Friday, 20 February 2015

Why I will never trust Science again.

On the 7th of December I submitted a paper about the spread of H5N8 bird flu via bird migration to Science. A pdf version of the file can be found here. Then I waited and went off for my Christmas vacation. That is why I did not see the final reply from Science until the beginning of January.


Biomedical Science
University of Westminster
Westminster None W1W 6UW

Dear Dr. Dalby

Manuscript number: aaa3940

Thank you for submitting your manuscript "The European and Japanese outbreaks of H5N* derive from a single source population that has been dispersed along the long distance bird migratory flyways. " to Science. Because your manuscript was not given a high priority rating during the initial screening process, we have decided not to proceed to in-depth review. The overall view is that the scope and focus of your paper make it more appropriate for a more specialized journal. We are therefore notifying you so that you can seek publication elsewhere.

We now receive many more interesting papers than we can publish. We therefore send for in-depth review only those papers most likely to be ultimately published in Science. Papers are selected on the basis of discipline, novelty, and general significance, in addition to the usual criteria for publication in specialized journals. Therefore, our decision is not necessarily a reflection of the quality of your research but rather of our stringent space limitations.


Caroline Ash, Ph.D.
Senior Editor

That was fine but the timing was a bit unfortunate and so delayed the paper being sent out to another more specific journal. I was happy with the paper but it was borderline in significance and Science has a lot more important manuscripts to publish.

So I sent it to Emerging Infectious Disease on the 9th of January in a modified form with some typos removed and a switch of emphasis on the epidemiology as that is what they need. The new manuscript for EID I sent is here. Again the paper was rejected on the 30th of January because it does not really fit with EID which wants manuscripts that are about diseases that affect human health and in this case it looks like it will only be an avian disease.

I was reading the Science weekly e-mail and saw that they were going to publish a paper on the spread of H5N8 by migratory birds in their Insights column. It is available here. This was even reported by the BBC. So it seems it was a more important story than I had thought.

Reading this I was rather angry that this was published and that my paper had been rejected as it comes to the same conclusions and so I wrote a short and quite angry e-mail to the editor of Science complaining about ethics and precedence. This was the reply which is in the name of Caroline Ash.

Dear Dr Dalby
Thank you for your message. I understand your concern that we should publish an item on the same topic as yours shortly after having  rejected your report. However, I should clarify. The Verhagen piece is published in the Insights section of Science and is therefore intended as commentary without data. Your paper was submitted as a formal research report with data that would normally be subject to peer review.
We receive many excellent papers, but we are limited in the number and subject areas we can pursue in each section of the journal and find ourselves rejecting the majority. Although we decided against in-depth review of your paper we enjoyed reading it and unless you have submitted elsewhere would encourage you to try our new journal Science Advances:
I hope this information is of some help and I am sorry your experience at Science was disappointing.
Kind regards
Caroline Ash
Caroline Ash
Senior Editor, Science;
ASI Science International, 82-88 Hills Road, Cambridge, UK, CB2 1LQ
+44 1223 326500;

So therefore anything we read in the Insights section of Science should be taken with a pinch of salt because it does not contain data and it is only a commentary. Anyway I went through the Science paper with a fine toothed comb and found a few errors that raise concerns. First there is s a different lineage in circulation in North America and more seriously the reference cited to support the figure and in fact the main conclusion about migration was wrong. So I submitted a letter to Science pointing out these faults. 

So I expected them to take this seriously as the error in the reference fundamentally undermines the paper and there is no alternative reference that collects the data that supports the figure and conclusion other than my own paper which is in PeerJ preprints. So I was fairly astounded by their reply.
Dear Dr. Dalby,

Manuscript number: aaa8769

Thank you for sending a Letter to Science. We have read your contribution but will not be able to publish it.  We invite you to leave an online comment instead.  To leave a comment, go and find the published paper to which your comment refers.  Then click Leave a Comment to submit.  Online comments should be no more than 300 words.  Excerpts from comments are occasionally published in the print Letters section of Science.

Note that we will post a correction to the reference you mention.

Please do not reply to this email, as it will not be read by Science. Unfortunately, the volume of submissions precludes specific discussions about individual submitted letters.


Jennifer Sills

I had asked for Caroline Ash to act as Editor on the letter submission as she had been the one who responded to my earlier e-mail and had been the signatory on the original rejection. I would say that my experience with Science goes beyond disappointing.  I would say that at this moment I am extremely angry with their behaviour. I would encourage anyone reading this to only support open access publication and transparency in peer review.

Sunday, 18 January 2015

Books I have read

When Bacon wrote his dictum about books there were so few that you could not be over-powered by their number. Now more than ever we are over-whelmed by writing and his dictum has become much more significant.

Now we have to distinguish the mundane from the profound, we have to distinguish the books that have an impact on the reader from the general background noise.  Not only are some books more significant, but they also take on a life of their own, moulding the experiences and beliefs of the reader.  Each book has its own time, it has order and it has age.

I keep a list of all of the books that I have read so that I can try and unpick the influences that they have on me. Now I have realised that just knowing what I have read is not enough. I need to know when I read it and in what order. For the last three years I have kept an ordered list, and pushed my reading to 50 books a year.

For example I read Brave New World in my 30s and for me it was a profound book because it struck a chord with my age, my experiences and the world in which I lived, but I doubt that the experiences of anyone else would put it into the same context. Reflecting on it, I think it is a book that is more likely to resonate with older readers with a wider range of experiences and I think that I would have appreciated it less if I had read it as a teenager.  The same is true of Borges, Labyrinths. Now for me it is an amazing book, but I do not think I would have grasped its many different layers and themes if I had read it in my teens or 20s. Reading it later I find that it has so many hidden ideas that make it a greater work of thought than many works of philosophy.

Saturday, 10 January 2015

The Downton Delusion

Downton Abbey seems to be a national obsession but I can't quite understand it myself. Why do we enjoy watching a generation of injustice, inequality and wasted opportunities and celebrate them like they were the "Good Old Days". There was nothing good about them but they seem to be the golden age to the British.

My grandma died this week. She was 95 which is a good age and she had loved through a lot of change. She got her first passport to come to my wedding in Spain when she was 81. She was an impressive and strong woman but I have to think what she would have been . Her parents were servants to the aristocrats. Her dad was the chauffeur and I think that her mother was the upstairs maid. She was born to Downton parents, those that lived at their masters wishes. My grandma went to school at Wyggeston Girls Grammar School where she was even a prize winner. I do not know when she left school and with what qualifications but this was a time when women were still not encouraged to continue their education. She had her teenage years in the depression and her early twenties were the war years. What saddens me most is what she could have been if she was born in 1979 and not 1919.

That is what we are celebrating with Downton, the inequality that wasted potential like my Grandma's. The wealthy had their great houses and the aristocracy had their protected lives, because some ancestor had done some favour to some monarch. But why because my ancestor's were successful should I expect to be successful as well? They had their privilege and success built in. This was first weakened by Lloyd-George's "People's Budget" but mostly the inequality and injustice was a consequence of the post-war second world war settlements. The returning soldiers and the women who had fought and worked at home wanted a different world and so the Downton Age passed. There were still pockets left but the 60's and 70's took care of them. I still remember the sense of deference amongst the farmers to the old aristocrats, who had once been their landlords.

Now we have this return to idolising the gilded Downton Age when we are in the middle of another depression caused largely by the same families who caused the last one. The aristocrats who we thought had been vanquished just became the much more diffuse "Establishment". Why do we idealise a time that was so unfair, so unjust and so unequal. We love Agatha Christie where Miss Marple and Hercule Poirot come from the same Downton world with trips on the Orient Express, or cruises down the Nile. We fantasize about a life that did not exist for most people and forget that it was the nineties and noughties when we really "Never had it so good". Now we are entering another age of inequality and instead of fighting against it we are embracing it. It seems that we want to be back in Downton, knowing our place and doffing our caps again.

Continuing the theme on Evolutionary Biology

Yesterday I was tumbling ideas around in my head but there is something important I missed and that is Monod - Chance and Necessity. Although philosophers have attacked it, it does contain a kernel of truth and the beginnings of an important theme. That is that evolution is random but selection makes necessary choices. So we have some developments which will happen over and over again such as eyes, long necks and photosynthetic systems and then we have accidents that are not required by the environment.

This theme is developed by Ian Stewart and Jack Cohen in all of their books and also by Murray Gell-mann in the Quark and the Jaguar where he talks about the amount of information needed to describe a system. Things that have to happen and that are homogeneous across a set require less description than the unique properties that are heterogeneous.

Where we lack theory is in describing the unique heterogeneous events - we struggle withe heterogeneous entropy or any systems because there are no statistical descriptions of the unique. You cannot average them. This is where we need to build our theories, on the edge of maths.


Monod - Chance and necessity
Ho - The Rainbow and the Worm
Gell-mann - The Quark and the Jaguar.
Stewart and Cohen - Figments of Reality
Stewart and Cohen - The collpase of chaos.
Stewart, Pratchett and Cohen - The Science of Discworld I-IV.

Friday, 9 January 2015

Trying to get my Head Around Evolutionary Biology

My mind goes round and round and round to the same ideas and the same connections but I am finding it very hard to out them all together. There is something very deep and fundamental that we are missing in biology, the reason why theories like relativity do not exist.

First is the stupidity of biologists trying to use statistical methods to "average out" historical events to eliminate "accidents". This all stems from Popper and his view of science, which is alright for physics but not appropriate for Biology. You ignore history in a biological problem at your peril. This was never clearer to me than at an ISMB meeting where I had been subjected to the same talk twice, by two different post-docs from the same group (the P.I. was on the organising committee) where the presenter was asked about how well the method worked on real data. The reply was that it didn't. It only worked on the model data. At that point I gave up on ISMB meetings because they are too incestuous.

The problem is that that synthetic data is all nNormals and Poissons and nothing like reality. Reality has nasty things like extinctions, bottle-necks, frozen accidents etc. Reality has population structures, isolation, incest, dispersion and above all else a richness of history that you cannot average out. This is why Mayr was so sceptical about the "bean counters" like Haldane, Fisher and Sewall-Wright. So trying to impersonate physics in quantitative biology throws the baby out with the bath-water. This is not to deny statistics its role but biology is full of what Taleb calls Black Swan problems. These are the out of the usual events, the unknown unknowns that mean the unexpected has a disproportionally large effect. So our knowledge and possibility of knowledge in biology is limited by the barrier of experience that Hume identified.

The error of ignoring history is compounded by excess reductionism that fails to look at the system. How can I judge the fitness of an organism in isolation from its environment? That is why in vitro and in vivo experiments differ so much (see Holmes on Viral Evolution). There have been those who have worked in solving these problems but usually they have been marginalised by the reductionist, statistical main-stream. Waddington stands out amongst these with his epigenetic landscape for development, but more important than that is extending this to evolutionary landscapes through evolutionary canalisation. Monod made some contributions towards this in Chance and Necessity where he introduced gratuity as a side-effect when there is a change in the landscape so evolution has access to new areas. Kaufman put these ideas into a computational and numerical frame-work. The recent appearance and very rapid disappearance of systems biology also produced a burst of activity particularly in the landscape view from Kitano.

The basis for where we need to go is already written but nobody has put it together in a useful way. There are so many works that are ignored and connections missed. These problems are hard - they frustrated Darwin.


Waddington - Towards a Theoretical Biology 4 volumes (The bible of real systems biology).
Waddington - The strategy of the genes (Canalisation - if an evolutionary biology text does not cite him do not believe them).
Taleb - Anti-fragile (His Magnum Opus about Black Swan problems and solving them).
Haldane - On the Causes of Evolution (One of the three founding works of evolutionary genetics).
Maynard-Smith - Evolution and the Theory of Games (Shows that mixed solutions work - not the message most take from it).
Axelrod - The Evolution of Cooperation (Tit-for-tat is the best and cooperation gives benefits).
Sewall-Wright - Evolution and the Genetics of Populations 4 volumes (His complete work on population genetics).
Kimura - The neutral theory of molecular evolution (An important assumption of coalescence).
Holmes - The Evolution and Emergence of RNA viruses (Quite specific and not always right but some good points).
Kaufman - Origins of Order (Has quite a lot of holes but it is a start).

Thursday, 13 November 2014

What does a graduate look like?

Why do companies hire graduates? Why is a graduate something different to someone who has worked their way up in the company? Why is there graduate level entry into most professions? Graduates have to be something different to those without a degree but what is it?

It isn't about knowledge.

There is no reason why a graduate should no more than a non-graduate. The same facts and information are available to both of them. A non-graduate can read a book or an article as well as a graduate. A non-graduate can look up the answer using wikipedia or Google as well as a graduate. I can often get the same degree of training whether I am a graduate or not a graduate. So why are graduates so desirable? 

It might be about expertise.

There is a difference between knowledge and expertise. You can fake knowledge, but you cannot fake being an expert. Perhaps the best description of this difference is by Harry Collins in his book "Are we all scientific experts now?" Where he describes how he has become a pseudo-expert in the sciences he follows as a sociologist/philosopher trying to understand how science develops. Although he can hold a conversation like an expert, he is not an expert because he does not actively contribute to the field. This is the same core argument in all the "Bluffer's guide to ..." and I have to admit that this has been one of my personal attributes. It is hard for me to determine if I am an expert in any particular field but I am a pseudo-expert in several fields. That is the problem of being multi-disciplinary. So by writing this do I go from being pseudo-expert in academic policy to a real contributing expert? Other examples are popular science writers whose expertise is in communication, not in science. 

Everyone says it is about "Critical Thinking".

The only problem with this is defining what critical thinking is. 

I was just asked to write a reference for a student and the first question they ask is, "Is the applicant capable of independent thought and learning?" Sadly too often I am starting to write no. Not because the students never had that ability, but because it has been beaten out of them by years of secondary education and the expectations imposed by £9000 a year fees. Students go from the wonder and exploration and flexibility of primary learning to the passive dependence of secondary education where teacher's salaries and jobs depend on league table positions and results. Then they go to university and want more of the same. Only better as now they are paying £9000 a year for that knowledge and those skills to be given to them while they passively wait for it to appear.

Critical thinkers are the students who can shake off this passive expectation. They are the students that realise that the £9000 a year is there to make them independent thinkers, confident in their own viewpoints and their own abilities. They realise that the future will not have jobs for life and that we all have to be flexible in what we do and that lifelong learning is going to be essential to their employability. Marcia Baxter-Magolda has written a lot about this process of students finding their own way and starting to author their own knowledge but this is not widely disseminated amongst the higher education community. 

Impacts on Higher Education.

For those who work in higher education the pressures on funding and work-load often come from research more than teaching, and research often where academics find most purpose in their careers. From a cynical viewpoint this leads to one of two approaches:

1) Select the students who are natural critical thinkers. These are the brightest and the best who can learn independently from the start and who would get the same results if you taught them nothing at university (see Academically Adrift for a survey of US universities showing that this actually happens). This gives you more time for research and teaching doesn't really matter. This is the preferred approach of the interview and A* entrance approaches.

2) Be less selective at entrance levels but then teach in the same passive and dependent way that they have been taught for the last 5 years to keep them happy and not rock the boat. Some students will find there own way to being critical thinkers and everyone else 

Both of these are appalling views, and they certainly exist even if they are not universal. Academics reading this know if they are following one of the two approaches although they will all deny it.

In truth there is a better way that is good for students, good for academics and good for research.

The better way.

Go back to primary school learning. Go back to exploration and play. Ditch a large part of the lectures and factual curriculum and focus on the skills that you need to be able to access those facts and that knowledge. The focus has to be on the threshold concepts that prevent students understanding at a higher level. Forget the fine details they are irrelevant in an information cheap age. Teaching should be research led and students should be research involved. Academics have to trust in student's ability. There are plenty of diamonds in the rough who had poor grades at A-level who can shine if you give them the right environment. There are also plenty of students with A*s who struggle to be independent critical thinkers. 

Students of all standards need to be treated equally in their expected outcomes. If you have the same high expectations for all students then they will push for those targets. If you set the barriers low, especially for independent thinking, you will get poor performance. If you think the students can't do it, then you are pushing them into failure. Until you try it out you don't know. Even from one year to the next there is more variation than you can predict. You have to give them a chance to succeed but also the possibility of failure and you have to put into place assessment that helps students to learn. It cannot be a one shot if you fail you fail approach. Students have to be able to fail without desperate consequences so that they can learn and get feedback and improve. 

When students need support then they should have it, but the need is not when they feel they need it, it is when the tutor feels that they need it.  To enable this successfully all academics need to be reflective practitioners and to explore what works and what does not. But this does not mean that as an academic your judgement should not over-ride that of the students. For now you are the expert and they are learning and sometimes students do not appreciate what you know is good for them.

To do this academics have to feel the same commitment and purpose in teaching as they do in investigation and teaching must not be undermined in terms of progression, as it is in some institutions. An academic's legacy should not be just judged on the volume of papers written, but also on the quality of the students taught.

Friday, 10 October 2014

Data Driven Biology

This is where biology is going to go. Everyone always thinks that biology is the easiest of the sciences, but in terms of building models and making predictions it is by far the hardest. Maths and physics are trivial by comparison to modelling even the simplest living creature.

We need more data, more computer power and more maths to generate theoretical biology. It has been tried many times before, the last version was systems biology that fell flat on its face with excessive claims and little foundation. So what next?

Biology with:

  • Remote sensing.
  • Continuous monitoring.
  • Multiple level measures (from the molecular to the whole organism).
  • Microfluidics.
  • Next Generation Sequencing.
  • Medical Informatics.