Sunday, September 01, 2013
Non-Darwinian evolution
Time to break out the popcorn! The internecine warfare among evolutionists rages on. Check out this wiki page for the various dissenting theories to the modern evolutionary synthesis or neo-Darwinism.
I'm guessing the only points of agreement are that creationists and ID advocates are essentially one and the same; that creationists and ID advocates are ignorant and immoral; and that all disagreements among evolutionists, no matter how significant, nevertheless lie squarely within the sound bounds of modern evolutionary theory, i.e., non-Darwinian doesn't mean anti-Darwinian! ;-)
A once-in-a-universe long shot
On the one hand, many scientists are proponents of the RNA world hypothesis for the origin of life on Earth. On the other hand, many of the same scientists believe life exists elsewhere in the universe. Indeed, many believe the universe is teeming with life.
However, if the RNA world hypothesis is true, then it's arguable the appearance of life on Earth was highly unlikely. In fact, the late chemist Robert Shapiro apparently said: "The appearance of such a molecule, given the way chemistry functions, is incredibly improbable. It would be a once-in-a-universe long shot. To adopt this [view], you have to believe we were incredibly lucky."
If life on a pale blue dot was so unlikely as to have been "a once-in-a-universe long shot," then how likely would life be elsewhere in the universe?
Saturday, August 31, 2013
Is a new evolutionary synthesis in sight?
"Darwinian evolution in the light of genomics" by Eugene Koonin.
"The Origin at 150: is a new evolutionary synthesis in sight?" by Eugene Koonin.
Evolution via the gradual accumulation of mutations
According to James Shapiro (2011, Evolution: A View from the 21st Century, p. 95):
The 2001 Nature report of the draft human genome contained two important figures illustrating what genome sequencing had taught us about protein evolution [382]. Using transcription factors and chromatin binding proteins as examples, the figures showed that these classes of proteins did not evolve one amino acid at a time [emphasis mine]. Instead, the two classes of protein "shuffled" and "accreted" copies of functional protein segments called domains as eukaryotes progressed from yeast through nematode worms and Drosophila fruit flies to mice and human beings. In other words, proteins diversify through a process of acquiring, amplifying, and rearranging coding sequences for subprotein structures that may be dozens or hundreds of amino acids in length.References
382. Lander, E.S. et al. Initial sequencing and analysis of the human genome. Nature 409, 860-921 (2001).
From the notebooks of the Lazarus experiment
According to Peter Ward ("What Will Become of Homo Sapiens?"):
Assuming that it does become practical to change our genes, how will that affect the future evolution of humanity? Probably a great deal. Suppose parents alter their unborn children to enhance their intelligence, looks and longevity. If the kids are as smart as they are long-lived - an IQ of 150 and a lifespan of 150 years - they could have more children and accumulate more wealth than the rest of us. Socially they will probably be drawn to others of their kind. With some kind of self-imposed geographic or social segregation, their genes might drift and eventually differentiate as a new species. One day, then, we will have it in our power to bring a new human species into this world. Whether we choose to follow such a path is for our descendants to decide.
Here's an excerpt from the ending of the original screenplay for the movie Gattaca:
A STARSCAPE
As we pan across the constellations, a title is superimposed
upon the starscape:
In a few short years, scientists will
have completed the Human Genome Project,
the mapping of all the genes that make
up a human being.
After 4 billion years of evolution by the
slow and clumsy method of natural selection,
we have now evolved to the point where we
can direct our own evolution.
The first title is replaced in the heavens by a second title.
If only we had aquired this knowledge
sooner, the following people would never
have been born:
A succession of portraits and photographs of RENOWNED and
HISTORIC FIGURES fades in and out of the constellations - the
accompanying titles list their affliction rather than their
accomplishments.
HOMER
Blind from birth
NAPOLEON BONAPARTE
Epileptic
COLETTE
Arthritic
LOU GERHIG [sic]
Amyotrophic Lateral Sclerosis
(Lou Gerhig's [sic] Disease)
RITA HAYWORTH
Alzheimer's Disease
HELEN KELLER
Blind and deaf
STEPHEN HAWKING
Lou Gerhig's Disease
JACKIE JOYNER-KERSEE
Asthmatic
CHARLES DARWIN
Chronic invalid
The face of Charles Darwin fades off and another title appears
out of the stars.
Even Charles Darwin, the man who told of
the survival of the fittest, numbered
amongst our frailest.
The title fades off and is replaced by one final title in the
night sky.
Of course, the other birth that would
surely never have taken place is your own.
CUT TO BLACKShould we make evolutionary biology a basic science?
On the one hand:
"Evolution: medicine's most basic science" by Randolph M. Nesse and Richard Dawkins.
On the other hand:
"Neo-Darwinism, the Modern Synthesis and selfish genes: are they of use in physiology?" by Denis Noble.
Researchers find surprising difference between human and chimp genomes
Old news, but FWIW:
Despite sharing 99 per cent of our DNA with chimpanzees, a certain key genetic process tends to occur at totally different places on human and chimp chromosomes. A study by Oxford statisticians and US and Dutch geneticists, published in Science, compared recombination in humans and chimpanzees and found a surprising difference between the species....Why these hotspots occur, and what triggers the swapping of DNA at those particular points, is a mystery. One theory was that the DNA code either side of hotspots controlled the activity. However, comparing chimps and humans showed that despite being so genetically similar, the species have totally different recombination hotspots....
'If chimps and humans do not share these recombination hotspots, then it means something other than the surrounding DNA code must be controlling the process of recombination - because the surrounding DNA code in chimps and humans is pretty much identical. This means that recombination is even more mysterious than we already thought: what is controlling it, and why does it occur so often at these particular places?
'The findings also tell us something else important: that the recombination landscape must be evolving extremely quickly. In humans and chimpanzees, the genome as a whole is very similar but the recombination hotspots totally different - so hotspots must be evolving much, much faster than the rest of the genome. That adds extra mystery to what drives these hotspots: why do they evolve so quickly?'
I believe this is the paper in question.
Are mutations random?
According to James Shapiro (2011, Evolution: A View from the 21st Century, p. 82):
There is one last area where the traditional assumptions about genetic change have been shown to be unrealistically restrictive. That is the question of targeting changes to specific regions in the genome. Conventional wisdom and the vast majority of evolutionists assert that there is no way natural genetic engineering functions can "choose" where to operate within the genome. This was a topic of active debate in 1988 when some adaptive mutation experiments were initially overinterpreted in neo-Lamarckian terms [2, 669, 670].Despite interpretive errors in the Lamarck vs. Darwin debate, a priori denials of the capacity for functional targeting of biochemical changes to DNA should be jarring to molecular biologists. We have over 50 years of investigation into the molecular basis of how cells regulate transcription, and all biologists agree that the transcription apparatus can be directed to specific, functionally appropriate sites in the genome. The reason for the denial in the case of mutation probably has to do with a continuing influence of the late 19th Century philosophical notion that "germ plasm" inheritance has to be isolated from the soma [671]. But in the 21st Century, when we know about transcriptional regulation, signal transduction from the cell surface to the genome, and the operation of natural genetic engineering in the germline, it is time to abandon this mistaken doctrine.
It is difficult (if not impossible) to find a genome change operator that is truly random in its action within the DNA of the cell where it works. All careful studies of mutagenesis find statistically significant nonrandom patterns of change [emphasis mine], and genome sequence studies confirm distinct biases in location of different mobile genetic elements. These biases can sometimes be extreme, as in the targeting of S. cerevisiae LTR retrotransposon insertions into regions just a few base pairs upstream of RNA polymerase III transcription start sites [672–674]. In many cases, we have some understanding of the molecular mechanisms and/or functional significance of the observed preferences (see Table II.11).
References
2. Sniegowski, P.D. and Lenski, R.E. Mutation and adaptation: The directed mutation controversy in evolutionary perspective. Annu Rev Ecol Systematics 26, 553-578 (1995).
669. Cairns, J., Overbaugh, J. and Miller, S. The origin of mutants. Nature 335, 142-5 (1988).
670. Maenhaut-Michel, G. and Shapiro, J.A. The roles of starvation and selective substrates in the emergence of araB-lacZ fusion clones. Embo J 13, 5229-39.
671. Weismann, A. The Germ-Plasm: A Theory of Heredity, (Charles Scribner's Sons, New York, 1893) (1994).
672. Bushman, F.D. Targeting survival: integration site selection by retroviruses and LTR-retrotransposons. Cell 115, 135-8 (2003).
673. Devine, S.E. and Boeke, J.D. Integration of the yeast retrotransposon Ty1 is targeted to regions upstream of genes transcribed by RNA polymerase III. Genes Dev 10, 620-33 (1996).
674. Bolton, E.C. and Boeke, J.D. Transcriptional interactions between yeast tRNA genes, flanking genes and Ty elements: a genomic point of view. Genome Res 13, 254-63 (2003).
Friday, August 30, 2013
Chris Pinto the "Kevin Bacon" of King James Onlyists
Peter
Gomes' dog is associated with Peter Gomes -->
Peter Gomes is associated with Harvard Divinity -->
Harvard Divinity is associated with Alan Kurschner -->
Alan Kurschner is associated with James White -->
James White is associated with Chris Rosebrough -->
Chris Rosebrough is associated with Brannon Howse -->
Brannon Howse is associated with Chris Pinto -->
Chris Pinto is associated with Chris Pinto's dog -->
Chris Pinto's dog must be promoting homosexual Christianity!
Peter Gomes is associated with Harvard Divinity -->
Harvard Divinity is associated with Alan Kurschner -->
Alan Kurschner is associated with James White -->
James White is associated with Chris Rosebrough -->
Chris Rosebrough is associated with Brannon Howse -->
Brannon Howse is associated with Chris Pinto -->
Chris Pinto is associated with Chris Pinto's dog -->
Chris Pinto's dog must be promoting homosexual Christianity!
“Cultural Catholicism” and the End of Life: “You Earned It”
I’ve mentioned that Roman Catholicism is so onerous because it puts its hooks in you at various times in your life – from baptism as a child, to “first confession” and “first holy communion”, then Confirmation as an early teen, then marriage, baptism of your own children, etc. It’s a programmatic cycle.
There is another point at which Rome is prominent, and that is at death. As the “Baby Boom” generation continues to age and die, people will continue to be focused on this phase of life, either as people focused on the end of their own lives, or that of their aging parents.
Paul Moses, a journalism professor at Brooklyn College/CUNY”, has written a piece for the Wall Street Journal this morning entitled “A Liberal Catholic and Staying Put”, which puts this in view.
There is another point at which Rome is prominent, and that is at death. As the “Baby Boom” generation continues to age and die, people will continue to be focused on this phase of life, either as people focused on the end of their own lives, or that of their aging parents.
Paul Moses, a journalism professor at Brooklyn College/CUNY”, has written a piece for the Wall Street Journal this morning entitled “A Liberal Catholic and Staying Put”, which puts this in view.
Thursday, August 29, 2013
Law and miracle
Debates about the scientific status of miracles have been going on for a long time, and often involve competing paradigms of natural law. For instance:
In his classic Adventures of Ideas (140-59), A. N. Whitehead describes two contrasting views of nature's laws as they obtained in much of the seventeenth and eighteen centuries:
(1) Theological voluntarism is the metaphysical idea that an omnipotent God endowed matter and nature with principles of motion that are passive and therefore completely dependent on God's volition; that since the properties of matter (atoms) are extension, impenetrability, and inertia, the motion of matter originates in God, the prime mover; that an active principle sustains motion and activity in nature by counteracting resistance; that this active principle is the source of gravity; finally, that the causes or laws of nature are therefore superimposed from the outside and are completely dependent on an omnipotent deity, who can abrogate or suspend these natural laws at will (miracles) to modify their course.
(2) Immanence is the view that activity and motion are inherent principles in matter and nature, that all movement in nature is governed by autonomous laws that constitute the interdependence of all activity in nature; that these immanent laws are so embedded in the structure of nature that they cannot be disrupted, that any disruption of the laws of nature (miracles) is impossible because it contradicts the principles of reason, order, and perfection–the attributes of God. Essentially voluntaristic, Newtonianism gave way in the eighteeth century to the view of immanent activity in nature that was essentially mechanistic, which is to say Cartesian. For according to Rene Decartes, the laws of nature were decreed by God and are–like his volition–immutable and universally efficient. That is why miracles contradicted God's immutable will–unless (perhaps) they were embedded in God's grand scheme from the beginning.
Cotton Mather's Biblia Americana: America’s First Bible Commentary, A Synoptic Commentary on the Old and New Testaments. Vol. 1: Genesis. Edited with an Introduction and Annotations by Reiner Smolinski (Mohr Siebeck and Baker Academic, 2010), 85-86n22.
In six days the Lord made heaven and earth
8 “Remember the Sabbath day, to keep it holy. 9 Six days you shall labor, and do all your work, 10 but the seventh day is a Sabbath to the Lord your God. On it you shall not do any work, you, or your son, or your daughter, your male servant, or your female servant, or your livestock, or the sojourner who is within your gates. 11 For in six days the Lord made heaven and earth, the sea, and all that is in them, and rested on the seventh day. Therefore the Lord blessed the Sabbath day and made it holy (Exod 20:8-11).
This text often crops up in debates over the days of Gen 1. Appeal is made to this text to establish two related points. The days in Exodus 20:8-11 are 24-hour days. And the days are consecutive. By parity of argument, so are the days of Gen 1. An uninterrupted sequence of 7 24-hour days. This is called the calendar-day interpretation.
There's obviously some merit to this argument from analogy. After all, this isn't just a reader's inference. The text itself invites that comparison.
However, there's also a danger of a modern reader unconsciously recasting the issue in provincial and anachronistic terms:
i) Ancient Israelites didn't think in terms of 24-hour days. That represents clock time. They didn't have clocks.
ii) Likewise, subdividing a day into 24 equal units of time is artificial rather than natural.
iii) There's an equivocation about the "day." It's not as if Israelites labored 24 hours a day, 6 days a week, before knocking off work. The workday actually stands for daylight hours. As a matter of fact, you took breaks between one day and the next day. You labored during daylight hours, and rested at night.
You were largely dependent on sunlight to be able to see. That could be supplemented a bit by firelight–or moonlight (a full moon on a clear night).
Folks who traveled by foot had to allow for enough time to arrive at their destination before they ran out of light.
iv) Moreover, day and night aren't like flipping a light switch, where it becomes instantly light at sunrise and instantly dark at sunset. First light precedes sunrise. Especially on a clear day, the sky brightens well before sunup, and darkens sometime after sundown. So the boundaries between day and night are fuzzy.
v) In addition, unlike clock time, which cuts across the natural divisions of day and night, sunrise and sunset undergo seasonal change. They vary every day. The daylight hours lengthen in the summer and shorten in the winter.
vi) Not only is this sensitive to the temporal orientation (i.e. time of year), but spatial orientation (latitude). If you live in Alaska, there are times of the year when you have continuous sunlight, and times of the year when you have continuous night. When the sun never dips below the horizon or rises above the horizon. One day blends into another day. One long day. A "day" that's longer than a week. So the duration of a day is not invariable. It depends on where you live, as well as when you live. So the duration of a "day" is variable both internally and externally. When a day naturally begins or ends is quite different from clock time or calendar time.
Of course, the Decalogue was originally addressed to people in the Mideast, but imagine applying it to someone living near the North Pole before the advent of electrical lighting. And Christian missionaries would have to make allowance for that contingency. Exod 20 does, indeed, draw a parallel between the ordinary workweek and the creation week. But the ordinary workweek doesn't necessarily map onto the creation week the way some modern readers routinely assume.
Secularism Without Atheism
Many apologists and apologetic organizations put a lot of focus on responding to atheism. They place a lot of emphasis on presenting arguments for the existence of God, arguing that miracles occur, etc. Doesn't that make sense in a society that's been growing increasingly secular?
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