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Friday, December 31, 2010

Sidebar into politics... A general and highly idealized way I look at political ideologies...

(Note: This was originally a FaceBook comment to a Libertarian friend's post about registering as a Republican and his friends' criticism of it as well as references to "the wrong party".)

It really depends on 1) How you much you value finances and 2) How far away they are making decisions.

Republicans/Conservatives spend money on defense and on policy that distinctly separates "us" and "them".  This doesn't mean that they try to hurt "them", but--when there's a preference, there's a difference.  A simpler way to think about it is that Republicans try break connections between the people they identify with and others with a high risk or a high cost to be associated with.

This means--if there actually is a meaningful distinction--like at the international level--it's a useful way of thinking.  Their fiscal policies are along the same lines except they tend to think of "us" as being the more contributing people and "them" as being the less-contributing people.

Democrats/Liberals, on the other hand, want to see everyone as equals.  Though idealistically noble, this is also their primary problem because this altruism makes them easy to take advantage of.  By distributing effort and resources across borders and without much reference to personal differences, they often develop policies that are expensive because people--who are often selfish--are abusing the system.
At home, in small, relatively homogeneous populations, this can be very helpful and encourage success by supporting the people who are key to our society.  At higher levels, unless the person has a definite attachment to a distinct group, you create problems.  ("Blue Dog Democrats" probably fall into the attached-category.)

Libertarians are sort of a different breed all together.  Their dividing line between "us" vs "them" becomes "me" vs. "you" vs. "them".   Where Democrats only see one set of ideal living situations and Republicans make a distinction between the in-group and the out-group, for Libertarians, there is an out-group writ large and it's okay for their to be differences between people inside the "in-group".

This is why the Libertarians have a lot of their political problems with numbers.  It's like herding cats.  Cats are--when they are mature--social creatures that create a hierarchy.  However, for the first half of their lives, they only associate with who they want to when they have to and only for as long as the other doesn't create some reason for conflict. 

This tendency does not lend itself to stand-alone success in a political system that is based on numbers and cohesiveness.  And--while it comes up with equitable--at least as far as effort invested--solutions to problems, selling them to others except where the borders of their political philosophy act, is often difficult.  In other words, guns and the Republicans, universal individual liberties and the Democrats, etc.

So, yeah, that's my take.  Pick your poison...

Monday, December 27, 2010

Odd dream...

Got a lot of money and a car in my dream--something I'm anticipating for some reason--and was downtown looking for a decent restaurant.  Only, it wasn't exactly Phoenix, Arizona.  It was a desert city on a grid and the area I was in had a lot of empty lots.  Anyway, I helped out someone that may have been homeless by giving them my pre-packed lunch.

I had stopped at a convenience store for something.  The convenience store was in an older, commercial area and was directly in front of an out-of-use commercial building, beside another which was still in use, and a large yard containing CONEX's, short sections of concrete traffic barriers, crates of this-that-and-the-other-thing, and a large number of pallets.

One thing led to another, and I found out there was a small group of them including a (putative) couple where the woman was pregnant, a guy that looked like a young Buddy Hackett, and some others.  In the process of being friendly, they raided my backpack and acquired some small bags of chips I had in there and one or two other things. 

I noticed a large, padded piece of cardboard that might be useful to them and pointed it out.  It was for packing and was probably about the area of a full-sized bed but only a few inches thick.  They pointed out it would be hard to carry around.  For some reason, I got the idea of wrapping it in plastic, tying a cord to one end, and storing it in a narrow vertical space, like between two buildings.  My thoughts were, it might be useful for a week or two.  They turned the idea down without thinking about it too much.

I was about to go when the manager of the business beside the store offered some of them some shelter in exchange for moving some of the short sections of traffic barrier inside.  I think he was primarily looking at the pregnant girl. 

The whole group sprang into action, manually manhandling the big concrete sections across the ground to the entrance of the working warehouse.  I don't know why, but I wanted to help.  I looked around for a lever and some form of skid or wheeled anything.  I found a low-slung wheeled trolley that would work, but I couldn't convince them to try and use it.  (Primarily, it was the guy that looked like Buddy Hackett.)

By this time, however, they had moved enough of them and the manager was happy.  He let in the pregnant women, another young woman, and the putative father.  Then, he closed the door and left the others outside.

Anyway, what it really got me thinking about were four things:

First, the lack of a durable social group among the homeless.  Personally, I saw them as a group when I walked up.  I expected them to function as a group.  The emotional read I got was that they were socially connected, but the end result was a complete focus on themselves and that was accepted by others.

Second, I really noticed the willingness to violate some of my expected personal boundaries and social norms.  This isn't any surprise for anyone who's had a lot of interaction with at least subsets of homeless people, but, hey!  It was my dream and my homeless people.

Third, I recognized that--at least as far as I've had real-life interactions with homeless people--and from conversations with others that have or have been homeless, they have an ongoing problem accumulating the "stuff" they need to survive and maintaining control over it.

Fourth, I contrasted them with what I learned this last semester about hunter-gatherer groups.  Both share a similar "problem"--lack of a static living situation, a very finite limit on what they can carry, and less control temporally on what resources they have available.

Then, I woke up.

My question is--and I would need to do a literature review to approach this--is how much of the homeless problem is simply the inability to form durable, interdependent social groups?

I mean, if social bonds (and social norms) are strongest between people who are the most familiar, have the ability to build reputations and reciprocal altruistic interactions, and have shared investment in mutual endeavors, could part of the homeless problem simply be a structural problem? 

Obviously, the reasons behind the breakdown of group building (or durability) could and probably are psychological--the effects of drug use on decision-making, for example, or simple mental illness--and I would need to identify or at least discriminate which group(s)/demographic(s) have this issue and why, but it's an interesting thesis.

Something to do while I wait for job offers... 

Saturday, December 25, 2010

Governmentally mandated paternity testing... (Part IV)

Analyses


Given the payoff matrices constructed last time, I constructed decision matrices for several sets of parameters.  I constructed tables for each type of payoff--prosocial, fiscal, and offspring quality--and reverse ranked each outcome within the table.  For example, the offspring with the highest quality had the highest numeric rank in the offspring quality chart.  I created a summary chart where the ranks for each payoff were added after being multiplied by a weighting parameter to allow for analysis of the priorities for each player.


The "basic" table looks like this:

Thursday, December 23, 2010

Governmentally mandated paternity testing... (Part III)

Starting with:


Payoff matrix with formulas.
Female payoffsMale payoffsOffspring payoffs
ProsocialFinancialProsocialFinancialOffspringFinancial
Marriage (2)P1 + P2 + bP1P2($1+$2)/2P1 + P2 + bP1P2($1+$2)/2
Separate (1+1)P1$1P2$2
Marriage (3)P1 + P2 + bP1P2pCON{[($1+$2)/3]} + (1 - pCON){[($1+$2)/2]}P1 + P2 + bP1P2pCON{[($1+$2)/3]} + (1 - pCON){[($1+$2)/2]}pCON{[(P1+P2)/2] + [(G1+G2)/2] + bP1P2G1G2}pCON[($1+$2)/3]
Alone/AbandonedP1pCON($1/2) + (1 - pCON)($1)P2$2pCON{[(P1/2) + [(G1+G2)/2]}pCON[($1)/2]
Alone/PayingP1pCON[$1/(2 - c)] + (1 - pCON)($1)P2pCON[$2/(1 + c)] + (1 - pCON)($2)pCON{[(P1/2) + [(G1+G2)/2]}pCON{{$1-[$1/(2 - c)]} + {$2-[$2/(1 + c)]}}
Alone/AdoptedP1$1P2$2pCON{ 0.75 + [(G1+G2)/2] + 0.56b(G1G2)}Max: $1 or $2
Grayed cells represent non-reproductive outcomes.

Tuesday, December 21, 2010

Governmentally mandated paternity testing... (Part II)

Deriving a payoff matrix
Before we can derive a payoff matrix, we can consider the fact not all combinations of choices are compatible.  For example, all results from a non-reproductive partner cannot produce a baby and therefore rule out all but two of the parental responsibility options.  If we go through the current process model and identify those sets of choices resulting in no baby (as seen marked in gray lines in the diagram below), a pattern can be discerned where non-reproductive relationships can only produce one of two basic outcomes: marriage [MRY] or abandonment in combination with alone [ABA x ALO] as the other outcomes require a baby. 




Monday, December 20, 2010

Governmentally mandated paternity testing... (Part I)

After watching Geraldo Rivera's governmental solution to absentee fathers, it got me thinking about father's and children's rights, primarily the sexual and parental support aspects of them.   Geraldo's basic assertions are absentee fathers are a major issue in poverty and the solution is a mandate for governmental compelled paternity testing to establish legal liability.


While I generally agree the most effective environment for raising children is a cooperative, mutually supporting environment, I think his solution has serious risks of unintended and perverse consequences on multiple levels.  Ignoring most of the legal issues for the time being, let's talk interpersonal relations.  


For argument's sake, let's break the process of having children into a 5-step process model:




Sunday, December 5, 2010

Blind men with jetpacks and altimeters...

I've been running MrBayes practically non-stop since I cleaned the last of the viruses off my PC.  For those who don't know, MrBayes is a phylogenetic software program that uses Markov Chain Monte Carlo methods in parallel to locate the most likely phylogenies for a given data set.

Most of you probably just went: "Markov...  Monte...  what?"

I don't blame you, so this is my explanation of what happens.

Imagine all of the possible phylogenies--ways a series of gene sequences might fit together--are actually a piece of land with mountains on it.  The mountains--the height above the ground--is how probable THAT phylogeny is given the sequence.  The higher the mountain, the more likely it's the right phylogeny.

So, the simple thing is to just look out over the landscape and pick out the highest peak, right?

One problem, it's pitch black and you can't see your nose in front of your face.

So, how do you find that peak?

Well, you recruit yourself some people--blind men--and you give them altimeters, radios, and jetpacks.  Their job is to go out, push the button on their altimeter and get a height.  Then, they take a step in a random direction and check their altitude again.  If they went up, there's a small chance they hit the gas and bounce away on their jet pack.  If they go downhill, the chance gets larger.

So, simple solution, you send out your 4 man team, they stumble around in the dark like blind men do and keep radioing in their location and altitude.  Except that would be a huge number of positions.

Instead, you have them only call in every thousand steps.  I mean, hey!  you jump more if you do downhill, jump a whole lot less when you're uphill, and that means--ideally--these guys will be walking around the hilltops in no time and stay there.

Only, how do you know THIS hilltop is the highest when you can't see?

Easy, you do two things.

One is, every 1000, the team members compare how high they are and the lowest swaps places with the highest.  This means--as far as the ex-lowest guy is concerned, he's now higher on his next step.  The ex-highest guy, however, is guaranteed to jump because he's now lower.  Sort of mixes things up, see?

The second thing is to bring two teams.  Both teams wander around on their own, totally oblivious of each other.  However, what you can do, is track and compare the heights they are reporting.  If Team A keeps reporting really different altitudes than Team B, you know that one or both just hasn't found the tallest peaks.  If that happens, you just send them more fuel, some hot chow, and tell them to keep trucking.

If instead, after a long, long time, both teams are reporting almost exactly the same heights...  You got a good chance they actually found the highest peak because that's the only place on the ground where there is an absolute upper limit to how high they can go.  If there were someplace higher, more than likely, given enough time and steps, even a blind man can find and climb Everest.

So, when you're done, what do you have?

You have several hundred or more locations and altitudes.  The first few--usually about 25%--are going to be crappy.  They'll be all over the place, but probably not that far up the mountain.  This is called the "burn-in" where your teams are getting their bearings.  So, you just rip those out and ignore them.  The rest, the last 75% or so, those are what you're after.  Those are the combinations of trees and other factors that "make the most sense" together and are most probably. 

But, with that many--say, 750 on a 1,000,000 step run--what can you do?  Why can't you just pick "the ONE" and be with it?

First, there's no guarantee your teams found the highest of the high.  Maybe they found K2 instead of Everest.  Maybe they just didn't get that lucky or Everest is on a diet and got really, really skinny and hard to find.  So, if you pick only one, you have no idea how much of the terrain you're actually looking at.

Instead, with 750 reports, you can identify where your team spent most of their time.  If there is--in fact--an Everest around and it's significantly higher than K2, you'll probably find reports telling you about one or more of your blind bouncers roaming around the shoulders of Everest.  Additionally, if all you find is that one, single major peak and all of your junior jetmen spent ridiculously large amounts of time and effort crawling around on the top of it, you can argue with a straight face you got the best and only one... or damn close to it.

So... that's why MrBayes makes me think of blind men with jetpacks and altimeters...

Friday, December 3, 2010

Update: Computer-wars

I have declared victory.  My last two problems--Java Virtual Machine not launching and random browser redirects--were likely caused by a single rootkit bug.  For those who don't know, a rootkit is a program or utility that stealthily co-opts system control be being able to intercept what the (authorized) user asks and then doing whatever the hell it wants to do.

After trying to explain what happened and why I was actually in the Computer Commons (the work must go on, even when viruses are about), I sort of felt nerdier-than-though when the computer-lab personnel looked at me with glazed eyes...

My solution was actually using several malware/virus checkers while looking for specific symptom combinations.  What I found was info on that rootkit and a combination of software that cleaned out all the temp files, caches, and such then quashed the rootkit.  A clean restart and scans by three different scanners and I'm tired, happy, and nerdier than ever.

*head desk*

Now, for a nap and--as soon as finals are over--real posts.

Thursday, December 2, 2010

Iterative methods and impending semester end...

The worst second worst possible thing for a student trying to complete a project depending on iterative, software-intensive methods has happened to me: a computer virus followed by an illustrative lesson paralleling why HIV and other STI's follow each other around.

Basically, I fell for a virus (ThinkPoint) that played off of my efforts to avoid infections by spoofing me with a pop-up looking exactly like a Microsoft Security Essentials (MSE) pop-up.  After having a hell of a time getting back on-line and avoiding the lovely re-directs away from informative sites--have to admire the bastard that developed it--by way of abusing MEGA's browser capabilities and incapacities, I was able to get rid of the virus. 

To be sure it wasn't also a corrupt MSE, I uninstalled it planning on reinstalling it immediately.  So, I restarted my PC, opened Internet Explorer, the MSE pop-up came up, and--even though I rationally knew I had uninstalled MSE--I clicked it...

ThinkPoint took 5 minutes to clean the second time, the only problem is that it brought friends the second time and I'm still trying to clean them out using several pieces of software that don't all seem to catch all of them but are highly recommended.  I still know SOMETHING is there because something kills Microsoft's Malicious Software Removal Tool as it pops up.

That and everytime I try to run a *.jar file, the window pops up with an error that Java Virtual Machine Loader can't start virtual machine.

So, this means I get to do some of my work on the school's PC's which--frankly--are slower than hell.  Which wouldn't hurt for some basic tasks--like internet--but when you REALLY want to run a BEAST run of several million cycles or even just a lowly jModelTest run, it takes forever.

I swear, if/when I get a real job, I'm buying two computers exactly alike just to have a spare...

Monday, November 22, 2010

The economics of hunter-gatherers...

Today, a presentation by Dr. Kim Hill, a rather prolific contributor to the evolutionary behavioral ecology end of anthropology, covered some basic concepts behind the resource sharing in hunter-gatherer tribes.  The crib notes of which can be summed as such:

Friday, November 19, 2010

Applied for yet another Epidemiology job...

It's funny, in a way, but I wouldn't have thought about applying for that field of work until recently.  Two things changed though, okay three things.

Tuesday, November 16, 2010

(A work in progress) My 10 tenets to handling overpopulation.

In response to a question on Yahoo! Answers, I've decided on some basic, first blush concepts to handle human overpopulation.  Obviously, there is a lot of cultural inertia and baggage to overcome before any of these could even remotely be feasible.

1) Dump the nuclear family ideal and force matrilinial, matrilocal extended families.

The nuclear family ideal pushed two things: spacial expansion and population expansion.  Additionally, an extended family with extensive familial support reduces familial competition and increases competition for women as mates providing a more stable society.

Monday, November 15, 2010

Quick thought on social and neuroscience...

Some of the recent studies showing continued brain growth in teenage brains (a "lite" report here) are being used as to push for an "extended childhood" for teens.  During the teenage years, the prefrontal cortex--the area of the brain concerned with "rational" decision making and courses of action--first grows and then prunes connections and myelinates particular areas.  (Myelination increases the speed a message can travel along a nerve, essentially "locking in" a particular message by reducing time to "consider" alternatives.)

In  several anthropology papers and courses, I've been shown patterns where young men (at least) may have greater strength and aptitude, but the peak age for production by hunting is upwards of 35.  This implies there is a context-specific experiential process at work for this socially important activity.  The fact it's a relatively smooth curve from onset of puberty to adulthood and a relatively monolithic (excuse the pun) adult culture in most cases says something as well. 

In some of the behavioral genetics heritability studies on certain traits like the heritability of religiosity, the heritability of the trait is seriously affected by age.  Those that are older often show an increase of heritability which wouldn't make sense if it was a basic additive genetic trait.  If it requires a (social) context-specific "burn-in" period, however, and is tied into a set of working behavior-governing institutions, that would make sense.

So...

My hypothesis is that the "developmental" period during puberty isn't part of an extended childhood, it's the intended developmental period for adulthood.  Essentially, the apprenticeship period for learning the rules and institutions in their social context in order to successfully function as an adult.  By removing the opportunity to develop in the adult society they will later be a part of, teens are rendered less prepared or with substitute, created variants of the "adult world" they have adapted to.

This would explain a number of things, least of all is the divorce rate and the periodic creation of sub-cultures based around teenagers.  Essentially, by "protecting" teens from the adult world, they learn and lock in (that's where the myelination comes in) rules that are appropriate for the limited situation they live through as teens and have difficulty adapting to the "responsible" adult world, a lot like Peter Pan.

How could you prove such a hypothesis?

The ideal situation would be somewhat ethically challenging in most places because it would require treating any subject post-puberty as an adult.  Alternatively, one could consider a cross-cultural study where adulthood is conferred at puberty, but the confounds would be ridiculous because most of these cultures also have a more simple overall culture.  If there were reason to believe different parts of this development process weren't very tightly integrated, one could use activities that are less regulated in this culture and create two experimental groups where "childhood" is enforced in one and adult activities are permitted/encouraged in the other.   Maybe something like hunting or finances may be of interest.

Just an idea.

Sunday, November 14, 2010

I love when people on Yahoo! Answers totally get the wrong area to post:

Found in the Anthropology section:

Question: What's the difference in Black Ops and Modern warfare 2?

I'm not talking about the missions! I'm talking about weapons!

Answer:
Regional variation in culture often result in differences in material culture including weapon design.  One example of this is the adoption of the Browning Automatic Rifle (BAR) in US forces during World War II and the adoption of the Bren Light Machine gun by the British.  The BAR was selected because if fit the US tactics of the time was one of small, similar units that swapped roles as maneuver, support, and assault repeatedly.  As such, the appropriate weapon design required the ability to provide supporting (automatic) fire and be easily maneuverable under fire.  Additionally, the M1 Garand and M1 Carbine--useful for both short range and volume fire compared to the bolt-action rifles of other nations--support this premise.
By contrast, the more hierarchical culture of the British created the organizational solution of specialized teams for maneuver/assault (riflemen) and support (light machine gun/PIAT).  This adoption of specialized solutions resulted in the adoption of specialized weapons for both types of teams.  As such, the Bren was heavier, less portable, and primarily intended for fire from the bipod with a dedicated person or persons to provide ammunition.  This allowed the British riflemen to employ "lighter" in terms of either volume of fire (SMLE rifles) or power (STEN submachine guns) successfully.
The follow-on developments tied to culture and tactics resulted in a number of different, more modern weapon designs including the American M60 machine gun series (intended to replace both the BAR in maneuver and the heavier medium machine guns), the M240/L7 series of GPMG's intended to supplant Bren's in a similar role), as well as the various assault rifle concepts including the bullpup designs and the AR15/M16.
Bullpup designs are a compromise between length of barrel, overall length, and possible length of sight radius.  Barrel length can be longer in these designs because the action is shifted into what was previously "unemployed" volume of the stock.  This results in a shorter overall design with a typically longer or similar length barrel providing good potential accuracy and power compared to similar length, short-barrel conventional designs.  The sacrifice comes primarily in the form of sight radius--which usually necessitates an expensive optical sight system--and the ability in most designs to fire off of the other shoulder to take advantage of tactical cover.
These designs are usually adopted by cultures with a long distinction between riflemen and other types of troops because--with the optical sights--they perform admirably in the rifleman role but less well--even in modified variants--in more general roles for the assault, support fire, and others.  The implication is again one of hierarchical, specialized solutions to tactical problems and over one of common, more generalist roles.
The competing paradigm--primarily demonstrated by the adoption of the AR15/M16-series--is one of modular flexibility.  These weapons are often selected by groups/military units with a high investment in individual skill and overall egalitarianism.  The design follows this trend by being easily modified and/or accessorized to allow the firer to perform most functions well in a variety of situations.  In this case, the focus of the weapon/user construct can change quickly and the design supports it. 
A third paradigm is one of the simple, primarily seen in the adoption of the AK47 and its descendants.  In most of these cases, the investment in training of weapon carriers is minimal and the design reflects this in being only moderately accurate but highly resistant to abuse.  Culturally, these groups often see the weapon as a symbol of power and or a means of inducing terror instead of a precision tool. 
In many cases, even those countries/cultures that employ a dedicated system at the basic troop level will use a different design where the subcultures exist--such as special operations or paramilitary troops.  The weapons employed and their design  or adoption in a competitive market is a reflection of cultural ideals mitigated by tactical necessity.
Now that you've read that, how about next time posting in a more appropriate forum, eh?

Thursday, November 11, 2010

The Utility of Religion...

Note: I have no intention to debate the existence or lack of existence of supernatural beings.  I acknowledge there are elements of existence that are not explained or even explainable as there is without debating the supernatural.

Many confuse the ideas of organizations and institutions.  Simply put, institutions are the sets of rules and norms that govern the behaviors of agents or people in a particular context.  These can be formal laws or merely suggestive norms.  Organizations, by comparison, are a combination of these institutions and a group of people.  

Monday, November 8, 2010

Have been busy...

Slamming an ethnography, trying to figure out how to run a Mac or Linux program using Xming on a Windows machine.

I'm decent with computers, but...

Monday, November 1, 2010

The discussion about last week's Science paper...

Led to a short discussion about the potentially massive data likely hid within the histories of massively multi-player online role-playing games (MMORPG's) and the issues of getting access to such a date mine.

My suggestion was to consider creating a new one in the name of science...

Essentially start from zero with an MMORPG run non-profit with permissions from the beginning to use non-personal data for research.  Sell it as fun to players, and create within it virtual research labs.  You could explore ecological and socio-ecological behaviors as well as simple social interaction.  If you could create a dynamic system in the game that--instead of a regular time-based "ecology" you get in many MMORPG's--current conditions could influence later conditions.

Another idea I would suggest incorporating would be the ability to create once-off or temporary "worlds" for use in specific, short term research projects.  Essentially, farm out some of the virtual "landscape" for use for student researchers.  It would require some level of modularity to ease the learning curve of academics and there would probably need to be dedicated programming staff as well as marketing...

...but I think it could be both fun and a useful tool to connect participants and academics in many of the up-and-coming interdisciplinary arenas.

Just an idea, eh?

Chaos...

The Complex Adaptive Systems seminar was today and--in the spirit of interdisciplinarity--today was a presentation by a mathematical modeler on chaos and complexity.  I think I had just enough math to get what he talked about, but--unlike most other presentations so far--today was really quiet on the question side of things.

For anyone who doesn't know, the idea of chaos isn't one of randomness (stochasticity), it's essentially one where you can predict an outcome with the probability of a specific outcome being greater closer to the origin and the probability of a general outcome (or distribution) being greater farther from the origin.  In other words, the closer to home you look at, say, a route taken bicycling, the more predictable you'll find the exact path the bike takes.  However, over time, you lose that ability but pick up the ability to predict a general group of paths usually taken.

It's interesting in an esoteric sort of way.  Ironically, my introduction to chaos as an idea came with discussions of mathematics in field artillery.  My first adult "job" was as a field artillery weather observer and--as part of the initial training--we were introduced to the artillery round-off rule that used the oddness or evenness of a the terminal digit to determine which direction to round an otherwise terminal 5.  This somewhat stochastic method was intended to avoid a directional tendency in the the rounding of the myriad of mathematical calculations required when artillery was targeted.  Because of the number of calculations, the number of times numbers are rounded, and the potential hazard of an incorrectly placed artillery round (typically, more than one), the concept was to try to make any error more uniformly distributed around the actual values being estimated.

(I think this connection between math and large things dropping out of the blue and going boom! is one reason I take mathematics a little more seriously than many of my friends.)

My second interaction with the idea was courtesy of Michael Crighton and--yes--Jeff Goldblum's voice creeps into the shadowy periphery of my mind every time I hear the word "chaos".  Given I read the book prior to the movie, I did get the more detailed if still fiction-driven conceptual explanation...

...but--as one of my oldest son's favorite movies as a kid was Jurassic Park--I can not begin to count the number of times I've seen the scene with the water off the hand explanation of initial conditions influencing outcomes.

Got to love popular culture.

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!