Slashdot Mirror
Computer Simulation of Cancer Growth
Roland Piquepaille writes "For a long time now, researchers and scientists have used computer simulations in the physical sciences: physics, chemistry, and engineering. But what about biology? An international team of U.S. and Scottish mathematicians and biologists has built a math model to predict tumor behavior. The researchers say their approach is similar to the one used by weather forecasters. So far, this approach is entirely theoretical. But the scientists see their effort as the beginning of a new era in cancer research — 'a sea change in how biology is being done,' as the lead researcher described it. Read more for additional references and illustrations about this use of computer simulation to predict a cancer evolution."
Programs and techniques be used wherever chaotic systems take place? I guess it's in the domain of the weather, disease rates and population growth.
It would be rather interesting to watch social networks in the similar style (Im not thinking of myspace gunk...).
Bioinformatics has been a growing area of research in Computer Science for over a decade now ...
Everything from developing algorithms to produce leafs/trees (for graphics) and to model pond-slime growth (for optimization problems) has been studied for awhile; hell, genetic algorithms and neural networks have been around for awhile.
But what about biology? An international team of U.S. and Scottish mathematicians and biologists has built a math model to predict tumor behavior.
In other news, an international team of U.S. and Scottish mathematicians and biologists has built a computer simulation of the RIAA's business model.
The theory of relativity doesn't work right in Arkansas.
But FFS I didn't need to see your face on a blog.
WTF are those glasses all about?
*off topic rant over* (someones gotta start it, might as well have a different angle to usual)
Back ontopic - if they are considering it like a weather model, just how many predictions end up in a whiteworld scenario?
liqbase
The researchers say their approach is similar to the one used by weather forecasters.
So its results are only accurate when looking about 4 hours into the future?
If I could sue my weather reporter for malpractice, I'd be rich enough to live somewhere there's no weather, only climate.
I should trust my cancer diagnosis to become as reliable as the rain forecast for the weekend?
--
make install -not war
I, for one, welcome our new Global Warming Tumor Overlords.
668: Neighbour of the Beast
First bugs, then viruses, then trojans, worms and other malware - now computers can get cancer!? What's next, liver disease?
The secret to creativity is knowing how to hide your sources. - Albert Einstein
Increasingly, researches seem to be finding a clear connection between stem cells, aging, and cancer. It looks like cancer depends on errant stem cells for its rejuvination - and years of cancer study supports this theory.
So, by all appearances, if we could destroy just the right cells, a small percentage (0.10%) of the tumor, the tumor goes away!
So, while the mathematical model of growth might represent some predictive value, it certainly will not effectively model new developments, such as the above, when they are found.
I have no problem with your religion until you decide it's reason to deprive others of the truth.
Let it be revealed!
... IF their proposed technique (which has not actually been tested against live cells) comes anywhere near a useful prediction. They haven't even done IN VITRO modeling yet. If this were a product announcement, I'd call it VAPORWARE of the highest order.
I've been hoping that eventually it will be possible to run a complete simulation of clinical research protocols long before any research participants are recruited. So this is very good news and a step in the right direction. Simulation cannot replace actual experimentation, but it can give you a very good idea of what to expect based on your theory which in the clinical sphere could have life saving potential.
To the making of books there is no end, so let's get started
Basically an oncologist should be able to get a rough guess of how a series of treatments will work, and if a set of treatments is just going to make a more resilient cancer, then they can consider more viable options. Cancer is tricky, and some treatments arent effective at the same stages.
Storm
"Live as if you'll die tomorrow." Ridiculous. You could die later today.
For a long time now, researchers and scientists have used computer simulations in the physical sciences: physics, chemistry, and engineering. But what about biology?
But the scientists see their effort as the beginning of a new era in cancer research -- 'a sea change in how biology is being done,' as the lead researcher described it.
I've read papers on maths models of tumours that are decades old. Even more sophisticated models like the one the scientists have done, have been done to death in recent years, on everything from angiogenesis to metastasis (I should know, I wrote one). There's also a wealth of work done tying down theory and experiments with gene circuits in phages. So what is new about this work? Their results that Roland (who wouldn't know how to do a literature review if it bit him on the proverbial) lists:
The findings suggest that current chemotherapy approaches which create a harsh microenvironment in the tumor may leave behind the most aggressive and invasive tumor cells.
certainly aren't new. A model of invasiveness with different levels of agressiveness isn't new either. There model does give nice results on the phenotypes of cells that are selected for, and the ways it allows them to control the microenvironment are certainly cute.
Eventually one cell has zero copies of at least a part of a chromosome, and that's when the fun really starts. One of the arms of chromosome 3, for example, appears to confer certain "superpowers" on any cell that loses it, since there appear to be certain tumor suppressor genes on that chromosome. As chromosome parts are gradually lost in the tumor population, the various superpowers of cancer become evident: growth in absence of any growth signals, loss of contact inhibition (you keep dividing even when you run out of room), the ability to ignore suicide signals from attacking white blood cells, the ability to promote blood vessel growth into the tumor, the ability to metastasize, etc. If a cell loses the right chunk of the right chromosome it can quickly take over the entire tumor, and you have a population of cells that are all missing that chromosome chunk and are ready to start losing more random chunks. So as you see, "very small changes in input parameters cause exponentially large deviations in output values".
I could be wrong but I think what they are modeling here is the genetic variation within the tumor, as evident in the chromosomal copy number within each cell.
In other news, Slashdot editors announce a mathematical model of the tumor-like growth of Rolaid Pinkeye's shameless blog-click-whoring....
biology is chemistry.
chemistry is physics.
physics is math.
but by the time you get from math to biology it becomes riddiculously complex.
...your comment piqued my interest. Whenever people start predicting the fall of the American Economy (offshoring, outsourcing) thoughts like yours cross my head. On a macro level industries like this replace our lost jobs overseas. I believe we are on the virge, a couple decades or so, of a BioMed Age and America and a select few other countries are on the forefront of these new technologies. The field is very young and we have just scratched the surface. If done right outsourcing, whatever, can be a good thing as it raises the bar for all of us and we can sell all our expensive bio stuff to the new middle class countries. Wishfull thinking?
"For a long time now, researchers and scientists have used computer simulations in the physical sciences: physics, chemistry, and engineering. But what about biology?"
Yes, scientists have used computer simulations heavily in biology too. Anything that can be mathematically modelled can make use of a computer. For years scientists have been using calculus and probability theory to model the way disease spreads, evolution, population growth etc.
These posts express my own personal views, not those of my employer
Posting anonymously,
I work for a cancer prognostics company that does something very similar: Aureon Laboratories. We do cancer prognostics primarily for prostate cancer right now.
There are other companies, such as Genomic Health, which work in breast cancer. Personalized predictive medicine, including prognostics, is really on the cutting edge and will be becoming more prevalent in the years to come.
Too bad for them it's just been determined that the consensus about cancer implantation has been turned upside down recently.
Am I the only person who is tired of hearing the phrase "sea change". It's one of those journalist fads that they will cram into every article just because everyone else is using it. Seriously, isn't their any other noun that could be used as adjectives instead?
,"I'm going to model how Dark Energy and Dark Matter form" when we still don't know what they even composed of. In Cell Biology nobody is even sure on how NADH is bound to lactate dehydrogenase (LDH), but I guess NIH reviewers are always too stupid enough to fall for such "computer modeling". If you really want free and accurate biological models see www.kintecus.com as it is the de facto state-of-the-art in bioinformatics and modeling...and even then, the software system with its models produce okay results for comparatively (relative to cancer chemical mechanism) small systems.
Programs and techniques be used wherever chaotic systems take place? I guess it's in the domain of the weather, disease rates and population growth.
The first thing these models will tell us is that cancer comes from too much CO2 in our system. But nobody will care until Al Gore does a movie about it.
You are running an ad campaign for an obscure proprietary software: "state-of-the-art in bioinformatics", "free and accurate", "de facto". What does it model? What processes does it describe? How? What methods and what data does it use? You said nothing.
TA is speaking about tissue-scale modelling of neoplasm growth. And these models are an interesting research tool. Yet theoretical for today. You are speaking about nothing.
Modelling cancer is difficult, because any model is a simplification. And it is not clear what is more important and what is less. And it is not clear what is the most suitable way to describe the growth of tissue mathematically.
I thought I'd point out that this isn't the only group in the world doing research like this--a friend of mine here is working on tumour modelling, and has been for several years now. The research group's homepage is http://www.maths.ox.ac.uk/cmb/Research/index.htmlh ere. I suspect there are probably many more, too, given there are journals devoted to this stuff.
How had this crap got itself published in Cell???
I do not believe in karma. "Funny"=-6. Do good and forbid evil. Yours, Oft-Offtopic Flamebaiting Troll.
I think when talking about cancer some people overlook one basic and some would say tragic fact of the whole principle of organization of higher eukaryots. Cancer is "natural" to a cell, the absence of it is unnatural.
Let me explain. Cancer involves at least two fundamental phenomena accompaniyng affected tissues: (1) uncontrollable growth (2) detachment from the base (other cells, other tissues, bones, other structural elements).
Both things are more basic to the commonality of cells than the mechanisms existing in higher eukaryots to suppress those things, namely (1) apoptosis (programmed cell death) and division regulation (most things continue doing what they are doing until some external factor stops them) and (2) ability to attach to other cells (most things do not stick to each other very good).
Cancer involves general principles of existence of all cellular organisms, stopping cancer involves more specific mechanisms. When the latter break, it is very hard to fix them. If heart fails, it is a quite specific complex organ designed for a very specific purpose, so one can replace it. If the artery gets clogged, it is also very speficific organ designed for a very specific purpose, so one can replace it. That is the other major cause of death in the world for you.
Cancer is not like that, it is not a failure of the organ, it is the nature of our cellular organization gone wild (wild in a sense that it is natural for cells to grow uncontrollably freely floating without attaching to anything).
This all sounds pretty generic, but I guessed that some people might not know that.
I do not believe in karma. "Funny"=-6. Do good and forbid evil. Yours, Oft-Offtopic Flamebaiting Troll.
I love how these press releases from universities pretend as if no one had ever even contemplated such an idea before the ground-breaking work mentioned in the press release. People have been doing mathematical modeling of tumors for years. Avner Friedman has been doing work since the late 1990's at least (see http://www.math.ohio-state.edu/node/22077, for example).
All is Number -Pythagoras.
The question on everyone's mind: does it spell out the GPL license text?
Burn the land and boil the sea, you can't take the sky from me