Too little science in my new "supervisor" group

Since October 2012 the administration of Swedish University of Agricultural Sciences, SLU is forcing me to accept a new group of supervisors. This group is not legitimate, because it was appointed in conflict with all prescribed rules. Anyway, new supervisors constantly gather for meetings and produce protocols. Reading these protocols makes me feel sorry for SLU administration: it so difficult to find smart people for a hatchet job. A true scientist would not take this job, and a fake scientist lacks accuracy and diligence to do it well. One of the first protocols that I got from the new “supervisor” group demonstrated it very clear.

At half-time my PhD project has “received praise from the external evaluator for the choice of fundamental biological questions to be investigated, as well as for the elegant systems which has been developed”. It was also obvious that obtained material would be more than enough for a PhD project. My new “supervisors” could not argue with this, instead, they said that the method that I used is outdated. They argued that it might be a problem to publish the results, and my work cannot be recommended for a PhD degree. Unfortunately for them, the statistics of the recently published articles shows that the method is not outdated (see comments below). Plus I did not have any alternative, because there were no other methods available at the Department at the time when I designed experiments and later I was never offered the opportunity to use new and expensive methods. When my new “supervisor” was caught in this attempt to discredit my research, he immediately stepped back, saying that he was misunderstood. Later, he was trying to pretend, that it was just a “scientific discussion”.

Below are my comments on a protocol from supervisor meeting and a response from a “principal supervisor” to these comments:

Why put DGGE method to death?

Comments on protocol from supervisor meeting for Elena K. 2012-12-03

I stated before and continue to insist that I nether recognize nor accept the supervisor group appointed for me by SLU administration in violation of the prescribed procedure. Particularly, I strongly oppose Mr. H and Ms. C candidacies, because I consider them biased toward my research.

Nevertheless, I would like to comment the protocol from supervisor meeting from 2012-12-03, signed by Mr. H and Ms. C, because the authors provided me with an opportunity to demonstrate their preconceptions.

Part I. DGGE is an adequate and not outdated method for microbial ecology

In the protocol from Mr. H and Ms. C there was no discussion about the scientific questions and the results of my projects. The main point of the comments was that DGGE method, used in my studies, is outdated . To make the discussion understandable for scientists from other fields of biology, a short introduction of our routine is necessary.

The subjects of studies in microbial ecology are microbial communities. Native microbial communities consist of many microbial species. Because we do not have detection systems that allow us to study microbial communities directly, the first step in each experiment is to amplify the signals from every group of microbes. This is done with polymerase chain reaction (PCR). So, PCR is simply the method to increase the signal up to detectable level.

The second step is to detect the amplified signal. For this there exist several methods. At our Department cloning-sequencing, T-RFLP, DGGE and NGS were/are used. Since, first two methods are already abandoned by our Department, I will compare the last two.

I. DGGE is about 100 times cheaper than NGS

Table 1. Cost of detection methods

Method of detection	abbreviation	Cost for 96 samples (plate)
Denaturing Gradient Gel Electrophoresis	DGGE	~750 SEK
Next Generation Sequensing	NGS	~100 000 SEK

2. DGGE is the only detection method that is left in the Department

DGGE is performed in home. NGS means buying a service. Next Generation Sequencing in spite that it sounds very impressive, on practice means that PCR is done at home and then products are packed into envelopes and sent to a company, which actually does sequencing. Results come as a huge dataset and processed with algorithm on an autopilot mode.

SLU is supposed to teach students and provide environment for them to master methods and techniques. It should be both, basic and advanced methods, because:

1. advanced methods does not always substitute basic ones
2. there are many students from the countries, where expensive techniques are not available

So, the main task of teaching unit should be preservation and improvement of basic methods and accommodation of new techniques that can be performed in home.

In spite of this, currently at our Department students can learn only DNA extraction and PCR. In seven years that I spent at the Department I could not master any new technology, which would make me more competitive at the work market after PhD. Even to study DGGE I went to the other laboratory, because there was no expert at home. No need to say that a student, in order to master a new method, needs supervision of an expert and a possibility to consult one on every day basis. Short-term visits to other labs do not provide necessary conditions to learn new methods.

In spite that DGGE currently stays the only one detection method available in home, there were constant and strong efforts to put it to death. The possible reasons for killing DGGE method are provided in the next paragraphs.

3. DGGE leaves no space for fraud and data manipulation

DGGE, as a method of detection, is absolutely intolerable to bad quality of PCR. If investigator gets bad PCR it is visible on a gel (examples are provided below). So, DGGE demands high accuracy of previous steps and leaves no space for fraud, since reviewers can easily request for original pictures of the gels.

In case of NGS, samples sent for sequencing do not pass proper quality control. Later, results arrive from company in electronic format (google can give examples of data from NGS on request). If there is no strict control for PCR quality BEFORE sending samples for sequencing, then there is a lot of possibility for incorrect results.

To illustrate this, I would like to show some results from my experiments.

Why there is a need for quality control?

Before starting to study natural communities I tested how the approach works on artificial simple community that consist of 4 bacterial species. So, if there are 4 species in the test tube, should be 4 different PCR signals and 4 bands on the gel (fig. 1)

However, polymerases (enzymes that perform PCR) that are in routine use at our Department were unable to amplify mixed template correctly (fig. 2A and 2b). Although there were only 4 bacterial species in a test tube, outcome results showed complex communities consisted of more then 20-50 species! So, being suitable for other purposes these polymerases cannot be used to study communities. After testing several options I found BioTaq polymerase that (in combination with certain primers) was suitable for routine use (fig 2 c).

Fig 2. What can happen when unsuitable polymerase is used for community analysis!

(Remember that it should be only 4 bands in mixed community and a single band for each individual species!)

1-3, 8-10, 15-17, 22-24, 29-31 – mixed community (3 replications); 4-7, 11-14, 18-21, 25-28, 32-36 – individual species A,B,C and D

(To whom it may concern) primer sets that were tested 1-7 – Muy1f-Muy2r; 8-14 – Eb246-1406R; 15-21 - EubB(27F)-U926R; 22-28 – EubB(27F)-U1510; 29-35 – BrunkBac 41-61-EubA(1522R)

a. DreamTaq polymerase

b. Phusion polymerase

100. 
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     с. BioTaq polymerase (in positions 22-28 PCR correctly reflected what was in test tubes)
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     So, for bacterial communities I managed to find suitable conditions, but...
     
     
     There is no way to study fungal communities with existing approaches!
     
     
     With fungal communities situation is worse. I did not find any PCR conditions that correctly reflected composition of artificial community consisted of 4 fungal species. It is not even possible to get only one band from single fungal species (fig 3). The prerequisite for community analysis is that each species gives single distinct signal. However, no difficulties were reported from other researchers from the department, who use NGS as a detection method.
     At least it remains very questionable approach to send samples for expensive sequencing without testing for PCR quality, and DGGE is a method of choice for such test.
     
     
     Fig 3. Fungal community never went fine!
     Amplification of artificial community consisted of 4 fungal species (named A,B, C, and D) under different conditions (the best outcome I managed to get)
     Mix A B C D Mix A B C D Mix A B C D Mix A B C D Mix A B C D Mix A B C D Mix A B C D
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     If PCR would work correctly then DGGE would be method of choice for studying fungal communities, since DGGE can easily resolve 60-70 bands and fungal community rarely exceeds this level of complexity (especially, when DNA is extracted from small (0.5 g) amount of soil). The main problem for studying fungal communities is inability of existing approaches to provide correct signal amplification from native communities. Before this problem would be solved none of the detection systems can compensate this drawback. However, NGS can easily hide it.
     
     
     
     
     3. DGGE is not that abandoned as it was presented!
     
     
     I never judge method by how fancy it is, but for modish persons there is some information below.
     Search in Scopus gave 842 hits for “denaturing gradient gel electrophoresis” published in 2012 with impact factor of journals (checked just on the first page) being:
     Clinical microbiological review 16.129
     ISME journal 7.375
     Bioresource technology 5.352
     PLoS ONE 4.351
     International Journal of Food Microbiology 3.847
     Environmental Microbiology 3.829
     FEMS Microbiology Ecology 3.408
     Molecular Ecology Resources 3.062
     
     
     
     
     
     
     
     
     
     
     Conclusions:
     1. DGGE is 100 times less expensive detection method that NGS.
     2. It can be done in home. It can be used at least to check the quality of samples before proceeding with expensive analysis
     3. The high resolution that NGS provides is not necessary for analysis of fungal communities, but this method provides good cover for errors.
        
        
        
        
     
     
     Part II. Advisers forgot what they said earlier, but “we have all moves written down”
     
     
     In their protocol Mr. H and Ms. C said:
     
     
     
     
     
     When I started my experiments in 2008, there was only two method of detection in use at the Department: T-RFLP and DGGE. So, counting on what there was available I designed experiments for which knowing names of each individual microbial species was not necessary for answering the questions. Nevertheless, I was ready to master any new method. However, when NGS became available at the Department I have never ever been offered an opportunity to use it.

     At my half time I have been recommended to cut bands form DGG gel, extract again DNA from each band, do PCR for each individual band separately and send product for sequencing to find out the name of the species. Here is a document:

     
     

     

     
     

Each band on DGGE is 0.1-0.3 mm thick (like a hair) and 3-4 mm wide. The distance between two adjacent bands is 0.3-3 mm. One sample produced from 30 to 60 bands and one experiment contains 124 samples to analyze. In addition these gels are very prone to cracking. If I should follow the advice given by Mr. H on my half-time seminar, all together I need to cut (doing it wearing a protection and under UV light!) and analyze from 3720 to 7440 bands . When I pointed out that such work would take at least a year, I was given an advice to cut at least “some of the bands”. On my question what should be criteria to select bands for analysis there was no answer provided...*

_______________________________________________

*Once upon a time rabbits became very tired of being bulled. They came for advice to old and wise owl and said: “O, owl! Please, teach us what we should do! We are so tired of being bulled by everyone in the forest!” Owl thought for a while and said:” Rabbits, you need to become hedgehogs!” Rabbits jumped away very happy, but after a while came back and asked owl again: “Owl, but HOW can we became hedgehogs?” Owl looked at them and said:” How should I know? I am not a tactician, I am a STRATEGIST!!!”

Part III. Even IF I would be able to follow Mr. H advice, does it worth to do?

After silver staining PCR is impossible. Other stains do not provide good resolution.

Gels after DGGE analysis are stained with silver. After silver staining DNA is not suitable for PCR (faint bands, fully developed), so it cannot be amplified for sequencing. SYBR green can be used to stain gel in order to be able to use DNA from band as template for PCR, but SYBR green is at least 5-10 times less sensitive and thus, reduce the value of analysis, which I need to perform to answer the main questions of the experiments.

Aiming to identify microorganism only by part of one gene – is overambitious and not scientific.

Even complete 16S rDNA or ITS region sequences are not enough for species identification. And identification is the first step BEFORE microorganism can be correctly classified. Sequences that are used for microbial community studies are far too short to provide reliable information for organism identification. Serious scientist discussed whether it is possible to identify species correctly even knowing sequences of several genes. Thus, sequencing alone does not provide correct information on taxonomy of microorganisms and therefor is useless.

More, Nesseria meningitidis and N. gonorrheae on the basic of their genomic and even metabolic properties would have been considered conspecific, however everyone knows the differences...

Do we have control of how many sequences are only the results of a polymerase mistakes?

Polymerases that are routinely used for community analysis usually do not have proof-reading activity. It means they do considerable number of mistakes when copy original sequence from bacteria or fungi. In manuals, the rate of mistakes that polymerase does is given for optimal conditions, however, environmental samples:

1. have damaged DNA
2. contain many impurities
3. often need PCR enhancers

And all these factors can alter polymerase behavior and increase the rate of mistakes. This is one of the possible causes for increase in the number of bands, compared with expected number after amplification with DreamTaq polymerase (fig. 2a).

Even if the name of microbe would be found and even if it would be correct how much information it gives about function?

The same microbial species can perform different functions in different communities, or under different environmental conditions (temperature, pH, availability of nutrients, etc).

This list can be continued...

Part IV. Conclusions.

Concluding all above mentioned, I state that:

1. My experiments were designed according the tools that were at my disposal at that time
2. I have never been offered an opportunity to apply NGS (if I would be offered now I will do it!)
3. Recommendations given to me by Mr. H and Ms. C I consider as non-scientific approach and not worth doing

Uppsala, January 7^th, 2013 

 Elena K

________________________________________________________

From: Nils H

Sent: 07 January 2013 23:01

To: Elena K; Marianne C; Martin W; Johan M; Pär F; Christer B

Cc: Jan S

Subject: Re: why put a method to death+ next supervisor meeting

Dear Elena,

You are right that the research questions are far more important compared

to methodology. In order to complete your thesis and for possible

discussions with the supervisor group you have to complete the study plan**

which was due to the faculty already Nov 15 2012. It is not possible to

have such an in depth discussion without a study plan as a basis. In the

supervisor group, we are prepared to have such discussions about your work

provided we have a study plan sent to us as a starting point for the

discussion. Furthermore, the work will not be fruitful if you are not

present yourself at the meetings.

The time for the next supervisor meeting is 13.00 Jan 10 in room A372 as

announced before.

Sincerely,

Nils H

** According the new "supervisor" group the information that my updated research plan lacked was:

The story of Professor James Mac Key

During my first year at SLU I met Professor James Mac Key. He is a legend for every plant breeder, one of the doers of the Green Revolution. He is a creator of a huge collection of plant material that can be used for plant breeding and to study genetics, physiology, and ecology of wheat, triticaly, barley, and oat. The significance and usefulness of his collection was beyond imagination. Part of his treasure was duplicated and stored at Nordic Gene Bank, but he had much more than that. When we met, he had some difficulties with walking due to his respectable age, but his mind is sharp and his memory admirable. It was enjoyable to talk to him.

What did SLU do to Prof. Mac Key? First, they threw Prof. Mac Key's collection out of the cold storage room. He was forced to keep part of his previously huge collection of seeds, at his small office, but these conditions were definitively not suitable for preservation.

Prof. Mac Key often came to his office to work on his book. Probably, even his appearance bothered SLU and one day they decided to take his office and to withdraw his access to the building. Of course, the proper explanations were provided and, of course, they did it for the better good! But these people with frostbitten brains, could not understand what work means for scientists like Prof. Mac Key. The ability to continue working, to stay a part of academia is vitally important for people like Prof. Mac Key.

I see two possible explanations for SLU behavior:

1. They have don’t have enough knowledge to understand the level Prof. Mac Key and the significance of his collection.

2. They feared to compare their results with his. Even if gathered together the practical results of all subsequent generations of SLU “professors” together would not outweigh results of Prof. Mac Key. All their articles and posters are good only as wallpapers at their offices. Of course, the mountain of real, genuine, and useful material was for them like a bone in a throat.

SLU “scientists” talk a lot about “visions” and “missions” and looks like they care about the University. But why they did not even bother to submit an article about Prof. Mac Key to Wikipedia? I keep looking for the article and still it is an empty place there. They must of have done it a long time ago, if not to express a gratitude to the World-class scientist, but at least to promote the University, about the future of which they talk so much.

How SLU appointed new supervisors

My PhD project went so difficult because SLU couldn't provide an adequate supervision. My former supervisor denied his duties, even when it came to publishing articles. I expected that my University would at least find me a new and effective supervisor for the final step of my project. However, six months passed before SLU took care of this question. And the way how my University did it surprised me.

SLU's rules say that a student should participate in discussion of candidates and, together with others, sign a proposal for a new supervisor. The discussion is especially important when the experience with the first supervisor was so damaging for the student's career. But this did not happened in my case. SLU decided to appoint me a new supervisory group in conflict with all the rules and when I refused to accept the obviously biased candidates, the University started to pressure me.

From: Jan S

Sent: 18 October 2012 16:40

To: Elena K

Cc: Rimvydas V; Roger F; Marianne C; Martin W; Johan M; Nils H; Lennart J; Christer B; Pär F

Subject: Supervisior group

Dear Elena,

I have now put together a new supervisor group for you.

The main supervisor will be Doc Rimvys V (Mykopat) and the co-supervisors Prof Johan M (VBSG), Prof Martin W (VPE), Prof Marianne C (Mykopat) and Doc Nils H (Mykopat). As you can see they are all highly experienced and merited in different aspects of your field of interest both from the technical, theoretical and applied side.

Shortly there will be a meeting where you will agree on a revised study plan that you can follow to finalise your studies.

Best regards,

Jan

From: Elena K

Sent: 18 October 2012 19:42

To: Jan S

Cc: Rimvydas V; Marianne C; Martin W; Johan M; Nils H; Lennart J; Christer B; Pär F; Björn A

Subject: RE: Supervisior group

Dear Prof. S,

I appreciate your efforts to create a group of supervisors for me. Since it is a crucial question for my career, I hope that I may express my opinion as well.

I would appreciate it if an external expert would become my main supervisor, since I have an impression that scientists from my Department are biased toward me and my projects.

I would be grateful if Prof. W would become my main supervisor. His knowledge in wheat biology and also his skills in statistics would be a valuable complement to my project.

I strongly oppose the involvement of Prof. C in supervising my project. Being a person, responsible for PhD education at our Department, she showed absolutely no consideration to my case.

If it is necessary to include experts from our Department into the group of supervisors, I would appreciate it if Dr. A would be considered. I highly acknowledge his experience and understanding of the modern agriculture.

Regards,

Elena K

From: Christer B  Sent: 19 October 2012 16:41To: Jan S; Elena KCc: Rimvydas V; Roger F; Marianne C; Martin W; Johan M; Nils H; Lennart J; Pär FSubject: Ang.: Supervisior group

Dear All

The faculty note the progress in this matter and is pleased to see the high competence and experience represented in the group of supervisors. 

Sincerely
Christer B
Forest entomology, Dept of Ecology
Swedish univ agricultural sciences
 

From: Elena K         Sent: 19 October 2012 17:50        To: Christer B; Jan S Cc: Rimvydas V; Marianne C; Martin W; Johan M; Nils H; Lennart J; Pär F; Björn A; Anna A         Subject: RE: Ang.: Supervisior group

Dear Dr. B,

I am afraid that it was something wrong with e-mail service again and you have not got my letter, which was sent yesterday. Here it comes once again. Sorry for repetition!

Dear Prof. S,

I appreciate your efforts to create a group of supervisors for me. Since it is a crucial question for my career, I hope that I may express my opinion as well.

I would appreciate it if an external expert would become my main supervisor, since I have an impression that scientists from my Department are biased toward me and my projects.

I would be grateful if Prof. W would become my main supervisor. His knowledge in wheat biology and also his skills in statistics would be a valuable complement to my project.   

I strongly oppose the involvement of Prof. C in supervising my project. Being a person, responsible for PhD education at our Department, she showed absolutely no consideration to my case.

If it is necessary to include experts from our Department into the group of supervisors, I would appreciate it if Dr. A would be considered. I highly acknowledge his experience and understanding of the modern agriculture.

 Regards,

Elena K

From: Jan S          Sent: 19 October 2012 18:21        To: Elena K; Christer B        Cc: Rimvydas V; Marianne C; Martin W; Johan M; Nils H; Lennart J; Pär F; Björn A; Anna A      Subject: RE: Ang.: Supervisior group

Dear Elena,

It will not be possible to have a main supervisor from another department.

Best regards,

Jan S

From: Elena K        Sent: 19 October 2012 19:18      To: Jan S; Christer B     Cc: Rimvydas V; Martin W; Johan M; Nils H; Lennart J; Pär F; Björn A; Anna A    Subject: RE: Ang.: Supervisior group

Dear Prof. S,

If it is not possible to have the main supervisor from another Department, then I would appreciate if two other options would be considered. The first is that my registration would be changed to the other Department; and the second is that I will just go on without main supervisor as I actually have been doing for all these years.  My only wish is to use the expertise of Prof. W and being able to consult him on an official ground. 

I am afraid, that the appointment of any scientist from our Department as my main supervisor might lead to a new conflict, which I wish to escape by any means. My wish from the begining was to solve this conflict within the Department. Unfortunately you have been very resistant to all my attempts. Now it is going too far and I am afraid I can not trust anymore to the internal experts. 

Best regards,

Elena K

From: Elena K           Sent: 21 October 2012 06:03     To: Rektor; Rimvydas V; Jan S; Christer B      Cc: IngridP (Forward); IngerA (Forward); BosseAJ; RolfL (Forward); JohanL (Forward); LennartB (Forward); EvaTh (Forward); Lena A-E; PeterS (Forward); Göran Er; Ingrid Ö; Inger Å; Saco-SLU Ordförande, Lars L; Roger A; Martin M; Martin W; Johan M; Nils H; Pär F; Björn A; Anna A          Subject: RE: Ang.: Supervisior group

Dear All,

Regrettably, the attempt to solve a problem with the supervision of my PhD studies came to a dead end. I feel a bit lost: on the same day I have got two contradicting messages from Dr. V (please, see below) and it is difficult to understand which of his intentions is the true one. This casus confirms my worse fears that Dr. V, if being appointed as my main supervisor, would like to use this position to discredit my reputation and to nullify my chances of completing PhD studies. I am afraid that it was a part of plan that the Head of our Department, Prof. S prepared for me long time ago.  

Unfortunately, in spite of many assurances of best intentions provided by Prof. S,   his actions contradict his words. My studentship was cancelled just few months before my PhD studies would be completed. It was done without warning and without any explanations. About each and every rule prescript in the Guidelines for Research Education in the Faculty of Natural Resources and Agricultural Sciences were violated during the procedure of the preliminary termination of my studies. Mention just that there were only two meetings during all these nine months that supposed to deal with the problem. Both of them were organized by my initiative and after my numerous requests. Also in spite of my frequent requests for appointment of new supervisor there was no any action taken during half a year. Finally, there was even an attempt to disable my access to the laboratory and e-mail/software services.

I am not psychologist, but to my humble opinion, Prof. S is affected by very personal and very negative feelings and is using administrative recourses to satisfy his revenge. If only he could explain me what triggered such negative emotions, I possibly would try to change my behavior. My worries are also that the next time, when Prof. S would dislike someone else (someone with less stable nervous system then mine) and would start a new hounding the University might be involved in dealing with suicide.

What I found even more disappointed and dangerous is that experts appointed by the Faculty to supervise the process of problem solving have been observing all violations of the rules with inexplicable indifference. Trigged by their passiveness I filed an appeal to the Swedish Agency of Higher Education. Currently, thanks to Dr. B´s and Dr. F´s lack of concern, the whole University is in charge for this problem. In this case, one can even suspect the intentional desire to transfer responsibility to the higher level. I felt extremely uncomfortable to blame innocent people in deeds they were not guilty at (in this case the SLU Authorities), but indifference of these two experts left me no other way out.

Although it might impose some exertion on your e-mail boxes, I would like to provide you all with detailed information regarding my case. So if you wish, you could make your own opinion about it. The files with my appeal to the Swedish Agency of High Education, the reply from the Department and my comments on this reply are enclosed into attachment.

Finally, my deep plea is, please, if you do not want to help me then at least stop installing new obstacles. My only desire is to finalize my PhD studies as soon as possible and leave you in peace. I have no bad feelings to my University, only a great disappointment in particular people.

Best regards,

Elena K

Dept. Forest Mycology and Plant Pathology

Swedish University of Agricultural Sciences

 From: Lena A-E           Sent: 24 October 2012 16:46         To: Elena K; Rektor; Rimvydas V; Jan ; Christer B; registrator      Cc: IngridP (Forward); IngerA(Forward); BosseAJ; RolfL (Forward); JohanL (Forward); LennartB (Forward); EvaTh(Forward); PeterS (Forward); Göran Er; Ingrid Ö; Inger Å; Saco-SLU Ordförande, Lars L; Roger A; Martin M; Martin W; Johan M; Nils H; Pär F; Björn A; Anna A; Lotta H            Subject: SV: Ang.: Supervisior group

Dear Elena K,

 I have been informed of your case and regret that your education is not proceeding according to your expectations. SLU has a keen interest in developing and improving the PhD education in general, but also in supporting PhD students if the study and work situation becomes hard to handle. Thus a PhD commissioner is supported by the university and available for you to contact. When it comes to more complicated situations it is the responsibility of the faculty board, with guidance of the university lawyer, to ensure that the case is handled by appropriate persons according to the legislation. According to my information, work is in progress and a solution will be suggested.

Best regards,

Lena A-E

Deputy Vice-Chancellor

Sveriges lantbruksuniversitet

Swedish University of Agricultural Sciences

Från: Elena K           Skickat: den 24 oktober 2012 20:28                Till: Lena A-E; Rektor; Rimvydas V; Jan St; C B; registrator                         Kopia: IngridP (Forward); IngerA (Forward); BosseAJ; RolfL (Forward); JohanL (Forward); LennartB(Forward); EvaTh (Forward); PeterS (Forward); Göran E; Ingrid Ö; Inger Å; Saco-SLU Ordförande, Lars L; Roger A; Martin M; Martin W; Johan M; Nils H; Pär F; Björn An; Anna A; Lotta H              Ämne: RE: Ang.: Supervisior group

Dear Dr. A-E,

Thank you for your replay and for the willingness to find a solution for this situation.

Today I have got a message from Högskoleverket with Mr. J’s remarks on my comments (the file is enclosed). I would appreciate if you can inform me whether the position that is formulated in Mr. J´s letter is the official position of our University.

One more time I appreciate for your concern and am looking forward for the win-win resolution of this situation.

Best regards,

Elena K

Dept. Forest Mycology and Plant Pathology,

Swedish University of Agricultural Sciences

________________________________________

From: Lena A-E                 Sent: 25 October 2012 17:46                  To: Elena K         Cc: registrator           Subject: SV: Ang.: Supervisior group

Dear Elena K,

Mr Jonsson, the university laywer, represents the universitet in this matter.

Best regards

Lena A-E

Deputy Vice-Chancellor

 Sveriges lantbruksuniversitet

Swedish University of Agricultural Sciences

From: Gabriella P H                Sent: 26 October 2012 11:47               To: Elena K               Subject: Decision regarding supervisors and formulation of a new individual studyplan

Please see attached decision.*

Yours sincerely

Gabriella P H

Utbildningshandläggare
Sveriges lantbruksuniversitet
Swedish University of Agricultural Sciences

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From: Elena K                       Sent: 29 October 2012 02:36                To: Lena A-E; Rektor; Christer B; registrator          Kopia: IngridP (Forward); IngerA (Forward); BosseAJ; RolfL (Forward); JohanL (Forward); LennartB(Forward); EvaTh (Forward); PeterS (Forward); Göran E; Ingrid Ö; Inger Å; Saco-SLU Ordförande, Lars L; Roger A; Martin M; Martin W; Johan M; Nils H; Pär F; Björn An; Anna A; Lotta H; Roger F                 Subject: RE: Ang.: Supervisior group

Dear All,

I apologize for bothering you again, but after nine months of discussions about my PhD studies I realized that appealing to several persons in charge might be the only way to get answer.

On October 26^th, I was informed about a new group of supervisors appointed for me by the NL Faculty (file Beslut Dnr Fe.2012.4.9 – 1257 is enclosed). My opinion on this crucially important issue was not even been inquired. To my point of view to assign superiors in autocratic manner is well expected at military organizations, understandable at private companies, but is out of place at academia environment. The inability or unwillingness of University (!) to maintain a constructive dialog and a clear tendency to eliminate problems by applying pressure is a scaring sign. 

After the first attempt to appoint a new supervisors group done by Prof. S, I explained my reasons for re-consideration of this proposal (file Supervisor group_sv is enclosed). Prof. S stated that it is impossible to have a scientist from another Department to be appointed as my main supervisor. The decision made by NL Faculty also did not take into consideration my request for external expert to be appointed as my main supervisor.

I regret to be a person, who need to remind SLU Authorities about the Rules prescribed by themselves, but according to the Guidelines for research education (third level programmes) in the Faculty of Natural Resources and Agricultural Sciences (Dnr SLU ua 40-1244/08) not only a scientist from another Department but even a scientist from other University can be appointed as a main supervisor for PhD student at SLU.

Particularly the paragraph §3 of the Guidelines says “A person who is an associate professor or professor, and employed at or visiting SLU may become the principal supervisor of a research student without a specific decision to that effect. A principal supervisor who is not an associate professor at SLU must have a recognised qualification in pedagogy of supervision.” (please, see the original document for more details at

https://internt.slu.se/Documents/internwebben/nl-fak/forskarutbildning/riktlinjer-eng_100701_antagn.ordn.101215.pdf)

Dr. H after being appointed as my main supervisor started with making a list of “must to do” tasks for me (see below). There was no any slightest concern whether it is feasible for me to do all these things. I have not been paid since the end of January 2012. My savings run off very quickly after this. Currently most of my time is devoted for making some modest living for me and my son. I have maximum two days in a week to dedicate to any other activities. In addition, the restricted diet for the last nine months seriously affects my health and diminishes my ability to work as efficient as I was able to work before.  Under these conditions I am not able to make any plans and/or to keep up with such plans.

Regretfully, the only solution that my University is ready to offer me is to put on additional pressure on me without providing any conditions that would allow me to fulfill these demands.

By the other hand, my former supervisor, Prof. F has got the incomprehensible protection from our University. He not only escaped questioning about the reasons why he did not find time within two years to read my manuscripts and to give his feedback on them, or why he was unable to guideline me through the basic statistical methods applied in his field of research; he even remained my supervisor until now according to the letter written by Mr. J to the Swedish Agency of Higher Education on October 24^th, 2012! So, attached to this message is a file with a formal request for withdrawal Prof. F from the position of my supervisor. I hope this request will be registered and processed according the prescribed protocols.

Under these circumstances, I think that disagreements between my University and me can not be resolved without the participation of a third part. My proposal for now is to leave this problem for the consideration of the Swedish Agency for High Education and wait for their decision.  

 Best regards,

Elena K

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I continued asking SLU for a proper procedure of appointing a supervisor, but University ignored my requests.   At the end of the year I needed to apply for a visa extension and sent a request to SLU for a issuing a certificate:

From: Elena K                  Sent: 30 November 2012 07:37                To: Gabriella P H              Subject: Decision regarding supervisors and formulation of a new individual studyplan

Dear Dr. P H,

My PhD studies are still not finished, so I need to apply for visa extend. To be able to do so I need to present to Migration Board several documents (http://www.migrationsverket.se/info/2973_en.html)

I would appreciate your assistance in obtaining a document referred in the second paragraph:

“a statement from your institution of learning showing that you have made acceptable progress in your studies. If your are studying at university or college, you are required to have taken 15 credits during the first year, 22.5 during the second year, and 30 credits during the third and subsequent years. If you are a graduate student, you should instead attach proof from your instructor confirming how your training is progressing and the planned dissertation date”

Thank you in advance!

Sincerely,

Elena K

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From: Gabriella P H                  Sent: 30 November 2012 13:27                 To: Elena K           Subject: RE: Decision regarding supervisors and formulation of a new individual studyplan

Dear Elena,

I'm afraid I can't help you with that kind of document. You have to ask your supervisor/department to help you. You have a meeting with your supervisors on Monday, right? A complete Individual study plan might be such a document that the Migration Board is asking for.

Concerning your Individual study plan (sorry I haven't had time to answer you earlier), it has to be completed and signed by your supervisor and head of department, and then sent to me. Hopefully that will be done by Monday.

Have a nice weekend!

Yours sincerely

Gabriella

From: Elena K                          Sent: 30 November 2012 14:21                   To: Gabriella P H Lena A-E              Subject: supervision group

Dear Dr. P H,

Thank you for your letter.

However, I am afraid, there is again misunderstanding. I have informed the SLU Authorities earlier that I can not agree with appointed supervisors' group since the process of appointment was autocratic and my request to have unbiased main supervisor has not been considered (please, see the letter below).

My favor to reconsider the decision about supervision group was repeated twice since that, but was refused to be noticed by SLU Authorities.

In case if my favor was not clear expressed, I need to repeat that I want to have any scientists from other Department to be appointed as my main supervisor. This request does not conflict with SLU Rules, so I do not understand why it was ignored.

Sincerely,

Elena K

From: Lena A-E                       Sent: 30 November 2012 16:54             To: Elena K           Cc: Gabriella P H; registrator

Subject: SV: supervision group

Dear Elena K,

The faculty board has the responsibility for the PhD education, and I have full confidence for their way of handling this issue. The faculty board decides upon the individual study plan and has appointed a new supervisory group. You will have to accept to meet the supervisors and to fulfil the study plan in order to successfully complete the studies.

Best regards,

Lena A-E

Deputy Vice-Chancellor