The Watchtower Society's commentary on the book of Jeremiah

JEREMIAH, BOOK OF

Prophecies and a historical record written by Jeremiah at the direction of Jehovah. Jeremiah was commissioned as prophet in the 13th year of King Josiah (647 B.C.E.) to warn the southern kingdom, Judah, of her impending destruction. This was less than a century after the prophet Isaiah’s activity and the fall of Israel, the northern kingdom, to the Assyrians.

Arrangement. The book is not arranged chronologically, but, rather, according to subject matter. Dating is presented where necessary, but the majority of the prophecies are applicable to the nation of Judah throughout the general period of the reigns of Josiah, Jehoahaz, Jehoiakim, Jehoiachin, and Zedekiah. God repeatedly told Jeremiah that the nation was incorrigibly wicked, beyond reform. Yet those with right hearts were given full opportunity to reform and find deliverance. As to being prophetic for our day, the arrangement does not affect the understanding and application of Jeremiah’s writings.

When Written. For the most part, the book of Jeremiah was not written at the time he declared the prophecies. Rather, Jeremiah evidently did not put any of his proclamations into writing until he was commanded by Jehovah, in the fourth year of King Jehoiakim (625 B.C.E.), to dictate all the words given him by Jehovah to date. This included not only words spoken about Judah in Josiah’s time but also proclamations of judgment on all the nations. (Jer 36:1, 2) The resulting scroll was burned by Jehoiakim when Jehudi read it to him. But Jeremiah was ordered to write it over, which he did through his secretary Baruch, with many additional words.—36:21-23, 28, 32.

The remainder of the book was evidently added later, including the introduction, which mentions the 11th year of Zedekiah (Jer 1:3), other prophecies that Jeremiah wrote down at the time he was to deliver them (30:2; 51:60), and the letter to the exiles in Babylon (29:1). Additionally, the proclamations uttered during the reign of Zedekiah and the accounts of the events after Jerusalem’s fall, down to about 580 B.C.E., were added later. It may be that, although the scroll written by Baruch was the basis for a large part of the book, Jeremiah afterward edited and arranged it when adding later sections.

Authenticity. The authenticity of Jeremiah is generally accepted. Only a few critics have challenged it on the basis of the differences in the Hebrew Masoretic text and the Greek Septuagint as found in the Alexandrine Manuscript. There are more variations between the Hebrew and the Greek texts of the book of Jeremiah than in any other book of the Hebrew Scriptures. The Greek Septuagint is said to be shorter than the Hebrew text by about 2,700 words, or one eighth of the book. The majority of scholars agree that the Greek translation of this book is defective, but that does not lessen the reliability of the Hebrew text. It has been suggested that the translator may have had a Hebrew manuscript of a different “family,” a special recension, but critical study reveals that this apparently was not the case.

The fulfillment of the prophecies recorded by Jeremiah, together with their content, strongly testifies to the book’s authenticity. Among the numerous prophecies of Jeremiah are those listed on the chart on page 34.

Principles and Qualities of God. Besides the fulfillments that we have listed, the book sets forth principles that should guide us. It stresses that formalism is of no value in God’s eyes but that he desires worship and obedience from the heart. The inhabitants of Judah are told not to trust in the temple and its surrounding buildings and are admonished: “Get yourselves circumcised to Jehovah, and take away the foreskins of your hearts.”—Jer 4:4; 7:3-7; 9:25, 26.

The book furnishes many illustrations revealing God’s qualities and his dealings with his people. Jehovah’s great loving-kindness and mercy are exemplified in his delivering a remnant of his people and finally restoring them to Jerusalem, as prophesied by Jeremiah. God’s appreciation and consideration for those showing kindness to his servants and his being the Rewarder of those who seek him and show obedience are highlighted in his care for the Rechabites, for Ebed-melech, and for Baruch.—Jer 35:18, 19; 39:16-18; 45:1-5.

Jehovah is brilliantly portrayed as the Creator of all things, the King to time indefinite, the only true God. He is the only one to be feared, the Corrector and Director of those calling on his name, and the one under whose denunciation no nation can hold up. He is the Great Potter, in whose hand individuals and nations are as clay pottery, for him to work with or destroy as he pleases.—Jer 10; 18:1-10; Ro 9:19-24.

The book of Jeremiah reveals that God expects the people bearing his name to be a glory and a praise to him and that he considers them close to him. (Jer 13:11) Those who prophesy falsely in his name, saying “peace” to those with whom God is not at peace, have to account to God for their words, and they will stumble and fall. (6:13-15; 8:10-12; 23:16-20) Those standing before the people as priests and prophets have great responsibility before God, for, as he told those in Judah: “I did not send the prophets, yet they themselves ran. I did not speak to them, yet they themselves prophesied. But if they had stood in my intimate group, then they would have made my people hear my own words, and they would have caused them to turn back from their bad way and from the badness of their dealings.”—23:21, 22.

As in other books of the Bible, God’s holy nation is considered to be in relationship to him as a wife, and unfaithfulness to him is “prostitution.” (Jer 3:1-3, 6-10; compare Jas 4:4.) Jehovah’s own loyalty to his covenants, however, is unbreakable.—Jer 31:37; 33:20-22, 25, 26.

Many are the fine principles and illustrations in the book, upon which the other Bible writers have drawn for reference. And many other pictorial and prophetic patterns are found that have application and vital meaning to the modern-day Christian and his ministry.

[Box on page 33]

HIGHLIGHTS OF JEREMIAH

A record of Jehovah’s judgment proclamations through Jeremiah, as well as an account of the prophet’s own experiences and of Babylon’s destruction of Jerusalem

Writing was begun about 18 years before Jerusalem fell, and was completed some 27 years after that event

Youthful Jeremiah is commissioned as a prophet

He will have “to tear down” as well as “build” and “plant”

Jehovah will strengthen him for the commission (1:1-19)

Jeremiah fulfills his commission “to tear down”

He exposes the wickedness in Judah and proclaims the certainty of Jerusalem’s destruction; the presence of the temple will not save the unfaithful nation; God’s people will be exiles for 70 years in Babylon (2:1–3:13; 3:19–16:13; 17:1–19:15; 24:1–25:38; 29:1-32; 34:1-22)

Judgments are announced against Zedekiah and Jehoiakim, as well as against false prophets, unfaithful shepherds, and faithless priests (21:1–23:2; 23:9-40; 27:1–28:17)

Jehovah foretells humiliating defeats of many nations, including the Babylonians (46:1–51:64)

Jeremiah carries out his assignment “to build” and “to plant”

He points to the restoration of an Israelite remnant and the raising up of “a righteous sprout” (3:14-18; 16:14-21; 23:3-8; 30:1–31:26; 33:1-26)

He also announces that Jehovah will conclude a new covenant with his people (31:27-40)

At Jehovah’s direction, Jeremiah buys a field in order to illustrate the certainty that Israel will return from exile (32:1-44)

He assures the Rechabites that they will survive, because they obeyed their forefather Jehonadab; their obedience shows up Israel’s disobedience to Jehovah (35:1-19)

He reproves Baruch and strengthens him with the assurance of surviving the coming calamity (45:1-5)

Jeremiah suffers because of his bold prophesying

He is struck and placed in the stocks overnight (20:1-18)

A plot is hatched to kill him for proclaiming the destruction of Jerusalem, but the princes deliver him (26:1-24)

The king burns Jeremiah’s scroll; Jeremiah is falsely accused of deserting to the Babylonians and is arrested and confined (36:1–37:21)

Finally, he is put into a miry cistern to die; Ebed-melech rescues him and is promised protection during the coming destruction of Jerusalem (38:1-28; 39:15-18)

Events from the fall of Jerusalem until the flight into Egypt

Jerusalem falls; King Zedekiah is captured, his sons are slain, and he is blinded and taken to Babylon (52:1-11)

The temple and great houses of Jerusalem are burned, and most of the people are led off into exile (39:1-14; 52:12-34)

Gedaliah is appointed governor over the few Israelites remaining, but he is assassinated (40:1–41:9)

Fearful, the people flee to Egypt; Jeremiah warns that Egypt itself will fall and that calamity will overtake them in that land (41:10–44:30)

[Box on page 34]

PROPHECIES RECORDED BY JEREMIAH

Ones That He Saw Fulfilled

The captivity of Zedekiah and destruction of Jerusalem by Nebuchadnezzar, king of Babylon (Jer 20:3-6; 21:3-10; 39:6-9)

The dethronement and death in captivity of King Shallum (Jehoahaz) (Jer 22:11, 12; 2Ki 23:30-34; 2Ch 36:1-4)

The taking captive of King Coniah (Jehoiachin) to Babylon (Jer 22:24-27; 2Ki 24:15, 16)

The death, within one year, of the false prophet Hananiah (Jer 28:16, 17)

Some of the Rechabites and Ebed-melech the Ethiopian surviving Jerusalem’s destruction (Jer 35:19; 39:15-18)

Others Concerning Which History Records Fulfillment

Egypt invaded, conquered by Nebuchadrezzar (Nebuchadnezzar) (Jer 43:8-13; 46:13-26)

The return of the Jews and rebuilding of the temple and the city after 70 years’ desolation (Jer 24:1-7; 25:11, 12; 29:10; 30:11, 18, 19; compare 2Ch 36:20, 21; Ezr 1:1; Da 9:2.)

Ammon laid waste (Jer 49:2)

Edom cut off as a nation (Jer 49:17, 18) (With the death of the Herods, Edom became extinct as a nation.)

Babylon to become a permanent desolation (Jer 25:12-14; 50:35, 38-40)

Those Having Significant Spiritual Fulfillment, as Indicated in the Christian Greek Scriptures

A new covenant made with the house of Israel and the house of Judah (Jer 31:31-34; Heb 8:8-13)

David’s house not to lack a man on the throne of the kingdom forever (Jer 33:17-21; Lu 1:32, 33)


Fall of Babylon the Great an enlargement and symbolic application of Jeremiah’s words against ancient Babylon, as the following comparisons show: Jer 50:2—Re 14:8; Jer 50:8; 51:6, 45—Re 18:4; Jer 50:15, 29—Re 18:6, 7; Jer 50:23—Re 18:8, 15-17; Jer 50:38—Re 16:12; Jer 50:39, 40; 51:37—Re 18:2; Jer 51:8—Re 18:8-10, 15, 19; Jer 51:9, 49, 56—Re 18:5; Jer 51:12—Re 17:16, 17; Jer 51:13—Re 17:1, 15; Jer 51:48—Re 18:20; Jer 51:55—Re 18:22, 23; Jer 51:63, 64—Re 18:21

The blind mariner II

Research by Dembski and Marks Makes Inroads in Technical Literature

Casey Luskin July 29, 2015 1:19 PM



Intelligent design is making unmistakable progress in mainstream scientific thinking. Here's an example from a new paper in the journal of Soft Computing, "Heuristic algorithm based on molecules optimizing their geometry in a crystal to solve the problem of integer factorization." It cites the work of leading ID researchers William Dembski and Robert Marks of the Evolutionary Informatics Laboratory -- quite favorably so, not in order to critique them.

The paper discusses integer factorization, or how we determine what prime numbers can be multiplied to yield another particular integer. This is essentially a search problem with applications in cryptography and other computer science questions. As the article explains:

Because of the computational intractability in factoring large semi-prime numbers, it is often used in public-key cryptography (PKC) such as RSA cryptosystems used in digital signatures, communication and e-commerce.
This is a very difficult problem but some algorithms have been developed to solve it. Which search algorithms are more efficient than others at solving the search? That is the precise question that Dembski and Marks set out to answer. The paper continues:
To quantify the quality of an objective function, we analyze our objective functions based on conservation of information in search theory (Dembski and Marks 2009).
Dembski and Marks have developed a principle called the "conservation of information" which says that if an algorithm does better than blind search, that is because it was given prior information, where the amount of prior information equals at least the measure of how far the algorithm outperforms blind search. Searches can thus perform better than a random search when they are fed information (called "Active Information") to help find the target. According to their methodology, Exogenous Information (I‡) represents the difficulty of a search in finding its target with no prior information about the target's location. Active Information (I+) is the amount of information smuggled in by intelligence to aid the search algorithm in finding its target. Endogenous Information (Is) then measures the difficulty the search will have in finding its target after the addition of Active Information. Thus, I+ = I‡ - Is.
After discussing various methods of solving the problem of integer factorization, the new paper in Soft Computing asks how the methods compare. They authors write:

In this section, we analyze our objective function based on conservation of information in search (Dembski and Marks 2009). We know that exactly two integers will exist, those are the prime factors of the semi-prime under consideration. Therefore for a semi-prime number, N, the probability of finding the two factors using a random search is

eq9.jpg (9)

Therefore, the endogenous information (Dembski and Marks 2009) measure is:
IΩ = -log p = 2 log N. (10)

Now, to measure the exogenous information (Dembski and Marks 2009), we need to know the problem-specific structure that the search algorithm takes into account. For example, if we just evolve one single factor using the objective function as defined in Eq. (3), then the probability of finding that factor is

q = 1/N (11)

Hence, the exogenous information measure (Dembski and Marks 2009) will be

Is = −log q = log N. (12)

Therefore, the active information measure (Dembski and Marks 2009) for this will be

I+ = log N (13).

After discussing how this methodology relates to solving a search question, they conclude, "The conservation of information in search provides a way to quantify the quality of an objective function."
What does all this have to do with Darwinian evolution? The research by Dembksi and Marks is applicable to essentially any search function. While this paper focuses on solving the problem of searching for prime numbers that can be multiplied to yield a given integer, Darwinian evolution is, at its heart, also a search algorithm. It uses a trial-and-error process of random mutation and unguided natural selection to find genotypes (i.e., DNA sequences) that lead to phenotypes (i.e., biomolecules and body plans) characterized by high fitness (i.e., fostering survival and reproduction).

Dembski and Marks explain that unless you start off with some information indicating where peaks in a fitness landscape may lie, any search -- including a Darwinian one -- is on average no better than a random search.

In some cases, even a random search can work when you have lots of probabilistic resources (i.e., time and opportunities for computation) or when there are lots of targets out there waiting to be found. Thus, Darwinian evolution can work when only one mutation is needed to give some advantage and when evolution takes place within a large, rapidly reproducing population (like we often see in bacteria).


But when targets are rare and there aren't lots of opportunities for the search (e.g., trying to evolve a complex multimutation feature in long-lived organisms like humans with small effective breeding populations), then such a random search won't work. The paper under discussion here doesn't get into any of that. It does, however, show the utility of Dembski and Marks's ideas in testing the efficiency of a search function -- an extremely important question in the context of evaluating Darwinian evolution.

Darwinism vs. The real world. V

Cardiovascular Function: What Happens When Real Numbers Are Wrong?

Howard Glicksman July 31, 2015 1:57 PM

Editor's note: Physicians have a special place among the thinkers who have elaborated the argument for intelligent design. Perhaps that's because, more than evolutionary biologists, they are familiar with the challenges of maintaining a functioning complex system, the human body. With that in mind, Evolution News & Views is delighted to present this series, "The Designed Body." Dr. Glicksman practices palliative medicine for a hospice organization.

Due to the laws of nature, the body must have enough energy for its trillions of cells to work properly. The body won't function very well if its cells don't have enough oxygen (O₂).

Evolutionary biologists claim that the organs described so far in this series, and the systems that control them, must have come about by chance and the laws of nature alone. But their theory seems to account only for how life looks and not how it actually works to stay alive under the laws of nature. Experience teaches that real numbers have real consequences when it comes to life and death.

Based on what we know about how the body actually works, our earliest ancestors had to be able to provide at least 3,500 mL/min of O₂, mainly to their muscles and heart, to be able to run fast enough and fight hard enough to win the battle for survival. That would have required their lungs to have a rapid enough airflow, a large enough volume, and an efficient enough gas exchange to bring in enough O₂. It would also have required that they have enough iron to make enough hemoglobin to be able to carry enough O₂ in the blood. And finally, their cardiac output (CO) needed to be at least 25 L/min to sustain the kind of activity levels needed to hunt rather than be hunted.

As I've noted in previous articles, lung function, hemoglobin production, and cardiac output are controlled by irreducibly complex systems, each consisting of sensors, integrators, and effectors that must also inherently know what is needed for survival. I call this natural survival capacity, because the systems involved must naturally have the capacity to keep a specific chemical or physical parameter within a certain range to allow for survival. We have looked at what happens to the body when its lung function and hemoglobin production do not measure up to what is needed. Now we will start to look at what happens when cardiac function is not up to snuff.

At rest the average male needs about 250 mL/min of O₂ to keep all of his organs working properly, and any increase in activity requires more. Walking slowly requires 500 mL/min of O₂; walking quickly, 1,000 mL/min; moderate jogging, 2,000 mL/min; and fast running, 3,500 mL/min of O₂. Since we know that the CO has to be at least 25 L/min for maximum activity, we can figure out what the minimum CO levels would have to be for lesser activity levels. We can do this by multiplying 25 L/min by the ratio of the lower and maximum O₂ consumption. So to jog at a moderate pace, the minimum CO would have to be 25 x 2,000/3500 = 14.3 L/min. To walk quickly would take at least a CO of 7.2 L/min, to walk slowly a CO of 3.6 L/min, and to stay at rest would need a CO of 1.8 L/min.

It is important to note here that these are real numbers that reflect real life and the laws of nature. No matter what evolutionary biologists say about how matter must have organized itself into the complex systems we know are needed for life, medical science tells you that if you don't have a CO of 7.2 L/min, you can't walk very quickly, if you don't have a CO of 3.6 L/min, it would be very difficult for you to walk even slowly, and if you don't have a CO of at least 1.8 L/min, you are probably dead. Certain parameters of cardiac function had to be met for our ancestors to survive within the laws of nature, and no expenditure of imaginary effort can deny this fact.

When real numbers lead to chronic debility with respect to the lungs, they usually involve problems with ventilation and/or gas exchange. But when dealing with chronic debility and the heart, we usually encounter four different problems. Each condition, individually, is capable of causing significant debility but, in real life, they often occur in combination. Just as adding a gas exchange problem to a ventilation problem can more quickly lead to worsening debility from pulmonary dysfunction, so too a combination of more than one of these cardiac conditions can quickly lead to significant weakness and a limited ability to be active and manage independently.

The commonest heart condition in developed countries, and what most people think of when they hear someone has heart trouble, is coronary artery disease. Even though the heart pumps blood throughout the body, it must also supply adequate blood flow to itself so it can do its job. As the blood flows out of the left ventricle through the aortic valve, the coronary arteries turn back over the surface of the heart. The heart is the hardest working muscle in the body and when its blood supply is compromised this can lead to significant debility and even death.

Another common cardiac condition is valvular heart disease. The "V" shaped one-way valves between the atria and the ventricles and the ventricles and their outflow tracts are structured in a way that allows them, when open, to facilitate the forward movement of blood, and when closed, to prevent blood from going backward. The efficiency of cardiac function is dependent not only on adequate coronary blood flow, but also on properly working valves. A valve can't be too tight, slowing forward blood flow, or too lax, allowing backward flow.

When the heart cannot meet the metabolic needs of the body it is said to be in heart failure. This third common cardiac condition can involve either the left or the right side of the heart alone, or both at the same time. In addition, left ventricular failure can be systolic, where reduced muscle contractility leads to weaker pumping action, and/or diastolic, where increased muscle stiffness reduces relaxation and the filling of the ventricle with blood. Both coronary artery and valvular heart disease are common causes of heart failure.

The fourth common cardiac condition is the cardiac arrhythmias. It is the sino-atrial node, the natural pacemaker in the right atrium that dominates the other excitable cells in the heart. It controls the heart rate and starts coordinated atrial contraction and the conducting system makes sure that coordinated ventricular contraction takes place soon afterward. Any disruption or short-circuiting of this signal formation, impulse conduction or coordinated muscle contraction can lead to significant debility and even death. All three of the conditions mentioned above, and other disorders, can predispose the heart to cardiac arrhythmias.

When real numbers lead to functional problems of the heart, these are usually the four main conditions that contribute to the situation. In the next few articles we will take a closer look at each of them.

It's Design all the way down III

The Puzzle of Perfection, Thirty Years On

Evolution News & Views July 31, 2015 3:18 AM 

Thirty years ago in his book Evolution: A Theory in Crisis, Michael Denton (above) posed "The Puzzle of Perfection" as a challenge to Darwinism. He described molecular machines in the cell as phenomena inexplicable by chance. He predicted that what was known in 1985 was sure to grow, concluding:

It would be an illusion to think that what we are aware of at present is any more than a fraction of the full extent of biological design. In practically every field of fundamental biological research ever-increasing levels of design and complexity are being revealed at an ever-increasing rate. The credibility of natural selection is weakened, therefore, not only by the perfection we have already glimpsed but by the expectation of further as yet undreamt of depths of ingenuity and complexity. (Denton, p. 82)

If the design argument is scientifically credible, it should get stronger with time. The counter-position of natural selection should correspondingly weaken. Was the perfection of cellular machines an illusion in 1985? Has Darwinian theory risen to the challenge in the meantime? Denton's prediction was made before details of ATP synthase, the bacterial flagellum, and kinesin had come to light (see Denton's 2014 description of kinesins and myosins here). And two recent papers suggest that, if anything, the evidence for design has only grown stronger.

The authors of the first paper, published in PNAS, seem hesitant to use the word "perfect" in their description of ATP synthase, the machine that generates energy currency for most cellular processes in all living things (see our animation of this amazing machine here). They use "near-perfect" in the title and throughout the paper:

ATP synthase produces most of the ATP in respiratory and photosynthetic cells. It is a rotary motor enzyme and its catalytic portion F₁-ATPase hydrolyzes ATP to drive rotation of the central γ subunit. Efficiency of chemomechanical energy conversion by this motor is always near-perfect under different ATP hydrolysis energy (ΔG_ATP) conditions. [Emphasis added.]

Any deviation from perfection, however, could be due to experimental error. In their graph, the error bars transverse the slope for 100 percent efficiency (that is, for conversion of chemical energy to mechanical work). It may well be as close to perfect as is physically possible. What's even more striking is that this "near-perfect" level of efficiency is maintained throughout a "broad range" of operation conditions.

The authors found a "simple" model that maintains this near-perfect efficiency. In the F₁ subunit of ATP synthase, where ATP is synthesized or dissociated (depending on the direction of energy flow), they deduced a spring mechanism that generates a "sawtooth" pattern of mechanical work. The spring automatically adjusts for varying conditions:

The chemomechanical energy conversion efficiency of F1 is close to 100% under various ΔG_ATP conditions. The torque profile found here explains how F₁ achieves this remarkable task. Fig. 5C illustrates how F₁ responds to the increase of [ATP] andadjusts its mechanical work accordingly. The equilibrium constants for nucleotide bindings/dissociations are functions of the γ angle. Therefore, as [ATP] is increased, the angular position of binding/dissociation of ATP shifts to the left (Fig. 5C, red arrow) at the point where the spring is shorter. The shorter the spring becomes, the greater the force to extend becomes because of the nature of a spring (Fig. 5B). This shift invariably increases the area of the sawtooth, that is, the mechanical work. This study shows that the following two properties of the torque profile of the F₁ motor ensure ∼100% energy conversion under various ΔG_ATP conditions: (i) shift of the angular positions of binding/dissociation of substrates according to their concentrations and (ii) changing its force (torque) according to the angular position of substrate binding/dissociation, which isreadily accomplished by a simple spring.

Since each of three catalytic sites has this mechanism, there are three springs in the motor. The "sawtooth" is the torque profile, consisting of three steep jumps and linear descents during each catalytic turnover. The shape of the sawtooth adjusts according to concentration or binding angle because of spring-like action inside the machine. It is "simple" only in the author's model to explain the observations. But hey -- if a simple mechanism achieves perfection, who's complaining? The authors didn't disparage this complex machine's efficiency. They twice called it "remarkable." By the way, is anyone surprised to hear that neither Darwin nor evolution is mentioned in the paper?

Perfection in Gene Translation

The second paper explores the amazing process of gene translation. A set of twenty machines helps translate the genetic code into the protein code. It's a shame the set doesn't have a cool name. They are called the "amino-acyl tRNA synthetases." Fortunately, we can call them aaRS for short. Their job is to read the transfer-RNA (tRNA) triplet codons and charge them with the appropriate amino acids. When the charged tRNAs match up with the messenger RNA (mRNA) codons in the ribosome (if the aaRS's did their job accurately), the correct string of amino acids links up to build a protein. The aaRS enzymes are the keys to the genetic code. They link the DNA code to the protein code.

There are twenty normal amino acids in proteins, but 64 possible combinations of triplet codons from the four DNA bases. The aaRS enzymes have to be able to handle situations where one amino acid may correspond to one to six codons. Not all codons link up with equal ease (there may be reasons for that). That's enough to make an aaRS enzyme's job hard, but it also has to discriminate between similar amino acids, like valine and isoleucine. (Remember, molecular machines have no eyes. This occurs in the dark, by touch.) Additionally, the aaRS enzymes have to work fast.

The d-value is a measure of the system's accuracy, with the maximum representing perfect accuracy. But like the auto mechanic dealing with a frantic businessman with a repair emergency, there's a trade-off: "You want it done fast, or you want it done right?" Since d-values can vary by a factor of 400, some situations could bring translation to a halt if accuracy is of paramount concern.

A team of four from Uppsala University, also publishing in PNAS, examined this trade-off problem. They found that cells are much more clever providing both accuracy and speed than anyone knew 30 years ago. First, a little history from 1957:

The existence of maximal accuracy limits (d values) in amino acid discrimination by an amino acid-selecting protein wassuggested years ago by Linus Pauling. He proposed that these dvalues would be very small for pairs of similar amino acids. For discrimination between valine and isoleucine he estimated a dvalue of 10, leading to the proposal of high intracellular amino acid substitution error frequency, which turned out not to be true. We now know that Pauling greatly underestimated the d value by which the isoleucine-specific aa-tRNA synthetase (IleRS) discriminates against valine, but the notion of d-value limits for enzymatic selections has since continued to guide experimental research on replication, transcription, and genetic code translation.

In fact, the discovery of substrate proofreading was inspired by the challenge of how to transcend the accuracy limits postulated by Pauling.

So there you have it. The cell has a way to get both arms of the tradeoff. First, it goes as fast as it can. Then, other molecular machines proofread the result! Here is a clear case where the expectation of design perfection inspired a major discovery. Somehow, the author's Lamarckian explanation is unconvincing:

From our results we suggest that proofreading has evolved in bacterial protein synthesis to minimize damage on the bacterial proteome by amino acid substitution errors due to initial tRNA selection error hot spots as identified here and maybe others that remain to be found from larger datasets.

While one shares their hope that "future extensions will serve as an inspiration and testing ground for theoretical approaches to explain the accuracy of codon reading," approaches based on design theory are bound to be much more productive than evolutionary approaches that hope perfection might be reached by blind processes.

The Puzzle of Perfection, c. 2015

As these papers illustrate, Denton was right. His "expectation of further as yet undreamt of depths of ingenuity and complexity" has been amply fulfilled.

But it's not just seen in the realm of molecular machines. Throughout all biology -- from the tiniest bacterial cell to the greatest of multicellular organisms -- we see exceptional ingenuity and complexity of design.

Illustra's new film Living Waters includes a wonderful example of an "engineering problem" that was solved ingeniously in the male reproductive organs of the humpback whale. The testes would have had to move inside the body cavity when the whale supposedly evolved from a land mammal, but the heat inside would have killed sperm cells, causing sterility -- the end of the line in evolution. We don't want to give away the solution before you watch the film; suffice it to say that Biologic Institute evolutionary biologist Richard Sternberg, who studied the situation, calls it "an elegant solution to the problem; it's beautiful. It's anatomically complex."

In the film, Tim Standish shows another example of design perfection in salmon, which can discriminate odors at the level of parts per trillion, recalling combinations of odors they had memorized as juveniles.

As Sternberg concludes, the flip side of Darwin's proposal of natural selection as a designer substitute is that "things look designed -- because they are designed." Whether in a whale or a bacterial cell, "things look too optimal," he adds, "to have been cobbled together by some haphazard mechanism."

The invincible scroll II

The Bible—A Remarkable Story of Survival

THE Bible is the most widely distributed book in history—an estimated 4.8 billion copies have already been circulated. In 2007 alone, more than 64,600,000 copies were produced. To put that into perspective, consider that the best-selling work of fiction that year had an initial printing of 12 million copies in the United States.

On its way to becoming the world’s most published book, the Bible survived many hazards. Down through history, it has been banned and burned, and those who would translate it have been oppressed and killed. Yet, one of the greatest threats to the continued existence of the Bible was, not the sudden heat of persecution, but the slow process of decay. Why so?

The Bible is a compilation of 66 smaller books, the oldest of which were written or compiled over 3,000 years ago by members of the nation of Israel. The original writers and those who copied the texts recorded the inspired messages on perishable materials, such as papyrus and leather. None of the original writings have yet been discovered. But thousands of ancient copies of small and large sections of the books of the Bible have been unearthed. A fragment of one of these books, the Gospel of John, dates to within just a few decades of the original document written by the apostle John.

“The transmission of the text of the Hebrew Bible [Old Testament] is of extraordinary exactitude, without parallel in Greek and Latin classical literature.”—Professor Julio Trebolle Barrera

Why is it remarkable that any copies of the Bible have survived? And how accurately do modern Bibles reflect the messages recorded by the original writers?

What Happened to Other Ancient Documents?

The survival of the Bible is extraordinary, considering what happened to the writings of nations contemporary with the Israelites. The Phoenicians, for instance, were neighbors of the Israelites during the first millennium B.C.E. These sea traders spread their alphabetic writing system throughout the Mediterranean area. They also profited from an extensive papyrus trade with Egypt and the Greek world. Even so, the National Geographic magazine observes regarding the Phoenicians: “Their writings, mostly on fragile papyrus, disintegrated—so that we now know the Phoenicians mainly by the biased reports of their enemies. Although the Phoenicians themselves reportedly had a rich literature, it was totally lost in antiquity.”

What about the writings of the ancient Egyptians? The hieroglyphics they carved or painted on temple walls and elsewhere are well-known. The Egyptians are also famous for developing papyrus as a writing material. However, regarding Egyptian records written on papyrus, Egyptologist K. A. Kitchen says: “It has been estimated that some 99 percent of all papyri written from circa 3000 down to the advent of Greco-Roman times have perished completely.”

What about Roman records that were written on papyrus? Consider this example. According to the book Roman Military Records on Papyrus, Roman soldiers were apparently paid three times a year, and a record of the pay was made on papyrus pay vouchers. It is estimated that during the 300 years from Augustus (27 B.C.E.–14 C.E.) to Diocletian (284-305 C.E), there were 225,000,000 individual pay records. How many have survived? Only two have been found that are legible.

Why have so few ancient documents written on papyrus survived? Perishable materials, such as papyrus and another common writing material, leather, decay quickly in damp climates. The Anchor Bible Dictionary says: “Because of the climate, papyrus documents from this period [the first millennium B.C.E.] are likely to be preserved only if they are in a dry desert and in a cave or shelter.”

What About the Bible Texts?

The original Bible books were evidently written on material as fragile as that used by the Phoenicians, Egyptians, and Romans. Why, then, did the material contained in the Bible survive to become the world’s most published book? Professor James L. Kugel provides one reason. He says that the original writings were copied “many, many times even within the biblical period itself.”

How do modern translations of the Bible compare with ancient manuscripts? Professor Julio Trebolle Barrera, a member of the team of experts charged with studying and publishing the ancient manuscripts known as the Dead Sea Scrolls, says: “The transmission of the text of the Hebrew Bible is of extraordinary exactitude, without parallel in Greek and Latin classical literature.” Respected Bible scholar F. F. Bruce says: “The evidence for our New Testament writings is ever so much greater than the evidence for many writings of classical authors, the authenticity of which no one dreams of questioning.” He continues: “If the New Testament were a collection of secular writings, their authenticity would generally be regarded as beyond all doubt.” Certainly, the Bible is a remarkable book. Do you make time to read it each day.

On Jesus's resurrection body.

After Jesus’ Resurrection, Was His Body Flesh or Spirit?

The Bible’s answer

The Bible says that Jesus “was put to death in the flesh but made alive [resurrected] in the spirit.”—1 Peter 3:18; Acts 13:34; 1 Corinthians 15:45;2 Corinthians 5:16.

Jesus’ own words showed that he would not be resurrected with his flesh-and-blood body. He said that he would give his “flesh in behalf of the life of the world,” as a ransom for mankind. (John 6:51; Matthew 20:28) If he had taken back his flesh when he was resurrected, he would have canceled that ransom sacrifice. This could not have happened, though, for the Bible says that he sacrificed his flesh and blood “once for all time.”—Hebrews 9:11, 12.

If Jesus was raised up with a spirit body, how could his disciples see him?

• Spirit creatures can take on human form. For example, angels who did this in the past even ate and drank with humans. (Genesis 18:1-8; 19:1-3) However, they still were spirit creatures and could leave the physical realm.—Judges 13:15-21.
• After his resurrection, Jesus also assumed human form temporarily, just as angels had previously done. As a spirit creature, though, he was able to appear and disappear suddenly. (Luke 24:31; John 20:19, 26) The fleshly bodies that he materialized were not identical from one appearance to the next. Thus, even Jesus’ close friends recognized him only by what he said or did.—Luke 24:30, 31, 35; John 20:14-16; 21:6, 7.
• When Jesus appeared to the apostle Thomas, he took on a body with wound marks. He did this to bolster Thomas’ faith, since Thomas doubted that Jesus had been raised up.—John 20:24-29.

Decanonising Science II

Should we have faith in science? Part II: peer-reviewed science papers
Thursday, February 26, 2015 - 12:51

Kirk Durston



The primary way scientific discoveries and advances are disseminated is through peer-reviewed papers published in scientific journals. The first step is to submit a paper to a journal. Those that survive preliminary filtering by the editor are sent out to be reviewed by qualified scientists in the field. On the basis of the reviewers’ recommendations, the paper is accepted or rejected. Only a fraction of papers submitted for publication make it through this peer-review process and are published.

One would hope that such a process would justify a high level of confidence in scientific publications, but recent findings suggest that our faith in peer-reviewed publications in mainstream journals of science may be on somewhat shaky ground.

The journal Nature, in a paper calling for increased standards in pre-clinical research, revealed that out of 53 papers presenting ‘landmark’ published findings in the field of haematology and oncology, only 6 could be confirmed by subsequent laboratory teams. For the 89% of papers that failed to have their results reproduced, it was found that blind control group analyses was inadequate or data had been selected to support the hypothesis and other data set aside.

Worse still, some of the papers that could not be experimentally reproduced, launched ‘an entire field, with hundreds of secondary publications that expanded on elements of the original observation, but did not actually seek to confirm or falsify its fundamental basis’.

Hundreds of other peer-reviewed, published science papers based on faulty initial papers!

Nature reported in October 2011 that although the number of submissions had increased by 44% over the past ten years, the number of retractions had increased by roughly 900%.

Austin Hughes, in a paper published in the Proceedings of the National Academy of Sciences, focusing on the origin of adaptive phenotypes laments, ‘Thousands of papers are published every year claiming evidence of adaptive evolution on the basis of computational analyses alone, with no evidence whatsoever regarding the phenotypic effects of allegedly adaptive mutations.’ He concludes that ‘This vast outpouring of pseudo-Darwinian hype has been genuinely harmful to the credibility of evolutionary biology as a science.’ Jerry Fodor and Massimo Piattelli-Palmarini write in New Scientist,

"Much of the vast neo-Darwinian literature is distressingly uncritical. The possibility that anything is seriously amiss with Darwin’s account of evolution is hardly considered. … The methodological skepticism that characterizes most areas of scientific discourse seems strikingly absent when Darwinism is the topic."

How can we distinguish the good papers from the poor? This can be very difficult without actually attempting to reproduce their findings. Short of that, apply the same critical thinking skills and healthy skepticism to scientific papers that you do for political, historical or religious claims. 21st century science can often be heavily influenced by poor experimental practices, unproven computational models, political agendas, competition for funding, and scientism (atheism dressed up as science). When going over a paper ask questions like, how large was the data set? What sort of statistical analysis was performed? Are there other papers that independently support or disconfirm these findings? What is not being discussed? One thing for sure, don’t accept something simply because ‘hundreds’ or even ‘thousands’ of papers say so, especially if Darwinian evolution is the topic. Practice critical thinking with the question in the back of your mind, 'Is this one of those papers that will be retracted?'.

Read Part III

Further reading:

http://www.nature.com/nature/journal/v483/n7391/full/483531a.html#t1

http://www.nature.com/news/publishing-the-peer-review-scam-1.16400

http://www.nytimes.com/2012/04/17/science/rise-in-scientific-journal-retractions-prompts-calls-for-reform.html?ref=science

http://dingo.sbs.arizona.edu/~massimo/publications/PDF/JF_MPP_darwinisms...


http://www.nytimes.com/2015/06/16/science/retractions-coming-out-from-under-science-rug.html?