A good example

There are lots of really fantastic things about my wife, but one of my favorites is that she is really open about who she is. She's straight up with you and doesn't go out of her way to be nasty, but doesn't pretend to like what you're saying or agree with you if she doesn't like what you're saying or agree with you. I learned at some point that smiling and agreeing was an easy way out of situations i didn't care to invest myself in, and I've really learned a lot from her about being open and honest about yourself. I really appreciate her example in that way.

Sepiolid Squid Symbiosis

As a student in microbiology I ask questions about how beneficial
bacteria associate with animals hosts: how they associate, what
benefits are exchanged through the association, and why sometimes
specific bacteria are included in an association while others are
excluded. The spin and the angle is usually to relate this back to
humans (think: why are certain species of bacteria in our mouths or
our intestines?), but there are many associations that are interesting
to study either for the novelty of the association (microbes that
provide nutrition from hydrothermal vents on the ocean floor to
tubeworm hosts), or for purposes that have economic value of their own
(a classic example is how nitrogen-fixing bacteria interact with their
plant hosts to fix gaseous nitrogen, which plants can't use, into
compounds that plants can use for growth).

In the field of beneficial microbial associations there are a number
of model animal-bacterial associations that are studied to help us
understand how partners interact in a more complex association.
Complexity can be measured as many things, but one complex factor is
the number of partners in the association. Humans carry greater than
5,000 different kinds of bacteria in our intestinal tract alone, so if
we wanted to ask how or if a specific species is maintained within the
intestine, and how, that's a difficult question to ask. In a model
where there is one animal host and one partner, you know exactly who
to look and and that the selective pressures are strong (perhaps - who
knows? - stronger than the forces our intestinal cells exert on
microbes they interact with).

One of the classic models for asking questions about how hosts and
symbionts recognize and interact with each other is the association
between a specific squid species and a specific bacterial species.
Adult sepiolid squids are about the size of a golf ball and associate
with bacteria that produce light in a special organ (called the light
organ) on the ventral side of the squid. The squid collects bacteria
from the environment through a series of selective processes, and once
inside the light organ the bacteria produce light. The light organ is
flanked by reflective tissue and lens tissue similar to our eyes that
moderates the amount of light that is reflected from the dorsal side
of the squid.

What's the benefit of the association to each partner? The light organ
is a beneficial place for the bacteria since they can reproduce more
inside the squid than outside the squid, and can be spread more widely
when released from the squid than if they were not associated. The
squid uses the light produced by the bacteria in a really cool way to
counterilluminate its shadow. The squid actively feed at night and
burrow in the sand during the day. While active at night, predators
looking up to the ocean surface from below the squid would see a
shadow cast by the squid against the moonlight. Light production by
the squid counterilluminates the shadow, and some very nice work has
showed that if you shine brighter light above the squid it will put
out more light from the organ by controlling how widely the lenses to
the organ are open.

Its a pretty neat biological phenomenon, and is just one of the ways
that bacteria interact with their animal hosts in beneficial ways. One
interesting thing is that the squid recognizes its beneficial bacteria
in many of the same ways we recognize pathogenic bacteria. This and
other work is starting to blur the distinction between beneficial and
pathogenic interactions.

Birthday Time

Today was my Granpda Chaston's birthday. As most grandparents are, he has been a great example to me in many ways. Here are three:

1) Whenever he asks you to help with something it always takes less time than he asks for. This makes it always a pleasure to help with something. Of course, since I usually expect things to take less time than they really do, it means that the first time he asked me to help him move something in the garage for 15 minutes i was flabbergasted about how it could take that long. Imagine my shock when we were dne 5 minutes later.
2) He talks to everyone. My Grandpa loves to talk to people and can talk to anyone anywhere, and it isn't awkward. People in line at the store, people in restaurants, and people you're supposed to talk to but usually don't talk to except about specific things (think: Checkers and Waiters/Waitresses). I don't at all but wish I did. I think there is hope for since my dad is becoming more like this every time i see him. It just takes a few years.
3) He works. First, i think he always had something like ten jobs at a time when my dad was growing up. Second, when he retired he didn't stop. He did the expected things - gardening, a little(which turns into a lot) of fixing up around the house, etc. But He and my Grandma have essentially gone on missions for our church since they retired. They've been out of the country at least twice (or maybe three times), but then when they come back they get asked to do family history missions in Provo or Salt Lake. And they've just done it over and over and over. My Grandma has dedicated a great deal of her life to geneaological research and my Grandpa has supported her both in the meaningful contributions she has made to the field, and in going with her to do some of it, too.

I should make a point #4. Nobody on Earth comes before my Grandma for him. She's still the world to him.

Not alone

Watched part of the movie "Fat Head" tonight. It's a comedic response
to "Super-Size Me" (which I've never seen) and it is on Netflix. It
also argues against making carbohydrates the staple of our diet. I
wasn't paying close attention, but I think it argued in favor of dairy
(see below).

It looks like he keeps a pretty good blog, too. His website is here: http://www.fathead-movie.com/

All I can say is that watching it makes me want to eat steak and eggs
for breakfast, spoonfuls of peanut butter for lunch, and T-bones for
dinner. Seriously, though, I do want to read more. The basis of the
arguments he cites are that humans haven't evolved to eat much
carbohydrate-wise or vegetable-fat-wise. Add to that dairy (which he
doesn't make much of a case against, and for which humans have
traditionally tolerated only as youngsters) and it certainly
recommends against most of what I eat all day long (think: oatmeal or
wheaties for breakfast, sandwiches for lunch, and rice or pasta with
something meat-like (or just 'meat') for dinner - vegetables and fruit
mixed in throughout) and like most people I'm pretty carb heavy.

Time for me to do some learning...

The Welfare System of the Church

This weekend commemorates the 75th anniversary of the welfare program of The Church of Jesus Christ of Latter-Day Saints. 

At least one rationale for the welfare program was to provide a way for those who were in need of assistance to make some form of compensation.

"In 1933 the First Presidency announced, "Our able-bodied members must not, except as a last resort, be put under the embarrassment of accepting something for nothing. . . . Church officials administering relief must devise ways and means by which all able-bodied Church members who are in need, may make compensation for aid given them by rendering some sort of service" (in James R. Clark, comp., Messages of the First Presidency of The Church of Jesus Christ of Latter-day Saints, 6 vols., 5:332–34, cited from http://lds.org/church/news/welfare-services-celebrates-75-years?lang=eng; note that the link provides a general history of the welfare program)

One really amazing part of the program is how the resources that are provided to those in need are collected. The money is donated by members of The Church who join in fasting (going without food and water) for two meals one day per month. In principle the donated money need only come from the cost of the meals that were skipped, but in practice many donate more than that amount. 

This practice is rooted in Biblical direction. The entire 58th chapter of Isaiah speaks to this idea:

6Is not this the fast that I have chosen? to loose the bands of wickedness, to undo the heavy burdens, and to let the oppressed go free, and that ye break every yoke?  7Is it not to deal thy bread to the hungry, and that thou bring thepoor that are cast out to thy house? when thou seest the naked, that thou cover him; and that thou hide not thyself from thineown flesh?

The rewards of the practice include: 

 8¶Then shall thy light break forth as the morning, and thinehealth shall spring forth speedily: and thy righteousness shall go before thee; the glory of the Lord shall be thy rereward. 9Then shalt thou call, and the Lord shall answer; thou shalt cry, and he shall say, Here I am. If thou take away from the midst of thee the yoke, the putting forth of the finger, and speaking vanity; 10And if thou draw out thy soul to the hungry, and satisfy the afflicted soul; then shall thy light rise in obscurity, and thy darkness be as the noonday: 11And the Lord shall guide thee continually, and satisfy thy soul in drought, and make fat thy bones: and thou shalt be like a watered garden, and like a spring of water, whose waters fail not. 12And they that shall be of thee shall build the old waste places: thou shalt raise up the foundations of many generations; and thou shalt be called, The repairer of the breach, The restorer of paths to dwell in.

The chapter continues to this effect, but this has always impressed me as a simple and elegant model for increasing reverential worship of God while providing for the temporal needs of those in need. Ideally it also helps us to remember that there are people in need so that we can assist when we aren't in need, and receive when we are. If we're in the mode of thinking about these things it can help us extend that beyond temporal necessities also.

revisiting some thoughts on evolution

Had some time this afternoon and wanted to revisit some thoughts on evolution - eventually I'd like to incrementally put down a whole bunch of different ideas that relate to why it is such an inflammatory subject and why it really doesn't need to be. 

As an aside, after writing the evolution post earlier I heard a very good, concise of reproductive fitness: fitness is the ability to pass on your genes to offspring that can pass on their genes. The example is that producing a mule doesn't contribute to reproductive fitness because mules don't reproduce. 

The thing that I'm really thinking about, though, is about defining evolution as a change in a population's allele frequencies over time. I'll get in trouble with some evolutionary biologists for cutting it down that far since there is a whole field that is devoted to understanding how the generational change in a population's allele frequencies can result in speciation, or the formation of new species. But making a distinction between evolution proper and speciation is an important thing for evolution's apologists to do (and, in my opinion, something that many seem unwilling to do at least in part for the reasons I stated in my earlier post on the matter) because: a) you can't argue that a change in allele frequencies happens over time since we can see it; b) it refocuses the debate about evolution onto evolutions core principles rather than its predictions. 

So for evolution to take place, you need two have multiple alleles for a given gene, you need to have an external pressure that causes having a particular allele to not be neutral (i.e. there is a benefit or cost to having the allele), and you need to have reproduction. If we use eye color, let's say that there are only two alleles for eye color - blue and brown. Let's also say that Debbie Gibson has blue eyes, and so all of the boys in the 1980s grew up with crushes on her and decided that they would only marry women who have blue eyes. All of the sudden, blue eyed girls all get to reproduce while some brown eyed girls don't get to. There will be more blue-eye alleles in the next generation, and presumably all of those blue-eyed children will be able to reproduce. Evolution just happened. Of course, the same thing could happen the following generation with Debbie Gibson's daughter, who has brown eyes, and the pendulum could swing back towards an increase in brown-eyed alleles the following generation. The most interesting changes will be permanent shifts in allele frequencies, and these will usually result from continuous or very strong pressures. 

The problem, of course, is that a change in the blue-eye color allele in the human population is less interesting than gamma-radiation from a special effects show at a Debbie Gibson concert causing everyone at the show to produce children that are actually a new species of Homo (called Homo gibsonii, this new species is actually born with eyes that are shaped like Ray-Bans and skin that looks like a jean jacket). The likelihood that a child will be born as a different species than its parent is extremely small (i doubt it could ever happen but never say never, right?), and so the question that arises is: how can a new species evolve? A more problematic, but related, question people like to ask is, "Why don't we ever see chimp-human hybrids if evolution is an ongoing process?" The former question is entirely appropriate but the latter is fundamentally flawed (another time...). At least one way that new species evolve is by isolation of individuals of that species by external barriers - such as geographic, social, or reproduction barriers between individuals in a population.

Can you see people who believe that the earth and all earth life was created by God being less resistant to teaching evolution if it focused on this?

As an aside, I thought it would be informative to check on a few definitions for evolution in online dictionaries. I was really surprised. Dictionary.com hit it on the head, but webster's is a bit off the mark, focusing not on the definition, but on the implications of the definition. I'm quick to add that I'm not aware of any evidence that contradicts Webster's definitions, but I think that defining evolution by its predictions and implications rather than by its underlying principles is flawed and causes a lot of unnecessary contention.

Dictionary.com :  change in the gene pool of a population from generation to generation by such processes as mutation,natural selection, and genetic drift.

Webster's: a theory that the various types of animals and plants have their origin in other preexisting types and that the distinguishable differences are due to modifications in successive generations; also : the process described by this theory

Future points: 

"can" vs. "do" pass on genes

speciation vs. evolution

geographical isolation

undirectional evolution

long term evolutionary vision

a problematic species definition

possible speciation mechanisms (egg and sperm mutations)

alleles arise by mutation

define "allele", "locus", etc

Revisiting some thoughts on evolution

Had some time this afternoon and wanted to revisit some thoughts on evolution - eventually I'd like to incrementally put down a whole bunch of different ideas that relate to why it is such an inflammatory subject and why it really doesn't need to be. 

As an aside, after writing the evolution post earlier I heard a very good, concise of reproductive fitness: fitness is the ability to pass on your genes to offspring that can pass on their genes. The example is that producing a mule doesn't contribute to reproductive fitness because mules don't reproduce. 

The thing that I'm really thinking about, though, is about defining evolution as a change in a population's allele frequencies over time. I'll get in trouble with some evolutionary biologists for cutting it down that far since there is a whole field that is devoted to understanding how the generational change in a population's allele frequencies can result in speciation, or the formation of new species. But making a distinction between evolution proper and speciation is an important thing for evolution's apologists to do (and, in my opinion, something that many seem unwilling to do at least in part for the reasons I stated in my earlier post on the matter) because: a) you can't argue that a change in allele frequencies happens over time since we can see it; b) it refocuses the debate about evolution onto evolutions core principles rather than its predictions. 

So for evolution to take place, you need two have multiple alleles for a given gene, you need to have an external pressure that causes having a particular allele to not be neutral (i.e. there is a benefit or cost to having the allele), and you need to have reproduction. If we use eye color, let's say that there are only two alleles for eye color - blue and brown. Let's also say that Debbie Gibson has blue eyes, and so all of the boys in the 1980s grew up with crushes on her and decided that they would only marry women who have blue eyes. All of the sudden, blue eyed girls all get to reproduce while some brown eyed girls don't get to. There will be more blue-eye alleles in the next generation, and presumably all of those blue-eyed children will be able to reproduce. Evolution just happened. Of course, the same thing could happen the following generation with Debbie Gibson's daughter, who has brown eyes, and the pendulum could swing back towards an increase in brown-eyed alleles the following generation. The most interesting changes will be permanent shifts in allele frequencies, and these will usually result from continuous or very strong pressures. 

The problem, of course, is that a change in the blue-eye color allele in the human population is less interesting than gamma-radiation from a special effects show at a Debbie Gibson concert causing everyone at the show to produce children that are actually a new species of Homo (called Homo gibsonii, this new species is actually born with eyes that are shaped like Ray-Bans and skin that looks like a jean jacket). The likelihood that a child will be born as a different species than its parent is extremely small (i doubt it could ever happen but never say never, right?), and so the question that arises is: how can a new species evolve? A more problematic, but related, question people like to ask is, "Why don't we ever see chimp-human hybrids if evolution is an ongoing process?" The former question is entirely appropriate but the latter is fundamentally flawed (another time...). At least one way that new species evolve is by isolation of individuals of that species by external barriers - such as geographic, social, or reproduction barriers between individuals in a population.

Can you see people who believe that the earth and all earth life was created by God being less resistant to teaching evolution if it focused on this?

As an aside, I thought it would be informative to check on a few definitions for evolution in online dictionaries. I was really surprised. Dictionary.com hit it on the head, but webster's is a bit off the mark, focusing not on the definition, but on the implications of the definition. I'm quick to add that I'm not aware of any evidence that contradicts Webster's definitions, but I think that defining evolution by its predictions and implications rather than by its underlying principles is flawed and causes a lot of unnecessary contention.

Dictionary.com :  change in the gene pool of a population from generation to generation by such processes as mutation,natural selection, and genetic drift.

Webster's: a theory that the various types of animals and plants have their origin in other preexisting types and that the distinguishable differences are due to modifications in successive generations; also : the process described by this theory

Future points: 

"can" vs. "do" pass on genes

speciation vs. evolution

geographical isolation

undirectional evolution

long term evolutionary vision

a problematic species definition

possible speciation mechanisms (egg and sperm mutations)

alleles arise by mutation

define "allele", "locus", etc