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.

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.

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 :)

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.

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.

In which she eats Belgian chocolate to celebrate

Eppendork sometimes says her prayers, tries to be a good person, scientist and hot babe (although somedays being hot is tough work), apparently someone was listening.  By someone, I mean the non-denominational fk-up fairy, who by some miracle absented herself and her absence allowed Eppendork to find some superduper hot stuff in her data.  

Figure 1: What I would've been doing if there was any one left in my office this afternoon!

Quite possibly wetting myself with excitement sitting in front of the computer I spent the afternoon with pretty coloured christmas-like light bulbs going off in my head - thinking nobody has described this previously and its hot!  I love my science - even tho' sometimes I'm not in love with it - although currently Eppendork is thinking wholeheartedly lustful thoughts about her science and is swooning over most recent results.  Apparently it is the season!

E.

I love Science, no really

Lately Eppendork has been using a particular technique involving total genomic DNA (useful for sizing genomes and identifying genome structures).  It takes a really, really long time to carry out and it's between one to two weeks before you get your results.  The real snotty thing about this technique is you don't know if it has worked until the end.   Using this technique has made and continues to make Eppendork feel a bit bipolar - OMG it worked and it's beautiful (seriously when it works it is just that hot), oh wow how hot am I? Oh no - (general expletives) grrrrrr - how much time have I wasted on this?  Deep breath - figure out what went wrong - if I cant identify where the problem crept in - nuke everything, scorched earth, don't pass go - start at the beginning again.  Part of the problem is the buglets I am working with at the mo take a really, really long time to grow and are superduper fastidious so starting again is not as easy as it sounds.  And then it works like perfectly and I think - that's hot,  Eppendork doesnt think she would last being bipolar without drugs.

Figure 1: Science drives me to it - honest ocifer - honest

Eppendork has also been working on another project for almost a year now - with very little in the way of sucess or results to show for it.  I hate this inability to get it to do what it should and constantly think that I could have been the original Imposter Syndrome model.  Which is why when the previously mentioned technique (which tbh Eppendork is Gold at, infact Big Sci boss has said my results are the best he has seen, ever) doesnt work because of fastidious bugs or unknown problem I feel like such a dork and think why am I doing this?  

Never mind next challenge (Phizzle Dizzle which more resembles previous MSc work) starts end of January. Eppendork is ready.  Bring it on.

E.