Postscripts

thehindu.com/sci-tech/science reported it first that marriage proposals have been placed in the acknowledgments

One such proposal published in a 2015 paper in Current Biology reads: “C.M.B. would specifically like to highlight the ongoing and unwavering support of Lorna O’Brien. Lorna, will you marry me?”

Another postscript in Global Change Biology is more worrying

Jos Barlow, a conservation scientist from Lancaster University in the U.K. and the Federal University of Lavras in Brazil, who led the team, wrote in the acknowledgement: “Some contributors declined authorship to maintain anonymity. We regret this was necessary and thank them for their important contribution.”

Climate refugees

People may be fleeing catastrophic events in their home countries. When preparing now a lecture on medical consequences of the climate crisis ( based on the 2019 Lancet  Report ) I found an intriguing piece at the UNHCR website.

According to the Internal Displacement Monitoring Centre, there were 18.8 million new disaster-related internal displacements already in 2017. Displacement across borders also occurs, and may be interrelated with situations of conflict or violence. From the legal side, however, there are no “climate refugees”, as a refugee is defined as a person who has crossed an international border

owing to well-founded fear of being persecuted for reasons of race, religion, nationality, membership of a particular social group or political opinion

The full document is at https://www.refworld.org/pdfid/5906e0824.pdf. The definition of a refugee certainly requires an immediate update including also climate related events.

Does smoking kill by accumulation of mutations or by repeated exposure until the final crack?

We have a new paper at Sci Rep “High degree of polyclonality hinders somatic mutation calling in lung brush samples of COPD cases and controls”. It took a long time from my initial grant application at Sander Stiftung in Dec 2009 (where it was rejected), to the field work within the scope of the EvA study (where the PI Loems Ziegler-Heitbrock retired). Followed by some first analysis together with Francesc at CNAG in Barcelona the final publication now appeared – my gratulations to Gian-Andri and Ivo Gut for their hard work!

Chronic obstructive pulmonary disease (COPD) is induced by cigarette smoking and characterized by inflammation of airway tissue. Since smokers with COPD have a higher risk of developing lung cancer than those without, we hypothesized that they carry more mutations in affected tissue.
We called somatic mutations in airway brush samples from medium-coverage whole genome sequencing data from healthy never and ex-smokers (n=8), as well as from ex-smokers with variable degrees of COPD (n=4). Owing to the limited concordance of resulting calls between the applied tools we built a consensus, a strategy that was validated with high accuracy for cancer data.
However, consensus calls showed little promise of representing true positives due to low mappability of corresponding sequence reads and high overlap with positions harbouring known genetic polymorphisms. A targeted re-sequencing approach suggested that only few mutations would survive stringent verification testing and that our data did not allow the inference of any difference in the mutational load of bronchial brush samples between former smoking COPD cases and controls.

So we would have probably needed a higher genome coverage on our brush sample mix. Or should we have sequenced more single cells as discussed in the paper? At least, we now know, that sequencing at rather low coverage rate is not a screening tool for upcoming tumours.  Maybe in this (pre-cancer) COPD epithelium there are less pre-malignant lesions than expected? In any case, in spite of higher susceptibility to lung cancer in COPD patients, sequencing to an intermediate read depth did not provide the resolution to detect somatic mutations in COPD airway brush samples. When looking at some other papers (Cancer Genome Atlas, esophagus, and more recently colon samples, I can only confirm what Iñigo Martincorena wrote

this study emphasizes how little we know about somatic evolution within normal tissues, a fundamental process that is likely to take place to varying degrees in every tissue of every species.

Somatic mutations accumulate with age, no doubt. There may be even more mutations in the aging esophagus than in sun-exposed human skin. Lee-Six estimates 43.6 mutations /year,

Martincorena 2018 https://science.sciencemag.org/content/362/6417/911

while I still have a gut feeling that there is no gradually accumulation of mutations (until the second hit) but a clonal expansion of a single bronchial cell, hit by a single smoke stream. With this hypothesis, smoking would not kill by accumulation of deleterious mutations, but by the never ending rexposure until the ultimate deleterious mutation occurs.

In human colorectal carcinoma, the total number of substitutions is about 15,000 (1,500 indels) which is about 5-fold than the approximately 3,000 substitutions (300 indels) that are found in normal crypts from 50–60-year-old individuals.

Many more of these timeline studies will be necessary to explain why the lung cancer risk drops immediately after you stop smoking.

Correlation of earth temperature and global mean CO2

For teaching purposes I need the CO2 concentration vs earth temperature by year. For that purpose we can use the Hadcrut 4 dataset created earlier while the global mean CO2 mix ratios (ppm) can be found at https://data.giss.nasa.gov/modelforce/ghgases/Fig1A.ext.txt.
After unscrambling that file and merging it to Hadcrut4 we can plot it

library(patchwork)
p1 <- ggplot(temp, aes(x=year, y=annual)) + geom_point() + stat_smooth(method="loess", span = .6) +
  scale_y_continuous( name="difference from baseline  [ oC ]", limits=c(-1,1) )

p2 <- ggplot(temp, aes(x=year, y=ppm )) +  geom_point() + stat_smooth(method="loess", span = .6) +
  scale_y_continuous( name=expression('ppm CO'[2]) )
p1+p2

Here are the two time courses

Time course of earth temperature (1850-2018) and CO2 (1850-2011)

while the correlation is higher than I expected

Correlation of earth temperature and CO2

 

References

  • 1850-1957: D.M. Etheridge, L.P. Steele, R.L. Langenfelds, R.J. Francey, J.-M. Barnola and V.I. Morgan, 1996, J. Geophys. Res., 101, 4115-4128,”Natural and anthroupogenic changes in atmospheric CO2 over the last 1000 years from air in Antarctic ice and firn”.
  • 1958-1974: Means of Scripps Institution of Oceanography Continuous Data at Mauna Loa and South Pole provided by KenMaarie (personal communication)
  • 1975-1982: Means of NOAA/CMDL in-situ data at Mauna Loa and South Pole. (P. Tans and K.W. Thoning, ftp://ftp.cmdl.noaa.gov/ccg/co2/in-situ)
  • 1983-2003: Global means constructed using about 70 CMDL CCGG Sampling Network station data. (P.P. Tans and T.J. Conway, ftp://ftp.cmdl.noaa.gov/ccg/co2/flask)
  • 2004-2007: Global mean growth rates. (T. Conway, ftp://ftp.cmdl.noaa.gov/ccg/co2/trends)

Zur Geschichte der Klimaforschung

Es ist nicht einfach, hier einen Überblick zu bekommen.

Jedenfalls sollte man von Qualität der Wettervorhersagen (die für die nächsten 24 Stunden von 75% auf über 90% in den letzten 20 Jahren gestiegen ist), nicht auf die Qualität der Klimavorhersagen schliessen.

Die Geschichte der Klimaforschung kann jedenfalls in drei Beiträgen lückenlos nachgelesen werden:

Wenn der Wind weht

Wenn der Wind weht” mit diesem Film (und seiner Titelmelodie von David Bowie) sind wir Mitte der 80er Jahre sozialisiert worden. Der drohenden Atomkrieg, das wardie reale und unmittelbare Gefahr dass eine der Pershing II in die Luft geflogen wäre.

Roland Emmerichs Katastrophenfilm The Day after Tomorrow 2004 konnte das nur schwer toppen. Experten sind aber der Meinung, dass die Spiefilme einen falschen Eindruck der Kimakrise vermittelt haben: zu sehr Katastrophen-orientiert, bekommt man allenfalls das Gefühl der Ohnmacht. Auch kommt neben der erfundenen Darstellung einer allumfassenden Katastrophe in dem Spielfilm die reale Erderwärmung vergleichsweise harmlos daher.

Oder doch nicht, wenn man sich “chasing ice” auf Youtube ansieht?

Urs Bruderer hat diese Frage in einem wunderbaren Essay über “Die große Überforderung” thematisiert

Ich habe die Klimakatastrophe viele Jahre kaum beachtet. Und hielt das für die klügste Entscheidung.
Seit Menschen denken können, warnen sie vor ihrem Ende.

Ob der Atomkrieg, das Waldsterben oder das Auslaufen des Maya-Kalenders im Dezember 2012, ob im Cern produzierte schwarze Löcher, Milleniumsbug oder Vogelgrippe – im Rückblick bewies jedes Weltuntergangsszenario nur, dass wir eine Lust an der Angst vor dem Ende haben.

Der Weltklimarat hat inzwischen unzählige Berichte und Sonderberichte veröentlicht. Die Warnungen wurden immer genauer und bedrohlicher. Und ich wurde immer besser darin, sie zu überhören.

Einen Artikel, den man vollständig gelesen haben muss.

Johan Rockström talking about tipping points

Last week I had the opportunity to attend a lecture by Johann Rockström explaining his most recent Nature commentary about tipping points “too risky to  bet against”.

The Intergovernmental Panel on Climate Change (IPCC) introduced the idea of tipping points two decades ago. At that time, these ‘large-scale discontinuities’ in the climate system were considered likely only if global warming exceeded 5 °C above pre-industrial levels. Information summarized in the two most recent IPCC Special Reports (published in 2018 and in September this year) suggests that tipping points could be exceeded even between 1 and 2 °C of warming.

Prof. Dr. Johan Rockström Nov 28, 2019 @ 1. Helmholtz Sustainability Summit Max-Dellbrück Zentrum in Berlin explaining his recent Nature paper. The full stream is at https://www.youtube.com/watch?v=Ppj04TGaX-Y&feature=emb_logo

This is a cruel message in particular as probably already one tipping point has been passed @ the Amundsen Sea embayment of West Antarctica. There is a thick ice sheet of about 3 km which forms one of the three major ice-drainage basins of the West Antarctic Ice Sheet. And it is melting rapidly – with the tipping point having been passed in 1996. And the Amazon is burning right now — the world’s largest rainforest. Estimates of the Amazon tipping point ranges between 20% and 40% deforestation.

Panel discussion 1st Helmholtz Sustainability Summit Max-Delbrück Zentrum Berlin. From left to right Prof. Dr. Thomas Hirth, Prof. Dr. Martin Visbeck, Prof. Dr. Otmar Wiestler, Prof. Dr. Heike Graßmann, Prof. Dr. Michael Backes, Heike Leitschuh. More talk than action.

Is the Loomis Hypothesis wrong?

I remember an old vitamin D book – I believe it was Feldman’s Vitamin D – that going down the Transsahara Route (Algier-Lagos) human skin color gets always darker towards Tamanrasset due to increased solar power (also known as Loomis Hypothese).

Let’s look at three maps now.

1. Solar power. Source: https://upload.wikimedia.org/wikipedia/commons/1/1e/Global_Map_of_Global_Horizontal_Radiation.png

The above map does not match the skin tones.

2. Skin tone. Source https://science.sciencemag.org/content/358/6365/867.full For full details see the original paper

Neither does a new vitamin D map published last week in the Lancet

3. Vitamin D map. Source: https://linkinghub.elsevier.com/retrieve/pii/S2214109X19304577 For full details see the original paper

Although the maps are still patchy, I think the Loomis hypothesis is wrong.

Wann sind Tiere am erfinderischten?

Die SZ weiss die Antwort

Womöglich gedeihen Innovationen manchmal ganz im Gegenteil besonders gut, wenn ein Tier genug hat: ausreichend Zeit und Energie, um etwa mit dem Schloss einer Futterkiste herumzuspielen. Neues ausprobieren kann vor allem, wer sich nicht rund um die Uhr mit Futtersuche, Wacheschieben und Revierverteidigung aufreiben muss, sondern derartige Verpflichtungen auch mal an Artgenossen delegieren kann.

Vermutlich ist es bei den Menschen auch nicht viel anders. Wenn man sich nicht rund um die Uhr mit Futtersuche, Wacheschieben und Revierverteidigung aufreiben muss.

Vitamin D3 in breast milk

1 µg/L D=> 40 IU/L D3 => 2,5 nmol/L D3

The detection limit in breast milk is 0,2 nmol/L = 0,08/µg/L = 3,2 IU/L according to vid Streym who measured a median of 0.34 nmol/L  25-OH-D3 in breast milk (approx 5,4 IU/L.

Li-Chieh Wang gives no detection limit but measures now approx 5 ng/mL = 5.000 ng/L = 5 µg/L = 12,5 nmol/L D3 in breast milk equivalent to 200 IU/L, the 40fold amount to vid Streym.

What is correct?

How to include a PDF in reveal.js

Right now there is a lot of information out there how to export a reveal presentation as PDF but much less not how to include a PDF document. The most natural way would be some embed

<section><object data="test.pdf" style="width:100%"><a href="test.pdf">PDF laden</a></object><section>

looks strange, not full frame, no handlers

<section data-background-iframe="test.pdf" data-background-interactive></section>

works but cannot jump to a certain page and cannot style the background.

So I am using now additionally the Chrome plugin that is based on pdf.js.

Tour de France average speed

Using the new TdT R package, I have re done the speed plot

library(remotes)
install_github("alastairrushworth/tdf")
library(tdf)
editions %>%
  ggplot(aes(x = start_date, y = distance / time_overall, color = edition)) +
  geom_point(na.rm = TRUE,size=4) + 
  geom_label_repel(data = editions, aes(label = winner_name), size = 4, na.rm = TRUE, segment.alpha = 1, point.padding=1) + 
  xlab('year') + 
  ylab('average speed km/h') +
  ylim(23,45)
click to increase Tour de France average speed by year