Thursday 15 August 2013

The cheapest way to get publishable results,


Or fungal hocus-pocus

Swedish University of Agricultural Sciences Swedish University of Agricultural Sciences
Swedish public invest huge resources into science. Swedish labs are rich and academia workers are well-fed. With such resources talented scientists can make useful discoveries or develop new technologies. Scientists that lack talent but still have dignity would at least provide the reliable & true results. What can you say about people, who spend huge resources to produce frauds?
Swedish University of Agricultural Sciences Swedish University of Agricultural Sciences
I will explain the main trick, which for the decades helps the “scientists” at the Department of ForestMycology and Plant Pathology, Swedish University of AgriculturalScientists get publishable results.
The story starts when a sample of soil is taken from a forest or a field. In old time scientists, who studied soil did enormous work: they dug deep pits, brought huge soil specimens, and took many samples to ensure that result are true. Modern academia inhabitants bring a pinch of soil to the lab, grimacing fastidiously even at this tiny amount of the real nature (see all the modern publications: 0.5 g and very rare 1 g of soil is used). From this point already a study loses realism. But who says that modern academia inhabitants care about realism? They care about “publishable results” (the favorite expression in modern academia)! So, although the pinch of soil cannot provide reliable results, it is enough to give the odor of environmental study. Now the task is to cook up the body.  
Swedish University of Agricultural Sciences Swedish University of Agricultural Sciences
So, a tiny sample arrives to a lab. Let's assume that this pinch of soil has 4 fungal species living there (pic 1). Swedish University of Agricultural Sciences Swedish University of Agricultural Sciences
Swedish University of Agricultural Sciences Swedish University of Agricultural Sciences
Pic 1
Swedish University of Agricultural Sciences Swedish University of Agricultural Sciences
The first step is to extract fungal DNA from soil. In a good lab researchers will prevent that any other fungi would contaminate the sample (pic 2)
Swedish University of Agricultural Sciences Swedish University of Agricultural Sciences
Pic 2
Swedish University of Agricultural Sciences Swedish University of Agricultural Sciences
In fraud-generation lab the point is to enrich samples! Fungi that live in a lab, or on human skin is only the minor source of contamination. Plus, they can be easily recognized as human-associated and will be interpreted as a sign of poor lab practice. The better source of contamination is required. And in our Department this source has been successfully created and maintained for decades! This source are the ghost fungi. The advantage of the ghost fungi are that they can be produced in the lab during the routine analysis. Swedish University of Agricultural Sciences Swedish University of Agricultural Sciences Swedish University of Agricultural Sciences Swedish University of Agricultural Sciences
The thing is that the amount of DNA extracted from a pinch of soil is so tiny that it cannot be detected. Thus this amount of DNA must be increased artificially up to detectable level. DNA amplification is done with so called polymerase chain reaction (PCR). PCR increase the amount of DNA approximately in 230 times. In other words, instead of one original molecule of DNA there will be 230 copies of this molecule after the reaction. PCR is an amazing tool in a knowledgeable hands. Unfortunately, as any powerful tool in the absent of control it can serve for mischiefs. DNA copies produced during PCR are very stable and can survive months if not years under lab environments. In the good labs leaking of DNA copies from test tubes is strictly prohibited. In my home lab it was not allowed even to open tubes with DNA copies. If anybody forgot about the taboo, this unmindful person would spend a week cleaning with a toothbrush every millimeter of the lab where the crime was done, corridors and all neighbor labs. But in the Department of Forest Mycology and Plant Pathology  DNA copies from all tests are dis-incarcerated. Tubes with DNA copies are left open. In few hours they dry into dust every speck of which contains trillions DNA copies (pic 3). This DNA dust spreads across by seriously looking people in white coats, darting between labs. Finally, all labs are heavily populated with the ghosts – copies of fungal DNA from all previous experiments.
Swedish University of Agricultural Sciences Swedish University of Agricultural Sciences

Pic 3

Swedish University of Agricultural Sciences Swedish University of Agricultural Sciences
Under such haunted environments all new samples will be contaminated (pic 4).
Swedish University of Agricultural Sciences Swedish University of Agricultural Sciences
Pic 4
Swedish University of Agricultural Sciences Swedish University of Agricultural Sciences
Swedish University of Agricultural Sciences Swedish University of Agricultural Sciences
But this level of contamination is still too little for the impressive results. Don't worry! The same PCR that helps to produce ghosts will help to obtain required results!
Well, now our sample with four fungal species undergoes PCR. If PCR analysis is done correctly, 4 fungi that were in the original sample will give 4 signals. Several types of control are used to prevent possible errors (pic 5).



Swedish University of Agricultural Sciences Swedish University of Agricultural Sciences
Swedish University of Agricultural Sciences Swedish University of Agricultural Sciences
Pic 5
Swedish University of Agricultural Sciences Swedish University of Agricultural Sciences
Swedish University of Agricultural Sciences Swedish University of Agricultural Sciences
In fraud-generating lab all controls are canceled and all errors are welcomed. Polymerase chain reaction has a highly creative nature and can join DNA molecules into combinations that never exist in the Nature. These new DNA-creatures even in scientific jargon are called chimeras. In addition to chimeras, PCR can create other types of monsters. As a result from 4 fungi, which originally inhabited the sample and 6 ghosts that arrived later, it is possible to get hundreds different signals (pic 6). In the end, it will look like not 4 but hundreds fungi lived in the original pinch of soil. In the publications the DNA copies from all PCR-monsters will be named “unculturable fungi” and their DNA copies will be saved in special repositories as a treasure.
Swedish University of Agricultural Sciences Swedish University of Agricultural Sciences




Pic 6
Swedish University of Agricultural Sciences Swedish University of Agricultural Sciences
Swedish University of Agricultural Sciences Swedish University of Agricultural Sciences
Now results already start looking impressive! 
Swedish University of Agricultural Sciences Swedish University of Agricultural Sciences
Compare: the correct procedure can provide only 4 fungi and to get such pauper result researcher needs sweating in the lab, preparing all kind of controls, preventing contamination and repeating analysis if errors are detected. In contract, control-free, quality-careless practice brings meaty results and demands very little efforts.
Swedish University of Agricultural Sciences Swedish University of Agricultural Sciences
Well, this is just one reason why this mis-practice has been adopted at the Department. The other reasons need special consideration and will be discussed later.

Swedish University of Agricultural Sciences Swedish University of Agricultural Sciences
Swedish University of Agricultural Sciences Swedish University of Agricultural Sciences