Search This Blog

Saturday, October 30, 2010

The Inupiaq Eskimos and Wage Disparity...

For a course, I'm reading through an ethnography of sorts of the Social Life in Northwest Alaska: The Structure of Inupiaq Eskimo Nations by Ernest Burch, Jr.  It primarily focuses on those Inupiat  living in the region between the Seward Peninsula and the region around Point Hope on the Chukchi Sea (near the Bering Straight) between about 1800 and 1850 when outside influence really hit them. 

Wednesday, October 27, 2010

Art and Science

Spent an hour or three assembling a set of DNA sequences for ape sex-determining regions of the Y-chromosome (SRY's) as well as one or two for macaques as an outgroup.  Several sequences included the 5' region and some were partial coding sequences.  This means--given the wide variety of lengths and evolutionary time--the software sort of ate it on the alignment.

Basically, the software tried to start the sequences in the middle and blew them apart trying to line them up.  Happily, one sequence, a human reference sample, covered the entire span and I could manually put them together.  The thing that really got me was how much SeaView (a program to edit sequences) and MEGA (a general purpose phylogenetic software) made the sequences look like a Scottish plaid, especially when some of the sequences are partially aligned.

Of course, it's not the first time I've connected art and science.  My pet name for microbiology was "art for science majors" because the tendency for others to stain various parts of their body.  (A secondary reason I dropped the pre-nursing idea, another being the number of my classmates showing an inability or unwillingness to wash their hands.)

In that case, it was accidental.  In other ways, like the manual alignments, it's an interesting connection between the rational, logical way to execute tasks and the somewhat intuitive means to accomplish the parts around the logical core.   Not de novo intuition, but informed intuition to be sure. 

I think that's one reason I like science: the integration of creativity in building research ideas and solving problems and then the logic of analysis.   

Monday, October 25, 2010

Science at work...

Learned at my seminar on Fundamentals of Complex Adaptive Systems (CAS) that I may have been a subject in a study of Social-Ecological Systems published in Science in April. The presentation today by Dr. Marco Janssen was essentially a brief on the study within the CAS context.

It was interesting hearing the theoretical interpretation of something I got to participate in.  The explanations of why we were asked to do certain things makes sense at this level. 

Although the article is linked to above, the basic research idea was to look at the effects of communication and punishment schemes in self-regulation of an artificial ecology.  Basically, the participants--5 to a group--"harvested" items from a closed space where the regrowth of the items depended on the density of items remaining.  (More dense areas = higher regrowth)  If the items were depleted, nothing grew back.  In scenarios where punishment was allowed, the participant could pay some of their harvested items to reduce the items of someone else.  When communication was allowed, there was a 4 minute text chat between scenarios. 

My personal experience with the game was one of frustration.  We had a group member that--to be blunt--was an antagonistic *insert expletive* who intentionally sabotaged any and all efforts for the rest of us to succeed.  After a while, the game devolved into a group effort to ensure the antagonist walked away with zero items.  We were awarded a small number of extra credit points based on our performance and I think only one or two of the group accrued more than the minimal amount.*  I have to be honest, I was a bit nihilistic in my pursuit of and punishment of the antagonist, primarily due to his harassment of the others.

What might be interesting--and what I suggested during the seminar--would be the ability to eject an antagonist like that from either the scenario or to create two areas within the scenario's field where a consensus of members could restrict another member (or members) from.  Essentially, using banishment as a cost of punishment reducer. 

A second idea would be to test the ability to set a leader who could punish at a lower (shared?) cost.  I can't remember where, I need to find the reference, but I was glancing over a paper that looked at leaders and hierarchy as a means to lower individual costs of costly punishment.  This could explain both the utility of hierarchy as territoriality shows up in studies of hunter-gatherers and some measure of the parochial altruism paradigm.

Regardless, it was enjoyable to see that study from both perspectives.



* - As befits a student of governance and social-ecological control, Dr. Janssen set up his extra-credit scheme so as to make it impossible to exceed 100% of the normal points.  Therefore, I didn't really need the points, it just would have been nice to be able to earn them.

Sunday, October 24, 2010

Yahoo Answers Reply: "Why do so many people attack Darwin and evolution?"

Here.

My answer:

"For most people, their day-to-day lives are heavily invested in trust relationships with those around them. These trust relationships often include rules and norms such as who may have sex with each other, who provides food or resources to each other, and what may each person do. These norms and rules are often derived from or derive power from one's religious beliefs.

Because these beliefs are so influential on people's lives and the belief system is tied into enforcement of these (costly) rules, surety of the correctness of the whole belief system is critical to maintaining these peoples' way of life.

Most religions are currently written religions where there is no/little area for reinterpretation and comparison--on a logical level--is simple. These religions were generally written and/or conceived of during a period of human understanding that did not include the ideas of evolution nor practical, recent knowledge of the biological relationships between humans and other species. Therefore, most religions have embedded in them the idea that humans are inherently and categorically distinct from the rest of the living world.

So, the reason why many people attack Darwin and evolution is that the principles and implications of Darwinian evolution-specifically the relationship between humans and the rest of living creatures and the implication of self-governing, complexity-producing process over a much longer period of time than their religion infers--challenges some elements of their belief system. This challenge puts their way of life at risk because it risks others not following otherwise costly rules and changing their ability to trust, find/keep mates, gain support/resources, etc. This paradigm also explains why people who are more self-sufficient and independent of religiously-driven social environments are more willing to consider Darwinian evolution on face value.

So, good luck with that, eh?"

 

Saturday, October 23, 2010

Social Networks and Infectious Disease...

Dr. James Holland Jones of Stanford gave a presentation yesterday at my school and I dragged my girlfriend to it.  Her eyes glazed over after the first couple minutes because she's seriously not into social networks or disease, but it was fascinating.

What he presented on was a combination of simulation and modeling work and an interesting empirical study looking at social structure within a school.  Primarily, his team applies graph theory as a tool to understand social networks as a basis for looking at disease transmission. 

Different types of behaviors influence the effective form of social networks in a way that influences disease transmission.  For example, the social mores connected to sexual behavior often promote a dendritic or long-chain network while other sorts of behavior can create clustering.

The differences in these patterns influence the transmission of disease, especially when one compares the degree of modularity.  When a population is tightly clustered with most connections being between people in the same cluster vs. people outside their cluster, disease transmission measured in total infected at a particular time looks "lumpy" as the infection passes quickly inside clusters and slower between them.  When the proportion of internal connections to out-of-cluster connections is higher, the infection spreads more quickly and is smoother with a higher portion of the overall population getting infected.

The theoretical background also looked at individual person/node traits like degree (number of connections from one node to others) and the potential effect of relationship/connection cost. 

The empirical study primarily looked at whether people follow one or more of the theoretical models in forming social groups.  The study used "motes" or small sensors worn on the front of the body that could detect the signals of other motes at very short, conversational ranges.  Essentially, because the mass of the human body blocks the signals, whenever the motes "ping" every 20 seconds and detect another mote, you essentially have a face-to-face interaction.  For disease transmission, these are the sort of encounters allowing for flu transmission.

After listening to this presentation and one on a study looking at social networking and health  by one of my instructors a few semesters ago, Dr. Matt Newman, at University of Texas at Austin using a timed recorders, it makes me wonder if this sort of technology might be useful for sexual behavior inventories.  Obviously, ethical issues might prevent actually recording sexual behavior as it happened on a large scale, but being able to compare self-reports and mote-derived data might be useful. 

Additionally, using the methodology to understand stress response modification through social interaction could be interesting and useful, but might require a "ruggedized" type of mote with a low maintenance and annoyance footprint for the participant.

Thursday, October 21, 2010

"15 Things Not to Say to Your Boss" and how many I have...

This article caught my eye because--first of all--I'm a sucker for any set of truisms, mostly because I like to look for exceptions.  Second, although I've not violated all of these, I've said a lot of them to bosses in one context or another.  So, here's my list:

1. "I’m only doing this job for the money."

One of the best things I ever did was be honest with my supervisor in the first civilian employer I had after the Army.  His name was Brian, the industry was pest--specifically, termite--control, and I was up front with him about why I was working there.  To be honest, I made it clear I liked my coworkers, I liked figuring out how to solve the testy problems and customers, but I was honestly only there for the money.

Brian recognized I was good at what I did and the fact my talent dealing with the unusual jobs and difficult customers was something most of his other employees had difficulty with.  He also knew I wasn't after his job and relaxed.  He then proceeded to ensure my pay was competitive to my peers and overtime was doled out based on who wanted it.

2. "I’m broke/in debt/one step away from bankruptcy."

I have an ex-wife.  I married up a class and the ex-wife still tried to live to the standards to which she was accustomed.  When the Army and every other major credit-card company gave us credit, she took it and ran with it.  So, about a year prior to me leaving the Army and after a permanent change of station to Alaska where one or more payments were misplaced to the line of credit for the Army and Air Force Exchange Service (AAFES or the military's "company store"), I found myself on the receiving end of paying back $2800 of debt in three easy monthly payments on an income of about $1800 a month.

I took this to my supervisor and I was honest about it.  There was nothing my chain of command could do to stop it, but what they did do was provide other types of support and assistance including authorizing selling vacation time to allow me added money for food and the like.   In many ways, I wish I had been more honest earlier because I may have been able to prevent some of the fallout.

3. "I’m going to quit after I (fill in the blank)."

To be honest, I think this statement, usually with the (fill in the blank) replaced by an education goal is one reason I've been let go when I have been.  If anything, I make a point to be honest about when my goals and priorities conflict with my employers in order to allow both parties to work things out.  In some cases, the employer pushes the timeframe forward for other reasons—like the economy dropping in a pay-to-play business or by changing their staffing requirements—but, for the most part, it works out.

4. "I partied a little too hard last night."

I'm not a drinker; I don't do drugs, so this one never came up.

5. "It’s not my fault."

This one didn't work out so well.

There was an issue with a company vehicle where someone (most likely) tried to pry open a driver's door with a crowbar after I was instructed to leave it unsupervised in a nearby parking lot.  Essentially, I was accused of damaging it myself, which didn't make much sense to me.  I declined to sign off on the financial responsibility form.  It essentially devolved into a "he said/she said" where the she was the management trainee who directed me to leave it in the parking lot.

Brian—who I mentioned in #1—was ordered to fire me if I didn't sign off on the form.  I declined again and made a call to the regional manager of the company who again offered to let me keep my job if I signed off on the form.  I declined to lie, filed for unemployment, and filed a complaint with the appropriate authorities.

I still lost the job, but they didn't take the $300 for the damage.  Call me a bit of a nihilist, but I'm not one for lying just to keep a job.

6. "I’m bored/this job is boring."

I haven't really used this one.  I'm a pretty task oriented guy, willing to change jobs if it's mind-numbingly boring, but I usually gravitate towards the interesting parts of the job anyway.  Often, my solution to boredom is finding a problem to solve or developing a new way to do a job more efficiently.

I killed termites (and other social insects) for several years.  Gives you a respect for them, but it's a combination of manual labor as well as problem solving and customer interaction.  One of the interesting, efficiency tasks was managing to treat a house quickly and efficiently in a way you could minimize both dust and dirt inside a house. 

For most houses in the Phoenix area, treating a house includes treating a trench around the perimeter; identifying, drilling and treating cracks, through the concrete floor slab; and treating the joint between the floor slab and the concrete stem wall that surrounds it either from the inside (through the floor) or through holes drilled in the stemwall.  So, the technical problem includes essentially treating the entire perimeter of the house twice (inside the stemwall and out) as well as cracks.

My favorite solution when using more than one team was to jump out of the truck, greet the customer and walk them through what we were doing, setting up inside drilling by lifting carpets and moving furniture as I went.  Then, before my teammates got busy, I set up there trenching tools, drills, hoses, and extension cords where I wanted them to start--generally the farthest interior starting point and the farthest exterior starting points.  They could have moved their gear and started elsewhere, but most of the time they simply started where I put them.

If any special circumstances existed--like an inside-the-floor koi pond--I would walk them through that as well.  The nice part is those jobs usually worked out to be a lower labor percentage (labor cost/contract price) and the lowest amount of man hours for most of the teams.

Not so much time to be bored.

7. “My job is too easy.”

I've probably used this, but I don't remember when.  There is always a way to make a job harder.  Challenging one's self for speed or perfection is one way.  Reworking job tasks for efficiency and picking up other, more interesting tasks can be another way.

My last pest control job was actually pretty easy.  I hated it most of the time because--unlike the termite work where you had several solutions to work out per job--the pest control job was essentially drive to the site, put on safety gear, spray the yard, leave a receipt, and go.  Typically, the expectation was about 30 houses a day.  If a client wanted more, they were expected to call in and we'd send someone back out.

Those call backs were what I really preferred.  Usually, it was some pest that the general treatment didn't cover.  Things like bedbugs or ants inside.

Most of the time, I "amused" myself by looking out for potential pest problems and harborage.  For example, noting where cracks in walls or stucco allowed access for crickets and/or scorpions, identifying moisture conditions where subterranean termites could take hold, or standing water for mosquitoes.  When I identified them, I communicated the problems with the customers so they had the chance to fix it.

To be honest, I lost that job because I was both starting college and I "didn't fit the business model" according to my supervisor.  My proactive efforts weren't part of the business model and my efforts for increased quality of service reduced the quantity of houses I treated per day from about 30 to about 26.

The irony is I was one of the more flexible and complimented technicians.

8. "I can’t work with so and so. I hate him."

Not a phrase I used, but one I wish I had used. 

One of my platoon mates in the Army had a reputation as a punk and tried to live up to it.  Personally, I have a thick skin when it comes to insults and the like, so I shrugged off his attempts at intimidation and did my job.  That worked until he tried to physically assault me.

It didn't work out well and it's one of the reasons I left the Army.  What I should have done, when his issues persisted and no one else said anything about him, was to approach my chain of command with the problem instead of simply working around him.

9. “I can’t do that because of my other job.”

I've only used this statement in the context of multiple duties within the same job.  I've never really moonlighted, but—at various times—I've had multiple duties within the same job that have come into conflict.  Typically, I would restrict this sort of phrase to situations where I can no longer maintain the appropriate standards for each job.  When I have used this phrase, I've always made attempts to offer suggestions allowing me to accomplish both duties. 

For example, I worked for several months in a single doctor medical office.  My primary duties was to research outstanding insurance claims and attempt to resolve who was fiscally responsible in order to get them paid.  An added duty was the entry of payment information from paid claims—often because of the outstanding claims I resolved.  When the priority became entering payments, I pointed out it conflicted with my primary duty and the existing procedure others used for trying to recover outstanding claims duplicated and delayed my efforts.

When the decision was made to share my primary task with another employee, I created a basic tracking form to allow us to track the work done, tasks required, and the recovered information for each client.  This allowed us to quickly move back and forth between duties and clients with little duplication in effort and be able to accumulate the information needed to resolve the claims without resorting to a default "send out another batch of claim forms" plan.

In many ways—with that job—I was a victim of my own success.

10. “Oh my Gawd! How did you do this job before the Internet/text messaging/Skype?”

I've used this one only in jest.  I make an effort to understand both the current method in use—for whatever job I do—as well as a little bit of history in methods.  Often, the "old methods" include how to do the same task when equipment fails or certain requirements are not met.  Also, being able to use a variety of technological tools allows me to be more flexible with solutions.

11. Sigh. Grimace. Eye roll. Wretching noises.

I've used these as well, mostly the grimace.

Some supervisors are dangerous.  Sometimes, it pays to be able to communicate your lack of confidence in a supervisor's ideas to others in order to facilitate changing from a potentially dangerous plan.  I loathe admitting this, but I've done this to communicate with patients and clients while a supervisor is present.

The first time I consciously did this, I was an Army medic and the patient had come in with swelling and pain in his hand after handling a pig's carcass with a cut on his hand.  The NCO in charge at the time suggested a simple non-steroidal anti-inflammatory for the "inflammation". 

Because of the rapid onset and the spreading of the swelling, I suspected it was something more and wanted our medical officer to see it.  I suggested as much to the NCO, he refused to listen to the explanation.  Normally, I would have left it at that, but this was something I recognized as being a decision above his pay grade.  I tried to communicate the problem non-verbally to the patient.  It didn't work.

When the NCO sent the patient out, I followed and told the patient to come back in a few minutes when our medical officer returned.  The patient chastised me for being disrespectful to the NCO.

The patient returned 4 hours later with his entire right arm swollen, hot to the touch, and inflamed.  The medical officer diagnosed it as cellulites—a rapidly moving infection—and initiated immediate medical evacuation and IV antibiotics.  Then he spent the next hour tearing the NCO and me a new one for letting the patient walk out that way in the first place.

Most of the time, I'm allowed to and able to communicate what the problem is to supervisors in such a way as to avoid such issues.  In general, if the supervisor's name is on the door or the business license or the hand receipts and I'm not being asked to lie, cheat, steal, or do something unethical, I'll roll with whatever a supervisor wants and I've done some silly things because a supervisor asked.  Only when someone's life, limb, eyesight, livelihood, etc. are involved and no one's willing to listen do I make efforts to communicate by other means or just say "no".

12. "Do it yourself!"

Used this as well, after a fashion.  Again, a stateside Army medic and a life, limb, or eyesight issue.  I ordered a Battery Commander—an Army Captain—to call for a helicopter medical evacuation while triaging a soldier of his in heat stroke.  Being the sole medically trained soldier present, I got a little bossy in order to overcome the Battery Commanders general reluctance to spend the Army's money that way. 

Because my priority was initiating treatment and treatment was critical, I used a tone I wouldn't normally in order to make it clear the situation was both real and necessary. 

13. “It’s always been done this way.”

I've used this one sarcastically.  I usually use this one in conjunction with a suggestion of an alternative method.  I usually simply offer suggestions when I see the potential for improvement. Knowing several ways to accomplish a task is something I prefer to learn and like to judge effectiveness of alternatives on merit.

I worked for a year in a veterinary hospital.  Given the fact we were open on weekends and saw exotic animals as well as birds, cats, and dogs, we had emergency calls often.  We ran into problems with triaging cases over the phone, especially when a pet owner called in with either an exotic pet (some of our vets didn't treat some types of exotics) or when they called in and had to decide whether or not they wanted to go there or somewhere else.

Because of the confusion between the receptionists and the vets or assistants, I developed a small in-house triage sheet that essentially pushed the reception person to ask the right questions so the vet could decide whether to see the pet and to track things like phone numbers and dispositions for those pets we hadn't treated before.  It also sped up the in-processing for pets and owners that were treated by the hospital.

14. "Let me set you up with..."

This one, I've never said.  Frankly, I try to leave the intimate relationships outside of the boss-employee purview.

15. "Sorry, I must have drifted off."

I haven't used this one.  In general, I'm disciplined enough to not sleep when I'm supposed to be working and--when I can't due to illness, etc.--to call in sick when I know I'm unable to perform my job safely or to standard.  I hate to leave coworkers unsupported, but I am conscious of workplace safety and health practices.  I get sick rarely, but take sick days when necessary to avoid getting my coworkers sick and to promote a safe work environment.

Research ideas...

I'm a little odd in the fact I go nowhere without something to write on and a writing utensil.  In some ways, I think, it's fear of boredom.  If I have something to write on, I can draw, sketch, think out loud on paper, or otherwise find something to do.

I also--for school--have this tendency to keep a variety of things in my pack.  Extra pens, pencils, and office-type supplies occupy one pocket.  Another pocket contain those little plastic note cards with things like "Deep Anatomy" or "Nutrition".  I also usually carry a really worn copy of the Penguin Dictionary of Biology.

One other book I don't leave at home when I go to school is a small composition notebook with "Research Ideas" on the cover. 

Inside, I scrawl, one to a page or--for a more detailed idea--several pages, research questions, concepts, and hypotheses.  Typically, it's based on something I hear in a class or in discussions with other people.  Some are just a statement of relationship.  Others are more formatted with diagrams, potential methods, and the like.

What my intent is--when I get time--to work through the literature and explore the possibility of actually running some of them.  The range of appropriate techniques runs from psychological surveys, mathematical modeling, agent based modelling, and/or ethnographic research.

I also tend to collect PDF articles from searches for coursework and the like in an archive for future use.  I plan on organizing a standard "research idea" format to use and create a project list. I figure I can work up some of these ideas to a point I can credibly search for an advisor or co-author.

Regardless, the idea of--and process of--research is a bit of a drive for me now.  There's just something almost tangibly satisfying about pulling off a successful project and finding something.

Monday, October 18, 2010

Games and simulations...

I'm currently auditing a graduate/undergraduate seminar on the Fundamentals of Complex Adaptive Systems (CAS) that is cross-listed between about 6 different course prefixes.  For the most part, the seminar is based around presentations by people conducting research on CAS.  Today, however, the presenter had to reschedule and--instead--we spent the hour or so discussing what we've learned so far.

While there were some general questions, most of the time was spent discussing modeling and simulation. The biggest question was "What does it mean?", in a somewhat paraphrased manner.  I also got the impression that most people in the seminar had a general idea of the concept of modeling and simulation, yet lacked an understanding of how to do one or the other.

To be honest, my attempts at mathematical modeling are rather simple and algebraic.  I understand what they can do, I just have a basic level of calculus so the transformation from concept to creating the parameters in the modeling is a little beyond me for some forms.  (One thing I intend to do--assuming time and resources--if I have a gap year between undergrad and graduate is to refresh and upgrade my math and/or statistics background.)  So, for the most part, I prefer working on agent-based models in NetLogo, primarily because I'm interested in social behaviors.

I seem to grasp the concepts and just what the basic utility of modeling and simulation on an intuitive level--partially because of the amount of coursework I've had in the sorts of systems they use for examples.  Another factor, I think, is a teenage and young adult history of playing war games like "Steel Panthers" and "Panzer Blitz".

What that form of war game has in common--whether played against a computer or another player--is the combination of hidden elements, heterogeneity of terrain, and interactive constraints for all the elements.  While most people can cognitively say these factors are present, after a while most (successful) players begin to make predictive assessments based on the interaction between the factors in a rewarded (win) or punished manner (loss).  The mental "conditioning" usually moves beyond the agent(simulation elements)/unit(game elements) toward sensing out how the interactions play out.

Doubly so with a human opponent.

It's unlike a conventional game like chess or Risk or even other computer games like first person shooters in the fact successful players integrate the partial knowledge they can know from the system/scenario with the knowledge underlying processes are at work unseen and are limited by the constraints of the model/scenario in such a way as to produce what they see.  Additionally, the understanding of path dependence (whether by terrain on the map or the parameters set such as opponent's nationality and date) becomes a somewhat default process.

Additionally, for anyone playing a number of such war games, the concept of scalability and aggregative processes is also quite clear.  What works at a "tactical" level doesn't necessarily show up at an "operational" level within such games.  Instead, you learn to focus on the processes at that level and identify what traits do carry over when you rescale as well as what might have a changed effect. 

(For WWII era gamers, German Tigers are loads of fun at a tactical level, but as soon as you start having to manage fuel and repairs in a game system you start seeing how the Allies won with primarily Shermans...)

Another use for the history of war gaming, is the simple idea of competitive situations.  It may be a bias of mine, but many of the other students I talk to are more emotionally invested in the ideals of cooperation and being nice than they are in rationally trying to understand systems and/or people.  This means they often are unwilling to see or insert conflict into their understanding of different systems.  Additionally, when they do, it comes across as simple and "reluctant"--more as a "token" effort than an attempt at making a good approximation of an adaptive system.

For war gamers, the idea of conflict in systems is why you usually play the game.  It doesn't help understand the "whys" beyond a basic level, but it helps you get in the mindset of "how" an opponent might game the system and to expect novelty in tactics used by human opponents*. 

In general, it makes gamers look for options--given the system and parameters--in creative ways that intentionally run counter to the expectations of even the initially programmed intention.  For the historically minded gamer, it also presents them with a better guess about path dependent effects as they ask "Why didn't/don't they do this in real life?".

That's what I was thinking about for most of the seminar...


*- For anyone who's played Steel Panthers 3, one of my favorite scenarios was a Russia vs. Germany battle set in 1999 against a human opponent.  He brought Leopard 2's and a lot of infantry.  I brought an insane amount to rocket artillery, light infantry as spotters, and engineers to lay mines.  He essentially kept searching for my tanks until all of his units were bled dry.

After that, I expected more novelty on his part after my example and--thankfully--got it. 

Projects 1-2: Interspecies and Intraspecies rates of evolution and relative effective population size.

(continued)

Lessons learned today:

1) mtDNA genome sequences are easy to find.  Trying to locate Y-chromosome sequences for primates, not so easy.
2) Running a maximum likelihood phylogeny with 500 repetitions of bootstrap analysis for confidence assessment on a set of 16,500bp sequences takes about an hour.  This will be important to remember later.
3) I've started keeping to segregate project information into a particular folder and incorporate a running text file log to track what program I did what with, the procedures, etc.  I've done something similar on past projects except using a Word document  and writing it up as I go as the Methods section of a paper.  This should make things faster, simpler, and still allow a write-up as necessary.
4) It is generally a bad idea to export gene sequences to a CSV (comma separated value) format for editing.  Locked up Notepad trying to replace the ","'s with "".  Word did it fine, but took a while for the set of sequences above.
5) Somehow, somewhere between ClustalX, jModeltest, and Mega, one of them "eats" taxon names if they are somewhat long.  Need to reformat names in the text file to "Genus_species|gi######" format so I don't get lost.
6) This should be fun!

Saturday, October 16, 2010

Projects 1-1: Interspecies and Intraspecies rates of evolution and relative effective population size.

I'm doing a project for my Phylogenetic Biology and Analysis course and--given my interest in sexual and structural systems--I've elected to make an attempt to examine whether there are differences in rates of genetic change by sex among the apes and some human populations based on mating practices and other potentially relevant factors.


My hypothesis is that variations in mating practices--such as monogamy vs. polyandry, etc.--and locality of mates--such as patrilocality vs. neolocality, etc.--will affect the effective population size (Ne) by sex and therefore the rates of evolution within sex-specific parts of the genome.  By comparing the rates of change in non-coding regions where selective pressure shouldn't have a strong effect and by using the rates of change in autosomal sequences to standardize the changes in mitochondrial DNA (mtDNA) and Y-chromosome sequences to correct for overall populations size (N), I can try to tease apart the average population ratios for the species within the apes.

If the phylogenies (mt-DNA, Y, autosomal) match in topography and I can get the ratios in the ape species, I want to run some human populations for the same data.  Finally, I want to run a multimodel inference to examine what factors--calculated ratios, social factors, sexual dimorphism ratios, typical living arrangements--are most likely to be driving the effective population size.

It should be fun.  I know I can get the mtDNA sequences, the others should be more fun.  I also plan on using as Gibbon sequences (if available) as a standard for the rest because of their unique characteristics.  Considering I'm relying on open access data... 

Thursday, October 14, 2010

Statistics...

Should be reading, instead, refreshing my familiarity with R.

For anyone that doesn't know, R is essentially an open-source (read: "free") software package using a command line interface (read: "You type commands, generally line-by-line") used to do statistics and some other data-handling tasks quickly.  The help manuals are written in language somewhere between a math text, a computer manual, and a guide to statistics where--if you don't know them all--the particular tests are described using the names for the test you didn't learn the first time.

Still, once you get a set of scripts you know works, it's mostly a matter of picking the right tests and changing the specifics in the script.  Which isn't all that hard.  Compared to SPSS, things run faster and you're in and out of the program quicker until you want to make your output pretty.  (My copy of SPSS is older, so I sort of just play with the settings until I get something good.)

The "problem" with R is you really have to be sure what you're doing procedure wise because it will merrily calculate almost anything if the math doesn't kick out an error or you type it in wrong.  Which--in spite of several statistics and analysis courses I've taken--the first thing I do when I have to use stats is actually dig out one of the several copies of the PowerPoint presentations (PPT's) and other, assorted information my Biometry Instructor piled on us in class.

I make a point to download every possible file from the course websites at the end of each semester and my Biometry course's folder is 286MB, many of them huge PPT's.  What Dr. Sabo did on every PPT was embed the MS Excel spreadsheets he used to run up the data he discussed.  What this means for me is not only do I get explanations in the presentations (and the textbook I kept) but also examples of how to run the procedure in Excel and (courtesy of the lab materials) in R or SPSS.

Really cool, huh?

Totally worth the money.  Oh, and you have to total respect an instructor who requires critiques of published research designs and analyses as a regular part of the course and even includes a paper he co-authored.

Makes me wish my Qualitative Analysis for Anthropology (QA4A) instructor had done something similar.  Maybe even actually used PPT's for later reference.  Oddly, beyond the briefest of forays into descriptive statistics (very brief in Biometry), the only real overlap between both statistics courses was actually non-repeated measures ANOVA and Chi-square. 

Where Biometry pulled apart a lot of the parametric and non-parametric ways of approaching hypothesis testing, crashed through things like bootstrapping, jackknifing, and multimodel inference (my favorite), QA4A really focused on probability and non-parametric tests of correlation and frequencies with almost everything plotted out by hand on paper.

Still, I learned a lot that way as well.  I just hope I can find and read my notes when I need to... 

Wednesday, October 13, 2010

Epidemiology


Never really considered epidemiology as a field, but I put an application in for a position as an epidemiologist for after I graduate.  Then, I started thinking...

I've had a ridiculous amount of related coursework, employment history, and no little amount of interest in the field and its social connectedness.  I've worked on the medical side with (para-professional) diagnosis and treatment of disease, disease reporting, disease prevention and even training others in disease prevention both medically and through sanitation efforts.  I've done record screening and reporting of tracked diseases as well as administered diagnostic tests.

I worked for a number of years in the pest control industry.  While my main focus was social insects which do not (generally) cause medical problems, I also helped others and received training in treatment of commensal pests--like rodents and bed bugs--as well as educating clients in avoiding potentially disease-causing pests through integrated pest management* (IPM) techniques.

In school, because I started out as pre-nursing, I took the full complement of basic healthcare core classes such as human anatomy, physiology, pathophysiology, and nutrition as well as microbiology and introductory chemistry.  After settling on the anthropology/psychology/biological trajectory of interest, I continued studying social and biological interactions which included a lot of coursework in sexual activity.

The last few semesters, I’ve been accumulating analytical tools in the form of statistics, analyzing institutions—including health related institutions—and agent-based simulation where—interestingly—the main group project was looking at influenza transmission and social networks.  Probably my favorite course was actually a summer course on Disease and Human Evolution.  

So, maybe my perspective on epidemiology is biased by discussions of Dr. John Snow and the legwork to identify Cholera in London as well as some of the genetic studies on HIV and tuberculosis, but I think it could be fun to do for a couple years.  

Who knows?  If I get lucky, maybe I could work while doing a graduate degree?  My interests in human interaction at a behavioral and biological level has a pretty good chunk of pathology involved as well.



*- IPM are methods to treat pest infestations by identifying environmental and social factors related to the pest and altering those in order to limit the need for pesticides.  An example is removing moisture near the walls of a structure against termites and clearing and removing harborage (living spaces) for crickets by sealing cracks in a house's walls.

Tuesday, October 12, 2010

Social Commentary I: Wages and Insurance

Two of my favorite books of all time are Why Things Bite Back: Technology and the Revenge of Unintended Consequences and The Psychology of Everyday Things. Both discuss the concept of design as a process and the consequences of design.  Why Things Bite Back goes further into the process and--as the title states--the unintended consequences of design.


Like most designs, there is usually a set of rational decisions made in an attempt to resolve a problem.  For example, the introduction of Eucalyptus trees to California was a solution to the needs of the railroads for cheap, sturdy railroad ties.  The lack of insight into the systems (Eucalyptus strength is due to developmental challenge from local pathogens) and the lack of foresight for alternative actions by others (resale of Eucalyptus as decorative trees in built-up areas) produces a recipe for disaster (Eucalyptus' propensity for burning + Santa Ana winds = wildfire risk).

So, where does this tie into wages and insurance?

Monday, October 11, 2010

Too little, too late...

I am auditing a seminar on the fundamentals of complex adaptive systems* and the presentation today was by Bert Hölldobler, an entomologist and ant expert.  The topic today was on the territoriality of three ant species, including one local species of harvester ants.

I am fascinated by social insects and have been since I was a boy.  Spending about 6 or 7 years killing (primarily) termites and other social insects created even more interest and actually respect for them.  So, last fall when I took a research techniques in animal behavior course, I elected to look at territorial behavior in Desert Harvester ants (Messor pergandei).

In part, it was a sample of convenience because I had multiple colonies in the fields surrounding the dorms.  So, my initial exploration was actually spending an afternoon watching them and observing them occasionally fight amongst themselves.  When the actual data collection started, I systematically introduced a number of workers near the entrances of other, distant colonies from within the roughly quarter-mile by quarter-mile area.

Oddly, they were suddenly peaceful.

Not a single ant attacked any newcomer.  I thought--at first--it was the solvent in the paint I misted over the newcomers.  So, I waited for an hour after the inititial 2 trials.  Still no effect.  I thought it might be contamination in the "test frame" I had made from a plastic container, so I washed it throuroughly with soap and water, ran water over it and manually scrubbed with clean paper towel.

Still no dice.

It made the statistics simple, but it still nags me why the same colonies that were agressively attacking some subset of ants the week before were suddenly pacifists.  My desire to explore alternate hypotheses was quashed the next week as the weather chilled.  I posited one potential explanation was the potential for inbreeding given the distance from ASU West's campus and the open desert miles away.

Then, today, I learned two things, both something I should have expected based on the theoretical background.  First, colony identification is typically imprinted and not genetically driven as I had been led to expect.  This meant there was little possibility those M. pergandei weren't telling each other apart because of genetic similarity. 

The second thing I learned today was how dependent ant aggression--specifically in the other Harvester Ant species locally--depended on the patchiness and availability of food sources.  This is something I knew in terms of primate ecology and somewhat in human ecology, but simply did not connect it to my situation in terms of timing. I likely elected to conduct my study at a time when the availability of food did not promote defensive behavior.

Ultimately, although I prefer looking at humans and would consider primates, I would like to explore the concept again.

* - For those not "up" on the terminology, in simple terms, a complex system is a combination of elements--typically considered agents--where the agents create an emergent or novel phenomena in combinations while following only simple rules.  A complex system becomes adaptive when the system changes in response to experience and "learns".

My relationship to the military...

I'm a veteran--technically--although the only foreign country I've been to (so far) is one corner of Canada I flew over en route to Alaska.  This predated the current unpleasantness (to re-appropriate a Robert De Niro line) and means my current involvement with the military is by proxy (a friend or two) or indirectly (my ex-wife is married to a soldier).

But, what is this doing in a science-oriented blog?

First, there is a somewhat common attitude from anthropologists I've taken courses from towards anyone associated with the military akin to the way most people treat someone with autism spectrum disorders.  They acknowledge their existence, but treat them as a person, but tend to assume their judgment is inexorably impaired.

For some, this is entirely understandable.  Their experiences with the military on a personal level are often derived from interactions with the military in the context of student protests during the Vietnam War.  Add to it potential interactions later in regions of the world where the only other Americans with institutional support is the military, and I can see where you can get such an attitude quickly.

As a student, I've avoided much of this issue by not talking about my history and the military or by reserving it for later interactions where it gives me useful examples on concepts like acculturation and social norms.  In many ways, it's a "stay in the closet" sort of idea.

Second, being a soldier as a young adult--even in peacetime--has given me a second set of insights beyond the academic.  The one common thread to all military training is a rapid, intensive acculturation.  For many people--especially academics--this process is one they look at in confusion and disdain because it attacks their very conception of identity.  In many ways, the acculturation is explicitly that--a challenge to the soldier's preconceived identity--and who comes out the other end is often someone different than who entered.  It is also done quickly, radically, and at such a pace you are left being able to rationally compare yourself before and after even as you change on the emotional level.

This actually helps one to understand cultural differences from a personal perspective because military personnel have two distinct cultures with two completely different sets of norms and values they have experience moving between, for some on a regular basis and in such a concise manner in order to allow comparison.

Third, my military history gave me some interesting skills, not the least of which is the ability to respectfully challenge authority figures.  On a personal level, I was better at soldiering (living the life, getting the mission accomplished) than I was at being a soldier.  I spent 7 years challenging authority when I felt I needed to and learning how to work in a new cultural system to my own advantage. 

One major lesson was--for every rule--there is often either an exception or a way to change the rule as long as you can grasp the reason behind the rule and apply the reason to the appropriate node in the network.  Admittedly, part of the insight came from what I did in the Army (weather observer and later medical specialist) as well as who I worked for (primarily warrant officers or commissioned ex-warrant officers).

Fourth, I acquired a skill set that may be of practical use.  Simply, I can perform detailed personal interviews and histories in an informative manner.  I can operate most of your basic camping and survival gear.  I can also sleep outside in the dirt without complaining (too loudly) and while remaining focused on whatever the task at hand is--say, observing people or animals--in lieu of focusing on how "scary" it is at night without a roof over your head.

Fifth, I share a training mindset with other veterans that simply says: With some training and a little practice, I can learn to do almost any task.  The expectation--for most soldiers and military personnel--is their job description changes often and learning new tasks or new ways to accomplish the same tasks is a de riguer part of the job throughout the lifespan of the job. 

Working in the blue-collar world after the "green-collar" world of the military, it was a shock to find people reluctant to continue to train in their own jobs, let alone training for advancement.  I think that shock is one of the reasons I'm interested in science and academia--the acceptance and expectance of continued learning through the career.

Finally, I--like many veterans--have a more of a mental flexibility than most "monocultural" people I've met. When it comes to social tasks, we maintain the ability to apply whichever set of norms (identity-driven "civilian", mission/cooperation-driven "military") is appropriate.  This allows us to work with people and in situations where others would have a "culture" or identity-threat to resolve.  In physical tasks, most veterans are more aware of their physical limitations over a long term than many others (barring athletes).  The combination is one reason most veterans have the ability to focus on and accomplish tasks other feel uncomfortable with.

To summarize, I think many people spend too much effort equating military personnel with "gun-carriers" and not recognizing the rest of the skillset required for going somewhere outside your social network, joining a new one, learning how to learn, and being able to rejoin your original network.  In many ways, the fields I'm interested in, especially anthropology, has some of the same characteristics.



Sunday, October 10, 2010

Fields of science and my personal place within the continuum...

I love college.  Essentially, I love to learn, to ask questions, and explore.  One thing I really enjoy is the fact I'm no longer being taught everything, but learning how to teach myself as well as the tools to learn on my own. 

Learning on my own becomes particularly useful as I realize, more and more, how atypical I seem to be within the fields I choose to study.  As a starting point, my declared degree program--two courses shy of completion--is a bachelors of science in psychology with minors in anthropology, biological sciences, and sociocultural anthropology*.  As such, most of my coursework is within the fields of psychology, anthropology, and biology with several courses being cross-listed for two or more of the fields.

I enjoy being a broad-based, physiologically grounded social science major most of the time, with a few exceptions. One of the nicer parts of my background is the fact all three of these fields are--at the theoretical level--quite integrated.  When you attach the field of experimental economics and complexity studies in general, you find the major components of the current theoretical explorations of human social behavior as described often in the pages of Science, Nature, and other prestigious journals.  My background--in conjunction with the accompanying reference library I've accrued--allows me to read and understand most articles and books across these fields**.

One type of exception happens when I find myself wanting to explore one field's focuses using other field's methodologies.  My sole human-subject experiment so far was a psychology experiment (survey-based, simulated game) to explore a anthropology focus (altruistic punishment) and included a biological statistical methodology (multimodel inference using AIC's).  The instructor got lost on what you could and couldn't do with multimodel inferences*** as well as my subject matter ("Too much jargon.").

A second exception occurs when I find myself fighting uphill battles to bring cross-discipline information into discussions where others have a single focus.  My best illustration of this was a discussion group on chimpanzee and bonobos as study models for understanding human behavior.  I found myself having to argue with others--primarily anthropology graduate students--whom I was actually in agreement with because they refused to consider a synergetic combination of inter-species effects and proximate, neural mechanistic effects for behavioral similarities and differences.

In most cases, I simply offer my two cents and deal with the fact people are invested in their own perspective...  Which is one reason I'm writing a random blog here.  What I wand to do--besides getting more into the habit of writing more--is to "think out loud" about things I hear and read and try to put them into context.  (Hopefully in a way that won't keep me from getting a job or into graduate school.)


* - Yes, my university allows one to minor in both anthropology and sociocultural anthropology because the minors are taught in two separate colleges.  I would have preferred to dual-major anthropology and psychology but I'm not too facile with other languages and the adoption of a bachelors of science in anthropology at my university arrived without one of the core courses required being installed in the course catalog as of yet.
** - I will admit my understanding of some of the statistical procedures isn't complete yet and some of the mathematical modeling is a little fuzzy...
*** - Multimodel inference is useful to explore the differences in effect for multiple independent variables.  What it doesn't do is give you a fixed p-value and let you hypothesize test with it.

Who am I?

I'm a mid-life college student, life-long student of behavior and conflict, and a closet wanna' be academic who is finally learning the tools of scientific exploration.  My primary interests now--as they have always been--are human conflict, sexual relationships, and family in a heterogeneous or adaptive context.  When I write fiction, it is most often based around the same interests and takes the form of humans adapting to a new or changing context.

From a philosophical perspective, I have a tendency toward starting with that of those around me, asking "What if?", and adjusting my perspective appropriately.  I also do not feel--unless there is serious evidence to do so--that there is only one, true way/path/solution to any problem.  This allows me to function with a more diverse network of friends and associates.  This acceptance or tolerance of alternative answers as a starting point mean I often find myself with beliefs at odds with those around me.  If this happens to be the case here, I apologize in advance.