Thursday, October 10, 2013
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
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!
Monday, September 9, 2013
|Grand Prismatic Spring, Yellowstone National Park|
Color variation due to microbial biofilms.
|Staphylococcus epidermidis, Common skin flora|
Scanning Electron Image
Thursday, August 29, 2013
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 [google.com].
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
(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."
When Species Mingle
|The Beautifully Illustrated Mountain of Mice|
Saturday, August 17, 2013
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
(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
"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
Write what you want to write and (more importantly) finish your drafts.
2. What's the best advice you heard/read about workshop, prior to coming?
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, Tor.com, 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
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.
Sunday, August 4, 2013
Wednesday, May 29, 2013
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.