It's hard enough to do biomedical research involving live animals without having to worry about bomb threats from activists, thanks very much.
Though I wonder if it is really as world-wide as they claim. My God -- can you imagine someone trying to "liberate" the lab animals from research in Egypt? More confusion! Or perhaps it is confusing enough over there that this is a small enough bleep that it won't even register on the radar....
[edit 8:24]
Forgot to comment on this XKCD comic. Or more precisely, how much it reminds me of my PI, since abuse of statistics (which, sadly, you do see in journals, even the higher tiered ones) is one of his favorite pet peeves. For historical reasons we use 0.05 as cut off and for basic tests, that's fine, but when you are testing a large number of hypotheses...well 0.05 is still a 5% chance of false positive, which means you'll find a "significant" result in one in twenty tests just by chance. (And why are they not using ANOVA, any way?) An example in my field, for instance, is testing the linkage between a certain allele of dopamine receptors and...say schizophrenia. There are different types of dopamine receptors. The researchers could start off by testing, say, D4, which they found no linkage. Lack of result = no publication and so, naturally they move on to test receptor D2...and so on. If they test 20 receptors (I don't think there are 20 types of dopamine receptors, but for the same of argument let's say they are testing all neurotransmitter receptors) there'll be one that's linked...if they test 40 there'll be two. If you repeat the 40 tests there might still be two that are positive, but it most likely be a different two because those two happened to be positive by chance. There are various ways to counter that. Bonferroni correction is the simplest and most commonly used for multiple-hypothesis-testing.
Also, yes, replication is important, technical replicates don't count (but biological replicates do), a minimum of 3 reps is good for the standards of most people, but our PI INSISTS on 5 reps whenever possible because of the robustness of stats. Scientific claims in popular news tend to give me headaches. Even pop-sci journals are better but alas, they don't have as strategic placement of splash pages.
Showing posts with label it ate my brain. Show all posts
Showing posts with label it ate my brain. Show all posts
20090606
Prospects ahead
I came up with a vague outline of my dissertation at around 7:15 this morning (those thoughts are immediately followed by "wow it ate my brain, clearly"). I'll need to check with my adviser to see how plausible it is.
Mostly I just feel like writing right now and can't afford to spend hours on it. I've slept lots last night (about ten hours -- great, isn't it?) and it (well, and the prospect of tea immediately after this) has put me in a chipper mode. (I think we can safely add "sleep" to the list of things that makes me happy.) I thought I should make a post with the images I've saved up this week while a) I still remember b) I still have the right laptop open and c) before incurable cases of brain disorder suck all the optimism out of me. (I could've chosen leprosy instead, and peripheral neuropathies, but it's hard to take something with armadillos seriously.)
Right. First of all, there was unexpected thunderstorm in SD on Wednesday. I was outside, eating lunch, when I noticed it getting darker and darker. Then it started sprinkling, and I thought, "Okay, well, odd SD weather, it'll probably pass because it's CA and it doesn't rain here in the summer." Shortly after that there was thunder and a downpour. I spent the rest of my break bemusedly trying to dry my glasses on my shirt in the bathroom.
I took two screencaps of my gmail, because I have the tree & sky background on and I've never seen a thunderstorm there before:
I do have my cell images on Ivy, too, but it's a) unpublished data, technically, and b) very large file so I'm not going to upload it.
Conferred with Lucy on who might be coming this summer (hi Victoria! I got the thing in gmail) and will be scrolling through more ads for housing this week to try to find a place and figure out the details for move-in when I do find the place. An option (if they're okay with partial rent and the rent is, in fact, cheaper than my current place) is for me to pay double rent for a month and a half, which will a) give people two places they can stay (hmm someone still need to bring an air mattress or sleeping bag or something; I have one spare cot mattress and a sleeping bag, that's all) at when they come down to SD and b) give me more time to move so that I can pack / move a little bit of stuff each day in the time after lab and c) still leave myself with enough time to clean up this place so I won't my deposit. (One of my classmate tried this last month and it seemed to work out okay with her.)
But yay, people! (Lucy, I think I have further proof that I should list each person as an individual item.)
Okay, tea and project.
Mostly I just feel like writing right now and can't afford to spend hours on it. I've slept lots last night (about ten hours -- great, isn't it?) and it (well, and the prospect of tea immediately after this) has put me in a chipper mode. (I think we can safely add "sleep" to the list of things that makes me happy.) I thought I should make a post with the images I've saved up this week while a) I still remember b) I still have the right laptop open and c) before incurable cases of brain disorder suck all the optimism out of me. (I could've chosen leprosy instead, and peripheral neuropathies, but it's hard to take something with armadillos seriously.)
Right. First of all, there was unexpected thunderstorm in SD on Wednesday. I was outside, eating lunch, when I noticed it getting darker and darker. Then it started sprinkling, and I thought, "Okay, well, odd SD weather, it'll probably pass because it's CA and it doesn't rain here in the summer." Shortly after that there was thunder and a downpour. I spent the rest of my break bemusedly trying to dry my glasses on my shirt in the bathroom.
I took two screencaps of my gmail, because I have the tree & sky background on and I've never seen a thunderstorm there before:
I do have my cell images on Ivy, too, but it's a) unpublished data, technically, and b) very large file so I'm not going to upload it.
Conferred with Lucy on who might be coming this summer (hi Victoria! I got the thing in gmail) and will be scrolling through more ads for housing this week to try to find a place and figure out the details for move-in when I do find the place. An option (if they're okay with partial rent and the rent is, in fact, cheaper than my current place) is for me to pay double rent for a month and a half, which will a) give people two places they can stay (hmm someone still need to bring an air mattress or sleeping bag or something; I have one spare cot mattress and a sleeping bag, that's all) at when they come down to SD and b) give me more time to move so that I can pack / move a little bit of stuff each day in the time after lab and c) still leave myself with enough time to clean up this place so I won't my deposit. (One of my classmate tried this last month and it seemed to work out okay with her.)
But yay, people! (Lucy, I think I have further proof that I should list each person as an individual item.)
Okay, tea and project.
20090521
The European Journal of Pain
My lab life ate my life.
I usually depart for school around 7:45 each morning and I've already had the pleasure of leaving lab at a quarter to 7, which means that by the time I got home, almost a full 12 hours would have past. The oddest part of this (after eight-to-five shifts of the previous rotation) is that I don't mind. Much. (I do mind when I don't get to eat lunch until 4:30, because being hungry for that long makes me cranky.) There is always something to do. Further more, there is always something I find interesting to do. My current philosophy seems to be that, if the PIs expect us to work 60 hours a week, I might as well as spend 60 hours a week on something that I'm interesting.
I.e. week two is progressing nicely.
My parents are paying a visit this weekend. Dad just came back from China on Monday. I may have to go in lab on Monday though, but we'll see.
And yes, that journal does exist. We're having a discussion on it. Now.
I usually depart for school around 7:45 each morning and I've already had the pleasure of leaving lab at a quarter to 7, which means that by the time I got home, almost a full 12 hours would have past. The oddest part of this (after eight-to-five shifts of the previous rotation) is that I don't mind. Much. (I do mind when I don't get to eat lunch until 4:30, because being hungry for that long makes me cranky.) There is always something to do. Further more, there is always something I find interesting to do. My current philosophy seems to be that, if the PIs expect us to work 60 hours a week, I might as well as spend 60 hours a week on something that I'm interesting.
I.e. week two is progressing nicely.
My parents are paying a visit this weekend. Dad just came back from China on Monday. I may have to go in lab on Monday though, but we'll see.
And yes, that journal does exist. We're having a discussion on it. Now.
20090509
20090317
Hard questions to answer
Example: proposing a new therapy for cancer (one that is not currently used or in clinical trials).
Note: there are many, many different types of cancer, and subtypes. There are many,many types of treatments out right now and many more in the pipeline (what pharm people call the series of trials to approve a drug for usage). There are research being done on many, many pathways.
I hope the PIs aren't really expecting something noteworthy out of us first years here. Like the next imatinib.
(I skipped the question about the upstream and downstream pathways. People spent 30 years studying one pathway in cancer. I have no idea how to even begin to describe the masses of pathways that are involved.)
(Thank you, Anna. I had chocolate. It did indeed improve my mood somewhat.)
Note: there are many, many different types of cancer, and subtypes. There are many,many types of treatments out right now and many more in the pipeline (what pharm people call the series of trials to approve a drug for usage). There are research being done on many, many pathways.
I hope the PIs aren't really expecting something noteworthy out of us first years here. Like the next imatinib.
(I skipped the question about the upstream and downstream pathways. People spent 30 years studying one pathway in cancer. I have no idea how to even begin to describe the masses of pathways that are involved.)
(Thank you, Anna. I had chocolate. It did indeed improve my mood somewhat.)
20090316
Finals week has begun
I went in to have my access card reset today. It turns out that somehow the card had defaulted back to its previous value, so that when you enter its ID number it shows that I belong to previous lab and not the lab I'm currently in. The person in charge was as bemused as I was.
Is it a sign? Hmm.
... ...
In other news, given that it is Monday and I have, by 1pm, not heard back from the PI about my proposal yet, I went over (while my experiment was at the "plug it in to electricity and wait" stage) to check, just to see what on earth happened and whether or not I should be waiting for an email at 3 in the morning tonight. Er. Tomorrow morning. When I went in the PI looked mildly surprised and mentioned that yes, she got the emails from me (yes, note the plural) and inquired as to whether or not I've attached my proposal to them. I informed her, very politely, that yes I did in fact attach my proposal. I attached it to all the emails I've sent to her. She said, mildly, "Okay, let me take a look then," went to her inbox, and there the emails were, with the attachments.
She decided to take a look at them while I was right there. (To save me the pain of staying up all night anxiously waiting for an email, but mostly just to get rid of me, I suspect.) Which is, to say, she skimmed over them, noted that I have more details than I need for the literature review (which I don't really consider a fault) and had me re-organize the entire experimental methods section because my aims needs to be numbered. She didn't actually comment at all about my experimental design, approach, or limitations. After she made sure I know how to re-organize the second half of my proposal (and part of the first half too, apparently background and literature review were supposed to be together for this proposal, and the sample proposal that I followed was for another type of proposal, nevermind that we weren't really told what type of research proposals we were doing to start with), she sent me on my way (no, literally, she said "Bye" to me). She was nice enough, I suppose. And technically helpful, since she gave me advice that I will take (she IS one of the graders for the proposal, after all). Mostly, though, I'm fuming slightly, because I sent that thing to her last Wednesday. For this.
Well, at least when I turn it in tomorrow it'll be over and done with. Good riddance. (For a 2 unit class too. ...If it weren't for the fact that I thought learning how to write a proposal was so important....)
Is it a sign? Hmm.
... ...
In other news, given that it is Monday and I have, by 1pm, not heard back from the PI about my proposal yet, I went over (while my experiment was at the "plug it in to electricity and wait" stage) to check, just to see what on earth happened and whether or not I should be waiting for an email at 3 in the morning tonight. Er. Tomorrow morning. When I went in the PI looked mildly surprised and mentioned that yes, she got the emails from me (yes, note the plural) and inquired as to whether or not I've attached my proposal to them. I informed her, very politely, that yes I did in fact attach my proposal. I attached it to all the emails I've sent to her. She said, mildly, "Okay, let me take a look then," went to her inbox, and there the emails were, with the attachments.
She decided to take a look at them while I was right there. (To save me the pain of staying up all night anxiously waiting for an email, but mostly just to get rid of me, I suspect.) Which is, to say, she skimmed over them, noted that I have more details than I need for the literature review (which I don't really consider a fault) and had me re-organize the entire experimental methods section because my aims needs to be numbered. She didn't actually comment at all about my experimental design, approach, or limitations. After she made sure I know how to re-organize the second half of my proposal (and part of the first half too, apparently background and literature review were supposed to be together for this proposal, and the sample proposal that I followed was for another type of proposal, nevermind that we weren't really told what type of research proposals we were doing to start with), she sent me on my way (no, literally, she said "Bye" to me). She was nice enough, I suppose. And technically helpful, since she gave me advice that I will take (she IS one of the graders for the proposal, after all). Mostly, though, I'm fuming slightly, because I sent that thing to her last Wednesday. For this.
Well, at least when I turn it in tomorrow it'll be over and done with. Good riddance. (For a 2 unit class too. ...If it weren't for the fact that I thought learning how to write a proposal was so important....)
20090209
It got a little hazy after the tenth plate
I have somehow accumulated many, many plates of cell cultures. Currently this is not a good thing. I wonder if I should be freezing down a sample of each plate when I leave, just because when you passage cells too many time they tend to become strange and disinclined to die when they're supposed to.
Today alternated between periods of downpour, where it is in fact accurate to use the word "downpour", and periods when it's sunny and massive fleets of clouds go sailing by overhead (way cool to watch if you've got the time -- for me it's mostly limited to glimpses between class and lab). The wind made me gasp, mostly because it's there and there was an unexpectedly lot of it. The presence of weather is almost soothing after the days in 80s. This could be why I'm having another good day today, despite of the fact that my troubleshoot experiment has failed. Or you know, I could just like being a lab minion / geek that much.
I got "I'm Feeling You" stuck in my head this afternoon, which is strange since I'm pretty sure I haven't heard that song in a very very long time. It's not even the entire song, just the part of the chorus that goes "I'm riding the highs / I'm digging the lows / cause at least I feel alive" ending right before the "I'm feeling you" part. I didn't know the lyrics until I looked it up just now. It has probably something to do with the rhythm of things, like the "The Hurlers", except I actually like "The Hurlers" and I'm not entirely sure I like the other song. (Oh and Annie, I recommend Seth Lakeman to you, his style a little bit like Leahy and...well...just look him up on youTube or something.)
Speaking of multimedia type things. I had an extra hour last night and so went to look up Pushing Daisies. Except I can't find season two on the abc site anymore. Lucy, is this because I was just browsing the wrong abc part or did they took it down?
I've structural biology papers. They are confusing. I mean I know those bits are hydrophobic, but so what?
Today alternated between periods of downpour, where it is in fact accurate to use the word "downpour", and periods when it's sunny and massive fleets of clouds go sailing by overhead (way cool to watch if you've got the time -- for me it's mostly limited to glimpses between class and lab). The wind made me gasp, mostly because it's there and there was an unexpectedly lot of it. The presence of weather is almost soothing after the days in 80s. This could be why I'm having another good day today, despite of the fact that my troubleshoot experiment has failed. Or you know, I could just like being a lab minion / geek that much.
I got "I'm Feeling You" stuck in my head this afternoon, which is strange since I'm pretty sure I haven't heard that song in a very very long time. It's not even the entire song, just the part of the chorus that goes "I'm riding the highs / I'm digging the lows / cause at least I feel alive" ending right before the "I'm feeling you" part. I didn't know the lyrics until I looked it up just now. It has probably something to do with the rhythm of things, like the "The Hurlers", except I actually like "The Hurlers" and I'm not entirely sure I like the other song. (Oh and Annie, I recommend Seth Lakeman to you, his style a little bit like Leahy and...well...just look him up on youTube or something.)
Speaking of multimedia type things. I had an extra hour last night and so went to look up Pushing Daisies. Except I can't find season two on the abc site anymore. Lucy, is this because I was just browsing the wrong abc part or did they took it down?
I've structural biology papers. They are confusing. I mean I know those bits are hydrophobic, but so what?
20090201
Upon reflection, it's really a new kind of pathetic
Sometime around 2am I woke up half way, thought about my reaction mix for an experiment I have to do on Monday, and calculated 18.5*33 in my head. Then in the morning I woke up, remembered that thought, laughed at myself, and checked and I've actually done it correctly.
On one hand: cool, I can apparently do two digit multiplications even half asleep.
On the other hand: my God I need to find something occupy my brain that's not school related.
Maybe Mike'd find this more impressive. Except for where he wouldn't because he can probably tell you the answer to 12! off of the top of his head at 6 in the morning with no caffeine.
Sometimes it's very awkward to write people who are smarter than you are. Especially if they happen to be the mouthy type of person.
Also I just realized that today, for the first time ever, I can't tell you right away where my sketchbook/notebook is. Remember high school? I used to carry that thing with me all the time. And throughout most of college too. This is the sad state of things.
On one hand: cool, I can apparently do two digit multiplications even half asleep.
On the other hand: my God I need to find something occupy my brain that's not school related.
Maybe Mike'd find this more impressive. Except for where he wouldn't because he can probably tell you the answer to 12! off of the top of his head at 6 in the morning with no caffeine.
Sometimes it's very awkward to write people who are smarter than you are. Especially if they happen to be the mouthy type of person.
Also I just realized that today, for the first time ever, I can't tell you right away where my sketchbook/notebook is. Remember high school? I used to carry that thing with me all the time. And throughout most of college too. This is the sad state of things.
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