Iconoclasm II

Now It's Whale Hips: Another Icon of Darwinian Evolution, Vestigial Structures, Takes a Hit

David Klinghoffer September 15, 2014 4:05 AM 

In the case presented by advocates of Darwinian evolution, vestigial organs are a star in the firmament, frequently and gloatingly pointed to. Darwin himself cited them as such in The Origin of Species and The Descent of Man, referring to body parts like the human appendix that, he believed, no longer serve a function:

On the view of each organism with all its separate parts having been specially created, how utterly inexplicable is it that organs bearing the plain stamp of inutility... should so frequently occur.

Of course the appendix is a great example of an organ once thought to be without utility that now turns out to serve a vital role.

In the catalogue of purported vestigial parts, whale hips are "the marquee example," writes Stephanie Keep at the absurdly named "Science League of America" blog populated by our Darwin-lobbying friends at the National Center for Science Education. Unfortunately whale hips have now gone the way of appendix. A paper in the journal Evolution reports that rather than being a useless reminder of the evolutionary past, when whale ancestor Pakicetus strode thThe pelvic bone supports the muscles that guide the penis. In male whales and other cetaceans, performance and thus successful sexual competition hinge on the size of the hips. The paper explains:

Male genitalia evolve rapidly, probably as a result of sexual selection. Whether this pattern extends to the internal infrastructure that influences genital movements remains unknown. Cetaceans (whales and dolphins) offer a unique opportunity to test this hypothesis: since evolving from land-dwelling ancestors, they lost external hind limbs and evolved a highly reduced pelvis which seems to serve no other function except to anchor muscles that maneuver the penis. Here we create a novel morphometric pipeline to analyze the size and shape evolution of pelvic bones from 130 individuals (29 species) in the context of inferred mating system. We present two main findings: 1) males from species with relatively intense sexual selection (inferred by relative testes size) have evolved relatively large penises and pelvic bones compared to their body size, and 2) pelvic bone shape diverges more quickly in species pairs that have diverged in inferred mating system. Neither pattern was observed in the anterior-most pair of vertebral ribs, which served as a negative control. This study provides evidence that sexual selection can affect internal anatomy that controls male genitalia. These important functions may explain why cetacean pelvic bones have not been lost through evolutionary time.

Under selection pressure from reality, Darwinists have already had to back away from Darwin's own understanding of what it means for a structure to be vestigial. Rather than serving no purpose, writes Jerry Coyne in Why Evolution Is True, now being vestigial can mean serving adifferent purpose than in one's distant ancestors. He defines "vestigial trait" this way:

A trait that is the evolutionary remnant of a feature once useful in an ancestral species but that is no longer useful in the same way. Vestigial traits can be either nonfunctional (the wings of the kiwi) or co-opted for new uses (the wings of the ostrich).

Stephanie Keep agrees:

[T]here's a problem when vestigial structures are defined as evolutionary remnants that have no function. As I discussed in a previous post, the correct way to describe a vestigial structure is to say that it no longer has its original function.

She is excited about Carl Zimmer's post on the subject, which elaborates:

While [whale hips] may not be essential for walking, they still matter a lot to whales. To see why, we have to go back to those hips of land mammals. They are important for walking on land, but they serve other purposes, too. Among other things, they anchor muscles that control the sex organs. If these muscles are anesthetized in men, for example, they have a hard time gaining an erection.

As whale hips stopped mattering to walking, they didn't stop mattering to having sex. In male whales, the pelvis controls the penis with an especially elaborate set of muscles. In some whale and dolphin species, these muscles make the penis downright prehensile.

You see the problem. Whale hips are "vestigial" yet still extremely important. Comments our colleague Michael Behe, "So doesn't that make everything a vestigial structure from a Darwinian viewpoint? And if so, of what use is the word?" Or as Jonathan Wells wrote here back in 2009 in reviewing Coyne's book ("The Myth of Vestigial Organs and Bad Design: Why Darwinism Is False"):

As [biologist Steven] Scadding had pointed out nearly thirty years ago, ... Darwin's argument rested on lack of function, not change of function. Furthermore, if vestigiality were redefined as Coyne proposes, it would include many features never before thought to be vestigial. For example, if the human arm evolved from the leg of a four-footed mammal (as Darwinists claim), then the human arm is vestigial. And if (as Coyne argues) the wings of flying birds evolved from feathered forelimbs of dinosaurs that used them for other purposes, then the wings of flying birds are vestigial. This is the opposite of what most people mean by "vestigial."

In this way, the concept of a vestigial trait is reduced to meaninglessness. In the most minimal definition, evolution denotes change over of time. No trait goes unchanged. Under the framework of Darwinian evolution, therefore, everything is vestigial. So nothing is.

This is not just our observation. The scientists who revealed the usefulness of whale hips are rethinking what it means to be vestigial. Or so it sounds from the remarks of biologist Matthew Dean at USC, a co-author of the paper in Evolution, commenting in Science Daily:

"Our research really changes the way we think about the evolution of whale pelvic bones in particular, but more generally about structures we call 'vestigial.' As a parallel, we are now learning that our appendix is actually quite important in several immune processes, not a functionally useless structure," Dean said.

Anyone who thinks whale hips are functionless, just like your appendix, should try telling that to a lonely gentleman whale. The career of this evolutionary icon isn't over yet, I'm sure, but its importance in the evolutionary pantheon is due for a serious downgrade.e land on all fours, they in fact serve an unquestionably important purpose.

Iconoclasm

Moth turns from black to white as Britain's polluted skies change colour

 The Peppered moth, which changed its colour from white to black in areas of Britain with heavy pollution, is now reverting to its original appearance.The moth was white with small black speckles but over time it evolved to being almost black in parts of the UK because of heavy industrial pollution. The change made it less obvious to predators against backgrounds of grime and soot.

Having declined by more than two thirds compared to 40 years ago, it is regarded as a classic example of natural selection and has consequently become known as "Darwin's moth."

Now in post-industrial Britain, 200 years after Darwin's birth, the moth is changing back to its original white colour.

Scientists at Butterfly Conservation, based in Dorset, are now appealing to the public for help in finding out how widespread this change has become.

As part of Garden Moths Count 2009 they want people to search their gardens for the moth and log their sightings.

"We have seen these moths making a big swing back to their original colour," said Richard Fox, project manager of Moths Count.

"It has been happening for decades as air pollution is cleaned up and with the demise of heavy industry in the big cities.

"The moths have been responding to this and the numbers of black and white moths will vary across the county.

"In Dorset it is very rare to see the moth in its dark form, but in industrial cities 150 years ago they were almost all black and that's where we will notice the greatest changes now."

He said they were also hoping to discover why the moth has been declining so dramatically since the 1960's.

"It's an iconic moth, the one that everyone learns about at school because it is such an amazing example of natural selection," he said.

"But it has actually undergone a major decline of 61 per cent since the 1960's and we don't know why.

"We will be fascinated to see where people are finding the two different forms of the moth and whether in fact people are finding it in their gardens at all."

Moth experts are also asking the public to look out for the beautiful day-flying Scarlet Tiger, which until recently was rarely seen outside South West England and South Wales.

In recent years the moth has spread to further parts of Britain as a result of climate change.

Scientists want to access how far they have flown to access the impact of climate change on our wildlife.

Garden Moths Count is part of the national Moths Count project, established after research indicated massive declines in moth numbers, especially in the southern half of Britain.

Some people are put off moths by the myth that they all eat clothes.

But in reality only half a dozen of Britain's 2,500 moth species do this - and they prefer dirty items that are hidden away in the dark in places where they are not disturbed.

Mr Fox added: "Moths are important indicators and observing them can tell us a lot.

"They are an essential food source for many birds and they are important pollinators in the garden.

"Some are very beautiful and, despite their recent decline, there are still very colourful moths to be seen in all of our gardens."

Sightings of moths seen by day or at night can be logged at the Garden Moths Count website www.mothscount.org .

Store bought sense V Horse sense II

The latest body blow to religious liberty in Russia

Russian Federation Supreme Court Decision Sets Dangerous Precedent for Jehovah’s Witnesses in Russia

On November 12, 2014, the Supreme Court of the Russian Federation upheld a lower court ruling that declared the Local Religious Organization (LRO) of Jehovah’s Witnesses in Samara to be extremist. The prosecutor’s office in Samara initiated its case against the Samara LRO in 2014 after law-enforcement officials searched facilities that the Witnesses rent for religious meetings and “found” a handful of their religious publications that have been banned nationwide. The banned publications had earlier been declared extremist by Russian courts and were posted on the Ministry of Justice’s Federal List of Extremist Materials. * However, the Witnesses in Samara had already complied with these Russian court decisions and removed the publications from the facilities that they rent for worship.

The Witnesses argued before the lower court and in the Supreme Court that the police conducting the search had planted the banned literature as a pretext to initiate charges. The Witnesses also explained that the European Court of Human Rights is currently examining the legality of earlier Russian court decisions that banned some of their publications. Additionally, the Witnesses argued that even if the Samara prosecutor’s allegations were true—that they had stored banned literature—the punishment was disproportionate for such a minor offense. Storing banned literature is an administrative violation punishable with a fine or a temporary suspension of the LRO’s activity, not the severe measure of liquidation. However, the Supreme Court dismissed these arguments.

Liquidation of a Legal Entity—One Step Closer to Criminal Prosecution?

The Samara LRO liquidation is following a pattern similar to that of the case in the city of Taganrog, where the Rostov Regional Court liquidated the LRO in 2009 on extremism charges. Subsequently, Taganrog law-enforcement authorities interpreted that decision as a de facto ban on the religious activity of Jehovah’s Witnesses in the area. Sixteen Witnesses in Taganrog were criminally charged in 2013 for merely carrying out their religious worship—the same practices that Jehovah’s Witnesses perform worldwide, including in Samara. Seven Witnesses were heavily fined; four of them, who are congregation elders, were also given lengthy prison sentences. However, the judge waived the fines because the investigation and trial exceeded the statute of limitations, and he imposed suspended sentences. The Witnesses have appealed these convictions, and on December 12, 2014, the Rostov Regional Court ordered a new trial with a new judge.

The 1,500 of Jehovah’s Witnesses living in the Samara region are now at risk of being criminally prosecuted merely for carrying out their worship. Where will it end? Russian authorities are conducting similar investigations of Witness LROs in various parts of the country. How these repressive state actions will affect the nearly 180,000 Witnesses living in Russia remains to be seen. However, the Supreme Court decision sets a dangerous precedent that jeopardizes the freedom of Jehovah’s Witnesses and other religious minorities in Russia.

Mark13:9NASB "But ^[e]be on your guard; for they will deliver you to the ^[f]courts, and you will be flogged in the synagogues, and you will stand before governors and kings for My sake, as a testimony to them."

Pointing out the emperor's nudity.

The Pope is wrong on religious speech

By Heidi Schlumpf

 

 

 

The popular Pope Francis is taking some hits himself after some lighthearted comments that included a pretend punch to a colleague. The comments came while trying to make the point that free speech should have some limits, including on the right to insult another's faith.

Speaking Thursday to reporters on the plane ride to the Philippines, the Pope gestured with a fake punch to demonstrate what he would do if someone were to say "a swear word against my mother."

Heidi Schlumpf

Most journalists interpreted it as a joke, not a justification of violence, especially since the Pope had also just forcefully stated that "one cannot kill in the name of God."

Still, the Vatican felt the need to clarify, in response to a later CNN question about the punch, that his words were "spoken colloquially" and consistent with the Pope's "free style of speech."

I don't for one minute think the Pope is advocating for any type of violence, whether religiously motivated murder or sparring among friends who dis each other's mamas.

 

What concerns me is his apparent belief that religion should have special protection when it comes to free speech.

"One cannot provoke, one cannot insult other people's faith, one cannot make fun of faith," he said. "There is a limit. Every religion has its dignity. ... In freedom of expression there are limits."

 

 

The Pope, responding to a general question about the interplay between religious liberty and free expression, was clearly referencing the massacre of journalists at Charlie Hebdo magazine by Islamist militants in Paris last week.

Although he did not say the slain cartoonists brought the attack upon themselves because of their satirical criticism of Islam, it's not a huge logical leap to that conclusion and raises the likelihood of such a misinterpretation.

Let's just say it's not what most public relations professionals would advise.

And while the Pope has been known to talk more informally with reporters on the papal plane (his "Who am I to judge?" comment about gay Catholics came on the return flight from Brazil in 2013), he's still on the record and obviously aware that his words will be reported and analyzed.

The Pope is not the only prominent Catholic raising the issue.

Bill Donahue, a self-appointed spokesman fighting "anti-Catholicism" as the president of the New York-based Catholic League, released a statement with the headline, "Muslims have a right to be angry," on the day of the killings.

 

On Thursday, his statement was headlined: "Pope sides with Catholic League." Such chutzpah.

While no one can match the offensive tone of Donahue, who actually said Charlie Hebdo's Stephane Charbonnier "didn't understand the role he played in his own death," the gist of the Pope's message was the same: Criticism of religion is problematic.

As an aside, I'll be curious to see if those who slammed Donahue have the same harsh words for the Pope.

Perhaps both of them should take a lesson from the response of another Christian, Jim Wallis, president of Sojourners, a progressive, evangelical community and publication. He had a different suggestion for how people of faith should respond to the Paris attacks:

"Jesus tells us to bless those who persecute us, to return love for hate and good for evil, and even to love our enemies," Wallis wrote. "Loving your enemies certainly includes supporting the foundational commitment to free speech, and defending the right of free speech, even, or especially, for those who offend you."

I think most American Catholics agree that while blasphemy -- offensive speech against God or religion -- is not particularly nice, it does not follow that it can or should be regulated or outlawed. In the United States, the Supreme Court outlawed blasphemy laws in 1952.

I'm hoping the Pope was only offering counsel to his followers, rather than advocating for any sort of legal position. No one has the right not to be offended. Even the Pope.

 

Bottled sunlight.

On separating science from mysticism

In Light of New BIO-Complexity Paper, Maintaining Neo-Darwinism Means Rejecting Established Methods of Historical Science

Casey Luskin January 23, 2015 4:31 AM

 

In the new BIO-Complexity paper, "Enzyme Families-Shared Evolutionary History or Shared Design? A Study of the GABA-Aminotransferase Family," Mariclair Reeves, Ann Gauger, and Douglas Axe find that modern enzymes cannot be easily mutated to acquire new functions. One 2009 study that their paper cites states, "[M]any attempts at interchanging activities in mechanistically diverse superfamilies have since been attempted, but few successes have been real¬ized." This suggests that modern enzymes are not amenable to evolutionary conversions. The typical response from evolutionists is that perhaps ancient enzymes were different, and more readily mutable to acquire new functions. Perhaps so. However, as Reeves, Gauger, and Axe explain, this means evolutionary scientists must then ignore experimental evidence showing that protein conversions require many mutations. That would reveal Darwinism as being grounded in speculation instead of experimental data. In their new paper they write:

We are asking whether the enzymes now pres¬ent in life are as amenable to functional conversion as ancient enzymes must have been in order for evolution to work. If the answer to this is No, then the classical recruitment scenario does not work today, anyway. That realization would be of consider¬able importance, in that it would call for careful consideration of how processes that do not work today somehow did work long ago. In other words, it would reinforce the importance of grounding evolutionary explanations in observable science.

The same rejoinder might be offered to defenders of the "promiscuity" hypothesis of protein evolution. According to this model, perhaps ancient enzymes performed many functions. Then, over time some of those functions may have been lost and others finely tuned, leading to today's enzymes which perform specific functions extraordinarily well. Do modern enzymes show the kind of promiscuity that ancient enzymes supposedly needed? That's not clear. Moreover, this model relies upon loss of function to explain enzyme specificity, and never accounts for the origin of new enzyme functions in the first place. Reeves, Gauger, and Axe continue:

This idea of functional divergence from promiscuous ancestral enzymes, though possibly of some value, leaves the most fundamental aspects of the origins question unchanged. Whether ancient enzymes resembled modern ones closely or only loosely, the modern ones are both the things to be explained and the things we can observe. The importance of grounding evolutionary explanations in actual study of modern enzymes therefore remains as important now as ever. Yet the promiscuity hypothesis leaves the actual origin of new enzyme functions unexplained. In the end, then, functional conversion by mutation is still the only evolutionary explanation for those first appearances.

As we saw previously, their experimental data suggests that many mutations -- including deleterious ones -- would be necessary to generate new protein functions. It would take enormously long periods of time -- longer than the age of the earth -- to generate the mutations needed for new protein functions. When the experimental data conflicts with the predictions of the theory, what is a Darwinian to do?
The answer is they ignore the experimental data. They assume that biological systems in the past could evolve because they worked very differently than they do today. This is not a scientific form of reasoning. It's a dictated not by the evidence but by faith in the overall Darwinian doctrine.
We saw the same kind of thing when UC Berkeley paleontologist Charles Marshall debated Discovery Institute's Stephen Meyer in 2013 on the origin of new biological information. A point that emerged was that Marshall simply pushed back the question of the origin of new information. He ignored the evidence showing that modern developmental gene regulatory networks (dGRNs) don't tolerate mutations, making it very difficult to evolve new body plans. When you mutate developmental gene regulatory networks, the organism dies. In response to Meyer, Marshall argued that perhaps in the past, dGRNs were more plastic than they are today, thereby allowing new body plans to evolve. Meyer explained in rebuttal that Marshall had stopped using uniformitarian reasoning:

Marshall and other defenders of evolutionary theory reverse the epistemological priority of the historical scientific method as pioneered by Charles Lyell, Charles Darwin and others. Rather than treating our present experimentally based knowledge as the key to evaluating the plausibility of theories about the past, Marshall uses an evolutionary assumption about what must have happened in the past (transmutation) to justify disregarding experimental observations of what does, and does not, occur in biological systems. The requirements of evolutionary doctrine thus trump our observations about how nature and living organisms actually behave. What we know best from observation takes a back seat to prior beliefs about how life must have arisen.

In light of the experimental data from Biologic Institute, much the same could be said of proponents of the co-option model of protein evolution. As Meyer artfully put it, those who simply assume that ancient enzymes were more amenable to evolutionary conversions "reverse the epistemological priority of the historical scientific method." Evolutionists are welcome to ignore the experimentally derived real-world workings of modern biology if that's what they want to do, but they should acknowledge that they are asking for special treatment for their theory. In defense of Darwinism, they have departed from the established methods of historical science.

Another side of the narrative

Its been said that there are at least three sides to every narrative.Without prejudice here is one of the at least two other sides to a narrative being widely broadcasted in the global press.

 

Chomsky: Paris attacks show hypocrisy of West's outrage

By Noam Chomsky

 

 

 

After the terrorist attack on Charlie Hebdo, which killed 12 people including the editor and four other cartoonists, and the murder of four Jews at a kosher supermarket shortly after, French Prime Minister Manuel Valls declared "a war against terrorism, against jihadism, against radical Islam, against everything that is aimed at breaking fraternity, freedom, solidarity."

Millions of people demonstrated in condemnation of the atrocities, amplified by a chorus of horror under the banner "I am Charlie." There were eloquent pronouncements of outrage, captured well by the head of Israel's Labor Party and the main challenger for the upcoming elections, Isaac Herzog, who declared that "Terrorism is terrorism. There's no two ways about it," and that "All the nations that seek peace and freedom [face] an enormous challenge" from brutal violence.

Noam Chomsky

The crimes also elicited a flood of commentary, inquiring into the roots of these shocking assaults in Islamic culture and exploring ways to counter the murderous wave of Islamic terrorism without sacrificing our values. The New York Times described the assault as a "clash of civilizations," but was corrected by Times columnist Anand Giridharadas, who tweeted that it was "Not & never a war of civilizations or between them. But a war FOR civilization against groups on the other side of that line. #CharlieHebdo."

The scene in Paris was described vividly in the New York Times by veteran Europe correspondent Steven Erlanger: "a day of sirens, helicopters in the air, frantic news bulletins; of police cordons and anxious crowds; of young children led away from schools to safety. It was a day, like the previous two, of blood and horror in and around Paris."

READ: Suspected ringleader of Belgian terror cell sought

 

Erlanger also quoted a surviving journalist who said that "Everything crashed. There was no way out. There was smoke everywhere. It was terrible. People were screaming. It was like a nightmare." Another reported a "huge detonation, and everything went completely dark." The scene, Erlanger reported, "was an increasingly familiar one of smashed glass, broken walls, twisted timbers, scorched paint and emotional devastation."

These last quotes, however -- as independent journalist David Peterson reminds us -- are not from January 2015. Rather, they are from a report by Erlanger on April 24 1999, which received far less attention. Erlanger was reporting on the NATO "missile attack on Serbian state television headquarters" that "knocked Radio Television Serbia off the air," killing 16 journalists.

"NATO and American officials defended the attack," Erlanger reported, "as an effort to undermine the regime of President Slobodan Milosevic of Yugoslavia." Pentagon spokesman Kenneth Bacon told a briefing in Washington that "Serb TV is as much a part of Milosevic's murder machine as his military is," hence a legitimate target of attack.

There were no demonstrations or cries of outrage, no chants of "We are RTV," no inquiries into the roots of the attack in Christian culture and history. On the contrary, the attack on the press was lauded. The highly regarded U.S. diplomat Richard Holbrooke, then envoy to Yugoslavia, described the successful attack on RTV as "an enormously important and, I think, positive development," a sentiment echoed by others.

There are many other events that call for no inquiry into western culture and history -- for example, the worst single terrorist atrocity in Europe in recent years, in July 2011, when Anders Breivik, a Christian ultra-Zionist extremist and Islamophobe, slaughtered 77 people, mostly teenagers.

READ: Why Islam forbids images of Mohammed

Also ignored in the "war against terrorism" is the most extreme terrorist campaign of modern times -- Barack Obama's global assassination campaign targeting people suspected of perhaps intending to harm us some day, and any unfortunates who happen to be nearby. Other unfortunates are also not lacking, such as the 50 civilians reportedly killed in a U.S.-led bombing raid in Syria in December, which was barely reported.

One person was indeed punished in connection with the NATO attack on RTV -- Dragoljub Milanović, the general manager of the station, who was sentenced by the European Court of Human Rights to 10 years in prison for failing to evacuate the building, according to the Committee to Protect Journalists. The International Criminal Tribunal for Yugoslavia considered the NATO attack, concluding that it was not a crime, and although civilian casualties were "unfortunately high, they do not appear to be clearly disproportionate."

The comparison between these cases helps us understand the condemnation of the New York Times by civil rights lawyer Floyd Abrams, famous for his forceful defense of freedom of expression. "There are times for self-restraint," Abrams wrote, "but in the immediate wake of the most threatening assault on journalism in living memory, [the Times editors] would have served the cause of free expression best by engaging in it" by publishing the Charlie Hebdo cartoons ridiculing Mohammed that elicited the assault.

Abrams is right in describing the Charlie Hebdo attack as "the most threatening assault on journalism in living memory." The reason has to do with the concept "living memory," a category carefully constructed to include Their crimes against us while scrupulously excluding Our crimes against them -- the latter not crimes but noble defense of the highest values, sometimes inadvertently flawed.

This is not the place to inquire into just what was being "defended" when RTV was attacked, but such an inquiry is quite informative (see my A New Generation Draws the Line).

There are many other illustrations of the interesting category "living memory." One is provided by the Marine assault against Fallujah in November 2004, one of the worst crimes of the U.S.-UK invasion of Iraq.

The assault opened with occupation of Fallujah General Hospital, a major war crime quite apart from how it was carried out. The crime was reported prominently on the front page of the New York Times, accompanied with a photograph depicting how "Patients and hospital employees were rushed out of rooms by armed soldiers and ordered to sit or lie on the floor while troops tied their hands behind their backs." The occupation of the hospital was considered meritorious and justified: it "shut down what officers said was a propaganda weapon for the militants: Fallujah General Hospital, with its stream of reports of civilian casualties."

Evidently, this is no assault on free expression, and does not qualify for entry into "living memory."

There are other questions. One would naturally ask how France upholds freedom of expression and the sacred principles of "fraternity, freedom, solidarity." For example, is it through the Gayssot Law, repeatedly implemented, which effectively grants the state the right to determine Historical Truth and punish deviation from its edicts? By expelling miserable descendants of Holocaust survivors (Roma) to bitter persecution in Eastern Europe? By the deplorable treatment of North African immigrants in the banlieues of Paris where the Charlie Hebdo terrorists became jihadis? When the courageous journal Charlie Hebdo fired the cartoonist Siné on grounds that a comment of his was deemed to have anti-Semitic connotations? Many more questions quickly arise.

Anyone with eyes open will quickly notice other rather striking omissions. Thus, prominent among those who face an "enormous challenge" from brutal violence are Palestinians, once again during Israel's vicious assault on Gaza in the summer of 2014, in which many journalists were murdered, sometimes in well-marked press cars, along with thousands of others, while the Israeli-run outdoor prison was again reduced to rubble on pretexts that collapse instantly on examination.

Also ignored was the assassination of three more journalists in Latin America in December, bringing the number for the year to 31. There have been more than a dozen journalists killed in Honduras alone since the military coup of 2009 that was effectively recognized by the U.S. (but few others), probably according post-coup Honduras the per capita championship for murder of journalists. But again, not an assault on freedom of press within living memory.

It is not difficult to elaborate. These few examples illustrate a very general principle that is observed with impressive dedication and consistency: The more we can blame some crimes on enemies, the greater the outrage; the greater our responsibility for crimes -- and hence the more we can do to end them -- the less the concern, tending to oblivion or even denial.

Contrary to the eloquent pronouncements, it is not the case that "Terrorism is terrorism. There's no two ways about it." There definitely are two ways about it: theirs versus ours. And not just terrorism.

 

The Holy Spirit ;Jehovah's active Force.But don't take my word for it.

Quotes: Holy Spirit is a Force from God, Trinitarians Admit

In the Old Testament (OT) it is clear that the inspired Bible writers intended holy spirit (ruah or ruach in Hebrew) to be understood as an invisible, powerful force from God. Even many trinitarian scholars will admit that.

For example, The Catholic Encyclopedia, p. 269, 1976, admits:

"In the OT the Holy Spirit means a divine power..."

And the New Bible Dictionary, Tyndale House Publishers, 1984, pp. 1136,1137, says:

"Spirit, Holy Spirit. OT, Heb. ruah 378 times ...; NT, Gk. pneuma 379 times." And "Divine power, where ruah is used to describe ... a supernatural force...." And "At its [the Old Testament's concept of ruah, God's spirit] heart is the experience of a mysterious, awesome power - the mighty invisible force of the wind, the mystery of its vitality, the otherly power that transforms - all ruah, all manifestations of divine energy." And "at this early stage [pre-Christian] of understanding, God's ruah was thought of simply as a supernatural power (under God's authority) exerting force in some direction."

The Encyclopedia Americana tells us:

"The doctrine of the Holy Spirit [as a person who is God] is a distinctly Christian [?] one.... the Spirit of Jehovah [in the OT] is the active divine principle in nature. .... But it is in the New Testament [NT] that we find the bases of the doctrine of the Spirit's personality." And "Yet the early Church did not forthwith attain to a complete doctrine; nor was it, in fact, until after the essential divinity of Jesus had received full ecclesiastical sanction [in 325 A.D. at the Council of Nicaea] that the personality of the Spirit was explicitly recognized, and the doctrine of the Trinity formulated." Also, "It is better to regard the Spirit as the agency which, proceeding from the Father and the Son, dwells in the church as the witness and power of the life therein." - Vol. 14, p. 326, 1957 ed.

And the Encyclopedia Britannica Micropaedia, 1985 ed., Vol. 6, p. 22 says:

"The Hebrew word ruah (usually translated `spirit') is often found in texts referring to the free and unhindered activity of God, .... There was, however, no explicit belief in a separate divine person in Biblical Judaism; in fact, the New Testament itself is not entirely clear in this regard....
"The definition that the Holy Spirit was a distinct divine Person equal in substance to the Father and the Son and not subordinate to them came at the Council of Constantinople in AD 381...."

Many historians and Bible scholars (most of them trinitarians) freely admit the above truth. For example: "On the whole, the New Testament, like the Old, speaks of the Spirit as a divine energy or power." - A Catholic Dictionary.

An Encyclopedia of Religion agrees:

"In the New Testament there is no direct suggestion of the Trinity. The Spirit is conceived as an impersonal power by which God effects his will through Christ." - p. 344, Virgilius Ferm, 1945 ed.

Even the trinitarian New Bible Dictionary tells us:

"It is important to realize that for the first Christians the Spirit was thought of in terms of divine power." - p. 1139, Tyndale House Publishers, 1984.

And the respected (and trinitarian) New International Dictionary of New Testament Theology confirms:

"As in earlier Jewish thought, pneuma [`spirit'] denotes that power which man experiences as relating him to the spiritual realm of reality which lies beyond ordinary observation and human control. Within this broad definition pneuma has a fairly wide range of meaning. But by far the most frequent use of pneuma in the NT (more than 250 times) is as a reference to the Spirit of God, the Holy Spirit, that power which is most immediately of God as to source and nature." - p. 693.

"The Spirit in the earliest Christian Communities and in Acts. `Holy Spirit' denotes supernatural power, altering, working through, directing the believer .... This is nowhere more clearly evident than in Acts where the Spirit is presented as an almost tangible force, visible if not in itself, certainly in its effects. This power of the Spirit manifests itself in three main areas in Luke's account of the early church [Acts]. (a) The Spirit as a transforming power in conversion. [p. 698] .... (b) The Spirit of prophecy. For the first Christians, the Spirit was most characteristically a divine power manifesting itself in inspired utterance. The same power that had inspired David and the prophets in the old age (Acts 1:16; 3:18; 4:25; 28:25) [p. 699] .... (c) The Spirit was evidently experienced as a numinous power pervading the early community ....
"The Spirit in the Pauline Letters. [p. 700] .... It is important to realize that for Paul too the Spirit is a divine power whose impact upon or entrance into a life is discernible by its effects." - pp. 693-701, Vol. 3, Zondervan, 1986.

"The emergence of Trinitarian speculations in early church theology led to great difficulties in the article about the Holy Spirit. For the being-as-person of the Holy Spirit, which is evident in the New Testament as divine power ..., could not be clearly grasped.... The Holy Spirit was viewed NOT AS A PERSONAL FIGURE BUT RATHER AS A POWER" - The New Encyclopedia Britannica.

 

Lucking out Darwinian style

 

Evolutionarily Unrelated Animals Use Geomagnetic Navigation

Evolution News & Views January 19, 2015 3:22

 

 

 

 

 

A female baby sea turtle hatches out of its egg in the sand on a Florida beach. It races for the ocean to catch the waves and swim out to the open sea. After years at sea traveling thousands of miles across the open ocean, the turtle, now a pregnant mother, finds its way back to the exact same beach where it was born. This amazing feat is described in a new paper in Current Biology by Roger Brothers and Ken Lohman at the University of North Carolina:

Ever since John James Audubon tied silver threads to the legs of young songbirds and observed their return the following year, evidence has accumulated that many animals return to their natal areas after migrating to distant locations. An extreme example exists in loggerhead sea turtles, which leave their natal beaches as hatchlings and traverse entire ocean basins before returning to nest, at regular intervals, on the same stretch of coastline where they hatched. How sea turtles accomplish natal homing has remained an enduring mystery of animal behavior. [Emphasis added.]

The biologists analyzed nesting sites over a 19-year period. They found that nest sites of returning sea turtles followed changing magnetic field lines. As the earth's magnetic field moves over the years, certain field lines of equal inclination, called isolines, move accordingly. In some years at a given location on the coastline, the isolines spread apart. In other years, the lines come closer together. The nest sites followed this same pattern, showing that the sea turtles were homing in on their natal beach by following the magnetic field inclination that matched their birth site. The hatchlings must have "imprinted" on that field line when they raced for the sea years earlier.
The precision of this sensory ability is incredible. Turtles are apparently able to gather information not just on the inclination angle of the magnetic field, but its intensity as well:

These results provide strong evidence that nesting sea turtles use Earth's magnetic field to locate their natal beaches. Although the exact geomagnetic component (or components) exploited by turtles cannot be determined from the analyses, the findings are consistent with the hypothesis that nest site selection depends at least partly on magnetic signatures consisting of inclination angle, field intensity, or a combination of the two.

Science Magazine gives a brief review of the findings:

Much like shifting sand, magnetic fields slide slightly over time, and their strength also increases as one moves away from the equator, akin to latitude. This property gives each stretch of coast a unique geographic marker, known as an isoline. The team found that in years when these magnetic isolines moved apart, the turtle nests spread out over a larger area -- by 1 or 2 kilometers. Conversely, when isolines converged, the nests squeezed into a smaller patch of beach, suggesting the turtles follow shifting magnetic tracks to their favorite nests. The findings also argue that a magnetic address is imprinted on loggerhead turtles at birth to point the way home.

The apparatus for sensing the earth's magnetic field appears to be in the turtle's brain, although this is still poorly understood. A news release about the paper from Cell Press says:

Brothers says that little is known about how turtles detect the geomagnetic field. Most likely, tiny magnetic particles in the turtles' brains respond to the Earth's field and provide the basis for the magnetic sense, but no one knows for sure.

Another clue indicates that turtles use more than a magnetic sense to find home. Some turtles nest on islands, where the isolines would spread out to the open sea at times. "In these cases," Brothers and Lohman suggest, "turtles might use magnetic cues to navigate to the vicinity of the island and then use odorants or other supplemental local cues to locate the nesting beach."
Remarkably, salmon show this same ability. Brothers and Lohman write:

In a previous study, the migratory route of salmon approaching their natal river was shown to vary with subtle changes in the Earth's field. Whereas the endpoint of the salmon spawning migration was presumably the same regardless of route, our findings demonstrate for the first time a relationship between changes in Earth's magnetic field and the locations where long-distance migrants return to reproduce.

Joining the contenders for this skill set are more unrelated animal types:

... our results provide the strongest evidence to date that sea turtles find their nesting areas at least in part by navigating to unique magnetic signatures along the coast. In addition, our results are consistent with the hypothesis that turtles accomplish natal homing largely on the basis of magnetic navigation and geomagnetic imprinting. These findings, in combination with recent studies on Pacific salmon, suggest that similar mechanisms might underlie natal homing in diverse long-distance migrants such as fishes, birds, and mammals.

So here we have a highly-precise navigational ability, able to cue on very faint properties in the earth's magnetic field, then on olfaction, and possibly on "other supplemental local cues" to find home across thousands of miles. The sensory "instruments" involved are integrated so that they are able to coordinate their functions for the same goal. Furthermore, the baby turtles, with their tiny brains, must have the ability to memorize the natal signatures of odors and magnetic field properties at birth, then recall those memories years later as large adults. (Sea turtles return about every two years to lay eggs.)
That would be a conundrum enough to explain by unguided processes like natural selection. But then, adding to the difficulty for Darwinism, similar abilities are found in distantly related animals like fish, birds, and mammals. Even if a Darwinian could show a possible line of descent from fish to mammal, the abilities involved would have been lost and regained multiple times, because not all fish, birds, and mammals use magnetic navigation. Given the complexities of the sensory systems involved, this would represent a case of "convergent evolution" on steroids. If the origin of this capability in one type of animal is highly implausible by mutation and selection, how about four times or more?
A design perspective, by contrast, would expect that unrelated animals on a common planet would share similar capabilities for their needs. The earth's magnetic field is global. It isn't surprising that very different animals would be designed to use that feature of the earth.

 

 

It's design all the way down

Protein Quality Control Surprise: An Enzyme Can Operate a Stalled Ribosome

Evolution News & Views January 9, 2015 5:17 AM | 

 

A cell is "a well-run factory," according to scientists at the University of Utah. Its protein assembly machines -- ribosomes -- do their work reliably and efficiently most of the time. On rare occasions, though, a nascent protein stalls inside the machine. When that happens, it's a crisis that can kill the cell or lead to serious diseases.

Fortunately, the cell has a plan to rescue itself:

Ribosomes are machines on a protein assembly line, linking together amino acids in an order specified by the genetic code. When something goes wrong, the ribosome can stall, and a quality control crew is summoned to the site. To clean up the mess, the ribosome is disassembled, the blueprint is discarded, and the partly made protein is recycled. (Emphasis added.)

A surprise surfaced when the Utah researchers, in an "extensive biochemical analysis," sought to understand the steps involved in tagging the stalled protein for destruction. Stalling causes the two parts of the ribosome, 40S and 60S, to separate. Immediately afterward, two "rare" quality-control proteins, Ltn1p and Rqc2p, bind to the stalled protein in the 60S part. Ltn1p binds near the exit tunnel and attaches the usual tag for destruction, ubiquitin. (Biochemists have a sense of humor sometimes; the "RING" domain of Ltn1p stands for "Really Interesting New Gene.")

It's the other participant, Rqc2p, that plays an unexpected role: it continues assembling the stalled protein without the benefit of a template or transfer RNA! "In this case, we have a protein, Rqc2, playing a role similar to that of mRNA" (messenger RNA), researcher Adam Frost says. "I love this story because it blurs the lines of what we thought proteins could do." But what kind of information can a template-free protein add to a stalled protein? The story gets even more bizarre:

Yet this study reveals a surprising role for one member of the quality control team, a protein conserved from yeast to man named Rqc2. Before the incomplete protein is recycled, Rqc2 prompts the ribosomes to add just two amino acids (of 20 total) -- alanine and threonine -- over and over, and in any order. Think of an auto assembly line that keeps going despite having lost its instructions. It picks up what it can and slaps it on: horn-wheel-wheel-horn-wheel-wheel-wheel-wheel-horn.

Is this a factory gone berserk? No. Using design thinking, the researchers figured there must be a purpose behind the seemingly wacky process:

Like a half-made car with extra horns and wheels tacked to one end, a truncated protein with an apparently random sequence of alanines and threonines looks strange, and probably doesn't work normally. But the nonsensical sequence likely serves specific purposes. The code could signal that the partial protein must be destroyed, or it could be part of a test to see whether the ribosome is working properly. Evidence suggests that either or both of these processes could be faulty in neurodegenerative diseases such as Alzheimer's, Amyotrophic lateral sclerosis (ALS), or Huntington's.

In fact, earlier experiments have shown a link between Rqc2p and the "heat shock" response of a cell under stress. This response up-regulates the manufacture of heat shock proteins. These proteins come to the aid of a cell that gets too hot, too cold, or oxygen deprived. The heat shock proteins act as chaperones and damage-control agents. They can re-fold partially folded proteins, tag misfolded proteins, or move proteins to safe-houses in the cell. In multicellular eukaryotes, they can even target proteins for the cell surface to be recognized by the immune system.

The linkage between Rqc2p and heat shock gave the researchers a clue. The alanine-threonine tags on the stalled protein (named, whimsically, "CAT tails" for "carboxy-terminal Ala and Thr extensions") might turn on the heat shock response. In their paper in Science, they put the story together:

Integrating our observations, we propose the model schematized in fig. S13. Ribosome stalling leads to dissociation of the 60S and 40S subunits, followed by recognition of the peptidyl-tRNA-60S species by Rqc2p and Ltn1p. Ltn1p ubiquitylates the stalled nascent chain, and this leads to Cdc48 recruitment for extraction and degradation of the incomplete translation product. Rqc2p, through specific binding to Ala(IGC) and Thr(IGU) tRNAs, directs the template-free and 40S-free elongation of the incomplete translation product with CAT tails. CAT tails induce a heat shock response through a mechanism that is yet to be determined.

It wouldn't be enough, in other words, for Ltn1p to tag the bad protein with ubiquitin. All that would do is silently send the protein to the trashcan (the proteasome). No, the cell needs an alarm signal that a ribosome might have gone haywire. The CAT tails added by Rqc2p somehow inform the cell that a heat shock response team is needed to investigate.

To add the CAT tails, Rqc2p cannot rely on the failed ribosome. It also cannot rely on the messenger-RNA and transfer-RNA pathways from the genetic code in the nucleus. Without a template, it has to work autonomously, using its own active sites for alanine and threonine, and the ability to fasten them to the incomplete protein. By stitching on these extra amino acids to the stalled protein, Rqc2p sends something like an SOS message to the cell, using the actual defective protein as evidence. It's all quite elegant and unexpected.

"There are many interesting implications of this work and none of them would have been possible if we didn't follow our curiosity," says Brandman. "The primary driver of discovery has been exploring what you see, and that's what we did. There will never be a substitute for that."

That statement is pregnant with design implications, however unintended. If the researchers stopped at Darwinian ideas of random, purposeless matter in motion, would they have found this new process? It was their curiosity about "what we thought proteins could do" -- what purposeful roles they could play -- that led them to expand our knowledge of cell quality control.

So whether or not these biochemists "believe in" intelligent design -- we assume they don't -- their actions speak louder than words. By viewing the cell as "a well-run factory" with "machines on a protein assembly line," they added to a growing view that "Nature is capable of more than we realize."

Lastly, don't miss that incidental statement about the "member of the quality control team" Rqc2p being "a protein conserved from yeast to man," implying that for hundreds of millions of years, evolution had nothing to do with it.

 

Survival of the kindest?

An Evolutionary Challenge: Explaining Away Compassion, Philanthropy, and Self-Sacrifice

Denyse O'Leary January 9, 2015 11:23 AM | 

 

 

Apart from religion, no subject has vexed naturalists more than why people sacrifice themselves and their wishes, hopes, dreams, and pleasures for others. Branding both philosophy and religion and popular arts and culture for naturalism includes explaining away compassion, philanthropy, and self-sacrifice.

Redefinition is a first step. This entire group of qualities is now loosely called "altruism," a trans-species concept by which, for example, worker ants pass on their genes by serving their queen, who lays lots of eggs, instead of reproducing individually (kin selection).

Kin selection grew legs in 1955 when British geneticist J. B. S. Haldane said, we are told, that he would risk his life for two brothers or eight cousins, to preserve enough of his own genes to justify his death. Evolutionist William Hamilton described the idea mathematically, calling it inclusive fitness. His calculations have been used ever since, and were a key inspiration for Richard Dawkins's The Selfish Gene.

Altruism has been described as "an anomalous thorn in Darwin's side" and a "conundrum that Darwinians would need to solve, given their view of the ruthless struggle among living beings for survival." So, if Darwinizing the mind through altruism and kin selection succeeds, we can account for such human behavior as if we were bees or beavers, which greatly simplifies matters.

E. O. Wilson is widely hailed as the founder of sociobiology (circa 1975), which expounded these theories. Sociobiology later morphed into evolutionary psychology. But then Wilson dramatically abandoned kin selection in 2010 in a Nature paper, "The evolution of eusociality," co-authored with mathematicians. He argued that strict Darwinism (natural selection acting on random mutation) "provides an exact framework for interpreting empirical observations," dispensing with the other theories he had promoted for decades. Over 140 leading biologists signed a letter to Nature, attacking the 2010 paper. Some called his new, strictly Darwin model "unscholarly," "transparently wrong," and "misguided."

What? All this is said of a Darwin-only model, the gold standard of naturalism?

New Atheist evolutionary biologist Jerry Coyne has weighed in, saying that Wilson et al. are "wrong -- dead wrong." Curiously, he admitted, "The 'textbook' explanation, based on a higher relatedness of workers to their sisters than to their own potential offspring, no longer seems feasible. ... But we've known all this for years!" If so, he and fellow evolutionary biologists have been very economical with their accounts of the failures. How else to account for the -- to many people, incomprehensible -- uproar at the time?

Evolutionary psychologist David Sloan Wilson, defending E. O. Wilson, scolded, "This degree of illiteracy about foundational issues is an embarrassment for the field of evolutionary biology." He is perhaps telling us more than he realizes. Neuroscientist Michael Gazzaniga, attempting to defend Wilson, offered:

In the end, Mr. Wilson comes down on the side of what is called multi-level selection -- the view that evolution involves a combination of gene selection, individual selection, kin selection, and group selection. Although he says his new theory opposes the idea of kin selection, in another sense he is simply maintaining that everybody is right. Genes are being selected to benefit the individual and their kin. Genes are also being selected that encourage the individual to participate in a group.

So if Wilson thinks everybody is right, why is Wilson so wrong? As John Gray put the matter in The New Republic, the debate is "an exercise in sectarian intellectual warfare of the kind that is so often fought in and around Darwinism." The uproar shows as well how flimsy the foundations of the Darwinian naturalist account of compassion, empathy, and self-sacrifice in humans have always been.

But that account meets a deeply felt need among naturalists. Generosity, we are told by one research group, leads to evolutionary success:

"When people act generously they feel it is almost instinctual, and indeed a large literature in evolutionary psychology shows that people derive happiness from being generous," [University of Pennsylvania biology Joshua] Plotkin said. "It's not just in humans. Of course social insects behave this way, but even bacteria and viruses share gene products and behave in ways that can't be described as anything but generous."

Elsewhere, we are told that altruism is just another form of manipulation, which greatly simplifies matters. Indeed, Northeastern University philosophy professor Rory Smead offers a Darwinian explanation of spite (why, counterintuitively, it is adaptive). Yet evolution is also moral, for it punishes the selfish and mean, according to two Michigan State University evolutionary biologists, who claim to disprove an earlier theory popularized in 2012.

We also learn that moral behavior is based on primitive disgust (not rational evaluation); altruism is really a form of sexual display; altruism is really just selfishness; a child must have a selfish motive for saving her sister's life; and why we don't (usually) hurt ourselves to hurt others.

Actually, it is far from clear that altruism selects for survival of selfish genes in humans. In addition to admirable self-sacrifice, there is also "pathological altruism" (often described as co-dependency), a common life- and health-endangering problem. In any event, as Oxford physiologist Denis Noble observes, "selfish genes" have no empirical basis in science. The idea, though "one of the most successful science metaphors ever invented," as David Dobbs tells us at Aeon, does not help us understand how actual genes work.

But never mind genetics, there is still neuroscience. Human brains, we are told, are "hardwired for empathy, friendship" (or they are wired to connect -- as Forbes puts it, "Study: To the Human Brain, Me Is We"). "Our self comes to include the people we feel close to," explains one University of Virginia research team.

This likely is the source of empathy, and part of the evolutionary process, [psychology professor James] Coan reasons.

But if the researchers wish merely to defend the thesis that humans are social rather than solitary, the word "hardwired" and its connotations are comically wrong. The word derives explicitly from devices that do not evolve. If the brain is indeed evolving, then nothing is hard-wired, though some types of experience and behavior may predominate over time and be reflected in brain organization. It is not clear, though, which came first.

A media-friendly approach is to study the animal mind. A cottage industry in this field is the study of primates. The empathy chimpanzees offer is, we are told, key to understanding human engagement. That said, some researcher think that humans are not as empathetic as apes because we are less likely to engage in contagious yawning. But still others say that we can't even predict the level of altruism in apes by their degree of kinship with humans.

"Humans and callitrichid monkeys acted highly altruistically and almost always produced the treats for the other group members. Chimpanzees, one of our closest relatives, however, only did so sporadically." Similarly, most other primate species, including capuchins and macaques, only rarely pulled the lever to give another group member food, if at all -- even though they have considerable cognitive skills.

It depends, these researchers find, on "cooperative breeding." "When our hominin ancestors began to raise their offspring cooperatively, they laid the foundation for both our altruism and our exceptional cognition." Maybe. Could they be cooperative before they were altruistic? On the whole, it is not clear what we can learn from altruism in primates.

Animals do show empathy. But that's part of the puzzle. Consider the monkey who rescued his electrocuted buddy. But then tortoises have been captured on film laboriously turning other upended tortoises back onto their feet.

The nature of the difficulty is apparent when we ask ourselves, what is the tortoise thinking? It is a reptile who cannot right itself, so how does it know enough to right another tortoise? When considering empathy in chimpanzees, we assume, with some justification, that the chimp who helps or shares has mental experiences analogous to those of humans. But if the famously slow-witted tortoise has such experiences as well, then there is not only no "Tree of Intelligence," there seems to be no Tree of Empathy either. Genetic closeness to humans may not have explanatory value for humans, any more than the supposed "selfish gene" does.

For human nature, evolution appears to be an endless well from which any lesson whatever can be drawn. And "evolutionary" explanations need not be informative; they need only be fully naturalist.