In case all of you haven’t already seen today’s xkcd:Win. The funny/sad thing is that I have actually done this. But no Punnett squares on the first date, I’m one of those girls who likes to take things slow.
In case all of you haven’t already seen today’s xkcd:Win. The funny/sad thing is that I have actually done this. But no Punnett squares on the first date, I’m one of those girls who likes to take things slow.
*takes a deep breath*
I’ve been dreading to write about this part of the Creation Museum trip because I know it will put me into a frothing rage all over again. But being a biologist, this is the part I should talk about the most. I’ll try to keep Caps lock and exclamation points to a minimum.
When I saw this sign, I went straight into the room:The whole theme of this part of the museum is that they accept natural selection and microevolution, but not macroevolution. Which makes no sense whatsoever, since microevolution over time leads to macroevolution. Actually, I hate those stupid terms anyway. Evolution is evolution, whether it’s a change in a trait or a change of a species – it’s just the change of genetic material from one generation to another. Since their stance makes absolutely no sense, they deal with it by repeating over and over again that things “are not evolution” even when they just perfectly described evolution happening.
They also never really talk about species, either. Instead there are just “Kinds.”
Their basic idea is that Noah took a certain “Kind” on the Ark, and then that differentiated after the flood. Horrifyingly enough, they have a made up word for creationists who waste their time studying “Kinds”: Baraminologists. Just because you can stick “ologist” at the end of a word doesn’t make it scientific. Here’s an example of “Kinds”:Noah took a small proto-horse, and that eventually evolved – sorry, gradually changed through time (wtf?) into modern horses, zebras, mules, etc. All the proto-animals Noah took were smaller than their modern day counter parts because that’s how they could fit on the boat (wtf?!). Their main argument is that all living equines aren’t really different species, because that would imply evolution. I don’t know why they even bother with all the microevolution stuff, because it just complicates their argument. Why not say Noah took two horses and two mules and two zebras on and they didn’t evolve at all? Why start redefining species and messing with all this “Kind” stuff?
The other thing they beat over your head is that God put so much genetic diversity into the animals Noah took onto the Ark, that once the flood was over, they were able to differentiate. Any geneticist can tell you this is pretty much impossible. Noah forced every single living creature into an extreme bottleneck of two individuals that would eliminate virtually all genetic variation present. Think of it this way: at a single gene locus, if both individuals were heterozygous, the maximum number of alleles you could have in the population would initially be 4. That is not a lot of diversity, and certainly not enough diversity to produce different “species” or whatever the hell they call them. And most likely, not every animal would be heterozygous, or they’d both share alleles that were common in the population. Have the people at the Creation Museum never heard of the Founder effect? It would take insane rates of mutation to make up for this, but they don’t claim that happened – they just say God filled the creatures with variation, which shows that they have absolutely no understanding of genetics.
Oh, but they did provide an answer to one of my favorite questions about the flood! How did the animals redisperse across the world once the flood was over and the Ark landed? It’s simple!
Yes, they really do claim that uprooted trees floated in all the oceans, and animals walked across these trees to get to the other side.
Let that sink in for a moment.
…
I really don’t understand how these people can NOT see how ridiculous this sounds. Have they ever tried to walk across floating logs before? How would a fucking mastodon walk on logs across an ocean? How many days would that take to get across, where the animals wouldn’t have food or would have to sleep on makeshift rafts without drowning. Keep in mind there are only TWO of each animal at this point. Better hope both of them make it! That must have been what happened to the unicorns.
On that note, how the hell did any of the plants survive? I’m pretty sure the vast majority of plants couldn’t survive being under salt water for months, dealing with whole continents moving and mountains being formed, all the soil be moved around so they’re ripped out, or having miles of soil being deposited on top of their seeds (if they even have them). Hell, most plants die if you water them too much! Even if only a couple plants died, it would cause huge complications since ecosystems are so interconnected. Or what about plants that needs specific animals or pollinators to survive? How do they know if that animal is going to end up in the same place since the animals now have to move all over the world? What if a plant that likes growing in a valley ends up on top of a mountain? IT DOESN’T MAKE ANY SENSE AT ALL!
*heavy breathing*
Ok, back to the Creation Museum raping genetics:
The whole point of this case was to say that all mutations are negative (mice with mutations are blind, sick, blah blah blah). They claimed no mutations are ever neutral or positive or produce anything new, which is an outright lie that has been debunked over and over again. It’s one thing to fabricate stories, but it’s another to try and use science and utterly fail. It just drives me mad that this stops being about religious beliefs and starts being about demonizing science. No where in the Bible does it say “all mutations are negative.” They can’t go around asserting that this is their opinion (not that opinions are sacred, but you know what I mean). They are just making shit up to discredit scientists and to promote their own cause. Another example:
I probably stood in front of this case for 15 minutes. First, I had no idea what it was trying to say. Second, the museum was making me feel so confused and stupid that I actually had a hard time reading full sentences to understand it. Third, once I understood what it was saying, I was so flabbergasted that I just stared at it with my jaw hanging open. The whole diorama isn’t there, so let me summarize for you:
1. Wild type bacteria + antibiotic = dead bacteria
Hmmm, that seems okay.
2. Mutant bacteria + antibiotic = living bacteria
Alright, still with you there.
3. Wild type and mutant bacteria WITHOUT antibiotic = living wild type, but dead mutant bacteria
…Wait, what?
The whole premise is that since there are ONLY negative mutations (aka, something destroying a receptor that an antibiotic targets), that without antibiotics present, mutant bacteria are less fit. This again is a downright lie. Proof? How about all the people who are infected with mutant, antibiotic resistant bacteria BEFORE they take any antibiotics? Those resistant bacteria seem to be doing just fine! There, in two seconds I debunked their entire display.
I still couldn’t stop staring at it though, because it angered me so much. Hemant finally appeared and gave me a hug, and after talking to him a bit I still stayed and stared at the stupid thing. Then PZ came through the entrance with Ashley (healthyaddict) who was videotaping this exchange, so I hope it goes up (with more accurate quotes):
PZ: *sees me staring forlornly at the thing* Hmm, so what’s this?
Me: *explains what I just said above*
PZ: …What.
Me: Yep.
PZ: That doesn’t make any sense.
Me: Have you seen the rest of this room?
PZ: …No.
Me: Have fun.
At that point I had to pry myself away or I was going to start crying.
(Thanks to Vanessa and Josh and robsterFDCD3 for extra photos)
Part1, Part 2, Part 3, Part 4, Part 5, Part 6, Part 7, Part 8, Part 9
Now that Adam and Eve ate the fruit, the world’s about to go to crap. We rounded the corner and found this pleasant scene:A very kids-friendly museum! Of course, it’s alright to scare little kids if it teaches them to follow the Bible – think hell houses. This was also in a dark scary room, but the flash from my camera kind of ruins that feeling. Anyway, this is supposed to illustrate their shame of being naked, and how they need to make animal sacrifices to God to make him happy.Please join me in facepalming: “But because humans are not related to animals.” So, let’s get cracking on the human sacrifices then with that logic! And as a side note, does God love nudists because they have no shame? …Moving on.
We meet Adam and Eve again, but now things are different. They have their sons, Caine and Abel, they have to produce their own food, Adam has put on a few pounds (sin = beer belly?), and Eve is barefoot and pregnant like she belongs (somehow I missed a photo of that, oh well). This seems tame enough, but things start getting really crazy here with a new theme: Before Adam’s Sin, and After (you really should click for a larger image and read these things, they’re terrible).
Plants aren’t alive? The hell? I guess we need to kick Botany out of Biology! What do those silly scientists know about what’s alive, anyway? I guess animals not dying for the short period of time they were in the Garden of Eden isn’t too preposterous. Well, immortality is silly, but it’s not like the entire ecosystem would be out of whack or overpopulated because of a lack of deaths. But this is the sign that killed me:
Wut.
…
They’re saying a T-Rex was a vegetarian until sin. I don’t think I need to explain why this makes no fucking sense. Why the hell did some dinosaurs have big freaking pointy teeth? So they could munch up lettuce better? I don’t think so. Either God did a shitty job at designing creatures and arbitrarily gave some useless teeth, or he already knew the fall was going to happen so he had some animals ready to fill the carnivore niche. In which case, did Adam and Eve really have free will if God already knew what was going to happen because it was part of his plan? Did God really just want an excuse to make bacon? EDIT: Apparently I missed a vital part of the exhibit: Velociraptors prior to the fall had MOLARS that through “natural selection” (not evolution, since that doesn’t exist) turned into canine teeth. What the HELL. NO.
Om nom nom. Meat is murder. Tasty, tasty murder.
Of course, I’m probably thinking about this too much. I’m sure there’s a simple explanation to all this. Oh…maybe that the Creation Museum is full of shit and denying everything science or even common sense has ever told us! That’s right, I forgot.
Yeah, I’m not even going to touch this one. It’s just here to show you how outstandingly stupid this room was.
Of course, once you think it can never get worse, it does. I stood in front of this sign for a good long time, probably with a look of confusion and rage on my face (click for larger):
God logic for why Biblical incest is okay but modern incest isn’t hurts my brain:
1. “All humans are related. So whenever someone gets married, they marry their relative.” You know, this is true with evolution too! But I think all reasonable people can see a difference between marrying your sister or cousin and marrying someone thousands of years removed from you.
2. Abraham was a cool guy and married his half sister, so that makes it okay! Well okay for then, then God changed his mind and now you can’t marry close relatives. So, are they actually saying that some of God’s laws were applicable for ancient times but not for modern times? I guess there’s hope for gay and women’s rights! Right?
3. We have inbreeding depression today because Adam’s sin caused mutations. Ugh, I hate when they bring in genetics to explain their crazy ideas.
4. Adam was genetically perfect, so inbreeding back then didn’t matter because there we less mutations. Man, at the mutation rate necessary to go from “genetically perfect” (whatever that means) to our current level of diversity in just 6,000 years, I’m surprised we don’t all have superpowers or extra limbs sprouting out of our foreheads.
5. Irrelevant comment about sex outside of marriage.
6. Lie about marriage being defined by God. You have no right to criticize the Bible if you don’t believe it. Wait…what? Well isn’t that convenient. Only the people who don’t have anything to criticize are the ones that can criticize it!
…
We all felt like soon we’d have no brain cells left, so we moved on.
The next room has a absolutely terrifying animatronic Methuselah. He was creepier then the little girl we first met, and I nearly jumped out of my skin when his eyes moved and looked right at me. I didn’t take a photo because I was afraid my camera would disintegrate from the pure evil emanating from this thing. They had a sign next to Methuselah with all the ages of various famous people from the Bible, and I think they were trying to show that people lived shorter and shorter lives since sin was introduced. I’m not quite sure how sin “builds up” over generations (I think they meant mutations), but I’m not sure about most of the stuff in this museum.
(Thanks to Vanessa and Josh for extra photos)
Part1, Part 2, Part 3, Part 4, Part 5, Part 6, Part 7, Part 8, Part 9
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.
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.
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.
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.
So what do I actually study?
Since I’m trying to milk this for all its worth, let’s just start with my study organism: kangaroo rats!
Specifically I study banner-tailed kangaroo rats, Dipodomys spectabilis. They’re nocturnal rodents that live in the Southwestern US and Mexico. Their entire diet consists solely of seeds – they don’t even drink water. They’ve adapted to the desert life by being extremely efficient at conserving water. For example, their urine (when they rarely pee) is 24% salt – ours is 6%. How do they do it? Simply put, the path from their lungs to the outside air is long enough that the water vapor cools and condenses before it escapes the body – and they sniff it back up. This allows them to only lose 5% of the water we’d lose in respiration.
Oh, and they’re adorable:That silver thing you see on it’s ear isn’t a staple of kangaroo rat fashion – they’re ear tags. Each contains a unique number, and we use them to keep track of each individual. We trap them during the summer and we’re able to tell if they’ve changed homes since last year, who they’re living with, how much they’ve grown, etc. We also take small ear snips so we have tissue to do DNA testing with. There’s really an endless about of studies we can do using this data, but so far most of the work has focuses on dispersal, inbreeding, and paternity.
Did I mention they were adorable?
Their main predators are coyotes (rarely), owls/hawks (commonly), and rattle snakes (frequently). I just because I was lucky to get the photo, here’s one in action (the krat was less lucky):This is post 23 of 49 of Blogathon. Pledge a donation to the Secular Student Alliance here.
So what do I actually study?
Since I’m trying to milk this for all its worth, let’s just start with my study organism: kangaroo rats!
Specifically I study banner-tailed kangaroo rats, Dipodomys spectabilis. They’re nocturnal rodents that live in the Southwestern US and Mexico. Their entire diet consists solely of seeds – they don’t even drink water. They’ve adapted to the desert life by being extremely efficient at conserving water. For example, their urine (when they rarely pee) is 24% salt – ours is 6%. How do they do it? Simply put, the path from their lungs to the outside air is long enough that the water vapor cools and condenses before it escapes the body – and they sniff it back up. This allows them to only lose 5% of the water we’d lose in respiration.
Oh, and they’re adorable:That silver thing you see on it’s ear isn’t a staple of kangaroo rat fashion – they’re ear tags. Each contains a unique number, and we use them to keep track of each individual. We trap them during the summer and we’re able to tell if they’ve changed homes since last year, who they’re living with, how much they’ve grown, etc. We also take small ear snips so we have tissue to do DNA testing with. There’s really an endless about of studies we can do using this data, but so far most of the work has focuses on dispersal, inbreeding, and paternity.
Did I mention they were adorable?
Their main predators are coyotes (rarely), owls/hawks (commonly), and rattle snakes (frequently). I just because I was lucky to get the photo, here’s one in action (the krat was less lucky):This is post 23 of 49 of Blogathon. Pledge a donation to the Secular Student Alliance here.
If you want to read some news articles about my lab’s research, here are some links:
Scientists are learning more about big birds from feathers
Study shows animal mating choices more complex than once thought
Sex lives of wild fish: genetic techniques provide new insights
Random picks better than complicated process in gene indentification
DNA from feathers tells tale of eagle fidelity
Road losses add up, taxing amphibians and other animals
Study rules out inbreeding as cause of amphibian deformities
Genetically modified fish could damage ecology
Speaking of our amphibian road kill project…to give you an idea of how bad it gets, here’s the carnage on a road in West Lafayette after it rains:The town literally has sweepers that come through and remove all of the frog bodies. Thousands die after a single rainfall.
This is why road planners need to talk to biologists before building a major road that bisects a marsh.
This is post 22 of 49 of Blogathon. Pledge a donation to the Secular Student Alliance here.