I, for one, welcome our midichlorian overlords


STAR WARS is really just a treatise on microbial evolution and the concept of the selfish gene. See below for more details.






So here’s the idea. The concept of midichlorians was introduced in the prequels. They are “a microscopic lifeform that reside within all living cells and communicate with the Force”. So essentially mitochondria, but powered by the Force. Han Solo has a great quote in episode IV,

Kid, I’ve flown from one side of this galaxy to the other, and I’ve seen a lot of strange stuff, but I’ve never seen *anything* to make me believe that there’s one all-powerful Force controlling everything. ‘Cause no mystical energy field controls *my* destiny. – Han Solo

But with midichlorians you now have a genetically discrete entity that is the sole communication with the powerful Force. The midichlorians want, in an evolutionary sense, to preserve and continue their lineage- they are ‘selfish’. So it stands to reason that they would have a say in what was going on with their hosts. A ‘host’ is simply a very large (relatively speaking) machine to enact the plans of the midichlorians. Of course. A kind of large biosuit for battle. So it’s amusing to think of them controlling all the battles like they’re playing video games.

Incidentally, this is not my first Star Wars inspired comic. That would be here.

Gravity Alternate Ending

This joke’s a SPOILER (at least in part) for the movie Gravity. I liked the movie a lot, thought it was an exciting drama/survival adventure. My wife wasn’t sold:

Her: “It’s too much like that movie with Tom Hanks”

Me: “Oh sure, Apollo 13”

Her: “No… the one with the volleyball”

Me: “Oh.”

She’s right, of course. It shares something in common with Castaway.

Anyway- here’s my idea for an alternate ending. You know, to sci-fi-it up a bit…



This one goes to 11…

The famous Spinal Tap quote (see the video here) is great because Nigel is explaining how  his amp is better than other rockers since you can turn it up to 11. “Why don’t you just make ten louder and make ten be the top number and make that a little louder?” asks the mockumentarian Rob Reiner. Good question.

The humor in this scene reminds me strongly of this recent paper on the introduction of an artificial nucleotide base pair into a bacteria. Essentially they got a bacteria to incorporate an artificial nucleotide pair into its DNA, it replicates stably (that is, the new pair stays in the bacterial DNA for generations), and its not removed by DNA repair mechanisms that look for problems in the DNA. Novel nucleotides are not new- researchers have created a large number of these and incorporation into DNA has been done in limited ways in test tube (in vitro) systems, not in a living organism. This is really a pretty cool technical achievement – the researchers had to solve a number of complicated problems to get this to work and, more importantly, it’s likely that they got very lucky with their choices (where ‘luck’ here is a combination of knowledge, trial and error, and actual bona fide luck).

The paper itself doesn’t really overstate the implications of this paper. The only implications statement in the paper comes at the end:

In the future, this organism, or a variant with the UBP incorporated at other episomal or chromosomal loci, should provide a synthetic biology platform to orthogonally re-engineer cells, with applications ranging from site-specific labelling of nucleic acids in living cells to the construction of orthogonal transcription networks and eventually the production and evolution of proteins with multiple, different unnatural amino acids.

And all of this seems very reasonable and potentially achievable.

However, as happens with many high profile papers, the press coverage I’ve seen on this is terrible. From Gizmodo touting that “scientists have created alien DNA” (only for a very limited definition of ‘alien’) to New Scientist stating that researchers have expanded the ‘genetic code’ of a bacterium (not really, a code needs to have meaning- that is, to be translatable into something that has meaning, this advance doesn’t yet). However, perhaps the most troubling is coverage from NPR, largely based on an interview with the senior author of the paper. In this piece Floyd Romesburg introduces a simple, and largely apt analogy, for what his work has done:

Maybe you get three consonants and one vowel. Maybe there are some words you can write and you can string them together to make, sort of, primitive stories. But if you could have a couple extra letters, there’s more that you could write. Having the ability to store increased information would allow you to write more interesting words, bigger words, more complicated words, more nuanced words, better stories. – from NPR interview

He goes on to say:

It’s not so much that I think life needs more genetic information but I think that there are things that we could really learn and drugs that could be developed by getting cells to be able to do more

So it’s not a bad analogy, but one where he’s essentially said: “This one goes to 11.” . And it points out exactly why this work is so limited in its implications (exactly the opposite of what he’s trying to point out by using it BTW). They have added, in a very constrained and limited way, added two letters to the standard ATCG alphabet used by nearly all life. Will this introduce the ability to build more complex or useful biological systems? Not in the slightest. Imagine that we added a couple of letters to the English alphabet. Now we give those extra letters to someone like William Shakespeare. Does anyone think that he would be able to do more with more letters? Write better, more complex, more interesting, more profound plays or sonnets? No, of course not. Even if you gave him a whole bunch of new words that contained the new letters (which they haven’t done at all in this paper- they haven’t actually introduced this new addition into the code itself, only into the alphabet), he would likely have produced very similar works. Maybe those works would be slightly shorter, but they would NOT contain more information. Adding a letter to the alphabet doesn’t increase the information or the complexity of the code. It just doesn’t. The computer that I’m writing this on is based on a binary alphabet (1 and 0 are the only letters it uses) and yet I’m able to put these together (with the help of the underlying OS and software) into complicated and information-rich constructs. Having a computer based on 0 , 1 AND 2 wouldn’t help me write this post any more better [sic].

An image of ACTUAL (fictional) alien DNA. This one has a 15 stranded double helix, which CLEARLY makes it more complicated than our humdrum double stranded type. Clearly. (from the movie The Fifth Element)

An image of ACTUAL (fictional) alien DNA. This one has an 8 stranded helix, which CLEARLY makes it more complicated than our humdrum double stranded type. Clearly. (from the movie The Fifth Element)

The idea that this would lead to development of new drugs, new forms of life, new biology is a far, far, far distant stretch that causes confusion and even fear. The problem here is not purely driven by misunderstanding and misrepresentation of the work by scientific journalists (though it looks like there’s some of that) but from the actions and statements of the senior author himself. As I mentioned, this is a sound paper and is pretty interesting- a technical achievement. It may indeed lead to some interesting new discoveries and methodologies that may be broadly applicable. But it’s not alien DNA and it’s not going to help us cure cancer with new drugs, and it’s not going to provide the ability to make the biology more complex, but it might make our rocker friends green with jealousy when we reveal that we have six nucleotide bases compared to their paltry four bases because “these go to eleven” (Nigel Tufnel)

Always use the right pen

Spike Lee’s 1989 classic “Do the Right Thing” is about a lot of things. It’s about life in general and I still don’t fully understand it’s message- why did Mookie throw the garbage can through Sal’s window. Was it the right thing to do?

It was NOT about life in academia – but did have elements about the conflict between the creative and destructive influences that I find very compelling. And Radio Raheem’s Love/Hate speech seemed to speak to me in a different way. Anyway, here’s an homage I did for fun.


How Big Collaborative Science is like Making a Movie

Disclaimer. I’m not involved in filmmaking, I’ve never been on a movie set, never even been to Hollywood. But I have watched a lot of DVD special features on making movies.

I am involved in science; big collaborative science as part of several NIH multi-institutional centers. Two systems biology centers funded by the NIAID (Systems Virology and Systems Biology of Enteropathogens) and a proteomics center part of the NCI Clinical Proteomics Tumor Analysis Consortium (CPTAC). I also work at a national laboratory where that’s the idea of how we’re organized- to do big science. So I know something about that.

Some of the worst movies have the best DVD special features. The League of Extraordinary Gentleman was a pretty bad movie, but it had something like four hours of special features on the DVD, all really interesting. Watching special features about making feature-length movies raised some very interesting parallels between big collaborative science and making movies (at least from my limited perspective.)

So first off, here’s how they’re different:

Goal and product: A movie project’s goal is to, big surprise, make a movie. A movie is a discrete chunk of a result. It gets made and released all at once, and there’s only one way to win: did you succeed in getting the movie made? A research project produces multiple different ‘products’-the chief of these is research publications. But these things are produced over time and released in different ways.

Having one end product, a finished movie, is also different. A research project will have many small projects that generally circulate around a set of central guiding hypotheses (that are at a very abstract level). This means that there will be gradations to successfully completing the project.

Evaluation: Bottom line, movies are successful if they make money. And they can be evaluated based on this by simple comparison with other movies. Research projects, because of the diversity of their different possible products, are harder to evaluate. Impact on the scientific community, high-impact publications, data released, etc. To be fair, a movie can be a classic work of art, and highly reviewed by critics, and so a ‘success’, without making a lot of money.

Now how they’re similar:

Funding: This is where I’m the most shaky in terms of making movies but it seems that there’s a funding agency (studio or often other entities) that basically pore over ‘proposals’ (screenplays, ideas, sequels, etc.) and award funding to people (directors) or groups (a director and their team) who they think can get the job done. It’s not unlike some scientific funding mechanisms- though it doesn’t involve the component of peer review, which many scientific funding agencies use. The funding agency is making an investment and they want to see a return on that investment.

Vision: This isn’t always true of big science, but it also isn’t always true of movies: A successful project must have clear and driving vision. Generally this is instituted by a central figure for the project, the PI or the director, depending. The vision isn’t just about the end product but also about how the end product(s) should be achieved. If the vision isn’t there then nothing will get done, or nothing will get done well.  (I guess I’m using this as equivalent to leadership, but it’s not really)

Organization: There are many parts to making a movie, and increasingly in big science, there are many different disciplines that need to come together to pull off a successful project. There have to be teams with different skills and expertise to work on the various parts of the project. So assembling the appropriate team with the right skills, the ability to get things done (critical), and work in a large project, is very important.

Collaboration/communication: So this is probably like many, many other large-scale projects (building a skyscraper, a ship, running a government, etc.) but I like the insight that the “making of” special features afford into this world. Collaboration is key. No one person, or one discipline can make it all work. Sure, the actors and actresses are important to a movie. But without everyone else working as a team and communicating efficiently at multiple levels they are just going to sit around and stare at each other. Making a movie at large scale seems incredibly complicated. So you need people who are specialists in what they do and probably know very little about what the other people do. Then you need people who glue those groups together, both from the top down, like a director, and from inside, like the leads from each team who can interface with other groups.

I really liked a quote I heard on a recent making of, but won’t be able to properly attribute it. It was the stunt coordinator talking about collaboration. He said (paraphrased), “we can both have different ideas of what a tree is. The best way to collaborate sometimes is to each go off and draw a tree and then come back and say, ‘is this what you meant?'” Successful collaboration can lead to great things that neither side thought of to start with and poor collaboration (in some cases no collaboration) can completely sink a project.

In my admittedly limited experience collaboration is the most important component. Of course, without the requisite technical skills in your collaborator you can’t actually collaborate effectively, so there is that, but the process of communication at all levels will determine how successful the project is and how happy everyone is about it.

Closing credits. Why is this comparison useful?

I think the most important takeaway- and one that I really haven’t discussed here- is that big science is substantially different from ‘traditional science’ (that is, individual researchers working on projects in their own labs, more-or-less by themselves). Thinking of the organization of big science projects in broader, more abstract terms actually seems to make them more approachable and understandable. This is in contrast to thinking of big science as traditional science, only with more people. In my experience this seems to lead to the use of big science funds to accomplish several disconnected traditional science projects, and misses the potential that big science offers. Big science projects have very similar parts and interactions as other large-scale projects. So how can ideas from these projects be used to improve how we do big science? That’s an open question but one worth thinking about.



Prometheus the creationist

This discussion probably contains spoilers, not really of the specific things that happen in the movie, but of the overall ideas. So if you haven’t seen it and are likely to watch it, keep that in mind.

Enough of the plot to get you going if you haven’t seen the movie. It’s the year 2093. Two scientists (maybe archaeologists? not really sure- but they sure is smart) discover an ancient cave drawing that (along with a bunch of other cheap knock-offs from around the globe spanning cultures and centuries) point them to a distant planet. A mysterious rich guy funds a spaceship (Prometheus!) to explore the planet and test the scientists’ hypothesis. Possibly the old guy has an ulterior motive or two? The hypothesis is that aliens created humans and they’re from this planet (see below for discussion). The spaceship reaches said planet, lands- the explorers start poking around and making the standard horror movie mistakes. Mayhem ensues.

So I loved it. Great action, great pacing, good characters, some suspense, a lot of grossness, a pretty self-consistent plot all-in-all (see my points below for how it doesn’t agree with science). However, there was one major problem for me that is hard to ignore. Why did the writers, as one character puts it in the start of the movie, “just throw away 300 years of [understanding of] Darwinian evolution?” The science part of the science fiction premise for the movie is on one hand a great one: humankind’s search for their own origins. As a scientific allegory this really works, and the addition of the extra layer, the human-created robot David, in the movie really works well. On the other hand, WTF!?! It makes really no sense in terms of anything scientific. Here are my main points:

  1. If the aliens planted us on Earth at sometime long enough ago to start the human race, how did they then communicate to different human cultures a pictogram map to the ‘home’ world? I guess you could argue that there were things that either weren’t known to science in the year 2093 or were known but not discussed in the context of the movie. Namely, that the aliens then returned and communicated with these various cultures- the logical resolution to this problem. We, as viewers, can fill this point in ourselves in a logical fashion.
  2. Here’s my big one: if aliens planted us on Earth at some point in the past, and our DNA is identical to their DNA, this raises a number of paradoxes that just don’t make even Sci-Fi sense:
    1. If we were planted along side a bunch of Earth-evolved animals how is it that we are so close in terms of DNA with other of these species. Mouse DNA and human DNA is something like 90% similar on the gene level. The aliens would have had to match that when they created us, but the Prometheus story is that they created us out of their DNA. Doesn’t make sense.
    2. If we were planted on Earth before the emergence of any animal life, then all other animal life (and plant too probably) would have to be derived from us so that everything is similar. Completely doesn’t fit with the fossil record, or any phylogeny of relatedness between species. We are not the progenitors of all other life on Earth- much closer to the reverse holds.
    3. So it seems that in the context of the movie either evolutionary science is all wrong, or that our understanding of the fossil record is all wrong or both. Or that there was something immensely complicated and unreasonable (in terms of amount of effort) that the aliens did to make things look like they do.
    4. The movie would make more sense and be more believable if there were some mention somewhere of these problems and some reasonable solution. For example, that scientists had made some big discovery sometime in the time between 2012 and 2093 that explained it all that is talked about in the movie but never explained, but the movie would have been better for it.
    5. Without such an explanation the “science” underlying it looks an awful lot like creationism with a big dose of intelligent design. The fossil record was manufactured (or we have consistently and massively misinterpreted it in many, many, many, independent ways), evolution is untrue or doesn’t work the way we think it does, and we have to look beyond evolution for the answers to our existence (which is, in my opinion, a total cop out). So that leaves me, on one level, fundamentally disturbed and unsatisfied by the movie.
    6. Nowhere in the movie is it ever explained why the scientists in the movie believe that this alien race “created” us. It seems more plausible to hypothesize that we descended from them, maybe from a marooned spaceship or something, given that their DNA is ‘identical’ to ours. I don’t really have a problem with this either way (except for the points I raise above), but it would have been nice for them to acknowledge this rather major plot assumption that doesn’t seem to have much basis. I’ll just chalk this one up to some scene that landed on the cutting room floor.
    7. Here’s a minor nitpicky science point: when they use carbon dating on the alien planet to determine the age of remains they discover. That’s really unlikely to work unless the particular distribution of carbon isotopes on Earth is found everywhere else in the universe. But that was pretty forgivable and more fun to find than annoying.

As I said at the start, I loved the movie. Thought it was great. It works really well as a science-based allegorical story about humans searching for meaning, and their own origins. No problems there. And I agree that the basic science plot is compelling: aliens created us and they planted us on Earth. It’s an idea that’s been explored before many times (though it would always suffer from the points I raise above). The big problem is that I just don’t understand why they didn’t address this, somewhere. Or maybe I’m asking too much of a sci-fi horror movie. Could be.


View the trailer here.