Allergy

FaRMI

I will add now a special collection of farming studies here as many of them are just candidates for the Ig nobel prize.

The most recent study introduces FaRMI, a “bacterial relative abundance farm home microbiota index”, probably introduced as the authors couldn’t find anything else. It reminds me very much to the polygenic risk score that rescues your study if you could not find the gene.

Asthma prevalence has increased in epidemic proportions with urbanization

Already the first sentence is wrong if we look at the following plot where asthma is clearly levelling off.

Urbanization happened in the late späten 19th century and not after 1950. Source of plot: The prevalence of asthma in children: a reversing trend ( ERJ 2005 )

 

Unfortunately, the difference between farm and non farm children is never explained in the Kirjavainen et al. paper. What is the average distance of a non farm house to a farm house? Are there any joint school or sports activities of children from farms and non farms (allergens travel in the classroom)? And why is there such a strong conclusion in the title?

Farm-like indoor microbiota in non-farm homes protects children from asthma development

A lower risk score is not equivalent to protection.

And did any reviewer ever look at the plots or tables?

I do not understand Figure 3c. It even makes only sense when I cross out the top labels. But even then it menas: GABRIELA does not show a significant replication.

 

What should these values tell us? 5 times p<0.05 in a grid of 6×11=66 tests? Quantile regression that has been “adjusted” by the data?

 

The FaRMI calculation is overly complicated. Probably the calculation can never be replicated by changing software, changing samples, unclear wording, suboptimal dimension reduction and data snooping.

Farm home microbiota-like community composition was modeled in LUKAS1 with logistic regression analysis (PROC LOGISTIC statement, SAS version 9.3). The home location on a farm or non-farm rural environment was the dependent variable and the main components of PCoA axis scores of β-diversity matrices were the predictor variables. Bacterial and fungal microbiota were investigated separately. For both bacteria and fungi, separate models were built using axis scores from PCoA of abundance-unweighted and -weighted β-diversity matrices. The PCoA axes were selected based on the scree plot method including axes above the point at which the variance explained by the additional axes levels off (Supplementary Fig. 3). The models give an estimate of the probability that the sample is from a farm home. The farm home likeness of the microbial composition in the LUKAS2 non-farm homes was then estimated by applying the regression coefficients obtained from the LUKAS1-based models to the corresponding microbial data from LUKAS2 samples.Some analyses were performed in non-farm homes of both LUKAS2 and LUKAS1 to obtain increased sample size and power if results remain comparable as was observed. Due to the discovered association with asthma, the probability that was modeled based on the relative abundance-weighted bacterial/archaeal β-diversity was named FaRMI and was studied further in greater detail.

And isn’t that  just an association that may have a rather simple explanation?

As FaRMI is weakly associated with muramic acid concentration in dust, the authors make Gram-positive bacteria responsible for the effect. The rhizosphere of soil is extremly rich of bacteria. The world’s first soil atlas showed  hundreds of taxa but never differentiated between water resistant, gram positive and less water resistant gram-negative taxa. Maybe Gram positive Streptococcaceae are ubiquitous and depend on where you draw your samples?

FaRMI is found in non farm / rural children by bacterial/archaeal operational taxonomic units (OTUs) of soil origin which basically confirms my initial assumption: There was the same contamination of soil both in farm and non-farm homes if we look at supplement table 6 where walking indoors with outdoor shoes results in significant higher FaRMI values…Maybe the microbiome hype is already over.

Our results warrant translational studies to confirm the causal relationship through indoor microbial exposure-modifying intervention that may also form a novel strategy for primary asthma prevention.

Good luck with your future studies.

 

BTW – The scripts at Github are useless references to shell and Python scripts that will never run due to “—” characters. And what about that baby code?

outfolder=getwd()
eigenfile <- paste(outfolder, "/", prefix, "_PCoA_eigenvalues.txt", sep="")
writerow <- paste("Eigenvalue min / max: ", min.eigen, " / ", max.eigen, sep="")
write(writerow, file=eigenfile, append=F)
writerow <- paste("Sum of all eigenvalues: ", round(neg.eigensum, digits=6), sep="")
write(writerow, file=eigenfile, append=T)
writerow <- paste("Sum of all eigenvalues (negatives as 0): ", round(nonneg.eigensum, digits=6), sep="")
write(writerow, file=eigenfile, append=T)
writerow <- "Eigenvalues (pos & neg): "
write(writerow, file=eigenfile, append=T)
writerow <- paste(pcoa$value$Eigenvalues, collapse="\t")
write(writerow, file=eigenfile, append=T)
writerow <- "Percents (Negatives as negatives): "
write(writerow, file=eigenfile, append=T)
writerow <- paste(paste(neg.percent, " %", sep=""), collapse="\t")
write(writerow, file=eigenfile, append=T)
writerow <- "Percents (Negatives as 0): "
write(writerow, file=eigenfile, append=T)
writerow <- paste(paste(nonneg.percent, " %", sep=""), collapse="\t")
write(writerow, file=eigenfile, append=T)

Using R heredoc syntax I can rewrite 20 unreadable by 8 readable lines.

tmp <- 'Eigenvalue min / max: min.eigen / max.eigen
Sum of all eigenvalues: neg.eigensum
Sum of all eigenvalues (negatives as 0): nonneg.eigensum
Eigenvalues (pos & neg): pcoa
Percents (Negatives as negatives):  neg.percent %
Percents (Negatives as 0): nonneg.percent %'
for (i in c("min.eigen","max.eigen","neg.eigensum","nonneg.eigensum","pcoa$value$Eigenvalues","neg.percent","nonneg.percent") ) { tmp <- gsub(i,get(i),tmp) }
write(tmp, file=paste(getwd(),out,"/")

 

And why moving to SAS for a simple logistic regression? Is there anyone else in the academic world who pays $8,700 annually for a basic SAS Windows Analytics package just for that reason?

 

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Philosophy

Den Fuss vom Gas

Ein lesenswertes Interview in der ZEIT mit Frank Trentmann “Die Herrschaft der Dinge“. Können wir mit Optimierungen im Alltag zu einem guten Leben gelangen?  Der Historiker Frank Trentmann sagt: Wir sollten endlich aufhören, unserem Ich hinterherzujagen.

Die Pensionäre, Manager, Millionäre hingegen hatten Muße. Zeit zu haben war Teil des gehobenen sozialen Status. Wer einen hohen sozialen Status hatte, gab damit an, dass er im Sommer für acht Wochen in seine Villa nach Baden-Baden oder an die Côte d’Azur fuhr. Heute ist es genau andersherum: Einen hohen Status haben jene Menschen, die ständig unterwegs und beschäftigt sind.

Und die Optimierung des Alltags in der Wissenschaft? Früher war es das Privileg von Wissenschaft, Zeit zu haben, zu lesen, nachzudenken, Schlüsse zu ziehen, Ideen zu skizzieren. Heute gibt es das nicht mehr, nur noch Emails, Benchmarks, Impact, Fly-in und Fly-out, Meetings, Skype, Hype und PR q.e.d.

 

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Software

Multisite WordPress user management is a pain

I installed the “Network Subsite User Registration” plugin which gives an extra menu point at each dashboard under Users>Registration>allowed  There is, however, a glitch as wp-activate.php redirects to the main site in “signup-welcome” and “lead-in” sections that need to be commented out.

After all, I changed to “Profile Builder“, but it had its own problems, missing functions, large overhead, $$$ for extras and strange formatting instead of using the theme definitions.

Finally, I ended up with https://userswp.io , a lightweight user profile plugin that features front end user directory, a registration and a login form. The only modification here is another line in my child theme to suppress the WordPress admin bar.

#wpadminbar { display:none !important;}

 

CC-BY-NC Science Surf accessed 20.01.2026
Genetics, Philosophy

Against DNA patenting

I remember a long struggle against gene DNA patenting in the 1990ies around the Venter case while Science magazine has now an update.

Patents balance providing incentives to take the financial risks necessary to convert an invention into useful products with the benefits of sharing information to drive other useful inventions. Since the advent of DNA sequencing and gene identification methods, patenting human genes has been controversial. A notable example involves patents for the genes BRCA1 and BRCA2, variations in which modulate risks for breast and ovarian cancer. These patents supported increased costs and hence, limited accessibility, for diagnostic tests for cancer patients and their families. In 2013, the U.S. Supreme Court ruled that these patents were invalid (Association for Molecular Pathology v. Myriad Genetics).

I still think that there is way to much money spent on rather trivial discoveries of natural products where purification doesn’t justify a patent. So maybe only now the existing law is being revised.

 

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Noteworthy

Die Zerstörung des Autos (6000 Tote XXIX)

Faktensammlung auf sz.de, Auszug “Ihr seid eine Plage” leider hinter Paywall, aber die Originalstudie (Link unten) ist frei verfügbar

Ein Berliner Projekt von Studierenden der Best-Sabel-Hochschule errechnete 2014, dass den Autos 19-mal so viel Fläche im öffentlichen Straßenraum zur Verfügung steht wie den Fahrrädern. 58 Prozent zu drei Prozent. Diese Autos, die in Werbespots ja immer so dynamisch durch malerisch endlose Fjordlandschaften düsen, stehen in Wahrheit mehr als 23 Stunden am Tag Stoßstange an Stoßstange im Stadtraum herum. In Berlin gibt es zehnmal so viel Fläche für Parkmöglichkeiten wie für Spielplätze. Laut dem dortigen “Flächen- Gerechtigkeitsreport” sind 19 Prozent der öffentlichen Verkehrsfläche parkenden Autos vorbehalten – ein Fünftel der Stadt ist Parkplatz.
Nun kostet ein Quadratmeter Bauland in Berlin im Schnitt 600 Euro. Ein Bewohnerparkausweis kostet aber nur 20,40 Euro. Für zwei Jahre. … Wer darauf hinweist, dass diese Parkgebühren doch absurd niedrig sind (in Amsterdam zahlt man 535 Euro für einen Jahresausweis in der Innenstadt, in Stockholm 827 Euro), der wird meist mit dem sozialen Argument ausgekontert: Parken müsse sich jeder leisten können. Komischerweise scheint dieses Argument aber nicht so wichtig zu sein, wenn es um Preiserhöhungen im ÖPNV geht: Seit 2004 verlangt die Stadt München die immer gleichen Parkgebühren pro Stunde (abgesehen von einigen Lizenzgebieten mit besonders hohem Parkdruck, in denen 2018 der Preis erhöht wurde). Im selben Zeitraum sind die Kosten für Einzeltickets und Monatskarten des ÖPNV um 40 beziehungsweise 60 Prozent gestiegen. Ähnlich ist es mit Regelverstößen: In den Niederlanden kostet Falschparken zwischen 50 und 140 Euro, in der Schweiz rund 100 Euro, bei uns kommen Falschparker oft mit 10 bis 20 Euro davon. Schwarzfahren kostet meist das Sechsfache.

Alle Zahlen in diesem Absatz stammen aus Untersuchungen der Berliner Mobilitätsforscherin Uta Bauer vom Deutschen Institut für Urbanistik.

Das Original bei Uta Bauer in “Parkraummanagement lohnt sich“.

 

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Philosophy

Scientific misconduct deserves more attention and better research committees

Misconduct is ever increasing with the increasing science industry. The spectrum of misconduct is large – as I explained some years ago with an extended version of the N-S-C Diagram. Unfortunately, protection of whistleblowers as well as quality of university investigations remain low (or are even suppressed for various reasons). This is also the view of a new Nature editorial “What Universities could learn from one of the biggest science’s fraud”

university investigations into research misconduct are often inadequate, opaque and poorly conducted. They challenge the idea that institutions can police themselves on research integrity and propose that there should be independent organizations to evaluate allegations of research fraud should.

I agree.

Too many research-misconduct investigations turn out to be inadequate or flawed, says Gunsalus, who had a hand in creating a 26-point checklist that university officials can use to guide probes into research misconduct, which Grey’s team used to rate the investigations.

The 2018 JAMA links to the checklist while the rights seems to be with the National Center for Professional & Research Ethics that has many more resources.

 

CC-BY-NC Science Surf accessed 20.01.2026
Philosophy

We don’t need Social Media in Science

Madonna eventually arrived at the same conclusion – we don’t need any Facebook and Instagram. Neither ResearchGate, LinkedIn and Academia.edu. Concentrating on your work gives you more satisfaction.

Madonna has about 14 million followers on Instagram, so the American singer knows first-hand how powerful the photo-sharing social network is for “influencing.” But now she’s speaking out against Instagram and the darker side of using it.
“You get caught up in comparing yourself to others,” the 60-year-old star tells The Sun in a new interview. “I think Instagram is made to make you feel bad.”
She says it’s especially hard for artists to develop their art and as people under the Instagram microscope.
“I was lucky enough to have a life as an artist before the phone and Instagram and social media because I did have that time to develop as an artist and a human without feeling the pressure of judgment of other people or comparing myself to other people,” Madonna states, adding that social media culture “runs people’s lives” and makes it harder for artists to “stick to your guns and be who you are.”

 

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Noteworthy

Nach dem Hype der 6000 Toten (XXXII)

Das Thema ist aus den Medien verschwunden, der Richter in BW wegen Befangenheit abgesetzt, nur das DÄ berichtet noch

Der EU-Grenzwert für Stickstoffdioxid ist nach neuen amtlichen Daten im vori­gen Jahr in 57 deutschen Städten überschritten worden. Wie das Umweltbundesamt (UBA) heute mitteilte, sank die Zahl der betroffenen Gemeinden damit um acht: 2017 war der Grenzwert noch in 65 deutschen Städten überschritten worden. UBA-Präsi­dentin Maria Krautzberger forderte weitere Maßnahmen, darunter die Nachrüstung von älteren Diesel-Autos mit „wirksamen Katalysatoren“.

Und es sind auch nicht Diesel, sondern Benziner die zurück gerufen werden

An verschiedenen Benziner- und Flüssiggasmotoren in den Modellen Opel Corsa und Opel Adam könnte die Lambdasonde nicht richtig arbeiten. Das könnte zu erhöhten Emissionswerten führen. Opel ruft europaweit insgesamt rund 209.000 Kleinwagen der Typen Corsa und Adam in die Werkstätten zurück.

Es gibt  weiterhin keine Diesel Nachrüstung, es kommt kein Tempolimit, auch keine Maut – und damit  ändert sich auch weiterhin nichts an der Verkehrsbelastung in Deutschland.

Und Umweltepidemiologie? Ist von Kritik unbeirrt, kassiert weiterhin exorbitante Kongresspreise (950€!) und vergibt davon Forschungspreise für Voodoo Assozationen.

 

CC-BY-NC Science Surf accessed 20.01.2026
Genetics, One World

The biggest problem

The biggest (scientific) problem currently for survival on earth?

The are many more interactive maps at the United Nations website.  And there is a new document out

Ten Key Findings
Citation: United Nations, Department of Economic and Social Affairs, Population Division (2019). World Population Prospects 2019: Ten Key Findings.

Nine countries will make up more than half the projected population growth between now and 2050: The largest increases in population between 2019 and 2050 will take place in: India, Nigeria, Pakistan, Democratic Republic of the Congo, Ethiopia, the United Republic of Tanzania, Indonesia, Egypt and the United States of America (in descending order of the expected increase).

 

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Software

How to interpret an odds ratio of less than 1

In a recent paper  (see page 122 ) I have read that an odds ratio OR of 0.7 means a 30% risk reduction which is wrong.

The OR is a measure of association not a risk ratio (which requires random sampling of the population and a slightly different formula)

Let’s have a look on the following table to see why this is all wrong

Disease+Disease-
Exposure+a=7b=10
Exposure-c=10d=10

The odds of an event is the number of those who experience the event divided by the number of those who do not.
Comparing the odds in an exposed and a not exposed group results in the simple odds ratio OR formula.

OR = (a/b) / (c/d)

The interpretation is straightforward for more patients in the exposed group: With a=13 we get an OR=1.3.

An odds of 0.7 however is less intuitive to interprete. 0.7 people will experience the event for every event that does not occur. This translates to one event for every 1,42 non-events, the reciprocal value of 0,7. The percent change PC is therefore

PC = 1/0,7 - 1 = 1,42 -1 = 0,42 = 42%

42% and not 30%.

Sorry not only the math, also the biology is wrong there.

 

 

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Genetics, Theology

Wann ist der Mensch ein Mensch?

Oder wie wird der Mensch zum Mensch? Hugo Lagercrantz, ein schwedischen Pädiater, versucht sich an der Antwort „Die Geburt des Bewusstseins“, das gerade erschienen ist.

Am 19. Tag bildet sich die Neuralplatte, aus der sich Rückenmark und Gehirn entwickeln werden. Aber während Organe wie Herz, Nieren, Leber nach drei Monaten fertig sind, gehen die Arbeiten am Gehirn auch noch nach der Geburt weiter. Hundert Milliarden Nervenzellen müssen erst durch Zellteilung entstehen, an den richtigen Platz wandern und sich miteinander vernetzen, um das Gehirn – und somit den menschlichen Geist – zu formen…
Ein wichtiger Schritt findet in der 24. Schwangerschaftswoche statt: Dann erreicht eine Gruppe von Nervenzellfortsätzen aus dem Zwischenhirn das, was einmal die Großhirnrinde sein wird. Ihr Anfang liegt im sogenannten Thalamus, eine Schaltstelle, die Wahrnehmungen unserer Sinne sammelt, sortiert und in Regionen weiterschickt, die damit weiterarbeiten sollen. „Erst wenn sich diese Bahnen bilden, können die Kinder bemerken, was ihre Sinnesorgane aufzeichnen. Und reagieren“, sagt Lagercrantz. Vorher erreichen Informationen aus dem Körper den Cortex gar nicht, und es kann eigentlich auch nichts geben, was der Fötus als Ich bemerken könnte.

Ja und nein, denn es kann natürlich auch ohne äusserlich wahrnehmbare Anzeichen Bewusstsein geben. Das Bewusstsein kann bei Narkose ausgeschaltet werden, aber es ist trotzdem jederzeit reaktivierbar und damit existent.

Sollte man daher Bewusstsein statt als etwas Eigenständiges mehr als die biologische Schnittstelle ansehen, das Interface  des eigenen Selbst oder der Seele mit der Umgebung?

 

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Genetics

Missing heritability

It is always nice if you are being cited after some years ;-)
There is an important article that I have been reading this morning “Missing heritability of complex diseases: case solved?” Emmanuelle Génin is correct by questioning the statistical models underlying our heritability measures.

It is therefore possible to directly quantify the contribution of these genetic variants to phenotypic variance and measure what is called “genomic heritability”. Briefly, the idea is to infer the proportion of variance that can be explained by a linear regression on a set of markers used as explanatory variables.

This genomic heritability seems to be in fact a poor mathematical representation of a biological trait. >1000 hits in >500.000 individuals, does that make any sense at all in terms of biology?

More recently, it was proposed that rather than polygenic, the genetic architecture of common diseases could in fact be “omnigenic” with mainly all active genes affecting every complex traits.

which is fatalistic but justified IMHO. But there could be solutions. We proposed undetected rare variants

When adding these rare and low-frequency variants to the common variants associated with height, 27.4% of the variation can be explained.

while the results are not impressive. We proposed also structural variants (CNVs), but again no convincing effect so far. Allele dosage? Disappointing . GxE, interaction with genome background? Difficult, highly complex. Epigenetic environmental influences ? Sure but where to start?

The “GIGO (Garbage-In Garbage-Out) syndrome in genetics” as coined by Emmanuelle Génin is one of the main reasons why I mostly dropped out of the field.

We believe that the “missing heritability problem” is an ill-posed problem. Solving it by refining over and over again statistical models derived under the “polygenic paradigm” or using more and more sophisticated sequencing machines will not answer the fundamental and biological question of why that individual is affected by the disease and that other individual is not.

My last sentence would be: Phenotypic correlations between relatives determine heritability. So we should go back to family studies if we want to explain heritability.

 

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