Archive for the 'bio' Category


Tuesday, May 29th, 2018

The frequent randform reader knows that a lot of randform posts are concerned with questions about how to keep earth as a habitat for humans. One of the biggest problems seems to be: population growth. That is humans are the root cause of “pollution”, they are to a great extend causing climate change, they massively reduced the habitat for other beings including those in their own food chain and if their own strive for efficiency keeps on like that, then they (partially?) need to abolish themselves and eventually (?) start the AI machine population explosion-if they haven’t wiped themselves out beforehand in their wars for ressources.

But what really are the reasons for this human population growth?

This seems to be a very deep systemic question, but for me it is rather suggestive that this strive or “competition for efficiency” is playing a major role here. So today I would like to discuss this quest for efficiency again a bit at the example of agriculture.


Mars on earth, part 2 and again on the loss of O2

Sunday, August 27th, 2017

A reoccurring question on randform is: how stable is the current ecosystem on earth? And in particular how stable is it as a not too hostile environment for humans?

A possibility to find out is to isolate living systems.
Some of these experiments of such (more or less) closed artificial ecosystems were mentioned in the 2006 randform post Mars on earth.

And at least one of these long-term experiments more or less partially failed (namely the First mission of Biosphere 2) because, as the Pittsburgh Post-Gazette wrote: Biosphere 2 members “aired out”:

With an admitted leakage rate of just under 10 percent of its atmossphere yearly, oxygen levels inside dropped gradually over the project’s first 15 months, eventually reaching the levels normally found atop a 13,400-foot mountain. Because the oxygen loss was gradual, the crew members were able to continue functioning but their physical activities were eventually reduced to about 70 prcent of normal because of oxygen deprivation before project staffers outside injected more air.

As far as I know the major reasons, why the oxygen levels dropped were never fully established.
The reasons given in the Pittsburgh are differing from what I thought and wrote about the major reasons in the Mars on earth blog post:

the air supply had to be reenforced due to a miscalculation of the air consumption of bacteria in the soil of the greenhouse

where in retrospective I am unfortunately not sure, whether this reason about the decline of oxygen was given in the TV documentation which I had seen about Biosphere 2 or whether this was just my own interpretation of what had most probably happened.

So the question about the stability of the earth ecosystem is last but not least a question of O2 or not O2. And the balance of very tiny organisms may play a very major role in that question.

So amongst others in the post How much O2 will be left? I suggested that

“melting of permafrost could not only lead to more CO2 in the air but also induce a reagression of O2 (which may e.g. be due to a sudden expansion of aerobic organisms)*”

There are also other randform posts which intrinsically look at the O2 (and also CO2) balance. In particular some posts are dedicated to the oceans via studying phytoplankta.
Like the 2009 post about “The tragedies of marine towns” or the 2010 post about phytoplankton decline. Amongst others the posts illustrate again how complicated it is to infer any future developments, and that is even not easy to monitor the developments of microorganisms. Whatsoever -it seems that rather big changes may be underway, which may point to an out-of-balance situation. But as said this is an ongoing discussion and e.g. the phytoplankton post needs to be updated with the finding that it seems (following an article in the new scientist ) that

The rate at which phytoplankton are disappearing as oceans warm has been vastly overestimated by a glitch in models.

And in particular that

Increased CO2 concentrations often have competing positive and negative effects on phytoplankton, with winners and losers among different species.

Where especially the abundance of diatoms seems to be controversial.
That is the NASA study from 2015 Sept. 23 in Global Biogeochemical Cycles sees a clear decline at least in northern regions, while Nature (pay wall) finds:

Climate change enhances diatom growth mainly owing to warming and iron enrichment, and both properties decrease cellular nutrient quotas, partially offsetting any effects of decreased nutrient supply by 2100.

There are some possibilities to get a better overview over the stability of ecosystems from an more abstract viewpoint (see e.g. this article on Quanta) but still.

And because the balance of the microorganisms is so complicated (and in fact heavily influenced by human activity even in a rather direct way (see e.g. algae fuel)) and since models are only models it is important to conduct concrete experiments with closed ecosystems and at least to monitor direct physical quantities like oxygen levels.

So in fact by looking at visualizations of oxygen concentration in various years at NOAA it had been written in another randform post of 2014 that oxygen saturation in the ocean especially in the north seemed to have declined and eventually likewise the oxygen concentration in the air.

Do we know more now?

Unfortunately it seems things got rather worse. That is despite the fact that meanwhile there had been flamboyant announcements by various people to establish even settlements on Moon and Mars, it seems research on closed environments is rather in decline (a brief update here). That is it seems BIOS 3 closed now for real (thats how it sounded following an article in novosti kosmonavtiki) and the last experiments in the direction of a closed system seem to have been the Yuegong-1 mission in May 2014, but maybe I oversaw something.

Worse however seems to me the fact that NOAA seems to have ceased to produce visualizations of the oxygen concentrations.
Is that true?

At least there seem still to be people who look at things. That is in a recent article my observation in this randform post about the decline in oxygen levels was confirmed. (via CNN)
The confirming article is behind a paywall but if you click on the link in the CNN article it is momentarily visible and it’s written:

We find that the global oceanic oxygen content of
227.4 ± 1.1 petamoles (10^15 mol) has decreased by more than two per cent (4.8 ± 2.1 petamoles) since 1960, with large variations in oxygen loss in different ocean basins and at different depths.


Five distinct regions with significant oxygen loss stand out that cannot be attributed to solubility changes. These are (1) tropical regions of all basins, which contain most of the upper ocean OMZ, (2) the North Pacific, (3) the South Atlantic, (4) the Southern Ocean and (5) the Arctic Ocean (Table 1, Fig. 1b, Extended Data Fig. 4).

The authors likewise see microorganisms as a potential major cause for the decrease:

This suggests that either multi-decadal variations or changes in ocean circulation induced ventilation, potentially
enhanced by increased upper ocean biological activity, are responsible
for the observed changes in oxygen below 1,000 m.

However as far as I understood their data went only until 2010 and my alarming observation was from the change between 2009 and 2013.

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

addition 04102017:
I detected an article which explains:
Why Quantum Coherence Is Not Important in the Fenna–Matthews–Olsen Complex

The authors, who apparently use certain Hierarchical equations of motion techniques claim:

Our exact results are then compared to calculations using the incoherent Förster theory, and it is found that the time scale of energy transfer is roughly the same, regardless of whether or not coherence is considered. This means that coherence is not likely to improve the efficiency of the transfer. In fact, the incoherent theory often tends to overpredict the rates of energy transfer, suggesting that, in some cases, quantum coherence may actually slow the photosynthetic process.

Remark: There exists now a Förster resonance energy transfer on Wikipedia, but I don’t know in how far this is related to (incoherent) “Förster theory”.