How can a computer scientist do research without using and producing only free and open source software?

This question is the corollary that follows from this hypothesis:

Free and open source software (FOSS) is the only way to produce and use software that follows the scientific method.

There are all sorts of reasons a human programmer might want to keep their computer code a secret.  But if that human is also a scientist, isn’t it their duty to produce science that can be verified?

Looking at the scientific method definition:

To be termed scientific, a method of inquiry must be based on gathering observable, empirical and measurable evidence subject to specific principles of reasoning.^[2] A scientific method consists of the collection of data through observation and experimentation, and the formulation and testing of hypotheses.

Often to verify science requires access to the same equipment – particle collider, electron microscope, or space-based telescope.  At some level, especially where the machinery is unique, the best method is to provide access to the machine for other scientists to verify. But where are you if your science can only be produced and reproduced using a black box that you have to buy, and that black box clearly has an influence on the outcome of the science?  How can you verify the science if you cannot study the insides of the black box to understand how it affects the outcome of the experiment?

How can I verify your science if your code isn’t open?  I have to be able to fully observe your experiment to verify your hypothesis.  How can I measure your evidence if the tools of measurement, your software code, are compiled and only available in binary form?

You could say that having non-commercial access to the source code would work for verifying the experiment.  That presupposes that the verification doesn’t require a commercial interaction that would be forbidden.  For example, if the code supports a new business method, I can’t verify that the code or method work without doing actual business with them.  Ultimately, these field of use restrictions block unknown usages of the science such as humanitarian or medical where the ethical situation is higher but couldn’t be predicted in advance (when choosing original licensing/release terms.)  These field of use restrictions also have a chilling effect on other scientists.  It’s less clear what is or isn’t a violation, so they seek a scientific solution in code (software) that is less ambiguous.

In addition, restrictive terms for viewing source code has the effect of tainting the recipient.  How is it scientifically ethical if you require a colleague to sign away an unknown number of enquiries in a liftetime of research for fear of violating a source code sharing contract?

There is a whole mess in here with patents, and this is related to why patents may be unethical for science.  In a machine patent, the science isn’t necessarily being patented; it’s the results of the science that is.  Any science that leads up to the machine patent should be open and visible for reproducing and verifying.

But a software patent is a slippery thing.  The patent may cover the science as well as the product of the science, in that both can be in the code.  There is an ethical dilemma for any scientist when they patent the science.  They are putting a price tag and control on reproducing and verifying the science.  Without verification, the science is invalid.

In case you are wondering if this is just semantics and word choices, it is.  Perhaps all of the people who call themselves computer scientists, shouldn’t?  I presume the word has meaning for them, as it does for the rest of us, and I expect them to act accordingly.

Being a scientist has a specific meaning that spans a long part of written history.  How long?  Several hundred to several thousand years, depending on what you are measuring.  It is clear that the scientific method has been followed since at least the Middle Ages.  It predates copyright and patent law by at least several centuries, if not nearly a full millenium.

It was Sir Isaac Newton, amongst others, who said,

If I have seen a little further it is by standing on the shoulders of Giants.

That, friends, is the whole point of FOSS.  It is, so far, the best way we’ve found as computer scientists (schooled/amateur/citizen) to live up to Newton’s ethics and methods.

I dubbed my point above as a hypothesis because I am opening this idea for debate by scientists, particularly computer scientists and scientific ethicists.

http://www.planetary.org/special/fromearth/bradbury

The greetings are limited to 250 characters, and I took advantage of a return character costing the same as a space or punctuation to write him this poem:

From first rocket to last pricking of thumbs,
your words and ideas carried our minds
out
past asteroid belts &
in
to the light and dark parts of the soul
Helping make the 20th century
using a mirror as a tool to
reflect the future in the past
Thanks

The gist of the movie is, GW McLintock (Wayne) is a tough but fair minded cattle baron in a US territory in the 1890s.  The relationship with the Comanche is interesting; McLintock is a former Indian fighter who speaks for the Comanche in a kangaroo court, and secretly supports their choice to die fighting instead of in prison.  The ranchers are at odds with the farmer settlers, who are looking for land to farm at 6000 feet above sea level (good luck.)

McLintock’s wife, Katie (Maureen O’Hara), is also tough, not fair, and rules her family with an iron parasol.  She has also separated from GW because of something she won’t talk about; she has moved out and comes back in the movie to help welcome home their daughter.

Said daughter falls in love with a young farmer, who happens to be a star pugilist who had to drop out of Purdue when his father died so he could help on the homestead.  Their love blossoms over fighting and, yes, when he spanks her for encouraging her father to shoot him, it’s clear love is in the air.

So the end is GW chasing Katie all over town, as she losses more and more clothing, until he finally catches her and spanks her in front of the whole town.  They he jumps in his carriage and leaves.  “Oh, no you don’t,” Katie cries, and suddenly able to run as fast as a horse in her heels (when she couldn’t outrun a Wayne-stride-through-town), she jumps on the back of the carriage.  Closing scene follows, with them embracing as silhouettes in the window.

Oh, did I mention, this is a comedy?

It is odd to watch a move like this, and both admire the slightly more respectful (for a cowboy movie) view of the Comanche situation in the 1890s.   Meanwhile, all the women in the film are just looking for the right strong man to tame them, break them like a wild horse.  Not even as an overtone — mother and daughter have multiple scenes where they slam a door or stalk off mad after being mistreated, then giving a sly sidelong glance and half smile at the abuser (husband, young beau.)

The sooner we erase these stereotypes from our cultures, the better the future will be.

Here is “Oh California”:

Here is “A Gust of Fall Wind”: