venerdì 27 luglio 2007

Ma se po' campà accusì?

Ma che é successo alla televisione italiana? Se la TV é lo specchio della nazione in cui viviamo (francamente non voglio crederci) mi sa tanto che siamo messi un pò giro per i canali vedo solo preti e poliziotti (a volte pure preti-poliziotto...roba da pazzi!) oppure cose peggiori...

Dopo 10 anni di assenza dall'Italia, ho trovato un paese più vecchio, più stupido, più triste e anche più cattivo di quello che mi ricordavo...

Ma se pò campà accusì?

Gabriele Amore

martedì 17 luglio 2007

On real time PCR, cDNA kits etc.

Hi there

A couple of (good) news for people dealing with real time PCR:

1-The Mj machine at the SBM can read a signal from a 8ul reaction. That means you can set your reaction using only 4ul of SybrGreen/replicate. However you really need a good pipette since small pipetting errors become critical at this point.

2- The QuantiTect cDNA kit from Quiagen is so far the least expensive and more efficient kit I had the chance to try. There is only one caveat: you need RNA already digested with DNAse. The kit includes a "genomic DNA wipeout reagent" to take care of genomic DNA before the cDNA synthesis, but as far as I can tell it's useless. Scaling don the reaction works fine, the kit works like a charm and it is really a pleasure to use (it's a 2 step process that only takes about 30').

Hope this is helpful

Till next one
Gabriele Amore

domenica 15 luglio 2007

Plastivik 4

Ed ecco la quarta puntata di Plastivik!
Ah! Dimenticavo: il nostro fumetto é liberamente ispirato a fatti realmente accaduti e a persone realmente esistite... alla SZN c' é davvero qualcuno che crede che la plastica sia una soluzione per l'effetto serra (la frase "viva la plastica" é stata effettivamente pronunciata)... così come c'é gente che strappa i volantini coi quali non si trova d'accordo... alla faccia del rispetto delle opinioni degli altri!

Hasta la proxima
Anton Dohrn Cafè

giovedì 12 luglio 2007

Plastivik siamo noi

No Comment

'till next one

Gabriele Amore

martedì 10 luglio 2007


To bring you music is what I'm here for....

Well, I ain't gonna talk about the overestimated Classical music!

Today I gonna take you a trip through the "pagan" and poetic music of a group

“The Waterboys”

Born in the beginning of 80s’(1983), under the simple rule of doing nice music and wonderful lyrics.
1983: The Waterboys
1984: A Pagan Place:
1985: This Is the Sea
1988: Fisherman's Blues
1990: Room to Roam
2000: A Rock in the Weary Land
2001: Too Close to Heaven (issued as Fisherman's Blues, Part 2 in the United States)
2003: Universal Hall
After four years, finally they came back again with the album,
2007: Book of Lightning
This time I don’t feel like writing a lot, probably because the only way to discover this group is through listening. Furthermore, there are several difficulties finding links with their music in good quality.
I give you only two links (due to scarcity of good quality of songs on the web) but enjoy the music and feel the

Come with me
On a journey beneath the skin
Come with me
On a journey under the skin
We will look together
For the pan within.....

The pan within
(This video is not original, for this reason is not beautiful, but not their music)
This is the sea

Red Army Blues

Your SDJ ..... Stilianos Arhondakis

domenica 8 luglio 2007

Plastivik 3

Ed ecco la terza puntata di Plastivik!
Ci vediamo la prossima settimana

Anton dohrn Café

PS se volete vedere le tavole precedenti cliccate sull'etichetta "Plastivik " in basso a sinistra.

venerdì 6 luglio 2007

About Microarrays

Dear all,

since I have the feeling that the interest in microarray , gene function annotation and experimental next steps is increasing in the Institute I would like to initiate something like a round table, even very relaxed. We can maybe meet outside this walls where we can not only enjoy discussions on scientific things but also a cold beer and some crackers. So whoever is interested can contact me via this blog or directly via mail:

So, lets start something

Alexander Luedeking

Veronica Hinman's Seminar today

Hi there!
Though it might be a bit late I want to take a minute to advertise today's talk by Dr Veronica Hinman....It is going to be great!
She is going to present a new way of looking at evolution and I can only recomend that you all come to hear her. Not only she is a very insightful scientist, she is als a very talented and effective speaker, like very few people around.

Hope you can all make it

Gabriele Amore

giovedì 5 luglio 2007

Blu blu blu le mille auto blu

Chiariamo subito una cosa: i Repubblicani non mi stanno simpatici (eccetto quelli tipo Lincoln). Però sentire che il sindaco di una città come New York se ne va al lavoro in metropolitana mi ha fatto un certo effetto. Niente auto blu e (credo) niente scorta. Non poco direi. Poi se ci aggiungi che negli USA ci sono solo 70.000 auto blu e le paragoni alle 500.000 che ci sono in Italia, cominci anche a pensare che non tutto il mondo é paese...

500.000 auto blu... costeranno i loro 30.000 euro l'una (o anche qualcosina in più)? Fa almeno 15 miliardi di euro...non male direi. Metteteci le spese di mantenimento e lo stipendio per gli autisti...mi sa che rispiarmiando 'sti soldi ci si potrebbe evitare tutti quanti una manovrina bellina bellina...

Simpaticamente vostro
Gabriele Amore

martedì 3 luglio 2007

The sound of nature

Pitagora once said that there is a music in nature. He also noted that we are not able to hear it and that is either because we just can't or because we are so used to it we cannot longer distinguish it from the background noise.

Take a look at this paper
Conversion of amino-acid sequence in proteins to classical music: search for auditory patterns
by Takahashi and Miller, and listen to the MP3 files that go along with it...looks like we are going old Pitagora was right after all!

till next one
Gabriele Amore

Ahmed e il ritorno dell'araba fenice

Ciao a tutti!

Eccomi qui, sono Giuseppe “Buccia” Bucciarelli...

Con alcuni di voi ho parlato meno di 5 minuti fa, con
altri non mi sento purtroppo da molto tempo.

Comunque! Volevo darvi una bella notizia...! Calmi!
Non mi sposo ne' aspetto un bimbo!

Forse sapete che ho prodotto e diretto un documentario
naturalistico sulla scoperta in Siria di un volatile
bizzarro e rarissimo, l' Ibis Calvo. Ebbene! Dopo
migliaia di ore di lavorazione, due versioni e un bel
po' di casini ecco a voi...:


il 29 di Luglio alle ore 21.00. Lo ridaranno in
replica anche il 30 luglio alle ore 13.00 e 19.30. e
il 31 luglio alle 08.00

Lo manderanno in onda anche nei mesi successivi ma
ancora non so quando.

Chi non mi vede da parecchio potra’ farsi un’ idea di
me, dato che scorrazzo in video per il deserto all’
inseguimento del mitico pennuto...

Baci a tutti!!

Giuseppe Buccia


You favourite SDJ [Scientific DJ] is back. Even if I’m not your favourite, I’m the only ONE, so you do not have any alternatives!

I can also understand that many of you may feel a bit uncomfortable of what I am going to write; well, in that case I have only a wise and precious advice for you:


Today the music trip will start with f€ew words upon the overestimated Classical music, and afterwards I will introduce you to the NEW Classical music, Electronic music!

Classical Music: just a musically poor passage.

Born during a period between the Baroque and the Romantic, by few known composers, i.e., Mozart, Beethoven, Clementi, Bach, called also “genius of music”. A music, that one should try to listen, and have respect. I tried (when I was able to resist to the sound that evokes), however, afterwards I always thought: “OVERESTIMATED”.

I guess that you have understood that I don’t feel part of this music, created from the so beloved and overestimated “genius” composers of the past. You may also think that what I have written is due to my ignorance towards the classical music. Well, it may be true, but sincerely I don’t care.

I am not here to fulfil your human expectation of being considered.

Society did its best to make us appreciate (poor feeling), and learn about these “genius fathers” of classical music, but nothing about their SONS, the new genius composers of music.

“Electronic music is not only a music created using devices, but a state of mind revolution, that travelled in every corner of the planet, and “sucked” the mind of million of people.”

Several composers, from Faithless, Chemical Brothers, DJ Shadow, Massive Attack, Fatboy Slim, Paul Oakenfold, Paul van Dyk, DJ Krush, DJ Shadow, Tobin have reached a level of music geniality overcoming that of their “fathers”.

A music, that unfortunately is also associated to different types of drugs (that’s you choice), and where as a consequence to be kept a certain “distance” of the society. Now try to listen (if you want) what follows, and since you are in the laboratory, I guess and I HOPE that you are not under the effects of some kind of natural/synthetic drugs!

Enjoy the trip!


DJ Krush:


Berlin 1998: 150 people gave the first party for love and peace.

10 years later, 1.500.000 people DANCE for EVERYTHING!

Love Parade

Music evolves by social and technological forces!

Stilianos Arhondakis AKA SDJ

lunedì 2 luglio 2007

Late reflections on the last Salvatore Lecture

Dear all,

With a terrible delay, which doesn’t really fit a blog, I wish to share with you some reflections on the last Gaetano Salvatore Lecture. Marc von Montagu, Belgian Geneticist and co-discoverer of the gene transfer mechanism between Agrobacterium and plants, is one of the pioneers of European agrobiotechnology. Beyond the scientific aspect of the technology, van Montagu was also much involved on the technological commercial side, as founder and head of two biotech start-up companies in the late Eighties and Nineties (see It is not difficult to imagine what the position of the man on the Agro-tech issue could have been. It was, indeed, a very one-sided, straight forward sermon, centred on the great potential of genetic engineering for the future of human societies and on the risks that might come from opposing or boycotting these new developments. Not a pale shade of doubt on the eventual risks that might arise from heavy and continuous human intervention on the environment.

What was surprising to me, given the one-sidedness of the speech, is that I actually found it almost totally convincing. Part of it must be due to the skill and experience of the speaker, as well as to my own ignorance. But I want to share with you some points that I found most compelling. I will do it in a rather unilateral fashion. I hope this will stimulate some discussion.

1. scientific evidence and precautionary principle

This is the most well known and “fashionable” issue, and also the most controversial. Ever since GMOs first appeared, all sorts of doubts and opposition have been aired by the press, by concerned citizens, political parties and movements. This movement first grew very strong in the UK, than in Continental Europe and, since recent times, is spreading wide in the US. Dr. Van Montagu in his lecture strongly objected to the almost universal value that the so called “precautionary principle” has acquired in the course of recent history. As a matter of fact, he stated, the presumed evidence on the environmental hazard (especially for the reduction of biodiversity) is overestimated. The only example I find in my notes is related to the problem of the “strong” engineered crops taking over the “natural” ones. To this, Dr. Van Montagu objected that it is difficult for a crop that has been designed for culture to spread over and survive on its own or, at least, to be so greatly successful in the outer world as to get rid of the “natural” competitors. To this I dare add that the very concept of “precaution” is still widely debated in the scientific and bioethical community. Moreover, I wonder what is the function of such a restriction when it only applies to limited parts of the globe.

We Europeans are very proud of our GMO(-almost)-free agriculture. Still, we buy huge quantities of gm products from abroad. Most of the soy that is being traded nowadays comes from GM germlines. The same could be said of our beloved Italian hard wheat: most of the sorts of this cereal we use today come from the Gamma field in Casaccia (Roma), where they were engineered by means of radiation in the Sixties. This takes us to the second point, namely:

2. who leads the game – and whose nature are we protecting?

The question regarding “who leads the game” is strictly related to that regarding the obstacles to experimentation raised by the precaution-oriented legislation. I must confess that this was the point I found most convincing, although one can well see its difficulties and the dangers it entails. The argument runs as follows: 1. one of the main objections to green biotech is that it is dominated by huge multinational food industries (mainly US, but also European with bases in America, as Unilever), whose main interest cannot possibly be very far from making profit; 2. this entails the interest to keep the customers in a state of dependance, which means 3. that the poor and backward countries, that need to improve their productivity to fight hunger, run the risk of being completely dependent on the private industry. vM’s objection to this is interesting. The argument (as I can see from my notes) runs as follows: SMEs cannot simply afford entering the Agrobiotech business, because the security requirements are so strict to raise experimentation costs beyond their possibilities. As things stand, says vM, the present regulation cooperates with the multinationals to keep the market closed. This is of course a major obstacle for finding new commercial and political solutions to a problem that, together with water management, is the most central to the future of mankind.

Is it possible that a more relaxed legislation allow new actors (SMEs, smaller States, consortia) to enter the game, bringing in a new logics and a new way to deal with this issue.

For medical research there already exist attempts to find new political-economical settlements to subtract relevant parts of the to the private sector: think of the Cuban biomedical industry, or of South Africa. We can object to the results and validity of these examples, but they show that some political alternative can be conceived. vM’s Institute in Belgium (IPBO, see also why IPBO?) can well be another example of this possible alternative, based on the “cooperation to development” scheme.

The role of Europe in this process is central. In my opinion, we cannot expect a culture based on free initiative and free market to provide different examples than free-competing hyper-powerful multinationals. This is no critique, I see it as a matter of fact. In the US there is no room for a direct intervention of the Administration beyond setting the rules. Europe has a different culture, and a different history. It is not understood that a European agro-biotech industry would be different, but the represent state of the regulations makes it simply impossible to assess it.

While Europe is busy protecting its own environment, the US and a number of Asian States, which are almost completely deregulated in this field, have gained a leading position, and are imposing their models. It seems at least difficult to me to gain a victory without competing.

My opinion is that the acceptance of the biotech (as well as the biomedical) challenge is a political fact. The main question, as I see it is: how much do we trust the present political and scientific authorities, especially in Europe? The answers can vary, but the question is by no means trivial. It is very important to ask ourselves wether we find a reason for hope in the present scientific and technological development or, to the contrary, we think it unavoidable that the scientific-technological dominion of a small part of the Western society (the big biotech multinationals) will be simply powered to the level of Imperialism by the new biotech tools.

The answer cannot be simple and straight, but the question must be taken very seriously. Acting in a risky business like this can be very dangerous. But the costs and risks of non-action must be considered as well.

3. what will we do of our biotech experts?

This final point I introduce with some hesitation. It was not part of the Lecture. It came to my mind only later. Since the 1987 Italian Referendum that banned Atomic Energy Plants, our engineering and nuclear physics faculties have gone on producing emigrants. Moreover, a number of research fields (including biology) that were scientifically or financially tied to nuclear research, have suffered from its crisis. Now we all agree that biotechnology and basic biological research are one of the most important avenues of the future development of science. Shall we go on training good researchers whose only destiny is to emigrate, because they cannot do here what they were trained for?

Links -
website on GM soy
IPBO website

Fabio de Sio

Plastivik 2

E come promesso, ecco la seconda puntata di Plastivik!
Ci vediamo la prossima settimana

Anton Dorhn Cafè

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