Pasteur's Blend

One of my favorite games is a card game called Munchkin.  There are some general rules, but every card also has rules.  Sometimes the rules on the card conflict with the general rules.  When there's a conflict, you follow the rules on the card.  Sometimes multiple players play cards at the same time that conflict with each other.  When this happens, you argue over the rules.  This is a major element of the game and it's actually a lot of fun.  It's not uncommon for a difference between boolean operators (and versus or) written on one card or another to be the deciding factor in the game.  (It's also hilarious when you turn the monster your roommate is fighting - a simple alarm clock - into a 'sneaky undead' alarm clock which he cannot defeat.

The first thing I tell people who are new to the game is "There is an exception to every rule - including the absolute immutable rule about what you have to do to win the game."  For me, part of the appeal of thi…

The first post in this series attempted to introduce the vast field of cancer, with an eye to describing what I expected would be represented in the new developments at ASCO this year.  In many respects, those expectations were realized and expanded upon.

The second post looked at combination therapies and how they're changing the cancer treatment landscape.  Now, the use of multiple drugs in combination isn't new to cancer research, so why did I devote a whole post to it?  Because the way we can use these approaches is changing in subtle but powerful ways.  In the past, we might focus on a small number of patients at research institutions whose cancer biology got additional attention.  In other words, we could look at a few 'example' patients and hope to learn information we could generalize to all cancer patients.  Of course, cancer doesn't work that way.  Each patient's cancer is different, and we've known that extrapolating out from one patient to many …

This is part of a series of posts about an update on the current state of cancer research, as I see it after attending the annual meeting of the American Society for Clinical Oncology (ASCO) this year.  In doing so, I'm trying to communicate impressions from a highly technical field into a format that is useful for a more general audience.  Therefore, I'm going to take a minute to talk about survival curves and what they mean in the context of clinical oncology.
I have young children, and one concept we try to help them understand is that they only get to choose among available options, not the universe of all imaginable options. For example, I'll offer them pancakes or cereal for breakfast and one of them will state (with finality) "I'm having muffins." When I point out we don't have muffins he'll double down, "I want a blueberry muffin."  What they have not yet learned, and what we try to teach them, is that they don't get to choose f…

I've been working on the promised updates from the annual meeting of the American Society of Clinical Oncology. I've also been working, so the updates aren't coming out as I'd hoped. Part of what I've struggled with is figuring it what level of detail to share. On one hand, I want this to be accessible to the audience who reads this blog, which doesn't assume a strong biology background.  On the other hand, to talk about what's new and exciting I'm the field of cancer research I have to get into the weeds a bit. Especially if I want to communicate why it's important.
This will probably take a few posts, but I want to focus on some themes to keep from getting so caught up in the weeds we miss the broader picture of what we're doing - and how we're succeeding.
In a previous post I talked about how robust biological systems tend to be. The image I used was of an engineer who is trying to bridge a river. Instead of building one sturdy bridge ac…

You may be familiar with fractals.  Fractals are often popularized as repeating patterns, but that's not really required as part of the definition.  Fractals are typically two-dimensional images (yes, I know, plus fractional dimensions, that's the whole point of calling them fractals) where you can zoom into any part of the image and additional complexity is revealed.  For example, if you want to draw the coast line of a nation like Great Britain, the level of detail you choose to include is entirely dependent on how far in you decide to 'zoom'.  There's no point at which we can say you've captured the 'true' coastline, because the complexity defies a solid definition by its very nature.

I want to make the case that biology approaches fractal complexity.  By this I don't mean that it's too complicated to study, or that it's infinitely complicated.  I think there is a finite amount of complexity to biology.  I'm invoking fractals as a way…

In the interest of brevity, I've decided to spin this post off into a sort of mini-series.  I first sat down to write some thoughts, but then realized I needed to explain other concepts that required other concepts and ...  I figure I'll capture each point in its turn, but in the process I want to get across an overall idea about open questions, hence the title of the mini-series.

To start, I'd like you to indulge me in a small experiment.  It's not a well-controlled experiment, but humor me.  First, go read this list someone generated of open questions.  Then come back here.  you don't have to read the whole thing, but get through at least six or seven of them.

I'll wait.

Done?  Great.  Did you notice that the author attempts - and generally fails - to identify explanations for each of the phenomena?  Other times there are multiple acceptable explanations and you the reader are left to guess at which is true.  Since the author was trying to write a list of uns…