A Biological Programming Language

I've often said to friends that if I could start my career over again I would go into biology instead of computer science. Now, perhaps, there is a way to have a foot in both worlds.

Little b is a programming language for modeling biological systems. Quoting from the languages site...

The little b project is an effort to provide an open source language which
allows scientists to build mathematical models of complex systems. The
initial focus is systems biology. The goal is to stimulate widespread sharing
and reuse of models. The little b language to allow biologists to build
models quickly and easily from shared parts, and to allow theorists to program
new ways of describing complex systems.

Currently, libraries have been developed for building ODE models of
molecular networks in multi-compartment systems such as cellular epithelia.
Aneil Mallavarapu is the author and inventor of little b, and runs the
project. Little b is based in Common Lisp and contains mechanisms for rule-based
reasoning, symbolic mathematics and object-oriented definitions. The syntax is
designed to be terse and human-readable to facilitate communication. The
environment is both interactive and compilable.

Makes me wonder if Mathematica would be a good enviornment for similar exploration but with more sophisticated tools already built in.

Top 10 Foolish Beliefs

In honor of April 1st, traditionally April Fool's Day in the US and some other countries, here are my thoughts on the top 10 foolish beliefs of all time.

10. Perpetual motion is possible.

9. The Earth is Flat

8. My religion is correct, all others are wrong.

7. Dianetics (Scientology) is not a cult.

6. There is a Devil who lives in hell.

5. Astrology is a valid methodology for understanding your life.

4. Numerology has something relevant to say about our personal destiny.

3. Noah's Ark existed and had two of every animal on board.

2. Intelligent Design is a rational model of the origin of life.

1. God (as in an intelligent animate being) exists.

You may wonder why the Devil is only 6 while God is 1, besides the obvious numerological reason :-) . I justify this ranking based on the observation that there is much more anecdotal evidence for Satan than God!

Micro vs. Macro Evolution

I suspect some of my readership may be getting bored with all this evolution vs. ID stuff so I promise after this post we will return to our regular scheduled programming!

A favorite ploy of creationism is to accept microevolution (e.g. Darwin's Finches) while rejecting macroevolution (new species, birds descending from some dinosaurs, etc.) There is plenty of credible discussion about micro and macro evolution on the web so I am not going to repeat it here. See Douglas Theobald , John Wilkins and Wikipedia. I'd like to instead address the kinds of drivel exemplified by the thousands of posts like this one. Here we see an author asking "When Did the Fish Sprout Legs?" and then denying such a leap is physically or biologically possible. Here is an excerpt:

When one examines the historical record of life, we find the absence of transitional forms between the major life groups such as fish and amphibians or reptiles and birds. The fossil record has failed to yield the host of transitional forms demanded by the theory of macro-evolution. Rather, the fossils show an abrupt appearance of very distinct groups of animals. Take, for
example, the supposed"fish-to-amphibian" transition. The general assumption has
been that the earliest amphibians evolved from the order of fish, the Rhipidistia. However, there are major differences between the earliest assumed amphibians, the Ichtyostega, and its presumed fish ancestor. The differences are not simply a few small bone changes but are enormous structural differences as can be seen in Figure 1.The first amphibian had well-developed fore- and hind limbs which were fully capable of supporting terrestrial motion. The transitions between the two are strictly hypothetical, and no transitional fossils have ever
been found ... only imagined and artistically drawn. The mechanism for the
supposed macro-evolution of the fish to the amphibian is purely hypothetical.

When I was a boy my family used to picnic at Westbury Gardens in Long Island. There is a large pond there where I used to love to catch frogs to take home. There was also a shallow area where there were steps leading into part of the pond. Around these steps swam hundreds of tadpoles. One day I decided it would be really cool to capture some tadpoles and take them home to watch the transition of a tadpole into a frog. So I caught about a dozen tadpoles and took them home and placed them in a fish tank. I waited and waited but they never turned into frogs. Clearly I did not provide them with the right environment and nutrients to allow this transition to occur.

Can we learn anything at all from my boyhood escapade? Well clearly I am not going to claim that the transition from tadpole to frog is an example of macroevolution at work. Clearly the transition is preprogrammed and does not involve any mutation or selection. But here is what is interesting and very instructive:

1. A tadpole looks far more like a fish than it does a frog.
2. Everyone knows that tadpoles do sprout legs and become frogs given the correct conditions.
3. We also know that the transition from tadpole to frog is not instantaneous and each intermediate form is viable.
4. We learn from my experiment that given the wrong environment a tadpole will remain a tadpole and eventually die.
   

So in a time frame far far shorter than any timescales on which macroevolution occurs we see a fish-like-thing turn into a frog. Fascinating really. What is fascinating is not that this is a proof of macroevolution. It is not. What is fascinating is that it is there is a stable trajectory through genotype space that leads to a stable trajectory through phenotype space that manifests itself as a fish transforming into a frog. The mechanisms by which genes switch on and off in the case of tadpoles are based in regulator genes, enzymes, etc. and not mutation and selection. But so what?

If you accept micro-evolution, whereby selection and mutation lead to small changes in form and you witness for yourself a purely biological process whereby a rather large morphological change can occur in a span of weeks, how can you not at least admit to the possibility of macroevolution? Oh right, it’s not in the bible. Sorry, I forgot.

p.s. I just found similar ideas by someone much more qualified than myself. Definitly worth a read.

A Lesson in the Process of Science.

I realize that I have been posting quite a bit about education and the evils of teaching creationism. These topics are a bit off topic for this blog but they are important in light of the fact that (a) this is an election year and (b) a new creationism propaganda film staring Ben Stein is about to be released.

This film and creationists in general claim that "big science" is stifling other viewpoints and that doing so is anti-scientific. However, this position has as much legs as the theory creationism itself(that would be none).

Allow me to illustrate how science actually works by considering another area that is not as emotionally charged as the origins of life. Let's consider physics and in particular Quantum Mechanics (QM). I am inspired to write this by a recent article in New Scientist titled Quantum Randomness may not be Random.

As most readers are probably aware, the meaning and interpretation Quantum Mechanics was hotly debated during the birth of modern physics (~1880 - 1930) . The two most famous individuals at the heart of this debate were Albert Einstein with his position best immortalized in the "God does not play dice" quote and Niels Bohr who argued for the abandonment of all notions of causality at the quantum level. Bohr's view point became known as the Copenhagen interpretation and it ultimately became the dominant viewpoint of physics and the one that the vast majority of physicists accept today. In fact, this interpretation of QM has the same status in physics as The Theory of Evolution has in biology.

The first point to be made is that during the evolution of modern physics there was certainly room for multiple viewpoints and these viewpoints were hotly debated. But these debates always followed a process of science which begins with the presentation of facts and uses logic and mathematics to reach conclusions. Of course, scientists are humans and a certain degree of emotion and bullying come into play as well but nothing is settled using these devices. They are only a back drop of the human saga that is science. However, this is not what is truly instructive.

Fast forward to 2008. Quantum Mechanics is the most successful theory in the history of physics and its equations are responsible for so much innovation in the modern world. Truly, QM has earned the right in physics to be untouchable dogma. Certainly any respectable physicist who would dare question the Copenhagen interpretation would be the laughing stock of his profession and his career would be ruined. Certainly the proponents of Creationism would have you believe that this is how science works. But they are wrong.

In the New Scientist article we learn that a respected physicist from Rutgers, Sheldon Goldstein, is trying to revive an older interpretation of QM called the Bohmian Model, after David Bohm. The details are not as important as the moral. Goldstein is not being mocked by physics (even though his views are squarely in the minority) because he and his peers question the dogma of QM on scientific grounds. He presents mathematical and logical arguments. When his peers raise objections he does not scream foul or prejudice but rather talks about possible experiments. He does not dismiss his peers arguments by arguing in circles nor does he draw on sources of mysticism that lie squarely outside of science. Goldstein and others can question Big Science while remaining well ground in the process that define the way science has always operated.

Creationist don't play by the rules of science but want the respect of scientists. They propose arguments which draw on misrepresentations of thermodynamics but when they are called out on this they jump to other arguments equally fallacious. It is not so much the argument of design that disturbs most scientists; its the lack of logical and consistent reasoning that pervades all of ID.

I doubt many proponents of ID read my blog but if there are any out there allow me to suggest the following analogy. Imagine a scientist walking into your church this Sunday and saying, "Listen all you Christians your whole process of worshiping Christ and interpreting the bible is wrong. You should interpret Mathew like such and such and Paul like this and that." Wouldn't you be furious? By what right does a heathen have in telling your preacher what the bible means. How dare he! Well I say to you, "How dare you! How dare you come into the house of science and tell it how it should be. By what right?!?. Please leave immediately! ... But if you'd like to drop a small monetary donation on the way out we'd gladly accept!

Intelligent Design Indeed.

Here it is in a nutshell why teaching ID in schools will create a country full of boobs (I mean more than the number we already have sitting in pews).

I was going to vote for John McCain...

John McCain pretty much had a lock on my vote for the 2008 election. The purpose of this blog is other than politics so I am not going to go into why I thought he was the best candidate. Instead I would like to discuss why I may have to change my vote.

The issue is "Intelligent Design" AKA "Creationism". Apparently McCain's views on the teaching of evolution and the teaching of creationism is that each is a point of view and each point of view should be taught.

Well, Senator, Astrology and Numerology are points of view. Should we teach them beside Astronomy and Mathematics? Phrenology is a point of view. Should we teach it beside neuroscience? I sincerely hope the senator would have the common sense, even though he says he is not a scientist, to see that "points of view" and "science" are not the same thing. Point's of view don't cure disease, solve problems in physics, help design the next generation of computers, launch a spaceship, etc. A point of view is not a scientific criteria. Scientists follow a process and within the boundaries of that process there can be different "points of view". "Intelligent Design" does not follow the process of science. This has been well established, so it would be silly to repeat the points here.

Can McCain be convinced to abandon this position? Well just to get my vote he probably can't but I think its time for a little grass roots action in the states where McCain has to have victory to become president. There must be enough rational folks out there to help convince the senator to abandon his foolhardy stance.