What your base criteria for data?

When reading a paper, how do you evaluate other peoples data? Do you look at an image and say, yes what you’re saying is obvious? Or do you look at the image and say, what you say appears obvious, but the quality of your image is not very good, so I don’t really trust it?

I am reading a paper that is quite important in my particular subfield. As I read the paper, I examined the microscopy images in detail as they were the first to demonstrate “colocalization” of my proteins of interest. IMHO, the images are not very good. As the authors used confocal microscopy, they either had too much ab, the detector pinhole set to > 1 airy disc or the pmt gain and offset settings were too high. They also stated that the 2 proteins colocalized without providing information on the voxel (a 3 dimensional pixel) size used to collect the images. Yes the 2 signals overlap, but is that because you used a 100 nm X 100 nm X 250 nm or because you used something greater than that? because if you used something bigger, I don’t care that signal from 2 proteins share the same space it doesn’t mean they interact. Heck signal from 2 proteins can occupy the same 100nm x 100 nm x 250 nm and that doesn’t mean they interact. In another set of images, as expected the images collected using GFP-tagged protein is much cleaner then images collected wheere an antibody was used to detect the protein. For those of you who don’t know, there will be additional noise with an antibody because of non-specific binding. It is for this reason, that is why you always take images of your cells, tissue, etc with no antibody (account for auto fluorescence), secondary only (non-specific ab binding) and / or an isotype control. I say and/or as I’ve heard legitimate arguments for an and against it – I just haven’t decided which side of the fence I sit on. These control images are used to remove “noise” or background (which should be stated in the methods section!!!)

As I explained my critique to a fellow lab member, they became somewhat defensive** and stated that when critiquing someone else’s data I should ask if it passes the bloody obvious question before slamming the quality of it. I don’t agree with this, because I know if MSc advisor had seen those images, he never would have let me publish them. Plus the images coming out of our lab do not look like that. Which brings me to my question for you dear readers? How do you evaluate data?

**although this individual was strongly annoyed with me (probably because they think I was being overly critical and they know how hard the first author worked), they were perfectly normal with me 10 minutes later. I love that we can be strongly opinionated on a subject and then be totally normal on the next topic.

An aunt twice over today!

Or at least in the next 24 hours. My sister just had a baby boy and my SIL is in labour and has gone to the hospital this morning. I am so excited!!!


I also have a whole bunch of emotions that are not happy, but I am trying to put those aside. These negative emotions stem from a whole bunch of family drama that was going on during monkeys birth, which resulted in alot of tension and a lack of celebration on my side of the family. It was really hard because when my sister had her first child I flew oversees to see them and I was annoyed that none of them could put aside there differences to celebrate in a traditional indian manner. I am not going to get bitter that the birth of her second child will be met with that celebration because they have sorted out their issues (which had nothing to do with me). Mr.SM's family was and always has been awesome. I love my sister and am super happy for her. That is what is important. Eventually I will get up the couragous to get to a therapist and deal with all the issues I have with my parents and family...

I am really am that pathetic

It is a beautiful sunday afternoon. The sun is shining, its warm and the monkey has gone with his dad for the day. You would think that I would be outside, enjoying the weather via reading in the sun or gardening. But nope I am in the lab, in dark room, deconvolving images. Why? Because I couldn't drive all the way out to campus and do nothing. Why did I drive all the way out to campus if I did not have to? Because I left the power supply to my computer there. Which shouldn't be that big of a deal since it is a nice day and I could be spending it outside without having to be eagle to keep an eye on the monkey, except the inability to check my email, read blogs and look up random shit was making me nuts. Yep, I am pathetic. On the plus side, I am finally looking at images that were collected a while ago...

RBOC

I know that setting up a committee and having committee meetings is an important part of grad school. Your committee can provide guidance and support on a variety of issues ranging from whether to quit, change supervisors to ensuring that you are not stuck with high-risk, impractical project, troubleshooting and fresh eyes. Yet I am terrified of them. I know they are there to support me and want me to succeed, but I still avoided setting up a committee or setting a meeting. Well after some gentle nudging from my PI and a slap on the hand from our department chair, I have done both. I have a thesis committee and will have my first meeting with them on May 19th. Freaking out is putting it mildy.

I also find it hard to troubleshoot experiments and do literature review (ie learning all about my field) simultaneously hard. I'm trying to get some critical data together so that I can put together a mini-proposal by May 6 (2 weeks prior to sending it committee so that PI can review and edit).

The boy is not listening to me. He is continuing to grow and change at exponential speeds. He is so cute and interactive, but totally independent and frustrating at the same time. Stubborn to the core...he gets that from his dad. Also his circadian rhythm is totally in sync with the sun, so we are entering that time of year where waking up at 6am raring to go is the norm and bedtime does not happen till after 9pm. Good time. The fall/winter sucks because my child goes stir crazy in the house and drives me bananas. The spring / summer sucks because my child can.not.wait. to get outside, and thus drives me bananas....

I have hit the age where if I don't run for 2 weeks I can literally see and feel the weight on me. I hate that. It means my hollow leg is filling up.

I am sitting on the toilet reading blogs while the boy baths. He has a new water gun and he squeals in utter and complete joy every time he shoots water at me. Unfortunately, water and Mac ibooks don't go together well.

I get to go get an iPhone on wednesday.

My parents are totally annoying me.

that is all.

One plus years

Its been over a year since I started blogging. Wow! I've hit some cool milestones: >163 posts, >50 regular readers, AND I'm just shy of 10000 page hits. Its nice to know that I've had some success in this blogging thing because when I started, I didn't really now what to expect as I didn't know the "type" of blogger I would be. My introduction into the blogosphere was thru the "mommybloggers" who got me hooked onto some political blogs (we had both US and Canadian elections going on!). I had no idea that there was this whole world of science bloggers. So when I started, I totally thought this would be all about my struggles as mom going through school, with the focus being on monkey. Thanks to Bean-mom and Mel, I discovered this awesome science blogging community. All of whom have encouraged me to (1) put myself first and find a new PI. (2) how to find myself in a better situation (3) trouble shoot experiments (4) get me through some hard sick days (5) cheer me on. (6) and most importantly, enjoy those monkey stories!

Thanks everyone. Thanks to your encouragement, I am in a new lab, here on a sunny saturday and not grumpy. I'm in a place where the fact that I am an adult and intelligent is acknowledged and respected.

Experience doing Westerns with Licor anyone!

If so do you know the answer to this Q:.

I was told by the rep that if I dry my membrane after staining with my secondaries, I will get a better signal, however I would not be able to strip and reprobe? does that mean I will also not be able to just reprobe?? I use nitrocellulose membranes

3 nights and 2 days

I have survived. 1 night and 2 days left. Its hasn't been too bad. Thursday we hung out at a friends out, we got home a bit after monkeys bed time, so a quick sponge bath and half a book later, he was out.
Friday he (WE!!!!) slept in, then off to a science museum thingy with a blog buddy and her son for the morning. They had a GREAT time together. Home before nap and then off to my sisters for dinner.
Today was harder. But he asleep. It was tough bedtime, largely my fault for thinking my child would actually watch KungFu Panda OR fall asleep with it on. Why would my child who rarely watch TV actually watch a movie???
Oh well. I can do 2 more days, the hardest part for me as been the lack of adult conversation and coming to bed alone.
I'm off to eat some popcorn and have beer while I watch the rest of KungFu Panda

Bad community member

So lab work is crazy busy, the monkey is thumbing his nose at my request and REFUSING to slow down and I'm a single mom this four day weekend. Yep Mr.SM is gone away during the FOUR day long weekend. To say I am terrified of having to be "ON" all weekend, with no help is an understatement. Single mom feel free to laugh at me now.

All of this is to say that I am going to continue to be a bad member of the blogging community. I've been reading all you gals/guys listed there in my blogroll, I'm just not commenting as I have no time. Sorry.

I'm sure you all understand. most of you are either PI's or grad students that are finishing up...

I really really deserve another vacation. must go to sleep before midnight....

New blogger in town

There is a new blogger in town: ArtGrphxJnky!

She's a friend IRL, has kept my blog a secret and has totally made it fun to come to work by being totally cool when I first came here. Lets make it fun for her to be here!

I so deserve these conditions!

We've taken a mini-ski vacation. 15 cm of new snow last night, 40 over the last 2 days! beautiful sunny clear skies! Check out the conditions. haha suckers!

Finished the fucking marking

OMG it was painful. though I dragged it out by only doing a few a night....oh and greys is getting sad..

An open letter to monkey

My dearest monkey,

You need stop. Stop right now.
Suddenly all those pants you got at Christmas / Birthday time fit. I'm not rolling the pant legs anymore and your rain boots don't fit. We went to the mall today to buy you new boots. You were quite confused that you got to try on so many different types and you definitely loved bright yellow boots the best. You put them on as soon as we got home and I swear you would've slept in them if I let you.
But you need to stop. You're having conversations with me and your dad at dinner, you're talking more and more. You are singing and animated. You have total and complete joy in life. You are understanding your boundaries, but are still trying to push them further out.
As much I love it, it needs to stop.
You are growing up way too fast. I blink and you're leaps and bounds ahead. I'm not saying that you have to stop forever, but can you please just stop for a bit. I know its not fair, but I'm really enjoying having you as my baby.
Gosh can I even call you my baby? You're so not a baby. You are little boy going at full throttle all the time. How about we make a deal? You don't necessarily have to stop, but how about you just slow down alot. Or promise me that you'll always be my little boy. You'll always give your mama kisses and hugs?
In case you didn't know, I love you!! I love you more and more each day. Everyday I think I couldn't love you more and everyday I do. Words can not describe out adorable and boyish you were today.
Hugs and kisses. Every morning, every night, every time you see me. Promise?