Yet more primeval tech v. Darwin.

Ribosomes Optimized for Speed, Flexibility
Evolution News | @DiscoveryCSC

The DNA translation machines in the cell show unexpected complexity, forcing molecular biologists to revise what they thought they knew about ribosomes. In particular, they appear optimized for speed of self-duplication and modularized for flexibility.

Last September, we evaluated a fascinating paper about ribosomes that showed how this molecular machine that translates DNA “requires the orchestrated function of hundreds of proteins” — and that’s just to get to the “pre-ribosome” stage! Ribosomes are marvels of organization and function. Since then, more discoveries have shown additional design features of ribosomes.

A cell doesn’t have all day to build and operate these machines. In July, a paper in Science Advances revised the half-life of RNAs significantly downward. Instead of 5-20 minutes to float around and get translated, most messenger RNAs (mRNAs) last only about 2 minutes before being degraded by complex recycling pathways (see this from the University of Basel ). The production rate and decay rate are important factors in gene regulation. So if you think of “orchestrated function” again, the sheet music won’t do any good if the stage isn’t already set up and the players aren’t in their seats.

The ribosome is composed of large RNAs and proteins. The paper doesn’t state the half-life of the ribosomal RNAs, which make up the bulk of the ribosome, but it’s safe to assume the lifetime of each RNA is finite — probably a matter of minutes. An extra reason for assuming this is the rapid doubling of ribosomes during cell division. Before the cell can divide, all the proteins needed by the two daughter cells must be translated. This requirement effectively doubles the work for these machines.

How does the cell prepare for this increased workload? Rather than speed up translation, the ribosomes first duplicate themselves, effectively doubling the production capacity. This means that they have to prepare and assemble all their own RNAs and proteins first. Without efficient ways to accomplish this prerequisite, cell division could be seriously delayed.

An interesting model, published in Nature by Johan Paulsson’s team at Harvard, suggests that “Ribosomes are optimized for autocatalytic production.” They knew that ribosomes are already optimized in three ways. Now, they add a fourth:

Many fine-scale features of ribosomes have been explained in terms of function, revealing a molecular machine that is optimized for error-correction, speed and control. Here we demonstrate mathematically that many less well understood, larger-scale features of ribosomes — such as why a few ribosomal RNA molecules dominate the mass and why the ribosomal protein content is divided into 55–80 small, similarly sized segments — speed up their autocatalytic production. 

The authors, as evolutionists, will assume that Darwinian processes achieved this optimization. In their own words, however, we sense their astonishment at what these machines accomplish.

Ribosomes translate sequences of nucleic acids into sequences of amino acids. Their features are therefore typically explained in terms of how they affect translation. However, in recent years it has also become clear that ribosomes are exceptional as products of the ribosomal machinery. Not only do ribosomal proteins (r-proteins) make up a large fraction of the total protein content in many cells, but the autocatalytic nature of ribosome production introduces additional constraints. Specifically, the ribosome doubling time places a hard bound on the cell doubling time, because for every additional ribosome to share the translation burden there is also one more to make. Even for the smallest and fastest ribosomes, it takes at least 6 min, and typically much longer, for one ribosome to make a new set of r-proteins (Supplementary Information); and this estimate does not account for the substantial time that is invested in the synthesis of ternary complexes. This bound seems to explain the observed limits on bacterial growth, because ribosomes must also spend much of their time making other proteins, and shows that ribosomes are under very strong selective pressure to minimize the time they spend reproducing.

Whether “selective pressure” is the mother of invention is debatable to those of us who are Darwin skeptics, but the authors point out something important. The “orchestrated function of hundreds of proteins” has time limits. The conductor is pounding his foot and tapping his baton on the podium, rushing the orchestra to get in place. Imagine how much harder if each player, instrument, chair, and music stand has to make a copy of itself first for a show across town!

Based on observed facts about ribosomal RNAs and proteins, and how quickly they duplicate, the team created a mathematical model based on the assumption that “selective pressure” forces cells to optimize their ribosomes’ doubling time. Although the model worked for fast-reproducing bacteria, they presume the same time pressure constrains eukaryotic cells:

Similar principles might also apply to some eukaryotes, because the ribosomes of eukaryotes are larger and slower. In fact, even organisms in which cell doubling times are not limited by ribosome doubling times would benefit from faster ribosome production, allowing ribosomes to spend more of their time producing the rest of the proteome. This efficiency constraint was recently shown to have broad physiological consequences for cells, and here we demonstrate mathematically that it might also explain many broader features of the ribosome 

In the figure, they show that ribosomes are dominated by a few large RNAs and lots of small proteins, about 55 to 80 of them of similar size. The reason for this arrangement has long puzzled molecular biologists. According to the new model, ribosomes can reproduce their parts quicker when the proteins are relatively short, and there are lots of them. The existing ribosomes can crank out smaller building blocks faster, and the construction workers can assemble them faster, than if they had to wait for long, complex pieces to arrive.

It’s not necessary to get into the weeds to see the elegance of the solution. Ribosomes assemble faster with more, smaller proteins, reducing the time to duplicate themselves, so that they can get on with their main job of translating all the other proteins the cell needs before dividing. The faster you double the translating machinery, the faster you can double everything else in the cell.

The model also needs to explain why ribosomes include a few large RNAs. Evolutionists have typically invoked the “RNA World” story to suggest that ribosomal RNAs represent transitional forms or vestiges from the origin of life before cells happened upon ways to make proteins. Paulsson’s model suggests a different reason — a functional reason. RNAs only need to be transcribed, not translated. RNA enzymatic activity is not as efficient as protein, but RNA is quicker to make. The cell, therefore, is better off using it when time is of the essence.

The above analysis suggests a great efficiency advantage of using rRNA [ribosomal RNA] over protein, whenever chemically possible, and so could explain why ribosomes defy the general rule that enzymes are made mostly of protein (Fig. 1). This finding does not mean that the role of rRNA is merely to ensure appropriate overall dimensions of the ribosome; however, it does provide a fundamental reason for why proteins must be used sparingly in the ribosome, for example, to increase accuracy or speed up translation, whereas rRNA should be used wherever possible without compromising function. If even one-quarter of the rRNA mass were replaced with r-protein without increasing translation rates, many bacteria would not be able double as quickly as they do 

Do you see  optimization (a form of intelligent design) at work? The authors go into more detail about why rRNAs must be large. Their model shows that small rRNAs, unlike the small ribosomal proteins, would actually slow down duplication. Suffice it to say that the observed ratio of rRNA to ribosomal protein increases the efficiency by two orders of magnitude. Here’s a pithy analogy from a layman’s summary of the paper at Science Daily:

“An analogy for our findings would be to think of ribosomes not as a group of carpenters who merely build a lot of houses, but as carpenters who also build other carpenters,” Paulsson said. “There is then an incentive to divide the job into many small pieces that can be done in parallel to more quickly assemble another complete carpenter to help in the process.”

One other mystery about ribosomes might be solved by looking at it as an optimization problem: why do ribosomes vary? Mitochondrial ribosomes differ from those in the cytosol. Eukaryotic ribosomes differ from those of bacteria. If they perform the same function, why aren’t they all the same? Here’s a paper in  PLOS ONE from last November that opens a window on a possible reason: ribosome structure is modularized. In “The Modular Adaptive Ribosome,” a team from India says this:

The ribosome is an ancient machine, performing the same function across organisms. Although functionally unitary, recent experiments suggest specialized roles for some ribosomal proteins. Our central thesis is that ribosomal proteins function in a modular fashion to decode genetic information in a context dependent manner.

Interested readers can delve further into this open-access paper to see why ribosomes vary in different cell types or different environments. “A clear example is nervous tissue that uses a ribosomal protein module distinct from the rest of the tissues in both mice and humans,” they say. “Our results suggest a novel stratification of ribosomal proteins that could have played a role in adaptation, presumably to optimize translation for adaptation to diverse ecological niches and tissue microenvironments.”

When it comes to ribosomes, it appears to be a case of optimization all the way down.

Let’s give the last word to the Science Daily article.

Rather than being mere relics of an evolutionary past, the unusual features of ribosomes thus seem to reflect an additional layer of functional optimization acting on collective properties of its parts, the team writes.

“While this study is basic science, we are addressing something that is shared by all life,” Paulsson said. “It is important that we understand where the constraints on structure and function come from, because like much of basic science, it is unpredictable what the consequences of new knowledge can unlock in the future.”

Notice how that downplays evolution’s role, in spite of the authors’ Darwinian views. It also, even if not intending to do so, supports a design pespective, while showing how such a focus leads to productive science.

Now the middle ages redux?

Experts Decry Russia’s Threat to Ban the New World Translation of the Holy Scriptures.

ST. PETERSBURG, Russia—Russian authorities are attempting to ban the New World Translation of the Holy Scriptures published by Jehovah’s Witnesses, labeling it as “extremist.”

Ironically, if the court rules in favor of the prosecution, any ban placed on the New World Translation would “violate the amendment to Article 3 of the Federal Law on Extremism signed by Mr. Putin in the fall of 2015,” according to Dr. Ekaterina Elbakyan, professor of sociology and management of social processes at the Moscow Academy of Labor and Social Relations. The amendment to Article 3 clearly states: “The Bible, the Quran, the Tanakh, and the Kangyur, their contents, and quotations from them cannot be recognized as extremist materials.”  

“Who would have imagined that adopting a law giving immunity to certain holy texts would provoke the banning of other holy texts?” states Dr. Roman Lunkin, head of the Center for Religion and Society at the Institute of Europe, Russian Academy of Sciences in Moscow. “The first to suffer have been the Jehovah’s Witnesses, along with their translation of the Bible.” 

Additionally, “as an ICCPR [International Covenant on Civil and Political Rights] member state, Russia’s attempt to ban such a Bible would be contravening freedom of religion conventions,” notes Dr. Jeffrey Haynes, professor of politics and director of the Centre for the Study of Religion, Conflict and Cooperation at London Metropolitan University. 

The case against the New World Translation is being held at the Vyborg City Court, 138 kilometers (85 mi.) northwest of St. Petersburg. On April 26, 2016, the second day of preliminary hearings, the judge granted the prosecution’s request to suspend the case, pending a court-appointed analysis of the New World Translation. The Witnesses were not given a chance to present their defense, and the court assigned the analysis to be done by the Center for Sociocultural Expert Studies, whose negative conclusions about the New World Translation served as the basis for the prosecutor’s original claim. Assigning the center to analyze the New World Translation again violates the precedent set by Russia’s Supreme Court to disqualify an expert if he has previously expressed his opinion about a subject being considered in court.

While the court-appointed analysis is pending, scholars have expressed their regard for the Witnesses’ translation. One such scholar, Dr. Gerhard Besier, director of the Sigmund Neumann Institute for the Research on Freedom and Democracy, comments: “The New World Translation has received high praise worldwide from Bible scholars representing diverse religious communities.”

Likewise, the Moscow-based SOVA Center for Information and Analysis stated in the February 2016 edition of their monthly news release Misuse of Anti-Extremism: “We don’t find any signs of extremism in the New World Translation.” Since then, in almost every monthly news release, SOVA Center has repeated its definitive position against Russia’s actions, such as was published in June 2016: “We would like to reiterate that we view persecution against Jehovah’s Witnesses in Russia and bans against their literature and communities as religious discrimination.”

Facts About the New World Translation

For over a century, Jehovah’s Witnesses in Russia worshipped using a variety of Bible translations, including the Russian synodal and Makarios translations. In 1994, the Witnesses embarked on what would be a 12-year project to translate the Bible into contemporary Russian. In 2007, the complete New World Translation in Russian was released. Since then, over 4.8 million copies in Russian have been produced. The New World Translation is available, in whole or in part, in 137 languages, with over 217 million copies printed. The nearly 175,000 Witnesses in Russia use a variety of peaceful and societally responsible methods to offer Bibles to interested ones free of charge.

Media Contacts:

International: David A. Semonian, Office of Public Information, 1-718-560-5000

Russia: Yaroslav Sivulskiy, 7-812-702-2691

Thanks to the modern cosmogony OOL science is not the only circus in town.

Cosmic Inflation Theory Loses Hangups About Scientific Method
Denyse O'Leary

Two features of our universe puzzle cosmologists: One is the horizon problem: The universe looks the same in all directions and the cosmic microwave background radiation is about the same temperature everywhere. As String Theory for Dummies puts it, “This really shouldn’t be the case, if you think about it more carefully.” Assuming that current measurements are correct, the radiation must have exceeded the speed of light if it really communicated in this way, but that is forbidden by the standard Big Bang model of the universe.

Then there is the the “flatness problem”: “The matter density and expansion rate of the universe appear to be nearly perfectly balanced, even 14 billion years later when minor variations should have grown drastically” (Dummies). Inconveniently, the apparent 1:10^66 fine-tuning  of the Big Bang, of which horizon and flatness are features, is frequently used as an argument for the  the existence of God.

Cosmic inflation theory, first proposed by Alan Guth  in 1981, modified the Big Bang theory (the Standard Model) by proposing that the universe, instead of unfolding at a steady pace, expanded rapidly shortly after it was created, which could account for apparent fine-tuning.

Inflation is not the only naturalist theory on offer. Perhaps the speed of sound was faster than the speed of light back then or else there were existence of extra dimensions of space-time, as postulated by string theory. But, as cosmologist Will Kinney admits, “The takeaway result here is that this idea of inflation turns out to be the only way to do it within the context of standard physics” (Phys.org).

It could have worked if the wheels hadn’t fallen off earlier this year. In “Pop Goes the Universe” (Scientific American, February 2017), Anna Ijjas, Paul J. Steinhardt, and Abraham Loeb (IS&L) advocated a different scenario: “[O]ur universe began not with a bang but with a bounce from a previously contracting cosmos.” The “bouncing cosmology” was initially proposed by Steinhardt and others in 2001, and fleshed out in 2014. When BICEPS II failed to find evidence of inflation in 2014, Michael Slezak  crowed at New Scientist “Inflation is dead, long live inflation! The very results hailed this year as demonstrating a consequence of inflationary models of the universe — and therefore pointing to the existence of multiverses – now seem to do the exact opposite. If the results can be trusted at all, they now suggest inflation is wrong, raising the possibility of cyclic universes that existed before the big bang.” Some were willing to trade the shadowy multiverse for (at least) one other (past) universe, however modest.

An exchange of letters followed, between the three authors (IS&L) and 33 cosmologists who defended early rapid inflation, among whom readers may recall Alan H. Guth, Sean Carroll, Andrei D. Linde, Stephen Hawking, Lawrence Krauss, Martin Rees, George F. Smoot III, Leonard Susskind, Alexander Vilenkin, and Steven Weinberg.

The 33 signatories pointed to the fact that 14,000 papers that use the word “inflation” or “inflationary” in their titles or abstracts have been written by 9,000 scientists. They were stung by the accusation that inflationary cosmology “cannot be evaluated using the scientific method” and that some proponents have proposed discarding a defining property of science: “empirical testability.” They retort that “it has been subjected to a significant number of tests and so far has passed every one.” That would settle the matter except that, as they admit, “Inflation is not a unique theory but rather a class of models based on similar principles.” Empirical science, they concluded with a flourish, “is alive and well!”

The trouble is, thousands of papers can indeed be wrong. One wonders how many papers were written on the formation of the continents before plate tectonics was proposed. And if cosmic inflation has passed so many tests, why do so many variant models survive? Planck data showed in 2015 that the simplest models are no longer tenable and need to be supplemented by exotic physics.

IS&L replied that “The claim that inflation has been confirmed refers to the outdated theory before we understood its fundamental problems,” including the fact that generic inflation leads to eternal inflation and, in consequence, a multiverse: “And if inflation produces a multiverse in which, to quote a previous statement from one of the responding authors (Guth), ‘anything that can happen will happen’—it makes no sense whatsoever to talk about predictions. Unlike the Standard Model, even after fixing all the parameters, any inflationary model gives an infinite diversity of outcomes with none preferred over any other. This makes inflation immune from any observational test.”

Science writer Dennis Overbye calls the inflation controversy a crisis in cosmology. But maybe it is more of a crossroads.

All parties to the dispute assume, as a metaphysical stance, that science cannot address the possibility that the universe shows evidence of design. Even if design turns out to be the best explanation and the most fruitful for progress, it cannot be accepted, as a matter of first principles.

So what options remain? One can earn a living in cosmology enforcing one problematic theory against its rivals. But the charges and countercharges between the three and the 33 raise a more promising possibility: Change the rules for evidence. For example, the 33 defend the multiverse: “If the multiverse picture is valid, then the Standard Model would be properly understood as a description of the physics in our visible universe, and similarly the models of inflation that are being refined by current observations would describe the ways inflation can happen in our particular part of the universe.”

But multiverse cosmology flourishes entirely without evidence. So, by its nature, it would be consistent with any finding whatever.

In 2014, not a good year for inflationary theory (gravitational waves were just dust), Steinhardt told Nature that the multiverse bubble had burst. But in the same piece, he warned that “the inflationary paradigm is so flexible that it is immune to experimental and observational tests.” In May 2017, for example, we were told by one team that dark energy is pushing the universe to expand but we have not established the existence of dark energy; it is itself a theoretical concept.

Experimental physicist Rob Sheldon offers some observations on the “firestorm” ignited by IL&S: Paul Steinhardt was an inflationary cosmologist himself in the early 1980s but he concluded in 2002 that it would not work.

The whole purpose of the inflationary theory is negated by its development. It was invented to explain the 1:10^66 fine-tuning of the Big Bang, but in the end, it required 1:10^10^100 fine-tuning. (The first number has 66 zeroes after it, the second number has a hundred, trillion, trillion, trillion, trillion, trillion, trillion, trillion, trillion zeroes after it.)

Steinhardt pleads ignorance as to why he advocated the theory in the first place. At the time it looked like it had just one or two zeroes after the probability, but research added a few more until the theory just wasn’t justified anymore. So the real question becomes, why do 33 famous physicists included Nobel prize-winners, still like the theory and think Steinhardt has lost his marbles?

Applying one of science philosopher Imre Lakatos’s concepts, Sheldon labels cosmic inflation a “seriously” degenerating science program. It illuminates only itself, not nature.

But is degeneration still a failure? What if naturalism changes the role of a science program? Perhaps stubbornly contrary evidence merely shows the need for more drive and zeal in generating new naturalist theories, not more reflection and evaluation of that direction. With enough such theories tried and discarded, more convincing ones will surely appear. Especially now because, the multiverse (“anything that can happen will happen”) is becoming so much a fixture of popular science culture that careers will thrive simply on formulating clever arguments for its existence, not on demonstrating it. Metaphysics again.

Lamarck redux v. Darwin?

Evolution’s Third Rail — Transgenerational Epigenetics Can Have a Profound Impact
Cornelius Hunter

In the spring of 2006 I gave a talk on the campus of Cornell University and afterwards was joined by then Cornell professors Richard Harrison and Kern Reeve for a sort of panel discussion or debate about biological evidences and origins. I presented a dozen or so interesting and important evidences that I felt needed to be recognized in any discussion of origins. The evidences falsified key predictions of evolution and so needed to be acknowledged and reckoned with, one way or another.

One of the items on my list was the so-called directed adaptation mechanisms which, broadly construed, can include everything from non-random, directed, mutations to transgenerational epigenetic inheritance. But I was in for a big surprise when Harrison and Reeve gave their response.

Directed adaptation is reminiscent of Lamarckism. Rather than natural selection acting over long time periods on biological variation which is random with respect to need, directed adaptation mechanisms provide rapid biological change in response to environmental challenges. Like physiological responses, directed adaptation can help an organism adjust to shifts in the environment. But those adaptations can then be inherited by later generations. Stresses which your grandparents were subjected to may be playing out in your own cells.

In the 20th century, evolutionists had strongly rejected any such capability. Lamarckism was the third rail in evolutionary circles. And for good reason, for it would falsify evolutionary theory. But empirical evidence had long since pointed toward the unthinkable, and by the 21st century the evidence was rapidly mounting.

While there was of course still much to learn in 2006 about directed adaptation (as there still is today for that matter), it could no longer be denied, and needed to be addressed. At least, that is what I thought.

I was shocked when Harrison and Reeve flatly denied the whole story. Rick waved it off as nothing more than some overblown and essentially discredited work done by Barry Hall and John Cairns, back in the 1970s and 80s (for example here ).

But there was a body of work that had gone far beyond the work of Hall and Cairns. Incredulously I responded that entire books had been written on the subject. Rick was quick to respond that “entire books are written about all kinds of discredited things.”

True enough. It was me versus two professors on their home turf with a sympathetic audience, and there was no way that I was going to disabuse them of what they were convinced of.

Confirmation testing and theory-laden evidence are not merely philosophical notions. They are very real problems. I’m reminded of all this every time a new study adds yet more confirmation to the directed adaptation story, such as the recent paper out of Nicola Iovino’s lab on transgenerational epigenetic inheritance in house flies, which states:

Gametes carry parental genetic material to the next generation. Stress-induced epigenetic changes in the germ line can be inherited and can have a profound impact on offspring development.

The press release gives little indication of the controversy as it admits that these findings were once considered impossible:

It has long been thought that these epigenetic modifications never cross the border of generations. Scientists assumed that epigenetic memory accumulated throughout life is entirely cleared during the development of sperms and egg cells.

It is hard enough to see how organisms can respond intra-lifetime to environmental challenges, but how can it be inherited as well? For epigenetic changes that occur in somatic cells, that information must enter into the germ line as well. Somehow it must be incorporated into the sperm and/or egg cells.

It is an enormous problem to explain how such capabilities evolved. Not only are a large number of mutations required to make this capability work, it would not be selected for until the particular environmental condition occurred. That means that, under evolution, it would be not preserved, even if it could somehow arise by chance.

Redundant no more?

Paper Finds Functional Reasons For "Redundant" Codons, Fulfilling a Prediction from Intelligent Design

Casey Luskin 

A new peer-reviewed paper in the journal Frontiers in Genetics, "Redundancy of the genetic code enables translational pausing," finds that so-called "redundant" codons may actually serve important functions in the genome. Redundant (also called "degenerate") codons are those triplets of nucleotides that encode the same amino acid. For example, in the genetic code, the codons GGU, GGC, GGA, and GGG all encode the amino acid glycine. While it has been shown (see here) that such redundancy is actually optimized to minimize the impact of mutations resulting in amino acid changes, it is generally assumed that synonymous codons are functionally equivalent. They just encode the same amino acid, and that's it.

Well, think again. The theory of intelligent design predicts that living organisms will be rich in information, and thus it encourages us to seek out new sources of functionally important information in the genome. This new paper fulfills an ID prediction by finding that synonymous codons can lead to different rates of translation that can ultimately impact protein folding and function.

This means that DNA contains multiple languages or encoded commands occupying the same string of contiguous bases. On the one hand, a string of nucleotide bases encodes amino acids. On the other hand, that same string contains information about the rate at which the ribosome should translate the protein so that it can properly fold into the right shape. The paper calls this "translational pausing." The ribosome is capable of reading both sets of commands -- as they put it, "[t]he ribosome can be thought of as an autonomous functional processor of data that it sees at its input." To put it another way, the genetic code is "multidimensional," a code within a code. This multidimensional nature exceeds the complexity of computer codes generated by humans, which lack the kind of redundancy of the genetic code. As the abstract states:

The codon redundancy ("degeneracy") found in protein-coding regions of mRNA also prescribes Translational Pausing (TP). When coupled with the appropriate interpreters, multiple meanings and functions are programmed into the same sequence of configurable switch-settings. This additional layer of Ontological Prescriptive Information (PI_o) purposely slows or speeds up the translation decoding process within the ribosome. Variable translation rates help prescribe functional folding of the nascent protein. Redundancy of the codon to amino acid mapping, therefore, is anything but superfluous or degenerate. Redundancy programming allows for simultaneous dual prescriptions of TP and amino acid assignments without cross-talk. This allows both functions to be coincident and realizable. We will demonstrate that the TP schema is a bona fide rule-based code, conforming to logical code-like properties. Second, we will demonstrate that this TP code is programmed into the supposedly degenerate redundancy of the codon table. We will show that algorithmic processes play a dominant role in the realization of this multi-dimensional code.

They write that the ribosome's ability to undergo translational pausing "reveal[s] the ribosome, among other things, to be not only a machine, but an independent computer-mediated manufacturing system." The paper even suggests, "Cause-and-effect physical determinism...cannot account for the programming of sequence-dependent biofunction."

Apart from ID's expectation of finding new layers of information in the genome, the paper implicitly challenges some common evolutionary assumptions. The notion that shared synonymous codons are functionally irrelevant has been used to buttress arguments for Darwinian evolution.

For one thing, some evolutionists claim that phylogenetic signals can be carried by the distribution of synonymous codons since they're functionally equivalent. This paper suggests otherwise.

For another, seeking to infer the activity of natural selection, evolutionary biologists statistically analyze the frequency of synonymous (thought to be functionally unimportant) and nonsynonymous (thought to be functionally important) codons in a gene. (We've discussed this previously here andhere.) As the thinking goes, if synonymous codons are functionally unimportant, then three conclusions may follow: a bias toward synonymous codons implies purifying selection in the gene, a bias towards nonsynonymous codons implies positive selection, and an equal balance implies neutral evolution (no selection). But if synonymous codons can have important functional meaning, then the whole methodology goes out the window, and hundreds of studies that used these methods to infer "selection" during the supposed "evolution of genes" could be wrong.

The evidence supports the view that synonymous codons have divergent effects upon translation, as the paper finds: "Data shows that with fixed levels of tRNA's, synonymously encoded mRNA's translate with different speeds" and "Recent work has built on the above observations showing a strong relationship between specific arrangements of codons in mRNA to the rate of translation." Genetic modifications in the lab can even induce translational pausing:

"Pausingfunction" is caused by specific mRNA codon sequences rather than by tunnel-protein interactions to amino acid sequences. This contention is supported by data involving the substitution of rare codons with synonymous codons in E. coli. If the pausing effect was solely related to the amino acid chain sequence, then replacing codons with synonymous codons should still produce the same folded amino acid chain with the same translation speed. However, substitution of rare codons with synonymous codons did produce a change in speed and conformation changes.

These changes in translational speed can have phenotypic effects:

For example, a silent mutation in the human gene ABCB1 caused a conformational change to occur in the P-glycoprotein. This protein folded differently caused by a temporal change in translation affecting the timing of the folding process. ... Thus, the protein folding pathways are affected by changes in the coding regions of DNA" (internal citations removed).

In short, "redundant" codons are not necessarily redundant at all. As the paper puts it: "we show why the term "degeneracy" is completely inappropriate. The dual coding functionality of redundancy is anything but 'degenerate.' It represents, instead, far more sophistication, layers, and dimensions of formal prescription." In fact, this paper "defines new universal linguistic-like rules needed to identify and characterize codon mappings of TP events." The authors write:

The TP code exhibits distinct meaning in relation to mappings between codons and pausing units. The TP code also exhibits a syntax or grammar that obeys strict codon relationships that demonstrate language properties. Because of the redundancy of the genetic code, it could be argued that the TP language is a subset of the genetic language. The subspace of the TP language resides, and thus appears to have a dependency on, the primary genetic code. Within this subspace, however, we argue that the TP language is decoupled from and remains independent of the protein-coding language.

Their conclusion about the high-information capacity of the genetic code is striking:

Redundancy in the primary genetic code allows for additional independent codes. Coupled with the appropriate interpreters and algorithmic processors, multiple dimensions of meaning, and function can be instantiated into the same codon string. We have shown a secondary code superimposed upon the primary codonic prescription of amino acid sequence in proteins. Dual interpretations enable the assembly of the protein's primary structure while enabling additional folding controls via pausing of the translation process. TP provides for temporal control of the translation process allowing the nascent protein to fold appropriately as per its defined function. This duality in the coding function acts to reduce the redundancy in the genetic code when viewed holistically. The functionality of condonic redundancy denies the ill-advised label of "degeneracy." When simultaneously combined with other coding schemas such as intron/exon boundary conditions, and overlapping and oppositely oriented promoters, multiple dimensions of independent coding by the same codon string has become apparent.

In his 2001 book No Free Lunch, William Dembski explained the primary prediction of intelligent design:

[W]hat about the predictive power of intelligent design? Intelligent design offers one obvious prediction, namely, that nature should be chock-full of specified complexity and therefore should contain numerous pointers to design ... This prediction is increasingly being confirmed. (p. 362)

Multidimensional codes and new levels of specified complexity are exactly what ID predicts, and they're exactly what this paper is reporting. It's this sort of sophisticated, information-rich control that is expected by intelligent design, in contrast to Darwinian biology which fails to anticipate it. On the contrary, Darwinian advocates publish mountains of papers banking upon the unquestioned assumption that there is no important, functional reason for the existence of "redundant" or "degenerate" features. Slowly but surely, the data are turning the tide in the evolution debate.

A mathematical examination of attempts to reduce consciousness to physics.

From Barren Planet to Civilization — Four Simple Steps

Granville Sewell

In the video “Why Evolution is Different,” above, I make the simple point that to not believe in intelligent design, you have to believe that the four fundamental, unintelligent forces of physics alone (the gravitational, electromagnetic, and strong and weak nuclear forces) could have rearranged the fundamental particles of physics into encyclopedias and science texts and computers and airplanes and Apple iPhones. I show that this belief runs contrary to the more general statements of the second law of thermodynamics, even if the Earth is an open system.

Whether or not it has anything to do with the second law, I can’t imagine anything in all of science that is more clear and more obvious than that unintelligent forces alone cannot produce such things as Apple iPhones. Yet materialists are not impressed. They believe they can explain how unintelligent forces alone could produce computers and airplanes. In the video, I outline the four steps in the materialists’ explanation of how advanced civilizations can spontaneously arise on barren planets, without design:

Three or four billion years ago a collection of atoms formed by pure chance that was able to duplicate itself.

These complex collections of atoms were able to preserve their complex structures and pass them on to their descendants, generation after generation.

Over a long period of time, the accumulation of duplication errors resulted in more and more elaborate collections of atoms.

Eventually something called “intelligence” allowed some of these collections of atoms to design buildings and computers and airplanes, and write encyclopedias and science texts.

The first step is the origin of life: even most materialists will admit that this is a very difficult problem which has not yet been solved by science. Regarding the fourth step, we may feel that we “understand” how humans design and build computers and airplanes, because we see it happen and perhaps even do such things ourselves. But seeing something happen and understanding how it happens are two very different things, and again I think even most materialists will agree that science cannot yet explain human consciousness or intelligence in terms of unintelligent forces alone.

Darwinists claim that the third step is well understood by science, that natural selection has organized these duplication errors into higher animals, and intelligent humans. The second part of my video disputes this claim, and argues that what we see in the fossil record — large gaps where major new features appear — actually looks more like the way human technology, such as software or automobiles, “evolves,” through testing and improvements.

When I point out, as I do in the second part of the video, the striking similarities between the evolution of life and the evolution of human technology such as the automobile, some people have responded by saying that of course cars cannot evolve like animals, because they cannot reproduce, so there are no “variations” for natural selection to work with. Actually the fact that natural selection cannot act on cars is irrelevant to the main point of this comparison, which is simply that similarities between “species” (of cars or animals) do not prove the absence of design.

However, even though it is irrelevant to my main point, let’s look at the argument that evolution is easier to explain if there is reproduction, because that brings us to the second step of the materialists’ explanation. That the third step seems even superficially plausible (until we look at it in more detail) depends completely on the second step, the fact that living things are able to reproduce, that “these complex collections of atoms are able to preserve their complex structures and pass them on to their descendants, generation after generation.”

Reproduction is the most fundamental characteristic of life. We see it happen everywhere, so we may feel there is no mystery to reproduction. But again, seeing something happen and explaining how it happens naturally are two very different things. Is it really true that if cars were able to give birth to other cars — that is, if they were able to reproduce themselves almost perfectly (the copies even retaining the ability to reproduce themselves in turn), with occasional minor errors — that would make the evolution of cars easier to explain without design than if individual cars experienced slight changes or improvements directly, through rust or crashes or other natural causes?

We are so used to seeing animals make nearly perfect copies of themselves that we dismiss this as just another “natural” process. However, if we actually saw cars that contained car-building factories inside with the ability to construct new cars — not just normal new cars, but new cars containing car-building factories — maybe we would realize what an astonishing process reproduction really is, and we might conclude that this would actually make automobile evolution even more amazing and even more difficult to explain without design.

Mathematicians are trained to value simplicity. When we have a clear, simple, proof of a theorem, and a long, complicated counterargument, involving controversial and unproven assertions, we accept the clear, simple, proof, and we know there must be errors in the counterargument even before we find them. The argument here for intelligent design could not be simpler or clearer: unintelligent forces of physics alone cannot rearrange atoms into computers and airplanes and Apple iPhones. And the counterargument consists of four steps, each of which — to put it very generously — is full of dubious and unproven assertions.

On removing ego from the equation(or not).

"Science Signaling"
David Klinghoffer March 24, 2016 11:42 AM

I keep circling back in my mind to the dramatic juxtaposition of atheist, theistic evolutionist (TE), and ID advocate in Saturday night's debate at the University of Toronto. I won't use names, since it was almost a clash of archetypes where the personal identities and personal circumstances hardly matter. That the TE persistently joined with the atheist in going after the ID'er speaks volumes.

An email correspondent, thinking along the same lines, offers the phrase "science signaling," a play on "virtue signaling." The latter refers to the habit of some in political and other debates to care more about signaling their own virtue than about winning the election or other contest against an opponent. The currency is feeling special and impressing strangers, not actually accomplishing anything.

In science signaling, the point is to signal that you're on the prestige side of any controversy. The theistic evolutionist in Saturday's event was true to type for many TE advocates. He seemed eager, pathetically so, to show the atheist that he "resonated" with him. While unctuously assuring the ID'er that they were on the same side spiritually (as "brothers in Christ"), even as the ID advocate talked science only and not religion, the TE's focus appeared to be on sharing some of the reflected prestige of the atheist scientist. He also did a fair amount of piety signaling to demonstrate to religious believers in the audience that, despite the seeming overlap with the atheist position, he's a strong Christian.

In this respect, for the theistic evolutionist, the science is almost beside the point. It's more of a tool for securing status, which may explain why TEs, like atheists, rarely grapple with the science of intelligent design. Science for many of them is a mask for pursuing other things.

Coincidentally, as I write this it's the Jewish holiday of Purim, when we read the Book of Esther. A custom is the wearing of masks and other costumes. Esther is a surprisingly secular and political story. That being the case, you naturally look for contemporary relevance. This year I'm struck, in the relationship between obsequious courtier Haman and the more ambivalent figure of foolish King Ahasuerus, by the pervasive theme of pride, prestige, status, craving for recognition, delight in royal recognition, and prestige by transference. Take 20 minutes and read it for yourself. You don't need to be religious to appreciate the astute psychology.

Much of the plot is about the ability of prominent, powerful people to take violent offense at having their status slighted. So violent that there must be a scapegoat -- whether the deposed Queen Vashti, or the unprotected Jews, whose scattered communities Haman wishes to see destroyed, all to assuage a bruised ego.

Try to name a contentious matter in science, politics, entertainment, and more that isn't fueled, at least on one side -- just behind the mask -- by status and threats to status. For example, how often does "defending science" really mean "defending or advancing your own sense of personal prestige"? Quite often.

In mainstream media coverage of the evolution debate, where a superficial grasp of the issues involved is almost an ironclad rule, 95 percent of what's said against intelligent design is about signaling, not science. It's a mask for other things.

On paradise:The Watchtower Society's commentary.

PARADISE

A beautiful park, or a parklike garden. The Greek word pa·ra′dei·sos occurs three times in the Christian Greek Scriptures. (Lu 23:43; 2Co 12:4; Re 2:7) Greek writers as far back as Xenophon (c. 431-352 B.C.E.) used the word (pairidaeza), and Pollux attributed it to Persian sources. (Cyropaedia, I, iii, 14; Anabasis, I, ii, 7; Onomasticon, IX, 13) Some lexicographers would derive the Hebrew word par·des′ (meaning, basically, a park) from the same source. But since Solomon (of the 11th century B.C.E.) used par·des′ in his writings, whereas existing Persian writings go back only to about the sixth century B.C.E., such derivation of the Hebrew term is only conjectural. (Ec 2:5; Ca 4:13) The remaining use of par·des′ is at Nehemiah 2:8, where reference is made to a royal wooded park of Persian King Artaxerxes Longimanus, in the fifth century B.C.E.—See PARK.

The three terms (Hebrew par·des′, Persian pairidaeza, and Greek pa·ra′dei·sos), however, all convey the basic idea of a beautiful park or parklike garden. The first such park was that made by man’s Creator, Jehovah God, in Eden. (Ge 2:8, 9, 15) It is called a gan, or “garden,” in Hebrew but was obviously parklike in size and nature. The Greek Septuagint appropriately uses the term pa·ra′dei·sos with reference to that garden. (See EDEN No. 1; GARDEN [Garden of Eden].) Because of sin, Adam lost his right to live in that paradise and his opportunity to gain the right to everlasting life, which right was represented in the fruit of a divinely designated tree in the center of the garden. The garden of Eden may have been enclosed in some way, since it was necessary to place angelic guards only at the east side thereof to prevent human entrance.—Ge 3:22-24.

What is the Paradise that Jesus promised to the evildoer who died alongside him?

Luke’s account shows that an evildoer, being executed alongside Jesus Christ, spoke words in Jesus’ defense and requested that Jesus remember him when he ‘got into his kingdom.’ Jesus’ reply was: “Truly I tell you today, You will be with me in Paradise.” (Lu 23:39-43) The punctuation shown in the rendering of these words must, of course, depend on the translator’s understanding of the sense of Jesus’ words, since no punctuation was used in the original Greek text. Punctuation in the modern style did not become common until about the ninth century C.E. Whereas many translations place a comma before the word “today” and thereby give the impression that the evildoer entered Paradise that same day, there is nothing in the rest of the Scriptures to support this. Jesus himself was dead and in the tomb until the third day and was then resurrected as “the firstfruits” of the resurrection. (Ac 10:40; 1Co 15:20; Col 1:18) He ascended to heaven 40 days later.—Joh 20:17; Ac 1:1-3, 9.

The evidence is, therefore, that Jesus’ use of the word “today” was not to give the time of the evildoer’s being in Paradise but, rather, to call attention to the time in which the promise was being made and during which the evildoer had shown a measure of faith in Jesus. It was a day when Jesus had been rejected and condemned by the highest-ranking religious leaders of his own people and was thereafter sentenced to die by Roman authority. He had become an object of scorn and ridicule. So the wrongdoer alongside him had shown a notable quality and commendable heart attitude in not going along with the crowd but, rather, speaking out in Jesus’ behalf and expressing belief in his coming Kingship. Recognizing that the emphasis is correctly placed on the time of the promise’s being made rather than on the time of its fulfillment, other translations, such as those in English by Rotherham and Lamsa, those in German by Reinhardt and W. Michaelis, as well as the Curetonian Syriac of the fifth century C.E., rendered the text in a form similar to the reading of the New World Translation, quoted herein.

As to the identification of the Paradise of which Jesus spoke, it is clearly not synonymous with the heavenly Kingdom of Christ. Earlier that day entry into that heavenly Kingdom had been held out as a prospect for Jesus’ faithful disciples but on the basis of their having ‘stuck with him in his trials,’ something the evildoer had never done, his dying on a stake alongside Jesus being purely for his own criminal acts. (Lu 22:28-30; 23:40, 41) The evildoer obviously had not been “born again,” of water and spirit, which Jesus showed was a prerequisite to entry into the Kingdom of the heavens. (Joh 3:3-6) Nor was the evildoer one of the ‘conquerors’ that the glorified Christ Jesus stated would be with him on his heavenly throne and that have a share in “the first resurrection.”—Re 3:11, 12, 21; 12:10, 11; 14:1-4; 20:4-6.

Some reference works present the view that Jesus was referring to a paradise location in Hades or Sheol, supposedly a compartment or division thereof for those approved by God. The claim is made that the Jewish rabbis of that time taught the existence of such a paradise for those who had died and were awaiting a resurrection. Regarding the teachings of the rabbis, Hastings’ Dictionary of the Bible states: “The Rabbinical theology as it has come down to us exhibits an extraordinary medley of ideas on these questions, and in the case of many of them it is difficult to determine the dates to which they should be assigned. . . . Taking the literature as it is, it might appear that Paradise was regarded by some as on earth itself, by others as forming part of Sheol, by others still as neither on earth nor under earth, but in heaven . . . But there is some doubt as respects, at least, part of this. These various conceptions are found indeed in later Judaism. They appear most precisely and most in detail in the mediaeval Cabbalistic Judaism . . . But it is uncertain how far back these things can be carried. The older Jewish theology at least . . . seems to give little or no place to the idea of an intermediate Paradise. It speaks of a Gehinnom for the wicked, and a Gan Eden, or garden of Eden, for the just. It is questionable whether it goes beyond these conceptions and affirms a Paradise in Sheol.”—1905, Vol. III, pp. 669, 670.

Even if they did teach such a thing, it would be most unreasonable to believe that Jesus would propagate such a concept, in view of his condemnation of the non-Biblical religious traditions of the Jewish religious leaders. (Mt 15:3-9) Likely the paradise truly familiar to the Jewish malefactor to whom Jesus spoke was the earthly Paradise described in the first book of the Hebrew Scriptures, the Paradise of Eden. That being so, Jesus’ promise would reasonably point to a restoration of such earthly paradisaic condition. His promise to the wrongdoer would therefore give assured hope of a resurrection of such an unrighteous one to an opportunity to life in that restored Paradise.—Compare Ac 24:15; Re 20:12, 13; 21:1-5; Mt 6:10.

A Spiritual Paradise. Throughout many of the prophetic books of the Bible, divine promises are found regarding the restoration of Israel from the lands of its exile to its desolated homeland. God would cause that abandoned land to be tilled and sown, to produce richly, and to abound with humankind and animalkind; the cities would be rebuilt and inhabited, and people would say: “That land yonder which was laid desolate has become like the garden of Eden.” (Eze 36:6-11, 29, 30, 33-35; compare Isa 51:3; Jer 31:10-12; Eze 34:25-27.) However, these prophecies also show that paradise conditions related to the people themselves, who, by faithfulness to God, could now “sprout” and flourish as “trees of righteousness,” enjoying beautiful spiritual prosperity like a “well-watered garden,” showered by bounteous blessings from God because of having his favor. (Isa 58:11; 61:3, 11; Jer 31:12; 32:41; compare Ps 1:3; 72:3, 6-8, 16; 85:10-13; Isa 44:3, 4.) The people of Israel had been God’s vineyard, his planting, but their badness and apostasy from true worship had caused a figurative ‘withering away’ of their spiritual field, even before the literal desolation of their land took place.—Compare Ex 15:17; Isa 5:1-8; Jer 2:21.

This undoubtedly provides the key for understanding Paul’s description of the vision (evidently had by him, since it forms part of his defense of his own apostleship) referred to at 2 Corinthians 12:1-7. Caught away to “the third heaven” (see HEAVEN [Third Heaven]), the vision viewer entered “paradise” and heard unutterable words. That this paradise envisioned could refer to a spiritual state among God’s people, as in the case of fleshly Israel, can be seen from the fact that the Christian congregation was also God’s “field under cultivation,” his spiritual vineyard, rooted in Christ Jesus and bearing fruit to God’s praise. (1Co 3:9; Joh 15:1-8) As such it had replaced the nation of Israel in God’s favor. (Compare Mt 21:33-43.) Paul’s vision, nevertheless, must logically have applied to some future time, so as to constitute a ‘revelation.’ (2Co 12:1) An apostasy was due to set in among the Christian congregation and was already working in Paul’s day; it would result in a condition like that of a field oversown with weeds. (Mt 13:24-30, 36-43; Ac 20:29; 2Th 2:3, 7; compare Heb 6:7, 8.) So, Paul’s paradise vision would not reasonably apply while such was the case but would evidently relate to the time of “the harvest season” when the genuine Christians would be gathered by the angelic reapers and would enjoy rich blessings and spiritual prosperity from God.

It is evident, however, that the restoration prophecies recorded by the Hebrew prophets include elements that will also find a physical fulfillment in the restored earthly Paradise. There are features, for example, in Isaiah 35:1-7, such as the healing of the blind and the lame, that did not have a literal fulfillment following the restoration from ancient Babylon, nor are they fulfilled in such a manner in the Christian spiritual paradise. It would be inconsistent for God to inspire such prophecies as those of Isaiah 11:6-9, Ezekiel 34:25, and Hosea 2:18, with the intention that they have only a figurative or spiritual meaning, without having a literal fulfillment of these things in the physical experiences of God’s servants.

Eating in “the Paradise of God.” Revelation 2:7 mentions a “tree of life” in “the paradise of God” and that eating from it would be the privilege of the one “that conquers.” Since other promises given in this section of Revelation to such conquering ones clearly relate to their gaining a heavenly inheritance (Re 2:26-28; 3:12, 21), it seems evident that “the paradise of God” in this case is a heavenly one. The word “tree” here translates the Greek word xy′lon, which literally means “wood,” and could therefore refer to an orchard of trees. In the earthly Paradise of Eden, eating of the tree of life would have meant living forever for man. (Ge 3:22-24) Even the fruit of the other trees of the garden would have been life sustaining for man as long as he continued obedient. So, the partaking of “the tree [or trees] of life” in “the paradise of God” evidently relates to the divine provision for sustained life granted the Christian conquerors, other texts showing that they receive the prize of immortality and incorruptibility along with their heavenly Head and Lord, Christ Jesus.—1Co 15:50-54; 1Pe 1:3, 4.