Archive for the 'bio' Category

p-values and Glyphosate animal tests

Thursday, May 19th, 2016

Dead marten in our garden. Cause of death unknown. The head was unexplainably jammed by twigs (see image). The animal was already stiff when I found it. Could have been there at most for a day.

Here a comment about a specific problem in statistics which is often ignored by (mostly) non-mathematicians.

I originally intended to leave the comment in a mathematicians forum where this problem is discussed. As an example I looked at the glyphosate Renewal Assessment Report from 2013 where I think this ignorance leads to very problematic conclusions. Warning: some details about the animal test results are rather explicit.


About maldeformation in Fallujah

Saturday, April 30th, 2016

image from Wikipedia by Vincent de Groot.

In the context of the last post about the WHO and the assessment of health problems due to radioactivity I wonder about one citation in the BBC report Falluja doctors report rise in birth defects. The BBC report was linked to from the Guardians WHO critique which I had mentioned in the last post.

According to the BBC report the citation was by “British-based Iraqi researcher Malik Hamdan:”

Ms Hamdan said that based on data from January this year, the rate of congenital heart defects was 95 per 1,000 births – 13 times the rate found in Europe.

Malik is a male name, so I guess this is a misprint and who is probably meant is Malak Hamdan.

Why did I wonder about that citation?


Volt ohne Raum

Wednesday, October 21st, 2015

Organic lettuce in Brandenburg


global warming didn’t stop

Saturday, July 11th, 2015

Image from NOAA (public domain if I understood correctly)

Those who follow the randform posts closely know that Tim and me had worked on a visualization of a main collection of global temperature stations. It was used in a post on Azimuth – a blog which is mostly concerned with environmental topics and which is run by the mathematical physicist John Baez. In the post I reviewed the temperature data, which was used by the IPCC for their sofar published climate Assessment Reports up to AR4 in 2007. I left the conclusions about the investigated temperature records and their quality to the reader, but in the comment section I became a bit more “direct” and wrote:

Well every reader may judge him/herself by looking at the visualizations. If you want my opinion: I think this is rather catastrophic. In particular I wouldn’t wonder if the “global warming hiatus” is connected to the gaps.

The “global warming hiatus” or “global warming pause” is a finding that the global temperature rise has approximately paused since 1998 and hence by making this comment I questioned this “warming pause” or at least its shape. Unfortunately my suspicion has now been more or less confirmed. That is there global warming continues.

The article “Possible artifacts of data biases in the recent global surface warming hiatus” by Karl et al. Science 2015 0 (2015)” in the journal “Science” has unfortunately to be rented for the prize of 20$/day for reading (so I haven’t looked at it), but NOAA has a summary, where it is written:

“Adding in the last two years of global surface temperature data and other improvements in the quality of the observed record provide evidence that contradict the notion of a hiatus in recent global warming trends,” said Thomas R. Karl, L.H.D., Director, NOAA’s National Centers for Environmental Information. “Our new analysis suggests that the apparent hiatus may have been largely the result of limitations in past datasets, and that the rate of warming over the first 15 years of this century has, in fact, been as fast or faster than that seen over the last half of the 20th century.”

About the newly included datasets it is written:

New analyses with these data demonstrate that incomplete spatial coverage also led to underestimates of the true global temperature change previously reported in the 2013 IPCC report. The integration of dozens of data sets has improved spatial coverage over many areas, including the Arctic, where temperatures have been rapidly increasing in recent decades. For example, the release of the International Surface Temperature Initiative databank, integrated with NOAA’s Global Historical Climatology Network-Daily dataset and forty additional historical data sources, has more than doubled the number of weather stations available for analysis.

I mentioned the International Surface Temperature Initiative (ISTI) in the Azimuth blogpost together with a citation from their blog:

The ISTI dataset is not quality controlled, so, after re-reading section 3.3 of Lawrimore et al 2011, I implemented an extremely simple quality control scheme, MADQC.

which doesn’t sound too great, if it comes to quality assessment.

But still: I suspect that the new temperature curves of that article match the real temperatures to a much better degree than the ones which were used for the IPCC reports until 2013.
It is though unfortunate that these new temperatures are not available, because I still have that suspicion that the role of methane in that warming trend is greatly underestimated and I still think it IS ULTIMATELY URGENT to investigate that suspicion. The exact shape of the curve would be rather important, because amongst others there was also a “hiatus” in the rise of methane and I think you can see that short pause in the above image.

Methane may however play eventually also a role in a way more dramatic environmental context. In my point of view that context should also be investigated URGENTLY, but it seems the view of methane is viewed controversely among climate scientists, at least Gavin Schmidt of the NASA’s Goddard Institute for Space Studies blurrily expressed anti-alarmistic words in an interview with John H. Richardson from Esquire (Esquire link via John Baez) by saying that:

“The methane thing is actually something I work on a lot, and most of the headlines are crap. There’s no actual evidence that anything dramatically different is going on in the Arctic, other than the fact that it’s melting pretty much everywhere.”

meat mast

Thursday, April 23rd, 2015

butchery goods

I had recently mentioned some practices in killing animals for meat production via socalled CO2 anesthesia. In this context it should be mentioned that there seem to exist also certain killing practices where the animal is not killed for consumption or disease prevention but in order to ensure something which some might interpret as “meat quality”.

There was recently an article in the german magazine Spiegel Online about a company here in Brandenburg which was in charge for duck mast. Activists had secretly filmed their practices. The breast of the specially fed ducks became so heavy that they partially couldn’t get back on their feet by themselves (warning: video behind the link). Moreover ducks which were not able to run fast and long enough (or which couldn’t get back on their feet by themselves) were slain with a pitchfork (warning: video behind the link). As the article says these marathon-slew practices seem to be illegal in Germany, but of course as one can see they seem to be not so easy to control, moreover there are countries where those practices seem to be legal.

As a matter of fact there seem to exist also cultural differences in mast practices. Like when I was working in Japan I met a woman from Bangladesh (a country which, as the reader probably knows, struggles with malnutrition and population growth), which did her Ph.D. on how to adjust nutrition for chickens in order to boost the size of chicken thighs, as apparently especially the thighs are very popular in Bangladesh. I didn’t ask her though about the use of tannery-scrap poultry feed because I didn’t know about this practice back then.

Lobetal – In food chains

Thursday, July 3rd, 2014



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.


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.

addition 24072014:

There is a new article in nature concerned with some of the above questions, in which Serial time-resolved crystallography of photosystem II using a femtosecond X-ray laser is used to investigate the catalytic processes in photosystems. I can’t read the article, but only the abstract and look the images, but that is already quite interesting. In particular concerning the above comment about the correlations one sees in image c how the spatial configuration of the molecules in the electron transfer chain looks like. After the photosystem II primary donor P680 one sees achlorophyll Chl_A and then a pheophytin Pheo_A. In the Wikipedia description of P680 it is written:

The primary donor receives excitation energy either by absorbing a photon of suitable frequency (colour) or by excitation energy transfer from other chlorophylls within photosystem II. During excitation, an electron is excited to a higher energy level. This electron is subsequently captured by the primary electron acceptor, a pheophytin molecule located within photosystem II near P680.

This sounds as if Chl_A is rather in charge of the excitation energy transfer to P680 than as part of the electron transfer from P680 to Pheo_A, which seems different from what the little orange arrows in image c indicates. So a question which arises here is wether one can here observe a long coherence between exiton states of Chl_A and Pheo_A (as it seems it exists for the case of BChl-b and BPh) and wether this involves P680 or not. It seems as if the grid like bubbles in the images g,h,i are eventually charge carrier configurations (? that is those seem to be electron density bubbles upon making a survey on the results of googleing what is an omit map). However I can’t even identify Pheo_A in those images.

addition 19092014:
The question about how the concrete energy transport pathway looks like concretely was raised also on the Azimuth forum

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

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 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.