[Ariew, '96]

Abstarct:

"Cognitive scientists often employ the notion of innateness without
defining it. The issue is, how is innateness defined in biology? Some
critics contend that innateness is not a legitimate concept in
biology. In this paper I will argue that it is. However, neither the
concept of high heritability nor the concept of flat norm of reaction
(two popular accounts in the biology literature) define innateness.
An adequate account is found in developmental biology. I propose that
innateness is best defined in terms of C. H. Waddington's concept of
canalization."

Full text via link at:

http://cogprints.soton.ac.uk/documents/disk0/00/00/03/30/

Jorolat

[Chicurel, Jun '01]

"Intriguing hints from cell and molecular biologists suggest that
they might, but evolutionary biologists are not yet convinced.

In November 1970, Miroslav Radman, a molecular geneticist now at the
Université René Descartes in Paris, stunned his colleagues with a
heretical proposal: that bacteria harbor a genetic program to make
mutations. Through this program, Radman suspected, bacteria can crank
up their mutation rates in stressful situations, helping accelerate
their own evolution. Virtually no one believed him.
But 3 decades later, with the discovery of a new family of DNA-
synthesizing enzymes, or polymerases, Radman feels vindicated."

Full text at:

http://www.sciencemag.org/cgi/content/full/292/5523/1824

[Access to this article may require free registration, if you have
any problems then please email: jorolat@...]

Jorolat

NATURE: The Cuckoo (Monday)

"..Davies has found that reed warblers are able to distinguish
between their own eggs and cuckoos eggs so the cuckoo tailors its
eggs to be identical to the reed warblers' eggs. Yet why doesn't the
reed warbler notice the difference once the chicks hatch out? Davies
has discovered through painstaking experiments that the cuckoo has
found a mechanism to fool the warbler so the chick can survive."
[Will be available all week]

LEADING EDGE: Noah's Flood (Thursday)

"New research questions Bill Ryan's theory that Noah's Flood might
have been the bursting of a dam between the Mediterranean and the
Black Sea."
[Will be available all week]

THE MATERIAL WORLD: Complex Life (Thursday)

"Quentin Cooper finds out how at a very early stage in the
development of complex life, two life-forms were fused as simple
organisms inserted themselves into our distant ancestors"
[Will be available all week]

QUIRKS AND QUARKS: Genetically modifying Mosquitos (Now)

"Mosquitoes are responsible for more than two million deaths from
malaria every year in the developing world, and another 300-500
million cases. We've tried pesticides and drugs with limited success
to control the disease. But now scientists are fighting back with a
new approach. They're working on genetically modifying mosquitoes to
prevent them carrying the malaria parasite. But not all scientists
think it's a good idea, or even technically possible."
[Available now and until next Saturday]

The 'Calendar' can be accessed from the group homepage or from here:

http://www.localendar.com/public/jorolat

Jorolat

A selection of today's Press Releases and News Headlines:

1) Space rock's close approach

Astronomers have revealed that on 14 June, an asteroid the size of a
football pitch made one of the closest ever recorded approaches to
the Earth. It is only the sixth time an asteroid has been seen to
penetrate the Moon's orbit, and this is by far the biggest rock to do
so. What has worried some astronomers, though, is that the space
object was only detected on 17 June, several days after its flyby.
http://news.bbc.co.uk/low/english/sci/tech/newsid_2056000/2056403.stm

2) Alternative cell source investigated

Adult stem cells could be just as versatile as embryonic stem (ES)
cells as a source of new tissue for transplant, according to research
just published. Scientists have been working with special stem cells
taken from the bone marrow of rats. These cells were injected into
mouse embryos, where they transformed into most, if not all, of the
cell types in the body, showing they have the potential to replace or
repair tissues which have become diseased.
http://news.bbc.co.uk/low/english/sci/tech/newsid_2056000/2056650.stm

3) Workmen Find Remains of 800-Year-Old Cyprus Palace

NICOSIA (Reuters) - Workmen breaking ground for a new town hall
stumbled across what are believed to be the 800-year-old remains of a
medieval Lusignan palace in Cyprus whose exact whereabouts were a
mystery for centuries. The discovery, in the heart of the capital
Nicosia, is a boon for archaeologists who enjoy a rich amount of
literature from the checkered history of medieval Cyprus, but very
little in the way of tangible evidence on the ground.

4) Curious Skeletons

Deep within the cells we're made of, squishy skeletons feel the
effects of gravity ... and respond in unexpected ways.
http://science.nasa.gov/headlines/y2002/19jun_cytoskeletons.htm

5) Man casts first stone

Our instinctive feel for the ideal projectile could explain the
design of hand-grenades, the collecting habits of geologists, the
size of handballs and the weight of the imperial pound, says an
engineer. Understanding that instinct could illuminate the lives of
prehistoric hominids, believes Alan Cannell, who lives in Curitiba,
Brazil. He thinks that selecting and stockpiling rocks as weapons may
have preceded sculpting them into tools.
http://www.nature.com/nsu/020617/020617-10.html

Jorolat

In 1640 Galileo Galilei wrote a letter to Fortunio Liceti in
which he said:

"If Aristotle were to see the new discoveries recently [made] in the
heavens, whose immobility he had asserted, because no alteration had
previously been seen in them, he would now without doubt state the
contrary." ['Galileo Galilei - Towards a Resolution of 350 Years of
Debate', Paul Cardinal Poupard].

   The above statement highlights the danger of placing
dependence on words frozen in time without taking into account how
different those words might be if their author had had access to the
discoveries that have since been made.

Lamarck, for example, published his "Zoological Philosophy" in 1809
and is today popularly associated with "the inheritance of acquired
characteristics" whereby organisms somehow <I>direct</I> their own
evolution. On the basis of Galileo's words, however, it could be
argued that had Lamarck been alive in the 1890s, over thirty years
after publication of Darwin's "On the Origin of Species", his views
would have progressed from the moment in time in which they had been
caught.

With access to the discoveries and discussions that occured
throughout the 19th Century it is conceivable that Lamarck might even
have reached broad agreement with J. Mark Baldwin over the latter's
proposal of an <I>indirect</I> factor in evolution, known today as
the "Baldwin Effect", and described in the 1896 paper "A New Factor
in Evolution" [American Naturalist].

    Pure speculation ,of course, but if sufficient to illustrate
a general principle (that "words frozen in time should be
differentiated from those cast in stone") then the inappropriateness
of interpreting new discoveries or proposals in 'Lamarckian terms'
is readily apparent.

Jorolat

[Boxmind, '01] "There is balance in a rainforest, structure in a reef
community, an elegant meshing of parts which recalls coadaptation
within an animal body. In neither case is the balanced unit favoured
as a unit by Darwinian selection. In both cases the balance comes
about through selection at a lower level. Selection doesn¹t favour a
harmonious whole. Instead, harmonious parts flourish in the presence
of each other and the illusion of a harmonious whole emerges.

The organism is a convincing vehicle because its parts harmonise to
achieve a common end. A cheetah has the teeth of a carnivore, the
claws of a carnivore, the eyes, ears, nose and brain of a carnivore,
leg muscles that are suitable for chasing meat and guts that are
primed to digest it. Its parts are choreographed in a dance of
carnivorous unity. Every sinew and cell of a big cat has meat-eater
inscribed through its very texture, and we can be sure that this
extends deep into the details of biochemistry. The corresponding
parts of, say, an antelope are equally unified with each other, but
to different ends. Guts designed to digest plant roughage would be
ill-served by claws and instincts designed to catch prey. And vice
versa. A hybrid between a cheetah and an antelope, even if it were
genetically possible, might be able to run very fast but otherwise it
would fall flat on its evolutionary face. Tricks of the trade cannot
be cut from one and pasted into the other. Their compatibility is
with other tricks of the same trade."

Click here to start:

http://www.boxmind.com/lectures/survivalofthefittest/frame1_56k.asp

Jorolat

[Gould & Lewontin, Royal Society of London, '78]

Abstract:

"An adaptationist programme has dominated evolutionary thought in
england and the United States during the past forty years. It is
based on faith in the power of natural selection as an optimizing
agent. It proceeds by breaking an organism into unitary "traits" and
proposing an adaptive story for each considered separately. Trade-
offs among competing selective demands exert the only brake upon
perfection; nonoptimality is thereby rendered as a result of
adaptation as well. We criticize this approach and attempt to
reassert a competing notion (long popular in continental Europe) that
organisms must be analyzed as integrated wholes, with baupläne so
constrained by phyletic heritage, pathways of development, and
general architecture that the constraints themselves become more
interesting and more important in delimiting pathways of change than
the selective force that may mediate change when it occurs. We fault
the adaptationist programme for its failure to distinguish current
utility from reasons for origin (male tyrannosaurs may have used
their diminutive front legs to titillate female partners, but this
will not explain why they got so small); for its unwillingness to
consider alternatives to adaptive stories; for its reliance upon
plausibility alone as a criterion for accepting speculative tales;
and for its failure to consider adequately such competing themes as
random fixation of alleles, production of nonadaptive structures by
developmental correlation with selected features (allometry,
pleiotropy, material compensation, mechanically forced correlation),
the separability of adaptation and selection, multiple adaptive
peaks, and current utility as an epiphenomenon of nonadaptive
structures. We support Darwin's own pluralistic approach to
identifying the agents of evolutionary change."

Full text at:

http://www.aaas.org/spp/dser/evolution/science/spandrel.htm

[Bookmarked]

Jorolat

[Barrier et al., PNAS, Aug '01]

Abstract:

"The disparity between rates of morphological and molecular evolution
remains a key paradox in evolutionary genetics. A proposed resolution
to this paradox has been the conjecture that morphological evolution
proceeds via diversification in regulatory loci, and that phenotypic
evolution may correlate better with regulatory gene divergence. This
conjecture can be tested by examining rates of regulatory gene
evolution in species that display rapid morphological diversification
within adaptive radiations. We have isolated homologues to the
Arabidopsis APETALA3 (ASAP3/TM6) and APETALA1 (ASAP1) floral
regulatory genes and the CHLOROPHYLL A/B BINDING PROTEIN9 (ASCAB9)
photosynthetic structural gene from species in the Hawaiian
silversword alliance, a premier example of plant adaptive radiation.
We have compared rates of regulatory and structural gene evolution in
the Hawaiian species to those in related species of North American
tarweeds. Molecular evolutionary analyses indicate significant
increases in nonsynonymous relative to synonymous nucleotide
substitution rates in the ASAP3/TM6 and ASAP1 regulatory genes in the
rapidly evolving Hawaiian species. By contrast, no general increase
is evident in neutral mutation rates for these loci in the Hawaiian
species. An increase in nonsynonymous relative to synonymous
nucleotide substitution rate is also evident in the ASCAB9 structural
gene in the Hawaiian species, but not to the extent displayed in the
regulatory loci. The significantly accelerated rates of regulatory
gene evolution in the Hawaiian species may reflect the influence of
allopolyploidy or of selection and adaptive divergence. The analyses
suggest that accelerated rates of regulatory gene evolution may
accompany rapid morphological diversification in adaptive radiations."

Full text:

http://www.pnas.org/cgi/content/full/98/18/10208

Jorolat

[Radman, Matic, Taddei]

Introduction:

"Evolution, the fundamental strategy of life, is an interplay of
genetic variation and phenotypic selection. Evolvability, or
evolutionary adaptability, is defined here as the capacity to
generate heritable, selectable phenotypic variation. 1 Whereas
selection is an easy concept that has been put into practice in plant
and animal breeding, the generation of genetic variability has been
considered, until recently, as a mere by-product of nature's
imperfection: an unavoidable stochastic error. However, mutation and
recombination processes which create the somatic genetic diversity of
the immune system are known to be well controlled and targeted to the
immunoglobulin genes. 2 Here we argue that the rates, and even
patterns, of genomic mutations in bacteria are also genetically well
controlled processes. The genetic control of mutation and
recombination is evident at the level of bacterial populations
(genetic mutators and/or hyper-rec mutants), individual cells
(inducible mutator and recombinator activity), and even particular
sequences (hypermutable genes and recombinational hotspots). Such
molecular strategies for controlling genetic variability all hint at
the trade-off problems between the cost and benefit of mutations.
Thus, every mutation-generating mechanism seems to have some cost
accompanying the benefit of rare favorable mutations. Even with
hypermutation in chicken immunoglobulin genes, where mutations result
from patchy recombination (gene conversion) between the different
germ-line V sequences 3 (i.e., such mutations result from new
arrangements of pre-existing sequences which have undergone natural
selection), 4 there is no evidence suggesting that the immunoglobulin
gene mutations are directly designed according to the nature of the
newly appearing antigen."

Full text at:

http://www.annalsnyas.org/cgi/content/full/870/1/146

Jorolat

A selection of today's Press Releases and News Headlines:

1) African Predator 'Rediscovered' in Tanzania

A WCS scientist working in southeastern Tanzania has rediscovered a
carnivore that has remained undetected for the last 70 years.
Photographed by a camera trap on the eastern side of Udzungwa
Mountain National Park, the Lowe's servaline genet - a three-foot-
long relative of the mongoose family - was previously known only from
a single skin collected in 1932.
http://wcs.org/7411/?art=59535

2) Causing Injured Nerve Cells In Rats To Regenerate

Using brain cells from rats, scientists at The Johns Hopkins
University School of Medicine and the University of Hamburg have
manipulated a molecular "stop sign" so that the injured nerve cells
regenerate. While their findings are far from application in people,
the prospects for eventually being able to repair spinal cord injury
are brighter, they say.
http://unisci.com/stories/20022/0620025.htm

3) Whale songs are mating calls, researchers say

Scientists lowered microphones into the Pacific Ocean and came up
with evidence suggesting that the booming songs sung by finback
whales are mating calls, rather than sonar-like navigation signals.
The findings raise concerns that shipping noises and other manmade
sounds at sea could interfere with the whales' breeding.
http://www.nandotimes.com/healthscience/story/440098p-3522003c.html

4) New Chemical Scenario For How Life Emerged On Earth

In order for life to emerge, both peptides and nucleic acids must
have appeared under "prebiotic" conditions. Despite numerous efforts,
the formation of these macromolecules without the help of modern
synthetic reagents has not been achieved in a laboratory. Now, for
the first time, researchers have proposed a mechanism by which the
formation of peptides could have occurred under prebiotic conditions.
http://unisci.com/stories/20022/0620021.htm

5) Earth pains?

To great fanfare, astronomers announced today the discovery of a
star, much like our Sun as an infant, that may be undergoing the same
processes that gave rise to the planets of our Solar System,
including Earth. Following a recent international campaign of near-
constant observation, the star's discoverers now believe they have
enough data to "guess" at what might be going on around it. Other
astronomers aren't convinced.
http://www.nature.com/nsu/020617/020617-8.html

Jorolat

Dr. James Watson, President of Cold Spring Harbor Laboratory. Dr.
Watson recounts events that led up to the discovery of the double
helix structure of DNA in 1953.

The video is 56 minutes long:

http://www.cshl.org/video/ddhall.ram

[Bookmarked in the "Recorded Programmes (Video)" folder]

Jorolat

[Wright, Journal of Bacteriology, Jun'00]

Introduction:

As this minireview is concerned with the importance of the
environment in directing evolution, it is appropriate to remember
that Lamarck was the first to clearly articulate a consistent theory
of gradual evolution from the simplest of species to the most
complex, culminating in the origin of mankind (71). He published his
remarkable and courageous theory in 1809, the year of Darwin's birth.
Unfortunately, Lamarck's major contributions have been overshadowed
by his views on the inheritance of acquired characters. In fact,
Darwin shared some of these same views, and even Weismann (106), the
father of neo-Darwinism, decided late in his career that directed
variation must be invoked to understand some phenomena, as random
variation and selection alone are not a sufficient explanation (71).

This minireview will describe mechanisms of mutation that are not
random and can accelerate the process of evolution in specific
directions. The existence of such mechanisms has been predicted by
mathematicians (6) who argue that, if every mutation were really
random and had to be tested against the environment for selection or
rejection, there would not have been enough time to evolve the
extremely complex biochemical networks and regulatory mechanisms
found in organisms today.

Dobzhansky (21) expressed similar views by stating "The most serious
objection to the modern theory of evolution is that since mutations
occur by `chance' and are undirected, it is difficult to see how
mutation and selection can add up to the formation of such
beautifully balanced organs as, for example, the human eye."

Full text at:
http://jb.asm.org/cgi/content/full/182/11/2993

[Bookmarked in the "Adaptive Mutations" Folder]

Jorolat

[Lewis & Palevitz, Jun '01]

"The Human Genome Project's discovery that the human body runs on an
instruction manual of a mere 35,000 or so genes--compared to the
worm's 19,000, the fruit fly's 13,000, and the tiny mustard relative
Arabidopsis thaliana's 25,000--placed humanity on an even playing
field with these other, supposedly simpler, organisms. It was a
humbling experience, but humility quickly gave way to awe with the
realization that the human genome might encode 100,000 to 200,000
proteins. Scientists base this number on the analysis of DNA
sequences--called expressed sequence tags, or ESTs--that are reverse-
transcribed from mRNAs. The question is, where is the information for
all those extra proteins?"

Full text at:

http://www.the-scientist.com/yr2001/jun/research_010611.html

[Free registration may be required to access this article]

Jorolat

The following audio files are in the Recorded Programmes folder
of "Booknarks" at:

http://groups.yahoo.com/group/evomech/links

Animal Intelligence (Oct '99)
"Have you ever been amazed at the spontaneity of improv artists? Two
bottlenose dolphins in Hawaii respond to the command of "do something
creative together" by making up synchronized routines. These animals
show evidence of abstract thinking, deception, and problem solving -
qualities we once believed were exclusively human."

Autobiography of a Species (Feb '00)
"We are living, Matt Ridley says, through the greatest moment in the
history of human understanding. He's not joking, and he's not alone
in his view. In the next year, or two or three, we will all be able
to read a book (the human genome) revealing more about our origins
and evolution, our nature and our behavior than all the efforts of
science before this."

Darwin's God (Jan '00)
"At a moment when school boards in Kansas and elsewhere want to get
evolution out of the curriculum and would love to get God back in,
Kenneth Miller makes no bones about having it both ways: biology
gives a much fuller account of God's methods and means than the Book
of Genesis did, he says; yet the God behind his Science, Ken Miller
says, is every bit as creative in the present as He was in the past."

Evolution's Workshop: The Galapagos (Apr '01)
"A hundred and sixty years, ago Herman Melville called the
Galapagos "evilly enchanted. The chief sound of life here is a hiss"
And Charles Darwin's first impression was equally bleak: "The Country
was what we might image the cultivated parts of the infernal regions
to be. " Darwin changed his tune when he closely examined the
wildlife he found there, and changed the course of intellectual
history as well. "

Mother Nature (Jun '00)
"The social anthropologist Sarah Blaffer Hrdy turns the maternal
image of the adoring, protective mother on its head. Mothers are not
the passive, coy, self-sacrificing creatures we like to think of, she
says, but rather calculating, aggressive and ruthless deal-makers."

Science, Reason and Genetics (Aug '00)
"The evolutionary biologist Richard Dawkins says your genes care
about themselves, not about you. You're just a vehicle to make more
genes."

Stephen Jay Gould (Dec '00)
"Stephen Jay Gould is the most popular modern guardian not just of
Charles Darwin's evolutionary science, but of the quasi-religious
enthusiasm that closes the "Origin of Speech," where Darwin
wrote "there is grandeur in this view of life." "

The Debate of Evolutionary Biology in Anthropology (Nov '00)
"At the end of the day, the socio-biologists have been trying to
teach us, we humans are biological organisms. To which to a lively
opposition keeps retorting: no, at the beginning of the day, we are
an evolving animal species, but by the end of the day, we're
something else again. We're human beings."

The Directionality of Evolution (Feb '00)
"It's a journalist this time, Robert Wright, who is presuming to
dress down and stir up some eminent Darwinians, with the argument
that evolution isn't quite random or blind, but has a direction,
maybe even a destination."

http://groups.yahoo.com/group/evomech/links

Jorolat

[Amaral, de Oliveira]

"Throughout its evolution, the human brain has acquired three
components that progressively appeared and became superposed, just
like in an archeological site : the oldest, located underneath and to
the back; the next one, resting on an intermediate position and the
most recent, situated on top and to the front."

Full text at: http://www.epub.org.br/cm/n05/mente/limbic_i.htm

[NB: The above is based on Paul Maclean's "Triune Brain" theory.]

Jorolat

A selection to today's Press Releases and News Headlines:

1) Sealed coffin found near pyramids

CAIRO, Egypt, June 17 —  Archaeologists have found the world's oldest
intact sarcophagus near the pyramids of Giza, and it could contain a
mummy 4,500 years old, Egypt's top antiquities official said Monday.
http://www.msnbc.com/news/768307.asp

2) China Scientists to Probe 'ET' Launch Tower

BEIJING (Reuters) - A team of Chinese scientists is to head out to
the far west of the country to investigate a mystery pyramid that
local legend says is a launch tower left by aliens from space, Xinhua
news agency said Wednesday.
http://story.news.yahoo.com/news?
tmpl=story&cid=585&ncid=753&e=1&u=/nm/20020619/sc_nm/china_aliens_dc_1
(If 'word-wrap' breaks the link cut & paste both halves into a
browser window)

3) Lower Jawbone Of Mammoth Embryo Found In Siberia

For the first time, a well-preserved lower jawbone of a mammoth
embryo has been found in Siberia. The discovery was made by
paleontologist E.N. Mashchenko and colleagues from the
Paleontological Institute of the Russian Academy of Sciences and the
Paleontological Museum of the Tomsk State University.
http://unisci.com/stories/20022/0619021.htm

4) Hints of solar system like ours spotted.

Astronomers have come a step closer to finding a solar system in deep
space that is similar to our own. US researchers have identified 15
new 'extrasolar' planets, some of which have similar characteristics
to those orbiting our Sun. [Contains movie clip]
http://www.nature.com/nsu/020603/020603-22.html#

5) Ruins uncovered in Israel believed that of Roman stadium

JERUSALEM (June 18, 2002 8:16 a.m. EDT) - On the shores of the Sea of
Galilee, Israeli archaeologists have uncovered what they believe are
the remains of a Roman stadium from the time of Jesus, where
thousands watched horse races, track events and boat races on long,
man-made pools.
http://www.nandotimes.com/healthscience/story/438030p-3507064c.html

6) New study sheds light on frog malformations

The appearance of strange deformities in amphibian populations across
the globe has been blamed on various culprits — from chemicals to
parasites. But a new study in Wisconsin and Minnesota wetlands shows
that ultraviolet radiation could be responsible for the freakish
frogs.
http://www.eurekalert.org/pub_releases/2002-06/acs-nss061802.php

7) Nerves Tell Arteries to Make Like a Tree

By the time an embryo's heart begins to beat, a vast network of
arteries has already branched out to supply tissues with oxygen and
nutrients. How arteries shape themselves into such fine patterns has
been an open question. Now, a study shows that arteries follow the
lead of another of the body's branching specialists--the nerves.
http://www.academicpress.com/inscight/06172002/grapha.htm

Jorolat

[18 Jun '02]

1) Press Release (UniSci)
2) Published article (Journal of Biology)

1) Genes Next To One Another May Be Expressed Together

"Our current understanding of gene expression, the fundamental
process by which proteins are made from the instructions encoded in
DNA, is that the process is tightly controlled so that the correct
amount of each protein is produced in the right place at the right
time.

But new research by Paul Spellman and Gerald Rubin of Howard Hughes
Medical Institute and University of California Berkeley indicates
that some groups of around 15 genes that just happen to be located
next to each other on chromosomes are instead routinely expressed
together."

Full text at: http://unisci.com/stories/20022/0618022.htm

2) Evidence for large domains of similarly expressed genes in the
Drosophila genome (Spellman, Rubin)

ABSTRACT

Background

Transcriptional regulation in eukaryotes generally operates at the
level of individual genes. Regulation of sets of adjacent genes by
mechanisms operating at the level of chromosomal domains has been
demonstrated in a number of cases, but the fraction of genes in the
genome subject to regulation at this level is unknown.

Results

Drosophila gene-expression profiles that were determined from over 80
experimental conditions using high-density oligonucleotide
microarrays were searched for groups of adjacent genes that show
similar expression profiles. We found about 200 groups of adjacent
and similarly expressed genes, each having between 10 and 30 members;
together these groups account for over 20% of assayed genes. Each
group covers between 20 and 200 kilobase pairs of genomic sequence,
with a mean group size of about 100 kilobase pairs. Groups do not
appear to show any correlation with polytene banding patterns or
other known chromosomal structures, nor were genes within groups
functionally related to one another.

Conclusions

Groups of adjacent and co-regulated genes that are not otherwise
functionally related in any obvious way can be identified by
expression profiling in Drosophila. The mechanism underlying this
phenomenon is not yet known.

Full text at: http://jbiol.com/content/1/1/5

Jorolat

[J. Rennie, Editor in Chief Sci-Am, Jun 17 '02]:

"Opponents of evolution want to make a place for creationism by
tearing down real science, but their arguments don't hold up:

When Charles Darwin introduced the theory of evolution through
natural selection 143 years ago, the scientists of the day argued
over it fiercely, but the massing evidence from paleontology,
genetics, zoology, molecular biology and other fields gradually
established evolution's truth beyond reasonable doubt. Today that
battle has been won everywhere--except in the public imagination.
Embarrassingly, in the 21st century, in the most scientifically
advanced nation the world has ever known, creationists can still
persuade politicians, judges and ordinary citizens that evolution is
a flawed, poorly supported fantasy. They lobby for creationist ideas
such as "intelligent design" to be taught as alternatives to
evolution in science classrooms. As this article goes to press, the
Ohio Board of Education is debating whether to mandate such a change.
Some antievolutionists, such as Philip E. Johnson, a law professor at
the University of California at Berkeley and author of Darwin on
Trial, admit that they intend for intelligent-design theory to serve
as a "wedge" for reopening science classrooms to discussions of God.

Besieged teachers and others may increasingly find themselves on the
spot to defend evolution and refute creationism. The arguments that
creationists use are typically specious and based on
misunderstandings of (or outright lies about) evolution, but the
number and diversity of the objections can put even well-informed
people at a disadvantage.

To help with answering them, the following list rebuts some of the
most common "scientific" arguments raised against evolution. It also
directs readers to further sources for information and explains why
creation science has no place in the classroom."

Full text at:

http://www.sciam.com/article.cfm?articleID=000D4FEC-7D5B-1D07-
8E49809EC588EEDF&pageNumber=1&catID=2

(If the above link has been broken in two by 'word-wrap' then cut &
paste each part into a browser window)

Jorolat

[Historical Review, Genetics, Dec '01]

Evolution by Jumps: Francis Galton and William Bateson and the
Mechanism of Evolutionary Change:

"FRANCIS Galton (1822–1911) genuinely disagreed with his cousin
Charles Darwin concerning the mechanism of evolutionary change (see
CROW 1993 ; MAYNARD-SMITH 1993 ; GILLHAM 2001 ). He felt that the
small, incremental steps by which natural selection supposedly
proceeded would be thwarted by a phenomenon he had discovered, which
he called regression (or reversion) to the mean. Hence, Galton
believed that evolution must proceed via discontinuous steps. We
would call them saltations, but he named them "transiliencies." This
was to some extent a throwback to views held earlier by Huxley and
Lyell, from paleontological observations (see, for example, LYONS
1993 , LYONS 1995 ). As fate would have it, Galton found himself
strongly allied with the young geneticist William Bateson, who would
become Mendel's great champion in Great Britain. This article
describes how Galton and Bateson came independently to the conclusion
that evolution must proceed in discontinuous steps."

Full text at: http://www.genetics.org/cgi/content/full/159/4/1383

jorolat

[Badyaev and Hill, June '02]

"Adaptation to the environment is the cornerstone of Darwinian
natural selection. Among the most conspicuous consequences of this
process are changes in the size and shape of animals in response to
climate. Nearly 200 years ago, long before the publication of
Darwin's Origin of Species, zoologists recognized that in wide-
ranging species, individuals that inhabit the colder parts of the
range tend to be larger and to have shorter limbs and appendages
(black bears and white-tailed deer, for example, show this trend in
North America). When one is considering species that have had stable
ranges over thousands of years, such changes in body size and shape
can be assumed to have evolved very slowly, by incremental stages,
over many thousands of generations. Biologists only rarely have a
chance to witness the pace of such changes when a population of
vertebrates spreads into a very new environment. Over the past few
years, however, we have documented rapid and adaptive changes in the
size and shape of one vertebrate species—the house finch—and we have
discovered a fascinating and unanticipated mechanism that allows this
bird to adjust quickly to local environments."

Full text at:
http://www.amnh.org/naturalhistory/0602/0602_feature.html

Jorolat

J. Mark Baldwin's Original Paper (published in 1896) in which be
proposed the concept known today as "The Baldwin Effect":

Abstract

    "In several recent publications I have developed, from different
points of view, some considerations which tend to bring out a certain
influence at work in organic evolution which I venture to call "a new
factor". I give below the list of references [1] to these
publications and shall refer to them by number as this paper
proceeds. The object of the present paper is to gather into one
sketch an outline of the view of the process of development which
these different publications have hinged upon.

The problems involved in a theory of organic development may be
gathered up under three great heads: Ontogeny, Phylogeny, Heredity.
The general consideration, the " factor " which I propose to bring
out, is operative in the first instance, in the field of Ontogeny; I
shall consequently speak first of the problem of Ontogeny, then of
that of Phylogeny, in so far as the topic dealt with makes it
necessary, then of that of Heredity, under the same limitation, and
finally, give some definitions and conclusions."

Full text at: http://members.aol.com/jorolat/baldwin2.html

This article will also appear in the "Bookmarks" section of the main
site.

Jorolat

[Press Release 17th June '02:]

"Life did not begin with one primordial cell. Instead, there were
initially at least three simple types of loosely constructed cellular
organizations. They swam in a pool of genes, evolving in a communal
way that aided one another in bootstrapping into the three distinct
types of cells by sharing their evolutionary inventions.

The driving force in evolving cellular life on Earth, says Carl
Woese, a microbiologist at the University of Illinois at Urbana-
Champaign, has been horizontal gene transfer, in which the
acquisition of alien cellular components, including genes and
proteins, work to promote the evolution of recipient cellular
entities."

Full article at: http://www.news.uiuc.edu/scitips/02/0617evoltion.html

Jorolat

The following audio files are available in the "Recorded Programmes"
folder of the "Bookmarks" section:

Anthropology Update / 'Future Evolution' (Mar '02)
"What will the Earth look like thousands of years from now? What will
the climate be like? The plants? The animals? And will humans be
around to see any of it?"

Birds from Dinosaurs? (Jun '98)
"It's a long-standing paleontological debate: are birds the
descendants of dinosaurs, or did they evolve separately? Ever since
the ancient bird Archaeopteryx was discovered back in 1861, the
question has bothered the scientific community. The discovery of
several new fossils, announced this week, may help settle the
dispute - although some doubts are likely to linger."

Die-hard Bacteria (Oct '00)
"Last week, scientists announced that they had isolated 250 million-
year-old bacteria that had been trapped inside a flaw in a salt
crystal. If true, the sample of Bacillus would contain by far the
oldest living creatures ever found."

Dinosaur Update (Nov '98)
"Last week, a group of paleontologists announced the discovery of a
new species of dinosaur found in the Tenere Desert of central Niger,
Suchomimus tenerensis. Suchomimus is estimated to have played the
role of the dominant African predator about 100 million years ago."


How and Why New Species Form (Oct '96)
"What does it take to make a new species? From finches in the
Galapagos Islands or fish in African lakes to fruit flies closer to
home, we'll talk to evolutionary biologists about how new species
develop, and how advances in molecular biology are helping scientists
trace evolutionary pathways."

Human Natures: Paul Ehrlich (Oct '00)
"How much do our genes determine our behavior? Is there such a thing
as "genetic destiny?" And is evolution merely a biological process,
or is it a cultural process as well? In this hour, we'll talk with
biologist Paul Ehrlich about human natures, how they change, and
about the history and future of human evolution."

Human Origins (May '97)
"Recent discoveries by fossil scientists may provide the earliest
documented evidence of toolmaking, and push the origin of homo
sapiens back more than 400,000 years. We'll talk about these latest
findings and the evidence for human evolution, with Donald Johanson,
the paleoanthropologist who discovered the famous Lucy skeleton in
1974."

Paleontology and Anthropology News (Aug '01)
"Recent reports of fossil finds in Ethiopia may change the way
scientists draw the human family tree. The fossils, over 5 million
years old, give new information about the way early hominids moved
and the habitats that they lived in."

The "Bookmarks" section is here:

http://groups.yahoo.com/group/evomech/links

Jorolat

Introduction:

"Through an experiment giving sight to a normally blind cave-dwelling
fish, researchers hope to get a better understanding of certain forms
of human sight loss by revealing the mechanisms of eye growth.

The current issue of Science* reports on the experiment involving a
ghostly pale, sightless cavefish which normally develops shrunken,
degenerate orbs in place of eyes. The researchers found that young
cavefish developed a normal eye after receiving the lens of a
sighted, surface-dwelling fish of the same species.

"We now have preliminary confirmation that the lens is the seat of a
signaling mechanism that somehow causes the eye to grow," explains
biologist William R. Jeffery of the University of Maryland at College
Park whose focus is on identifying basic developmental mechanisms in
fish embryos that can be studied in the laboratory."

Full text at: http://www.abc.net.au/science/news/stories/s156871.htm

*Science article info:
Central Role for the Lens in Cave Fish Eye Degeneration
   Yoshiyuki Yamamoto and William R. Jeffery
   Science 2000 July 28; 289: 631-633

This article will also appear in the "Bookmark" section at the main
site.

Jorolat

Introduction:

"Chapel Hill -- In 1862, British naturalist Henry Bates proposed --
but could not prove -- that over time, some animal and plant species
that taste good to predators come to resemble other animals and
plants that pose a danger to the hungry hunters.
By evolving in that way, the good-tasting species develop an
effective defense mechanism and are more likely to survive and
reproduce.

Although widely accepted and taught as early as elementary school,
Batesian mimicry has remained unconfirmed. Now, however, a University
of North Carolina at Chapel Hill scientist believes experiments he
and others conducted with fake snakes strongly show the Englishman
was right. Their report appears in the March 15 (2001) issue of the
journal Nature. Authors are Dr. David W. Pfennig, associate professor
of biology at UNC, undergraduate William R. Horcombe and Dr. Karen S.
Pfennig, postdoctoral fellow at the University of Texas at Austin...."

Full article at:
http://www.sciencedaily.com/releases/2001/03/010315075129.htm

Jorolat

TABLE OF CONTENTS

Foreword

Preliminary Discourse

PART ONE
Considerations of the Natural History of Animals, Their
Characteristics, Their Interrelationships, Their Organic Structure,
Their Distribution, Their Classification and Their Species

Chapter One
On the Role of Art in the Productions of Nature

Chapter Two
The Importance of Considering Affinities

Chapter Three
Concerning Speciation in Living Things and The Idea We Should Attach
to This Word

Chapter Four
General Observations on Animals

Chapter Five
On the Present State of the Distribution and Classification of
Animals

Chapter Six
The Degradation and Simplification in Organic Structure from One
Extreme to the Other of the Chain of Animal Life, from the Most
Complex to the Simplest

Chapter Seven
Concerning the Influence of Circumstances on the Actions and Habits
of Animals, and the Influence of the Actions and Habits of these
Living Bodies As Causes Which Modify Their Organic Structure and
Their Parts

Chapter Eight
Concerning the Natural Order of Animals and the Arrangement Which
Must Have Led to Their General Distribution to Make it Conform to the
Very Order of Nature

Click here: http://members.aol.com/evomech/index.html

This will also appear in the "Bookmarks" section on the main site.

Jorolat

Introduction:

"In 1988 a minor collision occurred between natural reality and
evolutionary theory when an article entitled "The Origin of Mutants"
[1] appeared in Nature Magazine. The authors (Cairns et al.) reported
experiments in which advantageous mutations in bacteria appeared to
have happened with a greater frequency than conventional theory could
account for. Subsequent experiments producing similar results have
been performed by other scientists one of whom, Barry Hall, has
said "Mutations that occur more when they`re useful than when they`re
not: that I can document any day, every day, in the laboratory" [2]."

     The above is the opening paragraph from an article [3] comparing
the reception given to the described phenomena (originally
called "Directed Mutation" but now more often "Stationary Phase
Mutations") and that accorded Galileo's Heliocentric Theory. In
another article that appeared in New Scientist [4] David Thaler, then
of Rockefeller University, is quoted as saying "In evolutionary
theory there has been an overemphasis on the power of selection as
opposed to the generation of diversity. Maybe this [the phenomena of
stationary phase mutations] will take it to another level". In
addition to providing a link between stationary phase Mutations and
the Baldwin Effect the following also attempts to bridge their gap
with Darwin`s principle of Natural Selection.

    Like all organisms bacteria are naturally integrated and though
there is an apparent diversity of results in experiments that have
produced stationary phase mutations there are also indications they
may be due to a single mechanism triggered by varying degrees of
disturbance to homeostasis [5]. It is proposed that such a mechanism
existed in the single-cell common ancestor and that when life became
multi-cellular so did the mechanism.

    To convey the simplicity of the concept the proposed mechanism is
initially presented (as a "fait accompli") for organisms that have
evolved beyond the notochord stage and a description given of how it
would account for the Baldwin Effect. It is then used to explain the
phenomena of stationary phase mutations in bacteria and in doing so
shows, as one would expect of a mechanism based on homeostasis
("staying the same"), how similar the basic mode of operation is for
both cases. Next, on the stated assumption that the proposed
mechanism also existed in the single-cell common ancestor,
evolutionary history is looked at for supporting evidence and this
ranges from the comparative sequencing of protein amino acids to
evolution of the brain. The premise underlying the proposal is that
the nature of life is simply to Be and continuity of Being is
maintained in a state of inner equilibrium.

     The basis on an extension to homeostasis means that the proposed
mechanism is testable and the appended (generic) Method of Testing is
currently illustrated by two experiments that inadvertently met it's
criteria. Finally the proposed mechanism is used to account
for "problem areas" of current theory such as the Common Origin of
the Pentadactyl Pattern in both the Fore and Hind Limbs of
Terrestrial Vertebrates."

Full article: http://members.aol.com/jorolat/TEM.html

This article will also appear in the "Bookmark" scetion of the main
site.

Jorolat

Abstract:

"Upon starvation some Escherichia coli cells undergo a transient,
genome-wide hypermutation (called adaptive mutation) that is
recombination-dependent and appears to be a response to a stressful
environment. Adaptive mutation may reflect an inducible mechanism
that generates genetic variability in times of stress. Previously,
however, the regulatory components and signal transduction pathways
controlling adaptive mutation were unknown. Here we show that
adaptive mutation is regulated by the SOS response, a complex, graded
response to DNA damage that includes induction of gene products
blocking cell division and promoting mutation, recombination, and DNA
repair. We find that SOS-induced levels of proteins other than RecA
are needed for adaptive mutation. We report a requirement of RecF for
efficient adaptive mutation and provide evidence that the role of
RecF in mutation is to allow SOS induction. We also report the
discovery of an SOS-controlled inhibitor of adaptive mutation, PsiB.
These results indicate that adaptive mutation is a tightly regulated
response, controlled both positively and negatively by the SOS
system."

Full article at:

http://www.pnas.org/cgi/content/full/97/12/6646

[Authors: Susan Rosenberg et al.]

A broader description of the SOS response than that given in the
article can be found here:

http://www.dubna.ru/~aksenov/sos/1.html

This article also appears in the "Bookmark" section of the main site.

Jorolat

Copy of a 1997 Scientific American article giving an overview of
events since the 1988 publication of John Cairns' (et al.) "Origin of
Mutants" article:

http://www.dhushara.com/book/evol/evev.htm

"Nine years ago John Cairns and his colleagues at the Harvard School
of Public Health reported in the influential journal Nature
sensational experiments "suggesting that cells may have mechanisms
for choosing which mutations will occur"-specifically, in ways that
give those cells an advantage in stressful conditions. This radical
proposal collided head-on with the sacrosanct principle of genetics
that mutations occur at a rate that is completely unrelated to
whatever consequences they might have.

Cairns's suggestion thus conjured the ghost of Jean-Baptiste Lamarck,
who argued in tile 19th century that species evolve through the
inheritance of "acquired" characteristics-ones that individuals
develop in response to environmental challenges. Cairns postulated
that bacterial cells, in effect, mysteriously know in advance which
mutations are likely to benefit them. Then, when'-investigators
stress the cells by starving them, the bacteria tip fate's scales so
that rare beneficial mutations happen more often than chance would
allow. This incendiary idea, known as directed mutation, ignited a
firestorm of debate."

This article also appears in the "Bookmark" section at the main site.

Jorolat

Schedules and appropriate links for the following programmes have
been entered in the Calendar
(http://www.localendar.com/public/jorolat):

Nature (UK Radio)
Discovery Science (UK Radio)
Leading Edge (UK Radio)
Science Friday (US NPR)
Quirks and Quarks (CBC Radio)

Please email me (jorolat@...) with any suggestions!

Jorolat