On letting the Bible speak for itself:The Watchtower Society's commentary.

“Let Us Compare Scripture With Scripture”

A MAN found a pamphlet on the floor of a railway car bound for New York City. ‘The human soul is mortal,’ said the pamphlet. Intrigued, the man, a minister, started to read. He was amazed because he had never before doubted the teaching of the immortality of the soul. At the time, he could not tell who had written the pamphlet. Still, he found the argument plausible and Scriptural and the material worthy of serious study.

The minister was George Storrs. The incident took place in 1837, the year that Charles Darwin first recorded in his notebook thoughts that would later develop into his theory of evolution. The world was still religious, and most people believed in God. Many read the Bible and looked up to it as having authority.

Storrs later found out that the pamphlet was written by Henry Grew of Philadelphia, Pennsylvania. Grew held fast to the principle that “the scripture . . . is its own best interpreter.” Grew and his associates had been studying the Bible with the aim of conforming their lives and activities to its counsel. Their studies revealed some beautiful Scriptural truths.


Stimulated by Grew’s writing, Storrs carefully looked into what the Scriptures had to say about the soul and discussed the matter with some of his fellow ministers. After five years of serious study, Storrs finally decided to publicize his newly found gem of Scriptural truth. At first, he prepared one sermon to give on a Sunday in 1842. However, he felt the need to give a few more sermons to do justice to the subject. Eventually, his sermons on the mortality of the human soul numbered six, which he published in Six Sermons. Storrs compared scripture with scripture in order to uncover the beautiful truth buried beneath the God-dishonoring doctrines of Christendom.

Does the Bible Teach the Immortality of the Soul?

The Bible speaks of Jesus’ anointed followers putting on immortality as a reward for their faithfulness. (1 Corinthians 15:50-56) If immortality is a reward for the faithful, Storrs reasoned, the soul of the wicked cannot be immortal. Instead of speculating, he went to the Scriptures. He considered Matthew 10:28, King James Version, which reads: “Fear him which is able to destroy both soul and body in hell.” So the soul can be destroyed. He also referred to Ezekiel 18:4, which says: “The soul that sinneth, it shall die.” (KJ) When the whole Bible was put into  perspective, the beauty of the truth stood out. “If the view I take of this subject be correct,” wrote Storrs, “then many portions of Scripture, which have been obscure on the common theory, become clear, beautiful and full of meaning and force.”

But what about scriptures like Jude 7? It reads: “Even as Sodom and Gomorrha, and the cities about them in like manner, giving themselves over to fornication, and going after strange flesh, are set forth for an example, suffering the vengeance of eternal fire.” (KJ) Reading this text, some may conclude that the souls of those who were killed in Sodom and Gomorrah are tormented by fire forever. “Let us compare Scripture with Scripture,” wrote Storrs. He then quoted 2 Peter 2:5, 6, which reads: “And spared not the old world, but saved Noah . . . , bringing in the flood upon the world of the ungodly; and turning the cities of Sodom and Gomorrha into ashes condemned them with an overthrow, making them an ensample unto those that after should live ungodly.” (KJ) Yes, Sodom and Gomorrah were turned into ashes, destroyed forever with their inhabitants.

“Peter throws light on Jude,” Storrs explained. “Both together show most clearly what displeasures God has manifested against sinners. . . . Those judgments inflicted on the old world, Sodom and Gomorrah, are a standing, and perpetual, or ‘eternal’ admonition, warning, or ‘example’ to all men to the end of the world.” So Jude referred to the effect of the fire that destroyed Sodom and Gomorrah as eternal. That in no way alters the fact that the human soul is mortal.


Storrs was not putting together scriptures that supported his view while ignoring others. He considered the context of each text as well as the overall tenor of the Bible. If a verse seemed to contradict other scriptures, Storrs looked into the rest of the Bible for a logical explanation.

Russell’s Studies in the Scriptures

Among those who became associated with George Storrs was a young man who was organizing a Bible study group in Pittsburgh, Pennsylvania. His name was Charles Taze Russell. One of his first articles on Scriptural themes was published in 1876 in the magazine Bible Examiner, edited by Storrs. Russell acknowledged that earlier Bible students had an influence on him. Later, as the editor of Zion’s Watch Tower, he appreciated Storrs’ giving him much assistance, by both word and pen.

At the age of 18, C. T. Russell organized a Bible study class and established a pattern for studying the Bible. A. H. Macmillan, a Bible student associated with Russell, described this method: “Someone would raise a question. They would discuss it. They would look up all related scriptures on the point and then, when they were satisfied on the harmony of these texts, they would finally state their conclusion and make a record of it.”


Russell was convinced that the Bible, when taken as a whole, must reveal a message harmonious and consistent with itself and with the character of its Divine Author. Whenever any part of the Bible seemed difficult to understand, Russell felt that it should be clarified and interpreted by other parts of the Bible.

Scriptural Tradition

However, neither Russell nor Storrs nor Grew was the first to let the Scriptures become their own interpreter. The tradition goes all the way back to the Founder of Christianity, Jesus Christ. He used a number of scriptures to clarify the true meaning of a text. For instance, when the Pharisees  criticized his disciples for plucking heads of grain on the Sabbath, Jesus demonstrated from the account recorded at 1 Samuel 21:6 how the Sabbath law should be applied. The religious leaders were familiar with that account, in which David and his men ate the loaves of presentation. Jesus then referred to the part of the Law that said that only the Aaronic priests were to eat the showbread. (Exodus 29:32, 33; Leviticus 24:9) Still, David was told to go ahead and eat the loaves. Jesus concluded his persuasive argument by quoting from the book of Hosea: “If you had understood what this means, ‘I want mercy, and not sacrifice,’ you would not have condemned the guiltless ones.” (Matthew 12:1-8) What a wonderful example of comparing a scripture with other scriptures to reach an accurate understanding!


The apostle Paul proved his point by references to scriptures
Jesus’ followers held to the pattern of using scripture references to shed light upon a scripture. When the apostle Paul taught people in Thessalonica, “he reasoned with them from the Scriptures, explaining and proving by references that it was necessary for the Christ to suffer and to rise from the dead.” (Acts 17:2, 3) In his divinely inspired letters too, Paul let the Bible become its own interpreter. Writing to the Hebrews, for instance, he quoted one scripture after another to prove that the Law was a shadow of the good things to come.—Hebrews 10:1-18.


Yes, sincere Bible students in the 19th and early 20th centuries were simply restoring this Christian pattern. The tradition of comparing scriptures with other scriptures continues in the Watchtower magazine. (2 Thessalonians 2:15) Jehovah’s Witnesses use this principle when they analyze a scripture.

Let the Context Speak

When we are reading the Bible, how can we imitate the fine examples of Jesus and his faithful followers? First, we can consider the immediate context of the scripture in question. How can the context help us understand the meaning? To illustrate, let us take Jesus’ words recorded at Matthew 16:28: “Truly I say to you that there are some of those standing here that will not taste death at all until first they see the Son of man coming in his kingdom.” Some may feel that these words were not fulfilled because all of Jesus’ disciples who were present when he said those words died before the establishment of God’s Kingdom in the heavens. The Interpreter’s Bible even says of this verse: “The prediction was not fulfilled, and later Christians found it necessary to explain that it was metaphorical.”


However, the context of this verse, as well as that of the parallel accounts by Mark and Luke, helps us understand the real meaning of the scripture. What did Matthew relate right after the words quoted above? He wrote: “Six days later Jesus took Peter and James and John his brother along and brought them up into a lofty mountain by themselves. And he was transfigured before them.” (Matthew 17:1, 2) Both Mark and Luke also linked Jesus’ comment about the Kingdom with the account of the transfiguration. (Mark 9:1-8; Luke 9:27-36) Jesus’ coming in Kingdom power was demonstrated in his transfiguration, his appearing in glory in the presence of the three apostles. Peter verifies this understanding by speaking of “the power and presence of our Lord Jesus Christ” with regard to his witnessing Jesus’ transfiguration.—2 Peter 1:16-18.

Do You Let the Bible Be Its Own Interpreter?

What if you cannot understand a scripture even after you have considered its context? You may benefit from comparing it with other scriptures, having in mind the overall tenor of the Bible. One excellent tool  for doing this can be found in the New World Translation of the Holy Scriptures, now available in whole or in part in 57 languages. This tool is a list of marginal references, or cross-references, that appears in the center column of each page in many of its editions. You can find more than 125,000 of them in the New World Translation of the Holy Scriptures—With References. The “Introduction” to that Bible explains: “A careful comparison of the marginal references and an examination of the accompanying footnotes will reveal the interlocking harmony of the 66 Bible books, proving that they comprise one book, inspired by God.”

Let us see how use of the cross-references can help us to understand a scripture. Take the example of the history of Abram, or Abraham. Consider this question: Who took the lead when Abram and his family went out of Ur? Genesis 11:31 reads: “Terah took Abram his son and Lot, . . . and Sarai his daughter-in-law, . . . and they went with him out of Ur of the Chaldeans to go to the land of Canaan. In time they came to Haran and took up dwelling there.” Just reading this, one might conclude that Abram’s father, Terah, took the lead. However, in the New World Translation, we find 11 cross-references on this verse. The last one takes us to Acts 7:2, where we read Stephen’s admonition to the first-century Jews: “The God of glory appeared to our forefather Abraham while he was in Mesopotamia, before he took up residence in Haran, and he said to him, ‘Go out from your land and from your relatives and come on into the land I shall show you.’” (Acts 7:2, 3) Was Stephen confusing this with Abram’s leaving Haran? Obviously not, for this is part of the inspired Word of God.—Genesis 12:1-3.

Why, then, does Genesis 11:31 state that “Terah took Abram his son” and others of his family and went out of Ur? Terah was still the patriarchal head. He agreed to go with Abram and thus was credited with moving the family to Haran. By comparing and harmonizing these two scriptures, we can see in our mind’s eye exactly what took place. Abram respectfully convinced his father to go out of Ur in accord with God’s command.


When we read the Scriptures, we should take into account the context and the overall tenor of the Bible. Christians are admonished: “We received, not the spirit of the world, but the spirit which is from God, that we might know the things that have been kindly given us by God. These things we also speak, not with words taught by human wisdom, but with those taught by the spirit, as we combine spiritual matters with spiritual words.” (1 Corinthians 2:11-13) Indeed, we must implore Jehovah for help to understand his Word and try to “combine spiritual matters with spiritual words” by checking the context of the scripture in question and by looking up related scriptures. May we keep finding brilliant gems of truth through the study of God’s Word.

And even yet more iconoclasm.

Scott Turner’s Purpose and Desire — An Important New Voice in the Evolution Debate
David Klinghoffer | @d_klinghoffer

The crisis of evolutionary biology is spoken of openly here and by scientists who are professed advocates of intelligent design. It is acknowledged in much more circumspect terms by other scientists who know they would be hounded and punished by colleagues for doing so in the public arena. You have to look carefully at what they admit in professional journals, when they think laypeople aren’t listening.

However, a forthcoming book by biologist J. Scott Turner,  Purpose & Desire: What Makes Something “Alive” and Why Modern Darwinism Has Failed to Explain It,  is a real shot across the bow. Dr. Turner’s last book, from Harvard University Press, was The Tinkerer’s Accomplice: How Design Emerges from Life Itself.  The new book, from HarperOne, is aimed not at an academic audience but straight at the broadest thoughtful reading public.

Turner is a delightful, clear, and highly engaging writer, and he sets out his argument against smug Darwinism forthrightly. As he shows, biology itself is in crisis, having failed to grapple with the enigma of what life really is.

From the Preface:

[T]here sits at the heart of modern Darwinism an unresolved tautology that undermines its validity. We scientists might not be troubled by this, but we should be, not least because the failure to recognize it closes off modern evolutionism from many big problems it should be capable of answering: the origin of life, the origin of the gene, biological design, and the origins of cognition and consciousness, to name a few. Intentionality and purposefulness are important to all these unresolved big questions, and yet we are very quick to fence these off behind a wall of denial. Instead of a frank acknowledgment of purposefulness, intentionality, intelligence, and design, we refer to “apparent” design, “apparent” intentionality, “apparent” intelligence.

The latest biologist to come out swinging at Darwinism, Turner is not an ID proponent. He teaches at the State University of New York College of Environmental Science and Forestry.

And this is not a review – you will be hearing more about Purpose & Desire, here and elsewhere, in weeks to come and more so when the book is published on September 12. Instead I want to invite you to take advantage of a great pre-order deal.  See here for details All you have to do is pre-order from Amazon, Barnes & Noble, or other selected venders, and you get two free e-books, Fire-Maker: How Humans Were Designed to Harness Fire and Transform Our Planet, by Michael Denton, and Metamorphosis, which I edited as a companion to the Illustra Media documentary of the same name.

It’s as simple as this: order, and then  click on the button at the bottom  to let us know your order number. The two free e-books are then yours. Needless to say, this deal is of limited duration, so don’t dawdle about it!

Between Necessity and sufficiency:Seeking answers on the OOl

Is the Universe “Rigged” for Life? Conversation with a Theistic Evolutionist, Continued
Douglas Axe | @DougAxe

This is the second part of my discussion with theistic evolutionist Hans Vodder about my book, Undeniable.See this earlier post for background. Hans replied to the response I gave there as follows:

In one sense, I might agree with you that “accidental explanations for life necessarily invoke unbelievable coincidences.” But I’m not sure this says anything definitive about the particulars of life’s history, specifically with respect to the question of whether or not some form of biological evolution occurred.

Continuing the Sahara scenario, a successful search would defy the odds and require an explanation. However, because there’s more than one way to “rig the game” (i.e., there are various possible restrictions which might all lead to a successful search), the historical particulars of those explanations may look very different. In other words, “design” is a multiply realizable concept.

If the ancient Earth’s conditions were conducive to biological evolution, this would be a form of restricted search. Biological evolution might be within the realm of possibility given the conditions of the early Earth (i.e., the specific restrictions), even if the very possibility of life in the universe still requires an explanation. In this way, empirical considerations and accurate probability measurements might be relevant for determining the restrictions that enable evolutionary searches to work, assuming they do.

Two questions suggest themselves here. First, would evolutionary explanations that depend in this way on restricted searches still qualify as “accidental explanations for life”? Or would they more accurately be considered the outcome of design once removed (or design “displaced,” as Dembski might put it)? Second, and related to the first question, is the primary target of probabilistic arguments biological evolution or metaphysical/philosophical naturalism?

I hope that clarifies my approach a bit and gives a sense of how I currently think about these things.

Yes, this is very helpful, Hans. We may have to circle back to these two questions in order to understand better how we think about “rigging the game.”

However the various kinds of life on Earth first came to exist, we agree that the physical circumstances that enable life to work — everything from the stable orbit of our planet to the extraordinary properties of water — seem remarkably well suited for life. As theists, you and I attribute these circumstances to God.

But as necessary as these circumstances are for life to work, I think it has become very clear that they aren’t at all sufficient to explain how the various kinds of life came to exist in the first place. So, I disagree with Francis Collins’s view that God’s role in creating life is hidden from our view by having been woven into the physical backdrop of the universe. In The Language of God, he put it as follows (p 205):

God could in the moment of creation of the universe also know every detail of the future. That could include the formation of the stars, planets, and galaxies, all of the chemistry, physics, geology, and biology that led to the formation of life on earth, and the evolution of humans…. In that context, evolution could appear to us to be driven by chance, but from God’s perspective the outcome would be entirely specified. Thus, God could be completely and intimately involved in the creation of all species, while from our perspective, limited as it is by the tyranny of linear time, this would appear a random and undirected process.

Contrary to Collins, I say random and undirected processes are clearly and obviously incapable of inventing new living things. God’s creative activity is therefore clearly attested to by each distinct form of life over and above his action in specifying a universe that produced a planet where life could flourish once it did exist.

I’m unclear where you stand on this, Hans. When you say “conditions” on early Earth may have been conducive to biological evolution, I’m thinking you’re referring to planetary conditions — prevailing aspects of the atmosphere, surface, crust, etc., under the influence of the sun and moon. And by “conducive to biological evolution” I take you to mean sufficient to cause biological evolution.

But I could be misreading you. Can you clarify this for me, Hans?

Looking for a diamond in the desert: OOL science's errand.

Undeniable? A Conversation with Theistic Evolutionist Hans Vodder
Douglas Axe | @DougAxe

Hans Vodder is a careful thinker, with graduate degrees from the University of St. Andrews (philosophy) and Northwest University (theology) to prove it. I met him a couple of months ago, just before I spoke at the community center in Port Townsend, Washington. Having read my book —  Undeniable  — Hans was instrumental in setting up that event to foster critical dialog over the book’s message.

Although we’re both people of faith, Hans favors the view that God used the evolutionary process to do his work of creating. In other words, while we agree that life is to be attributed to God, we disagree on the plausibility of the evolutionary explanation of life.

When disagreement leads to genuine dialogue, good things are bound to follow. Recognizing this, Hans and I agreed to convert our recent exchange of emails into a public discussion. We don’t know yet whether our conversation will bring us closer to agreement, but even if it doesn’t, each of us will have benefitted from understanding the other better. And we hope you will benefit as well by following the conversation.

Hans started by expressing the following concern about how I use probabilistic reasoning to argue against the standard evolutionary view:

It seems to me (Hans) that the probability distribution might make a big difference if the search has cumulative power and the search space is constrained by environmental factors. Whatever the situation was on early Earth, the specificity of certain features (geographical, climatological, chemical, etc.) would have favored certain outcomes over others: it wouldn’t have been a “level playing field” where any abstract possibility would have had just as much an opportunity for being realized as any other. In other words, might not the environment constrain the search space? If that’s right, the effective search map might be much smaller than a full-blown egg-hunt search.

How much smaller? It’s hard to say, as it seems very difficult to assign probabilistic values for historical events in general. I don’t think these considerations make the probabilistic arguments against evolution go away entirely: the odds do still seem against it. However, I remain extremely doubtful that one can assign anything like an accurate probability value to the historical circumstances under which life, if it evolved on Earth, would have emerged. From where I stand, considering the odds is a cause for caution and humility, but I think we’d be hard pressed to say whether or not a given biological event was “fantastically improbable” or merely “highly improbable.” The calculations cannot be precise enough, so far as I see, to constitute a knock-down argument against evolution.

I (Doug) answered:

I hope I can give you enough of my thinking on the probability question that we can understand each other iteratively.

Let me start by giving you an alternative to the single-sentence summary of the argument I make in Undeniable (see page 160). I could have summarized the argument this way: “Accidental explanations for life necessarily invoke unbelievable coincidences.”

To see why this has to be true, suppose I were to place a small diamond just below the surface of the sand in the Sahara Desert, and you were to set out to find it, knowing nothing other than that it’s in the Sahara. I think we can agree that the challenge for you is nearly impossible. Yes?

We come to that conclusion just by knowing how unsearchably large the Sahara is and how small the thing to be found is. We don’t have to make any assumptions about how you go about searching. Whether you devote years or decades to the diamond hunt, you can’t feasibly search more than an infinitesimal fraction of the Sahara. The fact that this one crucial resource – time — is in limited supply therefore tells us you have only an infinitesimal chance of success.

For example, if a third party (ignorant of the diamond’s location) were to impose geographical constraints on you by saying you can only look in a particular small patch of the Sahara, that wouldn’t help you at all — unless this happened to be the right patch. But for it to be the right patch would be a remarkable coincidence in itself.

The problem with all accidental explanations of life is like this, but far more extreme. You don’t need accurate measurements of probability any more than you needed an accurate measurement of the Sahara. Accuracy is only needed for judging close calls, and this isn’t a close call.

In the end, there’s no way around the fact that for any accidental causes to produce life amounts to a coincidence that’s far too extreme to be credible.

Or at least that’s how I’m thinking of it.

Editor’s note: The conversation continues on Monday.

Why OOL science needs to look past physics and chemistry.

Origin of Life and Information — Some Common Myths
Brian Miller

In previous articles (here,  here, and here) I described the thermodynamic challenges to the origin of life, and I explained the need for information in the first cell to originate from an outside source. Now, I will dispel many of the myths associated with attempts to circumvent the information challenge.

A common attempt to overcome the need for information in the first cell is to equate  information to a reduction in entropy, often referred to as the production of “negative entropy” or N-entropy. This connection is in certain contexts justified by the fact that both  entropy and the Shannon formulation for information use the same mathematics and can be related to probability and uncertainty. For instance, this approach can be used to calculate the amount of work required to  generate specific amounts of information in the amino acid sequences of proteins. However,  entropy is not equivalent to the information in cells, since the latter represents functional information To illustrate the difference, imagine entering the kitchen and seeing a bowl of alphabet soup with several letters arranged in the middle as follows:

REST TODAY AND DRINK PLENTY OF FLUIDS

I HOPE YOU FEEL BETTER SOON

You would immediately realize that some intelligence, probably your mother, arranged the letters for a purpose. Their sequence could not possibly be explained by the physics of boiling water or the chemistry of the pasta.

To continue the analogy, you mention your design inference to your friend Stanley Miller the Third who happens to be an origin-of-life chemist. Stanley believes any attribution of design to pasta sequences in soup is based on the concerned-parent-of-the-gaps fallacy, so he mocks your superstitious beliefs. He then states that the sequence could have come about as a result of the boiling soup cooling to room temperature. Since cold soup has a lower entropy than hot soup, he believes the reduction in entropy could have generated the information in the message. You would immediately recognize that a reduction in thermal entropy has no physical connection to the specific ordering of letters in a meaningful message. The same principle holds true in relation to the origin of life for the required sequencing of amino acids in proteins or nucleotides in DNA.

A related error is the claim that biological information could have come about by some  complex systems or non-linear dynamics processes. The problem is that all such processes are driven by physical laws or fixed rules. And, any medium capable of containing information (e.g., Scrabble tiles lined up on a board) cannot constrain in any way the arrangement of the associated symbols/letters. For instance, to type a message on a computer, one must be free to enter any letters in any order. If every time one typed an “a” the computer automatically generated a “b,” the computer could no longer contain the information required to create meaningful sentences. In the same way, amino acid sequences in the first cell could only form functional proteins if they were free to take on any order.

Moreover, protein chemists have determined that the vast majority of sequences in proteins today are indistinguishable from being purely random, which further confirms that those in the first cell also appeared random to first approximation. Any relevant divergence from pure randomness would have been due to  constraints associated with protein folding, such as the formation of a-helixes. To reiterate, no natural process could have directed the amino acid sequencing in the first cell without destroying the chains’ capacity to contain the required information for proper protein folding. Therefore, the sequences could never be explained by any natural process but only by the intended goal of forming the needed proteins for the cell’s operations (i.e., teleologically).

A third error relates to attempts to explain the genetic code in the first cell by a stereochemical affinity between amino acids and their corresponding codons. According to this model, naturally occurring chemical processes formed the basis for the connection between amino acids and their related codons (nucleotide triplets). Much of the key research promoting this theory  was conducted by biochemist Michael Yarus. He also devised theories on how this early stereochemical era could have evolved into the modern translation system using ribosomes, tRNAs, and supporting enzymes. His research and theories are clever, but his conclusions face numerous challenges.

For instance, Yarus’s experiments did not actually measure the direct attraction between individual amino acids and their related codons, but they tested for binding between amino acids and sets of generated nucleotide chains (aptamers). His team reported that certain amino acids bound to aptamers which contained a higher than random percentage of their corresponding codons or anticodons at the binding sites. However, other researchers were unconvinced by the findings. For instance, Andrew Ellington’s team questioned whether the correlations in these studies were statistically significant, and they argued that his theories for the development of the modern translation system were untenable. Similarly, Eugene Koonin found that the claimed affinities were weak at best and generally unconvincing. He argued instead that the code started as a  “frozen accident” undirected by any chemical properties of its physical components.

More significantly, even if such affinities existed, they would not help in any realistic origin-of-life theory. Yarus’s model centers on codons embedded in longer sequences of nucleotides folding around single amino acids. Any model for translating sequences of codons into chains of amino acids would require a much longer strand of RNA to fold around multiple amino acids and then consistently link them together in the right order. And, these RNAs would eventually have to lose the “non-coding” nucleotides surrounding the relevant codons – while somehow retaining the affinities which had previously required the removed nucleotides – in order to become modern versions of RNA and DNA. Even if such extraordinary feats could occur, the translation would take place in the wrong direction.

Within the presupposed RNA world framework, nucleotide sequences came into being which eventually evolved into RNA-based enzymes. A selective process was believed to replicate the more efficient enzyme-like sequences over others in order to eventually produce “ribozymes” which could perform all of the needed functions for some sort of protocell. However, the ribozyme sequences would have had no relationship via any code to amino acid sequences which could fold into functional proteins. Therefore, any process which could perform the translation would initially be completely useless. Instead, proteins would have needed to come into existence independently through their own selective process, and then their sequences would have needed to be encoded into new RNAs. However, Yarus’s model does not work in reverse. Another process would have been needed for the amino-acid-to-RNA encoding, but the underlying code would not have corresponded to Yarus’s affinity-based code. As a result, the decoding process would have lost the encoded information.

These problems simply highlight one of the challenges for the RNA world hypothesis and for any materialistic explanation for the genetic code. A viable theory would have to explain for both the encoding and decoding several steps:

Amino acids and nucleotides would have to be created in abundance and then brought together. They would have to originate in separate locations, since the conditions needed for their synthesis are quite different, and cross-reactions would have prevented the creation of either. (See  Shapiro’s Origins.)

A functional protein or RNA strand would have to unfold to allow for its sequence to be translated. And, such functional sequences would have to separate themselves from other useless chains. An enormous number of chains would have to exist for a useful sequence to have had any chance of forming.

Individual codons would have to be so strongly attracted to their corresponding amino acids, that they would attach to them for an extended period of time.

Some enzyme-like molecules would have to come along and then polymerize the nucleotides into strands of RNA or the amino acids into proteins.

All useful products would have to migrate to some safe location until they could be encapsulated into a cellular membrane. A viable membrane would have to be selectively semipermeable, so it would allow the right molecules to enter and waist products to leave.

Neither Yarus nor any other researcher has even come close to properly addressing any of these issues in a purely materialistic framework. Nor will they, for any realistic scenario requires intelligent agency to properly coordinate all of these fantastically improbable steps.

Physics v. OOL science.

Tornadoes, Ice, and Cells: The Challenge from Thermodynamics to Origin-of-Life Scenarios
Evolution News | @DiscoveryCSC

On a new episode of ID the Future, physicist and Center for Science & Culture research coordinator Brian Miller talks with host Sarah Chaffee about the thermodynamics of the origin of life. Dr. Miller has been unfolding a four-part series on the subject here at Evolution News, concluding on Monday.

Explaining why materialist theories of origins hit a wall when examining the physics of abiogenesis. Dr. Miller discusses the difference between systems such tornadoes, ice, and living cells. Learn more about equilibrium, self-organization, and how the cell defies natural tendencies towards high entropy and low energy.

Listen to the podcast here, or download it here.

As Dr. Miller concludes, referring to the origin of the genetic code and the information it bears at the heart of the cell:

The encoding and the decoding and the information had to be there all at once, which means it had to preexist the existence of the cell, because it had to exist before it was embodied in physical reality. But the only place that information in a code can exist outside of physical reality is in a mind, and that points very clearly to intelligent design.

Second only to cosmic fine-tuning, this would seem to be the most fundamental challenge to materialism there could be. With no original life, without the guidance and intervention of a designing agent, obviously Darwinian evolution is absolutely nothing even to begin to work with. This is a subject on which materialists are largely silent, and with good reason.

Unsettled science?

There's No Grand Unity Called "Science"
Ralph Dave Westfall 

Editor's note: We are delighted to welcome Dr. Westfall as a new contributor. He is an emeritus professor in the Computer Information Systems Department at California Polytechnic University, Pomona.

Doug Axe's piece at Evolution News the other day was very good ("Public Opinion Is the Ultimate Peer Review"), but it implicitly supports the misconception that science is one big thing. That idea is the primary basis for all pejorative propaganda attacking dissenters as being "anti-science."

It is false to say that there is one single activity to be identified as "Science." In truth, there are only individual fields of study, some of which deserve being called sciences, while others arguably do not. They don't all fit into one overarching category because the methodologies and criteria for what count as valid findings vary so greatly among them. (A cynic might suggest that in contrast to people who do research in psychology, physicists function in a different and not very parallel universe.)

The panorama can be taxonomized as follows. First, divide the fields of study into: (A) the natural or physical sciences, and (B) the social sciences. Then divide the natural sciences, separating (A1) those concerned with homogeneous entities and deterministic (at least in the aggregate) relationships, from (A2) the ones that deal with chaotic processes (like climatology).

Most of the progress in knowledge and technology comes from the (A1) category. Although researchers in the other categories would like you to think they are making comparable contributions to society, they are not.

In the public eye, most of the credibility of "Science" comes from tangible products resulting from the findings of computer science, physics, and chemistry -- for example, computers, jumbo jets, medical technologies such as MRI scanners, etc. Very few question the accomplishments of these kinds of sciences. But that doesn't mean that other sciences produce comparably valid results.

You can take this even further. Throughout history much of progress initially came from the tinkerers, inventors, and engineers. The relevant sciences were discovered or substantially elaborated after the fact to understand why the things they created actually worked. The Romans built great aqueducts two thousand years ago and the church produced grand cathedrals in the Middle Ages before materials science was developed. "The era of the steam engine ... was well into its second century before a fully formed science of thermodynamics had been developed." (See "Engineering Is Not Science.")

And unlike science, replication is not an issue in engineering. People may be able to get away with "scientific findings" that can't be reproduced, but not with bridges that collapse.

The climate change alarmists, for one, seem to think that just calling their opponents anti-science should be more than enough to shut them up, or at least convince others to ignore evidence contrary to their catastrophic warming narrative. However there is an implicit assumption in the "anti-science" epithet: that all sciences produce comparably reliable results. Say, that the science of climatology can be trusted as much as the science of aeronautics.

Here are a couple of thought-provoking questions to ask anyone who accuses others of being anti-science: Would you book a flight on an airplane that was as unreliable as weather forecasts more than ten days in advance? Or whose landings were as inconsistent as the frequently changing dietary recommendations from nutritional research?

No, there is no grand unity called "Science." It might clarify the public debate on these topics if we could help people understand this important point.

Protein folds v. Darwin.

Escape from Randomness: Can Foldons Explain Protein Functional Shapes?
Evolution News | @DiscoveryCSC

Does the subject of protein folding excite you? Read this to see why perhaps it should:

Protein folding is among the most important reactions in all of biology. However, 50 y after C. B. Anfinsen showed that proteins can fold spontaneously without outside help, and despite the intensive work of thousands of researchers leading to more than five publications per day in the current literature, there is still no general agreement on the most primary questions. How do proteins fold? Why do they fold in that way? How is the course of folding encoded in a 1D amino acid sequence? These questions have fundamental significance for protein science and its numerous applications. Over the years these questions have generated a large literature leading to different models for the folding process. [Emphasis added.]

In short, your life depends on protein folding, and the subject provides a classic contest between intelligent design and scientific materialism. That’s enough to make a thoughtful person take notice.

The quoted passage comes from a paper in the Proceedings of the National Academy of Sciences by two biophysicists at the University of Pennsylvania. They review the vast corpus of literature on the subject to assess the best current models for explaining how one-dimensional sequences of amino acids can end up as three-dimensional shapes that perform functional work. To appreciate the challenge, try to assemble a string of beads, some of which have electric charges or attractions to water, that will, when let go, spontaneously fold into a tool. Your cells do something like that all the time, and usually do it right.

Biologic Institute research scientist Douglas Axe has worked on the problem of protein folding for much of his career. He has been joined by another scientist, Discovery Institute’s Ann Gauger, to show why protein folding gives evidence for intelligent design. The subject is also discussed at length in Axe’s most recent book, Undeniable: How Biology Confirms Our Intuition That Life Is Designed (Harper One, 2016).

Here’s the problem for materialism in a nutshell: the number of ways you can assemble amino acids that won’t fold vastly exceeds the ways that will fold. To expect a random process to search “sequence space” (the set of all sequences of amino acids) and arrive at one that folds is so highly improbable, it will likely never occur in multiple universes. Axe followed Michael Denton’s hunch that “functional proteins could well be exceedingly rare” and put some numbers to it. He determined that there is only “one good protein sequence for every 10^74 bad ones” (Undeniable, p. 57). This was about 10 million billion billion billion times more improbable than Denton’s initial estimate.

As Axe goes on to say, materialists didn’t exactly put “out of business” signs on their doors when he published his results. That brings us to the current paper — one of the latest attempts to find a way to avoid the implications of design and find a natural, unguided means of searching sequence space for those elusive folds.

The authors, S. Walter Englander and Leland Mayne, know all too well that random search is hopeless. Even in the 1990s, “Levinthal had contributed the seminal observation that a random search could not account for known folding rates.” Most proteins find their native fold extremely rapidly — some in microseconds. Some need a little help from “chaperones” such as GRO-EL that allow the polypeptide to fold in a barrel-like chamber. In either case, the authors know that random attempts at finding the proper or “native” fold, even for a correctly-sequenced polypeptide, would be far too slow if there were many pathways to the correct fold. This led scientists early on to suspect that proteins follow an energy landscape that nudges them to the native fold, much like a funnel guides ball bearings down a narrow hole. The ball may bounce around in the funnel, but the shape of the energy landscape forces it in the right direction. This is known as energy landscape theory (ELT).

A critical feature of the funneled ELT model is that the many-pathway residue-level conformational search must be biased toward native-like interactions. Otherwise, as noted by Levinthal (57), an unguided random search would require a very long time. How this bias might be implemented in terms of real protein interactions has never been discovered.

The authors are not content with evolutionary just-so stories:

One simply asserts that natural evolution has made it so, formulates this view as a so-called principle of minimal frustration, and attributes it to the shape of the funneled energy landscape. Proteins in some unknown way “know” how to make the correct choices.

Sorry, no dice.

A calculation by Zwanzig et al. at the most primary level quantifies the energy bias that would be required. In order for proteins to fold on a reasonable time scale, the free energy bias toward correct as opposed to incorrect interactions, whatever the folding units might be, must reach 2 kT (1.2 kcal/mol). The enthalpic bias between correct and incorrect interactions must be even greater, well over 2 kcal/mol, because competition with the large entropic sea of incorrect options is so unfavorable. Known amino acid interaction energies, less than 1 kcal/mol (59), seem to make this degree of selectivity impossible at the residue–residue level.

Are we excited yet? This is getting really interesting. The suspense is growing. With randomness out of the question, what will they do?

They basically take a divide-and-conquer approach. Getting a big polypeptide to fold is too hard, but maybe if they can break the problem down into bite-size chunks, they can get to the target without intelligence. After all, it’s much easier to knit an afghan if the granny squares come ready-made so that you don’t have to make each one from scratch. “Quantized” in this manner, the problem becomes more tractable.

The structural units that assemble kinetic intermediates are much the same as the cooperative building blocks of the native protein. This strategy separates the kinetic folding puzzle into a sequence of smaller puzzles, forming pieces of the native structure and putting them into place in a stepwise pathway (Fig. 1B). This is the defined-pathway model.

They give the name “foldon” to a small chain of amino acids “perhaps 15 to 35 residues in size” that folds a little bit. If the polypeptide is composed of a number of these prefabricated foldons, maybe the whole protein will find its native fold quickly, descending the funnel in a stepwise fashion. Experiments unfolding and refolding some proteins actually show this kind of stepwise energy landscape. They like that:

The purpose of this paper is to consider the present status of these quite different models and relate them to the central questions of protein folding — how, why, and the encoding problem. We propose to rely on the solid ground of experiment rather than the countless less-definitive suggestions and inferences that have been so often used in this difficult field.

Empirical rigor; what’s not to like about that? So instead of imagining a correct sequence of amino acids from scratch, they substitute a sequence of foldons, increasing the probability of completing the search in time. Will this work in evolutionary terms?

The opposed defined-pathway model stems from experimental results that show that proteins are assemblies of small cooperative units called foldons and that a number of proteins fold in a reproducible pathway one foldon unit at a time. Thus, the same foldon interactions that encode the native structure of any given protein also naturally encode its particular foldon-based folding pathway, and they collectively sum to produce the energy bias toward native interactions that is necessary for efficient folding.

So how, exactly, did this clever solution emerge without intelligence?

Available information suggests that quantized native structure and stepwise folding coevolved in ancient repeat proteins and were retained as a functional pair due to their utility for solving the difficult protein folding problem.

“Co-evolution” again. So much for empirical rigor. They’re back to just-so storytelling mode. Let’s think this through. Each granny square in the quilt is a product of chance, according to materialist resources. Does a black granny square know that it will fit nicely into a complete quilt following a geometrical pattern of black, red and yellow squares? Unless each granny square has an immediate function, evolution will not preserve it. Similarly, no foldon will be “retained” with some future hope that it might have “utility for solving the difficult protein folding problem.” The foldon couldn’t care less! It had to be functional right when it emerged.

An intelligent designer could plan foldons as a useful strategy for constructing various complex proteins in a modular way. A designer could even preserve useful foldons, much like a computer programmer writes subroutines to use in other programs. Unless each subroutine actually does something useful for the system as a whole, though, what good is it? Say you have a subroutine that says, “Repeat whatever argument arrives in the input register.” Unless the system needs that function as part of what it’s doing, you can run the subroutine till the cows come home and nothing good will come of it.

In short, the foldon strategy doesn’t lower the probability of success, and it doesn’t solve “the difficult protein folding problem” for the evolutionist. It’s all divide and no conquer.

Englander and Mayne make a big deal out of “repeat proteins” that make up about 5 percent of the global proteome. These repeat proteins “have a nonglobular body plan made of small repeated motifs in the 20–40 residue range that are assembled in a linear array.” Are they good candidates for foldons? We know that many proteins contain repetitive structures like alpha coils and beta sheets, but the essence of a functional protein is not its repetitive parts but in its aperiodic parts. We’ve seen this requirement in other types of intelligent design, such as language. Sure; sometimes a series of dashes makes a nice separator between paragraphs, but you won’t get much meaning out of all repetitive sequences. Let’s see if they can do it:

The different families of repeat proteins are very different in detailed structure but within each family the repeats are topologically nearly identical. These observations suggest that repeat proteins arose through repeated duplication at an early stage in the evolution of larger proteins from smaller fragments. Available examples show that globular organization can arise from continued repetitive growth that closes the linear geometry, and by the fusion of nonidentical units, and so would carry forward their foldon-like properties.

The utility of foldons for the efficient folding of proteins might be seen as a dominant cause for the development and retention of a foldon-based body plan through protein evolution. In this view, contemporary proteins came so consistently to their modular foldon-based design and their foldon-based folding strategy because these linked characteristics coevolved. However, the fact that many known foldons bring together sequentially remote segments requires, at the least, some additional mechanism.

This sounds like the evolutionary story that duplicated genes became seeds of new genes. So if we duplicate the line of dashes, and then change some of the dashes to commas, will we get somewhere? Hardly. If we strip out the “mights” and “maybes” of their story, not much is left but the concluding admission that “some additional mechanism” is needed to get folded proteins. (We have one! Intelligence!) And get this: even if you get a polypeptide to fold into a globule, it’s trash unless it actually performs a function.

When scientific materialists began tackling the protein folding problem, they expected that biased energy landscapes leading to deterministic folds would soon be discovered. That didn’t happen.

However, how this propensity might be encoded in the physical chemistry of protein structure has never been discovered. One simply asserts the general proposition that it is encoded in the shape of the landscape and to an ad hoc principle named minimal frustration imposed by natural evolution.

Here they state Axe’s search challenge in their own words:

Quantitative evaluation described above shows that individual residue — residue interaction energies are inadequate for selecting native-like interactions in competition with the large number of competing nonnative alternatives. The assertion that the needed degree of energetic bias is supplied by the shape of an indefinite energy landscape because nature has made it so is — plainly said — not a useful physical — chemical explanation.

The foldon proposal that Englander and Mayne prefer, however, is not any better, despite their praise for it:

The question is what kind of conformational searching can explain the processes and pathways that carry unfolded proteins to their native state. The foldon-dependent defined-pathway model directly answers each of these challenges.

All they have done, however, is displace the challenges from amino acid sequences to foldon sequences. Since the foldons are composed of amino acid sequences, however, nothing is solved; it is still radically improbable to arrive at a sequence that will produce a functional protein without design. No amount of evolutionary handwaving changes that:

Evolutionary considerations credibly tie together the early codevelopment of foldon-based equilibrium structure and foldon-based kinetic folding.

So much for empirical rigor. Evolution did it. Problem solved.

We think not. To rub it in, consider that Axe’s calculation of one in 10^74 sequences being functional is way too generous. If we require that the amino acids be left-handed, and demand that all bonds be peptide bonds, the probability drops to one in 10^164. For a quick demonstration of why this is hoping against all hope, watch Illustra Media’s clever animation from their film Origin, titled, “The Amoeba’s Journey.”