Mythical Science: Mythodologies

Losing Our Myths

2012-01-08T08:59:00.000-08:00

I’ve just re-subscribed to the Chronicleof Higher Education (and I have no idea why I let it lapse, it feeds mybrain in all the right spots) and have been enjoying a backwards read throughmy favorite section of the publication, TheChronicle Review, sort of The NewYorker for college educators (oh, relax already; I read The New Yorker, too).

Anyway, in the November 25, 2011 edition of the CR, Pitzer College sociology Professor PhilZuckerman’s “TakingLeave of Religion” (subscription required) article describes a growingtrend, apostasy. He writes that there isn’t a lot of research on apostasy orthe leaving of one’s religion. He interviewed 87 apostates about why theybecame non-religious.

Quoting from ThePew Forum on Religion & Public Life’s Religious Landscape Survey, henotes that 16% of Americans are religiously “unaffiliated” and 17% claim “none”as their religion. These numbers are significantly higher than in previousyears. And one of Zuckerman’s predictions is that these numbers will continueto increase. [Geeky fan side note: he doesn’t mention how many Americans listed“Jedi” as their religion, but I checked the survey, and Jedi isn’t listed. It’sbigger in other countries, like in the UK.]

Zuckerman’s writes that what he learned in doing thisresearch is that “Religion is not universal or necessary.” CG Jung wrote aboutthe psyche’s transcendent function, which many people cite as a reason forreligiosity, but this can of course operate outside of organized religion orany form of theism. During my years of mythological studies at Pacifica Graduate Institute, there was oftena conversation about “people falling away from their myths (religions)” andwondering what would replace that lost faith. Zuckerman is saying that we don’tneed anything to replace them and in fact “many [non-religious] people preferit that way.” More generally, though, from a mythologist’s point of view, a lotreligion doesn’t have to be replaced by another religion or religious practice,specifically. We tend to talk more about another mythology replacing a lostreligion, and not all personal mythologies are religious, but they do inform apersonal worldview.

I know this where I should be prompted to write a lengthyexplanation as to why I’m an atheist, but it’s really not so complicated: I’m ascientist and I’m a lesbian. I’ve found that while one is a profession and theother a biological feature, neither is compatible with being a Baptist (the religion on both sides of my family). Orreligious. End of story.

I have a good friend at work who comes from a Catholic family,is sternly non-religious now, but has to deal with an overly-religious mother(and truly Irish Catholic, her mother is an Irish immigrant). I lent her my DVDof Julia Sweeney’s “Letting Go of God”-- a one-woman staged monologue about her quest for religious knowledge. Whenshe returned it, our conversation was full of some of the hilarious punch lines(“Have you READ that book?” “Deepak Chopra is full of shit!” At least theScientologists know to give you a personality test before telling you aboutXenu, the intergalactic overlord.”). Then there’s Sweeney’s impressions of herslightly dim mother, “This doesn’t mean you’ve stopped going to church now,does it?”

Interestingly, when I was out this morning getting a Los Angeles Times Sunday newspaper, Iheard an NPR story that featured quotes from the current batch of RepublicanPresidential contenders and their supporters talking about President Obama’swar on religious freedom. I don’t want to go into all of the reason why I findthe notion ridiculous, but checkout the story if you’re strong of stomach and can handle the kind ofreasoning that pushes why religious-based health charities should not fundcontraception or that LGBT rights is the biggest threat to American religiousfreedom today. Going back to the Pew Forum’s Religious Landscape Survey, 56% ofAmerican adults who leaveor switch their religious affiliation cite being “Unhappy with teachings onabortion/homosexuality” as a reason why they made the change.

All right, I’ve got to go and prepare for a daylong class I’mteaching in about a week. Be sure to check out Phil Zuckerman’s terrific listof 65Songs for Atheists and Agnostics.

The passing of James Hillman

2011-11-06T11:18:00.000-08:00

We were all deeply saddened to learn of James Hillman's passing on October 27th.

The Somatic Studies students were resident at Ladera on Monday, Oct 31st, so they were the first students on site after the news of Hillman's passing. We held a circle before class started in the morning. As we gathered quietly in the sun, after a time, a few students read passages from works by Hillman. Chris Downing was there (who is teaching in the Somatics program for the first time), and she noted that James Hillman died 50 years after Jung and at the same age, at 85. Joe Coppin told us he had heard that Hillman wanted to be buried in the Jewish tradition, without delay, but also because "he wanted to be able to hear each handful of dirt hitting the coffin."

During the faculty and staff memorial on Nov. 3rd, it was mentioned that a larger, more public memorial would be forthcoming in early December. Check the main Pacifica website for that information when it's available. Pacifica Graduate Institute's tribute page to James Hillman can be found here. [January 8, 2012 Update: A 2-day tribute to James Hillman and his work is planned for March 3-4, 2012 at Pacifica's Ladera Lane Campus. Check here for further information when it's available. I will post separately about this event when I know more details.]

Below is the James Hillman quote I shared with my class once we had assembled. This particular quote was helpful when I was writing my dissertation on the Human Genome Project because it quickly became obvious that it was the "root metaphors and operational myths" that needed to excavation and examination. I am so grateful for the few times I got to hear James Hillman lecture while I was a Mythological Studies student.

"Thescience fantasy with its reliance upon objectivity, technology, verification,measurement, and progress—in short, its necessary literalism—is less a meansfor examining the psyche than for examining science. Our interest lies not inapplying the methods of science in psychology (to put it on a “sound scientificfooting”), but rather in applying the archetypal method of psychologizing toscience so as to discover its root metaphors and operational myths.

Scienceis not soulless at all. It too is an activity of the psyche and of the archetypesin the psyche, one of the ways of enacting the Gods. By psychologizingscientific problems, methods, and hypotheses we can find their archetypalfantasies. For science, also, is a field for soul-making provided we do nottake it literally on its own terms."

—JamesHillman, Re-Visioning Psychology(1975), p. 169

Links with more information:
James Hillman's obituary at the New York Times online
Pacifica Graduate Institute's James Hillman tribute page
Thomas Moore remembers James Hillman at The Huffington Post
Remembrance at The Dallas Institute of Humanities and Culture where Hillman was a founder

On the Nature of Four: Jung's Quarternity, Mandalas, the Stone, and the Self

2011-10-22T07:31:00.000-07:00

This is a student paper I wrote back in 2005 for Glen Slater's "Jungian Depth Psychology" course. Glen's course was/is part of Pacifica's Graduate Institute's Mythological Studies program curriculum. What is odd about this paper is that it's taken on a life of it's own on the internet. I uploaded it to a bulletin board a few years back and since then it has appeared on a number of websites without my permission. If you do a Google search using "Jung" and "quarternity" or "mandala" this piece pops up. On many sites, they attribute the author to a "Carbonek" which is a handle I used in a particular online community, and anyone familiar with Charles Williams' Grail cycle of poetry will recognize the name. Oddly, the versions I've seen online don't include Ellenberger in the Work Cited, which is a big omission. Below is the entire paper and all mistakes are mine.

On the Nature of Four: Jung’s Quarternity, Mandalas, the Stone and the Self

During a difficult period in his life in which he withdrew from his teaching position and devoted much of his time investigating the nature of the unconscious, Jung frequently painted or drew mandalas, but only learned to understand the mandala symbology many years after he had begun creating the images. He understood only that he felt compelled to make the figures and that they comforted him, “Only gradually did I discover what the mandala really is: “Formation, Transformation, Eternal Mind’s eternal recreation”. And that is the self, the wholeness of the personality, which if all goes well is harmonious, but which cannot tolerate self-deceptions” (MDR 195-196).

Mandalas are defined by Jung as magic circles, containing certain design motifs that he found to have a universal nature, across cultures and across time, whether they are the transiently created mandalas from Tibet, sand paintings from the American southwest, or illustrations from ancient, medieval, and Renaissance alchemical works.

Jung believes that his mandalas were “cryptograms” of the state of the self as it was on the day the mandala was created. Each mandala that he spontaneously created was different from their predecessors and the paintings were precious to him, he “guarded them like pearls” (MDR 196). He also believes that mandalas appear in connection with dreams, chaotic psychic states of disorientation or panic (CW 9i 645) as they did in Jung’s own life, and that a function of the mandalas is to bring order out of chaos. Edinger agrees, “Quaternity, mandala images emerge in times of psychic turmoil and convey a sense of stability and rest. The image of the fourfold nature of the psyche provides stabilizing orientation. It gives one a glimpse of static eternity.” (Edinger 182).

Jung eventually came to believe that the mandala itself is an image of “squaring the circle” and as such could be called an archetype of wholeness (CW 9i 715).

Jung’s continuing practice of drawing and painting mandalas eventually leads him to understand them as symbols of the Self, that they are informed by archetypal forces in the unconscious that the artist is not aware of during the creation of the work.

Working with mandalas, Jung eventually realizes that like the designs he was drawing, his own life had been a series of meandering paths that bent back upon each other and yet always led back to the center. The mandala symbolically represents that path to the center, to individuation (MDR 196). Jung’s later practice of having his patients to spontaneously create mandalas is a prime example of Jung’s own explorations into the unconscious becoming effective tools in his psychiatric practice. In “Concerning Mandala Symbolism” several mandalas painted by some of Jung’s patients are reproduced and his commentary on each shows the universality of the symbolism across the patients’ cultural differences. He doesn’t go into the clinical details of the patients’ therapy but notes that “a rearranging of the personality is involved, a kind of new centering” over time as the mandala-creating process continued. (CW 9i 645). Jung’s reasoning for the similarity in mandala symbols created by his patients is that these symbols and images come from the collective unconscious and are therefore archetypes, or primordial images, which reside in each of us (CW 9i 711).

Jung also found that mandalas created by individuals often contain motifs related to the number four, which he terms a “quaternity”. The symbol might be “in the form of a cross, a star, a square, an octagon, etc. A form of this symbol is frequently found in alchemical texts as the “squaring the circle” or quadratura circuli (CW 9i 713). Jung thought that “squaring the circle” was a “problem that greatly exercised medieval minds” and this was also a “symbol of the opus alchymicum because it breaks down the original chaotic unity into the four elements and then combines them again in a higher unity” (CW 12 165). However, Jung is not the first to write about the symbolism of the quaternity as Ellenberger reports:

“In France Fabre d’Olivet had previously written about the same subject in the nineteenth century. However, Jung was certainly the first to relate it so closely to the process of individuation. The mandala is a circular figure ornamented with symbols that is generally divided into four sections. It is well known in India and Tibet, where it was used for centuries by ascetics and mystics to aid in contemplation” (712).

The fourfold symmetry of the quaternity eventually led Jung to study alchemical works and in these he found many examples, such the four main steps in the alchemical process: nigredo (black), albedo (white), citrinalis (yellow), and rubedo (red) (Henderson and Sherwood 5). Alchemical processes have fourfold properties such as hot, cold, wet, and dry while all materials are said to be combinations of the four elements: earth, air, fire, and water. He found that even the alchemical Philosopher’s Stone had a four-fold nature, “The lapis is called a “sacred rock” and is described as having four parts (CW 9ii 143). Elias Ashmole, in his Theatricum Chemicum Britannicum, an 18^th century collection of English alchemical texts, he even describes four different Philosopher’s Stones: Mineral, Vegetable, Magical, and Angelical, each with a different functionality (Edinger 264).

The alchemical arts have a dual nature, one which may be described as external, embodied and practical, and another which is internal, spiritual, and abstract (Henderson and Sherwood 7). While there were certainly those who practiced alchemy in a physical way, that is, with laboratory equipment with the goal of transmuting a base material into gold (chrysopoeia), or developing an elixir of immortality (spagyrics), it is clear that the metaphor of a laboratory process was more valuable to alchemists as a way to describe what was a psychological and spiritual practice in an attempt to improve themselves as human beings (Henderson and Sherwood 7). Jung "sees a projection of the process of individuation in the steps performed by alchemists" and "devoted many years to the psychological interpretation of alchemical symbology" (Ellenberger 719).

Edinger also sees the alchemical association between self and the lapis, “The goal of the individuation process is to achieve a conscious relation to the Self. The goal of the alchemical procedure was most frequently represented by the Philosophers’ Stone. Thus the Philosophers’ Stone is a symbol for the Self.” (Edinger 261).

The study of alchemy was essential for Jung’s understanding of the way to the Self, “Alchemy … made it possible for me to describe the individuation process at least in its essential aspects” (CW 14 792). And Jung notes that while medieval alchemists didn’t discover the structure of matter, they did discover the structure of the psyche, even if they themselves did not understand what it meant (CW 14 150).

We find a wide spectrum of four-fold symbols and systems in religion, myth, history, science and culture. There are four winds (Boreas, Eurus, Notus, Zephyrus), four seasons (winter, spring, summer, fall), four directions (north, east, south, west), four Evangelists (Matthew, Mark, Luke, John), four letters in the sacred name of God (YHVH), four ancient ages (gold, silver, bronze, iron), and four medieval humours: sanguine (blood), choleric (yellow bile), phlegmatic (phlegm), melancholic (black bile) to name a few. DNA is composed of four nucleotide bases, there are sixty-four triplet codons in the genetic code, and twenty common amino acids as a result of translating the genetic code.

Adding a fourth to an already established thee has a transformational effect. In geometry, a fourth point transforms the two-dimensional triad or triangle into a figure with depth, the cube and the tetrahedron (a form lapis). As the mathematician Michael Schneider observes, “There are always four ways (another quaternity) to look at any three-dimensional structure: as points, lines, areas, and volumes, or as corners, edges, faces, and from the center outward (63). Ellenberger notes that “The quaternity can appear as a geometric figure of square or sometimes rectangular shape, or it will have some relation wit the number four: four persons, four trees, and so on. Often it is a matter of completing a triadic figure with a fourth term, thus making it into a quaternity” (712). Jung searches for the quaternity when a trinity is encountered, “Jung over and over again in his writings returns to the alchemical question: “Three are here but where is the fourth?” (Edinger 189). The completion of the quaternity is seen frequently in alchemical works, even whimsically, “All things do live in the three/ But in the four they merry be” (quoted in CW 12 125).

One Trinity that was completed in the last century, with the bodily assumption of the Virgin Mary into heaven (defined as dogma in 1950 by Pope Pius XII), transformed the Christian Trinity into a Quaternity, and one that Jung believes was achieved by the overwhelming insistence of the Catholic masses (CW 9ii, 142). “… the quaternity is the sine qua non of divine birth and consequently of the inner life of the trinity. Thus circle and quaternity on one side and the threefold rhythm on the other interpenetrate so that each is contained in the other” (CW 11 125). Jung believes that this was the most significant religious event since the reformation (quoted in EJ 321).

Another quaternity that Jung develops is that of the four psychic functions: sensing, thinking, feeling, and intuiting. “The essential function of sensation is to establish that something exists, thinking tells us what it means, feeling what its value is, and intuition surmises whence it comes and whither it goes. (CW 6 983). Sensation and intuition he terms irrational types with thinking and feeling are rational types. Jung diagrams the four functions in a basic symbol of the quaternity, as a cross with the irrational functions at right angles with the ration functions. Along with what he terms the two general attitudes, extroversion and introversion, Jung feels that these now eight types provide a useful framework for these psychological concepts (CW 6 987). Jung’s suggestion that his psychological typology could be compared with a trigonomic net or a crystallographic axial system suggests the lapis, or Philosopher’s Stone once again circling back to alchemical concepts (CW 6 987).

During the years that Jung spends drawing and painting mandalas, he comes to understand that “the goal of psychic development is the self. There is no linear evolution; there is only a circumambulation of the self” (MDR 196). If there is one concept about the development of the self, of individuation that is important for those of us in the 21^stcentury caught in a Cartesian-Newtonian notion of reality is that “there is no linear evolution” for this process; that the process is one of circling, rotating, orbiting, circumambulating around the center – we must square the circle. We must create our own mandalas and go where they lead us. As much as we might wish for a clearly delineated way, here is no straight line to follow:

"From the circle and quaternity motif is derived the symbol of the geometrically formed crystal and the wonder-working stone. From here analogy formation leads on to the city, castle, church, house, and vessel. Another variant is the wheel (rota). The former motif emphasizes the ego's containment in the greater dimension of the self; the latter emphasizes the rotation which also appears as a ritual circumambulation. Psychologically, it denotes concentration on and preoccupation with a centre" (CW 9ii 352).

The circumambulation Jung describes, the process of “squaring the circle” or “circling the square” has an uncertainty built into the journey: do we ever achieve individuation or is it a goal that is ever just out of reach? It is important to take the path that the mandala represents, to revolve around the center, to rotate near and around the center, and hopefully, move towards the self.. As Jung remarks “… the self is our life’s goal, for it is the completest expression of that fateful combination we call individuality…” (CW 7 404).

Works Cited

Edinger, Edward F. Ego and Archetype. Boston: Shambala Publications, 1992.

Ellenberger, Henri E. The Discovery of the Unconscious. NY: Basic Books, 1970.

Henderson, Joseph L. and Dyane N. Sherwood. Transformation of the Psyche: The Symbolic Alchemy of the Splendor Solis. NY: Brunner-Routledge, 2003.

--- The Collected Works of C. G. Jung. Trans. R. F. C. Hull. Vol. 9. part i, 2^nd edition. Princeton: Princeton UP, 1968.

--- The Collected Works of C. G. Jung. Trans. R. F. C. Hull. Vol. 6, Princeton: Princeton UP, 1971.

--- The Collected Works of C. G. Jung. Trans. R. F. C. Hull. Vol. 12. 2^nd edition, Princeton: Princeton UP, 1968.

--- The Collected Works of C. G. Jung. Trans. R. F. C. Hull. Vol. 13, Princeton: Princeton UP, 1983.

--- The Collected Works of C. G. Jung. Trans. R. F. C. Hull. Vol. 14, Princeton: Princeton UP, 1989.

--- The Collected Works of C. G. Jung. 2^nd edition.Trans. R. F. C. Hull. Vol. 7, Princeton: Princeton UP, 1966.

--- The Essential Jung: Selected Writings. ed. Anthony Storr. Princeton: Princeton UP, 1983.

--- Memories, Dreams, Reflections. Revised edition. ed. Aniela Jaffe. Trans. Richard and Clara Winston. New York: Vintage Books, 1989.

Schneider, Michael S. A Beginner’s Guide to Constructing the Universe: The

Mathematical Archetypes of Nature, Art, and Science. NY: Harper Perennial, 1995.

Pleistocene Rewilding: its not what it sounds like

2011-04-02T15:00:00.000-07:00

Or, perhaps it is what it sounds like. The idea: "reinstituting ecological and evolutionary processes that were transformed or eliminated by megafaunal extinctions" (Donlan et al 661). The main reason for wanting to "re-wild" places that lost their megafauna (what scientists like to call large animals) due to various pressures is that since the demise of these animals, the ecosystems have been out of balance (Caro 281).

North American megafauna aren't available, but several authors have suggested that other species could serve as surrogates for the extinct animals, for example, endangered Bactrian camels for the camelids that used to reside here, or Asian elephants for the North American mammoth (Donlan et al 666-671).

Why am I interested in this when I'm not an ecologist, a vertebrate biologist, or a geologist interested in the Ice Age? I grew up visiting National Parks with my family and as an adult am a member of the National Parks Foundation and the Yellowstone Association. I visited Yellowstone National Park for the first time last year, heading up there the day after my PhD commencement. A really big attraction we have for Yellowstone is the chance to see larger animals -- and we did see quite a few, mostly buffalo, elf, deer, and moose. We did not see wolves, but overhead a lot of people talking about their sightings. Even though we don't seem to understand that our very presence in the park changes the behavior of the animals, we still want to go and get a glimpse of them. Here is my photo of a grouping of buffalo in the early morning:

Growing up in the Los Angeles area brought me into contact with the La Brea Tar Pits when I was about 9 or 10. The idea that mastodons, sabertooth cats, dire wolves, ground sloths, giant short-faced bears, and many other species used to roam the LA basin was one of my early educational experiences that showed me that the earth was a lot older than I was being taught in Sunday School.

I'll also point out that Homo neandertalensis went extinct around the same time as America's megafauna (though on different continents). The science isn't clear what happened to the megafauna or to the Neandertal, though we know part of the Neandertal genome survived in modern humans, thanks to some now obvious inter-breeding. Theories regarding Pleistocene extinctions vary from climate change to a large meteor/cometary impact. Some scientists are sure that humans didn't "overkill" the megafauna to extinction, though that theory has enough traction to be part of the rationale for rewilding programs.

I really can't speak to the idea of Pleistocene rewilding from a scientific standpoint; it's not my field. From a mythologist's viewpoint, there is something romantic about recreating the past in the present, in this case trying to recreate (or just approximate) an ecological system we have never seen ("we" meaning modern humans), one that existed 13,000 or so years ago. There is a little bit of a "back to the Garden" aspect in the idea of rewilding, even when couched in technical ecological concepts. There is a hubris in the thinking that we understand a natural system so well that we can tinker with it, even with all of the careful monitoring and pilot studies outlined.

While one of the papers observes that "Humans have strong emotional and cultural relationships with large predators and herbivores that began in the Pleistocene and have reached forward to contemporary times" it goes on to mention "ancient rock art, cars, and sports teams," but this seems to me to be a pretty thin argument (Donlan et al 666). Continued loss of biodiversity is a tragedy most of us would agree impoverishes nature and would like to see reversed. That diversity may possibly be maintained in new environments, even if those species did not evolve there, but there are many uncertainties in such a rewilding program. Suggested reading is below and I do recommend spending some time with the rewilding idea and some of the counter-arguments contained.

Pleistocene Rewilding References and Links

Caro, T. "The Pleistocene Re-wilding Gambit." Trends in Ecology and Evolution 22.6 (2007): 281-283.
Donlan, J. C., et al. "Pleistocene Rewilding: An Optimistic Agenda for Twenty-First Century Conservation." The American Naturalist 168.5 (2006): 660-681.
Donlan, J. et al "Re-wilding North America." Nature 436 (2005): 913-914.
Foreman, D. Rewilding North America. Washington, DC: Island Press, 2004 (link is to purchase signed copies from author).
Martin, P. S. Twilight of the Mammoths: Ice Age Extinctions and the Rewilding of America. Berkeley and Los Angeles, CA: U of CA P, 2005.
Richmond, O.M.W., et al. "Is the Climate Right for Pleistocene Rewilding?" PLoS ONE 5.9 (2010): e12899.
Rubenstein, D. R., et al. "Pleistocene Park: Does Re-wilding North America Represent Sound Conservation for the 21st Century?" Biological Conservation 132 (2006): 232-238.
Stolzenburg, W. "Where the Wild Things Were." Conservation In Practice 7.1 (2006): 28-34.

The Rewilding Institute -- TRI has three broad goals:

1) To effectively integrate conservation biology and wildlands and wildlife conservation.
2) To provide a long-term, hopeful vision for conservation in North America.
3) To create a North American Wildlands Network Vision and a strategy to implement it.

You'll find even more resources and links at TRI's Resource page.

Pleistocene Park -- LiveScience story about a preserve in northern Siberia where a number of species have been re-introduced, and not just megafauna.

Rewilding Megafauna: Lions and Camels in North America? ActionBioscience.org's informative and well-rounded interview with Connie Barlow discussing the idea of Pleistocene rewilding (if the science papers bore you, read this instead). There are a lot of resources and outlinks on this page as well.

Macs and the Trouble with Apostrophes and Quotation Marks

2010-02-14T13:41:00.000-08:00

During the copy edit of my dissertation, I discovered a truly disturbing "feature" in Microsoft Word for Macs; none of the fonts have regular apostrophes and quotation marks. Instead of the little curly marks we are used to seeing, on a Mac, these marks are 'tick marks' (like the ones to the left there, see what I mean?).

Why is this a problem? I have a MacBookPro at home and an HP PC at work and I'd been toggling back and forth between both computers as I wrote my dissertation. This has led to a mixture of tick marks and quotations marks throughout my dissertation, much to the proof reader's annoyance. I hadn't actually noticed the difference. However, a cheat sheet for you Mac users out there is below:

True right quotation mark ( ” ): Shift + Option + [
True left quotation mark ( “ ): Option + [
True apostrophe ( ’ ): Shift + Option + ]
True reverse apostrophe ( ‘ ): Option + ]

Problem solved. Now, on to other issues.

Human Genre Project

2009-12-17T04:44:00.000-08:00

Combine all 23 pairs of human chromosomes with short writings and poetry and what do you get? The Human Genre Project. The website is a simple and elegant page showing all of the chromosomes in order. Hover your mouse over a chromosome and a list of titles appears below. Click on a chromosome and the list becomes static and easier to click through.

I've not read all of the pieces and new ones are being added all the time. One piece I really like is "Meet Me at the Speed of Light" by Laura-Grey Street over on Chromosome 1. On Chromosome 17 you'll find a short but tough essay on breast cancer (BRCA1 is located on Chromosome 17) called "Knowing Who I Am" by Heather Fineman.

The Human Genre Project is taking submissions. Check out the "Contribute" link (you thought it was about monetary donations, didn't you?).

The Human Genre Project is funded through the ESRC Genomics Policy Research Forum in the UK, an organization that explores social issues and genomics.

December 9th @5PM Dissertation Defense

2009-11-21T14:22:00.000-08:00

Because this is being held at the Lambert campus, attendees must take a shuttle from the Best Western in Carpinteria (it's OK to park in the BW lot; meet the shuttle in front of the hotel).

Pacifica’s Shuttle Service
The reception desk at the Best Western will call Pacifica’s shuttle for you, or you may call the shuttle directly. The phone number is 805.896.1887 or 805.896.1888. Although it may not take more than 15 minutes, please allow one-half hour transportation time to the Lambert Campus once you reach the Best Western.

Clogston, C. (2009). Romancing the Gene: The Human Genome as Our 5 Million-Year-Old Story (Doctoral dissertation, Pacifica Graduate Institute, 2009).

ABSTRACT

One of the most heroic science projects undertaken in the last century is the massive and institutionally coordinated DNA sequencing of the entire human genome. Evangelically promoted by scientists to the general public, the Human Genome Project (HGP) developed a messianic veneer, promising molecular salvation for incurable diseases and nearly-divine control of our biological destiny. While the Herculean task of sequencing the entire human genome seems to literalize human condition to a set of DNA base-pairs, the meaning of the human genome has a mythic dimension: to definitively know the human genome is to ultimately know ourselves.

This dissertation examines the many metaphors used to promote and explain the HGP to various audiences. Scientists coined some of the most popular genome metaphors used to communicate the HGP’s value to governments, scientific organizations, and to the public. Many genome metaphors used in public discourse reveals an unconscious religious or mythological impulse: the Holy Grail of Molecular Biology, the Book of Life, a Form of Secular Soul, the Blueprint of Humanity, and a Human Map. However, not all human genome metaphors are equal; some are created with a particular social or policy agenda in mind.

This work considers the different ways the human genome is changing the way we are thinking about ourselves, as a species, as groups, and as individuals. Comparing our genomes to each other’s, to that of the chimpanzee and to Neanderthals, the human genome is reorienting humanity as a biological species. The HGP occurs during a time in the United States when the role of religion in society is once again, being hotly debated.

Looking at how the HGP has inspired a number of artists who use portions of human genome DNA sequences as the basic for creative works, it is clear that the human genome is more than just a DNA sequence. Considering the artistic forms that have emerged from the HGP, and how the Project is affecting our psychological and mythological processes, both personally and culturally, the human genome is a touchstone for an emerging creation myth, a new genomythology.

Ardi! Ardi! Ardi! Ardipithecus ramidus finally revealed

2009-10-04T09:40:00.000-07:00

You would have to be away from all electronic and print sources of news to miss the furor about Ardipithecus ramidus this week. The press releases and conferences hit the news cycle on Thursday followed by the publication of eleven (!) Ar. ramidus related papers in the weekly journal Science.

So what's the deal with Ardi? She is a partial skeleton of a hominid species ancestral to us and older than Lucy, the famous Australopithecus afarensis partial skeleton by a over a million years. Tim White and his team discovered "Ardi" in 1992, finding a molar and a lower jaw, which they published in 1994. Working on this find and the area where the partial skeleton was found in Aramis, Ethiopia, it took 15 years to complete. Instead of publishing a stream of papers as discoveries were made, White made the decision to hold off until a complete story could be told.

The wait has been worth it, considering the amount of information that the extended international team has been able to provide. Several ideas about human evolution will have to be reconsidered based on this species' attributes.

Ardipithecus ramidus lived in the trees but was also "intermediately" bipedal, based on analysis of pelvis, spine, legs, and feet. For the first time, a hominid species was found with a large opposable big toe, allowing for tree limb grasping. A theory about the development of bipedialism describes the needed walking trait in an African savannah environment, but Ardi walked even though she was also arboreal, living in a woodland environment.

Yet, Ardipithecus ramidus did not knuckle-walk, like chimpanzees or gorillas, the wrist and hand bone structure is not strong enough to support that kind of movement. "Ardi" is not chimpanzee-like, which is how most theorists described our earliest hominid ancestor.

This is the find of a generation and I'm sure there will be much more analysis and commentary in the years to come.

Great interactive site for general audiences can be found over at the Discovery Channel, which is a companion to the TV special.

Science has the scientific papers and news articles available with a free registration -- I recommend doing this because you can read the original papers yourself. There is also a good 10-minute video interviewing Tim White and explaining some of the significant features of "Ardi." I also highly recommend science-writer Ann Gibbons' NewsFocus article here entitled "A New Kind of Ancestor: Ardipithecus Unveiled."

I have one complaint about Science's handling of the general interest articles -- the introductory article prefacing the eleven scientific articles is entitled "Light on the Origin of Man" written by Brooks Hanson. The use of such sexist language in a major science journal in the year 2009 (and introducing such a major scientific discovery) is unbelievably crass. The language choice may have been unconscious, but it's stupid. I expect dumb headlines like the ones from the Los Angeles Times and the New York Times and we got them ("New Discovery Turns Evolution on its Head") at first, and then they were changed soon after. But Science? Ironically, the partial skeleton described (like "Lucy" before her) is female.

Milestones: Dissertation completed and accepted by my committee

2009-09-27T18:35:00.000-07:00

After 2 years of continuous researching and writing, I'm happy to say that I've submitted my dissertation to my committee and it has been accepted by all of them. The end process happened rather quickly; I submitted my final version on Friday, Sept 11th, and by the following Friday, I had all of the approved forms signed. Whew!

Next (and final) milestone: my dissertation defense. It's scheduled for Wed. Dec. 9th at 5PM at the Ladera campus of Pacifica Graduate Institute. Information for attending and an abstract will be posted here later.

Lev Grossman's "The Magician's" mini-review

2009-08-26T19:42:00.000-07:00

Just finished Lev Grossman's absorbing new novel The Magicians. I don't want to be too revealing about the storyline, but I found the story to be an homage to a number of well-known fantasy stories: the Chronicles of Narnia and Harry Potter series are the most obvious. But I detect some LOTR motifs and a few from the Arthurian legends. Quests abound, but this is not a kid's story; it's rather adult (yes I've read the HP books and know how dark they get as they progress). But dark is different from adult content.

The characters are young adults with all the issues that the age group experiences, but add some very intense magic, angst about love and sex, battling an odd assortment of creatures, and a really big theme of loss -- I found it an intense read. Not a light story but rather melancholy throughout, with a protagonist who is sometimes very hard to relate to or like. I need to re-read it again at a later date, but at the moment I'm not convinced by the ending, which seemed both too pat and improbable given the previous set of events in the story.

For readers who enjoy contemporary mythological fiction, particularly the works of Charles deLint, the story will resonate. deLint has written a number of works centering on managing tremendous loss, set in a mythologically-active, magical landscape. But I wonder if people will be distracted by the obvious HP and Narnia motifs in The Magicians. Read it and ping me about your observations.

Apollo 11 Anniversary -- 40 years since first Moon walk

2009-07-19T09:12:00.000-07:00

I was 11 years old when the Apollo 11 mission headed towards the Moon. I recall that the night of July 20, 1969 was warm in Los Angeles when my Dad called us in from outside (we were allowed to stay outside later than normal during the summer -- plus, it was hot and we had no air-conditioning in the house) to watch the TV broadcast from the Moon. I couldn't quite make out what I was seeing on the TV screen -- the contrast on the image was high. So, it took me a little while to recognize the outline of Neil Armstrong's suited body carrying the boxy EVA pack on his back.

People were on the Moon. Walking on the Moon. Not just taking pictures of it, actually walking on the Moon. This was so exciting to me and the event is one of those signposts that stand out in my memory. I often try to reconstruct my path to becoming a scientist and watching the first Moon walk is one of those moments, one of those points along the way. Mythologist Joseph Campbell wrote extensively about the space program, in particular the Apollo 8 mission, when sent back the first photos of the Earth hanging in space (the Big Blue Marble). Campbell felt that "Earthrise" was the beginning of a new myth.

Commenting on the 10th anniversary of the first Moon walk, Campbell reflects, "Men stood on the moon and looked back -- and by television we were able to look back with them -- to see earthrise. That is the symbol that enabled us to feel the truth of the discovery Copernicus made four and a quarter centuries ago."

(1979 interview with the NY Times, a copy of which is available here).

Campbell wrote quite a bit about the mythology of space exploration. Here is one more example: "The knowledge of space is the knowledge of our lives. We're born from space. It was from space that the Big Bang came that sent forth galaxies, and out of the galaxies, solar systems. The planet we are on is a little pebble in one of these things, and we have grown out of the earth of this pebble. This is the fantastic mythology that's waiting for somebody to write poems about." (Myths of Light xix).

You can watch a "replay" of the Apollo 11 mission on Twitter @ReliveApollo11. Nasa has paid to have TV images from the Moon restored (the original tapes were erased and reused, so the only images are from contemporary TV broadcasts, which varied greatly in quality. You can watch the restored footage here. Explore the surface of the Moon on Google.

I don't quite feel 11 again, mostly because I think the original sense of awe is difficult to revisit, especially 40 years later. But, I feel some measure of that wonder when I think about the fact that humans once walked, jumped, skipped, golfed, and drove on the lunar surface. Perhaps it will happen again and perhaps it will be as a waystation on the way to the next planet in the series, Mars. Then the footstep below would be in red Martian regolith.

That would be amazing.

Rita Levi Montalcini Turns 100 April 22

2009-04-19T07:23:00.000-07:00

I saw this news blip on Yahoo news and had to post it. Levi Montalcini's accomplishments began under the restrictions of Mussolini's ideology. As a Jew, Levi Montalcini could not practice medicine (she had just graduated from medical school) or work at the university. Undaunted, she created a home laboratory and continued her work in basic neurobiology. She moved to the United States after the war, and there she discovered what is now known as nerve growth factor (NGF), a small protein that stimulates the growth of nerve cells.

Nature has this extended profile "One Hundred Years of Rita" and describes her as the first Nobel Prize scientist to reach this life milestone. Great article.

The Nobel Prize site has a number of Levi Montalcini resources, including an autobiography, her Nobel lecture, and the original press release in 1986 announcing her prize, which was shared with Stanley Cohen, the discoverer of epidermal growth factor (EGF).

Photo from Nobel Prize site (1986).

(AP Photo/Riccardo De Luca) 2009

In the Dissertation Zone

2009-04-15T04:29:00.000-07:00

The Dissertation Zone: where those of us trying to finish sometimes get lost. That's where I am right now. Not lost, really, but not doing a lot other than working on my dissertation. Posting is necessarily sparse during this time. Perhaps later, when I emerge.....

In the meantime, here are a few things to keep you occupied:

Cloning animals is still popular -- 1st camel cloned reported here.

Want to peruse publications from the Human Genome Project?

All of Darwin's works are being made available online. I really like reading his correspondence.

Consider the International Genetically Engineered Machines competition.

Listen to some of Todd Barton's genomic music. I like "antibody" and trypsin."

Tonight: The Academy Awards

2009-02-22T08:42:00.000-08:00

I'm digressing from my usual Myth and Science analysis to mention one of the major popular culture events that happens this time of year. In an annual gathering at my house, a handful of our friends get together to watch the Academy Awards broadcast. What can I say? I live near Los Angeles, which abuts Hollywood -- this is a Company Town. And a few of my friends work in The Business, which I've found over the years is pretty normal here.

We watch films for entertainment, for escapism, and often mistakenly, for education (can you really learn about history in a Hollywood film? This is a rhetorical question and you are not required to answer). But films have another function -- modern film making is a form of mythopoesis, creating myths. Not all "movies" have a mythopoetic element, but some do, and you know the ones: they stick with you over time, you analyze and re-analyze portions of it, and you have memorized large chunks of dialogue.

Pacifica Professor Glen Slater relates, in defining the difference between "movies" and "films" that:

"Film demands that its visual presentation serves hidden depth -- shaded, secreted, semi-conscious or unconscious elements, the presence of which is first felt or intuited but may enter our awareness more fully only upon reflection. Depth makes meaning and brings poignancy. It results from patterned complexity and backward gazes into cultural history, ancestry, and personal pasts. Depth also occurs in the basic movement of our mind from the simple to the nuanced and subtle. If the cinematic arts have any fundamental characteristic, it is the call to create depth. This call makes film and psyche natural kin." ("Archetypal Perspective and American Film" pg. 1-2. Spring Journal 73 Cinema and Psyche).

I was thinking about Glen's distinction between "movie" and "film" as I pondered my own Oscar ballot for tonight's gathering. Which of the 5 nominees for Best Picture are "movies" and which are "films?" Which of the 5 stayed in my head the longest, was discussed the most, analyzed several times over several days, and has left lasting images in my mind's eye. Here they are, in order:

The Reader
The Curious Case of Benjamin Button
Milk
Frost/Nixon
Slumdog Millionaire

Each of the titles above is linked to the respective official site. I am reasonably sure that my list of nominees is not going to reflect the outcome of the awards tonight. There are also obvious mythic elements and conflicts in each of these 5 that are still operative in the American collective psyche today:

The Reader -- the Holocaust, personal responsibility, racism
Benjamin Button -- racism, ageism, the cult of youth
Milk -- homophobia, sexism, cultural exile
Frost/Nixon -- the Vietnam War, political corruption, power
Slumdog Millionaire -- racism, classism, materialism, violence against children

One thing that all of these have in common is that all of the main characters in these 5 works are trapped in a form of ghetto. Your opinion and your mileage may vary. Enjoy the broadcast tonight.

Darwin Day!

2009-02-12T08:07:00.000-08:00

I'm currently spending all of my free time working on my doctoral dissertation but I wanted to celebrate Darwin Day. Today is the 200th annivesary of the Charles Darwin's birth and you will no doubt see a lot about this in the media. If you would like to look at the many Darwin Day activities going on all over the world, and perhaps find one in your area to attend, a great place to start is here. If you haven't read any of Darwin's works, today is a very good day to begin, and you can do it for free online.

For now, I will leave you with the last paragraph of Darwin's On the Origin of Species, also known as the "Tangled Bank" passage:

"It is interesting to contemplate a tangled bank, clothed with many plants of many kinds, with birds singing on the bushes, with various insects flitting about, and with worms crawling through the damp earth, and to reflect that these elaborately constructed forms, so different from each other, and dependent upon each other in so complex a manner, have all been produced by laws acting around us. These laws, taken in the largest sense, being Growth with Reproduction; Inheritance which is almost implied by reproduction; Variability from the indirect and direct action of the conditions of life, and from use and disuse: a Ratio of Increase so high as to lead to a Struggle for Life, and as a consequence to Natural Selection, entailing Divergence of Character and the Extinction of less-improved forms. Thus, from the war of nature, from famine and death, the most exalted object which we are capable of conceiving, namely, the production of the higher animals, directly follows. There is grandeur in this view of life, with its several powers, having been originally breathed by the Creator into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved."

Darwin, C. R. 1872. The origin of species by means of natural selection, or the preservation of favoured races in the struggle for life. London: John Murray. 6th edition; with additions and corrections.

Rethinking the Wrinkling: Key Genes Cause Aging

2008-09-18T07:29:00.001-07:00

All of those "anti-oxidants" we have been striving to add to our diets may have no effect at all.

clipped from www.sciam.com

It afflicts every creature on this planet, and everyone dreams of an antidote. But even after decades of research, aging largely remains a mystery. Now new research findings suggest there is a good reason for this impasse: scientists may have been thinking about the causes of aging all wrong. Instead of being the result of an accumulation of genetic and cellular damage, new evidence suggests that aging may occur when genetic programs for development go awry.

The idea that stress and reactive forms of oxygen—“free radicals” that are the normal by-products of metabolism—cause aging has dominated the field for 50 years. Studies on the worm Caenorhabditis elegans have shown that reducing exposure to reactive oxygen species increases life span, and worms that have been bred to live longer are also more resistant to stress. But few studies have definitively linked oxidative damage to altered cellular function.

92% of Americans believe in God or a universal spirit, Pew survey finds

2008-06-23T15:03:00.001-07:00

Here is the link to the Pew Study: U.S. Religious Landscape Survey.

clipped from www.latimes.com

Americans overwhelmingly believe in God and consider religion an important part of their lives, even as many shun weekly worship services, according to a national survey released today that also found great diversity in religious beliefs and practices.

Ninety-two percent of those interviewed for the U.S. Religious Landscape Survey said they believe in the existence of God or a universal spirit, and 58% said they pray privately every day. But California, like other states along the country's two coasts, resisted the prevailing national tendencies.

Californians are less likely than other Americans to consider religion "very important" in their lives or to be "absolutely certain" in their belief in God.

Californians pray less than others in many parts of the country. They are less inclined to take the word of God literally. And they are ready to embrace "more than one true way" of interpreting their religious teachings.

California Challenges Genetic Testing Firms' Claims

2008-06-17T06:16:00.001-07:00

The state had been investigating consumer complaints for a while. GenomeWeb News notes that California is following a similar action by New York, Steve Murphy at Gene Sherpas has an acerbic take on the situation which he followed up with a detailed and reasoned post. I went to the websites of both 23andMe and Navigenics, two companies that have reportedly received letters, and couldn't find anything that tells Californian consumers that they cannot use their services without a doctor's prescription.

clipped from www.latimes.com

SAN FRANCISCO --
California health regulators have dealt a blow to direct-to-consumer genetic testing start-ups by demanding that 13 companies halt sales in the state until they prove they have met quality and reliability standards.

The Department of Public Health sent the cease-and-desist letters last week, after an investigation spurred by consumer complaints about the tests' accuracy and costs, a department spokeswoman said Monday.

The department said it would not identify the companies involved until it confirmed they had received the letters. It said they all advertised on the Internet. Two of the best-known companies to offer consumer genetic tests, Navigenics Inc. and 23andMe Inc., both confirmed receiving the letters.

Opponents of Evolution Adopting a New Strategy

2008-06-04T06:43:00.001-07:00

See the post below this one for a look at a recently published and lucid evaluation of the state of high-school biology education in the United States.

clipped from www.nytimes.com

DALLAS — Opponents of teaching evolution, in a natural selection of sorts, have gradually shed those strategies that have not survived the courts. Over the last decade, creationism has given rise to “creation science,” which became “intelligent design,” which in 2005 was banned from the public school curriculum in Pennsylvania by a federal judge.

Now a battle looms in Texas over science textbooks that teach evolution, and the wrestle for control seizes on three words. None of them are “creationism” or “intelligent design” or even “creator.”
The words are “strengths and weaknesses.”
Starting this summer, the state education board will determine the curriculum for the next decade and decide whether the “strengths and weaknesses” of evolution should be taught. The benign-sounding phrase, some argue, is a reasonable effort at balance. But critics say it is a new strategy taking shape across the nation to undermine the teaching of evolution, a way for students to hear religious objections under the heading of scientific discourse.
Already, legislators in a half-dozen states — Alabama, Florida, Louisiana, Michigan, Missouri and South Carolina — have tried to require that classrooms be open to “views about the scientific strengths and weaknesses of Darwinian theory,” according to a petition from the Discovery Institute, the Seattle-based strategic center of the intelligent design movement.

Evolution in American High Schools

2008-06-04T05:04:00.000-07:00

The new issue of PLOS Biology is online. For those of you not familiar with the PLOS journals, the Public Library of Science is a collection of peer-reviewed scientific journals that are freely available online. You can browse the list here.

In the new June 2008 issue is an article describing the current state of teaching high school biology in the U.S. As many of you are already aware, American high-school biology classes, are the crucible in which the current conflict between science and religion is most importantly being waged. While it is illegal to teach creationism or it's renamed twin, intelligent design, in public schools, this has actually not stopped the practice. The article in PLOS Biology provides some interesting data as to why:

About 1 in 6 High-school Biology teachers are young-Earth creationists. The article also shows in other data that some teachers feel community pressure to either gloss over or skip the concept of evolution entirely. 25% of teachers surveyed included creationism or intelligent design in their course curriculum and "nearly half agreed or strongly agreed that they teach creationism as a “valid scientific alternative to Darwinian explanations for the origin of species.”

Regardless of the outcome of high profile cases, such as the Kitzmiller decision, the message is not getting to teachers, or they are just ignoring it, "These findings strongly suggest that victory in the courts is not enough for the scientific community to ensure that evolution is included in high school science courses."

And it's clear that some teachers have had no education in evolutionary biology (it's not clear from the article whether any of the teachers surveyed would welcome one). The recommendation of the paper's authors is an educational standard for biology teachers that includes evolutionary biology, "Our study suggests that requiring all teachers to complete a course in evolutionary biology would have a substantial impact on the emphasis on evolution and its centrality in high school biology courses."

One thing is clear, bringing a personal belief in young-Earth creationism to the biology classroom, to mix an ancient mythology with modern science, is not a design of any intelligence that will increase American students' science literacy. Next year is a double Darwin anniversary: the 200th year of his birth and the 150th year of the publication of The Origin of the Species. It should be the perfect opportunity for high-school teachers to engage their students in the history of evolutionary theory.

Want to take bets that, in the U.S, it won't be?

Instant update: Only 1 hour after posting this, I found a related story at the NY Times.

Einstein Letter on God Sells for $404K at Auction

2008-05-19T05:30:00.001-07:00

How's your German?

The media loves to invoke "the culture war" between science and religion, which in this country means evolutionary biology and Christianity. Neither is mentioned in this letter.

The article mentions that Einstein said he fell out of his religion at age 12 and "never looked back" but he still seem to experience the numinous: "But he never lost his religious feeling about the apparent order of the universe or his intuitive connection with its mystery, which he savored. “The most incomprehensible thing about the universe is its comprehensibility,” he once said."

And this statement is even clearer: “If something is in me that can be called religious,” he wrote in another letter, in 1954, “then it is the unbounded admiration for the structure of the world so far as science can reveal it.”

clipped from www.nytimes.com

From the grave, Albert Einstein poured gasoline on the culture wars between science and religion this week.

A letter the physicist wrote in 1954 to the philosopher Eric Gutkind, in which he described the Bible as “pretty childish” and scoffed at the notion that the Jews could be a “chosen people,” sold for $404,000 at an auction in London. That was 25 times the presale estimate.
The Associated Press quoted Rupert Powell, the managing director of Bloomsbury Auctions, as describing the unidentified buyer as having “a passion for theoretical physics and all that that entails.” Among the unsuccessful bidders, according to The Guardian newspaper, was Oxford evolutionary biologist Richard Dawkins, an outspoken atheist.

NYT Book Review: Blood Matters: From Inherited Illness to Designer Babies, How the World and I Found Ourselves in the Future of the Gene

2008-05-11T20:06:00.001-07:00

Masha Gessen's new book is part memoir and part medical investigative thriller -- by chronicling her own story, Gessen lets us imagine what information obtained from a genetic screen can do to us psychologically, emotionally, and in some cases, physically, once we have that knowledge.

clipped from www.nytimes.com

One of the wonders of the genome is how it enables us to time-travel, both backward and forward. Scribbled within it are clues to our ancestry, which can give us an emboldening sense of continuity, coherence, place — how marvelous to imagine ourselves the sons of Levi, the daughters of African queens! But scrawled within it, too, are clues about our future, which can be downright terrifying. Rather than expand our sense of possibilities, they foreshorten them. There are dread mutations slumbering in our cells. From our genes, we learn how we may die.

Eleven years after her mother died of breast cancer, Masha Gessen, a Moscow-based journalist and the author of the fine family memoir “Ester and Ruzya: How My Grandmothers Survived Hitler’s War and Stalin’s Peace,” tested positive for a BRCA1 mutation, which disproportionately afflicts Ashkenazi Jews and significantly increases the risk of dying young.

Happy DNA Day!

2008-04-25T05:21:00.000-07:00

From the official website: " National DNA Day is a unique day when students, teachers and the public can learn more about genetics and genomics! It was created to commemorate the completion of the Human Genome Project in April 2003, and the discovery of DNA's double helix."

This is a great website to learn more about the human genome project -- the site has webcasts, presentations, and educational resources and links to even more information.

Senate passes bill baning genetic discrimination

2008-04-25T05:11:00.001-07:00

Finally, it looks like GINA will become law. Why is this important? In this new age of personal genomics, it's incredibly important that individuals are not discriminated against based on their DNA. It might be personally informative to go to DNA Direct and buy one of their direct-to-consumer disease tests, but what would happen to you if your insurance company got a hold of the results? Or your employer?

clipped from www.latimes.com

WASHINGTON --
The vast promise of an era of personalized medicine based on genetic testing long has been haunted by a disturbing possibility: The same data that could alert people to serious medical problems might be used to deny them jobs or insurance coverage.

But Thursday, the Senate voted 95 to 0 to outlaw such discrimination, with the House expected to add its approval quickly.

The bill, which President Bush has agreed to sign, does more than protect those who undergo genetic testing: It marks a significant milestone in the effort to develop a 21st century architecture of laws to govern the revolutionary changes sweeping science and medicine.

"It's the first civil rights bill of the new century of life sciences," Sen. Edward M. Kennedy (D-Mass.) said. "We made sure today that our laws reflect the [scientific] advances we are making."

America's Favorite Books is a Mythological Text: The Bible

2008-04-16T19:14:00.001-07:00

Somehow I'm not surprised by this outcome. But one really has to wonder if the people who chose the Bible has read it -- most people haven't. So, could it be the most favorite book American's haven't actually read?

clipped from news.yahoo.com

NEW YORK (Reuters Life!) - When it comes to literary pursuits in the United States most people agree on at least one thing -- the most popular book is the Bible, according to a new survey.

It came in first in a Harris Poll of nearly 2,513 adults but the second choice in the survey was not as clear cut.

"While the Bible is number one among each of the different demographic groups, there is a large difference in the number two favorite book," Harris said in a statement announcing the results.

Men chose J.R.R. Tolkien's "The Lord of the Rings" and women selected Margaret Mitchell's "Gone With the Wind" as their second-favorite book, according to the online poll.

But the second choice for 18- to 31-year-olds was J.K. Rowling's Harry Potter series, while 32- to 43-year-olds named Stephen King's "The Stand" and Dan Brown's "Angels and Demons."

Myth and Violence Conference

2008-04-06T16:53:00.000-07:00

Anne and I spent Friday and Saturday at the Myth and Violence Conference in Santa Barbara. This is the annual Myth conference organized by The Foundation of Mythological Studies and co-sponsored by Pacifica Graduate Institute and Spring Journal. The conference does continue through today, but we both needed today off as we'd already taken in a lot in the first two days.

If you don't see the connection between myth and violence, consider that most of the world's conflicts right now have a religious basis, which means people are at war over their mythologies.

Highlights were Chris Hedges, who spoke intelligently and eloquently about his experiences as a war correspondent for the NY Times, spending 20 years reporting armed conflict around the globe. Having an MDiv from Harvard Divinity School (though never ordained) has also given him the perspective of a religion scholar and his two latest works, American Fascists and I Don't Believe in Atheists has earned him the sharp enmity of both the New Religious Right and the New Atheists (he writes that both groups have developed a fascist ideology that threatens American democracy). It's important to note that the New Religious Right is a Christian group that the U.S. hasn't seen before -- they aren't the current Evangelicals or Fundamentalists we are used to, these are Dominionists, who are working for one goal: a completely Christian Government in the US (the Bible would be the basis of our legal system, etc....). Scary stuff.

Sarah Hussain, a Pakastani-American poet read some of her works. Very powerful and moving. She has also edited an anthology called Voices of Resistance: Muslim Women on War, Faith and Sexuality.

Psychoanalyst and religions scholar Lionel Corbett talked about the spiritual roots of war. He also psychoanalyzed GW Bush for a bit, noting that with only a couple of exceptions, all American Presidents had terrible childhoods (fearful, abusive parent, abandoned, etc...). Corbett suggested that a President who is so willing to go to war is enacting a revenge scenario to compensate for such a childhood.

Psychoanalyst and Pacifica faculty member Aaron Kipnis talked about the Psychopathic Nation, describing symptoms that sound very much like the current state of the U.S. He described six stages to a psychopathic society:

1. There is a positive regard for each others' differences.
2. An "other" is created. Differences are articulated and highlighted.
3. The dominant view thinks the "other" might be dangerous (pathologize the "other").
4. Dominant group is afraid of minority and isolates them. Creates gulags.
5. Bridges are destroyed (between the groups).
6. The holocaust stage -- penetrates the gulags and genocide takes place.

We were left to contemplate at what stage the U.S. has achieved so far.

We both attended sessions on juvenile offenders, violence in American society, violence in Japanese society, prison issues, the war in Iraq, America's Titanic Complex, the Jonesboro, Arkansas school shooting (1995), experiences in Nazi-occupied Amsterdam, scapegoating and American violence, psychopathy and training of American soldiers, and non-violent struggle.

There was a lot to consider and think about, taking today off seemed prudent.

Vatican updates list of sins

2008-03-11T05:37:00.001-07:00

This is interesting, the Vatican is literally trying to drag biotechnology into it's mythic shadow. This has actually been going on since the first recombinant DNA experiments were done a few decades ago (the potential for human cloning, using fetal tissue to establish stem cell lines, for example).

"Genetic manipulation" has it's own mythic shadow to deal with than trying to add it the one distributed by the Vatican's network. In biology, this process of engulfment is known as phagocytosis.

clipped from news.yahoo.com

VATICAN CITY - In olden days, the deadly sins included lust, gluttony and greed. Now, the Catholic Church says pollution, mind-damaging drugs and genetic experiments are on its updated thou-shalt-not list. Also receiving fresh attention by the Vatican was social injustice, along the lines of the age-old maxim: "The rich get richer while the poor get poorer."

In the Vatican's latest update on how God's law is being violated in today's world, Monsignor Gianfranco Girotti, the head of the Apostolic Penitentiary, was asked by the Vatican newspaper L'Osservatore Romano what, in his opinion, are the "new sins."

He cited "violations of the basic rights of human nature" through genetic manipulation, drugs that "weaken the mind and cloud intelligence," and the imbalance between the rich and the poor.

Too Bad Joe Campbell Never Got to See This

2008-03-05T05:26:00.001-08:00

Joseph Campbell saw the first photo taken by Apollo 8 astronauts of the earth in space (Earthrise) as an image of a newly-emerging mythology. Here is a photo that could only have been taken from much further away, Mars. NASA released an image of the earth and the moon in one picture, as seen from Mars. It was taken by the HiRISE Instrument on October 3rd, 2007.

This is an image of Earth and the Moon, acquired at 5:20 a.m. MST on 3 October 2007, at a range of 142 million kilometers, which gives the HiRISE image a scale of 142 km/pixel and an Earth diameter of about 90 pixels and a Moon diameter of 24 pixels. The phase angle is 98 degrees, which means that less than half of the disks of the Earth and Moon have direct illumination. We could image Earth/Moon at full disk illumination only when they are on the opposite side of the sun from Mars, but then the range would be much greater and the image would show less detail.
On the Earth image we can make out the west coast outline of South America at lower right, although the clouds are the dominant features. These clouds are so bright, compared with the Moon, that they are saturated in the HiRISE images. In fact, the RED-filter image was almost completely saturated, the blue-green image had significant saturation, and the brightest clouds were saturated in the IR image. This color image required a fair amount of processing to make a nice-looking release.

Beautiful!

Synthetic Genome: Signed Sealed, Decoded

2008-01-29T05:17:00.001-08:00

The NY Times writer fell for the "decoded" trope as most non-scientists do: the genome was sequenced, not decoded. The genetic "code" was "decoded" in the 1960s and there is no longer a "code" to "break."

However, this achievement is a benchmark and seems to point the way for truly artificial life built from the bottom up.

clipped from www.nytimes.com

You were expecting poetry, perhaps? The secret messages hidden in J. Craig Venter’s synthetic bacterial genome have now been revealed. They are Dr. Venter’s name, and that of his research institute and co-workers.

Dr. Venter announced last week in the journal Science that his team had become the first to synthesize the complete DNA of a bacterium. He revealed that the genome had five “watermarks,” sequences of genetic code that would spell words using the letters for the amino acids that would be produced by the DNA.
Wired Science reported Monday that it had ferreted out the messages, with help from government scientists. One watermark said “VenterInstitvte,” using the unusual spelling because there is no amino acid represented by the letter “u.”
The other messages were CraigVenter, HamSmith, GlassandClyde and CindiandClyde for his co-authors Hamilton O. Smith, Clyde A. Hutchison III, John I. Glass and Cynthia Andrews-Pfannkoch. A Venter spokeswoman confirmed them.
In 2003, scientists from Icon Genetics, a German biotechnology company, engineered the plant Arabidopsis thaliana to contain a line from Virgil’s “Georgics,” with the meaning “Neither can every soil bear every fruit.”

International Consortium Announces the 1000 Genomes Project

2008-01-22T15:12:00.001-08:00

Major sequencing effort will produce the most detailed map of human genetic variation to support disease studies.

clipped from www.genome.gov

Bethesda, Md., Tues., Jan.22, 2008 — An international research consortium today announced the 1000 Genomes Project, an ambitious effort that will involve sequencing the genomes of at least a thousand people from around the world to create the most detailed and medically useful picture to date of human genetic variation. The project will receive major support from the Wellcome Trust Sanger Institute in Hinxton, England, the Beijing Genomics Institute, Shenzhen (BGI Shenzhen) in China and the National Human Genome Research Institute (NHGRI), part of the National Institutes of Health (NIH).

Drawing on the expertise of multidisciplinary research teams, the 1000 Genomes Project will develop a new map of the human genome that will provide a view of biomedically relevant DNA variations at a resolution unmatched by current resources. As with other major human genome reference projects, data from the 1000 Genomes Project will be made swiftly available to the worldwide scientific community through freely accessible public databases.

"The 1000 Genomes Project will examine the human genome at a level of detail that no one has done before," said Richard Durbin, Ph.D., of the Wellcome Trust Sanger Institute, who is co-chair of the consortium. "Such a project would have been unthinkable only two years ago. Today, thanks to amazing strides in sequencing technology, bioinformatics and population genomics, it is now within our grasp. So we are moving forward to build a tool that will greatly expand and further accelerate efforts to find more of the genetic factors involved in human health and disease."

Pacifica Myth Classmate Book Just Published

2008-01-11T06:02:00.001-08:00

Congratulations to Annamaria Hemingway on her just-published book, Practicing Conscious Living and Dying: Stories of the Eternal Continuum of Consciousness. Annamaria is continuing her studies in near-death experiences for her dissertation. During our Dissertation Topic Formulation class (I was fortunate to be in the same group with Annamaria) she talked extensively about her research and her writings in this area, and the stories she has collected are compelling. NDEs are transformative, life-altering, and mythic in dimension, according to her research and I can't wait to buy a copy of her book.

Below is the flyer for an upcoming local book signing -- I will definitely be there. Also check out her website for more information.

FDA to Back Food from Cloned Animals

2008-01-05T07:13:00.001-08:00

Now, if they would just screen more animals then they currently do for BSE. Surveillance in that arena could be improved significantly.

clipped from www.washingtonpost.com

Having completed a years-long scientific review, the Food and Drug Administration is set to announce as early as next week that meat and milk from cloned farm animals and their offspring can start making their way toward supermarket shelves, sources in contact with the agency said yesterday.

The decision would be a notable act of defiance against Congress, which last month passed appropriations legislation recommending that any such approval be delayed pending further studies. Moreover, the Senate version of the Farm bill, yet to be reconciled with the House version, contains stronger, binding language that would block FDA action on cloned food, probably for years.

With a conference committee poised to finalize the farm bill in the next few weeks, that left the FDA a potentially narrow time frame within which to act if it wanted to settle the issue in sync with America's major meat-trading partners.

The DNA Shoah Project

2008-01-04T12:54:00.001-08:00

We've been seeing genealogic uses for DNA repositories. Using the same strategies for identifying the remains of 9/11 victims, this organization wants to reunite families that were separated during WWII.

Uses for the DNA Database:
* Assist in the identification of Holocaust victims whose remains continue to surface
* Aid in the future identification of mass-graves projects
* Assist global orphan-placement organizations to identify siblings and close relatives separated by World War II
* With signed permission, DNA data can be used to help in genetic disease research

clipped from www.dnashoah.org

The DNA Shoah Project is building a genetic database of people who lost family during the Holocaust. This database will help reunite families torn apart during wartime and aid in identifying victims of the Nazi regime who remain buried anonymously throughout Europe.
Today, as European countries expand their infrastructure, the remains of Holocaust victims continue to surface. In many cases, DNA can be readily obtained from victims' bones but, until this project, there has been no means or protocol for their identification.
DNA is the genetic material in our cells that makes us each unique. It may be obtained from living relatives with a gentle swab of the inner cheek. Ideal candidates for this project are pre-war immigrants, survivors, second- and third-generation family members. Participants will become part of the first-ever attempt to build a repository of genetic information for victims of the Holocaust.

Survey: 61 Percent Agree with Evolution

2008-01-02T20:50:00.001-08:00

clipped from www.livescience.com

Americans would rather hear about evolution from scientists than from judges or celebrities, according to a new survey that finds a majority agree that evolution is at work among living things.

A coalition of 17 organizations reacted today to the survey by calling on the scientific community to become more involved in promoting evolution and other aspects of science education.

The coalition, including the National Academy of Sciences, the American Institute of Physics and the National Science Teachers Association, released this statement:

"The introduction of 'non-science,' such as creationism and intelligent design, into science education will undermine the fundamentals of science education. Some of these fundamentals include using the scientific method, understanding how to reach scientific consensus, and distinguishing between scientific and nonscientific explanations of natural phenomena."

The Invisible Ingredient in Every Kitchen

2008-01-02T16:40:00.001-08:00

Ah, the alchemical fire of cooking! This is one of the ways in which a kitchen is exactly like a laboratory, even an alchemical laboratory -- where activities in both are concerned with putting together ingredients (or reagents) toward a goal. In both places fire is the transforming agency. It seems as though the home cook could use a little chemistry or alchemical knowledge. Alchemical Cooking -- there's a cookbook idea........

clipped from www.nytimes.com

OF all the ingredients in the kitchen, the most common is also the most mysterious.

It’s hard to measure and hard to control. It’s not a material like water or flour, to be added by the cup. In fact, it’s invisible.
It’s heat.
Every cook relies every day on the power of heat to transform food, but heat doesn’t always work in the way we might guess. And what we don’t know about it can end up burning us.
We waste huge amounts of gas or electricity, not to mention money and time, trying to get heat to do things it can’t do. Aiming to cook a roast or steak until it’s pink at the center, we routinely overcook the rest of it. Instead of a gentle simmer, we boil our stews and braises until they are tough and dry. Even if we do everything else right, we can undermine our best cooking if we let food cool on the way to the table — all because most of us don’t understand heat.

Science Names it's Breakthrough of 2007: Human Genetic Variation

2007-12-21T07:54:00.001-08:00

In this article, Elizabeth Pennisi writes "Already, the genomes of several individuals have been sequenced, and rapid improvements in sequencing technologies are making the sequencing of "me" a real possibility." Only 2 individual genomes have been "published", James Watson's and Craig Venter's, though Watson's is deposited in the database, Venter actually published his in a journal article. The era of personal genomics is definitely here.

Here's one of Science's predictions for next year:

Paleogenomics. Expect a very rough draft of the Neandertal genome by the end of 2008 and more comparisons between the genes of Neandertals and Homo sapiens that will continue to flesh out those fossil bones, filling out many features of this extinct human. Thanks to cheaper, faster technologies, there will be more genomes, from more extinct species, rolling out of the sequencing pipelines.

clipped from www.sciencemag.org

The unveiling of the human genome almost 7 years ago cast the first faint light on our complete genetic makeup. Since then, each new genome sequenced and each new individual studied has illuminated our genomic landscape in ever more detail. In 2007, researchers came to appreciate the extent to which our genomes differ from person to person and the implications of this variation for deciphering the genetics of complex diseases and personal traits.

Less than a year ago, the big news was triangulating variation between us and our primate cousins to get a better handle on genetic changes along the evolutionary tree that led to humans. Now, we have moved from asking what in our DNA makes us human to striving to know what in my DNA makes me me.

Genetic Genealogy

2007-12-21T06:56:00.001-08:00

The NY Times online must be fertile ground for DNA companies. Here is another company's ad with a completely different goal: tracing your ancestry via your genetic profile.

clipped from www.dnaancestryproject.com

deCode Me -- Ad found online at CNN.com

2007-12-20T08:11:00.001-08:00

You will be seeing more ads like this one. This is the company offering the $895 genetic scan product which I mentioned in an earlier post. Storefront genomics is here.

The small colored bars that make up the human figure on the left are meant to emulate a DNA-sequencing gel. However, there are more than four colors used in this graphic (there are only four different bases in DNA).

The ad copy flashes by too quickly but they state:

This is me.
This is myCode.
myCode is my DNA.
Know your Code.

On the website, you'll see what $895 will buy you (the links don't work):

For only $985, we scan over one million variants in your genome
Calculate genetic risk for 18 diseases based on the current literature
Find out where your ancestors came from and compare your genome with others
Get regular updates on future discoveries and a growing list of diseases and traits
New features:
- Easy family registration and family discounts
- Gift certificates for friends
- Recruit a friend and get a $50 refund of your Genetic Scan

clipped from ad.doubleclick.net

Mars Closest to Earth Tonight -- Best View until 2016

2007-12-18T18:40:00.001-08:00

clipped from news.nationalgeographic.com

The bright yellowish-orange "star" poised above the constellation Gemini is actually the planet Mars, and tonight the icy world will make its closest approach to Earth until 2016.

"Earth comes close to Mars because our planet is moving faster in its orbit, catching up to and passing Mars," said Jaymie Mark Matthews, an astronomer at Canada's University of British Columbia.
Tonight's passage happens while Mars is in retrograde motion, or appearing to move westward across the night sky.
"Thus, for the three months around closest approach, the yellowish-orange planet will appear to move slowly backward from the constellation Gemini into Taurus," said Edward Murphy, an astronomer at the University of Virginia.

What Your Brain Looks Like on Faith

2007-12-17T06:46:00.001-08:00

I don't have access to the Annals of Neurology, or I would try to blog from the peer-reviewed paper. Perhaps Harris will post it to his web site. So for now, here is Time Magazine's take on this paper. I'm sure this won't be the only report on this journal article. You can realistically expect lots of media attention over this paper.

clipped from www.time.com

Sam Harris is best known for his barn-burning 2004 attack on religion, The End of Faith, which spent 33 weeks on the New York Times best-seller List. The book's sequel, Letter to a Christian Nation also came out in editions totalling hundreds of thousands. Last Monday, however, the combative Californian produced a shorter (seven pages) and seemingly calmer publication that will be a hit if it reaches 10,000 readers: "Functional Neuroimaging of Belief, Disbelief and Uncertainty." It appears in the respected journal Annals of Neurology. And Harris, 40, claims it has little if any connection to his popular two books. Believers, however, may draw their own conclusions — and may want to read his subsequent neurological studies even more carefully.

F in Science, A in Self-Esteem

2007-12-10T04:07:00.001-08:00

Couple this assessment with the Chronicle of Higher Education's recent story on the lack of academic jobs for scientists (there has been a recommendation for some time to limit the number of graduate students going into science programs). Schools have so far refused to do this.

Back in the early 1980's when there was a similar glut of scientists, the new industry of biotechnology absorbed their numbers (and thereby creating the current biotech industry vs. academia social war). And now the biotech industry is not doing very well, in fact, it hasn't done well since the beginning, constantly growing and shrinking, hiring and firing in a roller coaster ride way that most people find untenable after a while (which is why there are so many MBAs out there with science degrees).

I grew up in the 1960s when the Space Race sparked an intense math and science resurgence in American public schools. What in the heck is happening now? Now, science teachers in K-12 have to fight pseudoscience in the classroom, illegally introduced by well-meaning but happily ignorant educational boards. With so many teachers trying to keep religion out of their science classrooms, is it a wonder that American kids aren't doing well in science?

clipped from www.latimes.com

American 15-year-olds go up against teens from around the world.

December 10, 2007

We could focus on the latest worrisome news in education: the results of an international test released last week that show American 15-year-olds don't know much about science and are falling behind their peers in other industrialized nations. But why get depressed?

There is an aluminum foil lining: The test also found that our teens don't let their ignorance bother them. They may not know as much as students in Finland, Canada or New Zealand, but they think they do. When asked to rate their own scientific abilities, they put themselves at the top with their better-educated peers.

Interesting Hearsay from Scientific American's Blog

2007-12-04T04:34:00.000-08:00

I found this little notice on SciAm.com's blog. deCODE's $895 genome scan is priced perfectly for Christmas giving! But seriously, the price shows how cheaply genomic sequencing and scanning has dropped. The really interesting bit is at the end, regarding Honest Jim Watson and his recent comments about Africans -- what's the old saying? something about throwing stones and glass houses?

"File Under: Hearsay: Earlier this week, Kari Stefansson, a well-known geneticist and the founder of deCODE, an Icelandic company specializing in translating human genetics into drug development and diagnostic tools, stopped by the Scientific American offices to talk about a new project: For less than $1,000, anyone can send his company a cheek swab and get his or her genome scanned. Then, via the decodeme.com website, they can review a number of predetermined complex genetic disorders to assess his or her relative risk for developing maladies such as diabetes, myocardial infarction and even restless leg syndrome.

In addition, you can check your ancestry to get an idea of the geographical distribution of their forefathers. According to Stefansson, when he put in James Watson's genome, which was sequenced earlier this year and made publicly available, the legendary geneticist turned out to be 20 percent African. (When we checked his claim, it was more like 16 percent, but with rounding, fine.) Stefansson remarked that the ancestry test suggests that Watson had at least one African ancestor within two or three generations of his birth.

Like I said, this is just gossip. But it would be ironic. Don't cha think? A little too ironic."

Another Scientist with a Mythic Imagination

2007-11-30T07:08:00.000-08:00

Henry Gee is an editor at the science journal Nature and is now also editor of the Tolkien Society journal Mallorn. He is the author of Jacob's Ladder: the History of the Human Genome (2004), In Search of Deep Time (1999), A Field Guide to Dinosaurs (2003), The Science of Middle-Earth (2004), and a new book this month Futures from Nature (2007). I read his blog on the Nature.com site occasionally, but this entry was really funny, in the middle of a commentary for the new Kindle ebook reader from Amazon.com:

"You’d think, that as an avid Tolkien fan I’d have a fine hardback three-volume edition of The Lord Of The Rings vacuum-packed in cellophane or stored in a vault in an argon atmosphere behind a 24-hour armed response unit. Not a bit of it. My copy of the timeless classic is a cheapo movie tie-in untimely ripped, much graffitoed with notes and marginalia, and stuffed with small pieces of paper (including a treasured admit-one pass for the party in LA hosted by TheOneRing.net to celebrate the Oscar-night sweep of The Return Of The King.) The book – now more like a mille-feuille pastry well past its sell-by date – is scuffed and multiply repaired with tape. When the time comes to recall my legacy, they shall call me ‘Spinebreaker’.

Hmmm. The previous sentence requires some more portentous capitalization and dramatic emphasis. They Shall Call Me … Spinebreaker. Actually, I quite like that. Henry Gee, Spinebreaker. When word got round that I was not only a Nature editor but the new editor of the Tolkien Society journal Mallorn, a colleague suggested that I should simply write, by way of manuscript rejection letters, something like this.

Dear Professor Trellis

Thank you for your manuscript entitled “On the positively negative interaction between one abbreviation and another abbreviation, conditional on the negatively double-negative interaction between a third abbreviation and one or other of the first two abbreviations”.

Please be aware that I am a Servant of the Secret Fire, Wielder of the Flame of Anor, and in that capacity I’m afraid to say that the Dark Fire will not avail you, Flame of Udun. I regret that your manuscript must go back to the Shadow. I am sorry to be the bearer of what must be disappointing news.

Sincerely

Dr Henry Gee
Spinebreaker.

PS - You Shall Not Pass!

Oh, I wish. But back to the Kindle. Now, the demise of books and their replacement by e-readers has been heralded more often and with more vigour than the retirements of James D. Watson."

As you were. Oh, BTW, the new book is a collection of SF short stories published in Nature every week under the title: Futures. I'm an avid reader of these -- there is something rather satisfying after reading peer-reviewed science journal articles to finish each issue with a little science fiction, or excuse, me SPECULATIVE FICTION. For some reason, SF is out of vogue for some.

Pandora Radio from the Music Genome Project

2007-11-29T15:06:00.000-08:00

There are a lot of free radio channels available on the Internet. I listen to NPR frequently and I have the choice of listening to stories directly on the main site www.npr.org or I can listen to programs on just about any member station -- most of them have direct broadcast feeds I can access with 2 clicks of my mouse.

Pandora Radio is different than a simple all-music station. This one is called the Music Genome Project (tm). The concept is that if you input a song or an artist (called a seed) the software will queue up additional music that it thinks you will like, based on your input. As the tunes are played, you can rate them (thumbs up, thumbs down) and adjustments will be made to your next song. There are pre-selected Pandora "stations" seeded with just about every genre of music you can think of (although they only added Classical Music this month).

While it's sort of cute that the company uses a tag such as the Music Genome Project, calling songs or artists "seeds" instead of "genes" means they haven't taken the metaphor to the extreme, though I'm guessing they were tempted. And with the name Pandora (all gifts) it was inevitable that I blogged about the service -- myth AND genome. They're as crazy as I am.

You will see ads on the webpage as you listen and they occasionally change as new music is queued up. They also sell small units that allow you to listen to Pandora as if from an AM/FM radio. But I don't find the ad intrusive -- I open a separate browser tab, open my Pandora account, and leave it alone. My tastes are very eclectic, some of my "stations" are:

Keltoi and Medieval
Metal Angst
Piano Concerti
Symphonic, Romantic period
Dead Can Dance Radio
Chamber, Baroque
Beatles Era
Jazz Holidays
Acid Blues Radio

Give it a try. It's free.

New Journal! "Evolution: Education and Outreach" free online for 2008

2007-11-28T07:45:00.000-08:00

Anyone interested in K-16 science education will be interested in this new journal aimed at science teachers, students, and the interested public. Written and edited by scientists and science educators, the inaugural issue comes at a critical time. Even though creationists and "intelligent design" proponents have lost several large court cases in their quest to teach a religious viewpoint in public school science classes, they haven't given up.

Writing in what will be a regular feature, "Overcoming Obstacles to Evolution Education", Glenn Branch and Eugenie Scott from the National Center for Science Education note that in the U.S., 30% of science teachers are still being pressured to either omit or downplay evolution in their lesson plans, wihle 31% report that they are being pressured to add "creation science" or "intelligent design" to their coursework (citing a 2005 National Science Teachers Association survey).

I've not read the entire first issue as of this writing, but I recommend paleontologist Ian Tattersall's letter essay "What's So Special About Science?" as well as evolutionary biologist T. Ryan Gregory's "Evolution as Fact, Theory, and Path." BTW, Gregory also has a truly excellent science blog.

The journal website is here and it will be open access throughout 2008.

What Makes Us Moral

2007-11-24T06:48:00.001-08:00

Time magazine has picked up a story that has had a lot of developments in the field of neuroscience, particularly this year. It has been nearly impossible to pick up a science journal without it including a new paper on the brain biology of morality. You'll find a library of popular science books and academic series on this subject. It's very much on peoples' minds.

Click the link below to read the entire article.

clipped from www.time.com

If the entire human species were a single individual, that person would long ago have been declared mad. The insanity would not lie in the anger and darkness of the human mind—though it can be a black and raging place indeed. And it certainly wouldn't lie in the transcendent goodness of that mind—one so sublime, we fold it into a larger "soul." The madness would lie instead in the fact that both of those qualities, the savage and the splendid, can exist in one creature, one person, often in one instant.

We're a species that is capable of almost dumbfounding kindness. We nurse one another, romance one another, weep for one another. Ever since science taught us how, we willingly tear the very organs from our bodies and give them to one another. And at the same time, we slaughter one another.

Are Scientists Playing God? It Depends on Your Religion.

2007-11-20T04:28:00.001-08:00

It's been reported in the science journals but not highlighted in the national media that stem-cell scientists are moving their entire labs out of the U.S. and into Asia in order to continue research. For leaders of a field of scientific inquiry to pack up and leave the country to work elsewhere is a new phenomenon -- and the resultant brain drain is growing.

clipped from www.nytimes.com

By JOHN TIERNEY

Published: November 20, 2007

Now that biologists in Oregon have reported using cloning to produce a monkey embryo and extract stem cells, it looks more plausible than before that a human embryo will be cloned and that, some day, a cloned human will be born. But not necessarily on this side of the Pacific.

American and European researchers have made most of the progress so far in biotechnology. Yet they still face one very large obstacle — God, as defined by some Western religions.
While critics on the right and the left fret about the morality of stem-cell research and genetic engineering, prominent Western scientists have been going to Asia, like the geneticists Nancy Jenkins and Neal Copeland, who left the National Cancer Institute and moved last year to Singapore.

Asia offers researchers new labs, fewer restrictions and a different view of divinity and the afterlife.

These Scientific Minds Think (and Drink) Alike

2007-11-17T20:10:00.001-08:00

Interesting -- science demonstrations and lectures as entertainment in bars. This is sort of the opposite of the "fermentation seminars" at Amgen or the Friday beer gatherings at Genentech -- both of these social gatherings for scientists are going away as biotech becomes more corporate. When scientists gather and share a round of beers, ideas are exchanged and experiments are considered and planned.

It's interesting that people will come to a NYC bar to listen to a science lecture -- I wonder if this same group would attend a lecture at the New York Academy of Sciences new headquarters at 7 World Trade Center? Maybe if the NYAS obtained a liquor license?

clipped from www.nytimes.com

CAFE PHYSICS Dave Maiullo stages experiments for a bar crowd.

By KAYLEEN SCHAEFER

Published: November 18, 2007

THE young men and women crowded into the basement of the Union Hall bar in Brooklyn looked as if they were used to spending time in dark steamy rooms. Dressed in plaid flannel shirts and corduroy coats, and carrying canvas bags, they could have come in search of the latest breakthrough band.

But on a recent Wednesday night, they were waiting to see a performance by Dave Maiullo, a support specialist for the Rutgers physics department, who stages demonstrations to illustrate scientific principles.
“I’m going to put on my glasses so I can pretend I know what he’s talking about,” said a woman in the second row.

Ancient and Modern Condors Coexisted

2007-11-10T06:17:00.001-08:00

Californians are serious about their condors, but you have to admit, this is one butt-ugly bird. It really looks like a Jim Henson creation to me. Despite a fairly successful breeding program, the released birds fall prey to toxins in the environment and idiot hunters who can't resist taking a shot at that enormous wingspan.

clipped from www.livescience.com

California condors are an endangered species. Captive breeding programs have boosted their numbers after poachers and habitat destruction pushed them to the brink of extinction. Credit: AP Photo

clipped from www.livescience.com

New comparisons of modern California condor bones to those found in Los Angeles’ La Brea Tar Pits show that two distinct species of these large vultures roamed the skies before the end of the last ice age, providing a compelling answer to a long-standing question.

At the end of the Pleistocene epoch about 10,000 years ago, when Earth was thawing out from the Ice Age, two types of condors competed over resources in what is now California, but it has been unclear if they were distinct species. The California condor seen in the skies today ultimately triumphed (though it is currently listed as Critically Endangered), while the others perished.

PBS Nova Program -- Documentary on Kitzmiller v. Dover

2007-11-09T12:51:00.001-08:00

Wow, I'm not going to miss this one. The science journal Nature gives this program a glowing review:

Excepts from Adam Rutherford's review in Nature:

"Conflict between religion and science has rarely been of more concern. Whereas the rhetoric of Richard Dawkins, Sam Harris and others has little measurable effect, the outcome of a juryless trial in a two-bit Pennsylvania town in 2005 had a profound impact on how science is taught throught the United States, and beyond"

"... the Kitzmiller v. Dover verdict, matched this September with the outlawing of intelligent design in the UK national curriculum, marked the official neutering of this unpleasant, sneaky movement in much of the western world. Judgment Day is just the sort of thoughtful programming that celebrates how sensible people -- faithful and otherwise -- can use science and reason to combat fundamentalism."

The web site for the program contains audio clips, additional resources, an educators guide, and links to all of the trial's legal documentation.

clipped from www.pbs.org

Comet is a rare sight for stargazers

2007-11-09T05:13:00.001-08:00

We've had dense fog every night and early morning, so I've yet to spot Comet Holmes myself -- but you don't need any kind of magnification -- your peepers will do. There is a wonderful photo of Comet Holmes taken in the Anza-Borrego Desert, but the photo is in the print edition only. If you go to latimes.com and click on "Print Edition" in the left collumn, you'll get a PDF of todays front page containing that photo. If I locate it elsewhere online, I'll post it here, too.

clipped from www.beloitdailynews.com

After seven years of hiding Comet Holmes is making quite the impression: on Oct. 24 it became visible to the naked eye and has yet to dim.

“It suddenly increased its brightness by one-thousand fold,” said Britt Scharringhausen, assistant professor of physics and astronomy at Beloit College.

The billions-year-old comet was discovered in 1892 by an Englishman named Edwin Holmes and was last seen in 2000. Then it appeared as a dim object seen in the telescope. The sight was not “nearly as spectacular” as it is now, Scharringhausen said.

Beloit resident Carl Balke, a 35-year stargazing enthusiast, first saw Comet Holmes about 10 days ago after he had heard about its appearance from someone else. Since then, he has spent at least three to four minutes a night to spot it.

“It looks like a big, out of focus light bulb,” he said. “The exciting part is this is the leftover debris from the big bang.”

StoryCorps: Listening Is an Act of Love

2007-11-08T16:46:00.001-08:00

During the NPR's Morning Edition this morning, I caught a story about a new book coming out about StoryCorps, a project that provides recording opportunities to people simply to tell their story. On Fridays, Morning Edition features one of those recorded stories and this has become my favorite "NPR moment" during the week.

Click the link above the photo to read the article. There is a link on the page that gives you excerpts from the book as well as an audio version of the story. This is not to be missed. And it appears, neither is the new book: listening IS an act of love.

clipped from www.npr.org

William Jacobs had a private conversation with his grandson that was overheard by millions of people. Their conversation was recorded and aired on Morning Edition in 2005 as part of the StoryCorps project, which has been capturing the stories of everyday Americans across the country.

In a separate conversation, Mary Caplan told a story about nursing her brother through AIDS.

Jacobs and Caplan are featured in a new book about StoryCorps called Listening Is an Act of Love, edited by StoryCorps founder Dave Isay.

Since 2003, when StoryCorps was launched, about 15,000 conversations have been recorded as part of the project.

The Brain's Technicolor Dreamcoat -- Brainbows

2007-11-07T04:39:00.000-08:00

From Scientific American online's gallery:

"Maybe the parents of neurons can tell their progeny apart, but researchers have a harder time disentangling one brain cell from the horde as they try to tease apart the inner workings of the brain's subsystems. A new labeling technique published in Nature may go a long way toward sorting out the chatter between cells. Researchers engineered neurons to randomly express one of nearly 90 different combinations of red, cyan and yellow fluorescent proteins, resulting in "brainbows" such as this set of multicolored axons projecting from the oculomotor nerve of a mouse."

Livet, J. et al. "Transgenic strategies for combinatorial expression of fluorescent proteins in the nervous system". Nature 450, 56-61 (2007).

Scientists Find Planet Orbiting Star

2007-11-06T15:57:00.001-08:00

Exoplanetary systems! So thrilling!

Joseph Campbell thought the next myth was about space exploration, the "Big Blue Marble" photo sent back by Apollo 8 gave us the first image of earth in space. While we aren't exploring in person, a number of satellites, telescopes, and explorer robots are doing it for us. And while this particular planet isn't earth-like, one's imagination can't help but speculate about possible life outside our solar system. Perhaps it can arise on a planet that isn't earth-like, perhaps not, but the search continues.

Homo sapiens is an explorer species, long-distance runners, actually. It's part of our evolution. It's bred into us -- a genetic legacy that may go back further than we can currently measure using modern fossil dating techniques. Sprinting from the original home savannahs of Africa out into Europe and Asia, our species rather quickly dominated the landscape. Our ancestral past as long-distance runners makes the current obesity epidemic dangerously ironic. If were were still a culture of long-distance runners, would the planet be in the shape it is currently?

clipped from news.yahoo.com

This artist rendering released by NASA/JPL-Caltech, Tuesday, Nov. 6, 2007, shows four of the five planets that orbit 55 Cancri, a star much like our own. The most recently discovered planet, and the fourth out from the star, looms large in the foreground. Astronomers said Tuesday they have discovered a fifth planet orbiting a sun-like star 41 light years away, making it the first planetary quintet outside our solar system. The newfound planet joins four others circling the nearby star 55 Cancri in the constellation Cancer. (AP Photo/NASA JPL CalTech)

Skeleton's Flesh Out Life's Past

2007-11-06T04:41:00.001-08:00

Book review by Carl Zimmer for a new coffee-table book entitled "Evolution". The book focuses on forms which reminds me of the last sentence in Charles Darwin's "Origin of the Species", "There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved."

clipped from www.nytimes.com

STRIPED DOLPHIN Stenella coeruleoalba.

By CARL ZIMMER

Published: November 6, 2007

About half a billion years ago, our ancestors were slender, jawless, fishlike creatures. Their backs were stiffened by a rod of cartilage, along which grew bony prongs. That smattering of bone was the forerunner of our vertebrae, and it gave us and all the other descendants of those ancient animals our name: the vertebrates. Vertebrates have evolved into tens of thousands of species dominating the ocean, land and sky. Much of their success is due to the many new forms their skeletons have taken. A new coffee-table-format book, “Evolution” (Seven Stories Press), offers hundreds of gorgeous photographs of those forms, as diverse as bats with fingers thinner than pipe cleaners and rhinos with skulls as stubborn as boulders.

Accompanying the photographs, by Patrick Gries, are essays by Jean-Baptiste de Panafieu, a French biologist and author.

When Science Comes Up Against a Mythical Creature

2007-11-05T07:48:00.000-08:00

Creature ID'd as coyote, not chupacabra

Phylis Canion holds the head of what she is calling a Chupacabra at her home in Cuero, Texas, Friday, Aug. 31, 2007. She found the strange looking animal dead outside her ranch and thinks it is responsible for killing many of her chickens. he results are in: The ugly, big-eared animal found this summer in Cuero is not the mythical bloodsucking chupacabra. It's just a plain old coyote. Biologists at Texas State University announced Thursday night Nov. 1, 2007 that they had identified the hairless doglike creature. 'The DNA sequence is a virtually identical match to DNA from the coyote,' biologist Mike Forstner said in a written statement. (AP Photo/Eric Gay)

You can read about it here.

Leslie Orgel, Biochemist Who Studied Origins of Life, 80

2007-11-05T04:26:00.001-08:00

Dr. Orgel, along with Francis Crick and Carl Woese are responsible for the "RNA World" theory -- an idea that the world biome was RNA-based before it was DNA-based.

clipped from www.nytimes.com

Leslie E. Orgel, a biochemist whose studies of early life on primitive Earth helped lead to the formation of a now widely accepted theory about the development of DNA, died Oct. 27 in San Diego. He was 80.

Dr. Orgel had also advanced a novel idea about life’s possible arrival from outer space.
The cause was pancreatic cancer, said a spokesman for the Salk Institute for Biological Studies in San Diego, where Dr. Orgel had been on the faculty since 1964.
Dr. Orgel and others began to pose seminal questions about DNA’s biochemical origins in the 1960s, as the molecular structure ohttp://www.blogger.com/img/gl.link.giff DNA, or deoxyribonucleic acid, was being unraveled and its role as a storehouse of genetic instructions was becoming more widely understood.

Hollywood Writers Cut to the Strike

2007-11-05T04:06:00.001-08:00

In the Land of Make Believe (where I live and work near) a writer's strike is one of the worst things that can happen. The Machine breaks down without writers. Some TV shows will have stockpiled some scripts, and some TV producers have writing abilities, but you will see the effects on serial TV if this strike lasts for any real length of time. This strike will only add to the economic woes in the area -- I hope that the WGA and the producers can come to an agreement quickly, but that isn't looking promising.

clipped from www.latimes.com

SIGNS OF CONFLICT: Writers Guild members load picket signs into vans Sunday afternoon in preparation for a walkout. The union planned to maintain picket lines at major studios and networks. “Once it starts,” a guild strike captain said, “it’s going to get ugly.”

The studios and the guild prepare for a long work stoppage. They remain far apart on Internet residuals.

By Richard Verrier and Claudia Eller, Los Angeles Times Staff Writers

November 5, 2007

Hollywood's film and television writers went on strike early this morning after last-ditch efforts to negotiate a deal with the major studios failed Sunday.

Despite the aid of a federal mediator and back-channel talks between top writers and studio executives, the sides were ultimately too far apart to bridge the massive divide between them and avert the first writers strike in nearly two decades.

The rest of the article can be found at the Los Angeles Times here.

King Tut in the Exposed Flesh

2007-11-04T12:53:00.001-08:00

For the first time since his tomb was opened in 1922, the face of King Tutankhamen is revealed to the public.

clipped from news.yahoo.com

The face of the linen-wrapped mummy of King Tut is seen in his new glass case in his underground tomb in the famed Valley of the Kings in Luxor, Egypt Sunday, Nov. 4, 2007. The mummy of the 19-year-old pharaoh, whose life and death has captivated people for nearly a century, was placed in a climate-controlled glass box in the tomb, with only the face and feet showing under the linen covering. (AP Photo/Ben Curtis)

Science news stories from around the web

2007-11-01T06:59:00.000-07:00

Washoe, the chimpanzee who had learned ASL, died Tuesday. Though chimpanzees have a variant of the FOXP2 gene, which is involved in speech ability, this isn't a barrier to learning a language.

The cat genome has been sequenced, though news stories insist on using the term "decoded". The DNA code was "decoded" in the 1960s. Genomes are sequenced, read, searched, annotated, or copied, etc. The cryptographic metaphors are so, like, 50 years ago. And in case you aren't a cat person, the dog genome was sequenced in 2004.

Craig Venter was on The Colbert Report Tuesday night talking about his autobiography, personal genomics, synthetic biology, and God's horrible mistakes. Good stuff. Several science bloggers have the video available in posts: The Tree of Life, and Eye on DNA among others feature the clip.

Wealth and Religiosity -- by Country

2007-10-31T06:36:00.000-07:00

The Pew Global Attitudes Survey results are out, with data from 47 nations. Topics include the economic globalization, immigration, religion and social issues, and views on democracy. You can guess which topic caught my interest, but the graph at the left gives it away.

From the report summary: "Global publics are sharply divided over the relationship between religion and morality. In much of Africa, Asia, and the Middle East, there is a strong consensus that belief in God is necessary for morality and good values. Throughout much of Europe, however, majorities think morality is achievable without faith. Meanwhile, opinions are more mixed in the Americas, including in the United States, where 57% say that one must believe in God to have good values and be moral, while 41% disagree."

The graph also shows that there are outliers, like Kuwait and the U.S. Garry Wills talks about the anomaly of the U.S.'s religiosity in comparison with the rest of Western Culture in his latest book Head and Heart:American Christianities (which I highly recommend if you are interested in the religious history of the founding of the U.S. and how it has affected politics today, in particular the current Administration).

Again, from the report summary: "The survey finds a strong relationship between a country's religiosity and its economic status. In poorer nations, religion remains central to the lives of individuals, while secular perspectives are more common in richer nations (1). This relationship generally is consistent across regions and countries, although there are some exceptions, including most notably the United States, which is a much more religious country than its level of prosperity would indicate. Other nations deviate from the pattern as well, including the oil-rich, predominantly Muslim -- and very religious -- kingdom of Kuwait."

A footnote at the bottom of the page shares the Pew's methodology on how religiosity was calculated: "(1) Religiosity is measured using a three-item index ranging from 0-3, with "3" representing the most religious position. Respondents were given a "1" if they believe faith in God is necessary for morality; a "1" if they say religion is very important in their lives; and a "1" if they pray at least once a day."

Coleridge and Darwin -- It WAS "in the air"

2007-10-30T07:43:00.000-07:00

Loren Eiseley, The Firmament of Time, 1960. pp. 61-62:

“Great literary geniuses often possess an ear or a sensitivity for things in the process of becoming, for ideas which are just about to be born. It is interesting in this connection to compare the remarks of Charles Darwin with certain observations on science made at a much earlier date by the poet Samuel Taylor Coleridge. Darwin, in his autobiography, protests that he saw no evidence that the subject of evolution was “in the air” of his time. “I occasionally sounded out not a few naturalists,” he remarks, “and never happened to come across a single one who seemed to doubt about the permanence of species.”

"By way of contrast, we may note that Coleridge, in a philosophical lecture delivered as early as 1819, makes reference to a belief which “has become quite common even among Christian people, that the human race arose from a state of savagery and then gradually from a monkey came up through various states to be a man.” Coleridge was not an evolutionist. He is, however, sensitive to a new doctrine, whose presence “in the air” Darwin had failed to discover. He observes in a very shrewd fashion … the way in which the intellectual climate of a given period may unconsciously retard or limit the theoretical ventures of an exploring scientist. “Whoever is acquainted with the history of philosophy during the last two or three centuries,” contended the great poet, “cannot but admit, that there appears to have existed a sort of secret and tacit compact among the learned, not to pass beyond a certain limit in speculative science. The privilege of free thought so highly extolled, has at no time been held valid in actual practice, except within this limit.”

Eiseley, a prolific science writer in the mid-20th century is a new discovery for me, though I understand he was very, very popular in the 1950s and 1960s. He doesn't provide citations in his works, though, using a more essayist style of writing. I was able to quickly find citations for the quotes of Coleridge and Darwin, thanks to Google Books.

Coleridge, Biographia Literaria. Vol. I (1817)
p. 140 paragraph 77

Darwin, Francis. The Autobiography of Charles Darwin. Austin, TX:1st World Publishing, 2004.
p. 65

James Watson Retires from CSHL -- sends his announcement to the NY Times and other news outlets

2007-10-29T12:06:00.000-07:00

Watson retires after all the hoopla of the last week. Burned by the public outcry over his remarks in UK media outlets, Dr. Watson emailed his retirement message to the NY Times.

Cold Spring Harbor Laboratory has published a press release as well. This press release contains no details, but Watson's email says that he will get to keep his home at CSHL.

Noah Gray posting on Nature's Action Potential Neuroscience blog has heard additional details, such as that Watson will keep his secretary, his office, and his salary, only losing the Chancellor nameplate on his office. Gray also calls this "a little finger-waggling" from the CSHL Board.

Arthur Kornberg (1918-2007)

2007-10-29T03:40:00.000-07:00

Without Arthur Kornberg's achievements, biotechnology would be a nice idea on paper, never realized. Intensely interested in enzymes, Kornberg discovered two families of DNA enzymes crucial for manipulating DNA: DNA polymerases and DNA ligases. Today, we buy these enzymes from catalogs that are as slick as any product catalog you receive just in time for the Christmas season. Kornberg, however, had to purify and identify these proteins from the cells that made them.

He won a Nobel Prize for this work in 1959 for DNA synthesis, sharing the prize with Ochoa, who won for RNA synthesis.

A lot of people who know about Kornberg's molecular biological achievements, might not know that he is also responsible for the research that showed that both folic acid and Vitamin K were essential nutrients.

His son, Roger, also a biochemist, won a Nobel Prize in 2006, making the Kornbergs only the second family to win multiple Nobels, the first being the Curies.

He was publishing up the end -- I checked PubMed and there is a paper in PNAS dated October 16, 2007, in which he is listed as the primary investigator (or PI):

Zhang H, Gómez-García MR, Shi X, Rao NN, Kornberg A. Polyphosphate kinase 1, a conserved bacterial enzyme, in a eukaryote, Dictyostelium discoideum, with a role in cytokinesis. Proc Natl Acad Sci U S A. 2007 Oct 16;104(42):16486-91

The Utopian Apocalypse

2007-10-28T09:02:00.000-07:00

That's the title of a book review in today's LA Times, though you don't get this rather emotionally-charged title with the online version. The review, by Michael Joseph Gross, concerns two books by Professor John Gray from the London School of Economics. The first one is entitled Black Mass: Apocalyptic Religion and the Death of Utopia and the second one is Straw Dogs: Thoughts on Humans and Other Animals. You wouldn't think of a Professor at an Economics school as a mythological writer, but excerpts from the book review reveal that Gray sees the world mythologically and bleakly:

"Straw Dogs considers what politics might be like if we took science seriously -- if we accepted the full ramifications of Darwin's finding that Homo sapiens is merely another kind of animal. If, as Gray writes, "species are only assemblies of genes, interacting at random with each other and their shifting environments," then humanity's ambition to master fate is absurd. Those who speak of "'the progress of mankind,'" Gray contends, "have put their faith in an abstraction that no one would think of taking seriously if it were not formed from cast-off Christian hopes."

Black Mass....."presents utopian politics from the French Revolution through America's project of spreading democracy in the Middle East as 'mutant version(s)" of an ancient, apocalyptic Christian belief that God will transform the world and evil will pass away."

"When the project of universal democracy ended in the blood-soaked streets of Iraq," Gray writes, "... Utopianism suffered a heavy blow, but politics and war have not ceased to be vehicles for myth. Instead, primitive versions of religion are replacing the secular faith that has been lost."

Finally, the reviewer writes that Gray's books "have the delighting, frightening, distracting and focusing qualities of a mist-to-dusk drive on the Pacific Coast Highway." I'll add his books to those of other European thinkers in this vein: Mary Midgely, Alex Mauron, and Peter Sloterdijk, all of whom are asking questions about the nature of science, it's involvement in modern politics, and what it really means to be human.

Some Neanderthals were pale and had red hair

2007-10-27T08:21:00.000-07:00

A new report in Science this week reveals that Neanderthals have a variant in a receptor involved in skin and hair color that made some of them look like modern northern Europeans: Lalueza-Fox, Carles, et al. "A Melanocortin 1 Receptor Allele Suggest Varying Pigmentation Among Neanderthals" Science Express (Advance of Print) 25 October 2007.

Abstract: The melanocortin 1 receptor (MC1R) regulates pigmentation in humans and other vertebrates. Variants of MC1R with reduced function are associated with pale skin color and red hair in humans primarily of European origin. We amplified and sequenced a fragment of the MC1R gene (mc1r) from two Neanderthal remains. Both specimens have a mutation not found in ~3700 modern humans. Functional analyses show that this variant reduces MC1R activity to a level that alters hair and/or skin pigmentation in humans. The impaired activity of this variant suggests that Neanderthals varied in pigmentation levels, potentially to the scale observed in modern humans. Our data suggest that inactive MC1R variants evolved independently in both modern humans and Neanderthals.

Certain mutations in the melanocortin 1 receptor effects pigmentation in humans, changing the levels of color in both skin and hair (particularly red hair, freckling, and sun-sensitivity (1). The variant that was found in one of the Neanderthal specimens is different than any seen in modern humans. The Neanderthal variant also causes changes in hair and skin pigmentation, resulting in red hair and fair skin, but this mutation arose independently of the ones in modern humans. The mutations evolved independently but the physical outcome (phenotype) is similar. Red hair in modern humans is not a trait we've inherited from Neanderthals, because this study, as others before it have shown, Neanderthals and modern humans did not interbreed.

The variant is a point mutation: one base in the DNA sequence is G instead of the expected A. This results in a single amino acid change at this position, from arginine (R) to Glycine (G) at position 307. This is abbreviated in the paper (and this is typical shorthand) Arg307Gly. This mutation affects the function of the resultant receptor and the pigmentation difference occurs.

The authors were also able to calculate that the frequency of red hair in Neanderthals would be about 1 in 100 if the individual was homozygous for the allele (two identical copies of the mutated gene).

(1) J.L. Rees. "Genetics of Hair and Skin Color". Annual Review of Genetics V37 (2003) p. 67-90.

"In Space, No One Can Hear You Scream"

2007-10-24T16:03:00.001-07:00

Bring Back the Greek Gods -- Did They Ever Leave?

2007-10-24T06:49:00.000-07:00

An Op-Ed piece in yesterday's Los Angeles Times penned by Wellesley Professor Emerita Mary Lefkowitz demands "Bring Back the Greek Gods."

Dr. Lefkowitz hits and misses with this essay. A serious miss: "Dionysus could alter human perception to make people see what's not really there. He was worshiped in antiquity as the god of the theater and of wine. Today, he would be the god of psychology." No way. Dionysus is all about wildness and loss of control, of "looseness" on every level, many of them physical. But God of Psychology? Perhaps a God of a psychological state, but then again, they are all Gods of psychological states. And they are still with us today.

"Openness to discussion and inquiry is a distinguishing feature of Greek theology." Lefkowitz begins her argument of polytheism over monotheism with this statement -- she says that religion isn't what is poisoning the world with violence and suffering, it's monotheism. Still, it's not polytheism that we need, but as Hillman has pointed out again and again, it's a polytheistic point of view. Obviously, we aren't talking about cultic practices, but ways of thinking about the world and our place in it.

Professor Lefkowitz ends her esaay with the observation, "Ancient Greek religion gives an account of the world that in many respects is more plausible than that offered by the monotheistic traditions. Greek theology openly discourages blind confidence based on unrealistic hopes that everything will work out in the end. Such healthy skepticism about human intelligence and achievements has never been needed more than it is today."

The biggest point that Dr. Lefkowitz misses about monotheisms is their ever-present apocalyptic view of the world. Until these religions stop focusing on the afterlife and stop preaching a rush to get to the "end", no one is safe. No one. Combine that apocalyptic view with a militaristic mindset and you have a powerful myth of TEOTWAWKI. Stopping THAT is what we really need today.

Woke up to more bad fire news -- 500K Evac'd in San Diego

2007-10-23T08:17:00.000-07:00

My friends in San Diego have evacuated and are safe (for now -- the winds keep shifting). One friend has been evacuated twice down there. It's nearly impossible for anyone to get North unless they are already near Interstate 5, so a lot of people have headed south into downtown San Diego, particularly Qualcomm Stadium, which has become a massive evacuation center. The situation is still dynamic, but the Witch fire is making it's unstoppable progress towards the ocean, and the new mandatory evacuation boundaries reflect that. The city is rising to the occasion, the Mayor's call for food for the evacuees at Qualcomm was quickly followed up by a call for refrigerated trucks to store all the excess food.

In Ventura County, Ranch fire, which has been the biggest generator of smoke and ash here (it being the largest fire north of San Diego) is now being joined by a new fire, the Magic fire, which started near Magic Mountain Parkway. This fire has already moved into Ventura County and is heading towards Simi Valley. The town of Piru is being evacuated and the firefighters are trying to keep the Ranch fire on the other side of Highway 126 -- I heard that if it jumps 126, it will burn to Simi Valley. So, right now Simi Valley is the new hot spot in Ventura County. Schools in Simi will be closed today.

The winds have continued to be relentless and made for a restless night. The winds are so fierce they are stripping all the leaves from trees -- it looks like early winter. Bizarre.

San Diego info sites:

http://www.cbs8.com for San Diego updates -- this is a great site, it's been completely converted to fire news only
http://www.signonsandiego.com -- another good San Diego news site, but their server is getting overwhelmed
http://www.sdcountyemergency.com -- the official site for San Diego OES -- info and maps in PDF of burn and evac areas

Ventura County info sites:

http://www.venturacountystar.com -- the local newspaper has coverage on local fires
http://fire.countyofventura.org -- FD of Ventura County -- official updates on both the Ranch and Magic fires
http://www.vcsd.org/oes/fire.html -- VC Sheriff's Dept site for evacuation information

Los Angeles info sites:

http://www.latimes.com -- doing a great job with updates, maps, and evacuation info, and some of the best photos
http://www.knbc.com/index.html -- Local NBC station has info, video, and a large number of viewer supplied photos
http://cbs2.com/firewatch/ -- Local CBS station has a web page for fire coverage -- heavy on video clips
http://abclocal.go.com/kabc/front -- More LA fire coverage with a live broadcast feed, too

California Office of Emergency Services
October Fires: http://www.oes.ca.gov/Operational/OESHome.nsf/ALL/876C5DEE11FE66808825737C005B8754?OpenDocument

The view in front of my house at 2:15PM

2007-10-21T15:00:00.000-07:00

This is the result of the fire that started up in Castaic and two fires closer to home in Moorpark. It was rather dumb for me to go outside and take this picture -- the air is unbreathable and I got ash in my eyes for the effort.

It's so dark that we've had to turn on the lights inside the house.

Craig Venter and an Amgen Molecular Biology Institute?

2007-10-20T09:06:00.000-07:00

I received my copy of Venter's autobiography, A Life Decoded, and went directly to the index in the back of the book. There are two entries for Amgen, the most interesting one is about the company's 1992 offer to set Venter up in a privately funded institute:

"... attempts to lure me away from NIH into a commercial lab continued. I was contacted by Amgen, which was netting more than $1 billion annually from biotech drugs and was now looking for new ways to invest its profits. A conversation with Lawrence M. Souza, the head of research, and Gordon Binder, CEO, turned to the concept of starting a new not-for-profit research institute in the Washington area. The Amgen team jumped at the idea, though while I envisioned doing basic research in a Venter Institute, they, of course, wanted me to do commercial work in an Amgen Institute. The subject was broached again during a visit to Amgen in Thousand Oaks, California. The company would give me a $70 million, ten-year commitment to establish the Amgen Molecular Biology Institute in Rockville, Maryland. I would serve as the institute president and be appointed a senior vice president of Amgen. The salary would be close to three times my NIH salary and would include stock options in Amgen. I still felt uneasy, but the offer was so generous that I promised that I would discuss it with my wife." (p. 153)

Venter explains his "unease" on the next page:

"Amgen offered stability, but I would be burdened with several new bosses and a drug company environment that did not appeal to me."

I'm confident that a corporate environment would never have appealed to Venter unless he was at the very top of it.

Neanderthals Had Speech Capacity. Also -- They Ate Their Own

2007-10-20T08:01:00.000-07:00

A lot of work is being done to completely sequence the Neanderthal genome. One of the groups involved in that genome project has just published a paper in Current Biology reporting that Neanderthals had a modern version of the FOXP2 gene, a gene that has been linked to speech and language ability. There are two point mutations in this gene that are the difference between humans and chimpanzees. The Neanderthals also have these same two point mutations.

This same research group has reported they find no genetic evidence that Neanderthals and modern humans interbred, and they report this again in this new paper.

But it's fun to speculate whether Neanderthals and modern humans were able to communicate with each other. Obviously, among Neanderthals, the entreaty, "Don't eat me!" had no effect, because Neanderthals, with all of their sophisticated culture, were cannibals.

Here is the NY Times take on this research, another from National Geographic online, and the Los Angeles Times article, which mentions the cannibalism.

Watson Fallout: He's Radioactive

2007-10-19T05:22:00.000-07:00

Cold Spring Harbor Laboratory has suspended James Watson as Chancellor:

"Earlier this evening, the Cold Spring Harbor Laboratory Board of Trustees decided to suspend the administrative responsibilities of Chancellor James D. Watson, Ph.D., pending further deliberation by the Board."

PZ Myers at Pharyngua is distressed by this development and disagrees with the CSHL Board's decision. Myers is wrong here -- CSHL has a certain reputation that needs to be maintained, for one, and Watson's roll as Chancellor was one heavily involved in fund raising, for another. But now, Watson's comments make him unsuitable as the public face of CSHL science or the scientists who work there. Myers is correct in that Watson has a right to say what he wants -- but Cold Spring Harbor also has a right to choose who represents them to the public. Rational individuals everywhere are distressed by Watson's morally objectionable invective and Cold Spring Harbor's action is not only understandable, but reasonable and inevitable.

And while Watson has now apologized, the damage is done. The most recent commentary, taken into account with his past gaffes, shows a pattern of bigotry. His time at a microphone should be over.

Watson Fallout: Press Releases Hit the Fan

2007-10-18T13:25:00.000-07:00

Thanks to Tim, who always sends info my way, both Cold Spring Harbor Laboratory and the Federation of American Scientists have issued press releases regarding Watson's latest gaffes.

The CSHL release is rather drab and overly polite:

“The comments attributed to Dr. James Watson that first appeared in the October 14, 2007 edition of The Sunday Times U.K. are his own personal statements and in no way reflect the mission, goals, or principles of Cold Spring Harbor Laboratory’s Board, administration or faculty. Dr. Watson is not the President of Cold Spring Harbor Laboratory and was not speaking on behalf of the institution.

"The Board of Trustees, administration and faculty vehemently disagree with these statements and are bewildered and saddened if he indeed made such comments. Cold Spring Harbor Laboratory does not engage in any research that could even form the basis of the statements attributed to Dr. Watson.

"Cold Spring Harbor Laboratory’s renowned commitment to scientific research in the areas of cancer, neurological diseases, and plant genetics has and continues to dramatically benefit human-kind throughout the world.”

The FAS, however, minces no words:

"The Federation of American Scientists (FAS) is outraged by the noxious comments of Dr. James Watson that appeared in the Sunday Times Magazine on October 14th. At a time when the scientific community is feeling threatened by political forces seeking to undermine its credibility it is tragic that one of the icons of modern science has cast such dishonor on the profession.

The scientific enterprise is based on the promotion and proof of new ideas through evidence, however controversial, but Dr. Watson chose to use his unique stature to promote personal prejudices that are racist, vicious and unsupported by science.

While we honor the extraordinary contributions that Dr. Watson has made to science in the past, his comments show that he has lost his way. He has failed us in the worst possible way. It is a sad and revolting way to end a remarkable career."

You can almost smell flesh sizzling.

James Watson's Obnoxious Personality

2007-10-18T06:33:00.000-07:00

James Watson's latest book, Avoid Boring People could easily be followed up with Avoid James Watson, because he is now persona non grata thanks to his latest newspaper interviews in the UK's Independent and Guardian this week.

His latest and probably most egregious gaffe in the Independent article is to say, directly, that Africans are less intelligent than Westerners. The Guardian article gives Watson a chance to once again sound off on his dead collegues and rivals, which is perfect for him, as the dead can't debate. His comments about Rosalind Franklin are beyond bullshit: "I think she was partially autistic. I'd never really thought of scientists as autistic until this whole business of high-intelligence autism came up. There is probably no other explanantion for Rosalind's behavior." As for Franklin not sharing the Nobel prize for elucidating DNA's double-helical struture, "No one thought about Rosalind, because she was dead." I do understand that Nobel's are not granted posthumously. I also understand that Photo 51 was taken from Franklin's laboratory and shown to Watson and Crick without her permission or involvement. This latest round of comments smears her memory and belies the fact that Franklin kept up a friendly and personal scientific correspondence with both Watson and Crick. Why Watson feels the need to excoriate Franklin almost 50 years after her death is unfathomable to me.

Science bloggers are universally roasting him (and not in a humorous vein). As scientists, we're embarrassed having to read Watson's imbecilic ravings. Here's a sampling of some good science blog posts on Watson's spew:

Thus Spake Zuska writes what I think is a typical reaction from a scientist, Greg Laden has decided that a more physical response is needed, PZ Myers over at Pharyngula puts it succintly, "Eminent scientist behaving badly", Hsien-Hsein Lei at Eye on DNA comments that Watson probably doesn't care and I think she is absolutely right.

Ventura County -- a new Biotech Beach?

2007-10-17T04:41:00.000-07:00

The most common subject brought up in regards to the recent layoffs and "early retirements" at Amgen is biotech start up companies. The amount of experience that walked out the door this month is enormous: 3,500 years (at minimum) in the volunteer pool alone. Among the couple hundred research scientists that left, the average Amgen experience was 18.1 years. On the low end in one department, the average was 12.7 years. So where is all that experience going to land? Most people I've talked to say in new companies all along the 101 corridor, from Thousand Oaks up to Carpinteria -- a Ventura County-centered biotech "Silicon Valley", if you like that analogy, though "Biotech Beach" would be more accurate. There are already some analytical and formulation companies in the area around CSUCI, started by Amgen employees who left years back. But the current talk around the campus is that many more companies will spring up -- and I think they are right -- I know several people who have already met with venture capital investors.

And the timing is perfect for anyone interested in "bio-similars" -- generic biotech drugs. Amgen's first 2 drugs, Epogen and Neupogen, will be going off patent soon, and who better to produce generic versions of these two blockbusters, but the very scientists who developed them in the first place?

Climate Change and the Nobel Peace Prize

2007-10-14T06:20:00.001-07:00

Unless you have no media access at all (and if you didn't you wouldn't be reading this blog anyway) Al Gore won the Nobel Peace Prize for his work on educating the world about climate change. You can read the news media accounts but don't forget to read what the Nobel Foundation committee wrote about this award. Gore shares the award with the IPCC, the Intergovernmental Panel on Climate Change, a UN group of scientists from all over the world.

From the press release: the prize is being awarded "for their efforts to build up and disseminate greater knowledge about man-made climate change, and to lay the foundations for the measures that are needed to counteract such change."

While naysayers still call the data behind the idea of human-caused climate change, "trash science," the scientific consensus is clear: we are affecting our environment in ways that endanger life on the planet. The Nobel Founation press release uses sexist language, but the point of argument is sound:

"By awarding the Nobel Peace Prize for 2007 to the IPCC and Al Gore, the Norwegian Nobel Committee is seeking to contribute to a sharper focus on the processes and decisions that appear to be necessary to protect the world’s future climate, and thereby to reduce the threat to the security of mankind. Action is necessary now, before climate change moves beyond man’s control".

"Amen" to that.

Survived the layoff

2007-10-11T14:40:00.000-07:00

I work for a very large biotech company and have been there for 20 years. After almost 2 months from the original announcement, the company's very first RIF (Reduction in Force) finally occurred yesterday. All North American sites RIF'd yesterday. It was leaked to us the day before, so many of us came to work in black, myself included, for Black Wednesday. I stopped at the local donut shop to buy a couple dozen because nothing is as comforting during high stress like sugar and saturated fats.

The day had a weird quality with everyone coming in and out of my office for a donut, but also not wanting to be too far away from their phone or email, because that was how the one-on-one meetings were arranged. Only one person from my group was laid off, and she was a volunteer (moving out of state and going to nursing school). We'd lost two members of our group last month who quit for personal or family reasons. So I think the fact that we'd already lost those two helped us out. Still, the numbers in my department were 20%. The estimated number for my location is 700.

Time seemed to stretch on forever as I began to get 'goodbye' emails from people who had been cut. People were mostly pretty happy with the severance, and the company left their badges active for 2 days so they could come back and clear out their offices. No security guards. No drama. Just some career counsellors in the large conference room in my building for post-meeting informational help.

I found out later last night that a good friend, someone who I had hired right out of college, 18 years ago, had lost her job. We had worked together for 10 years and then our paths diverged, though it wasn't planned, and we ended up working in different parts of the company. She was pretty upbeat about it and said that it was sort of a relief, she hadn't liked her job in a while and the stress from worrying about the layoffs had been really getting to her. She went out and bought herself a laptop and emailed me with it this morning to set up a lunch date next week. Another friend, who did not lose her job, just couldn't get out of bed today, and she emailed me from her laptop, still in bed, to ask about people in my department.

One of the things I noticed today in the cafeteria nearest my building, was that at lunchtime, people were hugging. "You're still here!" was the most common greeting I heard all day, but in the cafeteria, this was accompanied by lots of hugs.

So while I wasn't able to get any work done yesterday, today I went in and restarted where I'd left off. But, WOW, do I need a vacation.

2007 Nikon Small World Prize Announced

2007-10-09T06:59:00.000-07:00

If you've never seen the images recognized by this photomicrography competition, then you've missed out on some serious eye candy (not to mention that the images are actually scientific data). The 2007 winning image is of a double transgenic mouse embryo (shown on the main page). I really liked this image of a quartz sample because it looks like a great image to translate into an art quilt. I'm a sucker for bright saturated colors. These images are going on a musuem tour around the country -- so check out the tour page and see if the exhibit will be shown near you.

LA Times -- Al Martinez' Essay on the Dawn

2007-10-08T14:18:00.000-07:00

Al Martinez has a pre-dawn essay in today's LA Times that speaks to the stillness of that time of day. Sorry -- I know this is behind a registration wall, but registration is free.

I love the way the air feels just before the sun rises. Martinez got the feel of the change in air and light right. His first two paragraphs on the Greek goddess of the dawn, Eos (Aurora to the Romans) sounds like it was written for one of my two Greek Mythologies courses. I loved this, "By any name she brings tranquillity to the hesitant moment between night and morning -- an affirmation of renewal, a second chance for a new decision, a time not to be afraid anymore."

Great stuff.

Fall has arrived and brought the winds along, too

2007-10-07T06:21:00.000-07:00

Today, they are forecast to be as strong as 40mph and I can hear their effects from inside my house -- the trees and bushes are being whipped back and forth. The skylights on the roof are creaking and popping. I live on a hillside and on windy days like this it feels a little exposed to the elements. For me, the winds usher in Fall, and these come with much cooler nights that are not even hinted at in the warm, sunny days. Who says SoCal has no seasons? You have to develop the observational skills of a scientist and pay attention, but you can discern the differences if you try.

A beautiful crescent moon next to Venus and a bright Orion was in the sky as I walked out to pick up the Sunday newspaper. Early morning is my very favorite time of day -- I love the smell of the not-quite-dawn air and the beginning of sunrise. One of my nieces, never an early morning person, calls this time of day "the butt-crack of dawn." I've also heard it referred to as "o'dark early".

If I hurry, I'll have finished the Los Angeles Times before sunrise.

Twins -- and do they really skip a generation?

2007-10-02T07:45:00.000-07:00

There is an interesting but very short article in the science section of today's NY Times (it's Science Tuesday!) about the claim that twins can run in families but they skip a generation. The bottom line: twins can run in families but not necessarily skip a generation.

In my family, they have skipped 3 generations. On my father's side, my grandmother had twin sisters (Ruby and Ruth) and my grandfather had twin brothers (Ray and Roy). I have no idea why names starting with "R" were so popular 100 years ago, but I digress. There are more twin sets in my family (all on my father's side, BTW) but they've skipped 3 generations.

And naturally, the writer of this piece, Anahad O'Connor, uses the concept of myth in the Platonic way: "The notion that twins always skip a generation is also a myth." It would actually be a full-time job to try to correct this misuse of the word "myth" in the press, but it still makes me cringe.

Also strange is the illustration just below the large block words "THE FACTS" -- well, THE FACTS ARE that kids don't grow on trees, to be plucked from a branch like fruit. Creepy.

NY Times Science Tuesday -- It's All About Space

2007-09-25T07:15:00.000-07:00

Run, don't walk over to today's NY Times Science section, which is entirely devoted to space travel. Happy reading!

In the Shadow of the Moon

2007-09-24T03:54:00.000-07:00

I saw the documentary "In the Shadow of the Moon" yesterday at our local art house movie theatre, and thoroughly enjoyed it. Cutting between interviews with the now (mostly) septuagenarian astronauts and contemporary TV and film footage of the Apollo missions, the film covers missions 1, 8, and 11 and more detail. Most people recall, if they are old enough, that Apollo 1 never launched, the crew killed in a "plugs-out" test weeks before the scheduled lift-off. Apollo 8 was the first manned flight to the moon and the origin of the famous "Earthrise" photograph so extensively reproduced and written about. And Apollo 11 was the first moon landing, the first time a human being walked on a world other than earth.

The film's website is greatly interactive, filled with information about the astronauts, the Apollo missions, and a moon gallery.

Towards the end of the film, the astronauts talked more about what it felt like to see the earth from space and most of the commentary is one of wonder and awe. Edgar Mitchell recalls his experience of feeling as if all was one: the earth, the moon, the spacecraft, himself. Mitchell came down to earth and translated his experience of "oneness" into the creation of the Institute of Noetic Science, an organization in Northern California that sponsors research into human potential and consciousness. Other astronauts had experiences in space that can be categorized as religious but this aspect of the space flight experience is rather downplayed in the film.

I have a particular fondness for the Apollo program, not just because the idea of traveling to the moon caught my childhood imagination (it did and so began my lifelong love of science fiction) but because it's the reason I became a scientist. When I was in the fourth grade (age 10-11) I was chosen, along with a handful of other kids, to participate in an after school enrichment program. The initial program, as I recall, was about space: we studied astronomy and the biographies of early rocket scientists (like Goddard and Braun). I remember distinctly reading about the discovery of the solar system planets and the astronomers who discovered them. This was the same year, 1968, that Apollo 8 sent back the first "Earthrise" photographs, and it was the beginning of my life in science. While I went into the biological sciences in college and afterwards, it was astronomy that first caught my attention as a kid; and all of that is thanks to that after school program at Loma Vista Elementary school in Maywood, California.

"To the Moon, Alice! Right to the Moon!"

2007-09-17T06:53:00.000-07:00

This month's Scientific American has a long article on the Constellation Program, NASA's multi-billion dollar plan for putting a human presence on the Moon and for longer periods of time than the Apollo program achieved. The new vehicle being developed is called the Orion and will replace the Space Shuttle, which is scheduled for retirement in 2010. The U.S. Moon base will also support a future mission to Mars, which has long been in the human imagination.

The Russians have also announced that they will travel to the Moon. So have the Chinese.

And you had to bury your head under the covers to not hear about the X-Prize and Google's challenge, the Google Lunar X-Prize. This contest requires competitors "to land a privately funded robotic rover on the Moon that is capable of completing several mission objectives, including roaming the lunar surface for at least 500 meters and sending video, images and data back to the Earth." The prize itself is $30 million.

Joseph Campbell would think that all of this Lunar Madness is about time.... The image of the Earth seen by astronauts, the famous Earthrise photographs provided Campbell the idea that this view of the home planet would signify a new spiritual awareness. From Thou Art That:

"The reality of living in space means that we are born anew, not born again to an old-time religion but to a new order of things. There are no horizons -- that is the meaning of the Space Age. We are in a free fall into a future that is mysterious. It is very fluid and this is disconcerting to many people. All you have to do is know how to use a parachute" (105). For Campbell, the moon missions obliterated the divided model of Heaven and Earth. The division had been artificial. "Almost fifteen years ago we had the great symbol of change that has taken place. Men stood on the moon and looked back and by television we were able to look back with them -- to see earthrise. That is the symbol that enabled us to feel the truth of the discovery that Copernicus made four and a quarter centuries ago" (105).

September 11th

2007-09-11T10:14:00.000-07:00

Another anniversary of 9/11 and there is a lot out there to chew on if you so desire. The LA Times has a great editorial entitled "What We've Lost" and what we've lost are lives as well as freedoms.

No one has covered 9/11 like the NY Times and they have updated their special online section with new articles, new resources, and links to new digital museum exhibitions.

The Washington Post has a special section on the building of the Pentagon Memorial, called Sacred Ground.

NPR's story on today's ceremony can be found here.

Biology Professor PZ Myers over at Pharyngula has sharp words as usual; I do agree with his assessment that we need to stop living in fear. I disagree with his opinion about the remembrance services; the families are behind keeping the services going and it can be pointed out that we still mark events such as the Pearl Harbor bombing. But going back to his point about our need to stop living in fear, we Americans have practically made it into a sciene; check out Barry Glasner's excellent book The Culture of Fear: Why Americans Are Afraid of the Wrong Things.

We need to remember but also move on with our lives. These are not incompatible goals but for some reason the news accounts seem to think that you can have one but not both. That's crass. There is still mourning going on at the national level. The September 11th attacks not only punched a hole in American civic mythology, but created a wound through which we were violently pulled into the 21st century. We recognize that the culture has changed, we recognize that the way we see the world has changed, and we recognize that it may be, only in the retrospective view of history, that we fully understand those changes.

Friday Science Miscellany

2007-09-07T07:46:00.000-07:00

The disappearance of bees in North American, what has been called "colony-collapse disorder" may be caused by a virus that has been transmitted: IAPV, or Israeli Acute Paralysis Virus (the virus is not Israeli, but was first described there). National Geographic, the NY Times, CNN, and New Scientist have good summaries. The journal article on the virus was published online yesterday in Science and they have also published a news article on the bee-disappearing phenomenon. The Science content is behind a subscription wall, however.

The big news yesterday was the discovery of the asteroid collison in the belt between Mars and Jupiter that sent a large asteroid towards earth 65 million years ago, changing the Earth's climate and wiping out all the dinosaurs. Check out online stories about this at National Geographic, and Scientific American. A paper published in Wednesday's Nature (again, behind a subscription wall), describes a "family" of asteroids that appear to have come from the destruction of a 40-mile wide progenitor. One of the pieces from that explosion, which occurred 160 million years ago, headed toward Earth. Another impacted on the moon and created the crater Tycho.

I've posted on Craig Venter's personal genome yesterday, but if you aren't tired of Venter yet, Issue 221 of Edge: The Third Culture is out featuring an event called "Lief: What a Concept!" with Venter as one of the invited speakers. Other speakers were Freeman Dyson, George Church, Dimitar Sasselove, Robert Shapiro, and Seth Lloyd. Together and separately they discussed the concept of life, how it originated, did it exist outside Earth, and other related idea. The fall issues of Edge will feature transcriptions of all of the talks as well as video.

Happy Friday!

Dr. J. Craig Venter's personal genome published

2007-09-06T08:52:00.000-07:00

This has been pretty big news -- the publication of Venter's genome begins the era of personal genomics. Venter had previously acknowledged that the Celera-sequenced human genome published in 2001 was 60% his, but this sequence is 100% Venter's. James Watson's genome has also been sequenced (he received a DVD containing the sequence during a ceremony in Texas back in May, but has not published the results).

There are lots of places to go on the Internet for information about this milestone. Start at PLoS Biology for their Editor's Summary and the paper itself. You can also download a poster version of Venter's genome, but be aware that the file is nearly 90Megs in size and if printed would measure 40 by 60 inches in size.

It's interesting that Venter chose to publish this paper at PLoS rather than Science or Nature -- PLoS is an open access journal and that may be behind the choice: the other two would require a subscription to gain access, plus Venter has said publicly that he is trying to calm fears about personal genomics. Some strong federal legislation preventing genetic discrimination (GINA -- Genetic Information Nondiscrimination Act) would be a more comforting development, in my opinion.

If you want to muck around in the DNA sequences themselves, you can ftp it in winzipped chunks By the way, you can also download Watson's

Eye on DNA has a nice aggregation of news and blog posts about Venter's genome.

DNA, Art, and You

2007-06-05T08:14:00.000-07:00

I saw some of these links over at Eye on DNA wihch is a great science blog to check everyday.

Companies that use your DNA sample to create art:

DNA11.com
DNA Artisty
DNA-Art

All three of these companies use "DNA fingerprinting" techniques, which is extracting DNA from cheek cells (swabbed), purify the DNA, digest the DNA with restriction enzymes, and run the digests on a gel. An image of the gel is made and then that image is processed to enhance the image and add color. The exception is the 3rd company, which creates paintings inspired by the DNA gel -- based on client interviews and color preferences.

Want to see what your website looks like as a DNA digest gel? Check out Web2DNA This site analyzes your website and converts it into digital DNA and then creates a DNA digestion gel-like image of your site's contents. Interesting.

Dissertation Concept Paper 1st Draft

2007-05-19T07:37:00.000-07:00

I gave a copy of my draft concept paper to a Ph.D chemist at work who I admire and who has been a friend for over 15 years. He really liked the concept of the paper but he really hated MLA citation format. I laughed so hard because that was one of the things I had trouble getting used to as well -- MLA format. It's just so different than any format we use for scientific publishing. Dr. Bob spent a lot of time grousing about the MLA citation format. I sympathize.

We had a long talk about my concept paper and the difficulties I've encountered trying to bridge myth and science when both sides really aren't that interested in talking to each other. At least with religion and science there is a dialogue, even if at times it's a loud and contentious conversation.

The worst part is being ridiculed from people on both sides. Very recently, I travelled to the Salk Institute in San Diego to demo an X-ray diffraction scanning system made by a major X-ray manufacturer. After the demonstration (and wow did I want the system but lack the $650K to buy one) we went to lunch. In the group were the two of us from my lab, a crystallographer from Pfizer, and the two manufacturer reps, one an engineer. The sales rep asked about my graduate work and I told him it was in Mythological Studies -- everyone at the table laughed, as if I'd delivered a great joke and the punch line was hilarious.

In a recent reflection paper for my Religious Studies class, near the end I make the following observation:

"On a personal note, I feel a bit like Evans-Pritchard, being “a sort of double outsider alienated from both worlds” which is a lot to hold, let alone balance (quoted in Doniger 231). Studying mythology is not compatible with a scientifically constructed worldview and living in a scientific world is not compatible with the animus mundi. Wendy Doniger mentions it at the end of her article, but in my every-day laboratory existence, none of the work we have done in the last three years here at Pacifica is considered scholarly. And at Pacifica, there is a strong anti-Enlightenment, anti-rationalistic, and anti-science perspective. Some of that perspective I’ve found useful and some of it I’ve found to be just another bias."

Doniger, Wendy. “The Uses and Misuses of Other Peoples’ Myths.” Journal of the American Academy of Religion 54.2 (1986): 219-239.

So the big question in my mind is whether or not I will be able to bridge the two, myth and science, successfully for my dissertation topic. I've been told I need to provide a science Ph.D to sit on my committee but finding one who will be able to appreciate the mythic path this dissertation will take has been difficult. Dr. Bob wants to read my dissertation but doesn't feel he is social enough to interact productively with my committee. I've encountered Myth faculty who've told me straight up they wouldn't understand my topic, and scientists who have shown me that they don't understand the mythic or depth psychological aspects. In some ways, it seems as though I've made a connection between the two that others just cannot fathom.

Flock of Dodos documentary on Showtime starting May 19th

2007-05-12T12:16:00.000-07:00

Randy Olson's documentary about the intelligent design vs. evolution degate. Not to be missed! The DVD will be released at the end of August.

Time and description are from www.sho.com

FLOCK OF DODOS: THE EVOLUTION-INTELLIGENT DESIGN CIRCUS (PG) (2006)

Evolutionary biologist Dr. Randy Olson is the star of this tongue-in-cheek documentary that examines both sides of the evolution versus "intelligent design" debate, a controversial subject that has pitted faith against reason and school boards against scientists in an increasingly emphatic war of words and ideas. Which side will survive, and which will go the way of the now-extinct dodo bird?

Showtime May 17 8:30 PM
Showtime Showcase May 19 1:00 PM
Showtime Showcase May 19 3:15 AM
Showtime May 20 1:00 PM
Showtime Too May 21 8:00 PM

One of those "Blog Things" Quizzes

2007-05-09T18:20:00.000-07:00

You are 67% Aries

How Aries Are You?

I am an Aries but TBO and Pumpkin both say that I'm less of an Aries than TBO (also an Aries). Pumpkin maintains that one of her Gemini personalities is an Aries, so perhaps I should get her to take this quiz, too.

San Diego trip and Griffith Park Fire

2007-05-09T06:52:00.000-07:00

One of the Ducks and I took a day trip to San Diego to demo a piece of equipment that we really want but cannot afford: a compact X-ray device that would allow us to scan our protein crystals in the crystallization tray without physically manipulating the crystals (which can lead to damage). You can even get enough data from the images to index the crystals. But as I don't have a spare $650K handy, we will have to bypass this for the present.

The instrument we looked at was in a lab at Scripps Institute and it was the first time I'd been there. The particular building we visited had an enormous lobby with no ceiling and lots of open space decorated here and there with sculptures that would interest mostly scientists. The labs themselves were typical academic labs: overcrowded with equipment, lab "stuff", and people. The shelves were all overstuffed with consumables. There were -80C freezers lining the hallways. It's interesting to see the difference between academic and commercial labs -- the set-up of the academic labs I saw would have given our Safety people apoplexy. And all of that space taking up by the beautiful lobby would be seen as wasted space -- it would quickly be remolded as more labs and offices.

On the drive back home, we could see the Griffith Park fire all the way from the 405 Fwy, getting a really good view as we drove by LAX. The LA Times has some spectacular photos on their site this morning: http://www.latimes.com/news/local/la-me-fire8may09-pg,0,856526.photogallery?coll=la-home-center I really hope that the firefighters get it under control today. TBO used to be a LA City Park Ranger and Griffith Park was her territory so she was telling me about the areas that were burning; she knows them extremely well. She also had been telling me and Pumpkin for some time now that if Griffith Park burned, it would burn spectacularly because the city had stopped the control burns a number of years ago and much of the chapparell hadn't burned in many, many years.

What I'm Reading

2007-05-05T17:26:00.000-07:00

I'm working on my dissertation concept paper, so I'm concentrating right now on my bibliographic sources. Here is a relevant quote from Anthony Stevens book The Two Million-Year-Old Self, College Station, TX: Texas A & M Univ. Press, 1993:

"...I would have us journey far into the past and way over the horizon into cultures remote from the traditions of Western psychology. And rather than restrict ourselves to historical parallels from the relatively recent Sumerian, Egyptian, Greek, or Roman past, I would go back much further, back to the hunter-gatherer existence for which our psyches were formed, back to the archetypal foundations of all human experience, back to the hominid, mammalian, and reptilian ancestors who live on in the structures of our minds and brains. To do this is to discover within Jung's two million-year-old person, a 140 million-year-old vertebrate, which supports our finite existence and animates our dreams" (5).

It's Been Too Long

2007-05-04T15:04:00.000-07:00

since I've posted to this Blog. But work, school, and life have interferred (not necessarily in that order). Since the last time I've posted, I've completed my M.A. in Mythological Studies and have advanced to Ph.D candidacy. This means that I'm writing my dissertation. But at the moment I'm actually working towards that, writing my dissertation concept paper. This must be approved before I can form a committee. Once the committee is happy, THEN I can start the dissertation clock (which at Pacifica is 24 months).

More soon.

Synthetic Biology -- a new mythology?

2006-06-13T08:51:00.000-07:00

Still swimming in all of the continuing media stories about the human genome and new genetic findings connecting disease and behaviors to specific genes? Then you may have not read much about the new field of Synthetic Biology that has emerged. OK, I'm sure you saw the biological photographic images of the Flying Spaghetti Monster in the special issue of Nature in November of last year (featuring the results if the International Genetically Engineered Machine competition). This field is so new that it's proponents and practitioners cannot agree on what to call it exactly, I've found a number of monikers:

•Synthetic Biology
•Intentional Biology
•Constructive Biology
•Natural Engineering
•Synthetic Genomes
•BioHacking
•Biological Engineering

But Synthetic Biology.... what exactly is it? A short answer is "life from scratch". Synthetic Biology.org puts it this way:

Synthetic Biology is A) the design and construction of new biological parts, devices, and systems, andB) the re-design of existing, natural biological systems for useful purposes.

Declaration of the Second International Meeting on Synthetic Biology, which was held last month in Berkeley, CA can be found here http://syntheticbiology.org/SB2Declaration.html

Pertinent links

http://www.nature.com/nature/journal/v438/n7067/index.html (subscription required)
http://bbf.openwetware.org/ The BioBricks Foundation
http://www.intentionalbiology.org/ Intentional Biology Page
http://www.openwetware.org/wiki/Main_Page Open Wet Ware Wiki
http://parts.mit.edu/registry/index.php/Main_Page Registry of Standard Biological Parts
http://syntheticbiology.org/ Synthetic Biology.org

Angelism

2005-09-15T09:00:00.000-07:00

I was reading an essay by Phillip M. Thompson, "Thomas Merton and Leo Szilard -- The Parallel Paths of a Monk and a Nuclear Physicist" (Zygon Vol 39:979-986, 2004). It's a great read all by itself, but a section of the essay caught my eye. I'll quote the pertinent sections:

"... Their evolutions reveal some striking parallels, including the tendency at different times in their lives to break radically from and toward the world, a love for and ambivalence about their vocations, and a tendency towards angelism. (emphasis mine)

The tendency toward angelism is a temptation common to religious and scientists. Novelist Walker Percy describes angelism as not a love of angels but the tendency of intellectuals to zealously seek a specialized and esoteric knowledge that transcends ordinary human experience. Persons engaged in this quest often assume that their pursuit of an aspect of knowledge will yield some ultimate Truth. The inherent distortion in such a quest often eliminates or minimizes the value of other types of truth or reality. The seeker is propelled into an "orbit" of refined reflection that makes the reentry of the seeker into the normal flow of normal human life very difficult. A proper balance of physical, emotional, intellectual, and spiritual needs is lost to the demands of a pure and almost monomaniacal pursuit of the intellect or spirit (Percy 1983, Lost in the Cosmos, 115-19, 135, 160-75)."

I read this paragraph out loud to TBO after dinner last night and it sparked a good conversation. I had never seen before, in writing, an accurate description of what is going on with me internally. And what happens when your pursuit is both intellectual AND spiritual? TBO saw it immediately, of course, but also acknowledged my recent progress in moving towards a balance of "physical, emotion, intellectual, and spiritual needs". I struggle to contain my intense curiosity and need for informational input as well as control the monkish side to my personality, which always wants to withdraw into contemplative silence. The richness of my relationships with my partners is the pull in the opposite direction that keeps me from falling completely into my head. I feel very lucky to have them in my life.

Live Dangerously: Be a Scientist

2005-05-15T11:09:00.000-07:00

That's the headline of an article over on Whitley Streiber's Unknown Country site: http://www.unknowncountry.com/news/?id=4599

The gist is that scientists in certain fields (mostly anything to do with infectious diseases or molecular biology) are dying at an unusual rate (the article mentions 20) since January of 2004. But really, this is May of 2005 and listing 20 deaths of scientists in that time period doesn't make a pattern. Besides, several of the deaths listed are clearly natural, or caused by complications of surgery, or clearly accidental. A few appear to be suicides. A few look like murder.

But I'm wondering how many individuals from other professions died during the same 17-month period? Just as an example, how many lawyers or physicians died in the same period? I'm sure, worldwide, it was more than 20. This article is a good example of conspiratorial thinking, linking together disparate events and calling it "suspicious" or evidence of a "pattern".

I think my profession is still safe.

Mongolian Death Worm?

2005-05-02T16:25:00.000-07:00

You have to wonder about guys trekking off to Mongolia to look for a creature that may or may not exist. Doesn't anyone in this expedition have a day job? Apparently not. And like most online endeavors, this one features a Pay Pal button so you can donate to keep them in batteries for their GPS units.

Well, I wish them well, but this is seriously weird science.

http://cryptoworld.co.uk/