PhD Advice, possibly the best advice one can get before starting a PhD

I decided to write about this topic now that have some experience in the matter. I started this blog more or less a few months after started my PhD and now I am on my third year, so roughly 2 years are gone.

Over these two years many things happened, good and bad things, and obviously I have been realizing that I added a lot of knowledge not at the academic level alone but I am talking about living experience knowledge. This post will be all about life experience and almost nothing about the scientific content of my PhD, although it quite annoys me too...

Basically I wish I was aware of certain things I am now before I decided to start this PhD, and I hope that if you are reading this and considering doing PhD you will remember my advice :) or otherwise do not complain! ;)

First rule: Get to know your group first! This is so important, and I have been told about that, but for one reason or another I ended up forgetting to know more about the group I was going to be part of. It is really important that you like the group where you work, remember you will be there at least 3 years, the whole day, sometimes 7 days per week, you will possibly need to ask for help or one or two favours, you will be pleased to have colleagues that help you, that you identify yourself with, that you can hang out with, even if they are not or will never be your best friends, you will like to talk to them and enjoy the conversation. Remember that your supervisor must be a nice guy, in the end everything goes down to him, and he will be the responsible for you and your work, so your supervisor must be the guy that you will never feel angry with or have any problems.

So, to know the group is even more important than the subject of your PhD (actually the subject is not very important but I will come to that later). It is more important than the institution, it is more important than the place in the world. I believe that to feel happy at work with the people around it is already a very good help to get the work properly done, because you enjoy to be there, and best is when people work as a team and not like a bunch of selfish guys trying to see you is better like in a race where in the end things do not work and one feels very unhappy.

So do not forget, try to spend some time in a lab before you decide to stay there for you PhD, then you can make sure you are in the right place :))

Second rule: Supervisor success! I already said that the supervisor must be a nice guy, which is absolutely fundamental, you may not believe but that are really freaking supervisors around that can make your life a real nightmare, so be aware! Next important thing about your supervisor is he's rate of success at several levels but most importantly with publications. This is something very easy to track down, as in www.pubmed.com you can search for your potential supervisor's name and see which publications does he or she have. Be careful!! Sometimes there are people with the same name, so a quick look may make you overlook things, make sure the publications are all from the same person by for example checking the institution and the other people in the paper you will be able to track down who is working with etc... Obviously if your potential supervisor has been publishing like crazy in really good journals it is very likely that your project is going to be a success and you will probably enjoy it (but do not forget to check if the guy is nice.. it can be that he is a rubbish bastard scientist that slaves everyone in the lab to get all those papers out). By checking advisor's publications you will also be more aware of the work that is done in the lab, the techniques and methods in use, animal work and so on, so be sure that you don't chose a group that does something you are against or do not enjoy at all. Also very important is to know how many PhD students your supervisor had so far and if they all were ok, passed and published (in case there was a failure I would never go there, but that's just me)!

Third rule: Meeting with the boss! The meetings with your supervisor are very important moments of your PhD, so this advice is more for post-PhD beginning, but I decide to include it here because it is very very important. First, PhD students always think that the supervisor is watching them, or is thinking that they are not good enough maybe a bit stupid, basically in the beginning we all feel a bit overwhelmed by our supervisors, but everything we think is a myth and sooner or later we realize that... In fact our supervisors do not care that much about us.. and that's a problem because they do not remember what we discussed before, for example in the previous meeting, etc.. so meeting with your supervisor should be something very natural. please always feel or try to feel very confident when you talk to your boss, that will make you believable and you advisor will have a great (very temporary) impression of you, and probably will trust you sooner (meaning totally forget about you, which has the pro of at least you dont feel stupid anymore but the cons that you will have to run after your supervisor to have a meeting with him, otherwise he will never come to you). Most importantly, do not disregard these meetings as they are a confirmation of your success (hopefully), and usually your supervisor will guide you (if he is good) and give you ideas and tips that otherwise you would take a very long time to figure that out, and time is quite precious as it runs so fast..

Forth rule: Number of people around you! It sounds like what? but it is quite important that you are not isolated but also that you are not in a crowd all the time, so the amount of people you work with in a daily basis must be something balanced, so great enough for you to have choice, choice of friends, not to feel alone, it also helps to cope with the peer pressure, enough people to compare results with and to entertain the supervisor. On the other hand it is convenient that there are not too many people which could shadow you, or that your supervisor will be so busy taking care of them all that he will not have time for you.

Fifth rule: Institution/place in the world: Well this advice is very general, in fact the best place in the world is where you feel good, but you dont know before you stay there, so it is difficult to predict. Sometimes the most appellative place turns to be horrifying and vice versa, so here it will be very random and thats why the group is so important, because no matter where you are, if you are surrounded by the right people and nice people you will always be alright and feel good :) The institution matters a bit in terms of career for the future, so I would always look for the best ranked institutions first.

And there are some literature about it that you may want to read:

http://www.phdcomics.com/comics.php gives you an idea of how painful can this life be

How to get a PhD : a handbook for students and their supervisors / Estelle M. Phillips and Derek S. - gives you an extensive list of tips and advice on this topic.

Good luck and remember to be sure before you start, because then you commit to a three year nightmare or spend time till you decide to give up and start again or change your life. Nonetheless I can promise you it is not going to be easy even if you take all the advice possible!

Mathematical Modelling of Transcription Factors in Living Cells

or
How the mathematicians and the engineers meet the biologists

The subject of today involves a bit of my PhD's ideas and the one bit I am trying to work in at the moment (Although not too focused because I am doing the other bits too). I think generally speaking the title of this post sounds already a bit complicated but we are talking about PhD topics and subjects so there is no way to overcome complexity, the simple things are out there for everyone, the complex things are ignored by the most of you and deeply interesting to some of us. That’s not entirely my case though! I mean, I am slightly interested on them, but sometimes I just want to move over this and get a more simple life (I think I read it somewhere some time ago.. by that time I didnt quite understand it but every day that passes it sounds more and more familiar, so I already feel it too... it is unavoidable..) It appears that unless one is mental depressed and compromised he cannot enjoy this sort of life forever at least without questioning it (and I guess that may be part of the geniality of all this).
Ok, but regardless of my feelings I came out with this topic because I think it is interesting the way we can apply maths to explain how life works and on top of that there is not much being done in the area, just 2, maximum 3 groups in the world do something similar to this. Thought this is not my whole PhD, I couldnt just do that, but I will present a nice model (hopefully) and I think it will look pretty nice in my thesis..

Well I said hopefully because (maybe obviously) I still didnt solve the model but just some parcels, which is ok, nevertheless I need to solve the model.

Thats where I regret that my mathematics and physics knowledge is not very extensive so therefore I regret once again I didnt undertake the engineering degree :(
Some are medical frustrated, I am an engineer frustrated I am afraid... lol
On the plus side my boyfriend is an engineer and he is giving me a hand with the model, so thats where the biologist meet the engineers.. and this meeting is more than a meeting I hope, and it is genial ;)

So now I think with this precious help I am on the way to finish it and before I forgot I take the change to already acknowledge Pedro for his help ;) and once I finish this I will, I think, also publish something about it in a very practical and straightforward manner very different than what is in the literature I have been reading where one has to go through very complicated equations and protocols in order to maybe use a few of them applied to this sort of cases, it is not very clear how to do that and so on, basically I think the disciplines used to be too apart and they need to converge into a point, people need to work together!

Just to finish with my topic of today I leave a song that apparently represents me in a way, could be my song, it is one of many.. :)

Change everything you are
And everything you were
Your number has been called

Fights and battles have begun
Revenge will surely come
Your hard times are ahead

Best, you've got to be the best
You've got to change the world
And use this chance to be heard
Your time is now

Change everything you are
And everything you were
Your number has been called

Fights and battles have begun
Revenge will surely come
Your hard times are ahead

Best, you've got to be the best
You've got to change the world
And use this chance to be heard
Your time is now

Don’t let yourself down
And don’t let yourself go
Your last chance has arrived

Best, you've got to be the best
You've got to change the world
And use this chance to be heard
Your time is now

Pips go auctions?!

I have to share my experience of today's morning when me and Pedro decided to go to an auction here in Nottingham, but in the most dodgy area of Nottingham, by the way.. I havent been to an auction before, until today the closest thing to an auction I saw was the bids on ebay.. lolol so obviously I was not familiar with that at all, and thats why I probably went there, more in response to my curiosity than just to buy something. In fact I didnt spent a cent in there... but I am quite sure I could have done good business today, the offers are great, I should go back there with more time, like the whole day off!

Basically, after 10 minutes at Cripps health centre in the university, to take the stitches out of my forehead (consequence of my last trip to the snow), me and Pedro took a taxi to this place called John Pye Auctions in Radford. I got to know that through a friend that bought there a tv set some time ago but that place is apparently very popular, busy and known such that as soon as we got there it was full of people.

Before the auction starts people can look around the stocks. The reason why I went was to buy a tv, an LCD tv to put in our very nice living room. Basically we feel a bit poor with all the money we spent recently so any bargain is welcome! Nevertheless our budget was too low...

From the stocks we got interested in 7 or 8 LCDs. As soon as the auction started,
(late! I was really surprised!) we realized that we were surrounded by very strange people (actually I realized that as soon as we arrived but both of us just commented on that while sitting waiting for the bids to start). Mostly everyone was there purely for business reasons rather than buying for personal use, therefore everyone was very professional when bidding and we were like tw0 UFOs there..

And that was it, "our" LCDs were sold for about £200 and we didnt want to pay more than £100.. pity we still dont have the tv but I think we will just buy a new one sooner or later.

We keep the experience of being in an auction, real one, with that guy speaking out loud the prices and everyone seems to be hidden while bidding, I could actually hardly see who was bidding.. the gestures were too smooth.. like they were a bit embarrassed for being there! Like they felt they were committing a crime.. and there were those people on the phone, bidding for someone even more hidden... and there were those people that bought a lot of stuff, clearly they have a big business buying there to sell somewhere else..

Oh well, I should go back there one day, perhaps I could do a fortune out of it, but I am too afraid of high investment.. so back on my PhD life everything is calm and fine, I feel lazy today, I didnt want to come but ... thats life...
I feel I should get more fun :)

AHHHH I love you Google!

AHHHH I think I found the solution for my problems, yeahh Google's the best tool ever who didn't know that?? Doing FRAP experiments? Got lost and stuck, not sure what to do with your data?

Go here http://www.embl.org/cmci/downloads/FRAPmanual.htm

and the here http://www.wavemetrics.com/support/demos.htm

and at last here http://www.embl.org/cmci/downloads/frap_analysis.html

get this K_FRAPcalcV9e.ipf

and go on.. I assume you are smart enough to solve the puzzle from now on ;)
yeahhh

Biochemists versus Geneticists

"In general, assemblies of proteins have been analyzed using two complementary approaches: the biochemical and the genetic. In the well-known analogy to understanding how car runs, biochemists disassemble the engine, transmission and body, characterize all the pieces and attempt to rebuild a working vehicle. Geneticists, by contrast, break single components, turn the key and try to determine what effect the single missing part has on the car’s operation. This implies that genetic methods often require a specific phenotype before they can be carried out." (in Biol Proced Online. 1999 Oct 4;2:1-38).


Found this definition on my readings, quite nice one, I am both of them.

The Science of TODAY is NOT the Science of before

I think everyone who is involved with science nowadays and I don’t even say as involved as I am, but anyone who actual likes science or read scientific news on a magazine, someone who is generally interested on what is going on about new discoveries in physics, mathematics, genetics.... new technologies or whatsoever brings up a breakthrough on what is known so far may have thought the same thing:

The Science of TODAY is very different from what it used to be 10 years ago!

(In the past, but past in science is a very short time due to the speed of how things evolve and change and grow and.. ufff is exhausting!)

The reasons:

The most striking one is obvious: There was a lot more done in the past ten years than possibly in the 50 years before! It is just crazy the amount of findings that came out during the last decade! And of course, every time a step goes forward a new question arises or a new need arises taking the topic a lot further and further and then it’s just like a snow ball that goes faster down the mountain as soon as it gets bigger and bigger!

Also obvious is that the topics researched 20 years ago were different than what is going on now and that's always changing very quickly according to what comes out and what becomes needed and required and on the fields of medical research, pharmaceutics and IT it goes particularly more more fast!

Another big reason to explain this entire boost is INVESTMENT! Despite of the big economic crisis that is now spreading all over the world and the small ones that affected the USA and Europe, the principal scientific investors, there was a lot of money invested in science in the past decade. I am not going to tell you numbers but the results talk by themselves and since a lot more has been done it means there was money for that and that also generated more money! For instance, I noticed the amount of charity funded research provided by institutions fighting against cancer and other malignancies.

The chart below explains how science, technology and society talk among each others and the arrows connecting them, thanks to the big development in the IT fields are getting shorter and shorter and everything just happening very very fast.

The issue:
My personal reason why I am writing about this topic is because of my concerns on how do people are actually actively involved in this very fast circuit and how do they feel about it!

With everything moving and evolving very fast it is hard to stay on the front line and for a scientist that is absolutely essential! There makes no sense to research something that has already been unveil and published by someone else! That takes one to read and read and keep himself very up-to-date but that is a lot of time and then where is the time to perform the experiments? That is also a lot of time either! Shall we scientists become human robots and be design to perform science at the same speed it goes and forget about what behind it makes us human beings and not heartless machines?

How can a scientist succeed in THIS kind of life, professionally, having at the same time a family, a kid and a spouse? Most of them will definitely suffer. I just think that to be fairly recognized in this world one needs to work at least 16 hours a day, half of them reading and the other half performing experiments and the remaining 8 hours will be to eat/sleep and of course there will not be days off or holidays!
Personally I don’t feel programmed for that and I can’t cope with this fast, exhausting, pointless style of life, can you?

But then, since I have chosen that science is what I want to do, as my profession not as my whole live, I might not be taking it serious or enough serious and that means I might not get a job and then I might not work at all and then I cant have my private life because I wont be able to support it.. bla bla bla bla.. That is over then!

So, what way to choose? How far is this gonna be? How people are going to face this and cope with it?

How to quit smoking and learn a foreign language in a short period of time and other stories..

Some time ago I wrote about celebrations which were not actually that important, but today I am writing about a very important one: Tomorrow I am celebrating one month smoke free what literally means that I spent one month, 30 days no smoking at all! I am such a brave girl!!

But no, I am not that brave and now you wondering what the hell has quitting cigarettes to do with learning languages and bla bla bla..

Easy and simple:

MOTIVATION!

In fact this post is more about motivation and which kind of things makes a person undergo a certain effort to change her/his life! In my language we have a popular saying: QUERER E PODER, that means that wishing something is the way to get it!

And now the bridge to learn a foreign language... this makes sense here!

Amongst my group of friends we conclude some time ago that there are two major sources of motivation to learn a foreign language: either one learns it when a kid, in the cradle, or as an adult, in "bed". Of course, once a kid, the motivation is innate and comes from the need to understand the others and talk/express therefore communicate as a human being. From the adult perspective, that motivation is about LOVE! Ok, who says love, says something love-like and I just know so many people who are currently learning a language that they would never thought to learn as a way to impress their beloveds, or to make them happy, or to seduce them, or to date them, of simply to go to bed with them.. whatever the wills it entails motivation from the presence of a person who speaks a language one does not know.

So now I opened another bridge.. The bridge from MOTIVATION to FEELINGS!
The feelings are the other stories, that is so much about feelings and so many feelings in our human world and it is sometimes so difficult to control them: to understand them, to deal with them, to hide them, to show them!
But one thing one should bear in mind: feelings are a source of motivation! Motivation to learn a language, motivation to quit smoking, motivation to change life, motivation to travel, motivation to settle down, motivation to start again, to climb, to fight, to built, to stay or to go, to party and dance, to watch TV, to not watch TV, to change habits, to do sports, to smile and to cry and even to die for! And we can't deny our feelings, we can barely control them and they trap us sometimes taking us to situations that we think they could never happen! That’s so complex..

But not to make this post much longer because actually I just wanted to let you know I stopped smoking and I want as much people to know about this as possible people that I don’t want to let down and I think that will help me think twice before I lit up a next cigarette!
For those who read this and think about stop smoking or not and what would really change whether they would stop in terms of health benefits I leave you a list of What Happens to Your body if you stop smoking Right now?
by Wade Meredith on July 19th, 2006


This little timeline below is about some of the more immediate effects of quitting smoking and how that will affect your body RIGHT NOW (http://www.healthbolt.net/2006/07/19/what-happens-to-your-body-if-you-stop-smoking-right-now/)

• In 20 minutes your blood pressure will drop back down to normal.


• In 8 hours the carbon monoxide (a toxic gas) levels in your blood stream will drop by half, and oxygen levels will return to normal.


• In 48 hours your chance of having a heart attack will have decreased. All nicotine will have left your body. Your sense of taste and smell will return to a normal level.


• In 72 hours your bronchial tubes will relax, and your energy levels will increase.
  In 2 weeks your circulation will increase, and it will continue to improve for the next 10 weeks.


• In three to nine months coughs, wheezing and breathing problems will dissipate as your lung capacity improves by 10%.


• In 1 year your risk of having a heart attack will have dropped by half.


• In 5 years your risk of having a stroke returns to that of a non-smoker.


• In 10 years your risk of lung cancer will have returned to that of a non-smoker.


• In 15 years your risk of heart attack will have returned to that of a non-smoker.
  So, you have more immediate things to look forward to if you quit now besides just freaking out about not being able to smoke.

But above all, smoking is not popular anymore, its not fashion, it is not cool! It is very expensive, smelly and useless!
I quite enjoyed smoking and for me the most difficult part of it was because I wasn’t doing it for addiction but it was the pleasure of holding a cigarette and drinking a beer while talking to people, etc etc, I got rid of the nicotine addiction a long time ago, the real hard part of the quitting procedure are the social meetings. I don’t want to fail this time; tried a few times before with no success; but NOW I have got a lot of motivators! And I don’t even have to learn another language!! :)))

Plagiarism or how the proteins are synthesized, shown by a bunch of freaks!

Last time I visited my university ex class blog, that you can access here http://sexyhote.blogspot.com/ (written in Portuguese by the way), and where I took part in the past but never really wrote anything, I found the following video which I found so awesome that I couldn’t resist publishing it in my own blog.

It has so much to do with what I do although at the first sight it just looks like a bunch of freaks swinging and dancing around while an idiot freaky song plays. NO offence but really gets me an idea of a Hippie camping in the 70s where a group of hippies decided to do a colourful choreography!

BUT NO... that’s nothing like that!

It’s impressive but this video is SCIENCE and it is so good that I really believe that mostly everyone understands the protein synthesis after watching this! The video is long but worths the time to watch. Has a 3 minutes introduction where Paul Berg, Nobel Prize for Chemistry 1980 explains what’s going on and then, ENJOY!
This amazing educational film was used in schools to teach biochemistry to the kids!





Description of the film:Directed in 1971 by Robert Alan Weiss for the Department of Chemistry of Stanford University and imprinted with the "free love" aura of the period, this short film continues to be shown in biology class today. It has since spawn a series of similar funny attempts at vulgarizing protein synthesis. Narrated by Paul Berg, 1980 Nobel Prize for Chemistry.