The epigenome v. Darwin.

Electric DNA, Circular RNA, and Other Epigenetic Wonders
Evolution News | @DiscoveryCSC

Upon completion of the Human Genome Project, scientists were baffled at the unexpectedly low number of genes. How could so few protein-coding genes (about 20,000) build a human being? It turned out that genes are only one part of the action. The old Central Dogma that viewed DNA as the master molecule, RNA as the messenger boy, and protein as the end product is long gone. Now we are beginning to see that there are three “-omes” that interact in complex ways with other molecules, including lipids and sugars. Everywhere they turn, scientists are seeing molecular wizardry at work. Here are just a few recent examples.

Another -Ome with a Code of Its Own

The Bellvitge Biomedical Research Institute (IDIBELL) of Barcelona, Spain, assumes we know about the genome and the epigenome. Now,  news from IDIBELL draws our attention to another “-ome” that is rising in significance: the transcriptome, referring to the “epigenetics of RNA”:

“It is well-known that sometimes DNA produces a RNA string but then this RNA does not originate the protein. Because in these cases the alteration is neither in the genome nor the proteome, we thought it should be in the transcriptome, that is, in the RNA molecule”, Dr. Esteller explains.”In recent years, we discovered that our RNA is highly regulated and if only two or three modifications at the DNA level can control it, there may be hundreds of small changes in RNA that control its stability, its intracellular localization or its maturation in living beings”. [Emphasis added.]
For example, some non-coding RNAs are now known to be ‘guardian RNAs’ according to the modifications on their bases or sugars with methyl groups that act as tags. The field of transcriptomics is only about five years old; “It will definitely be an exciting research stage for this and the next generation of scientists,” Dr. Esteller says. See our recent article “RNA Code Surpassing DNA in Complexity” for more about this epicentric karma running over the Central Dogma.

Electric DNA

Here’s another way that DNA carries information that is rather shocking: it conducts electricity. Science Magazine describes “DNA charge transport” as an unexpected signaling system between the code and its reading machines.

DNA charge transport provides an avenue for rapid, long-range signaling between redox-active moieties coupled into the DNA duplex. Several enzymes integral to eukaryotic DNA replication contain [4Fe4S] clusters, common redox cofactors. DNA primase, the enzyme responsible for initiating replication on single-stranded DNA, is a [4Fe4S] protein. Primase synthesizes short RNA primers of a precise length before handing off the primed DNA template to DNA polymerase α, another [4Fe4S] enzyme. The [4Fe4S] cluster in primase is required for primer synthesis, but its underlying chemistry has not been established. Moreover, what orchestrates primer handoff between primase and DNA polymerase α is not well understood.
In the paper, seven researchers from Caltech and Vanderbilt tell about experiments they ran to establish the existence of electrical charge transfers between the double helix and the molecular machines that read it and duplicate it. “We demonstrate that the oxidation state of the [4Fe4S] cluster in DNA primase acts as a reversible on/off switch for DNA binding,” they conclude. And it’s not alone. Because DNA can conduct charges over long distances, “Such redox signaling by [4Fe4S] clusters may play a wider role in polymerase enzymes to coordinate eukaryotic DNA replication.”

Circular RNA

Some RNAs fold into stable loops. We have them in our brains. What do they do? When discovered, they were considered non-coding. Now, however, scientists at Hebrew University have found that they can indeed code for proteins. The paper in Molecular Cell, “Translation of CircRNAs,” opens up a new window of functional possibilities for these oddball transcripts.

Circular RNAs (circRNAs) are abundant and evolutionarily conserved RNAs of largely unknown function. Here, we show that a subset of circRNAs is translated in vivo. By performing ribosome footprinting from fly heads, we demonstrate that a group of circRNAs is associated with translating ribosomes. Many of these ribo-circRNAs use the start codon of the hosting mRNA, are bound by membrane-associated ribosomes, and have evolutionarily conserved termination codons…. Altogether, our study provides strong evidence for translation of circRNAs, revealing the existence of an unexplored layer of gene activity.
“Evolutionarily conserved,” of course, means not evolved. A layman’s account in Science Daily explains the significance of this finding.

This discovery reveals an unexplored layer of gene activity in a type of molecule not previously thought to produce proteins. It also reveals the existence of a new universe of proteins not yet characterized.
One possible function for circRNAs is stable storage of protein-coding data for regions far from the nucleus. The tips of axons, for instance, can be too far away for quick access to genes they need. “As circRNAs are extremely stable, they potentially could be stored for a long time in compartments more distant to the cell’s body like axons of neuron cells,” Science Daily says. “There, the RNA molecules could serve as a reservoir for proteins being produced at a given time.” One scientist not connected about the research expressed excitement about it. “This is a very important, promising and timely discovery that gives an important hint of the function of these abundant yet uncharacterized RNAs.”

Interdependent Modifications

As geneticists explore the universe of epigenetic modifications, they have been unable to replicate some of them in a lab dish (in vitro). Now, a reason for this is coming to light. A paper in Nature begins with surprising statistics in the number of epigenetic modifications known. Then the authors tell how they discovered a case of “interdependent” modifications:

Nucleic acids undergo naturally occurring chemical modifications. Over 100 different modifications have been described and every position in the purine and pyrimidine bases can be modified; often the sugar is also modified. Despite recent progress, the mechanism for the biosynthesis of most modifications is not fully understood, owing, in part, to the difficulty associated with reconstituting enzyme activity in vitro. Whereas some modifications can be efficiently formed with purified components, others may require more intricate pathways. A model for modification interdependence, in which one modification is a prerequisite for another, potentially explains a major hindrance in reconstituting enzymatic activity in vitro. This model was prompted by the earlier discovery of tRNA cytosine-to-uridine editing in eukaryotes, a reaction that has not been recapitulated in vitro and the mechanism of which remains unknown.
Sure enough, they found a case in a microbe where one modification was a prerequisite to another modification. The mechanism appears to provide quality control by preventing catastrophic modifications to every matching spot on a whole genome.

Here’s a case we can relate to. The human antibody response system rapidly mutates sequences looking for matches to antigens. How does activation-induced cytidine deaminase (AID) deaminate the immunoglobulin receptors (IgG) without affecting the rest of the genome? The answer may involve interdependent modifications:

In mammalian cells, AID plays a critical role in antibody class diversification by specifically targeting the IgG receptor genes, while generally leaving the rest of the genome unblemished. While the mechanism of this enzyme has been elucidated, the basis for its programmed specificity towards only a fraction of the genome is still unclear. The work presented here provides a rationale for controlling mutagenic enzymes through their interaction with other partners, as has been suggested previously. This, of course, leads to the question of how such substrate specificities evolved. Our data suggest that the answer may relate to the ability of certain protein–protein interactions to provide secondary functions based on extreme mutual dependability, as illustrated here by the interplay between TRM140a and ADAT2/3.

ID advocates are certain to catch the phrases “programmed specificity” and “extreme mutual dependency” in support of their view, while chuckling at the Darwinists’ quandary about “how such substrate specificities evolved.” Their suggested solution only appears to dig a deeper hole. They never quite get around to telling readers how “extreme mutual dependability” came up with “secondary functions” by sheer dumb luck, such that the result only gives an appearance of “programmed specificity.” ID, on the other hand, provides a common-sense answer. Programming presupposes a programmer.

on miracles and the miraculous.:The Watchtower Society's commentary.

MIRACLES

Occurrences that excite wonder or astonishment; effects in the physical world that surpass all known human or natural powers and are therefore attributed to supernatural agency. In the Hebrew Scriptures the word moh·pheth′, sometimes translated “miracle,” also means “portent,” “wonder,” and “token.” (De 28:46; 1Ch 16:12, ftn) It is often used in conjunction with the Hebrew word ʼohth, meaning “sign.” (De 4:34) In the Greek Scriptures the word dy′na·mis, “power,” is rendered “powerful works,” “ability,” “miracle.”—Mt 25:15; Lu 6:19; 1Co 12:10, AT, KJ, NW, RS.

A miracle, amazing to the eye of the beholder, is something beyond his ability to perform or even to understand fully. It is also a powerful work, requiring greater power or knowledge than he has. But from the viewpoint of the one who is the source of such power, it is not a miracle. He understands it and has the ability to do it. Thus, many acts that God performs are amazing to humans beholding them but are merely the exercise of his power. If a person believes in a deity, particularly in the God of creation, he cannot consistently deny God’s power to accomplish things awe-inspiring to the eyes of men.—Ro 1:20; see POWER, POWERFUL WORKS.

Are miracles compatible with natural law?

Through study and observation, researchers have identified various uniform operations of things in the universe and have recognized laws covering such uniformity in natural phenomena. One such is ‘the law of gravity.’ Scientists admit the complexity and yet the reliability of these laws, and in calling them “laws” imply the existence of One who put such laws into force. Skeptics view a miracle as a violation of laws they accept as natural, irrevocable, inexorable; therefore, they say, a miracle never occurs. It is good to keep in mind that their attitude is that if it is not understandable and explainable to us as far as we discern these laws, it cannot happen.

However, capable scientists are becoming increasingly cautious about saying that a certain thing is impossible. Professor John R. Brobeck of the University of Pennsylvania stated: “A scientist is no longer able to say honestly something is impossible. He can only say it is improbable. But he may be able to say something is impossible to explain in terms of our present knowledge. Science cannot say that all properties of matter and all forms of energy are now known. . . . [For a miracle] one thing that needs to be added is a source of energy unknown to us in our biological and physiological sciences. In our Scriptures this source of energy is identified as the power of God.” (Time, July 4, 1955) Since this statement was made, further scientific development has made it more emphatic.

Scientists do not fully understand the properties of heat, light, atomic and nuclear action, electricity, or any of the forms of matter under even normal conditions. Even more deficient is their understanding of these properties under unusual or abnormal conditions. For example, it is relatively recently that extensive investigations have been made under conditions of extreme cold, but in this brief time, many strange actions of the elements have been observed. Lead, which is not an ideal electrical conductor, when immersed in liquid helium cooled to a temperature of −271° C. (−456° F.) strangely becomes a superconductor and a powerful electromagnet when a bar magnet is placed near it. At such supercold temperature helium itself appears to defy the law of gravity by creeping up the side of a glass beaker and over the edge, draining itself out of the container.—Matter, Life Science Library, 1963, pp. 68, 69.

This discovery is one of many that have astounded scientists, seeming to upset their former ideas. How, then, can anyone say that God violated his own laws in performing powerful works that seemed amazing and miraculous to men? Surely the Creator of the physical universe has perfect control of that which he created and can maneuver these things within the framework of the laws he has made inherent in them. (Job 38) He can bring about the condition necessary for the performance of these works; he can speed up, slow down, modify, or neutralize reactions. Or angels, with greater power than man, can do so in carrying out Jehovah’s will.—Ex 3:2; Ps 78:44-49.

Certainly the scientist is not superseding or going beyond physical laws when he applies more heat or cold, or more oxygen, and so forth, to speed up or slow down a chemical process. Nevertheless, skeptics challenge the Bible miracles, including the “miracle” of creation. These challengers are asserting, in effect, that they are familiar with all conditions and processes that ever took place. They are insisting that the operations of the Creator must be limited by the narrow confines of their understanding of the laws governing physical things.

This weakness on the part of scientists is acknowledged by a Swedish professor of plasma physics, who pointed out: “No one questions the obedience of the earth’s atmosphere to the laws of mechanics and atomic physics. All the same, it may be extremely difficult for us to determine how these laws operate with respect to any given situation involving atmospheric phenomena.” (Worlds-Antiworlds, by H. Alfvén, 1966, p. 5) The professor applied this thought to the origin of the universe. God established the physical laws governing the earth, sun, and moon, and within their framework men have been able to do marvelous things. Surely God could bring the laws to play so as to produce a result unexpected by humans; it would present no problem for him to split the Red Sea so that “the waters were a wall” on each side. (Ex 14:22) Though, to man, walking on water is an astounding feat, with what ease it could be accomplished in the power of “the One who is stretching out the heavens just as a fine gauze, who spreads them out like a tent in which to dwell.” Further, God is described as creating, and having control of, all the things in the heavens, and it is said that “due to the abundance of dynamic energy, he also being vigorous in power, not one of them is missing.”—Isa 40:21, 22, 25, 26.

Since the acknowledgment of the existence of law, such as the law of gravity, presupposes a lawmaker of surpassing, superhuman intelligence and power, why question his ability to do marvelous things? Why try to limit his operation to the infinitesimally narrow scope of man’s knowledge and experience? The patriarch Job describes the darkness and foolishness into which God lets these go who thus pit their wisdom against his.—Job 12:16-25; compare Ro 1:18-23.

God’s Adherence to His Moral Law. The God of creation is not a whimsical God, unreliably violating his own laws. (Mal 3:6) This fact can be seen in God’s adherence to his moral laws, which are in harmony with his physical laws but are higher and grander than they are. In justice he cannot condone unrighteousness. “You are too pure in eyes to see what is bad; and to look on trouble you are not able,” says his prophet. (Hab 1:13; Ex 34:7) He expressed his law to Israel: “Soul will be for soul, eye for eye, tooth for tooth, hand for hand, foot for foot.” (De 19:21) When he desired to forgive helpless, repentant men for the sin that is the cause of their dying, God had to have a legal basis if he was going to adhere to his law. (Ro 5:12; Ps 49:6-8) He proved to be strict in his adherence to law, going to the point of sacrificing his only-begotten Son as a ransom for the sins of mankind. (Mt 20:28) The apostle Paul points out that, “through the release by the ransom paid by Christ Jesus,” Jehovah was able to “exhibit his own righteousness . . . that he might be righteous even when declaring righteous the man that has faith in Jesus.” (Ro 3:24, 26) If we appreciate that God, out of respect for his moral laws, did not hold back from sacrificing his beloved Son, certainly we can reason that he would never need to “violate” his physical laws to carry out anything desired within physical creation.

Contrary to Human Experience? Merely to assert that miracles did not take place does not prove that they did not. The truthfulness of any recorded event of history may be challenged by someone living today, because he did not experience it and there are now no living eyewitnesses to testify to it. But that does not change the facts of history. Some object to the accounts about miracles because, they say, they are contrary to human experience, that is, human experience that they acknowledge as true from observation, books, and so forth. If scientists actually took this position in practice, there would be far less research and development of new things and processes on their part. They would not, for instance, continue research on the curing of “incurable” diseases, or on space travel to the planets or even farther into the universe. But they do investigate and sometimes bring mankind into definitely new experiences. What is accomplished today would astonish men of ancient times, and a good share of modern mankind’s common daily experiences would be viewed by them as miracles.

Not “Explained Away” by Logic. Some opponents of the Bible account hold that Bible miracles can be scientifically and logically explained as merely natural happenings and that the Bible writers merely attributed these happenings to God’s intervention. It is true that such things as earthquakes were employed. (1Sa 14:15, 16; Mt 27:51) But this in itself does not prove that God did not take a hand in these events. Not only were the things powerful works in themselves (for example, the aforementioned earthquakes) but also the timing was such as to make the odds overwhelming against any chance happening. For illustration: Some have contended that the manna provided for the Israelites can be found in the desert as a sweet, sticky exudation on tamarisk trees and on bushes. Even if this doubtful contention were true, the provision of it for Israel is still a miracle because of its timing, for it did not appear on the ground on the seventh day of each week. (Ex 16:4, 5, 25-27) Furthermore, whereas it bred worms and stank if kept over until the next day, it did not do so when kept over for food on the Sabbath. (Ex 16:20, 24) It might also be said that the description of this manna as an exudation from trees does not seem to agree fully with the Bible description of the manna. The Bible manna was found on the ground and it melted in the hot sun; it could be pounded in a mortar, ground in a mill, boiled, or baked.—Ex 16:19-23; Nu 11:8; see MANNA.

Credibility of the Testimony. The Christian religion is interwoven with the miracle of the resurrection of Jesus Christ. (1Co 15:16-19) The evidence that it took place was not weak but powerful—there were more than 500 eyewitnesses to testify that it did take place.—1Co 15:3-8; Ac 2:32.

The motive of the persons who accepted the miracle of Jesus’ resurrection as true must also be considered. Many persons have experienced persecution and death for their beliefs—religious, political, and otherwise. But the Christians who so suffered received no material or political gain. Rather than get power, wealth, and prominence, they often suffered the loss of all these things. They preached Jesus’ resurrection but did not use any form of violence to promote their beliefs or to defend themselves. And one reading their arguments can see that they were reasonable persons, not fanatics. They lovingly tried to help their fellowmen.

Characteristics of Bible Miracles. Noteworthy characteristics of the Biblical miracles are their open and public nature, their simplicity, their purpose and motive. Some were performed in private or before small groups (1Ki 17:19-24; Mr 1:29-31; Ac 9:39-41), but often they were public, before thousands or even millions of observers. (Ex 14:21-31; 19:16-19) Jesus’ works were open and public—there was no secrecy attached to them; and he healed all who came to him, not failing on the pretext that some lacked sufficient faith.—Mt 8:16; 9:35; 12:15.

Simplicity marked both miraculous cures and control over the elements. (Mr 4:39; 5:25-29; 10:46-52) In contrast to magical feats accomplished with special props, staging, lighting, and ritual, Biblical miracles generally were performed without outward display, frequently in response to a chance encounter, a request, and that on the public street or in an unprepared place.—1Ki 13:3-6; Lu 7:11-15; Ac 28:3-6.

The motive of the individual performing the miracle was not for the selfish prominence of the individual or to make anyone wealthy, but it was primarily to glorify God. (Joh 11:1-4, 15, 40) Miracles were not mysterious acts performed merely to satisfy curiosity and to mystify. They always helped others, sometimes directly in a physical way and always in a spiritual way, turning persons to true worship. Just as “the bearing witness to Jesus is what inspires prophesying [“is the spirit of the prophecy,” ftns],” so, too, many of the miracles pointed to Jesus as God’s sent one.—Re 19:10.

Bible miracles involved not only animate things but also inanimate ones, such as calming the wind and sea (Mt 8:24-27), stopping and starting rain (1Ki 17:1-7; 18:41-45), and changing water into blood or into wine (Ex 7:19-21; Joh 2:1-11). They also included physical cures of all types, such as “incurable” leprosy (2Ki 5:1-14; Lu 17:11-19) and blindness from birth. (Joh 9:1-7) This great variety of miracles argues for their credibility as backed by the Creator, for it is logical that only the Creator could exercise influence in all areas of human experience and over all forms of matter.

Purpose in Early Christian Congregation. Miracles served a number of important purposes. Most basic, they helped to establish or confirm the fact that a man was receiving power and support from God. (Ex 4:1-9) Both with Moses and Jesus people drew this correct conclusion. (Ex 4:30, 31; Joh 9:17, 31-33) Through Moses, God had promised a coming prophet. Jesus’ miracles helped observers to identify him as that one. (De 18:18; Joh 6:14) When Christianity was young, miracles worked in conjunction with the message to help individuals to see that God was behind Christianity and had turned from the earlier Jewish system of things. (Heb 2:3, 4) In time miraculous gifts present in the first century would pass away. They were needed only during the infancy of the Christian congregation.—1Co 13:8-11.

In reading the history of the Acts of Apostles, we see that Jehovah’s spirit was working mightily, speedily, forming congregations, getting Christianity firmly established. (Ac 4:4; chaps 13, 14, 16-19) In the few short years between 33 and 70 C.E., thousands of believers were gathered in many congregations from Babylon to Rome, and perhaps even farther west. (1Pe 5:13; Ro 1:1, 7; 15:24) It is worthy of note that copies of the Scriptures then were few. Usually only the well-to-do possessed scrolls or books of any sort. In pagan lands there was no knowledge of the Bible or the God of the Bible, Jehovah. Virtually everything had to be done by word of mouth. There were no Bible commentaries, concordances, and encyclopedias readily at hand. So the miraculous gifts of special knowledge, wisdom, speaking in tongues, and discernment of inspired utterances were vital for the congregation then. (1Co 12:4-11, 27-31) But, as the apostle Paul wrote, when those things were no longer needed, they would pass away.

A Different Situation Today. We do not see God performing such miracles by the hands of his Christian servants today, because all needed things are present and available to the literate population of the world, and to help those who cannot read but who will listen, there are mature Christians who have knowledge and wisdom gained by study and experience. It is not necessary for God to perform such miracles at this time to attest to Jesus Christ as God’s appointed deliverer, or to provide proof that He is backing up His servants. Even if God were to continue to give his servants the ability to perform miracles, that would not convince everyone, for not even all the eyewitnesses of Jesus’ miracles were moved to accept his teachings. (Joh 12:9-11) On the other hand, scoffers are warned by the Bible that there will yet be stupendous acts of God performed in the destruction of the present system of things.—2Pe 3:1-10; Re chaps 18, 19.

In conclusion, it may be said that either those who deny the existence of miracles do not believe there is an invisible God and Creator or they believe that he has not exercised his power in any superhuman way since creation. But their unbelief does not make the Word of God of no effect. (Ro 3:3, 4) The Biblical accounts of God’s miracles and the good purpose that they accomplished, always in harmony with the truths and principles found in his Word, instill confidence in God. They give strong assurance that God cares for mankind and that he can and will protect those who serve him. The miracles provide typical patterns, and the record of them builds faith that God will, in the future, intervene in a miraculous way, healing and blessing faithful humankind.—Re 21:4.

Is political atheism's calling political theism violent the pot calling the kettle black?

A Dehumanizing Ideology Unsurprisingly Catalyzes Violence
Michael Egnor

Evolutionary biologist Jerry Coyne, who denies the existence of free will and has endorsed social control of human beings that is hardly distinguishable from animal training, insists that religion is a significant motivation for violence.

Coyne, who claims that in human affairs "reason is no different from a kick," is of course right, in a sense. There is no question that religious belief can motivate and has motivated violence. We are currently experiencing violence in many parts of the world motivated by Islamic beliefs, and historically many faiths and ideologies have at times motivated wars and repression.

He writes:

...[O]ver at [Why Evolution Is True] we don't find it so hard to understand that religious beliefs could motivate violence. After all, other ideologies like Communism or Nazism, are well known for promoting violence... Wed that to religion's claim of absolute truth and its promulgation of a moral code, and you have an automatic recipe for "othering".

Yet Coyne omits candid discussion of the violence -- the extraordinary violence -- caused by atheist ideology during the past century. He refers to "Communism," but if we are to single out "religion" for violence, we must compare it to "irreligion," not merely to "Communism." And it is precisely the metaphysical commitments Coyne has championed that have catalyzed atheist violence -- the denial of an objective moral law, the denial of eternal accountability for transgressions, the reduction of human beings to animals or even to meat robots, deprived of free will or of any claim to human exceptionalism. These are all tenets of atheist belief, and Coyne himself is one of the loudest salesman for the dehumanizing ideology inherent to atheism.

Just how violent and repressive can atheism be? The most inhuman tactic of Islamic terrorists -- suicide bombing -- was first employed by atheist Tamil Tigers in Sri Lanka. John Gray in the Guardian notes:

Islamists owe as much, if not more, to the far left, and it would be more accurate to describe many of them as Islamo-Leninists. Islamist techniques of terror also have a pedigree in secular revolutionary movements. The executions of hostages in Iraq are copied in exact theatrical detail from European "revolutionary tribunals" in the 1970s, such as that staged by the Red Brigades when they murdered the former Italian prime minister Aldo Moro in 1978.

Many of the inhuman tactics used by Islamists today were first used systematically in modern times by the atheist Left. In the past century, a number of nations have been governed by explicitly atheist governments. Atheist governments murdered more than 100 million people during the 20th century. See here for a comparison of violence and political repression between nations with established Christian churches or cultures, Islamic nations, and nations governed by atheist ideologies during the 20th century.

Looking at modern history, we see: Christian culture creates reasonable and tolerant democracies. Islamic regimes create repressive theocracies. Atheist regimes create totalitarian hellholes.

The denial of free will and the other anti-human inferences inherent to atheism are not merely theoretical affronts to humanity.

The fact is that atheism is the most violent ideology in the 20th century, and given its short run and unprecedented rate of state-sanctioned murder, it is also the most violent and repressive ideology in human history.

Ps. almost all instances of so called religious violence when carefully examined turn out to be political violence.Politics is in fact a requirement for the weaponisation of religion.That is why throughout history members of politicised religion are far more likely to kill there co religionists for political/ecomomic reasons than unbelievers or other believers for purely religious reasons in fact they will often join with unbelievers/other believers with whom they share common political aspirations/ideologies against fellow believers.That may explain why atheistic regimes have outdone political theists in state sanctioned violence for the atheist politics is religion.

On the struggle to publish Jehovah's word in the 16th century.:The Watchtower society's commentary.

Lefèvre d’Étaples—He Wanted the Common People to Know God’s Word

ON A Sunday morning in the early 1520’s, the inhabitants of Meaux, a small town near Paris, could not believe what they heard in church. They had listened to the reading of the Gospels in their mother tongue—in French instead of Latin!

The Bible translator who was behind this initiative, Jacques Lefèvre d’Étaples (Latin, Jacobus Faber Stapulensis), later wrote to a close friend: “You can scarcely imagine with what ardor God is moving the minds of the simple [people] in some places to embrace his Word.”

At that time, the Catholic Church and the theologians in Paris opposed the use of translations of the Bible in common languages. So, what moved Lefèvre to translate the Bible into French? And how did he manage to help the common people to understand God’s Word?

SEEKING THE TRUE MEANING OF THE SCRIPTURES

Before becoming a Bible translator, Lefèvre had dedicated himself to restoring the original meaning of classical works of philosophy and theology. He noted that ancient texts had often been corrupted by centuries of misleading renderings and errors. In his search for the true meaning of ancient writings, he started studying closely the standard Bible of the Catholic Church, the Latin Vulgate.

His earnest study of the Scriptures led him to the conclusion that “study of divine truth alone promises . . . the highest happiness.” Therefore, Lefèvre turned away from studying philosophy and devoted all his energy to translating the Bible.

In 1509, Lefèvre published a comparative study of five different Latin versions of the Psalms, * including his own correction of the Vulgate. Unlike theologians of his time, he endeavored to find the “natural sense” of Bible passages. His method of interpreting the Scriptures had a strong influence on other Bible scholars and reformers.Born a Catholic, Lefèvre was convinced that a renewal of the church could be possible only if the Scriptures were properly taught to ordinary people. But how would the common people benefit from the Scriptures at a time when those sacred writings were mostly in Latin?

A BIBLE TRANSLATION ACCESSIBLE TO ALL.

Lefèvre’s deep love for God’s Word made him determined to make it accessible to the greatest number of people. To achieve that goal, in June 1523, he published a French translation of the Gospels in two pocket-size volumes. This small format—which cost half the price of a standard edition—made it easier for people with little means to obtain a copy of the Bible.

 The response of the common people was immediate and enthusiastic. Both men and women were so eager to read Jesus’ words in their mother tongue that the first 1,200 copies printed were out of stock after just a few months.

A COURAGEOUS STAND FOR THE BIBLE

In the introduction to the Gospels, Lefèvre explained that he had translated them into French so that “the simple members” of the church “can be as certain of evangelical truth as those who have it in Latin.” But why was Lefèvre so eager to help the common people to get back to what the Bible teaches?

Lefèvre was well-aware that human teachings and philosophy had corrupted the Catholic Church. (Mark 7:7; Colossians 2:8) And he was convinced that the time had arrived for the Gospels to be “purely proclaimed throughout the world, so that people may no longer be led astray by alien doctrines of men.”

Lefèvre also endeavored to expose the faulty arguments of those who opposed the translation of the Bible into French. He denounced their hypocrisy, saying: “How will they teach [the people] to observe all that Jesus Christ commanded, if they are quite unwilling that the simple folk should see and read the Gospel of God in their own language?”—Romans 10:14.

 Not surprisingly, theologians at the University of Paris—the Sorbonne—soon attempted to silence Lefèvre. In August 1523, they objected to vernacular translations of and commentaries on the Bible, considering them “harmful to the Church.” Had it not been for the intervention of French King Francis I, Lefèvre would have been condemned as a heretic.

THE “SILENT” TRANSLATOR COMPLETED HIS WORK

Lefèvre did not allow heated debates on his works to distract him from translating the Bible. In 1524, after completing his translation of the Greek Scriptures (the so-called New Testament), he released a French version of the Psalms so that believers might pray “with greater devotion and deeper feeling.”

Theologians at the Sorbonne lost no time in going through Lefèvre’s works with a fine-tooth comb. They soon ordered that his translation of the Greek Scriptures be burned publicly, and they denounced some other writings as “favoring the heresy of Luther.” When the theologians summoned him to justify his views, Lefèvre decided to remain “silent” and fled to Strasbourg. There, he discreetly continued translating the Bible. Even though some considered his stance to be lacking courage, he believed that it was the best way to respond to those who had no appreciation for the precious “pearls” of Bible truth.—Matthew 7:6.

Almost one year after his flight, King Francis I appointed Lefèvre tutor of his four-year-old son, Charles. This assignment gave Lefèvre plenty of time to finish his translation of the Bible. In 1530, his translation of the complete Bible was printed outside France, in Antwerp, with the approval of Emperor Charles V. *

GREAT HOPES, LAST REGRETS

Throughout his life, Lefèvre hoped that the church would abandon human traditions and return to the pure knowledge of the Scriptures. He strongly believed in “the right, indeed, the duty, of every Christian to read and learn the Bible personally.” That is why he worked so hard to make the Bible accessible to all. Although his desire to see the church reform itself failed to materialize, Lefèvre’s legacy is undisputed—he helped the common people to know God’s Word.

How Martin Luther Was Influenced by Lefèvre

Martin Luther was still an obscure monk when he carefully studied Lefèvre’s works. The young Luther noted that Lefèvre expounded Biblical passages in a clear and simple way, without resorting to fancy allegories as did the scholars of his time. Lefèvre’s method of interpretation exerted a strong influence on Luther as well as on Bible translator William Tyndale and Reformer John Calvin. Although Lefèvre remained a Catholic until his death, his works marked a turning point in Bible translation and paved the way to the Reformation.

On chemical equilibrium.

A brief history of the Olympics.

On how practice makes perfect.

File under "Well said" XLIX

As we must account for every idle word, so we must for every idle silence.

BENJAMIN FRANKLIN

On a Titan's titan.

Today's science fiction is tomorrow's science fact?

Socrates on democracy v. demagoguery.

A Brief history of theistic monism

By Peter Clarke

Tom Chivers' lively description of his interview with neuroscience professor Patrick Haggard highlights the fundamental question of whether brain research undermines our belief in free will and responsibility. Our brains determine our thinking and behaviour, and our neurons obey the laws of physics and chemistry, so how are we different from neural machines? As Tom points out in a second article, a lot depends on how you define free will.
On this issue, philosophers are divided into two camps: “libertarians“and “compatibilists”. For libertarians, free will is almost by definition incompatible with brain determinism. They argue from our experience of making choices that somewhere in the brain there must be indeterminate events. Most modern libertarians, including Robert Kane, invoke Heisenbergian uncertainty as the source of brain indeterminism, despite scepticism among scientists. In contrast, compatibilists argue for a different definition of free will. They make the distinction between external and internal constraints. The difference is illustrated by the following two excuses: “It’s not my fault I broke the window, my brother pushed me”, and “It’s not my fault I broke the window, my brain caused me to do it”.
Few people would accept the second excuse, which seems strange at best. If my brain did not cause me to break the window, I was certainly not responsible, so how can brain causation be an excuse? Of course, simple arguments like this are only a start in a complicated debate, but compatibilists are currently in the majority in claiming that the “varieties of free will worth wanting” (to quote Dennett) do not require indeterminate events in the brain. The debate is by no means over.
Our attitude to the free will question is intimately linked to the dualism-monism debate. Dualists believe that there are two separate entities, soul (or mind) and brain, and most maintain that they somehow interact, following Descartes. Monists deny a separate soul, saying that everything is matter. This links in with the question of free will, because if you believe in a separate nonphysical soul/mind that somehow influences the brain, you must assume that conventional physical and chemical forces do not completely determine brain function.
This debate is sometimes caricatured as a rearguard defense by religious or spiritually minded traditionalists against the attacks of modern science and atheistic philosophy, but there is not such a neat dividing line. The first philosophers to invoke physical indeterminism as necessary for free will were the materialists Epicurus and Lucretius, who denied life after death and supernatural intervention in the world. Judaism was monistic throughout the Old Testament era, and early Christianity appears likewise.

It is true that neo-Platonist dualism was incorporated into the philosophies of many leading Christian thinkers including Augustine, Luther and Calvin, but over the last couple of centuries these were opposed by equally Christian monists such as Joseph Priestley, the nonconformist minister famed for isolating oxygen, who argued that dualism was a contamination of biblical Christianity by Platonic philosophy. Over the last 60 years monistic philosophy of mind has gained ground among Christians because of increasing evidence that the biblical conception of man is monist, not dualist. For example, the Hebrew word Nefesh, traditionally translated as “soul”, does not refer to a separate, Platonic soul and is nowadays usually translated as “being”.
But how can a monistic conception of the mind-brain be reconciled with humanist notions of freedom and responsibility and with a theistic belief in life after death? Several solutions have been proposed, but the dual-aspect monism of protestant neurobiologist-philosopher Donald MacKay is justifiably one of the most influential, as is reflected in the writings of many subsequent theistic monists such as Malcolm Jeeves, Nancey Murphy and Warren Brown. According to MacKay, my subjective conscious experience and an objective neurobiological account of my brain are two complementary views of a single entity. There is no separate Platonic soul that floats out of the brain at death. MacKay couples this dual-aspect monism to a compatibilist approach to free will. Thus, protestant MacKay and atheist Daniel Dennett share common ground as far as the mind-brain relation is concerned.
But how could the inevitable destruction of the brain at death square with any idea of an afterlife? The New Testament does not teach an eternal soul, but a resurrected “spiritual body”. This is not defined precisely, but the idea seems to be that the information structure of the real “me” will somehow be restored into a very different embodiment, just as a poem can retain its essence when copied or a computer programme can be reinstalled on a new computer.
There is still plenty of debate even among theists. Monism and compatibilism dominate among protestant neurobiologists and philosophers, whereas Roman Catholic and Orthodox scholars (e.g. Richard Swinburne) tend to favour dualism. If a line can be drawn through the diversity of opinions, it may be the ancient divide between Aristotelians and Platonists. The monistic view of soul/self as information structure is close to that of Aristotle, whereas the most widespread forms of dualism are neo-Platonist. But there is no neat division between dualistic, libertarian theists and monistic, compatibilist atheists.
Peter G H Clarke is an associate professor of neuroscience at the Département de Biologie cellulaire et de Morphologie at the Université de Lausanne.

Continuing to rethink the unrethinkable

Yet more predarwinian tech takes the witness stand for design.

The Machine that Fuels ATP Synthase

Evolution News & Views

Why do you need oxygen to breathe? Oxygen actually plays a secondary role in the amazing process of respiration. What you really need are protons (hydrogen atoms). For every proton captured from your food, there's an electron needing proper disposal. Oxygen is just an electron receptor at the end of a long chain of processes, driven by molecular machines, that captures protons for fuel. The machines translocate the protons across a membrane, creating a pool of protons that enter the ATP synthase rotor and make it turn (see our animation, "ATP Synthase: The Power Plant of the Cell"). In a sense, the whole job of respiration is to set up a proton gradient in the mitochondrial membrane to serve as fuel for ATP synthase.

A bit of background: The protons turn the rotor in ATP synthase like a carousel or waterwheel. This, in turn, rotates a camshaft to mechanically force ADP and phosphate into ATP in the catalytic center of the motor. The energy from your food (or from sunlight in plants) thus transforms chemical energy to electrical energy to mechanical energy and, finally, to another form of chemical energy. Most of the other processes in the cell use ATP for their energy.

We've heard of the mitochondrion as the "powerhouse" of the eukaryotic cell. That's because it creates the ATP to power everything else. Along its folded inner membranes, called cristae, molecular machines pump protons to one side of the inner membrane where they can be channeled into the "turbines" of ATP synthase. In plants, chloroplasts serve this function, capturing energy from sunlight. Bacteria have the same basic machinery in their inner cell membranes. Since we are eukaryotes, let's look at what's going on in our mitochondria, where thousands of molecular machines are working 24/7 to set up the proton gradient, a literal "voltage" to run your motors.

The first of those machines has a cumbersome name, NADH:ubiquinone oxidoreductase (sometimes NADH dehydrogenase). We can use its nickname "Complex I" for convenience. It's one of five "complexes" in the electron transport chain of respiration (also called oxidative phosphorylation), ending with ATP synthase as Complex V. The last of the molecular machines to be elucidated, Complex I has just been described in unprecedented detail by scientists from the molecular biology laboratory at Cambridge.

For many years, scientists knew the general function of Complex I. Its job is to generate four protons for the proton gradient from each input. It does this by taking electrons from NAD (nicotinamide adenine dinucleotide), a sugar phosphate first described in 1906. The reduced form is called NADH.

Now for some terminology: For historical reasons, removing electrons is called "oxidation", and donating them is called "reduction." Together, these are abbreviated "redox" reactions. But since negative electrons and positive protons are involved, it might help to think of 'reduction' as reducing the number of protons. Oxidizing a molecule leaves it with fewer electrons, resulting in a positive charge -- i.e., with extra protons. Reducing a molecule leaves it with a negative charge, or a reduced number of protons. A proton is the same as a hydrogen ion (H+).

The docking site of Complex I oxidizes NADH to NAD+, passing two captured electrons to a cofactor called ubiquinone. In the process, by passing the electrons through a series of iron-sulfur clusters (Fe-S), the machine pumps four protons through the inner mitochondrial membrane, contributing about 40 percent of the proton gradient needed by ATP synthase. You can watch a simplified animation from NDSU Virtual Cell showing how the complexes move electrons and protons around.

The mitochondrion is where the well-known "citric acid cycle" takes place. Students often hear about the chemistry of life, but not as often about the mechanics. They learn how energy from food is transferred through various molecules to make ATP as we breathe in oxygen and breathe out carbon dioxide and water vapor. That's great to know, but what is more fascinating is how these reactions require machines with moving parts. Let's see what scientists have discovered about Complex I, in terms of its structure and dynamics.

Complex I is a huge enzyme, one of the largest in the cell. In mammals, it has 14 core subunits and 31 "supernumerary" (fancy word for "extra") subunits, adding up to a whopping mass of 980 kilodaltons (kDa). (A Dalton is about the mass of a hydrogen atom; technically, 1/12 the mass of a carbon atom.) Such high mass implies over 7,000 properly-sequenced amino acids. That's one huge machine, considering the average size of an enzyme is about 300-400 amino acids. The bacterial Complex I, lacking many of the supernumerary subunits, is still gigantic, weighing in at 550 kDa.

In appearance, Complex I resembles a boot, with the ankle inside the mitochondrion and the sole anchored in the crista. NAD enters the ankle. The protons exit the sole into the inner membrane. But what actually goes on in this structure? Research published in Nature in 2010 suggested the possibility that the bacterial enzyme moves with an action resembling a piston.

The overall architecture of this large molecular machine is now clear. F-ATPase has been compared to a turbine. In a similar vein, complex I seems to resemble a steam engine, where the energy of the electron transfer is used to move a piston, which then drives, instead of wheels, a set of discontinuous helices. The full mechanistic details remain to be clarified by atomic structures of the membrane domain and the entire complex.
A subsequent paper in Nature in 2014 called the piston-like motion into question, at least for the mammalian version, but it did not rule out smaller-scale motions (called "conformational changes" in the literature).

Now, using cryo-electron microscopy, the Cambridge team has described all 45 subunits of Complex I from bovine mitochondria. In Nature, they mention having found moving parts:

We have located and modelled all 45 subunits, including the 31 supernumerary subunits, to provide the entire structure of the mammalian complex. Computational sorting of the particles identified different structural classes, related by subtle domain movements, which reveal conformationally dynamic regions and match biochemical descriptions of the 'active-to-de-active' enzyme transition that occurs during hypoxia. Our structures therefore provide a foundation for understanding complex I assembly and the effects of mutations that cause clinically relevant complex I dysfunctions, give insights into the structural and functional roles of the supernumerary subunits and reveal new information on the mechanism and regulation of catalysis.
The supernumerary subunits "are central to the structure, stability and assembly of the complex, and some also have regulatory or independent metabolic roles," they say. Some of them may serve a role in anchoring the machine to the membrane. That makes sense if the machine is vibrating from moving parts. What do the dynamic regions do? Later in the paper, they explain:

The two states of mammalian complex I described support the idea that dynamic, flexible regions at the hydrophilic-membrane domain interface are important for coupling ubiquinone reduction to proton translocation.
They go into detail about additional movements in a chain reaction, concluding:

Thus, a cascade of events originating from the ubiquinone-binding cleft may couple ubiquinone reduction and protonation to proton translocation. Although all such mechanisms for complex I are currently hypothetical, cryoEM now provides a powerful tool to study individual trapped conformations or separate mixed states computationally in order to determine how conformational changes are initiated, coordinated and propagated.
Currently, biochemists are limited to catching snapshots of the action. In the future, will they be able to watch Complex I move in real time? That's something to look forward to!

Students are likely to be much more interested in cell biology if they learn about molecular machines with moving parts. Who wants to memorize the chemical reactions in the citric acid cycle when you can watch rotors, pistons and pumps? That's what really goes on. We are privileged to live in a time when these realities are coming to light.

The authors point out two other observations of interest for intelligent design. One is that mutations in these machines cause disease and death; they cannot tolerate much change, meaning that the specificity in the amino acid sequence is vital to the function. That's why they say that the core machinery is "conserved from bacteria to humans."

The other observation is that the machines have to be assembled to work in the first place. It's like Scott Minnich's comment in Unlocking the Mystery of Life that the assembly instructions for the bacterial flagellum are even more complex than the machine itself. A machine needs a plan (encoded in DNA). It needs materials that must be delivered to the right place at the right time, in the right quantities. The parts have to be assembled in a coordinated sequence. Each step requires inspection, so that the cell doesn't waste time building something that won't work. That's true of Complex I and the entire factory of machines in the electron transport chain that make life possible. We see similar requirements in the construction of a house or manufacturing plant. It's Undeniable that we compare these processes and intuitively understand that intelligent causes must have been at work in the design of molecular machines.

Let's end with a look at one more level of organization. We mentioned cristae, the folds in mitochondrial membranes where these machines reside. A paper in the Proceedings of the National Academy of Sciences shows that the machines are arranged on the cristae in such a way as to maximize efficiency. In particular, the ATP synthase engines form V-shaped pairs, offset with respect to neighboring pairs so that their moving parts do not conflict but rather promote their respective operations. The spacing and angular displacement of the pairs, furthermore, results in the characteristic curvature of the cristae, which maximizes the proton gradient by creating local concentrations of protons aimed at the engines.

And this was found in Paramecium.

The Science delusion.

Two Kinds of Science "Skepticism"
David Klinghoffer

Over the weekend in New York, the excellent science journalist John Horgan spoke at a convention of "Skeptics," the Northeast Conference on Science and Skepticism, and absolutely flailed crowd. I wish I could have been there. Even better, he published his comments at Scientific American. This is a man after my own heart. He begins:

I hate preaching to the converted.
Ditto.

If you were Buddhists, I'd bash Buddhism. But you're skeptics, so I have to bash skepticism.
I'm a science journalist. I don't celebrate science, I criticize it, because science needs critics more than cheerleaders. I point out gaps between scientific hype and reality. That keeps me busy, because, as you know, most peer-reviewed scientific claims are wrong.

Preach it! Horgan makes the great distinction between "skepticism" directed at "soft" versus "hard" targets. Capital-S "Skeptics" have a tendency to bullying. Almost exclusively, they go after the weak and easy targets -- Bigfoot, UFOs, homeopathy, that kind of thing. It's their way of identifying as a tribe, says Horgan:

So I'm a skeptic, but with a small S, not capital S. I don't belong to skeptical societies. I don't hang out with people who self-identify as capital-S Skeptics. Or Atheists. Or Rationalists.
When people like this get together, they become tribal. They pat each other on the back and tell each other how smart they are compared to those outside the tribe. But belonging to a tribe often makes you dumber.

Here's an example involving two idols of Capital-S Skepticism: biologist Richard Dawkins and physicist Lawrence Krauss. Krauss recently wrote a book, A Universe from Nothing. He claims that physics is answering the old question, Why is there something rather than nothing?

Krauss's book doesn't come close to fulfilling the promise of its title, but Dawkins loved it. He writes in the book's afterword: "If On the Origin of Species was biology's deadliest blow to supernaturalism, we may come to see A Universe From Nothing as the equivalent from cosmology."

Just to be clear: Dawkins is comparing Lawrence Krauss to Charles Darwin. Why would Dawkins say something so foolish? Because he hates religion so much that it impairs his scientific judgment. He succumbs to what you might call "The Science Delusion."

"The Science Delusion" is common among Capital-S Skeptics. You don't apply your skepticism equally. You are extremely critical of belief in God, ghosts, heaven, ESP, astrology, homeopathy and Bigfoot. You also attack disbelief in global warming, vaccines and genetically modified food.

These beliefs and disbeliefs deserve criticism, but they are what I call "soft targets." That's because, for the most part, you're bashing people outside your tribe, who ignore you. You end up preaching to the converted.

Meanwhile, you neglect what I call hard targets. These are dubious and even harmful claims promoted by major scientists and institutions.

Yes. My goodness, how I loathe tribal thinking -- perhaps to a fault.

What the genuine soft targets have in common is that, besides being encumbered by major and easily identified holes in them, they don't matter much. (I would exclude belief in God in both these respects.) If Sasquatch does or does not stalk the wildernesses of the Northwest, it hardly impacts our lives or our outlook on the meaning of existence. Also, there's no powerful Bigfoot "establishment" ready to mercilessly defend its preferred view or penalize you for your wayward thinking. Mocking Bigfoot belief costs the Skeptic nothing.

Not so with the "hard" targets, associated with prestige academia and government support. Horan's illustrations include "Multiverses and the Singularity," "Overtested and Overtreated for Cancer," and "Mental-Illness Over-Medication."

On the multiverse:

For decades, physicists like Stephen Hawking, Brian Greene and Leonard Susskind have touted string and multiverse theories as our deepest descriptions of reality.
Here's the problem: strings and multiverses can't be experimentally detected. The theories aren't falsifiable, which makes them pseudo-scientific, like astrology and Freudian psychoanalysis.

Some string and multiverse true believers, like Sean Carroll, have argued that falsifiability should be discarded as a method for distinguishing science from pseudo-science. You're losing the game, so you try to change the rules.

Physicists are even promoting the idea that our universe is a simulation created by super-intelligent aliens. Last month, Neil de Grasse Tyson said "the likelihood may be very high" that we're living in a simulation. Again, this isn't science, it's a stoner thought experiment pretending to be science.

He loses me at the end when he advocates for extreme skepticism directed at war. Pacifism and anti-war thinking can be all too comfortable ceding ground to evil, a luxury that may feel good but leaves the weak, innocent, and threatened to fend for themselves. Otherwise this is bracing stuff. Read it.

Of course among the hardest targets of all are the prestige scientific ideas about life's origins, especially the Darwinian explanation of how major novel biological structures arise. The "Skeptics" really steer clear of challenging those.

In the context of some of the discussions we have here, the critics are happy to go after a soft target like creationism. But they keep a safe distance from tackling the massive and serious critique of the Darwinian mechanism articulated by Meyer, Axe, Sternberg, Berlinski, Behe, Gauger, Wells, Nelson, et al. That's very telling.