Category Archive

Comprehending exponential timescales is one of the greater challenges of the human mind. As Brent pointed out:

You need a thorough understanding of the multiple levels of computing.  Programming requires understanding more levels of complexity than a mathematician, physicist, chemist, or structural engineer.

Cosmology and astrophysics as well require similar comprehension of scale from atomic fusion to stellar and galactic furnaces, and to a lesser extent geology depends on understanding the vast ages of the planet and universe.

Magnitudes such as these are difficult to understand fully, which I think contributes to the continuing challenges in the classroom over the theory of evolution. A majority of Americans do not fully accept the implications of common descent, preferring views which maintain a special status for humans, partially because it is difficult for most people to conceive of a time when there were no humans! Thinking about the world ten million years ago is daily work for a geologist, but it is nearly inconceivable for many others.

In a culture where we constantly reinforce the faith-based belief in parentism–the notion that parents are the source of Christmas presents–thankfully this season External Delivery The Future presents a critical examination of this debate, the problems with parentism, and the scientific validity of external delivery theory.

Is External Delivery the same as Santa Clausism?

No. The theory of external delivery is only concerned with empirically testing whether Christmas presents are delivered by an external agent, or an internal agent such as your parents. Santa Clausism typically starts with the premise that Santa Claus is delivering presents, and then seeks to fit the evidence to that theory. The theory of external delivery has developed strictly from objective interpretations of the empirical evidence.

(Thanks to Exploring Our Matrix for bringing this to attention.)

My NaNoWriMo novel is finished, and I am quite pleased with the result. The story Inhabitants of Eternity is a journey of philosophical and spiritual ideas set in the context of near-future scientific discoveries. In particular, the Terrestrial Planet Finder mission will be capable of observing terrestrial planets around other stars, which includes the ability to determine the gases present in the atmosphere. It is conceivable, then, that in the next century we will observe a planet that, at a distance, looks nearly identical to our own life-filled world. Though we have continually been pushed into mediocrity by the discoveries of astronomy and cosmology, Earth is still the only inhabited planet that we know of, and so the uniqueness of Earth’s phenomenon remains a steadfast truth for many people. Set in the near future when this mission first starts surveying the skies, Inhabitants of Eternity explores the implications of such a discovery on both religious and secular thought.

The story takes place through a series of dialogues that explore our conception of knowledge, the implications of biological evolution, the likelihood of extraterrestrials, and the relationship between religion and science. The main character is also a dreamer, which provides a unique setting for his own exploration of these personal and profound ideas. I have written several essays that touch on some of the themes in this story, but I until now I had not outlined the totality of these thoughts into a single work of discussion. I certainly learned a lot from this process, and I am looking forward to what the eventual finished work will look like. I like to give my writings time to ripen, so I will likely not start revisions until January or February; revision seems most beneficial with a fresh look at the manuscript.

For thus says the high and lofty one
     who inhabits eternity, whose name is Holy:
I dwell in the high and holy place,
     and also with those who are contrite and humble in spirit,
to revive the spirit of the humble,
     and to revive the heart of the contrite. (Isaiah 57:15)

Most of our conceptions of religious expression are fundamentally based on practices that are biologically human. For instance, religious books or texts require literacy, which in turn requires the development of abstraction coupled with a language–all of which resulted from increased brain size. Congregational worship is reasonable for our species since we are biologically social creatures, and our primate hierarchies form a convenient basis for the worship of a personal God.

What about other creatures, though? If squirrels, dolphins, and owls are spiritually active, how could we tell? Since most outward expressions of human religiosity are based on biologically human traits, it seems that we are largely unqualified to identify non-human spirituality by simple comparative means.

Given that we do not see these obvious parallels between human and non-human spirituality, we are led to one of three conclusions:

1) Spirituality is a result of intelligence (or some other uniquely human biological trait)

2) Non-human spirituality exists with qualities unique to each species/sub-community

3) Humans alone possess a divine spiritual gift (e.g., an immortal soul)

#1 suggests spirituality is a biological peculiarity and likely absent in non-human communities. #3 is a popular religious assumption, implying the dominion of humanity over the biosphere. Given our inability to find non-human spirituality with the comparative method, #1 and #3 are the most commonly believed conclusions; yet the absence of evidence is almost never a strong argument. Perhaps spirituality is uniquely human, but then again perhaps our religious experiences are so narrow that we constantly overlook the signs of spirituality outside of our realm.

My essay I wrote for the Pale Blue Dot III workshop was published in the August issue of the journal Astrobiology. The paper discusses the conflict that often occurs between the belief in intelligent design or creationism with the theory of evolution, particularly because the underlying story for describing both of these perspectives is sometimes similar.

View a PDF of the complete article.

Awhile back I wrote an essay on the loss of hair in human evolution. There are a few plausible reasons as to why humans became naked, but there is no strong evidence to prefer any of the ideas.

I wonder, though, what the impact on modern collective thought would have been if humans had not lost their hair. The theory of evolution repulsed many people because they did not want to draw a connection between humanity and animals–after all, humans were a status above the animals. Yet eventually sufficient evidence accumulated to suggest that humans indeed were closely related to the other great apes on the planet. Among the great apes, though, we physically stand out because of our nakedness. If we had retained our full coat of hair, would our perception of relationship to the animal world have been greater? Might this have been enough to avoid the idea of human-animal separation to begin with?

Perhaps not–but then again, hairlessness was specifically noted when Adam was becoming fully human:

They heard the sound of the Lord God walking in the garden at the time of the evening breeze, and the man and his wife hid themselves from the presence of the Lord God among the trees of the garden. But the Lord God called to the man, and said to him, ‘Where are you?’ He said, ‘I heard the sound of you in the garden, and I was afraid, because I was naked; and I hid myself.’ He said, ‘Who told you that you were naked? Have you eaten from the tree of which I commanded you not to eat?’ (Genesis 3:8-11)

The evolutionary mechanism is not a linear process of ever-increasing increasing complexity (as is unfortunately still sometimes depicted in textbooks with this classic linear human evolutionary sequence) but instead produces a tree of increasing genetic diversity.

Speciation occurred because genetic diversity is beneficial for survival. Environmental shift can cause the extinction of any single population; if there are two different populations, though, there is a greater chance that one of them will survive. The diversity of species is a device for protecting the continuity of life on Earth. Certain species may not be able to withstand catastrophic flooding, meteorite impact, or climate change as well as others, but throughout Earth’s history there has always been some species capable of continuing the community of life. Complexity is a product of this genetic diversification, but greater complexity does not have any more inherent “goodness” to it.

Diversity is the fundamental good.

One of the defining traits of our species is what we call intelligence and self-awareness. Too often, though, these traits are cited as a defining separation between man and beast; that is, owing to our intelligence we have somehow transcended the animalistic level.

Ignoring for now that this view presumes no other significant life forms other than animals and humans, this still ignores the notion that human intelligence–just like any other trait–developed over time with selection effects. Intelligence makes us superior to lizards in the same way that wings make birds superior to us. We value intelligence only because we posses it. And since our culture has lost a connection with the community of life, we often interpret this value as superiority at best–and a mandate to dominate at worst.

It was brought to my attention that the Creation Museum in Petersburg, KY has now been open for one month. I’ll limit my commentary and simply feature some excerpts from the Creation Museum brochure. Let’s dive in.

So, what is the Creation Museum all about?

The Creation Museum presents a unique and unparalleled experience, a walk through time portraying significant, life-altering events from the past, illuminating the effects of Biblical history on our present and future world.

Sounds exciting! What can I expect to see there?

Walk through the Garden of Eden. Introduce yourself to our chameleons. Examine bones, the clutch of eggs from a dinosaur, an exceptional fossil collection, and a mineral collection. Enter the Cave of Sorrows and see the horrific effects of the Fall of man. Finally, see the sacrificial Lamb on the cross, and the hope of redemption.

A walk through the most important events in the 6000 years of human history–great! But what about science and discovery today?

Each seat is a rocket launching pad in our Stargazer’s Planetarium. Prepare for lift-off. The Digistar3-SP2 digital projector showcases a spectacular spaceflight, a thrilling 22 minute ride billions of light years away to the vast outer regions of our universe. Breathtaking images and inconceivable distances make this cosmic journey under the dome a fully engaging experience.

And animitronic dinosaurs to boot! Certainly a place the whole family can enjoy. But wait a minute–will I have to sit through a preachy sermon that tells me I’m going to Hell unless I convert?

The Bible speaks for itself at the Creation Museum. We’ve just paved the Way to a greater understanding of the tenets of creation and redemption. Our exhibit halls are gilded with Truth, our gardens teem with the visible signs of Life. (Emphasis in original.)

Sounds like quite the adventure. I know that if I am ever near the viscinity of the Museum, I will certainly make the effort to take a tour (really). The brochure leaves me with one question, though: how can young-Earth creationists talk about objects being billions of light years away? Then again, maybe the Creator simply made it look as if celestial objects are billions of years old. Tricksy.

Iowa State astronomy professor Guillermo Gonzalez–well known for being a proponent of Intelligent Design–was recently denied tenure. The Discovery Institute obviously expressed concern, but the decision also prompted some criticism from the general public.

In general, tenure exists to permit the unrestricted exploration of ideas in academia. A professor who is granted tenure can pursue research interests that may be seen as controversial or speculative without risking their job security. From this argument, some claim that Gonzalez was denied tenure in order to maintain scientific homogeneity of ideas–in particular with relation to Intelligent Design.

There is a basic flaw in this line of reasoning, though. Gonzalez and others maintain that Intelligent Design is a scientific theory, an assertion rejected by most of the scientific community. This is not a bias toward one theory over another; rather, it is an acknowledgment that Intelligent Design is not science, and therefore is best left outside of the scientific realm. An idea is a valid scientific hypothesis if it is falsifiable in principle. Gravitation, relativity, string theory, astronomy, and evolution cannot ever be demonstrably proved, but all of these ideas can be falsified–that is, we could design an experiment that, if successful, would show the idea to be false. Intelligent Design, however, fails this criterion: no conceivable physical experimental outcome can falsify the notion of a Designer.

The Discovery Institute and other Intelligent Design proponents will no doubt try to make Gonzalez out to be a martyr, but this is expected since they are trying to force the acceptance of an outdated (and useless) definition of science. There is nothing wrong with a scientist who also happens to believe in a designer, but there is a problem–as Iowa State properly recognized–when a professor insists on applying non-scientific principles within the scientific community.

Over a much longer time period than intended, I sketched out some of the primary scientific challenges to a common cultural worldview in our modern global society. The Copernican Revolution placed our planet in a typical galactic environment, and the discovery of fossils shattered the notion that life on Earth was permanent. The Darwinian Revolution placed humans in the same biological arena as the animals, and the realization of human-induced climate change make this assertion even more apparent.

The modern global culture is resistant to the full implication of these ideas, since acceptance would require a behavioral change. Humans are not the masters of the world but are a single organism on the planet, subject to the same environmental pressures and feedback as any other creature. Yet the lifestyle of the modern global culture is one of consumption; the rate at which resources are used increases with time. The ideas sketched above imply that no society can biologically claim to supersede the biosphere–that is, all creatures are a component of the community of life.

The modern global culture insists on living above the biosphere, yet because we are a part of this system it is biologically disastrous for our culture to maintain the status quo.

The theories of Copernicus and Darwin are not shocking to most people today, even though the implications of Darwin’s ideas are knowingly or unknowingly rejected at times. Today global climate change has taken the stand as the “controversial” scientific theory. The perceived controversy does not stem from division within the scientific community, though, but instead from the implications of accepting human alteration of the biosphere.

The global cultural worldview was shaken by the heliocentric and evolutionary theories because they challenged the notion that humans are not subservient to the biosphere but instead are masters of the world, whether by superior intellect or divine providence. Global climate change has taken this challenge one step further by showing our culture that consumption without regard can have real and lasting impacts on the biosphere. And in spite of the superior intellect that supposedly makes us “greater than the animals”, there is no obvious technological solution to a human-induced alteration of the climate system. It is much easier to try and explain any and all climate effects as “natural variability”, because acknowledging human-induced climate change implies that people are part of the biosphere. Just as Darwin’s ideas suggest, people are simply one of many animal species on the planet. And like any other species, natural selection is always in effect to remove harmful individuals–and species–from the gene pool in order to maintain the community of life.

Done with the semester and finally getting back to exploring some Big Ideas in science.

The specific criticisms of evolutionary theory by opponents has changed over the years, but the basic premise for the opposition has not. The debate is often separated into the “science vs. religion” groups, but–especially when Darwin published his ideas–this opposition is more fundamental than a religious objection.

The discovery of fossils caused people to realize that organisms were not permanent players in the arena of life; life has remained present on Earth, but organisms have come and gone. The idea of extinction shook a basic premise of a prevailing worldview, but Darwin’s idea took this realization to a new level.

With the Origin of Species, Darwin did more than provide a mechanism for speciation: linking together all organisms on the planet led to the conclusion that humans are animals as well! We are the member of a species, subject to the same selection effects as any other living creature. We may have heightened reasoning abilities compared with fish, but that does not isolate us from the rest of the community of life. Religious objections were specific, because humans were “made in the image of God”, but non-religious objections had similar reasons. Humans were assumed to have a special status, whether divinely ordained or intellectually grasped, and evolutionary theory challenged this fundamental assertion. The world did not belong to human beings, but instead humans were part of the world. This was one of the greatest paradigm shifts since the Copernican Revolution.

Life did not take ~4 billion years to evolve on Earth.

This statement often appears in conversation and print, but it grossly misrepresents the evolutionary mechanism. Current estimates suggest life originated between 3.9 and 4.1 billion years ago, which means life took between 400 and 600 million years to evolve. The origin of eukaryotic cells is estimated to be 1.6 to 2.1 billion years ago, corresponding to an evolutionary time of 2.4 to 2.9 billion years to develop.

The 4 billion year number comes from the Cambrian explosion, which took place around 542 million years ago. Thus, the statement people actually mean to make is: “Complex animal life took ~4 billion years to evolve on Earth.” And, of course, when people are talking about the development of complex animal life, they often have the appearance of humans in mind. But life is far more persistent than that. Without the Cambrian explosion, Earth would still be a vibrant planet thriving with life.

The discovery of fossils on a large scale gave rise to the idea of extinction. Somehow, the imprints of non-existent creatures were in the geologic record. Barring supernatural influence, it soon became clear that these creatures lived long ago–before humans, even! This is not surprising news today, but at the time it was a revolutionary discovery. The prevailing worldview assumed human civilization had always existed in some form; this idea was present in the Christian theology of the time, but non-Christian views of the world also shared similar assumptions.

Look backward, there was a thriving community of life long before humans ever appeared on the planet. And looking forward, the discovery of fossils foreshadowed the eerie possibility of human extinction. Humans were thought of as different from the rest of life, though, so the ramifications of this conclusion did not fully set in until the ideas of Charles Darwin.

In 1725 in Würzburg, Germany, Dr. Johann Beringer made a startling discovery. Occasional fossils had been found earlier, but only now were geologists and natural scientists locating large quantities of fossils that questioned their view of the world. Organisms were not known to go extinct, but scientists were finding organisms in rocks that were not observed in the present.

Beringer believed that a perfect Creator could not make an imperfect creation, so it was impossible for fossils to be the remains of extinct life. Fossils, he reasoned, must have been placed by God in order to test mankind’s faith. Unfortunately for Beringer, not everyone shared his opinion. He soon became the victim of a famous geologic hoax, where he came into possession of a vast number of fossils such as those pictured below.

For about a year, Beringer collected these fabricated fossils and wrote a book describing his findings. Soon the fossils took more esoteric shapes, such as shooting stars and Hebrew scripts. He even discovered the name of God among the fossils, confirming his theory! Finally, he discovered a fossil with his own name on it; Beringer then realized that he had been the victim of an elaborate and extended hoax.

While we cannot fault Beringer for pursuing his beliefs, his famous lying stones remain in Würzburg as a testament to the pursuit of a fallible worldview.

The realization that the Earth is not at the center of the Solar System or the Universe is known to modern minds, but when Copernicus published his ideas they were not received with enthusiasm by everyone. Historically, the Catholic Church was the primary antagonist against a heliocentric view of the Solar System. Some of the basis for the Church’s opposition is the literal interpretation of certain Biblical passages to infer a physical cosmology. Religious doctrine only provided a vehicle for expressing distaste for the idea, however; if Biblical influences had not been present, other oppositions would have arisen. The problem is not religious but cultural.

Around 10,000 years ago in the Fertile Crescent, a group of people began practicing totalitarian agriculture. That is, they farmed and created surpluses, and they used the land to the exclusion of other organisms. With the food surpluses came rapid population growth that led to expansion–expansion not only of people, but also of ideas. Totalitarian agriculture spread from the Middle East, and along with these farming practices came a new worldview: the people of this culture assumed 1) they were the most superior creature, and 2) they knew the one proper way that people should live. As this culture continued to spread over the years, this centrism continued to develop; after all, if they had not found the right way to live, then why were they so apparently successful?

The first blow to this worldview was the relocation of Earth from the center of the cosmos to a rather unremarkable location. It was not a terminal blow, for the culture was able to continue growing and expanding. But it was the first of many signs that the culture had adopted a fatal worldview.

Certain ideas are unpalatable to some people. Criticism of these ideas is often attempted in a logical or scientific framework, but opposition to the idea is often more fundamental than a disagreement in methods. Over the next week or so, I will devote separate entries to each of the four ideas listed below. Some of these ideas carry more modern dissenters than others, but the collective significance of these four ideas is important in understanding our place as part of the community of life.

1) Copernican Revolution - we are not the center of the Universe

2) Discovery of Fossils - extinctions happen

3) Theory of Evolution - we share ancestors with other creatures

4) Global Climate Change - we are capable of altering our environment

Let’s condense the 4.6 billion year history of the Earth to 1 year.

The rise of atmospheric oxygen in the Paleoproterozoic occurred around 6 months ago.

The Cambrian Explosion took place about 1.5 months ago.

The K-T extinction event (that killed the dinosaurs) was 5 days ago.

Humans and human ancestors appeared about 7.5 hours ago.

The Agricultural Revolution (and rise of civilization) took place one minute ago.

It’s interesting to consider how much importance we put on that last minute.

I was digging around in my computer file archives this afternoon and came across this essay I wrote for an undergraduate seminar. It was fun to re-read, so I thought I’d post it here.

The extinction of the dinosaurs signaled the end of the reptilian era, allowing mammals to fill the now devoid ecological niches and develop in their own right. Primarily insectivores, these small mammals began to specialize: some moving underground, some taking to the fields as carnivores, others taking to the treetops and subsiding on a diet of fruits and nuts. The tree-dwellers developed into the pre-primates, ancestors of all species of ape seen today; and yet a comparison of these modern apes results in a startling observation: humans are the only primates that are virtually hairless! The evolutionary development of humans from their tree-dwelling ancestors resulted in attributes such as bipedalism, tool use, and larger brain size, but all of these traits have obvious advantages for a creature that has left the trees for the plains; however, the loss of a protective furry coat is not apparent, as all other apes–as well as most hunting animals in the plains–have retained their hair. (Indeed, in the mammalian kingdom almost all animals have kept their hair, with the exceptions of those who have moved underground or to the sea.) However, given the ecological success of humans there must be some evolutionary benefit to nakedness that aided the early hominids in their competition with the plains carnivores.

Declines in forestation caused the early tree-dwellers to diversify and seek out new habitats in order to thrive. Those who remained developed into the chimpanzee, gorilla, gibbon, and orangutan, and have since been declining in numbers. The pre-hominids ventured out into the plains, to compete with the big cats and other carnivores for a diet of meat–contrasted with the former fruit and nut diet. Nevertheless, the tree-dwellers had a fairly robust digestive system, so the progression to include meat in the diet was not necessarily a leap. Larger brain size and the emergence of bipedalism were paramount in the rivalry with other carnivores, but it seems likely that the simultaneous disappearance of body hair contributed to this advantage as well.

An idea that has gained recent popularity is that hair was shed to reduce susceptibility to disease and parasites, especially as hominids began to dwell in dens and caves. As clothing and fire could be used to control the local climate, the coat of hair may have been less necessary and its loss would have provided a decrease in health risks. (For example, because most primates are nomadic, they are not plagued with lice in the same way as wild dogs or cats; this is due to the fact that lice eggs are actually laid in the skin waste of the host’s den–only after two weeks of development do they attach themselves to the creature.) This motivation also carries with it the benefit of increased sexual attractiveness, as potential mates would be able to clearly identify fit, healthy partners. A verification for this theory is the prediction that humans who developed in regions higher concentrations of disease-carrying parasites will have less body hair than others, and indeed this is found to be true of the African races.

Clearly the sanitary motivation for becoming hairless has some merit, although it is a bit odd that no other den-dwelling mammal has taken the same preventative measures in their evolutionary history. An alternative explanation provides a more direct advantage in hunting competition against other plains dwellers. As simply a cooling device, it is not immediately beneficial to lose one’s protective coat, as exposure of the skin not only increases heat loss but also increases heat gain and risks damage from the sun’s rays (which is why heavy, loose clothing is worn in hot Arab countries). But perhaps there is a reason that the hominids would make this sacrifice in exchange for a competitive advantage. When the pre-hominids moved out to the plains speciali
zed hunting animals already dominated it, and even with larger brains they did not possess the sprinting ability to compete with the large cats and other predators. In this case, a thick coat of fur was a hindrance to hunting, as it would result in considerable overheating. The disappearance of hair and the increase in bodily sweat glands would produce significant cooling for the crucial moments of the chase, allowing the hominids to remain competitive. Interestingly enough, the loss of hair was accompanied by the development of an insulating layer of fat, providing a means of heat retention in colder weather.

More than likely, no single factor can be assigned to the loss of hair in human evolution, but rather a conglomerate of several necessary adaptations. The inability of fossils to provide specific information regarding hair and skin details makes it difficult to construct a timeline for this occurrence, but it is at least true that nakedness in hominids, while not employed by most primates, is one of the significant factors leading to the continuity of humans on the planet.

While preparing a presentation for some of my research on the climate of Archean Earth, I stumbled across an interesting excerpt from the Catechism of the Catholic Church. The Vatican’s official position on science and faith is not new to me, but I think the wording in the document carries the point well.

159. Faith and science: “…methodical research in all branches of knowledge, provided it is carried out in a truly scientific manner and does not override moral laws, can never conflict with the faith, because the things of the world and the things of faith derive from the same God. The humble and persevering investigator of the secrets of nature is being led, as it were, by the hand of God in spite of himself, for it is God, the conserver of all things, who made them what they are.” [Vatican II GS 36:1]

Pope John Paul II spoke directly about the church’s acceptance of the theory of evolution. It would be wise for Protestant leaders and churches to heed the worldview so eloquently put in the Catechism. Evangelical movements often seem to be characterized by a fear or mistrust of science, specifically concerning the theory of evolution. Yet it is not the Creator who is being replaced in these scientific ideas; of course evolution does not presuppose or eliminate a deity or designer. It is unfortunate that in the United States this ancient so-called battle between science and religion is still prevalent, but fortunately there are strong religious groups in addition to scientific communities that see this as a false conflict. After all, what kind of Creator would create purposefully misleading scientific evidence?

On this date 147 years ago Darwin’s pivotal work was published with the full title: On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life. In addition to changing the biological sciences, the work generated enormous controversy with the public. This controversy continues today in some places, most recently last year in Dover, PA where intelligent design was put on trial against the theory of evolution. I had the opportunity to attend a day of this fascinating trial, and I thought today would be fitting to post my reflections on that day in court. (I wrote this immediately after I attended court, but I never posted it here.)

I just returned from a full day at the trial in Harrisburg (Kitzmiller et al vs. Dover School Board). Today was probably the only day in the entire 5-week trial that I could attend, and I think I lucked out: the defense began testifying yesterday, beginning with Professor Michael Behe (the ID biochemist). Behe testified all day yesterday and half of today. Cross-examination went until the end of today, and I expect will continue for at least another day or two. Must more interesting and exciting than a bunch of school board members on the stand…

Behe began with the example of blood clotting as an “irreducibly complex” system; irreducible complexity comprised most of yesterday’s testimony as well. He maintained that no scientist has sucessfully described the blood clotting cascade with a Darwinian mechanism. He proceeded to refute the claims by Doolittle that the problem had been solved by pointing to popular magazine articles, omitting any mention of the peer-reviewed literature. When he finally addressed the scientific literature, it was to point out that none of the literature was relevant because the exact phrases “random mutation” and “natural selection” did not appear in the body of the papers in his sample.

He continued to refute several specific papers by bold underlining words like might, argue, and could, as the presence of these words clearly indicates the conclusions are not conclusive.

Behe spent a good deal of time describing and refuting the molecular clock hypothesis. I found this part very odd, because everything he said about the controversy surrounding the molecular clock hypothesis was true—and largely irrelevant. Near as I can tell, he was attempting to make the judge believe the molecular clock hypothesis was generally accepted in the scientific community (which it is not) and synonomous with the theory of evolution (which it is not). Unfortunately I think it would be tough to catch that without some former knowledge of the molecular clock theory.

Behe also took every possible opportunity to compare Intelligent Design with the Big Bang theory, mostly because they both could have religious/philosophical implications; but he also made the comparision in many other contexts as well. (Behe quote: “I’m surprised I didn’t mention it [in this article], I try to mention the Big Bang as often as I can.”) Of course there was also the comparision to the SETI project a few times.

Lastly, he asserted that the theory of evolution was a “special case” from other scientific theories, since it had far-reaching implications in non-biological fields (psychology, political science, etc.). He even went so far as to say the teaching of Darwinian evolution furthered the liberal political agenda (which I find odd—which party seems to operate under the auspices of “survival of the fittest”?).

The plaintiff’s job is essentially one of reduction: show that the theory of ID (as defined by the Dover School Board) is creationism in disguise and the case is won. They nearly finished one avenue of reasoning in cross-ex today, with success, and I can tell they have many more lines to pursue.

At the very least, once all is said and done I would be shocked if the school board continues to recommend the same reference book on ID (Of Pandas and People) as it was clearly demonstrated today that the multi-authored book is filled with internal contradictions on the actual meaning of ID (one chapter asserts ID does not allow for common descent, another chapter allows for it, etc.). But the plaintiff seems to have a relatively strong case, and removal of ID from the biology curriculum seems like a reasonable outcome.

Just in case you never followed this story the plaintiff won the case, and the school board was forced to remove mention of ID from the curriculum. The school board members who supported the ID initiative were also all ousted by the Dover, PA voters that year. Unfortunately, this battle still continues in other places around the nation (but interestingly enough, only in the United States). Dover was a landmark victory, though, and it will hopefully set a precedent for cases in the future.

Just yesterday I saw an interesting George Carlin video clip on environmentalism and our relationship with the planet. At first it seems like general criticism of certain environmental movements, but as he continues he actually raises some very important points: namely, the planet is not in trouble; it is people who are in trouble.

What about plastic? Although partially comedic, Carliln raises an interesting point about the disposal of non-biodegradable plastics. After all, the planet has been around for over 4 billion years, while humans civilization has only existed for around 10,000 years–and only a fraction of these years involved plastic production! The Earth system (or Gaia, if you prefer) has been able to regulate itself against severe climate and cosmological changes, which has led to both speciation and extinction. Individual species come and go, but the community of life has so far been persistent. We are part of this community, but we often like to view ourselves as separate, so the thought of our extinction can be frightening. But if a species is not beneficial to Gaia, then regulating mechanisms will tend to eliminate said species. And maybe Gaia just needed a plastic component in the biosphere system. Humanity’s purpose in the community could be the production of plastic goods that will fully enter the Earth system once humans have disappeared.

It is impossible to know the direction of a Gaian mechanism, but it is also unwise to try and fight one. And as long as we consider ourselves apart from the global community of life, we will always pose a threat to Gaia.

Today, marks the birthday of our very own Universe, which was apparently born on October 23, 4004 B.C.–at least according to the Ussher-Lightfoot Calendar. The calendar originates by a reading of the Bible by Anglican Archbishop James Ussher in 1650. Working backward from Biblical genealogies of Israelite kings, Ussher was able to deduce not only the year in which God created the Universe, but also the month and exact day (a Sunday, obviously).

Today is also Mole Day, the day we pay homage to Avagadro’s Number. Someday, celebration of this day will include the congregation of a mole of moles…but that would certainly be a lot of moles in one place.

And according to the left-hand side of my blog, today is also Cambodia Peace Treaty Day. Maybe today marks the anniversary of God’s peaceful creation of a mole of Cambodians.

This post could work with a variety of creatures, but I seem to enjoy talking about dolphins.

Many human civilizations that developed counting systems used a base of ten–and obviously the most prominent modern mathematical convention is to use base ten. It is simple enough to consider a reason for choosing to base a counting system on ten: we have ten fingers. Perhaps other factors came into play and perhaps not, but it is a reasonable enough guess.

Now let’s apply this same conclusion to dolphins. In a few million years, say that dolphins evolve to a higher level of intelligence and develop their own counting systems. Assuming dolphins do not develop fingers or any additional appendages they would have two front flippers, a dorsal fin, and a tail. Following the human convention for selecting a counting base, we might expect dolphins to use a binary (base two) counting system (counting with each flipper). Computer systems presently operate with a binary system, as a zero and one can be designated easily with low and high voltage, respectively. If binary computing is an advantage, then perhaps a dolphin society that primarily uses a binary counting system will have a technological advantage at some point in their development.

I’m telling you, watch out for the dolphins–but at least they’re friendly.

It is often used in conversation as one of the fundamental paradoxes of the Universe: which came first, the chicken or the egg? In the absence of evolutionary theory this is a problem in causality, as a chicken cannot exist without first being an egg and an egg cannot exist without being produced by a chicken.

This is no longer a paradox. Chickens are birds, and birds are the evolutionary ancestors of dinosaurs. And dinosaurs–they laid eggs. We do in fact know which came first. It is understandable that the phrase is used in the colloquial sense, but I find it especially amusing when used in an academic discussion at an astrobiology meeting, where evolutionary theory is frequently discussed.

From China’s Maternal and Infant Health Care Law (1995):

Article 10: Physicians shall, after performing the pre-marital physical check-up, explain and give medical advice to both the male and the female who have been diagnosed with certain genetic disease of a serious nature which is considered to be inappropriate for child-bearing from a medical point of view; the two may be married only if both sides agree to take long-term contraceptive measures or to take ligation operation for sterility.

Most people are aware of China’s restriction on the number of children per married couple, but this mandatory genetic testing before marriage is less well-known. Ignoring any particular comments regarding the Chinese government, I do wonder where the line should be drawn in the so-called self-improvement of our own genetic pool. The desired effect of the Chinese policy is to remove certain genetic diseases from the population, ideally never encountering these again once they have died off. But where is the line in terms of “diseases”? Many people with mental disabilities of a genetic nature do not die early and have led fulfilling lives. What about something as simple as eyesight? Many people require corrective lenses to have sufficiently functional vision. Perhaps if we artificially selected in favor of 20/20 vision glasses and contacts would eventually become a thing of the past. What about baldness, or height, or obesity?

In the United States this is of course not mandatory. However, some of these issues are more relevant than one might suspect, as fertility clinics are becoming increasingly able to offer certain genetic choices to their clients. It’s a brave new world out there.

Sigmund Freud and others have suggested a subconscious Oedipus complex (the desire of a man to kill his father and possess his mother) as an explanation for various behaviors and attractions. Assuming that this does exist in most men to at least some degree (whether or not this is valid), we can come up with an evolutionary basis for the Oedipus complex.

Part of the drive for mating in humans is the act of passing one’s genes to the next generation. However, perhaps this is not a sufficient reason for males to reproduce (perhaps due to overcrowding, social restraints, or other factors). Pair-bonding and copulation may be desired, but reproduction leads to unnecessary complications (i.e. babies). However, the presence of an Oedipus complex may tip the balance in favor of raising a family. If a male has some subconscious maternal desire, it is unlikely that he will act on this directly; but this may translate into raising a family which his partner who has taken on the “pseudo-mother” role. That is, a female partner that cares for children sufficiently satisfies the Oedipus complex as a maternal substitute. And evolutionarily, this encourages the male to produce children with the same partner.

Maybe not, but it could be…

We are genetically programmed to safeguard our genes. This is not only limited to the genes in our body, but also those of our parents, offspring, siblings, and other family. I have sometimes wondered if our affinity for a particular familial relationship is influenced by the degree of genetic similarity. A parent is always 50% genetically similar to its child. Two siblings, however, can be anywhere from 0% to 100% genetically similar, with a mean of 50%. An uncle and niece will have a mean similarity of 25% in the range [0%, 50%]. Two cousins will have a mean similarity of 12.5% in the range [0%, 50%]. (These values are inclusive of identical twins, exclusive of incest, and assume normal transmission of genes from parent to offspring.) So on average, it is genetically advantageous to have greater affinity to your immediate family than your extended family. Makes sense, right?

But what about that one cousin that you get along so well with? What is the probability that a person is more genetically similar to their cousin than their sibling? I decided to ask my good friend, Monte-Carlo simulation. I whipped up a quick script and ran off one million cases to find the result: there is a 0.64% chance that a person is more genetically similar to their cousin than their sibling.

It’s not terribly likely, but it is a high enough probability that it certainly occurs. I wonder if in these cases there actually is a greater outward affinity toward the cousin as a result of the genetic similarity.

(I should also note that my personal sibling affinity is greater than my cousin affinity, regardless of genetic similarity.)

It’s a classic experiment to determine when “self-awareness” occurs: a monkey (or child, or other creature) is placed in front of a mirror. A hat, food item, or other object is placed on the subject’s head. If the monkey reaches toward the image in the mirror, it is assumed that the monkey thinks there is someone sitting in front of it. If, however, the monkey looks in the mirror and proceeds to reach on top of its own head to retrieve the object, then the monkey is said to be self-aware–because it knows that the image in the mirror is itself.

Although the experiment itself is interesting, I have always had a problem with the conclusion. Does this really test self-awareness, or is it simply a way of assessing a creature’s learning ability (i.e. when does a creature learn how a mirror works?). Just because a monkey/baby/whatever reaches for the images doesn’t mean they aren’t self aware; it doesn’t even mean they don’t recognize their own image. All it means is that they do not understand the reflective properties of a mirror (after all, why wouldn’t they assume that a duplicate was created in the image of the mirror?). Self-awareness is indeed a difficult thing to assess, but often it seems to me that the methods for quantifying this are vague at best.

A thousand monkeys may be able to randomly pound out the works of Shakespeare, but in all probability it would take longer than the age of the Universe. Creationists will often use this line of reasoning as a refutation of evolution, but the evolutionary process–although containing random elements–is not identical to the classic monkey paradox. Instead, it is more akin to a SuperMonkey, which I have coded below in Python for your amusement (and yes, I know the code could be more efficient). SmartMonkey pounds keys at random, but once a character has correctly been entered in its proper place, it is locked there. If you want to run this code, you also need to use this sample-with-replacement method.

A better monkey-model when making an evolutionary analogy, my SmartMonkey pounded out Hamlet in just 1215 iterations (~18 minutes on a dying PIII 750MHz laptop). Even for a slow SmartMonkey, this type of result could certainly be achieved well within an acceptable timeframe.

import random
import sys
import psyco
psyco.full()

if len(sys.argv) < 2:
   text = "My hovercraft is full of eels."
   desc = "Phrase: \"" + text + "\""
else:
   fid = open(sys.argv[1],’r')
   text = fid.read()
   desc = “File: ” + sys.argv[1]

charset = ['A','B','C','D','E','F','G','H','I','J','K','L','M','N','O','P', \
'Q','R','S','T','U','V','W','X','Y','Z','a','b','c','d','e','f','g','h','i', \
'j','k','l','m','n','o','p','q','r','s','t','u','v','w','x','y','z','1','2', \
'3','4','5','6','7','8','9','0','~','!','@','#','$','%','^','&','*','(',')', \
'-','_','+','=','[', '{',']‘,’}',’\\’,'|’,':’,';’,'\”‘,’\”,’,',”, \
‘/’,'?’,’ ‘,’\n’,'\r’]
test = range(1,len(text)+1)
itercnt = 0

print desc
print “SmartMonkey is pounding the keyboard…”
while sum(test) != 0:
   monkey = sample_wr(charset,len(text))
   for i in range(0,len(text)):
      if monkey[i] == text[i]:
         test[i] = 0
   itercnt = itercnt + 1
print “Number of iterations:”, itercnt

The observation that mitochondria have their own unique set of DNA when compared against the rest of the cell is an indicator that in the development of the cell, a symbiotic relationship was formed. That is, cellular mitochondria may have been independent organisms that became incorporated into a larger cell structure for mutually beneficial reasons. Although we recognize this as an evolutionary development, today we refer to the system as “a cell”, not “a cell and mitochondria”. The degree of symbiosis is such that to the human eye there is a single functional unit.

At what point does is this distinction made? A cell without its mitochondria may not be able to produce enough energy on its own to survive. So what about humans? If not for a symbiotic relationship we share with certain bacteria in our digestive systems, we would die. Certainly we share a significant symbiotic relationship with these organisms. But when we want to refer to “a person”, is that inclusive or exclusive of the symbiotic bacteria? After all, the bacteria could find another non-human host where they could survive just as well–but the human would not fare as well without the bacteria. While the cell and mitochondria have evolved to be mutually interdependent, the human-bacteria relationship seems to lean a bit to one side.

A common (not necessarily incorrect) anthropocentric opinion is that humans are the sole “intelligent” creature on Earth, intelligence is a binary construct (either you’re self aware, or you aren’t), and behavior of other animals that may mimic certain human behavior is classified as “instinct”.

A less anthropocentric view (not necessarily correct) is that intelligence and self-awareness comprise a spectrum, with humans perhaps the most developed along this continuum. Observations of dolphins and whales indicate complex language and social behaviors that could be indicative of intelligence and/or awareness. But then again, how would one design an experiment to test this hypothesis? If intelligence is a binary construct, then it could perhaps be demonstrated with reasonable certainty that dolphins are unintelligent. If a spectrum exists, however, then we return to the curse of the astrobiologist: a sample size of one.

Philosophically I have an easier time believing that humans are not so unique that we operate based on intelligence while dolphins and blue whales (which have very high brain/body ratios) operate entirely on instinct. The Copernican principle is always present, especially in matters of life and our place in the Universe. At least in my mind, the distinction between human intelligence and animal instinct is a remnant of the geocentric view, even if the name no longer persists. There’s more than one way to say “potato”.

They say a picture is worth a thousand words, so I’ll just let the image do the work today.

This is a continuation of yesterday’s post, so be sure to read it first.

Today, let’s go back 650 million years in Earth’s history. Using our time machine, we end up on a late proterozoic beach and wander around a bit. Eventually, we spot a creature–a jellyfish–floating in the water, and (as in all good science fiction) this jellyfish is able to speak with us. Suppose we were to ask this jellyfish our question: “how did things come to be?”. The response might be something like this:

How things came to be
Once the Earth cooled down, oceans began to form. Soon after this, conditions allowed for the formation of amino acids and proteins that developed into more complex molecules and then into living cells. For over a billion years this life remained simple single-celled organisms. But eventually some of the cells began to form multicellular systems and increase in complexity. Certain cells took on specific functions so that the organism would be able to have unique abilities for metabolism and motility. And finally, after millions of years of evolution, finally jellyfish appeared!

Using this as an example, hopefully it’s a bit more obvious that I’m not looking at the data/theory being presented, but rather the way in which we tell the story.

How have things come to be? This is one of the most ancient and profound questions that has been asked since the beginning of time. Answers to this question have taken religious, political, and scientific overtones (and probably others as well). Let’s listen and hear what “Mother Culture” has to say about this. (This should be familiar if you’ve read Ishmael.)

How things came to be
About 13.7 billion years ago, the Universe came into existence via the Big Bang. This formed a lot of hydrogen, some helium, and a trace amount of lithium but not much else. Eventually, a non-uniform distribution of these elements resulted in gravitational attraction that eventually formed stars capable of fusing hydrogen into helium (and other heavier elements). When these stars reached the end of their lives, they dispersed heavier elements into space, allowing other stellar and planetary systems to form. In the third stellar generation, the solar system formed around the Sun. As the planets formed and cooled, one of them, Earth, retained liquid water on its surface. Eventually, conditions allowed the synthesis of amino acids, proteins, and other building blocks that led to the emergence of life. For over a billion years this life was simple and mostly single-celled. Over time, this life evolved into multicellular oceanic life. The development of ocean life was followed by the colonization of land by plants and amphibians. Reptiles and mammals came to flourish on the land, with mammals gaining an upper hand with the K-T extinction. Over the millions of years that followed, these mammals evolved, primates developed in the jungle, and eventually humans emerged as grassland-dwelling primate hunters.

This a familiar version of “Mother Culture’s” creation story. Do you see the problem? Look closely, or recite your own favorite version of this story, to see if you can figure out why I’m bringing this up and linking it with some “Mother Culture” (this has nothing to do with scientific accuracy, either).

A few million years from now (give or take), let’s say humanity has annihilated itself and evolution proceeds in other species. Perhaps dolphins would continue to develop their intelligence and maybe even have a technological revolution of their own. Of course, there is no reason to expect that advanced dolphin intelligence would have a lot of outward similarities to human intelligence, but there would likely be some. What about the urge to explore beyond one’s own environment? I imagine that these evolved dolphins would eventually embark on discovery journeys onto land, similar to our exploration of the oceans. And then…a dolphin space program? Just try and picture what that would look like!

Consider a simple ecosystem in balance (that some people may recognize from Ishmael by Daniel Quinn): lions, gazelle, and grass. The gazelle eat the grass, lions eat the gazelle, and the grass gains nutrients from the activity of both animals. It is easy enough to see that if, for example, there is a lot of rain and the grass becomes particularly rich and plentiful, the gazelle population will increase. As a result, the lion population will also increase with their food supply. Conversely, in a period of drought, both animal populations will decrease.

But now what happens in a period of severe drought (or freezing, or other catastrophe)? With no grass to eat, the gazelle population would vanish, followed by the lion population as well as the grass. Although this ecosystem was in equilibrium and could withstand minor perturbations, a significant shift in climate or other external forcings was sufficient to eliminate the system.

So, how does nature protect against this? Simple: lots of life, in all sorts of shapes, sizes, and environments. Death is not unnatural, nor is extinction. Nature (or Gaia, as some of us prefer for poetic reasons) does not act to preserve any particular species, but rather strives for the longevity of the community of life. Why save the whales? Because someday, whales may be the hope of this community.

There are approximately 240 M dwarf stars within 10 parsecs of Earth. M dwarfs (small, cool, dim stars) are thought to make up about 75% of the stars in the universe, although they are too faint to be detectable by the naked eye. The expected lifetime of an M dwarf is >100 billion years–much longer than the current age of the universe, so there have probably been very few M star deaths thus far.

Given the age and number of M stars, if life exists elsewhere in the universe then the life around M stars might have a significant evolutionary advantage to us Earthlings. We only got in the game a little over 4 billion years ago (when the Sun formed), but these guys could have had up to 13 billion years of development! Assuming that they didn’t blow themselves to bits in some massive civil war, there could very well be a highly advanced M star civilization out there, simply given the amount of time they could have had. Of course, self-destruction of an “intelligent” civilization is a separate matter of speculation. Maybe tomorrow I’ll go through the Drake Equation for fun. But I still like to think that somewhere out there is an M star system teeming with life.

In order to further the cause of the Church of the Flying Spaghetti Monster, Bobby Henderson graciously revealed The Gospel of the Flying Spaghetti Monster on the 28th of this month. Bobby also included some of the work done by the FSM Enlightenment Institute, including a study conducted by Michael B. Larson and myself. The work will also be published in an online periodical later this month, so for now I will simply provide the abstract to our study. The full article is found on pages 149-153 of Bobby’s book. (I still have mixed feelings about this being my first publication. Fortunately, I am also co-author on a peer-reviewed journal article currently in preparation. That should offset things a bit.)

Piracy as a Preventor of Tropical Cyclones (abstract)
Recent hurricane seasons have been characterized by intense and frequent tropical cyclones. One contributor is increased sea-surface temperature, which is caused by decreased upwelling of cold deep-ocean water. We demonstrate that decreased Pirate activity results in less upwelling. This suggests that the only viable solution to intense tropical cyclones is to increase Pirate activity.

Just an interesting tidbit today: thinking back to biology, recall the famous Miller-Urey experiment that was able to produce amino acids from atmospheric chemistry in an analogue of Earth’s early atmosphere. Subsequent variations were able to produce all amino acids necessary for life. Of course, it’s the atmosphere that interests me the most. Earth’s early atmosphere was certainly nitrogen-rich, and possibly contained a significant amount of methane (at least in the archean); the rise of atmospheric oxygen, however, did not occur until photosynthetic cyanobacteria began to have a significant ecological footprint. Of course, most of the life that we think of today is intimately dependent on an oxygen rich atmosphere, whether for respiration or photosynthesis. Here’s the interesting thing: none of the Miller-Urey experiments is successful when atmospheric oxygen is present. Reduction by oxygen does not allow for the formation of the very building blocks of life. I find it fascinating that life as we know it is so dependent on a molecule that had such little involvement its conception. Atmospheric oxygen is a rich topic for exploration; there will certainly be more later.

As of today, the paper “Piracy as a Preventor of Tropical Cyclones” by Michael Larson and myself has officially been accepted as one of the 18 (out of 120) submissions suitable for the Church of the Flying Spaghetti Monster’s Enlightenment Institute. The articles will be published online in the Science Creative Quarterly, which is not actually a quarterly publication. The winner of the coveted $100 worth of Ramen noodles has yet to be announced.

In any case, the article will also be in Bobby Henderson’s Gospel of the Flying Spaghetti Monster, available March 28. And I just might end up giving a seminar on the current state of pirate-hurricane research sometime soon.