Ice Ice Baby
Did you know that hot water actually freezes faster than cold? Strange right? One would think cold water would freeze faster given that it's already somewhat closer to freezing temperature. This "hot water freezing faster than cold" is known as the Mpemba effect.
But as I mentioned in a previous post, sometimes what seems to be the most logical answer a) isn't the answer and b) isn't so logical.
Physicists from Nanyang Technological University in Singapore believe this effect can be attributed to the chemical bonds that hold water together (i.e. hydrogen bonds).
They report that water molecules in close contact cause the molecules to repel from each other (like with a magnet), resulting in the stretching of the covalent bonds. As the liquid warms the hydrogen bonds stretch and the water becomes less dense. This stretching allows the covalent bonds to give up their stored energy, resulting in freezing.

If this is true we can presume the same process is active before the final freezing. We can do a fast and dirty experiment and find out if this is true. Take a 1 cup of cold water (from the sink) and 1 cup of hot water. Measure the temperature of both and separately measure the temperature of the fridge (should be colder than the cold water). Place both in the fridge. Which cools down to the temperature of the fridge faster? Let me know if the experiment works for you!

And there ya have it. Another mystery mayhaps solved except not really. It's a working theory, sure, but they haven't actually proven this is the case. Unless we see some molecular structures I'd say this case is still open.

Given Halloween is approaching I figured I would post about the scaries of science.
Today's edition:
Ethidium Bromide, EtBr.

If you've ever worked in a lab that does genotyping you've likely heard of it. You've also likely seen the bench space devoted just to it with hazard warning labels: BEWARE, CARCINOGENIC or some such. But how dangerous is it? I often wondered given that even as much as one tries, somehow it spreads throughout the lab like a virus. I can't imagine where it wouldn't be found if we brought in a UV light.

So that's when I decided to actually look it up and see just how bad is it and you know what? Turns out, it's not that dangerous!
Sure it makes all my bands show up nicely but what exactly is it?
Ethidium bromide is genotoxic, a frame-shift mutagen and teratogen.
It intercalates double stranded DNA (inserts itself between the strands), deforming the DNA and increasing chance of mutations (M.J. Waring, 1965). Because it's a fluorescent compound, when exposed to UV light it will fluoresce with an orange color. 

Since EtBr has been administered for treatment of African Sleeping Sickness in cattle you would think there would be a lot of increase in tumorigenesis... but there isn't! Appears that it is less genotoxic in animal systems compared to the in vitro tests performed. There is actually no evidence that direct exposure to EtBr has caused any tumors.

I'm not suggesting we should start gurgling with it. I'm just saying maybe we can tone it down on the EtBr disposal as incinerating anything that came in contact with it, putting it into activated charcoal, using hydrophosphorous acid or sodium nitrate are much more dangerous than it is itself.

Perhaps the largest real hazards associated with use of EthBr in molecular biology are the methods used to inactivate it. Some labs now incinerate all waste containing even a trace of EthBr, and others absorb it onto activated charcoal. Harsher methods involve use of bleach and sodium hydroxide, or hydrophosphorous acid and sodium nitrite, all much more dangerous than EthBr. - See more at: http://rrresearch.fieldofscience.com/2006/10/heresy-about-ethidium-bromide.html#sthash.yOLIpwZi.dpuf

bleach and sodium hydroxide, or hydrophosphorous acid and sodium nitrite, all much more dangerous than EthBr. - See more at: http://rrresearch.fieldofscience.com/2006/10/heresy-about-ethidium-bromide.html#sthash.yOLIpwZi.dpuf

Here is a great article on heresy about EtBr.

Why is it dark at night?

Now I know what you'll say. The sun isn't there and gets replaced by a less bright rock (i.e moon) that just reflects the sun's light. But the more I think about it the less it makes sense. The sun is HUGE. Way bigger than Earth. Other stars that we see are also huge, some far bigger than our sun. How is it that it's so dark merely because the Earth has flipped to the other side?
And then I read this:

“If the Universe is infinite and contains an infinite number of stars, then any direction we look should point to a star. Therefore the sky should be as bright as the surface of the Sun both day and night. Since it’s not, the Universe must not contain an infinite number of stars and therefore, the Universe must be finite.” - Olbers.

How amazing that from a seemingly obvious observation such a profound conclusion can be reached.
That is science. It's not just doing the brunt work and getting the data. It's the analysis that comes at the end of all that. What's the bigger picture from all those little bits? 

Although the idea here is good Olbers' premise was actually incorrect. But that's science. Take an observation, propose a hypothesis and TEST it. The reason it's not quite right has to do with the idea of infinite sets such as the one in Hilbert's Paradox of the Grand Hotel.

Gel Questions

As a graduate student you're expected to know certain things. What I've learned the hard way is that I definitely don't know them!
Reading and analyzing scholarly articles takes a whole new training. I'm still trying to get the hang of it, hence my stupid question for today.

In particular lets just look at figure B here.




(Xiao-Dong Yang et al, 2011)

What is this figure trying to show? Obviously you can see a band (that black elongated blob) shifted down in C delta 39 in the 1st panel. In the 2nd panel there are some solid bands along with lanes that have multiple bands in one. What does this all mean?
The fact that you don't have those multiple bands in the top lane shows that pop-1 alone is not phosphorylated. This is not due to any sort of mutation as even the wt doesn't show phosphorylation.  In the 2nd panel pop-1 in the presence of wrm-1, and lit-1 acheives phosphorylation in the wt (DUH), D8E, ExpA, ExpD, etc. suggesting that phosphorylation of pop-1 requires the presence of wrm-1 and lit-1. Though it may have been interesting to see pop-1 with wrm-1 alone and with lit-1 alone to see if perhaps both are not required (possible this is done in the supplemental). What we also see in this figure is that pop-1 even in the presence of wrm-1 and lit-1 is still not phosphorylated for T425D, ExpA T425D,  ExpD T425D, and C delta 4, suggesting the mutations present in these somehow inhibit phosphorylation of pop-1.

And there you have it! This is how you read a gel and analyze it.

But I'd also like you to pay attention to the 3rd to last column of ExpD... is that...? Why yes it is PHOTOSHOPPED in. At this point how can you trust any other information the authors provide? Why did they choose to cut and paste instead of just rerunning a blot with all the necessary components? Shady stuff, people, shady stuff! 

Introductions

You may be just like me. I'm that terrified PhD student who feels too stupid, too unprepared, and mistakenly accepted into a program far above my capacity. I have to keep reminding myself that my brain is still making synapses (there's hope)!

"Why couldn't I think of that experiment?"
"How do they know so much? They're the same year as me!"

These were my thoughts and I am making this blog in part to pretend long enough that I do belong here and in part to help others who feel as inadequate as I do. 

I think the main issue is that  institutions teach science the wrong way. They teach to memorize and not to think. What this does is stifle creativity and frankly, makes science boring. Of course memorization plays a role but alone it just makes you a record player (and unless you have the equivalent of photographic memory for audio, a rather poor one).

So here I'll allow myself to question things I'm too scared to ask my labmates lest they think I'm stupid AND I'll even go so far as to try and find answers. Even if they're wrong initially (heck, even nature papers get retracted)!
Basically, I'm going to let myself ASK without fear of what others will think of my intelligence.

I hope to reignite my passion for science and scientific thought. To resurrect thought experiments.

The main goal here is to use the basic facts about science and apply them in a wider framework.

Feel free to leave me questions you would be interested in seeing answered.

Science doesn't need to look like this:

to be fun or thought provoking.