Decanonising Science

Science, Now Under Scrutiny Itself
By BENEDICT CAREYJUNE 15, 2015

The crimes and misdemeanors of science used to be handled mostly in-house, with a private word at the faculty club, barbed questions at a conference, maybe a quiet dismissal. On the rare occasion when a journal publicly retracted a study, it typically did so in a cryptic footnote. Few were the wiser; many retracted studies have been cited as legitimate evidence by others years after the fact.


Retracted Scientific Studies: A Growing List

“Until recently it was unusual for us to report on studies that were not yet retracted,” said Dr. Ivan Oransky, an editor of the blog Retraction Watch, the first news media outlet to report that the study had been challenged. But new technology and a push for transparency from younger scientists have changed that, he said. “We have more tips than we can handle.”

The case has played out against an increase in retractions that has alarmed many journal editors and authors. Scientists in fields as diverse as neurobiology, anesthesia and economics are debating how to reduce misconduct, without creating a police-state mentality that undermines creativity and collaboration.

“It’s an extraordinary time,” said Brian Nosek, a professor of psychology at the University of Virginia, and a founder of the Center for Open Science, which provides a free service through which labs can share data and protocols. “We are now seeing a number of efforts to push for data repositories to facilitate direct replications of findings.”

But that push is not universally welcomed. Some senior scientists have argued that replication often wastes resources. “Isn’t reproducibility the bedrock of science? Yes, up to a point,” the cancer biologist Mina Bissell wrote in a widely circulated blog post. “But it is sometimes much easier not to replicate than to replicate studies,” especially when the group trying to replicate does not have the specialized knowledge or skill to do so.

The experience of Retraction Watch provides a rough guide to where this debate is going and why. Dr. Oransky, who has a medical degree from New York University, and Adam Marcus, both science journalists, discovered a mutual interest in retractions about five years ago and founded the blog as a side project. They had, and still have, day jobs: Mr. Marcus, 46, is the managing editor of Gastroenterology & Endoscopy News, and Dr. Oransky, 42, is the editorial director of MedPage Today (he will take a position as distinguished writer in residence at N.Y.U. later this year).

In its first year, the blog broke a couple of retraction stories that hit the mainstream news media — including a case involving data faked by an anesthesiologist who later served time for health care fraud. The site now has about 150,000 unique visitors a month, about half from outside the United States.

Dr. Oransky and Mr. Marcus are partisans who editorialize sharply against poor oversight and vague retraction notices. But their focus on evidence over accusations distinguishes them from watchdog forerunners who sometimes came off as ad hominem cranks. Last year, their site won a $400,000 grant from the John D. and Catherine T. MacArthur Foundation, to build out their database, and they plan to work with Dr. Nosek to manage the data side.

Their data already tell a story.

The blog has charted a 20 to 25 percent increase in retractions across some 10,000 medical and science journals in the past five years: 500 to 600 a year today from 400 in 2010. (The number in 2001 was 40, according to previous research.) The primary causes of this surge are far from clear. The number of papers published is higher than ever, and journals have proliferated, Dr. Oransky and other experts said. New tools for detecting misconduct, like plagiarism-sifting software, are widely available, so there’s reason to suspect that the surge is a simple product of better detection and larger volume.



The increasing challenges to the veracity of scientists’ work gained widespread attention recently when a study by Michael LaCour on the effect of political canvassing on opinions of same-sex marriage was questioned and ultimately retracted.
Still, the pressure to publish attention-grabbing findings is stronger than ever, these experts said — and so is the ability to “borrow” and digitally massage data. Retraction Watch’s records suggest that about a third of retractions are because of errors, like tainted samples or mistakes in statistics, and about two-thirds are because of misconduct or suspicions of misconduct.

The most common reason for retraction because of misconduct is image manipulation, usually of figures or diagrams, a form of deliberate data massaging or, in some cases, straight plagiarism. In their dissection of the LaCour-Green paper, the two graduate students — David Broockman, now an assistant professor at Stanford, and Joshua Kalla, at California-Berkeley — found that a central figure in Mr. LaCour’s analysis looked nearly identical to one from another study. This and other concerns led Dr. Green, who had not seen any original data, to request a retraction. (Mr. LaCour has denied borrowing anything.)

Data massaging can take many forms. It can mean simply excluding “outliers” — unusually high or low data points — from an analysis to generate findings that more strongly support the hypothesis. It also includes moving the goal posts: that is, mining the data for results first, and then writing the paper as if the experiment had been an attempt to find just those effects. “You have exploratory findings, and you’re pitching them as ‘I knew this all along,’ as confirmatory,” Dr. Nosek said.

The second leading cause is plagiarizing text, followed by republishing — presenting the same results in two or more journals.

The fourth category is faked data. No one knows the rate of fraud with any certainty. In a 2011 survey of more than 2,000 psychologists, about 1 percent admitted to falsifying data. Other studies have estimated a rate of about 2 percent. Yet one offender can do a lot of damage. The Dutch social psychologist Diederik Stapel published dozens of studies in major journals for nearly a decade based on faked data, investigators at the universities where he had worked concluded in 2011. Suspicions were first raised by two of his graduate students.

“If I’m a scientist and I fabricate data and put that online, others are going to assume this is accurate data,” said John Budd, a professor at the University of Missouri and an author of one of the first exhaustive analyses of retractions, in 1999. “There’s no way to know” without inside information.

Here, too, Retraction Watch provides a possible solution. Many of the egregious cases that it posts come from tips. The tipsters are a growing cadre of scientists, specialized journalists and other experts who share the blog’s mission — and are usually not insiders working directly with a suspected offender. One of the blog’s most effective allies has been Dr. Steven Shafer, the current editor of the journal Anesthesia & Analgesia who is now at Stanford, whose aggressiveness in re-examining published papers has led to scores of retractions. The field of anesthesia is a leader in retractions, largely because of Dr. Shafer’s efforts, Mr. Marcus and Dr. Oransky said. (Psychology is another leader, largely because of Dr. Stapel.)

Other cases emerge from issues raised at post-publication sites, where scientists dig into papers, sometimes anonymously. Dr. Broockman, one of the two who challenged the LaCour-Green paper, had first made public some of his suspicions anonymously on a message board called poliscirumors.com. Mr. Marcus said Retraction Watch closely followed a similar site, PubPeer.com. “When it first popped up, a lot of people assumed it would be an ax-grinding place,” he said. “But while some contributors have overstepped, I think it has had a positive impact on the literature.”

What these various tipsters, anonymous post-reviewers and whistle-blowers have in common is a nose for data that looks too good to be true, he said. Sites like Retraction Watch and PubPeer give them a place to discuss their concerns and flag fishy-looking data.

These, along with data repositories like Dr. Nosek’s, may render moot the debate over how to exhaustively replicate findings. That burden is likely to be eased by the community of bad-science bloodhounds who have more and more material to work with when they pick up a foul scent.

“At this point, we see ourselves as part of an ecosystem that is advocating for increased transparency,” Dr. Oransky said. “And that ecosystem is growing.”

Darwinism vs. the real world IV

Computing the "Best Case" Probability of Proteins from Actual Data, and Falsifying a Prediction of Darwinism

Kirk Durston July 28, 2015 4:52 PM | 

 

 

Biological life requires thousands of different protein families, about 70 percent of which are "globular" proteins, with a three-dimensional shape that is unique to each family of proteins. An illustration is shown in the picture at the top of this post. This 3D shape is necessary for a particular biological function and is determined by the sequence of the different amino acids that make up that protein. In other words, it is not biology that determines the shape, but physics. Sequences that produce stable, functional 3D structures are so rare that scientists today do not attempt to find them using random sequence libraries. Instead, they use information they have obtained from reverse-engineering biological proteins to intelligently design artificial proteins.
Indeed, our 21st-century supercomputers are not powerful enough to crunch the variables and locate novel 3D structures. Nonetheless, a foundational prediction of neo-Darwinian theory is that a ploddingly slow evolutionary process consisting of genetic drift, mutations, insertions, and deletions must be able to "find" not just one, but thousands of sequences pre-determined by physics that will have different stable, functional 3D structures. So how does this falsifiable prediction hold up when tested against real data? As ought to be the case in science, I have made my program available so that you can run your own data and verify for yourself the kinds of probabilities these protein families represent.
This program can compute an upper limit for the probability of obtaining a protein family from a wealth of actual data contained in the Pfam database. The first step computes the lower limit for the functional complexity or functional information required to code for a particular protein family, using a method published by Durston et al. This value for I(Ex) can then be plugged into an equation published by Hazen et al. in order to solve the probability M(Ex)/N of "finding" a functional sequence in a single trial.
I downloaded 3,751 aligned sequences for the Ribosomal S7 domain, part of a universal protein essential for all life. When the data was run through the program, it revealed that the lower limit for the amount of functional information required to code for this domain is 332 Fits (Functional Bits). The extreme upper limit for the number of sequences that might be functional for this domain is around 10^92. In a single trial, the probability of obtaining a sequence that would be functional for the Ribosomal S7 domain is 1 chance in 10^100 ... and this is only for a 148 amino acid structural domain, much smaller than an average protein.
For another example, I downloaded 4,986 aligned sequences for the ABC-3 family of proteins and ran it through the program. The results indicate that the probability of obtaining, in a single trial, a functional ABC-3 sequence is around 1 chance in 10^128. This method ignores pairwise and higher order relationships within the sequence that would vastly limit the number of functional sequences by many orders of magnitude, reducing the probability even further by many orders of magnitude -- so this gives us a best-case estimate.
What are the implications of these results, obtained from actual data, for the fundamental prediction of neo-Darwinian theory mentioned above? If we assume 10^30 life forms with a fast replication rate of 30 minutes and a huge genome with a very high mutation rate over a period of 10 billion years, an extreme upper limit for the total number of mutations for all of life's history would be around 10^43. Unfortunately, a protein domain such as Ribosomal S7 would require a minimum average of 10^100 trials, about 10^57 trials more than the entire theoretical history of life could provide -- and this is only for one domain. Forget about "finding" an average sized protein, not to mention thousands.
As we all know from probabilities, you can get lucky once, but not thousands of times. This definitively falsifies the fundamental prediction of Darwinian theory that evolutionary processes can "find" functional protein families. A theory that has an essential prediction thoroughly falsified by the data should have no place in science.
Could natural selection come to the rescue? As we know from genetic algorithms, an evolutionary "search" will only work for hill-climbing problems, not for "needle in a haystack" problems. There are small proteins that require such low levels of functional information to perform simple binding tasks that they form a nice hill-climbing problem that can be easily located in a search. This is not the case, however, for the vast majority of protein families. As real data shows, the probability of finding a functional sequence for one average protein family is so low, there is virtually zero chance of obtaining it anywhere in this universe over its entire history -- never mind finding thousands of protein families.
What are the implications for intelligent design science? A testable, falsifiable hypothesis of intelligent design can be stated as follows:

A unique attribute of an intelligent mind is the ability to produce effects requiring a statistically significant level of functional information.

Given the above testable hypothesis, if we observe an effect that requires a statistically significant level of functional information, we can conclude there is an intelligent mind behind the effect. The average protein family requires a statistically significant level of functional, or prescriptive, information. Therefore, the genomes of life have the fingerprints of an intelligent source all over them.

 

A line in the sand XVIII

Tom Wolfe calls out the Darwinian Gestapo

In The New Yorker, Tom Wolfe Compares Persecution of Intelligent Design Advocates to the "Spanish Inquisition"

David Klinghoffer July 28, 2015 10:44 AM

How did we miss this? The comment is brief but pungent to say the least.Interviewed by The New Yorker earlier this year, the great novelist and journalist Tom Wolfe acknowledged that he's writing a book about evolution -- actually, "a history of the theory of evolution from the nineteenth century to the present." No indication of what his overall thesis might be, but he "invokes the Spanish Inquisition when discussing how academics have cast out proponents of intelligent design for 'not believing in evolution the right way.'"

The metaphor is apt, since the Spanish Inquisition was all about rooting out people who held the wrong beliefs in secret. The expulsion of the Jews from Spain in 1492 had already pushed out anyone openly professing Judaism. It was converted Jews, claiming to be loyal to the dominant faith, who were the focus of the inquisitors.

No metaphor is an exact equation between two things -- it wouldn't be a metaphor if it were. But uncovering and punishing those with secret sympathies for ID is indeed a priority for zealous evolutionists, who insist everyone needs to believe in evolution in "the right way." The anxiety this provokes, especially in academia, is something we deal with all the time behind the scenes.

I don't have any idea what view Wolfe takes on ID other than his obviously deploring such intimidation. But we noted a while back that he was seen in the audience when Eric Metaxas interviewed Stephen Meyer about Darwin's Doubt at the Union League Club. It was already known then that Wolfe was writing a book called The Human Beast.

His attitudes are now slowly coming into focus, demonstrating once again the Thomas Nagel Principle, aka the Tom Stoppard Rule: when you reach a certain level of fame and accomplishment, if you are independent-minded, you can say whatever you want without fear. Which in turn gives courage to others lacking your bullet-proof armor. This, I predict, is going to be good.

Origin of life science's blind ally

For the Origin of Life, on Earth or Elsewhere, "Ingredients and Conditions" Aren't Enough
David Klinghoffer July 24, 2015 12:45 PM 


You carefully set out the implements and ingredients on the kitchen counter. Two cans of tuna, bag of egg noodles, block of Cheddar cheese, onion, frozen green peas, condensed cream of mushroom soup, can of sliced mushrooms, a cup of potato chips (for the topping).

Lined up at the ready, a mixing bowl, baking pan, and a pot with water for the noodles. Also a can opener, a grater for the cheese, colander for the pasta, cutting board and knife to chop the onion. Set one burner to high, and the oven to 425 degrees F.

Your family is hungry, but everything is in place! The easy-to-follow recipe gives a prep time of 15 minutes, and 20 more to cook. Of course that's approximate.

Now sit back and relax. How long before these items assemble themselves into a tuna casserole? Pour yourself a glass of wine and watch what happens.

Oh, you're concerned that the stuff has no means of coming together physically? Well, as days pass and you continue to stare intently at your unassembled casserole, perhaps that promised Seattle mega-earthquake comes along and jostles things around.

The cheese collides with the grater. A tuna can knocks into the can opener. The water sloshes in its pot and some gets on the unopened bag of pasta. Throw in a few aftershocks for good measure.

Ridiculous? No more so than stories that are a regular feature of science news that expect incomparably greater wonders to follow automatically when the "ingredients" of life, or some of them, appear to be in place -- whether on a distant, Earth-like exoplanet or on the early Earth itself. This week's pairing comes from NASA and Nature.

NASA reports the discovery of a new world, Kepler-452b some 1,400 light years away, that is seemingly Earth-like in key respects, orbiting in the "habitable zone" around a star like our sun. From Science Daily:

"We can think of Kepler-452b as an older, bigger cousin to Earth, providing an opportunity to understand and reflect upon Earth's evolving environment," said Jon Jenkins, Kepler data analysis lead at NASA's Ames Research Center in Moffett Field, California, who led the team that discovered Kepler-452b. "It's awe-inspiring to consider that this planet has spent 6 billion years in the habitable zone of its star; longer than Earth. That's substantial opportunity for life to arise, should all the necessary ingredients and conditions for life exist on this planet." [Emphasis added.]

Meanwhile on Earth, we're told that the origin of complex life from simpler forms must be even more of a snap than previously assumed. Earlier theorizing said it required a generous infusion of oxygen in the early seas. Now that addition must be seen as more modest. Again, from Science Daily:

If oxygen was a driver of the early evolution of animals, only a slight bump in oxygen levels facilitated it, according to a multi-institutional research team that includes a Virginia Tech geoscientist.

The discovery, published in the journal Nature, calls into question the long held theory that a dramatic change in oxygen levels might have been responsible for the appearance of complicated life forms like whales, sharks, and squids evolving from less complicated life forms, such as microorganisms, algae, and sponges.

The researchers discovered oxygen levels rose in the water and atmosphere, but at lower levels than was thought necessary to trigger life changes.

"We suggest that about 635 million to 542 million years ago, Earth passed some low, but critical, threshold in oxygenation for animals," said Benjamin Gill, an assistant professor of geoscience in the College of Science. "That threshold was in the range of a 10 to 40 percent increase, and was the second time in Earth's history that oxygen levels significantly rose."

Do you follow the logic? If oxygen was "a driver of the early evolution of animals," then only a "slight bump" was needed since that's all that was available.

We've said many times before that whether on our planet or any other, "ingredients and conditions" fall wildly short of being enough to explain the development of life from non-life, or complex from simple.

ENV observed recently:

Visualize an exoplanet far away: dynamic, comfortable, yet lifeless. It has water, plate tectonics, volcanoes, an atmosphere and all the ingredients for life -- but no life. What would be the primary factor distinguishing it from Earth? A new paper in PLOS Biology suggests that its chief drawback, all things being equal, would be a lack of complex specified information.

As for the oxygen idea, that's hopeless. It isn't merely oxygen, but information, that's needed. From our post "Cambrian Animals? Just Add Oxygen":

Once again, we see Darwinists dodging the main problem with the Cambrian explosion: the sudden appearance of biological information necessary to build tissues, organs, limbs, eyes, systems, and body plans. This is the focus of most of Part II of Stephen Meyer's book Darwin's Doubt. Mystically, they imagine animals as eager to evolve but, like racehorses at the gates, held back by environmental barriers.

Actually, that tuna casserole stands a better chance than either of these notions -- expecting life based on "ingredients and conditions" -- since at least the recipe is known. Identifying the ingredients and lining them up in a working kitchen is different from knowing how they're supposed to come together. If life has a recipe, we are utterly ignorant of what that might be, otherwise we would have sparked life ourselves in a laboratory by now.

Your casserole is a complex structure, in the sense of being an unlikely assemblage, but it is also specified or functional. (The function is to serve as a tasty and nutritious meal, more so than the unprepared ingredients.) So too with the structures of life, which in addition give evidence of irreducible complexity.


If you're hungry now, do you think it's only a matter of time before the table can be set and the food served? With these science news items, that is the level of absurdity we're talking about.

1Peter1-5 New American Bible

1)Greeting.*
1
Peter, an apostle of Jesus Christ, to the chosen sojourners of the dispersion* in Pontus, Galatia, Cappadocia, Asia, and Bithynia,a
2
in the foreknowledge of God the Father, through sanctification by the Spirit, for obedience and sprinkling with the blood of Jesus Christ: may grace and peace be yours in abundance.b

Blessing.
3
* Blessed be the God and Father of our Lord Jesus Christ, who in his great mercy gave us a new birth to a living hope through the resurrection of Jesus Christ from the dead,c
4
to an inheritance that is imperishable, undefiled, and unfading, kept in heaven for youd
5
who by the power of God are safeguarded through faith, to a salvation that is ready to be revealed in the final time.
6
* In this you rejoice, although now for a little while you may have to suffer through various trials,e
7
so that the genuineness of your faith, more precious than gold that is perishable even though tested by fire, may prove to be for praise, glory, and honor at the revelation of Jesus Christ.f
8
Although you have not seen him you love him; even though you do not see him now yet believe in him, you rejoice with an indescribable and glorious joy,g
9
as you attain the goal of [your] faith, the salvation of your souls.
10
* Concerning this salvation, prophets who prophesied about the grace that was to be yours searched and investigated it,
11
investigating the time and circumstances that the Spirit of Christ within them indicated when it testified in advance to the sufferings destined for Christ and the glories to follow them.h
12
It was revealed to them that they were serving not themselves but you with regard to the things that have now been announced to you by those who preached the good news to you [through] the holy Spirit sent from heaven, things into which angels longed to look.
Obedience.
13
* Therefore, gird up the loins of your mind,* live soberly, and set your hopes completely on the grace to be brought to you at the revelation of Jesus Christ.
14
Like obedient children, do not act in compliance with the desires of your former ignorance*
15
but, as he who called you is holy, be holy yourselves in every aspect of your conduct,i
16
for it is written, “Be holy because I [am] holy.”j
Reverence.
17
Now if you invoke as Father him who judges impartially according to each one’s works, conduct yourselves with reverence during the time of your sojourning,k
18
realizing that you were ransomed from your futile conduct, handed on by your ancestors, not with perishable things like silver or goldl
19
but with the precious blood of Christm as of a spotless unblemished lamb.*
20
He was known before the foundation of the world but revealed in the final time for you,
21
who through him believe in God who raised him from the dead and gave him glory, so that your faith and hope are in God.
Mutual Love.*
22
Since you have purified yourselves by obedience to the truth for sincere mutual love, love one another intensely from a [pure] heart.n
23
You have been born anew,o not from perishable but from imperishable seed, through the living and abiding word of God,*
24
for:
“All flesh is like grass,
and all its glory like the flower of the field;
the grass withers,
and the flower wilts;p
25
but the word of the Lord remains forever.”

God’s House and People.
1
* Rid yourselves of all malice and all deceit, insincerity, envy, and all slander;a
2
like newborn infants, long for pure spiritual milk so that through it you may grow into salvation,
3
b for you have tasted that the Lord is good.*
4
Come to him, a living stone,* rejected by human beings but chosen and precious in the sight of God,c
5
and, like living stones, let yourselves be built* into a spiritual house to be a holy priesthood to offer spiritual sacrifices acceptable to God through Jesus Christ.d
6
For it says in scripture:

“Behold, I am laying a stone in Zion,
a cornerstone, chosen and precious,
and whoever believes in it shall not be put to shame.”e



2)7
Therefore, its value is for you who have faith, but for those without faith:
“The stone which the builders rejected
has become the cornerstone,”f
8
and
“A stone that will make people stumble,
and a rock that will make them fall.”
They stumble by disobeying the word, as is their destiny.g
9
* But you are “a chosen race, a royal priesthood, a holy nation, a people of his own, so that you may announce the praises” of him who called you out of darkness into his wonderful light.h
10
Once you were “no people”
but now you are God’s people;
you “had not received mercy”
but now you have received mercy.i
Christian Examples.
11
* Beloved, I urge you as aliens and sojourners* to keep away from worldly desires that wage war against the soul.j
12
Maintain good conduct among the Gentiles, so that if they speak of you as evildoers, they may observe your good works and glorify God on the day of visitation.
Christian Citizens.*
13
Be subject to every human institution for the Lord’s sake, whether it be to the king as supremek
14
or to governors as sent by him for the punishment of evildoers and the approval of those who do good.
15
For it is the will of God that by doing good you may silence the ignorance of foolish people.
16
Be free, yet without using freedom as a pretext for evil, but as slaves of God.l
17
Give honor to all, love the community, fear God, honor the king.m
Christian Slaves.
18
* Slaves, be subject to your masters with all reverence, not only to those who are good and equitable but also to those who are perverse.n
19
For whenever anyone bears the pain of unjust suffering because of consciousness of God, that is a grace.
20
But what credit is there if you are patient when beaten for doing wrong? But if you are patient when you suffer for doing what is good, this is a grace before God.
21
For to this you have been called, because Christ also suffered* for you, leaving you an example that you should follow in his footsteps.o
22
“He committed no sin,p
and no deceit was found in his mouth.”*
23
When he was insulted, he returned no insult; when he suffered, he did not threaten; instead, he handed himself over to the one who judges justly.q
24
He himself bore our sins in his body upon the cross, so that, free from sin, we might live for righteousness. By his wounds you have been healed.r
25

For you had gone astray like sheep,s but you have now returned to the shepherd and guardian of your souls.*

Christian Spouses.
1
* Likewise, you wives should be subordinate to your husbands so that, even if some disobey the word, they may be won over without a word by their wives’ conduct
2
when they observe your reverent and chaste behavior.a
3
Your adornment should not be an external one: braiding the hair, wearing gold jewelry, or dressing in fine clothes,b
4
but rather the hidden character of the heart, expressed in the imperishable beauty of a gentle and calm disposition, which is precious in the sight of God.
5
For this is also how the holy women who hoped in God once used to adorn themselves and were subordinate to their husbands;
6
thus Sarah obeyed Abraham, calling him “lord.” You are her children when you do what is good and fear no intimidation.

7
c Likewise, you husbands should live with your wives in understanding, showing honor to the weaker female sex, since we are joint heirs of the gift of life, so that your prayers may not be hindered.*
Christian Conduct.*
8
Finally, all of you, be of one mind, sympathetic, loving toward one another, compassionate, humble.
9
Do not return evil for evil, or insult for insult; but, on the contrary, a blessing, because to this you were called, that you might inherit a blessing.d
10
For:
“Whoever would love lifee
and see good days
must keep the tongue from evil
and the lips from speaking deceit,
11
must turn from evil and do good,
seek peace and follow after it.
12
For the eyes of the Lord are on the righteous
and his ears turned to their prayer,
but the face of the Lord is against evildoers.”



3)Christian Suffering.*
13
Now who is going to harm you if you are enthusiastic for what is good?
14
But even if you should suffer because of righteousness, blessed are you. Do not be afraid or terrified with fear of them,
15
but sanctify Christ as Lord in your hearts. Always be ready to give an explanation to anyone who asks you for a reason for your hope,f
16
but do it with gentleness and reverence, keeping your conscience clear, so that, when you are maligned, those who defame your good conduct in Christ may themselves be put to shame.
17
For it is better to suffer for doing good, if that be the will of God, than for doing evil.
18
For Christ also suffered* for sins once, the righteous for the sake of the unrighteous, that he might lead you to God. Put to death in the flesh, he was brought to life in the spirit.g
19
In it he also went to preach to the spirits in prison,*
20
who had once been disobedient while God patiently waited in the days of Noah during the building of the ark, in which a few persons, eight in all, were saved through water.h
21
This prefigured baptism, which saves you now. It is not a removal of dirt from the body but an appeal to God* for a clear conscience, through the resurrection of Jesus Christ,i
22

who has gone into heaven and is at the right hand of God, with angels, authorities, and powers subject to him.j

Christian Restraint.*
1
Therefore, since Christ suffered in the flesh, arm yourselves also with the same attitude (for whoever suffers in the flesh has broken with sin),
2
so as not to spend what remains of one’s life in the flesh on human desires, but on the will of God.
3
For the time that has passed is sufficient for doing what the Gentiles like to do: living in debauchery, evil desires, drunkenness, orgies, carousing, and wanton idolatry.a
4
They are surprised that you do not plunge into the same swamp of profligacy, and they vilify you;
5
but they will give an account to him who stands ready to judge the living and the dead.b
6
For this is why the gospel was preached even to the dead* that, though condemned in the flesh in human estimation, they might live in the spirit in the estimation of God.

4)Christian Charity.*
7
The end of all things is at hand. Therefore, be serious and sober for prayers.
8
c Above all, let your love for one another be intense, because love covers a multitude of sins.*
9
Be hospitable to one another without complaining.d
10
As each one has received a gift, use it to serve one another as good stewards of God’s varied grace.e
11
Whoever preaches, let it be with the words of God; whoever serves, let it be with the strength that God supplies, so that in all things God may be glorified through Jesus Christ,f to whom belong glory and dominion forever and ever. Amen.*
Trial of Persecution.*
12
Beloved, do not be surprised that a trial by fire is occurring among you, as if something strange were happening to you.g
13
But rejoice to the extent that you share in the sufferings of Christ, so that when his glory is revealed you may also rejoice exultantly.h
14
If you are insulted for the name of Christ, blessed are you, for the Spirit of glory and of God rests upon you.i
15
But let no one among you be made to suffer as a murderer, a thief, an evildoer, or as an intriguer.
16
But whoever is made to suffer as a Christian should not be ashamed but glorify God because of the name.
17
For it is time for the judgment to begin with the household of God; if it begins with us, how will it end for those who fail to obey the gospel of God?j
18
“And if the righteous one is barely saved,
where will the godless and the sinner appear?”k
19

As a result, those who suffer in accord with God’s will hand their souls over to a faithful creator as they do good.

5)Advice to Presbyters.*
1
So I exhort the presbyters* among you, as a fellow presbyter and witness to the sufferings of Christ and one who has a share in the glory to be revealed.
2
Tend the flock of God in your midst, [overseeing] not by constraint but willingly, as God would have it, not for shameful profit but eagerly.a
3
Do not lord it over those assigned to you, but be examples to the flock.
4
b And when the chief Shepherd is revealed, you will receive the unfading crown of glory.*

Advice to the Community.*
5
Likewise, you younger members,* be subject to the presbyters. And all of you, clothe yourselves with humility in your dealings with one another, for:
“God opposes the proud
but bestows favor on the humble.”c
6
So humble yourselves under the mighty hand of God, that he may exalt you in due time.d
7
Cast all your worries upon him because he cares for you.e
8
Be sober and vigilant. Your opponent the devil is prowling around like a roaring lion looking for [someone] to devour.f
9
Resist him, steadfast in faith, knowing that your fellow believers throughout the world undergo the same sufferings.
10
The God of all grace who called you to his eternal glory through Christ [Jesus] will himself restore, confirm, strengthen, and establish you after you have suffered a little.g
11
To him be dominion forever. Amen.
12
I write you this briefly through Silvanus,* whom I consider a faithful brother, exhorting you and testifying that this is the true grace of God. Remain firm in it.
13
The chosen one* at Babylon sends you greeting, as does Mark, my son.
14

Greet one another with a loving kiss. Peace to all of you who are in Christ.h

On Religious Images

What does God’s Word say about the making of images used as objects of worship?

Ex. 20:4, 5, JB: “You shall not make yourself a carved image or any likeness of anything in heaven or on earth beneath or in the waters under the earth; you shall not bow down to them or serve them [“bow down before them or worship them,” NAB]. For I, Yahweh your God, am a jealous God.” (Italics added.) (Notice that the prohibition was against making images and bowing down before them.)

Lev. 26:1, JB: “You must make no idols; you must set up neither carved image nor standing-stone [“sacred pillar,” NW], set up no sculptured stone in your land, to prostrate yourselves in front of it; for it is I, Yahweh, who am your God.” (No image before which people might bow in worship was ever to be set up.)

2 Cor. 6:16, JB: “The temple of God has no common ground with idols, and that is what we are—the temple of the living God.”

1 John 5:21, NAB: “My little children, be on your guard against idols [“idols,” Dy, CC; “false gods,” JB].”

May images be used simply as aids in worship of the true God?

John 4:23, 24, JB: “True worshippers will worship the Father in spirit and truth: that is the kind of worshipper the Father wants. God is spirit, and those who worship must worship in spirit and truth.” (Those who rely on images as aids to devotion are not worshiping God “in spirit” but they depend on what they can see with their physical eyes.)

2 Cor. 5:7, NAB: “We walk by faith, not by sight.”

Isa. 40:18, JB: “To whom could you liken God? What image could you contrive of him?”

Acts 17:29, JB: “Since we are the children of God, we have no excuse for thinking that the deity looks like anything in gold, silver or stone that has been carved and designed by a man.”

Isa. 42:8, JB: “My name is Yahweh, I will not yield my glory to another, nor my honour to idols [“graven things,” Dy].”

Should we venerate “saints” as intercessors with God, perhaps using images of them as aids in our worship?

Acts 10:25, 26, JB: “As Peter reached the house Cornelius went out to meet him, knelt at his feet and prostrated himself. But Peter helped him up. ‘Stand up,’ he said ‘I am only a man after all!’” (Since Peter did not approve of such adoration when he was personally present, would he encourage us to kneel before an image of him? See also Revelation 19:10.)

John 14:6, 14, JB: “Jesus said: ‘I am the Way, the Truth and the Life. No one can come to the Father except through me. If you ask for anything in my name, I will do it.’” (Jesus here clearly states that our approach to the Father can be only through him and that our requests are to be made in Jesus’ name.)

1 Tim. 2:5, JB: “There is only one God, and there is only one mediator between God and mankind, himself a man, Christ Jesus.” (There is no allowance here for others to serve in the role of mediator for the members of Christ’s congregation.)

See also pages 353, 354, under the heading “Saints.”

Do worshipers have in mind primarily the person represented by an image, or are some images viewed as being superior to others?

The attitude of worshipers is an important factor to consider. Why? Because a key difference between an “image” and an “idol” is the use to which an image is put.

In the mind of the worshiper, does one image of a person have greater value or importance than another image of the same person? If so, it is the image, not the person, that the worshiper has primarily in mind. Why do people make long pilgrimages to worship at certain shrines? Is it not the image itself that is viewed as having “miraculous” powers? For example, in the book Les Trois Notre-Dame de la Cathédrale de Chartres, by the canon Yves Delaporte, we are told regarding images of Mary in the cathedral in Chartres, France: “These images, sculptured, painted or appearing on the stained glass windows, are not equally famous. . . . Only three are the object of a real worship: Our Lady of the Crypt, Our Lady of the Pillar, and Our Lady of the ‘Belle Verriere.’” But if worshipers had primarily in mind the person, not the image, one image would be considered to be just as good as another, would it not?

How does God view images that are objects of worship?

Jer. 10:14, 15, JB: “Every goldsmith blushes for the idol he has made, since his images are nothing but delusion, with no breath in them. They are a Nothing, a laughable production.”

Isa. 44:13-19, JB: “The wood carver takes his measurements, outlines the image with chalk, carves it with chisels, following the outline with dividers. He shapes it to human proportions, and gives it a human face, for it to live in a temple. He cut down a cedar, or else took a cypress or an oak which he selected from the trees in the forest, or maybe he planted a cedar and the rain made it grow. For the common man it is so much fuel; he uses it to warm himself, he also burns it to bake his bread. But this fellow makes a god of it and worships it; he makes an idol of it and bows down before it. Half of it he burns in the fire, on the live embers he roasts meat, eats it and is replete. He warms himself too. ‘Ah!’ says he ‘I am warm; I have a fire here!’ With the rest he makes his god, his idol; he bows down before it and worships it and prays to it. ‘Save me,’ he says ‘because you are my god.’ They know nothing, understand nothing. Their eyes are shut to all seeing, their heart to all reason. They never think, they lack the knowledge and wit to say, ‘I burned half of it on the fire, I baked bread on the live embers, I roasted meat and ate it, and am I to make some abomination of what remains? Am I to bow down before a block of wood?’”

Ezek. 14:6, JB: “The Lord Yahweh says this: Come back, renounce your idols [“dungy idols,” NW] and give up all your filthy practices.”

Ezek. 7:20, JB: “They used to pride themselves on the beauty of their jewellery, out of which they made their loathsome images and idols. That is why I mean to make it an object of horror [“uncleanness,” Dy; “refuse,” NAB] to them.”

How should we feel about any images that we may formerly have venerated?

Deut. 7:25, 26, JB: “You must set fire to all the carved images of their gods, not coveting the gold and silver that covers them; take it and you will be caught in a snare: it is detestable to Yahweh your God. You must not bring any detestable thing into your house or you, like it, will come under the ban too. You must regard them as unclean and loathsome [“thoroughly loathe it and absolutely detest it,” NW].” (While Jehovah’s people today are not authorized to destroy images that belong to other people, this command to Israel provides a pattern as to how they should view any images in their possession that they may have venerated. Compare Acts 19:19.)

1 John 5:21, Dy: “Little children, keep yourselves from idols [“false gods,” JB].”

Ezek. 37:23, JB: “They will no longer defile themselves with their idols . . . They shall be my people and I will be their God.”

What effect could use of images in worship have on our own future?

Deut. 4:25, 26, JB: “If you act perversely, making a carved image in one shape or another [“some idol,” Kx; “any similitude,” Dy], doing what displeases Yahweh and angers him, on that day I will call heaven and earth to witness against you; . . . you shall be utterly destroyed.” (God’s viewpoint has not changed. See Malachi 3:5, 6.)

1 Cor. 10:14, 20, JB: “This is the reason, my dear brothers, why you must keep clear of idolatry. . . . The sacrifices that they offer they sacrifice to demons who are not God. I have no desire to see you in communion with demons.”

Rev. 21:8, JB: “The legacy for cowards, for those who break their word, or worship obscenities, for murderers and fornicators, and for fortune-tellers, idolaters or any other sort of liars, is the second death [ftn., “eternal death”] in the burning lake of sulphur.”

Ps. 115:4-8, JB (113:4-8, second set of numbers, Dy): “Their idols, in silver and gold, products of human skill, have mouths, but never speak, eyes, but never see, ears, but never hear, noses, but never smell, hands, but never touch, feet, but never walk, and not a sound from their throats. Their makers will end up like them, and so will anyone who relies on them.”

On Apostolic Succession

Was Peter the “rock” on which the church was built?

Matt. 16:18, JB: “I now say to you: You are Peter and on this rock I will build my Church. And the gates of the underworld can never hold out against it.” (Notice in the context [vss. 13, 20] that the discussion centers on the identity of Jesus.)

Whom did the apostles Peter and Paul understand to be the “rock,” the “cornerstone”?

Acts 4:8-11, JB: “Peter, filled with the Holy Spirit, addressed them, ‘Rulers of the people, and elders! . . . it was by the name of Jesus Christ the Nazarene, the one you crucified, whom God raised from the dead, by this name and by no other that this man is able to stand up perfectly healthy, here in your presence, today. This is the stone rejected by you the builders, but which has proved to be the keystone [“cornerstone,” NAB].’”
1 Pet. 2:4-8, JB: “Set yourselves close to him [the Lord Jesus Christ] so that you too . . . may be living stones making a spiritual house. As scripture says: See how I lay in Zion a precious cornerstone that I have chosen and the man who rests his trust on it will not be disappointed. That means that for you who are believers, it is precious; but for unbelievers, the stone rejected by the builders has proved to be the keystone, a stone to stumble over, a rock to bring men down.”
Eph. 2:20, JB: “You are part of a building that has the apostles and prophets for its foundations, and Christ Jesus himself for its main cornerstone.”
What was the belief of Augustine (who was viewed as a saint by the Catholic Church)?
“In this same period of my priesthood, I also wrote a book against a letter of Donatus . . . In a passage in this book, I said about the Apostle Peter: ‘On him as on a rock the Church was built.’ . . . But I know that very frequently at a later time, I so explained what the Lord said: ‘Thou art Peter, and upon this rock I will build my Church,’ that it be understood as built upon Him whom Peter confessed saying: ‘Thou art the Christ, the Son of the living God,’ and so Peter, called after this rock, represented the person of the Church which is built upon this rock, and has received ‘the keys of the kingdom of heaven.’ For, ‘Thou art Peter’ and not ‘Thou art the rock’ was said to him. But ‘the rock was Christ,’ in confessing whom as also the whole Church confesses, Simon was called Peter.”—The Fathers of the Church—Saint Augustine, the Retractations (Washington, D.C.; 1968), translated by Mary I. Bogan, Book I, p. 90.
Did the other apostles view Peter as having primacy among them?
Luke 22:24-26, JB: “A dispute arose also between them [the apostles] about which should be reckoned the greatest, but he said to them, ‘Among pagans it is the kings who lord it over them, and those who have authority over them are given the title Benefactor. This must not happen with you.’” (If Peter were the “rock,” would there have been any question as to which one of them “should be reckoned the greatest”?)
Since Jesus Christ, the head of the congregation, is alive, does he need successors?
Heb. 7:23-25, JB: “Then there used to be a great number of those other priests [in Israel], because death put an end to each one of them; but this one [Jesus Christ], because he remains for ever, can never lose his priesthood. It follows, then, that his power to save is utterly certain, since he is living for ever to intercede for all who come to God through him.”
Rom. 6:9, JB: “Christ, as we know, having been raised from the dead will never die again.”
Eph. 5:23, JB: “Christ is head of the Church.”
What were “the keys” entrusted to Peter?

Matt. 16:19, JB: “I will give you the keys of the kingdom of heaven: whatever you bind on earth shall be considered bound in heaven; whatever you loose on earth shall be considered loosed in heaven.”

In Revelation, Jesus referred to a symbolic key used by himself to open up privileges and opportunities to humans
Rev. 3:7, 8, JB: “Here is the message of the holy and faithful one who has the key of David, so that when he opens, nobody can close, and when he closes, nobody can open: . . . I have opened in front of you a door that nobody will be able to close.”
Peter used “keys” entrusted to him to open up (to Jews, Samaritans, Gentiles) the opportunity to receive God’s spirit with a view to their entering the heavenly Kingdom
Acts 2:14-39, JB: “Peter stood up with the Eleven and addressed them in a loud voice: ‘Men of Judaea, and all you who live in Jerusalem . . . God has made this Jesus whom you crucified both Lord and Christ.’ Hearing this, they were cut to the heart and said to Peter and the apostles, ‘What must we do, brothers?’ ‘You must repent,’ Peter answered ‘and every one of you must be baptised in the name of Jesus Christ for the forgiveness of your sins, and you will receive the gift of the Holy Spirit. The promise that was made is for you and your children, and for all those who are far away, for all those whom the Lord our God will call to himself.’”
Acts 8:14-17, JB: “When the apostles in Jerusalem heard that Samaria had accepted the word of God, they sent Peter and John to them, and they went down there, and prayed for the Samaritans to receive the Holy Spirit, for as yet he had not come down on any of them: they had only been baptised in the name of the Lord Jesus. Then they laid hands on them, and they received the Holy Spirit.” (Verse 20 indicates that Peter was the one taking the lead on this occasion.)
Acts 10:24-48, JB: “They reached Caesarea the following day, and Cornelius [an uncircumcised Gentile] was waiting for them. . . . Peter addressed them . . . While Peter was still speaking the Holy Spirit came down on all the listeners.”
Did heaven wait on Peter to make decisions and then follow his lead?
Acts 2:4, 14, JB: “They were all filled with the Holy Spirit, and began to speak foreign languages as the Spirit gave them the gift of speech. . . . Then [after Christ, the head of the congregation, had stirred them up by means of the holy spirit] Peter stood up with the Eleven and addressed them.” (See verse 33.)
Acts 10:19, 20, JB: “The Spirit had to tell him [Peter], ‘Some men have come to see you. Hurry down, and do not hesitate about going back with them [to the home of the Gentile Cornelius]; it was I who told them to come.’”
Compare Matthew 18:18, 19.
Is Peter the judge as to who is worthy to enter the Kingdom?
2 Tim. 4:1, JB: “Christ Jesus . . . is to be judge of the living and the dead.”
2 Tim. 4:8, JB: “All there is to come now is the crown of righteousness reserved for me, which the Lord [Jesus Christ], the righteous judge, will give to me on that Day; and not only to me but to all those who have longed for his Appearing.”
Was Peter in Rome?

Rome is referred to in nine verses of the Holy Scriptures; none of these say that Peter was there. First Peter 5:13 shows that he was in Babylon. Was this a cryptic reference to Rome? His being in Babylon was consistent with his assignment to preach to the Jews (as indicated at Galatians 2:9), since there was a large Jewish population in Babylon. The Encyclopaedia Judaica (Jerusalem, 1971, Vol. 15, col. 755), when discussing production of the Babylonian Talmud, refers to Judaism’s “great academies of Babylon” during the Common Era.

Has an unbroken line of successors been traced from Peter to modern-day popes?

Jesuit John McKenzie, when professor of theology at Notre Dame, wrote: “Historical evidence does not exist for the entire chain of succession of church authority.”—The Roman Catholic Church (New York, 1969), p. 4.

The New Catholic Encyclopedia admits: “ . . . the scarcity of documents leaves much that is obscure about the early development of the episcopate . . . ”—(1967), Vol. I, p. 696.

Claims of divine appointment mean nothing if those who make them are not obedient to God and Christ

Matt. 7:21-23, JB: “It is not those who say to me, ‘Lord, Lord’, who will enter the kingdom of heaven, but the person who does the will of my Father in heaven. When the day comes many will say to me, ‘Lord, Lord, did we not prophesy in your name, cast out demons in your name, work many miracles in your name?’ Then I shall tell them to their faces: I have never known you; away from me, you evil men!”

See also Jeremiah 7:9-15.

Have the claimed successors to the apostles adhered to the teachings and practices of Jesus Christ and his apostles?

A Catholic Dictionary states: “The Roman Church is Apostolic, because her doctrine is the faith once revealed to the Apostles, which faith she guards and explains, without adding to it or taking from it.” (London, 1957, W. E. Addis and T. Arnold, p. 176) Do the facts agree?

Identity of God
“The Trinity is the term employed to signify the central doctrine of the Christian religion.”—The Catholic Encyclopedia (1912), Vol. XV, p. 47.
“Neither the word Trinity, nor the explicit doctrine as such, appears in the New Testament . . . The doctrine developed gradually over several centuries and through many controversies.”—The New Encyclopædia Britannica (1976), Micropædia, Vol. X, p. 126.
“There is the recognition on the part of exegetes and Biblical theologians, including a constantly growing number of Roman Catholics, that one should not speak of Trinitarianism in the New Testament without serious qualification. There is also the closely parallel recognition on the part of historians of dogma and systematic theologians that when one does speak of an unqualified Trinitarianism, one has moved from the period of Christian origins to, say, the last quadrant of the 4th century.”—New Catholic Encyclopedia (1967), Vol. XIV, p. 295.
Celibacy of the clergy
Pope Paul VI, in his encyclical Sacerdotalis Caelibatus (Priestly Celibacy, 1967), endorsed celibacy as a requirement for the clergy, but he admitted that “the New Testament which preserves the teaching of Christ and the Apostles . . . does not openly demand celibacy of sacred ministers . . . Jesus Himself did not make it a prerequisite in His choice of the Twelve, nor did the Apostles for those who presided over the first Christian communities.”—The Papal Encyclicals 1958-1981 (Falls Church, Va.; 1981), p. 204.
1 Cor. 9:5, NAB: “Do we not have the right to marry a believing woman like the rest of the apostles and the brothers of the Lord and Cephas?” (“Cephas” is an Aramaic name given to Peter; see John 1:42. See also Mark 1:29-31, where reference is made to the mother-in-law of Simon, or Peter.)
1 Tim. 3:2, Dy: “It behoveth, therefore, a bishop to be . . . the husband of one wife [“married only once,” NAB].”
Before the Christian era, Buddhism required its priests and monks to be celibate. (History of Sacerdotal Celibacy in the Christian Church, London, 1932, fourth ed., revised, Henry C. Lea, p. 6) Even earlier, the higher orders of the Babylonian priesthood were required to practice celibacy, according to The Two Babylons by A. Hislop.—(New York, 1943), p. 219.
1 Tim. 4:1-3, JB: “The Spirit has explicitly said that during the last times there will be some who will desert the faith and choose to listen to deceitful spirits and doctrines that come from the devils; . . . they will say marriage is forbidden.”
Separateness from the world
Pope Paul VI, when addressing the United Nations in 1965, said: “The peoples of the earth turn to the United Nations as the last hope of concord and peace; We presume to present here, together with Our own, their tribute of honor and of hope.”—The Pope’s Visit (New York, 1965), Time-Life Special Report, p. 26.
John 15:19, JB: “[Jesus Christ said:] If you belonged to the world, the world would love you as its own; but because you do not belong to the world, because my choice withdrew you from the world, therefore the world hates you.”
Jas. 4:4, JB: “Don’t you realise that making the world your friend is making God your enemy?”
Resorting to weapons of war
Catholic historian E. I. Watkin writes: “Painful as the admission must be, we cannot in the interest of a false edification or dishonest loyalty deny or ignore the historical fact that Bishops have consistently supported all wars waged by the government of their country. I do not know in fact of a single instance in which a national hierarchy has condemned as unjust any war . . . Whatever the official theory, in practice ‘my country always right’ has been the maxim followed in wartime by Catholic Bishops.”—Morals and Missiles (London, 1959), edited by Charles S. Thompson, pp. 57, 58.
Matt. 26:52, JB: “Jesus then said, ‘Put your sword back, for all who draw the sword will die by the sword.’”
1 John 3:10-12, JB: “In this way we distinguish the children of God from the children of the devil: anybody . . . not loving his brother is no child of God’s. . . . We are to love one another; not to be like Cain, who belonged to the Evil One and cut his brother’s throat.”
In the light of the foregoing, have those who claim to be successors to the apostles really taught and practiced what Christ and his apostles did?