Category Archives: Information

Breakend Orientation Guide

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A Brief Guide to Complex SV Orientations – a cartoon by Sage Wright – July 23, 2018

I don’t know about you, but sometimes in VCF files when I run into complex breakends and translocations, the formatting can get a little confusing. I made this handy cheatsheet that should hopefully help explain what’s going on should you come across these interesting structural variations.

Breakpoint Orientation Guide

 

Let me explain the table on the left side of this picture.. ±25 indicates the direction you should traverse the genome in order to gain sequence information about that particular region.

For example, if my VCF file said (This is taken directly from the VCFv4.3 documentation):

#CHROM POS ID REF ALT QUAL FILTER INFO

2 321681 bnd_W G G]17:198982] 6 PASS SVTYPE=BND

We would know that this is a +- orientation from the table shown in the picture above. If we wanted to get the 100 bp before the breakpoint on chr2, we would need to start from chr2:321681 and SUBTRACT 100 base pairs–so we would need the range of chr2:321681-321581.

If it were a -+ orientation, we would need to ADD 100 to the starting position. If this is confusing, consider this if we use the terms of  chrA and chrB. According to our VCF file, we are moving from chromosome 2 to chromosome 17. As shown beneath the table, the from chromosome is chrA, and the to chromosome is chrB.

If you have anymore questions regarding this concept, please let me know and I can try my best to answer your question. Or, if I’ve accidentally made an error in this chart, please let me know so I can fix it!

The VCF file format specification is another great resource if you want to try and understand this a bit better. However, it is heavy with jargon, which is why I tried to create this alternative. Regardless, I recommend reading it as it offers an additional reinforcement of these ideas in a way that might make more sense to you than my silly drawings. Cheers!

 

Gentle Giants

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A Brief Introduction to Redwood Forests – an essay by Sage Wright – July 12, 2018 

I write this essay already knowing that my words will not give this tree justice, because there are no words that can properly describe the majesty and grandeur of the coastal redwood. But first, if you don’t know what a redwood tree is, let’s back up and talk about a different tree first and make some comparisons before I go into any detail.

Alright. Take a look at that figure from Save the Redwoods League, just for a second. Most of us have heard of sequoias. Think about sequoias while I tell you that all of the following numbers and values are from a publication found on this webpage titled “The Three Redwoods”. Alright. Back to giant sequoias. They look something like this:

(Thanks Jim Bahn for this picture of General Sherman!)

That’s one big tree. And that’s not a joke– they are the widest and thickest trees, getting up to a 30 foot diameter. That’s a massive circumference, roughly 94.2 feet. That means if we wrap fifteen jump ropes that are as long as my husband is tall around that tree’s base, it still wouldn’t be able to enclose it. That’s gigantic. So obviously, sequoia trees get pretty tall. Seriously tall, hundreds of feet tall–the tallest trees ever, right? That would make sense–but no, that’s actually not true. We’re wrong there. Even though giant sequoias have the widest bases, they are not the tallest trees. I may have mislead you with that first figure, because here is what it actually looks like:

No, its the coast redwood that wins the award for the tallest tree in the world, even though it’s max diameter is about 4 feet shorter (26 feet), meaning that I only would need 13 husband-length jump ropes. So, I mean, a difference of two husband-length jump ropes seems fairly significant? Granted, these are maximum measurements, so we should expect that in a regular tree, the number of husband-length jump ropes might differ more dramatically.

But how much taller? That picture doesn’t really make them seem that much taller. But that’s because we’re comparing them to an apple tree. In actuality, they’re surprisingly almost 100 feet taller. The maximum height of a giant sequoia was about 314 feet. The corresponding listing for the coast redwood is to 379 feet or more. That’s right. We don’t know how tall these trees can get–they don’t seem to reach a “maximum height” (although Koch, et al., predicted in 2004 that a redwood tree maximum height would peak around 425 feet due to the theory of evapotranspiration). Not to mention redwood trees still seem to grow as much as a foot a year. Here’s one lovely tree, featuring a burl (which is a knobby growth which is full of bud tissue that stores and preserves the genetic code of the tree, so if anything untoward happens to the tree, the burl can sprout so the tree can continue to exist). Note just how tall this tree is.

Lots of scrolling, huh? It’s even more impressive in person. And I’ll guess that this could be a second-growth tree, because there are a lot of skinny trees surrounding it. Keep that in mind, as we’ll talk about the difference in old-growth and second-growth forests later, but it’s true– there are a ton of trees and measuring each and every one can get fairly difficult. How do we know which one is the tallest? And since the location of the tallest coast redwood tree, Hyperion, is not revealed as per long-standing botany traditions to protect important specimens, it’s not like we can all march out there with our rulers to find larger trees and start shouting out “Oi! This a-one’s a big tree, ova’ here mate!” and have our friends all yell out encouraging groans and then we carve our names into the tree’s side so everyone for all generations of time will know that we were there first so hah.

Um, yeah, no thanks. Botanists try to avoid that exact situation, which is why we will never actually know the actual location of the tallest and largest plants in the world. It’s to protect them–and for good reason (at least, that’s what I’ve read in numerous blog posts and the first fifty pages of a book by Richard Preston, and on this database that lists the tallest redwood trees).

These trees grow up on the California/Oregon coast, and they used to have a range of over 2,000,000 acres, but since these trees are so massive, early loggers thought they would be brilliant sources of income so they cut them all down. Currently, less than 40,000 acres remain of the original old-growth forest (though some claim that there are actually 110,000 acres left, but if you take a look at the map below, I think that’s a massive overestimation).

While that map is roughly seven years old, the only real difference between more current versions is that the original extent of the old-growth forests has expanded to reach toward Napa, CA, and is much more coastal north of Eureka, CA. Still, the range of the forest shies away from the western-most point that is north of Mendocino and south of Eureka, which is directly tied into how these trees obtain water. When you see maps that claim that western-most area had old-growth redwood trees, you can be sure that they were incorrect. This is due to the precise mechanisms needed to generate massive amounts of fog that enable the trees to obtain the hundreds of gallons of water necessary each day.

Because let’s be real here–we have trees hundreds and hundreds of feet tall. We’re talking trees that are at their maximum 68 husband-length jump ropes tall. And let’s not forget that trees are plants, and plants need water. And a 400 foot tree? It’s gonna need a lot of water. Typically, most plants get their water through their extensive root systems. You would think that a tree like the coastal redwood would have an extensive root system that burrows deep into the earth to get all of that necessary water, right?

Nope! Redwood trees don’t have a taproot. According to the National Park Service, redwood tree roots only extend about 10-13 feet into the ground (about 2 husband-length jump ropes). So this presents an interesting conundrum. These trees extend far into the sky, but have very little anchoring them to the ground. Wind is the second-greatest danger to these trees falling, right after logging. If you go visit the redwoods, you will undoubtedly see a fallen redwood.

But before a redwood falls, they obviously will need water. A paper published in 1998 suggested around 600 quarts of water are needed each day. That’s about 150 gallons. Or a 150 milk jugs, if you’d like. That much milk will definitely not fit in your fridge. The original old-growth forests typically had only 5-15 trees in an acre, which makes sense in order to accommodate their massive water needs. However, there wasn’t that much available ground water year round to accommodate all of the tree’s needs. The dry season in the summertime led to a reduction in ground water, due to the lack of rain and lower levels in the streams and creeks. So what do the trees do to make it through the dry season? They need to find alternative water sources, but it’s not like they can walk around to sit down at another spot. And so this is where the most beautiful part of redwood ecology comes into play. They survive because of fog.

That’s right, fog. The fog that is created from the nearby Pacific ocean flows inland and then condenses on the needles of these trees. The water falls onto the ground, and then that enables the tree to be able to use it to live. That’s why these trees can only live in a certain part on the Northwest coast. They need a place where the fog will be consistent enough to provide them with enough water to make it through the summertime.

T.E. Dawson, the author of that paper published in 1998, measured the amount of rainfall and the number of “fog days”– days where visibility was severely decreased and the fog typically lasted for greater than 12 hours. You can see this trend in Figure 1, below. Click on it to make it bigger and easier to look at.

But the pattern here is pretty easy to see: when the rain is low, the fog days increase. It explains the pattern. Fog is what is able to make these trees get enough water year round. It’s frankly incredible, in my opinion. Nature is so cool.

Now, I mentioned that old-growth forests have only 5-15 trees per acre, and that’s because they need sufficient water. These old-growth forests also have rich diversity on the forest floor, and have open spaces where light can reach the ground; it’s a proper functioning ecosystem. Second-growth forests face a different problem.

When logging was occurring, private planes and helicopters had planted thousands and thousands of Douglas-fir and redwood trees. They were crowded close together and competed heavily for light, making the forest floor dark, and with little room for secondary plants to grow. There were over a thousand trees per acre. That’s right–over a thousand trees per acre. But these trees aren’t meant to live like this–well, no living thing is really meant to live like that.

The NPS went about trying to restore these forest by thinning out the Douglas-fir trees. They called it “restoration thinning,” which sounds much nicer than “we’re cutting down more trees because we’ve got too many of them.” And really, what they’re doing is absolutely necessary. These forests aren’t healthy. If we want to try and restore some of the forests to their magnificent state before the logging craze, then we need to do everything we can, even if it sounds a little unintuitive.

Maintaining these environments, and these glorious trees, is absolutely necessary. My family has a yearly tradition where we go and camp in a redwood state park. We’ve been doing it since my mother was a kid, and we’ll be still doing it when my siblings have kids of their own. We love the redwood trees. There’s something just absolutely incredible about them that words cannot describe. If you have not been to the redwood forest, then it’s probably difficult to imagine the awe these trees inspire.

The whole forest holds such great memories for me. The nostalgic smell of the tanin-rich trees, the sounds of the birds and the creeks, the feel of walking on the forest floor’s duff. The redwoods are not just trees. They are a part of who I am. They are a sacred space to me. In the groves of gentle giants, I find hope. I find wisdom, I find passion. I find home.

—

Here is a list of book suggestions that may interest you if you want to learn more about the redwood forests or sequoia trees. It includes children’s books (fiction and non-fiction) in addition to adult non-fiction. I must admit, this book is adorable if you have a really tiny kid because it rhymes and talks about the tree ecology and it’s just wonderful.

You Don’t Stand Alone

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A Brief Look at Sexism in Science – an essay by Sage Wright – October 13, 2017

Image result for gender workforce science cartoon

Above comic from Getting more girls into science, technology, engineering and mathematics degree courses by Global Education Monitoring Report

You’d think I’d be used to being the only girl in all of my classes. Maybe at one point in my life, I was happy about it. I liked being the odd one out, having all of the attention from the boys, but that was back in middle school. I’m in graduate school now, and I no longer care about getting boys to like me (it might have something to do with being married), but I’m sad to say things really haven’t changed and that oftentimes I’m still the only girl. But things are looking up — 26% of the graduate students in the Bioinformatics and Genomics program at Penn State are girls, 9 out of 34. Not to mention that 20% of the Fall 2017 cohort was female: 1 out of 5 (that’s me!).

I can’t help but admit that I find it shameful that I say that 26% is looking up. Because it shouldn’t be. There should not be such a massive underrepresentation of women in science. But it’s obvious and true, and the data clearly shows it. I’m not going to beat around the bush and whine about how it’s not fair and hopefully get straight to the point I’m trying to make.

This can’t continue to happen. Women need to be equally represented in STEM fields.

I’m in Bioinformatics — an interesting combination of both the computer science and biology fields. And there’s a spectrum–some individuals are strictly computational, and others are more analytical, dealing more with the biology. For the sake of this essay, I’ll report statistics for both biology and computer science; or, when available, interdisciplinary sciences.

According to Scientific American, 26% of PhDs in computer and mathematical sciences were awarded to women. 45% of PhDs in physical and biological sciences were awarded to women. But before you say that those numbers aren’t a good representation of all women in the United States, I will mention that 61% of non-science PhDs were awarded to women. And that’s not what I’m even concerned about.

It’s not that women aren’t obtaining PhDs, it’s that there are so few women in STEM fields. And I strongly believe that it is not due to “lack of women interest.” It’s because our society has been so strictly immersed in a sexist society that if some women aspire to a higher degree than her Bachelor’s, she will have no support. Her family will convince her to settle down instead, and that she should find a nice man to take care of her, and that her talents are better suited elsewhere. I’m not saying that this is the case for everyone–but I know too many women personally that have had to give up their dreams of a PhD because of societal expectations.

I’m one of the lucky few. I’m married–and I honestly felt that my husband wanted me to go to graduate school more than I did (which was a lot, don’t get me wrong). He was so supportive, and it’s because of his influence that I’m even able to do it. But we have a unique situation. We don’t subscribe to traditional gender roles. He does the laundry and dishes, while I bring home the big bucks so we can buy food and really comfortable sweaters. Although granted, that’s mostly due to the fact that I get a stipend in graduate school and medical school tends to steal your money right out of thin air.

My husband supports me, and wants me to achieve my educational dreams. And I’ve certainly dreamt about getting a PhD–since 6th grade, actually, when I was enrolled in a part-time STEM school program. Our principal was a woman, and she had a PhD. She also wore killer heels that terrified all of us because whenever she came walking down the hallways we knew and we scrambled to make sure we behaved. And I’ve come full circle. I was the only girl in my class, and I looked up to our principal. She was absolutely inspirational, and her story about obtaining her PhD thrilled me. Orientation day, and she was told to look to the person on her left, and then to the person on her right. “Neither of those people are going to be here at the end.” And she remembered being panicked, because she was on his left and her right, and she really wanted to finish the program. She had drive, determination, and guts. She was my inspiration, and every since 6th grade, I wanted to be like her. I didn’t even really know what a PhD meant when I was that young, but it didn’t matter to me. I wanted it, so I could walk down hallways in high heels and scare those annoying boys into obedience.

Now I want it for different reasons. But seeing a women in science inspired me to go to science. At school, all the girls were part of a “buddy” system where we corresponded with women at the local IBM. I was painfully shy, and probably disappointed my buddy horribly, but the experience kept with me. I could grow up and be like one of these women. Maybe I could have a 6th grade buddy, who I could hopefully inspire to go into science.

According to information from the NSF, it was reported that in 2012 only 3,067 women were part of interdisciplinary graduate programs. In 2015, that number increased to 3,922.

But women earn 57% of undergraduate degrees— no one can deny that women want education. While some might say that women just don’t want to work in the “more difficult” fields, that’s simply not true. Resources are not available for women who want to go into those fields. And when they do, they face tremendous discrimination. Especially in computer science. I have never had a female computer science professor. I couldn’t have even if I tried–there wasn’t a single woman professor in the computer science department at my university.

Some of my most painful memories involve my jobs as a teaching assistant for computer science classes. I was immensely qualified for the job–having achieved nearly perfect grades for both classes. But it would happen when someone came in to ask a question, realize that it was a woman instead of a man, and then proceed to immediately demean me with their body language, basically telling me that I didn’t really know what I was talking about, and that I couldn’t possibly understand their problems.

Going to computer science TAs on my own time resulted in similar situations. I had to mentally prepare myself for every occasion, by carefully formulated a very specific question instead of going in for general guidance (because otherwise they’d be rude to me and make me feel uncomfortable). I would go up to them, wait my turn politely, then say something along the lines of “I’m having difficulties in the algorithm for transversing the sphere in a counter-clockwise direction. I walked through the situation in the debugger, and couldn’t find any issues in my calculations. I looked up the question on Stack Overflow, but what they suggested didn’t work. I even tried changing the signs of all comparisons. What do you suggest? Can I walk you through my algorithm so you can help point me in the right direction to find what I missed?”

It was honestly absurd. The guys in the class could just go up to them, shove their computers at the TAs faces and blurt out that it just “doesn’t work,” and then the TA would respond to them like they were a normal human being not an idiot–which was how they treated every woman. The other women in my computer science classes had similar experiences. We would often group up together to work on problems together outside of class to spare us the pain of going to see TAs.

So even if a woman manages to get through her undergraduate in the sexist STEM world we live in, the next hurdle is trying to explain her research interests to her interviewers in industry jobs or graduate schools. And if she manages to get into graduate school, she has an uphill battle trying to get funding and recognition. She struggles to get published.

According to a paper published in Nature in 2013, “Globally, women account for fewer than 30% of fractionalized authorships, whereas men represent slightly more than 70%.” In the United States, the female-to-male relationship (where numbers closer to 0 represent higher male representation) is 0.428–the lowest of the three North American countries (although Mexico and Canada aren’t much better at 0.508 and 0.459, respectively). Paper’s authored by women are also cited less than papers with men as primary authors.

But take a look at one of the most revolutionary breakthroughs of the decade: CRISPR-Cas9. Pioneered by a group of people, but most importantly a woman named Jennifer Doudna. In case you missed it (though I seriously doubt you have), CRISPR-Cas9 is a technology that allows for rapid and easy genome editing. The amount of searches related to CRISPR has skyrocketed in recent years (see the Google Trends results for yourself). Thank you, Jennifer. A woman was one of the primary driving forces behind such monumental technology that has already changed our world.

Now, imagine if women weren’t in science. Imagine the world without Marie Curie (who won two Nobel Prizes (Physics and then Chemistry), something accomplished by only three other people–excuse me, men). Marie was influential, and inspired her daughter, Irène Joliot-Curie to win a Nobel Prize in Chemistry as well. Now try to imagine the word without Rosalind Franklin. We can pretend all we want that Watson and Crick were the actual discoverers of DNA structure, but they really just stole Rosalind’s work and took all the credit. She really does not get the credit she deserves. Like most women in science. Who here has heard of Maria Goeppert-Mayer? She proposed the nuclear shell model — the idea that electrons inhabit different spaces around the nucleus due to differing energy medals. That won her the second–and last–Nobel Prize in Physics awarded to a woman.

Women have been awarded a Nobel Laurette only 5.2% of the time. That’s only 44 women. Over 116 years, only 44 women have been awarded the prize. 36% of the 44 women won the Nobel Peace Prize award. Only 4 in Chemistry. Only 2 in Physics.

Now I don’t know about you, but I know for certain that women do not take up only 5.2% of the population. As of 2016, it’s something more like 49.56%. In the United States, though, it’s 50.5%. That’s more than half. And worldwide, only 5.2% of the Nobel Prize–the most prestigious award around, really–winners have been female.

Something seems off there. This isn’t just about science. This is about everything. Women have been constantly underrepresented in governments, religions, occupations, Nobel Prize winners. You name it.

But the problem here is that most women do nothing to stop this. We just let it happen. I’ve just let it happen. The only reason why I’ve been able to go so far in my career is because of a supportive husband. If he didn’t want me to, I probably wouldn’t have put up a fight, and would have lived with regret for the rest of my life. Because I was taught as a young girl, that I need to obey the authority figures, who were usually men. I was taught to obey men. I was taught in church that my purpose in life was to get married, have lots of babies, and be a homemaker. I was told that I had great “child-bearing” hips when I was twelve. And then I was trained as a teenager to fear men, to walk a little faster when you’re alone and a man is loitering on the side of the street, to not get in fights, to not flip men off in fear of retaliation. I learned as a young women that men will just use you, and then throw you aside once they’ve had their fill. It’s been engrained in me since I was an infant, when I was given a baby doll to take care of. Women are raised to become mothers.

The majority of women who are not working claim that it’s because of family, and the trend is especially prominent in Asian women (38.7% of responses, higher than any other). Note that in this figure, respondents were able to pick more than one option. And I guarantee that most all women also selected “Retired” as a reason, instead of just only putting “Family.” Family nearly always ranked last for men (in underrepresented minorities, family was 11.5% of responses and layoff was 11.1%), no matter the ethnicity. Women are pressured to take care of the family. Women are called bad mothers for putting their child in childcare–which is an insult that strikes most people deep, since that’s what we were raised for, wasn’t it?

I know that this isn’t the case for all women, and I’m glad if you don’t fall into these generalizations I’ve been spewing. But this is the case for a lot of women. And it’s just plain wrong. Women are just as smart as men. We have always been that way, and we always will be. Men are not better than us. We are equals. But until we do something about it, we might as well not be.

Some steps we can take involve increasing outreach to women who may be interested in science. More “buddy” programs like the one I was in all those years ago, perhaps. Volunteer in schools. Fund women in science initiatives. Maybe convince your university to become a partner of the Association of Women in Science. March for Science. March for Women’s Rights. Tutor young girls in science. Run an after school coding camp. Teach our children, or our friend’s children, or our neighbor’s children, that just because you don’t pee the same way doesn’t mean you’re worth any less.

Let me know about your experiences as a woman in science, or about other ways we can contribute to helping other women join STEM fields in the comments or in an email.

But before you do anything, take a look at some of these sources for yourself. Don’t let me just spew numbers at you–find out for yourself. After all, we’re scientists.

Global Gender Disparities in Science Interactive Figures

Women in Science and Engineering Statistics

NSF’s 2017 Women, Minorities, and Persons with Disabilities in Science and Engineering Report

Scientific American’s How Nations Fare in PhDs by Sex

Women in STEM – 2014 in Review

Above comic by Eric Mills in Witnessed

Note: I initially wrote this on October 14, 2017. It is over nine months later. I have not updated any of the numbers of values written here, or looked at hardly any additional sources (save for the addition of the two comics that I found to be relevant), but I think that the information presented continues to be true.

Insert Profound Quote Here

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Welcome to the blog portion of this website! This is the area where I post short impromptu essays about various topics related to science, music, or anything else that inspires me to write–which may/will cover a very wide array of topics.

All posts will have relevant tags so you can sort through the essays in order to find which will best suit your interest. That search function is still under construction as I rarely spend time working on the functional portion of this website. Regardless, all of the topics presented are in my opinion great conversations that I would love you have with you. Please advance through the posts by using the upper right hand arrows.

And a final public announcement: I am likely going to be very slow to get new posts out as I try and make sure that they have at least some reputable sources from newspapers or scientific articles, and I usually only spend about ten minutes at a time working on these essays as that’s usually how long it takes for a program to run. You get the drill. I am open to requests on particular topics, but I doubt I have any interesting opinions so that will likely never happen. We shall see.