Torpedoing the fun

This is a trailer for The Master, an awesome movie about a WWII sailor who returns home to found a new religion inspired by the story of Scientology, but I wanted to mention something neat that you might not have noticed,

The torpedo that Freddie Quell was depicted drinking from looks an awful lot like a Mark 14 torpedo, which would have meant that the fuel he would have been drinking was methanol.

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Then the absolutely predictable happened.

When I was in college, I had this very good friend who is generally pretty awkward, though in a wonderfully sincere and good natured way, and who occasionally did profoundly bizarre things. The craziest involved a can of beef stew and his misapplied education as a talented physics major.

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Synthetic biology from a religious perspective

If there is a God of creation that went around designing the genomes of all of the living things on Earth, they are the sloppiest, most frustrating, terrible programmer you could possibly imagine. The Intelligent Design proponents are particularly frustrating to me as a biologist having seen how fundamentally unintelligent the design of living critters actually is when you get down to the real moving parts. At least it is designed according to a sort of logic so fundamentally alien to our own that by any human standard we couldn’t help but call it stupid.  Looking at life through the lens of Max Delbrück’s slowly fulfilled dream of a science of molecular genetics to replace the stamp collecting of Drosophila genetics1, the organization of information, regulation, and function in genomes makes precious little intuitive sense in terms of human logic. When you think about it; silly things like fundamentally unrelated systems being piled on top of each other such that one can’t be manipulated without messing up the other – necessitating otherwise functionless patches to the paired system whenever the other is modified, or Rube Goldberg-esque fragile systems of regulation that respond to all kinds of wrong stimuli, or systems of global regulation that are pretty analogous to reading the same giant program in either Python or C++ to produce one of two desired global results, or the kinds of systems that you can just tell are 99.9% amateur patch jobs are really what you would expect from systems designed exclusively by the entropic trial and error of evolution.

If you guys remember all of the big genome sequencing projects of the 90s and the early aughts, they’ve been continuing and the amount of raw data they have been giving back to us has exponentially accelerated. However, those of us trying to understand the biological realities of what all of those sequences actually mean were very quickly left behind and have been falling further and further behind as the advance of sequencing technology accelerates faster than we could ever hope to keep up with. The central problem is that while it turns out that we can get computers to do our pipetting for us if we pay engineers enough – we can’t get computers to do our thinking for us. Like mathematicians with some of the fanciest calculators imaginable, we can get the tools NCBI gives us to show us amazing things in amazing ways, but they can’t tell us what it all means. For the genomes we get to make any kind of sense a human being has to abstract meaning from it and communicate that meaning in understandable language – and there is no way around that limitation – there will only ever be ways to optimize it.  This is really what synthetic biology is trying to do from its own weird and attractive but easily deceptively simplistic perspective.

For more information here are,

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We can do better.

Last year Bill Nye described in a Youtube video why he thinks that Creationism is inappropriate for children. Representatives of the Creation Museum had a response,

There is a lot about the character Bill Nye plays on TV that rubs me the wrong way, all it really manages to accomplish is to celebrate a hollow cargo-cult-like impression of science with a precious little bit of (unfortunately often incorrect) education; beakers without things to mix or measure, fuming liquid nitrogen without things to keep cold, experiments without questions to answer. However in this video Bill Nye is largely incoherent, repeatedly demonstrably wrong in trivial ways, doesn’t put forth or prove a meaningful thesis, and fails to present evidence for his points or meaningfully engage with the ideas of the people he is opposing.  We can do better.

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A brief introduction to how I am going to be approaching biblical exegesis in this blog

It would be unimaginably awesome if we had contemporary accounts by perfectly disinterested observers, or better yet multiple independent ones, but the contents of the bible really is pretty much the best we’ve got for figuring out what the dude actually said. Unfortunately, after the less scketchy of Josephus’ two brief mentions of Jesus in 90 CE, the earliest undisputed account that we have like this is from Pliny the Younger who, as a governor, writes to the Emperor in 112 CE that there are “Christians” about who are meeting illegally and who “worship Christ as a God,” all he wants is advice as to how to handle the situation. The next earliest is by Pliny’s friend Tacitus in 115 CE in his history of Rome where he mentions that the great fire, supposedly set by Nero, in 64 CE was blamed on “the Christians.” He seems largely uninterested in the scapegoats, but does mention that they got their name from Christus and that the “superstition” spread from Judea to Rome after Pontius Pilate executed Christus under the reign of Tiberius. This is still seventy nine years later. The earlier stuff that we have is indeed pretty terrible by the kinds of standards used to asses modern history, though is importantly a pretty standard level of terrible for the age. The accounts we have are written by true believers, who were not themselves eyewitnesses, who for the most part spoke a different language and lived in a different country than the eyewitnesses, they are not free from collaboration (With Mark being used as a source for Matthew and Luke), and they are pretty wildly inconsistent in both details and global understandings. However, there is still a lot we can do to get decent information out of what we’ve got.

Here is a brief introduction to how scholars approach figuring out what we know about Jesus

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