On the last day of the genetics congress the halls of the spacious ICC were very empty. On previous days, many halls were could not seat everyone interested and overflow rooms had to be arranged.

Today, even George Church presented his fascinating technologies in a small yet half empty auditorium. But maybe real geneticists do not listen to lectures by George Church because he is experimenting with E. coli and avoid talks about yeast (the plenary lecture by Yoshinori Ohsumi this morning), or trees.

The latter were discussed in the last plenary lecture by Antoine Kremer , a forest geneticist, who reviewed and predicted the effects of climate change on forest trees. The migration patterns of oaks after the ice age in Europe can be traced reliably by preserved specimen. By relating the temperature increases due to human action and the natural warming of the ice ages, one can make predictions how trees will react to global warming. An early report from 1997 in PNAS explains the methodology.
I had no idea how advanced the field of forest genetics is and the organizers selected an fascinating speaker on a very timely subject.

I wonder whether I got his conclusion correct – oaks are probably better adopted than humans and France will largely be devoid of oaks by 2080 – but he, like many other presenters before him, was signaled to conclude by the chair of the session and had to leave out a couple of explanations. The following closing ceremony was short and painless.

The 21. genetics congress will be held in Singapore in 2013. Five years is a long time; in 2003 we barely had a decent sequence of the human genome, today we have sequencing technologies that allow medium sized labs to profile eukaryotic genomes independently. The advances of stem cell technology are equally amazing if viewed on this time scale. Eric Lander predicted in his plenary lecture that in five years we should be able to profile cancers genetically on a routine basis, which would hopefully improve the survival chances of many people. Who would have thought several years ago that simple sequencing could make a direct and important contribution to health?

[Some left overs and scribbles will follow]

Well, I’ll be frank: After lively and long discussions on every night of the genetics congress, it was time to get some sleep for me. Rudolf Jaenisch, our guest yesterday, was in the best hands and I sneaked out fairly early. From what I heard today, the meeting continued well after midnight.

The next gathering of the Berlin group will probably be in September. There are plans beyond a simple pub night, those of you who have met Phil won’t be surprised. Stay tuned!

Svante Päabo has a mission: The genome sequence of the Neanderthal. Amongst the attendants of the congress his report and strong opinions on the possibility, usefulness and quality of the sequence data could be heard at several occasions. His plenary lecture addressed most of the concerns that I had heard earlier, about degradation, contamination and sequencing quality. He promised the 1x coverage genome for the turn of the year. This corresponds to a large number of runs of 454-sequencers because the vast amount of DNA in the available samples bacterial. The “junk” would probably make a nice metagenomics project on its own.

Bacterial sequences should sufficiently different from but what about human DNA contamination? The trick to ensure a high quality extraction builds on the availability of the mitochondrial genome of the Neanderthal. By comparing it to the known and well established mitochondrial sequences in an extraction, one can measure the ratio of contaminant human DNA and he showed that indeed, only few extractions were really usable. The openness in error reporting certainly convinced me.

The precautions go much further and includes the use of special linker sequences for Neanderthal to ensure that there is no carry over of DNA from within the sequencing machines.

From everything I saw today, it seems as if a good portion of the Neanderthal genome will be available in a reasonable amount of time. But will we get to see more human fossils sequenced? Svante Päabo’s answer to the question after the talk was sobering. In his opinion, degradation of the DNA will make it impossible to sequence older hominids like Australopithecus. But even specimen from the human lineage younger than the 40.000 year old Neanderthals will not be available because it will be impossible to separate contaminated samples from pure ones due to the lack of a mitochondrial standard.

That was this morning but an article in PLoS ONE now reports the isolation the mitochondrial sequence of a Cro-Magnon and validation of the originality by comparing it with all seven people that were in contact with the sample. That could mean that Svante Päabo’s a little too pessimistic. But he surely wouldn’t mind to err.

A press conference was held yesterday at the genetics congress regarding the heated discussion on stem cells in Germany. One remarkable note was a complaint of the German stem cell researcher Hans Schöler from the MPI for Cell and Developmental Biology on the reports of breakthroughs in the German press. Results had not appeared in peer reviewed journal yet and were presented “to scientists only” but were picked up by a major newspaper, the FAZ whose science section is considered highly even in the science community. The article also included doubts (“practically artifacts”) about the results of other researchers by Schöler himself, who now claims to be quoted out of context. The scientists, whose results were criticized, responded acridly in another newspaper .

The case has not been picked up by non-German media but check the Ärzteblatt for a reasonable report, SpOn has more extensive but somewhat tendentious coverage. This case is complicated and I am not sure what to make of it. But the mass media are not the very best way to discuss scientific results and I am afraid that cases like this will rather mute open scientific discussions.

Peer Bork, Eric Lander and Dinshaw Patel were the guests for NN dinner yesterday. The picture below was taken shortly after Eric Lander (center left) sat down. He caught the rapt attention of the students immediately even though not everyone knew the details about his contributions to genetics or heard the stellar plenary lecture he had given at the conference on Monday. Peer Bork (left) and Dinshaw Patel got their turn to talk later. We had many attends from the conference this time and filled the patio in the back yard of the Meierei .

Organizing these dinners was really rewarding. Particular in the context of a larger conference whose size is limiting interactions, sites like Nature Network provide a nice platform for local groups. Tonight, our guest will be Rudi Jaenisch and conclude the fringe dinners for the congress.

The NN Berlin group organized a series of dinners to bring students in Berlin in contact with some of the high profile scientists attending the genetics congress currently held here. The majority of scientists contacted accepted the Phil’s invitation instantly, showing there is a interest in communication, which we can only applaud.

Yesterday night, it was nice to see that we had even reached even undergraduates from the Free University who were later chatting with a Elisa Izaurralde, director at the MPI in Tübingen and Frank Uhlmann, group leader at the Cancer Research UK in London quite openly about pretty much everything about becoming a scientist and in particular, living abroad for an extended period of ones life. I wish I would have had the opportunity when I was a student.

Berlin felt deserted at 8 a.m. on a Monday during vacation time and I got to enjoy the fresh and shiny morning. It was odd hear about the processes of aging to my first plenary lecture of the XX. Genetics congress and .

Then again, Elizabeth Blackburn’s (UCSF) presentation was quite jolly and the amazing processes around telomeres and telomerases were stunning even if they are text book knowledge by now.

After the initial presentation of the basic players and the consequences in senescence, cancer and activities in regular tissue, she started to discuss high level implications of psychological stress and telomerase activities that felt almost dubious in contrast to the basic molecular biology presented earlier.

I seemed to have not been alone with that uneasiness and picked up similar comments on the way out the auditorium. Not that I have any grounds to doubt her findings. I might be simply old school when it comes to studying genetics and psychiatry side by side. In the context of Elizabeth Blackburn’s complete work, this seems to be a rather minor part anyway and I wished there would have been more time for discussion of the matter. Nonetheless, that was a very nice start.

The Nature Network group Berlin is growing and we found a group blog to be timely. So despite running under my user name, this is fully devoted to Berlin and the research that happens here.

We – mostly me in the next couple of months – will use it for feed back on activities of the groups and coverage of conferences and meetings in Berlin or the area, which we believe is best served by a blog.

For content with more persistence and grounds for discussion, we will use the forum.