Category: Science

Animals, Genetics, Scarlett, Science

Merle, Merle, On My Dog…Who’s The Cutest of Them All

Meet Our Mascot.

This is Scarlett. Named after The Grateful Dead song, “Scarlett Begonias.” “Scar” for short. “ScarJo” for fun. @scar_struck on instagram. Honestly, it doesn’t matter what you call her: she’ll never be able to hear it.

Scarlett is an Australian Shepherd mix who is blind and deaf, the result of backyard breeding gone wrong.

In the daylight, though, it’s hard to tell. She can play fetch with her tire chew toy, bark at passing firetrucks, and hide from the cats. She’ll follow you around the house when you get up, and don’t even think about leaving food out. But as soon as the lights go out, you can see her have to navigate a whole new world.

Scarlett spent her early months wandering the streets of Mississippi, covered in fleas, ticks, and parasites. She was likely let go after anyone failed to adopt her. Then she was picked up at 4 months old by the amazing people at Wolftrap Animal Rescue in Virginia, beginning her journey to recovery. There it was determined that she is mostly blind – able to see light, shadows, and bright color – and completely deaf.

Despite that, her ears still move, conveying her excitement, curiosity, or dismay, but they can’t send any signal to her brain. And one of her eyes never developed, severely inhibiting her vision, particularly on the left side.

Okay – now for the genetics part.

Basically, every cell you have has two copies of a gene, these copies are known as alleles. These alleles are copies you got from your parents. However, there are a select few cells that have only one copy – for when you’re ready to become a parent. These cells are known as gametes – sperm or egg cells – that have only one allele. This results from a process called meiosis, which splits cells into gametes. Then, when two individuals love each other very much…they combine their gametes via fertilization which creates a zygote with two alleles. This random splitting and combining of alleles is the reason siblings look different and you don’t look like a clone of your parents.

Humans have anywhere between 20,000-25,000 genes according to the Human Genome Project. Dogs have about 19,000.

One of those 19,000 genes is the Merle gene, which affects the production of eumelanin, the dark brown or black pigment protein associated with darker skin and hair and is also responsible for eye development. Its dominant form is denoted by a capital ‘M’ and its recessive counterpart by a lowercase ‘m’. Different types of dominance exist, but thankfully this one is pretty simple: if the dominant merle gene is present, it’ll have an effect on the phenotype, or expression, of the gene more than the recessive allele. Dogs with a marbled coat, referred to as a common Merle, have heterozygous alleles, which just means one dominant and one recessive allele (Mm). Breeding them together is the problem.

Why?

Combining two Double Merle (MM) alleles can potentially result in a slew of developmental issues.

A basic punnett square of the merle gene after breeding two heterozygous dogs.
a punnett square

Let’s start here: this is a punnett square, a way of visualizing the genetic probability of a given gene(s). They can get pretty complicated, but this one is simple.

Either side of the square is a parent – mom or dad, and in this case it doesn’t matter which. (Some genes exist exclusively on sex chromosomes, so then it starts to matter which parent, but the merle gene isn’t one of them).

In this case, the parents are each heterozygous for the Merle gene (Mm). These dogs would have marble-colored coats (as shown in the heterozygotes below).

To determine the probability of their offspring’s genotype – or the allele combination they get – use a punnett square. To do so, take one allele from each parent and match it with another in the corresponding square. One ‘M’ from one parent and an ‘m’ from another create heterozygous offspring. In this case, you get two boxes of Mm babies. 2/4 = 1/2 = 50% chance of having a heterozygous offspring. These are healthy, marble coat babies and the reason a lot of backyard breeders breed Merle dogs together in the first place. Do the same for another pair of alleles: one ‘m’ from one parent and another ‘m’ from the other. This combination produces healthy, regular coat babies. 1 square out of 4 = 25% chance of this combo.

I bet you can see where this is going.

This leaves us with our final square. Both ‘M’s from the parents. Here you have the double Merle babies. Also a 25% chance.

So think of it like this:

A punnett square with pictures depicting the different merle phenotypes and the percentage probabilities.
A super visual representation of Merle genetics

If both alleles present are dominant, those big Ms make some big changes. The double dominance is the reason Scarlett’s coat is mostly white with marble coloring, why her left eye is underdeveloped, and why her ears can’t pick up noise. Double Merles can’t generate enough eumelanin, meaning their hair and skin lack pigment and the eyes don’t develop properly. This also underlies albinism.

So, fun fact: pigment follicles in your ear are involved with translating the vibrations of sound into a neural signal. Thus, missing these pigmented cells – known as cilia – can mean deafness. Double Merles often suffer from this.

Double Merle dogs often have blue eyes because of the lack of pigment in their eyes. This can also cause eye developmental issues including corectopia, where the pupil is subluxated or out of place, starburst pupils where the pupil is spread out with irregular edges, and micropthalmia a condition resulting in small eyes.

In Scarlett’s case, her left eye is both subluxated and starburst, which causes her blindness.

Scarlett’s pupils are both subluxated and starburst.

Double Merle dogs are a prime example why understanding genetics is necessary when breeding dogs – especially given how many animals are killed every year when they can’t get placed in homes.

While genetics may seem overwhelming, the discipline is vital in determining the etiology of genetic disorders, the effects of our environment on our genes, and it’s the whole principle behind ancestry tests.

I met Scarlett in late April 2019 when my neighbor was fostering her. And it was love at first sight meet. My boyfriend and I adopted her a few weeks later. Even people who don’t normally love dogs, can’t help but be taken by her sprightly personality.

At a year old, Scarlett is a well-behaved, loving little tank with some of the strongest back legs I’ve seen on a dog. She’s a thick 40lbs and has a knack for chewing (everything). She’s done growing, so her ears are perpetually large and animated and her claws are like talons. She rarely barks, except when she ‘hears’ a high pitch or when she’s dreaming. She loves to sleep under a blanket, has to be touching someone at all times, and loves her stegosaurus chew toy. And she hates the rain.

The most common question we get asked is how we train her. Simply, using tactile stimulation with butt scratches or a spray bottle of water, depending on what she’s doing. Oh and lots of treats.

She really is a normal dog, who just so happens to not be able to hear or see very well. She’s clever, entertaining, and unconditionally loving. Proof it’s nurture and nature.

Remember to adopt, don’t shop! Contact your local animal rescue if you’re looking for a new furry friend.

Hobbies, Mental Health, Relationships, Science, Self Care

Autonomy, Autophagy, and Apple Pie

A look at self care, coping with trauma, and making a stressful field a little less stressful

TW: Mental illness, sexual assault

I. Autonomy

At sixteen, the human brain is entering the final stages of development. Synaptic pruning begins to die down. Neurogenesis and migration have already plateaued, but executive functioning is solidifying connections and the myelination of neurons continues to increase.

In short, a sixteen-year-old’s brain is almost done developing, but oh boy is it emotional. Everything has salience and it feels like the end of the world.

You remember puberty.

So, at sixteen, when a boy robbed me of my autonomy and justified it by citing my ass as the only redeeming quality of my intellectual inadequacy, it was a little salient. So salient, in fact, that I stopped confidently participating in classes. I stopped participating at all. It exacerbated my pre-existing mental illnesses and sent me spiraling down a rabbit hole that would make Alice prefer her own.

Like 40 million other people in the United States, I struggle with anxiety disorders. As a kid I learned to navigate it, living in between the shallow breaths of panic attacks and limited minutes of sleep. As long as I was busy and distracted, I was good. Not necessarily a healthy coping mechanism, but a coping mechanism nonetheless. For the type of problems I was having, it worked.

Until it didn’t. Because sexual assault wasn’t the type of problem that I previously had. Because, you know, no one should have that problem (despite the fact that one in three women in the U.S. do). So I repressed it, wrapping it in the stress of the event that preceded it – the reason we were working together – shoving it as deep into the recesses of my memory as I could.

I had convinced myself it was my fault. If I had been smarter, or smaller, or stronger or something, it wouldn’t have happened, that’s what my friends told me.

Naturally, unhealthy coping mechanisms turned to worse coping mechanisms — and also stress baking which was beneficial from a utilitarian perspective — until I was in therapy a year later where I stumbled upon the memory I tried so hard to bury. Words caught in my brain like a splinter, and tore the memory out.

II. Autophagy

At sixteen, I saw the quote circulating around tumblr:

Today my professor told me every single cell in our entire body is destroyed and replaced every seven years.
How comforting it is to know that one day I will have a body you will have never touched.

unknown author, plenty of known reposters

This, of course, is mildly misleading. We don’t morph like Mystique, suddenly shedding our cells for a whole slew of new ones. Instead, they turnover gradually, some dying here, some dying there, but as long as we’re alive it won’t ever be every cell in the entire body. We’re stuck with whatever neurons we’ve got, everybody.

Skin cells, though? Get him off of me.

The biological inaccuracy doesn’t negate the weight of what the quote is implying.

And I know, Em, stop being melodramatic.

Except, no. Because when we’re kids, everybody warns us about the strangers out to hurt us. Not the people you know who think they deserve to know more. They don’t warn you about the self-loathing that comes after. There’s not a disclaimer that if it happens to you, you’ll feel like a stranger in your own body. Everybody warns you not to put yourself at risk, but nobody warns you about the risks you start to crave after. The nightmares, the anxiety, the triggers, the flashbacks are all listed as symptoms on pamphlets you only see after you’re able to process it happened. Only in the past decade was post traumatic stress disorder (PTSD) even recognized in survivors of sexual assault, up to half of whom are at risk of suffering long-term.

The subtext of that “corny” tumblr post speaks volumes.

So, stop thinking I’m being dramatic and pay attention.

The biological process of programmed cell death, apoptosis, is a natural phenomenon that promotes healthy cell turnover. To assist in apoptotic regulation, cellular components within the cytoplasm are broken down in a tightly regulated process otherwise known as autophagy.

Autophagy also plays a super important role in butterfly metamorphosis. Do you remember being in grade school and raising butterflies from caterpillars? Remember the magic of watching them emerge after weeks of being in a chrysalis? Remember that magic?

Autophagy.

A caterpillar’s transformation into a butterfly is a grueling process. A delicate packet of goo, or more specifically, digested caterpillar, turns into a whole new organism.

And, yes.

Caterpillars literally digest themselves whilst in their goo packet…in fact, they are the goo. Then they reconstruct themselves and emerge as a butterfly. Or a moth if you’re a man I guess (haha, cryptid humor. We have fun here).

But in all seriousness, being a butterfly takes a lot of work. It’s an easy analogy to make – a metamorphosis for when it feels like the end of the world. It’s a beautiful metaphor (call it “metaphorosis”) to mask the pain-staking time and energy it takes to get through it.

But Maya Angelou, like the icon she is, summed it up best.

We delight in the beauty of the butterfly, but rarely admit the changes it has gone through to achieve that beauty.

Maya Angelou

Was she right or was she right? When was the last time you looked at a butterfly you thought was beautiful or aesthetic or whatever and appreciated its auto-digest journey?

When was the last time you looked at yourself and appreciated your auto-digest journey?

III. Apple Pie

At sixteen, I thought twenty-one was going to look a lot different. By now my brain is almost fully developed, an organ shaped by my experiences as much as my genetics. I’m a neuroscientist entering graduate school with a full-time job and thriving with the help of my incredible support system, including two cats who drag me out of bed for catnip. I do yoga regularly to practice mindfulness and bake in my spare time instead of when I’m stressed.

Eevee (left) and Oliver (asleep) will wake me up and meow at me until I feed them. They’re cute.

On this particular day, I baked banana bread. Now, I’m sitting outside with my dog at my childhood home. The way the light shines through the trees stirs a memory that regularly plays peekaboo in my hippocampus. It smells like spring and it feels so good to breathe it in and fill my lungs with it. With my eyes closed the memory is dancing in my synapses and suddenly I can see it.

The light, just like that, shining gently through the trees onto the water flowing downstream. It spotlights fish swimming below and highlights the grass in every direction. Birds flit through the air in an intricate dance. It’s quiet until I hear my dog bark excitedly that she retrieved her throw. I am happy.

I remember.

I exhale and it fades away but the contentedness stays. It’s been five years since I splintered. It’s taken about as long to get to the point that I can write something like this. And getting to this point, where I can take a deep breath and say I made it, was hard.

And every day is a new trial of making it. Some days are harder than others. Some days are just about looking in the mirror and saying I made it. There are still days I can’t get out of bed because everything is too heavy, too loud, too much. And that is okay. I’m learning to make peace with that.

This is just my story, my timeline, my lessons learned. Every person has a different healing process, and that is perfectly and completely okay, too. Caterpillars take 5 to 21 days to do their thing. The great thing about healing is that there’s not a right way to do it. I baked 73 cookies one day and filled up a journal the next. I had to retake a major class after missing too many because I couldn’t get out of bed. It’s taken a lot of therapy, reconciliation, and acceptance to understand what happened to me is not my fault. Taking steps to get better is. My success is. And in the long run, if you are doing things that help you, it’s a step in the right direction.

It’s difficult going through any of this by yourself. It’s sometimes even more difficult to talk about any and all of these things with other people. There’s a stigma for everything. But your experience doesn’t warrant an explanation. Literally everything about this is exhausting, let people help you rest.

It’s not just coping mechanisms that need work. Schools, elementary to university, need to better accommodate their students’ mental health needs. Normalized abusive behavior needs more comprehensively addressed and all together changed. Self-care needs to be a priority not a privilege. The current environment, both socially and academically, boasts of advocating for self-care, mental health and sexual assault resources, which wildly exaggerates the reality. Students are forced to sacrifice their well-being to make deadlines or attend classes without adequate resources to supplement their mental health. The gross mishandling of sexual assault cases bears little explanation.

Individuals who suffer from mental health issues and sexual assault survivors have enough to worry about. Society needs to pick up some of the slack. And that means talking about it. Check on your friends. Look out for your loved ones. Say something because some people can’t. Let’s do better.

If nothing else, imagine how many of your cells have already turned over. Keep drinking water, keep feeding yourself, keep helping them do it. You’re gonna make it.

Neuro, Science

We Get It, You’re A Science Major

“They said, if you aren’t studying cellular/molecular mechanisms, you’re not studying neuroscience,” one kid from my seminar class told our professor. “I told her she was wrong. I’m right, right?”

My professor nodded. Another girl chimed in, “I bet they’re a CST neuro major.” Murmurs of how she was “the worst” made their way around the small group of us that stood in front of our professor, waiting patiently for her answer.

I graduated with a B.S. in Neuroscience from the College of Liberal Arts (CLA) at Temple University. This is the same B.S. in Neuroscience given by the College of Science and Technology (CST). They are two completely different programs; CST has eleven required labs in their curriculum, CLA only has three, and where CLA focuses on behavior and systems, CST is rooted almost entirely in cellular and molecular.

Guess which program “doesn’t count” in the eyes of most neuro majors.

I’ll give you a hint: it’s the one I graduated from.

“You’re right,” my professor replied kindly. “One without the other doesn’t mean much.”

The room was mostly empty except for the maybe six of us huddled in the front of the room after class. It sounded a lot louder than that as everyone erupted into their own questions, comments, and opinions. Some of these same people held similar reservations until I joined the class. Suddenly CLA wasn’t as washed up as everyone thought it was. I didn’t just know the molecules, I knew the pathways, I knew behaviors, I knew neuro.

Because it’s the same degree.

But this whole CLA-CST beef isn’t a new phenomenon (duh, have you seen the Tupac and Biggie docuseries on Netflix?). But, it is a microcosm of how annoyingly elitist some scientists get.

I hope some of you are reading this wondering what the hell I’m talking about – keep that innocence.

For the rest of you who know what the hell I’m talking about – choose your fighter: The Geneticists versus the Biochemists versus Everyone Else; The Physicists versus the Chemists; Internal Med versus Surgeons.

These kinds of feuds are not new. And that’s annoying!

I have had an internal medicine doctor scoff at a surgeon’s opinion because they “slice and dice” and “don’t know actual medicine.” (Which, first of all, sir, have you seen some of the absolute ninnies that work in INTERNAL? Not the point, let’s discuss that another time). A week later, that same surgeon rolled his eyes at the internal doc for “reading so many books” that he “forgot the actual medicine.” Unsurprisingly, that project never really took off.

I’ve had professors tell me my degree wasn’t “real science” because it was just biology and some people think that’s a soft science. Others have split opinions because genetics is better than biochemistry is better than behavioral research. Don’t get me started on the rifts between graduate programs.

I say this coming from the unlisted, unforeseen option: journalism. I was two semesters deep when I switched into neuroscience, with three electives too many to join CST and still graduate on time. So I switched to CLA. I have had to explain this to every doctor, researcher, or both that I have worked with. And that’s annoying. I have had to defend this against peers who questioned my ability because I came from the school across campus. And that’s Annoying.

It’s the same degree. But it’s not just about the degree; I’m almost expected to look down on the field I fell in love with. However, I am not a jaded ex.

This pseudo-elitism that any one science, specialty, or concentration is better than another while both are simultaneously more valuable than any humanities or arts degree is complete, utter nonsense. (Unless you’re in evolutionary psychology and trying to justify your opinion that women are inferior, in which case I’ll have a post just for you.) If everyone was in science, we would know a lot about the world, with no way of interpreting it or escaping it or any of the million other things arts, humanities, and trades do for us as a society. And honestly, if your field was for everyone, you’d probably be out of a job.

This, of course, is not to say that I would excel at a physics or organic chemistry-heavy course, and it’s definitely not to say that we don’t need anyone in a given discipline. Instead, this is more of a hypothesis. If we stopped focusing so much on the discipline and more on the scientific end-goal of answering questions, then science would move a lot faster.

The best illustration I can think of is the field of neuroimmunology (we get it, you’re a neuro major). Up until five or ten years ago, the fields of neuroscience and immunology were two very separate, distinct fields. Then the lymphatic system was discovered in the brain, and voila, neuroimmunology was born. Since its advent, neuroimm has specialized even further, encapsulating research in the gut microbiome, traumatic brain injury, developmental disorders, and a whole host of other topics. But without merging these fields, we would still probably think that the nervous system was independent of the rest of the body’s immunity.

Despite the unnecessary explanations and inquiries laced with condescension, I still wouldn’t change the college I got my degree from. The CLA neuro program, though aggravating in its newness and non-CST reputation, prepared me for neuro better than the plethora of lab courses woven into the CST curriculum. That’s not to say those labs aren’t important, but I’m the kind of neuroscientist that consults someone else about the physics of an MRI.

Differences aside, the neuro programs at Temple gave me a chance to do what I love. And as corny as it may be, I love learning especially about the brain and its many complexities. My mentor, who fostered my curiousness about the nervous system, evolution, and cellular brain mechanisms, teaches out of CLA. The professors of the neuro electives in CST also fostered my love of learning. All of them got me to believe I could make it in this field. And what else? They’re mostly women.

These women and their respective colleges taught me a lot, both academically and personally, and not once did they seem bothered about which college it was. As far as the pettiness of scientific elitism, that taught me something too.

I want to be the science major who loves it, not the one who has to prove I know it.