Robotics in the lab -SPRi and Mass Spectrometry

In the team of Dynamics of Macromolecular Complexes at the LBPA  we developed a technique to transfer material from an SPRi prism to a SELDI (mass spec) slide. This technique had already been published by us some years ago (see Bouffartigues 2007):

Using the Hamilton Starlet robot we were able to automate this such that a given spot on the surface could be treated with a chaotropic solution then transferred to a SELDI surface for identification by mass spectroscopy. We used a pin tool and modified the programming to reduce contact between the pin tool and the rather fragile (50nm thick) gold surface of the prism.

A pretty amateur film can be seen by clicking on the link below

Next time we will get David Arraez to shoot it for us 🙂

click here for Movie

Robotics in the lab -spotting

We are increasingly using automation even in research. We are very interested in spotting biological material on biochips. This video shows spots of around 400µm diameter being deposited on a gold coated prism.

We use a Vikalex ink jet spotter. Again thanks to David Arraez for the video and image.

PhAST Technology

The team of Dynamics of Macromolecular Complexes at the LBPA has developped  an  approach  to use the probability of UV induced cyclobutane dimer formation between adjacent pyrimidines on the same DNA chain in naked and bound DNA as a probe of changes in local base structure not only between naked DNA and reconstituted nucleosomes but also at different stages of nucleosome formation. This technique of Photo-chemical Analysis of Structural Transitions (PhAST) induces photo-chemical alterations in DNA pyrimidine dimer formation. The location and intensities of these alterations are themselves affected by external agents that reshape the DNA structure and thus alter the photo-chemistry. Thus, the technique provides unique information on the local structure at a base level of the DNA. We reveal photochemical products using a simple primer extension technique coupled to capillary electrophoresis. Our approach confers high-resolution, excellent quantification, application in vitro and in vivo, and the possibility of high-throughput since practically any size DNA sample may be analysed in a fashion analogous to genome sequencing.

Concerning nucleosomes, a recent result, which can be found here: 2016 Hatakeyama 

demonstrated that, for the first time we are
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Letter to the People of Earth

Dear People of the Planet Earth

As is the custom amongst you I would like to begin this letter by hoping that it finds you in good health.

Unfortunately, this is blatantly not the case and is the reason why I have been designated to inform you officially of our decision to cease all preparation of contact with you.

As a conscious species with a respectible level of intelligence, surprising for a carbon based life source, we were pleased to note that you ticked most of the boxes in your progress curve towards civilisation. Although a belligerent species, we felt that you demonstrated considerable potential especially technologically and artistically.

However, where you have totally failed is in terms of social development specifically with respect to what you call religion. I will not discuss with you in detail what you refer to as spiritual matters; quite frankly if you were smart enough to understand why then I wouldn’t have to explain. However, and this then is the crux of the matter you are unable to establish and live by a set of ethical rules that are not based on a doctrine derived from the word of a fictitious deity dictated to some enlightened individual or group of individuals. You invent some preposterous object called god, to whom you attribute a whole set of do’s and do nots of which the most stringent and enforced is not the obvious “only do unto others what you would have done unto yourself”, thus encompassing the o so necessary dont kill other people, but rather is very emphatically centred on the need to never ever question either the presumed existence of this god and most certainly never dispute its code of conduct.

Large swathes of your population adhere without question to this fantasy. We believe that this is symptomatic of a pathological mind set that you call religion and that is unfortunately now endemic to your planet. We believe that you are incapable of dealing with this and that there is a real threat of contamination.  Collectively, you are manifestly unable to progress beyond this primitive social state to create a fair and equitable society, you are unable to establish a sustainable economy, of managing your ressources and of tapping into your cerebral potential. Your adherence to a faith based society is in great part responsable for this social stagnation.

The elected leader of the most technologically advanced nation state (G. W Bush Jr) on your planet once engaged in a commercially inspired war with a major ressource producing nation; this leader admits to having been inspired by conversations he had had with his societies version of god. Even more recently some unstable individuals, even though resident and products of a laic society killed a number of people who had dared to poke fun at their version of god and justified this by claiming that their god may never ever be insulted or even represented graphically. I have neither the patience nor the will to catalogue all the instances of religious inspired stupidities that your species have and continue to perpetrate. Neither do I have an optimistic message to send you concerning your capacity to contain and cure this epidemic of religion. You cannot and you will not.

I am empowered to tell you one thing only, knowing that it will have no effect whatsoever since the enlightened few amongst you already know, and the majority afflicted by this disease will of course not want to understand. There is no god; you have only one chance to experience consciousness and this during an infinitely short period of time. You squander and waste this unique opportunity. As a species you are therefore destined to remove yourselves from the cosmos.

The ridiculously small region of space that you have occupied over a very short period of time (100 000 of your years) will be maintained as a no go zone until all risk of contamination has disappeared.

This decision is irrevocable.

You have I believe the custom of wishing your god to go with you. We are pleased to confirm that this will indeed be the case.

Why I am an atheist

Je suis Charlie


Over the last week we have seen vicious attacks on these fundamental pillars of our society perpetrated in the name of religion. The potential consequences of the barbaric attacks which were carried out in France this week could have diverse negative effects and be distorted by the ever present undercurrents of racism and fundamentalism that are running through our society. It is an attack on our culture, and by our I mean human.

I wish to categorically state that the motor for the horrendous events that took place this week is religion, religion in all its forms, but predominantly in its monotheist formulation. I hold that religion has no place in human culture. Iwish to attack religion, I do not intend to concentrate on fundamentalists or extremists. J’accuse all religion and all those who are duped by its well organised PR machine. This letter will necessarily be aggressive, but you will not die by reading it, your brain may perhaps ache afterwards but it wont be splattered across the office wall, the only thing to be buried may be some misguided beliefs not a bullet ridden body.

So, for those of you who entertain some religious beliefs, there is probably no god. there is as much evidence for the existence of a supreme deity than there is for Santa Claus, the tooth fairy, or a life after death. Lets not get bogged down into questions of the meaning of life. We have a very good idea of how the universe started, how life began and how we as conscient creatures evolved. We have no idea why. There is no need to invent a god to explain the how, there may be a need to explain the why, but having invented a god then you have to explain where the god came from, maybe made by another god, maybe always present, who knows? it doesn’t answer anything, so whichever way you look at it there is probablyno god or absurdly, there is a Russian doll infinity of gods.

That’s that out of the way. No god, good, so what about our ethics? How can we live without the ten commandments etc?  Would you not have thought that one of the most important tenets of a book of rules for a society would be “do unto others what you would have them do to you”, well no, in fact this one doesn’t exist anywhere in the code books of the major monotheist religions. The most important message is don’t question the existence of god and don’t ask questions of (or disrespect)  god. This is the reason why so many brave human beings were butchered this week in Charlie Hebdo. Are you impressed by this code of conduct. I am not.

What else do we have in these codes of conduct? I will pass on the dietary advice, on what sexual perversions you should or should not practice on your livestock or how you organise your working week. What is notably underplayed in all cases is don’t kill. Why should such a fundamental concept not take pole position? Because the major monotheistic religions aim to answer a fundamental question that has bothered mankind from the onset of collective consciousness, notably what happens when we die. All the evidence, not the majority, but all the evidence shows that when a living organism dies it ceases to exist. The body, the personality, all the elements that made up an individual occupy the same state that they had a nanosecond before conception. If you want an idea of the afterlife then remember how you felt a year before your birth. For any normal human being this is inacceptable. Apart from the innate desire to live, the intense pain felt upon the loss of someone close is unbearable. How much easier to imagine that they (and eventually us) are continuing somewhere else and we will see them again. How easy then for the shamans to manipulate this to then suggest that yes of course there is life after death, but only accessible if you believe in their god and subscribe to their code of conduct. How convenient also to suggest that other tribes/cults/groups in competition with their tribe etc for limited ressources obviously have an inferior religion that must be destroyed, whence all the stuff about jealous gods, false idols etc. Indeed in the Islamic faith if you martyr yourself in response to a real or imagined insult to ones god you get automatic admission into a paradise complete with explicit sexual favours (interestingly only if you are male however).

Such is the scenario that has lead to the disgusting events that took place this week in Paris, that are taking place all over the world everyday, stonings, beheadings, amputations, slavery, rape, sexual mutilations, flogging and so forth. All in the name of religion.

What to do? It is time, it is long past the time, that a serious religious figure, a Pope, a Mullah, a Rabbi, stood up and had the courage to say, “look, frankly we haven’t a clue, please stop killing and mutilating in gods name”. Is this going to happen? No, its not going to happen. At least not spontaneously.

So my letter is a simple request to two groups, first so called religious leaders, do you have the courage to stand up and say “we have no better idea about god, life after death or how best to organise your life than anyone else”

Second, to all human beings, ask yourselves honestly if you can accept that in all likelihood we live only once, there is no life after death and no god who is personally interested in you and you alone, and that life is sacred and under no circumstances be taken from someone simply because that person indulges in one of the fundamental rights of man, the right of free speech.