Geoff Barton's blog

Computational biology and more...

FizzBuzz and Vectors

 

Another un-posted thing from a few years ago!  I guess I figured we had already discussed on twitter so “what’s the point”.  Still, nice to summarise with a few more words here…

Chris Cole (@drchriscole) posted a link back in 2019 to

https://www.r-bloggers.com/fizzbuzz-in-r-and-python/

on twitter (you can see the thread here), which poses a simple coding problem that is claimed to be used often to test a candidate’s coding knowledge:

In pseudo-code or whatever language you would like: write a program that prints the numbers from 1 to 100. But for multiples of three print “Fizz” instead of the number and for the multiples of five print “Buzz”. For numbers which are multiples of both three and five print “FizzBuzz”.

The author of the article shows some simple and clear ways to solve this problem in R and Python that would certainly convince a possible employer that you knew how to do basic coding. 

for (i in 1:100){
 
  if(i%%3 == 0 & i%%5 == 0) {
    print('FizzBuzz')
  }
  else if(i%%3 == 0) {
    print('Fizz')
  }
  else if (i%%5 == 0){
    print('Buzz')
  }
  else {
    print(i)
  }
 
}

Chris though correctly pointed out you can solve the problem with only two “if” statements and wrote some pseudocode to show how:

I only have my phone, but pseudo-code would be something like this.




for i in 1:100
outstr = ""
num = i

if i divisible by three
 outstr = "fizz"
 num = ""

if i divisible by five
  outstr = outstr + "buzz"
  num = ""

print num + outstr

The big strength of R though is that it is a vector language so I (@gjbarton) came up with the following:

My version in R but with three “if”s. There is prob. a really elegant way to do this in R...

a = 1:100
b = a %% 3
c = a %% 5
d = b + c
t = replace(a,b==0,"Fizz")
t = replace(t,c==0,"Buzz")
t = replace(t,d==0,"FizzBuzz")
t

I'm a very rusty R programmer, first code in at least 3 years probably :-(

Here I create three vectors, b,c,d that have zeros at positions where the number is divisible by 3, 5, or both 3 and 5.  I then substitute the appropriate text for zero in the result array t using the built-in “replace” function.

David Martin pointed out that I actually used zero if statements… so I guess this is a “win” ?

You might ask why solve the problem like this?  It appears to hide the basic logic that is very clear in the first solution with an “if” block.   For a very small task like this, the “if” block is probably clearest, but as soon as you start to extend the logic, if blocks can get very messy and hard to read.  For example, it would be easy to extend the vector method to include more options such as “also divisible by 7” or to explore all combinations while still maintaining fairly concise code.

There is also an efficiency consideration as the size of the vector grows.  Generally, computers are great at running down a big vector and doing the same simple operation on it.   Once you introduce complex nested “if” statements on each element of the vector then the code has multiple possible branches and so takes more steps to execute at the CPU level.  This can mean it runs a lot slower or that it might run into memory issues.   If the code is compiled though, the compiler might be able to spot things like this (The people who write compilers are true artists!) and so there will be no performance advantage.

 

Why “Validate Experimentally” is wrong. “Seeking Consistency” is right!

I hate the expression “Experimentally Validate…” or “Validate Experimentally…” particularly when applied to computational biology studies.

There is an assumption in biological sciences that the only way to be sure of a result suggested by computational analysis is to perform an experiment.   However, it does not make sense if you have used sophisticated computational methods to analyse the results of thousands of experiments published over decades to arrive at a conclusion, to then run a handful of experiments to “validate” your findings!

In biology, since the systems being studied are complex it is hard to minimise the variables down to one under investigation.   As a result, it is usually very difficult for a single experiment to “prove” a finding.   The very low threshold of statistical significance that is acceptable in biology is a consequence of this problem.  Whereas in most physical sciences you need a 5 or 6 sigma result to publish, in biology (and medicine) the threshold is 1.6 sigma.  In other words, about a 1 in 20 chance that the result is wrong.

Accordingly, experimental biology works by starting with a hypothesis and then gathering evidence for and against that hypothesis by carrying out a series of experiments that address the question from different angles.  At some point, enough evidence is gathered to support the original hypothesis or a hypothesis modified in the light of the experimental data gathered in the laboratory and from work published or otherwise communicated from laboratories world-wide.   This may be enough evidence to justify writing up for publication of the study with some conclusions based on all the evidence accumulated in favour of the hypothesis.  Although rarely combined into a single statistic, the combination of multiple lines of evidence that are consistent provides confidence that the result is real and not a chance artifact.

Of course, many experiments don’t work or perhaps give ambiguous results, or possibly give results that contradict what all other experiments on the system seem to indicate.   Contradictory results suggest further investigation is necessary: “Can I believe these contradictory results?   Do I trust that single experiment more than all the others?”   Further experiments might be designed to test this, or perhaps in the worst case, the investigator might put those contradictory results to one side as untrustworthy and push ahead to publish the positive data.   This is not necessarily wrong if the experimental method being excluded is generally known to be unreliable.  Also, it is rarely possible to explore every possible angle in a single study; time and money are not limitless and there is value in publishing results even if not completely conclusive.  However, the emphasis in the current publishing model is that only positive results are valuable, so scientists gain skills in putting a positive “spin” on their data and conclusions when writing up.  This also requires readers of the scientific literature to “read between the lines” of the positive spin to understand the true confidence in the result.

Referees of papers may spot potential deficiencies in the justification of the results given the experimental data and so suggest further experiments or analysis.  Authors may have to do these experiments and present results that satisfy the referees in order to get their work published.  In this way, the final published account should be as good a representation of understanding as is possible with the resource and minds that have been thinking about it.

Of course, it may turn out that the one experiment that did not fit the hypothesis was actually showing something fundamentally wrong with the hypothesis.    This may not be obvious immediately, but only emerge years later after substantial resources have been spent building on the erroneous findings.

Good experimentalists are highly skilled at identifying possible flaws in their own experiments and those of others.  They are superb at suggesting further experiments to carry out to help eliminate possible artefacts in the study.   This critique of their own work and that of others is what drives science forward and while many results will be misleading and contradictory, leads ultimately to greater understanding of biology.

“Validation” in experimental terms might mean using multiple technologies that explore different aspects of the biological system.  For example, NGS to look at transcript expression, proteomics to probe protein complement, the response of both to chemical probes that are known to affect specific processes and pathways, the effect of “knocking down” a specific gene and so on.

However, “validation” is not really the right word to use.  What is being done is seeking support from complementary methods.  A better word would be “Consistent”.  In other words, that the results of analysing experiments from multiple techniques are consistent with an underlying hypothesis.   The scientific process is to “Seek consistency” towards a clearer understanding.

Computational analysis is no different in this respect.  It is fine to do some new experiments based on the computational study to look for consistency.  Indeed, the goal of an analysis is often to suggest new avenues of experimentation.  However, this is rarely a true validation of the computational analysis.

 

What should you call your research group?

After studying really hard, getting a good B.Sc., flying high in your Ph.D. and as a postdoc, you have finally amassed enough research experience and scientific research publications to apply for Principal Investigator (PI) positions.   You succeed in winning, against massive competition, a prestigious Fellowship or other grant to start a research group in a great department and so can now start to forge your own independent research career as a PI!  Fantastic!   As I explain in my summary of Academic research careers this is in some ways, just the beginning!

Once your group grows beyond yourself, there is one important question.  What do you call the Group?

There is a long tradition, at least in places I have worked, to call the group after the person who forms it.   Some would argue this is egotistical and somehow gives the impression that all the work is done by the PI and that the group members are just a supporting act.   I think it is very rare for this to be true though – science is a team effort and in my experience, most PIs do a lot to acknowledge and and support their team.    In fact, the  “Group called after the PI” tradition reflects the realities of how research groups are created and funded in Universities and many research institutes.  They are built around a PI.  If the Group is to succeed, the PI, with the support of colleagues in their group has to win grants, support and train research students and postdocs and steer the Group to publish scientific papers and other outputs that advance the field.   If the PI decides to leave their job or retires, then typically the group dissolves.

Some argue that it is better to call the group after the research theme that the PI works in.   Some do this and that is fine.  Unfortunately, PIs often shift the direction of their research, so a group that is called one thing when the group is first created, may become unconnected with what the group actually does a few years later.  I suppose you could change the group name if that happens, but that is a chore, particularly if the name is used on the Web and Social Media such as twitter.

That’s the generalities, what about me? 

I first established an independent research group in the Laboratory of Molecular Biophysics, Department of Zoology, University of Oxford in 1989.  The Laboratory head was (Sir) David Phillips to begin with and then Louise Johnson (later Dame Louise).  The Laboratory had 8 or 10 research groups in it, each led by an individual PI and the groups were all referred to by the PIs name (e.g. Johnson Group, Stuart Group, Barford Group and so on…).  Naturally, when I joined, my group was called the Barton Group by the Laboratory and the Department. 

I can’t remember if I thought this was weird or egotistical or not.  I do remember as a fresh PI, enjoying the fact that I was independent of what the other groups were doing and our Head of Laboratory (Louise Johnson for most of the time I was there).  The group name also made clear that I was not someone else’s postdoc, though as is common with young PIs, I had to point this out to people a lot in my early career.

There is a slight computational twist to this.  When I started as a PI I had just enough equipment funds to buy a Unix workstation (A Sun SPARCstation 1) to use for my research.  I had to configure this and manage it myself.  At one point in the slow installation of the operating system from tape, I had to provide a name for the computer.  I was stumped, “Err, what do I call it?”  Since this was the first time I had ever “owned” a computer, I decided for some reason to call it “geoff”.  I thought, “I can change that later to something more sensible…”.  However, I didn’t know how to change the name (it was harder to find out things like this without Google) and so the name stuck.

So, the network name for my computer was “uk.ac.ox.biop.geoff” which, when we went fully onto the internet became “geoff.biop.ox.ac.uk” .  I was one of the first in the UK to establish a group web site in about 1993 I think, so naturally, it was called the Barton Group website and was hosted on www.geoff.biop.ox.ac.uk.  Sigh…   This was a real embarrassment but at least it did make clear whose group it was…

Roll the clock forward a bit to 1997.  I went to work at the European Bioinformatics Institute near Cambridge, UK.   In the early years of the EBI the tradition for the few research groups was to call them after the surname of the PI.  So, my group site became “barton.ebi.ac.uk” alongside “sander.ebi.ac.uk” for Chris Sander’s group and others.

When I moved to the University of Dundee in 2001, I compromised by keeping the name of my group as Barton Group, but naming the website, “compbio.dundee.ac.uk”.   This gave continuity and “Brand identity” since by this time we provided a number of bioinformatics resources to the world and it made them easier for people to find.

This is pretty much where we are today…. There is a problem though.  The generic domain name “compbio.dundee.ac.uk” is just “Barton Group” but in 2013 we formed a Research Division of which I am one of six PIs, which after much discussion is also, confusingly called “Computational Biology” – it has its own simple webpages on lifesci.dundee.ac.uk.

Ho hum…

Thoughts about Brexit and Scottish Independence – after the Conservative Party victory in the UK General Election

Introduction

I live in Scotland and I’m strongly pro-EU and pro-UK, but the election result on Thursday and the now inevitability of the UK leaving the EU mean it is time I should re-evaluate my position on Scottish Independence.

In my post from March 2019 I explained why I did not support breaking up the UK or the UK leaving the European Union.  Fundamentally, I believe that Nationalism reinforces differences rather than embracing them and people achieve more when they work together at all levels.  I think we should be working to build stronger links with other nations, not finding ways to make ourselves different. 

So, as you can imagine I had hoped that Brexit would not happen.  Whatever you measure, Brexit is a bad idea for the UK.  It separates us from one of the largest trading blocks in the world, it introduces extra complexity and costs into almost every aspect of our international relationships.  It moves us from being rule makers as a major economy in the EU to being rule takers in order to trade with our former partners.  It reduces our bargaining power in relationships with major economies like the USA or China.  Brexit removes the right for UK citizens to live and work in EU countries and so makes it harder for UK citizens to move to where the best job opportunities are.   It also makes it more difficult for UK business and public sector such as the NHS to recruit and retain the best people from the world to build and sustain our economy, our health care system, our scientific research and education systems.

However, with the election result on Thursday, Brexit will now happen for sure.  We’ll leave the EU at the end of January 2020 and there will follow a difficult time of negotiations about our future relationship with the EU.   As many have said, this is not the end of the process, but just the first step.  The entire business of splitting away from the EU will be costly and those costs will likely be felt greatest by the poorest in society.   This makes me sad.

Scotland after Brexit

As well as providing Boris Johnson with a strong position to push his party policies, the election result has emboldened the SNP in Scotland with the election of 48 MPs to the Westminster Parliament, 13 more than they had in the last parliament.   There are now many questions about whether it will be possible for Scotland to hold another referendum on independence (IndyRef2) in the near future and what the result might be.   I have to decide whether I would support independence in IndyRef2 or not.   Here are some pros and cons as I see them at the moment, but I am happy to listen to reasoned arguments about this position:

Scotland Staying in the UK

Positives

  • We already have our own Government.
  • We have control of the NHS in Scotland.
  • We have control of the education system in Scotland.
  • We have control of the legal system in Scotland.
  • We print our own bank notes.
  • We have strong representation in the UK parliament (59 MPs).
  • We have the economic cushion of the UK economy (which will still be big even after Brexit).
  • We have the protection of the UK armed forces.
  • We do not have to replicate all government services but can take advantage of UK economies of scale.

Negatives

  • We don’t have full control of taxation.
  • We will leave the EU.

 

Scotland leaving the UK

Positives

  • We’ll still have control of everything we already have control of as part of the UK.
  • The Scottish Parliament will have full control to make decisions/borrow money etc.
  • We can apply for EU membership independently of the UK.

Negatives

I spell these out more fully in my March post.

  • We lose the economic cushion of the UK.
  • We still won’t be part of the EU – membership should be possible, but will take time to negotiate and for Scotland to meet economic requirements of membership.
  • If we do join the EU then we will be a much smaller player in that Union than we are currently in the UK.
  • We won’t have automatic access to all the services we currently enjoy as part of the UK.
  • Funding for Science will be uncertain.
  • It will cost a lot to split away from the UK and will take time.  Likewise, if joining the EU is possible, there will be costs and it will take time.  The poorest in society will suffer in the transition.

Summary

I don’t vote on emotional grounds.  For me, how I campaign and vote in a future IndyRef2 rests on clarity of the deal and process for leaving the UK and potentially joining the EU.  

If we get to vote again on independence, then I would want to see clear evidence from those promoting independence that a path to full EU membership had been agreed ahead of the vote.  Without EU membership, it seems likely that Scotland would struggle to balance the books as a nation.  I’d also want to see a clear and detailed agreement with the UK government on what the divorce deal with the UK would be.

Since I work in a University and do scientific research, I’d need to see hard evidence that Scottish institutions that currently rely heavily on UK charities and government funds would still be able to obtain funding from those sources.  There were no such guarantees in the lead up to the last independence referendum.  Indeed, it was not even clear what currency we would have used had the vote been Yes.  There were huge questions around pensions that had not been answered and many, many more issues.

I hope that the SNP and colleagues who promote independence for Scotland will not follow the path of the Brexiteers by peddling untruths in support of their cause.    Rather, I look forward to hearing concrete, well-research data on which I can base my decision.

 

Thoughts about the Scottish Referendum on breaking up the United Kingdom – parallels with Brexit

Prologue

I wrote this in Summer 2014 before the referendum on Scottish Independence that was held on 18th September that year.  While it refers to Scotland leaving the UK, many of the arguments are the same for why the UK should stay part of the EU.  I have not published it before, but given the parallels with Brexit I thought the time was right.

Background

I am British and have lived in Dundee, Scotland for the last 13 years.  Previously I worked in London, Oxford and Cambridge.  On the 18th September 2014 I will get to vote on whether Scotland should leave the United Kingdom (UK) and go it alone as an independent country.  Here are some of the reasons why I will be voting NO to breaking up the United Kingdom.

Philosophy

Philosophically I believe we should be drawing countries together, not splitting them up. There are enough problems generated in the world by nationalist groups or groups that only care about a subset of the population divided on historical or religious grounds. We need to learn to work together with people of all beliefs and origins. The UK has done this successfully for 300 years and is rich and successful because of it.  Why change now?

Being a Scientist

I am a research scientist and I moved with my young family to Dundee in 2001 because of the excellence in Life Sciences and Medical Research at the University of Dundee. As such, you could say I am a part of the “Brain Gain” that has made Life Sciences at Dundee the top Life Sciences research department in Scotland and one of the top 5 in Europe. I have seen the department I work in grow over the last 13 years to around 900 people with annual income last year of  £90 million.  This funding has nearly all come from UK Government and charity sources.  I have seen two fantastic new research buildings open in this time thanks to generous funding from charities and UK Government.  My own team moved into the latest building, the Centre for Translational and Interdisciplinary Research (CTIR) in July.  Establishing such a success story in science takes decades, but as I will show below, this is all under threat if Scotland votes YES to independence.   

Like all research, mine is international in scope and I rely on winning research grants from government agencies and charities in competition against scientists across the UK and Europe.   The research grants pay the salaries of the highly skilled staff in my research team and so support the shops, taxis, restaurants and other services in Dundee.

Science funding in the Life Sciences is dominated by UK-Government funding agencies and UK-based charities such as the Wellcome Trust.  However, there is no clear message about what would happen under independence.  The Wellcome Trust who fund 60% of my team’s work might impose the same model as they do in Ireland and only fund 50% of project costs, or they might choose to fund nothing in Scotland.  Unfortunately, these possibilities have not been considered by the Scottish Nationalists so there is huge uncertainty about what would happen to our funding.  Perhaps some deal would be worked out with the rest of the UK after independence, but this will take time.  Science moves very fast and we cannot afford to tread water and wait years for politicians to negotiate such a deal when we are in competition with scientists across the world.  In any case, science funding is likely to be low on the list of priorities for an independent Scotland.  Sorting out the currency, major industries, banking and pensions will likely absorb all the time first.    

Although my own job will probably be secure, my ability to do my job will be made very difficult by a YES vote.  My job is already more difficult because of the referendum.   Since the referendum was announced, I have had problems with recruiting the skilled people I need to do my research.  Previously, if I advertised a job I would have 60 or 70 applicants, many of whom would be from Cambridge, Oxford or London Universities or other top centres in England and around the world.  Now I see hardly any applicants from these institutions.  People tell me this is because of the uncertainty about what might happen after 18th September if there is a YES vote. 

Science does not stand still, it is international and we are losing out because of this uncertainty.  If there is a YES vote, not only will recruitment become even more difficult but worse, many of my highly skilled and successful colleagues say they will look to leave Scotland due to the huge uncertainties about science funding and the wider implications for their pensions and savings.   People with these high skills always have other options for jobs so this Brain Drain would seriously damage and possibly destroy the international reputation of the institute I work in that has been built up in Dundee over decades.

Where will the people come from?

The Brain Drain raises a further question. Where will the skilled people come from who will be needed to run an independent Scotland? How will an independent Scottish Government attract the very best and brightest people from the world to run the country and its major industries when there will be enormous economic uncertainty in a newly independent country?

Will Scotland be better off?

Nobody really knows whether Scotland would eventually be better off independent of the rest of the United Kingdom. However, what I can say with certainty is that, if independence is chosen by the residents of Scotland on 18th September, the transition will be very long, disruptive, and painful to many people. Think of any major change such as a marriage breakup or the breakup of a large company.   With divorce, the transition away from a partnership is very difficult for both partners.  Even if one partner is initially pleased with a new relationship, there is no guarantee that relationship will be as happy as the old one in a few years time.   Likewise, with a company breakup, it may make sense to shareholders or others that this is the best course, but many people lose out in the process.  A YES vote would tear apart a relationship that has lasted for 300 years and made the UK one of the most successful nations on earth.  What can we possibly gain from such a break up?

Uncertainties of transition to an independent Scotland.

(a) Even if one were to accept that Scotland could be better off as an independent country, the transition would take decades to complete and consume vast resources.  It is pure fantasy to suggest it can all be done in 18 months.    Just about everything would have to be negotiated, from currency, nationality, transport, BBC, etc etc etc etc.  In science funding if as the SNP would like, we keep a science funding area and keep the BBSRC, MRC etc with money provided by Scottish Govt to Westminster, then the level of this funding would have to be negotiated, probably every year.  At the moment, Scotland does better per-capita than the rest of the UK out of science funding, but this does not seem to be factored into any of the SNP budget plans.

(b) Disruption to recruitment etc.  We have already seen problems with recruitment due to the uncertainty introduced by the referendum.  People from the rest of the UK are applying to us in smaller numbers and if from outside Scotland, when invited to interview, always ask “what will happen if Scotland goes independent?”.  We have to put a positive spin on this, but no one knows the answer.  One colleague told me that a very talented Chinese student he offered a highly prestigious and fully-funded Ph.D. to turned it down because he had seen the news about “political unrest” in Scotland and did not want to risk coming to a country like that!

(c) By going independent, Scotland would be breaking new ground.  The UK would be the first prosperous nation to break up without violent conflict.   Every institution that we currently take for granted would have to have its terms renegotiated with what was left of the UK.  For those organisations that the YES campaign would like to keep sharing with the rest of the UK (e.g. science funding) the details of the funding model would have to be negotiated.  This will take years, not months to achieve and all for what?

We already have a devolved government

In Scotland we already have control over major parts of what matters to people. For healthcare, the NHS in Scotland is separate from the NHS in England and so less vulnerable to the creeping privatisation that the current conservative government is introducing in England.   The Scottish education and examination systems are also under control of the Scottish Parliament, so allowing for free tuition at university.  The legal system is independent and has allowed Scotland to lead on many issues.   

Currency?

The SNP want to keep the pound in a currency union. They want to keep other UK-based institutions such as the Research Councils that fund scientific research. There are probably other UK institutions they would like to keep.  In Scotland we already have control over health, schools, universities and law.  Under the SNP plans for independence we would also keep the same currency and other UK organisations so why introduce all the complications and expense of splitting up the UK?

EU Membership?

There is no clear message on whether an independent Scotland would be able to remain a member of the EU.  If Scotland does remain in the EU then there will be big implications for any company or public sector pension schemes that are UK wide.  Such cross-border schemes would have to be in credit.  Few if any are at the moment. What would that mean for all those with such pensions?

Citizenship?

If Scotland were to go independent, we would have the option of a Scottish Passport. However, it is not at all clear whether all current British Citizens living in Scotland would also still be eligible for a British Passport.  Would children born in Scotland after independence automatically have the right to British Citizenship?  Would those who only had Scottish Citizenship receive the support of British Embassies and Consuls overseas or have to rely on completely new Scottish Embassies that currently don’t exist and would have to be set up at huge expense?

Representation in Westminster

In the televised debate with Alistair Darling on 5th August, Alex Salmond (leader of the Scottish Nationalist Party) repeatedly said that for more than half his life, Scotland had not got the UK government it voted for.  One could make the same argument for many other parts of the UK, indeed most individuals, but they are not asking for independence!  In the 2010 elections even London elected more Labour MPs (38) than Conservative (28)! 

Who stands to gain most from a YES vote?

I think this is just the politicians who are clamouring for more power. All we hear from the SNP politicians is their thirst for power.  The significant powers they already have in the devolved government are not enough for them, they want more.   They are not really thinking about the consequences for the rest of the people in the country, just their own selfish gain, their moment of glory as they celebrate leading Scotland away from its partners in the UK.

Summary

There is no strong economic or social case for splitting up the successful UK.   A strong Scottish Government within the UK is the best option for Scotland. It gives the ability to make decisions locally while having the security of being part of one of the strongest economies in the world and avoids the huge risks and uncertainties of breaking up the UK.

Epilogue – written on 24th March 2019

Well, Scotland voted to stay part of the UK and people like me breathed a big sigh of relief and got on with life.  Unfortunately, the UK Government then took us into yet another referendum, this time  on membership of the European Union.  As we know, they did not get the result they expected, nor did they get the result that the majority in Scotland voted for or the majority in many other parts of the UK such as London.   This leads some in Scotland to argue more stridently for another independence referendum.  While I am very unhappy about the way we have been ‘led’ since 2010 by Westmister,  I stick by my view that whatever happens with Brexit, people in Scotland will still be better off over the coming years as part of the larger United Kingdom.

 

 

 

The Fragility of our Civilisation’s Knowledge…

In my more pessimistic moments, I consider it likely that, driven by climate change and the inevitable conflicts that will follow, our civilisation will collapse over the next 50-100 years.

The totality of human knowledge, history and civilisation used to be stored on a medium that had been shown to be stable over hundreds of years:  Paper.   Until just a few years ago, the core of human knowledge in science, the arts, social development and so on was replicated in libraries across the globe as well as in private collections.  Replication protected the backbone of our civilisation from localised disasters brought on by climate or war.  Today, the same knowledge and more is stored on electronic media that is vulnerable in ways that paper never was and is inaccessible to a human being without multiple layers of technology to read it.

Having worked with computers for over 30 years I am a bit obsessive about doing backups to multiple locations and media.  My work-related research data, writing, presentations etc are all on redundant disk arrays that are backed up nightly to tape in two geographically separate locations.  Personal stuff like my 80 or so thousand photos is stored locally and on at least one cloud provider.   I replicate my laptop to two bootable external drives in two locations.  Companies take securing their data against disaster very seriously since the data are central to the success of their businesses.   Data replication technologies are routinely used to secure against disasters in one location, so you might say all is well?  Unfortunately, it isn’t!

Clearly, the many advances that have occurred in the modern world are absolutely dependent on computer technologies.  With each passing decade, the possibilities for creativity and for understanding expand thanks to the increasing sophistication of computers and associated devices.  My entire career has been built around such developments!  Now the research outputs we produce are mostly stored and made available only through electronic media on the web.

Unfortunately, our reliance on computer technology makes the archive of human knowledge and expertise acutely vulnerable to disaster.  Yes, data are replicated around the globe, but how well this is done is patchy and often unknown to the end user of a service or repository.  For example, I have no idea how robust the infrastructure is that this blog is written on! 

Even if we accept that all the data services we rely on are robust and replicated across the world, civilisation’s knowledge is highly vulnerable to major events that might impact the network of computer systems.  Networked systems are built on a pyramid of technology from the electricity generation and cooling to the data centre, the hardware, firmware and software running on individual computer nodes and storage devices, to the high-level applications that users interact with.  Central to keeping the pyramid working is the human expertise and ingenuity that builds and maintains the systems at all levels.  This expertise is in itself dependent upon those same systems – after all, when was the last time you consulted a paper manual?

While once, a human being could leaf through boxes of dusty records or books to seek out knowledge from past generations, a future archaeologist aiming to learn of our civilisation’s treasures would be left with decaying ranks of hard disks.  Even if functional and an access device could be made, those ranks of disks would be impossible to decode without knowledge of the underlying architecture and encryption methods.   In the unlikely event that an entire data centre was powered up, the lack of knowledge about how to log into the system would defy access.

Civilisations rise and fall.  If our global civilisation does go the way of so many from the past then little will be left for those that follow us to rebuild from.

 

Save Civilisation – the planet will be fine

Here’s a cheery little post for a Sunday evening!

We often hear people talking about what we can do to “save the planet”. Really though, what is meant is “Save Civilisation”.  If the nations of the Earth continue in the way they are currently, then we will see a collapse in the incredible civilisation that has built up over the last few hundred years.   To the planet, the period of industrialisation, fossil-fuel burning and waste will be just a blip on a billion-year history.  The planet has coped before with catastrophes and will cope with what humankind has done to it.  Life will go on, but human civilisation as we know it won’t survive.

We know that human action has led to climate change. We know what we have to do to counter this and how urgently, but nothing is happening fast enough.  The nations of the world bicker about internal politics like Brexit in the UK and the Wall in the USA and worry about “threats” from each other for dominance in the markets but ignore the impending disaster brought on by our actions.

It is wonderful then to see children across the world reacting to this threat and showing they have a voice through marches and school strikes.   Like many others, they realise that if urgent action is not taken to tackle climate change then it is their generation that will live through the depravations brought on by the neglect of the current rulers.

As ecological change hits, then whole populations will become unsustainable where they are.  It will be harder to provide water and food for millions of people and we will see migration on a huge scale.  This will lead to humanitarian crises and conflict over resources and lands where water and good crop growing conditions still exist.   In the worst case this will lead to all-out war, with increasing desperation leading to the use of nuclear weapons by smaller nations threatened by those such as the USA with massive armies.

This won’t just be a crisis for developing nations.  Rich countries will need to cope with hugely increased demands from migrants, but within rich countries like the USA there will be critical resource issues in areas affected by drought and the loss of biodiversity.  This will lead to massive migration and starvation within the country as regions become unsustainable for crop growing and human existence. 

Rich countries around the world are currently reacting to perceived threats from increasing immigration, but these are nothing compared to what will come with ecological changes that will happen over the next 50 years.  In my lifetime, I am sad to say, I will witness the breakdown of the great global civilisation that has built up over the last few hundred years as increasingly desperate groups look to preserve and protect what they have, rather than work cooperatively to find the best solutions for the majority of the world.

The sad fact is that we are already seeing this inward-looking protectionism in Europe and the USA.  Couple this with a “head in the sand” attitude to the unequivocal scientific data about climate change that has been building for decades and we are doomed.

It is very sad to think that this apocalyptic future is all avoidable, but we seem powerless to act fast enough to have any real effect.  I’m sure that ancient civilisations had the same problems, vested interests in locations and ways of life blinded those in power to the impending disasters of drought or sea level rise. Civilisations fall, it seems likely ours will too,  but the planet will be fine.

 

 

 

 

Publishing Research… Part 2

Sales and Marketing in Research: About being a “Booth Babe”, Performing Arts and Science

I wrote Part 1 over a year ago!  It highlighted one example, where in my (completely unbiased 🙂 ) view, four editors got it wrong.  Of course, this is not unique in science, or indeed to science.   J.K. Rowling, author of the Harry Potter books and one of the top 10 selling authors of all time, was rejected multiple times by publishers who could not see the appeal of her stories.  She has also famously shared rejection letters for her first book written under the pseudonym Robert Galbraith.  History is littered with people making decisions which in the light of history seem like obvious oversights.

Back in March 2016 I spent three days with Dr Suzanne Duce, promoting our free research software Jalview (www.jalview.org) and some of our other resources such as JPred (www.compbio.dundee.ac.uk/jpred) at the Microbiology Society Annual Conference in Liverpool.  You can see a cute (?) timelapse of the stand here.

This was a bit of experiment to see if we could reach new audiences for our tools. The Wellcome Trust (wellcome.ac.uk) and BBSRC (www.bbsrc.ac.uk ) both fund our projects and gave us some money to do this sort of thing in our last grant renewal.  Did it work?  Well, yes!  We met a lot of people who were not using our tools but probably should be at least trying them, we reconnected with some users of the tools and introduced them to some new features, and we set up some new collaborations.   Was it worth me spending three days on a stand? Maybe yes.  It was a good experience and I just transplanted my office there for the duration so could get on with other stuff too!  Maybe no, but more of that later.

One of my former group members who has been in the USA for a lot of years called what I did in Liverpool as being a “Booth Babe”.  This conjures up all kinds of horrible stereotypical and sexist images, but made me think more broadly about what we do in science and how much what we do centres around Sales and Marketing.

Publishing Research and the Importance of Marketing

In the world of musical performance, competition is intense, so success is a combination of:

  1. Talent
  2. Marketing (getting noticed and continuing to get noticed)
  3. Timeliness (having the right sound or stage presence)
  4. Perseverance (coping with failure and not giving up)
  5. Being attractive, unusual and/or flamboyant

All can  help in promoting your “brand”.  There are very many people with the talent to be a top performer, but few gain international success and acclaim.   The most successful usually combine 1-5 in varying degrees.

I don’t think the situation is any different in science.  We scientists would like to think it is all about the purity of the research, but that is only part of what makes up a successful career.  If we take 1-5 above and map them onto a science career:

Talent.

Well, you need to be able to “do” science.  What that means is field dependent, but you identify problems interesting to study, design experiments, methods or observation strategies, carry them out, interpret the results, put them in context and so on.

Marketing

It doesn’t matter how smart your research is, if you don’t tell anyone about it, it is invisible to the world.  A bit like a musician playing awesome guitar riffs in their bedroom but never performing them to anyone else.  In science, you need writing and other communication skills.   The biggest way you “sell” science is through the peer-reviewed literature, so publishing your excellent research in journals is key to success.  However, where should you publish?

There is a massive preoccupation with publishing “well”. Publishing the results of your research in “high profile” journals.  Why is this?  On the face of it, it should not matter where you publish if the research is sound, but it certainly does make a difference.  In my view, it is all about marketing.

If you publish in a little-known journal then it may take months or years before anyone notices, even if that research is paradigm shifting.  At best, the people who should read your research won’t notice it, at worst they will just dismiss it because (a) they have never heard of you and/or (b) think it is not even worth reading due to where it was published.  If the journal is behind a paywall, then the chances of your work being noticed are even more remote.  If it is open access then at least it is visible to all, but (a) and (b) will likely play a part in it getting ignored.

It is a sad fact that if you publish in “high profile” journals like Nature or Science, then your work will be noticed, even if it is not the best in the field.  Most scientists look at these journals, journalists look at these journals, your work will reach a wide audience.  You will be more likely to get invitations to speak at conferences, your CV is more likely to get noticed when you apply for jobs and so your career is more likely to take off.  Sigh…

Timeliness

It doesn’t matter how exciting you think your research is, if you are just doing some incremental additions to a well understood problem, then even if it is really important, it won’t get a lot of attention.  If your work is a long way ahead of its time, then the risk is no one else will understand why it matters!  If you are really on top of your work then you will be ahead of the world, that is the point of research, but unfortunately, you will always be the world expert on what you do so explaining the magnitude and importance of your discovery or technical innovation to others can be hard.   This is where your marketing and political skills come in.   Sadly, however much you try to explain something to your senior or more established colleagues they may still not “get it”!

Perseverence

You need a lot of this to be successful in science.   Ideas don’t always pan out, experiments fail relentlessly, bugs creep into code only to reveal themselves late in the publication process (OK, that wasn’t a big bug, but…), good papers don’t get sent to review ( 😉 ), grants get turned down… You have to be able to cope with this all and have confidence in what you are doing to keep trying!

Being Attractive and/or Flamboyant

I’d really hope that how you look is not important to scientific success. However, if you can communicate well and get along with other people then you will be more likely to build up your network of scientific colleagues.  The thing is to be confident about what you have done and what you know about and not be afraid to defend your point of view.  If you are a naturally gregarious person and have a flamboyant style, it probably helps get attention of peers and beyond.  Of course, having a great delivery style has to be backed up by solid science…

The changing face of publication

When I started my scientific career in the 1980s, the only methods to advertise research were through journal publications and presentations or discussions at other institutions and conferences.  These remain major and important ways to advertise and disseminate research.   Preprint servers such as arXiv and bioRxiv make getting your original research seen early, much easier.

In the early 1990s http came along and so we could advertise and promote research through a web site.  Here is a copy of mine from 1996, though it looked much the same in 1993/4 when we first created it.

Today, there are many ways to disseminate research and draw attention to your work.  This blog is one, some entries focus on specific research we have done, others like this are more general.

One has to be careful reading blogs, including this one!  Some scientists use their blog as a platform to attack other scientists since this is difficult to do in a conventional peer-reviewed publication.   I don’t think this is the most productive way to settle differences of opinion.   Of course, being controversial in a blog, draws attention to yourself, but personally, I would rather not write something that deeply upset another person, however strongly I felt about the topic.  If anyone reads my blog or anything else I have written and are upset, then please let me know, so I can learn why.

Twitter (in my case: @gjbarton and @bartongrp) is great for advertising new work, new job opportunities etc., but relies on building up a follower network.   I’m not sure how effective it has been in finding people for me, it is hard to judge, but I know some who have found jobs through twitter ads and exchanges.   Direct messaging on twitter is also invaluable as a communication method with fellow scientists.

Facebook can be useful too, we use this to promote Jalview, though since I manage the page, I have to remember to update it!  Facebook is an easy platform to use to advertise basic news etc.   Of course, there are many other platforms that you can publish on:  LinkedIn, ResearchGate, etc., etc., …  it is just a question of spending the time keeping them up to date.

Social media, blogs etc  may or may not help improve your scientific profile though, which is still built primarily on high-quality research written up clearly in the scientific literature!   With the scientific literature, there are now many experiments with different publishing models – open peer review, peer review after publication etc., but change is difficult and slow when the majority of science is still published by conventional journals.

As with musicians, scientists must balance advertising and promotion of what you have already done, with doing the next new thing.   I am demonstrating by writing this blog rather than my next grant application that it can be easy to get distracted from the “doing new science” thing…

Finally, was the booth at Liverpool worthwhile?

As I said above, overall yes, some new contacts were made that have led on to new collaborations and also opportunities to teach about Jalview at other institutes.  The caveat is that we reached around 200 people at that meeting.  In contrast, Dr Suzanne Duce who manned the stand with me, has prepared >20 instructional videos about Jalview as well as other videos about what we do (even some of me giving some lectures…   ).  These videos have reached 10s of thousands of people world-wide.   A conclusion would be that if time is limited, then making videos and using social media/web promotion has to be more efficient and effective than talking to people individually. However, one cannot beat face-to-face meetings for explaining complex concepts.  Face-to-face gives the opportunity for questions and discussion, particularly in a small group and so while reaching a smaller audience, it provides a richer way to communicate.  Overall, we have to do a bit of everything and adapt as new technologies and opportunities present themselves

Thoughts on age in science…

I saw a twitter discussion last year from a young Professor in the USA who was saying something along the lines of “why do people not realise I am a Professor?”  I think she was about 30 years old.   She commented that she was tired of hearing people, mostly men, say to her, “You don’t look like a Professor” or you “Look too young to be a Professor”.   This was a thread about discrimination in the University workplace against people who were not white middle-aged males.   Reading about her concerns reminded me of my own experiences as a young group leader.

When I was 17 I really did not know what to do.  I was privileged to have the opportunity to go to University, but did not know what subject, or even what University was all about since no one in my family had ever had that experience.   In the end, I went to study mechanical engineering, after a year switched to biochemistry and then finally began to enjoy myself when I started a Ph.D. in computational biology.  Thanks to excellent mentoring and a fair bit of luck, 5 years later at the very young age of 28 I was awarded a Fellowship that allowed me to start my own independent research.  A year later, I was sole supervisor to a bright new Ph.D. student…  Oh, I also taught undergraduate students a bit too.

So, I was very young to be a group leader.   This was unusual then and still is today, but I was certainly not unique in gaining independence at a young age.    One consequence though, was that until I was about 36 or so, I was frequently mistaken for a Ph.D. student or post-doc.  I lost count of the number of times people asked me “Who do you work with?” or “Whose group are you in?” and I had to explain patiently that I had my own group.   This was particularly true when I travelled to give talks outside the UK where it was even more unusual for someone of 30 to be running a group.  I remember visiting the NIH at Bethesda when I was about 31 and having a 1:1 discussion with a postdoc.  I mentioned that my Ph.D. student was working on something – he looked at me amazed and said: “You have a Ph.D. student???!”.  On that same trip, I had various senior staff saying: “So, you are here looking for a postdoc position then?”.   On another similar occasion, I was visiting a University in Australia.  I’d given a talk and afterwards was doing the rounds of scientists, people thought I would be interesting to meet or vice versa.   When I met one person he said something along the lines of: “Sigh… you are another one looking for a job here then?”.  I got the impression he thought I was the latest in a long line of job hunters he had been asked to talk to.

At the University I worked in at the time, I was made a member of Congregation, which is the governing body of the University.  Not such a big deal, this group had all the academic staff in it but I had had to be nominated since my salary was externally funded.  I recall getting a letter about new ID cards being issued and being instructed to go to a particular office to get it done.  I turned up at this office in an ancient building and told the lady at the desk why I was there.  She rather brusquely told me I was in the wrong place and should go to the Student help centre!  I was a bit put out by this, but showed her the letter I had that explained I should go to this office!  She glanced at it and said: “Oh!  You are a member of Congregation, so sorry Sir…”   I think that is the one and only time I have had someone in the UK call me “Sir”.

So, it was a pretty common experience for me to be mistaken as a student or postdoc even after several years as an independent scientist, what would be called a “Professor” in some countries.  I don’t recall being offended by it, though the guy in Australia did irk me a little with his attitude, he softened once I explained I had a job and was just interested in his research.    I don’t think I was discriminated against on age.  I did see other kinds of discrimination based on where I went to school, but by and large I worked in those early years in an institution that judged people by what they could do rather than what they looked like or how they behaved.

I know as a white male, I have not had to deal with the biases (unconscious or otherwise) that other genders or races have to deal with in many institutions.    Despite this, I have noticed a difference in attitude to me and what I say as I have got older, especially  now I am a grey, bald, Professor (in the British sense) and so fit the appearance stereotype.

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