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Too much phosphorus

It seems the big paper about the Arsenic which I’ve talked briefly on the previous post lacks a lot of precision and that the impurities presents in the medium will give room to the possibility that actually the bateria is not using arsenate, but still phosphate.

We were not really convinced at lunch discussion and then it seems we are not the only ones.

More info here. Especially interesting these criticisms . ).3 µM of Phospate is quite a lot in a P-/As+ medium.

I guess there is room to have another look at this bacteria.

The other way

I’m still amazed by the subs of the Phosphorus with Arsenic as found out and report in Science here

So life can have a completely different way for working… It’s also true that the Arsenic sits just under the Phosphorus, so it share a lot of chemical property, but still is the first time we have an example of something living without Phosphorus. Some questions just right off the bat:

  • What’s going on with the Adenosin Three Phosphate (main energy molecule in all cells)?
  • Is that thing using an ATA (Adenosin Three Arsenate) ?
  • Is that stable/does it even exist?
  • Which are the pathways? All the kinase/phosphatase system is just working with ATA? I guess we need to change the phosphatase names if that is the case..
  • Which kind of evolution?
  • Where is on the phylogenetic tree?
  • Is it on the phylogenetic tree?

Time to read the paper.

Best LaTeX editor: Gedit on steroids

Looking for a really powerful editor in GNOME is one of my constant research.

However it seems now it’s close to an end and it need just a small tilt to achieve perfection.
Right now I’m using Gedit with LaTeX plugin . It works amazingly and it does it jobs. The spellchecker is available and everything works properly.
I’m using Evince to actually check the complied PDF instead of the third panel, but that is a preference thing.

However the best tool out there to enjoy creative writing is definitely Scrivener. The main features of Scrivener is the ability to completely shiedl the user from the managing of the files and names, giving the possibility to focus on:

  • the status of it’s work (todo, draft, revision…)
  • the ability to shuffle and reorder the pieces of work as it best fit.
  • the main idea to use scrivener, or autonomous chunk of text which can be combined in an easy way

Writing books or big documents from scientific papers to PhD thesis it’s a main effort, which need constantly the main vision, but also the attention to details. Some parts will be ready before others, some pieces have a different evolution than others. The chunked text is the best way to go and I think it will really make the users’ life easier while battling with writing massive document.

The main problems with Scrivener are three according to me:

  • is available only for Mac and Windows, although there is a not supported version for Linux
  • the way the references are managed is not ok for scientific papers (BibTex does a perfect job)
  • not able to control easily the results of the compiled files.

This is the impression I’ve got when I used it for a really small period of testing. Although the User Interface is amazing.

Therefore we should create our own Scrivener, where the three points over stated should be addressed.

Gedit is a very good candidate to evolve, due to use of plugins, to a similar User Experience. Using the LaTeX plugin is already possible to holds and manage complicated text and notation and have a top-notch quality results.

What we are missing is the managing of the files a la Scrivener, where each file is a just a chunk of text which can be a subsection, a section up to even a chapter. Each file should be indexed and the metadata of each file should be tracked, like the revision status and the part status. A project manager, which will holds all this file and it will open them and make them always available to the user. The best would be to have a project manager which holds all the files, and a third panel where the status of the file and the type of the file is tracked properly.

Any chunk of test should be written in LaTeX and could be combined according of the order in the Outline, using the  input command.

Unfortunaly I’m not too familiar with Gedit from the programming point of view, however if there is anyone who thinks is a good idea and want to give a try I’m happy to be a beta tester and give an hand.

If interested, leave a comment, or send me an email. There is a starting (hopefully) discussion also on the Gedit ML

Git tutorial pushing branch

This is a very good and clear tutorial how to push a local branch to a remote with git.

In a nutshell:

1. Creating a the remote branch

git push origin origin:refs/heads/new_feature_name

2. Updating the branch list
git fetch origin

3. Just double check if it is really there
git branch -r

4. Track the remote branch on a new local one
git checkout --track -b new_feature_name origin/new_feature_name

5. Classic pull. All branches will be pulled now
git pull

Symphony of Science

Great video about science and a way of thinking.
[youtube http://www.youtube.com/watch?v=1PT90dAA49Q]

Best quotes:

Plait:
Teach a man to reason
And he’ll think for a lifetime

Randi:
Enjoy the fantasy, the fun, the stories
But make sure that there’s a clear sharp line
Drawn on the floor
To do otherwise is to embrace madness

One regret

The only thing I’m really missing right now, it’s not to be in Italy to actual join the manifestation going on in the country against the infamous reform ‘Gelmini’ which is a disastrous choice for the Public school and Italian University.

Anyway I’m supporting, from here. For now.

Does Stagecoach got ears?

Today I’ve tried to get the City7 from Cambridge to Hinxton. Usually I take the shuttle bus in the morning and in the afternoon, but if you’ve got stuff to do in town, you have only two options left:

  • taking the train + bike
  • taking the city7

The train+bike means boarding your bike @ Cambridge station and getting out at Whittlelsford Parkaway station and then cycle to the Genome Campus and cycle back in the evening.

The path is really nice, especially in summer, but right now it gets dark rather too quickly, and the road from the Genome Campus to Whittlesford ParkAway is completely without any kind of illumination. So not available in the winter.

[googlemaps http://maps.google.com/maps/ms?ie=UTF8&hl=en&msa=0&msid=117346831772329393426.00048f2f5310609e8b669&ll=52.091784,0.172152&spn=0.025068,0.029241&t=h&output=embed&w=425&h=350]

The other option is to catch the City 7.

Now, the problem with the city 7 is the service is quite disastrous. There is only one city7, that goes hourly from CB to Hinxton, where the Genome Campus and the EBI is based and it’s never on time. We actually call it the “Unpredictable city 7”.

Real life experience, today the bus @11.05 never show up and I was forced to take the one @12.05. I was at the bust stop from 10.40 (to not miss it if was going to pass really early), so I waited 1 hour and 30 mins. Oh yeah!

I think those guys can do better than this. So I wrote the letter below. Feel free to send them an email as well if you care about this. You can use mine as template if you like.

Their email address is cambridge.enquiries@stagecoachbus.com .

Dear Stagecoach,

The the City 7 line, specifically the one that goes from Cambridge to Saffron Walden has a very sloppy service for an amazing high price.

While I understand you can’t provide a service every 10 mins I think it’s outrageous that your bus is most of the time either late or too early in respect of the schedule.

When I started my PhD, 3 years ago, the frequency of the bus was every half hour for 2.80 £. Right now the service is hourly and the price is 3.10 pounds. As I already stated the punctuality is not a strength.

I’m working @ the EMBL-EBI which is in the Wellcome Trust Genome Campus, together with the Sanger institute and the Hinxton Hall Conference Center. The Campus is very close to the Hinxton Village.

The Genome Campus has roughly 4000 people and I can tell you I’m not the only one who would enjoy a better service. Most of the people I know have completely given up the idea to take the public bus, in favour of cycling or going by car or other means because of its unreliability.

I think there is enough potential to try to run things differently.

Other City 7 lines stops at Duxford and the Duxford museum. Maybe you can run a trial and extend those services to Hinxton, which is just few miles away.

If you can provide a reliable schedule with an increased number of services maybe the perception would change and more people will use those service more often.

That would be a better service for us and a good business for you.

I hope you will take those suggestions in consideration.

Thanks for your time.

Best regards,

Michele Mattioni.