M T Fahey

Archive for May, 2011|Monthly archive page

A Historical Comment on “Physics and the Immortality of the Soul”

In General, Philosophy, Science on May 29, 2011 at 5:12 am

I am not a physicist, professional philosopher, or interested in participating in the massive and fiery atheist v gnostic feud that takes place all over the internet every day.

I just finished reading a post by Sean Carroll over at Discover’s physicist and astrophysicist blog Cosmic Variance.  Sean writes:

Claims that some form of consciousness persists after our bodies die and decay into their constituent atoms face one huge, insuperable obstacle: the laws of physics underlying everyday life are completely understood, and there’s no way within those laws to allow for the information stored in our brains to persist after we die. If you claim that some form of soul persists beyond death, what particles is that soul made of? What forces are holding it together? How does it interact with ordinary matter?

Everything we know about quantum field theory (QFT) says that there aren’t any sensible answers to these questions. Of course, everything we know about quantum field theory could be wrong. Also, the Moon could be made of green cheese.

He slaps down the Dirac equation, the rather triumphant mathematical union of quantum mechanics and special relativity. He asks: What would you change to make the soul fit?

Carroll’s objection is not new.  It is, in essence, an updated version of the argument made by Princess Elizabeth of Bohemia (1618-1680) in her letters to Descartes in 1643. In Treatise of Man, Descartes identified the pineal gland as the “seat of the rational soul,” where (much like Carroll’s “blob of spirit energy,” which “drives around our body like a soccer mom driving an SUV”) it receives sensory information from flowing “animal spirits” and controls the body’s movement through interactions with the ventricles.

Descartes picked the pineal gland because it was singular, central, and small enough for the spirits to move it around:

“My view is that this gland is the principal seat of the soul, and the place in which all our thoughts are formed. The reason I believe this is that I cannot find any part of the brain, except this, which is not double. Since we see only one thing with two eyes, and hear only one voice with two ears, and in short have never more than one thought at a time, it must necessarily be the case that the impressions which enter by the two eyes or by the two ears, and so on, unite with each other in some part of the body before being considered by the soul. Now it is impossible to find any such place in the whole head except this gland; moreover it is situated in the most suitable possible place for this purpose, in the middle of all the concavities; and it is supported and surrounded by the little branches of the carotid arteries which bring the spirits into the brain” (29 January 1640, AT III:19-20, CSMK 143)

Princess Elizabeth’s objection was one having to do with Descartes own distinction and their (shared) contemporary understanding of physics: How does a substance not extended in space exert an influence on physical objects extended in space?  The problem raised in her letters was one of soul-brain interaction:

“I beseech you tell me how the soul of man (since it is but a thinking substance) can determine the spirits of the body to produce voluntary actions. For it seems every determination of movement happens from an impulsion of the thing moved, according to the manner in which it is pushed by that which moves it, or else, depends on the qualification and figure of the superficies of this latter. Contact is required for the first two conditions, and extension for the third. You entirely exclude extension from your notion of the soul, and contact seems to me incompatible with an immaterial thing.”

Although our understanding of the physical world has increased quite a bit since 1643, Descartes was unable to coherently respond to this challenge within the framework of the time (he suggested that the Princess conceive of the soul as extended, even if it really is not, and suggested that the soul’s ability to change the physical is simply an empirical fact).

How can the soul move an electron, something in an exhaustively equation-defined system, without being a part of that system (a term in the equation)?  If Descartes was alive today, he would probably be worrying about other things.

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A Post about Open Science and Incentives

In General, Science on May 25, 2011 at 9:04 pm

Slate Magazine recently published an excerpt from Tim Harford’s new book, Adapt: Why Success Always Starts with Failure. The selection recounts the story of researcher Mario Capecchi’s work on gene targeting, funded by the NIH despite strong recommendations from grant reviewers that he abandon the project in favor of less speculative work. His risk-taking was rewarded by a Nobel Prize, and his reviewers later wrote to him in apology: “We are glad you didn’t follow our advice.”

In defense of his book’s title thesis, Harford invokes an economics study on the effects of financial incentives on creative scientific achievement. The paper tests the theoretical framework suggested by Gustavo Manso (2009), in which particular incentive schemes increase the production of innovative ideas (in Harford’s words: “insanely great ideas, not pretty good ones”). According to the researchers:

“The challenge is to find a setting in which (1) radical innovation is a key concern; (2) agents are at risk of receiving different incentive schemes; and (3) it is possible to measure innovative output and to distinguish between incremental and radical ideas. We argue that the academic life sciences in the United States provides a near-ideal testing ground. ”

It was an ideal testing ground. The Howard Hughes Medical Institute (HHMI) investigator program, one source of funding, has long renewal cycles (5 years), a robust and detailed review process, and the stated goals to fund “people not projects” and to “push the boundaries of knowledge.” This leads to a system which gives investigators flexibility in the projects they pursue and time to invest in exploratory efforts. In contrast, the National Institute of Health (NIH) R01 grant program has a shorter funding period (3 years), a stricter review process with less feedback, and an emphasis on funding specific projects. By measuring the number of publications from each investigator that fell into the top citation percentiles, the novelty of the attached keywords (in relation to the entire body of literature and the researcher’s past work), and the range of journals that cited the work, the researchers found evidence that HHMI investigators produced more novel research and more high-profile papers (while also producing a greater number of flops) than NIH controls.

The researchers are careful to note that their findings “should not be interpreted as a critique of NIH and its funding policies.” After all, researchers that are awarded HHMI grants (and the NIH MERIT controls) have been judged to exhibit extremely high potential. The investment in time (detailed project reviews) and risk (a high degree of freedom and low expectations for immediate results) for the program suggests that it may not be beneficial to replace the NIH incentive structure with HHMI-like criteria. The ideal situation may be closer to the one currently in place — a combination of the two incentive systems. A more project-based system may be better for younger, less experienced scientists, while the HHMI system would be best reserved for the select group who would flourish with less constraints.

How else might small differences in incentive structure determine the quality of scientific output? What implications does the confirmation of the Manso model have for the future direction of scientific investigation?

The incentive structure in scientific research is likely to change drastically in the next decade. Like the field of journalism (another information-gathering and sharing enterprise), the practice of science is poised at the edge of an internet-driven revolution in connectivity. Driving this change are journals like the Public Library of Science (PloS), which makes scientific papers available to the public via the internet using an author-pays model, and groups like openscience.org, which encourages the free sharing of methodologies and datasets with the public. Some major academic publishers are also moving to a hybrid system in which authors can pay a fee to have their paper publicly available, and groups like HHMI have agreed to cover the extra charge for their grantees.

The poster child of the open science movement is the Human Genome Project, which sequenced and published the entire human genome in 2003, in the process narrowly routing a proprietary attempt to do the same. Following in the footsteps of that success, all DNA sequences generated by recipients of NIH grants are required to be entered into the GenBank database, creating a massive searchable repository of our genetic knowledge. Open science has the potential to help scientists wade through massive amounts of data, to find patterns in extremely complex systems, and to substantially increase the speed of scientific progress.

Despite the success of these open science experiments, scientists are understandably slow to switch over. Dan Gezelter at openscience.org writes:

“Right now, the incentive network that scientists work under seems to favor ‘closed’ science. Scientific productivity is measured by the number of papers in traditional journals with high impact factors, and the importance of a scientists work is measured by citation count. Both of these measures help determine funding and promotions at most institutions, and doing open science is either neutral or damaging by these measures. Time spent cleaning up code for release, or setting up a microscopy image database, or writing a blog is time spent away from writing a proposal or paper. The ‘open’ parts of doing science just aren’t part of the incentive structure.”

Time investment is not the only reason the scientific community is resistant to moving to the open system. Opening up your data to analysis by other scientists is necessarily risky, and not something scientists are likely to do en masse until it is fully expected by the community. It involves massive reform of the scholarly publication system, as well as the reputation bookkeeping done by that system. It requires researchers be comfortable with managing their online identity and with using new software tools. It will involve sweeping changes in the way science is reported.

An online publishing system, especially one that encourages self-publishing, would allow scientists to publish smaller chunks of work at a time. Results from individual experiments could be made available as soon as data is gathered. Data analysis and interpretation could become a much more open process. The smallest publishable unit would shrink, allowing researchers across the world to build on each other’s findings in a fraction of the time it currently takes. Many of the publishing biases that plague the current system (eg unwillingness to publish replication of experiments or negative results) could be eliminated.

It is possible that the ability to publish in this manner, with atomized units (maybe single experiments), would lead to the expectation that scientists publish much more frequently. Having shorter periods of expected achievement would mimic the incentive structure of the NIH rather than the HHMI; in the same way that shorter review periods prevent exploration, expected rapid publication of data on the internet could incentivize less risky experimentation.  In this case, perhaps an increase in HHMI-like funding incentives would be appropriate.

There is a sense in which faster publication in smaller units could cheapen the value of a publication. There would be less effort, less time, and less reputation at stake for each piece released. The current system, with the huge time investment necessary to get a paper published in a traditional journal, encourages lumping of many experiments and forces researchers to piece all of their work together into a convincing narrative.  A scientific paper today may span many years of work. It puts all of a researcher’s eggs into one basket.

Rapid publication of open data prevents researchers from shuffling their experiments to tell a better story. It makes it difficult to change how data is perceived by changing the way it is presented. Peer review could be done online, transparently, by a larger group of people. The shorter time between finishing and experiment and publication would automatically help put experiment in context with other work being done. Review and meta-analysis would be more important than ever to retain the continuity and coherence of the scientific narrative being created (this could be a new role for journals as they lose their base of readers and contributors).

The face of science could be changed for the better, medical advances could be faster, and public understanding of the sciences could be improved, and it could all happen very soon if institutions with pull in the scientific community (the NIH, HHMI, journals, and universities) created the right incentives.

BBC documentary — Everything and Nothing (Nothing)

In Science on May 13, 2011 at 3:49 am

A great BBC documentary featuring Professor Jim Al-Khalili.  Describes the history of the science of the vacuum and gives a very accessible account of quantum mechanics. Second part of a two-part series, but can stand alone.

Old video (2009): Clay Shirky on the future of accountability journalism

In General on May 4, 2011 at 8:44 am

Great informal talk by Clay Shirky at the Joan Shorenstein Center on Press, Politics, and Public Policy at Harvard’s Kennedy School.

“So I have no idea how long this transition will take. But I don’t think that some degree of failure and decay is avoidable. I think our goal should be to minimize the depth of that trough, to constrain that trough to the areas we can constrain it to, and to hasten its end. But I don’t think we can get away with a simple and rapid alternative to what we enjoyed in the 20th century — in part because the accidents that held that landscape together in the 20th century were so crazily contingent.”

Or the complete transcript

Julian Assange Interview

In News, Politics on May 3, 2011 at 9:23 am

A Russia Today (RT) interview with Julian Assange on the Arab revolutions, social media, and recent Wikileaks activity. On Facebook: the “most appalling spy machine that has ever been invented.” On Wikileaks partner redacting (Guardian, New York Times): “It is part of that mesh of corporate and state interests.”

Bin Laden’s Death and Pakistan

In General on May 3, 2011 at 5:21 am

The killing of Osama Bin Laden by US military forces has prompted a number of official comments from leaders around the world, varying from condemnation (Ismail Haniyeh, Hamas) to enthusiastic support. A summary of official reactions can be found at Al Jazeera.

Perhaps one of the most pointed responses came from the Indian home minister, who said:
“We take note with grave concern that part of the statement in which President Obama said that the firefight in which Osama bin Laden was killed took place in Abbottabad ‘deep inside Pakistan’. This fact underlines our concern that terrorists belonging to different organisations find sanctuary in Pakistan.”

Not a surprising comment given India’s uneasy relationship with their neighbor, and pertinent to the United States, whose operations in Afghanistan are not at all independent from events in Pakistan. Although the US tends to emphasize successful cooperation with Pakistan in the War on Terror, the recently-released Wikileaks files contribute to the conspicuous pile of evidence that groups within Pakistan are actively subverting US efforts. The successful Bin Laden operation is attributable in part to the President’s decision to keep the Pakistani government in the dark.

Great article by famed foreign correspondent Robert Fisk on Bin Laden (whom he interviewed three times) and Pakistan.

From the Telegraph on Wikileaks and Pakistan’s aid to Bin Laden.