Engineering the Future of Developmental and Stem Cell Biology

Final poster.001A meeting was held recently at the Pasteur Institute on the topic “Engineering the embryo: beyond Systems Biology”. The event brought to my mind a question I pose to the final year undergraduate class: how should we approach a biological problem? like physicists or like engineers?

The relationship between Physics and Biology has a long and very distinguished history, strewn with technical contributions that have often changed the direction and pace of biological research. Microscopy and X-ray crystallography would not have happened without the intervention of the physicists. To see this you don’t need to go further than the 2014 Nobel prize to E. Betzig, S. Hell and W. Moerner for the deep developments in superresolution techniques that are having a most dramatic impact in cell and developmental biology. However, there are also profound and long lasting conceptual contributions. Neurobiology has benefitted enormously from the input of physicists and molecular biology was shaped by Schrodinger’s “What is life?” and Max Delbruck’s Phage School. More recently, over the last twenty years, a cadre of young physicists have led a renaissance of the relationship between Physics and Biology. Single molecule and single cell techniques have opened up our eyes to the statistical processes underlying molecular and cellular Biology and taught us the beginning of how to deal with them. For those of us who have been lucky to be part of this feast, it has been both fun and insightful. If you have missed it, I suggest you catch up.

The fact that a biological system integrates multiple variables was never in doubt but it has been our ability to access those variables that has changed the game. Faced with a deluge of information of specific processes, we have learnt to measure and to use models to understand those measurements and, in turn, perform precise experiments. In many ways we are at the beginning of this game but the input of the physical sciences forged over the last ten years has already left an important imprint permeating much of forefront biological research. There is much to do and we now know how. Why then mulling over engineering?

The word ‘engineering’ has many meanings but, in general, evokes images of machines and blueprints. If you belong to the last century, like some of us do, you might think of steam engines, bridges, chemical plants, of belts and braces. If you belong to this century you might think of jets, computer chips, speed trains and clean technology, of electronics. Engineering is, in many ways, applied Physics. It is about toiling with materials to do something useful in a reproducible manner. Where a physicist uses an equation to understand/explain a process, an engineer uses it to explore a practical solution to a problem. Where a physicist uses a phase space to explore the behaviour of a system, an engineer will look at it seeking the domain that might work for a specific process in the real world. A phase space may often be the end game of the physicists work, for the engineer it is the starting point. While much of engineering deals with the physical world, there have been many inroads into Biology and, as in the physical world, there are many kinds of engineering in Biology: fermenters, biochemical reactors, bacterial circuits, mechanical organs are examples that come easily to mind. A good example of bioengineering you can relate to is beer making (yeast engineering in disguise). However, over the last few years, two fields -developmental and stem cell biology- have been coming together unknowingly with a common nexus through Engineering, a new kind of Engineering that was the motivation of the Pasteur meeting. Let me explain.

It is about five years that the tragically late Yoshiki Sasai surprised everybody by showing that Embryonic Stem (ES) cells could be coaxed into forming eye cups and forebrains1,2. His work coincided with the observation that intestinal stem cells would build crypts on their own3 and was followed by a plethora of other reports showing that (but not how) embryonic and adult stem cells can give rise to tissues, organs and structures. These observations are often hailed as the dawn of a new field, organoid biology, though one wonders if this is not, really, Developmental Biology by another name and with one significant difference: embryos, the realm of Developmental Biology, are reproducible, organoids more often than not, aren’t; this has consequences and sets a target.

Sasai was, at heart, a developmental biologist and, having worked with Eddy de Robertis (but probably from before) he was aware of classical experiments in which when animal caps from frogs are left to their own devices, they will make eye cups and forebrains (see Hurtado and de Robertis for a practical review 4). Furthermore, as shown in an insightful review in Development 5 he clearly knew the early development of the eye cup and the lens and thus understood the necessity to relate whatever happens in an ES cell culture to what happens in embryos. Thus he had a good sense for the fact that the autonomous potential of ES cells to organize into tissues autonomously was neither new nor unusual, it reflected what those cells are meant to do. The autonomous gastrulation of frog tissue (exogastrulae), the ability of cells from limb buds to to self organize into digits and the remarkable but much forgotten experiment 6 in which when frog animal cap cells are jumbled up, reagregated and exposed to signals they organize in space as the normal animal caps do, are some examples of this. If you allow me,  ‘organoid biology’ is a rebranding of ‘tissue and organ morphogenesis’ with, perhaps, the added spice that it is making use of our ability to differentiate stem cells rather than the material provided by embryos. It also carries a lot of hype.

The sight of disembodied organ-like structures in culture dishes easily captures the imagination. Probably it is for this reason that the report that a human brain had been grown in a dish 7sparked a huge amount of attention and interest amidst researchers and the public. The press fuelled this interest with headlines such as “Mini brains allow scientists to study brain disorders” or ‘lab grown minibrains aid Alzheimer disease researchers’ that created expectations. What had been achieved did not live up to the billing. What had been observed was not that different from what had been achieved in the mouse system but the fact that it was human, as these things tend to be, and that it had been achieved from iPS cells (genetically engineered ES cells) was an irresistible combination. There was also a sideline about microcephaly and the possibility of modelling brain diseases but one wonders how much of this had to do with journal headline and how much with real science. We certainly look forward to further reports on this front.

There is little question that this was an achievement but what the media forgot to say is that the events that led to those structures are the creations of cells over which we have little control. Furthermore, that in the v1.0 there were no brains as such but rather whimsical structures with a mixture of elements from a brain (forebrain, midbrain and eye tissue), that the system was hardly reproducible, that we had little understanding over what had happened. Feynman famously left on his final blackboard the statement “that which I cannot build, I do not understand’. If in ignorance we extrapolate this to the organoids that grow in culture dishes we would have to say: that which we can build we do not understand. The reason is, of course, that we have not built anything ourselves, that it is the cells -with rules that at the moment we cannot fathom- that have done it (as they are programmed to do), that we are at the mercy of the cells, privileged spectators of their productions. Can we change this? What is missing? Enter the engineers.

Figs for Paris.002If the system was engineered it would be reproducible and this would allow us to learn. Reproducibility is a first and most important target of the organoid game at this stage and it is where the interaction with engineers is key. Embryos are reproducible systems and it is because they are reproducible that we can use them to learn, that we can detect small changes in patterns to obtain clues of how genes relate to the building of tissues and organs. As F. Jacob pointed out, organisms are the result of evolutionary tinkering, bricolage, a more rudimentary form of engineering and so, perhaps, a way to understand them is to look at them from the point of view of engineering. The goal is not to GUESS how an organism is made, BUT to KNOW how it is made and for this only if we obtain reproducibility shall we understand. If we want to use organoids, we need to strive to make them reproducible and then, not only we shall be able to use them but, they will also teach us about the processes and interests that they represent. Recently there has been some progress in some of the organoid cases and the possibilities are clear. Thus an engineering of the minibrain system has allowed insights into the working of the Zika virus and promises more 8,9, and an engineering of the already robust intestinal organoids, has created the conditions for a sophisticated degree of reproducibility that will contribute to ongoing studies10. These are examples to follow because for the most part the field (if we admit that it is a field) remains hostage to the vagaries of the interactions between cells and culture.

Figs for Paris.003If we agree that the solution is to engineer the process, we need to use the Physics of the system, which, like in any engineering process, underpins the events. This means that in our attempt to engage cells into building tissues and organs we need to engage developmental biologist. If stem cells are the materials, developmental biology is to organoids what Physics is to Engineering, and we need to use it like that. And by Developmental Biology I do not simply mean the garden variety that dabbles in genes and cells but the more quantitative systems one that strives to integrate the rapidly emerging data into models that identifies parameters and tells us how the different variables interact. Just like Evolution tinkers, we shall tinker. At this, as Peter Zandstra exhorted us at the meeting, we need to use what we know in a realistic manner. Build models that contain real dimensions and time scales and use them, like engineers do, to improve, to build, to understand.

Organoids, in its many varieties (embryonic and adult stem cells, micropatterned cell arrays, scaffolding of cells from different tissues) promise much but we need to accept that the process is more important than the end, that understanding their beginnings and how they unfold will allow us to understand and improve the end product. One intriguing feature emerging from the current studies and that we shall have to address, concerns the differences between the events that we see in the dish and what we observe in an embryo (see refs 5 and 11 for discussions). It is too early to say whether these differences are important but, it might be that as in engineering there are many ways to make a bridge or a jet or a computer, the same might apply to a tissue and an organ; to put it clearly, there are many molecular solutions to an organ or a tissue and the embryo uses one but we might be able to use others that are simpler. Much interesting and unknown lies ahead but one of the most exciting prospects is the possibility to explore human developmental biology and, in the end, to create a proper organ and tissue engineering as a first step for a regenerative medicine. But we should not cut corners.

Much of this was discussed on and off stage at the Pasteur meeting which had a sense of first encounter between engineers, developmental and stem cell biologists and of expectation of what can be achieved by working together. There will be a report of the meeting in the Development journal, but importantly interesting things will happen. Stay tuned.

1.         Eiraku, M. et al. Self-organized formation of polarized cortical tissues from ESCs and its active manipulation by extrinsic signals. Cell Stem Cell 3, 519-32 (2008).

2.         Eiraku, M. et al. Self-organizing optic-cup morphogenesis in three-dimensional culture. Nature 472, 51-6 (2011).

3.         Sato, T. et al. Single Lgr5 stem cells build crypt-villus structures in vitro without a mesenchymal niche. Nature 459, 262-5 (2009).

4.         Hurtado, C. & De Robertis, E.M. Neural induction in the absence of organizer in salamanders is mediated by MAPK. Dev Biol 307, 282-9 (2007).

5.         Sasai, Y., Eiraku, M. & Suga, H. In vitro organogenesis in three dimensions: self-organising stem cells. Development 139, 4111-21 (2012).

6.         Green, J.B., Dominguez, I. & Davidson, L.A. Self-organization of vertebrate mesoderm based on simple boundary conditions. Dev Dyn 231, 576-81 (2004).

7.         Lancaster, M.A. & Knoblich, J.A. Generation of cerebral organoids from human pluripotent stem cells. Nat Protoc 9, 2329-40 (2014).

8.         Qian, X. et al. Brain-Region-Specific Organoids Using Mini-bioreactors for Modeling ZIKV Exposure. Cell 165, 1238-54 (2016).

9.         Xu, M. et al. Identification of small-molecule inhibitors of Zika virus infection and induced neural cell death via a drug repurposing screen. Nat Med 22, 1101-1107 (2016).

10.       Gjorevski, N. et al. Designer matrices for intestinal stem cell and organoid culture. Nature 539, 560-564 (2016).

11.       Turner, D.A., Baillie-Johnson, P. & Martinez Arias, A. Organoids and the genetically encoded self-assembly of embryonic stem cells. Bioessays 38, 181-91 (2016).

Preprints in the Biomedical Sciences: The Future is Here

IPPA few days ago, fittingly in the context of Open Access week, we had an event to explain what are preprints and how they have the potential to change communication and career development in the biomedical sciences. You can follow the recording here: The event counted on the participation of publishers, funders and users; a summary has been posted in The Node and I encourage you to look at it and contribute to the discussion. There is much to talk about in the wake of the event. Here I shall concentrate on a few issues in the context of publications which highlight the momentum for change.

Preprints are not peer-reviewed papers but importantly, they are nothing new as they have been tried and tested in the Physical sciences for over twenty years, with much success. Interestingly, at the time of the event EMBO J published an article from P. Ginsparg, the founder of arXiv, the Physics preprint server, called  ‘Preprint deja vue’   (; I recommend everybody to read it and reflect on what it says about the biomedical sciences for it shows us up (my reading, I hasten to say) as a small minded community, with a narrow notion of competitiveness and an overreliance on commercial publishing for the evaluation of our work.

Preprints and preprint servers are a rising culture and are emerging as a good first solution to some of the problems. But we have to get it right. There are two concerns that are often levelled to preprints: the worry about their lack of peer-review and the fear of being scooped. Both fail to recognize the essence of Science and the crisis of the peer-review process in the biomedical sciences. For example, on the first one, it would be foolish not to recognize that an important element fuelling the rise of the preprint culture is the degradation of the peer-review process which, up to now, has been the cornerstone of modern science. Nobody can deny that papers improve with peer-review but it is obvious that from a system of checks and balances and with the connivance of journals, the peer-review process has become –particularly at the high end of the market- a device to delay publications and, in the process, to give reviewers the power to determine the content of the work and, in some instances, use the anonymity of the process to produce unfair allegations and decisions. Much has been written about the anonymity (blind, double blind, open reviews) but it has always worried me that one of the arguments to preserve the status quo is said to be the protection of young PIs from retributions that established peers might launch in the face of the criticisms that might be levelled to them. How come we cannot own what we say and think? What this says really is that the reason for the anonymity is FEAR, a typical situation in totalitarian systems. How come fear is a justification for anonymity? It should give us pause for thought. Where have we taken our scientific culture: people afraid of signing what they believe in? It would be good if we could change the scientific culture, if we could encourage and practice more an open discussion of our work (which let us not forget, goes on in private, in journal clubs and cafeterias). Journals give you the option of commenting and discussing but only after publication. A preprint is there for discussion, so you can comment, openly, and influence its shape and help, rather than hinder, the authors.

But, in the end, we have to ask what is the purpose of peer review? It has been suggested that it is validation of the research and yet, if you ask (and we did at the event) how many people have failed to reproduce a published piece of work, the answer will be loud and clear: many, most. So, peer-review is not validation. It is a form of certification of the quality of work, like that of the rating agencies on credits and, as it was the case in the financial crisis, there are too many subprime papers AAA rated because they are bundled in HIF journals with a few quality ones. We have lost our bearings and it is unfortunate that we value our work not for its intrinsic merits but because of where it is published.

The issue of scooping cannot be separated from the strange contraption that the peer-review process has become. Here, again, we biologists have a very different understanding of a notion (scooping) that highlights our small mindedness. As Ginsparg puts it (see EMBO J above) ““scooping” in the context of biology research appears to mean the race between laboratories working on overlapping” and herein we highlight again that the form matters more than the content. There is little question that posting your work, whether in preprint or peer-review form, gives you priority… if there is anything to give priority for………… In Physics there is no question, again Ginsparg: “Posting work on arXiv gives authors a datestamped priority claim, which is accepted by the community, and gives immediate visibility to authors’ work”. I and many agree. The large number of papers with 0 citations in HIF journals is a sad comment on the huge amount of work that in the biomedical sciences goes into useful pieces of information but largely irrelevant pieces of science. How much money and pain would those authors have saved if they had posted their work in a preprint server! I shall leave you to take it from here but in my mind, there is little to fear about posting your work in a preprint server and much to be gained. In many ways, preprints are the “ultimate open access”. Preprints can create a more democratic, cost effective way of managing science and at the event it was excellent to see Journals promoting them and seeing their value.


There is much to work on to get the community to embrace preprints. We were lucky to have exceptional speakers at the event where the Wellcome Trust, as a funder, expressed their support for the culture and explained their own efforts towards it (Wellcome Open Research & the Open Science Prize). Interestingly, shortly afterwards we learnt that EMBO will allow for preprints to be cited as evidence of output (as long as they are accompanied by at least one peer-reviewed paper). I am aware of efforts along these lines in the US where many institutions already encourage applicants for jobs to cite preprints. This is good news because it does unshackle students and postdocs from the handicap of not being able to refer to their toilings when they are looking for fellowships and jobs. Preprints are here to stay. The reasons are many and being increasingly discussed and if you wanted a particularly one, this one was stated by Richard Farndale (Dpt of Biochemistry, University of Cambridge): preprints give us a way to let funders know that the work that they gave money to do, has been done. This simple statement alone, makes the point of what preprints are for and should lead funders not only to encourage preprints but to demand them. It should be the funders and not the journals, who decide whether the work has been done.

There is much being said and written about the current situation which really is an expression of movement. A particularly thoughtful piece by P. Walter and D. Mullins appeared recently in the ASCB: ‘on publishing and the sneetches: a wake up call?’ ( ). Much to mull over here and many arguments for preprints. The article ends up on a note “The end goal seems obvious: The knowledge that we produce in our publicly funded works belongs to humankind and must not be locked up behind pay-walls— newly submitted papers should be open-access and older ones open-archive. Our real challenge is to find the paths that get us there.  But major change can happen, even if it seems impossible to imagine now” I say, let us use preprints. Not only use them but work, together, to shape the future of biomedical science communication.

Further readings on preprints from this blog:

New publication on “symmetry breaking in ensembles of ES cells”


The left picture is a group of ES cells bearing a reporter for Wnt signalling (red) in adherent culture, the middle one is the same cells in an elongating ‘organoid” which we call a ‘gastruloid” -notice the localize expression of the reporter-; finally the picture on the right is an embryo bearing the Wnt reporter at a stage we reckon mimics that of the aggregates in the middle. Picture on the right courtesy of Christoph Budjan.

New publication on “symmetry breaking in ensembles of ES cells”

Progress on our attempts to understand the connection between genes, signals, cells and embryos have just been published in Development. In a first paper we describe a new experimental system in which we coax mouse Embryonic Stem cells to make structures with an anterior posterior axis and a germ layer organization that resembles that of an embryo ( In a second paper we use this experimental system to gain some insights into the emergence of the spinal cord (

You can see a movie and some thoughts on the experiments here:

More on this will follow soon.

Farewell to Pedro Machado


IMG_0666 copy

Yesterday we wished farewell to Pedro Machado, a young physicist who has been in the lab for the last few years, educating us in the use of measurement and theory to understand biological systems. Pedro came to Cambridge four years ago fresh from a PhD in Holland on quantum gravity and a great interest in understanding the emergent properties of cells within tissues. At the time Nicole Gorfinkiel had started a trip trying to put some physics in the process of ‘dorsal closure’, a morphogenetic event at the end of Drosophila embryogenesis we had been working on for some time. So, Pedro’s arrival and interest was timely. Overall, as a group, we had decided that a physical sciences inspired approach to Biology was the way forward. Pedro was the first physicist to reside in the lab and I can see now that in his time with us he has learnt and we have learnt. Pedro is a brilliant, imaginative and inspiring scientist with, as befits a good theorist, a great eye for beauty in the structure of a thought or an idea and with a great way of discussing about Nature.



Pedro tried to fiddle with fly embryos but this did not last long. Needles, slides and microscopes, not to mention eggs, are a far cry from quantum gravity. Around him, in the ticky-tacky room (as it is called) Pedro with Jonathan, Pau, Sabine and, throughout the years, a small group of visitors have been teaching us how to put and interpret numbers in Biology and, in exchange we hope to have given him something to think about. I guess at the end of this stretch of his journey Pedro will be happy to have dabbled with Biology and, hopefully, have learnt to accept that Nature is noisy, also reliable, but noisy. Ever since he arrived he has worked in close association with Nicole and the problem they set out to solve has taken more time than they thought it would. Miraculously it was solved a few weeks ago and I am pleased for both of them; it soon will be in manuscript form. How cells turn tissues into continua with material properties is not an easy problem, but one that, probably, is at the root of many morphogenetic processes and we need to understand through a cycle of theory-measurement-modelling-experiment. Pedro and Nicole with the help of their collaborator Guy Blanchard have been doing just this.



Like all physicists, and unlike most biologists, the quantitative skills that Pedro carries will open him doors. For the moment he is going to London, to work on an exciting new venture which looks at how to interface computers, data and medical intervention. An exciting new field to which, we are all sure, Pedro will contribute enormously.

We shall miss Pedro, his class, his kindness, his brilliance and panache when explaining something. But we shall continue to work together. As I always tell him, Einstein did not do his best work from a University or a research institute but rather from his spare time in a patent office in Zurich.  We still have some unfinished business and we shall always have questions and data for him to explain, for us to discuss. And we look forward to this and more.


New Publication: “Quantifying ES cells: A ß-catenin driven protein interaction network that buffers Oct4 to maintain pluripotency”

Muñoz-Descalzo, S., Rue, P., Faunes, F., Hayward, P., Jakt, L.M., Balayo, C., Garcia Ojalvo, J. and Martinez Arias, A. (2013) A competitive protein interaction network buffers Oct4-mediated differentiation to promote pluripotency in embryonic stem cells. Mol. Sys. Biol. 9 Article number: 694  doi:10.1038/msb.2013.49

The model that represents the competition between the different complexes and a comparison of the distributions of Oct4, Nanog and ß-catenin in ES cells grown in Serum and LIF or in 2i conditions; in the top is data, at the bottom is the result of the simulations of the model on the left.

Pluripotency refers to the property of a cell population to give rise to all cell types of an organism. Embryonic Stem (ES) cells are pluripotent and are able to self renew this property in culture. ES cells have become an important focus of research. From the biomedical point of view because they hold a promise for regenerative medicine, from the basic science point of view because they offer a useful experimental system to understand how cells make decisions in development.

Work over the last ten years has identified a core set of transcription factors that are necessary and sufficient for the establishment and the maintenance of pluripotency with two of these factors, Oct4 and Nanog, at the center of the network. However, how they function together to achieve this state has remained elusive. Most of the models focus on transcriptional gene regulatory networks assembled from interactions between these factors. However we have shown recently that pluripotency is characterized not by the absolute amount of any of these factors but by specific ratios of Nanog and Oct4 (Muñoz Descalzo et al. 2012 Correlations between the levels of Nanog and Oct4 as a signature for naïve pluripotency in mouse embryonic stem cells Stem Cells 30, 2683-2691). Furthermore, it appears that the amount of ß-catenin is key to the stability of the state. In this work we use a combination of quantitative immunofluorescence, genetics and modelling to show that pluripotency is dependent on a competitive protein network whose function is to buffer the levels of Oct4. ß-catenin emerges as the anchor of the network and the one element whose fluctuations determine the stability of the state.

While not doing away with Gene Regulatory Networks, this study raises the power of protein networks as the information processing units of the cell.

News – AMA Lab retreat at Clare Hall Cambridge

Last Friday we had what they called a ‘retreat’, a day out to get a view of what we all do in the lab. It is true that there are lab meetings but one of these events allows us to get a global view of the activities of the group. Given our interest in heterogeneities, it is not surprising that we are a number of variations on a theme: how cells make decisions and how we can bridge this at several scales. We also are pleased to have a number of important collaborations and contributions from outside the lab, which were much in evidence during the day.

It all started with Christoph Budjan (working jointly with Emma Rawlins and us) who made a lucid and clear discussion of what is the role of signals in development beyond the classical linear view suggested by Genetics. This was followed by two talks by David Turner (the onset of Brachyury in cultured ES cells) and Christian Schroeter (decision making in the Primitive Endoderm/Epiblast lineages) who made explicitly clear how quantifications of cell fate decision processes leads to interesting insights into the mechanisms underlying the events (and sometimes these are not obvious). We then entered a more biochemical theme with our collaborators (Claire Mulvey and Andy Christophorou) from the proteomics group led by Kathryn Lilley, showing us the beauties and promise of proteomics as applied to ES cells and Penny Hayward discussed her progress on the long treck to understand the role of ß-catenin in pluripotency and the exit from pluripotency.

On either side of a great lunch we heard two of our theoreticians discussing fine grained (Peyman Gifani) and coarse grained (Pedro Machado) approaches to infer rules and networks involved in decision making in ES cells. It was interesting to get a fresh view of notions that have been around for a while. With increasing amounts of information from single cells, these kind of approaches which use hybrids of statistical mechanics, population biology and bioinformatics, become increasingly significant and influential. And with these talks we looked at the home straight in which Joaquin de Navascues gave us an account of how a classical developmental geneticist from Madrid has been transformed into a cell population biologist. He aso discussed his plans for the forthcoming move to Cardiff to work in the European Cancer Stem Cell Institute led by Alan Clark ( Cassie Yu Bian presented us some exciting and insightful data on Notch signalling in the intestinal stem cells of the gut which challenges everything that is published on the subject. The reason being that it is quantitative dynamic data.

The day was capped with a guest talk from Tristan Rodriguez (Imperial College, London: who discussed his recent results on cell competition in the early mouse embryo under the title “Surviving pluripotency, who picks who will live and who will die”.

The day was a bit warmer than it has been and we could see (and feel) all seasons through a very nice set of glass windows on the side of the room. The venue was wonderful and Clare Hall did a great job. We want to thank Sung Ly for organizing everything. We ended up, as it is customary on these occasions, going to the pub and later to dinner. This was, however, not a normal occasion as we said Good Bye to Jamie Trott, who having finished his PhD with us is moving to Singapore where he will be working in the group of Ray Dunn ( Jamie leaves much behind and will be missed, We still have much to wrap up concerning his work in single cell transcriptomics during differentiation (you will hear more about this soon).