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Not only is our biography of
Robert Boyle complete, we just added a
page of his writings so you can read
Boyle in his own words.
Check it out!
Sexual Selection for the Masses 06/30/2003
The July 2003 National
Geographic has arrived in homes across the world. It contains an article by
Virginia Morell on Darwins theory of sexual selection: The Animal Mating
Game: Its his show, but its her choice. The pictorial entry,
replete with flea penises, bellowing elk and strutting cocks, recalls how Darwins
theory that sexual dimorphism evolved by a means other than natural selection
had a rough time gaining acceptance, presumably from British white guys unwilling to
grant such power of choice to females. She quotes Therese Markow (University
of Arizona) saying (p. 48), Theres no question Darwin was right about the power of
female choice. It can shape males and it can make new species.
This is why the Teach the Controversy approach
would be good for science. Popular magazines like NG have free rein to distort
the evidence to fit their beliefs. Why dont they report what you have read
here, that the origin of sex is the
queen of evolutionary problems, and
that results are equivocal? Sexual selection
is a collection of just-so stories that can be spun
to explain any observation, and prominent evolutionists are announcing that it has
no effect on speciation, or that
sexual selection is plain wrong. Even
the classic example of the peacock tail, the thought of which made Charlie sick,
is a tormented just-so story according to NG's own
news division, with many unanswered questions that have not been answered satisfactorily
to this day. So why does NG sanitize this controversy for the eyes of impressionable
students in their flagship magazine? Its their show, but its your choice.
Next headline on: Darwinism and Evolutionary Theory.
The Mystery of the Ultra-Pure Sandstones 06/27/2003
R. H. Dott, Jr (Univ. of Wisconsin) has a problem. Hes been trying
to explain a geological puzzle for 50 years, and it is still unresolved.
All around the world, sandstones are found that are remarkably pure
that seem nonactualistic (jargon for They cant really
be there). These pure quartz arenites, as they are called, were
considered a major puzzle half a century ago, when Dr. Dott was a student.
Some of them extend laterally over vast areas encompassing one or several states,
and they cover vast areas of Africa and Arabia, the Great Lakes region, South America,
Australia, and more.
These sheet sands (as they are nicknamed) are part of a notorious
gang: Together with the origin of dolomite, red beds, black shale,
and banded iron formation, they made up a group of seemingly intractable
geological problems (emphasis added in all quotes).
Dott tells autobiographically, Having lived literally upon quartz-rich
sandstones for almost 50 years, I have come to regard supermature quartz
arenites as natures finest distillatealmost as remarkable
as a pure single malt Scotch whiskey.
In the July
2003 Journal of Geology, he has written a lengthy paper addressing
the mystery of the quartz arenites, and the status of current hypotheses.
It amounts to a veritable State of the Century address to sandstone geologists.
He explains the puzzle in the Introduction:
What is the quartz arenite problem?
Foremost is the extreme compositional maturity of sandstones composed
of more than 95% quartz. Furthermore, the quartz consists almost
exclusively of grains of unstrained, single-crystal units. Very
rare lithic [rock] fragments consist only of durable polycrystalline
quartz types such as chert or vein quartz. In addition, the extremely
rare accessory mineral suite (generally <0.05% by weight) is dominated
by durable zircon, tourmaline, ilmenite, and leucoxene. Where
present, associated conglomerates also consist only of durable clasts
of vein quartz, quartzite, or chert. How can we explain the
complete disposal of at least 75% of any ultimate parent igneous or
metamorphic rock to yield a residue that is at least 95% quartz sand?
Extreme textural maturity is also characteristic of many, but not all,
examples. A high degree of sorting has always been
emphasized, with high rounding being common but not universal.
Both properties imply much abrasion by one or more of natures
most physically vigorous processes, such as surf and strong eolian [wind]
or aqueous currents.
Dr. Dott mentions additional puzzles about these formations:
- Thin, tabular geometry: layers tens or hundreds of meters thick, very flat over vast regions,
yet Paleozoic in age i.e., prior to the emergence of land plants.
- A paucity of associated shale, in contrast to other sandstones.
- Interstratified with shallow marine carbonate strata.
- A lack of volumetrically significant analogues forming today (i.e.,
nothing on that scale can be seen forming now). This implies
weathering processes orders of magnitude greater in the past.
- Very rare body fossils, and some burrows.
- Frosting of the grains, making the rough on microscopic scales.
- Underlying mature shale high in kaolinite (clay) or illite.
- Even more pure quartz arenites, even thousands of meters thick, in Precambrian strata.
- Many of them underlain by paleosols (ancient soils) that show a
high degree of chemical maturation.
According to Dott, wind erosion is the most efficient, but not the only, agent for
rounding of the sand grains. Some geologists have resorted to
theories of multicycling to explain the
weathering and maturation of the grains, but theories of single cycles
under intense tropical weathering also go back decades, and
he cannot rule them out.
(Though there are small examples forming in isolated river deltas today, their
grains are not nearly as rounded.) The chemical maturation suggests
that impurities were dissolved away, a process called diagenesis, but
that is not possible in the presence of wind.
The paradox of the compositional maturation of the
sand seems to require some additional factor to reconcile
geomorphic conditions that could have enhanced the transport
and abrasion of enormous volumes of pure quartz sand, on the
one hand, but could have allowed exceptional chemical maturation
of soils on the other hand, as indicated by profiles beneath,
and the composition of pelitic [mud, clay] strata interstratified
within, many quartz arenites.
Dott introduces his theory at this point. To solve
the paradox, he postulates thin microbial crusts or mats of cyanobacteria
formed over the soils, similar to
the stromatolites and cryptogamic soils seen forming in some regions today.
These might
have protected the underlying paleosols while allowing wind transport of
sand above. The lack of trees and shrubs might have allowed much
more energetic winds. This assumes that the first land invaders
were cyanobacteria, although the fossil record has seemed mute
on this point. In a sense, these crusts formed a cap that protected
the lower strata while the high winds deposited the sand (although he does
not propose sources for the sand).
He ends with one other paradox; without land plants,
unless the landscape were perfectly flat, how could it be stable enough
to allow the chemical weathering of both the sand and underlying paleosols?
The abundance of medium-grained to coarse-grained sand and associated
pebbles required streams with sufficient gradients to transport such
materials, which in turn points to at least moderate topographic relief,
which exacerbates the stabilization problem, he says.
His best guess, in conclusion, is the microbial mat theory; this formed a
crust enough to stabilize the landscapes for up to two billion years
while these puzzling structures formed.
This was an interesting paper about an interesting puzzle that some readers
may wish to investigate further.
Does his explanation satisfy you?
Notice how these formations are huge, and exist on every continent.
Notice how thick and flat they are. Notice how they are interspersed
with clays and soils, yet are exceptionally pure, natures finest
distillate. Notice how they give evidence of being deposited
via natures most
vigorous and energetic forces. Doesnt this sound like global
cataclysm? Since catastrophism
is back in vogue, should we not follow the evidence where it leads?
Next headline on: Geology.
Cell to Phagocyte: Im Dying Eat Me 06/27/2003
Cells go the way of all the earth, but their society cleans up
after them. This occurs through an elaborate signalling procedure
that biochemists are beginning to uncover, as explained in a Minireview
in Cell,
June 27 by Kodi S Ravichandran (Univ. of Virginia). A cell
undergoing death throes by caspase activation (in itself an elaborate
shutdown process) sends out eat me signals that are
recognized by the roving clean-up squad, the phagocytes.
Normally, a cell wears a Dont eat me tag, but this
is removed and a phosphatidylserine (PS) tag pops up on the outer
membrane. Simultaneously, LPC and/or other signals are secreted
in search of a nearby phagocyte, with a silent invitation to
dinner. The dying cell wears the Eat-Me
signals on its outer membrane. An approaching phagocyte turns
on anti-inflammation signals, as if to say to others nearby,
Nothing to get inflamed about; I can handle this one.
After engulfing the dying cell, it re-arms the inflammation alarm.
Through this system, needless inflammation is avoided,
and the streets and alleys are kept clear of cellular corpses.
The author summarize, An evolutionarily conserved machinery
exists for engulfment of apoptotic cells from worm to mammals.
Lets clear the air in that sentence:
if machinery is evolutionarily conserved,
it is not evolutionary at all. Conservation is not evolution.
Such doubletalk that injects evolution into the phraseology contradicts
these observations. Nothing has evolved. The cleanup crew
has been around since it first appeared, fully functional, in the
lowly roundworm. (Undoubtedly, similar mechanisms go back even further;
scientists just happened to study this mechanism in a favorite lab worm,
C. elegans.) There are at least seven
genes involved in corpse clearance, he says.
So the Creator thought of everything. Nothing
is wasted; when the cell has hit its threescore and ten, the parts are
recycled, and the tissues are kept clear of debris.
The authors diagrams
show cells with happy faces wearing the Dont eat me
tag and sad faces advertising Eat me. This is not
just a cute trick that animals do; he says, Accumulating
evidence suggests that failure to clear apoptotic [dying] cells
promptly has serious consequences for inflammation and
autoimmunity.
In the same issue of Cell, 25 scientists published
a paper entitled,
A
Panoramic View of Yeast Noncoding RNA Processing in which they
describe the huge number of noncoding RNA that is functionally
conserved over evolution [there they go again] and
plays a role in
basic cellular processes. But this RNA is not going to
help their RNA World hypothesis for
the evolution of life, because these RNAs depend on proteins to
manufacture them: Predictive analysis using publicly available
yeast functional genomics and proteomics data suggests that
many more proteins may be involved in biogenesis of ribonucleoproteins
than are currently known (emphasis added). It just keeps
getting harder to hang on to the Darwinian story line. Let go and
let God.
Next headline on: The Cell.
Hunting for the Common Ancestor of Chordates 06/27/2003
Chordates have a chord, a nerve chord, part of their central nervous
system. They include all vertebrates, including people.
Did whales, kangaroos, camels and mice evolve from a common ancestor?
Thats the conventional wisdom, and in the
June
27 issue of Cell, Diethard Tautz is optimistic that
evolutionists are starting to make progress figuring out the chordate
family tree, but he makes some rather
damaging admissions along the way (emphasis added):
- The study of comparative anatomy is one of the great traditions
of biology. The intellectual challenge of inferring hidden
relationships and devising consistent schemes for placing
seemingly disparate morphological types into a logical [sic] order
has always attracted biologists, but also other great thinkers. ...
Probably the most fascinating aspect of comparative anatomy is that
it has remained impossible to propose a grand scheme that places
the phyla into an undisputed evolutionary context.
- It is usually assumed that the evolutionary advance
[sic] of centralizing the nervous system has occurred only once,
implying a direct relationship between the central nervous system of
arthropods and chordates. However, the nerve chord is dorsal in
chordates and ventral in arthropods. Thus, if there was only a
single origin of the central nervous system, one has to propose an
axis inversion during evolution ....
- The alternative, namely at least two independent events
leading to the evolution of a central nervous system from an ancestor with a
diffuse system, has seldom been discussed, mainly because the
traditionally assumed phylogenetic relationships among phyla
would have made this unlikely.
Tautz refers to a paper in the same issue by nine cell biologists (Rowe
et al.),
Anterior
Patterning in Hemichordates and the Origins of the Chordate Nervous
System that hypothesizes that acorn worms might be the
missing link. Along the way, these authors also make embarrassing
admissions about the usual story:
- Despite considerable paleontological work and molecular
analysis, mystery still surrounds the origin of our own phylum,
the Chordata.
- Early deuterostomes [chordates + hemichordates + echinoderms] were
clearly established by the Lower Cambrian, as documented in
recent excavations.
- Identifying morphological homologies among these phyla has
been fraught with difficulties, as their adult body plans appear
so divergent.
- However, the homologies [chordates with hemichordates] are easily
controverted and hemichordates were reclassified into their own
phylum by the 1940s.
- Three hypotheses currently account for the origin of the
chordate nervous system, all consistent with recent molecular
phylogenies, yet all mutually incompatible.
- A more classical perspective of nervous system evolution
that has not enjoyed much support from recent molecular analyses
is the proposal that the bilaterian ancestor had a diffuse nervous system
that was centralized independently in different bilaterian lineages. ...
Since there has been no molecular evidence for an extant group of
animals with such a well-patterned but diffuse nervous system, it was
not clear such an organism could exist.
- The nervous systems of hemichordates and chordates are so
different morphologically that it has been difficult to make
valid comparisons. This study provides a rational basis for
investigating the possibility of structural homologies between
the two groups by restricting direct morphological comparisons
to regions that develop from the same expression domains of
the two maps, as shown in Figure 7.
- At this stage in our
analysis, we do not suggest any structural homologies of
the respective nervous systems of the two groups but do call attention
to corresponding parts that evolved [sic] from the same domains
of the deuterostome ancestor.
- Although we raise the possibility of a diffuse nerve net in
the deuterostome ancestor, evidence is still equivocal.
- The deuterostome ancestor we propose, with its complex
anteroposterior organization but diffuse nervous system, may already
have had some other differentiated characteristics of the chordate
lineage, ... In general though, the conserved domain map appears
very weakly linked to the particular morphologies of
different evolutionary lines.
- Although the ancestor of bilateral animals probably had
complex anteroposterior organization based on many of these domains,
this organization set few limits on morphology and
cytodifferentiation in subsequent evolution. The existence of
a modern hemichordate with a highly patterned but diffuse nerve net
suggests that the nervous system may be very plastic in its
evolutionary possibilities and that its exact neuroanatomy
may tell us little about the early branching of metazoan phyla.
In short, they find some conserved developmental genes, not clear
morphological (bodily) evidence of a relationship.
Back to Tautz. He finds the data and analysis by
Lowe et al a
refreshing new view on an age-old discussion of evolution,
but concludes, Alas, even these excellent data are open to more
than one interpretation, ensuring that the discussion will go
on.
One participant not invited in this
discussion is the one who says there is no evolutionary relationship,
that this is all force-fitting data into a belief system, and that
highly conserved and complex mechanisms that are well adapted to each
organisms needs imply intelligent design.
So after all this time as the official soothsayers of
biology, all that evolutionists can describe are widely divergent groups with
no clear common ancestor; conserved (unevolved) genes and
development patterns (see previous headline commentary); and complex,
highly adapted systems that were already fully formed in the lower
Cambrian, i.e., the first fossil layers. All they can propose are
suggestions (i.e., stories; heres another,
different one) that are open to more than one interpretation and
fraught with difficulties. To adapt a
favorite political slogan, are you better off than you were 144 years
ago when the Darwin Party came to power?
Next headline on: Darwinism and Evolutionary Theory.
Upward Lightning Shocks Atmospheric Physicists 06/26/2003
Caught on film was a totally unexpected find: gigantic electrical
discharges reaching upwards from thunderclouds to the edge of earths
atmosphere. A Taiwanese team photographed the bolts that last
only milliseconds but are 55 miles long and are unrelated to normal
lightning. Evidence for transient luminous events
have been anecdotal by pilots for decades, and smaller events like sprites had
been discovered in 1989, but these are whoppers: over 25 miles wide at the top
and occupying 7200 cubic miles each.
It is believed these gigantic jets as they have been called
play an important role in the global electric circuit
that surrounds the Earth, helping reduce the huge differences in
charges that build up between the surface and the ionosphere,
says National
Geographic News. They could also help life on earth by
fixing nitrogen and producing ozone for our UV-shielding ozone layer.
Physics Web also
talks about this find.
The original paper by Su et al is published in
Nature
June 26. In a
News and Views
summary in the same issue, Victor Pasko
says the study of what impact these 300,000-volt discharges have
on environmental chemistry is in its infancy.
Here another phenomenon has been
discovered that contributes to the life and health of earths
inhabitants. That something this large could go unnoticed for so long
hints that there is more design in our environment than we know.
Welcome to Earth: the electric planet.
Next headline on: Physics.
Next amazing story.
Trees, Water Pumps Extraordinaire 06/26/2003
The worlds tallest tree stands over 367.5 feet tall, which means
every needle up there has to get water pumped up to it from the ground.
Did you know scientists have been puzzled for centuries how this is done?
The leading theory taught in schools, the Cohesion-Tension Theory (C-T), has
been controversial for a long time.
Even Francis Darwin said when it was proposed,
To believe that columns of water should hang in the tracheals like solid bodies,
and should, like them, transmit downwards the pull exerted on them at their upper
ends by the transpiring leaves, is to some of us equivalent to believing in ropes of sand.
Even today, Michael Tyree of the USDA Forest Service, writing in
Nature
June 26, explains other, more serious problems with the idea that transpiration at
the leaves somehow 'pulls' the water up the vessels:
I can think of no other botanical theory that has engendered more
incredulity among physical scientists and animal physiologists than the C–T theory,
because it requires us to suppose that water is transported in a metastable state.
If an air-bubble or vapourvoid of sufficient diameter were to arise in a xylem conduit
under negative pressure, the water column would cavitate and the void would expand to
displace the water, making the conduit dysfunctional.
Despite these criticisms, no one has had a better idea.
Recent measurements, however, seem to indicate that the C-T mechanism actually
does work in spite of cavitation,
because there are billions to trillions of conduits in a tree and because
adjacent conduits are isolated from each other by primary cell walls in pits.
So the huge number of conduits guarantees that some
cavitation in individual tubes will not reduce the overall success of the water pump.
In addition,
tall trees and ground-hugging plants have to balance trade-offs between vessel diameter
and gas exchange rate through the leaves. Fast-growing species have
large, efficient conduits that are highly vulnerable to embolism; such plants
perform poorly in drought. Slow-growing species have small, inefficient
conduits that are very resistant to cavitation, Tyree explains.
Some puzzles remain, but An understanding of this legacy of natural selection
should allow us to breed or engineer improved drought-resistant or fast-growing trees,
he says (emphasis added in all quotes).
This story would be so much more enjoyable without
the useless Darwinspeak. Tyrees article starts out,
Like their animal counterparts, large multicellular plants need to supply all their
cells with fuel and water. For animals, the solution was the evolution [sic]
of a vascular system, with a pump to circulate an isotonic blood plasma that
prevented cell rupture through the osmotic inflow of water. Plants took a
different route to solve the problem [sic] of osmoregulation, encasing each
cell in a rigid exoskeleton, the cell wall. But this rigidity brought with it
a lack of mobility — for whole organisms and also for tissues and cells. Plant
tissues were too rigid to evolve a pump mechanism for long-distance transport.
So plants found another solution and invented high-efficiency pumps
that could transport water hundreds of feet into the air without cavitation loss, etc. and so on.
Is this kind of personification
of plants and animals enlightening? How did a plant, without a brain, figure out
this trick: Plants seem to retain and transport water in conduits while under
pressures as negative as -1 to -10 megapascals (MPa) — that is, pressures 10 to
100 times more negative relative to atmospheric pressure than a perfect vacuum.
Evolutionary gibberish about plants inventing pumps that solve the cavitation problem
and animals that invent vascular systems is devoid of logic.
Nature should abhor a vacuum.
Next headline on: Plants.
Next amazing story.
Sea Shells: Shed Sell Em If She Could Manufacture Them 06/26/2003
The common seashell: extraordinary. Michael Rubner in the
June
26 issue of Nature is rhapsodic over the lowly items picked
up daily by children on the beaches of the world:
For a materials scientist, cross-sectional images of the complex
microstructures of naturally occurring hard materials such as
bones and sea shells are awe-inspiring. Over many
millions of years [sic], nature has devised schemes [sic]
to combine seemingly incompatible building-blocks — soft
organic proteins and hard inorganic particles of calcium
carbonate — in a manner that produces composite materials with
the unusual combination of high strength, hardness and toughness.
(Emphasis added in quotations.) So
how does nature do it?
To be strong, hard and tough, a material must be able to absorb a large
amount of energy during mechanical deformation and also maintain
high stiffness. In bone or shell, this desirable combination
of properties is made possible by one key attribute — a
bricks-and-mortar-like structure, made up of strongly interacting,
nanometre-size building-blocks. The 'hard' bricks and 'soft'
mortar are complementary in their response to stress and strain.
Shellfish use calcium carbonate particles for bricks, and
specially-designed proteins for mortar.
Human attempts to mimic this ability have failed to produce a substance
with similarly impressive mechanical properties.
Most artificial efforts have had problems with adsorption of water, that
reduces the strength, and controlling the assembly of nanometer-size objects.
But once again, Nature has no such difficulty with nanoengineering.
Rubner describes some recent successes, but as man inches along toward
mimicking the manufacture of similar materials, he must stand in awe
of clams and scallops and conches that do it every day without a thought.
If you took the childish Mother Nature
talk out of science journals, evolutionary theory would gasp for hot
air. So Nature devised this over millions of years?
Nature has nanoengineers better than our PhDs? Such nonsense
isnt worth two clams.
On the beach this summer, go shell collecting with your
kids. Make it a teachable moment about the wisdom of God.
Next headline on: Ocean Life, Fish etc.
Next amazing story.
Hubble Outdoes Itself 06/25/2003
Many will remember the Hubble Space Telescopes memorable 1995
Deep Field image of 1600 galaxies within a tiny point of sky.
Now, it has really delivered the GOODS (Great Observatories Origins
Deep Survey): twin photographs equalling 60 Deep Fields. For
photo and description, see the
Hubble
Press Release or the
NASA Press Release.
The images, one from the southern hemisphere and one from the northern,
contain a combined total of about 50,000 galaxies. The fields will
also be scrutinized by the Chandra X-Ray observatory and
SIRTF, the giant infrared telescope launching this August.
What can anyone say in response
to such awesomeness? Write your own commentary on this one.
Next headline on: Stars.
Next amazing story.
Medical Schools Dont Teach Enough Evolution 06/25/2003
A questionnaire was sent to the deans of all the medical schools
in America asking them how much evolution was part of their
curriculum. Of those responding, only 48% considered evolution
an important part of the curriculum, only 32% actually taught at
least 8 of 16 core topics in evolutionary biology, and
only 16% actually had a faculty member with a PhD in evolutionary
biology. The most common reasons evolution was not given more
coverage was lack of time and lack of faculty expertise.
Specifically, they said the factors that made it difficult to
incorporate teaching evolutionary biology were:
87% Lack of curriculum time
53% Lack of faculty expertise
34% Lack of funding
33% Lack of agreement about relevance
24% Difficult finding/hiring qualified faculty
11% Political controversy
05% Lack of confidence in scientific status of evolutionary biology
Source: Evolutionary Biology in the Medical
School Curriculum, by Randolph M. Nesse (professor of psychiatry,
Univ. of Michigan) and Joshua D. Schiffman (Dept. of Pediatrics,
Stanford), published in
BioScience, June 2003.
They say, We conclude that the role of evolutionary biology
as a basic medical science should be carefully considered by a
distinguished group of biologists and medical educators.
In the meanwhile, undergraduate educators need to recognize that,
for now at least, most future physicians must learn evolutionary
biology as undergraduates if they are to learn it at all.
See our
January 13 commentary on this subject.
The statistics above are quite revealing. A third of deans of
medical schools dont believe evolution is relevant to their
curriculum, and 5% do not have confidence that evolution is science.
11% are afraid it will embroil them in political controversy.
One wonders whether the other reasons were just polite cloaks for their
lack of confidence in Darwinians. There does not seem to be a
lot of interest in teaching evolution. If it were that important
and that relevant, would they not make time for it in the curriculum,
rather than 87% of them saying they couldnt give it the time of day?
How can it be that after a century of indoctrination, less than half of
medical school faculty feel qualified to teach it?
The lack of funding reason almost implies a sarcastic smirk:
You want us to teach more evolution? Send me a check.
How essential is it for doctors to
know evolutionary theory? It depends on what you mean by evolution.
Change happens: everybody accepts that. These authors undoubtedly
mean the whole worldview of Darwinian evolution, that human patients in
hospitals have evolved from slime over time.
Each of the 16 core concepts that medical
schools are presumably lax about teaching are either irrelevant
to medicine, or irrelevant to Darwinian evolution. Table 1 of the
paper lists these concepts and the degree of coverage in medical schools
according to the deans that responded. Here they are:
- Antibiotic resistance: 94%. Yes, it is important for doctors
to understand that certain populations of pathogens are resistant to
antibiotics, but this is microevolution at best. Since the pathogens
are most likely losing information, this is irrelevant to Darwinian
evolution: i.e., the de novo emergence of new
functional information.
- Virulence evolution: 83%. Since virulence genes appear to move
about by horizontal gene transfer, it is equivocal whether evolution
had anything to do with it. A doctor needs to know how to treat
a pathogen, not its assumed family history.
- Population genetics: 79%. A knowledge of how traits shift within
populations may be interesting, but probably not helpful to a medic.
This subject can be treated without reference to common ancestry.
- Selection for disease genes: 72%. Understanding how artificially
imposed environments might exacerbate the prevalence of pathogens is
important for doctors and hospitals to know, but again, what does common
ancestry really have to do with it?
- Mutation selection balance: 55%. The relevance of this
triple-noun jargon is questionable. Mutations: yes, they occur.
These result in devolution. Selection: natural selection operates as
a conservative force. Balance: we all need balance. Who made up
this phrase and appraised it one of evolutions core concepts?
- Levels of selection: 51%. Not all selection pressures have the
same effect. Big deal. Your doctor probably does not know
or care about this one.
- Host-pathogen arms races: 43%. This is one of evolutionists
many personification fallacies.
Germs dont care if they win or lose a war. If existing strains
already have resistance, they will proliferate, and hosts having resistance
to those will also proliferate. Proving a trail of tit-for-tat
evolution becomes questionable after a generation.
- Novel environment causing disease: 30%. A med student should
be expected to know that there are risks going into a strange environment,
but claiming this causes disease
is a non-sequitur.
It might just awaken what was already present.
- Tradeoffs: 26%. Another personification fallacy.
Intelligent designers often make tradeoffs between competing requirements
to achieve optimum design, so what does evolution have to do with it?
See the May 2002 example about the eye.
- Comparative anatomy: 21%. This subject was alive and well long
before Darwin, but when usurped by the evolutionists, it became the
argument from homology. Jonathan Wells in Icons of Evolution
has demonstrated this to be a
circular argument when used to argue evolution.
- Defense regulation: 20%. Humans and animals have highly functional
defense mechanisms that are regulated. Does anybody have a clue why
this is a core concept of evolution, rather than evidence for
intelligent design? This is like saying, Tax relief is a
core concept of the Democratic Party.
- Life history evolution: 19%. Dr. Average Dean was probably
scratching his head on this one.
- Design flaws from path dependence: 17%. Ah, now they want to
impugn God. Evolutionists think that presumed suboptimal design shows
that our ancestors took opportunistic paths to obtain functional traits.
Favorite examples include the pandas thumb and presumed inverted
wiring of the mammalian retina. Both work as excellent adaptations for
their users; calling them flaws is subjective, and path
dependence is just-so storytelling. Doctors need observations,
not stories.
- Primate phylogeny: 9%. Totally useless, and 91% of medical
schools agree. Nobody, not even young-earth creationists, disputes
that humans and apes have physical similarities. Perhaps it would
be useful to doctors to be able to tell one from the other when their
patients walk into the office. A circus vet might need to know
how to treat the chimpanzee differently than its trainer. But does
any doctor care about the ape-to-man story line?
- Kin selection: 9%. Aha! These authors are
group
selectionists. Michael Ruse, get on their case.
Does a doctor need to know what evolutionists are arguing about?
Hes got better things to do.
- Proximate/ultimate distinction: 5%. Another head scratcher.
What does this have to do with evolution, medicine, or the price of
tea in China?
The authors apparently feel that listing these assumed core
concepts will cause Marcus Welby to think, Hmmm, I never
learned about that; maybe I should go back to Darwin school to improve
my career. But look at each one, and they are either not the
sole property of the Darwin Party, or have nothing to do with macroevolution,
or have nothing to do with medicine. We repeat: medical schools do
not waste valuable time teaching evolution, because it is useless.
Next time you go to the hospital, you had better hope your
doctor knows more about intelligent design than evolution, or he might
yank something out and say, You dont need this; its
just a useless vestige of a tree shrew in your ancestry. Or s/he
might let you die, believing that (1) the pathogen has just as much a
right to a living as you do, or (2) natural selection needs to let
the fittest survive, and the germs are clearly the fittest in the
evolutionary arms race going on in your body. Wait till these
evolutionists wind up on a hospital bed themselves. Chances are
they wont care much about the evolutionary qualifications of the
surgeon. Rather, they will be praying earnestly for the likes of a
Louis Pasteur instead of a Dr. Mengele.
Next headline on: Schools.
Next headline on: Darwinism and Evolutionary Theory.
The Mountains of the Sun 06/24/2003
The suns surface has been imaged in 3-D for the first time
by the Swedish 1-m Solar Telescope and is featured on
Astronomy
Picture of the Day. The surface is seen as a constantly
churning plasma of granules with steep edges, some reaching 200 miles
above the average surface height. Thats higher than 34
Mt Everests stacked on top of each other.
For more descriptive details and images,
including time-lapse movies, see the
Lockheed Martin
Solar and Astrophysics Lab press release.
Other stars are known to be violent
and sometimes explosive. How our own can be so gentle and benign
despite a violently churning, pulsating, complex interior and
surface (photosphere) is due to a large number of lucky
accidents, including our protective storm
windows here at earth. These detailed images will provide
insight for solar astronomers seeking to explain many mysterious
features of the sun.
Next headline on: Solar System.
Next headline on: Stars.
Next amazing story.
Sea Monsters Brought Up from the Deep 06/24/2003
Not exactly dragons, but fish and other creatures that look like
the stuff of nightmares have been brought up from 1.3 miles deep
off the coast of New Zealand, reports and
BBC News.
One species of fish has fangs bigger than its head. To avoid
piercing its own brain when it shuts its mouth, the article
explains, its teeth fit into opposing sockets. In addition
to fish, new species of armored shrimp, squid, and a spider with long
legs and a tiny body were found. 500 species of fish and 1300
invertebrates were discovered, living in complete darkness and pressures
hundreds of times greater than at the surface. They also found
a fossil shark tooth they claim had been lying undisturbed on the
sea floor for millions of years.
The sea floor was not supposed to be
undisturbed for so long. The tooth is evidence that the creature
did not die millions of years ago.
Unheard-of wonders remain to be
discovered on this living planet. Ugly as they are to our
sensibilities, these creatures are all remarkably adapted to their
extreme environment. Many of them have features not seen in
other members of their orders and families. And they represent
arthropods, bony fish, cartilaginous fish, crustaceans, cephalopods,
echinoderms and more totally different groups of animals,
all with adaptations to high pressure and darkness.
The writer
of Psalm
104 didnt know a thousandth of the amazing details in
the sea when he exclaimed, O LORD, how manifold are Your works!
In wisdom You have made them all. The earth is full of Your
possessions-- this great and wide sea, in which are innumerable teeming
things, living things both small and great. There the ships sail
about; there is that Leviathan which You have made to play there.
Next headline on: Fish.
Next headline on: Bugs and Creeping Things.
Next headline on: Fossils.
Next amazing story.
Evolution Drives Mars Quest 06/23/2003
Its the phylogeny, stupid: What draws humans to the Red Planet
after so many failures? asks James B. Garvin in
The
Orlando Sentinel.
The reply is obvious: Its simple -- life.
But not just life per se: he means life that evolved from nonlife.
A new awareness of the biological evolution of our
own planet
is motivating us to reach out and find it in space.
If we find life on Mars, he thinks, then the prospects for life
elsewhere in the solar system and beyond would be magnified
enormously. He likens us to new explorers launching
out into Terra Incognita:
Two hundred years ago, our fledgling nation chose to send Lewis and
Clark and their Corps of Discovery on one of the greatest overland
expeditions in history, and within a generation the discoveries they
made reaped benefits for the entire country. Today, we send
robotic explorers to the planet Mars as a bold step forward in our
quest for understanding the prospects for life elsewhere
in our solar system and to lay the groundwork for future human voyages
to the Red Planet.
In conclusion he writes,
Mars is indeed a terra incognita that may tell us ultimately
we are not alone, or, better still, that our origins are
traceable to other worlds whose histories can tell us about parts of
our long-lost past here on Earth, he writes. But he hedges
his bets whether life will be found:
We arent sure what we will ultimately learn and discover,
but the quest will teach us how to better understand [sic - split
infinitive] ourselves and
our place in the universe. (Emphasis added in all quotes.)
Significant difference: Lewis and
Clark were not trying to discover primordial soup. This was
56 years before Darwins book, when most scientists still believed
life had been created. Part of their mission was to examine new
varieties of life they already knew existed on the Blue Planet.
This essay, so typical of Darwinian daydreaming, makes it
seem the Darwinists are lonely. Since they have cast out belief
in a God and an afterlife, maybe they want to share their despair
with some other despairing beings in this interlude between a bang
and a heat death. Misery craves company.
Ever notice how evidence for evolution
is always in the future tense? If we find life on
Mars, then we can really bash those creationists.
If not, well just move the battlefield farther out,
ad infinitum. But why should finding life elsewhere prove
evolution? Isnt God omnipresent and omnipotent?
Next headline on: Mars.
Next headline on: Origin of Life.
Kin Selection Studies Produce Mixed Results 06/23/2003
Two different investigations of kin selection, an
offshoot of Darwinian natural selection proposed by W. D. Hamilton 40 years ago
to explain altruism and group behavior, have produced mixed results.
Swedish and Spanish researchers studying
carrion crows concluded that their work, published in the
June 20
issue of Science, supports the theory.
But American and French scientists publishing
another
paper in the same issue about blue side-blotched lizards got results
that contradict it. They conclude,
Our experiment rules out kin philopatry or kin attraction as
settlement mechanisms; rather, settlement must arise from the mutual
attraction of genetically similar types.
In their summary of these papers,
Desperately
Seeking Similarity, Dickinson
and Koenig say these two studies shed new light on this
problem, but admit that in the lizard study Kin
selection is apparently
not driving these behaviors, at least under the experimental conditions
enforced by Sinervo and Clobert. Where to go from here?
Progress in understanding social evolution, they conclude,
will involve teasing apart the importance of kinship
from other forms of selection based on genetic similarity as
distinct and potentially important pathways to social behavior
(emphasis added).
Too bad they didnt read the
PNAS paper May 2002 by Oxford
scientists.
It would have saved them a lot of needless energy.
Those who think Darwinian evolution is a coherent theory,
embraced by all scientists unquestioningly, fail to recognize the deep
divisions within the Darwin Party.
This is one of them: the individual selectionists
vs. the group selectionists. The blind are only fighting the blind,
however, because neither of them seem able to explain the strange,
altruistic behavior of Presbyterians.
Next headline on: Birds.
Next headline on: Darwinism and Evolutionary Theory.
Searching for the Dork Side of the Farce 06/20/2003
Dark Matter is the subject of a special section in the
June
20 issue of Science. Seven feature articles discuss
the unknown quantity that supposedly makes up 96% of the universe
(emphasis added in all quotes):
- Welcome
to the Dark Side: Delighted to See You by
Linda Rowen and Robert Coontz introduces the dark subject:
Dark stars, the dark age, dark matter,
and dark energy are the major components of the dark side of the
universe: 96% of the universe consists of mass and energy we
cant see and dont really understand.
- The
Warped Side of Dark Matter by Robert Irion examines whether
dark matter can be detected through weak gravitational lensing.
Astronomers are lining up to survey the sky looking for the effect,
but have not detected it yet.
- Dark Energy Tiptoes Toward the Spotlight by Charles Seife
introduces the new and radical concept of dark energy.
Astronomers studying Type 1a supernovae first postulated in 1997
an antigravity force causing the universal expansion to accelerate.
On the face of it, this was an absurd conclusion, he
admits, but formerly timid astronomers are now boldly charging into
this dark region:
These are baby steps into a new realm of physics that was
entirely obscure until a few years ago--and scientists are
just beginning to figure out its properties. Id
love to be able to take a lump of dark energy and see what happens when
you knock it about, squish it, drop it on the floor, says
Campbell [sic; Caldwell? the article mentions Robert Caldwell of
Dartmouth]. But short of that, observations of
supernovae and eventually the evolution of distant galaxy clusters
and galaxies will begin to pull back the veil over dark energy.
Until then, dark energy will likely be the darkest mystery in a
very dark universe.
- Evidence
for Black Holes by Mitchell C. Begelman explores the overwhelming
circumstantial evidence for black holes, though the measurements
discussed so far do not establish that the dark masses and compact objects we
detect are the black holes whose properties are predicted so precisely by
general relativity. Begelman does not make it clear what the
connection is between black holes and dark matter or dark energy.
- New
Light on Dark Matter by Jeremiah Ostriker and Paul Steinhardt
discusses what the mystery material might be. WIMPs (weakly interacting
massive particles) are a leading contender, CCDM (cold collisionless dark
matter) is a runner-up, but there are seven alternatives invented to explain
problems with the front runners. Where did the Dark Matter and
Dark Energy concepts come from? They explain:
After the introduction of inflationary theory, many cosmologists
became convinced that the universe must be flat and that the total
energy density must equal the value (termed the critical value) that
distinguishes a positively curved, closed universe from a negatively
curved, open universe. Cosmologists became attracted to the
beguiling simplicity of a universe in which virtually all of the
energy density consists of some form of matter, about 4% being ordinary
matter and 96% dark matter. In fact, observational studies were
never really compliant with this vision. Although there was a
wide dispersion in total mass density estimates, there never developed any
convincing evidence that there was sufficient matter to reach the
critical value. The discrepancy between observation and the
favored theoretical model became increasingly sharp.
Dark energy came to the rescue when it was realized
that there was not sufficient matter to explain the structure and nature
of the universe. The only thing dark energy has in common with
dark matter is that both components neither emit nor absorb light.
- Throwing
Light on Dark Energy by Robert Kirshner attempts
...to learn whether the dark energy is a modern version of Einsteins
cosmological constant or another form of dark energy that changes with
time. Either conclusion is an enigma that points to gaps in our
fundamental understanding of gravity.
Is it justified, though, to posit invisible entities?
In the self-proclaimed age of precision cosmology, we
know the amount of each component to a few percent, but in the spirit
of honest cosmology we also have to admit we do not know
precisely what either of them is. But we are not helpless.
We can observe light emitted by supernova explosions to trace the
history of cosmic expansion to learn more about the invisible forces
that shape the universe.
Kirshner reviews the evidences for cosmic expansion and acceleration,
but more and better observations are needed. Nevertheless, he
ends on an optimistic note:
Theorists may be wary of the coincidence between the present and
the onset of cosmic acceleration. Observers are delighted by this
coincidence and by the coincidence between our own brief lives and the
instant when technology has made these measurements possible.
We are incredibly lucky to be working just at the moment when the
pieces of the cosmic jigsaw puzzle are falling into place, locking
together, and revealing the outline of the pieces yet to come.
Dark energy is the biggest missing piece and a place where
astronomical observations point to a gaping hole in present knowledge
of fundamental physics.
In the end, dark matter and dark energy are still invisible and unknown.
Their presence is only inferred from the most popular models that match
certain observations (and many assumptions) about the nature of the universe.
For a simplified review of these articles, see
National
Geographic News.
Attractive models are not reality, and hopes are not done deals.
Since we are not impressed by such things here, we always sweep it away
look for any kernels of hard evidence behind the fluff of words
and abstruse math. Consider several things from the above quotes:
- The holes in our knowledge involve fundamental things, not
details. There are, as stated, gaping holes.
- Dark matter made its debut because of the attractiveness
of the inflationary big bang cosmology.
- Dark energy made its debut to rescue dark matter from observations
that conflicted with inflationary theory.
- Nobody knows what either of these entities are. The proportions
between them are due not to observational evidence, but what is needed
to sustain the most popular inflationary models.
- Evidence is always in the future tense.
- Observational studies were never compliant with the vision.
- The conclusions are absurd.
- We need more funding.
- More funding and honest cosmology do not necessarily go hand in hand.
It appears that cold dark matter was invented as a cosmic fudge factor to make the
models work, but when the most popular model got too convoluted to
expect CDM to do it all, they needed a bigger, better fudge factor;
thus was invented dark energy. So now there are two ghosts, the big
ghost and the little ghost. When the little ghost cant
take the heat, the big brother ghost comes to bat.
If this dark stuff comprises 96% of reality, then it
should be right here: right on earth, all around us, even passing through
our bodies without interacting with ordinary matter. Yes, Mr. Peabody,
you are surrounded by WIMPs you cannot see, but they control the origin
and destiny of the universe. Is this dorky, or what?
Its as weird as Star Wars, with some invisible spiritual entity
permeating space and explaining everything. Trust your
feelings, Luke! I can feel the hate [against creationism] rising
within you. Let go, give in, yield to the dark side!
You will become more powerful, and a part of ... The Empire.
Science is supposed to be about observable, repeatable,
measurable phenomena, not invoking dark, dark, dark entities to explain things that
dont fit ones favorite model. Science says, if the model doesnt
work, chuck it. If the assumptions are unjustified, scuttle
them. If the philosophy behind the assumptions is unsupportable,
change it; but that takes courage and can incur the wrath of The Empire.
If a metaphysical cosmology is wrong, dont become seduced by the
dark side of the farce, no matter how big the Empire that supports it.
Dont trust your feelings, Luke. Do the right thing.
Join the rebellion:
come
to the light.
Next headline on: Cosmology.
Scientists Watch Motors Unwind DNA 06/19/2003
Andrew Taylor and Gerald Smith from Fred Hutchinson Cancer
Research Center (Seattle, WA) announced in
Nature June 19
that RecBCD enzyme is a DNA helicase with fast and slow
motors of opposite polarity. In the same issue,
Mark S. Dillingham, Maria Spies and Stephen C. Kowalczykowski of
U.C. Davis came to a similar conclusion. Working independently,
these teams watched an important molecular motor in action and determined
that it is two motors in one, with a slow motor and fast motor working
side by side on the same track. How can that be, and why?
RecBCD helicase is the molecular
machine that travels along a DNA double helix, unwinds it, and
separates the strands so that the translation machinery can
get to it. This combination enzyme
(RecB + RecC + RecD) is a member of a superfamily of helicases, or
enzymes able to unwind and separate DNA. Simpler helicases separate
the two DNA strands into a Y-like tail, but RecBCD has the unusual property
of creating a loose tail on the RecD side and a loop and a short tail
on the RecB side (RecC, not a motor, appears to help RecB in its action).
Combined, RecBCD is among the fastest of helicases: it can
cover 370 base pairs per second, according to Taylor and Smith,
or up to 1000 base pairs per second, according to Kowalczykowski et
al.
Both the RecB and RecD motors
can travel along DNA separately, but are polar opposites: one moves
along one strand, one along the other. Of the two, RecD is the
speed demon; RecBC only moves 20% as fast. The motors are not
nearly as fast or stable acting alone. Separately, they fall off the
track after 50 base pairs, but together, can cover 400-600 times as much
ground: 20,000 (Taylor and Smith) or 30,000 (Kowalczykowski) at full
speed.
So why two engines in this race car? Taylor and
Smith suggest that it adds stability; a motor is less likely to fall off
the DNA track when combined with another, but why the speed difference?
This will take more study. All they can conclude is, This
asymmetric feature might impart RecBCD enzymes asymmetry in
other aspects of its promotion of genetic recombination.
Were going to stick our neck out
and offer a hypothesis. First of all, it is apparent from the
speed and processivity (ability to process lots of letters without
failure) that RecBCD is very well designed. It doesnt seem
to slow RecD down to have the slower RecBC motor on the other track,
but why dont they both run at the same speed?
There must be a reason, and maybe the loop that RecBC forms is the clue.
In a fast winding device, like a tape drive, engineers
often design a slack-uptake mechanism to prevent breakage if there
is a sudden stop. In older computer tape drives, for instance,
a vacuum column maintained a loop of tape that could act as a buffer
when the motors stopped or reversed direction. Because RecBCD
is so fast, maybe it was designed with a similar slack-adjusting loop
on one side.
Well have to wait and see whether this hunch
has any merit. Suffice it to say that we have again watched
scientists uncover a superbly-efficient, highly-accurate biological
machine, made up of multi-component parts, that does just what the
cell needs doing. For security reasons, DNA is tightly
wrapped and hard to get to. Once the helicase machinery is
authenticated and allowed in, it needs to do its job fast, and
that it does, exceptionally well. 1,000 base pairs a second:
imagine! It has to melt the chemical bonds between
DNA letters at that high rate without causing collateral damage for
its 20 to 30 second roller-coaster ride down the DNA tracks.
A good typist works about 70 words per minute; with an average word length
of 5, thats 350 letters per minute, or just under 6 letters per
second. A speed reader can go faster, but can anyone claim to
read 200 words per second? Behold RecBCD, the champ.
Its busy at work inside your every cell, right now. And
oh, by the way, these scientists did their studies on those simple,
primitive, lower forms of life: bacteria. As you might expect,
neither paper dares mention how these little machines could have evolved.
Next headline on: The Cell.
Next headline on: Genes and DNA.
Next amazing story.
Constantine Converted by Asteroid? 06/19/2003
Swedish geologists are claiming an asteroid hit the Apennine Mountains
outside Rome, and the resulting mushroom cloud was the basis of
Constantines vision of the Sign of the Cross that converted him
to Christianity on his way to conquering Rome, reports
Ananova.
The BBC News
has a picture of the crater and says this blast saved Christianity.
How can anyone possibly know that?
You cant go back and ask Constantine what he saw, and you cant
date an asteroid impact precisely to the very day his army was crossing
the Tiber. Why didnt the enemy see the same sign and convert?
Constantine may well have had ulterior motives other than visions for what
he did. There are limitations to what science can tell us.
Stories like this are idle speculations, essentially worthless.
Next dumb story.
Recent Archaeological Finds: Fakes? 06/19/2003
Israel Insider
reports that the Israeli Antiquities Authority (IAA) announced
June 18 that the James ossuary is fake,
and also that the Joash inscription
is a forgery. Both items were owned by the same collector,
who is alleged to be a dealer of questionable reputation.
The Biblical
Archaeological Society, which announced the ossuary last fall,
is withholding judgment on it until a forthcoming scientific
report from the IAA is completed, but is pretty convinced the
Joash
inscription was too good to be true; that inscription
leaves little doubt that we are dealing with a forgery,
and that, unfortunately, it is a rather poor forgery,
according to Harvard professor emeritus Frank Moore Cross.
Regarding the ossuarys authenticity, the controversy revolves
around the inscription. The box appears to date from the
right period, but some are claiming at least part of the text
(especially the part that says brother of Jesus) was
added in modern times. See also a report on
National
Geographic News.
A good lesson in not jumping to
conclusions. We advised cautious optimism with both these finds,
and the caution appears to have trumped the optimism in at least one case,
maybe both.
Perhaps the ossuary may still prove genuine, but we should assume it is
not till proven otherwise.
We also reminded readers that the
authenticity of the Bible does not depend on relics.
National Geographic makes this absurd statement:
If the 2,000-year-old ossuary were genuine, it would be the
first archaeological proof that Jesus existed. Up until now,
all references to the three men [i.e., Jesus, James, Joash]
have been found only in manuscripts. Why are not manuscripts
considered evidence potentially as solid as etchings in rock?
Is the only evidence for American presidents the engravings
of four of them on Mt. Rushmore? Dont presidential libraries
and manuscripts provide even better evidence? Come on.
Manuscripts, when adjudged to be genuine, were written by contemporaries
just as surely as a stonemason with a chisel and they can provide
a much greater wealth of detail.
Evaluate the Biblical manuscripts with good historical-grammatical
technique, and you do not need to find the name Jesus etched in a
bone box to provide proof he existed.
Meanwhile, there is much more to dig and discover
out there, but it is not always easy to find. Consider that only
one wall remains of Herods huge temple, but no one doubts the rest of
it existed. There is plenty of hard archaeological evidence
already to confirm the genuineness and historical accuracy of the
Biblical manuscripts. Dont expect to find a stone inscription
of Jesus under every tree in Israel. The more valuable a relic,
the more eagerly sought by thieves or destroyed by enemies.
If we have seen as much destruction and looting as took place in Iraq
in one month, how much has been lost in thousands of years of major wars
and occupations? Read
the
manuscripts.
Next headline on: The Bible.
Is Modern Cosmology on the Right Road? 06/18/2003
Many science news sources have been giving the impression that
inflationary cosmology is all wrapped up now, and we can all go home except
for mopping up a few details. Steven Gratton and Paul Steinhardt,
writing in the
June
19 issue of Nature, seem to share that assessment, yet
raise some caveats that do not seem trivial in their News and Views
article, Cosmology: Beyond the inflationary border.
Some excerpts (emphasis added in all quotes):
- The standard model is less a solid edifice than a scaffolding
with many gaps, resting on uncertain foundations.
- The story has become familiar, but consider its foundations.
Is there really a beginning to the Universe? What events led to
the onset of inflation? And does the Universe even contain the
ingredients necessary for inflation (in particular, the inflaton
field that purportedly drives inflation and then decays into
hot matter and radiation)? Without answers to these questions,
the model is incomplete. Most cosmologists have set
these questions aside, assuming that advances in fundamental physics
(such as string theory) will address them.
They give some details why eternal universe or eternal oscillation
models do not work; so the question of what happened before
inflation seems hard to avoid.
- The Hartle-Hawking 'no boundary proposal' [proffered
in Stephen Hawkings best seller A Brief History of Time]
deals with the transition from quantum to classical cosmology,
and many have hoped that this would naturally lead directly
to a description of inflation on the classical side.
Unfortunately, instead it leads typically to an almost empty
universe in which little or no inflation occurred.
Their last paragraph sounds like an accountant with bad news interrupting
the company sales celebration:
The work of Borde* et al.
combined with these other attempts, forces us to realize
that the inflationary story is still incomplete.
And this is not the only unresolved issue. The model
predicts the total energy density in the Universe correctly, but
the nature of 96% of that energy is unknown.
Furthermore, despite two decades of studies, the fields responsible
for driving inflation have not been identified, and there is
no accepted explanation for the finely tuned interactions
that the fields must possess for inflation to end smoothly.
So, there are good reasons to cheer [sic] the recent breakthroughs, but there
are also many fundamental issues that remain to be explored.
And there is perhaps even room for radical alternatives.
*They refer to a recent paper in Physical Review Letters 90:151301
(2003) by Borde, Guth and Vilenkin.
Were lost! the wife
laments as a couple roams down a country road in the rain at night.
Dont worry, honey. I know right where we are,
the husband replies cheerfully.
Why are you so stubborn? Why dont you ever
want to stop and ask for directions? she whines.
Real men dont need directions. Everything is under
control. Well be there in no time at all, you just wait.
But weve never been there before! We have been driving
on this road for hours now, we cant see a thing ahead, it
doesnt look anything like we thought it would, and the directions
we were given were vague and dont match what we are seeing, which is
precious little at the moment. And you claim we arent lost.
Can we please ask someone from around here who knows the way?
Trust me, honey, well get there eventually. Look
on the bright side. At least were ahead of schedule!
Ponder the seriousness of the issues Gratton and Steinhardt
raise, and ask yourself whether this joke fits the current situation
in cosmology. Perhaps there is even room for radical
alternatives, they say, but which cosmology is radical
is in the eye of the beholder. Some consider it radical to
ask for directions.
Next headline on: Cosmology.
Surprise: Y Chromosome Protects Itself with Palindromes 06/18/2003
Cheer up, men: your Y chromosome is not going extinct.
Since the Y has no backup copy, geneticists thought it might mutate
itself into useless junk in just 10 million years. Well, the
Y chromosome map has just been completed, reports
Nature
Science Update, and of all the clever things, the Y has built-in
self-defense in the form of palindromes. Just like the phrase
Madam, Im Adam can be read the same backwards and
forwards, there are large gene-coding regions on the Y that can be
decoded in either direction. The article explains:
These palindromes house many genes - which means that there is a copy
at each end of the palindromic sequence. These provide back-ups
should harmful mutations arise. The mirror-image structure also
allows the arms to swap position when DNA divides. Genes are
shuffled and bad copies are purged.
David Page at MIT remarked, The Y chromosome is a hall of
mirrors. More surprises are expected now that the full
map of the chromosome has been published (its the cover
story of Nature June 19).
Now that the male chromosome reveals that we have underestimated
its powers of self-preservation, maybe men will finally start
getting some respect.
Male chromosome full of surprises, is
the way Science Now
entitled their summary of the findings. The Y is not a graveyard
of genes, nor a shriveled up remnant of the larger X chromosome.
Its new-found capabilities, dynamically shuffling its genes to weed
out defects, has given scientists a new appreciation for it.
As one researcher put it, this has brought a lot of honor to males.
For this system to work, the decoding
and translation mechanisms, and the epigenetic controls, also have
to know the trick. This is a remarkable and unexpected finding.
The article states, The male-defining chromosome was previously
thought of as a wasteland where genes go to die.
To that idea we say, hasta la vista, baby.
You will see design or chance in this story
depending on your philosophy. Huntington Willard commented,
No one had contemplated that there would be this level of gene
conversion in our own genome. It gives us a glimpse of how
the Y has protected itself. [How can a string of DNA
protect itself if a Programmer did not design the function?]
On the other hand, the article states,
Other researchers see swapping as an
evolutionary accident, not a safeguard.
Only an evolutionist
could see a self-defense mechanism and call it an accident.
One of the palindromes is nearly 3 million letters long.
Experiment: try writing your own original palindrome with just one
thousandth of that: 300 letters. Follow up experiment: now
try getting a palindrome of similar length by shuffling random
Scrabble letters on a table.
Next headline on: Human Body.
Next headline on: Genes and DNA.
Next headline on: Intelligent Design.
Next amazing story.
Short Takes 06/17/2003
- Hearing:
Max
Planck scientists have discovered the elusive channel that
converts mechanical energy into electrical signals in sensory
hair cells, such as those in the cochlea of the human inner ear.
They found this in zebrafish, but worms and fruit flies have similar
mechanisms. This means,
they claim, It is very likely that this particular
sensory system evolved in an ancestor common to both arthropods
and chordates.
- Intelligent Design:
William Dembski has a forthcoming book The Design Revolution:
Answering the Toughest Questions About Intelligent Design.
For the outline and preface, see
Access
Research Network.
- Insect Flight:
Flies fly on automatic pilot. An article from the New York
Times 6/10/03 is reproduced on
Access
Research Network.
- Genetics: A comparison of human and mouse genomes
shows that differences do not appear at random breakpoints around the
chromosomes, but only at certain fragile sites
in only 5% of the genome.
This overturns a thirty year old hypothesis.
Story on SciNews;
original paper on
Proceedings
of the National Academy of Sciences.
- Disease: The complete genome of a liver carcinogen
Helicobacter hepaticus shows that the disease-producing agent
inhabits a pathogenicity island that is missing in non-virulent
strains of the bacterium. The authors of the paper in the
Proceedings
of the National Academy of Sciences feel this 71-kb island may have
entered the genome by horizontal gene transfer from another organism.
- Brain:
Glia cells in the brain are more than just the side-kick of the
celebrities, the neurons. Neuroscientists are now catching
up and discovering that glia not only support a number of essential
neuronal functions, but also actively communicate with neurons and with
one another. By doing so, glia influence nervous system functions
that have long been thought to be strictly under neuronal control,
writes Beth Stevens in the June 17 issue of
Current
Biology. Neuroscientists should have known better,
she quips, because over a century ago, Roman y Cajal had predicted that
they would be important due to their sheer numbers (they outnumber
neurons by a factor of 10). But his work
was largely ignored, and glia
were considered to be space-filling junk,
or mere scaffolding for the glitzier neurons.
- Dolphin Sonar: Dolphins perform automatic gain control
on their sonar pulses, but unlike bats, they do it on the transmitter,
not the receiver. See News and Views by Amanda Tromans in the
June
19 Nature, reporting on the research paper
by Whitlow Au and Kelly Benoit-Bird in the
same
issue. See also
Science
Now, Why Dolphins Aren Deaf (because without
gain control, return pulses from their clicking sounds would be deafening).
Next headline on: Fish.
Next headline on: Bugs.
Next headline on: Mammals.
Next headline on: Human Body.
Next headline on: Genes and DNA.
Next headline on: Intelligent Design.
Bacteria More Orderly Than Previously Known 06/17/2003
Bacteria are not simple bags of protoplasm. Since they lack the
organelles and nuclei that eukaryotic cells possess, scientists
used to think their contents were fairly unstructured and homogeneous.
That view is changing,
say Zemer Gitai and Lucy Shapiro in the June 16 online preprints of
the Proceedings
of the National Academy of Sciences. Historically,
they agree, perhaps because of their general lack of
compartmentalized organelles, bacteria were viewed as relatively
uniform at the subcellular level. New microscopic techniques
are unveiling highly ordered structures, like protein spirals and rings
that oscillate between the poles and allow the cell to locate the
midpoint for cell division. Perhaps the most important
lesson to be learned from the work by Shih et al,
(who imaged the spiral proteins) is that the more closely
we look, the more order we see within bacterial cells.
The fact that the phrase bacteria are not just small bags
of enzymes has become cliché is a sign that bacterial cell
biology is coming of age.
For a related story, see our Jan
16 headline about spiral action of the bacterial cytoskeleton that
repairs the inner cell wall.
Hmmm, wonder why there is no mention
of the word evolution in this paper. Maybe we need to
return to the view of Antony van
Leeuwenhoek, the first man to see bacteria. Even in 1702
he realized,
From all these observations, we discern most plainly the
incomprehensible perfection, the exact order, and the inscrutable
providential care with which the most wise Creator and Lord of the
Universe had formed the bodies of these animalcules, which are so
minute as to escape our sight, to the end that different species of
them may be preserved in existence. His exemplary
observational scientific work led him to wholeheartedly reject
and refute the doctrine of spontaneous generation.
By the way, do bacteria really lack organelles?
This scientist at
University
of Illinois at Urbana-Champaign reported today that he found one, and that it
is challenging commonly-accepted evolutionary ideas. Dr. Roberto Docampo
said, It appears that this organelle has been conserved in evolution from
prokaryotes to eukaryotes, since it is present in both. This argues
against the belief that all eukaryotic organelles were formed when early
eukaryotes swallowed prokaryotes. This also means that prokaryotes are
not more primitive, and that the complexity of organelles goes way back into the
smallest, allegedly simplest, forms of life.
Next headline on: The Cell.
Update on RNA Quality Control: See
February 20 headline.
Picture of Protein Evolution Emerging? 06/16/2003
Most proteins have been formed by gene duplication, recombination, and
divergence, declare scientists from Cambridge and Stanford in the
June 13 issue
of Science. Proteins of known structure can be matched to
about 50% of genome sequences, and these data provide a quantitative description
and can suggest hypotheses about the origins of these processes.
With growing numbers of genomes decoded, they feel we
are well on the way to answering fundamental questions about how the huge
assortment of proteins arose (emphasis added in quotes):
During the course of evolution, forms of life with increasing complexity have
arisen. What are the mechanisms that have produced the increases in
protein repertoires that underlie the evolution of more complex forms
of life? How are proteins organized to form pathways?
Answers to such questions at the molecular level began to appear 40 years ago,
but it is only with the advent of complete genome sequences that we have begun
to get a comprehensive view.
At present, they admit, only close
to 50% of the sequences in the currently known genomes are homologous to proteins
of known structure, yet this half of the protein repertoire have given
us a detailed picture of its evolution.
They discuss how proteins fall into domains, and these are organized into families
that seem to obey a power-law
distribution; i.e, A few families have many members and many families
have a few members. Even proteins with different sequences can often be matched
with others possessing similar structure. Many of these are paired with other
domains. Of all the million-plus possible pairs of known families, only a few thousand
are used. This, they feel, is evidence of selection for function.
Also, the fact that combinations of particular pairs of domains are found in only
one sequential order ... suggests that conservation of sequential order in
domain combinations is usually found because the combinations descend from a
common ancestor.
The authors feel confident that
we understand the basics of how new complexity arises from the protein pool:
It is now clear that the dominant mechanisms that produce increases in protein
repertoires are (i) duplication of sequences that code for one or more domains;
(ii) divergence of the duplicated sequences by mutations, deletions, and insertions
to produce modified structures that may have useful new properties and be selected;
and, in some cases, (iii) recombination of genes that results in novel arrangements
of domains.
But how would metabolic pathways arise? They introduce the problem:
Proteins do not function by themselves but as part of an intricate network
of physical complexes and pathways. How does the duplication, divergence,
and recombination process fit into the formation or extension of pathways?
They propose that mutated proteins might either be recruited to new substrates within
existing pathways, or jump to different pathways. They observe,
An examination of the functions of the members of different families of
domains shows that, nearly always, it is the catalytic mechanism or cofactor-binding
properties that are conserved or slightly modified and the substrate specificity
that is changed. This suggests that it is much easier to evolve
new binding sites than new catalytic mechanisms. This tends to scramble the
evolutionary picture, though: This has led to a mosaic pattern of protein
families with little or no coherence in the evolutionary relationships in different parts
of the network. Can the evolutionary history be seen by comparing unrelated
organisms, then?
The comparison of enzymes in the same pathway in different organisms also shows
that proteins responsible for the particular functions can belong to unrelated
protein families. This phenomenon is called nonorthologous
displacement. Variations come not just from changes in specific enzymes.
In some organisms, sections of the standard pathway are not found and the gaps are
bypassed through the use of alternative pathways. Together, these variations
produce widespread plasticity in the pathways that are found in different organisms....
One final question remains: how did the first proteins originate?
And are new ones originating now?
The earliest evolution of the protein repertoire must have involved the
ab initio [Lat., from the beginning] invention of new proteins.
At a very low level, this may still take place. But it is clear
that the dominant mechanisms for expansion of the protein repertoire, in biology
as we now know it, are gene duplication, divergence, and recombination.
Why have these mechanisms replaced ab initio invention? Two
plausible causes, which complement each other, can be put forward. First,
once a set of domains whose functions are varied enough to support
a basic form of life had been created, it was much faster to produce
new proteins with different functions by duplication, divergence, and
recombination. Second, once the error-correction procedures now present
in DNA replication and protein synthesis were developed, they made the
ab initio invention of proteins a process that is too difficult to be useful.
In conclusion, they remind the reader that genome size is not the measure of
complexity (rice has more genes than people); instead, complexity does
seem to be related to expansions in particular families that underlie the more
complex forms of life. So the key to understanding the evolution of
the protein repertoire will be to compare how families of proteins in diverse
organisms have been duplicated and recombined.
We quote extensively from this article to let them dig their own trap.
Read again and look specifically for the origin of information
tied to function that has actually been observed to occur, anywhere. Is it not
all inference and deduction based on a prior acceptance of evolution?
Similarities are used to prove common ancestry, and common ancestry is used to
prove similarities. Round and round we go.
Protein
domains may behave in a certain sense like Lego parts, although this is a grossly
unfair oversimplification. The evolutionists are looking only for the Lego
blocks that look similar, and assuming the similarities (homologies) derive from
common ancestry.
What about the differences? They choose to focus on
similarities for philosophical reasons, but perhaps the differences raise the more
fundamental questions. Furthermore, they steadfastly refuse to consider that
the similarities might be due to an intelligent cause.
After all, we all inhabit the same
planet, whether bacteria, birds or people. It would only be expected that design would
produce similar metabolic pathways, requiring similar proteins (with some differences due to
differing needs, or from mutation or recombination, which are not sources of new
genetic information). For a discussion on whether duplication
and recombination can produce function, see the
07/09/02 headline on this subject.
The fact is, functional proteins appear fully formed
from the simplest organism on, and many are highly conserved a phenomenon
that led some Harvard scientists last year to announce the
protein big bang theory.
In todays
article, notice how these believers in protein evolution use a semantic trick to
sidestep around the problem of the origin of
functional information. That trick is to use passive
voice verbs, infinitives and subjunctives that contain no subject, so that it
remains nebulous who did the action. For example, from the last
paragraph quoted above,
- The earliest invention must have involved the ab initio invention of new
proteins. [Who, or what, was involved?]
- Once a set of domains whose functions are varied enough to support a basic form of
life had been created... [by whom? God? If that is what they meant,
the creationists would shout Amen!, but clearly they mean the naturalistic
magic trick of emergence, in which the miracle-worker
is an unnamed combination of impersonal natural laws and chance, using unspecified
mechanisms.]
- Once the error-correction procedures now present in DNA replication and
protein synthesis were developed... [Who did the developing?]
Suggestion for tough-minded thinkers: do not let them get away with this dodgeball game.
Stop them in mid-sentence and ask them to name the Subject. Who did the
creating? Who did the developing? Who was involved? It will
push them against the wall of chance, from which there is no escape.
If you are a consistent, doctrinaire evolutionist, there is no Who.
The ab initio invention of proteins has no Inventor.
To get even to a minimalist basic form of life you will need at
least 239 proteins to emerge or
the Ruse is over. Good luck.
Youll need it..
Next headline on: The Cell.
Next headline on: Origin of Life.
Next headline on: Darwinism and Evolutionary Theory.
Darwin or The Angel of the Lord: Who Guards the Tree of Life? 06/13/2003
The phrase tree of life appears in the first, last, and middle
books of the
Bible; it is the centerpiece of the garden of Eden, the
multi-fruited tree lining the river of heaven in Revelation,
and a metaphor for wisdom and joy in Proverbs. Solomon spoke
of wisdom, righteousness, a wholesome tongue, and hope fulfilled
all as being a tree of life.
These days, the phrase means
something quite different. Charles Darwins only illustration in
The Origin of Species was a diagram of organisms branching
into a tree-shaped array, all descended from a common ancestor.
This concept expanded during the Darwinian revolution to represent
a view that all life had arisen from a warm little pond, without
design, without God, without a creation, and without a heaven.
Rather than being
a source of righteousness, hope and wisdom, Darwins tree of
life stood for a world of uncaused, purposeless natural processes
that presumably had led, quite by chance, to the great diversity of
living creatures from bacteria to porpoises to orchids to people
through an unguided process of mutation and natural selection.
The June 13
issue of Science has a special section on the
Tree of Life, namely, Darwins. The series of articles
presents a collage of confusion mixed with confidence; confusion,
in that much debate surrounds the placement of species, genera, families
and orders in the branching timeline; confidence, in that evolutionists
are certain they are on the right track, and that with new data from
genomics and tree-building algorithms, a complete picture of the
tree is only a matter of time. Here is a brief outline of the series
(emphasis added in all quotes):
- In the lead story Charting the Tree of Life, the editors begin,
We are part of a tree of life that germinated at the dawn of
evolutionary history [sic] and encompasses a vast diversity that we are
only beginning to understand [sic]. Its a daunting task
to reconstruct the tree, especially for eukaryotes, but finishing the
job will have practical applications, they claim, such as helping formulate
conservation policies by providing insight into the history of extinctions.
- Elizabeth Pennisi begins with three articles. In
Modernizing
the Tree of Life, she discusses new techniques taxonomists are
using to create phylogenetic trees.
- In Drafting a
Tree, Pennisi portrays the tree-builders world as
confidence mixed with frustration: Systematists often say the
tree of life is in good shape. But ask them to illustrate this
notion with a single diagram, and most throw up their hands in
frustration. She unveils Science magazines
latest consensus tree, based on input from a dozen systematists,
which (though she admits specialists may take issue with parts
of the tree), gives a sketchy picture of a work in
progress. A larger version of the tree is provided as a
web feature.
About half the lines are shaded with a color indicating controversy.
- In Plants
Find Their Places in the Tree of Life, Elizabeth Pennisi
claims the botanists are way ahead of the zoologists in building their
phylogenetic trees: Researchers trying to piece together the tree of
animal life are hacking through dense foliage, barely able to see the
top branches, never mind the distant twigs (see main text). But
their colleagues studying plants have many of their phylogenetic trees
neatly pruned and manicured, she says.
- In Dating
the Tree of Life, Michael Benton and Francisco Ayala admit
that morphologists and molecular phylogenists have differed in placement
of groups by a factor of two, but claim the discrepant groups are
converging toward consensus.
- In The
Deep Roots of Eukaryotes, S.L. Baldauf examines the recent
revolutionary view that eukaryotes branched off much earlier than thought.
The article talks about radically revising this picture
again and fundamental rethinking of the position
of the root. Together these data suggest major gaps in our
understanding simply of what eukaryotes are or, when it comes to the
tree, even which end is up. Sections are entitled:
Eukaryotic Diversity: To (Nearly) Every Rule There Is an
Exception and What We Thought We Knew But Didnt.
Here is an excerpt from the section The Root of All Roots,
about the radical new idea of placing the root of the eukaryote tree
between opisthokonts (animals, fungi, and their allies, including people)
and nearly all the other major eukaryote taxa (emphasis added in all quotes):
Essentially, it turns the tree on its head, rooting it within the
former crown radiation. This is a radical
reinterpretation and would mean that opisthokonts branched off
very early from the main line of eukaryote descent. The
LCA [last common ancestor] of all extant eukaryotes would then
have been a far more complex organism than previously envisioned,
and any any similarities between, e.g., animals and plants
would simply be universal eukaryote traits. It also
suggests that opisthokonts may be older than previously thought,
consistent with the diversity of single-celled protists now thought
to be closely allied to animals and/or fungi.
Before this, they said The most important point in a phylogenetic
tree is its root. The root is the oldest point in the tree and
corresponds to the theoretical last common ancestor (LCA) of
everything in the tree.
- In Phylogenomics:
Intersection of Evolution and Genomics, Jonathan Eisen
and Claire Fraser of Rockville, Marylands Institute of
Genomics claim that evolution is helping us understand genomics:
Although it is generally accepted that genome sequences are
excellent tools for studying evolution, it is perhaps less well accepted
that evolutionary analysis is a powerful tool in studies of genome
sequences. In particular, evolutionary analysis helps to
place comparative genomic studies in perspective.
- In Preserving
the Tree of Life, Macy, Gittleman and Purvis discuss how the
emerging tree of life is informing policy on conservation.
- In View from a Twig
Jennifer Graves summarizes the grand sweep of Darwins picture:
More than 100 years ago, Charles Darwin systematically charted
relationships of organisms in space and time. What emerged was
the concept of the Tree of Life, a cornerstone in evolutionary theory
that, as well as classifying organisms, has the potential to make
sense of all biology.
She thinks this big picture, despite
the confusion in the details, needs to be inculcated in the schools
early on:
The concept of the unity of life--the most simple and general
rules of molecular structure, chemistry, and genetics that apply to
all organisms--should be introduced in grade school. These rules
can be linked firmly to an understanding [sic] of the way in which the
genome has gradually changed over the more than 3 billion years
that life has been unfolding [sic]. The fascinating descriptive
biology of diverse organisms that my generation grew up on can come
later, once there is a framework to hang it on. That way,
future generations will be able to appreciate the beauty of the
Tree of Life without its form being obscured by the tangle of
twigs and leaves.
There is so much verbiage in these
articles, and so many revealing quotes, that it would be impossible to
deal with it fairly in a Headlines service trying to encapsulate it.
The bottom line impression these authors present is, We know the
Big Picture is right, but the details are confusing and
contradictory. This is a recipe for self-deception.
When the deceived hold the power, and want to force their belief
on the children, it is a recipe for self-perpetuating deception.
Since we are not impressed by bluffing
and glittering generalities here,
we took a look at three sample papers from the most recent issue of
Molecular
Phylogenetics and Evolution (28:1, July 2003). In
each case, the authors were having difficulty resolving the roots
of their trees, found groups they could not resolve, and found
contradictions between morphology and genes.
This has been
the pattern, not the exception, in every molecular phylogeny story
we have reported over the last two years.
One would think,
if the Big Picture were so clear, one could see it in the details,
but the opposite is true. Never do they ever consider alternative
explanations for similarities found. And throughout, complex
features abruptly appear, fully formed, without ancestors, earlier
than thought possible. Recall that last
July, scientists portrayed tree-building as an impossible task,
and we deduced that it was only possible by assuming what needed to
be proved (Darwinian evolution), a clear case of
circular reasoning.
In short, molecular phylogeny appears to be
a deductive approach, based on the prior belief that Darwinian
evolution is true, therefore these confusing details must fit
together somehow. If so, it is not science; it is faith.
In the Biblical story, an angel guarded the way back to the Tree of
Life after Adam and Eve sinned. A new way beyond death to the
Tree
of Life
was made available by Christ through his death on the cross.
Now, the evolutionary establishment is guarding the way out of
the fallen world with the sword of political and educational power.
They are saying to the children, The tree of life is not
over there; that was just a myth. The tree of life is
behind you. You dont want to pass through the Brandenburg
Gate to freedom. You already live in the freest land of all, right
here. Stay with us. Our tree of life will give you
wisdom, wholeness, and hope. We are evolving. Someday,
we will be like gods, knowing good and evil.
Next headline on: Darwinism and Evolutionary Theory.
Next headline on: Genes and DNA.
Next headline on: The Bible.
Research Leads 06/13/2003
The current issue of Annual
Review of Earth and Planetary Sciences (Vol. 31, 2003) covers
interesting topics some readers may wish to pursue:
- Fossilization (Taphonomy): What conditions are required to
make a fossil? Derek
E.G. Briggs of Yale reviews minerals, microbial activity, types
of organisms and other factors required to preserve soft tissues.
He focuses on the remarkable extent of detail preserved in fossils of
certain soft-bodied animals. In the paper, The Role of Decay and
Mineralization in the Preservation of Soft-Bodied Fossils,
the stem rapid appears 11 times.
- Ancient Oxygen: In Phanerozoic Atmosphere Oxygen,
five
geologists examine whether atmospheric oxygen has fluctuated in the
past, possibly reaching levels as
high as 35% in Carboniferous times. The subject of
oxygen level variation has been essentially ignored or assumed
to be held to an almost constant level till now.
They believe higher oxygen levels might explain the giant
insects found fossilized in Permo-Carboniferous strata. But they
wonder whether it would also have led to catastrophic wildfires.
- Io Volcanoes:
Paul
Geissler of Lunar and Planetary Lab, University of Arizona, Tucson
surveys the main Voyager and Galileo findings into a state of the moon
address, examining evidence for high-temperature ultramafic lavas,
mass loss to the Io torus surrounding Jupiter, rapid resurfacing rates,
uniform global heat output and the characteristics of specific volcanic
features. Many basic questions and puzzles remain.
- Black Sea Flood:
William Ryan and colleagues
attempt to defend the Black Sea Flood hypothesis against criticisms.
- Meteorites: In the June 12 issue of Nature,
Conel Alexander puzzles over A Question of Timing, how to
get the contents of meteorites in sync. The chondules have
CAIs (calcium-aluminum inclusions) containing short-lived radionuclides
and show evidence of melting at temperatures up to 2000K.
Next headline on: Geology.
Next headline on: Solar System.
Honing the Concept of Biological Information 06/12/2003
Well established is how Jack W. Szostak (Howard Hughes
Medical Institute) describes the concept of biological information
in the
June 12 issue of Nature.
We are all familiar with the idea that it is the sequence of
the nucleotides or amino acids that make up DNA, RNA or protein
molecules that determine their structure and function, he
says, and this constitutes a type of molecularly coded information.
But how do we define information in proteins, when we find
numerous examples of different sequences that perform the same
biological function? And how do we measure the amount of
information in a biological molecule? A new concept of information
is needed to deal with the special case of biological complexity.
He examines the old approaches before suggesting an alternative:
- Information content is usually thought of in terms
of the amount of information required to specify a unique sequence
or structure. This viewpoint derives from classical information
theory, which does not consider the meaning of a message, defining the
information content of a string of symbols as simply that required to
specify, store or transmit the string. Thus, the unannotated human
genome sequence can be encoded in a 750-megabyte file, but this could be
greatly reduced in size by the application of standard data-compression techniques to account for internal repetitions.
- Algorithmic complexity approaches further define the amount
of information needed to specify sequences with internal order or
structure, but these also fail to account for redundancy due to
related sequences that are structurally and functionally equivalent.
- Physical complexity addresses this objection. It is
a rigorously defined measure of the information content of such
degenerate sequences, which is based on functional criteria and is
measured by comparing alignable sequences that encode functionally
equivalent structures. But different molecular
structures may be functionally equivalent, he says, pointing out
another shortcoming of the above approaches.
Szostak suggests this alternative:
- A new measure of information - functional information -
is required to account for all possible sequences that could potentially
carry out an equivalent biochemical function, independent of the
structure or mechanism used.
How would functional information be measured? He describes
it mathematically, but then gives an analogy:
Imagine a pile of DNA, RNA or protein molecules of all possible
sequences, sorted by activity with the most active at the top.
A horizontal plane through the pile indicates a given level of activity;
as this rises, fewer sequences remain above it. [An illustration
shows a cone with the vertex at top, intersected by a plane.]
The functional information required to specify that activity is
-log2 of the fraction of sequences above the plane.
In other words, the more activity the molecule can perform, the fewer
sequences would be likely able to perform it.
The probability decreases as you proceed up the cone.
Because there can be more than one way to achieve a function,
the probability of achieving that function from a random sequence will
be higher than if a specific sequence were required. Nevertheless,
measuring the amount of functional information is difficult,
because precisely how much more functional information
is required to specify a given increase in activity is unknown.
What is the probability a random sequence will perform a function?
One experimental example indicates this probability is
very low: the extreme rarity of functional sequences in
populations of random sequences (typically 10-10 to
10-15 for aptamers and ribozymes isolated from random
RNA pools. Typical lab searches can bias the results:
Unfortunately, the original
distribution of functional molecules can be obscured by biases in
replication and selection efficiency that accumulate over cycles
of enrichment. So he suggests,
A radically different approach would be to apply the
new single-molecule fluorescence methods to the direct analysis of
large sets of random sequences.
As the concept of functional information advances,
he thinks it will be interesting to see if the
relationship between functional information and activity will be
similar in many different systems, suggesting that common principles
are at work, or whether each case will be unique.
A central claim of intelligent design theory is that complex specified
information is a reliable indicator of an intelligent cause.
Its good that Szostak has brought the concept of biological information
to the attention of Nature readers, and has offered some insight into
what it is and how it is measured, even if he had little to say about
where it came from (his views on this are not apparent in the article).
Notice that he considers the idea of biological information
well established.
There is no question that biomolecules are carriers of information,
and that this information is not just meaningless (Shannon
information, named after pioneer information theorist Claude Shannon),
but tied to function. Szostaks cone diagram can be expanded to
a landscape with hills and valleys, with hills representing energy
barriers and high levels of functional information. The steepness
of the hill can represent the amount of specificity, and the height
the level of functional activity. The probability that a
random walk may reach a hilltop may be higher somewhat if there are
several routes to get there (a concept called degeneracy), but the
steeper the peak, the fewer the options and the more improbable a
random walk will arrive at the summit, or at a specified level where the plane
intersects the cone: i.e., where a desired level of function is achieved.
With this in mind, consider real biomolecules.
There are protein machines featured in previous headlines that perform
very precise, multiple functions with low tolerance for error
(see last weeks headline on tRNA synthetase),
or exhibit irred |