Category Archives: Science & Scams

fMRI studies crap due to software failure.

Having developed software myself for retarded biologists, I can say that this problem has two sides.

  1. programmers that have insufficient experience with statistical methods and just work their way through bullet points from a powerpoint slide to satisfy the customer.
  2. biologists who do not want and often simply refuse to understand anything of statistics. They insist on ‘buying’ the solution as a black box (hint: there are no useful black-box statistical techniques).

https://www.newscientist.com/article/2097734-thousands-of-fmri-brain-studies-in-doubt-due-to-software-flaws/

Published in Nature Oncogene

I just found out that I apparently published in Nature Oncogene a couple of years back. Didn’t know that since the relations with that lab broke down after they decided to add authors to the paper just ‘because of politics.

In 2004/2005 I created the correlation maps between leukemia patients and their P53 isoforms on 2D gels. This was about 96G of data, based on 2D gels, mainly created by Nina Anensen and Bjorn Tore Gjertsen. Given that this paper is about the results of the analysis, you would think the PhD student to be the first author, and the one who did the analysis the second author.

However, because BTG can’t write an English sentence that is not contorted, (english sentences contorted three time was made), the paper got delayed and delayed and delayed. A couple of years later, Nina left the lab (and I had the feeling she didn’t want to be involved much more with that paper nor with BTG). I also changed jobs.

By now, I had managed to get the technique published in BMC Bioinformatics. BTG had to be the last and corresponding author on that paper otherwise he would refuse that we could publish it. There was no reason in his arguments, aside from ‘I pay you’, which was actually not true. He paid maybe a couple of weeks, while my employer at the time paid more than two years. Of course, it helped him to obtain his professorship that same year.

Nina gone, me gone; with new technicians, he still had to publish that research. How do we publish that ? Add some more pointless ‘validation’. Let’s ‘prove’ the P53 isoform correlations and when we’ve done that, let’s move Werner further down the line because you know, he actually screwed the patent we were going to take on this method. Let’s place some Norwegian lazy fuck, who in all likelihood had had more coffee and cake in his hand than lab material, at his place. Oh yes, and of course, don’t forget to add some well connected politicians to the end of the list, that should help his career as well.

http://www.nature.com/…/journ…/v31/n12/full/onc2011348a.html is the pay-walled article.
http://analysis.yellowcouch.org/2dcor.html is a description of the method I created.
http://werner.yellowcouch.org/Papers/p53cor/index.html is a demo of the output of the analysis

This was truly a disappointing experience. Everything for the career and high impact factor. He probably snorted lots of cocaine or speed to just get through the correlations maps. Otherwise his brain would not process what he saw.

Now, you would say, the story is finished there. Not really. A year later, I moved to ETH Zürich where I ended up in a similar situation. Did an analysis that noone else could perform (two research groups had tried to analyze some NOTCH data, yet couldn’t even normalize their data properly, and could produce nothing of interest). So, I did the analysis. Everyone was ‘wow’ and ‘great’; yes Werner you _might_ be on the paper as well. Again I ended up at third position, they threatened to sue me if I shared information. And within 2 weeks the paper was published in Cell Developmental. In this case because the lab head was editor of Cell. Fucking political business.

If you ask me, why I left academia: it is because of shit and disrespect like this. It is because of scams where ‘impact factor’ and political positioning is more important than sharing the knowledge that was learned with taxpayers money.

Piss on high impact academics. I’ve been there, I’ve seen it and it should all be thrown out. Universities should be recreated from scratch. You want creative and intelligent people; not paper pushing bureaucrats who know how to ‘score’ and use other people abilities so they can get the paycheck.

AdMob a Scam ?

admob_iconI recently considered adding advertisement to my app to see whether that could be a viable method to generate revenue. In the past Google adsense turned out to be an important income for my website. So I thought admob would be as well.

Boy was I mistaken.

First of all, using the admob API is hard work. Some of the problems I encountered

  • Getting it linked in. The Android SDK for eclipse is so unstable that it just never worked. Switching to Android studio made it easier but then still it took a couple of days.
  • Resource issues After linking the library in, everything worked but Admob kept on spouting resource errors. Days later, I found a post by the admob team that I can simply ignore that error. Can’t they simply remove that error then instead of sending me on an egg hunt ?
  • The problem of API8. The Admob SDK just doesn’t support older phones, so that cuts down the market already. On older phones admob just stopped working. (Lucky people who are staring at all those black boxes)
  • No keywords The API normally allows you to add keywords so that the ads are better targeted. No luck there, as soon as you use some weird UTF8 characters (as can appear in song titles), the thing CRASHES. Can you imagine that ? A support library that is supposed to make me money crashes my app, which would lead to negative reviews ? So no keywords then.
  • Performance sucks Then there was the problem of performance: the admob runtime is not the most efficient one can imagine. While my app is rendering audio, providing the user interface and actually doing things, admob just seems to hog resources. Probably while waiting for a network connection or who knows what. 35% CPU time was used, while the mp3 decoder only used 7%. Seriously ? What is so difficult on serving adds that you need the resources of five mp3 players ?

Let’s say implementing the ads through the admob SDK took around 1000 EUR (a week work). Now it was time to actually get to the revenue…

Well… forget it… The estimated revenue per thousand impressions on admob is so so low (0.02 EUR !) that you will not see any money. That means that in order to obtain that 1000 EUR back, before even starting to make any profit, the app needs to generate 50’000 impressions. Now, you might think this is reasonable. But it is a magnitude difference compared to the old adsense ads. And the fact remains it isn’t reasonable. After all you provided something: screen real estate. It got used, yet whether you get paid or not depends on whether someone clicked on that ad or not. If impressions aren’t worth shit then why do we see so much advertisement ? Compare this to an auto route with advertisement billboards: What Google wants is that you give them the billboards and then they will see whether someone was really interested before actually paying you.

Of course, you could say: this is how it works… Well, I’m telling you: this is not working anymore. For very few people. Just search for ‘admob low cpm’ and you will see quite a lot of stories of people that have millions and millions of views to earn next to nothing.

So, that was it for admob. It was nice to know you. Or not. It took a lot of investment from my side. Your support sucked, your development team sucked and your payout sucked. Goodbye.

NCF tries to kill Kenny

In the article http://www.ncf-net.org/forum/CallForResignation.htm the NFC Board calls for Kenny De Meirleir‘s resignation because he choose not to publish his findings in officially recognized journals.

I would not publish there either. You have to pay the idiots and you know that your findings will be ‘reviewed’ by other groups and then probably published at the same time by this other competing group. Why would anyone choose to go through such charade ?

Quoted: … Dr. De Meirleir neglected to publish in peer-reviewed medical journals, although he carefully put his work into patents […] as well as in a book he published, […] His important discovery is in his own chapter and was discovered by the medical director of the NCF. Without publication in a medical journal, it went unnoticed and unread by most researchers….

The entire complaint reads as a political attack out of spite. Shouldn’t those that are complaining look in their own backyard. Hint: the ‘processing fees’ journals ask for publishing are ridiculous. Maybe they can consider that journals are in the business of hiding knowledge, and letting people pay for it, as opposed to disseminating it.

Quoted from the complaint: The National CFIDS Foundation, Inc., upon hearing of this important work that went unpublished, immediately asked other researchers to look into doing this work and have, since, funded them for the work.

This is of course a lie. The work was published in patents and in a book. Aside from the appalling attack on someone’s reputation. It is also an unnamed and undated post. And as always: they will take the research and start publishing their own findings, which is nice enough, but I don’t have the feeling it has to do with knowledge here. Instead, I have the feeling it is about politics.

Fuck the establishment. Go Kenny.

Open Access: it’s just a word, it doesn’t really mean anything

oa_sure1

Recently I was interested in downloading an article as a non scientist; and since it was open access I thought it wouldn’t be much of a problem.

The article in question can be found here: http://www.informaworld.com/smpp/content~content=a781790162 Although clearly marked as an ‘open access’ article, you should pay the, not so inconsiderable, price of 37 USD ! Of course the logo suddenly disappeared. It’s also an odd article to be placed by the psychology press, but anyway 🙂

Telephone Sanitizers are Taking over the World

I’m dissatisfied with the direction society goes to. More censorship, more control over content, less real content and what makes it really worse is that a huge amount of telephone sanitizers (a term taken from Douglas Adam to refer to administration and bureaucracy) that did not create content but want utter control over it regardless.

Some examples of what I mean:

  • A university I worked at sent me an official letter to state that I was not allowed to mention which research they were conducting.
  • The university of Tromsø does not allow employees to have their own homepage and publish research through such medium.
  • A poster produced by a research group I worked with contained false information because of potential ‘patent’ opportunities.
  • A former employer of mine tried to patent correlation (for those knowledgeable: maybe the old Greeks could have patented multiplication !) and claimed it was a ‘prediction’ tool. Clearly nonsense. Of course those idiots refused to provide the undersigned with a payment for the invention I created.
  • Halfway a project involving 4 universities, the document template we had to use suddenly had a ‘confidential’ tag. Of course on the documents that I wrote I removed this, but it gives clearly the impression in what direction things move
  • Often I get emails from researchers asking me whether a comment I made online was ‘already published’. What is the point of this ? Does it make it less scientific or do they want to publish a comment I made ? Well, maybe I read too much in their statement, but it has nothing to do with science whether it was already put to paper or not.
  • On many researchers’ site there are (too) many pages that cannot be shown due to copyright transfer or due to ‘intellectual property’.

Aside from this, I often bump into researchers who have an rather large ego and in accordance with the size of their ego they want to be involved in patents (whether they materialize in a true accepted patent and one which makes money is completely immaterial to them). They want their articles to be considered so important that they happily sign away the copyright. It is hopeless at universities. And without exception, the inflation of their ego is inverse proportional to the work they did themselves and the creative ides they themselves had. (Similar arguments can be found at Celia Greens site). Sadly enough none of them realize that the only thing which surpasses the current publishing infrastructure is the content itself if it is widely accessible.

So that is my stance on the current state of ‘content’ versus ‘big publishing’.

Potental Backcovers as written by Scientific Reviewers

You probably know how back cover texts on books are always positive. No surprise there: they are written and/or selected by the publishers themselves, and they want to sell the book. Recently though, I wondered how they would read if scientific reviewers got their hand on the back-cover ?

Given my own experience with this breed of vultures, I believe the opinions will be wide-ranged, but will in general be self-involved and with an absolute disregard for the actual content. This is what I came up with:

1. This author paid us a lot, so it must be a good book.
2. This is really a boring book. We didn’t not get past the first chapter. Not even on the toilet. Probably it is good though. Good luck with this read !
3. We at Oxford/Stanford publishing recognize the excellent sales this book will offer to our partners.
4. This book has great potential.
5. We tried to read the book backward and couldn’t follow it. It’s probably scientific.
6. We didn’t like the font of the book.
7. There were no nice pictures in the book.
8. Why couldn’t the author give a dense outline of the book before starting with that lengthy introduction ?
9. As a professional editor and a high selling author of two and a half book, I believe our own work is so much more interesting than what you are holding in your hands right now. For instance, we ‘develop’ our characters in our manuscripts and we ‘work’ with the reader to achieve a greater understanding of the book’s emotional plot.
10. I had to read it and was not really interested. I finished the 540 pages in 3 hours and am not impressed.
11. I only read the first sentence of each page and the story still made sense. Amazing.
12. If chapter 3 would be scrapped and the introduction placed at the end, the book would certainly have a bit more of a David Lynch feeling.
13. If you picked up this book, you probably liked the front-cover. Lets hope you like the back-cover as well because the content is worthless.
14. The HERO died !!! Hopefully this is the last in the series.
15. Carefully consider other books before buying this miserable heap of recycled paper.
16. Hopefully the hero stays dead this time.
17. I loved the little troll on page 603.
18. The footnotes really deepened the story.
19. The book has a beginning, a middle and an end.

Obviously I’m highly frustrated with scientific reviewers 🙂

Applied Biosystems & Celera Genome Identifiers

It is widely known that there is some tension in the scientific community between Celeras genome project and the more open state funded genome project. Up to now I never stood still about this but recently it came to my attention that a particular micro array (Applied Biosystems) manufacturer actually tries to force this issue. The Applied Biosystems 1700 scanner I’m talking about is the one at Tromsø’s university and my experience with AB on this matter is less than optimal. The first major problem I encountered was that the output of the machine produced a large collection of hCG or mCG genes, none of them which follow standard annotations. The only database able to actually understand these genes is the pantherDB, but that database is not the one I would prefer. I would rather have an annotation that actually uses standard nomenclature (NCBI, Swissprot for instance). So, after trying to get my hands on more information with this respect I figured out that the AB software should be able to export these columns as well. Good. So I tried to export all columns. Well, it didn’t work. The machine plainly refuses to export everything that I wanted. After 48hour of ‘export in progress’ not a single byte was written to the export-file.

Of course, I contacted Applied Biosystems regarding this issue. Below is the transcript.

12 April 2007 undersigned wrote
Hello, exporting the standard collection of columns works. However, as soon as I try to include all the gene-related attributes, I find that the process hangs. Is it correct that to assume that the machine requires an Internet connection ? (It doesn’t have one at the moment).

17 April 2007 Even O. for Applied Biosystems Technical Support wrote
You do not need an Internet connection for this step. However, depending on the number of arrays to be exported the export process can become very slow or even freeze if you include all the columns. Try with less columns (they only need SIGNAL, S/N, FLAGS, eventually coordinates and).

18 April 2007, undersigned wrote
Hello, In order to export all necessary information from 7 arrays, I waited for more than 48 hours ! Since you are aware of the problem I can only comment that your solution (‘just wait’) is completely unacceptable. Even from a programmatic point of view there is no reason at all why an export should take such a prohibitively long time. We are prepared to install new versions of the software, or to talk about better solutions than the one you propose. If you want I can have a look at the software together with the developers.

18 April 2007, Even O. wrote
I am sorry if I have given you the impression of “just wait”. That was not the meaning at all! I have taken this problem up with my network group, and I will respond to you as soon as possible. Ok?

18 April 2007, 3 hours later, Even O. wrote
Hi again, exporting 7 arrays should not take that much time. I will contact service and let them check the status of the Oracle database. I’m really sorry for your problems with the exporting time. We will have this fixed as soon as possible.

27 April 2007, undersigned wrote:
Hello, do you already have a solution for this export problem ?

27 April 2007, Even O. wrote
I have taken this problem up with my network group. Can you send me your phone number so I can call you?

2 May 2007, undersigned wrote
Hello, that would be good. My phone number seems to be +xx xx xx xx

8 May 2007, undersigned wrote
Hello, I still didn’t get a phone call regarding the mentioned issues. Please contact me either by email (preferably) or if necessary by phone: +xxxxxxxx would be my phone number,

Of course, a call never came. Why is vendor lockin always of a lower quality than leaving people to freely choose what they need and feel is the most appropriate in a certain situation ? If they make a scanner they should not force me to use their retarted nomenclature.

Researchers: Why would we even want to cooperate ?

While working for a Norwegian company, I was involved in project acquisition. The institute was somewhere between industry and university: an applied research institute. On one side we needed university partners, on the other side we needed partners in the industry. Finding partners was in all cases difficult. Below is a list of excuses people used to avoid cooperating with us.

Suppose you approach somebody with the question: Hello, I have this problem and we would like to research this further:

1. Your proposal is not interesting
2. You are too expensive
3. You have a bad CV / Your company has a bad CV ( Interestingly it is always the worst CV which is taken)
5. Yes, extremely interesting; somebody else should have done that
6. No, we are in the same pool, cooperation with you might lessen our changes for our pet-project.
7. No, but if you had called last month.
8. Are you involved in an EU project ?
9. Yes, somebody else (better and probably the best in the world) already does this
(a) and thus we don’t cooperate with you
10. Can you send me an abstract
(a) and then hear nothing
(b) find out it is used somewhere else
11. You cannot get money to do new things
12. What do you get out of this ?
13. Yes interesting, but we’ll just use a PhD for that
(a) even if it ain’t research
(b) even if the guy in question is not qualified
14. No, we already have expertise
15. No, we want to own the expertise
16. No, you have a bad reputation
17. A bad reputation actually carries far: No, we know somebody related to you and we don’t like them, so we don’t want to talk to you (with friends like these)
18. Interesting ! Want to do it for free ?
19. Sounds interesting ! Do you have money for us ?
20. Interesting but we don’t have money
(a) Can you do it for 1% of the actual cost ?
(b) No, then we will silently ignore the problem
21. Why should we want to cooperate ? Leave me alone.
22. Very interesting, somebody else is already doing that.
23. Did you already publish that ?
(a) on paper ?
(b) in color ?
(c) was it peer reviewed ?