TonySeb's Commonplace Blog

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

2007-05-18T16:20:00.001-07:00

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

2007-05-06T11:03:00.001-07:00

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

2007-04-29T14:11:00.000-07:00

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

2007-02-01T19:35:00.000-08:00

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

2007-01-29T20:37:00.000-08:00

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

2006-11-30T19:18:00.000-08:00

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

2006-09-20T13:51:00.000-07:00

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

2006-04-07T15:55:00.000-07:00

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

2006-04-02T12:31:00.000-07:00

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

2006-03-30T17:08:00.000-08:00

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

2006-02-23T19:54:00.000-08:00

[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”

2006-02-20T21:04:00.000-08:00

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

2006-02-18T13:40:00.000-08:00

“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?”

2006-02-14T20:05:00.000-08:00

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

2006-02-09T16:13:00.000-08:00

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

2006-02-01T17:17:00.000-08:00

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

2006-01-31T15:48:00.000-08:00

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"

2006-01-29T20:21:00.000-08:00

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

2006-01-28T20:39:00.000-08:00

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

2006-01-22T15:50:00.000-08:00

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?"

2006-01-22T12:53:00.000-08:00

“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?

2006-01-16T14:50:00.000-08:00

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

2006-01-14T20:31:00.000-08:00

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

2006-01-14T20:05:00.000-08:00

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

2005-12-27T20:06:00.000-08:00

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.