Meta Blogging – How do I wake up?

Throw away post, sorry.

I’m starting to feel the effects of sleep, and I still have at least seven hours of blogging left. Usually 2 am doesn’t affect me like this, but I woke up at 7am and I’ve slept like crap the last three days. I think I can stay awake, but the hard part is actually coming up with coherent thoughts. Before I was ahead by a half hour, now I feel like I have about 15 minutes a post because I’m starting to move slower and slower.

So, suggestions? Caffeine? Running around to music? Giving up and letting my inner insanity take over my posts?

PS: Lost at the art contest, aw. Oh well.

This is post 35 of 49 of Blogathon. Pledge a donation to the Secular Student Alliance here.

Porn? Too silly!

WATCH OUT boys and girls! It’s late night with the Blag Hag! Aka, I’ve finally cracked and it’s time to get to the dirty stuff. The rest of this night probably will be mildly NSFW, unless you don’t have to worry about curious coworkers peeping over your shoulder.

Why don’t women watch as much porn as men? I think someone finally got it right:

“For me, the real problem with most porn is its hokeyness — the ridiculous costumes, the awful cinematography, the ludicrous story lines, the terrible acting (not to mention how scary the close-ups sometimes look, how fake the boobs are, how some starlets really sound like injured animals…).”

One hundred percent agreed.

I’m not sure why it seems like guys don’t have a problem with this – they are the ones watching the majority of porn, after all. But silliness in porn drives me nuts. Even at peak horniness, an ugly pair of socks (why the hell are you still wearing them?), unrealistic people, fake moans, funky disco music, or cats walking by in the background will just ruin it for me. It’s not necessarily that I react in a disgusted way – usually it just distracts me. Sometimes it’s so funny that I keep watching to laugh at it instead of enjoying it the way Aphrodite intended. I’ve even wished there was a blog devoted to making fun of the ridiculous stuff in porn. I’d do it myself, but I kind of don’t want my name eternally associated with that.

So guys, enlighten me. How do you do it? Do you just not notice it in the heat of the moment?

This is post 34 of 49 of Blogathon. Pledge a donation to the Secular Student Alliance here.

Jennifer Jennifer Jennifer

And like Beetlejuice, I appear out of nowhere magically! Along with the five billion other Jennifers.

It really bugs me to have such a common name. There always seems to be at least one other Jennifer in my classes. The laboratory where I work had three Jennifers in it at one point in time out of 20 people. Hell, in the Blogathon chat room 2/17 people are named Jennifer. It’s gotten to the point where if I walk down the street and someone says Jennifer, don’t even bother to turn because it’s rarely ever for me. This annoys the heck out my friends who are actually trying to get my attention.

So one day I asked my dad, why the hell did you name me Jennifer? Why such a common name? Did it have some sort of significance for you?

Why?

Both of my parents are teachers.

When you have so many students, less common names always conjure the image of a specific student. Veronica? Ugh, sooooo annoying. Courtney was a nerd. Meredith? Not the brightest crayon in the box. But Jennifer? So many of them, no one student popped in mind!

So thank you mom and dad. I was named to be bland and unmemorable.

Just kidding, I think this is pretty hilarious. Better than just naming someone after a relative, I think.

This is post 33 of 49 of Blogathon. Pledge a donation to the Secular Student Alliance here.

Drawing Challenge

There’s a new challenge at the Blogathon for $5 – draw something related to Blogathon! Well, this is basically how I feel right now: going insane and jacked up on caffeine.
Though it’s a bit of a stretch. I really only have a couple Pepsi cans surrounding me, and they’re not ginormous. Unfortunately I didn’t have to take too much artistic liberty with the deranged look on my face.

This is post 32 of 49 of Blogathon. Pledge a donation to the Secular Student Alliance here.

Friendly vs Outspoken Atheism

Another guest post from Mark:

Now that I’ve had a little bit of booze in me… I don’t know much about Christmas, but Bailey’s, Peppermint Schnapps, and chocolate milk is fine by me.

My hat goes out to Jen here. I would not be able to blog every half hour. I don’t have that many things to say.

That being said, here’s Guest Post #3 from me!

I was asked by Jen to discuss the difference between the so called “Friendly Atheist” vs the so called “Outspoken Atheist.”

Here, I think, are the pros and cons of each at their most extreme:

The Friendly Atheist is sort of seen as the apologetic atheist. They are there to be a spokesperson of atheism to religion. As a result, these people tend to be less outspoken about their own atheism in hopes that they can act as ambassador to the religious.

On the other hand, we have the Outspoken Atheist. The Outspoken Atheist is out there to let people know that he exists and doesn’t care about your shenanigans. If you say or do something stupid, they will let you know because they’re Atheists and they are the guardians of logic and the path of scientific enlightenment.

I think it is possible to conserve the best traits of each. It is possible to be an Atheist who is quite staunch in his beliefs and not be a dick about it. Certainly you may come across people with stupid beliefs. However, in my opinion, if they aren’t bothering you, it is perfectly fine to leave them the heck alone.

As a general rule, when I meet a person, I try to judge them on their merits. I am, indeed willing to ignore the faults of a person if I find they are a positive influence on my life.

For example, a very close friend of mine, “Barry,” is very religious. He went to a school system run by a Baptist church and is a very active member of his congregation and a very religious individual. However, as a person, he is an incredibly good one. He’s a talented musician of many stripes, an incredibly intelligent person, and an all around good guy. As a result, I have no problem with him as one of my closest friends. Sure, we disagree on certain things, religion being tantamount among them, but that is a small part of our relationship. We recognize that we have an incredibly different opinion, and recognize that, in the end, we are unlikely to change each others minds…so we don’t bother mentioning it. Incidentally, he helped to build the museum that we are going to in two weeks. (LOL *cough*)

It is possible to be an ambassador to other faiths without compromising your integrity just as it is possible to be outspoken without being intrusive.

When it comes to these two archetypes, I don’t think they need to be different.

This is post 31 of 49 of Blogathon. Pledge a donation to the Secular Student Alliance here.

Why do people have favorite colors?

Random thought time.

Why do people have favorite colors? It may be like having a favorite food, which I assume is basically chemical in food > taste buds > signal to brain > release of happy chemicals (very scientific discorse following my last posts). I guess a favorite color would go more like certain light waves > particular stiumlation > signal to brain > release of happy chemicals.

But is that really how it works? With food, I will pick my favorite over others, and I will go “mmmmm” when a delicious piece of cheesecake is in my mouth. But my favorite color is blue, and the sight of blue doesn’t necessarily make me elated. I don’t jump for joy when I see a blue car over a red car. My closet isn’t just full of blue clothes – if I got a wonderful psychological reaction of of blue, you would expect it would be. But at the same time if you asked me my favorite color, I was not hesitate to say blue.

My guess is that having a favorite color is a cultural meme. We’re asked at an early age what our favorite color is, and we’re expected to have a quick answer. I wonder if younger children have to think longer about their choice than older children, or if younger children change their mind more and then their favorite color becomes permanent. I’m not sure how that initial color is picked – maybe it’s the color of their room, their blanket, their favorite toy – or maybe it’s completely arbitrary and then they stick with it. And from that point on, it starts reinforcing itself. I know blue is my favorite color because I said it was my favorite color. I like blue more because people start buying me blue things that I like (my mom basically bought me nothing but blue clothes when I was little). After a while I can’t come up with a logical reason why I like the color blue – I just do. It seems instinctive. Yet I have a hard time believing my preference for blue has a genetic basis – but who knows, weirder things have been found.

Keep in mind this is arm chair speculation – it could be complete BS. But what do you think? Any hypotheses? Any sources I should have tried to find?

This is post 30 of 49 of Blogathon. Pledge a donation to the Secular Student Alliance here.

I'm a scientist! Pt 5

So the previous project I described is what I worked on most of my junior year and is in the process of being transformed into a paper (which I’ll likely get to be first author on – huzzah!). What other lab work have I been doing recently?

This wasn’t even meant to be a full project, but really started out of curiosity (like all good science does). One of my professors, Prof W, was doing some collection in the krat’s breeding season (Novemberish) instead of our usual July. During his trapping he was lucky enough to discover some copulatory plugs.

What the hell are copulatory plugs, you ask? Basically it’s a secretion the male deposits during mating that hardens into…well, a plug that takes time to remove. This makes it harder for the female to mate with another male later for obvious reasons. Or to steal a good analogy from Wikipedia, it’s a biological chastity belt.

Most rodents and some insects use copulatory plugs but they’re still a bit of a mystery. There’s not much literature on them in rodents, and virtually none on kangaroo rats. So we thought, what the heck can we do these things? Hmmm, let’s chop them up and genotype them!

We cut the plug into four segments, so one segment 1 would be the most internal in the female, and segment 4 would be the most external. We digested the plug and extracted DNA, then genotyped the DNA using various genetic markers. We then compared the results for these markers to the genotypes of the females we retrieved the plugs from. The tricky thing here is that you have a mixed sample, something they have to deal with a lot in forensic cases. Think of a rape case – you may have a semen sample, but it’ll have DNA from the female in it too. How do you know which belongs to which when you’re looking at something on a screen?

This is an example of what you would see (each number represents an allele):

Female: 130, 142
Mixed sample: 130, 136, 138, 142

You know that 130 and 142 most likely came from the female, and the new 136 and 138 came from the male. So the male is 136, 138 right? Well…it’s a bit more complicated. Maybe there are two males, and one is 130, 136 and the other is 138, 142. Or maybe one is 136, 138, and the other is 138, 142. What if there are three males?

Thankfully, there are ways around this. One is by comparing the relative strengths of each allele (not going to explain that, sorry). Another is using multiple markers. Another is assessing the probability of the combination using statistics. And finally, you can use the exclusion principle – see what males absolutely cannot possibly have contributed those alleles, and see who’s left and how the puzzle fits together.

I think you can imagine that this project is the ultimate puzzle. It can be a pain in the butt deciphering everything, but it’s really rewarding once you crack the code. And what have we figured out so far? Well, we have a pretty good guess of what male contributed to the plug, and in some cases more than one male appears to have contributed to the same plug, with their contributions separated by location in plug. Aka, the male that got their first formed the most internal part of the plug, and the second male formed the most external.

And before I start talking too much about rodent sex, I’m going to leave the implications of that up to your imagination.

This is post 29 of 49 of Blogathon. Pledge a donation to the Secular Student Alliance here.

I’m a scientist! Pt 5

So the previous project I described is what I worked on most of my junior year and is in the process of being transformed into a paper (which I’ll likely get to be first author on – huzzah!). What other lab work have I been doing recently?

This wasn’t even meant to be a full project, but really started out of curiosity (like all good science does). One of my professors, Prof W, was doing some collection in the krat’s breeding season (Novemberish) instead of our usual July. During his trapping he was lucky enough to discover some copulatory plugs.

What the hell are copulatory plugs, you ask? Basically it’s a secretion the male deposits during mating that hardens into…well, a plug that takes time to remove. This makes it harder for the female to mate with another male later for obvious reasons. Or to steal a good analogy from Wikipedia, it’s a biological chastity belt.

Most rodents and some insects use copulatory plugs but they’re still a bit of a mystery. There’s not much literature on them in rodents, and virtually none on kangaroo rats. So we thought, what the heck can we do these things? Hmmm, let’s chop them up and genotype them!

We cut the plug into four segments, so one segment 1 would be the most internal in the female, and segment 4 would be the most external. We digested the plug and extracted DNA, then genotyped the DNA using various genetic markers. We then compared the results for these markers to the genotypes of the females we retrieved the plugs from. The tricky thing here is that you have a mixed sample, something they have to deal with a lot in forensic cases. Think of a rape case – you may have a semen sample, but it’ll have DNA from the female in it too. How do you know which belongs to which when you’re looking at something on a screen?

This is an example of what you would see (each number represents an allele):

Female: 130, 142
Mixed sample: 130, 136, 138, 142

You know that 130 and 142 most likely came from the female, and the new 136 and 138 came from the male. So the male is 136, 138 right? Well…it’s a bit more complicated. Maybe there are two males, and one is 130, 136 and the other is 138, 142. Or maybe one is 136, 138, and the other is 138, 142. What if there are three males?

Thankfully, there are ways around this. One is by comparing the relative strengths of each allele (not going to explain that, sorry). Another is using multiple markers. Another is assessing the probability of the combination using statistics. And finally, you can use the exclusion principle – see what males absolutely cannot possibly have contributed those alleles, and see who’s left and how the puzzle fits together.

I think you can imagine that this project is the ultimate puzzle. It can be a pain in the butt deciphering everything, but it’s really rewarding once you crack the code. And what have we figured out so far? Well, we have a pretty good guess of what male contributed to the plug, and in some cases more than one male appears to have contributed to the same plug, with their contributions separated by location in plug. Aka, the male that got their first formed the most internal part of the plug, and the second male formed the most external.

And before I start talking too much about rodent sex, I’m going to leave the implications of that up to your imagination.

This is post 29 of 49 of Blogathon. Pledge a donation to the Secular Student Alliance here.

I'm a scientist! Pt 4

So what do I specifically study about kangaroo rats using genetics? Well, there’s been a long standing debate in our lab if our two study sites are actually separate genetic populations, or geographic locations. They’re separated by about 30 miles, and krats don’t disperse that far in a year – usually 100 meters. However, the sites are connected by a valley that’s full of kangaroo rats. If they’re a single population, their long term population histories and genetic variation would be similar. If they’re two populations, you would see some difference. That’s what I’m trying to solve.

How do you look thousands of years back into the past using just the DNA you have now? You use a molecular clock. DNA mutations accumulate at certain rates in certain areas, and you count the number of mutations. For example, if you know in one gene you get one mutation every ten million years, and you see three mutations, that probably took 30 million years to accumulate.

I specifically use the control region of mitochondrial DNA. The control region is a noncoding region that accumulates mutations quickly since it doesn’t undergo any type of selection. It accumulated mutations so quickly that you can see differences within individuals in a single population by just looking at a couple hundred base pairs of sequence data. For example, these may be two individuals:

krat 1: AATCGTT
krat 2: GATCGTT

Each variation of sequence is called a haplotype. You may know the term “genotype” – the main difference here is that since we’re dealing with mitochondrial DNA, it’s haplod (only has one copy). More than one individual usually share haplotypes unless it’s a rare one. If the two populations are isolated, you would expect to see differences in haplotypes. We didn’t see any differences, which indicate these two locations aren’t as isolated as we may have thought.

There’s some more in depth analysis going on, but I’m not going to bore you with those bits.

This is post 28 of 49 of Blogathon. Pledge a donation to the Secular Student Alliance here.

I’m a scientist! Pt 4

So what do I specifically study about kangaroo rats using genetics? Well, there’s been a long standing debate in our lab if our two study sites are actually separate genetic populations, or geographic locations. They’re separated by about 30 miles, and krats don’t disperse that far in a year – usually 100 meters. However, the sites are connected by a valley that’s full of kangaroo rats. If they’re a single population, their long term population histories and genetic variation would be similar. If they’re two populations, you would see some difference. That’s what I’m trying to solve.

How do you look thousands of years back into the past using just the DNA you have now? You use a molecular clock. DNA mutations accumulate at certain rates in certain areas, and you count the number of mutations. For example, if you know in one gene you get one mutation every ten million years, and you see three mutations, that probably took 30 million years to accumulate.

I specifically use the control region of mitochondrial DNA. The control region is a noncoding region that accumulates mutations quickly since it doesn’t undergo any type of selection. It accumulated mutations so quickly that you can see differences within individuals in a single population by just looking at a couple hundred base pairs of sequence data. For example, these may be two individuals:

krat 1: AATCGTT
krat 2: GATCGTT

Each variation of sequence is called a haplotype. You may know the term “genotype” – the main difference here is that since we’re dealing with mitochondrial DNA, it’s haplod (only has one copy). More than one individual usually share haplotypes unless it’s a rare one. If the two populations are isolated, you would expect to see differences in haplotypes. We didn’t see any differences, which indicate these two locations aren’t as isolated as we may have thought.

There’s some more in depth analysis going on, but I’m not going to bore you with those bits.

This is post 28 of 49 of Blogathon. Pledge a donation to the Secular Student Alliance here.