Tuesday, June 19, 2007

Moving to Nature Networks

Dear everybody.

From now on this blog is moving to Nature Networks. Find it following this link.

See you there!

Tuesday, June 12, 2007

Mini workshop in Oxford

Today Marcus Tindall has organised a mini symposium (for lack of a better name) for me and the guys here working on mathematical models of cancer to get to know each other. I have given a very small presentation [PDF] (<30m) that covers stuff I presented before.

From the CMB I got to know the work of:
  • Philip Murray, who has created a CA model to study the role of the cell cycle in tumours and that is now trying to obtain a continuous model that displays the same behaviour.
  • Alex Fletcher who studies hypoxia in tumour development at the sub-cellular scale.
  • Matt Johnston who works with W. Bodmer (whose game theory models have inspired my own work) to study the dynamics of cell populations in a colon crypt in colorectal cancer. His model shows how a homeostatic population could explode by slightly altering some of the paramers.
  • Natasha Li who collaborates with Gatenby to study, using Cellular Automaton and continuous models, the role of glycolysis in tumour invasion and the influence of the stromal environment. This is specially relevant to me since it is one of my two main lines of work at the moment. She mention in her talk that glycolytic cells are especially sensitive to glucose deprivation.
  • Rebecca Carter works on multiscale models of fluid and drug transportation in tumours.
  • Marcus Tindall gave a brief introduction to his multiscale model of interaction between the cell cycle and cell density.
The presentations were all quite short but I hope to hear more from these people in the coming days.

Tuesday, June 05, 2007

Queerer than we can suppose

I found this video from a Richard Dawkins's talk in which he talks about the strangeness of science.

He talks that science is about truth but that our brain is evolved to cope with every day's reality, within the scope of the reality we have to live with. He cites the example that matter is mostly composed of space but we do not perceive it like that since it is more useful for us to perceive it as solid and opaque. He argues that a living being of the size of a neutrino and capable of vision would see matter as mostly empty space only by the nature of the space it inhabits. Similarly, things that look entirely unlikely to us (the existence of life) become inevitable when considering the vast amounts of time and space the universe has been going on compared to the space and time of our human lifetimes.

More shockingly to me he claims that humans are more akin to automata than to agents seeking what they consider positive things and avoiding negative things. The reason being that evolutionarily we rather model fellow humans as people with a purpose than as systems made of components whose design and integration we ignore.

In any case this is an important issue for scientists and philosophers of science: our brains have evolved for certain purposes and with certain biases and that should impose some limitations and constraints in what things we can understand and how we chose to interpret natural phenomena.

Sunday, June 03, 2007

Oxford

I will be staying one month at the Centre for Mathematical Biology directed by Philip Maini at the University of Oxford. With a little of luck I will be able to meet people interested in mathematical discrete models of cancer evolution and angiogenesis.

In the Centre they have some interesting (and relevant) research lines like "individual and collective behaviour in ecology" and of course "cancer modelling". The Centre is pioneering (with Arizona's Gatenby and Oxford's Comlab Gavaghan) the idea that glycolytic acidity promotes invasion. Maybe this could be an opportunity to test my hypothesis that this invasion comes in waves.

Friday, June 01, 2007

Talk in Girona

I have been invited by Josep Vehi to give a talk about my research at the institute he directs at the University of Girona.

In this talk I have introduced for the first time the game theory model in which I have worked with people in Dresden (Andreas Deutsch, Haralambos Hatzikirou) and Bonn (Matthias Simon) in which I study Gatenby's hypothesis of acid mediated tumour invasion. I have also talked about the Cellular Automata model I have developed with Benjamin Ribba (Lyon) to study the microenvironmental influence in cancer evolution which I have previously presented in Lyon, Dundee and Dresden.

The presentation can be found here in PDF format.

Tuesday, May 29, 2007

cancer and the cell cycle

Last Friday I came to the Max Planck Instute for Cell Biology, at the other side of Dresden, to attend a series of seminars including one from a colleague and friend of mine, Babis Hatzikirou, about the cell cycle.

The classical view on the cell cycle can be seen in this picture that I took from Babis's presentation (and which I suspect he took from somewhere else :)):
This is quite interesting although not precisely research news. Most of the cell cycle is of course devoted to interphase and only a minority of the time (assuming that the cell is not in arrest mode) is devoted to create a copy of itself (through mitosis and cytokinesis). The cell cycle is controlled by a finely tuned balance of proteins cdc2-cdc13 and a number of checkpoints make sure that before changing the phase of the cell cycle everything is in order. These checkpoints and their associated proteins (such as the famous TP53) are quite critical to prevent tumour formation as they impede the growth of cells that need DNA repair.

Friday, May 18, 2007

What science is not

From an extract of the book The invisible sex: Uncovering the true roles of Woman in Prehistory (review in Nature 3rd of May issue).

"science is not truth; it is, instead, a method for diminishing ignorance"

Wednesday, May 16, 2007

A 3D model of human breast cancer

This has been covered in a few places like the BBC and ScienceDaily. It seems that some researchers at Queen Mary College in London have recently come with a non animal 3D human breast cancer model.

This is interesting at more than one level. Their research was funded by a research charity (Dr Hadwen Trust) that supports the development of methods that avoid animal experiments. Working with rats is not that satisfactory for ethical reasons and also because there are many cases in which the results of rat experiments cannot be extrapolated to humans (seems we are not so similar in some respects after all). It is also much more realistic than just taking some human cancer cells and studying them on a petri dish.

Being capable of performing experiments using realistic 3D models quickly and efficiently is one of the holy grails of theoreticians since it would make experimental validation of our models much easier (confusingly enough what theoreticians call model, eg, equations or computer rules, is not what experimentalists understand as a model, eg. rat, arabidopsis or drosophila). This validation is quite complicated as I have already mentioned in another post. Making this validation easier and more convenient will go a long way in terms of making our work more reliable and quantitative.

Monday, May 14, 2007

Somatic and non somatic evolution

Many ecologists study evolution of the non somatic kind. That is, evolution that happens as a consequence of mutations in the germ line of multicellular organisms during reproduction. The evolution of cancer is of the somatic kind. This means that it affects cells of the soma, the ones that are not transmitted to the offspring.

Some time ago I got this paper from Crespi and Summers (nicely enough, publicly available). I will probably talk about this paper, entitled Evolutionary biology of cancer (and presented to a readership of ecologists) some other time but I liked a table in which they compare somatic and non somatic evolution.

Phenotypic variation. In most ecosystems of multicellular organisms variation is attained through genetic recombination (sexual reproduction) and mutation. In a tumour we also have to consider also genomic instability (a hypothesis by which some individuals have a higher probability of mutation) and epigenetic alteration (the environment also affects the behaviour of cells in ways that could make tumour progression to cancer more or less likely).
Selection. In most ecosystems it means dealing better with competitors, avoiding predators, parasites and producing many fit successors. In a tumour means being good at competing for resources with other cells (tumour or otherwise), avoiding the immune system and coping with environmental signals designed to maintain homeostasis.
Drift. That is similar in both types of evolution.
Inheritance. In many cases that involves the transmission of genes from parents to offspring through sexual recombination. In tumours there is no sexual reproduction.
Result. In most ecosystems the result is adaptation across generations. In a tumour the end results is in many cases the death of the individual and thus of all the cells in the body, including the cancer cells.

I think that this is a quite interesting and useful comparison of evolution although I am not sure I agree with all the differences suggested. In my view the evolution in a tumour does not differ much from other types of evolution. For instance, epigenetic changes do play a role in other ecosystems asides from cancer. Genetic instability is not a source of variation, genetic mutations are (genetic instability just makes genetic mutations more likely). Also the fact that tumour cells reproduce asexually is not a big difference with more conventional ecosystems. At the end of the day most of the biomass of the planet is made of bacteria that reproduces asexually. What it is true is that as far as we know, the end result of cancer evolution is either the end of the cancer itself or the end of the individual that hosts the cancer and thus the end of the cancer cells. Thus the only way tumour cells have to be successful is to evolve in such a way that the life of the host is not threatened (you can call that tumour sustainable growth).

Wednesday, May 09, 2007

Autophagy and cancer

This is a new cellular mechanism I did not know about: autophagy. Nature's issue of April 12th (I am bit behind I know) has an interesting article in the section Q&A on autophagy and its role in cancer.

Autophagy is the process by which cells degrade faulty or redundant components. It is used by cells when they need to reuse molecules for other uses and also it plays an important role in complementing apoptosis. Both apoptosis and autophagy are connected to cell death but in the case of autophagy cell death is not always the outcome although it can be a substitute when the apoptotic mechanism is crippled. In that case the cell literally eats itself to death.

The image bellow comes from the article. Autophagy has the potential of being useful for cancer supression but also for cancer promotion. The balance is important, too little and you get cell death when the cell cannot produce things it needs by reusing parts of itself. Too much of it and you also get cell death since the cell can eat itself. Altering this balance in a tumour cell could be the source of a new therapy although as usual it is important to remember that cells might evolve mechanisms to avoid the trouble of autophagy, maybe by inactivating the atophagy mechanism all together. Even in that case the tumour cell would be less capable of surviving in situations of stress since it would not be able to recycle material.

Autophagy seems to be a mechanism whose precise role in cancer has not been fully studied yet but could be a promising extra target for a multi target therapy that could hinder cancer evolution and growth.

Monday, May 07, 2007

Evolution and medicine

Catriona MacCallum, an editor at PLoS Biology has posted the following essay (being PLoS, it is available to everybody) about medicine and evolution.

According to the article, physicians do not get much of a training in evolution as a method to study the origin of diseases. That is because most of the training of physicists is not to make them good scientists but to make them good at treating patients. Quoting the article: "does a mechanic need to understand the origins, history and technological advances that have gone into the modern motor vehicle in order to fix it?".

This approach is not entirely wrong and once can treat things that are the result of an evolutionary process without having to spend too much time studying evolution. A different thing is when the disease is not a result of evolution but they are evolution itself. They never mention cancer in the article but cancer and infectious diseases are clear cases of diseases in which evolution should be dealt with if the disease is to be cured or even contained. Without an understanding of evolution a physician will be unable to understand how the bacteria or cancer cells will react and evolve when a treatment is used or what phenotypical traits are more likely to be evolved and thus cause problems to or be exploited by the medical community.

Friday, May 04, 2007

Cell article on science blogs

Blogs as a way to communicate science. This is quite an unusual topic for Cell that, as opposed to Science and Nature journals, devotes less space to the non-technical side of science. For those of you that are subscribed, the article is here.

According to the article there are approximately 20000 blogs with the label 'science'. That is quite an impressive number since most of my colleagues seem to be doing lots of things but not blogging. It seems that most of these science blogs are actually about pseudo science which would be the number of more conventional science blogs to around 1200 (always according to sources cited in the article). These are generally blogs like mine (of course in many cases better written and updated more often) which deal with fairly specific issues in a specific field of science.

These science blogs can be just about anything. Many do like I do and comment (what we personally find) interesting stuff in our own field of research that we find reading, mostly, papers and journals. Some do also include bits about their own lifes and produce some sort of hybrid between the conventional blog (understood as a personal diary) and the scientific blog. Some take the idea of science blog a step further and every day record their latest results online (although in some fields, like biology, this behaviour seems to be quite rare due to the extreme levels of competition between experimental biologists).

Why would any one start a science blog? On top of the conventional reasons why people start a blog (and weighted down by the fact that most of us do not carry sizable audiences) is the thought that when you write something with the expectation (as unlikely as it might be) that someone will read it that surely helps to clarify that something in your mind.

Wednesday, May 02, 2007

Mini workshop on cancer and cellular automata

Today we are hosting in our group at TU Dresden a mini workshop on cellular automata in biology. Three talks (one in the morning and two in the afternoon) are actually about CAs and cancer. It will be a busy but interesting day.

The booklet for the afternoon part of the workshop (the longest part of it) is here.

Friday, April 27, 2007

evolution of multicellularity

A friend of mine has found this interesting essay in Nature entitled "Unity from conflict" that deals with the evolutionary mechanisms that allowed the emergence of multicellular organisms.
The problem of how multicellular organisms came about from single cells is quite intriguing. I heard from Lewis Wolpert that this is probably the most important of the seven transitions in evolution as described by Maynard Smith and Szathm√°ry in their book. In retrospect it is clear that such a transition is possible (since we are here) but, why did it happen?

Paul Rainey (whom I suspect might be a microbiologist) seems to be suggesting that with the right mutation rate (or right mutation bias) multi-cellularity should be possible. Organisms such as myxobacteria seem to be able to alter their mutation rate in response to stress in the environment so I guess that evolution fiddling with the right mutation rate is not unreasonable. In any case I'd rather see it from the point of view of my friend, that is, a harsh environment does enforce cooperation in a way that makes cheating very costly. In reality I would imagine that other factors such as the immune system (that in a way can be though of a police on the lookout for cheaters) or the fact that cells in a multicellular organism share the same DNA could also help explain why there is not that much cheating in our bodies.

This article is quite interesting for any one interested in cancer. At the end of the day a cancer cell is a normal cell that due to genetic or epigenetic reasons stops cooperating. Once they evolve the means to avoid the immune system and other mechanisms designed to maintain homeostasis I would imagine that the life expectancy of a tumour cell should be rather short (necrosis, running behind in the evolution game or due to a poor microenvironment) and thus crime might not pay, at least in the mid/long term (which still would leave room for a benefit in the short term that would be enough to kick-start somatic evolution).

It should be possible using a computational model to demonstrate that an aggressive microenvironment would favour cell cooperation. A mutlicellular organism in which individual cells suffer when exposed to the exterior would evolve a morphology that would minimise the interface with the outside world. it would be also quite likely that a niche of stem cells would evolve to be in charge of generating the cells in this interface that would be in need of constant repair and maintenance. That is what happens in places in which the environment is hostile to cells like the colon or the skin. If cells in the model are allowed to cheat (by means of mutations leading cells to try to avoid being part of the interface if that is their role) that would presumably affect negatively the overall fitness of the organism. However I am not sure that this would rule out other explanations for the evolution of multicellular organisms.

Monday, April 23, 2007

Acceptance of evolution around the world

National Geographic has published this chart that depicts the public acceptance of Darwinian evolution in 34 countries around the world. As a Spaniard I am happy to see that evolution is widely accepted in my country, with a higher acceptance rate than even in Germany where I currently live although not as high as in Scandinavian countries or in the UK (the birthplace of Darwin). In the U.S. less than half of the population (if the results of the poll can be extrapolated) have at least some reservations towards evolution although the country (of all those polled) that seems most hostile to it seems to be Turkey.

Tuesday, April 17, 2007

The laws of biology

The side effect of having spending so much time traveling these last months is that I have this stack of Nature and Science journals (I switched from the former to the latter a month ago to see the difference) which I am going through quite slowly.

In a Nature from the 7th of February there is an interesting essay about the clash of cultures between biologists and physicists working on biological topics written by a physicist from MIT (good to know where the bias will come from). Physicists have a long tradition of studying an (increasing) range of phenomena and producing theoretical models that characterise as many of those phenomena as possible. These are what are called the laws of physics. The question is if biology can have also models and laws that represent biological phenomena.

Although there are some (fairly generic and neat) biological laws (thing of Darwin's evolution and Mendel's genetics) most biologists seem to be more interested in fact collecting than in putting the available information in the form of theoretical models and universal laws of biology. The physicists (and mathematicians) coming to the field have not much knowledge in how the facts are collected (which it is easy to imagine as the source of many frustrations) but a deep interest in integrating those facts into models (especially when it involves using their favourite tools such as phase transitions, fractal analysis, power laws or networks). It remains to be seen if (in the view of the author) these general laws are possible at all and if (not my view but at least my question) the tools that were useful in physics will be that useful in biology (which does not mean they could at the very least, constitute a good starting point).

Tuesday, April 03, 2007

Back from Scotland and Gatenby's talk

I am back from sunny Scotland in sunny Saxony. Of the remaining speakers in Dundee, the one whose talk I was looking for the most was the one from Robert Gatenby, Arizona University (as with Vito Quaranta, a life scientist).

I know the work of Gatenby because he is one of the few researchers involved in using evolutionary game theory (although not of the most conventional, fitness-and-payoff-table kind) to study cancer evolution. Specifically he is working on how acidity due to glycolysis (the anaerobic metabolism that constitutes and advantage for tumour cells that lack oxygen due to the distance to a blood vessel) is a necessary step in the evolution towards cancer. The so called Warburg effect is the result of a well known biochemical mechanism but, what is the evolutionary advantage?

As he has shown in other papers, the advantage for glycolytic cells is that the poison the environment of other cells so they face less competition. They also degrade the connective tissue and thus increase the motility of cells, which is a required step for a tumour to become invasive. From my point of view it is interesting that he seemed to imply that this acidification of the microenvironment is not only a facilitator for cancer but a necessary step. I guess that Hanahan and Weinberg could include this in the section for mechanisms for invasion and metastasis.

From the therapeutic point of view, his research suggests that either alkalising the microenvironment (to counteract the progressive acidification resulting from the glycolytic metabolism) or making it even more acidic by reducing the pH in the blood (and thus contributing to self poisoning of glycolytic cells) would be something worth trying.

Thursday, March 29, 2007

The cost of validation

Many interesting speakers in this workshop in Dundee but most of them fall in the mathematics part of biomathematics. Among the few who do not is the biologist Vito Quaranta (Vanderbilt University). Although I have been told many times that things are changing for the better in that respect, the scarcity of life scientists and medical doctors in these type of conferences tells me that there is still a lot of work to do to convince them that computational and mathematical biology is not only relevant but necessary.

The talk from Vito Quaranta was not so much about science as about doing science at the interface between theory and experiments. He is lucky to count with the resources of the Vanderbilt Integrative Cancer Biology Center. Otherwise the problem of validating the mathematical and computational models with theoreticians come with would be next to impossible. This theoretical models make a number of assumptions about the properties of tumour cells, tissues and micro environments and predict outcomes that in many cases have to be contrasted with in vivo and in vitro experimental results. This experimental work is really challenging given the level of fragmentation of knowledge and expertise in biology and medicine. Different labs with different experimental techniques, machinery, cell lines and the necessary permissions to perform animal experiments and access human clinical data are required to validate one single theoretical model. That means that unless centres like the one in Vanderbilt become much more common most theoretical models will remain experimentally untested unless they proof to come out as the result of the consensus of the theoretical biology community.

Monday, March 26, 2007

Cooperation in a tumour and workshop in Scotland

I find myself in Dundee, in Scotland, attending a workshop entitled Mathematical modelling and analysis of cancer invasion of tissues. It promises to be an interesting event and some of the attendees are working on topics that are very close to mines so it is good to know what is their contribution to the state of the art.

When I arrived this morning I was expecting good stuff from people like Philip Maini (Oxford), Bob Gatenby (Arizona), Vito Quaranta (Vanderbilt) and Sandy Anderson. Still today's most relevant talk for me was given by Anna Marciniak-Czochra (Heidelberg) who presented work based on the research presented very recently by Robert Axelrod (and reviewed in this blog here). Axelrod's work is about how the collaboration between tumour cells could mean that cells do not have to acquire all the necessary capabilities (mentioned in Hanahan and Weinberg's 2000 work) in order for the tumour to become agressive. This is a word model but in Marciniak-Czochra's presentation a mathematical description was shown in which the characteristics of the growth factors (eg. diffusion strength) can determine how useful this collaboration is. It looks like an interesting model and hope a paper will come out soon so I can take a look. Still it seems that a paper that covers Axelrod's work more comprehensively is still work to be done.

Wednesday, March 21, 2007

The links between scientific disciplines

I have just found this amusing article about how some guys took more than a million and a half scientific papers from 776 different branches of science and came with the graph included in this post. You can find a larger version (5Mb) of it at this site. It shows how often papers from different disciples are cited by the same paper so it can give a measure of what fields are more likely to inspire interdisciplinary work.

Most of the research seems to be in Medicine and biochemistry (including all the -omics stuff). Math seems to be more unconnected to many other branches of science that I thought but to be honest I am not very sure about the methodology. More about it can be found in Mapofscience.com.

Sunday, March 18, 2007

World Community Grid and Cancer

Since the guys at SETI came with the idea of using the CPU time of internet users when they are not using their computers, several other projects draw inspiration from this idea to obtain some sort of highly distributed high performance computing when the funding is not there.

One of these projects is called the world community grid which involves many research centres and universities and tries to tackle several problems that should be of general concern. One of the projects is about Cancer. One of the ways to go about cancer research is by using tissue microarrays in which samples of tumour cells are treated differently and the results of the different treatments can be obtained and compared in a comparatively efficient way. I am writing this from Columbus airport but when I get the chance of getting back to Dresden I should install this client on my Linux workstation. They do have versions for Linux, Mac and Windows.

Of course one thought is that if I know that I will not use the computer in a while the right thing to do (assuming one cares about the world) is to switch the computer off but I guess that those times in which the screen saver kicks in I would be happier thinking that my computer is doing something interesting instead of just displaying pointless and CPU intensive openGL pictures.

Tuesday, March 13, 2007

Columbus workshop and interactions with life scientists

Being a workshop on mathematical biology one of the issues we all face here is how to work with life scientists and thus one of the panel session yesterdays was precisely about that.

It seems that there are different kind of problems theoreticians might find when dealing with clinicians and experimentalists depending on a number of factors:
  • What kind of people are they? Are they 'math-skeptic'? do they have affinity towards theory?
  • Do you want them to share their expertise with you or do you want to influence the experiments they perform so they can be used in your theoretical model? The latter is significantly more difficult.
  • Do you work with biologists or with physicians? There is a real difference between the average PhD and the average MD that does some research on the side when it comes to understand the usefulness of theory.
Some tips where also offered by some participants on how to make finding and establishing collaborations. Mainly it helps to attend seminars from the life sciences departments, get yourself familiar with their stuff and get your face known to them so you don't come as a complete stranger.

Friday, March 09, 2007

Workshop in Ohio

I will not probably have much time for posts next week since I plan to attend a workshop in Columbus, Ohio. The workshop is organised by the Mathematical Biosciences Institute of the Ohio State University and is entitled Workshop for young researchers in mathematical biology (remember what the meaning of young researcher is from my previous post from my visit to Barcelona :().

At any rate there will be some interesting people both in the category of keynote speakers and "young" researchers. Some of them doing bio mathematics of cancer so expect a report on that when I come back.

Thursday, March 08, 2007

cancer genes

The information can be found tailored for all types of users. For those who want an easy take here is the BBC version. Nature has a nice overview and the article proper.

Here is my take: a (fairly large) group of researchers mainly at the Sanger, in UK have studied hundreds of genes that are mutated in about 200 types of cancers. The trick here is to find what genes DO drive cancer as opposed to 'just happen to be mutated' in a cancer. At the end of the day your average tumour cell in an advanced stage tumour is likely to contain several mutations and many of them will probably be hitchhikers not necessarily contributing to the overall fitness of the cell. Unfortunately the result of the research is that the number of genes mutated in many cancers is higher than expected and telling apart driving genes from others will be a challenging task. One thing of working with so many types of cancers (200) is that genes that might not play any significant role in one type of cancer might turn to be important in the next.

Wednesday, March 07, 2007

Telomeres, cancer and aging

One quite fascinating thing in animal biology is the question of immortality or, to be more precise, the lack of it. While most unicellular organisms can divide for as long as they have the luck to find resources and space to do so, human cells can divide only a limited amount of times (approximately around 50 times, although this does not apply to stem cells that can divide an unlimited amount of times). In principle the limitation in divisions for most human cells is due to a mechanism that has been evolved and is not an intrinsic limitation. The cancer hypothesis is that the limitation makes the appearance of cancer more unlikely. If a cell is limited to just a few divisions, if it acquires a mutation that mutation is unlikely to spread to far.

The reason for this limitation are the telomeres, situated at the end of the chromosomes, that get shorter each time the cell divides. Once these telomores reach a critical size and become to small the cell will enter a state called senescence by which they will not divide again.

This is an interesting link in which they talk about this and how in the next few decades we might know enough about the effects of limited cell replication in human life expectancy, how to increase it (maybe for ever) and how to do that avoiding nasty side effects (like increased probability of dying from cancer). The website in which this is hosted is covering all sorts of news, many of them of dubious scientific interest, but the information in the link looks sound.

On the other hand in a more reliable source (PNAS) there is a nice study on how telomere dysfunction can cause genetic instability. They work on a disease known as Werner syndrome but it is quite useful stuff for cancer research. This Werner syndrome results in people aging prematurely and researchers at the Salk institute have found how extra short telomeres can be the source of the problem.

Monday, March 05, 2007

Bioinformatics and google

First of all, I am not a bioinformatician. I even thought I had an idea of what is the aim of bioinformatics but after a visit to the group of Nuria Lopez Bigas at the Biomedical Research Parc in Barcelona I realised that the scope of what I thought the field is about was too narrow (they do some nice machine learning and statistical work on disease related genes).

I have seen this video on Google video (only one of these sites that allows the user to download the video for offline use) some time this weekend. It is just a talk by David Vise, the author of a book about Google, to staff at Google Inc. Google is one company that fascinates (and in a sense, worries) me tremendously. As a side note, this blog is posted in one of their servers.

The thing is that at the end of the talk, David mentions the interests of one of Google founders (I think it is Larry Page) on biology. Then I thought (and I am sure that I will be the last of a long list of people) that, wow, that is really a good match: google and bioinformatics. Biology until know was mostly a science in which practitioners collected facts. There is loads of data and little idea of how to make sense of it, asides from evolution and a few other very general ideas. One of the aims of google is precisely to find patterns in the zitabytes of information stored in their servers. I have the feeling that we will see more of Google in that field.

Thursday, March 01, 2007

Old Dawkins video on cooperation

I have found this video on google video. It is an old Richard Dawkins BBC TV programme in which he goes through some topics of which I am quite fond and which I personally think have some yet-to-be-explored relevance to cancer research.

The documentary was produced a few years after Dawkins wrote The selfish gene and not long after Robert Axelrod had written The evolution of cooperation. It takes from Axelrod's research on cooperation (whose own take on how this can be observed in cancer has been mentioned in this blog before) to illustrate how cooperation might evolve in an place in which agents (say humans, bacteria or buffaloes) are selfish. The topics are the usual ones in game theory such as prisoners dilemma (how playing if for an undetermined number of times changes what is the best strategy), tragedy of the commons (if everybody is overusing a resource why shouldn't you, and if few people overuse, why shouldn't you since it will make no difference whatsoever?).

The tragedy of the commons seems to me a suitable game to model global warming (why should your country cut on carbon emissions if nobody else does or why should you if everybody does? this seems to apply to most countries but the likes of U.S. and China whose weight is to big to be considered just another player) or cancer (at the end, tumour cells do kill the host and thus themselves).

Friday, February 23, 2007

In Barcelona

I have finished my stay in Lyon and arrived to Barcelona to attend a round table for young researchers organised by the Universitat Autonoma de Barcelona. Interestingly enough the definition of young researcher seemed to include any researcher after the PhD but without a stable contract (that is, postdocs, non tenured group leaders and people in teaching positions).

I was a rather interesting discussion that dealt with things that I imagine are common worries for young researchers across Europe and elsewhere. Mainly the difficulty of living on short term research contracts, (for those of us postdocing somewhere else) the strain of keeping up with friends, relatives and former colleagues while living abroad, the gap between our real age (late twenties or early thirties) and how our status is perceived by the rest of the population (not like assistant professors or people with "real" jobs and more like students with a fancy "Dr." in front). Other issues that I found very relevant not only for young researchers are the link between research and teaching (in Spain, like many other countries, university lecturers are paid to teach but their progress on the career ladder depends exclusively on publications) and linked to that if the main duty of academic staff is to perform research or to teach (there seemed to be some consensus that universities should be free to chose wether to have a research profile or a teaching profile).

Tuesday, February 13, 2007

Lenski et al: Balancing robustness and evolvability

R. Lensi, J. Barrick and C. Ofria. Balancing robustness and evolvability. PLoS Biology, Vol. 4, 12, pp 2190-2193

This paper has not much to do with cancer but I have been interested in evolvability issues for a while so I decided to take a look at it. Tumour evolution has many but not all the features of the evolution involving longer time scales but its evolvability is not a thoroughly investigated topic. That is a shame because it seems that, given enough time, one would expect that tumour cells will not evolve only towards phenotypes that can take better advantage of the environment but also to genotypes that allow evolution to adapt better to that changing environment.

This paper does not explore this but something also interesting: that robustness and evolvability might be desirable but incompatible aims. Robustness can be seen as he ability to counteract change while evolvability represents the capability to adapt. In general it is true that species must strike some sort of compromise between these two abilities since organisms need the robustness provided, for instance, by the DNA repair mechanism but species need mutations that actually allow these organisms to better adapt to the environment. This is not always true and there are cases in which robustness and evolvability can go happily hand by hand. One such case is genomic redundancy. Up to a point, genomic redundancy improves robustness since functionality is kept in more than one location making it less vulnerable but also it helps evolvability since it allows duplicated genes to evolve different functions.

The general rule though is that organisms cannot be entirely robust to change in the form of genetic mutations since such an organism would freeze from an evolutionary point of view and thus subject to become extinct when a fitter rival comes around. I guess that that is a good explanation to cancer, a perfect reproduction mechanism would have not led from simple organisms to humans.

Monday, February 12, 2007

Cancer and biofuels

I have recently commented how (in my particular view, especially at the theoretical level) research in some area can be used in a different one but I guess I did not expect this: Cancer research may help biofuels.

It seems that, inspired by research done at the Fred Hutchinson Cancer Research Center in Seattle, a company called Targeted Growth is doing to corn the opposite of what oncologists do to human cancer cells taking advantage of the fact that some pathways in these two different cells are similar. The idea is to promote plant growth by overriding the genetic clock that tells the cell when to stop growing. The advantage is that plants thus modified are not transgenic (whith the load that this label carries to many consumers) and that it can lower the price of growing them as biofuels and thus promoting them as a good value alternative to oil.

Friday, February 09, 2007

Axelrod et al: Evolution of cooperation among tumor cells

R. Axelrod, D. Axelrod and K. Pienta: Evolution of cooperation among tumor cells. PNAS vol 103, 36, pp. 13474-13479, 2006.

A few months ago a friend of mine from Vienna send me the link to this paper (thanks Peter!) and although I skimmed through it at the time only now did I have the chance to read it with a little bit more of care. Robert Axelrod is well known in the complex systems and game theory communities. The research he did almost a quarter of century ago (detailed in his book: The evolution of cooperation) explained how cooperation can be established between two agents (people, elephants or cells) even when the mechanisms of the cooperation have not been agreed beforehand and the agents could gain more in the short term by not cooperating.

Now Axelrod and coauthors speculate on how this approach could be used to study carcinogenesis. They present this in the framework of Hanahan and Weinberg and the six capabilities required to progress towards cancer (self sufficiency in growth signals, ignoring anti growth signals, evasion of apoptosis, angiogenesis, limitless replicative potential and invasion/metastasis).

Now, this paper is no regular paper. Most research papers I read describe a particular piece of clinical research (we have investigated this gene in this context...), mathematical or computational model (in this paper we introduce a model that explains the influence of acidity in...) or are review papers. This one does not describe new clinical research nor does propose a formal way to describe any aspect of oncology nor represents a review of carcinogenesis research from the cooperation point of view. This is not meant to be a criticism. The paper represents for me a new category of papers, one whose aim is not as much as telling finished research as to suggest to the reader new venues of research under a particular perspective.

If that was indeed the aim then this is a good paper. According to the authors, the conventional view on tumor progression using the Hanahan and Weinberg framework is that cells have to acquire all the six capabilities but under the new cooperation based view this is no longer necessary. It could be possible that, at least some of this capabilities are provided by some cells to others and thus cancer could occur when groups of cells displaying a mixed set of capabilities collaborate to create the same effect of a single cell acquiring all the capabilities and reaching fixation (taking over the tumour population) by clonal expansion. One of the things that I was not very comfortable with is that the authors state that cancers are the result of genetic (or epigenetic) instability. Readers of this site probably know that this is currently a hotly debated topic (something as fundamental such as: what starts carcinogenesis) and that in front of the Weinberg school (cancer starts from genetic instability) is the , say, Tomlison school (a bigger number of cells and selection suffices to explain the start of cancer). My view is that if tumour cells can cooperate in order to share capabilities and progress down the path of carcinogenesis then having a higher mutation rate might not be so relevant and thus a cooperation based view on cancer would favour the view that cancer does not really need genetic instability to get started. If this view of mine turns out to be a stupidity remember that you read it here first.

The paper provides a number of examples of capabilities in which cooperation can happen. In angiogenesis (where cells can produce growth factors that benefit not only the producing cell but others in the neighbourhood), self sufficiency from (certain) growth signals (there is a certain amount of growth signals which can be produced in paracrine or autocrine fashion) and in invasion/metastasis (collaboration to degrade the ExtraCellular Matrix).

The authors point out that this view of carcinogenesis arises a number of new research questions such as what are the resources that can be shared among cooperating tumour cells, what mechanisms are used to share these resources, how does this affect the order in which mutations appear (since mutations can appear in parallel)? Interesting questions but it might take some for someone to come with the answers...if it is that answers can be found using evolutionary cooperation.

Tuesday, February 06, 2007

Mitochondria and apoptosis

A couple of posts ago I mentioned this research in which RNAi was used to restore the functionality of the mitochondria, especially its role in apoptosis. Now I read that the same results are being obtained by Dr. Michelakis and colleagues at the University of Alberta in Canada using a well known drug, dichloroacetate (DCA).

DCA is an affordable drug that has been previously used to treat metabolic disorders so it is known to be safe and has no patent. What should have been a blessing could also be a curse since there is little incentive to large pharmaceutical companies to finance the clinical trials. The news has been reported in all sorts of news outlets from Cancer Cell to Slashdot and including The Economist. In this website you will be able to find the latest results as well as information on how to donate money so Dr. Michelakis and his group can finance the clinical trials.

Incidentally, in the link pointing to these news in the online version of The New Scientist, a researchers from Dundee mentions something I did not think of at that time. It could be that the metabolism and not genetic mutations spark cancer. Of course for the metabolic switch to take place you will still need hypoxia (low oxygen due to distance to vasculature) which means, if I am not wrong, a neoplasm.

Monday, February 05, 2007

World cancer day

I guess I missed it. It seems that yesterday, 4th of February, was the world day of cancer. As many other "World day of...", this WOC was one of these events designed to raise awareness of the problem of cancer in the world, although given that cancer is in the top two of the diseases that are responsible for more deaths in the developed world I guess that many people are more than aware of it.

The headlines I am reading sound actually quite optimistic. Death rates are decreasing due to early detection and improved therapies. Of course nobody is suggesting that cancer will be eradicated but that it will become a chronic disease. I am not sure of how much impact has mathematical oncology had on all these successes but I suspect that it has been limited. For one, mathematical oncology is a fairly relative newcomer in the world of oncology and oncology is a discipline in which cutting edge discoveries take many years (or decades) to reach the public. For another one, I think it is highly unlikely that there will ever be headlines of the kind "theoretician cures cancer". Theoreticians deduce rules or laws that try to describe things like, for instance, cancer growth. These can be used by experimentalists to focus on the more promising areas of research and design the therapies with more likelihood of success faster.

Another added advantage of theoreticians is that they can connect research in different areas. Things that apply to cancer evolution can also be used to study the evolutionary dynamics of other diseases. Many diseases are dangerous due to their capability of evolving and being able to tell what (phenotypes) to expect in the near future from what is there now (genome) would be crucial to deal with them. This week's issue of science carries a paper (http://www.sciencemag.org/cgi/content/abstract/315/5812/655) about how the H5N1 virus (infamous for the avian flu) suggest that only two mutations stand between the current problem and one in which the virus could affect and spread in humans causing a global pandemic. Is there anything that we know about how a tumour evolves that could be used here? I would not be surprised if the answer turns to be positive.

Monday, January 29, 2007

Mitochondria and glycolysis

As mentioned in a previous post the acquisition of the glycolytic metabolism is regarded by many researchers as a necessary step on the carcinogenic path (this is known as Warburg effect). Compared to healthy cells, glycolytic cells do no need oxygen for their metabolism and although this is very inefficient it has advantages such as the capability of surviving in environments that do not have vasculature in the vicinity and the capability of acidifying the environment (which makes other cells go to programmed death and leaves glycolytic cells room to grow). The reason that healthy cells have a more efficient metabolism is due to the mitochondria, the cellular organelles that oxidises sugar molecules to produce energy. Mitochondrias are what remains of symbiotic bacteria that in the last couple of thousands of millions of years have became integral parts of the cells of many living beings. Glycolytic cells seem to revert to a premitochondrial state thus forfeiting the need of oxygen.

Researchers at the university of Harvard Medical School have created a method based on RNAi (RNA interference, the revolutionary method to knock out genes using double stranded RNA which was the work that has rewarded its authors the Nobel prize in medicine in 2006) in order to put the mitochondria back to work not with the purpose of normalising the metabolism of tumour cells but for the role they play in programmed cell death. The result of applying this therapy on animals resulted in a surge of tumour cells performing apoptosis and a significant increase in the survival rate.

Wednesday, January 24, 2007

Spencer et al: Modeling Somatic Evolution in Tumorigenesis

S. Spencer, R. Gerety, K. Pienta and S. Forrest. Modeling Somatic Evolution in Tumourigenesis. PLoS Computational Biology, Vol 8, 2, pp 939-947.

Because the paper has been published in an open source journal it means that any reader, regardless of location or affiliation, will be able to download and print it.

I am spending the remaining of this month and most of February in Lyon working with Dr. Benjamin Ribba, from the University Hospital of the University of Lyon. The month will be busy so I am not sure of how much time will be left for posts in this blog but at least on my way here I had time to take a look at the paper mentioned at the beginning.

This paper, together with the one mentioned in a previous post from Anderson et al, tries to create a mathematical framework in which to study the phenotypical view of carcinogenesis presented by Hanahan and Weinberg in their paper. As in Anderson's case, they use a Cellular Automata in which tumour cells occupy the discretised space and can grow and produce angiogenic factors in order to provision themselves with oxygen. The CA is let to evolve the initial population of cells in which mutations might alter the phenotype and acquire any of the six capabilities (ignoring antigrowth signals, production of paracrine growth signals, limitless replicative potential, evasion of apoptosis, angiogenesis and invasion/metastasis). Additionally a tumour cell might acquire genetical instability which significantly increases the mutation rate during mitosis. Cancer is assumed to take place whenever the cells grow over the natural boundaries of the tissue and claim 90% of the total space. This definition of cancer is, at least from my not so extensive experience, quite unconventional since it seems to allow no role to the phenotypes present in the tumour or the the shape of the tumour. At any rate, tumour growth is determined by the ability of the tumour cells of proliferating AND of surviving.

With this not too complicated system, the authors use several simulations to explore different tumourigenetic paths (or as they call them, pathways to cancer). This is how early mutations determine the likelihood of other mutations to appear successfully (the mutant cell has to survive and have other successful offspring) and how some mutations lead to early or later cancer (which I translate as the speed of the tumourigenesis).

So what do they find? They find that the mutator phenotype should play an important role in the case of early onset tumours but not necessarily in others that take more time to develop. They also find that not all the 'pathways to cancer' are equally probable and that is on its own something quite interesting. If in a particular tumour it was possible to see what genes are responsible for particular capabilities in the Hanahan&Weinberg description, then a genetic analysis of representative cells in the tumour could be used to see what further mutations would be the more likely to be successful and maybe design a therapy for it or try to alter the microenvironment to favour other competing mutations.

They also study the heterogeneity of the tumours which is an important feature when designing a therapy. They use a metric based on what it is done in evolutionary biology. The diversity is measured by aligning the different mutational paths of the different cells in the tumour and counting all the ones that have a different path. This seems to me a strange approach given that they treat tumour cells at the phenotypic level. I wonder if it would be better just to count the different phenotypes (defining phenotype in this case as a particular combination of H&W capabilities, regardless of what was the path to reach them)?

To conclude this review: it is clearly a theoretical model aimed to provide qualitative, not quantitative, results. It is probably complicated enough that biomathematicians might not feel very comfortable with it. The results are mainly simulations and it is unlikely that physicians could devise experiments to compare results with the model. Still I have to say that I like it, the quantitative results are interesting enough and the implementation of the word-model is very easy to follow.

Saturday, January 20, 2007

The Darwinian perspective, the mutator phenotype and response to stress

Although today I will be writing about a paper recently published in the international journal of Epidemiology and authored by Paolo Vineis and Marianne Berwick, this is not going to be a review in the usual sense. This time I would like to write about the ideas and make no reference to the methodology.

The Vineis and Berwick emphasize the role of population dynamics on cancer progression. The usual view on cancer is that cancer cells grow at a faster rate than normal cells and that is the reason why they end up (if successful) killing the host. Growing populations can be due to this but they can also be the result of other factors (think of longer lifespan). The authors hint that the success of most cancers (with respect to taking over a tissue) lays on the fact that cancer cells have a greater proportion of replicating daughter cells. That makes sense to me. For instance, in a tumour whose cells that are capable of dividing near the tumour growth front (let's call them motile tumour cells) will have an advantage over other non motile but faster proliferating tumour cells in terms of how many of its daughter cells will be in position to proliferative (regardless to the speed at which they can divide).

The authors have also something to say about the highly controversial topic of the mutator phenotype. Quick reminder: the amount of time to pick up all the mutations necessary for a neoplastic cell to become a cancer cell is, according to some researchers, big enough as to be unlikely to happen in our life time. Thus cancer is the consequence of a single mutation that makes the cell more likely to produced mutated offspring. To prove their point they compare tumour cells to the behaviour of E.coli under stress. Under normal circumstances the mutation rate of the E.coli is low but when the going gets tough the mutation rates increases significantly. The speculation is that this is no accident but a feature of the bacterial DNA that in such a way can explore a genetic solution out of the problem. Could tumour cells be attempting something similar?

I find this hypothesis quite interesting and from my limited experience it seems quite novel. It should be interesting to do some experimental work (maybe more than theoretical) to see if there are any molecular mechanisms that might have an effect on the probability of mutation (say, the DNA repair mechanism) that could be held down when there are 'stress' signals in the environment. It could even be that the mechanism is similar to that of the E.coli although since bacteria are far simpler cells than human cells that could be unlikely (not having any experience with molecular biology should make any one be skeptic about statements like this).

Wednesday, January 17, 2007

Edge of existance

Researchers of the Zoological Society of London have started a new campaign (called EDGE) to promote the protection of certain species that might not be so close to extinction as some other more famous ones (say, whales?) but whose impact on the survival of other species might be significant. The news can be found in BBC or for those of you that can read Spanish in El Pais.

Now, this is probably not something that many people might find relevant to cancer research but I think that there might be a connection. In ecological systems (and here I assume that a tumour is one of those) species depend on other species for their survival. This dependency does not need to come in terms of food webs (a species needs other to prey on) but also in the way that one species can change the environment for the benefit (or not) of the other ones. The idea then would be to identify 'agents' in a tumour whose role in principle might not look so relevant but that might provide support to other more important but less vulnerable targets. Given the current emphasis on the role of the microenvironment in cancer research I would be surprised if there was not already some work pointing in this direction.

Monday, January 08, 2007

Online introduction to computational oncology

I have recently found an interesting introduction to computational oncology on the website of Paul Macklin, a graduate student at UC Irvine.

The website comes complete with the stages of cancer evolution (not the usual 6 capabilities of Hanahan & Weinberg but a version a little bit coarse grained for my taste) and therapies. He also points out some of the challenges that need to be addressed such as explicitly incorporating the tumour microenvironment (it is a well known fact that some tumour cells behave like regular healthy cells if left in a different microenvironment from the one it comes from). Useful for people who might want to understand some of the aim of the papers I mention in my reviews.

Monday, January 01, 2007

Merlo et al: Cancer as an evolutionary and ecological process.

L. Merlo, J. Pepper, B. Reid and C. Maley. Cancer as an evolutionary and ecological process. Nature reviews cancer, Vol 6, pp 924-935, December 2006.

New year and (maybe not so) old traditions: the review of a paper. Nature reviews cancer is one of the world's top scientific journal in terms of impact factor for a reason: they publish very interesting and comprehensive reviews in a field of such importance and as crowded as cancer research. Review papers are comparatively more likely to be cited than the ones about one group's research, review papers in cancer research are normally highly cited since there are so many researchers working in the field. Review papers in a prestigious journal like Nature reviews cancer are thus bound to be cited once and once again and one would expect that only very good scientists would be invited to write for them (I believe that is only by invitation that you get to publish in these journals).

This review covers a topic that is very close to my interests: cancer from an evolutionary and ecological point of view. This view sees a neoplasm, a tumour, as a population of cells with a diversity of inheritable features. This means that evolution will happen and the fitter phenotypes will tend to be more abundant in the tumour population. Questions that might arise are how to alter the mutation rates, clone expansion and how does this expansion happen. Furthermore, given that in many cancers we can find mutations in vast areas of DNA, how do these cells retain enough genetic material to even function? The authors put forward the idea that this could be because most of the human genome is devoted to the development and homeostasis of a multicellular body and thus has no effect on the survival of the single cell in a tumour.

Having a diverse range of individuals whose uniqueness is inheritable is only one of the requirements of evolution. The other one is selection. In a tumour we have two sources of selection. Natural selection is the one that takes place in any tumour when there is scarcity of resources (oxygen, glucose, space). Under these circumstances some phenotypes are bound to be better at surviving and dividing than others. Additionally there is artificial selection which is the result of a therapy applied to a patient with a tumour. Artificial selection changes the fitness landscape, hopefully in such a way as to make survival impossible to every tumour cell. Unfortunately that is somewhat difficult so in many situations is worth altering the fitness landscape in ways that promote the survival of the least aggressive (that is, less likely to be able to invade and metastasise) tumour cells. In any case, altering the fitness landscape in favour of the patient is significantly easier when the tumour did not have much time to evolve.

Evolution in a tumour is not entirely the same as the one in organismal populations. That is to be expected given that tumour evolution lacks something of great importance: time. That is why during chemotherapy, surviving tumour cells are not the ones that develop mechanisms to resist but the ones that due to other reasons (genetic drift for example) already had the capability to resist before the therapy was used. Other differences include the reliance on stem cells for population diversity or that reproduction is asexual (which, incidentally, makes mathematical treatment much easier).

If a tumour resembles an ecosystem we should expect things such as cooperation, competition or parasitism. It seems that you get some of that. Like in an ecosystem individuals compete for the available resources (there is some speculation about that in the paper from Tomlinson reviewed the 10th of October of last year). There are predators if we understand as predation the behaviour of the cells from the immune system when they meet tumour cells. There should be parasitism, mutualism and commensalism (although the authors provide no evidence for that).

I found this a very nice and readable paper. I think it will make a good introduction to any cancer researcher that wants to study the evolutionary aspects of it. My only criticism of a paper that claims to deal with cancer as an evolutionary and ecological process is that the ecological part is significantly weaker than the evolutionary one.