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 BLACK
Should 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 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”
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
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).
Secularism Without Atheism
Darwinian evangelicals: a love–hate relationship
"There are a number of good books available on reconciling science and Christian theology, particularly creation and evolution. The value of such books to various audiences depends, of course, on some shared assumptions. Carlson and Longman's book [Science, Creation and the Bible: Reconciling Rival Theories of Origins] is especially important for anyone who perceives conflict between evolutionary theory and Scripture. While sharing a commitment to scriptural infallibility and a generally literalist reading, they nonetheless show that none of the multiple creation stories in the Old Testament precludes the acceptance of contemporary science. I recommend it highly."
—Nancey Murphy, professor of Christian philosophy, Fuller Theological Seminary
http://www.ivpress.com/cgi-ivpress/book.pl/review/code=3889
But at the heart of liberalism is the denial of purpose in nature. Historically, the key turning point was Charles Darwin. The central elements in Darwin's theory -- random variations, sifted by the blind, automatic process of natural selection -- were aimed specifically at getting rid of the concept of purpose or design in biology. As historian Jacques Barzun says, "This denial of purpose is Darwin's distinctive contention."
Today we are seeing the real-world results of this denial. Transgenderism treats the scientific facts of human biology as having no intrinsic purpose or significance. It treats the body as nothing but a piece of matter that gives people no clue about who they are as persons. It is a self-alienating worldview that teaches people that their identity as male or female has no inherent purpose or dignity. (For more, see chapter 3 in my book Saving Leonardo.)
This article is adapted from Saving Leonardo, by Nancy Pearcey, director of the Francis Schaeffer Center for Worldview and Culture at Houston Baptist University and editor at large of The Pearcey Report.
http://www.pearceyreport.com/archives/2013/07/nancy_pearcey_transgender_politics_vs_facts_of_life.php
Wednesday, August 28, 2013
The music of life
http://www.musicoflife.co.uk/pdfs/The%20Music%20of%20Life-sourcebook.pdf
Cut out the middleman
From a recent WSJ article:
Most people are unaware that if they don't use insurance, they can negotiate upfront cash prices with hospitals and providers substantially below the "list" price. Doctors are happy to do this. We get paid promptly, without paying office staff to wade through the insurance-payment morass.
Read the rest here.
Who's redefining what?
So look, here's my modest proposal: If we aren't going to start with sound exegesis of the Bible and be content with that…
Same thing for all their other redefinitions. If they wanted some holy status for their errant feelings and hunches and "leadings," they should never have assaulted the well-known and well-defined Biblical phenomenon of prophecy, and embarrassed themselves by trying to redefine it to suit their experiences.
Prophetic sayings and speeches preserved in early Christian sources exhibit a wide variety of forms and styles. Even though we have somewhat overconfidently proposed a typology of six types of basic forms of prophetic speech and three kinds of complex forms, it is apparent that only the presence of formal framing devices betrays the possible presence of Christian prophetic speech…There is therefore no such thing as a distinctively characteristic form of Christian prophetic discourse that is recognizable apart from the presence of formal framing devices. The only real exception to this generalization is the apocalyptic vision report, a literary form which we have not considered in any detail and which requires careful study in its own right. D. Aune, Prophecy in Early Christianity and the Ancient Mediterranean World (Eerdmans 1991), 337-338.
See, that's where the modern inventors of Charismaticism/"continuationism" went wrong. Parham and his poor dupes were originally seeking the Biblical gift of tongues. That is, they expected to be able to speak in unlearned human languages supernaturally. And when they started babbling and gobbling, they were convinced it had to be that, that Biblical gift, that falsifiable gift with defined contours and edges. So they went off to mission fields, expecting to be understood by the Chinese... but, yeah, you know how that went. Natives shrugged and, in effect, made little circular gestures by their temples. Incomprehensible babble.
So here's where the first-gen errorists went afield. They were sure their experience was valid (Charismaticism 101), so then took some large hammers and saws to the Bible, and eventually changed the interpretation of what "tongues" meant from, well, what it meant, to what they were doing. They took a well-understood gift and invented something that gave cover to their experience.
The ambiguous evidence regarding the exact nature of tongues raises the question of whether even Paul himself or the other earliest Christians knew the exact nature of the phenomenon. R. Ciampa & B. Rosner, The First Letter to the Corinthians (Eerdmans 2010), 586.
From the way Paul speaks of this phenomenon [tongues] in the rest of this chap. [12] and in chap. 14, however, it seems best to recognize it as some form of noncommunicative utterance or incoherent babbling.
The phenomenon cannot mean speaking in foreign tongues…it denotes here [14:2] some sort of utterance beyond the patterns of normal human speech. J. Fitzmyer, First Corinthians (Yale U. Press 2008), 470, 510.
Second, Paul understands these utterances to be addressed to God (14:2,14,28) and not to humans (14:2,6,9). It is not a language of normal human discourse, but something mysterious and "other," which may give it its appeal. It consists of "mysteries in the Spirit" that are unintelligible to humans (14:2 ) and that benefit only the speaker (14:4). It communicates with God through prayer and praise (14:15) in ways that analytical speech do not…This rules out the view that tongues refer to the miraculous ability to speak in unlearned languages or to speak in one's native language. D. Garland, 1 Corinthians (Baker 2003), 584.
Edwards declares: "It is evident that the Corinthians did not use their gift of tongues to evangelize the heathen world. They spoke with tongues in their Church assemblies, and not once does the Apostle urge them to apply the power to the purpose for which it would be so eminently serviceable."
If there were any hint of this use, Paul could not have said "the person who speaks in a tongue speaks not to people but to God" (14:2), let alone, "the person who speaks in a tongue builds up only himself (14:4). But we saw that insofar as Chrysostom, Cyril, Thomas, and most especially Theodoret and Calvin were concerned, the whole point of using foreign languages was strictly to serve the proclamation of the gospel as part of the mission to the world. But if we decontextualize the gift from mission (as Paul clearly does in 1 Cor 14), the basis for the gift has disappeared.
Tongues may then be viewed as "the language of the unconscious" because it is unintelligible (unless it is "interpreted") not only to others but also to the speaker, A. Thiselton, The First Epistle to the Corinthians (Eerdmans 2000), 977, 988.
The weight of the textual evidence, however, does not support this understanding of tongues as real human languages. The Pentecost story does emphasize the intelligibility of the tongues spoken, but a careful reading indicates that the miracle occurred in the hearing rather than in the mode of speaking. The bystanders do not ask, "How can they all be speaking our native languages?" but rather, "Since all who are speaking are Galileans, how is it that we hear them in our own native languages" (Acts 2:8).
As for Paul,he could hardly emphasize more strongly that in his view–and he was a speaker in tongues himself (14:18)–glossolalia is an intrinsically noncommunicative form of utterance (1 Cor 13:1; 14:2,4,7-9,16-17,23).
In summary, the convergence of evidence suggests that glossolalia is a verbal expression of a powerful emotional state. It is not a real language but a kind of structured or ordered babbling, "Glossolalia and the Embarrassments of Experience," L. T. Johnson, The Princeton Seminary Bulletin (1997), 117-118, 121.
Every time we're trying to talk God's Word, someone is sure to ask, "So, what about when X happens? or when Y happened in 1843? How do you explain that, huh?" As if this is what really should consume the Christian, because we already have so well mastered all that actually-in-the-Bible stuff.
But then again, really, since the whole point is that we've got this imperative (we must validate the Charismatic's experience and his special powers)…
Biblical longevities
Caught your article about biblical genealogies.
I also ran across this...
Creation Research Society Quarterly, "Biblical Longevities: Some Questions and Issues"http://www.asa3.org/ASA/PSCF/2011/PSCF12-11Huebner.pdf
The author also ignores the clear lack of expected randomness in many of the entries of Table 1. In the best example, Noah (ordinal 10) was 500 years old when his sons were born and the Flood followed 100 years later when he was 600. His son Shem (ordinal 11) became a father when he was 100 years old and he lived 500 more years, dying at the age of 600. The chance of this being anything other than a fabricated, symbolic use of special numbers is miniscule.
You asked what signs we would need to be able to judge a person's age at death if all we had was the skeleton.
Youngblood doesn't bother to explain how paleoanthropologists would be able to determine the age of prediluvians from skeletal remains. If, say, they aged very slowly, could you tell that from skeletal remains?
Don't we generally determine age of death from skeletal remains by comparison with normal lifespans?
So what would be the frame of reference in the case of prediluvians? By definition, they fall far outside normal standards of comparison.
But when you're talking about people who allegedly lived way past 100 some basic considerations come to mind such as the fact that tooth enamel does not grow back but continues to wear out. So do the inside of joints, where the surfaces touch one another, literally wearing down the joint surfaces over time, even in a young healthy person who overuses their joints. It's true that tortoises can live for 200 years but they have beaks that continue to grow slowly, and they either move slowly, or swim in water which probably slows the deterioration process, but they probably suffer broken down joints all the same once they reach that age. One could hypothesize that the patriarchs were blessed with genes for growing multiple sets of teeth for as long as they lived, though very few humans are blessed with those same genes today (a few today are blessed with some extra teeth that come in after the second set, but we don't grow teeth as easily as sharks do). As for joints, even young healthy people can wear those out, so people living past 100 would probably have increasingly more trouble with their joints.
How The Apostles Died
Tuesday, August 27, 2013
Genuine “Good Works” vs “The Precepts of ‘The Church’”
Monday, August 26, 2013
Rat nirvana
Although the experiments were done in rats, Borjigin thinks they have implications for the near-death experiences (NDEs) reported by one in five people who are resuscitated after their hearts stop. Although they were unconscious, unresponsive and clinically dead at the time, they come back with stories of bright lights, “realer than real” memories, and meetings with people they knew. Some scientists have dismissed these accounts outright. Others have taken NDEs as proof of a religious afterlife or a consciousness that lives on outside the body, as popularised in a recent bestseller of dubious provenance.
But Borjigin’s research suggests that these experiences could just be a natural product of a dying brain. That doesn’t make them any less real, but it does root them in the natural world, without the need for a “super-“ prefix.
http://phenomena.nationalgeographic.com/2013/08/12/in-dying-brains-signs-of-heightened-consciousness/
Sunday, August 25, 2013
Against the Gods
I have a few reservations. Although his position on the birth of Moses is defensible, I also think it's unnecessary. But my major disappointment is with his handling of the Enuma Elish. Here I prefer John Oswalt's treatment, in The Bible Among the Myths.
Christians who take an interest in this issue would do well to read both scholars.
I'd add that Currid has covered some, but not all, of the same ground in his earlier Ancient Egypt and the Old Testament. His new book is pitched at a more popular level.
Three-story eschatology
“The Current State of Rome”
Hop On the Sacramental Treadmill |
Eric Charter has pulled them together for his Literate Comments blog. Here is a taste of it:
You’ve engaged a group who are themselves in the middle of a fight for the soul of their communion. They’ve just seen the heyday of their conservative ‘renaissance’, which best I can tell lasted about 15 years, from early 90′s till about 2007. And actually Ratzinger, in lobbying for the office, was a last ditch effort to keep the movement on life support. I was just going back through Pachence’s notes after I left and it looks to be about ’92 when he starts to notice a swing in the seminarians coming through the formation center. And it looks to be what you’re seeing now is the Vat II vanguard pushing back and gaining steam right around the time Ratzinger took office, which is a great deal of why he quit shortly thereafter. So, now you’ve got both sides marshalling different bishops, theologians, and putting them forward as the ‘official position’. You even had Ratzinger making movements toward SSPXers trying to shore up the conservative flank.
Remember ‘interpretation’ in Rome is a multi-headed beast. There isn’t ONE conclusion, there are multiple and since 2005 now officially,-not ex cathedra(huge loophole) the only bounding that has been set is “no rupture”. Well if no definitive bounding(single conclusion) was set at Vat II, and the hermeneutical purpose was to allow for multiple interpretations so that Rome could effectively morph pastorally with modernity you will forever have swings one way or another, you will effectively have sects, factions, movements all LEGITIMATELY being able to claim grounding in ALLOWABLE interpretation. Which is why you have Anglo-catholic communions, SSPXers(dissent), Vat II ‘liberals’, Latin-rite communions, the Network, social conscience academics, etc.
Now they want to say this isn’t confusion, like what you see in protestantism because sacramentally we are all on board. Well, I’ll grant that everybody, who practices, goes to mass. Let me be generous here; I’d say 1 in 200 catholics can explain to you their sacramental theology. …
What you have is a religious communion grounded in the priestly charism of the ordinary magisterium. They have sacerdotalism. They have grace and benefit mediated to them per priestly mediation and justification/salvation conveyed by way of ontological renovation and purgation. Now, 1 in 1000(uber-generous) could explain that to you. But since you have ex opere operato at work, and your official posture is to want to receive the benefit conveyed, you’re still good…. Most people’s religious expression in RC amounts to; “I go to mass, went to mass, tried to do right, went to confession a few times and I hope the priest gets there in time for last rites.”
Read it all here: http://literatecomments.com/2013/08/23/the-current-state-of-rome/
Please note: an earlier version of this post had erroneously attributed the Literate Comments blog to Darryl Hart.
Catholic Converts and “Buyer’s Remorse”: Permitting “Pitifully Low Standards” to Overcome It
The Real Roman Catholic Hierarchy |
Are Catholics really that desperate to enlist among their ranks of apologists converts that have been enlightened a mere one year? That's rather telling in my opinion. By their measure, he's been teaching and preaching heresy for the last 20 years, but now, in the last year he's some how finally gotten it right and is qualified to lead others? Those are some pitifully low standards.
He really answered his own question. I responded: “My thought is that the whole ‘Catholic Convert’ schema has been set up to allay the buyer’s remorse that many of them have upon finding out what they've really gotten themselves into.”
Another Called to Communion writer has portrayed that feeling as “a marriage, in which romance does not reduce to sentimentalism, nor prescind from difficulty and pain, but rather flows from the realities of a life shared together, come what may”.
In other words, the newness comes off, and the Roman Catholic convert who falls in love with “The Church” wakes up one day and finds that the purported “Bride of Christ” really does have warts.