Expensive or Insightful Biology?: Single Cell Analysis as a Symptom

160727_800px-Musei_Wormiani_HistoriaLists, catalogues and classifications have always been the business of the biological sciences. The nature cabinets of the XVII and XVIII centuries, the collections that occupied much of the XIX century and which fuelled the work of Darwin are good examples of this. Beetles, butterflies, fish, pigeons, plants occupied (and occupy) the time of individuals, often amateurs, interested in Nature. The nature of this enterprise is captured in Umberto Eco’s book “The Infinity of Lists”

When we don’t know the boundaries of what we want to portray, when we don’t know how many things we are talking about (….) when we cannot provide a definition by essence of something and so, to be able to talk about it, to make it comprehensible or in some way perceivable, we list its properties (…………….). We call this representative mode the list, or the catalogue

Indeed: to make something whose limits or meaning we ignore, we make lists, if they are organized according to some criterion (and since Linnaeus but even before, they are) they have the potential to reveal something of the essence of that which is being classified. Physicists and chemists know well how this works: stars, spectra and the elements come to mind. But the level and intricacy of what the biological world offers to the catalogue aficionado is different, probably, boundless. To go back to Eco, it is unclear where the limits of the biological world lie. No wonder E. Rutherford said that one could reduce the sciences to Physics and stamp collecting; he may have had the biological (then natural) sciences in mind and this perhaps is why S. Brenner famously retorted that what Rutherford did not know is that there are some stamps that are worth collecting.

In the History of Science lists have the potential to highlight generalities which allow precise questions to be asked and answered. Physics and Chemistry have been good at reaping the benefits of this activity. In Biology a most famous outcome of this cataloguing is, of course, Darwin’s great work which revealed a principle running through the continuum of transformations that stares from large collections, ordered collections (the word ordered and in what manner the order comes about being important here), of plants and animals. In a different way, the work of Mendel is a culmination of less structured but no less significant collection of lists of the output of many lists; after all, it is seeing patterns in the outcome of crosses of plants that leads to genetics. In all cases the assumption is that if the lists are arranged according to the right criterion, they will reveal an order and, behind that order, some mechanism -in the sense of a causal explanation for a set of observations and not as the usual Figure 7 characteristic of modern biology papers- that will provide an insight into a system. In the end, sometimes, the insight can lead to the manipulation of the system for the benefit of the observer: lists lead to science that leads to engineering which leads to progress.

There is a danger in these lists and it is that they might become an end of themselves. That the scientist becomes a collectionist, forgets Brenner and gives credence to Rutherford. Surely the lists are valuable resources for those that want to ask questions, but the truth is that as we turn into list makers, we can forget that there are questions behind the observations and habit turns us lazy and content in our collecting. Sometimes one feels that this is happening in the biological sciences, that biologists are becoming professional collectionists. There might be a reason for this:  the essence of biological systems is the generation, selection and competitive propagation of novelty and variation. As a result, every species, every genome, every cell in every genome, every organelles in the cell, every protein in the organelle, is subject to this continuous generation of variation, to the exploration of a large space of form and functions. If one assumes that every cell type in an organism is different and that these differences are species specific, one can do a simple calculation: the range of different cell types varies between 3 in a plachozoan to about 1014 in a human and if, as it is currently assumed, there are on the order of 8.5 x 106 organisms on the earth, one could say that there might be on the order of 1020 different cell types to explain (NB this is assuming that all individuals within a species are similar and forfeiting the development of an organism during which large numbers of transient cell types are generated that differ from their final types). This number, 1020 , is already a large number relative to the approximate number of stars, 1012 . It may be small relative to number of atoms, 1080 in the Universe –and one has to remember that atoms need to be proportionately distributed into 117 elements which is where the differences appear i.e all atoms of an element are essentially the same and thus, the 1080 number needs to be tempered by its being bundled up in the abundance of each element. It is here, in this notion of similarity of all the atoms of an element, that the main difference between the biological and physical systems appear. The stars are very similar to each other in composition, and this is why we can study them from a distance by using the spectra. On the other hand, every organism, every cell type in every organism is different, unique. In fact you and I are very similar but our cells in similar places in similar organs are likely to be different. Enter DNA, which is the way to explain uniqueness in Biology: if we accept, as we must, that every cell type responds to a ‘transcriptional code’ of sorts, and we focus just in humans with our approximate 20,000 genes (I am not interested in philosophical discussions of what is a gene and hope that you and I will agree that this is a lower bound), simple calculations allow for 220000 combinations, to account for those 1014 different cells (and don’t forget those developmental intermediates). If you throw this number into your calculator, it will be confused as it will approach infinity. Of course, the toilings of Natural Selection ensure that only part of that repertoire is used but still, the number is large and dwarfs anything the inorganic world can produce. Surely we are stardust, like the moons of Jupiter, but DNA and RNA have found a way to turn that dust into a creative material device.

Where am I going with this? Over the last few years technical developments have allowed us to peer into single cells at the level of their transcriptional complement and, with increasing accuracy, at the level of their genomes. The observation is that even within what histologically is a (one) cell type, there is a great deal of heterogeneity. It is difficult to silence the genome, and we are learning that cells –particularly in development- are exploring their transcriptional space in a dynamic manner. The result is that within an organism much of that space of 220000 combinations is likely to be explored and much of it represented. The technical developments are allowing increasing volume and accuracy in the observation of this process (gene expression at the level of single cells) and of the delivery of these results. In consequence this creates interesting challenges for classifying, for making lists, which are taken on by groups of computational biologists whose interests lie in dealing with complexity rather than in understanding its meaning. Meetings are held on the subject of gene expression at the level of single cells and while at the moment the possibilities lie in honing our ability to describe the expression patterns of single cells and of characterizing the genomes of cells in tumours, the holy grail on the horizon is the analysis of epigenetic marks at the level of single cells and the ambition of getting the genome, epigenome, transcriptome and proteome in single cells. Our infatuation with these techniques, what it reveals and the possibilities associated with it are powerful and thus reviewers and editors lurk in the background to ask you for a single cell analysis of your favourite system, if everything else has failed to hamper the publication of your work. But, at the moment, it is also expensive and begs the question of where does it lead to? What is the meaning of this work? Are we paying lip service to Rutherford?

160727_Untitled.001The analysis of single cell gene expression can have -and sometimes had- an impact in three areas of Biological research: Cancer Biology, Immunology and my area of interest, Developmental Biology, which aims to understand how an organism builds itself. In all cases, single cell analysis allows the identification of ‘rare cells’ which sometimes have a function and sometimes, they don’t. The issue is that more often than not and in the best tradition of Biology, these studies reveal the temptation of collecting data under the banner of its ‘importance’ without realizing that we have fallen to a fad, that cataloguing has taken precedence over understanding. The description of a biological process demands a link between a cellular and a genetic description of the process and there is little doubt that the arrival of single cell transcriptomics and associated techniques, particularly single cell lineage tracing, has revolutionized the field. However we should be careful not to be swayed by the collectionist syndrome and remember that behind the data there are questions and that if we cannot see them, we should acknowledge that. We should not confuse cataloguing and collecting with Science. In some ways there is no great difference between beetles and genes, and we might be developing a XXI cabinet of genes and cells. It might require more challenging techniques than those collections of the past but there is no difference between collecting one or the other. Already papers in journals tend to be divided into two: either analysis of gene X in tissue Y in organism Z, or increasingly, single cell analysis of process W in organism Z. And in the best tradition of classical Systems Biology, one hopes that in the analysis of the data, the question and the answer will emerge at the same time as one stares in hope at the data.

Single cell analysis of expression is the epitome of this strange hypothesis-free science that is often hailed in reviews and social media. We are in the midst of it. Slowly we fool ourselves that large data and cataloguing will lead us to the essence of a process, that it will allow us to talk about something that we cannot define. And while it is true that Biology has a habit of revealing principles from lists I cannot help but thinking that with this trend of hoarding data, we are losing perspective of the processes that still need addressing. It would be good if, as R. Feynman said, we don’t confuse naming something with understanding something. Developmental Biology in particular, is losing itself in this naming game and single cell analysis will –unless checked- provide the ultimate distraction from questions that are there but we are too…..may I say ‘lazy’? to ask. We should not forget that there are things to explain, that cataloguing is a way to answer, and sometimes to unlock, those ‘things’ but also that we need to make an effort to search for them.

The allure of the information that can be gathered in one of those experiments is enormous but one needs to remember that in addition to being expensive and data rich, it needs to be insightful. The difference between a collectionist and a scientist should lie not in the ability to make observations but in the ability of the second to use the observations to answer specific questions about Nature. Biological systems have a boundless ability to generate (constrained) variability and it seems to me that the challenge is to understand the nature of the machine –for it is a machine- that generates, processes and uses that variability, written in that tape that is the DNA, interpreted by the transcriptional machinery and supervised by Natural Selection. It is the process, not its output, that needs to be explained. Questions are cheaper than data gathering but good questions are hard to come by.

Epilogue

One of the most disturbing aspects of the current trend in the single cell field is the lack of cross reference or discussion of the data. Often the same system is surveyed in more than one paper without any reference to the other, related, pieces of work or even, on occasion, to the general problem. While this is in keeping with the current trend in the biological sciences in which the publication rather than the finding is what matters, it is no less disturbing. If we do not get hold of the boundless nature of that data by using questions to clean it up and thus reveal what is good and bad data, we shall do a disservice to the system that puts up the money for that research and, more importantly, to Science itself. Surely, there is meta-analysis, Darwin’s great work can be construed as a meta-analysis- but nowadays, often this is done not so much with a question in mind but with the idea of multiplying the data-analytical power. The boast tends to be not in what has been learnt but in how large the data set is. And in the end, the danger is that, increasingly, what we do is expensive collecting; XXI century cabinets of genomic data, without a good reason, without a good question –which exists. We seem to have relinquished our ability to interpret what we observe and lost our interest in asking questions because, I agree, it is easier to order and catalogue this diversity that we call Biology. Still, the issue buzzes in the back of my mind: there are questions, important questions, to be asked and….all that data!

Brexit: The Pyrenees, the Channel and the Ocean

Pyrenees_1

I few months ago I was asked to speak at the Society of Spanish Researchers in the UK (SRUK) annual Symposium in London. SRUK is a grass roots organization which has evolved over the last few years to act as a reference for Spanish researchers in the UK and as a vehicle between the UK and Spain in scientific matters. With this in mind and having been asked for a perspective on Science in the UK and Spain from my experience as a researcher and teacher here, I gave a title (The Pyrenees, the Channel and the Ocean) based on three geographical barriers which acted as cultural barriers for Spanish people of my generation. I wanted to emphasize the value of breaking those barriers, how good this feels, how important this has been for Spain and how the UK as a cultural melting point with strong and (in my experience) welcoming institutions is a working example of this. Then, June 23rd, Brexit, happened.

The UK is my home and has been my home for the last 33 years. I realize that my view of the UK is a biased one (from Cambridge and London) but having lived here so long I have had a chance to experience a broader Britain and I can say that have never felt a foreigner here. Have never felt glass ceilings in Cambridge and have always found the UK an exciting and forward thinking multicultural place anchored in worthwhile traditions. It is here that I have learnt much of what I know about how to do and run Science, where I have come to appreciate the structure and value of a scientific culture that would be good to export to Spain. I have also come to appreciate the value of a society which, at the grassroots level, I find kind and integrative with much that can serve as a model for others. It is here where my wife and I have developed our lives and our careers, where our children have grown up, where I have learnt to look at and to see Spain and, importantly where over the years I have received young people in search of a future -which many times could be and has been here- and have help them to graft into this interesting place which is Britain. These people come from many places, mostly continental Europe, and have always taught me something and I have seen them change their views of their countries through their experience in the UK: it is in this cultural tradeoff that one becomes richer at so many levels. It is from here that I have seen, and have had the opportunity to contribute –in a small manner- to the enormous transformation of the biomedical sciences in Spain, particularly, over the last 15 years and my what I have learnt by being here has been crucial for this. And it is for all these reasons, but significantly because through my personal experience I am well aware of the effects that isolationism, that I am sad for what has happened and what it has revealed to me about a UK which, I guess, I did not know or I had missed. Or perhaps I had ignored.

 

Like many people I had a strange sense of anger and disbelief on the morning of the 24th and felt like saying much –which I did- just to vent the frustration. At the time (I guess) there were two things that fuelled my feelings. The first one was the way the debate had been conducted and what it revealed to me about an isolationist craze hidden outside London-Oxford-Cambridge-Scotland; how this debate revealed a fear of foreigners – which I had taken as part of a humorous past- and its consequences. The second one was the fact that I -and some millions like me who have lived and paid taxes for a long time, could not vote on something that mattered to us and our families- had not been allowed to vote (for those that complained about lack of democracy in the EU, what kind of democracy is that?). I felt like venting my frustration with a few lines but realized that this would be more emotional than reasoned and decided to wait. The SRUK event gave me more ammunition and some distance to reflect from. In that event I wanted to reflect on what breaking barriers meant to a country like mine from the perspective of an open one, the UK. Brexit cast a shadow on those thoughts. The SRUK symposium, where I had a chance to meet many Spanish researchers spread through the UK, was proof of the value of the open society that Britain has been up to now. At the meeting there were postdocs but also fellows, lecturers, readers, professors and all with a positive experience of their time in the UK, sharing that they have learnt here and, judging by their work, contributing to the growth of this society.

 

There is much that is uncertain at the moment, and not just about Science. There is also a lot of fear about what might happen and some short term consequences of this uncertainty. For example, we are all pragmatic and perhaps it is not surprising, that EU wide projects will look with some suspicion at the potential participation of UK groups. After all, Science is (increasingly) very dependent on collaboration and money that attracts money; if the UK is not going to be part of the game and wants to take more than it gives, it should be looked at with suspicion. I appreciate this and also that the result of the referendum has come as a surprise to many, that there is no plan for the situation in which we (because I and others like me are part of this society) find ourselves, but it would be good to hear soon from the government that Science, which is such a central element of this society, will continue to play the leading role that it has up to now. The repeated emails from the vice-chancellor of my University are reassuring, strengthen the concerns and single voice view of the academic community, but also highlight the extraordinary circumstances we have been thrown in.

 

It is very difficult to say anything new, original or inspired about the situation we live in. We are all waiting and whoever reads this is, anyways, a convert that much of what was in place with the EU is good and that what is wrong can only be repaired from being in. However, I shall say that I know what barriers do, how taking advantage of geographical and economic barriers leads to a cultural isolationism that is harmful and how when inward looking attitudes prevail, when a nation closes upon itself, Science and culture suffer and a social decay follows quickly. When I grew up in Spain, the Pyrenees were much more than a mountaneous ridge, they were a symbol of a cultural barrier that set us aside and apart from the rest of Europe. We, Spain, had the Pyrenees on one side and the Ocean on the other and although we did not have much at the time, we did not get much from the outside either. I remember the first time I crossed the into what we then called Europe (at the time we were only part of it geographically), my bewilderment at the world that I found, its wealth and its allure. Later when I crossed the Channel (the British Pyrenees) and the Ocean, this impression got magnified and I discovered a world that changed my life and one of the elements of that world that I have come to appreciate as the most important one, was its multicultural nature, what the US called “the melting pot”. Who I am has been shaped by my interactions with people from other cultures, nationalities and beliefs.

 

I left Spain in 1978 and have followed the transformation that it ensued from abroad, have witnessed how, as barriers fall, a country is enriched, becomes known abroad and, in contributing to the rest of the world, the rest of the world contributes to it. From the US and the UK I have seen how, over the years, Spain has turned from a culturally isolated country, to one exporting academics, to one which, using the lessons from other countries, welcomes foreigners and integrates them into its society. The benefits of being culturally open need time to emerge but it is easy to see in places like the UK and, of course, the US. Can one imagine US science without immigration?  Openness and integration are essential elements of social and academic progress because they promote tolerance and also, in the blending of views and attitudes, cultural development. In contrast with the slow development of cultural interactions, the losses created from isolation can be fast and become engrained before one realizes they exist.  Above all, what I learnt when I looked at Spain from abroad is how poor a country becomes when it isolates itself.

 

As I have said, it is difficult to say much that has not been said but I want to emphasize the dangers that will ensue from severing the structure of interactions that have emerged over 40 years with continental Europe. Science is a central part of those interactions and I am well aware of how much the British point of view is valued in those interactions. Brexit, if implemented in the way the Brexiteers want, will deprive Europe from the British input but, worst and importantly, slowly and inexorably it will make the UK a culturally poorer place and one in which, at a time in which science and technology are global endeavours, it will not be able to share and participate in those enterprises. As a biologist I know well the value of exchanges of genes and memes as well, and as much, as the damage that isolation can do to a group. I can hear some people thinking about the power base of British science and technology but these people will be living at the beginning of the XX century rather than in the global and interactive society of the XXI century. It is true that the UK has much that is good and solid, but by sharing it with the rest of the EU in an open manner it does much to promote its valuable institutions and influence. At the SRUK meeting I was asked what would I take to Spain from my experience in the UK. I did not hesitate: from the point of view of Science and technology, many of its institutions and their organization.

 

I am optimistic by nature and want to believe that in the end, sense will prevail, that whoever will do the necessary negotiations (and as of today it looks as if these are going to be hardcore Brexiteers) will see that much of what is in place in Europe is good, that freedom of movement within the EU has more positives than negatives and that this, and the structural benefits it brings along, are something worth preserving. It is possible (though I think unlikely) that the government will find a way to provide the funds that will be lost if the negotiation is not done with the UK’s real interests at heart. It is, as I say, possible, however, what the government can’t do is to buy what people coming to the UK, like I and many do, with open minds and eyes, to learn and, in the process, contributing, positively to the growth of a global society in which individual countries adapt to their idiosyncrasies the valuable aspects of other societies. You don’t lose your individuality in an open society, you enrich it. Brexit is a step backwards, the expression of a yearning for an order and a society which do not exist any more, that is encapsulated in that apocryphal headline “Fog in the channel, the continent isolated’; yes, a small island looks at a continent.

 

Let’s hope that sense will prevail and in the end, as the Prince says in Il Gatopardo: ‘everything has to change for everything to remain the same’.

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ASAPbio: The Dusk of Peer-Reviewed Glamour (a report from a virtual attendance)

The issue of publications of science manuscripts is reaching breaking point. Breaking in the sense of tearing down the enthusiasm of young investigators, the patience of seasoned ones and generating a lot of debate at institutional level. A few days ago, a survey by Nature News showed that more than 35% report taking 1-2 years to publish a manuscript and 20% 2-5 years (http://www.nature.com/news/does-it-take-too-long-to-publish-research-1.19320). What the bottom line of the article hid is that the time does not mean time sitting in the same journal –though some times it does- but time from submission to the first journal. For a more informed case study of the topic you should look at several posts in the always excellent S. Royle’s blog (https://quantixed.wordpress.com/); in the context of this post, I particularly like this one https://quantixed.wordpress.com/2014/04/15/some-things-last-a-long-time/. The point is that in science, but particularly in the biological sciences, something very fundamental has changed. Scientific publishing is an evolving enterprise but over the last twenty years it has moved, imperceptibly, from a medium scientists use to report their findings to a consumer good that uses scientists to develop its business model. It could be argued that this should not be a blanket statement but, actually it is pretty much that, particularly in the non-academic tier. Compound this with a sociological trend of too many scientists, disenchantment with career prospects and the emergent importance of media and this explains why scientific publishing has become a source of employment and a business that, as has been repeated many a time, uses scientists at all ends –from the bench to the editorial desk- of its fabric.

The problem is that the essence of the enterprise: finding-report-publication, has not evolved and what we have is a system that, basically, cannot cope with its essential fuel: science. Too much is being produced, all needs to be peer reviewed and peer review has evolved into an interesting sociological contraption that at some point should be the subject of some PhD thesis. The aim of peer review in its current incarnation is not to improve the work (this is the gimmick) but to ensure that a paper takes the longest possible time to be published and that its cost escalates to the point that what is considered good research is, basically, expensive research. And so it is against this backdrop (a much simplified version of it) that last week a meeting took place at HHMI headquarters with the cunning acronym of ASAPbio (Accelerating Science and Publication in biology: http://asapbio.org/). The meeting gathered an interesting mixture of senior scientists, administrators and editors with the aim of discussing preprints and preprint servers in Biology. For those of you who have not heard of preprints (and surprisingly there are many out there who haven’t and people at ASAPbio who acknowledged that they did not know they existed before the meeting!), a preprint -in the context of science communication- is a manuscript which has not been subject to external peer review and which is posted in a site for public viewing; it even has a Wikipedia page (https://en.wikipedia.org/wiki/Preprint), whose first words are “Publication of manuscripts in a peer-reviewed journal often takes weeks, months or even years from the time of initial submission,…..”, it says all.

ASAPbio was broadcast live on the internet and you could follow it on Twitter and social media; some of us did and you can see the videos now at the site (http://asapbio.org/). It was interesting. The gathering was representative of what we could call the establishment of science, principally the US establishment, and gave careful consideration to the culture of preprints and its future. Perhaps the most surprising thing to come out of it is that we have to fight a fear to preprints as forms of unvalidated science, preprint postings as a danger to “true research” and, surprisingly, some of these voices from qualified scientists (yes, the ones who have created and control the system we enjoy –or endure, as you choose-). There were exceptions amidst the old guard. The objection raised by those who worried was that preprints are not ‘controlled’, are not reviewed (forgetting really what lies at the heart of a manuscript at the time of submission), vetted. One had the impression that preprints are some kind of modern samizdats (in case you have not heard this word: https://en.wikipedia.org/wiki/Samizdat) forgetting that samizdats were a good thing in the cold war era. In fact, as a response to ASAPbio some went as far as posting tweets wondering whether what is in preprints is true or safe for consumption!. The answer to this question is simple: read the paper. Furthermore, physicists have been using preprint servers since 1991, particularly in the form of their very successful arXiv (http://arxiv.org/) home to over one million e-prints on all aspects of physical and mathematical sciences. Paul Ginsparg, founder of arXiv, participated at the meeting providing details of its history, value, mechanics and validation of and making clear that in many ways, preprints (e-prints at arXiv) are the bread and butter of the physics community. He also reminded (in some cases revealed) to the audience that arXiv introduced a section on quantitative biology which is proving popular. Along these lines a few years ago under the initiative of John Inglis, CSH started a parallel server, bioRxiv, which aimed at catering to do for Biology what arXiv does for Physics and Mathematics. There are other preprint servers of different flavours but bioRxiv aimed from the beginning to be arXiv like i.e. community oriented, user friendly, data rich. As it was reported at the meeting (and you can read here http://asapbio.org/biorxiv) bioRxiv is succeeding and that many of us –who have been using bioRxiv from the beginning- believe that it is a seed for and leads the way to the future of bioscience publishing.

The problem, for now, is that Biology lags culturally and practically behind Physics and this is reflected in many practical aspects, not only the publication ethos. Biology, as a science, hiding behind mindless collection of data has become more a culture of glamour than of content, of haves and have nots in which a good idea or a good point is likely to go amiss and where many bad ones get too much fleeting attention by virtue of where they are published. The question people most often ask you when you try to tell them about your work is not WHAT is it about, but WHERE have you sent the manuscript or, often, how big is your group. The science of the bioscience is a means to an end and so, it is not surprising that publishers have latched on to it and make the most of it. I don’t want to be misunderstood, there is a lot of good science around, it is just that not all that appears as good science is good science (though all data are useful). And thus it emerges the current tangled web of bioscience publishing. You, like me and many, have felt the dismay of starting the path of trying to publish something in what some people would call a ‘decent journal’. By now it is clear that the demands of peer review are not very different in most of those ‘decent journals’, that the difference between them is that in NCS you get rejections with arrogant and patronizing demands and messages from the editors, whereas in other journals you just get a directive to answer the often arrogant and patronising comments of the reviewers. I shall not bore you with details, we all have our stories. As has been said before, when people finally publish, there is a sigh of relief more than of elation. There are exceptions and I can only cite, within the realm of what I know, EMBO Press and The Company of Biologists. I wished I could cite eLife and PLoS but I am afraid that each in their own ways have failed to live up to their expectations (PLoS ONE has done a lot of good but has become slow and cumbersome as reviewers ask for more and more work, and PLoS Biology has become a place where people go when their papers have been rejected from NCS; in the case of eLife, with much that is good, it is unfortunate that so much power and resources are being channelled to beat NCS at their own game rather than in being really creative –for those who praise their excellent reviewing methods of eLife, you should know that EMBO journal had been using them for several years before eLife.

So, in terms of publication time and effort, things are getting worst all the time (see above). Enter preprints, that apparently dangerous and unsafe way of disseminating science. I must say that to label a preprint as dangerous or scientifically unsafe is to miss the point that publications in NCS can be worst because, as has been pointed out many times having been ‘peered reviewed’ they show the cracks of the system and the pitfalls of the glamour world those magazines promote: Arsenic life, the STAP problem or cold fusion come to mind and, in the case of STAP, don’t forget it led to the humiliation of a world renowned institute and the suicide of a much respected scientist with little consequence to the journal which published the manuscript in the first place. To say that preprints are dangerous is to overlook where the real danger lies and where the pursuit of glamour over science has led and leads. For those who say that preprints will be honey for garbage I shall say that having followed bioRxiv from the beginning, one thing has surprised me: there has been almost zero crank science. BioRxiv has had a steady increase in submissions and all of them -up to now it is possible to follow most of them- are sound science, no less controversial than what is published after peer review. If anything, one of the valuable aspects of preprints –if properly used- is that they represent raw science, before it is tampered with by editors and other scientists, who often have more competition in mind than the advancement of he science. It is clear that preprints in Biology are here to stay and that in the future will be the best way to present your science. I suggest that you go to the ASAPbio site and read through some of the views of the meeting and even if you have time, watch some of the discussions. More importantly, make sure that you use preprints to disseminate your science.

There were two other important issues discussed at the meeting. The first one was whether preprints should be allowed as an evaluation of scientific research. In theory, and in the light of DORA, this is a no-brainer but the discussion is important as the people gathered at ASAPbio represented a significant element of the establishment. Despite some concerns, it was also reassuring that, for the most part, people saw this in a positive light and many pledged not only to accept preprints (in preprint servers) as evidence of scientific quality, but to encourage their citation in job and fellowship applications. Many young scientists will appreciate this and I suspect that we shall see more of this in the future. The second issue was the mechanics and detail of such a cultural change. You cannot move this idea forward without attention to the organizational mechanics of the server, something arXiv and now bioRxiv know well. There were several references to this and it is important that in the enthusiasm of the move, we do not forget this important aspect of the enterprise.

ASAPbio was led by Ron Vale, whose excellent http://biorxiv.org/content/early/2015/07/11/022368.article-metrics served as a fuse for the meeting. There were well known people in the audience, like Michale Eisen, who have been doing a very open campaign for open science. However, while Eisen is good as a ramming bat against the establishment, we should not forget the many who in a quiet way have been adding to the momentum of preprints by convincing students and postdocs of the value for their careers and science of preprints servers. We need the chief scientists and administrators on board but, more than that we need the inertia created by people submitting their papers to preprint servers commenting on those servers (and don’t forget that you can comment in PubMed through PubMed Commons). It is clear when you come to think of it, that not only there is nothing to be lost by using e-print/preprint servers, but much –all- to be gained, particularly if you are a young Scientist. What is good for physicists cannot be bad for biologists.

ASAPbio was a formal recognition that something is changing and hopefully a formal start of a much needed move into new directions. I can see the worries of so called major publishers about the watershed that is coming, they might lose their stranglehold on the Science they own and shape, but a date comes to mind, 1789, and a voice that reportedly said “let’em eat brioche”. There will be no blood here but much needed change and a recovery of what is scientists’ privilege, the control over their work. I get the impression that something is moving. I sense not the dawn of a new era but the dusk of a short lived one based on much that is wrong and that we need to turn around. As it is being said these days, make sure that your next paper goes to a preprint server as it goes, or before it goes, to peer review. One senses that this is the way to solve, not only the emerging tyranny of journals but also peer review itself.

Season’s Greetings from the AMA Lab

With Christmas just around the corner, we have been adding a touch of festive cheer to the lab with a decorations competition. Novel uses were found for Falcon tubes, polystyrene packaging and Eppendorfs – in the end the prize went to the bay with the snowman!

We also gathered for our annual Christmas lunch, which was a great chance to get out of the lab and to share a meal together.

From all of us in the lab, have a very merry Christmas/happy Hanukkah and all the best for 2016!

Lab Decorations

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The case of the Irish Elk, a parable for the weight of the glamour journals

The case of the Irish Elk, a parable for the weight of the glamour journals

Irish Elk 2In one of his wonderful and educational essays, SJ Gould discusses the story of the Irish Elk, a spectacular species of elk that became extinct because……well, it is unclear why but the late specimens did have a very visible trait: enormous –and I mean enormous- antlers; the elk was over 3 meters tall and had antlers 3.3 m across. There have been many theories to explain the mysterious extinction of this magnificent animal but the one Gould discusses and the one I like to think about in certain contexts is that the Irish Elk was brought down by the weight of its own pride. The speculation goes that selection was in action for bigger and bigger antlers which, in the end, brought down –literally- the elk. And for selection, read in many instances, sexual selection. I am aware of the controversies associated with deciding whether selection is involved in a process or not and, more so when sexual selection is involved but, have always been interested in the Irish Elk as a parable from that perspective.

As a practicing biologist these days it feels like groundhog day in certain issues, particularly that of publications/glamour journals/Impact Factors (IF)/evaluations and the like. By now we all agree, more or less explicitly, that the biological sciences (I can only speak about them) are in a crisis because of a change of emphasis: what matters is the publication and not necessarily the research. Of course, there is some correlation between the two and so called high IF publications tend to publish more appealing reports than others, but it is difficult to accept that ‘more appealing’ means ‘better science’. In fact how we measure good science is something that is rarely debated outside the arena of the IF/h-indexes and related metrics and perhaps we should reflect upon this and try to return to value science for its intrinsic value, for the question that the scientist asks. I see few debates about what is a good question, what are the important questions but, in the context of my comments about the “LMB hut” probably this –questions in the biological sciences- is another issue that should go down to the fossil record of the history of science. Be that as it may, in the midst of the latest storm about how to deal with journal glamour (the latest idea to remove journal titles from websites) it is difficult to feel optimistic about any change soon, though it is clear that change is needed and, as I say, not only in our appreciation of the just value of scientific outputs, but about the actual value of the science we do. But…sorry, perhaps inevitably, I digress….allow me a thought.

Maybe the NCS’s (Nature Cell Science for those who are not familiar with the acronym) and the likes, there are some crude imitators around –are like the antlers of the Irish Elk. They are useful in mindless combat, they have a selective value, but as they grow they become more important than other body parts and, above a certain size, they will bring the organism down. I suppose the only response to that would be to grow a body size that keeps up with the size of the antlers. This did not happen in the case of the elk -though their body mass did increase and they were formidable specimens- and certainly cannot happen in the case of the biological sciences. The impression of many is that the kind of pressure that exists to value publications is distortive, creates serious problems for the development of the biological sciences and is certainly affecting the development of careers (the antler v the body and the long term survival of the organism). The question is not as simple as some people would make it sound and this is why nowadays, at meetings, there are entire sessions devoted to discussions of the issues associated with this topic. The problem, I think I have said it before, is that we are running a XXI century enterprise with a mid XX century business model, one that catered for a smaller, more focused community, a content centred enterprise with a smaller constituency. Today there is too much, too much that is good –at least technically sound- and a very large constituency. We need to evolve. Unfortunately the way we are doing it now is by selecting for bigger antlers without thinking about the consequences. There is too much talk about the form (publications) and very little about the content (science) and, slowly we are forgetting what this is about. Look at the indexes of most journals and have a think. The mantra that the science has become the publication is true and, because of its nature, the biological sciences will lend themselves to this gimmick because you can always find a new gene, a new function for a known gene, a new cell, a new drug, a new technique, any of which will be hyped by the impact department of any of ‘those journals’. No wonder some of us often ask if there are any Questions left.

The main problem with, let us call it, the IF question, is that it is breaking up the biomedical sciences into two: those who can afford to publish in certain journals and those who can’t. It is not only about science and ideas, it is about whether you have the stamina and the resources to deal with the whims of editors and reviewers. As it has been pointed out before, the editors have lost the plot and they will ask for bigger antlers (experimental responses to reviewers’ comments) that add very little to the content of the paper, propagate the myth of the specific journal as a tough place to publish and conflate the antlers with the rest of the body. Of course, not everybody will be in a position to respond in kind to the reviewers’ comments, to grow bigger antlers. The consequences of this are dire in the short term though I am convinced that in the large canvas of history the system, like the Irish Elk, will be extinct (don’t forget that this is an evolving system) and in the future we shall look foolish from the perspective of a more sensible science adapted to the times and to the people.

The good news is that slowly, and certainly in Great Britain, I begin to see some sense emerging and while there are still some old fashioned colleagues looking at the publication, more and more are realizing that in this manner you select, mostly, for antler size. If that is what you want, go ahead, grow your antlers and, on the side of the panels and the editors, pick your elks. Content, Science is something else.

NB SJ Gould essay follows an article he published: Gould SJ (1974) The origin and function of the bizarre structures: antler size and skull size in the Irish Elk. Evolution 28, 191-220.  The picture is a modified version of a picture first published by JG Millais in 1897, often reproduced in the web and shown in Gould’s essay: Natural History. 82 (March): 10-19 which you can read in Gould, S.J. 1977. The misnamed, mistreated, and misunderstood Irish Elk. Pp. 79–90 in Ever Since Darwin. W.W. Norton, New York. The person at the bottom of the picture could be construed as a panel member looking for some substance that can keep the elk up.

 

Good bye to a hut and to all that

“On a summer day in the late fifties a delegation from the Soviet Union appeared in Cambridge demanding to see the “Institute of Molecular Biology”. When I took them to our shabby prefabricated hut in front of the University Physics Department, called Cavendish Laboratory after its nineteenth century benefactor, they went into a huddle until finally one of them asked me: “And where do you work in winter?” They wanted to know how I had planned our successful Research Unit, imagining that I had recruited an interdisciplinary team as Noah had chosen the animals for his ark: two mathematicians, two physicists, two chemists, two biochemists and two biologists, and told them to solve the atomic structure of living matter. They were disappointed that the Unit had grown haphazardly and that I left people to do what happened to interest them” Max Perutz Nobel lecture http://www.nobelprize.org/nobel_prizes/themes/medicine/perutz/

"The Hut"The other day getting into work through my favourite route, the New Museum site next to the old Cavendish laboratory in the Center of Cambridge –nothing scenic, by the way-, I noticed a dramatic change, a hole in a familiar landscape. A small one floor building in the form of a large bungalow or hut occupied by Rolls Royce for the last few years, was gone. Instead, one of those modern multi story bicycle parking lots had been erected. But the loss was, is, historic as this was the old ‘hut’, home to the toilings of Max Perutz, Sydney Brenner and Francis Crick amidst others in the 1960s when they were laying down the basis of Molecular Biology (picture from http://www2.mrc-lmb.cam.ac.uk/?attachment_id=2631). It was in that hut that myoglobin was crystallized, that phage mutations leading to the genetic code were isolated and interpreted. That was the place of interesting discussions to which we owe much of what we do in Biology today. Surely one could take a moment to reflect. Change is necessary and, after all, the hut was a relic without much use or future, hardly noticed by passers by and in any case hardly known by many of the people who work around the site on a daily basis. Its demise led me to reflect on a number of issues that are associated with the hut and made me think that a way of doing Science so attached to the spirit of the hut, has also gone. The reflection that followed, and that follows here, is not intended as a nostalgic yarn but as a statement of fact, as a wake up call to a reality that we need to accept and work around. Science, Biology, as we have known them, is gone and is not coming back.

If you have read some of the classics of the history of molecular biology: “The eighth day of creation”, “Phage and the origins of molecular biology” to cite but two of the greatest, you will not find there stories of discussions with editors, rejected papers or grants or glossy statements in High Impact Factor magazines/journals. Instead you will find a riveting story of pursuit of some of the deepest secrets of Nature. The heroes that we so often praise did not spend their time arguing with editors, or doing experiments to satisfy reviewers and editors comments. They spent their time doing experiments, writing and publishing progress reports –which did not go through two rounds of review and excess comments by editors- and, within a competitive environment, moving on and along. There was a collective sense of what was important, people competed but also respected each other and the experiments and Science, rather than the publication, was what mattered; as it ought to be. They did not ask ‘where did you publish’ but rather ‘what did you publish?” “what did you find?”. Those were different times. I cannot imagine M. Nierenberg in the famous Moscow meeting at which F. Crick saw the tip of the genetic code, trying to catch the interest of an editor of Cell, Nature or Science. It is difficult to imagine Brenner having anything but contempt for journals telling him how to shape his legendary paper on phage mutations and the genetic code and I really can’t imagine J. Watson –whatever I or you think of him- in front of a career development award panel. The focus of Science then was research and important questions not careers or publications. When I came to Cambridge in the early 1980s there was still some of that spirit. The question at the time was not the molecular basis of heredity or the genetic code but, equally enthralling, the molecular underpinning of embryonic development. And we pursued this with a spirit not dissimilar to that of the 60s: toiling with questions and techniques, trying to get answers to questions we felt would be important. Journals were, still –but just-, vehicles to report progress, subservient to our needs. Change, however, had started and in some ways the emergence of Cell –run by an ex-lecturer from the University of Sussex and aiming to shape the content and form of contemporary Biology- was starting to take hold of the field. Then imperceptibly and in parallel with an explosion in terms of the number of researchers, fields of studies and journals, all changed.

Today it is unclear what is the relationship of what we do to Science as understood in the past. Nothing wrong with this but I do feel uncomfortable when at some meetings, panels of over 50s scientists gather with students and postdocs to advice them on their future. Often they tell them how they –the old guard- became great and that all the young generation has to do is follow the same steps. This is, at the very least misleading if not disingenuous. To survive today in Science, particularly in Biology, requires more than a good question or an original idea, much more than focused hard work, good judgement and luck. I say survival with intent and don’t mention “success” because this, more than ever, is relative. Today you need a combination of ingredients of which good Science (in the old fashioned way) is just one. If you try the old recipe, unless you are very lucky, you will fail. Times change and the advice need to go with the times. My advice is that if you are starting a lab today you should not model it on the attic at the Institut Pasteur where Lwoff, Jacob and Monod peered into the secrets of gene regulation, but on a small business. What you will face is the need to get funds to maintain an enterprise which, if you are lucky (which these days often mean to end up in a well endowed institute for a few years), will be close to your interests but which, in general, will have to adapt to fashions and funding needs. Your currency will not be your ideas or your results but your publications and while we wean ourselves off the pernicious influence of the HIF journals, you will have to keep an eye on them and live under their shadow because them (and the scientists that form their core) determine the agenda -my heart sinks every time I hear the pernicious and mistaken mantra that you need a HIF publication (warholian fifteen minutes of fame) to get a job, that the perception of the value of those papers, when published, will determine your value in some virtual and ethereal stock market of labs which, in turn, will determine how much funding you have and thereby the performance of your business. Things are changing and we have to push for change but, for now and while change comes, we need to be aware of the reality. In this climate you have to be careful and strategic.

And as part of this advice let me tell you that the best time to do Real Science today is your PhD because, if your supervisor allows you, it is the only time in your career when you are going to have some time to explore freely what you want to do. Afterwards, your work will be marked in a more or less open manner by a business model in which the name of the game is to survive, you will have to think carefully about what you do because your future will depend on it and this will become more apparent if you are not in one of those large Institutes which have the potential of doing a lot of good (and many do) but which for the most part suck resources from the environment and contribute to an increasing gap between different tiers of research. There is a lot of technical quality around and most people can do a competent job which increases competitiveness. Furthermore, Biology will never fail to produce a ‘new’ situation, either a new job for a well known gene or a new gene for a well known function and there are endless way of looking at DNA and RNA. This means that competition for resources is fierce and how you ‘sell’ what you do is more important (or at last as important) as what you sell (do). And the problem is that (maybe just my opinion) a question, let alone a good question, is not easy to find (see Coda on Einstein and Valery) and gets buried in a sea of data and techniques. While we are good at finding flaws in papers, we are not good at defining their context and, for the most part, we get lost in a forest of three letter acronyms and data. Unfortunately, in an age of shrinking budgets, translational pressures, data collection and technology driven projects, good old fashioned real questions and problems is not what shines (though I should say that come committees and institutions can sometimes throw a surprise or two of judgement).

It is difficult to gauge what is fundable and target it. It is not easy to tread the thin line between real science and a business model. If you want to survive and have the small amount of shallow success that will allow you to get funding, you need to go to meetings, be some part of the small circus that journals have created, talk to editors, to PIs who like to feel important and are influential. More importantly, be aware that the short term future of Biology lies in collaborations, formal collaborations. Brenner, Perutz, Crick, Sanger, the inhabitants of ‘the hut’ were collaborative, intellectually, they fed on their discussions and each other’s ideas but now it is different. One has to show coherence, added value, joint up projects. This is the reality and there is no point in looking away.

As I said above and repeat here, I do not yearn for bygone times, the spirit of the hut or the way science was done. I like to read and think about all this and feel proud to be part of that tradition. I am not nostalgic for history but, it is important that we know and accept that today those times and places are not a model for us more than Newton is a model for modern physicists at CERN. It is not right to tell people today that because they do good science they will succeed (whatever this means). The definition of good science has changed. Today people will not recognize a good idea if they see one; what matters is how you sell what you do. Ah, and as an average PI you will find yourself chasing money, going to meetings, dealing with editors and reviewers and, if you are in a high profile institute you will have to deal with periodic reviews. Nothing like the ‘spirit of the hut’. It is important to acknowledge where we are and look for ways to evolve it and to make the most of it.

IMG_6049For me the disappearance of ‘the hut’ has been a statement of the times and a reminder that a way of doing Biology is gone and that, like the hut, is not coming back. Perhaps there is something metaphorical in that the space of the hut has been occupied by a bicycle parking because this, in some ways, what has happened to Biology. What you will get with your PhD is a bicycle which you should use to move around and sell your skills which are not the same that they would have been if you had been working in Biology 40 years ago. I insist, nothing wrong with this, just be aware of it and don’t try to follow the paths of those days; they don’t work. In this regard I shall finish by saying that I do not expect The Crick, one of the examples of corporate science in the UK, to produce anything like what the hut did. The reasons for this is the changes I have been discussing. Science today is different……

CODA on ideas: It is said that Paul Valery, french poet and philosopher with an interest in the nature of creativity and the process of creation once met Albert Einstein. In the course of the conversation Valery asked Einstein how he worked to which Einstein explained that often he took walks and that during the walks he ran thoughts through his mind. Valery quickly retorted that surely he would have a pencil and a paper with him. Einstein was puzzled: a pencil and a paper? What for? Valery sighed; but ‘bien sure’ when you have an idea you write it down. Ah, now I understand; you see, Einstein said, I do not need those items, an idea is so rare that if I had one, I would remember it.

Boltzmann, Darwin and THE current challenge of the life sciences

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Ludwig Boltzmann 1844-1906 (http://en.wikipedia.org/wiki/Ludwig_Boltzmann)

The XIX century will be called the century of Darwin (L. Boltzmann)

While most people have heard of Einstein and Newton and Feynman, Boltzmann is not a household name when thinking about famous physicists. Ludwig Boltzmann was a theoretical physicist extraordinaire who at the end of the XIX century, in that Vienna that was going to give so much to the world in the ensuing years, taught us a most interesting way of thinking in material terms about the structure of matter and abstract concepts like heat and energy. Spurred by his philosophical inclinations, in his latter years he wanted to transcend what he had done and thought, by looking at Evolution from the physical perspective. In this process he clearly absorbed much of Darwin at a time that darwinism was not as popular as it would become later: “… If you would ask me about my heartfelt conviction, whether the nineteenth century will be called one day the iron century or the century of the steam engine or the century of the electricity, I answered without any doubt it will be called the century of the mechanistic conception of nature, the century of Darwin…”. There is little doubt from this statement that Boltzmann understood Darwin but there is also an inkling, if you know something about the work of each of these individuals, that he might have had a deeper insight than he let us know in his writings.

Physics and Biology share one challenge: the mechanistic understanding of the relationship between events that happen at the limit of our visual detection –the microscopic world- and what we can observe and sense i.e. measure (any act of perception is a more or less conscious measurement) at the macroscopic level. The way we do this is nicely put in a statement attributed to the physicist Jean Perrin, which suggests that one of the cornerstones of Science is the craft of revealing the invisible through the visible. In some respects this is what we do in Biology when we draw those diagrams that are meant to represent events supposed to happen inside cells. While some of them are probably accurate (and for accuracy on the basis of our current understanding of our molecular structural knowledge, see D. Goodsell visions of the cell: http://mgl.scripps.edu/people/goodsell/) others do not capture, yet, what they want to represent. And so, there is a two way road from the macroscopic to the microscopic. A topic of many talks in Biology is, we are told, that what we want to know is the relationship between the genotype and the phenotype, between the genes and the cell. However, behind this statement there is the dream of some sort of a linear relationship between both which has not and will not be found because 1) it does not exist and 2) this might not be the right question to ask. If you are an evolutionary biologist you spend a great deal of time relating genes to the structure of populations and therefore you know about the problems of simple linear models and of the slippery nature of quantifiable variables which are sometimes needed to deal with biological systems. However, it is precisely in the challenge of relating genes to, for the sake of argument let us say phenotypes, that the connection between Boltzmann and Darwin emerges and might provide some inspiration for today’s challenges.

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Figure 1. One of the big challenges in Biology is how to relate the events that are described by molecular networks with the organs and tissues that characterize the make up of an organism.  It is obvious that cells and their lineages are the vehicles for this transformation.

The breakthrough of Boltzmann stemmed from his belief in the reality of atoms and their fundamental role in the understanding of physical systems. A belief it had to be since at that time it was impossible to penetrate the structure of a cell, let alone that of a molecule or an atom. Taking this view as a starting point, he developed a theory which provided a mechanistic explanation (watch it, not in the sense of the modern biologists i.e. figure 7 of your NSC paper, but rather, to quote my colleague Ben Simons, as a causal explanation for an observation) for observables like Pressure, Temperature or Energy. He showed how if one accepted the existence of atoms, one could derive these properties from the spatially constrained interactions between them. Since the number of molecules in a macroscopic observable is enormous (remember Avogradro’s number is 6.02 X10 23 molecules in a mole), even those who were interested in the subject, found it very difficult to comprehend how could one devise a mechanistic and mechanical way to connect these large numbers to the observables. If you were a committed newtonian you would have to calculate the trajectories and energies of every atom and its interactions with all the other atoms and then find a way to compute the total sum (or product) of the resulting numbers! The way forward, as Boltzmann saw, was assuming the reality of the atomic structure of matter, to perform a proper statistical analysis of the behaviour of ensembles of molecules in different conditions. He reckoned that with such large numbers, the connection between the elements and the properties of the system was through statistics –in its infancy at the time- and that under the simple conditions of an ideal gas, a statistical treatment of the kinetic relationships between individuals in populations of molecules (microscopic) would yield the macroscopic measurable (Pressure, Temperature, Kinetic Energy…); a proper treatment of the problem shows how the observables result from the constrained averaging of the individual variables. It was a deep insight that what mattered were the statistical properties of the population rather than the details of the individual behaviours which became averaged at the higher level. This work provided a solid foundation for the work of the Scottish physicist JC Maxwell who had calculated the distributions of velocities of an ideal gas on similar terms, thus laying a significant foundation for the kinetic theory of gases -this is why today we talk about the distributions of velocities and energies in physical systems as the Maxwell-Boltzmann distribution. But Boltzmann took the basic ideas of a statistical analysis of the structure of matter further and provided a material basis for that most elusive notion: Entropy (which in thermodynamic terms can be defined as the amount of energy, thermal energy, which is not available to do mechanical work). With apologies to the physicists (if any reads this) for the simplification, he envisioned matter as a problem in combinatorials of its constituents: a particular structure being one, and only one, of a huge number of configurations of its constituent elements. If that structure disappears, or changes, it means the system has acquired a new configuration and will search for the original one in the large space of all the other configurations. Not surprisingly it will find many ‘disorderered’ ones before finding the original one. Entropy, Boltzmann saw, is a measure of that number of non-structured configurations. He extrapolates this to the Universe and suggests Life as the chance result of a fluctuation in a small space of a large heat bath. It is these thoughts about the Evolution of physical systems that probably led him to consider darwininan concepts: “… The struggle for existence of the living beings is not a fight for basic materials—these materials are available in air, water and soil in sufficient quantities for all organisms—it is also not a fight for energy that is available in the form of inconvertible heat in every body but it is a fight for [negative] entropy, which becomes available by the transition of energy from the hot Sun to the cold Earth. In order to exploit this transition as much as possible, the plants spread out the incredibly large surface of the leaves and force the energy of the Sun before it falls down to the temperature of the Earth in a not yet understood way to perform synthetic chemical reactions that are still completely unknown in our laboratories. ..”. Much food for thought here and I shall leave it for another time. Suffice to say that the deep gauntlet that lies in here was taken later by E Schrodinger who in his famous book “What is Life” discussed at length some of these notions and introduced the eye catching but misleading notion of negative entropy, free energy really (Gibbs or Helmholtz); he might have been influenced by his youth in Vienna studying Physics under the aura or the great Boltzmann.

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Figure 2. Boltzmann’s insights that allowed him to use statistics of the mechanical properties of the particles under several constrains to deduce the macroscopic properties of the system. In the process he provided a physical description of Entropy (S) in terms of the configurations of the system (W).

What does this have to do with where we are at the moment? What is the point of all this to modern Biology? The current challenge, as some of us perceive it, is not to see how genes generate a phenotype but to link the molecular and the cellular realms. To explain cellular activities (motility, change of fate, higher order structure and dynamics of cell populations, etc) in terms of their molecular underpinning. In all this and what has become a game changer is our ability to measure or, if you will, to see and then to measure, and to be able to do this at the level of individual cells. What we are getting out of this process is large amounts of data, information, that we are accumulating in databases that are more or less centralized and organized. What we are lacking is not just methods to process this information, but questions, conceptual frameworks to interpret what the analysis of the data (which is more data) yields. The question then can be reduced to how the myriads of genes, proteins and their interactions at one level, generate behaviours at a different scale. How do the macromolecular complexes that underpin cell movement  and shape, the structure of a tissue or the dynamics of a tissue in homeostasis, generate those observables?. In this work, there are two connected relations: from the molecules to the cell and then from the cell(s) to the tissue. This statement contains the implicit statement that THE CELL is a vehicle to link molecules to tissues and organs. The numbers of the game are very large (genes, transcripts, cells) and become larger if we consider single cells, which is becoming routine. It is here that the work of Boltzmann becomes an inspiration. The secret will be the averaging and the way biological systems do what physicists call coarse graining, will provide the understanding; but first we need to define the variables that need to be averaged and the calculations that need to be made. Progress is being made but it is slow because, unfortunately, the emphasis is still in mindless data collection and on the naïve belief that describing it is understanding.

It was probably this deep insight into the population averaging of the properties of very large number of components of a system that led Boltzmann to have an intuitive understanding of Darwin. After all, the importance of large numbers and their dynamics is implicit in Darwin’s theory of natural selection and becomes explicit in the postdarwininan interpretation as in the work is R. Fisher, S. Wright and others, genes play the role of the atoms, and statistics is not just central, but develops around these ideas. Qualities, phenotypes, arise from the multivariate statistics of the effects of multiple genes. It is interesting, as has been discussed by J Gunawardena that much Genetics was developed without an understanding of the molecular structure of the gene and that for many years, the gene was a mathematical entity  (Biology is more theoretical than Physics, Mol Biol Cell. 2013 Jun;24(12):1827-9).

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Figure 3. Outline for a statistical mechanics inspired solution to the problem (for further thoughts see references at the end). At the more microscopic level there are Gene Regulatory Networks (GRN) which generate dynamic (revolving arrows) patterns of activity at the level of single cells (intrinsic component). An interaction between these patterns and external signals (extrinsic components) generate patterns of fates at the cellular level that result in distributions of cell populations which are the result of distributions of gene expression in those populations. In turn these interactions across scales result in macroscopic structures. At the moment we do not know what these significant variables are nor what are their relationships but there are glimpses of this in the literature (see references at the end).

We need to look at Physics for inspiration and the current impasse needs, quickly, some new paradigms to move from description to understanding. The single cell analysis of developmental processes and, in particular stem cell populations has raised the possibility that statistical mechanics can offer a useful paradigm. What you have read for the last few minutes is a statement in support of such programme. But what we shall need is to define the macroscopic and the microscopic variables in a precise and meaningful manner. Then, progress will follow. Perhaps Boltzmann was right and the XIX century belongs to Darwin, as much as the XX belongs, at least in Biology, to the gene. In this series, the XXI should be the century of the cell and I hope that it does not take us 100 years to realize that to name and count genes and proteins is as futile a task as that which Boltzmann circumvented: to calculate the position and momentum of every particle of a gas. In many ways Biology is the unwritten chapter of statistical mechanics, the chapter that beckons at the end of any text book in the matter.

Darwin gave Biology a way to use the information that has been collated by naturalists in their collecting frenzy (which Darwin practiced in his early days). Today, instead of beetles and plants, we collect sequences and genomic landscapes and this is important and useful. However, the wonder of these objects and the useful information they contain should not deter our attention from the real task in hand which is to formulate the questions that will allow us to link genes (and epigenes) to cells and cell populations and through these to tissues and organs.

A brief list of related references (to build a field: the statistical mechanics of biological processes)

Karsenti E. Self-organization in cell biology: a brief history. Nat Rev Mol Cell Biol. 2008 Mar;9(3):255-62. doi: 10.1038/nrm2357 (E. Karsenti is a pioneer of the attempts to understand biological systems bridging the microscopic and macroscopic realms. He has done most of his work trying to understand how molecular ensembles generate cells which is a first step towards higher levels of understanding. His work is very influenced by I Prigogine).

Lander AD. Making sense in biology: an appreciation of Julian Lewis. BMC Biol. 2014 Aug 2;12(1):57. With Julian Lewis in mind, an insightful meditation of models in Biology.

Gunawardena J. Beware the tail that wags the dog: informal and formal models in biology. Mol Biol Cell. 2014 Nov 5;25(22):3441-4. doi: 10.1091/mbc.E14-02-0717. Models? What kind of models?

The next three references deal with the all important issue of time which is not dealt with here but is very important in linking molecular, cell and developmental biology:

Kicheva A, Cohen M, Briscoe J. Developmental pattern formation: insights from physics and biology. Science. 2012 Oct 12;338(6104):210-2. doi: 10.1126/science.1225182.

Kutejova E, Briscoe J, Kicheva A. Temporal dynamics of patterning by morphogen gradients. Curr Opin Genet Dev. 2009 Aug;19(4):315-22. doi: 10.1016/j.gde.2009.05.004.

Nahmad M, Lander AD. Spatiotemporal mechanisms of morphogen gradient interpretation. Curr Opin Genet Dev. 2011 Dec;21(6):726-31. doi: 10.1016/j.gde.2011.10.002.

The next four references discuss in an explicit manner the need for an approach based in statistical mechanics to understand the dynamics of cell populations in development.

Chalancon G, Ravarani CN, Balaji S, Martinez-Arias A, Aravind L, Jothi R, Babu MM. Interplay between gene expression noise and regulatory network architecture. Trends Genet. 2012 May;28(5):221-32. doi: 10.1016/j.tig.2012.01.006.

Garcia-Ojalvo J, Martinez Arias A. Towards a statistical mechanics of cell fate decisions. Curr Opin Genet Dev. 2012 Dec;22(6):619-26. doi: 10.1016/j.gde.2012.10.004

MacArthur BD, Lemischka IR. Statistical mechanics of pluripotency. Cell. 2013 Aug 1;154(3):484-9. doi: 10.1016/j.cell.2013.07.024.

Trott J, Hayashi K, Surani A, Babu MM, Martinez-Arias A. Dissecting ensemble networks in ES cell populations reveals micro-heterogeneity underlying pluripotency. Mol Biosyst. 2012 Mar;8(3):744-52. doi: 10.1039/c1mb05398a.

On the dynamics of cell populations:

Klein AM, Simons BD. Universal patterns of stem cell fate in cycling adult tissues. Development. 2011 Aug;138(15):3103-11. doi: 10.1242/dev.060103. This is an important insight from physics on the dynamics of cell populations.