# fibonacci

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1. ## Molecular bio novice, a little help?

I'm trying to figure out how to sequence a gene I'm interested in from mRNA. Typically the way the lab does qrtPCR is they first make cDNA. using Applied Biosystems high capacity RNA to cDNA. Does this create full length cDNA of every RNA? For example, one gene I want to study is 5000 bp long in its mRNA. Does the reverse transcriptase make a full length cDNA? Next, what do I do with the cDNA? If I design primers using standard protocols that use online software, it gives me a pair of primers that are somewhere in the middle of the cDNA. Once I do PCR, will it amplify the whole cDNA o
2. ## Why are experiments run in triplicate?

Good points. I agree, magnitude of effect and biological importance should be the most important concept to analyze for a biologist, but too often journals won't accept a manuscript if they don't see "statistical significance" , which in the end is meaningless without effect size. If one knows what statistical test they want to run on the data that they are going to obtain, I was under the impression POA should be used to determine how many times to run the experiment. Why is it then so many journals accept n=3 without justification for 3? I don't understand the rule of thumb I guess if the
3. ## Why are experiments run in triplicate?

I don't think each cell counts as an individual "n". See: http://labstats.net/articles/cell_culture_n.html N should be the number of times your run your experiment independently. For example, let's day I do the tox test above on the cells day 1 with technical triplicates, repeat again on day 2 w/ technical replicates, and repeat again on day 3 with technical replicates. My n is still only 3 even if each sample I tested on those days contained millions of cells.. I've never seen a literature example where they run an ANOVA on a n=millions of cells. Cell culture cells al
4. ## Why are experiments run in triplicate?

Ok, for a very easy example: Let's say I want to test drug X on cancer cells to test for toxicity. I test 0, 50, and 100 uM of the drug on the cells and then count them to determine toxicity. The typical way to complete this experiment would be to repeat this experiment 2 more times and then run ANOVA or some other statistical test to determine statistical significance between concentration and cell count. This would be acceptable for many journals. What I'm hung up on, is why is n=3 by far and away accepted as a default number of times to run an experiment like this? Shouldn't o
5. ## Why are experiments run in triplicate?

Right, experiments are done in triplicate so that statistical tests that generate P values can then be used to show "statistical significance". However, if your study is underpowered statistically, you run into all sorts of problems with type II errors and over estimating the mean effect size from an experiment. I'm under the impression that in cell culture work, each cell doesn't represent an independent measurement. Anytime you obtain a sample and assay your cells, the sample as a whole only counts as one measurement (technical replicates do not count of course). Am I confus
6. ## Why are experiments run in triplicate?

I don't understand why many biological experiments in literature are automatically run in triplicate. What's so special about the number 3? Why is it automatically assumed that a study run in triplicate has enough statistical power to make the observations from that study meaningful? Don't you have to run power of analysis first before determining proper sample size? Why is "triplicate" a mindless automatic default for number of times to do an experiment? I even see papers that get published in Nature and Science with experiments "done in triplicate". I don't understand why so much of the li

Let's say you messed up big time and took a course that is impossibly difficult to pass with the minimum grade. Is it bad to withdraw from a class in grad school? Let's say I don't even give a crap about teaching in academia after getting a PhD and that I can take a summer course to supplement the credits needed. What would you do if you knew you couldn't pass an insanely hard class that's not required but one of your electives?
8. ## anyone else losing weight in grad school?

I've lost 22lbs while in grad school thus far, not because of some strict regimen of working out and dieting, but because of the fact that I simply don't have time to eat. Many days I only eat once per day. I wasn't that big to begin with, just slightly overweight (161 lbs for a male) and am now down to 139lbs. I haven't been this light since my freshman year in high school. At this rate, ill be sporting a 6 pack soon all without even trying, and ive never had a 6 pack in my life. Anyone else losing a ton if weight because they slend more time doing work than having time to eat?
9. ## don't think I'm going to make it

Know how you feel. I'm older too, and went back to school after a half decade in industry. Your academic skills definitely deteriorate while working BUT you have working experience which most lunatics in academia have never had in their life. No one really cares about your grades in grad school, just pass the courses you need to and do interesting research. If you're getting A+s in your classes, that means you are spending too much time doing class work and not enough on research. Sometimes I think the undergraduates in some of the classes I take are way smarter than me, but just I realiz
10. ## how to deal with F\$(&\$ING stupid post doc in lab?

The postdoc we have in lab is starting to drive me crazy. She now thinks someone is sabotaging her experiments when she isn't around, and has now started whining to the PI about it. I know she's probably narrowed it down in her head to either me, or another guy in the lab. It just irks the sh!t out of me, that I'm probably being falsely accused of sabotaging her experiments behind my back. Now that she thinks sabotaging is going on, she's moving stuff around the lab and taking over cabinets and putting locks on them so someone can't "sabotage" her experiments. NO ONE IS SABOTAGING H
11. ## Why do publishing companies own access to taxpayer funded research information?

It's time universities should start creating their own open access journals and peer review them among themselves. The publishing cartels charge outrageous fees that do nothing more than increase tuition costs for everyone. The vast majority of the work that goes into academic journals mostly come from tax payer http://www.guardian.co.uk/commentisfree/2011/aug/29/academic-publishers-murdoch-socialist
12. ## What's your opinion of the "Occupy Wall St." movement?

Look at that, Bank of America just dumped \$75 trillion in derivatives liabilities onto the US tax payers: http://seekingalpha.com/article/301260-bank-of-america-dumps-75-trillion-in-derivatives-on-u-s-taxpayers-with-federal-approval This country is so screwed beyond belief because we let a few wall street banksters and politicians in Washington get away with rigging the system in order to makes millions, if not billions, on it for their own personal selves while it costs us a country as a whole trillions in losses. LIke the author said, these people privatize profits, but socialize all

And it has only been 7 weeks in. I'm struggling with course work right now because I really don't see the point of all this BS. Course work is such a stupid formality, I just hate how I can't get to work in the lab right away because we all know that's what I'm there for anyway. Just learn the science you need as you go along with research, why all the useless coursework that you'll probably never or hardly use again? Also, sometimes I bother wondering why I went to grad school anyway. The economy sucks, and it will for a LONG time. We're training way too many PhDs for number of positi
14. ## Important article for PhD students to read

if you haven't already: http://www.miller-mccune.com/science/the-real-science-gap-16191/ That article also recently won the American Association of University Professor's award for excellence in coverage in education.

It's because the majority on here don't want to believe that the mantra they've been fed their whole life--that more education is always better no matter what the cost--is really not that true at all. Next year when the department of education starts tracking default rates on student loans out to 5 years the default rate on student loans is projected to almost double from 7% up to 14%. Only 40% of student loans are currently in repayment, the rest are either in deferment or are in default. The US has a massive ticking time bomb with regards to education and debt. The numbers don't lie, ed
16. ## Recent grads, how's the job search going?

The jobs that are being created by this economy are for the most part non exportable service and construction jobs, not jobs which require a college degree. During the years of 01 and 06, when times were still "good" and we hadn't entered into a Depression, the information sector of the US economy lost 645,000 jobs or 17.4% Computer systems design and related lost 116,000 or 8.7% of its work force. During that period of time, Oracle moved 2k jobs to India, among others including WS firms which moved their back room tech and analysis work overseas as well. And this was during the time when this

Yeah, run for cover. These days you are lucky if you can get a \$50k a year job with a PhD. The US economy is absolutely hemorrhaging high tech jobs and other well paying work like a slit wrist. Once we get out of this depression most of the jobs that will have been created will be in retail sales, janitor and cleaning services, food prep, RNs, nursing aides, and other low paying service jobs that can't be outsourced. Many new jobs won't need even a college degree. It's highly likely you are probably better off with your masters than a PhD.
18. ## Working in "industry" vs. academia

I don't understand what students mean when they say they want to work in "industry" after they get out when they're asked "so what are your future goals and career aspirations?" Basically it means they have no idea what the hell they're doing and they're just hoping, maybe even expecting, that there will be a job there for them waiting when they get out. Sorry, a PhD after your name doesn't mean there will be anything there after you graduate. Being honest with yourselves, how many of you are hiding out there in grad school really only because you have no idea what you want to do wi
19. ## Coffee! How do you get your buzz?

Been trying cold drip brewing recently. Much much smoother, less bitter, and less acidic. You can definitely tell a major difference. Some people won't like a cold brew while others may vastly prefer it.
20. ## Bikes

^ nice bike. Fixie skid stop
21. ## Bikes

I don't see why this wouldn't be a decent fixie bike for the average commuter (they even have one for short people): http://www.amazon.co...07679311&sr=1-2 They have a red one with straight bars if you don't want to get all low and in a race position with the drop bars. For \$300, you probably won't be able to find a 'good' bike per say anywhere. You'll have to get an old one off of ebay or craigslist if you want better quality. Spend \$250 and then take it to the bike store to get it converted to a fixed gear bike. Just be aware with a fixed gear bike, the pedals constantly move, y
22. ## Taking Calculus 3 after...

Just go into Calc 3. Calc III doesn't really emphasize tricky integrals it's more about the concepts behind using multivariables. Unless you have a huge jerk for a professor, you really won't be doing ludicrously difficult integration.
23. ## Bikes

I'd highly recommend for most of you to fall in line w/ the hipster crowd and simply go with a 'fixie' road bike. I've fixed bikes for years when I was younger. The more moving parts a bike has, the bigger pain in the ace it is to fix it. Fixing something simple like a chain popping can be a huge pain on a bike that has multiple speeds. A fixed cog will be fine for probably 90% of people simply using a bike to just commute and get around town.
24. ## The DIRTY BUSINESS of college education

It also doesn't help when you have multi BILLION dollar entities like JP Morgan, Wells Fargo, etc. rigging the system so that students can't get out of loan debt while simultaneously selling their debt on Wall Street to investors which is putting the pedal to the floor on tuition inflation. There are clear conflicts of interest at almost every single level with regards to student loans, lenders, and borrowers. I suspect that universities too may also be investing in SLABS, which is down right sickening. That would give them incentive to have their students in debt and to constantly raise tu

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