I has surfaced...

Hello faithful readers - I have been a very lax sci blogger. In fact, some would say I had fallen off the face of the earth since August. Well for all intents and purposes I had, I consider it a well need vaykay or more accurately post stress funk, truely considered walking away from science as my psyche and ego had taken a bit of a battering, but I bend I don't break. This time it was was an extended held pose, consequently I am well stretched and have started applying for jobs again in the science field of mine - some not. Just thought I would let you all know I am alive and am doggy paddling again.

Just to keep you remembering how cool science is - it even does christmas:

Paediatr Anaesth. 2004 Dec;14(12):1016-20.

A Christmas tree in the larynx.

Philip J, Bresnihan M, Chambers N.

Department of Anaesthesia and Department of Ear, Nose and Throat, Princess Margaret Children's Hospital, Perth, WA, Australia. jennyphilip@hotmail.com

A 2 year-old boy presented with acute upper airway obstruction following a 15-month history of noisy breathing and hoarseness. An urgent laryngotracheal bronchoscopy was performed following inhalational induction of anesthesia. Using a fiberoptic bronchoscope, visualization of the larynx through a laryngeal mask airway revealed a flat plastic Christmas tree embedded within granulomatous cords causing almost complete obstruction and requiring tracheostomy prior to extraction. Twelve days later, the tracheostomy was successfully decannulated with the child's voice beginning to normalize. The family remembered the decoration from Christmas celebrations 2 years prior and recalled a coughing episode that predated the onset of hoarseness.

You gotta love it.

E.

You know I loves Science

but I just don't love scientists (well that's a sweeping generalisation) but flow with me here.  Officially Eppendork doesn't love hates a system that tolerates unprofessional behaviour because you are a leader in your field and you bring in the big bucks.   My supervisor is a great scientist (I completely respect his science) but his managerial skills are absolute crap, and if I had to I would say they are non-existent.   I have never ever been managed so badly by a supervisor, never.  Nor have I ever been so stressed out and paranoid about making mistakes as I have been in the past few months, I have been a complete fking wreck (hence the lack of blogging).  He just has no stop measure on his temper - there is a zero to 100 in terms of anger in like 5 seconds and just lets rip on the person - alone, in front of people, in front invited guests.  He just doesnt give a shit and everyone takes it because with his name on a paper you are going to get it published in one of the big ones.    He is a micromanager, in and out, in and out - unless he has some one else distracting him that he can 'help' them see the error of their ways (cause they arent thinking just like him), you never get time to do stuff and he continually adds things to your list of stuff to do.

I have been contemplating in the last week or two whether he is a workplace bully or he is just insensitive to the dignity of others, and to be honest I think it's the later and has no control over his temper.  He had threatened me twice with being 'fired' from this PhD project - the first time was like - OMG he's threatening me - WTF?? This was after he and my other supervisor had a meeting and worked out a plan for me to improve my performance to be reviewed in three months at which point we as a group would decide if this project was to go forward.  The last time he told me 'you dont know how close you are to being fired!' and in my head I was just like - meh if you are going to do it, do it (the reader must realise at this point I had got my head around the fact that he and i shouldnt be working together cause we are a really bad fit) I dont care that much.  But I still thought I had my now two months to prove myself worthy of his godlike tuterage, unfortunately this morning he had decided he had enough and told me I was fired from the project.  And you know what (having spent my weekend working my arse off for him) just sat there and went thank fucking God - thank you Jesus.   It had been taken out of my hands and I am glad cause me being stubborn and not wanting to give up on something until the last possible moment would have sat there a stressed out, wreck of a person, a shell of the person I walked in here as and I can tell you I would have lost my love of science.  It was ridiculous how much lighter I felt walking back into my office - one of them (who is in my office but not in the group but see how he behaves to all of us) - was like 'Oh Eppendork I am so happy for you - this is a really, really good thing!'.   Every one including the tech who is also leaving soon because of his behaviour (although she gave him another reason cause she needs a good reference), was like it is a positive positive thing.

And dear readers it is!  It really, really is!  Just have to go find me another job and explain why I spent x amount of time on a PhD project that has come to nothing - but I can live with that, I still love science and tonight Im not a wreck!!  I might just sleep soundly for the first time in months as well....

Hallelujah, Hallelujah, Hallelujah.

E

xxx

Eppendork's terrible, horrible, no good, very bad six months

I confess I have a problem. It is all to do with my love of praise and dislike of disappointing people and feeling like a failure. I have spent the last six months spending more of my time feeling like I am dog paddling in the pool of wanton science dreams. Yep you heard floating/dog paddling and not swimming and I am getting tired. I desperately want to get my shit together and I am hoping my research proposal will meet with supervisor A and supervisor B's approval so that i can get my shit together. My manic depressive relatonship with supervisor A is not helping my balance - he is a really high achieving and extremely well respected in our field (which makes lit reviews fun when he's on half the papers you are talking about), he has high expectations of all his staff and students and gets all disappointed (verbalises this both in front of other people and has been known to lose his temper at people in front of people even at visiting students - which reduces you and whoever else is around to feeling super duper crap). He does give you praise and its honest not manipulative praise - when i get it im like omg the world is brighter, better more fabulous place and then in the next breath he will go 'I'm disappointed' or I dont have time for this go away and do it again (tbh some of the time its me thats cocked up - but more often he changes his mind about what he wants after I spend ages on it and I have to do it again. Or he just doesnt listen and you have to push the point and make him hear you or he will walk all over you with his assumptions.  I made a choice I chose this project this supervisor go me!

Having said that i love this field, I love the kind of work I am and have been doing. I am not stupid. I will resolve it. I just need a really big wine right now. Tommorrow is a new day - I have a project proposal to work on and hopefully they will buy it and not throw me out on my ear.

E.

Be scared, be very scared and dont fall asleep!

Get Your Cyborg Name

Heehehe - eat my cyborg dust science!

That is all.

E

Everybody say Yey-ah! Yey-ah!

I got the script to work :-p which is good and maybe i will share with you maybe I wont in the future - probably will! But then in future planning will remember about the primary key needing to be the same as the key you want to join the tables with :-p but i think that is relatively easily solved I think a new_list.remove will work - let us all cross our fingers and tune in next time for when we hear Eppendork say Yey-yah! uhuh! Yey-yah!

E.

Calling all Pythonistas!

Okay so I have a question:

I have a pile of sequences (200+) in fasta format in a text file eg 

>geneA

asdfdfasfsdfasdfsdfsdfsfdsfsdfsdfsdfasdfsdfsdfasdfasfsdfafasdfsdsdfsfs

afasdfasdfasdfsdfasdfdfafdasdfsdfafasdfasfafdsfasfafsdfsdfasfsfasdfsdf

>geneB

asdfdfasfsdfasdfsdfsdfsfdsfsdfsdfsdfasdfsdfsdfasdfasfsdfafasdfsdsdfsfs

afasdfasdfasdfsdfasdfdfafdasdfsdfafasdfasfafdsfasfafsdfsdfasfsfasdfsdf

>geneC

asdfdfasfsdfasdfsdfsdfsfdsfsdfsdfsdfasdfsdfsdfasdfasfsdfafasdfsdsdfsfs

afasdfasdfasdfsdfasdfdfafdasdfsdfafasdfasfafdsfasfafsdfsdfasfsfasdfsdf

I need to make it into columns like this:

geneA asdfsdfasdfsdfsdfsdfasdfsfasdfsdfafsdfsdfasdfasdfsdfasdfs

geneB asdfsdfasdfsdfsdfsdfasdfsfasdfsdfafsdfsdfasdfasdfsdfasdfs

geneC asdfsdfasdfsdfsdfsdfasdfsfasdfsdfafsdfsdfasdfasdfsdfasdfs

all in one line.  I want to have the text file set up like this because i want to use python to stuff the text file into an SQL table - only I dont know how to do it - I can concatenate the sequence bit of it in excel for one of the sequences but that doesnt work for the 200+ other sequences I have.  Everything I have found on fasta and or concatenation involves simple exercises or pulling down individual fasta sequences from genbank which didnt help me a lot.

So what I want to know is how do i get the sequence name in one column and all sequences in the other so that I can make an output file that I can open using a python script then stuff into an SQL table.  Any ideas?

E.

It's a good day today

I feel slightly like I have a manic-depressive relationship with my supervisor.  One its good and he's happy and all is right with my world (sometimes I feel really good).  Then the next day he will just be tearing strips off me and handing my arse to me on a plate and I feel like what the hell was I thinking doing a Phd.   Kinda like this:

SELECT * FROM "Eppendork"

WHERE "EmotionalState" LIKE  'F%'

ORDER BY "Dayoftheweek" 

AND "Houroftheday"

Which roughly would give you the hours and days of the week where I felt F**d or Fabulous. Yes this week has been good for SQL and me making a start on learning Python.  I got excited today by:

n = int(raw_input('What's my favourite number?: '))

if x >4:

print 'No that is not my favourite number!'

elif x<4:

print 'No that is not my favourite number!'

else:

print 'Yes that is my favourite number! Woot!'

I know baby steps - its the small things.

E.

Reality sux, but in the meantime I have Chilli-tomato lentils

So I have been burying myself in my literature review basically to distract myself and avoiding the very real family crisis that is going on at the moment - given I am far, far away and feeling a little helpless.  My mum has been told that her heart is so badly traumatised by her congestive heart failure (not to mention al the other things) that they cant replace the pacemaker that is currently failing - she wont survive any type of surgery and they basically they have sent her home with the expectation that she wont see out the year.  So Im gutted.  My supervisor has been good and said I can take time off to go home - but I need to time it right given I cant afford to make the trip more than once.  I was trying distraction but apparently not that well.

So I was head down bum up trying really hard to focus on the lit review - but with the help of a friend realised that to a large extent what i was writing was skimming the surface, trying to cover too much and not enough detail.  It also hasnt been any near where the level of my writing usually is - so it is in other words crap! So i have set it aside and made up a new plan of attack hopefully supervisor will agree to it.  Starting next week after an intensive programming course which I had asked for earlier prior to the current goings on but I need to get my shit together and get things done - focus Eppendork - focus!  But it's hard.

E.

And on and on and on and on and on infinitum

Notice no fullstop at the end of infinitum because although you can get to the end of the word infinitum the concept itself just goes on and on and on and on and on. Much like lit review writing, thesis writing and the writing of those loverly journal articles we all like to prize above all else epeshially if they manage to get snagged by the she daddies of the science world in terms of journals. Eppendork is not so lucky. Although she has two more articles out of her MSc .than previously (they are still in the process - one in press the other submitted) neither of them will be submitted to the double mecca of dynastic scitholicism, just plain ole respectabible journals that dont do the bells and whistles and pretty sequins. No, no she is currently writing for a lit review and my what fun she is having - gee if i had known it would all be picnics and fuzzie bunnies I would have done this sooner!

Figure: I love this cartoon - it just makes me laugh!

Note to self: sarcasm may go over heads of readers - I don't think its fluffy bunnies at all and if the weather would just stay sunny for a while it may be picnic weather. It's Saturday and I have been head down bum up for way longer than I care to admit - and I may be just procrastinating now and yes, yes I am procrastinating. Rather I am giving the brain a little rest and I will be back into it asap because really chickens I do see the light at the end of the tunnel today - didn't yesterday - its babysteps.

E.

Pink No More

Tired of gingham - so March!  I am had long day at the Biosafety cabinet chickens so Eppendork is tired and thought about Abel Pharmboy's little titilating rant about vaccintions and sexy, sexy videos.  I was going to have a rant balanced discussion about the pro's and con's of vaccinating your beautiful children - very little con's lots of pro's to be very honest and how more discussion and talking with people who don't have 7 year degrees is a good thing (and I realise here that saying if you have Phd or a MD you are going to vaccinate your child is not always true but more likely I think if the PhD is in some form of Science).   How ever I don't think it matters how much we the microbiologists, the medical plethora and other scientists say vaccinate your child those who really dont want to aren't going to. Which saddens me but not a lot you can do about it.  I still think it does border on child abuse - when a disease is preventable it should be prevented.  Fullstop.  End of story.  If you want a nice discussion about how vaccines work ToasterSunshine has one.  I am just too sleepy.

E.

I wonder

I wonder if the person giving a presentation on their past year or two's work should feel insulted that a lead PI nodded off during their presentation? What do you think?

Eppendork may have a little crush on Mr Nick Cave

I love this song - PJ Harvey rocks the house too.

I am up to eyeballs in Lit review at mo - so not too much blogging going on unfortunately.

E.

PS fave Nick Cave song - Into my arms - seriously good song - the man's a genius.

On why Macs rock da hizzle

I Eppendork own a Mac - it's true.  I haven't always been a fan Mac's used to be very naf and then one day they weren't they were sexy and sleek and did all sorts of hot funky things and the whole no virus thing is da bomb, well the world was mac's oyster.  With itunes/ipod, iphone and beautiful Mac laptops well they can do no wrong really.   There is even a documentary about people who love their Macs. Now the iphone is truely an ass kicking hot piece of technology - it is just that sexy - love playing with it a lot.   I havent manned up and brought one yet but I know some one who has one and they let me play with it if I'm good.   The reason for this little ramble into Eppendork's sometimes mac fetish was this little slide show in the New York Times - what to do when you have too much time on your hands.

Figure 1: Ooooosh!  

Ask me again why I think Mac's are da bomb - they're like little cockroaches of the computer world...

E.

I'm so sick

So sick that I wrote sik three times before I could get the word spelt properly.  I wanna bitch about American Idol - are you all so stupid that if they tie them up with a bow they're gonna make it in the fickle, fickle world out there?  Removing anyone of any real interest - bar the guy with the indie bent - makes AI a dull show - cookie cutter molds are destined to fail - cause the flavour is going to change and no one wants your gingernuts any more.  And really why isnt there a Science Idol - hmmm?  Well I realise there is the Nobel prize but thats for people who have been there done that a lot - kinda the point of the prize.  Seriously, where is the competition for noobs who have talent but just lacked their 'big break' - huh?  

I may need some more flu meds.  

E. 

The Leslie Winkle experimental methodology

Okay so as I write this I am tucked up in bed with the flu, I have my lemon, honey and ginger tea next to me, on the other side is the work I brought home with me that I have yet to pick up yet.  Very hard script is on top of the pile mocking me with its brilliance - I made a little progress on understanding it - upside is I have realised I will have to learn how to script in python - although I am told once I know how to script in it - I wont ever go back - bit like the dark side really.  Any who I was reading Juniper's blog, about her current trevails and trials in her pathway to become a real scientist, and I thought to myself damn - how can it be so hard?   Then as I do in my slightly drug-induced fluey state I thought - things happen for a reason and sometimes we dont get what that reason is until we get to a place where we do.   

For me I wanted to do science when I left high school - but due to a mixture of severe lack of intellectual self esteem and generally propensity to take the easy way out (when I was 17) I enrolled and completed a very average BA and then took up the only career I believed was open to me.   Turned out I was good at it but I felt like my true potential was being smothered and I just couldnt do it anymore - so I stepped outta my comfort zone a long way outta my comfort zone and found the confidence to do what I wanted to do in the first place, science.  I thought of doing medicine so I started there and my undergrad was focussed on that goal - but in the end I decided Micro was where it was at and battabingbattaboom whaddya know here I am.

Course it didnt happen all nice and neat like that - when I said I wanted to do science, my then partner basically laughed and fully expected me to fall flat on my face and go back to doing what I did before within a year of starting my undergrad.  It felt good to show him the straight A's I got in my first year - I didnt give up I worked two part time jobs and was a full time student and a mother.  It wasnt easy and I have to say the first year of my MSc was the most stressful year I have ever experienced in my whole life - I wouldve lost the plot completely had it not been for a very good friend of mine who I love dearly.  Needless to say my relationship with my ex didnt last, but my relationship with science is still going strong.   When I think about it now - if I had of tried to do my science straight out of high school I would have crashed and burned majorly - I didnt have the motivation or the self confidence to do the work that had to be done.  I couldn't see that at the time.  I do now - I had to go through a shit load of growing up to realise I had a brain in my head was useful for something other than sleeping and breathing.

Juniper sweet cheeks - I almost feel like you need to take a time out and center yourself and make a plan.  OMG I am such a control freak - I am such a planner - I like to know what to expect - go figure.   You need to focus your efforts, don't disperse them left right and center - get a piece of paper out - write down what you want, what you want to do and how you are going to get there.  Find places that are doing what you want to do - then ring them up and explain your situation - could you intern for them? Could you do an MSc with them?  You never know your luck - and believe that half of the science opportunities start because some is in the right place at the right time.   You are a kick ass writer - your blog shows that - figure out what you want to happen and then make it happen - you are the only person who can do it for yourself and you are the only person who can stand in your own way.  Focus chick focus.

E.

PS:  Still fluey  gotta love viruses - they are little pieces of God's own glory they are, they are.  Mmmmm I have M&M's as well - purely for medicinal purposes you understand.  

Old Skool Styles

Vintage just says Im Styling hot Science Chick - dont make me take off my sunnies and come over there!

So I took a facebook quiz to burn a little time - Eppendork decided that if Isis can blog about Barbie then I can certainly take a quiz to find out just what sort of Barbie I am.  So I took it and the news is out - Eppendork is old skool - Vintage Barbie - classic down to her mean patent pumps and kick ass corset figure.  Did I mention I have a slight girl crush on Ms Von Teese?  I wish I looked that good!

That is all.

E.

A good use of Resources - Methinks

So trawling through the internet one fine day - I found this:



Not for the squeamish - forewarned is forearmed. Couldn't do it these days....

E.

I'm out and I'm proud

Hello my name is Eppendork and I write a pseudononymous sci-curious blog.  I started this as a way for me to blog about (crap) important stuff that was going on in my search for just the right kind of scientist I wish-hope-wanna be.  Little did I know I would find out that I had a latent talent girls and boys - not hula hoop dancing, not how many M&M's could possibly fit in your mouth should you ever try, not intuitively knowing Gregory House style that the cat likes the warmth feverishly dying people give off.  No darlingks I Eppendork - Current Queen of the Pink Gingham - have (Eppendork hangs her head - sigh) an apparent latent talent for writing scripts - computer program scripts - not pharmaceutical scripts before you get excited.  

Figure 1: Yes, Eppendork does look this hot, but will try hard in the future not to search for hot geek girl or eve comp geek girl in Google.

I wrote my first real script today that actually did something useful rather than "Hello World" or similar.  It was a short little script and it really only changed a few things in the database but it saved me work and I wasn't expecting to feel proud of myself for doing it - but I did (blush).    I kinda feel like scripting will save a shedload of time and effort in taking care of my db's (eww listen to me db's) in the future.    

E.

Open Letter to Adobe

Dear Creators of Adobe Illustrator,

I am a great fan of Adobe - where would be without our faithful versions of journal articles?  I for one am really, really grateful - I love my interesting reading and pretty, pretty pictures therein associated with said articles.  However, Eppendork is not a computer geek - although evidence to the contrary (learning various scripting languages should not be taken as evidence of the former), and finds programmes such as Illustrator very cool, just not very intuitive at all.  

Figure 1: Any of these geeks will do - I am sure the Apple guy will know!

I spent an hour and a half this morning trying to figure out how to import a picture and then recolour it - figured the first bit out pretty quick - the rest of the time to figure out the later.  Sufficient to say Eppendork is not stupid - just hasn't worked with your program before.  I would be completely in your debt if your computer savvy boffins could figure it out for me and other non-computer geeks. 

Luv and Hugs,

Eppendork. 

Apparently I am not the only one...

I now have had Waterloo running around in my head all week - that will teach me to share the ABBA love.   I do have things I want to blog about soon - but they need to ruminate a bit so they get all nice and smelly and good.

That is all.

E.

For Phizzle and Juniper! Abba's got your back!!!

For Phizzle cause some times doing PhD bump and grind is more grind than bump and Juniper I have fingers crossed - Abba is the cure - there is no ill they cannot cure - also Muriel's wedding will just cheer you up so I give you "Waterloo" Muriel styles.

Love and hugs

E.

Although Im not comfortable with a shiney white catsuit - have totally danced like this before.

Slick moves by the ID God squad

So Eppendork was sitting contemplating her bejewelled navel, as you do on a slow Monday morning, when she came across a pretty cool paper. And now I think the mechanisms behind diphasic flagella in Salmonella are pretty fucking cool.  I mean the switch mechanism is just that hot. So here’s how it goes – Salmonella have two flagellin loci in the genome – not terribly unusual for bacteria – kinda cool not that that interesting – the interesting bit comes in the form of the switch that allows the Salmonella cell to express only one form of flagellin subunit either fliC or fljB (the genes are only expressed alternately, such that you can have only one form of flagellin - no mixies going on, or so they thought).  

As far as I can tell fliC is transcribed constitutively by the cell – which is fine if that’s all it ever does then it will only have a phase 1 flagellin – however if the fljB is thrown – well it all gets interesting (if it is you get a phase 2 flagellin).  The flagellin 'switch' are two proteins Hin and Fis, working in conjunction with each other to cause the inversion of the the fljB/fljA operon, which is normally inverted.  Normally this operon remains dormant and isn’t expressed, but invert it and bobs your uncle you have a working operon.  And this is where it gets cool – fljA is expressed, it then latches on to the constituitively expressed fliC rendering it unable to be translated! It never gets translated so fljA acts as a gatekeeper/mediator of fljB/fliC expression. And export! Previously it was thought that if fljB is expressed then fljA must be acting as a transcription repressor – but it’s not its working posttranscriptionally – how cool is that? Eppendork thinks its hot shit so to speak. 

Figure 1: Salmonella rocking an improperly prepared egg sandwich somewhere near you this lunchtime....

Which of course made me think about intelligent design – cause you gotta admit the complexity of this switch could give the foaming at the mouths id nutters cause for joy.  The complexity and yet at the same time simplicity of it is stunning (the science to prove it was very cool - kudos people).   So one thing lead to another when you are moi and here is where I ended up - that’s right peoples the concept of irreducible complexity – id proponents favourite chew toy.  So I will dissemble for the non up-to-date with a quick evolution primer: the idea floating around is that there are certain biological systems are too complex to have evolved as they are – that there had to be an intelligent designer ie a God figure that created them just so and that if you took one piece of the design away it would all fall to pieces and all would be lost (IC has validity - just not the denial of evolution which is just sniffing some bad mojo).  I may sound a bit sarky over here at the real scientists table but I have had this q and a with many different people - I am still firmly Darwin's bitch. But any who, nuff said on the snarchasm between Eppendork and the ID God squad.    

The problem with the ID God squad is that they are slick - they have some pretty "solid" evidence - eyeballs, the bacterial flagella, antibodies, gene cascades - the "list" goes on - and they present pretty vids with tbh sexy cgi, and if you didnt know better you would think - that's reasonable. Well sorry sonny-Jim it isnt reasonable - it's insidious - i mean seriously have you looked at bacteria lately?  Huh? Have you?  They are like the poster child for Natural Selection and evolution - now showing in your local armpit! and you guys are holding them up as perfect examples of the Creator's intelligent design?? FFS - scuse Eppendork's language - she may be ranting now.  So I am putting the verbal crow bar down now and walking away - I found this on youtube (may I say god bless spewtube for all its unsolicited and uncensored offerings) I like it - it's reasonable and based on the dirty word round the ID halls of residence (S.C.I.E.N.C.E).

Figure 2: Good point!

E.

PS: Eppendork is not an Atheist - she fully believes in God - just not licentious ID dribble - that is all.

PPS:  My favourite bits about the you tube videos are the unsolicited comments - god bless them all :)

Warm Fuzzies

So a post or two ago I blogged about foetus scientist and their possible plagiarism.  It turns out after I read the lit review - it was just bad writing and not understanding the project or the field very well at all - rather than purposeful plagiarism.  I talked to fs made it abundantly clear what needed to happen I think I repeated myself about four times in one email (I emailed the lit review back to them with appended comments) - I even used italics and exclamation marks.  I think they got the point - they have a practice 10 minute presentation soon - we shall see.

Figure 1: 

H o w E p p e 

n d o r k c 

u r r e n 

t l y f 

eel

s.

Apart from that I am just tired - I have been doing my best sponge impersonation - some of it is working.  I am also currently thinking I need glasses I am finding it hard to read text on the computer screen from more than 30 cms away these days.  I turned the text size up and I am currently sitting about 30 cms away from it and it is nice and clear.  Joy - another gem of my old age.

E.

Hap Hap Happy V'day to you all

Figure 1: Eppendork's beating V. day heart

So feeling particularly in a happy full on, doped out high on sugary self bought chocolate and a few glasses of rose (cause it was valentines day (now isn't as Eppendork fell asleep due to wine but had good intentions) and her beloved is a million miles away doing man stuff) - I found this beautiful little geek fest Vday poem.

# open HEART by Eric Windisch, Feb 15, 1999

open (HEART, ">for_me");
for ($this-valentines-day; $you and $me; $together++) {
$you = "My special one";
$me = "Your darling";
}

%time = ($you => $me, $together => "forever");
while ($you = push(@me, @away)) {
foreach (@second) {
die a_bit to my $death;
goto hell;
}

pack $my_bags, @and_leave;
package my_love;
unless(!$i_see_you) {
write YOU_SOON;
}
}

reverse keys %time;
bless me;
for (last; kill $me;) {
if ($you) {
die;
}
}

Oh be still Eppendork's beating heart - the Sandy kind not the Edgar Allen Poe kind.  I do love me some comp geek (and yes my own beloved is a comp geek, tho he refuses to admit to it).  I now have an inane desire to sing "I love you in the morning and in the afternoon.  I love you in the evening and underneath the moooooooooon!".  Which may well just be extra chocolate I found that was left over from yesterday - cause really Eppendork doesnt hang out with too many purple dinosaurs that she knows of.

Happy Vday to you all.

E.

OMG - That's Fantastic

Sometimes when Eppendork needs a bit of an uplift (I was going to write a blog about my recent programming marathon with two particularly good programmers and baby programmer E - but that can keep for another blog) - now after a long day doing stuff I myself signed up to do and enjoy doing I am tired.  This darling readers was Eppendork's up lift for today - words to the effect of OMG that's fantastic may have been heard to come from my lips.   I seriously think that had I not jumped on the Bacteriology wagon - I would have been a full on, card carrying, gun toting Parasitologist - they are just that cool.

PS:  Lovely Isis since you were distracted  and couldn't do Hot shoe of the week I your faithful follower have shoed it out for you with these hot hot hot babies which I think I may just cry over cause they are just that beautiful.

That is all for now.

E.

Make Someone Happy - Cause it tis a lazy Sat

Eppendork is enjoying her lazy Sat afternoon and realises that there may not be that many more of them for a while so is fully appreciative of it.  I found this at AA - I embraced it cause it looked like fun :)  I took out the d - f steps cause I couldn't be arsed on my lazy sat.

RULES:
a) Put your MP3 player, iTunes, Windows Media Player, etc. on shuffle
b) For each question, press the next button to get your answer.
c) YOU MUST WRITE THAT SONG NAME DOWN NO MATTER HOW SILLY IT SOUNDS

1. IF SOMEONE SAYS 'ARE YOU OKAY' YOU SAY?
"That's the way I wanna rock n roll" - AC/DC

2. HOW WOULD YOU DESCRIBE YOURSELF?
"Shameless" - Ani DiFranco

3. WHAT DO YOU LIKE IN A GUY/GIRL?
"Sleep" - Kimya Dawson

4. HOW DO YOU FEEL TODAY?
"I know this bar" - Ani DiFranco

5. WHAT IS YOUR LIFE'S PURPOSE?
"Another man's vine" - Tom Waits

6. WHAT'S YOUR MOTTO?
"Does your mother know?" - ABBA

7. WHAT DO YOUR FRIENDS THINK OF YOU?
"The girl at the bottom of my glass" - Nick Cave and the Bad Seeds 

EEEK!! Eppendork is not really a Lush

8. WHAT DO YOUR PARENTS THINK OF YOU?
"You know that I'm no good" - Amy Winehouse

9. WHAT DO YOU THINK ABOUT VERY OFTEN?
"Blood" - My Chemical Romance

10. WHAT IS 2 + 2?
"Jack the Ripper" - Nick Cave and the Bad Seeds

11. WHAT DO YOU THINK OF YOUR BEST FRIEND?
"Hast thou considered the tetrapod?" - The Mountain Goats

12. WHAT IS YOUR LIFE STORY?
"1234" - Feist

13. WHAT DO YOU WANT TO BE WHEN YOU GROW UP?
"If you knew" - Neko Case

14. WHAT DO YOU THINK WHEN YOU SEE THE PERSON YOU LIKE?
"I'm sticking with you" - The Velvet Underground

15. WHAT WILL YOU DANCE TO AT YOUR WEDDING?
"Turn me on" - Norah Jones

16. WHAT WILL THEY PLAY AT YOUR FUNERAL?
"Lay all your love on me" - ABBA

17. WHAT IS YOUR HOBBY/INTEREST?
"Through the morning/ Through the night" - Robert Plant & Alison Krauss

18. WHAT IS YOUR BIGGEST FEAR?
"Beautiful Disaster" - Kelly Clarkson

19. WHAT IS YOUR BIGGEST SECRET?
"Serpentine" - Ani DiFranco

20. WHAT DO YOU WANT RIGHT NOW?
"And no more shall we part" - Nick Cave & the Bad Seeds

Eppendork may have a lot of Nick Cave and Ani DiFranco - but oddly correct re #20

21. WHAT DO YOU THINK OF YOUR FRIENDS?
"Over Protected" - Britney Spears

22. WHAT WILL YOU POST THIS AS?
"Make someone happy" - Jimmy Durante

I have eclectic tastes...

E.

Someday I'll be Saturday Night....

But currently it just feels like an eternal Wednesday - humpday - where it's almost painful.  One day Eppendork will be Saturday night, but that day is not today or within the next two months - why?  Because her lab - love it tho she might - isn't quite set up yet so she cant just jump in and lay down some blazing hot burn ya grandmother's knickers off science yet.   

Figure 1: Yup still smoking hot as the day I first realised you existed age 10 and 3/4's

I spent today reading manuals - for a loverly robot that when working properly will just be smoking hot and plow through the buzzkill work that I need to get through to get my data. Another part of my day was spent trying to get another robot to work properly - this was done in collaboration with sexy scientists A (who really knows who stuff) and B (who like me is in awe of scientist A).  Main thing I came away with was robots are like kids - they wont do what you want them to do unless you make it so damn clear that its crystal and squeaky.    Have also taken up programming (very slow progress here) - am officially uber-geek.  

Last time I checked it's still Wednesday - it may Thursday in two or three months.

E.

More on Pretty

Pretty in Pink - Eppendork loved the movie the first time round and every single time after that! So running with the pretty theme she has changed the very staid and sciencey theme to a more pretty friendly pink.  It may stay or it may not stay but for the moment I am feeling verrrry pretty! 

In the words of Duckie somewhat revised "(That Eppendork) is a really volcanic ensemble you're wearing, it's really marvelous!".  

Marvelous chooks Marvelous!

E.

PS: Blog roll has disappeared - will have to fix that after I get back from my Welcome to the lab dinner!

I feel pretty oh so pretty...

That's right folks - I feel pretty, oh so pretty.  Well in Eppendork's lalalala land of sleep deprivedness and inserting herself into a new time zone kinda way she is preeetty!   Anywho I spent this week learning more about the city and lab I have plonked myself into and there is good news afoot (notice pretty sparkly shoe to distract from dark circles under well defined baby blues).  

Figure 1: OMG did you see those shoes Mr Isis was wearing???    Kidding!! Minus the rollers and Eppendork swears it could've been the mirror she was looking at yesterday.

I like my new lab - it has lots of really good equipment and anything we don't have we are to add it to the list of things to sort out - although I cant see anything we really, really need at the moment.  I like the people in my office and the people in my lab(s).   I am adjusting to my new supervisors way of dealing with things and have figured out in short order that Eppendork has to have her shit together (well together) before she asks questions and or for help.  Eppendork sat quietly (because I'm new and it's always good to observe the lay of the land before sticking your neck too far) while he toastly grilled someone until they were golden on the outside (not quite but you get the idea) for not doing something which she shouldve done and tbh what he was saying was correct and I would have made that call but not quite the way he did so.  Having said that he is a star in the field and I can get on with him and learn from him.   

Eppendork now has a list of things to do longer than her arm (she has short arm syndrome) that I have to work through in the next six months or so - am set just have to press go!  In the mean time I shall enjoy my somewhat quiet time and go in search of a few glasses of the good stuff as reward for having survived her first week in her new lab - which she has given the moniker of ILA - International Lab A - not too creative but seriously that Eppendork can string words together is a good sign at this stage anyway.

E.

PS: There are no shoes in this blog - I forgot to put them in here - and didn't notice until now - suspect sleep may be the answer.

OMG it's cold

Let us just review the past 48 hours or so - Eppendork packed her bags (forgetting her raincoat grrrr - just stupid) and hopped on the first of four planes to get to her new home town for the foreseeable future.   I have made a few observations about travel and the new country so far:

1. Eppendork has the demeanour and face of a nefarious person.  To count I was wanded four times during the trip and for want of a better word "felt up" by an overenthusiastic female guard at Airport 4 of the five airports I visited.  I also had a delightful conversation with another customs lady at Airport 2 who engaged me by enquiring about what I was doing on my travels and then we talked about my upcoming Phizzle Dizzle - during which time she wanded me and swiped both of my bags for drug residues all with a smile on her face.  Mental note: baby steps maketh the evil scientist. 
2. Two empty seats on plane B = sleep budget business class styles.  One seat squished next to strange man = one hour of sleep because you are so so tired that it is impossible for you to stay awake and 11 hours of watching movies and tv of varying quality.  Eppendork can now officially say that she can fall asleep at the drop of a hat - after much sleep deprivation.
3. Airline food is not always good - worse when one meal is good and the next is very bad.
4. When people tell you it is cold where you are going - believe them and remember your raincoat.  Standing in the pouring, driving ran (when the sun has started to disappear at 3 pm) for twenty minutes huddled in the doorway of a hairdresser who looked at you funny when you rock up bags in hand and asks if she minds if you use her phone and stand in her doorway, is not fun.  Landlord eventually arrived but not before I got very cold and somewhat wet.
5. Rain will stop when you purchase the umbrella you didn't have last night.

Eppendork starts her Phizzle Dizzle tomorrow - wish me luck!

E.

Possibly Procrastinating Now

Figure 1: I shall call him Bob - wait we arent meant to name them are we?

So Eppendork is procrastinating just a little, just enough to cast her purtty blues over the online New York Times when I came across this little gem of an article.   It amused Eppendork greatly - although if she was being serious then using your offspring as test subjects may well be ethically dodgey - but look at that picture - how cute is that kid????   It sparked off a bit of debate in the readers comments but I personally think its about where the lines are drawn if I just video tape my kid unobtrusively for the first year of his/her life and they dont know about it - how is that harming the child?  I don't think it is - when you take them out of the home setting doing MRI's etc on them that's when it steps over the line for me.  What do you think?

E.

I cannae doit any morrrr captin!

Eppendork believes she may well be turning into bare-arsed bluebottle with amount crap she has been sorting out and taking care of.  I mean really how much stuff (which may include one large forest plantation - non native of course) can one person accumulate in the space of a year (which is the amount of time since last large clean out)?  Lots and lots and lots apparently, and not much of it could i actually throw out in the recycling either so a lot of it became fuel for a fire that burned nicely.   Moving to another country will do that for ya - woot! Seriously last move it was five car loads, stacked to the eyeballs - and quite frankly am surprised I didnt get stopped by any one for a traffic violation.  Today it was one partially full car - it helps to have a friend look after a couple of boxes for me - but the majority of stuff I am keeping came with me.

   

Figure 1: Eppendork is pleasantly surprised by how much stuff she can fit into her decrepit little people mover.

I am pleasantly surprised, LB believes it is his no nonsense, only bare essentials, minimalistic style of living is rubbing off on me.  I hate to shatter his unfounded belief - I will invariably start collecting crap as soon as I land on non-native tarmac, which will occur in four days.  Four days - arggggghhhh!  I still have way too much to do - sigh, back to doing stuff.

E.

I love Science - fullstop

I love bacteria! And this always makes me feel good.

E.

Very cool

Eppendork has a very large tattoo on her back - it is beautiful and it hurt lots - especially over the spine.  However, I don't have one of my science and now I am thinking I want one - where should I start methinks?  I do believe it will require much thought - the last one took around 10 years to happen. What made Eppendork think about this?  I was reading Carl Zimmer blog "The Loom" and I came across this - the Science Tattoo Emporium and it's tre cool.  I also love Carl Zimmer's Parasite Rex - a very rocking parasite book - it's still on my bookshelf.  You should read it.

Check out those fangs! How cool is the very ordinary tapeworm?!  Click on the picture it will take you to Parasite Rex.

E.

PS:  Did anyone see that House episode where they pulled the twenty foot tapeworm from inside someone who couldn't feel pain - awesome!                   

In which Eppendork gets punKd so to speak...

Eppendork, I don't understand your fear. Just how easy do you think it would be for one to isolate some anthrax from the soil and then grow it in a way that it could be "released or weaponized", that is, if one didn't expose oneself to the agent during the process? These Chicken Little posts about mere possibilities have to have more substance than the usual "no, i'm scared, its bad" that is floating around the blogaspheres. Would you enlighten me?

Figure 1: Eppendork doesnt think GMO is wrong or evil or bad - there is a time and place

Biopunk raised an interesting viewpoint about whether the previous post was just good old fashioned scaremongering which in Biopunk’s words is “floating around various blogospheres”. Eppendork will enlighten you Biopunk – she is good like that. The availability and viability of any bacteria is a moot point – microbes are everywhere – you the backdoor/garage scientist just has to know where to look and have a basic knowledge of how to use the internet. Now Eppendork loves the internet as much as the next person – information at her gorgeously manicured fingertips both delights me and disturbs me.  However, a little information can be a dangerous thing – and to be honest I think that is a fair call. I mean look how easy it is to get a recipe for bomb making – Wikipedia god love them (I really wouldn’t trust them either about being a accurate source of information, however the BioPunk article was interesting) – has pages dedicated to all manner of microbes and their growth conditions. Just type in Anthrax, Media and growth conditions and see what pops up – you don’t even have to use the correct species name. I imagine safety gear is just as easy to acquire. A piece of information, a recipe or a formula taken out of context and given to a lay person who may or may not consider the wider consequences of their actions disturbs Eppendork. To be honest with you Biopunk I like freedom of speech and I like the availability of the information but I do think there are limits to where it is a good thing. That is why public debate both within the blogosphere and without is an excellent idea and I fully support that.

The following is just my personal opinion as a Molecular Microbiologist and is actually what I was thinking about when I composed the previous blog. I personally don’t think GMO bacteria should be created or released outside of a PC2 Lab. At the end of the day bacteria are just big fat dirty ho bags who will, given half a chance either willingly share their plasmids with each other and/or their chromosomal dna. If you give a colony a particular plasmid and you let it go say “go free – multiply my pretties” they will do just that and then they will add their own spesh additions on to the dna plasmid or not that you have given them. Whether it be plain old recombination or just simple normal everyday synonymous base substitutions, it will happen. Bacteria scavenge dna just as a normal everyday occurrence, it will happen. My field loves those little changes a lot – they excite me when I see them – because they tell me a lot. Natural selection will always occur in all living species – it just happens and you can see it happening very quickly with bacteria - the acquistion of new dna happens to help it survive long enough for it to pass it on to the next generation - gotta love it. The problem I have with using or creating GM bacteria outside of a controlled lab is that you just cant control what those cells will do in terms of sharing dna or modifying the dna you have given them. To be honest you can’t really control it in the lab either but you can contain it and destroy it easily.

I think that if you cannot predict or at least compensate for the potentially negative outcomes you should not be doing the experiment, and unless you have a PC2 lab and are following tight governing authority guidelines at home you should not be doing GMO experiments, least of all in your wardrobe. I don’t think that creating GMO’s at home is being responsible as a scientist – and it falls on our shoulders as scientists to be responsible for the creation and disposal of all GMO organisms. Responsible, ethical science is really important whether your particular GMO be an E.coli you have generated, Dolly the sheep or a reverse engineered virus. Don’t you agree BioPunk?

So to recap:

1. The evolution of microbes is happening as we speak - not a damn thing you can do to stop and why would you want to? Eppendorks science would fall over and that would be a sad, sad day in her book. However, human intervention and creation of GMO's will push the evolution of these organisms in possibly a completely different direction to that which they would have gone naturally. The release of these organisms in to the wild will either mean they die (and we have dodged part of a bullet, as the dna may yet be taken up) or they will survive and share willi nilly their fabulous dna with other bacteria who dont give a rats where it came from - think natural selection it just happens people. Release of these human generated organisms into the environment accidental or not shouldn't happen.
   
   
2. I applaud you and your BioPunk kin rocking out in a scientific way - becauses let's face it Science is da bomb. However, there are rules and regulations and committees for a reason - it is necessary to follow these regulations so that we can be responsible, ethical scientists as well as human beings. This article gives an overview of biosafety measures - it's readable you should read it.
   
   
3. My main concern is about control and disposal of the GMO's you create because I know how promiscuous bacteria are - bacteria have no ethics and dont give a rats about anything else because the only thing they are programmed to do is survive and pass on their genes to the next generation.  I realise natural GM of organisms has been going on for billions of years - its's why we are here today - but that GM is unlikely to have turned rabbits fluorescent or given tomatoes mamalian genes or archael genes to E. coli via plasmids (although you never know with that one), and it is a lot easier to control a transgenic animal or plant than it is to control bacteria. The point is if you can't control the organism and dispose of it responsibly you shouldn't be doing it (that goes for any transgenic experiment).
   
   

E.

PS: Eppendork realises she anthropomorphised a lot during this discussion but thinks it worked anyway.

Science as Spectator Sport

Now Eppendork loves her science and is quite willing to admit to anyone this fact. I have also been known to extol the virtues at home and abroad about my science. However, my science has a time (all the time) and a place (in the lab or lab office) not, I repeat not (because I just feel strongly about this) at home. That's right people not at home, not in your wardrobe, not in your bathroom, not in the garage and definitely not in the kitchen. What brought this particular rant to the fore I hear you say? This article in the New Scientist that Eppendork stumbled across today. My favourite quote comes from Katherine Aull, Ms Aull decided to make a GMO in her closet (her wardrobe!) - the story opens with "Down here I have a thermocycler I bought on eBay...for 59 bucks....the rest is just home brew". Eppendork's mouth may have dropped open when she read on further in the article about people "tinkering" with DNA as their hobby.

Figure 1: My face may have looked a bit like this

Now I realise everyone needs a hobby but it disturbs Eppendork greatly when she thinks about the hoops she has to jump through for her science. There are rules and regulations for a reason - bacteria are quite frankly promiscuous they don't need any help to take up any new and "interesting" genes. Who the fk is monitoring these backyard geniuses? No one - who is going to admit to tinkering with Ebola or E. coli OH157? Or Anthrax? admittedly Ebola maybe harder to get hold of but seriously what do you think you are doing?

The final straw was Ms Aull saying that she thought the warnings of danger were overblown. Ms Aull I am sure you will make a brilliant scientist - go to school get yourself an MSc or a PhD and practice your science in the lab - where science that involves GMO belongs. Eppendork's rant may now be over.

That is all.


E.


PS: I just re read the article (Eppendork may have missed the following point about Ms Aull) - she is already a scientist a "synthetic biologist" (presumably with a PhD or similar) - should this mean she should already know better than to fiddle with GMO stuff at home? I mean this screams containment issues for me - any thoughts on this one?

I wanna work in Dita's Lab

Dr Isis - I do believe she out does you on the shoes this time!

E.

Karma's a bitch

Eppendork is not full of vim and atem today - I am tired and am thoroughly over Christmas holidays.  I love my family but sometimes I wonder what sort of person I must have been in a past life to be surrounded by these ones in this life.  Sometimes famdamnly are hard work and require much bubbly.  Give me a week I will be back to level soon.

E.