James ch.4 King James Version

 

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◄ James 4 ►

King James Bible 

1From whence come wars and fightings among you? come they not hence, even of your lusts that war in your members? 2Ye lust, and have not: ye kill, and desire to have, and cannot obtain: ye fight and war, yet ye have not, because ye ask not. 3Ye ask, and receive not, because ye ask amiss, that ye may consume it upon your lusts. 4Ye adulterers and adulteresses, know ye not that the friendship of the world is enmity with God? whosoever therefore will be a friend of the world is the enemy of God. 5Do ye think that the scripture saith in vain, The spirit that dwelleth in us lusteth to envy? 6But he giveth more grace. Wherefore he saith, God resisteth the proud, but giveth grace unto the humble.

Drawing Near to God

7Submit yourselves therefore to God. Resist the devil, and he will flee from you. 8Draw nigh to God, and he will draw nigh to you. Cleanse your hands, ye sinners; and purify your hearts, ye double minded. 9Be afflicted, and mourn, and weep: let your laughter be turned to mourning, and your joy to heaviness. 10Humble yourselves in the sight of the Lord, and he shall lift you up.

11Speak not evil one of another, brethren. He that speaketh evil of his brother, and judgeth his brother, speaketh evil of the law, and judgeth the law: but if thou judge the law, thou art not a doer of the law, but a judge. 12There is one lawgiver, who is able to save and to destroy: who art thou that judgest another?

Do Not Boast about Tomorrow

13Go to now, ye that say, To day or to morrow we will go into such a city, and continue there a year, and buy and sell, and get gain: 14Whereas ye know not what shall be on the morrow. For what is your life? It is even a vapour, that appeareth for a little time, and then vanisheth away. 15For that ye ought to say, If the Lord will, we shall live, and do this, or that. 16But now ye rejoice in your boastings: all such rejoicing is evil. 17Therefore to him that knoweth to do good, and doeth it not, to him it is sin.

The bible's counsel in this age of rage.

 Ecclesiastes 7:9NIV"Do not be quickly provoked in your spirit, for anger resides in the lap of fools." 

Even when anger is justified ,it can be a tool of Satan and his henchmen. That is why we are warned in scripture ,

James1:20NIV"because human anger does not produce the righteousness that God desires." 

As for JEHOVAH'S servants or sincere truth seekers we have been forewarned, as to what to expect from this civilization whose prince is the Father of lies, see John8:44,John14:30 

Matthew 10:25NIV"It is enough for students to be like their teachers, and servants like their masters. If the head of the house has been called Beelzebul, how much more the members of his household!"

Our Lord counseled us aquire the wisdom of a serpent even as we maintain the blamelessness of a dove, see Matthew 10:16 ,we can safely add the hide of a rhinoceros to the list of qualities needed to maintain our integrity.

Remember: James4:4NIV"You adulterous people, don’t you know that friendship with the world means enmity against God? Therefore, anyone who chooses to be a friend of the world becomes an enemy of God."

 

Pope Pius XII and Hitler.

 Vatican documents show secret back channel between Pope Pius XII and Hitler

Jun 7, 2022 6:35 PM EDT 

A series of recently opened Vatican archives are shedding new light on the relationship between Pope Pius XII and Hitler as he led Nazi Germany during World War II. A new book takes a deeper look at these revelations. Historian David Kertzer, author of “The Pope At War: The Secret History of Pope Pius XII, Mussolini, and Hitler,” joins Amna Nawaz to discuss.

Read the Full Transcript

Judy Woodruff:

A series of recently opened Vatican archives are shedding new light on the relationship between Pope Pius XII and Adolf Hitler as he led Nazi Germany during World War II.

Amna Nawaz looks at what we are learning and how it changes our thinking about the Vatican during that time.

Amna Nawaz:

Judy, in 2020, the Vatican released millions of documents on Pope Pius XII that were previously hidden from public view. These include transcripts of negotiations between the pope and Nazis.

A new book published today takes a deeper look at these revelations. 

Historian David Kertzer is the author of that book. It's called "The Pope at War: The Secret History of Pius XII, Mussolini, and Hitler."

And he joins me now.

David Kertzer, welcome to the "NewsHour." Thank you for being here.

So a lot of folks know previous versions of history around Pius XII went one of two ways, right? He was either called Hitler's pope and an antisemite, or the story was that he did everything in his power to save as many Jewish people as he could during the war. 

After reviewing the documents, what's your understanding?

David Kertzer, Author, "The Pope at War: The Secret History of Pius XII, Mussolini, and Hitler": Well, I think neither one is really accurate. They're both extremes.

The fact is, Pius XII was afraid of, certainly in the first years of the war, that the Nazis were going to win. And so he felt he had to plan for a Europe that was going to be under Nazi control with their pal Mussolini helping out.

So his main concerns in those earlier years, say '39 to '42, was to protect the church in a time when it would — Europe could be under Nazi control. It wasn't that he loved the Nazis, much less Hitler, but this was his thinking. 

Amna Nawaz:

Well, what does that mean, when you say protect the church?

For example, we mentioned these — these meetings that we now know happen between the pope and a personal envoy of Hitler. What did we learn about those? What were those talks like? 

David Kertzer:

Well, probably the most shocking finding from these newly opened Vatican archives that just opened two years ago, after 50 years of pressure and interest in being able to see what they contain, is that, within weeks of Pius XII being elected pope — he is elected in early 1939 — Hitler saw an opportunity and decided to send a personal envoy, who himself is a rather colorful character.

It's the great-grandson of Queen Victoria of England, a Nazi prince, who is married to the daughter of the king of Italy. And he would begin to shuttle back and forth between Hitler and the pope over the next two years, engaged in secret negotiations. We didn't know about these until just now. 

Amna Nawaz:

David, when it comes down to what Pope Pius XII did or didn't do, in terms of saving Jewish lives, you tell the story about one October night in 1943 in Rome.

What happened then? 

David Kertzer:

Well, on October 16, 1943, the S.S. had lists of all the Jews in Rome, and went door to door and tried to arrest all of Rome's Jews, thousands of them.

They found about 1,260 arrested them, brought them to a military college just outside the walls of the Vatican, and held them there for two days. What we now learn from these recently opened archives is that the Vatican worked very hard to show that some of them had been baptized and therefore shouldn't be considered Jews, from the point of view of the church, and, therefore, should not be he shipped off to Auschwitz with the rest of them.

And, in fact, about 250 of those who were originally rounded up were freed before, two days later, they were put on a train, 1,007 of them, of whom I think about 16 would be — would survive. And most, in fact, a week later on arrival at Auschwitz were immediately put to death.

The pope did send his cardinal secretary of state to meet with the German ambassador to the Holy See to say, do you really need to go through this? Can you do something about this? But the ambassador told the cardinal secretary of state, this has been ordered by the highest level, namely, Hitler, and you really don't want me to protest on your behalf, do you?

And the cardinal secretary of state basically said, no, I'm not insisting on any protest. 

Amna Nawaz:

Dave, I'm curious.

I know, previously, the Vatican has come forward when previous allegations were made similar to this about Pope Pius XII. Have they responded in any way to your book or to the reporting that's in this book? 

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Vatican documents show secret back channel between Pope Pius XII and Hitler

Jun 7, 2022 6:35 PM EDT

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A series of recently opened Vatican archives are shedding new light on the relationship between Pope Pius XII and Hitler as he led Nazi Germany during World War II. A new book takes a deeper look at these revelations. Historian David Kertzer, author of “The Pope At War: The Secret History of Pope Pius XII, Mussolini, and Hitler,” joins Amna Nawaz to discuss.

Read the Full Transcript

Judy Woodruff:

A series of recently opened Vatican archives are shedding new light on the relationship between Pope Pius XII and Adolf Hitler as he led Nazi Germany during World War II.

Amna Nawaz looks at what we are learning and how it changes our thinking about the Vatican during that time.

Amna Nawaz:

Judy, in 2020, the Vatican released millions of documents on Pope Pius XII that were previously hidden from public view. These include transcripts of negotiations between the pope and Nazis.

A new book published today takes a deeper look at these revelations.

Historian David Kertzer is the author of that book. It's called "The Pope at War: The Secret History of Pius XII, Mussolini, and Hitler."

And he joins me now.

David Kertzer, welcome to the "NewsHour." Thank you for being here.

So a lot of folks know previous versions of history around Pius XII went one of two ways, right? He was either called Hitler's pope and an antisemite, or the story was that he did everything in his power to save as many Jewish people as he could during the war.

After reviewing the documents, what's your understanding?

David Kertzer, Author, "The Pope at War: The Secret History of Pius XII, Mussolini, and Hitler": Well, I think neither one is really accurate. They're both extremes.

The fact is, Pius XII was afraid of, certainly in the first years of the war, that the Nazis were going to win. And so he felt he had to plan for a Europe that was going to be under Nazi control with their pal Mussolini helping out.

So his main concerns in those earlier years, say '39 to '42, was to protect the church in a time when it would — Europe could be under Nazi control. It wasn't that he loved the Nazis, much less Hitler, but this was his thinking.

Amna Nawaz:

Well, what does that mean, when you say protect the church?

For example, we mentioned these — these meetings that we now know happen between the pope and a personal envoy of Hitler. What did we learn about those? What were those talks like?

David Kertzer:

Well, probably the most shocking finding from these newly opened Vatican archives that just opened two years ago, after 50 years of pressure and interest in being able to see what they contain, is that, within weeks of Pius XII being elected pope — he is elected in early 1939 — Hitler saw an opportunity and decided to send a personal envoy, who himself is a rather colorful character.

It's the great-grandson of Queen Victoria of England, a Nazi prince, who is married to the daughter of the king of Italy. And he would begin to shuttle back and forth between Hitler and the pope over the next two years, engaged in secret negotiations. We didn't know about these until just now.

Amna Nawaz:

David, when it comes down to what Pope Pius XII did or didn't do, in terms of saving Jewish lives, you tell the story about one October night in 1943 in Rome.

What happened then?

David Kertzer:

Well, on October 16, 1943, the S.S. had lists of all the Jews in Rome, and went door to door and tried to arrest all of Rome's Jews, thousands of them.

They found about 1,260 arrested them, brought them to a military college just outside the walls of the Vatican, and held them there for two days. What we now learn from these recently opened archives is that the Vatican worked very hard to show that some of them had been baptized and therefore shouldn't be considered Jews, from the point of view of the church, and, therefore, should not be he shipped off to Auschwitz with the rest of them.

And, in fact, about 250 of those who were originally rounded up were freed before, two days later, they were put on a train, 1,007 of them, of whom I think about 16 would be — would survive. And most, in fact, a week later on arrival at Auschwitz were immediately put to death.

The pope did send his cardinal secretary of state to meet with the German ambassador to the Holy See to say, do you really need to go through this? Can you do something about this? But the ambassador told the cardinal secretary of state, this has been ordered by the highest level, namely, Hitler, and you really don't want me to protest on your behalf, do you?

And the cardinal secretary of state basically said, no, I'm not insisting on any protest.

Amna Nawaz:

Dave, I'm curious.

I know, previously, the Vatican has come forward when previous allegations were made similar to this about Pope Pius XII. Have they responded in any way to your book or to the reporting that's in this book?

David Kertzer:

Well, unfortunately — I mean, other national Roman Catholic Churches, for example, in France and in Germany have come to terms with this history.

And part of the history is how it was that, in the middle of the 20th century, the — millions of Jews could be massacred, little children, old people, by people who thought of themselves as Christian, more or less half of them Roman Catholics, but also Protestants, of course.

And in other countries, in Germany and France, the clergy has come to terms or begun to come to terms with it. But the Vatican has not. The Vatican released a statement in, I think, 1998, we remember, in which they said the — their own demonization of the Jews had absolutely nothing to do with the Holocaust.

So this is — I think my book is probably not entirely appreciated by many in the Vatican, although there are those in the Vatican when I worked in the archives who had whispered to me they're happy that this is finally coming out. 

Amna Nawaz:

What about how we view, all these years later, the role of Pope Pius XII's leadership of the church, I mean, especially with his — there being a push for his sainthood, right? How should we look at that when you step back? 

David Kertzer:

Yes, so the popes have tried to beatify and canonize, make Pius XII a saint. He is a hero of the right wing or the conservatives in the church, who see the church as having gone wrong after his death with the Second Vatican Council under his successor, John XXIII.

I wish that — first of all, I wish they'd read this book, but I also wish they'd be willing to consider this history anew. But I'm afraid, for those — those really don't have an open mind, and it's unlikely that it will change their mind. So I think the drive to make a saint of Pius XII will continue. 

Amna Nawaz:

That is historian David Kertzer, author of the new book "The Pope at War: The Secret History of Pius XII, Mussolini, and Hitler."

David Kertzer, thank you so much. 

David Kertzer:

Thank you.

Darwin, Wallace and class.

 Why Darwin Eclipsed Wallace: Darwin and the English Class System 

Neil Thomas 

The theory of natural selection was the co-discovery of two men, but by the mid 1860s one of its progenitors began to reject his own theory, scarcely more than a half decade after first announcing it to the world. Towards the end of his life Alfred Russel Wallace would resolve the conceptual confusion surrounding the curious “half-and-half” dualism which initially prompted him to claim that it was only mankind’s mental faculties which had been designed, natural selection having fashioned our bodies. That improbable thesis was later to be replaced by his contention that the totality of (wo)man — body and mind — had arisen from what today would be called intelligent design, and, moreover, that the same applied to the whole sentient universe. This was indeed a root-and-branch “apostasy” from his prior convictions.

Why have people not registered this rejection of the theory by its co-author more strongly? Why is it Charles Darwin’s view which has persisted while Wallace’s has been airbrushed out of history? Predictably, the quintessentially English subject of class has been invoked to answer this question. Sociologists of science often point to the fact that the progress of scientific ideas advances in part as a form of social process, and Darwin, unlike the impoverished and socially less well-placed Wallace, was fortunate to have an upper-middle-class support group to promulgate his ideas. 

How convincing is this thesis as an explanation for Darwin’s greater success? I have argued elsewhere that the major role in the acceptance of Darwinism depended not so much on social factors but on the truly seismic changes in attitudes to religion experienced by all classes of society by the middle of the 19th century. But this does not mean that social factors played no part at all. How might those factors be characterized?

With a Little Help from His Friends

There are indications that Darwin over time gained something of the de facto status of a cult leader (in an unexceptionably benign sense). There cannot be many natural scientists who have inspired a follower to write a fulsome, 50-page poem in their memory, but after Darwin’s death in 1882 this is precisely what occurred. A younger acolyte, the naturalist George Romanes (pictured above), venerated Darwin so greatly — “this side idolatry” seems the entirely appropriate phrase — that he chose this form of laudation for a commemorative poem titled with lapidary simplicity, “Charles Darwin: A Memorial Poem.”1 There is ample evidence in Darwin’s voluminous correspondence with both indigenous and overseas scholars —continued without interruption even when chronic illness kept him house-bound — and in the “pilgrimages” to Down House he inspired from his old boys’ network of former college friends and tutors, that he had an enviable gift for friendship, even to the point of being able to inspire forms of fraternal love.

Only on the assumption of such personal magnetism can we understand such things as his limitlessly supportive inner circle meeting regularly to discuss matters of personal and professional interest with him. The severe-looking photographs of the bearded patriarch that have come down to us clearly give few hints of the sheer charisma he must have projected to inspire such admiration and affection. Romanes’s poem, which set off the high honour already accorded to Darwin in his burial in the north aisle of the nave of Westminster Abbey, near to Sir Isaac Newton, might have suggested to some an aura close to sanctity or at the very least a symbolic assumption into a form of scientific empyrean. 

The Darwin Circle: A Small World

To those acquainted with modern Britain, a place which frowns on nepotism and cronyism (at least officially), and which has opened itself up to meritocratic selection procedures and the importation of foreign talent, it is rather surprising that the same cast of characters keep popping up again and again in the drama of Darwin’s life.2 Clergyman and botanist Professor John Stevens Henslow (1796-1861)3 would regularly hold soirées at his home, attended by Darwin and Darwin’s Cambridge tutors, William Whewell and Adam Sedgwick, the latter having been Darwin’s companion on a number of geological field trips when Darwin was younger and in better health. Henslow’s daughter was later to marry one of Darwin’s closest friends, the botanist Joseph Dalton Hooker. It was Henslow who recommended Darwin for the Beagle expedition in the early 1830s and again Henslow who chaired the famous Oxford debate in 1860 where Bishop Wilberforce squared off against Darwin’s “bulldog,” Thomas Henry Huxley. Despite his reservations about Darwin’s ideas, Henslow’s avuncular relationship with Darwin bade him always do his best to protect Darwin from harsh criticism.4 The same was the case with Adam Sedgwick. Sedgwick disagreed with Darwin’s ideas in the Origin so radically that, far more in sorrow than in anger, he once described Darwin’s ideas in a confidential letter to palaeontologist Richard Owen as being at one and the same time saddening and risible. For him, his erstwhile protégé was “a teacher of error instead of the apostle of truth.”5 Notwithstanding these reservations, he remained on commendably friendly terms with Darwin for the remainder of his life.The recipient of this amount of indulgence from his friends clearly had every reason to feel secure in the knowledge that he commanded a supportive in-group whose loyalty he could depend on absolutely. So it was that in 1856, at a hush-hush meeting at Down House convened by Darwin, he took soundings with Hooker and Huxley as to how best to proceed with his heretofore secret ideas concerning evolution. Huxley, despite the fact that he had condemned ideas similar to those of Darwin when they had been presented in Robert Chambers’s Vestiges of the Natural History of Creation (1844), and that he would never reconcile himself with Darwin’s special theory of natural selection, immediately volunteered to defend Darwin’s ideas, being more than willing to take Darwin’s corner against the high authority of Richard Owen. In the words of Iain McCalman, alluding to the fact that so many of Darwin’s intimates were part of an old sea-dog confraternity who had made voyages of scientific discovery of their own, Huxley had come aboard and “joined Darwin’s fleet.”6 Huxley might have been, in Peter Bowler’s phrase, a “pseudo-Darwinian” (that is, a believer in evolution but not natural selection), yet he would not hear a word said against Darwinism in any of its facets.There is no getting away from the socially parochial aspect of English life at this time. The same names recur in the Darwin story simply because debate about matters of high import at the time were debated and largely decided by an “upper crust” of ex “public”7 school boys and Oxbridge graduates. These persons would typically not even meet, let alone converse with members of “lower” social classes (except in trading transactions) because it was tacitly accepted that it was only the views of the social elite which counted.

Tomorrow, “Why Darwin Eclipsed Wallace: Darwin Comes to America. 

Ps. Ecclesiates9:16KJV"Then said I, Wisdom is better than strength: nevertheless the poor man's wisdom is despised, and his words are not heard."

Resistance is futile.

Ecclesiastes7:13KJV"Consider the work of God;

For who can make straight what He has made crooked?"

Here is the expositor's commentary on this passage: ); once let him see that the thing is crooked, and was meant to be crooked, and he will accept and adapt himself to it, instead of wearying himself in futile attempts to make, or to think, it straight.:  Now consider our Lord words at John17:9KJV"I pray for them: I pray NOT for the world, but for them which thou hast given me; for they are thine." And also Jeremiah7:16KJV"Therefore pray not thou for this people, neither lift up cry nor prayer for them, neither make intercession to me: for I will NOT hear thee."  It is waste of time and resources to attempt to save any nation or civilization rejected by The Lord JEHOVAH. Individuals who humble themselves and prove to be of a different spirit to their contemporaries may be shown mercy. But their is truly no straightening of what the Lord JEHOVAH has decreed crooked.

The prosecutor's fallacy: a brief history.

 Prosecutor's fallacy 

The prosecutor's fallacy is a fallacy of statistical reasoning involving a test for an occurrence, such as a DNA match. A positive result in the test may paradoxically be more likely to be an erroneous result than an actual occurrence, even if the test is very accurate. The fallacy is named because it is typically used by a prosecutor to exaggerate the probability of a criminal defendant's guilt. The fallacy can be used to support other claims as well – including the innocence of a defendant. 

A simple example illustrating the prosecutor's fallacy. (The hypothesis is the possibility that the defendant is guilty, whereas the evidence found refers to a positive test result, such as a DNA or blood type match.) Although the probability that evidence is found on the real culprit may be quite high (in this case, two-fifths, or 40%), the probability that a certain individual is guilty given that said evidence was found in him is unrelated to the former, and will often be much smaller (in this example, only two-eighths, or 25%). For instance, if a perpetrator were known to have the same blood type as a given defendant and 10% of the population to share that blood type, then one version of the prosecutor's fallacy would be to claim that, on that basis alone, the probability that the defendant is guilty is 90%. However, this conclusion is only close to correct if the defendant was selected as the main suspect based on robust evidence discovered prior to the blood test and unrelated to it (the blood match may then be an "unexpected coincidence"). Otherwise, the reasoning presented is flawed, as it overlooks the high prior probability (that is, prior to the blood test) that he is a random innocent person. Assume, for instance, that 1000 people live in the town where the murder occurred. This means that 100 people live there who have the perpetrator's blood type; therefore, the true probability that the defendant is guilty – based on the fact that his blood type matches that of the killer – is only 1%, far less than the 90% argued by the prosecutor. 

At its heart, therefore, the fallacy involves assuming that the prior probability of a random match is equal to the probability that the defendant is innocent. When using it, a prosecutor questioning an expert witness may ask: "The odds of finding this evidence on an innocent man are so small that the jury can safely disregard the possibility that this defendant is innocent, correct?"[1] The claim assumes that the probability that evidence is found on an innocent man is the same as the probability that a man is innocent given that evidence was found on him, which is not true. Whilst the former is usually small (approximately 10% in the previous example) due to good forensic evidence procedures, the latter (99% in that example) does not directly relate to it and will often be much higher, since, in fact, it depends on the likely quite high prior odds of the defendant being a random innocent person. 

Mathematically, the fallacy results from misunderstanding the concept of a conditional probability, which is defined as the probability that an event A occurs given that event B is known – or assumed – to have occurred, and it is written as P(A|B). The error is based on assuming that P(A|B) = P(B|A), where A represents the event of finding evidence on the defendant, and B the event that the defendant is innocent. But this equality is not true: in fact, although P(A|B) is usually very small, P(B|A) may still be much higher. 

 

And still yet more on why primeval tech is the bane of Darwinism.

 Yes, a “Host of Machines” Are at Work in the Cell 

David Coppedge 

Much as we love the old standbys (the flagellum, cilium, ATP synthase, etc.), we should never assume that the case for intelligent design is restricted to those iconic favorites. In 2002, Jed Macosko claimed in Unlocking the Mystery of Life that there are “a host of machines” at work in the cell — as many as there are functions that the body has to perform. Each machine is a marvel of engineering and precision. Let’s visit a few more of them.Another Topoisomerase

Discovery Institute’s recent animation of a Type 2 topoisomerase dazzled us with its ability to accurately cut DNA and stitch it back together to fix twisted loops that could send a genome into a tailspin. The family of topoisomerase machines, though, includes six types just as amazing. Topoisomerase 3β (abbreviated TOP3B) received an ovation this month from Yang et al. in Nature Communications. This one “regulates R-loop dynamics and mRNA translation, which are critical for genome stability, neurodevelopment and normal aging.” TOP3B is a Type 1 topoisomerase that repairs one strand of DNA (see below for a simple video demonstration). The details are more complex than shown, as this excerpt from the paper demonstrates:

As a Type IA topoisomerase, TOP3B acts by general acid-base catalysis to break and rejoin single-stranded DNA. Passage of a second DNA strand through the transient break permits dissipation of hypernegative DNA supercoiling and catenation/knotting. Additionally, hsTOP3B was recently demonstrated as the human RNA topoisomerase, required for normal neurodevelopment and proposed to be a potential anti-viral target upon RNA virus infection. Here we elucidate the biochemical mechanisms of human TOP3B. We delineate the roles of divalent metal ions, and of a conserved Lysine residue (K10) in the differential catalysis of DNA and RNA. We also demonstrate that three regulatory factors fine-tune the catalytic performance of TOP3B: the TOP3B C-terminal tail, its protein partner TDRD3, and the sequence of its DNA/RNA substrates.One other surprise is worth noting: the need for metal ions to cut the nucleic acids: “addition of Mg2+ and to a greater extent Mn2+ stimulated DNA binding and cleavage by TOP3B.” Is it fair to say that this machine has metal cutting blades?

Another Dart Gun 

We’ve learned about the Type 3 Secretion System and the Type 4 Secretion System in bacteria that shoot molecules outside their membranes, but there’s another we haven’t considered for a while: Type 6. An Evolution News article in 2015 discussed its firing mechanism. Now, Lin Lin and colleagues at the University of Basel, Switzerland, have published an open-access paper in the EMBO Journal describing T6SS assembly. The machine looks like a cannon or bazooka in the figures. Remarkably, this “large nanomachine that can deliver toxins directly across membranes of proximal target cells” appears to assemble rapidly on contact when the bacterium encounters a rival in “interbacterial competition.”We identified a class of diverse, previously uncharacterized, periplasmic proteins required for this dynamic localization of T6SS to cell–cell contact (TslA). This precise localization is also dependent on the outer membrane porin OmpA. Our analysis links transmembrane communication to accurate timing and localization of T6SS assembly as well as uncovers a pathway allowing bacterial cells to respond to cell–cell contact during interbacterial competition.

This implies that the components are stored locally throughout the inner membrane to avoid the cost of maintaining an arsenal all over the cell. It also implies contact sensors to activate the assembly — which the authors found.In this work, we reveal a mechanism of localization of a complex nanomachine in response to contact with another cell. Such precise positioning likely requires temporal and spatial coordination of many regulatory proteins at the membrane. Since many T6SS accessory proteins remain uncharacterized, we propose that some of these proteins might be required for spatiotemporal regulation of T6SS assembly. We expect that additional mechanisms of dynamic localization of T6SS will be identified in more bacteria and shown to play an important role in their pathogenesis or ecology.

The authors use strategic mission terms like “attack” in their belief that the T6SS “likely evolved to allow efficient killing of target cells.” But we shouldn’t take the warfare motif too seriously. They’re just bacteria. Maybe the colony is programmed to regulate its surroundings this way. They expect that higher resolution imaging will “unravel additional intricate mechanisms of T6SS targeting.”Nitrogenase Black Box

One of the most important enzymes in all nature, nitrogenase has defied analysis. This multi-part machine with metals in its core is the only enzyme that can split the tough triple bonds of atmospheric nitrogen. The enzyme is only found in bacteria that form symbiotic relationships with the roots of some plants. Biophysicists have tried for years to open the black box of nitrogenase, but its conformational changes are fleeting and difficult to capture. 

Reduced forms of nitrogen are essential for the biosynthesis of amino acids and nucleic acids as well as the production of fertilizers and many commodity chemicals. As the only enzyme capable of nitrogen fixation, nitrogenase catalyzes the eight-electron reduction of atmospheric nitrogen (N2) and protons (H+) into ammonia(NH3) and hydrogen (H2) (Fig. 1A). Nitrogenase is a two-component enzyme, which, in its most common form, consists of the iron protein FeP (a γ2 homodimer) and the molybdenum-iron protein MoFeP (an α2β2 heterotetramer) (Fig. 1B) (4, 5). Nitrogenase is distinct from most redox enzymes in its requirement for adenosine triphosphate (ATP) hydrolysis to enable the successive transfer of electrons and protons for substrate reduction. 

As stated, this machine can precisely break and re-join single strands of DNA to untie knots. Like its Type 2 counterpart that can cut and splice two strands at a time, TOP3B works in a “three-step strategy — DNA cleavage, strand passage, DNA rejoining.” It requires three fine-tuned regulatory cofactors to work. And it is required for normal neurodevelopment. Hannah L. Rutledge at UC San Diego (Science) used cryo-electron microscopy and abundant ATP to capture a few more frames in the “movie” of this remarkable and unique machine. Based on the states they were able to capture, they think they see how the game is being played:

Given the asymmetry between the FeMoco’s in the two αβ halves, it is tempting to propose a “ping-pong”–type mechanism in which the cofactors proceed through each of the eight catalytic steps in an alternating fashion. This scenario would assign a dual role to FeP: (i) to deliver an electron to one αβ subunit of MoFeP and (ii) to suppress FeP binding to the opposite αβ subunit while priming it for catalytic transformations through long-distance activation of electron, H+, and/or substrate access pathways to the distal FeMoco. Establishing whether such a mechanism is operative will require future studies, but our current work illustrates that it is possible to characterize nitrogenase under turnover conditions by cryo-EM at near-atomic resolution, representing a critical step toward understanding the mechanism of this enigmatic enzyme in full structural detail.

When that day comes, it could revolutionize agriculture. An article from Tsinghua University Press (Phys.org) says that “major breakthroughs are still badly needed” to replace the energy-intensive Haber-Bosch process which “is disrupting the planet’s nitrogen cycle, warming the globe, and potentially risking the health of millions.” Imitating the way cells do it might allow scientists to fix nitrogen at ambient temperatures. Nitrogenase is a molecular machine to watch! 

Rubisco Geometry

Another vital enzyme for the biosphere is Rubisco, which fixes carbon for conversion to sugars. Emily Reeves wrote about how it works last year, so readers are referred to that article for background. A new open-access paper in Nature Communications by Lauren Ann Metskas et al. adds some interesting details about its geometry: it forms a lattice inside tiny geometric domes. 

This arrangement preserves freedom of motion and accessibility around the Rubisco active site and the binding sites for two other carboxysome proteins, CsoSCA (a carbonic anhydrase) and the disordered CsoS2, even at Rubisco concentrations exceeding 800 μM. This characterization of Rubisco cargo inside the α-carboxysome provides insight into the balance between order and disorder in microcompartment organization.The research team points out that many prokaryotes segregate their machines into microcompartments like this, contrary to earlier assumptions that the enzymes just float around in the interior. Like the cell’s outer membrane, a proteinaceous shell “selectively restricts passage of key intermediates and improves on-target catalysis.” 

Interest in “microcompartment bioengineering” has grown in recent years, the authors say. The paper shows electron micrographs of some of these remarkable geometric compartments with the Rubisco enzymes neatly packed inside but “surprisingly” not in contact with the shell. “The six-fold lattice may therefore be a packing mechanism to preserve function at concentrations that could otherwise crystallize or sterically impede function.” That makes design sense.

Microcompartment bioengineering is a growing field, and this polymerization-based mechanism for efficient, functional, and controlled packing of enzymes may be useful for future discovery and designs in both CBs [carboxysomes] and other microcompartments.Once again, observation and expectation of design from an engineering perspective is proving fruitful in opening the black boxes of the cell and peering at the watch-like moving parts inside. The future looks bright for nanobiotechnology, and with it, increases in global human flourishing. Intelligent design is proving to be “useful for future discovery and designs.”