Category Archives: Science

Science

What are the best utilities in Mac OS X?

There are whole websites dedicated to answering these kinds of questions. However, for the kind of work I do as a computational scientist, I have found some favorites over the last seven years of using Mac OS X. From now on, my current favorites with brief rationale for each one will be posted on the tools page of this blog. That page has also been added to the navigation bar at the top.

Please let me know if your favorites differ from mine and why — there might be a better program out there that I’m missing out on!

Happy Darwin Day!

Charles Darwin was born 199 years ago today. From the Darwin Day press release,

Recent Gallup polls show that 43 percent of Americans reject the theory of evolution and instead believe that “God created human beings pretty much in their present form at one time within the last 10,000 years or so.” And at least four 2008 presidential candidates have said they do not believe the theory of evolution.

“There is a continuous threat to evolutionary biology and to science in general that has been posed by fundamentalists who reject entirely a Darwinian worldview because they feel it threatens their religious beliefs,” said Massimo Pigliucci, Ph.D., a professor of evolutionary biology at the State University of New York-Stony Brook.

43% — Keep in mind that while these people think God created humans in the last 10,000 years, we have evidence that dogs were domesticated by humans some 4000-7000 years before that.

Mind/Brain Duality (or lack thereof)

What is the mind? Is it a product of the brain, or does it come from somewhere else? Is there a ghost in the machine?

A number of things have brought this source of controversy to my mind recently. One is that I just finished the second season of Ghost in the Shell: Stand Alone Complex (not as good as the first season). The Ghost in the Shell franchise is largely an exploration of the implications of mind/brain duality and how it may actually become a reality as technology improves. Another is that I’m still reading Gödel, Escher, Bach: An Eternal Golden Braid by Douglas Hofstadter, a book that (among many other things) is largely about the origin of consciousness. Yet another is that there was a great party at the Mind/Brain Institute here at Hopkins last Friday. The final thing is that over the weekend I have gotten into some arguments with anti-choice people on YouTube (I know, bad move).

First, a disclaimer — here are the things that I believe, after a lot of reading and thinking:

  • The mind exists as a result of things that happen in the brain.
  • As it stands now, the mind cannot exist without the brain.
  • It is conceptually possible that the mind could be ‘liberated’ from the physical hardware of the brain, but it would require some other equivalent physical hardware. The most computationally difficult and brute-force version of this would be to accurately simulate a physical brain on a computer.
  • Humans are not the only conscious animals on this planet.
  • Not all humans have the same level of consciousness. For instance, a baby in the womb or even a newborn is not likely conscious in the sense that adults or older children are. Probably many animals are more conscious than a one-year-old.

The alternative view, as far as I can discern it, is that the mind is something special that sort of “sits on” the brain, but can be liberated from it should the brain fail (read: die). This consciousness (or “ghost”) can then go on to lead an afterlife. This is an extremely common perception, though it’s highly unlikely, and it is the basis of some very common and heated controversies. It leads to statements of belief (contrasted with mine above) like this:

  • As soon as a zygote is formed, it has a soul and is a person. It has feelings and cries out in pain if aborted, thinking “Why does my mommy not love me?“
  • Humans have a soul and are special. Animals do not, and are not essentially ‘special’.
  • When the body dies, the soul lives on. Its future can contain things like heaven, hell, joining with the universal consciousness from whence it originally came, and so on.

This is why anti-choicers insist that abortion is murder. They will swear up and down to you that abortion is taking a “life”, but try to pin them down on what “life” is and why it’s more valuable than the life of the mildew in their shower or the pregnant woman, and they start to stutter and dive into circular logic. We can pose some difficult questions that will reveal this:

  • What is an aborted foetus’s soul like in Heaven? Does it remain always a baby? Does it grow into an adult?
  • Do people with life-long brain dysfunction on earth (say, from Down’s Syndrome) become different, more intelligent, and function better when relieved of their physical brain?
  • Do people who have suffered head injuries on earth that allow them to survive but damage their ability to function, or people who have survived a stroke regain full function in the afterlife?

These questions are designed to bring attention to conflicting beliefs held within the same mind. That is, if one believes that a head injury causes its mental effects via damage to the brain, and not because it allows a demon into the soul, the rest of the ghost-in-the-machine belief system comes into question. The latter explanation is still accepted by some uneducated people (think rural west Africa) and crazy people in the developed world. The questions make it harder for people to rest assured that they hold reasonable beliefs on the nature of the brain and that these beliefs do not jeopardize their religious convictions.

What are your views on the subject? Do you disagree with me? Can you think of similar and better questions to bring out this sort of thing?

Updates to Google Notebook Make It Even Better As a Lab Notebook

In October of ’07, I posted about my move to Google Notebook as my primary lab notebook. It has not only continued to serve me well since then, but now serves me even better with the addition of a few features:

  • Auto-dated notes: I’d be happier if I could opt for auto-timestamps as well, but Google now adds the date a note was created (not sure if it updates it when edited but I don’t think so) to the upper right-hand corner. Now instead of putting the date and location at the top of each note, I just put the location.
  • Sharing: It’s now easy to share with others. I’ve shared my notebook with my advisor so that she can follow along if she likes. I used to do this on our lab wiki as well. It would also be possible to have a shared notebook between all of the people on a project, almost like a private blog. I think this latter use has a lot of potential
  • Labels: Google has added labels (in practice the same thing as ‘tags’), making it possible to tag each entry with the projects to which it is related. Pulling up all of the notes on a project is then as simple as selecting the appropriate label.

It keeps getting better. Hopefully, they will add those automatic time stamps at some point.

Infinity and Beyond

My friend Rob has another excellent mathematical post up. It has, in fact, been up since December 14th, but I’m only now catching up with my starred RSS items from last month.

This post is on the nature of infinity and other large numbers, and how we mentally relate to and handle them. Here’s a taste:

[I]f you look at infinity from a size standpoint, infinity is dizzyingly terrifying. Most people don’t have a proper concept of what “large” means, but mathematicians know better:

  • The universe is 13.7 billion years old, or 4.3*10^-17 seconds. Current quantum theory has trouble measuring time below Planck’s time constant, or 1.855×^-43 s. If we treat the idea of time as a discrete number of Planck’s constants, then the age of the universe is 8*10^60 of these constants. Infinity is bigger than this.
  • The number of atoms in the universe is estimated to be around 10^80.
  • The biggest number ever seriously used in mathematics is Graham’s number. The number is an upper bound for some mathematical property. The number is so huge that it cannot be written with scientific notation (the exponent would have more digits than atoms in the universe). Still, infinity is bigger than this number.
  • The Ackermann function is a strange non primitive recursive function:
    ackermann function

    This function generates huge finite numbers. For example, A(5,2) is so large that it cannot be describing it with common math notation would take more letters than there are atoms in the universe (this includes 9^9^9^9^9^9… etc.). Still, infinity is bigger than this number.

Read the whole thing here.