Thursday 31 August 2017
In Russia;A return to Bible burning?
Russia Declares the Bible “Extremist”
On August 17, 2017, the Vyborg City Court declared “extremist” the Russian version of the New World Translation of the Holy Scriptures, a Bible published by Jehovah’s Witnesses in numerous languages. * This decision marks the first time that the Bible has been banned in a country where the majority of its citizens claim to be Christian.
In late July 2017, the Vyborg City Court resumed its hearing of the case, which had been adjourned since April 2016 to allow time for an “expert study” of the Bible. The judge had ruled in favor of a claim filed by the Leningrad-Finlyandskiy Transport Prosecutor to appoint an “expert study” of whether to declare the New World Translation to be “extremist.” After numerous delays, the study was completed and was submitted to the court on June 22, 2017. The study concluded that the Bible is “extremist” literature, following the same pattern as previous court-appointed studies of the Witnesses’ publications by so-called experts.
“Expert Study” Based on Theological Beliefs, Not Facts
To justify its conclusion, the study went so far as to claim that the New World Translation is “not a Bible.” By making this claim, the study attempts to circumvent the Law on Counteracting Extremist Activity, which forbids declaring extremist sacred texts such as the Bible. Yaroslav Sivulskiy, a representative for the European Association of Jehovah’s Christian Witnesses, stated: “For as often as Russian authorities have misapplied the law on extremism to our religious worship, now they are trying to bypass it—claiming that the New World Translation is not a Bible so that they can declare it extremist. It’s just another example of how far Russian authorities will go to malign Jehovah’s Witnesses.”
The main pretext that the study used to support its claim that the New World Translation is “not a Bible” is that it renders God’s personal name represented by the Tetragrammaton * as “Jehovah.” Lawyers representing Jehovah’s Witnesses presented evidence to challenge this reasoning. The lawyers introduced to the court ten other Russian Bibles that use the name Jehovah, as well as poetry by Tsvetaeva and Pushkin and books by Kuprin, Goncharov, and Dostoyevsky and excerpts from other classic Russian literature. They also pointed to the 19th-century Russian-language Makarios Bible, produced by Orthodox translators, in which the name Jehovah occurs more than 3,500 times.
Additionally, the court allowed two experts to present testimony that the New World Translation is a version of the Holy Bible. At the trial on August 9, Professor Anatoliy Baranov, * a respected linguist, testified that differences in wording between the New World Translation and the synodal Bible do not mean that the New World Translation is not a Bible. Such differences are expected between different translations. To evaluate the accuracy of a modern Bible translation objectively, it must be compared to the original-language texts (in Hebrew, Aramaic, or Greek) rather than to an older translation in the same language.
During the court session on August 16, Mikhail Odintsov, * a religious scholar, testified that the text of the New World Translation does not differ in substance from other Russian Bibles and that it conforms to the generally accepted Bible canon. Regarding the use of God’s name, Mr. Odintsov confirmed that “Jehovah” has been used by other Russian translators, including the translators of the synodal Bible, where the divine name occurs some ten times.
The study also claimed that the New World Translation is not a Bible because it does not expressly say that it is one. However, Mr. Odintsov explained that the words “Scriptures” and “Holy Scriptures” are quite appropriate to describe the Bible.
New World Translation Hearing—Another Injustice Targeting Jehovah’s Witnesses
The Vyborg City Court’s decision is not yet in force, and the New World Translation has not been added to the Federal List of Extremist Materials. The Witnesses will appeal the decision to the Leningrad Regional Court within 30 days.
The decision to ban the Bible that Jehovah’s Witnesses use in worship is just the latest injustice in a more than decade-long, government-orchestrated campaign of persecution against them. This campaign culminated on July 17, when Russia’s Supreme Court confirmed its earlier ruling to criminalize the activity of Jehovah’s Witnesses in Russia. With this latest decision in the Vyborg City Court, Russia continues its unjust persecution of the Witnesses.
Truth in Translation
An earlier “expert study” that was used to refuse importation of the New World Translation into Russia said this: “To interpret sacred texts correctly one must have a thorough knowledge of the Sacred Tradition. The Orthodox Church is guided by a self-evident principle when explaining the meaning of God’s Word: The Holy Scriptures must be understood within the context of the Sacred Tradition.” According to this view, translation of the Holy Bible is subject to the primacy of church tradition.
In contrast, J. D. BeDuhn, Professor of Religious Studies at Northern Arizona University, evaluated the New World Translation (NW) with seven other modern Bible translations and concluded that “the NW emerges as the most accurate of the translations compared.” In explaining how Jehovah’s Witnesses came to produce what he regarded as the least biased of the translations, he remarked that the Jehovah’s Witnesses movement “really sought to re-invent Christianity from scratch.” He observed that this “resulted in the Jehovah’s Witnesses approaching the Bible with a kind of innocence, and building their system of belief and practice from the raw material of the Bible without predetermining what was to be found there. Some critics, of course, would say that the results of this process can be naive. But for Bible translation, at least, it has meant a fresh approach to the text, with far less presumption than that found in many Protestant translations.’”—See Truth in Translation: Accuracy and Bias in English Translations of the New Testament, by Jason David BeDuhn, pages 161-165.
Why Jehovah’s Witnesses publish the New World Translation
It is free and is available in more than 120 languages, in formats such as print, audio, and sign-language video and at jw.org
Time Line of Russia’s Case Against the New World Translation of the Holy Scriptures
August 17, 2017
Vyborg City Court grants the prosecutor’s claim to declare the New World Translation “extremist material”
August 9, 2017
Vyborg City Court resumes hearing on the case examining the New World Translation
June 6, 2017
Report from Center of Sociocultural Expert Studies concludes that the New World Translation “is not a Bible” and is “extremist” literature
December 23, 2016
Supreme Court of the Russian Federation upholds lower court decisions to seize all Bibles confiscated in July 2015
April 26, 2016
Vyborg City Court orders the Center of Sociocultural Expert Studies to examine the New World Translation for signs of “extremism”
March 15, 2016
Based on a claim filed by the prosecutor, hearings begin in the Vyborg City Court to declare the New World Translation “extremist”
December 29, 2015
Arbitration Court of St. Petersburg and the Leningrad Region denies Witnesses’ claim against illegal seizure of the Bibles
August 13, 2015
Vyborg Customs officials rule to seize all 2,016 Bibles in the July 13 shipment, claiming that they may contain signs of “extremism”
July 14, 2015
Vyborg Customs officials seize three copies of the Bible for an “expert study” to justify the seizure
July 13, 2015
Vyborg Customs officials stop a shipment containing only Russian-language copies of the New World Translation
Wednesday 30 August 2017
On Darwinism's explanatory shortcomings from an evolutionist.
Evolutionary Theorist Concedes: Evolution “Largely Avoids” Biggest Questions of Biological Origins
Evolution News | @DiscoveryCSC
Evolution News | @DiscoveryCSC
At this past November’s Royal Society meeting, “New Trends in Evolutionary Biology,” the distinguished Austrian evolutionary theorist Gerd B. Müller gave the first presentation. As we’ve noted before, it was a devastating one for anyone who wants to think that, on the great questions of biological origins, orthodox evolutionary theory has got it all figured out. Instead, Müller pointed to gaping “explanatory deficits” in the theory. Now the Royal Society’s journal Interface Focus offers a special issue collecting articles based on talks from the conference.
Let’s see what Dr. Müller has to say in an article titled, “Why an extended evolutionary synthesis is necessary.”A friend highlights the following paragraph.
As can be noted from the listed principles, current evolutionary theory is predominantly oriented towards a genetic explanation of variation, and, except for some minor semantic modifications, this has not changed over the past seven or eight decades. Whatever lip service is paid to taking into account other factors than those traditionally accepted, we find that the theory, as presented in extant writings, concentrates on a limited set of evolutionary explananda, excluding the majority of those mentioned among the explanatory goals above. The theory performs well with regard to the issues it concentrates on, providing testable and abundantly confirmed predictions on the dynamics of genetic variation in evolving populations, on the gradual variation and adaptation of phenotypic traits, and on certain genetic features of speciation. If the explanation would stop here, no controversy would exist. But it has become habitual in evolutionary biology to take population genetics as the privileged type of explanation of all evolutionary phenomena, thereby negating the fact that, on the one hand, not all of its predictions can be confirmed under all circumstances, and, on the other hand, a wealth of evolutionary phenomena remains excluded. For instance, the theory largely avoids the question of how the complex organizations of organismal structure, physiology, development or behavior — whose variation it describes — actually arise in evolution, and it also provides no adequate means for including factors that are not part of the population genetic framework, such as developmental, systems theoretical, ecological or cultural influences.
Uh, whoa. Or as our friend says, “BOOM.” Read that again. Müller says that “current evolutionary theory…largely avoids the question of how the complex organizations of organismal structure, physiology, development or behavior…actually arise in evolution.” But how stuff “actually arises” is precisely what most people think of when they think of “evolution.”
Says our friend, see Michael Behe in The Edge of Evolution, where Dr. Behe asks, “The big question, however, is not, ‘Who will survive, the more fit or the less fit?’ The big question is, ‘How do organisms become more fit?’” Müller concedes that conventional evolutionary thinking “largely avoids” this “big question.” Though expressed in anodyne terms, that is a damning indictment.
Here are some other gems from the paper.
A rising number of publications argue for a major revision or even a replacement of the standard theory of evolution [2–14], indicating that this cannot be dismissed as a minority view but rather is a widespread feeling among scientists and philosophers alike.
That could have appeared in a work from an intelligent design proponent. But wait, it gets even better:
Indeed, a growing number of challenges to the classical model of evolution have emerged over the past few years, such as from evolutionary developmental biology [16], epigenetics [17], physiology [18], genomics [19], ecology [20], plasticity research [21], population genetics [22], regulatory evolution [23], network approaches [14], novelty research [24], behavioural biology [12], microbiology [7] and systems biology [25], further supported by arguments from the cultural [26] and social sciences [27], as well as by philosophical treatments [28–31]. None of these contentions are unscientific, all rest firmly on evolutionary principles and all are backed by substantial empirical evidence.
“Challenges to the classical model” are “widespread” and “none…are unscientific.” Wow — file that one away for future reference.
More:
Sometimes these challenges are met with dogmatic hostility, decrying any criticism of the traditional theoretical edifice as fatuous [32], but more often the defenders of the traditional conception argue that ‘all is well’ with current evolutionary theory, which they see as having ‘co-evolved’ together with the methodological and empirical advances that already receive their due in current evolutionary biology [33]. But the repeatedly emphasized fact that innovative evolutionary mechanisms have been mentioned in certain earlier or more recent writings does not mean that the formal structure of evolutionary theory has been adjusted to them.
Orthodox Darwinists of the “All Is Well” school meet challenges with “dogmatic hostility”? Yep. We were aware.
Here he obliterates the notion, a truly fatuous extrapolation, that microevolutionary changes can explain macroevolutionary trends:
A subtler version of the this-has-been-said-before argument used to deflect any challenges to the received view is to pull the issue into the never ending micro-versus-macroevolution debate. Whereas ‘microevolution’ is regarded as the continuous change of allele frequencies within a species or population [109], the ill-defined macroevolution concept [36], amalgamates the issue of speciation and the origin of ‘higher taxa’ with so-called ‘major phenotypic change’ or new constructional types. Usually, a cursory acknowledgement of the problem of the origin of phenotypic characters quickly becomes a discussion of population genetic arguments about speciation, often linked to the maligned punctuated equilibria concept [9], in order to finally dismiss any necessity for theory change. The problem of phenotypic complexity thus becomes (in)elegantly bypassed. Inevitably, the conclusion is reached that microevolutionary mechanisms are consistent with macroevolutionary phenomena [36], even though this has very little to do with the structure and predictions of the EES. The real issue is that genetic evolution alone has been found insufficient for an adequate causal explanation of all forms of phenotypic complexity, not only of something vaguely termed ‘macroevolution’. Hence, the micro–macro distinction only serves to obscure the important issues that emerge from the current challenges to the standard theory. It should not be used in discussion of the EES, which rarely makes any allusions to macroevolution, although it is sometimes forced to do so.
This a major concession on the part of a major figure in the world of evolution theory. It’s a huge black eye to the “All Is Well” crowd. Who will tell the media? Who will tell the Darwin enforcers? Who will tell the biology students, in high school or college, kept in the dark by rigid Darwinist pedagogy?
Evolution has only “strengths” and no “weaknesses,” you say? Darwinian theory is as firmly established as “gravity, heliocentrism, and the round shape of the earth“? Really? How can anyone possibly maintain as much given this clear statement, not from any ID advocate or Darwin skeptic, not from a so-called “creationist,” but from a central figure in evolutionary research, writing in a journal published by the august scientific society once presided over by Isaac Newton, for crying out loud?
To maintain at this point that “All Is Well” with evolution you have to be in a state of serious denial.
Too tough for Darwinism?
Inside the Bizarre Genome of the World’s Toughest Animal
Tardigrades are sponges for foreign genes. Does that explain why they are famously indestructible?
The toughest animals in the world aren't bulky elephants, or cold-tolerant penguins, or even the famously durable cockroach. Instead, the champions of durability are endearing microscopic creatures called tardigrades, or water bears.
They live everywhere, from the tallest mountains to the deepest oceans, and from hot springs to Antarctic ice. They can even tolerate New York. They cope with these inhospitable environments by transforming into a nigh-indestructible state. Their adorable shuffling gaits cease. Their eight legs curl inwards. Their rotund bodies shrivel up, expelling almost all of their water and becoming a dried barrel called a “tun.” Their metabolism dwindles to near-nothingness—they are practically dead. And in skirting the edge of death, they become incredibly hard to kill.
In the tun state, tardigrades don't need food or water. They can shrug off temperatures close to absolute zero and as high as 151 degrees Celsius. They can withstand the intense pressures of the deep ocean, doses of radiation that would kill other animals, and baths of toxic solvents. And they are, to date, the only animals that have been exposed to the naked vacuum of space and lived to tell the tale—or, at least, lay viable eggs. (Their only weakness, as a researcher once told me, is “vulnerability to mechanical damage;” in other words, you can squish ‘em.)Scientists have known for centuries about the tardigrades’ ability to dry themselves out. But a new study suggests that this ability might have contributed to their superlative endurance in a strange and roundabout way. It makes them uniquely suited to absorbing foreign genes from bacteria and other organisms—genes that now pepper their genomes to a degree unheard of for animals.
Thomas Boothby from the University of North Carolina at Chapel Hill made this discovery after sequencing the first ever tardigrade genome, to better understand how they have evolved. Of the 700 species, his team focused on Hypsibius dujardini, one of the few tardigrades that’s easy to grow and breed in a lab.
At first, Boothby thought his team had done a poor job of assembling the tardigrade’s genome. The resulting data was full of genes that seemed to belong to bacteria and other organisms, not animals. “All of us thought that these were contaminants,” he says. Perhaps microbes had snuck into the samples and their DNA was intermingled with the tardigrade’s own.
But the team soon realized that these sequences are bona fide parts of the tardigrade’s genome.
By expelling their water, tardigrades have ironically become a sponge for foreign genes.
That wouldn't be unusual for bacteria, which can trade genes with each other as easily as humans might swap emails. But these “horizontal gene transfers” (HGT) are supposedly rare among animals. For the longest time, scientists believed that they didn't happen at all, and reported cases of HGT were met with extreme skepticism.
Recently, more and more examples have emerged. Ticks have antibiotic-making genes that came from bacteria. Aphids stole color genes from fungi. Wasps have turned virus genes into biological weapons. Mealybugs use genes from many different microbes to supplement their diets. A beetle kills coffee plants with a borrowed bacterial gene. Some fruit flies have entire bacterial genomes embedded in their own. And one group of genes, evocatively called Space Invaders, has repeatedly jumped between lizards, frogs, rodents, and more. But in all of these cases, it's usually one or two genes that have jumped across. At most, the immigrants make up 1 percent or so of their new native genome.
But Boothby found that foreign genes make up 17.5 percent of the tardigrade's genome—a full sixth. More than 90 percent of these come from bacteria, but others come from archaea (a distinct group of microbes), fungi, and even plants. “The number of them is pretty staggering,” he says.
Claims like these have been debunked before, so the team took extra care to confirm that the sequences did indeed come from outside sources.
For a start, they re-sequenced the genome using PacBio—a system that decodes single unbroken strands of DNA without first breaking them into smaller fragments. This revealed that the foreign genes are physically linked to the tardigrade’s native ones. They are all part of the same DNA strands, which means they couldn't have come from other contaminating microbes. They have also gained several features that are characteristic of animal genes, like an animal gloss over their fundamental bacterial character. John Logsdon from the University of Iowa, who studies genome evolution, is certainly convinced. “It’s a very interesting and technically robust paper,” he says.
So, how did these genes get into the tardigrade's genome in the first place? Boothby thinks that the answer lies in three quirks of tardigrade biology. First, they can dry themselves out, a process that naturally splits their DNA into small pieces. Second, they can stir back to life by rehydrating, during which their cells become leaky and able to take in molecules from the environment—including DNA. Finally, they are extremely good at repairing their DNA, sealing the damage that occurs when they dry out.
“So we think tardigrades are drying out, and their DNA is fragmenting along with the DNA of bacteria and organisms in the environment,” explains Boothby. “That gets into their cells when they rehydrate. And when they stitch their own genomes together, they may accidentally put in a bacterial gene.” By expelling their water, tardigrades have ironically become a sponge for foreign genes.
Do these genes do anything? So far, the team have found that the tardigrades switch on several of their borrowed genes, which, in other organisms, are involved in coping with stressful environments. That's pretty tantalizing: It suggests that these animals might owe at least part of their legendary durability to genetic donations from bacteria.
Boothby imagines something like this: Ancient tardigrades could dry themselves out to an extent, which allowed some foreign genes to enter their genome. If some of these genes made them more tolerant to drying, the animals would have become even more susceptible to horizontal gene transfers. “This positive feedback loop builds up over time,” says Boothby. “That’s speculation on our part.”
It certainly bolsters his case that another microscopic animal—a rotifer—can also dry itself out during tough times, and also shows signs of extensive horizontal gene transfer. Almost 10 percent of its genes came from foreign sources. Boothby’s team now wants to check for similar genetic infiltrations in other animals that tolerate desiccation, including some nematode worms, fish, and insects. They are also planning to gradually inactivate the tardigrade’s borrowed genes to see if that compromises its fabled invincibility.
Ralph Schill from the University of Stuttgart also points out that Hypsibius dujardini is something of a wuss among tardigrades, and isn't actually very good at surviving desiccation. Perhaps the genomes of its hardier relatives—the ones that shrug off extreme cold, extreme heat, and open vacuums—will yield even bigger surprises.
Tardigrades are sponges for foreign genes. Does that explain why they are famously indestructible?
The toughest animals in the world aren't bulky elephants, or cold-tolerant penguins, or even the famously durable cockroach. Instead, the champions of durability are endearing microscopic creatures called tardigrades, or water bears.
They live everywhere, from the tallest mountains to the deepest oceans, and from hot springs to Antarctic ice. They can even tolerate New York. They cope with these inhospitable environments by transforming into a nigh-indestructible state. Their adorable shuffling gaits cease. Their eight legs curl inwards. Their rotund bodies shrivel up, expelling almost all of their water and becoming a dried barrel called a “tun.” Their metabolism dwindles to near-nothingness—they are practically dead. And in skirting the edge of death, they become incredibly hard to kill.
In the tun state, tardigrades don't need food or water. They can shrug off temperatures close to absolute zero and as high as 151 degrees Celsius. They can withstand the intense pressures of the deep ocean, doses of radiation that would kill other animals, and baths of toxic solvents. And they are, to date, the only animals that have been exposed to the naked vacuum of space and lived to tell the tale—or, at least, lay viable eggs. (Their only weakness, as a researcher once told me, is “vulnerability to mechanical damage;” in other words, you can squish ‘em.)Scientists have known for centuries about the tardigrades’ ability to dry themselves out. But a new study suggests that this ability might have contributed to their superlative endurance in a strange and roundabout way. It makes them uniquely suited to absorbing foreign genes from bacteria and other organisms—genes that now pepper their genomes to a degree unheard of for animals.
Thomas Boothby from the University of North Carolina at Chapel Hill made this discovery after sequencing the first ever tardigrade genome, to better understand how they have evolved. Of the 700 species, his team focused on Hypsibius dujardini, one of the few tardigrades that’s easy to grow and breed in a lab.
At first, Boothby thought his team had done a poor job of assembling the tardigrade’s genome. The resulting data was full of genes that seemed to belong to bacteria and other organisms, not animals. “All of us thought that these were contaminants,” he says. Perhaps microbes had snuck into the samples and their DNA was intermingled with the tardigrade’s own.
But the team soon realized that these sequences are bona fide parts of the tardigrade’s genome.
By expelling their water, tardigrades have ironically become a sponge for foreign genes.
That wouldn't be unusual for bacteria, which can trade genes with each other as easily as humans might swap emails. But these “horizontal gene transfers” (HGT) are supposedly rare among animals. For the longest time, scientists believed that they didn't happen at all, and reported cases of HGT were met with extreme skepticism.
Recently, more and more examples have emerged. Ticks have antibiotic-making genes that came from bacteria. Aphids stole color genes from fungi. Wasps have turned virus genes into biological weapons. Mealybugs use genes from many different microbes to supplement their diets. A beetle kills coffee plants with a borrowed bacterial gene. Some fruit flies have entire bacterial genomes embedded in their own. And one group of genes, evocatively called Space Invaders, has repeatedly jumped between lizards, frogs, rodents, and more. But in all of these cases, it's usually one or two genes that have jumped across. At most, the immigrants make up 1 percent or so of their new native genome.
But Boothby found that foreign genes make up 17.5 percent of the tardigrade's genome—a full sixth. More than 90 percent of these come from bacteria, but others come from archaea (a distinct group of microbes), fungi, and even plants. “The number of them is pretty staggering,” he says.
Claims like these have been debunked before, so the team took extra care to confirm that the sequences did indeed come from outside sources.
For a start, they re-sequenced the genome using PacBio—a system that decodes single unbroken strands of DNA without first breaking them into smaller fragments. This revealed that the foreign genes are physically linked to the tardigrade’s native ones. They are all part of the same DNA strands, which means they couldn't have come from other contaminating microbes. They have also gained several features that are characteristic of animal genes, like an animal gloss over their fundamental bacterial character. John Logsdon from the University of Iowa, who studies genome evolution, is certainly convinced. “It’s a very interesting and technically robust paper,” he says.
So, how did these genes get into the tardigrade's genome in the first place? Boothby thinks that the answer lies in three quirks of tardigrade biology. First, they can dry themselves out, a process that naturally splits their DNA into small pieces. Second, they can stir back to life by rehydrating, during which their cells become leaky and able to take in molecules from the environment—including DNA. Finally, they are extremely good at repairing their DNA, sealing the damage that occurs when they dry out.
“So we think tardigrades are drying out, and their DNA is fragmenting along with the DNA of bacteria and organisms in the environment,” explains Boothby. “That gets into their cells when they rehydrate. And when they stitch their own genomes together, they may accidentally put in a bacterial gene.” By expelling their water, tardigrades have ironically become a sponge for foreign genes.
Do these genes do anything? So far, the team have found that the tardigrades switch on several of their borrowed genes, which, in other organisms, are involved in coping with stressful environments. That's pretty tantalizing: It suggests that these animals might owe at least part of their legendary durability to genetic donations from bacteria.
Boothby imagines something like this: Ancient tardigrades could dry themselves out to an extent, which allowed some foreign genes to enter their genome. If some of these genes made them more tolerant to drying, the animals would have become even more susceptible to horizontal gene transfers. “This positive feedback loop builds up over time,” says Boothby. “That’s speculation on our part.”
It certainly bolsters his case that another microscopic animal—a rotifer—can also dry itself out during tough times, and also shows signs of extensive horizontal gene transfer. Almost 10 percent of its genes came from foreign sources. Boothby’s team now wants to check for similar genetic infiltrations in other animals that tolerate desiccation, including some nematode worms, fish, and insects. They are also planning to gradually inactivate the tardigrade’s borrowed genes to see if that compromises its fabled invincibility.
Ralph Schill from the University of Stuttgart also points out that Hypsibius dujardini is something of a wuss among tardigrades, and isn't actually very good at surviving desiccation. Perhaps the genomes of its hardier relatives—the ones that shrug off extreme cold, extreme heat, and open vacuums—will yield even bigger surprises.
Reports of I.D's demise have proved premature.
Ten Myths About Dover: #10, The Intelligent Design Movement Died After the Dover Decision
Sarah Chaffee December 11, 2015 11:20 AM
Editor's note: The Kitzmiller v. Dover decision has been the subject of much media attention and many misinterpretations from pro-Darwin lobby groups. With the tenth anniversary of Kitzmiller approaching on December 20, Evolution News offers a series of ten articles debunking common myths about the case.
In December 2005, Judge John E. Jones ruled that intelligent design is not science, but religion. Critics predicted this would mean the end of the ID movement.
Expert witness Kevin Padian and Nick Matzke of the National Center for Science Education, for example, wrote:
It's over for the Discovery Institute. Turn out the lights. The fat lady has sung. The emperor of ID has no clothes. The bluff is over. Oh sure, they'll continue to pump out the blather. They'll find more funding, at least for a while, from some committed ideologue or another. But no one with any objectivity will take them seriously any longer as scientists.
Similarly, Matzke told Nature that "Intelligent design as a strategy is probably toast."
Barry Lynn, Executive Director of the Americans United for Separation of Church and State, predicted in September 2005, "I believe that we will be successful in the Dover case as far as it goes in the federal court system, and that it will prove to be the death knell for intelligent design as a serious issue confronting American school boards, period. I think this will be the last case."
But in December 2015, the ID movement is not only still alive -- it's thriving. This holds true across the board, in education, science, and the public dialogue.
Over the past decade, academic freedom and objective education on evolution have advanced, reflecting the growth of scientific research and scholarship critical of neo-Darwinian theory and supportive of intelligent design.
Currently, ten states have science standards, laws, or other provisions that support the rights of teachers and/or students to critically analyze evolution: Minnesota, Missouri, Mississippi, New Mexico, Pennsylvania, South Carolina, Alabama, Tennessee, Louisiana, and Texas. Louisiana passed its academic freedom policy, the Louisiana Science Education Act, in 2008. Tennessee followed in 2012. Neither of these policies has been challenged in court.
In Texas, students are required to examine "all sides of scientific evidence" for explanations and to "analyze and evaluate" scientific evidence regarding evolution. South Carolina expects students to "Summarize ways that scientists use data from a variety of sources to investigate and critically analyze aspects of evolutionary theory."
The cause of academic freedom has also seen significant victories. In one case, as we reported here, "[T]he University of Kentucky paid $125,000 to settle a lawsuit by astronomer Martin Gaskell who was wrongfully denied employment because he was perceived to be skeptical towards Darwinian evolution." Two other Darwin skeptics received settlements for discrimination. Applied Mathematics Letters retracted mathematician Granville Sewell's article critical of neo-Darwinism; a lawsuit followed, leading to a public apology and $10,000 payment to Sewell. After the California Science Center (CSC) cancelled the showing of an intelligent design film, Darwin's Dilemma, the American Freedom Alliance sued. The CSC paid $110,000 to avoid going to trial over the evidence that they discriminated. And the film Expelled drew over 1.1 million viewers to movie theaters to learn about discrimination against scientific dissenters from Darwinism.
Public outreach on intelligent design is also doing very well post-Dover. In 2009, Stephen Meyer published Signature in the Cell, which received praise from famed atheist philosopher Thomas Nagel, who named it "Book of the Year" in the respected Times Literary Supplement of London.
In 2013, Meyer published Darwin's Doubt which made the New York Times and Los Angeles Times bestseller lists. That book was endorsed by scientists including Harvard geneticist George Church and Mount Holyoke College paleontologist Mark McMenamin. UC Berkeley paleontologist Charles Marshall gave Darwin's Doubt a serious review in the top journal Science and participated in a radio debate with Meyer.
Illustra Media has released a slew of excellent video documentaries since Dover, including their Design of Life series: Metamorphosis, Flight, and Living Waters. Discovery Institute has produced a series of science videos, which have collectively received over half a million views on YouTube, including molecular machine animations of ATP Synthase and Kinesin, along with Journey Inside the Cell. Our latest video, Information Enigma, was released this fall.
The ruling sure hasn't stopped young people from getting excited about ID. Since Dover, over three hundred students -- many of them graduate students who are pursuing careers in the sciences -- have attended Discovery Institute's Summer Seminar on ID. Intelligent design is making an impact on the rising generation of scientists, which means far from being over, ID has excellent prospects for the future.
Finally and most importantly, science supporting ID continues to move forward. Several areas of research have seen groundbreaking progress, including work by the Evolutionary Informatics Lab (using computer models to test Darwinian evolution) and Biologic Institute (exploring evidence for ID in biology). To date, there are more than eighty peer-reviewed articles supportive of intelligent design, with over fifty of them published post-Dover. Casey Luskin has documented much of this work:
[T]he ID research community has published dozens of pro-ID peer-reviewed scientific papers advancing the scientific case for ID since Dover. This includes experimental research demonstrating the unevolvability of new proteins, as well as theoretical papers refuting alleged computer simulations of evolution, showing that intelligence is needed to produce new information.
This research is being presented at scientific conferences, such as a major ID research conference held at Cornell University in 2011, which led to the publication of the volume Biological Information: New Perspectives through World Scientific, a major mainstream scientific publishing house.
Even non-ID researchers have unwittingly and decisively confirmed ID predictions since Dover. In 2012, an international consortium of researchers published the ENCODE project, supporting the longstanding ID prediction that "junk DNA" would turn out to have function. Likewise, the burgeoning field of epigenetics has validated ID's claim that we will find new layers of information, code, and complex regulatory mechanisms within biology.
At the same time, Darwinian arguments have suffered. Brown University biologist Kenneth Miller's main argument at the Dover trial was that a stretch of DNA called the beta-globin pseudogene was "non-functional" junk, supposedly demonstrating our common ancestry with apes. In 2013, however, a paper in Genome Biology showed the "pseudogene" was functional, refuting his argument.
Likewise, in 2014 a favorite argument against pro-ID biochemist Michael Behe was overturned as chloroquine-resistance turned out to be a multimutation feature that is difficult to evolve.
Meanwhile, the past 10 years have seen a flood of peer-reviewed scientific papers critiquing core tenets of neo-Darwinian theory, and concessions from influential evolutionists that neo-Darwinism faces serious scientific criticisms. Couple this with major admissions from leading atheists like philosopher Thomas Nagel that ID arguments have merit and should be taken seriously, and the anti-ID intelligentsia is not happy.
What all this shows is that Michael Behe was correct when he said of Judge Jones's decision:
[It] does not impact the realities of biology, which are not amenable to adjudication. On the day after the judge's opinion, December 21, 2005, as before, the cell is run by amazingly complex, functional machinery that in any other context would immediately be recognized as designed. On December 21, 2005, as before, there are no non-design explanations for the molecular machinery of life, only wishful speculations and Just-So stories.
Given how quickly ID scholarship is moving forward in so many areas -- science, public policy, and culture -- we can only anticipate how much stronger ID will be twenty years after Dover.
Sarah Chaffee December 11, 2015 11:20 AM
Editor's note: The Kitzmiller v. Dover decision has been the subject of much media attention and many misinterpretations from pro-Darwin lobby groups. With the tenth anniversary of Kitzmiller approaching on December 20, Evolution News offers a series of ten articles debunking common myths about the case.
In December 2005, Judge John E. Jones ruled that intelligent design is not science, but religion. Critics predicted this would mean the end of the ID movement.
Expert witness Kevin Padian and Nick Matzke of the National Center for Science Education, for example, wrote:
It's over for the Discovery Institute. Turn out the lights. The fat lady has sung. The emperor of ID has no clothes. The bluff is over. Oh sure, they'll continue to pump out the blather. They'll find more funding, at least for a while, from some committed ideologue or another. But no one with any objectivity will take them seriously any longer as scientists.
Similarly, Matzke told Nature that "Intelligent design as a strategy is probably toast."
Barry Lynn, Executive Director of the Americans United for Separation of Church and State, predicted in September 2005, "I believe that we will be successful in the Dover case as far as it goes in the federal court system, and that it will prove to be the death knell for intelligent design as a serious issue confronting American school boards, period. I think this will be the last case."
But in December 2015, the ID movement is not only still alive -- it's thriving. This holds true across the board, in education, science, and the public dialogue.
Over the past decade, academic freedom and objective education on evolution have advanced, reflecting the growth of scientific research and scholarship critical of neo-Darwinian theory and supportive of intelligent design.
Currently, ten states have science standards, laws, or other provisions that support the rights of teachers and/or students to critically analyze evolution: Minnesota, Missouri, Mississippi, New Mexico, Pennsylvania, South Carolina, Alabama, Tennessee, Louisiana, and Texas. Louisiana passed its academic freedom policy, the Louisiana Science Education Act, in 2008. Tennessee followed in 2012. Neither of these policies has been challenged in court.
In Texas, students are required to examine "all sides of scientific evidence" for explanations and to "analyze and evaluate" scientific evidence regarding evolution. South Carolina expects students to "Summarize ways that scientists use data from a variety of sources to investigate and critically analyze aspects of evolutionary theory."
The cause of academic freedom has also seen significant victories. In one case, as we reported here, "[T]he University of Kentucky paid $125,000 to settle a lawsuit by astronomer Martin Gaskell who was wrongfully denied employment because he was perceived to be skeptical towards Darwinian evolution." Two other Darwin skeptics received settlements for discrimination. Applied Mathematics Letters retracted mathematician Granville Sewell's article critical of neo-Darwinism; a lawsuit followed, leading to a public apology and $10,000 payment to Sewell. After the California Science Center (CSC) cancelled the showing of an intelligent design film, Darwin's Dilemma, the American Freedom Alliance sued. The CSC paid $110,000 to avoid going to trial over the evidence that they discriminated. And the film Expelled drew over 1.1 million viewers to movie theaters to learn about discrimination against scientific dissenters from Darwinism.
Public outreach on intelligent design is also doing very well post-Dover. In 2009, Stephen Meyer published Signature in the Cell, which received praise from famed atheist philosopher Thomas Nagel, who named it "Book of the Year" in the respected Times Literary Supplement of London.
In 2013, Meyer published Darwin's Doubt which made the New York Times and Los Angeles Times bestseller lists. That book was endorsed by scientists including Harvard geneticist George Church and Mount Holyoke College paleontologist Mark McMenamin. UC Berkeley paleontologist Charles Marshall gave Darwin's Doubt a serious review in the top journal Science and participated in a radio debate with Meyer.
Illustra Media has released a slew of excellent video documentaries since Dover, including their Design of Life series: Metamorphosis, Flight, and Living Waters. Discovery Institute has produced a series of science videos, which have collectively received over half a million views on YouTube, including molecular machine animations of ATP Synthase and Kinesin, along with Journey Inside the Cell. Our latest video, Information Enigma, was released this fall.
The ruling sure hasn't stopped young people from getting excited about ID. Since Dover, over three hundred students -- many of them graduate students who are pursuing careers in the sciences -- have attended Discovery Institute's Summer Seminar on ID. Intelligent design is making an impact on the rising generation of scientists, which means far from being over, ID has excellent prospects for the future.
Finally and most importantly, science supporting ID continues to move forward. Several areas of research have seen groundbreaking progress, including work by the Evolutionary Informatics Lab (using computer models to test Darwinian evolution) and Biologic Institute (exploring evidence for ID in biology). To date, there are more than eighty peer-reviewed articles supportive of intelligent design, with over fifty of them published post-Dover. Casey Luskin has documented much of this work:
[T]he ID research community has published dozens of pro-ID peer-reviewed scientific papers advancing the scientific case for ID since Dover. This includes experimental research demonstrating the unevolvability of new proteins, as well as theoretical papers refuting alleged computer simulations of evolution, showing that intelligence is needed to produce new information.
This research is being presented at scientific conferences, such as a major ID research conference held at Cornell University in 2011, which led to the publication of the volume Biological Information: New Perspectives through World Scientific, a major mainstream scientific publishing house.
Even non-ID researchers have unwittingly and decisively confirmed ID predictions since Dover. In 2012, an international consortium of researchers published the ENCODE project, supporting the longstanding ID prediction that "junk DNA" would turn out to have function. Likewise, the burgeoning field of epigenetics has validated ID's claim that we will find new layers of information, code, and complex regulatory mechanisms within biology.
At the same time, Darwinian arguments have suffered. Brown University biologist Kenneth Miller's main argument at the Dover trial was that a stretch of DNA called the beta-globin pseudogene was "non-functional" junk, supposedly demonstrating our common ancestry with apes. In 2013, however, a paper in Genome Biology showed the "pseudogene" was functional, refuting his argument.
Likewise, in 2014 a favorite argument against pro-ID biochemist Michael Behe was overturned as chloroquine-resistance turned out to be a multimutation feature that is difficult to evolve.
Meanwhile, the past 10 years have seen a flood of peer-reviewed scientific papers critiquing core tenets of neo-Darwinian theory, and concessions from influential evolutionists that neo-Darwinism faces serious scientific criticisms. Couple this with major admissions from leading atheists like philosopher Thomas Nagel that ID arguments have merit and should be taken seriously, and the anti-ID intelligentsia is not happy.
What all this shows is that Michael Behe was correct when he said of Judge Jones's decision:
[It] does not impact the realities of biology, which are not amenable to adjudication. On the day after the judge's opinion, December 21, 2005, as before, the cell is run by amazingly complex, functional machinery that in any other context would immediately be recognized as designed. On December 21, 2005, as before, there are no non-design explanations for the molecular machinery of life, only wishful speculations and Just-So stories.
Given how quickly ID scholarship is moving forward in so many areas -- science, public policy, and culture -- we can only anticipate how much stronger ID will be twenty years after Dover.
Saturday 26 August 2017
On the NWT's rendering of Matthew 24:3
New World Translation - Parousia ("Presence") (Mt. 24:3)
Some New Testament Greek words, like modern English words, can have more than one meaning. When translating those words one must carefully determine as best as possible which meaning was intended by studying the context. It may still be impossible, at times, to be absolutely certain which meaning was intended. In cases like this it is to be expected that the translators' own understanding and interpretation will decide which meaning to use.
Many translator's understanding and interpretation of Mt. 24:3 is that when speaking of Christ's parousia, the Bible writers meant his visible, physical coming to earth. Therefore, most "orthodox" members of Christendom, want parousia to mean "coming" in all such instances. This does not make it so!
It is readily admitted by all NT Greek scholars that parousia "lit[erally means] a presence, para, with, and ousia, being" - W. E. Vine, p. 201, An Expository Dictionary of New Testament Words. No one disputes this literal meaning of parousia. Even Young's Analytical Concordance gives this as the literal meaning (" a being alongside, presence" - p. 188.)
As J. B. Rotherham (noted Bible scholar and translator of The Emphasized Bible) wrote in the appendix of his translation:
"in this edition the word parousia is uniformly rendered `presence' (`coming,' as a representative of this word, being set aside). .... The sense of `presence' is so plainly shewn by the contrast with `absence' (implied in 2 Co. x.10, and expressed in Ph. ii. 12) that the question naturally arises, - Why not always so render it? The more so, inasmuch as there is in [2 Peter 1:16] also, a peculiar fitness in our English word `presence.' This passage, it will be remembered, relates to our Lord's transformation upon the Mount. The wonderful manifestation there made was a display and sample of "presence" rather than of "coming." The Lord was already there; and being there he was transformed (cp. Mt. xvii. 2)" - p. 271. [Also cf. 2 Pet. 1:16, Young's Literal Translation; and Lattimore's translation]
In other words, context clearly demands "presence" in some instances. And, although context would allow either "presence" or "coming" in other instances, why should a translator insist on "coming" when the word in question does not even mean that in the first place? Rotherham's answer to this question was to render all uses of parousia into "presence" in his translation.
So it is the meaning "coming" that demands a clear need from context to establish its use instead of the more literal "presence"! If context clearly shows that "presence" cannot be properly used, then, and only then, we may properly consider a different meaning. (For more on this subject see The Watchtower, 15 August 1996, pp. 9-14 and Insight on the Scriptures, Vol. 2, article entitled "Presence" - also compare pp. 201 and 1271, W. E. Vine. Also compare the Ref Bible ('84) Appendix 5B on "parousia".)
Posted by Elijah Daniels
Darwinism's apologists are yet to get the memo re:free lunches.
Evolutionary Computing: The Invisible Hand of Intelligence
The best explanation for sophisticated engineering remains a skilled engineer II
Cell Vesicles Wear Sophisticated Coats
Evolution News & Views
Envision a day when self-driving cars make driving obsolete. Now, imagine a far-future day when you don't even have to get in the car. Instead, as you walk out the front door, a car assembles around you, lifts off the ground, floats you to your destination, then disassembles in anticipation of picking up the next passenger. Something like this actually happens in living cells. According to news from the European Molecular Biology Laboratory (EMBL):
Researchers at EMBL Heidelberg have produced detailed images of the intricate protein-coats that surround trafficking vesicles -- the "transport pods" that move material around within biological cells. The study, published today in Science, provides a new understanding of the complex machines that make up the cells' logistics network.
Vesicles are responsible for transporting molecules between the different compartments within a cell and also for bringing material into cells from outside. There are several types of vesicle: each has a specific type of coat which is made up of different proteins and assembles onto a membrane surrounding the vesicle. [Emphasis added.]
There are three models of "transport pods" that molecular biologists know about, each with its own specific coat proteins: Coat Protein 1 (COPI), Coat Protein 2 (COPII), and clathrin-coated vesicle (CCV). Each coat has its own proteins, adaptors, and functions. The first paper in Science looks in detail at COPI; but first, let's mention COPII. This type of vesicle takes proteins from the endoplasmic reticulum (ER), where they were assembled, to the Golgi apparatus where they will be packaged for delivery. This is called anterograde (forward) transport.
COPI is the reverse; it takes proteins from the Golgi back to the ER, or to different compartments of the Golgi. This is called retrograde (backward) transport. Surprisingly, the coat proteins on these vesicles are very different. COPII coats are made of four proteins that assemble with four-fold symmetry in a sequential manner, using separate adaptor proteins. COPI is more complicated. It has seven discrete proteins that come together simultaneously, forming complexes with triangular symmetry that include the adaptor function (i.e., allowing the complex to attach to the vesicle membrane).
The EMBL researchers pushed the envelope of cryoelectron microscopy to determine the nature of the "triads" called coatomers that make up the coat. They found that the seven proteins form two complexes that overlap into a layer 14 nanometers (nm) thick -- a substantial fraction of the typical 100-nm-diameter vesicle. A Perspective article in the same issue of Science says there's still a lot to learn about these coats: "it remains to be determined what specific roles these conformations play in the respective coat functions," Noble and Stagg write. What is known is that the coatomer triads make contact with up to four neighboring triads. This gives them structural flexibility that is distinct from the other coated vesicle types. The authors of the paper speculate about the reasons for this:
In existing models for clathrin and COPII vesicle coats, multiple identical subunits each make the same set of interactions with the same number of neighbors. Structural flexibility allows formation of vesicles from different total numbers of subunits. Based on these principles, both clathrin-like and COPII-like models have been proposed for the assembled COPI coat. We found instead that assembled coatomer can adopt different conformations to interact with different numbers of neighbors. By regulating the relative frequencies of different triad patterns in the COPI coat during assembly -- for example, by stabilizing particular coatomer conformations -- the cell would have a mechanism to adapt vesicle size and shape to cargoes of different sizes.
The paper includes color models and two motion animations of how the proteins fit together, protecting the cargo as it rides to its destination from organelle to organelle.
Clathrin Coats
A better-understood protein coat is made of clathrin. The name comes from a Latin word for lattice. Individual clathrin molecules, made of 3 heavy chains and 3 light chains, look like a three-spoked pinwheel called a triskelion. They fit together beautifully around the vesicle into a cage-like structure that resembles a geodesic dome. A beautiful animation from Harvard Medical School shows how numerous other proteins work with clathrin to form the vesicle coat and disassemble it after use, so the triskelia can be recycled. The vesicles can import and export molecules to the exterior of the cell or transport them within the cytoplasm. Clathrin proteins are also implicated in cell division, where they assist in arranging chromosomes on the spindle.
The animation will need an update, because something new was reported about clathrin-coated vesicles (CCV) and the pits (CCP) that form when the membrane invaginates to bring cargo in from outside. Another EMBL team, also reporting in Science, found that clathrin is more gymnastic than previously recognized.
Unlike as shown in the animation, the clathrin lattice forms flat on the inner membrane surface before invagination begins. Then, as the membrane folds inward, the lattice stretches and reconfigures itself, maintaining the same surface area but following the shape of the vesicle as it elongates. With its cargo safely inside, the vesicle pinches off and forms a sphere. The press release from EMBL expresses the surprise at the shape changes:
John Briggs, senior scientist at EMBL Heidelberg, said: "Our results were surprising, because the proteins have to undergo some complicated geometric transformations to go from a flat to a curved shape, which is why the second model was favoured by scientists for such a long time."
(The "second model", now falsified, refers to the idea that "clathrin assembles directly, assuming the shape of the membrane as it is drawn inwards.") The paper describes how the growing cage must change its geodesic structure as the vesicle forms:
In order to bend, flat lattices composed primarily of hexagons must acquire pentagons requiring extensive molecular rearrangements and removal of triskelia.
Why would the cell perform this more difficult gymnastic routine? The final paragraph offers some possible reasons:
Recruitment of clathrin before membrane bending provides a flat, dynamic array as a platform for cargo recruitment. This implies that the membrane to be internalized and the size of the future vesicle are not determined by clathrin geometry during assembly into a curved cage but rather are selected before invagination during cargo recruitment. Rapid clathrin exchange is consistent with a dynamically unstable lattice -- dynamic instability is a common property within networks of low-affinity protein interactions. It would allow for stochastic abortion of sites that initiate but fail to cross a growth- or cargo-mediated checkpoint before investing energy in membrane bending. During invagination, further exchange would allow clathrin reorganization and bending of the lattice into a defined cage that requires active disassembly.
One thing not mentioned in the articles is the rapidity of vesicle formation and disassembly. Suffice it to say that clathrin-coated endocytosis and exocytosis occur at the tips of nerve cells, where electrical signals must cross synapses. The vesicles form at one nerve, cross the synapse carrying the cargo, and are taken in by the next nerve cell in line. How long does it take your brain to feel pain from a stubbed toe? A lot of CCVs formed, crossed synapses, and disassembled in that very quick response!
Evolution or Design?
As usual, the articles and papers say very little about evolution. If mentioned at all, it was about the lack of evolution: e.g., "The archetypal protein coats COPI, COPII, and clathrin are conserved from yeast to human." Only the Perspective piece by Noble and Stagg ventures further:
Individual proteins in the three different coat protein complexes share similar folds and are proposed to be distant evolutionary relatives. Despite these similarities, the coats have evolved different functional mechanisms....
One possibility is that the proto-COPI coat evolved the four different linkages to expand the repertoire of geometries that the coat can accommodate and thus adapt to the secretory needs of the cell.
These suggestions amount to little more than after-the-fact assertions of evolutionary belief. One cannot invoke a blind, unguided process to say that it "evolved to" meet the needs of the cell. Darwinian natural selection has no foresight.
The complexity of these coats, and the accessory proteins that build them, attach them to vesicles and disassemble them, defy unguided evolutionary explanations. They exhibit irreducible complexity; they don't work unless all the protein parts are present simultaneously. They exhibit beauty in the way they organize into geometric shapes. The shapes, in turn, are dictated by digital codes in the genome that produce sequences that fold into building blocks. These building blocks, like the triskelion of clathrin, have no knowledge of the elegant geodesic domes that they will be fitted into. The triskelia are also blind to their attachment points that will be used by two other proteins that will disassemble the vesicle.
We see only glimpses of structures we don't yet fully understand. Why are separate coats needed for the three types of transport? What types of vesicles need the different coats? What specific advantages do the different coats provide for transport in one direction and not the other? What molecules need coated vesicles opposed to uncoated vesicles? What function does each protein in the coat provide?
Further research at higher resolution will undoubtedly yield more knowledge about vesicular transport. One thing is clear so far; the elegance of these systems, their ability to reshape their geometry as they grow, their adaptability to cargoes of many sizes, the rapidity of their action, and their conservation from yeast to humans all proclaim, "design!"
Evolution News & Views
Envision a day when self-driving cars make driving obsolete. Now, imagine a far-future day when you don't even have to get in the car. Instead, as you walk out the front door, a car assembles around you, lifts off the ground, floats you to your destination, then disassembles in anticipation of picking up the next passenger. Something like this actually happens in living cells. According to news from the European Molecular Biology Laboratory (EMBL):
Researchers at EMBL Heidelberg have produced detailed images of the intricate protein-coats that surround trafficking vesicles -- the "transport pods" that move material around within biological cells. The study, published today in Science, provides a new understanding of the complex machines that make up the cells' logistics network.
Vesicles are responsible for transporting molecules between the different compartments within a cell and also for bringing material into cells from outside. There are several types of vesicle: each has a specific type of coat which is made up of different proteins and assembles onto a membrane surrounding the vesicle. [Emphasis added.]
There are three models of "transport pods" that molecular biologists know about, each with its own specific coat proteins: Coat Protein 1 (COPI), Coat Protein 2 (COPII), and clathrin-coated vesicle (CCV). Each coat has its own proteins, adaptors, and functions. The first paper in Science looks in detail at COPI; but first, let's mention COPII. This type of vesicle takes proteins from the endoplasmic reticulum (ER), where they were assembled, to the Golgi apparatus where they will be packaged for delivery. This is called anterograde (forward) transport.
COPI is the reverse; it takes proteins from the Golgi back to the ER, or to different compartments of the Golgi. This is called retrograde (backward) transport. Surprisingly, the coat proteins on these vesicles are very different. COPII coats are made of four proteins that assemble with four-fold symmetry in a sequential manner, using separate adaptor proteins. COPI is more complicated. It has seven discrete proteins that come together simultaneously, forming complexes with triangular symmetry that include the adaptor function (i.e., allowing the complex to attach to the vesicle membrane).
The EMBL researchers pushed the envelope of cryoelectron microscopy to determine the nature of the "triads" called coatomers that make up the coat. They found that the seven proteins form two complexes that overlap into a layer 14 nanometers (nm) thick -- a substantial fraction of the typical 100-nm-diameter vesicle. A Perspective article in the same issue of Science says there's still a lot to learn about these coats: "it remains to be determined what specific roles these conformations play in the respective coat functions," Noble and Stagg write. What is known is that the coatomer triads make contact with up to four neighboring triads. This gives them structural flexibility that is distinct from the other coated vesicle types. The authors of the paper speculate about the reasons for this:
In existing models for clathrin and COPII vesicle coats, multiple identical subunits each make the same set of interactions with the same number of neighbors. Structural flexibility allows formation of vesicles from different total numbers of subunits. Based on these principles, both clathrin-like and COPII-like models have been proposed for the assembled COPI coat. We found instead that assembled coatomer can adopt different conformations to interact with different numbers of neighbors. By regulating the relative frequencies of different triad patterns in the COPI coat during assembly -- for example, by stabilizing particular coatomer conformations -- the cell would have a mechanism to adapt vesicle size and shape to cargoes of different sizes.
The paper includes color models and two motion animations of how the proteins fit together, protecting the cargo as it rides to its destination from organelle to organelle.
Clathrin Coats
A better-understood protein coat is made of clathrin. The name comes from a Latin word for lattice. Individual clathrin molecules, made of 3 heavy chains and 3 light chains, look like a three-spoked pinwheel called a triskelion. They fit together beautifully around the vesicle into a cage-like structure that resembles a geodesic dome. A beautiful animation from Harvard Medical School shows how numerous other proteins work with clathrin to form the vesicle coat and disassemble it after use, so the triskelia can be recycled. The vesicles can import and export molecules to the exterior of the cell or transport them within the cytoplasm. Clathrin proteins are also implicated in cell division, where they assist in arranging chromosomes on the spindle.
The animation will need an update, because something new was reported about clathrin-coated vesicles (CCV) and the pits (CCP) that form when the membrane invaginates to bring cargo in from outside. Another EMBL team, also reporting in Science, found that clathrin is more gymnastic than previously recognized.
Unlike as shown in the animation, the clathrin lattice forms flat on the inner membrane surface before invagination begins. Then, as the membrane folds inward, the lattice stretches and reconfigures itself, maintaining the same surface area but following the shape of the vesicle as it elongates. With its cargo safely inside, the vesicle pinches off and forms a sphere. The press release from EMBL expresses the surprise at the shape changes:
John Briggs, senior scientist at EMBL Heidelberg, said: "Our results were surprising, because the proteins have to undergo some complicated geometric transformations to go from a flat to a curved shape, which is why the second model was favoured by scientists for such a long time."
(The "second model", now falsified, refers to the idea that "clathrin assembles directly, assuming the shape of the membrane as it is drawn inwards.") The paper describes how the growing cage must change its geodesic structure as the vesicle forms:
In order to bend, flat lattices composed primarily of hexagons must acquire pentagons requiring extensive molecular rearrangements and removal of triskelia.
Why would the cell perform this more difficult gymnastic routine? The final paragraph offers some possible reasons:
Recruitment of clathrin before membrane bending provides a flat, dynamic array as a platform for cargo recruitment. This implies that the membrane to be internalized and the size of the future vesicle are not determined by clathrin geometry during assembly into a curved cage but rather are selected before invagination during cargo recruitment. Rapid clathrin exchange is consistent with a dynamically unstable lattice -- dynamic instability is a common property within networks of low-affinity protein interactions. It would allow for stochastic abortion of sites that initiate but fail to cross a growth- or cargo-mediated checkpoint before investing energy in membrane bending. During invagination, further exchange would allow clathrin reorganization and bending of the lattice into a defined cage that requires active disassembly.
One thing not mentioned in the articles is the rapidity of vesicle formation and disassembly. Suffice it to say that clathrin-coated endocytosis and exocytosis occur at the tips of nerve cells, where electrical signals must cross synapses. The vesicles form at one nerve, cross the synapse carrying the cargo, and are taken in by the next nerve cell in line. How long does it take your brain to feel pain from a stubbed toe? A lot of CCVs formed, crossed synapses, and disassembled in that very quick response!
Evolution or Design?
As usual, the articles and papers say very little about evolution. If mentioned at all, it was about the lack of evolution: e.g., "The archetypal protein coats COPI, COPII, and clathrin are conserved from yeast to human." Only the Perspective piece by Noble and Stagg ventures further:
Individual proteins in the three different coat protein complexes share similar folds and are proposed to be distant evolutionary relatives. Despite these similarities, the coats have evolved different functional mechanisms....
One possibility is that the proto-COPI coat evolved the four different linkages to expand the repertoire of geometries that the coat can accommodate and thus adapt to the secretory needs of the cell.
These suggestions amount to little more than after-the-fact assertions of evolutionary belief. One cannot invoke a blind, unguided process to say that it "evolved to" meet the needs of the cell. Darwinian natural selection has no foresight.
The complexity of these coats, and the accessory proteins that build them, attach them to vesicles and disassemble them, defy unguided evolutionary explanations. They exhibit irreducible complexity; they don't work unless all the protein parts are present simultaneously. They exhibit beauty in the way they organize into geometric shapes. The shapes, in turn, are dictated by digital codes in the genome that produce sequences that fold into building blocks. These building blocks, like the triskelion of clathrin, have no knowledge of the elegant geodesic domes that they will be fitted into. The triskelia are also blind to their attachment points that will be used by two other proteins that will disassemble the vesicle.
We see only glimpses of structures we don't yet fully understand. Why are separate coats needed for the three types of transport? What types of vesicles need the different coats? What specific advantages do the different coats provide for transport in one direction and not the other? What molecules need coated vesicles opposed to uncoated vesicles? What function does each protein in the coat provide?
Further research at higher resolution will undoubtedly yield more knowledge about vesicular transport. One thing is clear so far; the elegance of these systems, their ability to reshape their geometry as they grow, their adaptability to cargoes of many sizes, the rapidity of their action, and their conservation from yeast to humans all proclaim, "design!"
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