Summer is finally here

I missed a couple of days blogging this weekend, so here's a quick update:

Friday we helped some friends pack up for their move.

Saturday we had a lovely night out with friends' for a barbecue. Tons of great food, bocce ball, board games and delicious desserts!

Sunday we rented a canoe from Tussey Mountain Outfitters in Bellefonte, PA. Our friends came in their kayaks (and rented one more).

Central PA is really quite beautiful.


The canoe was good for a leisurely ride,


but I think a kayak would be a little easier to maneuver.


And, to round out the day, I made some banana bread:


Today, we went into work for awhile, took the dogs to the dog park - there weren't too many dogs there, so we came home made banana smoothies and took them for a long walk around the neighborhood.

NPR continues to enchant me

I only caught a little of this show, so I think I'll try to go listen to the podcast, but what I did year was worth sharing here:

"... being selfish bastards, we will go into the forest and shoot squirrels, and bring them home and make squirrel tea"

"if you don't believe in evolution, there are bags in the back you can put on your head and run around in"

Raj Patel, The Art of Democracy

As heard on Alternative Radio, on NPR.

Dessert tonight: homemade lemon cake

In an effort to continue to blog with some consistency (no matter how short!), tonight I'll tell you about dessert.

I haven't really been hungry for desserts lately - the hot weather kind of takes it out of me, and I just want a glass of cold water (or cold mint tea), but tonight I decided to make lemon cake.

Well, originally I was going to make chocolate chip cookies, but we had no chocolate chips, and being too lazy deciding to conserving natural resources, I opted for lemon cake instead.

Most of the recipes I found online are for lemon pound cake, or lemon bars, no light and fluffy lemon cake. So, deciding to Betty Crocker it up, here is my lemon cake recipe (would omit the oil for applesauce or yogurt, if I had any).

-- As a brief aside: This is one of the many times I wish the US were more like Denmark, or any other number of European countries, with a grocer within walking distance of nearly every house. But, I suppose if I could have easily walked to the store, I would be eating gooey delicious boring chocolate chip cookies instead of waiting for my new creation to emerge from the oven. --


Lemon Cake
1c unbleached flour
.5c wheat flour
1c sugar
2 eggs
1tsp vanilla
.5c skim milk
1.5Tbs lemon juice
1/3c oil
1tsp baking soda

Preheat oven to 350
Mix all ingredients
Pour into 8x8 glass pan
Bake for 30 min, or until toothpick comes out clean


Final verdict: It's a little sweet, but pretty good. If I made it again, I'd leave out a bit of the sugar.

Si tu savais

lyrics

Bonjour!

Je suis en forme. :)

I've decided to try to learn some French before my trip in July. My friend recommended Coffee Break French, and I have to say after only a day, it is tres bien (sorry for the lack of accents). There are 80 lessons, but I don't want to be overly-ambitious (considering I'm also trying to get some serious work done this summer). I think I can get through half of them before July 3. I changed my facebook to read in French - it may not be super-helpful, but will remind me to practice. And help me with reading, because I'm mainly listening to the podcasts.

In other news, we got our first CSA (Community Shared Agriculture) from Plowshare Produce yesterday - and added a fantastic loaf of kalamata olive bread (bread AND olives, in one?!... genius!!!). We were able to meet one of the farmers, Bethany. She was lovely.



Yesterday for dinner and today for lunch we had salads, and tonight I made an Rustic Potato soup (with hot chicken sausage instead of kielbasa, a large yellow onion instead of leeks and omitting the butter). It was fantastic.

good news and bad news

good news: Today is the first day of the Plowshare Produce pickup in State College:
"This Week’s Veggies: salad mix, spinach, kale, pea shoots, kohlrabi, hakurei turnips and/or radishes, maybe a little broccoli, asparagus (from Village Acres and just for Friday folks; Tuesday shareholders will get theirs next week!"

bad news: The oil spill is having a tremendous and destructive impact on the environment (pics here).



This week is shaping up to be a pretty busy week:

1. Prepare a presentation for Friday's lab meeting on the Neandertal genome paper:
A draft sequence of the Neandertal genome (Green et al, 2010)
Science 7 May 2010:
Vol. 328. no. 5979, pp. 710 - 722
DOI: 10.1126/science.1188021

2. Submit draft of Y overview to Nature Scitable.

3. Work on Male Mutation Bias manuscript, especially figures.

4. Work on Pseudogene project with undergrad (a. hashing out the procedure for her to follow, and b. computing the math for the Confidence Intervals).

5. Start drafting letters to potential postdoc advisors.

6. Put down some concrete ideas for NSF postdoctoral fellowship application.

7. Start assembling the program for National GWIS meeting.

8. Put together concepts for my guest lecture (Comparative Mammalian Sexuality) for the Tuesday June 15th class of Human Sexuality. It is going to be awesome, so you should all come!

you will do foolish things,

but do them with enthusiasm.

Sidonie Gabrielle Colette (b. Jan 28 1873, d. Aug 3, 1954, French Novelist)



She had an extraordinary and controversial life, considering when she was born.

I would like to read some of her work, but I wonder how well the material translates to English. I just bought a compilation of three short stores, "Gigi, Julie de Carneilha, and Chance Acquaintances: Three Short Novels". Although I won't be able to comment on the translation, I'll be sure to write about the stories themselves.

My two most foolish (and wonderful) acts this weekend:
1. driving to NY, spending less than 24 hrs and driving back
2. getting into an argument with a goose

Both were completely worth it. :)

Grégoire - "Toi + Moi"

Lyrics in French and English. :)

A different perspective on autism

This guy has a pretty unique perspective on autism. I don't know enough about the history of autism research to be entirely critical of his assessment, but I do think that there is a lot of room for new hypotheses.

He postulates that:

"A simple possibility would be that there is a fundamental problem in the interaction between the child and its parent, usually the mother. It has been known for many years that if this interaction is seriously disturbed - if you can't achieve what's called joint attention with your mother or care giver - then you don't learn to speak, you don't learn social skills, and you develop restricted interests and, not infrequently, repeated stereotypic movements."

But continues:

"Autism is the most genetic of the neuropsychiatric disorders. So the child seems genetically impaired in his or her ability to interact, and the question is what is the nature of the impairment. There are lots of ideas about this. One is that autistic children don't process faces normally, which interferes with their interactions with people. Another is that they don't have the special interest in biological as opposed to inanimate things that normal children have. And another idea is that they can't figure out what's going on in somebody else's mind - called mind blindness or a 'theory of mind problem'.

I think it is very unlikely that any of those are the primary problem. I think a more likely explanation is that there is a problem with attention - a particular type of attention problem. There's increasing evidence that these children have what's called sticky attention, which is a problem with attention disengagement. When autistic children are focused on something, it's very hard to disconnect them and get them to focus on something else. So shifting attention from one thing to another seems to be a problem."

My favorite part, however, is that he does reiterate that vaccinations are not linked to the development of autism:

"But there have been ten or more studies that show pretty unequivocally that vaccination is not involved in the autism spectrum disorders. One of the best was from Denmark, which showed that the prevalence increased about 15-fold from 1990 onwards, yet MMR was introduced in Denmark in the 1970s, and thermasol was removed in the 1990s with no apparent impact. So I think it's safe to say that vaccination is a red herring. Autism spectrum disorders are now recognized to be a fairly common condition, affecting almost 1% of children, and so there will be a substantial number of coincidences in which vaccination seems to trigger the condition."

Saturday is Harvey Milk Day!

State College will be celebrating with the following:

HARVEY MILK DAY EVENTS BRING AWARENESS TO LGBTQ EQUALITY:

Rally, March, and Film Viewing to be Held in Downtown State College on Saturday, May 22

Harvey Milk’s legacy as an advocate for LGBTQ equality will be commemorated in downtown State College on Saturday, May 22. The AIDS Project, Justice League –Activate!, Penn State LGBTA Student Resource Center, and RISE Advocacy will sponsor a rally, march, and film viewing. This is the only Harvey Milk Day event that will be held in Pennsylvania and will bring advocates from across the state to State College.

The rally will be held at the Municipal Building Plaza at 12:00pm. State College Mayor Elizabeth Goreham has issued a proclamation in recognition of the day and will present it at the rally. The rally will also feature musicians, speakers, and artwork.

A march through downtown State College will follow at 1:30pm. The march will make multiple stops at places of significance to allow individuals to share their stories, discuss discriminatory policies, and other issues of relevance.

University Baptist and Brethren Church, located at 411 S. Burrows St., will sponsor a viewing of the award winning documentary, The Times of Harvey Milk at 4:30pm. All events are free and open to the public.

In addition to the event, State College organizers plan to advocate for policy changes that will broaden the inclusivity of the State College Fair Housing Ordinance and Home Rule Charter non-discrimination statements. At a May 17, 2010 State College Borough Council Meeting, an event organizer detailed to the Council instances of bigotry in the process of collecting signatures from local businesses for the Application for Use of Public Property. Caryn Winters asserted, “Council, I assure you that this is a State College issue.”

Harvey Milk Day was designated by the California State Legislature in 2009. May 22, 2010 will be the first annual Harvey Milk Day commemoration.

Justice League –Activate! is a network of people headquartered in State College, PA advocating for civil rights and social justice for LBGTQ individuals and communities. To get involved, contact Audrey Smith at justiceleagueactivate@gmail.com

Happy Birthday!!!

The E. coli experiments in Richard Lenski's lab are now in their 50,000th generation!

If 75 days = 500 generations, then this experiment has been going on for over 20.5 years. Wow. This is spectacular.

E. coli are a wonderful model system because their generation time is so short that it allows us to observe evolution in action. From this we can make inferences about how evolution works in longer-lived species.

Some people choose not to accept observations, however. View the dialogue between Dr. Lenski and Mr. Schlafly. I think Dr. Lenski states the case for responding to creationists well:

"I offer this lengthy reply because I am an educator as well as a scientist. It is my sincere hope that some readers might learn something from this exchange, even if you do not."

At my poster presentation to the public (at the Graduate Exhibition), I am fairly confident one of my judges was a bigoted creationist, and another asked me, "How do you respond to creationists who approach you about your work?" My response, fitting after the previous judge, was that if someone approaches me, with ideas that are not founded in anything but their own desire to desperately believe them, there's not really any evidence I can provide that will convince her or him otherwise. It may be a side-step, but I try to focus on parts of the science where I can find common ground, if said person is honestly interested in the research, but find that it is not only useless, but counter-productive to try to teach the basic concepts of molecular evolution in a 5-minute conversation.

One of my favorite quotations was shared by my uncle with me:

"You can't reason out what wasn't reasoned in."

Quite true.

So, rock on E. coli, rock on.

Nature Scitable

I am in the process of writing an article for Nature Scitable about Y chromosome evolution (in between writing paper 2, researching paper 3, attending conferences and looking for postdocs).

I wanted to take the time, however, to point you to the Nature Scitable website, for example, this article on the Neutral Theory of Evolution by a scientist I recently met, Laurent Duret. It is an ever-growing collection of approachable science articles, written by primary researchers, aimed at high school and undergraduate students, but should be accessible to the general public. The concept, I think, is similar to Wikipedia, only the articles are peer-reviewed and supported by well-researched results.

Go have a browse!

Teach Evolution.

Courtesy of http://shorthand-hero.deviantart.com/gallery/

Difficult to catch an optical illusion

I am a huge proponent of encouraging skepticism among all people. Even so, optical illusions are still quite a lot of fun. This one is still challenging my brain a bit:

PJAS

The PJAS (Pennsylvania Junior Academy of Sciences) State competition was help today at Penn State, University Park. I've judged before and have always had a wonderful time (if your in State College, look for it next Spring!). This year I judged 9th grade Biology and 8th grade Physics. Both had some projects that were quite impressive for students just starting in the Sciences, although I'm sure they had some help from their parents/teachers/sponsors, in coming up with the ideas.

I met some parents, and some teachers.

One of the teachers, a middle school science teacher, was complaining about the state science standards, and how evolution is required on the Keystone standards and how she absolutely refuses to teach evolution to her middle school students. What!?! I couldn't let it go. I might have alluded to that attitude being self-defeating and cowardly, in so many words. What chance does Science education have if our teachers refuse to teach?

Her attitude was in contrast to the students we had just judged, one of whom referenced the evolutionary origins of the plants he was studying.

Moral of the day: Fourteen-year-olds may, at times, have more brains and guts than fourty-something inept middle school Science teachers.

Writing

I'm still having a little trouble finding a "niche" for my blog. Basically it is a random assortment of my thoughts, interspersed with music or news/science that I find interesting.

I like the concept of a blog more than social networking sites, like facebook. I am just throwing my thoughts out to the ether, and people are welcome to read, or not read, at their preference, whereas with facebook updating a status or adding photos or changing anything is automatically added to a feed that everyone is nearly compelled to at least glance at. Someone has to make some sort of effort to go to a blog (or add it to Google Reader).

Although I officially have five followers (thanks to those brave souls for publicly following), I'm sure there are others who peruse with some regularity - thanks to you too!

I'm always looking for suggestions for what to blog about, and am happy to start some discussion topics here - feel free to email me things you find interesting or relevant to the content I've posted previously.

One comment was to post more pictures - I'll do my best with that. To start with, here's a recent photo of the Makova Lab. Enjoy! :)

The Biology of Genomes

Just returned from Cold Spring Harbor, The Biology of Genomes.

I decided to sign up for twitter because of the benefit of being able to tweet thoughts and questions about the research during the sessions. Twitter was... inconsistent. I'm not sure that I will use twitter much outside of meetings, but I think it is a fantastic, and potentially very powerful tool to use during scientific meetings.

Hashtags can be used to collect the thoughts, comments and questions from the audience, and save them to be reviewed later. Discussion is facilitated, and potential collaborations introduced by shared interest that arises from comments during the seminars. Oftentimes there is only time for one or two questions after a presentation, but surely many, many more questions remain unanswered in the audience. Twitter, potentially, is a venue for some of these questions to be brought up and addressed.

Maybe Twitter isn't the best venue, because of its character restriction, and also because of its inconsistency, but it is a good start for now. The problem that I encountered with Twitter is that the "searchability" of my hashtags was very inconsistent. The first posts I tagged showed up in the feed, then the afternoon posts did not work. The next day again my hashtags showed up for only a few sessions, and then did not show up. I am still trying to figure out what the problem with the hashtags is, but in order for Twitter to be the useful tool it could be for conferences, it needs to be figured out.

The benefit of a character limit is that it ensures attendees won't be so easily distracted during the seminars; one can simply tweet as the thought arises, similar to taking notes (which I do on my laptop anyway). Only now these thoughts can be shared with the rest of the community.

If you'd like to see the comments from the meeting, search twitter for #bg2010. Some of my posts are there. :)

In preparation for SMBE

I'll be attending the SMBE (society for molecular biology and evolution) meeting in July. This year it will be in Lyon, France, so I figured I should start learning a little French - at least to show I'm trying. What better place to start than music. Not sure how I found it, but I really like this song (at least the melody). :)

CSH day two

Day two of the Biology of Genomes conference and I'm pretty exhausted. It runs from 9am-11:30pm, but I have to tack on an extra two hours before (to catch the bus and get breakfast) and hour afterwards (to catch the bus back to the hotel), so it's making for pretty long days.

Tonight and tomorrow morning I'm one of the people in charge of walking the microphone around. Should be good to start to recognize people, although I wish they would state their name and affiliation before asking a question. Should be a pretty good deal.

I've met a good deal of people already - wonderful scientists from all over. I met a fantastic Medical Dr/Researcher named Jim Wilson (like my grandpa!) who I took to right away. I'm hoping to keep in touch with some people after the conference, or at least meet up with them at other conferences.

I'm really looking forward to the talks tomorrow, and especially Friday morning. I'll likely blog more about the content tomorrow. Just getting ready for the evening session to start, but wanted to give a quick update.

morality

There is no such thing as absolute morality, it changes, as a culture evolves, and differs from culture to culture.

"The research suggests that intuitive judgments of right and wrong seem to operate independently of explicit religious commitments."

the incredible, edible, egg

Poor farming practices aside (I haven't gotten to that chapter of "Slaughterhouse" yet), there seems to always be debate about whether eggs are good for you or not.

Here is a pretty comprehensive collection of information about studies related to the egg. Basically it comes down to - everything in moderation - even eggs, are okay. :)

There are no miracle foods, not even the incredible, edible egg, but it has a lot of redeeming qualities.

what color is my skin?

I've sat on a lot of panels addressing diversity, working to increase diversity and tolerance, and assessing attitudes about diversity. One of my facebook friends posted this link today, and it got me thinking about an issue raised during these panels/meetings.

In the most recent discussion, the terms to distinguish based on ethnicity are "whites" and "people of color". Basically, Eastern-european descent and everybody else. I suppose, when dealing with diversity there has to be a description (hopefully relatively accurate) of each of the discriminated groups, but I don't really like the "people of color" classification, because everyone, except people with albinism, and other melanin-disorders, have melanin, and hence, color, in their melanocytes (skin cells). It seems just as divisive, and just as inaccurate, as saying "black", "yellow", and "red".

One solution would be to have a scale measuring the level of pigmentation, based on the melanin content in ones skin cells, say an average measurement of three locations on the body, using photographic technology. A problem with this would be that people tan, and the range for various ethnic groups overlaps. However, it would be a step closer in the right direction. Plus, we could have more than two classes - it could be measured on a continuum. Especially because there is evidence that even among different ethnic groups there is discrimination based on the relative darkness of skin. A measurement based on range of pigmentation would help discern this.

Another idea, with the advent of cheap, efficient, sequencing technology, is to run a very basic genotype of each person, say, when you go to get your photo id from the government (driver's license or whatnot), looking for markers indicating which ancestral populations lie in your genome, and each person could report the number of markers they have relative to each of the studied ancestral populations. This would be more accurate, but perhaps not always as effective for researchers, because some discrimination is based on what people see, and heritage is sometimes hidden in our genomes.

slacking a little

I've been slacking a bit writing here, so I thought I'd take a break to give an update on research.

I'm running some programs now that are taking for-ev-er! I got chided for using too much of the server space, so I've had to limit the number of jobs I submit to 1,000. I have 13,200 jobs that need to run, each job takes approximately 48 hours to run...that means with the new limitation imposed, it is going to take me quite some time to finally get to the results. Oh, and I have to run this whole scenario twice.

In the meantime, I am writing and testing some other programs, and will try to focus on writing the bulk of the paper. Then, hopefully, I'll just have to update it with the new results.

The next week is going to be pretty busy:

Saturday: Genetics Symposium

Monday: Take Aro to get neutered (he desperately needs it!)

Tue-Sat: Cold Spring Harbor, Biology of Genomes Conference

When I get back, I'm hoping to really start moving forward with my last project needed to finish before graduation.

I now have an estimated graduation time of late September/early October - Yay! I'm planning to meet some potential postdoc advisors at the conference next week, as well as the SMBE meeting in Lyon, in July.

Adventures in baking

I've given up caffeine the past couple of months, and yes that includes caffeine, so I've been working on finding other tasty drinks/sweets to take the place of caffeine-filled delicacies.

This is inspiring me to get back into cooking. I really enjoy cooking, not enough to devote an entire blog to it, but you'll definitely see food pop up here now and again. I haven't felt so great, so have slacked off of cooking for the past few weeks. Still feeling a little queasy, but in a mood to get back on the horse, as it were.

Yesterday I made some rockin' oatmeal raisin cookies (and chocolate chip oatmeal for Scott, who has not given up caffeine).

Today I'm making pizza (dough completely from scratch), cheesy potatoes, and testing out three kinds of bread: 1) italian spices, 2) raisin, 3) regular white bread.

The cheesy potatoes are something my mom used to make growing up and I loved them.

Here's the recipe I've worked out so far, with advice from my mom. I haven't done the calorie count, but as far as cheesy potatoes goes, they aren't terrible:

Melissa's cheesy potatoes:

4 medium potatoes, cleaned, skinned and diced

2 cups skim milk

2 tablespoons butter

1/4 cup flour

pepper to taste

shredded cheese of your choice (cheddar is good, but anything you like will work)

1. Boil diced potatoes until just fork tender, then drain and place in 8x8 glass oven-safe pan

2. In a separate pan make a roux of the flour and melted butter on medium low

3. Add 2 cups milk to the roux

4. Cook milk mixture until it thickens on medium

5. Add pepper to taste to the milk mixture (you can also add salt and garlic powder if you like)

6. Pour thickened milk mixture over potatoes (note potatoes will still be slightly firm, so will soak up additional liquid from the milk mixture)

7. Cover with aluminum foil and bake at 350F for 20 minutes

8. Uncover, top with shredded cheese and bake another 10 minutes, or until crispy on top (if you like it crispy)

And deliciousness!

Overcast evening

It's been raining on and off all day today (which I'm hoping the onions, radishes and snow peas I just planted will love!), the dogs are desperately trying to get my attention (because I forgot I laid a handful of treats on the bookcase and they now smell them), and I haven't posted for awhile.

Here's your smile for the day: http://www.mouthman.com/category_s/31.htm

In other news, I made some rockin' oatmeal chocolate chip cookies and oh-so-tasty oatmeal raisin cookies. Just trying not to devour them before the cool.

As a side note, Chip is now sitting on top of the folded down blanket that is laying on top of the GIANT pile of laundry, on the couch - he had to climb his way up there, but there was no way he was letting Aro have it... silly dogs.