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The Brachistochrone Curve

We’ve always been told that the fastest way from point A to point B is a straight line, right? Well, as it turns out, this isn’t always true! If the concept is considered in three dimensions – such as when a ball is rolling down a hill – the fastest way is actually a curve.

Say what?

I’d never heard of a brachistochrone curve before, and to be honest I can barely pronounce it. The name comes from the Greek words for “shortest time,” referring to a really cool property of this shape. Namely, that a ball rolled down this type of curve will reach the end faster than any other type of slope… including a straight line.

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In fact, the straight line is the SLOWEST path from point A to point B

 

I realize that computer generated models are not the most convincing – so let’s check it out in real life courtesy of Vsauce and Adam Savage, of MythBusters.

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Full video here

It’s not even a close race – the brachistochrone curve CLEARLY wins! So what the heck is happening? First, let’s define the geometry of the shape. A brachistochrone curve is drawn by tracing the rim of a rolling circle, like so:

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As it turns out, this shape provides the perfect combination of acceleration by gravity and distance to the target. The steep slope at the top of the ramp allows the object to pick up speed, while keeping the distance moderate. There is a necessary trade off between the two variables… the shortest distance (the straight line) also has the least amount of acceleration. Alternatively, the fastest acceleration (the extreme curve) also has the longest distance. The brachistochrone curve is the baby bear – it’s juuuuust right.

BUT WAIT – THERE’S MORE!

This curve has a super amazing bonus feature – it’s also a tautochrone curve, meaning “same time.” An object released at any point on the curve will take exactly the same amount of time to reach the end… no matter if it starts at the very tippy top, in the middle, or near the bottom.

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(forgiving slight variation by human error and friction)

It’s almost as if they’re waiting for each other! But really it’s just physics at work.

I find this relationship between the radius of a circle and the properties of motion to be SO ELEGANT! The simplicity of their demonstration is perfect, and I’m happy to say that I learned something new today.

🙂

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What is Genome Sequencing?

In one of my recent posts, I talked about personalized medicine and how genomics will likely become standard medical practice one day, so this seemed like a great time to discuss what the term “genome sequencing” means. In my next post, I’ll go even deeper and describe something called next generation sequencing (NGS), but first, let’s cover what the genome is, why it’s important, and why we would want to sequence it.

1. What is a genome? The genome is the complete set of genetic material or genes present in an organism. It’s made of DNA, and pretty much all of your cells have a full copy of it. You inherited your genome from your parents – so you can thank them for your unique combination of traits – like eye color, hair color, height, complexion, propensity to grow weird body hair, etc.

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“Gene Girls”

2. What is a gene? It’s a small region of the genome that encodes a protein. The gene acts like a blueprint and tells the cell how to synthesize that specific protein from scratch. All of your cells require proteins to survive, so these genetic blueprints are VERY important. Without proteins, your cells die (and so do you).

3. What makes up a gene? Your entire genome is made of only four chemicals, called nucleotides. They are cytosine (C), guanine (G), adenine (A), and thymine (T). These four chemicals link end to end in a specific order to “spell out” the blueprints for a protein. Just like the letters in this sentence, order is crucial for you to understand the meaning. For example… SANTA and SATAN use the same letters, but the slight differences have a big impact on meaning.

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You can see why typos would be easy…

4. What is “sequencing?” This term means reading the order of the nucleotides in a gene, just like reading a book. Like a really boring book that only uses 4 letters. Sequencing can be on a small scale (single gene) or on a large scale (whole genome). For reference, the human genome has ~3 billion nucleotides.

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That’s more than the number of Gangnam Style views on YouTube

Okay so now that we’ve got the basic terms, let’s talk about why sequencing the genome is so rad. First of all, it’s pretty new to us. We only finished the Human Genome Project in 2003. At the time, this was an ENORMOUS amount of work – in fact it took 13 years to complete – and it’s paved the way to new advancements in fields like molecular medicine, evolution, forensics, and so much more. And in recent years, new developments have dramatically decreased cost, making this tech more accessible to the scientific world.

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In 2007, traditional “Sanger” sequencing was replaced by “Next Generation” sequencing – causing prices to plummet. More on Next Gen in my next post!

So why should you care about genome sequencing? Well, some diseases are caused by known genetic mutations, or changes in the DNA code. Sometimes they are large changes, like the deletion or rearrangement of entire genes… and sometimes they’re nothing more than a single nucleotide “typo.” We’ve been able to pinpoint the genetic mutations that cause many genetic mutations, like Huntington’s, Cystic fibrosis, Sickle cell anemia, color blindness, and some forms of cancer. But there are many, MANY more that have not yet been discovered. Easy, cheap access to genome sequencing will help researchers unlock more of these genetic mysteries.

Currently, we don’t have the technology to “fix” DNA mutations in living humans, but understanding the root of genetic disorders will allow researchers to develop these types of cures. It may seem like science fiction, but scientists have actually been working on gene therapy methods for years. With access to cheap, reliable genome sequencing these efforts will be accelerated – and medical science will certainly benefit! Now we just need servers that can handle the tsunami of data we’re going to generate…

 

CRISPR

I just saw this incredible video about the inevitable future controversies of CRISPR gene editing. I really like how they blend science, technology, and society – and humor! – so I wanted to share it with you guys.

Listen, this technology is going to affect all of our lives someday. And sometimes technologies this powerful can seem scary, because with great power comes great responsibility. So that’s why educating ourselves about how these technologies work, what they’re capable of doing, and how they’re being regulated is the most important thing we can do!

So check out the video, learn about the light and dark sides of this amazing science, and empower yourself to bridge the gap between science and society.

If you like this video, check out more by Kurzgesagt, here! #knowledgeispower

Personalized Medicine

As medical science marches forward, the prospect of personalized medicine becomes more exciting than ever. The basis is simple – treat patients according to their specific disease, drug sensitivities, and genetic makeup. Different diagnostic tools are used to determine the unique needs of each patient, allowing doctors to select appropriate treatment regimens with less guesswork.

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“lol pick one” – Morpheus

It sounds like kind of a “duh” thing, right? Well, that’s because it is. In fact, the concept of personalized medicine dates all the way back to Hippocrates, who assessed the four “humors” of blood, phlegm, yellow bile, and black bile to determine the best course of action for his patients. The idea was revolutionary, but medical technology just wasn’t ready to execute it effectively. (Obviously).

Now, because we live in the FUTURE, we use something called genome sequencing to analyze the unique genetic makeup of a patient. This provides us with information about their DNA – which can be immensely helpful in detecting and treating disease. Perhaps more importantly, it can actually help prevent disease by identifying risk factors in each patient. And since your genome is more or less static, most people would only need to have it done once. Their sequence could be referenced later if they develop a new disease, become resistant to a drug, or are being considered for new drug treatments.

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Cheers to that

Cancer is the perfect poster child for personalized medicine. One of the most prominent examples is a hereditary form of breast cancer caused by mutations in the BRCA1 and BRCA2 genes that predispose women to high risk of breast and ovarian cancer. Genome sequencing allows for early detection, proactive disease prevention, and diligent screening regimens. In addition, about 20-30% of breast cancer patients have mutations causing over-expression of the protein HER2. This *specific* type of cancer can be effectively treated with a drug called Trastuzumab. Therefore, genome sequencing helps doctors know whether Trastuzumab treatment is worthwhile, or if they need to proceed directly to other options.

Cancer is a huge example, but by no means the only kind of disease that would benefit from personalized medicine. Identifying risk factors associated with cardiovascular disease and hypertension can help people make smarter lifestyle choices. Antidepressant dosages can be honed based on an individual’s response, metabolism, and adverse reactions to specific drug combinations. Aging diseases like Alzheimer’s and Parkinson’s could be detected earlier, and early intervention could postpone onset, improve quality of life, and perhaps even extend lifespan. I should mention that it’s not a silver bullet, though. Just knowing the sequence of your genes doesn’t mean we know how to cure everything – but more on that in my next post. Which I know you’re all dying for because you are amazing humanoids who loves swear words and knowledge, just like me. 😉

But I digress. Anyway – overall, personalized medicine sounds like a slam dunk. Right? Well… kinda.

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Not only would widespread application of personalized medicine be crazy expensive, it would also be controversial. First of all, although sequencing technology becomes faster and cheaper every day, it’s still hella pricey. I don’t know about you, but my itemized medical bills are more ridiculous than a Ticketmaster checkout these days. I swear there are fees for other fees – and a service charge for the person who compiled the fees. Something like genome sequencing, which actually DOES cost of a lot of money, would generate thousands of dollars in bills that neither the patient nor the insurance company want to pick up.

Which leads me to the next, sorta conspiracy-theory problem – fear of insurance discrimination. If a person has certain genetic predispositions or risk factors, could insurance companies choose not to cover them? Would their premiums be higher because they’re “riskier” clients? Theoretically this is illegal, but there will be a big grey area until regulations and legislation can be nailed down. Also, how can we ensure confidentiality and privacy for a person’s genetic code? The data files will be so large, they’ll have to be stored in this “cloud” thing everyone keeps talking about – aka the internet – aka the safest place ever.

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Heh.

Of course I would love to say that all of this is phooey nonsense, but we have to face the realities if we want personalized medicine to work. Like almost all revolutionary technology, genome sequencing is a double edged sword. Glorious access to our unique genetic information can be used for good (medicine) or for evil (discrimination). Just like splitting atoms creates access to cheap, clean energy, it also makes bombs. If Spiderman has taught me ANYTHING, it’s that with great power comes great responsibility. But I think the benefits of personalized medicine are going to far outweigh the risks, which is why scientists are striving so hard to make this happen.

But yes – routine genome sequencing will be a reality someday, which is amazing because scientists will be able to use that wealth of information to discover new cures, develop new drugs, and learn more about how diseases happen. Knowledge is power! It’s a really freaking cool time to be alive, guys.

Impostor Syndrome

In this post, I want to talk about the fun little bag of emotions called Impostor Syndrome. I’m willing to bet that many of you have experienced this phenomenon, even if you didn’t realize it had a name.

I was a first year grad student when I learned about Impostor Syndrome. Overwhelmed with my new environment and surrounded by people who seemed to know WAY more than me, I worried constantly that someone would “find me out.” It honestly felt like I’d been accepted to the program by accident. Had a drunk intern at the admissions office accidentally dropped my application into the “accepted” pile? Even though I was doing as well as my peers, these nagging feelings wouldn’t go away… so I just pretended to know what I was doing and hoped no one would realize I was a fraud.

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Life as a young grad student

So if you’ve ever felt this way in the past, or if you’re currently feeling this way, fear not. You’re normal! Depending on your personality, it might be something you experience for your entire life (lol join the club).

So what is Impostor Syndrome? Well first of all, it’s not actually a “syndrome,” because it doesn’t meet the qualifications to be a mental illness. It’s just a catchy name that was coined by clinical psychologists Dr. Pauline R. Clance and Suzanne A. Imes back in the 1970s. They recognized that many high-achieving, highly successful females were unable to internalize their accomplishments. Instead, these women would attribute their success to luck rather than merit. They experienced fraudulent feelings and often expressed concern that someone would soon discover they were incompetent.

Although the initial research was focused on females, we now know that men experience “impostor” feelings just as frequently as women. Interestingly, men were more likely to report these feelings when the surveys were given anonymously, suggesting there are unique social pressures on the male sex to appear confident and competent.

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You don’t say…

This chronic self-doubt is different than low self-esteem, because people who experience Imposter Syndrome don’t necessarily feel bad about themselves. Rather, they discount their successes as luck, or feel they somehow hoodwinked everyone into believing they were qualified. It’s extremely common in graduate students, who have to meet high achievement standards that are both extrinsically and intrinsically set for them. It’s compounded by the fact that many people pursuing higher degrees have been labeled as “the smart one” since they were very young, so they feel pressure to live up to that standard.

So if you’re sitting there reading this frankly illuminating blog and thinking, “Gosh! That sounds like me!” – then let me assure you that you aren’t alone. Research shows that at least 70% of people have “Impostor” feelings at some point in life. Often it is in a professional setting, but it can happen in pretty much any scenario. Once recognized, it can also be managed. This little graph provides a nice illustration of perception vs. reality when it comes to Impostor Syndrome:

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The people around you are always going to know things that you don’t know. But don’t forget that it goes both ways – YOU know lots of things THEY don’t know either. The smaller the overlap between your Venn diagrams, the bigger your “impostor” feelings might seem, but rest assured that there’s a good chance the others are feeling the same way about you.

Impostor Syndrome can be very common when starting a new job, being promoted, joining a new social network, etc. If something like this ever triggers Imposter Syndrome for you, try to remember that everyone has to start somewhere. Just because you’re new to the game doesn’t mean your unqualified. And no matter the situation, never let these feelings convince you that your success happened by accident!

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Flailing my way into industry

As I mentioned in an earlier post, I decided after grad school that I no longer wanted to pursue a career in academic science. Don’t get me wrong, I have nothing but respect for tenure-track professors. The job is incredibly demanding – they have to secure grants, train grad students and postdocs, publish papers, and teach courses to snotty nosed undergrads. And they have to possess a special kind of personality, passion, and ability to focus on unraveling a particular scientific mystery for years. 

I knew that lifestyle wasn’t a perfect fit for me, so I wanted to explore other options. The problem was, I honestly had no idea what careers even EXISTED for someone with my training. There was only one career path that had ever been laid out for me: PhD > postdoc > professor. Anything that strayed from this path was considered an “alternative career.” WHICH IS STUPID – because according to the 2012 NIH Workforce survey only 8% of people entering PhD programs will end up as tenure-track professors.

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If you’re a PhD student and like crying yourself to sleep, click here to see an enlarged version

The persistent stigma around leaving academic science is baffling to me. Times have changed, and what used to be the most prominent career path simply isn’t anymore. It’s not a big deal, except some people in academia still make it one. As a student, I actually heard people say that taking a career in biotech was akin to “selling your soul to the devil.” It’s a weird combination of upholding an outdated tradition and shaming people into a certain career path – one that mathematically cannot hold the volume of PhDs that are currently graduating.

So if the majority of us don’t end up in tenure-track faculty jobs, why the hell are the other career choices considered “alternative?” And why don’t we provide tools and resources to help people succeed after earning their degree, no matter what direction they choose? Why are we setting all these poor (literally poor) graduate students up for failure? It doesn’t make any sense to me!

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So when I graduated, I had no professional guidance or career development training for a job in biotech. Nonetheless, I slapped together a resume and started sending it off to every job posting I could find. I applied to nearly 100 positions and was met with nothing but crickets. I later learned that academic and industrial resumes are completely different – honestly, my resume was so off the mark that my chances might have been better if I’d mailed them “HAVE PHD WILL WORK” in macaroni art.

No one gave a shit about the details of my thesis project that I had lovingly spelled out. They wanted me to sell my skills to them, to show them why I would be valuable. They wanted to know how I optimized lab work to improve experimental outcomes, save time, save money, or ideally, all three. They wanted to know about leadership and project management experience. I’m sure these specifics will vary depending on what field you work in, but the point is I hadn’t done my homework.

So how does one “study up” on their career options? The answer my friend, is conducting informational interviews! If you’ve never done one of these, I highly recommend it. You basically chat with someone about their career – what led them to that job, what does their daily work consist of, do they have to travel or work long hours, etc. Keep it short and simple, and most importantly DO NOT ask them for a job. The point of the interview is to gain perspective about different career options and to build your professional network. Asking the person for a job is rude – you’re not using them, you’re learning from them. If they know of a job opening they’ll probably tell you on their own, anyway. So just be cool, ok?

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I know social skills are hard, but you can do it. I believe in you.

I had some great informational interviews with people that worked in the biotech industry. Having been in my shoes, many of them understood my confusion and were more than happy to help me succeed. Some of them even sent me their resumes to help me improve my own. For example, they taught me the importance of using the exact keywords in a job posting, because most resumes have to go through an HR computer filter before they ever seen human eyes. I incorporated all the things I had learned and eventually managed to land a job. YAY ME!

I wont lie, the transition has been crazytown. I feel like I have impostor syndrome all over again, because everyone speaks in acronyms and I have no idea how business works. Half the time I speak to my manager I run back to my computer and google the acronyms she used to figure out what the heck she was talking about. Smile-and-nod-and-figure-it-out-later.

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*internally screaming*

After talking to some friends, I realized these feelings aren’t unique to my field. Lot’s of people feel overwhelmed when they dive into a new job, because coming up to speed is awkward! After three months at my current job, the majority of what I’ve learned has nothing to do with experiments. It’s mostly learning how a company works, which is VERY different than how a university lab works. Even though it’s intimidating, I’m slowly growing a backbone and learning that it’s safe to assert myself as an educated member of the team. I swear, I’ve learned more in my first three months here than I did in the last 3 YEARS of grad school.

I’m still doing informational interviews every chance I get – they’re so valuable! Networking never stops guys. I know it’s awkward but it’s probably the most important thing you can do for your career. I lost count of how many people told me they landed their dream job because they happened to know the right person. You can leverage your connections in so many ways, and building your network is probably the most critical thing you can do to ensure your future success. I know it’s hard and it’s uncomfortable and you hate it, but get your ass out there and network.

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You can’t spell network without “work” – AMIRITE?

Hop onto LinkedIn and check out your connections. Do they have job titles that intrigue you? Ask them about it! Do they work at a company you might want to work for? ASK THEM ABOUT IT! You’ll be surprised how many people are willing to chat on the phone, meet for coffee, or even just answer your questions via email. A great resume only gets you so far. A great resume with an actual human connection gets you a hundred times further.

I learned how to get a job the hard way, but that doesn’t mean you have to. Learn what your resume should look like. Get your butt out there and make some connections. And most importantly, don’t be discouraged. Job hunting is hard for everyone and involves a lot of frustration. But if you just do your homework, you’ll be miles ahead of chumps like me! 🙂

You want me to move to… Texas?!

In our generation, moving up the career ladder often involves ACTUALLY moving. Unfortunately, job-hopping has become not only normal but sometimes necessary for establishing a successful career. But you know what sucks? Ambitious people are often in relationships with other ambitious people, and amazing job opportunities don’t seem to come in pairs. This leads to tough, unfair choices and unequal sacrifices that have to be made. I think A LOT of us will experience crappy dilemmas like this, so why isn’t anyone talking about it??? Well, I recently lived through it relatively unscathed, so I want to share my experience should any of you find yourself in a similar position.

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Let me be your spirit guide.

I planned to stay in Seattle for at least a few years after grad school. The job market is good for scientists, and the Pacific Northwest is so beautiful it should be illegal. I had built a decent professional network, lots of great friendships, and a pretty darn perfect (and serious) relationship. Everything was coming up Milhouse.

But then one day my boyfriend called and said he’d been offered a huge promotion… in Texas. I think my initial response included the f-word as a verb, noun, adjective, command, and adverb. It was colorful. First of all, Texas. Scoff. But on top of that, I just got my doctorate! I was on the precipice of my new life and my career options were limitless! And now the person I care about the most had the audacity to rip that away from me? Didn’t my advanced degree make my career equally, if not MORE, important? HOW WOULD I EVER SURVIVE IN A PLACE LIKE TEXAS? I have a flair for the dramatic – the meltdown went on for a long time. You get the picture.

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In summary.

To his great credit, Boyfriend was patient and understanding. He respected my feelings, and since we were both invested in this relationship he would turn down the offer if it really couldn’t work. But there was one condition – we had to actually visit Austin. In fact, his company wanted him to take the job so badly that they offered to fly us down, all expenses paid. I was certain I would never agree to move to Texas, but hey! A free trip is a free trip! Plus, I was a broke-ass grad student, so the prospect of eating free room service like a $ophisticated adult person was very enticing.

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So I turned my Judgement Eyes up to level 11 and boarded a plane for Austin. And you know what happened when I got there? I didn’t find any of the negative stereotypes I was expecting. In fact, Austin turned out to be pretty freaking cool even though it was hotter than Hades. I had been using the excuse that I could never see myself living in Texas as a “get out of jail free” card, but apparently that wasn’t true.

This realization forced me to admit/confront my real hangups. Mainly, that there were very few jobs for PhD level scientists in Austin, and I felt cheated by having to sacrifice my own career goals to accommodate the career goals of someone else. Especially because I was a woman, and following a man’s career is just so cliche it hurts.

So that brings me to the meat of this post. A lot of us are going to face this situation, and I wish I had been given, I dunno, a heads up or something? You see, I never wanted to stand in the way of Boyfriend’s success. But if I’m really, selfishly honest… it felt like he was doing that to me. We agreed that although long distance can work great for some people, it wasn’t something we wanted to do. So for him to accept this huge opportunity meant a huge *loss* of opportunity for me.

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This job was going to pay him big bucks, certainly more than what I was pulling as a postdoc (not that that’s hard lol). So should the person making more money get the final say? If I did this now, would he be willing to make sacrifices for MY career in the future? If I moved to Austin and couldn’t find work right away, would he support me financially (including my gigantic mountain of student loan debt)? In short, whose career was more important right now?

Of course the answers to these questions will be different for every couple, so I have no magic cure-all advice. But for those of you who will face a similar experience in the future, here are the major lessons we learned.

1. Compromise. Unfortunately, there is no way to make these sacrifices fair. NEWSFLASH! Life isn’t fair. You have to search for compromises to help balance the scales, even if they’re small. For example – once I got a job in Austin, Boyfriend agreed to live somewhere that was more convenient for me although it meant a much longer commute for him.

2. Be empathetic. You have to be honest and open, even if it’s uncomfortable. Put your dealbreakers on the table, and actually discuss them with an open mind. If you don’t, you’ll just resent the crap out of each other. You have to consider how the other person feels and how much you’re asking of them – if the tables were turned, would YOU be willing to agree? This is true whether you’re the making the sacrifice or the one asking for it. I eventually realized that my needs were not higher priority because I had a higher degree, and that we should work together to support mutual success rather than competing over whose career was more important. Neither. They are both important.

3. Take risks. Change is scary as hell! But fear of the unknown can prevent you from all kinds of cool opportunities. One of the biggest things I’ve learned through professional networking is that people rarely follow a straight path to success, and lots of them end up in jobs they love but never expected to do. As it turns out, moving to Austin landed me a job at a huge biotech company. The science is rad, and my resume is getting stronger by the day. Risks are scary, but getting outside your comfort zone can help unlock doors you didn’t even realize you wanted to open.

4. Never move to Texas. HA – jk Austin is great! After living in Seattle for so long, I’m literally high on Vitamin D all the time now.

So there you have it. Hopefully my experience can give you insight to keep your head up if you ever need to make these crappy adult choices. Things have a way of working out if you’re willing to let them, you know?

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