Looking For Some Expert-Guided Free Encyclopedia Articles In Biology?

Try the new expert-guided wiki encyclopedia, Citizendium . Some approved biology articles:

Bacteriophage
Biology
Horizontal gene transfer
Life
Metabolism
RNA interference

Many more in progress. If you have something to add or emend, register with Citizendium and offer your knowledge. Or apply for editorship yourself if you have the expertise.

Polytheistic Atheism

If everything, every event, has its own god, then the big god does not exist. I suppose you might postulate a god of all gods, but then what about the god of the god of all gods?

The sun god, the god of rain, the god of planetary engineering, the god of planetary development, the god of the first law of thermodynamics, the god of protons, the god of quarks, the god of forks, the god of computer chips, the god of bicycling, the god of blowing your nose — ad infinitum.

Try it, at table, in conversations, in everything you do. The god of blogging inspires me to write this, and the god of Dell XPSs helped along the way.

The god of planetary engineering and the god of planetary development presented us with a garden of eden.

The god of rain soaked the soil.

The god of sun warmed the soil and showered the plants with photons.

The god of energy capture decreased the entropy of the plants while more than compensatorily increasing the entropy of the universe.

That clever devil.

The god of information processing oversaw the parts production.

The god of self-organization let it happen.

The flowers bloomed, and the god of reproduction let them spread.

The god of flower pickers smiled.

The god of mother's day smiled, too.

Citizendium - An Expert-Guided Free Wiki Online Encyclopedia

Looking for a new online free encyclopedia with reliable information, check out Citizendium at Citizendium Homepage.

Citizendium, a start-up, recruits editors with credentialed expertise segregated into subject-area workgroups (economics, biology, arts, etc.) and subgroups. Those editors write and/or edit articles written by registered (Real Name required) users (free registration), and approve them for access to readers.

Registered users, whether experts or not, can write and edit articles, but all articles require fact-checking, clarity-checking, coherence-checking, and general quality-checking before approval. After approval, authors/editors can work on the latest pre-approval draft, and with further quality improvements, the new updated draft replaces the previously approved version.

If you'd like to participate as an expert editor, check out Citizendium's Homepage for a way to apply and for other ways you can participate.

Longevity: Part I

Cell homeostasis, tissue homeostasis, and organ homeostasis determine organismic homeostasis (Adam and Eve Don't Want to Get Old: New Strategies for Fighting Aging. Annals of the New York Academy of Science, Annals Extra. 8-29-2006). Therefore the efficiency of cells, tissues and organs in maintaining homeostasis would likely influence the longevity of the emergent organism.

To quantify the homeostasis efficiency of a complex system even low in hierarchy, like a eukaryotic cell, one might try valuating the degree/promptness of homeostasis of its major subsystems in response to a perturbation spectrum. But that could only quantify efficiency under the environmental conditions of the studies. Each condition might affect efficiency differently, and variably differently, in the various subsystems. Because an enormous number of environmental conditions test homeostasis-maintaining ability of the organism during a lifespan, one would need to obtain and integrate too much detail of human subsystems’ properties for any valuation of efficiency of homeostasis to have practical value in controlling human lifespan.

The property of the human system, viz., lifespan, emerges only when organismic homeostasis fails completely and death results. A model that could predict lifespan long in advance of death, even one that age-modified the prediction, might lend itself to teaching how to treat the system to improve the efficiency of homeostasis of its subsystems.

What form would such a model take? For personal benefit—a major product of aging research—the model would seem to require itself to interrogate the individual human system before running its lifespan-predicting algorithm. And do so each time as time goes by. One would want the model’s systems readout, however implemented and interpreted in relation to previous readouts, followed by a prediction of lifespan as well as a prescription of steps to take to reverse damage and improve homeostasis-maintaining ability. A massive-load-capable information-gathering-and-processing method, abstract, computational: a cyber-smart doctor, distributed geographically or miniaturized.

But that ideal model allows control of lifespan for extreme longevity, as opposed to merely extending it substantially beyond present norms. Yet, learning to extend lifespan substantially may crucially underpin any model that permits control of lifespan for extreme longevity. Minimized energy consumption as food extends lifespan in diverse genera. That would seem to have potential for obese humans, but not necessarily for non-obese humans. We do not know whether calorie minimization, ceteris paribus, extends lifespans in non-obese humans. If so, we might want to revise our quantitative criteria for obesity to retain its connotation of poor health. We have no firm idea what body mass indexes, or percent body fat, however adjusted for other anthropomorphic variables, associate with human lifespans substantially greater than current norms.

Depending on how extreme the possible longevity, achieving it may require the complex task of controlling the entire human environment, the biosphere at minimum. Hopefully, but likely, all humans will require a large core-biosphere-set of common conditions, however geo-regional, for super-efficient organismic homeostasis. In recognizing that, the motivation of individuals for youthful longevity may impel them to interact in ways to achieve that common set of conditions. Sacrifices might involve opposing nature’s algorithmic drive to reproduce. Doing that would step us closer to the question of optimal sustainable population size, and how to achieve that ethically.

The property of lifespan has interest because the desirer of longevity wants a long healthy mental life, a long-lived kingdom of the mind. Why? Because as one’s knowledge increases so do the number of paths for curiosity to pursue—and a healthy youthful mind dictates the exercise of curiosity. Because often one has ambitions and goals that require many prolonged stages. Because those who do believe in ‘afterlife’ feel they should get the greatest possible satisfaction from living before dying. Because living longer increases the chances of participating in breakthroughs to extreme longevity.

Though some suggest the possibility that someday supercomputers, perhaps quantum computers, will have the ability to simulate the processes that generate conscious and self-conscious experience in simulated humans living in a simulated biosphere (Tipler FJ. (1994) The Physics of Immortality: Modern Cosmology, God and the Resurrection of the Dead. New York: Doubleday). For all I know, I live as a simulation in a simulated world, as an experiment, perhaps an iterative run of a model program developed by model-building systems scientists beyond my ken.

Consciousness Made ‘Easy’: The Perspective of a Lay Enthusiast

As David Chalmers discovered in searching for a fundamental theory of consciousness, taking as starting point the assumption that conscious experience resides in a domain of the mind separate from that of cognitive functioning creates an explanatory ‘hard’ problem, in that no matter how much progress one makes in elucidating the mechanisms underlying cognitive functioning, the question always remains why does conscious experience accompany all that cognitive functioning.

Chalmers was inspired by that problem to postulate an extension of physical reality in which the apparent explanatory gap becomes bridged by laws of a ‘psychophysical’ nature.

A similar ‘hard’ problem of consciousness does not emerge, however, if one starts with the assumption that only one domain of the mind exists: cognitive functioning. In that case, one could only find conscious experience in the cognitive domain, and therefore the activity of a particular kind of cognitive process renders conscious experience as much subject to functional analysis as such cognitive functions as perception and learning. One can then understand consciousness-constituting cognitive functioning at the same level of understanding as that which one understand other cognitive functions.

Progress in that approach, however, requires a conception of conscious experience in terms of cognitive functioning, a conception that accords with our intimate acquaintance with conscious experience, yet does not leave open the question why conscious experience should accompany the cognitive functioning. We can derive such a conception from the postulation that whenever experiences an object consciously, the cognizing system concurrently cognizes two different realities: (1) the reality of the object itself, and, (2) the reality of the activity of cognizing the object. Just as the external object qualifies as a reality that serves as the object of cognitive functioning by the cognizing system, the activity of that cognitive functioning itself qualifies as a reality that may serve as the object of cognitive processing. In the absence of this additional information processing, the perception of object presumably occurs non-consciously—-in the dark—-since by our starting assumption no separate domain of conscious experience exists for it to reside in.

Extra work in the cognitive domain needs doing for the system to experience the object consciously. That extra work: cognitive processing of the information consisting of perceiving and reacting to that object. In cognitive terms, a system that consciously experiences an external object does so in virtue of its concurrently cognizing object and cognition of object: co-cognition of object and cognition of object. The object not only gets perceptually cognized, but at the same time cognized as getting perceived. The system not only reacts to the object but to it as an object.

The project of understanding conscious experience then becomes the admittedly nontrivial but Chalmerian 'easy' one of understanding how the experiencer applies cognitive processing of information to the real activity of cognitive processing of information about the realities of our potentially consciously experienceable world.

Religion: In 50 years

In one evolutionary biologist's opinion: Religion in 50 years:

“Third, evolutionary moral psychology will reveal the social conditions under which human moral virtues flourish. The US will follow the UK in realizing that religion is not a prerequisite for ordinary human decency.

“Thus, science will kill religion - not by reason challenging faith, but by offering a more practical, universal and rewarding moral framework for human interaction.

“A naturalistic moral philosophy will replace the rotting fictions of theological ethics. In these three ways, applied evolutionary psychology will help Enlightenment humanism fulfill its long-stalled potential to make us all brighter, wiser, happier and kinder.”

From:
18 November 2006
New Scientist

Geoffrey Miller

From EDGE: "GEOFFREY MILLER is Senior Research Fellow, Centre for Economic Learning and Social Evolution, University College London. He is a widely respected evolutionary psychologist, whose work (research focusing on evolutionary psychology and sexual selection) is in the tradition of scientists such as Richard Dawkins, Daniel Dennett, and Steven Pinker. He is the author of The Mating Mind: How Sexual Choice Shaped Human Nature.”

On Words and Writing: A Few Quotations

Words constitute the ultimate texture and stuff of our moral being, since they are the most refined and delicate and detailed, as well as the most universally used and understood, of the symbolisms whereby we express ourselves into existence.—Iris Murdoch

Good prose is like a windowpane.—George Orwell (1903-1950)

You don't write because you want to say something, you write because you have something to say.—F. Scott Fitzgerald

One must be drenched in words, literally soaked in them, to have the right ones form themselves into the proper patterns at the right moment.—Hart Crane, poet (1899-1932)

By words the mind is winged.—Aristophanes

Words are miraculous things. They describe, captivate, provoke, vivify, encompass, pervade, inspire, preserve, and comfort. So much more than that, in fact, so as to leave me at a loss of . . . words.—Whitaker

Words, as is well known, are the great foes of reality.—Joseph Conrad

The most essential gift for a good writer is a built-in, shock-proof, shit detector.—Ernest Hemingway

All first drafts are shit.—Ernest Hemingway (contribution of Peter Mc [peter@the beagleproject.com]

REDUCIBLE MOLECULAR COMPLEXITY: MIGHT SURPRISE ADVOCATES OF INTELLIGENT DESIGN

REDUCIBLE MOLECULAR COMPLEXITY: MIGHT SURPRISE ADVOCATES OF INTELLIGENT DESIGN

TonySeb: Advocates of Intelligent Design invoke a concept called “irreducible complexity”, in which the function of a complex system (e.g., a molecular system in a living organism) depends on all of its components working together, implying that building the system as a whole must occur to achieve the function of the system, and implying that gradual stepwise Darwinian evolution could not have built the system. Research reported in the journal, Science, provides contrary evidence.

Science 7 April 2006: Vol. 312. no. 5770, pp. 97 - 101DOI: 10.1126/science.1123348

http://www.sciencemag.org/cgi/content/abstract/312/5770/97

ABSTRACT

Evolution of Hormone-Receptor Complexity by Molecular Exploitation

Jamie T. Bridgham, Sean M. Carroll, Joseph W. Thornton*

According to Darwinian theory, complexity evolves by a stepwise process of elaboration and optimization under natural selection. Biological systems composed of tightly integrated parts seem to challenge this view, because it is not obvious how any element's function can be selected for unless the partners with which it interacts are already present. Here we demonstrate how an integrated molecular system—the specific functional interaction between the steroid hormone aldosterone and its partner the mineralocorticoid receptor—evolved by a stepwise Darwinian process.

Using ancestral gene resurrection, we show that, long before the hormone evolved, the receptor's affinity for aldosterone was present as a structural by-product of its partnership with chemically similar, more ancient ligands. Introducing two amino acid changes into the ancestral sequence recapitulates the evolution of present-day receptor specificity.

Our results indicate that tight interactions can evolve by molecular exploitation—recruitment of an older molecule, previously constrained for a different role, into a new functional complex.

Center for Ecology and Evolutionary Biology, University of Oregon, Eugene, OR 97403, USA.

* To whom correspondence should be addressed. E-mail: joet@uoregon.edu (image placeholder)

Excerpt from “God and the Founders”, By Jon Meacham, Newsweek

April 10, 2006 issue, taken from MSNBC’s Newsweek Society

http://www.msnbc.msn.com/id/12115700/site/newsweek/

“However dominant in terms of numbers, Christianity is only a thread in the American tapestry—it is not the whole tapestry. The God who is spoken of and called on and prayed to in the public sphere is an essential character in the American drama, but He is not specifically God the Father or the God of Abraham. The right's contention that we are a "Christian nation" that has fallen from pure origins and can achieve redemption by some kind of return to Christian values is based on wishful thinking, not convincing historical argument.”

“Writing to the Hebrew Congregation in Newport, Rhode Island, in 1790, George Washington assured his Jewish countrymen that the American government "gives to bigotry no sanction." In a treaty with the Muslim nation of Tripoli initiated by Washington, completed by John Adams, and ratified by the Senate in 1797, we declared "the Government of the United States is not, in any sense, founded on the Christian religion. ... " The Founders also knew the nation would grow ever more diverse; in Virginia, Thomas Jefferson's bill for religious freedom was "meant to comprehend, within the mantle of its protection, the Jew and the Gentile, the Christian and the Mahometan, the Hindoo and infidel of every denomination." And thank God—or, if you choose, thank the Founders—that it did indeed.”

TonySeb: Can we have religious freedom without freedom from religion?

Recommended reading: Fogel, Robert W. The Fourth Great Awakening and the Future of Egalitarianism. Chicago: University of Chicago Press, 2000.

Excerpted from:

http://www.press.uchicago.edu/Misc/Chicago/256626.html

The Phases of the Four Great Awakenings
Robert William Fogel
from The Fourth Great Awakening & the Future of Egalitarianism

“To understand what is taking place today, we need to understand the nature of the recurring political-religious cycles called "Great Awakenings." Each lasting about 100 years, Great Awakenings consist of three phases, each about a generation long.”

“A cycle begins with a phase of religious revival, propelled by the tendency of new technological advances to outpace the human capacity to cope with ethical and practical complexities that those new technologies entail. The phase of religious revival is followed by one of rising political effect and reform, followed by a phase in which the new ethics and politics of the religious awakening come under increasing challenge and the political coalition promoted by the awakening goes into decline. These cycles overlap, the end of one cycle coinciding with the beginning of the next.”

TonySeb: According to Fogel, we find ourselves now in the fourth great awakening. How long before we begin the “…phase in which the new ethics and politics of the religious awakening come under increasing challenge and the political coalition promoted by the awakening goes into decline”?

Power of Prayer: Negative Test by Harvard Scientist Principal Investigator

According to MSNBC News, reporting on The Associated Press March 30, 2006:

“In the largest study of its kind, researchers found that having people pray for heart bypass surgery patients had no effect on their recovery. In fact, patients who knew they were being prayed for had a slightly higher rate of complications.”

Full story: http://www.msnbc.msn.com/id/12082681/

Full scientific article:

Benson H, Dusek JA, Sherwood JB, Lam P, Bethea CF, Carpenter W, Levitsky S, Hill PC, Clem DW, Jr., Jain MK, Drumel D, Kopecky SL, Mueller PS, Marek D, Rollins S, Hibberd PL. Study of the Therapeutic Effects of Intercessory Prayer (STEP) in cardiac bypass patients: a multicenter randomized trial of uncertainty and certainty of receiving intercessory prayer. Am Heart J 2006;151:934-42.

“Critics said the question of God's reaction to prayers simply can't be explored by scientific study.”

One wonders what those critics would have said had the study turned out positive.

Dr. Harold G. Koenig, director of the Center for Spirituality, Theology and Health at the Duke University Medical Center, who didn't take part in the study, said that science "is not designed to study the supernatural."

That conclusion, of course, assumes the existence of the supernatural, for which science finds no evidence.

The philosopher, Daniel Dennett, makes a strong argument for religion, and its adherents’ belief in a deity that wields supernatural powers, as a “natural phenomenon”. By that he means, as I interpret it, that religion and the belief in the supernatural emerged naturally in the course of human evolution, based on the natural selection of genes for particular mental structures (e.g., the predilection for detecting or assigning agency; the intentional stance) and the natural selection of cultural replicators (memes). As a natural phenomenon, religion and its belief in the supernatural admits of scientific inquiry just as does other natural phenomenon.

See: Dennett DC. Breaking the Spell: Religion as a Natural Phenomenon. New York: Penguin Group, 2006.

Michael Shermer has reviewed numerous intercessory prayer studies and notes the flaws in those claiming positive results. See:

Shermer M. Flying carpets and scientific prayers. Scientific experiments claiming that distant intercessory prayer produces salubrious effects are deeply flawed. Scientific American 2004;291:34.

Shermer ends his article thus:

“The ultimate fallacy is theological: if God is omniscient and omnipotent, he should not need to be reminded or inveigled into healing someone. Scientific prayer makes God a celestial lab rat, leading to bad science and worse religion.”

One must remember that negative studies like the Harvard study indicate only absence of evidence not evidence of absence. The Harvard study could not exclude a small positive effect (less than 10%).

Added 040404: Also see:
http://www.nature.com/news/2006/060327/full/060327-16.html

Howard Hughes Medical Institute 2005 Holiday Lectures: Evolution – Constant Change and Common Threads

[Click picture to enlarge]

On-Demand Webcasts of the lectures available free.



View webcasts here.

The lectures targeted to a high school audience:

Endless Forms Most Beautiful
Selection in Action
Fossils, Genes and Embryos
From Butterflies to Humans

Read text summaries of lectures here.

TonySeb: Fun lectures, basic evolutionary principles.

Defining “Experience” As Prerequisite To Explaining “Conscious Experience”

By Anthony Sebastian

Abstract accepted for presentation at the “Toward a Science of Consciousness” international meeting in Tucson, April 2006.

See meeting website.

ABSTRACT:

Lack of a precise definition of the word “experience” acts as an obstacle to formulating a fruitful explanation of “conscious experience” at the most general level of narrative explanation. The practice of synonymizing “experience” and “conscious experience” occasions a missed opportunity to understand “conscious” as a quality of “experience”, which can have qualities other than “conscious”.

After Leslie Dewart, I suggest a physiological definition of “experiencing” applicable to all sentient creatures. Organisms must perform a physiological activity in experiencing events of reality, first by receiving information about the event, then processing that information so as to generate a response (physical, mental) that serves the organism’s biological and/or cultural imperatives, directed ultimately to the production of biological and/or cultural progeny: genes and/or memes. The experience-initiating events may reside/originate in either the world outside the organism (external reality) or the world inside the organism (internal reality).

In performing the physiological activity of experiencing events of reality in the elemental sense as defined above, the organism lacks what generally goes by the term “conscious awareness”, either of the event experienced or of the ongoing activity of its experiencing the event. Elementally then, organisms perform the physiological activity of experiencing objects/events of reality “non-consciously”.

I emphasize that organisms perform the physiological activity of experiencing, just as they perform other physiological activities, such as regulating arterial blood pressure, walking, etc. As with any performance, performance of physiological activities admit of qualities of performance, for example, efficient or faulty regulation of arterial blood pressure, slow or brisk walking, articulate or stuttering speech. In that context, we can take the view that an organism’s performance of the physiological activity of experiencing may admit of different qualities of performance.

Humans can perform the physiological activity of experiencing events of reality “consciously”, a quality of performance that I next show admits of physiological definition. It does not stretch to recognize that performance of the very activity of non-consciously experiencing an event in, say, the external world, itself qualifies as an event of reality (i.e., an event of internal reality). As such it therefore potentially could initiate, within the organism, the performance of the activity of experiencing it as an event of reality, given the organism’s ability to experience events of reality, as I have defined “experiencing” as performed elementally. A cognitively advanced organism might have the ability to receive information about that mental (physiologically-based) activity of its non-conscious experiencing of an event of external reality, leading it to generate an adjustive response.

Performance of the physiological activity of an experiencing-complex consisting concurrently of experiencing the activity of a non-conscious experiencing has the quality we may define as “conscious”, as it speaks appositely to our intuitive conception of “conscious” and our intimate acquaintance with conscious experience. This formulation provides a physiological explanation of “conscious experience” at the most general level of narrative explanation.

A more proximate explanation requires understanding how we perform the physiological activity of receiving and processing the information about our receiving and processing information about objects/events of reality.

See: Dewart L. (Evolution and Consciousness: The Role of Speech in the Origin and Development of Human Nature. Toronto: University of Toronto Press, 1989.

Human Evolution: The Future

“Human evolution at the crossroads: Genetics, cybernetics complicate forecast for species”

Read article.

By Alan Boyle, Science editor, MSNBC
Updated: May 2, 2005

Excerpts:

The evolutionary future of humans:

“Evolutionary biologist Richard Dawkins says it's the question he's most often asked, and "a question that any prudent evolutionist will evade."”

“In the book "Future Evolution," University of Washington paleontologist Peter Ward argues that we are making ourselves virtually extinction-proof by bending Earth's flora and fauna to our will.”

“"The big thing that people overlook when speculating about human evolution is that the raw matter for evolution is variation," he said. "We are going to lose that variability very quickly, and the reason is not quite a genetic argument, but it's close. At the moment we humans speak something on the order of 6,500 languages. If we look at the number of languages we will likely pass on to our children, that number is 600."”

“Global epidemics or dramatic environmental changes represent just two of the scenarios that could cause a Unihuman society to crack, putting natural selection — or perhaps not-so-natural selection — back into the evolutionary game. Then what?”

“If different populations develop in isolation over many thousands of generations, it’s conceivable that separate species would emerge. For example, that virus-resistant strain of post-humans might eventually thrive in the wake of a global bioterror crisis, while less hardy humans would find themselves quarantined in the world’s safe havens.”

“Imagine improvements that could keep you in peak working condition past the age of 100. Those are the sorts of enhancements you might want to pass on to your descendants — and that could set the stage for reproductive isolation and an eventual species split-off.”

“[computer scientist Bill] Joy speculated that a truly intelligent robot may arise by the year 2030. “And once an intelligent robot exists, it is only a small step to a robot species — to an intelligent robot that can make evolved copies of itself,” he wrote.”

Books mentioned:

Future Evolution, Peter Ward, W. H. Freeman, 2001, ISBN: 0716734966

The Time Machine, H.G. Wells

Evolution (A Novel), Stephen Baxter, Orion Pub Co, 2002, ISBN: 0575073411

Radical Evolution : The Promise and Peril of Enhancing Our Minds, Our Bodies -- and What It Means to Be Human, Joel Garreau, Doubleday, 2005, ISBN: 0385509650

TonySeb: Interesting article, superficial.

“Is Human Evolution Over?”

Asks Robin McKie in The Guardian Unlimited:

Read article.

McKie comments on the split among scientists.

TonySeb: I say, human evolution not over so long as the natural selection and random genetic drift of genes and memes continues to operate. What can stop them?

Even if we learn to outsmart our genes and memes, we won't want to stand still.

Darwin Day Celebrations Berkeley & San Francisco, Tuesday, February 14, 2006

Presented by Bay
Area Biosystematists, UC Berkeley Entomology
Students Organization, and the Essig
Museum of Entomology

The Essig Museum holds an open house each year to celebrate the contributions of Charles Darwin to evolutionary thought. Researchers and the general public are welcome to view displays, talk shop, and enjoy presentations.

In 2006, Darwin Day will be celebrated on Tuesday, February, 14th from 1:00 to 5:00 pm. 2009 will mark Darwin's 200th birthday and the 150th anniversary of the publication of "On The Origin Of Species" with celebrations spanning the globe.

For more information about other Darwin Day activities,
please visit the Darwin Day Celebration: An international Recognition of Science and Humanity webpage.

Darwin Day (week) Events

Essig Museum of Entomology Open House (Wellman Hall): Open to the public - Posters and exhibits are available for viewing. Graduate student lead tours of the museum will begin on the hour at 2:00, 3:00, and 4:00 pm. Classes welcome (if more than 20 people please contact Cheryl Barr <cbarr@nature.berkeley.edu>).

A toast to Darwin (Wellman Hall): Limited to BNHM and BABS members - Cake and drinks in the Essig Museum at 5:30. Please RSVP to Steve Lew <stevelew@nature.berkeley.edu>

Talks and Discussion (2050 Valley Life Science Building):
Open to the public - Beginning at 7:30, all are invited to attend the following talks:

"The continuing Darwinian revolution" by Michael Ghiselin (California Academy of Sciences)

"Intellegent Design: A view from the trial" by Kevin Padian (University of California, Berkeley)

"From the Galapagos to the genome: Evolutionary biology in the 21st century" by Patrick O'Grady (University of California, Berkeley)

Nature documentary seminar (412 Wellman Hall): Open to the public - All week long, 12-1 pm, bring a lunch and enjoy a screening of the NOVA/WGBH series, "Evolution" (February 13, 15-17) and "Life in the Undergrowth - Intimate Relations" by David Attenborough (February 14 only).

Download or print a copy of our Darwin Day Flier

Understanding Evolution -- UC Berkeley Website

Below find link to the revised UC Berkeley evolution site that I discussed in a previous post (Dec. 25, 2005):

Understanding Evolution

Outstanding resource, including an Evolution 101 course, excellent illustrations, references, links to other sources. Possibly the best one-stop source of information on evolution.

A few topics:

What is evolution and how does it work?
What is the evidence for evolution?
What is the history of evolutionary theory?

Merriam-Webster Online Reports “Agnostic” Among Top Twenty Most Looked-Up Word in December, 2005

Agnostic

See etymology in their January 2006 online: Click title this post.

TonySeb: Of course, everyone knows who coined the word.

"Despite Appearances, Science Doesn't Deny The Existence of God"

The Wall Street Journal Online, January 27, 2006

Read entire article, click on this post’s title, or

http://online.wsj.com/article/SB113832581304557736.html

SCIENCE JOURNAL
By SHARON BEGLEY

January 27, 2006; Page B

Excerpts and comments:

“…science has been saddled with the canard that it arbitrarily and a priori rules out the existence of a deity.”

"It is a serious error to arbitrarily insert God or the supernatural as explanations for scientific mysteries," says biologist Richard Colling of the evangelical Olivet Nazarene University, Bourbonnais, Ill. "But it is equally unjustified to claim science excludes God."

TonySeb: Or that it excludes other mysterious supernatural forces, or even denizens from a parallel universe.

“As Barbara Forrest, a philosopher of science at Southeastern Louisiana University, Hammond, explains, ‘Science doesn't rule out anything a priori. Saying it does is false, and makes science look dogmatic.’

TonySeb: Yes, scientists must keep an open mind, but not so open that their brains fall out.

Charles Darwin: Evolution of a Scientist

Newsweek article [for complete article, click on title of this post]:

By Jerry Adler, with Anne Underwood and William Lee Adams

A few excerpts:

“He had planned to enter the ministry, but his discoveries on a fateful voyage 170 years ago shook his faith and changed our conceptions of the origins of life.”

“His own life exemplifies the painful journey from moral certainty to existential doubt that is the defining experience of modernity.”

“To a world taught to see the hand of God in every part of Nature, he suggested a different creative force altogether, an undirected, morally neutral process he called natural selection.”

The authors conclude:

“For all his nets and guns and glasses, Darwin never found God; by the same token, the Bible has nothing to impart about the genetic relationships among the finches he did find. But it is human nature to seek both kinds of knowledge. Perhaps after a few more cycles of the planet, we will find a way to pursue them both in peace.”

TonySeb: “Human nature”—perhaps.

See:

Breaking the Spell: Religion as a Natural Phenomenon,
by Daniel C. Dennett, Penguin Group, 2006

Evolution: The Remarkable History of a Scientific Theory,
by Edward J. Larson, Random House, 2004

Charles Darwin on “natural selection”, from the first edition of Origin of Species

NATURAL SELECTION. CHAP. IV., pp. 80-81

HOW will the struggle for existence, discussed too briefly in the last chapter, act in regard to variation? Can the principle of selection, which we have seen is so potent in the hands of man, apply in nature? I think we shall see that it can act most effectually. Let it be borne in mind in what an endless number of strange peculiarities our domestic productions, and, in a lesser degree, those under nature, vary; and how strong the hereditary tendency is. Under domestication, it may be truly said that the whole organisation becomes in some degree plastic. Let it be borne in mind how infinitely complex and close-fitting are the mutual relations of all organic beings to each other and to their physical conditions of life. Can it, then, be thought improbable, seeing that variations useful to man have undoubtedly occurred, that other variations useful in some way to each being in the great and complex battle of life, should sometimes occur in the course of thousands of generations? If such do occur, can we doubt (remembering that many more individuals are born than can possibly survive) that individuals having any advantage, however slight, over others, would have the best chance of surviving and of procreating their kind? On the other hand, we may feel sure that any variation in the least degree injurious would be rigidly destroyed. This preservation of favourable variations and the rejection of injurious variations, I call Natural Selection. Variations neither useful nor injurious would not be affected by natural selection, and would be left a fluctuating element, as perhaps we see in the species called polymorphic.

From:

ON THE ORIGIN OF SPECIES BY MEANS OF NATURAL SELECTION, OR THE PRESERVATION OF FAVOURED RACES IN THE STRUGGLE FOR LIFE. BY CHARLES DARWIN, M.A., October 1st, 1859 [First Edition].


Excerpt taken from:

The writings of Charles Darwin on the web
by John van Wyhe

Whye website: click title of this post

"Acts of God?"

“Acts of God?”

Editorial by Donald Kennedy, Editor-in-Chief of Science

“We know with confidence what has made the Gulf and other oceans warmer than they had been before: the emission of carbon dioxide and other greenhouse gases from human industrial activity, to which the United States has been a major contributor. That's a worldwide event, affecting all oceans.

“When Katrina hit the shore at an upgraded intensity, it encountered a wetland whose abuse had reduced its capacity to buffer the storm, and some defective levees gave way.

“Not only is the New Orleans damage not an act of God; it shouldn't even be called a "natural" disaster. These terms are excuses we use to let ourselves off the hook.”

Science 20 January 2006: Vol. 311. no. 5759, p. 303;
DOI: 10.1126/science.1124889

TonySeb: Comments?

Read the entire Editorial: click title this post.

http://www.sciencemag.org/cgi/content/summary/311/5759/303

Did viruses invent DNA, enabling them to invade the earliest RNA-containing cells?

On January 12, 2006, the editor of the science journal, Nature, introduced a “News Feature” in the journal that reported on the idea of evolutionary biologist Patrick Forterre (University of Paris-Sud, Orsay) that viruses “…invented DNA as a way around the defences of the [RNA] cells they infected.”

The editor’s note, entitled, “War of the worlds”, referring to the RNA and DNA worlds, reads:

“In life's early days, most biologists believe, there was no DNA; instead, life stored its information in RNA, a versatile molecule that can also act as an enzyme. So how did DNA eventually take over this 'RNA world'?

“Evolutionary biologist Patrick Forterre suggests that viruses, not cells, triggered the change, adopting DNA not because of its merits as an information store but because it allowed them to evade the defences of RNA-based cells. The rest is evolutionary history.”

John Whitfield, a freelance science writer. wrote the “News Feature”, entitled “Origins of DNA: Base Invaders”, Nature 439, 130-131 (12 Jan 2006) doi: 10:1038/439130a.

You can find Forterre’s original article, “The two ages of the RNA world, and the transition to the DNA world: a story of viruses and cells”, in the journal, Biochimie, Vol. 87, pgs. 793-803, 2005

doi: 10.1016/j.biochi.2005.03.015

The Abstract of Forterre’s article reads (paragraphing added for ease of reading):

“Most evolutionists agree to consider that our present RNA/DNA/protein world has originated from a simpler world in which RNA played both the role of catalyst and genetic material. Recent findings from structural studies and comparative genomics now allow to get a clearer picture of this transition. These data suggest that evolution occurred in several steps, first from an RNA to an RNA/protein world (defining two ages of the RNA world) and finally to the present world based on DNA.

“The DNA world itself probably originated in two steps, first the U-DNA world, following the invention of ribonucleotide reductase, and later on the T-DNA world, with the independent invention of at least two thymidylate synthases. Recently, several authors have suggested that evolution from the RNA world up to the Last Universal Cellular Ancestor (LUCA) could have occurred before the invention of cells.

“On the contrary, I argue here that evolution of the RNA world taken place in a framework of competing cells and viruses (preys, predators and symbionts). I focus on the RNA-to-DNA transition and expand my previous hypothesis that viruses played a critical role in the emergence of DNA.

“The hypothesis that DNA and associated mechanisms (replication, repair, recombination) first evolved and diversified in a world of DNA viruses infecting RNA cells readily explains the existence of viral-encoded DNA transaction proteins without cellular homologues. It also potentially explains puzzling observations from comparative genomic, such as the existence of two non-homologous DNA replication machineries in the cellular world.

“I suggest here [in the article] a specific scenario for the transfer of DNA from viruses to cells and briefly explore the intriguing possibility that several independent transfers of this kind produced the two cell types (prokaryote/eukaryote) and the three cellular domains presently known (Archaea, Bacteria and Eukarya).”


TonySeb: Quite a story. Check out the “News Feature” and Forterre’s article.

Human-modified ecosystems and future evolution

Article:

Western D. Human-modified ecosystems and future evolution. PNAS 2001;98:5458-65.

Full-text of complete article for free-viewing and/or free-downloading at:

http://www.pnas.org/cgi/content/full/98/10/5477

I present the Abstract below, which I paragraphed for ease of reading.

“Our global impact is finally receiving the scientific attention it deserves. The outcome will largely determine the future course of evolution.

“Human-modified ecosystems are shaped by our activities and their side effects. They share a common set of traits including simplified food webs, landscape homogenization, and high nutrient and energy inputs.

“Ecosystem simplification is the ecological hallmark of humanity and the reason for our evolutionary success. However, the side effects of our profligacy and poor resource practices are now so pervasive as to threaten our future no less than that of biological diversity itself.

“This article looks at human impact on ecosystems and the consequences for evolution. It concludes that future evolution will be shaped by our awareness of the global threats, our willingness to take action, and our ability to do so.

“Our ability is presently hampered by several factors, including the poor state of ecosystem and planetary knowledge, ignorance of human impact, lack of guidelines for sustainability, and a paucity of good policies, practices, and incentives for adopting those guidelines in daily life.

“Conservation philosophy, science, and practice must be framed against the reality of human dominated ecosystems, rather than the separation of humanity and nature underlying the modern conservation movement. The steps scientists can take to imbed science in conservation and conservation in the societal process affecting the future of ecosystems and human well-being are discussed.”

Tonyseb: PNAS has many other articles on the future of evolution in the same issue one finds the above article: A Colloqium on the Future of Evolution.

See:

http://www.pnas.org/content/vol98/issue10/index.shtml

Q & A on Evolution and Intelligent Design

From the American Association for the Advancement of Science (AAAS)

Q & A on Evolution and Intelligent Design

See: www.aaas.org/news/press_room/evolution/qanda.shtml

Below, I list the question. See AAAS’s answers with link above.

What is evolution?

Is evolution "just a theory?"

Is there "evidence against" contemporary evolutionary theory?

Is there a growing body of scientists who doubt that evolution happened?

What is intelligent design?

Is intelligent design a scientific alternative to contemporary evolutionary theory?

Why did AAAS boycott the recent Kansas State Board of Education hearings on evolution?

Aren't scientists really just afraid to debate proponents of intelligent design?

Doesn't fairness require that alternatives to contemporary evolutionary theory be taught in the public schools?

Still, it appears that scientists are arrogant or elitist when they refuse to participate in debates.

Are scientists trying to stifle discussion of intelligent design?

Are science and religion inherently opposed?

Can science stimulate religious thought?

Is the science classroom the appropriate place to discuss the religious interpretations of science?

Have scientists underestimated the impact of the intelligent design movement?

What are the stakes?

Tonyseb: I would answer some questions differently, especially those that include mention of “faith”. Thoughts?

Major Darwin exhibit at New York’s American Museum of Natural History

November 19, 2005, to May 29, 2006

Exhibit website, includes videos:

http://www.amnh.org/exhibitions/darwin/

From the journal, Nature (Nature 438, 741 (8 December 2005) doi:10.1038/438741b):

“The American Museum of Natural History in New York bills its new exhibition, Darwin, as the most in-depth ever mounted on Charles Darwin's life and thought. It's also well timed, coming as it does in the midst of litigation over 'intelligent design' in Dover, Pennsylvania, and in the run-up to the bicentennial of Darwin's birth in 2009. All that aside, Darwin is splendid: evolutionary biologist Niles Eldredge's exhibition takes us on a fascinating tour through the life of a great thinker, in what is a superb example of the curator's art.”

TonySeb: If you can’t visit, visit the rich, extensive website.

Understanding Evolution: 2005 Year-End Items

ITEM #1:

The University of California Berkeley has marvelously upgraded it “Understanding Evolution” website. Give it a look see, test its ability to answer your questions and help you find evolution information and resources:

http://evolution.berkeley.edu/


ITEM #2:

Science magazine (http://www.sciencemag.org/), in its Dec 23 2005 issue reports as breakthrough of the year: “Evolution in Action”.

In addition to the article summary, the article list many important 2005 pubscientific articles reporting advances in our understanding of evolution.

Also, the article lists many interesting websites, including:

The Evolution Project

Nature Web Focus: The Chimpanzee Genome

Ensemble Chimp Resource

Becoming Human

Kimball's Biology Pages: Speciation

Evolution 101: Speciation

And much more. Get your hands on a copy. Some fee articles on the web edition.


ITEM #3:

Evolution: Modern Darwinism paints a more flattering portrait of humanity than traditionalists might suppose

The Story of Man
The Economist, print edition, Dec 24th 2005

Includes a survey on human evolution:

The proper study of mankind: New theories and techniques have revolutionised our understanding of humanity's past and present, says Geoffrey Carr (interviewed).

The long march of everyman: It all started in Africa. [TonySeb: Happy New Year, fellow Africans, every one. See also: Dennell R, Roebroeks W. An Asian perspective on early human dispersal from Africa. Nature 2005;438:1099-104.]

Meet the relatives: A large and diverse family. [TonySeb: Our genealogy.]

If this is a man: Why it pays to be brainy. [TonySeb: How much does it pay?]

The concrete savannah: Evolution and the modern world. [The Paleolithic paradigm; agriculture as a Faustian bargain; evolutionary psychology.]

Starchild: Evolution is still coming. [TonySeb: Argument for present-day continuing natural selection of genes in humans; cultural influences on genetic evolution.]


TonySeb: Pick up the Dec 24th print edition of The Economist, with “the story of man” on the cover. Some free articles on the web edition:

http://www.economist.com/

Evolution for Everyone

Evolution for Everyone: How to Increase Acceptance of, Interest in, and Knowledge about Evolution

Essay by David Sloan Wilson

David Sloan Wilson is with the Departments of
Biology and Anthropology, Binghamton University,
Binghamton, New York, United States of America.
E-mail: dwilson@binghamton.edu

Wilson describes a single-semester college course, with no pre-requisites, designed to make evolution acceptable, interesting, and relevant to anyone, regardless of preconceptions. And much more happening to promote understanding of evolution at Binghamton University.

Citation: Wilson DS (2005). PLoS Biol 3(12): e364

Open access to article at:
http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0030364

View/download article at:

http://www.msnusers.com/AnthonySebastianMDFiles

From the Introduction:

“There appear to be two walls of resistance [regarding evolution], one denying the theory altogether and the other denying its relevance to human affairs. This essay reports a success story, showing how both walls of resistance can be surmounted by a single college course, and even more, by a university-wide program. It is based on a campus-wide evolutionary studies program called EvoS

http://bingweb.binghamton.edu/~evos/

initiated at Binghamton University in 2002, which currently includes over 50 faculty members representing 15 departments.”

TonySeb: Wilson published his essay/report in the open-access journal, PLoS Biology, which allows unrestricted distribution of the article. Spread it around, especially to educators.

Richard Dawkins says, “Read Sam Harris and wake up.”

Dawkins refers to Sam Harris’s recent book, The End of Faith: Religion, Terror, and the Future of Reason.

Available in hardcover: Norton, ISBN 0393035158, 336pp
Available in paperback: Norton, ISBN 0393327655, 224pp

Dawkins writes in “The Guardian”: “The End of Faith: Religion, Terror and the Future of Reason by Sam Harris is a genuinely frightening book about terrorism, and the central role played by religion in justifying and rewarding it…Even moderate religion is a menace, because it leads us to respect and "cherish the idea that certain fantastic propositions can be believed without evidence".”

Table Of Contents
1 Reason in Exile 11
2 The Nature of Belief 50
3 In the Shadow of God 80
4 The Problem with Islam 108
5 West of Eden 153
6 A Science of Good and Evil 170
7 Experiments in Consciousness 204
Epilogue 223
Notes 229
Bibliography 293
Acknowledgments 323
Index 325

Winner of the 2005 PEN Award for Nonfiction

About PEN:

“PEN American Center is the largest of the 141 centers of International PEN, the world's oldest human rights organization and the oldest international literary organization. International PEN was founded in 1921 to dispel national, ethnic, and racial hatreds and to promote understanding among all countries…PEN American Center builds upon the achievements of such dedicated past members as W. H. Auden, James Baldwin, Willa Cather, Robert Frost, Langston Hughes, Thomas Mann, Arthur Miller, Marianne Moore, Susan Sontag, and John Steinbeck.”

“The Economist” published an extensive review of Harris’s book. You can read the full review at:

http://www.samharris.org/index.php/samharris/full-text/economist-review/

“The Economist” review begins:

“THIS book will strike a chord with anyone who has ever pondered the irrationality of religious faith and its cruel and murderous consequences—from the Spanish Inquisition to the suicide bombs of devout young Islamists. After noting that a majority of the world's population still believes in some kind of divine creator, Sam Harris goes on to show how one holy book after another promises paradise to believers and damnation to all others. Deuteronomy tells believers to have no mercy on apostates ("You must stone him to death, since he has tried to divert you from Yahweh, your God"); death is the punishment for anyone breaking the Ten Commandments; and "those that deny Our revelations shall be punished for their misdeeds," says the Koran.”

TonySeb: I consider this an important book, both for brights and believers. Because attacks on faith generally strengthen the faith of the faithful, as Dawkins has pointed out, the faithful might want to read this book in an attempt to strengthen their faith. I forewarn them, however, of the insidious power of reason.

Thanks to Robert J. Stephens, PhD, President of the international annual “Darwin Day Celebration”, for introducing me to Harris’s book. Check out:

http://www.darwinday.org/

and join in the 2006 celebration.

P.S. Bob, I’ve started my second read.

What Do You Make of “Focus Fusion”?

A non-radioactive fusion device of moderate size that generates electricity directly sufficiently cheaply to power a neighborhood.

See:

http://www.focusfusion.org/index.html

Hocus focus?
Fusion illusion?

I remain skeptical.

The Big Questions Facing Scientists Today

—What Scientists Do Not Know—

In celebrating its 125th anniversary in July 2005, the journal Science listed 125 big questions facing science today. The top two:

What is the universe made of?
What is the biological basis of consciousness?

See: Science, Vol 309, Issue 5731, 78-102 , 1 July 2005. DOI: 10.1126/science.309.5731.78b

The website gives commentary perspective on each question.

http://www.sciencemag.org/sciext/125th/

The entire list:

What Is the Universe Made Of?
What is the Biological Basis of Consciousness?
Why Do Humans Have So Few Genes?
To What Extent Are Genetic Variation and Personal Health Linked?
Can the Laws of Physics Be Unified?
How Much Can Human Life Span Be Extended?
What Controls Organ Regeneration?
How Can a Skin Cell Become a Nerve Cell?
How Does a Single Somatic Cell Become a Whole Plant?
How Does Earth's Interior Work?
Are We Alone in the Universe?
How and Where Did Life on Earth Arise?
What Determines Species Diversity?
What Genetic Changes Made Us Uniquely Human?
How Are Memories Stored and Retrieved?
How Did Cooperative Behavior Evolve?
How Will Big Pictures Emerge from a Sea of Biological Data?
How Far Can We Push Chemical Self-Assembly?
What Are the Limits of Conventional Computing?
Can We Selectively Shut Off Immune Responses?
Do Deeper Principles Underlie Quantum Uncertainty and Nonlocality?
Is an Effective HIV Vaccine Feasible?
How Hot Will the Greenhouse World Be?
What Can Replace Cheap Oil -- and When?
Will Malthus Continue to Be Wrong?
Is ours the only universe? What drove cosmic inflation?
When and how did the first stars and galaxies form?
Where do ultrahigh-energy cosmic rays come from?
What powers quasars?
What is the nature of black holes?
Why is there more matter than antimatter?
Does the proton decay?
What is the nature of gravity?
Why is time different from other dimensions?
Are there smaller building blocks than quarks?
Are neutrinos their own antiparticles?
Is there a unified theory explaining all correlated electron systems?
What is the most powerful laser researchers can build?
Can researchers make a perfect optical lens?
Is it possible to create magnetic semiconductors that work at room temperature?
What is the pairing mechanism behind high-temperature superconductivity?
Can we develop a general theory of the dynamics of turbulent flows and the motion of granular materials?
Are there stable high-atomic-number elements?
Is superfluidity possible in a solid?
What is the structure of water?
What is the nature of the glassy state?
Are there limits to rational chemical synthesis?
What is the ultimate efficiency of photovoltaic cells?
Will fusion always be the energy source of the future?
What drives the solar magnetic cycle?
How do planets form?
What causes ice ages?
What causes reversals in Earth's magnetic field?
Are there earthquake precursors that can lead to useful predictions?
Is there--or was there--life elsewhere in the solar system?
What is the origin of homochirality in nature?
Can we predict how proteins will fold?
How many proteins are there in humans?
How do proteins find their partners?
How many forms of cell death are there?
What keeps intracellular traffic running smoothly?
What enables cellular components to copy themselves independent of DNA?
What roles do different forms of RNA play in genome function?
What role do telomeres and centromeres play in genome function?
Why are some genomes really big and others quite compact?
What is all that "junk" doing in our genomes?
How much will new technologies lower the cost of sequencing?
How do organs and whole organisms know when to stop growing?
How can genome changes other than mutations be inherited?
How is asymmetry determined in the embryo?
How do limbs, fins, and faces develop and evolve?
What triggers puberty?
Are stem cells at the heart of all cancers?
Is cancer susceptible to immune control?
Can cancers be controlled rather than cured?
Is inflammation a major factor in all chronic diseases?
How do prion diseases work?
How much do vertebrates depend on the innate immune system to fight infection?
Does immunologic memory require chronic exposure to antigens?
Why doesn't a pregnant woman reject her fetus?
What synchronizes an organism's circadian clocks?
How do migrating organisms find their way?
Why do we sleep?
Why do we dream?
Why are there critical periods for language learning?
Do pheromones influence human behavior?
How do general anesthetics work?
What causes schizophrenia?
What causes autism?
To what extent can we stave off Alzheimer's?
What is the biological basis of addiction?
Is morality hardwired into the brain?
What are the limits of learning by machines?
How much of personality is genetic?
What is the biological root of sexual orientation?
Will there ever be a tree of life that systematists can agree on?
How many species are there on Earth?
What is a species?
Why does lateral transfer occur in so many species and how?
Who was LUCA (the last universal common ancestor)?
How did flowers evolve?
How do plants make cell walls?
How is plant growth controlled?
Why aren't all plants immune to all diseases?
What is the basis of variation in stress tolerance in plants?
What caused mass extinctions?
Can we prevent extinction?
Why were some dinosaurs so large?
How will ecosystems respond to global warming?
How many kinds of humans coexisted in the recent past, and how did they relate?
What gave rise to modern human behavior?
What are the roots of human culture?
What are the evolutionary roots of language and music?
What are human races, and how did they develop?
Why do some countries grow and others stagnate?
What impact do large government deficits have on a country's interest rates and economic growth rate?
Are political and economic freedom closely tied?
Why has poverty increased and life expectancy declined in sub-Saharan Africa?
The following six mathematics questions are drawn from a list of seven outstanding problems selected by the Clay Mathematics Institute.
Is there a simple test for determining whether an elliptic curve has an infinite number of rational solutions?
Can a Hodge cycle be written as a sum of algebraic cycles?
Will mathematicians unleash the power of the Navier-Stokes equations?
Does Poincaré's test identify spheres in four-dimensional space?
Do mathematically interesting zero-value solutions of the Riemann zeta function all have the form a (image placeholder)bi?
Does the Standard Model of particle physics rest on solid mathematical foundations?

Evolutionary Perspective on the Acid-Base Effects of Diet: The Paleolithic Paradigm

“Evolutionary Perspective on the Acid-Base Effects of Diet: The Paleolithic Paradigm”

See:

http://groups.msn.com/AnthonySebastianMDFiles

File consists of text and figures of a lecture I gave on the occasion of the University of California San Francisco’s Academic Senate 5th Distinguished Clinical Research Lecture, October 12, 2005.

Comments welcomed.

Darwinism and Bishop Spong

“The challenge of Darwinian thinking to traditional Christianity is deep and profound. That means that Christianity's survival depends on its being big enough to embrace a post-Darwinian world. If we cannot then Christianity will surely die.”

US Anglican bishop John Shelby Spong commentating in his weekly newsletter (28 September)

From: New Scientist, 8 October 2005, page 18
http://www.newscientist.com/

John Shelby Spong’s HomePage:
http://www.dioceseofnewark.org/jsspong/index.html


Spong’s call for a new reformation:
http://www.dioceseofnewark.org/jsspong/reform.html

TonySeb: Bishop Spong worries that Christianity will die if it doesn’t “embrace a post-Darwinian world”. If Christianity embraces Darwinian evolution and the modern science worldview, shall it not die anyway?

Favorite Quotation 092705 [Ralph Waldo Emerson]

Earth laughs in flowers…

--Ralph Waldo Emerson(1803-1882)

Source: The Columbia World of Quotations, 1996
http://www.bartleby.com/66/

Why the laughter?

…to see her boastful boys,
Earth-proud, proud of the earth which is not theirs;
Who steer the plough, but cannot steer their feet
Clear of the grave.

From his poem, “Hamatreya”
Full-text at:
http://www.emersoncentral.com/poems/hamatreya.htm

Understanding Evolution IV -- Origin of Complex Biological Systems

If you still have doubts that complex biological systems (e.g., the human eye) can come into existence through evolution characterized by a serious of simple, random events, you might want to deepen your knowledge of molecular biology.

In the journal Nature, scientists from the Netherlands and Sweden show how uncovering the structure of a vital protein we use for defense against damaging biological invaders can reveal how that kind of evolution can occur at the molecular level. The details fascinate and edify.

The full article:

Janssen BJC, Huizinga EG, Raaijmakers HCA, Roos A, Daha MR, Nilsson-Ekdahl K, Nilsson B, Gros P.

Structures of complement component C3 provide insights into the function and evolution of immunity.

Nature 2005;437:505-11. (22 September 2005)
doi: 10.1038/nature04005

A “News and Views” report in the same issue summarizes the findings and implications:

Liddington R, Bankston L. Structural biology: Origins of chemical biodefence. Nature 2005;437:484-5.
doi: 10.1038/nature04005

Richard Dawkins explains how complex biological systems can arise through a series of simple random events over evolutionary time in his book:

Dawkins R. Climbing mount improbable. New York: Norton, 1996.

Understanding Evolution III -- Richard Dawkins

Perhaps the leading teacher of the wonders of science and the meaning of evolution. They called Henry T. Huxley "Darwin's Bulldog". Some call Dawkins "Darwin's Rottweiler". He writes accessibly and engagingly.

Richard Dawkins featured on the EDGE website:
http://www.edge.org/

Bio:
http://www.edge.org/3rd_culture/bios/dawkins.html

Article -- Science, Delusion and the Appetite for Wonder
http://www.edge.org/3rd_culture/dawkins/lecture_p1.html

Article -- A Survival Machine
http://www.edge.org/documents/ThirdCulture/j-Ch.3.html

Consciousness --- Machine Consciousness

Conference: Toward a Science of Consciousness 2004
"Tucson VI"
April 7-11, 2004

Abstract accepted for poster session.

Author: Anthony Sebastian *

A Gedankenexperiment that Establishes In Principle the Ability of Humans To Construct Consciously Experiencing Machines.

Abstract:

In his JCS article on machine consciousness, "The Borg or Borges?" [Journal of Consciousness Studies, Volume 10, No. 4-5, April-May 2003], William Thompson writes humorously and allusively, yet makes some claims clear enough for response. He writes, for example: "An engineer can be clever and construct a machine that says 'Ouch!' instead of flashing a red light, but this gnostic demiurge is mimicking consciousness to trick humans. The machine is not a sentient being capable of suffering, and….experiencing compassion for the suffering of other sentient beings."

Not clever enough, Thompson’s engineer, I say. Thompson’s and related views seem not to recognize that, first of all, all "sentient being[s]" own the essential requirements to qualify as machines. One may call them organic multi-cellular machines. One would find it difficult to argue convincingly that humans fail to qualify as machines. Merriam-Webster’s 3rd International Unabridged Dictionary states “MACHINE applies to a construction or organization whose parts are so connected and interrelated that it can be set in motion and perform work as a unit.” Sounds like my fifth-grader daughter.

One must recognize the mind-boggling level of complexity of the human machine, and realize that it acquires conscious cognitive functionality only in a socio-cultural matrix comprising other consciously experiencing machines. If nature can engineer such machines, and license the appropriate socio-cultural matrix that enables conscious experiencing, then we, who have caught on to so many of nature's machinations, can conceivably do so too.

For one example, with a not unrealistically advanced and not too future-remote technology, and sufficient knowledge of the human genome and cell structure, conceivably we could build an entirely artificial human being, from raw materials, atom by atom, starting with a single manufactured cell, a zygote, implanted in a surrogate human for gestation. Such an artificial machine, flawlessly constructed, and nurtured in the human environment, predictably would learn to speak and to experience objects and events of reality consciously.

Thus, one way to construct consciously experiencing machines involves constructing proto-machines that self-develop to an enormous level of complexity that emulates the functionality of human beings, all the while nurturing those self-developing machines in the human environment, as fully fledged members of human society. Such machines would grow and develop as nascent humans do, emotionally and cognitively, learning the trick of experiencing consciously from the natural human machines who already know the trick, just as happens with natural children.

Accordingly, this gedankenexperiment establishes conclusively in principle that we can construct from raw materials consciously experiencing machines. Issac Asimov (“I, Robot”) and Robert Heinlein (“Friday”) understood the basic requirements decades ago. If possible in principle, its implementation just needs clever enough engineers, cleverer than the ones Thompson imagines.

* My first post on the subject of conscious experiencing.

Favorite Quotation 091105

Nothing you do is important, but it is very important that you do it. —Mahatma Gandhi

I read that as: You cannot do anything truly important, but you cannot then just sit around doing nothing.

Other readings?

Favorite Quotation 090505

It is not the strongest of the species that survive, nor the most intelligent, but the one most responsive to change.

—Charles Darwin

TonySeb:

What changes in our environment, in its broadest sense, will we face to meet the qualification “most responsive to change”?

I will start the list:

(1) the rapidly diminishing availability of cheap energy;

(2) the coming of the "Singularity", the time point when machine intelligence outstrips human intelligence;

(3) ...

Interesting Article: Finding Structure in Raw Data

A computer program that can uncover structure from raw data (“corpora of raw symbolic sequential data”): For examples, see Abstract below.

Unsupervised Learning Of Natural Languages

Zach Solan*, David Horn*, Eytan Ruppin**, and Shimon Edelman***

*School of Physics and Astronomy and **School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel; and ***Department of Psychology, Cornell University, Ithaca, NY 14853

Proceedings of the National Academy of Science (PNAS) 2005 102: 11629-11634; published online before print as 10.1073/pnas.0409746102. [Need subscription to obtain full text online; university libraries carry print journal; academics can access online through their library]. Free full-text of lead-up publications at http://kybele.psych.cornell.edu/ADIOS/publications.html.

Address correspondence to Dr. Shimon Edelman: se37@cornell.edu.

Abstract:

We address the problem, fundamental to linguistics, bioinformatics, and certain other disciplines, of using corpora of raw symbolic sequential data to infer underlying rules that govern their production.

Given a corpus of strings (such as text, transcribed speech, chromosome or protein sequence data, sheet music, etc.), our unsupervised algorithm recursively distills from it hierarchically structured patterns. The ADIOS (automatic distillation of structure) algorithm relies on a statistical method for pattern extraction and on structured generalization, two processes that have been implicated in language acquisition. It has been evaluated on artificial context-free grammars with thousands of rules, on natural languages as diverse as English and Chinese, and on protein data correlating sequence with function.

This unsupervised algorithm is capable of learning complex syntax, generating grammatical novel sentences, and proving useful in other fields that call for structure discovery from raw data, such as bioinformatics.

NB: For further details see Zach Solan’s Ph.D. thesis:

"The Syntax of Nature" - "The Nature of Syntax": a study of the hidden structures in human language and in other raw sequential data such as music, proteins, DNA and more...

http://www.tau.ac.il/~zsolan/

TonySeb: What use could you get out of ADIOS? Perhaps we could learn how to “talk” to birds, dolphins, à la Dr. Doolittle.

More on scienceblog: http://www.scienceblog.com/cms/node/8802

Important Article: A Must Read for Human Life-Fulfillment in the 21st Century

An energy emergency looms—we all know it, though with heads buried in the sand.

--Shall we ration?
--Invest more in technological solutions?
--Throttle our gross materialism?

Read, free online:

The Joseph Strategy. David Ehrenfeld. Orion Magazine, September-October, 2003.

http://www.oriononline.org/pages/om/03-5om/Ehrenfeld.html

Other generic strategies, anyone?

Books 090105

The Modern Library’s List of the 100 Best Non-Fiction Books of the 20th Century


Selected by the Modern Library’s board of authors, historians, critics, and “a scientist”.

[Which have you read? Add your own choices to the list, and explain why you consider them among the best.]

-------------
THE EDUCATION OF HENRY ADAMS by Henry Adams
THE VARIETIES OF RELIGIOUS EXPERIENCE by William James
UP FROM SLAVERY by Booker T. Washington
A ROOM OF ONE'S OWN by Virginia Woolf
SILENT SPRING by Rachel Carson
SELECTED ESSAYS, 1917-1932 by T. S. Eliot
THE DOUBLE HELIX by James D. Watson
SPEAK, MEMORY by Vladimir Nabokov
THE AMERICAN LANGUAGE by H. L. Mencken
THE GENERAL THEORY OF EMPLOYMENT, INTEREST, AND MONEY by John Maynard Keynes
THE LIVES OF A CELL by Lewis Thomas
THE FRONTIER IN AMERICAN HISTORY by Frederick Jackson Turner
BLACK BOY by Richard Wright
ASPECTS OF THE NOVEL by E. M. Forster
THE CIVIL WAR by Shelby Foote
THE GUNS OF AUGUST by Barbara Tuchman
THE PROPER STUDY OF MANKIND by Isaiah Berlin
THE NATURE AND DESTINY OF MAN by Reinhold Niebuhr
NOTES OF A NATIVE SON by James Baldwin
THE AUTOBIOGRAPHY OF ALICE B. TOKLAS by Gertrude Stein
THE ELEMENTS OF STYLE by William Strunk and E. B. White
AN AMERICAN DILEMMA by Gunnar Myrdal
PRINCIPIA MATHEMATICA by Alfred North Whitehead and Bertrand Russell
THE MISMEASURE OF MAN by Stephen Jay Gould
THE MIRROR AND THE LAMP by Meyer Howard Abrams
THE ART OF THE SOLUBLE by Peter B. Medawar
THE ANTS by Bert Hoelldobler and Edward O. Wilson
A THEORY OF JUSTICE by John Rawls
ART AND ILLUSION by Ernest H. Gombrich
THE MAKING OF THE ENGLISH WORKING CLASS by E. P. Thompson
THE SOULS OF BLACK FOLK by W.E.B. Du Bois
PRINCIPIA ETHICA by G. E. Moore
PHILOSOPHY AND CIVILIZATION by John Dewey
ON GROWTH AND FORM by D'Arcy Thompson
IDEAS AND OPINIONS by Albert Einstein
THE AGE OF JACKSON, Arthur Schlesinger by Jr.
THE MAKING OF THE ATOMIC BOMB by Richard Rhodes
BLACK LAMB and Grey Falcon by Rebecca West
AUTOBIOGRAPHIES by W. B. Yeats
SCIENCE AND CIVILIZATION IN CHINA by Joseph Needham
GOODBYE TO ALL THAT by Robert Graves
HOMAGE TO CATALONIA by George Orwell
THE AUTOBIOGRAPHY OF MARK TWAIN by Mark Twain
CHILDREN OF CRISIS by Robert Coles
A STUDY OF HISTORY by Arnold J. Toynbee
THE AFFLUENT SOCIETY by John Kenneth Galbraith
PRESENT AT THE CREATION by Dean Acheson
THE GREAT BRIDGE by David McCullough
PATRIOTIC GORE by Edmund Wilson
SAMUEL JOHNSON by Walter Jackson Bate
THE AUTOBIOGRAPHY OF MALCOLM X by Alex Haley and Malcolm X
THE RIGHT STUFF by Tom Wolfe
EMINENT VICTORIANS by Lytton Strachey
WORKING by Studs Terkel
DARKNESS VISIBLE by William Styron
THE LIBERAL IMAGINATION by Lionel Trilling
THE SECOND WORLD WAR by Winston Churchill
OUT OF AFRICA by Isak Dinesen
JEFFERSON AND HIS TIME by Dumas Malone
IN THE AMERICAN GRAIN by William Carlos Williams
CADILLAC DESERT by Marc Reisner
THE HOUSE OF MORGAN by Ron Chernow
THE SWEET SCIENCE by A. J. Liebling
THE OPEN SOCIETY AND ITS ENEMIES by Karl Popper
THE ART OF MEMORY by Frances A. Yates
RELIGION AND THE RISE OF CAPITALISM by R. H. Tawney
A PREFACE TO MORALS by Walter Lippmann
THE GATE OF HEAVENLY PEACE by Jonathan D. Spence
THE STRUCTURE OF SCIENTIFIC REVOLUTIONS by Thomas S. Kuhn
THE STRANGE CAREER OF JIM CROW by C. Vann Woodward
THE RISE OF THE WEST by William H. McNeill
THE GNOSTIC GOSPELS by Elaine Pagels
JAMES JOYCE by Richard Ellmann
FLORENCE NIGHTINGALE by Cecil Woodham-Smith
THE GREAT WAR AND MODERN MEMORY by Paul Fussell
THE CITY IN HISTORY by Lewis Mumford
BATTLE CRY OF FREEDOM by James M. McPherson
WHY WE CAN'T WAIT by Martin Luther King by Jr.
THE RISE OF THEODORE ROOSEVELT by Edmund Morris
STUDIES IN ICONOLOGY by Erwin Panofsky
THE FACE OF BATTLE by John Keegan
THE STRANGE DEATH OF LIBERAL ENGLAND by George Dangerfield
VERMEER by Lawrence Gowing
A BRIGHT SHINING LIE by Neil Sheehan
WEST WITH THE NIGHT by Beryl Markham
THIS BOY'S LIFE by Tobias Wolff
A MATHEMATICIAN'S APOLOGY by G. H. Hardy
SIX EASY PIECES by Richard P. Feynman
PILGRIM AT TINKER CREEK by Annie Dillard
THE GOLDEN BOUGH by James George Frazer
SHADOW AND ACT by Ralph Ellison
THE POWER BROKER by Robert A. Caro
THE AMERICAN POLITICAL TRADITION by Richard Hofstadter
THE CONTOURS OF AMERICAN HISTORY by William Appleman Williams
THE PROMISE OF AMERICAN LIFE by Herbert Croly
IN COLD BLOOD by Truman Capote
THE JOURNALIST AND THE MURDERER by Janet Malcolm
THE TAMING OF CHANCE by Ian Hacking
OPERATING INSTRUCTIONS by Anne Lamott
MELBOURNE by Lord David Cecil

Recently Read Books 082505

Cassidy DC. J. Robert Oppenheimer and the American Century. New York: Pi Press, 2005.

Blom P. Enlightening the World: Encyclopaeie, the Book that Changed the Course of History. New York:l Palgrave Macmilan, 2005.

Sturgeon T. More than human. New York: Farrar, Straus and Young, 1953.

Simmons D. Olympos. New York: HarperCollins Publishers, 2005.

Durham DA. Pride of Carthage: A Novel of Hannibal. New York: Doubleday; A Division of Random House, Inc., 2005.

Huxley E. Red Strangers. London: Penguin Books, 1999.

Coelho P. The Alchemist. San Francisco: HarperSanFrancisco, 1993.

Surowiecki J. The Wisdom of Crowds: Why The Many Are Smarter Than The Few And How Collective Wisdom Shapes Business, Economies, Societies and Nations. New York: Doubleday, 2004.

Greenblatt S. Will in the World: How Shakespeare Became Shakespeare. New York: W.W. Norton and Company, 2004. -- [Greenblatt knows the plays like the back of his hand; the back of his other hand has the history of the times.]

Shakespeare's The Tempest. CliffsComplete. Foster City, CA: IDG Books Worldwide, Inc., 2000. -- [Complete play, plus commentary & glossary] See: http://www.cliffsnotes.com/WileyCDA/CliffsTitle/productCd-0764585762,categoryNavId-106166.html

Poem: A Few Words

A Few Words

“In the beginning was the Word…”—
World-building Lego pieces.

Lego, Goddess of words.
Always hungry, we feed Her lexicons.

How many words to build the world?
Two, two bits. One ought...to know.

Two bits we call a quarter,
A quarter of a buck. Any one of four.

Four-play, word-play, on an okay day
In a world of words, you have your say.

Some new words—
Bacedif, bacedifog, bacedifoguh.

When we discover something new,
Lego forbid we don’t clothe the naked thing.

So few vowels. We need more.
We need to genegineer an extra tongue.

Tongues. Useful little devils. For cursing,
The specialty of devils. And praying.

The specialty of saynts.
Say it ayn’t so, Lego Jo.

—TonySeb


NB: All neologisms dedicated to Lego. Lego my foot.

Favorite Quotation 081905 [Martin Luther King, Jr.]

Every man must decide whether he will walk in the light of creative altruism or in the darkness of destructive selfishness. --Martin Luther King, Jr.

Questions:

Either or? Can one 'decide'? Definition of altruism? Whatever definition, what 'motivates', 'actuates', 'drives', etc.?

Makes one think.

History and Future of the Universe

History and Future of the Universe

PBS-Nova offers a one-page illustrated chronicle of the universe's history and projected future. Worth a glance, at:

http://www.pbs.org/wgbh/nova/origins/univ-nf.html

Food and Health - I [Green Tea and Cancer]

Green Tea and Cancer

Studies have shown that green tea affords protection in animals against cancers caused by polycyclic aromatic hydrocarbons, standard combustion products of automobiles and airplanes, formed and released in the atmosphere during the incomplete burning of coal, oil and gas, garbage, or other organic substances (e.g., in wild fires).

Beliveau R, Gingras D. Green tea: prevention and treatment of cancer by nutraceuticals. Lancet 2004;364:1021-2. doi: 10.1016/S0140-6736(04)17076-1

Park OJ, Surh YJ. Chemopreventive potential of epigallocatechin gallate and genistein: evidence from epidemiological and laboratory studies. Toxicology Letters. 2004;150:43-56. doi: 10.1016/j.toxlet.2003.06.001

Information on sources and toxic effects of polycyclic aromatic hydrocarbons: http://www.atsdr.cdc.gov/tfacts69.html.

Technical Point: Green tea contains a substance called epigallocatechin gallate, a member of the class of plant phytochemicals called polyphenols, that may mediate green tea's cancer-protecting effect by indirectly inhibiting the transcription of a gene, aryl hydrocarbon, known to mediate the toxic effects of numerous environmental contaminants, including the cancer-producing polycyclic aromatics hydrocarbons.

Palermo CM, Westlake CA, Gasiewicz TA. Epigallocatechin gallate inhibits aryl hydrocarbon receptor gene transcription through an indirect mechanism involving binding to a 90 kDa heat shock protein. Biochemistry 2005;44:5041-52. doi: 10.1021/bio47433p

For more on green tea, plus red wine, read:

The Elixir of Life: Green Tea or Red Wine?, by William H. Baarschers, SKEPTICAL INQUIRER Volume 29, Issue 5, September/October, pp 30-33.

The article identifies the author as:

“William H. Baaschers is a professor emeritus of chemistry at
Lakehead University in Thunder Bay, Ontario. His research
interests have included the chemistry of medicinal plants, synthetic chemistry, environmental science, and industrial toxicology. He is currently an advisor to the university’s Resource Centre for Occupational Health and Safety. He is the author of Eco-Facts and Eco-Fiction: Understanding the Environmental Debate (Rutledge, 1996).”

Future blog-entries: More on polyphenols; more on doi’s.

Questions: Which cancers protected against? How much green tea required, and for how long?

Favorite Quotation 081505

By words the mind is winged.

—Aristophanes, Greek Playwright, comic dramatist (c. 448-c. 385 B.C.)

For a brief bio from the Columbia Encyclopedia:
http://www.bartleby.com/65/ar/Aristph.html

From Wikipedia:
http://en.wikipedia.org/wiki/Aristophanes

Understanding Evolution - II

Click on this blog-entry's title to enter the website of the National Academies developed for easy access to resources on evolution education and research, including books, research papers, position statements, and links to outside resources.

The National Academies comprise the National Academy of Sciences, the National Academy of Engineering, the Institute of Medicine and the National Research Council.

If title link not operative, click:
http://nationalacademies.org/evolution/

Understanding Evolution - I

Click this blog-entry's title to enter a website developed by evolutionary scholars for teachers, to help them learn more about evolution so that they might improve their teaching of the subject.

But the site has value for anyone interested in learning more about evolution.

Website covers: nature of science; evolution 101; relevance of evolution; evidence; misconceptions; history of evolutionary thought; pitfalls; roadblocks; and much more.

If title-link non-operative, click here:
http://evolution.berkeley.edu

Poem: The Words on This Page

The Words on This Page

the burst
of electric cognition
that spattered them there

the crackle of synapses,
the hum of ionic pulsations
that gave them their chance

the hectic committee
of word agents
that compiled them

the Darwinian selection
that composed them
as thoughts

of themselves
as words on this page

--Anthony Sebastian

Non-Material Resources Required for Life-Fulfillment

Consider these non-material resources, and how together they give you what you need to live a fulfilling life:

• a sense of purpose
• a vision of opportunity
• a sense of the mainstream of work and life
• a strong family ethic
• a sense of community
• the capacity to engage with diverse groups
• an ethic of benevolence
• a work ethic
• a sense of discipline
• the capacity to focus and concentrate one's efforts
• the capacity to resist the lure of hedonism
• the capacity for self-education
• a thirst for knowledge
• an appreciation for quality
• self-esteem

--by Robert William Fogel (1926-), Nobel laureate, Economics

In, The Fourth Great Awakening and The Future Of Egalitarianism, The University of Chicago Press, Chicago and London, 2000

For a review of the book, click this blog-entry’s title.

Additions to the list welcomed: non-material resources.

Favorite Quotation 081405 [Iris Murdoch]

Words constitute the ultimate texture and stuff of our moral being, since they are the most refined and delicate and detailed, as well as the most universally used and understood, of the symbolisms whereby we express ourselves into existence. —Iris Murdoch, English novelist and philosopher (1919-1999).

To see a list of her publications, click this blog-entry's title.

Tonyseb's Blog Goals

I plan to make entries in this blog as one would make entries in a commonplace book: "a book of literary passages, cogent quotations, occasional thoughts, or other memorabilia" --[Merriam-Webster 3rd International (MW3)].

Also, I will post information (including excerpts and links) on various topics: nutrition, evolution, human physiology, cognition, consciousness.

"Occasional thoughts" may take the form of poetry.