to an undergraduate journal, and am very curious to see how it all works. The paper will still be peer-reviewed by two faculty members at Berkeley. Similar to traditional journals, it can be accepted, accepted with minor revision, accepted with major revision, or rejected. But, I am not sure what criteria they use to judge the submissions. The journal accepts papers from any scientific discipline, and also works under the assumption that the work is completed by undergraduates. 

Here are the title and abstract for our petite paper:

Title

Evolution of the phosphatase gene family across nematode worms and flies 

Abstract

Phosphatase genes have been shown to be involved in male meiosis in the nematode worm, Caenorhabditis elegans, and are expressed in the testis in the fruit fly, Drosophila melanogaster. However, the evolution of this multi-gene family among nematodes and flies had not previously been investigated. We conducted a phylogenetic analysis of all genes in the phosphatase gene family across nematodes and flies using sequences from a 6-way alignment of nematode worms and a 15-way alignment of insects, including 12 Drosophila species. We found that: 1) multiple alignments contain spurious alignments that should be filtered for quality control; 2) several gene sequences with incomplete open reading frames are highly conserved, so may actually be functional genes; and, 3) the phosphatase gene family appears to have expanded independently in the common ancestor of worms, and again in the common ancestor of flies (but not all insects). 

Wish us luck!