Thursday, October 10, 2013

On Shutdowns and Science

I'm not one to typically advocate for political topics. Usually I  don't feel that my opinion on matters I haven't researched are of any real value. I don't have an economics degree or have any sense of how the governmental politics works on anything other than a broad level. I am however rather informed on how the U.S. scientific community works and am becoming increasingly distressed by the implications of federal spending shutdown. I don't like talking politics, but this is something that needs addressing.

As pretty much everyone knows, the federal government shutdown on October 1st until the budget can be renegotiated. I honestly don't care how or why this has happened, because to be honest it really doesn't matter to me. What matters to me is that this has happened and we have already felt the impact. What matters to me is that even if the budget is resolved tomorrow, we are going to be feeling it in the scientific community for a long time.

If you didn't know, research at public universities is deeply connected to the federal spending budget. A majority of biological research is funded by the National Institutes of Health, including but not limited to the National Center for Biotechnological Information which houses the databases that almost every biologist uses to compare and research biological information.

(Such as the BLAST tool which is invaluable. I only use it all the time to do research, not that big a deal. The vitriol I have for this particular point is mostly just personal inconvenience.)

From this breakdown, we can see that there are a number of safety mechanisms that are currently not functioning. The least extent of this is the cancelation of medical trials for disease study. To put an ethical spin on this, it means that children aren't getting accepted to cancer trials that can provide them with potentially life saving treatments. (Kids with cancer are being refused treatment. I don't think I could try to play that more empathetically if I wanted to.)

Besides the long term effects that come from delaying every single federally funded medical trial until this all blows over, which means denying sick people medical attention and setting back all trial based research for an unknown period of time, we are looking at a current 0% acceptance rate for grant proposals during this time (which is a slight step down from the already low 14% acceptance rate from the sequestration cuts previously this year.) This means that labs have to shut down their research and cut back on their staff even more than they have already.

It's not just biology though: just look at NASA's website. Our scientific community is at a standstill, and I highly doubt that "non-essential" research is going to be reinstated before the rest of the budget. The real issue is that these labs can't exist without funding indefinitely. Given enough time, the delay in new grant money is sure to sink many labs that are already struggling.

Really though, if you aren't involved in the scientific research community none of that really affects you, right?

Well, the FDA isn't currently running trials either. Which means no new drugs are being approved, and they aren't able to keep up their food inspections. You're poultry and beef are fine as the USDA is still running tests even if their website isn't up, but testing facilities for other food disease outbreaks from fish or produce aren't running. Which is fine, right? I mean, we haven't had a major food poisoning outbreak since... August. But it's not like there's an outbreak happening right now or anything.

Oh right. Now that 300 people have salmonella from a multi-state outbreak, we should probably bring the CDC back online. That's a good idea. Huh, maybe it wasn't the best plan to shut down our nation's ability to monitor and regulate infectious disease outbreaks. Someone should have thought that through.

The real problem is that we still aren't monitoring any of the imported foodstuffs that the FDA normally has jurisdiction over. The CDC is a reactionary agency, and they only have the ability to limit the spread of diseases after they've started. Without the ability to shutdown potential threats, we are going to be looking at a higher incidence of outbreak and we are restricted to catching diseases after they've occurred.

As I said before, I really don't care about the politics behind the shutdown. I do care about our nation crippling itself and allowing both it's scientific research community and disease control protocols to become essentially non-functional. It is literally appalling that we have let this occur. I cannot stand silently as people are suffering because we are unable to fund the most basic preventative measures to keep our populace protected. I cannot think of any reason that we as a nation would allow this to happen, and I cannot condone anyone who thinks this is an appropriate measure to challenge any kind of public policy.

Thursday, September 12, 2013

Life Update: The Proofening

Hey everybody!

It's been a couple of busy weeks here in Pittsburgh. I've been up to my neck in school work while settling into the new city. I'm having a real blast, but it is a truly exhausting experience. (Anyone that follow my twitter: I'm sorry. I'm so sorry.) Between all of the work and balancing socialization time, I've been teetering in my usual emotional levels of "Everything is amazing!" to "What in the world am I doing with my life!?" I have been assured that this is a completely normal human response and that it will level out fairly soon.

I've started fencing again so that I can keep my skills from completely rusting away. I found some people to swing swords at and carpool, so I've got some motivation, though I made the distinct tactical error of forgetting my electric equipment back in the lovely state of Michigan. Of course this means I will have to recover it before I can even think about becoming more competitive. This also involves having free time to actually travel to tournaments, and since I currently lack anything that amounts to free time or spare cash, this could be regarded as a positive problem.
(On a side note, it doesn't appear that the state of Pennsylvania actually uses the AskFred database. That means that I have no idea about what sorts of tournaments and ratings are doing around here, which is quite aggravating.)

As far as writing goes, I've gotten a couple of rejections for some stories (which is still promising) and a possible novel outline to completely ignore during my first draft. I'm mostly putting my stuff on the back burner until I can get some solid classwork footing. Possibly jumping into Nanowrimo if everything seems to in good shape. I've only got a month to work myself into a frenzy before that prospect becomes impossible, but it looks good in the distance.

In the "spare time" that I have left for reading, I've been working through Ted Chiang's collection of short stories "The Story of Your Life and Others" which has been an amazing read so far. The story Division by Zero was especially poignant as I'm frantically working on my proof-based math homework. If I write anything that approaches what Ted is able to do with his pieces, I will be exceedingly happy with myself. I doubt that will happen for a while, but I feel it's a good, lofty aspiration.
I've also picked up the third volume of "Locke and Key: Crown of Shadows", written by the ever talented Joe Hill. It should be noted that Gabriel Rodriguez's art is gorgeous as usual. It is an excellent continuation of the storyline and I'm really excited to see where the series is heading in future volumes.

Other than that I'm just polishing my resumé and ironing my suit for interview for possible internships this summer. It seems like all of the companies that I'm looking at are arriving on campus in the next few weeks which gives me plenty of time to panic uncontrollably. Hopefully I'm not just stuck watching Netflix and eating popcorn during a few months this summer, as appealing as that sounds. (It would let me catch up Breaking Bad though, so not an awful plan. Still not ideal.)

Oh! If you guys had science questions that you wanted answered in simple terms, feel free to aim a tweet or comment my way. I'm always happy to give my best attempt at clear answers, and as you can tell that something that I've been trying to work on for the blog.

That's about everything (minus stressing more about homework load) so mostly I just need to keep my head down and keep working. I've got a lot of good things happening, and it's nice to be doing something that I love. I'll try to update more as things go forward!

Have a great week everyone, and take some time to relax and enjoy yourself!

~ Patrick

Monday, September 9, 2013

Stupid Simple Science: Microbes and You

As someone who studied microbiology in undergraduate, I can be a little bit dense on what the general public knows about my field. So today, I'm going to talk about the microbiome, specifically your microbiome. This is going to be the briefest touches into the complicated relationship we have with microbes and hopefully this will help you understand things a little bit better.

First off, I didn't realize how lacking this stuff was in pop consciousness. There aren't any youtube videos about this with more than 5k views, only one TED talk. The only real stuff that starts hitting the public image is probiotics (which are marginally effective at best) and honestly is putting practical application to something we don't know the intricacies of just yet. (Also to sell you pills. Don't take probiotic pills. Eat yogurt, it's cheaper. Obligatory: this is not medical advice.)

Grand Prismatic Spring, Yellowstone National Park
Color variation due to microbial biofilms.
The second bit is that most scientists really don't do a good job at explaining cutting edge science for people that don't speak their sub-variant of geekenese. I'm going to try and do this justice with links and other good things. The first thing you have to know about microbes is that they are everywhere. Literally almost everywhere. Except in specifically sterile places and on molten rock surfaces, there are microbes on and in everything. Boiling pools of sulfur? Totally. Thriving in the hearts of glaciers? Of course. In solid rock miles under the earth's surface? You betcha. Six miles into the sky riding on updrafts? I'm certainly glad I'm not.

The long story short is that wherever microbes can live, they will. Some of these things eat sulfur, arsenic with a side of methane for breakfast, and others only divide once every millenia and a half. Quite a few of these things think that the conditions that humans need for life are extremely toxic (namely oxygen, but anaerobes are finicky to say the least), but there are entire communities that not only live with the same conditions that humans do, but need conditions that humans create. I'm not talking the fungi that live in dishwashers, but almost every surface of our body is completely coated in microbes.

**A quick side note: surface means "not in the body". Your intestinal tract, your sinuses, insides of your lungs, and inner ears are all outside your body as much as your skin is. (Yes they are all coated in microbes too.) Pretty much all animals that developed past sponges are roughly donut shaped with regards to body surface.**

Before you get the hand sanitizer and start dipping yourself in it, know that this is a good thing. A really good thing. All those pathogens that are constantly trying to infect you and eat you? They have to not only get past the body's defenses but also out compete an entire ecosystem of microbes that have specifically adapted to your body conditions. Not your friend's body conditions either: every person has a completely unique set of microbes and every single surface of your body has a different set of flora specifically evolved to grow there.  Your skin microbes that grow on your elbows are different from those that live in your scalp, from those that live in your armpits, from your eyelids, and even your bellybutton.

They eat pretty much everything that can be eaten and actively hate on anything that is trying to make a foothold on your body that isn't already there. Now anything and everything that you touch puts new microbes on your skin and puts your skin microbes on everything that you touch. This includes other people

Staphylococcus epidermidis, Common skin flora
Scanning Electron Image
So you have this really badass crew of microbial bodyguards on your skin. What about everywhere else? Well, we know a lot but we don't know everything. We know that your gut microflora produces vitamins (primarily K) and breaks down things that we can't normally process. Neither cows nor termites can break down cellulose in plants, but they both have closely symbiotic microbes that do that job for them. That's cool and everything, but I mean it's not like there are that many microbes on us, right? We can't even see them! 

Ha. Yeah. Nope. You are only 10% Human. Out of the entire biomass that you occupy, only 1 in 10 of your cells contains your DNA sequence. The rest are many, many, many varieties of microbes each with their own set of genes, proteins, and enzymes. Your initial set of microbes is from when you are born and come into contact with your mom, and breastfeeding is shown to pass along and promote gut microflora. Everything from there is gathered as you go. If you've been somewhere once, you probably have some microbes that are unique to that exact location. Heck, if you meet someone from somewhere you've never visited, you might have picked up microbes unique to that location from them!

Every single person is completely coated in unique, human-specific organisms whose community composition dictates how we break down food, smell, develop cavities, maintain clear skin, derive nutrients, avoid infections, and much more that is still being discovered. Trying to get rid of them is pointless and ultimately harmful. 

Also, please wash your hands: they are really disgusting.

Thursday, August 29, 2013

Stupid Simple Science: Eyes

Why do most complex organisms only have two eyes, and only in the front?

That is a very good question. I'm going to avoid taking the microbiologist answer of "because multicellular animals are weird" and try to give some good concepts. We'll break this down into a few different questions and I'll try to explain the ideas behind each.

Why eyes to begin with?

Eyes are really important for most organisms, but almost none so much as humans. Our eyes give not only light input, but also allow us to interact socially and detail written information and so such humanities nonsense. We think of them as all important, whereas a dog might sooner go blind that lose its sense of smell.

Why do we use light for one our senses? Above water, it travels farther and faster than sound, pressure, heat, and molecular diffusion (smell/taste) and it allows us to perceive minute chemical differences in materials without ingesting them. (There are lots of chemicals that have colors outside of our range of vision, then tend to show up white or clear depending on their state.) This means that we have access to information more quickly and at a greater distance than any of our other senses.

Why in the front though?

Most animals have optic sensors near their brains to allow for optimal reaction speed. There is a maximum speed that your nerves can transmit information at, and in order stay relevant to something that is moving at the speed of light, they have to be as close to the brain as possible. 
Human nerves can transmit information from 30-120 meters per second. [Bullock, H, (1965), Structure and Function in the Nervous Systems of Invertebrates], compared to light's blisteringly fast 299,792,458 meters per second [].

This means that any eyes that aren't optimally close to the brain are going to suffer from some serious lag in responsiveness. Well, more so than we suffer from already. Brains, for whatever reason, are usually situated in the front of the organism.

Why multiple eyes?

Ok, so being able to see and interpret light is a good thing. So why in the world do we have more than one? It's not like we are going to be able to react soon enough to quick light stimuli with our signals to our muscles creeping along at a mere 120 m/s (which is a cool 268.432 mph for our imperial friends) so why do we need the same input multiple times? Well, it's not the same input exactly.

You've heard this before, as humans have excellent depth perception being hunters, but the slight difference in the image produced by two eyes that close to each other allows our fantastically bored brains to infer the difference in distance of multiple objects. This is primarily hunters though, as most herbivores have shifted their eyes to the sides of their heads to create a much larger field of vision but at the price of their depth perception.

The reason for multiple eyes is generally to create better depth perception or to increase range of vision. Outside of that there is little reason to generate new eyes, (though the infrared sensors in snakes could technically be considered eyes as they interpret a specific set of low wavelength radiation. I'm not a herpetologist though.)

Ok, but why two?

Two eyes? Oh, right. That thing that happens in most mammals, reptiles, amphibians, fish, birds, and almost everything with a vertebra. The first things with vertebras probably developed two eyes (because of bilateral symmetry) and then went "Guys! This is in 3D!" and didn't move on from there. Pretty much what they movie industry has been doing for a while now. (You think they would just get over it.)

Monday, August 19, 2013

Stupid Simple Science: Species

In an effort to reach out to the general public, I'm going to tackle one of my favorite subjects: the concept of Species. Most people outside the field of biology don't realize that this isn't some dry definition in a textbook, but is one of the more debated definitions in the field and changes wildly on context. I'll get started with the macro-biology term (where things make a little sense) and then move into the real fun stuff.

(I'm going to warn you ahead of time that this doesn't have a cut and dry answer, and I'm touching on very few of the big complex arguments and am doing none of them justice. So please excuse me as I butcher these arguments and examples. Feel free to ask any questions. I will try to clarify further.)

(Also, I'm going to do a lot of linking to Wikipedia. Bear with me please, none of the links are really necessary outside of providing easy routes for further research on your behalf.)

Species: A Definition

"The major subdivision of genus or subgenus, regarded as the basic category of biological classification, composed of related individuals that resemble one another, are able to breed amongst themselves, but are not able to breed with members of another species."
    ~ (Not filling space or anything)

So basically a species is a group of organisms that can breed within themselves to produce offspring that can also reproduce. That sounds simple, right? It's not though. 

There are three major criteria for what can and can't breed. First off, if two organisms do not have functioning biological that connect properly (Tab A into Slot B and all that jazz) then they aren't the same species because they cannot physically mate. A Tree and a Duck for instance. Literally two different pieces of equipment.

Second off, if two organisms could breed but cannot genetically produce viable offspring, then they aren't the same species because their genes are incompatible. Donkey and Horse producing a Mule are a good example. Mules can't breed further, and are sterile therefore ending the line.

Finally, even if two organisms can produce viable offspring but never encounter each other in nature because of basic behavioural or geographic differences, they are considered separate species. Nocturnal versus Diurnal animals for instance. Also geographic isolation can cause a speciation event if enough difference is generated for one of the first two criteria to take place before they are rejoined.

You got that? It's pretty straightforward. Two organisms fit into the same species if they mechanically, genetically, and temporally interact in order to generate more organisms that can also do the same. Really cut and dry. Absolutely nothing that could possibly go wrong with this definition.

When Species Mingle

Well, almost nothing could go wrong with that definition except for humans generating fertile crossbreeds between species... but that's unnatural. Human interaction can overrule the first and third rules of species definition fairly easily. (Physical and temporal constraints are easy enough for our engineering.) But if two genomes don't want to exchange information, there isn't much we can do outside drastic genetic modification. With that in mind, we'll ignore human meddling for defining species. That'll make things easier, right?

Well, let's talk for a moment about Ring Species. Let's say that we have a mountain that has two species of mice on the South facing side. (The actual real life example of this are species of arctic seabirds.) 

These are genetically incompatible species we will refer to Normans and Robertas. On the East facing side of the mountain there are a subspecies of Normans called Spotted Normans, which can interbreed with Normans just fine but just have spots. To the Western face, we have Striped Robertas which can interbreed with Robertas, and of course they are striped. On the Northern side we have Striped Spotters, which can interbreed with both Striped Robertas and Spotted Normans. All of these are mice that live on the same mountain, and some can interbreed with others, but not all. What does this mean?

To clarify: 
Normans<->Spotted Normans<->Striped Spotters<->Striped Robertas<->Robertas

The Beautifully Illustrated Mountain of Mice

But: Normans < X > Robertas

What we have here is two mice species that can exchange genes through genetic exchange (though not directly) and are still considered separate species. What does this mean? Well what you have to understand is that humans created the idea of species. Nature didn't come up with it and it's mostly an artifact of our brand of sexual reproduction needing similar genetic makeups for proper homologous pairing. 

Why Does This Matter Again?

(This section is science lingo dense. If you don't follow, I'll sum it up in the next section.)

Ok, here's the fun part. So far we've been going through the species as defined by macro-organisms, specifically macro-organisms that use sexual reproduction. What happens in the world of single celled asexual organisms? No mating. None.

So wait, how do we use those three rules for defining species of bacteria, archaea, and asexual eukaryotes? (Those are the domains of life for those that don't speak biology geek.) How do we define E. coli, Botulism, and Lactobacillus as different species? They don't follow any of the rules that we associate with macro-organisms as far as mating goes, and physical characteristics won't always give us clear answers. Instead we use genetics.

Specifically we use a 97% similarity benchmark for comparison of the ribosomal DNA between two organisms to determine if they are similar enough to be called the same species. (Yes that's a mouthful.)

Why do we use such a strange criteria for defining microbial species? Can't we just come up with some nice laws like we have for the macro-organisms? It's not really that easy. We take the most widely shared, conserved gene known to science (every living organism needs a ribosome to translate the genes in DNA into proteins, we found that everything else is possibly optional) and we compare the sequence, and if 97% of the As, Ts, Gs, & Cs match between the two, they're a species. (We even have really handy database that stores this info.)

This means that two strains of the same bacteria that have the same symptoms that are the same species can have drastically different genetic makeups

Mind you, this is 97% of a fairly conserved gene, not the ones that are fairly variable. One human's genome is 99.9% similar to another human's genome. That's regardless of race, creed, or nationality. That's also 99.9% of the entire genome, not just one gene. By the criteria that we have microbial species, if the ribosomal DNA between two organisms has more than 97% similarity, they would be considered the same microbial species.

I haven't done the math, but we'd be lumping significant lumps of the animal kingdom in as the same species with these sorts of terminology.

Once again, with normal words.

Chickens share 60% of their genes with humans. Two strains of Escherichia coli that cause almost the same exact infection had only a few genes in common, but were still considered the same species, and until recently were probably confused as the same strain. This isn't to say that we classify bacteria wrong, but rather they play by such different rules on the microbial level that the terms 'species' don't really apply as we know them on the multi-cellular scale. The term 'species' doesn't even work properly on the multi-cellular scale. 

Species means a whole lot of different things. All of those definitions are just human words that don't really fit onto the complex concept properly and don't really imply the drastic changes and subtle variances that we see in the world's vast populations of organisms. At the same time, we can't make up a better word for it. It's not a perfect definition, but it's the best that we currently have. To be fair, nothing in biology is really divided. Everything is connected, related, and constantly changing. 

It's messy, it's life, and it's all we have.

Saturday, August 17, 2013

Bad Science

I love science. It's not just a hobby for me, but a way at looking at the world to see the intricate beauty that permeates everything. In the same regards, I loathe pseudoscience. I despise it with a passion. It is detrimental and disgusting. As someone that prizes our ability as humans to rationally attack an argument, pseudoscience is one of the most filthy concepts that I can think of.

To note, I am not talking about science fiction (a literary field that I love very dearly and has no pretenses about being fictional) or theoretical science (which we have no way of properly testing as of yet, but offers interesting explanations) but rather ideas that wear the guise of legitimately tested science without the actual rigor or repeatability.

Show me the Citations

When looking at a supposedly scientific document, look at what it cites as its sources. Nothing cited? That's extremely suspicious. Never trust anything that doesn't have citations if it purports itself as a scientific document or scientific article. Notice that this document does not cite things. It is an opinion piece, not a scientific article. You can safely ignore opinion pieces as they are opinion and not fact. Lots of people have opinions and very few people have tested facts. Myself included in this matter.

A good rule of thumb : if a news report has some shocking scientific breakthrough, you can safely ignore it unless they cite some other sources of information or papers. This is doubly true if the title is a question.

"Does the newest research show that wallpaper causes bronchitis?"
Probably not, but if it were true they might have written
"Newest research shows that wallpaper causes bronchitis."

Note that I put probably there. There are legitimate cases where these tabloidesque articles are true and full of legitimate, factual information. The chances that they will not cite relevant papers and have their title as a question while still being accurate and relevant are extremely low.

Legitimate Citations Please?

Ok, you've looked it over and it cites three different articles on three other websites. Good, right? Not so much. Take a look at what those sources actually are. Let's say you've got a link to the main page of The Society of Homeopathy, a video of a perpetual energy machine, and the ever lovely theory of Time Cube. They are all bogus. These range from statistical tricks, to sheer impossibility, to... I'm not actually sure what Time Cube theory presents. I just really love their font choices.

(I really do truly swear that anything that purports homeopathic effects is lying to you. It's just placebo. Diluting anything does not make it more effective in the way that they are claiming. It literally does nothing.)
(Likewise, I promise that if perpetual energy machines weren't just garbage and flashing lights, and even if the US government was hiding it all from us, every other country in the world would be jumping on it like nobody's business.)
(You can believe the Time Cube stuff if you want. It's pretty trippy.)

A paper is only as good as its sources. If it has shitty sources, the science held within is also highly dubious. A good way of searching for the credibility of sources is looking up the exact opposite of what the article is purporting and seeing what the other side is saying. Please, do research. Don't just take my word on this. Look up stuff and see what people are actually throwing money at.

Look at what scientists actually think about it, though really only trust ones that are in that field. If you ask me about some advanced quantum effect that manipulates spacetime and results in a cubed field of time that swirls around the planet, I honestly don't have any idea. I'm a biologist for god's sake. Go talk to a planetary physicist. They do that stuff for fun.

Now the real problem isn't when you've gotten really spectacularly bogus stuff like above. The real problem is when you have semi-credible sources, or the science they are showing you isn't shown in the papers they are citing. This is fine if they show their own research and provide detailed methods for replicating it, but then you actually have some insight into what they are doing to determine if it's good science.

Do we really have to bring statistics into this?

If you're a lay person, you're good. You've got an article. It's got data and credible sources. It's got revered sources even, stuff that people have been saying is the cornerstone of the field. From an outside perspective, it looks good and it checks out. If it's got a spot in Nature or one of the other big scientific publishing houses, you should be good.

Just know that people suck at statistics. There is no way of certifying things one hundred percent. People also make stupid math errors, and people who have a lot to lose will sometimes make stuff up. It is for these reasons that I hate pseudoscience. Not because science is so great, but because science is so very fragile.

We can have findings that aren't statistically significant. Our best methods typically have a certainty factor of ninety five percent. We build a web of knowledge on strands of trust and probability. After enough time and enough trials of experiments, we can hold fast onto some knowledge as truth, and each fact is hard won.

When people mock science and intellectualism, they don't realize that everything we have is a delicate victory against a difficult and hostile universe that we must fight as a species to gather knowledge about. I do not hate pseudoscience because it dares to question the authority of some greater group, but because it destroys the fragile trust that we as scientists try to establish in our brief academic lives. It mocks the rigorous methods that have stood the test of time and it uses our hard work as a thin veil to push unsupported opinions as fact.

This is merely my opinion. As someone who has done promising work only to have it break apart upon scrutiny of statistics, I can only say as personal anecdote how frustratingly difficult science can be. It is fickle and temperamental. It will never show you the results you want, but it will show you what is true.

Whether you recognize the truth when you are staring at it is another matter entirely.

Monday, August 12, 2013

Welcome to Pittsburgh

It's about 11pm here in Pittsburgh. I've gotten done with my first day of orientation here at CMU and have settled in quite nicely. I moved in late last evening to the first room that I have had to myself.

(Before I continue to whine about myself, a special shout out to my family for not only driving out to help me lug all my stuff, but also stuck around and helped me unpack. They then braved the roads for the trip all the way back to Michigan even later into the night.  After an action packed Saturday and a very grumpy Patrick, their levels of dedication to getting me out of the state approached divine. I really do love you guys.)

It's an odd feeling being here. I've been going over manuscript critiques on a short story that I'm almost happy with, (Fourteen scenes in just under 4k words. What was I thinking?) and suddenly I'm missing people pretty badly. I'm missing my fellow Clarionites. I'm missing my fellow Spartans. I'm missing my family. The people I met today are really interesting and brilliant, and I'm a little worried about what exactly I plan on doing here.

This is my problem. I wanted to be here. I want to be here. Unfortunately I work out most of my problems by writing about it. It's sort of like talking to myself through a problem except that everyone on the internet can hear you... maybe this wasn't such a good idea either.

Let me start again. I miss people. This is normal. But I am letting these feelings of nostalgia get in the way of me being able to actually pursue what I want. I want to learn and be good at what I do. To do anything that might get in the way of that is wrong. I am not here to do things that are going to interfere with my becoming a kickass guru of computational biological goodness... but what if I've already started? There are so many things to do and -- nope. That's not how this problem is going to be solved. Let's try this one last time.

Hello Pittsburgh. My name is Patrick J Ropp. I'm here to do science and be awesome. Get used to it. 

Yeah. I think that has the right ring to it.

Friday, August 9, 2013

The Stupid Guard Dilemma

The Trouble with Guards

A real trouble I have with my first drafts is the fact that my guards suck at their jobs. This is something that I heard quite a bit of as I hastily nailed plot to paper. No matter what they said, how adamant that they were, or if they actively questioned what was going on, they still were stupid. The protag skips past them and goes on to steal the MacGuffin.

I heard this several times, and I wanted to figure out how and why I wrote stupid guards in my drafts. My first instinct is that I didn't want to leave the cell unattended or the vast pile of loot unsupervised, which is intelligent on my part as who really wants their stuff just sitting around to get stolen or blown up? Because I had other things in my mind and bigger portions of plot that I needed to attend to, I still wanted my protags to be able to pass right through the guards and continue on with the story. There were castles to raze, gangster hideouts to blow up, and honestly what were a couple of guards going to do?

I was setting them up as a just another security device or booby trap. They were something to be easily outwitted and then ignored. What I didn't realize at the time was that I was introducing characters without actually treating them like it.

Realizing and Acknowledging Intelligence

So, what do I do with the fact that we are introducing intelligent characters as another obstacle? Give them a backstory. Until a character comes from somewhere and is going somewhere else, they don't own any action that they perform. The NPC (Non-Protagonist Character) is just a temporary personification of plot unless they are given the same weight of backstory as our protags. Once they are given their own wants and desires, then their actions begin to align properly.

A zealot for the cult who has given up everything to bring back their family, a Yakuza who secretly just wants to be a popstar, a rent-a-cop that is working extra shifts to help feed his kids, or a government spook that had her boyfriend shot in a drug trade. These aren't just guards anymore, they are characters. Any one of them is just as interesting as the main protag might be, and that gives them weight. Even the briefest of character sketches that are discovered make a world of difference.

These aren't just guards anymore. These are intelligent and motivated actors in the world. Now that we know that, it becomes a little more complicated. It becomes part of a bigger story.

Guns, Explosions, and Grey Moral Choices

Now that we have characters and have given them motivations, the rest becomes trivial... at least that what it appears to be. But these aren't just automated defences anymore, they are characters and that means that you now have to devote page space to develop them a little bit. In novels, this is easier because you can just write more. In short stories and flash, you really have to think about it. Every guard that you add needs to be a semi-fleshed out character and that really eats into what you can do with a limited word count. Some of the approaches I have considered (each with their own pros and cons) are Killing them, Distracting them, and Failing them.

"Shot first and ask questions later." Guards aren't an issue if your protags have no qualms about killing them quickly. This doesn't really fly for me. Looking over the stories that I have written, I realize that I have never shown a gun going off on the page. I don't like guns in fiction, or rather I am not inclined to write them. The actual weight of shooting someone is something that I don't take very lightly and maybe that's something I need to address in my own work. A way to do this more palatably is to flesh out the guards after they're dead.

"Make bigger problems." If your protags make a bigger mess somewhere else, the vault might be unguarded, but probably not. Breaking up the normal guard schedule because of what your protags do means that you can have the guards acting abnormally and in less or greater numbers. Throwing them off of their game can make them more or less likely to stop doing their job properly. Having different reactions to the same event also means that smart protags can take advantage of this. This really works best with fleshed out guards that can disagree with one another.

"Write a short tragedy." The one I'm most likely to follow through on. Give a guard a personality with a flaw. Have protag realize it, or not realize it, and then exploit that flaw for the guard's downfall. Creates subtext, flavors your protag, and might create something more dynamic than just a regular shoot 'em up. This does require more weight to a scene, but that just means that you have more text to set the tone of the piece in.

"Where'd they go?" If your protags evade the guards, then the guards might be looking for them. An early success does not mean that the guards are dealt with for good and that goes with any problem that the protags face. Reintroducing them as a recurring threat ups the stakes and gives tension. It also means that the guards have learned, thereby creating a mini character arc.

This is not an exhaustive list, and none of these are prescriptive for any draft problems. They are merely some of the options and alternatives that could be brought up. The best problems are ones that don't have a clear right and wrong choice, or ones that might make the right choice far more difficult than the wrong choice. That is an entire other discussion though. The author has the best sense for what the characters are likely to do, and what their choices will do to them. Motivations are the name of the game.


When you create flat characters, characters with just names, or even just cardboard cutouts with the word "Guard" spray painted across them, you cannot give a character actions that do not fit with the characters motivations. Guards guard things, and so if they stop guarding things, they better have a damn good reason to do so. Making them more than just guards means that they can stop being guards for a second and let their other motivations take hold.

"Wait Patrick! We already knew that," you might say. "I write all my characters with complex motivations."

You might be right and this is just another silly problem that I have. It is a personal dilemma of my drafts that often goes overlooked when I'm initially plotting and writing. It is too easy to write characters without actually writing them as characters. Taking time and giving people reasons to perform the actions that the plot demands takes actual effort that I'm not always willing to give a first draft. This is something I prefer to fill in during later drafts, and with the consequence that I might need to shift the entire plot around to make it believable.

In short, never lose sight of any character's motivations during a conflict. (Especially the motivation of the security staff.)

Tuesday, August 6, 2013

Advice to Future Writers

A good friend and Clarion alumni, Isa Yap, came up with a set of questions for people that are interested in attending Clarion in the future. (This has also been addressed by Marie (another Clarion Alum) as well.) In answering these I attempt to construct insightful and creative responses that people will undoubtedly disagree with. Take them at face value. 

1. Any advice for people applying to Clarion in future years?

Write what you want to write and (more importantly) finish your drafts. 
There is a lot to write about, and very little time to write all of it. Don't waste your time writing things that you think you should be writing, spend your time writing stuff you want to write. Better yet, write the things you want to read. If an idea floats into your head and you think that it would make a good story, don't be afraid to write it. An amazing number of silly ideas become moving stories with the right wit and presumption behind them. 
With that thought in mind, never be upset about how your first draft is coming out. Never stop writing and say "this is stupid" because despite your best efforts, your first draft will suck. Your first draft will be the biggest most plot hole-y, hokey thing that you have ever read. With that in mind, you will never improve if you never finish anything. The best pieces of writing take many edits to polish so don't worry if your draft is a little off or doesn't read well. Alternately, if you think you've finished something perfect, you need to sit on it for a while and then read it to see what you are simply overlooking.

2. What's the best advice you heard/read about workshop, prior to coming?

Get sleep, and don't ignore your fellow students.
You think better if you sleep. If you have to cut back on the depth of critiques for a day in order to get a reasonable amount of sleep, do so. Sleep deprivation will kill you slowly and degrades both your writing and your reading. There is no reason that you need to write at 3 in the morning (unless it's due in the morning, and then it's your own damn fault.)
If you only read and write, by the end of the workshop you'll only have six shitty first drafts. You are going to be with ~17 extremely gifted writers that are going to write things that are completely different from anything you might normally read and write in a way that may be completely foreign to you. Take breaks. Have fun. These people and your relationship with them will last far longer than any drafts that you might finish. Cherish them. Keep in touch.

3. 3-5 biggest takeaways from workshop?

Write what you want to read.
I've already said this, but I want to hit this home. Do not write things that people say you should write. Do not write things because you think that they are more commercial. Do not write to the lowest denominator. Do not write things that bore you.
Write what you want to read and write what excites you. There are stories that only you can tell and these are the stories that only you can write. Even if you don't think you have anything to say, I promise that if you write what interests you, it will interest other people.

If writing is running, reading is eating.
You can only really write what you know. Reading expands what you know, so read everything. Fiction is great and helps you to write fiction, but non-fiction helps you write too. Read things you think are good so you can steal ideas off them, and read some select things that are bad so you know what to avoid. If you write science fiction, read fantasy. If you write fantasy, read science fiction. If you write both, read literary. If you write anything, read non-fiction because the real world is far stranger than anything that we could ever dream up.

Don't submit work to a publication that you don't enjoy reading.
When you are trying to submit work, work that you love and you have poured your soul into, don't settle for shitty publications. If you don't enjoy reading it, people won't enjoy it either. The people that share your interest in what you are writing will share your interest in what you are reading. If you absolutely love a publication, send it there.
Second part to this, go from the top to the bottom. Send it to the big names first. Asimov's, F&SF,, and the list goes on and on. Never sell your work short, because the worst that these publications can do is say "no." Dream big or go home. Writers need a thick skin and a bigger ego.

Never be afraid to kill your darlings.
This goes for your prose, this goes for your characters, and this especially goes for your plots. Nothing you write is ever above being cut. The more that you love a phrase, the more likely that someone else will hate it. Your lovely, flowery adjectives must die, your precious adverbs must be brutally burned, and every noun that can be replaced by "said" and "asked" must be unceremoniously ripped out. Strip your prose down the the barest structure and then read what you have written. This is what you are actually saying. If you want to say more, think carefully about it.
Don't pull punches and don't think death is the worse thing you can put a character through. No character is ever above being brutally beaten to within an inch of their life, letting them barely live, and then letting it haunt them for the rest of their lives. Always remember that killing them off is far cheaper than making them suffer. If they need to die, make it sudden and thoughtless (because that is often what death is) and make it hurt to everyone else.
Nothing you do is ever clever enough. Your well intentioned, carefully planned, meticulously outlined plots will drown to death on the page. Your characters will have no trouble gleefully forgetting about what you had intended them to do and are content to be quite contrary to anything you had in store. Never let your cleverness get in the way of the story that is trying to be told.

Writing is hard and thankless.
Anyone that tells you that you can make a career of writing is probably lying to you. Unintentional, but true never the less. Writing is not something you should do if you are expecting to be famous from it. Writing is not something that will come easily or naturally every day. Writing is not something that will make a steady or sizeable income. Do not expect your book to be famous. Keep your day job and make it one you find tolerable. If you romanticize the idea of publishing something, it is going to be very bad news once you get into the grit of what it actually means to produce publishable work.
Writers are masochists. They do not care if they type deep into the night fueled by some strange fancy. They do not care how many people hate their work and take the time to write them long letters informing them of such. They do not care how many rejection letters they have already gotten from every publication house under the sun.
They didn't all start that way, but that's what you have to become. In becoming a writer, many people have become very kind, understanding, and generous. They understand that rejection is normal, and they ignore it for the people that genuinely care about the story they are trying to tell. Write because you love writing. Write because you love people reading your work. Write because you cannot think about doing anything else with your time. Write because you love writing, and know that it won't always love you back.

4. If we were maybe wondering, "oooh, I wonder what -your name- considers his/her biggest 
influences," what would you tell us?

This is going to be kind of sad and embarrassing. As a kid I read a lot of stuff, and a lot of it got lost somewhere down the dark passages of my grey matter. Instead of thinking long and hard and impressing you with the  I will write a short list of names that have gotten me through my awkward teenage years and into my awkward early-twenties.

Terry Pratchett, Neil Gaiman, Isaac Asimov, Douglas Adams, Anne McCaffrey, and JRR Tolkien.

These are the authors I read growing up as a kid. These are the worlds that I traveled through during middle school and high school. They are staples of fantasy and science fiction, but they are the people that brought me the greatest joy when I was trying to figure out life in all its complexities.

5. Best book you read this year?

This is the part that is going to get me into a lot of trouble. I actually have only read probably four or five books this year, and while I have enjoyed all of them I struggle to think of which would be the best. I think I will settle for the strangest one that I would recommend.
House of Leaves by Mark Z. Danielewski was a very strange and compelling book. I personally think that some of the theatrics of the formatting are a bit over the top (which many people will either fiercely agree or disagree with), but the premise and the general oddity of the construction make it very entertaining to both read and think about.

That is almost everything that I want to say about these subjects for the moment.
G'night folks.

Sunday, August 4, 2013


While currently sitting at home suffering jet-lag, I feel like I've just woken up from a strange dream. This is my first day home from Clarion 2013, and I don't entirely know what to do with myself. I've recolored the blog here and hooked up my various social medias a bit better. (Tumblr and Twitter are becoming a bad habit of mine.) There is just too much running around my head for me to rest properly and maybe I just need to go over everything one more time. I guess I can recap just a little bit for you guys.

A common description of post-Clarion is scuba decompression. The pressure of forcing words for six weeks and having a constant stream of other's first drafts to read turns the brain into a strange stew that is both anxiety ridden but also strangely intoxicating. It is this addictive latter part that makes Clarion so powerful, but also so very difficult to adjust from once we come home. The pressure of all the words surrounding us is suddenly released and seep out of us leaving us unable to properly eat, plot, or sleep. I've heard this from many people -- instructors and alumni alike -- and what everyone has recommended is time. 

Over the course of Clarion I have written five new first drafts, typed over 40k words, read roughly 100 stories (at least twice apiece) and provided each a heartfelt and head scratching critique. All of this over six weeks, but in reality recounting these numbers doesn't mean anything to me. They don't describe the entertaining frustration of reading a story constructed almost entirely of non-linear footnotes (which was eventually cut up and reassembled on the floor), the sudden realization that you are reading someone's semi-fictional biography (which had multiple occurrences and was equally heartbreaking each time,) or the satisfaction you get when you hear someone yelling in rage from the other room while they are reading your draft. (It was about grammar. I'm not going to lie.) These numbers are merely placeholders for the things that I have done and goals for the work that I still need to do. Numbers speak nothing of the many brilliant people that I have met during my time here.

These six weeks have introduced me to 17 other aspiring writers from a diverse age range and background, and I have fallen deeply in love with all of them. (This speaks completely separately from our brilliant and benevolent instructors who are a constant inspiration.) From east coast, west coast, and even from down under, each and every one of the members of this Clarion class have inspired me at least once (and usually multiple times a person.)

I'm not sure if this strangeness has seeped into my bones for good or if it is but a passing plague, but part of me really hopes that it has nested as a chronic habit. My other hope is that that this habit is contagious. If you have an itch to write, attending Clarion at some point during your short time on earth would be a highly advisable option. Even if life takes a different path, don't stop writing. 

I hope I've entertained, informed, and potentially inspired you, but mild amusement is acceptable too. It's almost one in the morning here and I think I've decompressed enough for this session. I think I can finally sleep.

G'night folks.

Wednesday, May 29, 2013

Sketches and Love Letters

I recently watched at TED talk (recently being a few hours ago) while being stuck inside due to the beautiful Michigan weather (rain, still.) I was inspired, a little bit at least, because I finally figured out how visual artists manage to post all of these things online (via tumblr or blogs or any number of different things) and still be able to pursue their craft more formally. They show sketches. They show little pieces of things that aren't exactly finished product, but are still good. Still at the heart of what they do and produce.

I wanted to share a sketch of mine with you guys. I know that I don't get a lot of comments on here, (something that really was brought home as the first comment on my blog was "test" just a few days ago) but I'd like criticism, and I want to sort of know what people think about it. I tend to write this blog in a more personable way (at least I think so) and... I don't know. Maybe these love letters to the internet are a little taxing to write when you never get a response.

Sorry about all of that, but sometimes it's nice to hear back. I submitted a few works recently, and it'll be a while to hear back from them, but I can share something I've been working on. It's a little rough, but I have a feeling it needs to be a much longer piece than I can write right now. Maybe I'll pick it up at a later point and polish it properly, but right now it's just a sketch.

The Shaman

Thomas was known to most as a skilled bike mechanic with a head for numbers, but he truly had a heart of iron and breath of smoke. His family had come over from the old country, from the highlands, years and years ago. He grew up with his mother and younger sister, and though not easy, life was never bad for them. He had a knack for getting machines to work properly, which seemed magical to most, but to be honest: he just read a lot of manuals and had the right tools. A logical mind his teachers would call him, but they didn’t have funds for college so he just sat around the garage fixing bikes and the occasional car, but only an easy fix. He made enough cash to spend on his personal ride and enough to keep his family comfortably living, but that was all he asked for.
There was a lot that he could do that might seem magical to most: clear a fuel line properly, set wheels spinning symmetrically so that they wore even, and could put a bike together from parts in just an hour or two. These were skills to Tom, not tricks. He never boasted about how to get a bike tuned so tight that it could off road without new shocks, or how he could make a three-eights outside hex fit every bolt. These were just things that people expected mechanics to be able to do, and so he did them. He always did little things wrong when someone knew what they were doing though. It made them feel a bit better to get to yell at him, but the results were always what mattered and he delivered.
There was little magical about what Tom did when he was fixing bikes, but that wasn’t the case for when he rode them. To him, riding a bike was a religious experience. There was a transformation occurring, turning gas into energy into life. It made the bike pulse under his hands and breath under the saddle. The roar of a bike was like a song conducted by an orchestra, and he could hear every part clicking together. He could even tell you when your brakes were going bad just by the sound of your engine turning over.
When he rode, the bike didn’t feel like and extension of himself, as many others would describe it, but as a living thing that he meshed with so perfectly it was hard to see a real difference between the two. He once sent a kid to the hospital for spitting on his bike. Not in any malicious way, but people get violent when other people spit in their face. The air rippled across his skin and against the metal of the bike when they rode. He could feel it as well as the beating of the pavement under the wheels and the circulation of gas and oil through its veins. He was alive when he was riding, and though he wasn’t like a bird soaring through the sky, it must be a similar experience.
There was a difference between his bike and cars. He didn’t care for driving cars, but not for the reasons you’d expect. They were still alive, but they were a different beast. They were more docile and more skittish than a bike. You could run them for harder and longer, but they had a heavier sense of self. You could get lost in a car, all the parts spinning and flexing like some great oxen, but a bike was a mutual thing. You felt the bike and it felt you. That’s what Tom always believed at least.

They had asked him to do a speed run. That’s what Tom was good at, and honestly he didn’t need the pay but they insisted and they cashed out very well. Small package, but that had never affected the run or payment before. The went over the route, and Tom made sure that he mentally shaved off seconds with shortcuts and free speeding areas. The item was only going to be available for a second or two, so the timing was critical. He was good at that timing though. He set out, his bike sporting a fresh set of black coverings and a spoofed license plate, and began. The most difficult part of these jobs was thinking about the job. He fell into the speed, the exhilaration and the feeling of the machine rush with him. He never had to check where the other vehicles were, he just could tell with that same sense as when he drove. He felt them on the roads, plowing along, unconnected to their drivers. Sometimes he would feel another true rider, but that was a very rare event. 
The package was being switched between two individuals and he simply had to cut between them and grab it. This was the hard part, but even then he knew when they would be there. They had people that knew these sorts of things, but he never questioned the timing. The timing was always right with these people. He just had to be there to take advantage of it. He saw the scene as they described it: a woman in a yellow dress and a man in a tattered suit. He honked as they held the package between them, startling them both. He gripped it as he pushed between them, and kept going. This was the point where he could just let go.
He revved the engine and let the road take him. The sooner he got there, the better, and the faster that meant he could go. The wind rushed in his air and he weaved through the traffic like smoke. This why he did the job: the feeling of true speed and purpose for his gift. This is what he considered to be close to flying. Then something went wrong. 
There was another rider there with him. Not on another car or bike, but riding with him in his bike. It felt strange, like someone watching you make love or staring at you while you slept. He didn’t like this feeling, but he didn’t know what to do about it. He clicked the radio button at his helmet and voiced a concern. They sounded alarmed at the other end. They wished him luck, but that they wouldn’t be there when he arrived. He wouldn’t get paid, and if he made it out of this that he should never contact them again. For safety reasons, they explained and then wished him luck again. The radio went dead silent, and Tom would have felt truly alone if he didn’t have someone riding in the bike with him.
He put extra gas in the engine and gave the issue a serious thought. What was he going to do about this? He didn’t know his employers real well, and he certainly didn’t know what to do about the package safely nestled behind his handlebars. What was he going to do about the extra person riding with him in spirit? He though it over as he took a short cut and then came up with an idea. He looked at the man like he looked at bikes when he was fixing them. He saw the person behind the facade, and then he pushed. 
Kicked would be a better word for what he did. He mentally kicked the rider in the face, or the face equivalent and felt as their grip left the bike and it disappeared behind him. He then sped up. He took a slightly longer route home. Went past a few spaces that were out of his way, and though spaces that normally weren’t open to the public. When he got home, the plates and covers came off as quickly as he could shut the garage. He would deal with them later.
His mother was taking a mid-afternoon nap and his sister had yet to come back from high school. He began to put some ramen on the stove for himself when the doorbell rang. He opened the door carefully, and there stood the man that had hitched a ride, standing on his door mat. He looked different from when he was riding: the hair was dyed and the teeth weren’t as perfect, but he was unmistakable. The man saw Tom and just smiled. Tom reached over to the hall table and picked up the small package and handed it to the man, who began laughing when he saw it.
“Well, that certainly saves me a lot of trouble,” said the Rider as he took the package from Tom’s hand, “and I don’t suppose that you are looking for new employment, are you?”
Tom just nodded slightly. 
“Good.” The man smiled again, “Because I have a job that I think you’d be well suited for.”
It was at that point that Tom could tell that this was the beginning of a interesting series of events.