Archive for the 'bio' Category

FuturICT

Monday, February 4th, 2013


Musician Imogen Heap in her tech wear

In a recent comment on randform randform reader Bibi asked:

You had written at Azimuth that your idea to use MMOGs for simulating economic and political real world scenarios

seems to have recently been picked up for the Global Participatory Platform of the 2013 Flagship proposal FucturICT

It seems also that your scientific platform idea had been picked up for that ICTfutur grant proposal.

What about your intellectual property?

The FuturICT application for 1 billion Euros had though been turned down, will you now write an EU grant proposal?

Answers to this comment after the click.

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au courant

Friday, October 5th, 2012


image by Curtis Neveu on wikipedia

About five years ago there was on randform a question regarding the possibility to study the electron transport in a pigment-protein complex via some optical methods in the attosecond regime. Understanding this may be important for the development of new types of solar cells. From the randform post:

It would be interesting to know wether such high temporal resolution could also be used for investigating electron tranfer in pigment-protein complexes such as in a photosynthetic reaction center (see image above)(correction 05.10.2012: in a FMO complex (the reaction center seems to be a part of this complex)), which was done by researchers in Berkeley e.g. in a 3 pulse two-color electronic photon echo experiment with 750 and 800 nm pulses in the femtosecond range (science 316 (5830)) or wether the high energies of the corresponding laser pulses would alter the corresponding structures, which apparently happenes if one shoots with gamma rays on a pigment.

In a press release which reports about measurements at the photosystem 1 (PS 1) protein (which appears to be even more complex than the above mentioned FMO complex) it seems that one can at least measure the speed of charges in a photosystem with the help of optical devices.

Not only the press release but even the article itself:
Photocurrent of a single photosynthetic protein, by Daniel Gerster, Joachim Reichert, Hai Bi, Johannes V. Barth, Simone M. Kaniber, Alexander W. Holleitner, Iris Visoly-Fisher, Shlomi Sergani & Itai Carmeli
is actually still currently available on the nature nanotechnology website.

The results of their research makes the researchers write (see article):

Our results demonstrate that individual PS I units can be integrated and selectively addressed in nanoscale photovoltaic devices while retaining their biomolecular functional properties. They act as light-driven, highly efficient single-molecule electron pumps that can function as current generators in nanoscale electric circuits.

Instead of directly shooting with lasers the researchers were here however “exciting the PS 1 with a “633 nm laser light with a power of ~4 mW “from the back of the tip” (see figure 1 in the article), which I understand as that the laser light went through the glass of the tip of a scanning near-field optical microscope before it entered the PS 1 (the PS 1 was “glued” via cysteine mutation groups to the glass tip). Moreover the light makes electrons travel through the protein (as I understand with the help of a voltage through the protein i.e. between the tip and the ground) and this can be measured as a current:

The photocurrent was measured by means of a gold-covered glass tip employed in a scanning near-field optical microscopy set-up. The photosynthetic proteins are optically excited by a photon flux guided through the tetrahedral tip that at the same time provides the electrical contact.

The researchers sketched out the whole reaction-centre electron transfer chain and showed electron transfer and recombination times (see figure 2). I didn’t understand where the detailled knowledge for this figure came from, however their measurement seems to be in good agreement with this knowledge, they write:

One of the most significant results in our experiment is the intriguingly large value of ~10 pA for Iphoto. This translates into a turnover time of ~16 ns; in other words, every ~16 ns, an electron transverses the PS I covalently bound between the two electrodes.

(remark: with electrodes the researchers mean here probably the tip and the ground)

The wavelength in the experiment was 633 nm laser light with a power of ~4 mW but I have no feeling how the light is altered by the scanning near-field optical microscope. In particular I still don’t know wether one could use the high resolution laser pulses to investigate the traveling electrons within a photo system without destroying the photo systems.

Because in principle it seems one could make interesting films with this, similar to what had been done for topological insulators.

addition 090113:

It seems there are already some applications underway, which use PS1, which seems also to be up for a patent. I can’t read the original article , but there is some english description e.g. on nanowerk. Found via Sascha Peters on Liligreen.

I haven’t written this explicitly, but may be I should. PS1 is interesting not only because it has a high quantum efficiency (here a current record for quantum efficiency in quantum dots) and because it is usually available in ecofriendly materials like spinach but amongst others also because it seems that the charge carrier separation works rather well. The above work seems to be amongst others probably concerned with studying the involved mechanisms of charge carrier separation, i.e. last but not least it is concerned with the mechanisms of electron transfer.
On that issue I had written five years ago: “electron transfer in the photosynthetic reaction center of Rhodobacter sphaeroides in the above experiment seems to be highly efficient due to the long coherence between the exiton states of two chromophores corresponding to the bacteriochlorophyll b (BChl-b) molecules and bacteriophaeophytin b molecules (BPh) of a photosynthetic reaction center.”” (the comment was based on observations of the Fleming group) but I haven’t found the time and means to look into these mechanisms much further.

focus and context, part II-2: brain childs and their evolution

Monday, February 20th, 2012

This post is a follow-up to the last post. There is also a copy of this essay at the Azimuth project.
If you read the essay you will in particular understand that I profoundly disagree with most of the key concepts as formulated in the video by Kirby Ferguson, who also investigated intellectual property in the context of evolution.

Feb22: some additions to the essay in orange more additions eventually on Azimuth
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diversity maintenance

Saturday, November 19th, 2011

“Dreimäckriges Blauquallendrachengespenst verwandelt sich in einen Kugelblitz um die ausgecyborgte, zweigebeinigte “Jeanne die Arge”, zu töten”. Artwork by Hugo Buster, acrylic paint and pencil

Just a quick link to what seems to be an interesting study about biodiversity with the title Experiment gives insight into how species maintain diversity (via physorg.com). In the study it was investigated how biodiversity could be maintained despite dominance. Experiments with male voles, ordered by testesterone level, were performed:

when they released just a few of the high testosterone males and lots of low testosterone males into the same area, the males once again reigned supreme with the ladies. But when they released lots of high testosterone males with lots of lots of low testosterone males, the males with the lower levels actually did better than those with the high levels, indicating that there was something clearly at play. The researchers suggest that such results came about because the high testosterone level males spent more time fighting or showing off than mating, which gave the low testosterone males more of a chance to mate.

Holograms Reveal Brain’s Inner Workings

Wednesday, August 17th, 2011


“HirniKoppic”, Copic Markers on paper, by artist “nettwürg” on the occasion of the rumors about the possibility of closing the Medizinhistorisches Museum (Berlin Medical Historical Museum) of the Charité.

Using Digital Holographic Microscopy (DHM) researchers of EPFL gathered quite some interesting images from inside the brain:

->Holograms Reveal Brain’s Inner Workings.

When do we get to see brain images from image imaginations? and when can others recognize these?

plastic surgery

Monday, June 20th, 2011


Photography: Pal Lindlund

This post is like the previous post a comment to the discussion about human-machine hybrids in the recently uploaded game-scheme article.
In a passage from human to a human-machine hybrid the tolerance towards body modifications plays an important role.
There was recently an interesting interview in the english newspaper “The Guardian” wether cosmetic surgery does help or damage people.
The interview however didn’t really touch the issue of how strongly plastic surgery (and other body modifications) is influenced by cultural predispositions (which are of course often influenced by economic considerations, but not only by these). In particular it also didn’t touch upon the question in how far the design of the human outer appearance via cosmetic surgery (especially its current boom) etc. might be seen as a step in a human-machine-hybrid transition.

New economic schemes in games

Friday, March 25th, 2011

In the blogpost on the return of investments I proposed to use games for testing new economical scenarious. I currently try to make an article out of that.
In the draft I sofar have given an overview about games and roughly motivated why I think that it may be a good idea to introduce new economical schemes. In particular I talk about the limitations of this planet, design and in particular about something that I dubbed “recycling-run-away effect”.

Amongst others I also try to line out why I think that the nuclear waste problem may be a worse problem than the safety of reactors (see also the first post on Fukushima).

Comments are appreciated, here is the draft:

update (06072011) : This blog post is now used as a referrer URL for the game scheme article, thus newer versions of the article and comments will be uploaded more or less regularily. Please note that this offer to our randform readers costs our private money. Since randform is currently purely financed by Tim Hoffmanns income as a math professor, we may eventually be forced to reduce or close this offer, depending on download rate, inflation, etc. Most of the content of the article is also spread on the Azimuth project like the section about the Game environment. The Azimuth updates are usually more current.

->version July 06, 2011

The most essential content article of the article was presented on July 1st at the open knowledge conference 2011 in Berlin:

Talk: “Testing new toy economies/political structures in MMOGs” at slideshare.net

older versions of the article:

->version May 25, 2011

->version april 26, 2011

-> New economical schemes in games, version march 25, 2011

about competition, part III

Wednesday, January 26th, 2011

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around teufelsee

Tuesday, October 19th, 2010

On the occasion of the current convention on biodiversity some images from a green part of Berlin, called Teufelsee (the “satanic lake”) in the district of Köpenick.

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phytoplankton decline

Thursday, July 29th, 2010

koi1-IMG_9885-450

In todays nature magazine there was an article about the “Global phytoplankton decline over the past century”. I have no access to the article however in an article by Markus Becker – a reporter from the german news magazine Spiegel Online – it was reported that since 1950 on average the mass of phytoplankton declined globally by 40%. Since phytoplankton are amongst others a major food source for food webs this affects e.g. the abundance of fish. Moreover phytoplankton are responsible for much of the oxygen present in the earth’s atmosphere. A main reason for the decline of phytoplankton is climate change.

-> related article on randform about oceans and climate change
->related article on randform on microorganisms and oxygen supply
-> see also here
update 30.7.10: You might also want to kick into the subject by reading
about the decline in fish occurence:
->Elizabeth Kolbert on overfishing on Azimuth
-> randform post about fish consumption and nutrition

some koi after the click
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