The unending tedium of writing up

[sophster]

Anyone around here currently doing a PhD. I'm finally at the writing up stage (yeah yeah I know I should have been doing it as I was going along ). Where is everyone else at, what's your topic of research?

[Dak]

I'm currently doing by BSc dissertation.

 

It's due in friday.

 

To anyone reading: seriously, seriously, do not leave your dissertation or, presumably, your PhD wright-up to the last minute. under ANY CURCUMSTANCES!

 

argh!

[Cap'n Refsmmat]

If you'd like I'll ban you from SFN until Friday so you can finish, Dak

 

Procrastination is a college student's worst enemy.

[ydoaPs]

procrastination is, however, the high school student's best friend.

[sophster]

What's the dissertation on? Maybe we can help?

 

My BSc dissertation was a nightmare as I got labyrinthitis (a horrid ear/balance infection) the week before it was due in. I got an extension but it wasn't much help as I was also meant to be revising for finals. Argh - the stress.

[Dak]

If you'd like I'll ban you from SFN until Friday so you can finish, Dak

 

lol, you just want to use you'r l33t new moderation skilz

 

What's the dissertation on? Maybe we can help?

 

My BSc dissertation was a nightmare as I got labyrinthitis (a horrid ear/balance infection) the week before it was due in. I got an extension but it wasn't much help as I was also meant to be revising for finals. Argh - the stress.

 

I hear you there. A mixture of medical problems, uber-stress and stupidity meant that i didn't actually start the actual wright-up of my dissertation untill about a fortnight before it's due in (ie, last week). 'Argh-the stress' indeed.

 

the title's "potential uses of restriction enzymes in the ablation of HIV infection/AIDS", and cheers for the offer of help but there's not really anyway anyone could help (plus, it'd be cheating)

 

what's your PhD investigation (thesis?) on?

[sophster]

Has it been a practical dissertation or just a literature review Dak? Sounds interesting though.

 

My PhD has been using an electrochemical method to characterise non-labeled biological affinity interactions (mostly an antibody-antigen interaction) at phospholipid surfaces. It's totally not what I set out to do at the start (I was meant to be using phage display to make novel antibodies) but it's been pretty interesting (and way too much hard work!)

[Dak]

mixture between a literature reveiw and, i suppose, a thereoretical experiment outline. it (probably) wouldnt be possible to do as an actual experiment, due to the vast number of unknowns in the outline (ie, will restriction enzymes be faithfully transcribed by eukaryotic cells, is there a 4-methyl-cytosine glycolysate in humans etc), so i'm doing it (rather badly i fear) in dissertation form instead.

 

"electrochemical method to characterise non-labeled biological affinity interactions"... does that mean a way of assessing wether, say, an antibody has bound it's antigen without having to label either of the molecules?

 

If so, that'd be a pretty useful technique.

[sophster]

I see. So are you thinking of it as a sort of gene therapy type of treatment where you would deliver the gene for the restriction enzyme to the cells of the immune system (I never did much immunology during my degree or get to grips with the immune system, I got distracted by more biophysical topics). Or could you deliver the enzyme directly to the HIV infected cells, possibly by tagging the enzyme to one of the receptors found on the HIV surface so you have a therapy similar to ADEPT (antibody directed enzyme prodrug therapy - IIRC this actually works fairly well and is in clinical trials for treating certain types of cancer)

[Dak]

both.

 

briefly, the main benifits of using restriction enzymes against hiv is that the hiv would be unlikely to evolve resistance, especially if you use a 4-cutter. no matter how fast HIV evolves, its unlikely that it will, for example, be able to completlely remove the sequence GATC from its genome whilst retaining functionality.

 

the main disadvantage is that the human genome is also made out of DNA, thus neccesetating a mechanism to protect the uninfected human genome from restriction.

 

the four methods im speculating about are:

 

1/ HIV induced restriction enzyme gene, to act as a fast suicide gene upon hiv infection

 

2a/ something similar to ADEPT to target huge (too big to diffuse through the nuclear membrane) restriciton enzymes to CD4+ cells' cytoplasm, to restrict cytolic viralDNA whilst leaving nuclear dna alone in non-dividing cells

 

2b/ a gene for a large restriction enzyme that hooks into the cell-cycle regulatory gubbins, so that the level's of the restriction enzyme drop off leading up to nuclear dissolution during M-phase

 

3/whach a methylase gene into CD4+ cells, wait a bit, and then whack a restriction enzyme gene into CD4+ cells, so that they have a full-blown res/mod system, to restrict viral DNA whilst ignoring their own (methylated) dna.

 

hmm... that's probably why i've run out of words without having done my discussion yet...

[sophster]

That sounds really cool. Shame you haven't been able to do any practical for your project, the doing part of science is always my favourite bit.

 

What university are you at, if you don't mind me asking.

[CharonY]

Actually it is traditional to write up till the last minute.

On the other hand, I found writing my phd thesis (Ok, it is a little while back, but not that long that it is totally blurry), somewhat less tedious than writing the papers.

I mean the thesis only goes to your prof and other usually benevolent reviewers, while the latte actually tend to go to experts and more often than not competition in the same field ;-P

[sophster]

Benevolent reviewers. I wish.

 

My internal examiner has a reputation for being a total meanie and making people cry in their viva . Also I've found that I've got to cover so much more background theory in this thesis than I would in a paper (mostly because I'm technically in the biology faculty and all the experimental theory is hard chemistry and physics - which I'm struggling to teach myself and regurgitate in a semi-understandable fashion ).

[CharonY]

Ah, OK cross-faculty theses are little bit harder, I suppose. However, most reputations of mean examiners tend to be exaggerated (well, I managed to get some diploma students crying myself).

But if he is a real meanie, well you are the expert in your field. He is not

[swansont]

I acquired a neck/shoulder problem from non-ergonomic equipment combined with less than perfect posture when I wrote my thesis (which would be 11 years ago). I had to get a fair amount of treatment when I was a postdoc, and it still flares up occasionally. The tedium was really the single-mindedness of it all — you had no other problems on which to work when you got stuck with the equivalent of writer's block.

 

I agree pretty much with CharonY — the bulk of the write-up isn't/can't be done until you have finished the research. And one difficulty of writing papers is trying to be concise. At least in a thesis you have the ability to take the extra space if you need it, add in extra diagrams if they are helpful, etc. Many journals (with which I am familiar, at least) have page limits.

[CharonY]

And in addition to page limits there are page charges. I think for my last paper we had to cough up over 2k euros. I should learn to use fewer, or at least shorter words.

Ow and by reading swansont's post I have to add, take breaks every few hours. Your wrists and back will love you for this

[Dak]

That sounds really cool. Shame you haven't been able to do any practical for your project' date=' the doing part of science is always my favourite bit.

 

What university are you at, if you don't mind me asking.[/quote']

 

Cheers. and actually, i kinda suck at wet research (have to learn fast when i do my PhD )

 

And sorry, but i'm not confortable giving out personal info over the internet (dont mind you asking tho )

 

And in addition to page limits there are page charges. I think for my last paper we had to cough up over 2k euros. I should learn to use fewer, or at least shorter words.

 

dont journals pay you for your research?

[sophster]

Good luck with starting your PhD Dak. After my experiences I can't say I'd ever recommend one. Are you staying at your current place and a familiar supervisor and lab or are you off to pastures new.

 

I suppose the one thing I like about writing my thesis rather than writing a research paper is that I get to present all my hard collected data, rather than just a few salient points. And I get to spread them out into the most clear representations and all in glorious technicolour.

 

I hate the way journals sting you for colour plates in papers. I'm a really visual person and hate seeing loads of scrunched up little graphs and photos in black and white rather than distinctive colours.

[swansont]

dont journals pay you for your research?

 

No, at least for any journal with which I have experience. You have a research grant, typically, from some source (could be government, industry, or private foundation or even individuals, depending on what you are doing). Journals are usually funded through subscriptions only, and not a very large subscription base, so they defray publication setup costs and administrative costs (or so I've always understood) by charging the authors a fee.

[Dak]

Good luck with starting your PhD Dak. After my experiences I can't say I'd ever recommend one. Are you staying at your current place and a familiar supervisor and lab or are you off to pastures new.

 

Cheers.

 

I can't say ive thought about it that much yet (im gonna take atleast a year break first). I guess it depends on how good their genetic enginering/viriology departments are (which are my main interests).

 

No, at least for any journal with which I have experience. You have a research grant, typically, from some source (could be government, industry, or private foundation or even individuals, depending on what you are doing). Journals are usually funded through subscriptions only, and not a very large subscription base, so they defray publication setup costs and administrative costs (or so I've always understood) by charging the authors a fee.

 

So... let me get this strait... people pay journals to publish their results, and then other people pay the journals so that they can read about them.

 

sounds like the jourals are on to a good thing

 

hmmm... do journals just print papers, or do they do other stuff like check results/lab books, repeat experiments etc? if it's just a case of printing, they could surely publish online and ignore the majority of the publishing costs?

[5614]

My physics teacher was telling me about his PhD the other day, how it was a few hundred pages long and he was giving it on the last day but he had to photocopy it several times for various different people and the scanner which scanned in multiple pages automatically broke down, so he had to scan in each individual page and photocopy it a few times and compile all the copies and rush, rush, rush etc.

[CharonY]

Dak, journals typically only publish the results.

Although in some cases I have heard that they also pay other labs for verfication of certain results (only heard it from a physics journal, though. not really my field of expertise).

In almost all cases (at least of journals I know of) the editors are scientists themselves, though. Of course they are responsible for the review process, however the reviewers are not paid.

More recently some online journals indeed started to appear. Most of them allow free access to the articles, but still charge money from the authors (often less, then many print journals though).

I do have the feeling that it is not always about covering costs from the journals as the charges can vary extremely.

[swansont]

So... let me get this strait... people pay journals to publish their results' date=' and then other people pay the journals so that they can read about them.

 

sounds like the jourals are on to a good thing

 

hmmm... do journals [i']just[/i] print papers, or do they do other stuff like check results/lab books, repeat experiments etc? if it's just a case of printing, they could surely publish online and ignore the majority of the publishing costs?

 

 

As CharonY said, they are responsible for the review process, and this is no small responsibility, as quality correlates with prestige. The circulations of many journals is small, so the economies of scale don't really kick in; many of the subscribers are institutional (e.g. university) libraries, so that all of the institution can effectively use that one subscription.

 

For journals that have online acess, some of what you are paying for is also access to their database of old journals.

[sophster]

I really need to get this finished up really properly asap as I start a post doc job in just over a week. Eeeeek.

[scicop]

I really need to get this finished up really properly asap as I start a post doc job in just over a week. Eeeeek.

 

Good luck! I finished my PhD 2 years ago, and I was in your shoes! Two weeks before the postdoc and still had to get my thesis approved by the librarian (very anal about formatting).

take it easy there "doctor"