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Paleys Watch Found in Bacteria 10/31/2008

Oct 31, 2008 A clock with cogs, gears and ratchets that keeps accurate time
what more could William Paley wish for? The 18th century natural theologian used
the illustration of stumbling upon a watch in a heath as an example of reasoning from
design to a Designer as from watch to watchmaker.
Skeptics like David Hume challenged such reasoning of the natural theologians as a mere argument from
analogy: living things are very different from mechanical
machines, he argued. One can only wonder how their debate would unfold with the
discovery of a ticking watch inside one of the simplest forms of life.
Scientists have long wondered how living things keep time.
We are all aware of our own natural cycles throughout the day. Organisms without
eyes and ears, though, like bacteria, also keep time with diurnal cycles. How do
they do it? The secret has only been coming to light in the last few years
(see 05/17/2005)
Johnson, Egli and Stewart wrote a review article in Science this week that
describes what is currently known about the circadian clock present in cyanobacteria.1
They could not help but use mechanical terms for this biological machinery.
It began right in their opening paragraph:
An endogenous circadian system in cyanobacteria exerts pervasive control
over cellular processes, including global gene expression. Indeed, the entire
chromosome undergoes daily cycles of topological changes and compaction.
The biochemical machinery underlying a circadian oscillator can be reconstituted
in vitro with just three cyanobacterial proteins, KaiA, KaiB, and KaiC. These
proteins interact to promote conformational changes and phosphorylation
events that determine the phase of the in vitro oscillation.
The high-resolution structures of these proteins suggest a ratcheting
mechanism by which the KaiABC oscillator ticks unidirectionally.
This posttranslational oscillator may interact with transcriptional and translational
feedback loops to generate the emergent circadian behavior in vivo.
The conjunction of structural, biophysical, and biochemical approaches to this
system reveals molecular mechanisms of biological timekeeping.
Conformational change is jargon for bending, springing, unfolding and other
kinds of motion that take place as the proteins operate. Proteins are therefore
the moving parts of the clock.
Later, they spoke of cogs and gears in the clockwork mechanism
evident in the Kai-ABC proteins. Each protein, in turn, is made up of multiple
parts, composed of hundreds of amino acids. KaiC, for instance, is a barrel
mechanism with two donut-shaped rings, each made of six toothed parts that make it
look like a gear wheel. The clock runs on ATP energy pellets. It accumulates
hydrogen bonds through phosphorylation events that force it to tick like a
ratchet in one direction. It keeps an accurate 24-hour cycle, releasing its
energy for the next round in conjunction with feedback loops from the nucleus and
cytoplasm. These, in turn, affect what genes are expressed by the transcribers
in the nucleus and translators in the ribosomes.
In his description of the clock posted last April on
Reasons to Believe,
Dr. Fazale Rana described how the KaiA and KaiB parts interact
with KaiC like a rotor and wing nut.
He made the same connection to Paley. Describing this as a biochemical watch
on a heath, he showed how it refutes David Humes criticism of natural
theology. The discovery of molecular machines like the circadian clock have
revitalized the watchmaker argument for the existence of God, he said.
The Science article pointed out that several questions remain.
How is the clock robust against temperature fluctuations? Does the eukaryotic
clock, which employs very different molecular systems, operate on similar design
principles? They referred to evolution twice, but only in a very indistinct, indirect way:
The benefit of a clockwork that is imperturbable even when
buffeted by the massive intracellular changes of cell division could have provided
an evolutionary driving force for convergent circadian clock mechanisms among
diverse organisms.
We now recognize KaiABC as a dynamically oscillating nanomachine
that has evolved to precess unidirectionally and robustly.
These sentences, however, merely assume that evolution produced the machines in
the first place. Since the clocks are present in some of the simplest forms of life,
it would seem a grand challenge to believe that a blind, directionless process
stumbled upon all this interacting, mechanical system by chance. Incidentally,
they pointed out that each cell has 10,000 KaiC proteins. If it is difficult
to imagine getting one clock by chance, imagine getting 10,000 that tick together.
The challenges ahead, they ended, are to delve deeper into the
molecular nature of its temperature compensation ... and to discover if the clocks
in our own cells have attributes that are similar to those of bacteria.
1. Johnson, Egli and Stewart, Structural Insights into a Circadian Oscillator,
Science,
31 October 2008: Vol. 322. no. 5902, pp. 697-701, DOI: 10.1126/science.1150451.
Oh, for the sight of David Hume and Charles Darwin
being confronted with a ticking clock inside a simple cell.
We can get an idea of their reaction, though, by looking at the fact that the
three authors of this review, after having described an intricate mechanism of oscillators, ratchets
and feedback loops, attributed it all to evolution. The many biochemists
aware of these and other exquisite molecular machines follow suit. In spite
of overpowering evidence for design, their minds are made up: they will follow
Charlie to the bitter end and die with him rather than acknowledge design.
The Apostle Paul said in Romans 1 that the evidence for God
and His attributes is
clearly seen in creation, so that men are without excuse. Each generation has
evidence of sufficient clarity for its knowledge base. For the Romans and
Egyptians, the diurnal cycles of the sun, moon and stars have been more than sufficient
to remove their excuses for unbelief and mistaken belief. For todays scientists,
the diurnal cycles of nanoscopic protein clocks throughout life is more than sufficient.
The true challenge ahead is not just to delve deeper into the molecular nature of
the design we already see, but to hold it up for display and preach the implications,
so that it takes effect in the human mind as Paul said,
casting down imaginations, and every high thing that exalts itself against
the knowledge of God (II Corinthians 10:5; cf.
01/17/2007).
Next headline on:
Cell Biology
Amazing Facts
A swarm of bee stories abuzz with design, from 10/27/2006.
FrankenTitan Comes to Life 10/30/2008

Oct 30, 2008 Theres electricity at Titan, the large moon of Saturn.
That can only mean one thing: life! Electricity Found on Saturn Moon--Could It Spark Life?
asked a headline on National
Geographic News by Rebecca Carroll. Visions of spark discharge tubes in a
mad scientists lab arise in the imagination. Recently identified electrical
activity on Saturns largest moon bolsters arguments that Titan is the kind
of place that could harbor life.
Carroll quickly pointed out that at -350° F, any Titanian life
would not resemble life as we know it. Initial indications of
electrical activity in the thick atmosphere of this unusual moon have been
confirmed in data from the Huygens Probe that landed in 2005
(see 01/15/2005,
01/21/2005). With that spark of imagination,
the L-word leaped up from the reporters table:
But a new study reports faint signs of a natural electric field in Titans
thick cloud cover that are similar to the energy radiated by lightning on Earth.
Lightning is thought to have sparked the chemical reactions that
led to the origin of life on our planet....
Jeffrey Bada, of the Scripps Institution of Oceanography, believes
the process that allowed lightning to spark life on Earth is universal
and could happen in many environmentsincluding on Titan.
Confirmation earlier this year of Titans hydrocarbon lakes
makes the Saturnian moon the first place other than Earth where open bodies of
liquid have been found.
Hydrocarbons are organic molecules, and the fact that they
exist in large quantities on Titan suggests that life could take root there
under the right conditions.
Alas, the water required for life is locked up in rock-hard ice. The precursor molecules
formed by lightning acting on hydrocarbons could go no further without water, Bada said.
But then perhaps the ice could melt under certain circumstances. Maybe
a meteor impact would melt the ice long enough for interesting things to happen.
Titans water is currently frozen into chunks as hard as granite. If those
ice rocks were to melt, however, the environment could become
more hospitable to the building blocks of life.
With liquid water, the planet could host the formation of amino acids
and then full proteins, which drive all biochemistry and set the stage
for more complex molecules.
I look at Titan as a big, frozen, prebiotic casserole,
Bada said, referring to the state before the emergence of life.
The idea that life could be widespread in the universe,
I think, is very credible.
Juan Antonio Morente of the University of Granada in Spain, the lead author of the
study, seemed less enthusiastic about the possibility of life on Titan. He said
that Titan is exposed to deadly cosmic rays because it lacks a stable magnetic field.
Without stable protection from radiation, Morente said, the existence of
life is very unlikely.
In all, Carroll used the L-word life 11 times in her short
585-word article. It seems strange Carroll would focus on life now when discussing
Morentes paper. For one thing, its not news; the paper was published
in June.1 And the team never used the L-word in
the paper. Apparently Jeffrey Bada,2 a well-known origin-of-life researcher
at Scripps, who was not involved with Morentes study, made the
statements about electricity, hydrocarbons and life recently or maybe Carroll
was looking for a story with a tie-in to Frankenstein right before Halloween.
1. Morente, Porti, Salinas and Navarro, Evidence of electrical activity
on Titan drawn from the Schumann resonances sent by Huygens probe,
Icarus,
Volume 195, Issue 2, June 2008, pages 802-811, doi:10.1016/j.icarus.2008.02.004.
The only statement in the paper that comes close to the idea of life on Titan is
in the first paragraph: Lightning activity would considerably increase the
probability of organic and pre-biotic molecules being formed.
2. Jeffrey Bada was part of another Halloween prank last week: see the
10/20/2008 entry.
Creepy. To learn about the real Frankenstein, listen to this
podcast.
Truth is stranger than fiction.
Next headline on:
Solar System
Origin of Life
Dumb Ideas
Scientific Terms Can Obfuscate, Not Enlighten 10/29/2008

Oct 29, 2008 When scientists classify things and use scientific terms,
are they really shedding light on nature and natural history? Its possible
they may just be glossing over their own ignorance, suggested three articles in
Nature last week. They underscore cases where subjective human conventions are
falsely assumed to correlate with external realities. They lead us to ask,
what do we mean by meaning?
- Words demean things: Apparently the editors of Nature have
had it with certain clichés. One editorial, published also on
Nature News,
pointed out the ambiguity of popular words and phrases used in scientific papers
and by science reporters. The editorial began,
To a great extent, science is about arriving at definitions.
What is a man? What is a number? Questions such as these require substantial
inquiry. But where science is supposed to be precise and measured, definitions
can be frustratingly vague and variable.
As examples, the editorial reviewed the terms
paradigm shift, tipping point, race, epigenetic, complexity, stem cell, consciousness
and significant. Those terms may seem intuitively obvious but in fact
have multiple definitions. For the word consciousness to have meaning,
for instance, there must be a physical basis for it but none has been found.
And significant is in the eye of the beholder, despite mathematical crutches
like p-values that lend a false air of confidence in scientific results.
Scientists often use a 5% confidence level as a measure of significance.
That number, though, is an arbitrary convention and often a useless one:
Even if a result is a genuinely statistically significant one, it can be virtually
meaningless in the real world. A new cancer treatment may significantly
extend life by a month, but many terminally ill patients would not consider that
outcome significant. A scientific finding may be significant without
having any major impact on a field; conversely, the significance of a discovery might
not become apparent until years after it is made. One has to reserve
for history the judgement of whether something is significant with a capital S,
says Steven Block, a biophysicist at Stanford University in California.
- Class warfare: What do we mean by a class of objects? Take
terms like species and planet: which objects belong in the class, and which are
excluded? Its not always easy to decide, said Jeffrey Parson and Yair
Wand in an essay in last weeks Nature.1
The authors illustrate problems with these two examples. Look at the conflict
over Pluto: is it a planet, a minor planet, or a plutoid? Depending on
which properties of objects in space are considered useful to humans,
it could be any one of these things yet Pluto itself
hasnt changed. Plutoid is a recently made-up word about a class of objects
of which Pluto is the best-known example. Just because the International Astronomical Union declares
that from henceforth and forevermore Pluto is a plutoid, that does little more than
provide a consensus for human beings and their nomenclature. Similarly, the
term species contains considerable uncertainty, as even Ernst Mayr realized
when he tried to define a species as a class of organisms that can produce fertile offspring (the
biological species concept). Too bad that doesnt work for
the vast majority of organisms asexual microbes and fossils.
Some classifications can lead to false and even fatal
results. Consider the word disease, which originally just meant discomfort
or not at ease. The classification of diseases has usually been centered on etiology,
or causes of disease. These fall into 3 subclasses: genetic, environmental or
pathogenic. For nearly 40 years, the authors said, doctors misdiagnosed
ulcers because they could not bring themselves to believe that a bacterium, H. pylori
was capable of living in the acidic environment of the stomach. When
considering the reasons why the bacterial hypothesis was missed for such a long time
(and then not readily accepted), the main problem was the misattribution of the
property cannot grow in the acidity of the stomach to the class of bacteria,
they explained. Re-evaluating this fundamental property involved
a major mind-shift that was difficult to accept.
Classification is a human enterprise. The authors gave an evolutionary
spin on this skill: Classification ... is recognized as an evolved mechanism
that supports survival. Supposedly it helps humans get food and shelter.
They did not ask whether lions and lizards needed to evolve the mechanism to sort out
their food and shelter, too. They tried to distinguish between
categories and classes by defining the former as a group of
objects with shared properties, and the latter as a category that allows humans to infer
further information consistently over a reasonable time period.
A little reflection, however, shows that they have simply
substituted the word class for a meta-category with the same difficulties.
The information that can be inferred from a class is simply a collection of objects with
shared properties things that humans find useful. Their final paragraph,
though, revealed that they are aware of the main pitfall of classification: it
happens in the mind, not in the external world.
Taking a classification perspective on scientific discourse suggests a sequence of questions to ask when studying a domain of phenomena. What are the properties of interest of these phenomena? Are there stable sets of properties common to these phenomena? Are there stable relationships in some of these sets? And finally, and most importantly, what is the evidence or rationale that these relationships reflect the true nature of the phenomena? This perspective has two important implications. First, scientists should make every effort to ensure that the assumed relationships among properties are indeed correct. Second, rather than arguing over which of several classification schemes is preferable, researchers should recognize that several correct and useful schemes can coexist. And overall, scientists should recognize that classification happens in the mind and, as a result, it can be influenced by beliefs and emotions. This is where science can go astray.
- The human element: The lead editorial in Nature last week
brought these lessons home to the human species. What does it mean to be
human? the editors asked.2 The Delphic oracle may
have advised Know thyself, but that is often hard to follow, they said.
Watch the editors balance their confidence in Darwins ability
to help us know ourselves with doubts about the evidence:
Modern science can help, but using it to uncover truths about ourselves
can also be fraught with difficulty. Consider, for example, that an important
first step towards understanding contemporary human behaviour establishing
the evolutionary context in which it emerged means piecing together
odd scraps of evidence left by our hunter-gatherer ancestors tens of thousands
of years ago. The paucity of data makes it all too easy to come up with untested,
and even untestable, Darwinian versions of Rudyard Kiplings Just So Stories.
After acknowledging that sciences just-so chickens have come home to roost,
the editors resurrected an old conflict that illustrates the impossibility of speaking objectively
about ourselves without wandering into politics:
Another major challenge for researchers is being objective about a topic as philosophically, politically and ethically charged as human nature. Take the sociobiology wars of the 1970s and 1980s. Left-wing scholars rejected biological explanations for phenomena such as gender roles, religion, homosexuality and xenophobia, largely because they feared such explanations would be used to justify a continuation of existing inequalities on genetic grounds. The resulting debates became hugely political.
The combustibility of the interface between science and society is one major reason for the extraordinary fragmentation of research that tackles human behaviour. In part because of the sociobiology battle, most social scientists still steer clear of using evolutionary hypotheses. And even researchers who do work under the unifying framework of evolution tend to fall into distinct camps such as gene-culture co-evolution or human behavioural ecology their practitioners divided by differences of opinion on, say, the relative importance of culture versus genes.
The editors clearly think that evolutionary theory deserves to be a unifying
theme, but have just cast doubt on the evidence behind it and the pragmatics of using
it. They attribute the problems to the complexity of our species and the lack
of interdisciplinary communication. In a belief that their magazine can help, they
said they are starting a series of essays which, though they might make for
uncomfortable reading, will try to draw lines between human evolutionary
prehistory and the complex societies we live in. The first was by Pascal Boyer about
the evolution of religion. Did it accomplish its purpose?
See our review in the 10/26/2008 entry.
1. Jeffrey Parson and Yair Wand, A question of class,
Nature
455, 1040-1041 (23 October 2008) | doi:10.1038/4551040a.
2. Editorial, A look within,
Nature
455, 1007-1008 (23 October 2008) | doi:10.1038/4551007b.
It was good for Nature to point out these
problems with scientific terminology. Unfortunately, their brains are so
completely sold out to Darwin they are incapable of looking in the mirror.
Thats why one moment they can be admitting the evidence is so scanty it
gives ease to untested, untestable Just-So Stories about human evolution, then
the next moment they give their editorial blessing to a stupid Just-So Story about the evolution of religion
(10/26/2008).
Philosophy of science is a vital topic for anyone interested in
science or apologetics or both. In philosophy of science you learn to ask
questions that scientists themselves rarely ask. Consider the important
topic of classification, brought up in bullet 2 above. Scientists too flippantly
invoke class terms that are totally subjective when scrutinized. For instance,
what is a predator? We think we understand the term, but in the class of
predators you can find snails, tigers, and even the Venus Flytrap. The
differences between these objects in the class predator seem more
significant than the property they share: that they eat animals. In addition, each
object belongs to multiple other classes that either distinguish it or include
it: organism, vertebrate or invertebrate, plant or animal. The class you
focus on is the one that is useful at the moment. If you are playing Twenty
Questions, for instance, the categories initially useful to you are animal,
vegetable or mineral, where animal could be anything from a flatworm to
a giraffe, vegetable could be anything from algae to a redwood tree, and mineral
could include diamonds and space stations. A corollary of this
idea is that classes are merely human constructs not necessarily ways of dividing
up the world as it really is, or as Plato is said to have worded it, carving
nature at its joints.
In his excellent lecture series on philosophy of science for
The
Teaching Company, Jeffrey L. Kasser used a humorous illustration. He
invented a word broccosaxodile, which he defined as anything that is broccoli, a saxophone,
or a crocodile. While one might question the usefulness of such a composite classification,
he asked if it is any less meaningful than predator which, as we said, includes
things just as diverse. Predator is just a shorthand word for a
composite category that we could just as well call a snail-tiger-VenusFlytrap.
Lets add another example: what is a fossil?
If you immediately picture bones in rock, you are ignoring the fact that fossils can include
whole insects in amber complete with their soft tissue, footprints, petrified wood,
and mere impressions of jellyfish or leaves, like shadows, without any bones at all.
Fossils are not permanent, either: the dinosaur trackways in the entry below
(10/28/2008) are eroding and will eventually disappear.
In that sense, a corpse in a morgue is a fossil, or the ashes of a cremated person
sitting in a bottle in the heartbroken spouses bedroom. (Not to be morbid,
but it is almost Halloween.)
A classification is meaningless
without a context in which the term is useful to some human being for a subjective
purpose. There is nothing objective about a class if you want to think of
it as referring to something that is out there in the world which
scientists discover without bias. This should be a lesson to
evolutionists who think they are talking objectively when they use class terms like
missing link, transitional form, ancestors, phylogenetic tree, homologous traits
or innovation. Such terms are employed for their utility in this
case, the utility of making evolutionary theory appear scientific.
Application. Lets apply what weve learned to a Biblical
example some find embarrassing. Many skeptics have ridiculed the Bible for classifying bats with birds in
Leviticus 11:13-19 (see EvidentCreation.com).
OK, their point is? This classification was amply useful to Moses, who was
helping the Israelites distinguish what they were allowed to eat. The property
apropos to their circumstances was clean and unclean edible animals.
Moses, or God for that matter, was under no obligation to use modern scientific taxonomy
for the purpose. In fact, it would seem much more helpful to Israelites
wandering in the wilderness to point out which
of those things flying around in the dark was safe to eat. Those of you who have
camped in the desert know that swifts and bats can look very similar in the way
they dart about. Formally, we can say that the property at issue in the class being
defined was flying things call them volant vertebrates
if it makes you feel better not whether the things had fur or feathers
or laid eggs. Moreover, it would be an unfair disparagement of the mental capabilities
of people who grew up in the advanced Egyptian
civilization and their well-educated leader to assume they didnt know the
difference between birds and bats. We mustnt be chauvinistic.
They probably possessed more savvy about nature than the typical modern couch potato.
Exercise. Teachers and home-school parents: here is an opportunity to
introduce your precocious young thinkers to some philosophy of science.
Have them invent categories similar to broccosaxodile (above) and make lists
of objects that fit. Is the category useful in some way? Does it allow
inferring additional information? Which members belong to other categories?
Silly categories: Make up your own silly category and defend its usefulness:
vege-toy-mobiles, dirt-bike-chocolate, sister-TV-cotton
(anything that is either a sister, a television, or made of cotton), etc.
Trivial categories: Round things, small potatoes, friends, food, containers,
pets, creeping things, rhyming words, oxymorons, shapes, etc. Think of more.
In what circumstances are these useful categories? What are examples of extremely
different things that can fit in the same category? Can you dream up a story
to explain how the category evolved?
Scientific categories: omnivore, migratory species, gene, hybrid, moon, cloud,
field, particle, wave, force, reagent, network, factor, family, biome, ecosystem,
riparian dweller, marine invertebrate, intelligent life, sentient being.
List some extremely different objects that fit into the same category. Pick an object
in the category and list what other categories it belongs to. How well does the category
reflect distinctions in the external world? What kinds of observations are
required to make the distinction? Who does the observing?
When is the category useful and not useful? Are the evolutionary stories told about
these classes the only possible ways to understand them? What does understanding
mean without the preconditions of immaterial concepts, reason, truth, and mind?
Next headline on:
Early Man
Philosophy or Theology
Evolutionary Theory
Darwin Myths Debunked By Darwinist 10/28/2008

Oct 28, 2008 An aura of legend has enveloped the memory of Charles Darwin.
To many, the white-bearded father of evolutionary theory was like a saint on a white horse,
rescuing science from an age of superstition. The true history is much more
interesting.
Darwin Day is coming next February 12. It marks Darwins
200th birthday and also the 150th anniversary of the publication of his Origin of
Species. The Darwin Exhibition, a multi-million-dollar display produced by
the American Museum of Natural History
(09/22/2005), is making the rounds of major museums,
culminating in the 2009 Darwin Bicentennial year.
Hiram Caton (Griffith University, Australia)
felt compelled to pen Getting Our History Right when he saw the
Exhibitions devotion to the legend at the expense of fact.
Here are six mythbusting theses Caton defended in his article:
- Publication of the
Origin was not a sudden (revolutionary) interruption of Victorian societys confident
belief in the traditional theological world-view.
- The Origin did not revolutionize the
biological sciences by removing the creationist premise or introducing new principles.
-
The Origin did not revolutionize Victorian public opinion. The public considered Darwin
and Spencer to be teaching the same lesson, known today as Social Darwinism, which,
though fashionable, never achieved dominance.
- Many biologists expressed significant
disagreements with Darwins principles.
- Darwin made little or no contribution to the
renovation of theology. His public statements on Providence were inconsistent and the
liberal reform of theology was well advanced by 1850.
- The so-called Darwinian revolution was, at the public opinion level,
the fashion of laissez-faire economic beliefs
backed by Darwin and Spencers inclusion of the living world in the economic paradigm.
Where did Hiram Caton print this Darwin-deflating piece?
Not in a creationist magazine, but in Evolutionary Psychology.1
(See 06/06/2008.)
He is no creationist; he just worries that distorting publicity can backfire.
As a cadre who bear a public trust to get the facts right,
he ended, we are obliged to correct misrepresentations directed to schools
at a time when evolution is under challenge.
Besides, science history that includes the quirks, baseless claims, cheating, and battles
is more engaging than the sanitized history
meant to instill unquestioning acceptance.
1. Hiram Caton, Getting Our History Right: Six Errors about Darwin and His Influence,
Evolutionary Psychology,
www.epjournal.net 2007. 5(1): 52-69.
What, exactly, are we supposed to be celebrating
next year? Ineptitude? The gullibility of the public? The
power of fashionable ideas to distort history? The inability of
reasonable scientists with their significant disagreements to stop bad ideas
at their onset? Darwin Day can still be a worthy holiday if we make these
the lessons. We agree with Caton; first, we have to get the facts right.
Next headline on:
Darwin and Evolutionary Theory
Education
Darwinists refute ID claim about irreducible complexity! See the
10/31/2005 entry.
Monster Mash 10/28/2008

Oct 28, 2008 Just before Halloween, its time for tricks and treats
about monsters in the fossil record. Heres a list of recent stories
about scary beasts:
- Dino Dance: Are these potholes tracks or weathering marks?
PhysOrg and
Science
Daily were among news outlets reporting a new interpretation of formations
by a grad student at the University of Utah in Navajo Sandstone near a popular
photographers locale
called The Wave.
Winston Seiler claims the round holes represent tracks of three different kinds
of dinosaurs, complete with tail drag marks. Other dinosaur tracks are
known in the area; this one is unusual for the number and density of tracks,
what Seiler calls a trample surface.
National
Geographic also joined the dance party.
Update 11/10/2008: The party dispersed when some
science cops showed up. PhysOrg
reported that A group of paleontologists visited the northern Arizona wilderness
site nicknamed a dinosaur dance floor and concluded there were no dinosaur tracks
there, only a dense collection of unusual potholes eroded in the sandstone.
One of the co-authors of the dance floor thesis agreed to work with the skeptics:
Science is an evolving process where we seek the truth, she said.
So she turned around and changed the dance to The Shake: This is how science
works, and well have to see how it shakes out in the end.
- Hornblower: The unusual head crests on duckbill dinosaurs were
used for shouting, claim scientists in a report on
Live
Science and PhysOrg.
The nasal passages on lambeosaurs and corythosaurs connected with passages in the head crest to
produce resonant, bellowing calls (see diagrams on
Science
Daily). The pitch of the calls probably deepened as the dinosaurs
aged. Perhaps they had a tonal language for communication, with special
calls for Run for your lives! A T. rex is coming! Veteran
dinosaur hunter Jack Horner (Montana State) noted that, Its difficult to infer the function
of structures in an extinct dinosaur when there is so little resemblance to any living animal.
- Taking the plunge: How do you interpret dinosaur tracks that
gradually fade away? The track-maker must have gone for a swim, reported
Science
Daily. Debra Mickelson of University of Colorado even thinks she knows
what they were doing going out to sea to feed, 165 million years ago.
- Migrants: Dinosaurs werent the champion migrators of the
ancient world, contrary to the usual view, said Phil Bell (U of Alberta) in a report on
Science
Daily. How could he and colleague Eric Snively figure that out?
They calculated the energy requirements for a herd of herbivores like
Edmontosaurs, and believe it would have limited their travel to 3000 km round trip
half the previous estimate.
- Microsaur: We tend to think of dinosaurs as mighty tyrants of the
early earth, making the ground shake with every step.
Science
Daily reported the finding of the smallest dinosaur ever seen.
The juvenile Heterodontosaurus (mixed teeth) had a skull less than two inches
long and would have weighed less than two sticks of butter. Its
likely that all dinosaurs evolved from carnivorous ancestors, said co-author
Laura Porro (U of Chicago); Since heterodontosaurs are among the earliest
dinosaurs adapted to eating plants, they may represent a transition phase
between meat-eating ancestors and more sophisticated, fully-herbivorous
descendents.
- Megasaur: A dinosaur graveyard has been found in Utah, reported
Live
Science. Remains of a large number of herbivores were found, including
one well-preserved skeleton and a 5-foot humerus from a brachiosaur, one of the
largest dinosaurs known. Tracks have also been found. Another surprise
was a Deltapodus stegosaur previously known only from Europe.
How did brachiosaurs get so huge? Another story on
Live
Science claims they ate high-energy foods whole, without chewing.
- Sniffer rex: Halloween wouldnt be quite the same without mention
of everyones favorite dinosaur nightmare: the Tyrannosaurus rex.
A report on Live
Science claims the monsters had a good sense of smell vital for hunting
down prey. They believe this based on the size of the opening in the skull
where the olfactory bulb an organ of smell was located.
The article speculated on evolution of birds from dinosaurs:
Most of todays birds have keen eyesight but lack a good nose, suggesting
smell became less important at some point in birds ancestral history,
the researchers said.
Its clear that dinosaur hunting is still a popular sport for
paleontologists, especially ones with vivid imaginations.
Dinosaurs are for kids including the grown-up kind. Who doesnt
enjoy learning about this large and varied class of extinct animals that roamed the whole
earth? Imagining things is fun, too. Just dont confuse it with
science. There are limits to how much can be known about dinosaurs from
their tracks and bones. We dont know, for instance, their favorite
dance steps, to say nothing of how they decided to give up meat, reduce their
noses and fly like Tweety rex. The beasts are scary enough without
the evolutionary monster tales around the campfire.
Next headline on:
Dinosaurs
Fossils
Evolution
Bible Was Right: Edom Thrived in Solomons Time 10/27/2008

Oct 27, 2008 High-precision radiocarbon dates have confirmed that Biblical
Edom was active with industrial-scale metal production in the 10th and 9th centuries.
Archaeologists publishing in PNAS said,1
The methodologies applied to the historical IA archaeology of the Levant have
implications for other parts of the world where sacred and historical texts interface
with the material record. In other words, sacred and historical texts
should sometimes be taken seriously not dismissed out of hand.
The authors viewed their results as a challenge to recent minimalist
re-interpretations of the Bible that try to relegate the stories of David and Solomon
to myths and legends by saying that Israel was too tiny to support the wealth and
power described in the Bible. They also challenge the ridicule that has been
heaped on those who took the Bible as a reliable guide for archaeologists.
Heres how they started their paper:
In 1940, the American archaeologist Nelson Glueck summarized
his extensive 1930s archaeological surveys in Transjordan in his
book The Other Side of the Jordan, asserting that he had
discovered King Solomons mines in the Faynan district (the
northern part of biblical Edom), ~50 km south of the Dead Sea in
what is now southern Jordan. The period between the First and
Second World Wars has been called the Golden Age of biblical
archaeology when this subfield was characterized by an almost
literal interpretation of the Old Testament (Hebrew Bible, HB) as
historical fact. Archaeologists such as Glueck metaphorically carried
the trowel in 1 hand and the Bible in the other, searching the
archaeological landscape of the southern Levant for confirmation
of the biblical narrative from the Patriarchs to the United Monarchy
under David and Solomon to other personages, places, and events
mentioned in the sacred text. Beginning in the 1980s, this paradigm
came under severe attack, primarily by so-called biblical minimalist
scholars who argued that as the HB was edited in its final form
during the 5th century (c.)BC, any reference in the text to events
earlier than ca. 500 BC were false. Accordingly, the events
ascribed to the early Israelite and Judean kings from the 10th-9th
c. BCE were viewed as concocted by elite 5th c. BCE editors of the
HB who resided in postexilic times in Babylon and later in Jerusalem.
Some of the casualities [sic] of the scholarly debate between the
traditional biblical scholarship and biblical minimalists has been the
historicity of David and Solomonthe latter of which is traditionally
cross-dated by biblical text (1 Kings 11:40; 14:25; and 2 Chronicles
12:2–9) and the military topographic list of the Egyptian Pharaoh
Sheshonq I (Shishak in the HB) found at the Temple of Amun in
Thebes and dated to the early 10th c. BCE (5).
....The 14C dates associated with
smelting debris layers from Faynan reported here demonstrate
intensive 10th–9th c. BCE industrial metallurgical activities conducted
by complex societies.
The analytical approach advocated here argues for an historical
biblical archaeology rooted in the application of science-based
methods that enables subcentury dating and the control of the
spatial context of data through digital recording tools.
The researchers carefully dated carbon-bearing materials from the site discovered
in 2005 (see 02/18/2005) as a candidate for the
massive copper-mining operation of Edom described in the Bible. The
paper describes in detail the methods they used: carbon dating charcoal pieces
from the site with high precision equipment. Some of the dates stretch well
before 1000 BCE before Davids kingdom. The paper contains pictures and sketches of
the complex smelting operation with its copper slag mounts found at the likely
site of Biblical Edom across the Arabah from southern Israel.
The researchers concluded that the
revisionist, minimalist dates of 7th century BCE are no longer tenable.
What are the implications?
These new data indicate the need to revisit the relationship between the
early IA history of the southern Levant [eastern Mediterranean] among other
things. Perhaps other minimalist dates will be falsified under the new scientific
techniques used by this team thus lending credibility once again to the
practice of digging with a Bible in one hand, a trowel in the other, and a
radiocarbon dating machine back in the lab. In their words,
the question of whether King Solomons copper mines have been
discovered in Faynan returns to scholarly discourse.
The day after our entry on the Levy et al paper appeared,
Science
Daily posted its report and other news sites followed.
National
Geographic News reported that some of the funding for the project came from
the National Geographic Society. Todd Bolens
Bible
Places Blog contains pictures of the site and links for more information.
Update 10/29/2008:
Bible
Places Blog posted another report from an archaeological dig relating to the time
of David and Solomon: Biblical Gath, home of Goliath. The team excavating Tell es-Safi
used joint on-site analytical methods unparalled at ANY excavation in Israel,
and in fact, in the world, Todd Bolen, a professor in Israel for 11 years, said.
After reviewing the teams report, he added, For many reasons, this excavation looks like it will be
extremely beneficial for archaeological and biblical studies.
1. Levy et al, High-precision radiocarbon dating and historical biblical archaeology in southern Jordan,
Proceedings of the National Academy of Sciences
USA, published online before print October 27, 2008, doi: 10.1073/pnas.0804950105.
Bible scholars will surely find this paper
interesting. Theres something satisfying about debunking the
debunkers. Congratulations to National Geographic News, usually a Darwinist
propaganda bullhorn, for giving a fair report on the story without disparaging the Bible in the
process. Time to minimize minimalism in Biblical archaeology. Minimalists?
Dont need em in Edom.
Next headline on:
Bible
Dating Methods
Habitable Zones Are Not Forever 10/27/2008

Oct 27, 2008 A new realization has broken on the astrobiological community:
planetary habitable zones have no fences. Michael Sherber wrote for Astrobiology Magazine
(see Space.com)
that planets around low-mass stars tend to be pulled out of the habitable zone toward
the star. They have just a billion years before migration can pull them in and cook them.
Planets around small mass stars may only have a billion-year window during
which life can form. He did not indicate whether that life would be very
happy, though, knowing a fiery hell awaited it. Habitability is not a
permanent property of a planet, the article said.
Rory Barnes (U of Arizona) who thought about this, wondered if it
could be a test of the Gaia Hypothesis something he termed a grand
picture of evolution. Maybe the lifeforms could adapt as the planet migrates
inward by altering the planets climate and geochemistry. Maybe we could
even learn how life mitigates disasters and adapts to climate change,
he said.
Meanwhile, Clara Moskowitz at
Space.com
had more optimistic news. Some planets once thought inhospitable might actually
be able to support life. The [habitable] zone may not be so fixed,
it turns out, she said. Some extrasolar planets that one might
assume are too cold to host life could in fact be made habitable by a squishing
effect from their stars, a new study found. If the planet has an oblong
orbit, the tidal heating would heat it up. Maybe this could melt the ice of
a planet outside the zone and give it hope for life. Maybe it could start
volcanoes and plate tectonics. Thats a lot of maybes. One thing
we know: it all comes together just right where we live: Plate tectonics is
a definite boon for life, she said, because stirring up the surface
layers helps to regulate the amount of carbon dioxide in the atmosphere, since
rock absorbs CO2 from the air.
That perfect balance helps a planet maintain that just right
temperature range.
Quiz question: what is an evolutionists
favorite word? Oh, you want a free hint? Maybe, baby.
Next headline on:
Solar System
Stars
How do plants wax their leaves? Its an elaborate task. Its much
easier for an evolutionary biologist to make up a fable about it and win Stupid Evolution Quote
of the Week see 10/27/2004.
Snails Walk on Water 10/27/2008

Oct 27, 2008 Why is that scientist staring at a snail? Hes
watching a miracle: walking on water. This is not our exaggeration: Matt
Kaplan on National
Geographic News entitled his article, How Snails Walk on Water Is a Small Miracle.
If we can figure out the trick, we might be able to make little robots do it
even if we dont know why we would want to yet, other than it would be cool.
Snails are small enough to be naturally buoyant, but needless to say,
getting traction on water is a challenge. The snail apparently does this by
making small ripples. The ripples are just the right size to give the snail
traction without breaking the surface. Its a unique method of propulsion
unknown till Eric Lauga, a professor of mechanical and aerospace engineering at the
University of California, San Diego, decided to investigate.
For a human to do this would require shoes as big as a football
field, the article said.
Many capabilities of animals and plants
seem miraculous to us, but we sometimes use the word too carelessly.
Jesus walked on water barefoot or on sandals. Thats a real miracle.
Next headline on:
Biomimetics
Terrestrial Zoology
Physics
Amazing Facts
Evolutionizing Religion: Whos Assuming What? 10/26/2008

Oct 26, 2008 Findings from cognitive psychology, neuroscience,
cultural anthropology and archaeology promise to change our view of religion,
said Pascal Boyer in Nature.1 His essay
summarized studies that offer an evolutionary explanation for mankinds
propensity to embrace religion. We can probe the shared assumptions
that religions are built on, however disparate, and examine the connection between
religion and ethnic conflict, he said. Lastly, we can hazard a
guess at what the realistic prospects are for atheism.
Boyer weaved together evolutionary explanations for several features
seemingly common to all religions: belief in things for which there is no evidence,
ritual, morality, metaphysics, and social identity. There is no one place
in the brain, a religious center, he said. Rather,
religious thoughts seem to be an emergent property of our standard cognitive
capacities. Just as the brain was not made specifically for music, politics,
ethnic groups and family relations, religion is just an emergent response to
super stimuli, he said. Religious concepts and activities
hijack our cognitive resources, as do music, visual art, cuisine, politics,
economic institutions and fashion. In evolutionary terms, the brain
evolved for skills to aid survival, but religion simply takes advantage of those cognitive
faculties and meshes them in an unexpected way. The mind has myriad
distinct belief networks that contribute to making religious claims quite natural
to many people, he said.
Central to Boyers case are that religious people make tacit assumptions
they never notice. They may be able to describe their core beliefs,
But cognitive psychology shows that explicitly accessible beliefs of this
sort are always accompanied by a host of tacit assumptions that are generally
not available to conscious inspection. The details of religious
beliefs may differ, he said, but the tacit beliefs underlying all religious are
remarkably similar. To him, this can only mean that we have similarly
evolved brains that exercise the tacit assumptions in diverse ways.
He began his essay with
a listing of various reactions to the scientific study of religion:
Is religion a product of our evolution? The very question
makes many people, religious or otherwise, cringe, although for different
reasons. Some people of faith fear that an understanding of the
processes underlying belief could undermine it. Others worry
that what is shown to be part of our evolutionary heritage will be interpreted
as good, true, necessary or inevitable. Still others, many scientists
included, simply dismiss the whole issue, seeing religion as childish,
dangerous nonsense.
Such responses make it difficult to establish why and how religious thought is so pervasive in human societies an understanding that is especially relevant in the current climate of religious fundamentalism. In asking whether religion is one of the many consequences of having the type of brains we come equipped with, we can shed light on what kinds of religion come naturally to human minds
Those human minds, we can safely assume he believes, are also products of evolution.
Throughout the article, Boyer promotes the idea that gods and beliefs are not real,
but rather manufactured by the cognitive and social psychology of humans and their
evolved brains. Imagining supernatural beings may be a natural way,
he said, for human products of evolution to process information:
The findings emerging from this cognitive-evolutionary approach challenge two central tenets of most established religions. First, the notion that their particular creed differs from all other (supposedly misguided) faiths; second, that it is only because of extraordinary events or the actual presence of supernatural agents that religious ideas have taken shape. On the contrary, we now know that all versions of religion are based on very similar tacit assumptions, and that all it takes to imagine supernatural agents are normal human minds processing information in the most natural way.
Implicit in this idea is the position that atheism is a more scientific world view.
His last paragraph, though, gives little hope for his fellow atheists to gain a
foothold in the culture: the evolutionary deck is stacked against them.
Some form of religious thinking seems to be the path of
least resistance for our cognitive systems. By contrast, disbelief
is generally the result of deliberate, effortful work against our natural
cognitive dispositions hardly the easiest ideology to propagate.
For previous entries on the evolution of religion, see
03/16/2005,
02/02/2006,
09/25/2006 and
05/27/2008.
1. Pascal Boyer, Being human: Religion: Bound to believe?,
Nature
455, 1038-1039 (23 October 2008) | doi:10.1038/4551038a.
How otherwise intelligent people can continue to be so blind
to their own biases after decades, nay centuries, of philosophers and theologians
and logicians pointing them out, is stunning.
Nature has just published another in a long series of
self-refuting essays. A freshman CEH
reader can probably refute this article in a sentence or two. If not, you need
to apply yourself to stopping by here more often.
What is it about their brains that predisposes evolutionists to think
this way? You notice that we put the shoe on the other foot. Thats
fair, because to him, we are all equally evolved. By what standard of measure
can he insist that his tacit assumptions are better than anyone elses?
By the standards of science? Ha! Only if he is a logical positivist
another self-refuting belief system. If this is not obvious, go back and read Wolperts ideas
from the 10/16/2008 entry and the commentary
on logical positivism from 05/10/2007 before
continuing. If Boyer assumes that testable predictions render
evolutionary psychology scientific, he has not learned about the dubious logic of
predictive success in science. Its the main reason Karl Popper rejected
predictive success as a criterion of science, and promoted falsification instead.
(Falsification, alas, was also later rejected as a foolproof criterion.)
Boyer came close to recognizing the self-refuting nature of his
beliefs by mentioning people who worry that what is shown to be part of our
evolutionary heritage will be interpreted as good, true, necessary or inevitable.
(For elaboration on that point, see the
05/09/2006 commentary,
bullet 5.) He should be worried. To
what universal standard could he appeal to decide that religion is an emergent
property of the brain, but science is not? And why would he lament
that atheism is hardly the easiest ideology to propagate? At least he admitted it is an ideology.
But to what universal moral standard would he appeal to say that propagating his atheistic world view would
be a good thing? He said that science may one day find that religion
contributed to fitness in ancestral times. On what grounds, then, can he
say it hijacked mans cognitive abilities? If it produced fitness,
it is just as much an intrinsic benefit to human evolution as the brain itself.
Boyers essay
is plagued with other fallacies. For one, he
generalizes all religions, no matter how
opposite, in a highly simplistic manner: he puts the witch doctor and the Oxford
Scholar into the same fundamentalist bucket, also a form of
ridicule. By excepting his own reasoning
from those of religious nuts, of course, he has also divided the world into
us-vs-them, the either-or fallacy: i.e., you
either belong to the People of Science or to the People of Faith (whatever that
broad-brush category means). Students want extra credit can hunt for
begging the question fallacies,
non-sequiturs,
the post-hoc fallacy, misuse of
circumstantial evidence,
reductionism,
subjectivity and
other fallacies.
The card-stacking fallacy is
notable in this article. He only offered three responses to the idea that
religion evolved: (1) Worry by religionists that it will undermine their beliefs.
(2) Worry by evolutionists that religion, if part of our evolutionary heritage,
will be seen as good, true, necessary or inevitable. (3) Disgust by
scientists that religion is childish, dangerous nonsense.
Why did he not consider the possibility that theologians and knowledgeable
scholars will consider his evolutionary theory or religion to be regarded
as childish, dangerous nonsense? Is that not what we have just illustrated?
Another example of his card stacking
was to list only things like ritual, metaphysical beliefs, social identity and
moral codes as the characteristics of religion. Why didnt he mention
evidence and apologetics? Those things may be lacking in the cultic
or ritualistic religions, but the Bible is filled with historical references that
can be cross-checked, and appeals to remember what the people knew to be true from
evidence, reason and eyewitness testimony. Paul and Peter claimed to
be eyewitnesses of the risen and glorified Christ and emphatically denied that they were
following cleverly devised fables. They also warned people against falling for
fables. If Boyer likes prediction so much, he should consider the prediction
Paul made in II Timothy 4:4
that in the last days people will turn their ears away from the truth and turn aside to myths,
of which evolution is a prime example, because the evidence for God is clear from
creation (Romans
1:18-20). Peter, similarly, predicted the coming of belief in
uniformitarianism. He predicted that mockers would deny the evidence for creation and the flood
(II
Peter 3:3-9). Do those predictions count? Must be consistent.
Boyer and his fellow atheistic evolutionists arrogate to themselves the chair of
science, but have no floor to put it on: not a scientific floor, or a philosophical
floor, or an evidence floor. He needs the Judeo-Christian floor to be able to
reason about truth, morals, and evidence at all. Like Yoda, he speaks ex cathedra from some
exalted plane above the rest of humanity, telling us about our tacit assumptions
while ignoring his own (08/13/2007).
He tells others what makes them tick without understanding that what makes him
tick is rebellion against his Creator. He couldnt
slap his Fathers face without first sitting in His lap. Pascal
Boyer should sit quietly like a good boy and read Pascal.
Next headline on:
Evolutionary Theory
Human Body
Theology
The Life and Death of Oxygen 10/24/2008

Oct 24, 2008 The oxygen in our atmosphere has the energy equivalent of
20 thousand billion billion hydrogen bombs. To maintain the oxygen level
in our atmosphere, that amount of energy would have to be spent in manufacturing
molecular oxygen every 4 million years (a thousandth the assumed age of the earth).
Now that we have your attention, lets think about the role
of oxygen and life. The statistics above were estimated by Paul G. Falkowski
and Yukio Isozaki in Science this week.1
Unlike nitrogen, which is inert, oxygen is lively it oxidizes, or burns
things not only in fire, but in cells, where the element must be handled
gingerly by molecular machines to avoid damage. Thats also why you
take antioxidants in your food. Keeping oxygen away from the
primordial soup at the origin of life is understandably a serious problem
(10/20/2008).
Evolutionary biologists do not believe earths oxygen is primordial (i.e.,
that it formed when the earth formed). They believe it was generated by
living organisms when they evolved to use oxygen for electron capture in metabolism.
This conveniently keeps oxygen out of the picture at the origin of life (though
some atmospheric oxygen forms spontaneously by the dissociation of water).
Oxygen could also be sequestered from the air in continental rocks: silicates,
carbonates and sulfates.
Oxygen reached levels of 10 to 30% only in the last 550 million years, evolutionists say.
Its 4-million-year lifetime is 0.4% the estimated 1 billion
year lifetime of the atmospheres most abundant gas, nitrogen.
How did oxygen, with its relatively short lifetime, become the second most abundant
gas in the atmosphere? The story is not as simple as it might first appear,
said Falkowski and Isozaki. One has to calculate when and how it was first
generated, and how it persists in its high concentration.
Some oxygen is continuously formed by the breakup of water molecules
by ultraviolet light in the atmosphere (at least till ozone forms and shields the upper
atmosphere from excess UV). If biology is the source, how does life produce
it from water and minerals?
The overwhelming source of O2 on Earth is photobiological oxidation of water; neither the evolution nor the mechanism of this process are completely understood. Apparently it arose once in a single clade of bacteria and was then appropriated via a single event, in which one cell engulfed another (endosymbiosis) to form a new symbiotic organism. The latter became the progenitor of all photosynthetic eukaryotes, including algae and higher plants.
The core of the oxidation machinery is photosystem II, a large protein complex containing four manganese atoms that are photocatalytically oxidized to create electron holes upstream.
They stressed that this arose once most likely because of the improbability
that a large protein complex of oxidation machinery could
arise by chance. Nevertheless, assuming plants and bacteria produce it, the
equation is balanced by the animals that consume it:
On time scales of years to millennia, these reactions are closely coupled to the reverse process of respiration, such that net production of O2 is virtually nil. That is, without burial of organic matter in rocks, there would be very little free O2 in the atmosphere. Hence, the evolution of oxygenic photosynthesis was a necessary but not a sufficient condition to oxidize Earths atmosphere.
So the second problem is getting molecular oxygen up to the level of 10-30% that
has been maintained for 500 million years. If a small amount is subducted
into the mantle by plate tectonics, or captured in stable continental rocks,
an atmospheric excess could be built up to a stable concentration without
runaway production. The balance between burial of organic matter and its oxidation,
they said, appears to have been tightly controlled over the past 500
million years. This balance requires an ongoing
process of long-term storage within the earth. The picture becomes complicated
by the fact that volcanoes can re-release oxygen back into the atmosphere.
The presence of O2 in the atmosphere requires an imbalance
between oxygenic photosynthesis and aerobic respiration on time scales of millions
of years, they said; hence, to generate an oxidized atmosphere, more organic matter must
be buried than respired.
How well do scientists know how oxygen concentration has varied over
geologic time? Perhaps surprisingly, not very well. Comparison
of isotopes in carbonates and sulfates provide clues. They believe the initial
oxygen concentration produced by the first photosynthetic bacteria was quite low.
It rose when eukaryotes appeared, and then, according to the evolutionary timeline,
became much more abundant in the Neoproterozoic corresponding to the period just before
the Cambrian Explosion. The eukaryotic oxygen increase would have had to
coincide with enhanced subduction in the lithosphere.
Was the Cambrian Explosion a cause or effect of the rise of oxygen?
They suggested the latter: The burial of large amounts of organic carbon
over the past 750 million years is mirrored in a substantial rise in atmospheric
O2, which may have triggered the Cambrian explosion
of animal life.
Another balance of geology and biology would have had to occur in the
Carboniferous. The doubling of oxygen production by trees and ferns had to be balanced by
further increases in burial efficiency they said. How the continental
plates coordinated their behavior with the evolution of plants, they did not say.
Throughout the remainder of earth history, this balance was maintained within comparatively
narrow limits 10 to 23%. The relatively narrow range of variability
suggests tight controls on the rate of burial and oxidation of organic
matter on Earths surface. They did not say who or what is controlling
these rates, other than to say that the burial of organic carbon is roughly
balanced by oxidation and weathering.
How valid is this story? They think the broad picture is understood,
but the details remain sketchy particularly, how photosynthesis splits water,
how oxygen concentration is controlled in the atmosphere.
Could Woodward W. Fischer in Nature help the story?2
How good is the evidence to support the rise of the first photosynthetic bacteria?
Go back to Archaean time, the interval of Earths history between about
4 billion and 2.5 billion years ago, he began, and were in
largely unknown biological territory.
While Fischer was concerned primarily with debunking claims of eukaryotes
too early for comfort (i.e., before the rise of atmospheric oxygen), his report contained
reason to doubt the validity of the timeline. The new evidence may remove an
embarrassing puzzle of how photosynthesis could arise 300 million years before the rise
of atmospheric oxygen, but
does it close the gap between the morphological and molecular-fossil records
of the evolution of eukaryotes? he asked himself.
He answered himself, Not yet. Other scientists are not
conceding the debunking of 2.7-billion-year-old photosynthesis. A news item
about this on Nature
News agrees the debate is far from over.
For problems with oxygen at the birth of the solar system, see
bullet one of the 09/24/2008 entry.
1. Paul G. Falkowski and Yukio Isozaki, The Story of O2,
Science,
24 October 2008: Vol. 322. no. 5901, pp. 540-542, DOI: 10.1126/science.1162641.
2. Woodward W. Fischer, Biogeochemistry: Life before the rise of oxygen,
Nature
455, 1051-1052 (23 October 2008) | doi:10.1038/4551051a.
OK; how convinced are you that the evolutionary
storytellers are compelled by the evidence to embrace their billions of years
saga of a history they cannot observe? Its a magical history, in which
complex oxidation machines arise by some unspecified natural magic.
(Note that if something arose once, it is not following a natural law).
Lacking evidence, they can build models that include the natural
magic built-in. By tweaking parameters here and there, and trying to debunk
contrary evidence, they can get it to work sort of. It continues to
amaze them how finely balanced it is.
So much for this space fantasy.
The atmosphere on Darwins imaginary world is too rarefied
to breathe. Lets head back to the real world.
Next headline on:
Geology
Physics and Chemistry
Origin of Life
Dating Methods
Read about the fast-forward scanner on a translating machine in the
10/23/2003 entry. Where is it?
In your body, working as you read this.
Minding the Brain, or Braining the Mind? 10/23/2008

Oct 23, 2008 Theres a battle brewing over who controls your brain:
nature or your mind. Materialist scientists are recognizing that creationists
are getting a foothold on this hill and declaring war over the brain,
according to an article in
New
Scientist. Psychiatrist Jeffrey Schwartz fired this salvo:
Materialism needs to start fading away and non-materialist causation needs
to be understood as part of natural reality.
Amanda Gefter, author of the article, also took note of the book
The Spiritual Brain: A neuroscientist's case for the existence of the soul
by OLeary and Beauregard. Schwartz and Beauregard were among the
speakers at an international symposium in Manhattan called Beyond the Mind-Body
Problem: New Paradigms in the Science of Consciousness. Gefter listed
several fronts in the war to reclaim the mind: Schwartz and Beauregard are
part of a growing non-material neuroscience movement, she
explained. They are attempting to resurrect Cartesian dualism
the idea that brain and mind are two fundamentally different kinds of
things, material and immaterial in the hope that it will make room in
science both for supernatural forces and for a soul.
After giving adequate white space for proponents of the non-materialist
view (including Angus Menuge, J. P. Moreland and the Discovery Institute),
Gefter clearly wanted to throw her vote to the reigning materialist paradigm
on this matter of mind. She commented on an experiment Schwartz
used to support the independent existence of mind, saying, these experiments
are entirely consistent with mainstream neurology the material
brain is changing the material brain.
In the middle of her article, Gefter got really serious:
Clearly, while there is a genuine attempt to appropriate neuroscience, it will not influence US laws or education in the way that anti-evolution campaigns can because neuroscience is not taught as part of the core curriculum in state-funded schools. But as Andy Clark, professor of logic and metaphysics at the University of Edinburgh, UK, emphasises: This is real and dangerous and coming our way.
He and others worry because scientists have yet to crack the great mystery of how consciousness could emerge from firing neurons. Progress in science is slow on many fronts, says John Searle, a philosopher at the University of California, Berkeley. We dont yet have a cure for cancer, but that doesnt mean cancer has spiritual causes.
And for Patricia Churchland, a philosopher of neuroscience at the University of California, San Diego, it is an argument from ignorance. The fact something isnt currently explained doesnt mean it will never be explained or that we need to completely change not only our neuroscience but our physics.
To Gefter, the debate is just a quibble over words:
The attack on materialism proposes to do just that, but it all turns on definitions. At one time it looked like all physical causation was push/pull Newtonianism, says Owen Flanagan, professor of philosophy and neurobiology at Duke University, North Carolina. Now we have a new understanding of physics. What counts as material has changed. Some respectable philosophers think that we might have to posit sentience as a fundamental force of nature or use quantum gravity to understand consciousness. These stretch beyond the bounds of what we today call material, and we havent discovered everything about nature yet. But what we do discover will be natural, not supernatural.
Andy Clark continued his tone of alarm over this battle, calling the intelligent-design
position an especially nasty mind-virus because it piggybacks
on some otherwise reasonable thoughts and worries. He argued that it
is a non-sequitur to leap from the empirical
evidence that we can change our brains with our minds to the conclusion that the
mind is non-material. That doesnt follow at all, he said,
applying his material brain to the process of logic.
Theres nothing odd about minds changing brains if mental states
are brain states: thats just brains changing brains.
Gefter became enough alarmed over this new front in the creation-evolution
battle to suggest some strategy.
If people can be swayed by ID, despite the vast amount of solid evidence
for evolution, she worried, how hard will it be when the science
appears fuzzier? She reminded scientists of criticisms that they
have already been too lax in teaching the public about evolution. Its time to get on offense.
Maybe now they need a big pre-emptive push to engage people with
the science of the brain and help the public appreciate that the brain
is no place to invoke the God of the gaps.
Apparently the irony of this article was completely
lost on Amanda Gefter and her materialist experts. They were all using
their minds to argue and debate about immaterial concepts. If nothing more
was happening than molecules bouncing around in their skulls, how could they
even know what they were saying?
Remember when Mom, Dad, or some other childhood mentor showed you that
when you point an accusatory finger at someone else, three other fingers are pointing back at you?
Clark just lectured us on logic. Flanagan just lectured us on
definitions. Gefter just lectured us on God-of-the-gaps arguments.
All three have just shot their little finger-guns right back into their own
skulls. Example: Gefter dismissed Schwartzs empirical evidence that
the mind can change the brain by saying, the material brain is changing the
material brain. OK, class, whats the next question?
Think about it (yes, think), [Jeopardy tune plays], and the bell rings
Aha! Who is making the material brain change the material brain?
And who is observing the change?
Now, if you
think that is just a logical trick, you have to realize that without a person
doing the changing, no one would ever know a change had occurred. This is
a mind-body problem that cannot be so easily swept away. If you could
shrink yourself to the size of a cell and wander through the brain, you would
no more see thought than if you wandered through Big Ben could you see time.
Time and thought live in the conceptual realm, not the material realm.
Suppose you walked through a computer chip like a pedestrian on the streets of
London. Would you see Boolean logic? Oh, you might see
certain switches light up, and perhaps you could perceive electrons
in a diode or transistor junction flowing one way instead of the other.
But it is not the chip that would be sensing that logic is occurring: it would be
you, the Observer. The operation of a physical system is not the same as
concept behind the system. A system cannot tell itself the purpose of the
system in a way that brings understanding. That takes a Person.
Consider: if Amandas mind is not directing her argument, how could she
have any free will to believe that her argument is true, and that ID is so false it
should be pre-empted? And to what is the pre-emptive strike referring, if
not some well-intentioned but misguided appeal to immaterial truth and morals?
Gefter and Flanagan dismissed this all as quibbling over definitions.
But look at the fingers pointing right back at them: they suggested that any
possible concept might be enveloped within the words material or
natural even things like sentience, a quantum-gravity theory of
consciousness, or any future discovery of science. These stretch
beyond the bounds of what we today call material, and we havent
discovered everything about nature yet. But what we do discover will
be natural, not supernatural. This is a rescuing device to
end all rescuing devices. No matter what the evidence, they can envelop
it, like The Blob, into their materialistic worldview.
OK, lets push that envelope. Suppose they find irrefutable
evidence for angels. Will they call them material? Will they be a part
of the natural universe? Even God has a divine nature.
The word nature or natural is so slippery it can mean a dozen different
things including immaterial things like natural laws (Note: material things may
obey natural laws, but laws are not material). Materialists constantly invoke
non-material things in their reasoning: mathematics, abstract logic, scientific
methods to name just a few. They also frequently make reference to unobservable
entities information, feedback, signal transduction, classification, reason, honesty
and much, much more. They help themselves to immaterial concepts and stuff them into
their materialist bag, oblivious to who is doing the classifying.
God-of-the-Gaps: J. P. Moreland, who was mentioned in Gefters
article, has three comeback arguments to the perennial charge that Christians
fill gaps in scientific knowledge with appeals to God. Paraphrasing, he says,
(1) Christians would not expect there to be many gaps. The Biblical worldview
indicates that the world runs according to predictable patterns (natural laws)
most of the time. In fact, it is only the Biblical worldview that makes
sense of the concept of natural laws. (2) Some gaps are getting wider.
Scientific discoveries about the cell and the origin of life and the fine-tuning
of the universe are resisting all attempts at materialist explanations.
We should follow the evidence where it leads. If that evidence is pointing
to design, so be it. (3) Materialists are just as guilty of the charge.
Whenever some incredibly-complex mechanism is discovered in a cell, for instance,
they assume that natural selection produced it, or assume that some day in the
future, a material cause will be discovered. This is nothing more than
naturalism-of-the-gaps.
The material/spiritual and natural/supernatural distinctions are
false dichotomies. They cannot stand up to
a half-hour of scrutiny by a skilled philosopher. What it boils down to is
this: naturalism is anything and everything that allows a scientist (or a party
animal on drugs) to avoid responsibility to their Maker. Thats the
real argument from ignorance. They can believe
in space aliens or unobservable multiverses anything, no matter how crazy,
as long as they never have to bow the knee and confess, Thou art worthy,
O Lord, to receive glory and honor and power, for Thou hast created all things,
and by Thy will they exist, and were created
(Revelation
4:11).
You can put
a brain into a jar of formaldehyde, and you can throw a used computer onto a junk pile,
but the concepts of mind and design, like Halloween ghosts, will always find the
materialists haunted house and come back to join the party.
Next headline on:
Human Body
Intelligent Design
Theology, Philosophy or Religion
Another Strange Chinese Fossil Found: Dinosaur or Bird? 10/22/2008

Oct 22, 2008 Feathers and wings are among the most distinguishing characteristics
of birds. Integumenary features have been found on some dinosaur
fossils, and true feathers have been found on some strange-looking extinct birds.
The news media often try to marry the two into a committed relationship using
exaggerated artwork. They have been found imagining
feathers on fossils where the data are dubious or even missing
(09/29/2008,
06/13/2007). What makes a structure a true
feather? When does it support linking an unknown species into an evolutionary
relationship to birds?
The latest case involves a strange fossil from China reported in
Nature.1 Dated Middle to Late Jurassic in age, it is one
of the earliest species to sport integumentary structures (see
10/06/2004,
10/12/2005), but it was nearly contemporary
with early birds having true feathers. The media reports typically announce
a feathered dinosaur has been found (e.g.,
BBC News
New feathered dinosaur discovered and
National
Geographic First Dinosaur Feathers for Show, Not for Flight?)
though some titles leave other interpretations open (e.g.,
Live
Science, Bird-Like Dinosaur Sported Bizarre Tail Feathers).
Instead of allowing for the possibility that unrelated species had similarities,
the articles often state matter-of-factly that birds evolved from dinosaurs.
The BBC article was the most blatant in this regard, referring to the critical
transition from dinosaurs to birds and quoting a paleontologist at Londons
Natural History Museum stating, It provides fascinating evidence of
evolutionary experiments with feathers that were going on before small
dinosaurs finally took to the air and became birds.
The original paper did use the word feathers for the structures
in the fossil of the new pigeon-sized creature from the Middle or Late Jurassic
they named Epidexipteryx, but a closer look
shows some findings that may not help the evolutionary scenario.
- None of the structures were pennate feathers, that is, with barbs and
barbules from a central vane. The integumentary structures fell into two categories:
- Shafted feathers Connected to the last ten tail vertebra were found two
membranous structures consisting of parallel shafts that each branch once.
Each shaft has a thin unbranched vane of material, like a coating, along a central rachis.
The result appears as four long nearly-parallel rods that join at the base.
Collectively they are nearly as long as the skeleton of the creature. Mark Norell
(American Museum of Natural History) commented, These seem to lack that main
shaft down the middle and are just a really long collection of very long,
filamentous-like structures.
- Non-shafted feathers These are rows of integument
found outside the outline of skeleton, presumably from the skin. They
all end in parallel rows of barbs, nothing like the cross-cutting structure of
bird feathers; the BBC article calls it a fluffy, down-like covering.
The authors stated, the free distal barbs of Epidexipteryx
arise from the edge of a membranous structure (Fig. 2b, c, d, d'), an arrangement
that has never previously been reported.
- Some of the structures bear similarities to those on Jeholornis, a creature interpreted
as being capable of powered flight (see 07/24/2002).
- The authors allowed for the possibility that this creature was
secondarily flightless i.e., that it once had feathers like
a bird, but lost them; if so, it was not evolving from a dinosaur into a bird.
- The authors suggested that the feathers on Epidexipteryx were used for
display, not for flight, but the LiveScience article hypothesized they
likely helped the creature balance on tree branches.
- The animal had a curious mosaic of traits. National Geographic remarked,
Epidexipteryxs anatomy seems to be a hodgepodge of features taken
from a variety of animals. It seems to have been the platypus of
the Jurassic an improbable mixture of traits from different groups.
- Since the creature had a surprising combination of physical features
(BBC News), it should not be envisioned as a transitional form from one lineage to
another. The BBC News article
complicated the evolutionary story by stating, The discovery adds
yet more complexity to the early history of the era when small meat-eating
bipedal dinosaurs evolved into birds. The evidence, therefore,
makes the explanation more complex, not simpler, in contradiction to Occams Razor.
- The evolutionary date is too late to represent a pre-bird. The BBC article
said, whereas other feathered dinosaurs [sic] date from after
the appearance of the first known bird, this fossil appears to be much closer in age,
so it opens a new window on the evolutionary events at the critical transition
from dinosaurs to birds. Live Science says that the dates are uncertain;
at best it was slightly older than Archaeopteryx. If it
was nearly contemporaneous with a fully-feathered bird that was most likely
capable of powered flight, it could not be a pre-bird, bird ancestor or missing link.
- The evolutionary link to birds is only inferential. Live Science quoted
one of the authors saying, Although this dinosaur cannot be the direct
ancestor for birds, it is one of the dinosaurs that have the closest
phylogenetic relationship to birds.
- Mark Norell hinted that this fossil has more to say about diversity, not evolution.
Things more primitive than this have fully formed feathers he said.
This is just some weirdo kind of thing this animal has.
The Live Science article elaborated on Mark Norells comments about diversity
within groups:
As scientists and others discover more and more dinosaur fossils with bird-like features,
the picture of such creatures is becoming more complex, said Norell, who
was not involved in the current study.
Just like the bird diversity we have living today goes all
the way from hummingbirds to ostriches to toucans, its incredibly diverse,
Norell said during a telephone interview. Now were starting to
see that sort of diversity extends not only in birds but also in the close bird
relatives [which] were just as physically diverse as modern birds are.
To infer evolutionary relationships, scientists conduct two kinds of studies. One is
the cladistic study, that measures the number of specific characteristics in a
fossil or creature, like the angle of its pelvic bone or ratio of skull length to
skull width, and scores it in relation to other similar creatures. The other,
when possible, is the genetic study of DNA similarities and differences.
Assuming that common descent is true, they produce phylogenetic diagrams of
ancestral relationships based on degree of similarity. Norells comments
suggest that among a highly diverse set of organisms, the possibility of subjective
inferences to ancestry is high meaning that other inferences are legitimate,
depending on which similarities are measured, and the relative weights
assigned them by human minds.
1. Zhang et al, A bizarre Jurassic maniraptoran from China with elongate ribbon-like feathers,
Nature
455, 1105-1108 (23 October 2008) | doi:10.1038/nature07447.
The artists renditions go far beyond the
evidence: theyve put vibrant colors on the alleged feathers and given the
creature a whole life and personality. The structures cannot be called feathers except
by stretching the definition of the term. The tail structures look like long
rods. The down-like coating could be flayed skin, given that the
creature was exceptionally well preserved. It may represent a mutant dodo-line
of ancient birds that went extinct, or a member of a subclass of dinosaurs that
shared the most similarities with birds without being related to them.
Scientists should be very careful about making inferences about any
complex set of data. The bones do not jump up and announce that they were
evolving into birds. The supplementary data in the paper show nearly 300
traits that had to be compared to make a cladistic analysis. The significance
of any one of them requires a human judgment. Which traits are you going to
focus on? Humans share traits with this fossil, too: vertebrae, teeth,
radius and ulna, and many organs not visible from the bones. It is conceivable
that the scientists in another civilization might consider size, habitat, lifestyle or some
other characteristic to be the overriding concern in their way of classifying things.
What kind of inferences would they draw? Complexity, diversity and mosaics
of traits throw simplistic schemes into disarray. How would you rearrange your
Evolutionary Tree of Tools if somebody handed you a Leatherman tool with a
knife, screwdriver, pliers and scissors in a leather pouch?
Even granting, for the sake of argument, the most generous leeway
to the evolutionists and calling the structures on this thing feathers does not help their story.
Other feathered birds were nearly contemporaries. If this was an evolutionary
dead end, where is the highway? A collection of dead ends may keep you
busy, but is not going to get you anywhere.
Next headline on:
Dinosaurs
Birds
Fossils
How Not to Teach Evolution 10/21/2008

Oct 21, 2008 Current Biology usually interviews a scientist for each
issue. In the October 14 issue,1 the subject was
Dyche Mullins, a molecular biologist at UC San Francisco. His story of how
evolution was taught in high school should make teachers and parents take notice.
After the usual anecdotal fluff about what kind of cookies he likes
and what bicycles he prefers, Mullins was asked what turned him on to biology after
so many years (he did not become interested till graduate school).
Good question. In part, it was the way I was taught biology in high school. My teachers refused to teach anything about evolution. In fact, the only time I remember hearing the E word in high school was when we dissected frogs. After explaining to a room full of queasy kids how understanding the anatomy of a frog could help us understand the basics of human anatomy, the teacher paused thoughtfully and said, Now Im not talking about evolution here, so dont go home and tell your parents that Im teaching evolution. And that was it. The rest of high school biology was just a collection of evidence supporting Dobzhanskys claim that Nothing in biology makes sense except in light of evolution. We collected insects and looked at pine cones, and we had a hamster that we taught to go to the bathroom through a hole in the side of its cage. That was pretty much it. Biology seemed more like an eccentric hobby than a coherent body of knowledge. Mercifully, we were spared any discussion of Intelligent Design....
I started reading more deeply in biology and realized just how flawed my early education had been. I read Darwin and I discovered T.H. Morgan and Max Delbrück and the Phage Group. The only advantage of coming to biology so late was that I found almost everything that I learned new and exciting. Reading about solving the genetic code, thirty years after the fact, made me as excited as if it was happening at that moment, in a lab down the hall. I was astounded by the calcium ATPase: a single molecule that can discriminate, with remarkable specificity, between similar divalent cations and use chemical energy to pump calcium against a 10,000-fold concentration gradient.
In the ellipsis, Mullins had described his educational diversion into physics and mathematics.
Apparently his teachers on those subjects did a better job, because he dove into
them headlong with gusto. What made him turn back to biology was seeing living systems
for the first time as computer-controlled machinery:
To my engineers mind, a living cell was now just a complex, feedback-controlled system.
I could imagine writing equations to describe biochemical pathways, cellular functions,
and, eventually, entire living cells. Nowadays this kind of thinking would be
called systems biology. And while it is not exactly the way I approach
biological problems in my lab now, it was the kind of thinking that made biology intelligible to me.
When outside the lab, Dyche takes off the white coat. You can watch him ham it up
with comedy country blues boys on YouTube,
singing, Man of Constant Sorrow.
1. Q&A, Dyche Mullins, Current
Biology, Volume 18, Issue 19, 14 October 2008, pages R895-R896, doi:10.1016/j.cub.2008.07.056.
Biology teachers should have constant sorrow, too
after reading this story. This is how to turn a bright young inquiring mind into a
self-contradicting smart aleck. Cant this blues boy realize that
complex, feedback-controlled systems dont just happen? This man of constant
sorrow can stare at intelligent design right in front of his face, like that biological
machine that can discriminate, with remarkable specificity, between similar
divalent cations and use chemical energy to pump calcium against a 10,000-fold
concentration gradient, and turn right around and praise Darwin and
Dobzhansky. Step back a second and realize how insane this is. This same
dude would never step into a computer room and insult the designers, but can
stare at even more complex systems and call them cobbled jumbles of time and chance.
Its enough to make you want to yank his beard and knock on his skull and
ask, Anybody home? (Caution: Do NOT do that to anybody except yourself,
women and obsessive shavers excepted.) The interviewer, as usual for Current Bilge,
just slurps it all up like fine whine.
Teachers: pay attention. You cannot solve the creation-evolution
controversy by ignoring it. This does more harm than good. Students
want answers. They are curious about evolution. Those from religious
homes may be worried about it, while those from secular humanist homes may have
moms and dads ready to sue. You cannot push this subject off. One cannot
understand modern history or science without understanding Darwin. The next
Dyche Mullins in your classroom will remember how you sloughed off the subject as
if it were taboo, then a Darwin dogmatist in college will sweep him off his feet
with visions of the alluring explanatory power of evolution.
In private or home schools,
the solution is simple: teach all about Darwinism all its strengths and weaknesses,
the stuff the textbooks leave out. In public schools, the courts and the
school boards have often become so paranoid they will try to persecute or dismiss
any teacher who teaches scientific facts about Darwin, like they did to Roger
DeHart. Sometimes the thought police go after not what you say, but what they think your
motivation is. You have to know your principal, your state, and your school
board. Thankfully some states are passing academic freedom laws. Many
teachers have found the right way to present Darwinism honestly without dogmatism.
Who could fault that? Science is supposed to be the opposite of dogmatism!
Dont expect all parents and school boards to be rational, though, on this hot topic;
the Discovery Institute can provide
valuable help for negotiating the fine legal lines involved. Whether public or private
or home school teacher, your goal is to help students become familiar with the evolutionary theory
in its historical, political and scientific contexts; to understand the arguments Darwin
and his critics have made, and while at the same time to develop critical thinking skills
to be able to separate dogmatic claims from scientific evidence.
Lets use this entry also to cogitate on the nature of science.
We tend to pigeonhole subjects into watertight categories: a scientist is someone
who does science, and science is what scientists do. Is that necessarily the case?
When Mullins is clowning around with the country band, is he doing science then, just
because he is a scientist by profession? Obviously not. All right, then;
is |