The Watchtower Society's Commentary on the book of Ezra.

EZRA, BOOK OF

A record showing how Jehovah fulfilled his promises to restore Israel from exile in Babylon and reestablish true worship in Jerusalem. Included are the imperial orders to restore Jehovah’s worship among the Jews after the 70-year desolation of Jerusalem and the account of the work done, despite obstacles, to achieve this. Ezra stuck closely to the above purpose throughout the book. This is apparently the reason for the omissions of what went on during certain lapses of time, such as between chapters 6 and 7 of the book, for the writer was not trying to give a complete historical account of the times.

Writer. Ezra, as a priest, scholar, skilled copyist, and man who had “prepared his heart . . . to teach in Israel regulation and justice” and to correct the things wanting in the worship of Jehovah that was carried on among the repatriated Israelites, was eminently qualified to write the book bearing his name. The royal power granted to him by the king of Persia would give him added reason and authority to do the research necessary, and it would be logical for such a man to write a record of this important segment of his nation’s history. (Ezr 7:6, 10, 25, 26) The book is honest, therefore, in its use of the first person for the writer from chapter 7, verse 27, through chapter 9. Most scholars are in agreement that the book of Ezra carries on the history at the point where the Chronicles leave off, as a comparison of 2 Chronicles 36:22, 23 with Ezra 1:1-3 will show. This again points to Ezra as the writer. Jewish tradition likewise assigns the writership to Ezra.

Authenticity. The book of Ezra is included in the Hebrew canon. Originally it was combined with Nehemiah to form one scroll. The Babylonian Talmud (Bava Batra 14b) follows this tradition, but since the 16th century, printed Hebrew Bibles mark a division, although they count the two books as one in the total number of the books of the Hebrew Scriptures. The Douay Version uses the designations First and Second Esdras, following the Greek form of spelling. It notes, however, that the second book is also known as Nehemiah. There is an apocryphal book in Greek called Ezra III. This is composed of passages from Second Chronicles, Ezra, and Nehemiah as well as certain popular legends; also there is the book falsely called Ezra IV.

The greater portion of Ezra was written in Hebrew. But a sizable portion is in Aramaic, since Ezra copied from the public records and official documents. These include the copies of letters sent to the Persian kings by officials “beyond the [Euphrates] River” and the royal replies and decrees imposing commands on these officials. Also, Ezra supplied a brief connecting history linking these documents. Aramaic was the diplomatic language and that used in international commerce of Ezra’s day. The Aramaic portions are found in chapters 4 to 7. Some of Ezra’s information was copied from Jewish archives, and this part is, of course, in Hebrew. These facts also strengthen the argument for the authenticity of Ezra’s account.

Ezra 7:23-26 records that the Persian government approved the Law of Moses as applicable to the Jews and that the Persians thus had a hand in restoring true worship. Ezra’s references to the Persian kings put them in their accurate order. Today the majority of scholars accept the accuracy of the book, The New Westminster Dictionary of the Bible frankly saying that “there is no doubt about the reliability of the historical contents.” (Edited by H. Gehman, 1970, p. 291) The record in the book is, therefore, dependable, and Ezra was a historical person.

Time and Setting. The book of Ezra was written about 460 B.C.E., along with the books of Chronicles. Ezra begins by relating the decree of Cyrus for the restoration of the Jews from Babylon. It was in the first year of Cyrus that this Persian king issued a restoration proclamation. (Ezr 1:1) Judah and Jerusalem had been left desolate of inhabitants, in the autumn of 607 B.C.E., when those left by Nebuchadnezzar moved to Egypt. The 70th year of Jerusalem’s desolation, the last enforced sabbath on the land, would end in the autumn of 537 B.C.E. Cyrus’ decree must have been issued late in 538 B.C.E. or early in 537 for two reasons. The desolation had to last until the 70th year ended, and the released Israelites would not be expected to travel in the winter rainy season, as would have been the case if the decree had been made a few months earlier. Likely it was issued in the early spring of 537 B.C.E. in order to give the Jews a chance to travel during the dry season, arrive in Jerusalem, and set up the altar on the first day of the seventh month (Tishri) of the year 537 B.C.E., September 29 according to the Gregorian calendar.—Ezr 3:2-6.

After describing the Passover and the Festival of Unfermented Cakes that were held after the temple was completed in 515 B.C.E., Ezra passes over the subsequent period of time until the seventh year of the reign of Artaxerxes, the king of Persia, 468 B.C.E., when Ezra personally comes into the picture. Ezra uses the first person from chapter 7, verse 27, to chapter 9 but changes to the third person in chapter 10, putting himself in the background to concentrate on the activities of princes, the priests, the Levites, and the rest of those who had been repatriated, especially dealing with correcting the situation of the ones who had married foreign wives.

[Box on page 799]

HIGHLIGHTS OF EZRA

The rebuilding of the temple in Jerusalem and the restoration of true worship there after the Babylonian exile

Covers a period of some 70 years following the return of the Jews from exile in Babylon

Cyrus issues liberation decree, and a remnant of Jewish exiles return to Jerusalem (in 537 B.C.E.) to rebuild the temple (1:1–3:6)

Rebuilding of the temple (3:7–6:22)

Foundation laid in second year of the return from exile

Enemies repeatedly interfere with temple rebuilding and finally succeed in having the work stopped until the prophets Zechariah and Haggai, in the second year of Darius I (520 B.C.E.), encourage the people to resume construction

An official investigation of Persian records in Babylon and Ecbatana reveals that the temple rebuilding was authorized by Cyrus, so Darius I decrees that the work continue without hindrance, stipulating the death penalty for violators

In the sixth year of Darius I (515 B.C.E.), temple construction is completed, after which the building is inaugurated and the Passover observed

Ezra goes to Jerusalem (in 468 B.C.E.) with gifts for the temple and to appoint judges (7:1–8:36)

Permission for the trip granted by Persian monarch Artaxerxes (Longimanus)

Ezra and about 1,500 men, besides 258 Levites and Nethinim from Casiphia, depart from a point of assembly at the river Ahava with gold, silver, and utensils for the temple; they arrive in Jerusalem over three and a half months later

Cleansing of Israel, including the priesthood (9:1–10:44)

Learning of the defilement from marriage to foreign women, Ezra makes public confession in prayer to Jehovah

Shecaniah acknowledges sin and proposes the making of a covenant to put away foreign wives and their offspring

All former exiles are commanded to assemble at Jerusalem; a decision is then made to have princes investigate the individual cases of defilement progressively


Priests, Levites, and the rest of the men follow through in dismissing foreign wives and sons

The perpetual information machine:another magical beast from the atheistic universe.

Rob Sheldon: Increasing the heat energy leads to decreasing the information

Published on August 22nd, 2015

Written by: News

Further to Origin of complex cells: Can energy create information? (Lane seems to think that energy can create or substitute for huge amounts of information. This seems wrong but it is apparently acceptable to The Scientist, Rob Sheldon, noting that reader’ thoughts were solicited, writes to say,

In thermodynamics, we have the fundamental thermodynamic relation or defining equation dU = dQ + dW = TdS – PdV, where U=internal energy, Q=heat, W=work, T=temperature,S=entropy, P=pressure, V=volume, and “d” means “the change of”. In a closed system that is “reversible” , (no eddies, turbulence etc) and the volume doesn’t change much (incompressible like water), then we can eliminate the work and get the equation dQ = TdS, which is to say, the change in heat energy of our system is equal to the temperature times the change in entropy of the system. Or we can rewrite this dQ/T = dS.

What does this mean?

Well, since S is the entropy, and using Shannon’s definition, -S = Information, then dQ/T = -d(Info)

So addressing Lane’s book, heat energy is not information. Increasing the heat energy leads to decreasing the information. The same amount of heat energy at higher temperature has more information than the same heat at lower temperature. For life to extract information from a heat source, it must be a heat engine, extracting high temperature energy and excreting low temperature energy. Heat engines do this feat by incorporating carefully constructed linkages and machinery to prevent the work from vanishing in the turbulent, diffusive, entropic working fluid. If the machinery has to be made out of the same material as the working fluid, then it is like saying “a high information dense state can process heat energy to extract information”.

Well, doesn’t this process produce more information than at the beginning? Wouldn’t this allow for an infinitely great amount of information inside the system, the “Borg” of cellular automata?

No, because entropy is a fluid property, and it wants to diffuse away. The more information that gets concentrated, the greater the gradients, and the more work expended keeping those gradients. Therefore for a fixed energy flow, there is a maximum entropy gradient, a maximum entropy density, where all the effort is expended just staying alive. For heat engines like your car, this is given by the maximum temperature the engine can run at before it melts, and Sadi Carnot used the formula (Ti-Tf)/Ti to describe this “Carnot efficiency”. For cells, we’ll call this maximum achievable entropy gradient “the life efficiency”, and I think it is fair to argue that the more efficient a heat engine, the more information it must contain. (Have you looked at the number of sensor wires under the hood of a late model car and compared it to, say, a VW bug engine?)

But one thing it cannot do, cannot allow, is “a low information state can process heat energy to spontaneously become a high information state that processes heat energy”. This is the proverbial “perpetual motion machine” now operating on entropy, it is the “perpetual information machine”. For just as Clausius and Kelvin showed that heat engines that produced too much work (too efficient) could be linked together to produce a perpetual motion machine, so also fluid “life” machines that produce too much information can be linked together to produce perpetual motion. This proves that no such machine is possible or else biology would long ago become a perpetual motion machine that never eats.

So why do these erroneous views keep propagating, having spontaneous information arising from energy gradients?

Because they fudge the bookkeeping. Entropy is notoriously hard to measure, and so for example, they might underestimate the information in the cellular machinery and think that a temperature gradient has more than enough entropy to create the cellular machinery. Or as Granville Sewell argues, they have an open system that allows entropy to arrive and disappear without proper accounting, so that information accumulates inside the cell, which they then misattribute to temperature gradients. But if any of these papers were even within hailing distance of being correct, then perpetual motion would be commonplace by now, and you and I would spend our days wondering what to do with all our free time.

Other reader’s thoughts?

See also: Granville Sewell’s important contribution to physics: Entropy-X

The Watchtower Society's commentary on ' the lake of fire'

What Is the Lake of Fire? Is It the Same as Hell or Gehenna?

The Bible’s answer

The lake of fire is a symbol of eternal destruction. It is the same as Gehenna, but it is different from hell, which is the common grave of mankind.

Not a literal lake

The five Bible verses that mention “the lake of fire” show it to be a symbol rather than a literal lake. (Revelation 19:20; 20:10, 14, 15; 21:8) The following are cast into the lake of fire:

• The Devil. (Revelation 20:10) As a spirit creature, the Devil cannot be harmed by literal fire.—Exodus 3:2; Judges 13:20.
• Death. (Revelation 20:14) This is not a literal entity but represents a state of inactivity, the absence of life. (Ecclesiastes 9:10) Death cannot literally be burned.
• “The wild beast” and “the false prophet.” (Revelation 19:20) Since these are symbols, doesn’t it seem reasonable to conclude that the lake they are thrown into is also a symbol?—Revelation 13:11, 12; 16:13.

A symbol of eternal destruction

The Bible says that the lake of fire “means the second death.” (Revelation 20:14;21:8) The first kind of death mentioned in the Bible resulted from Adam’s sin. This death can be reversed by resurrection and will eventually be eliminated by God.—1 Corinthians 15:21, 22, 26.

There is no release from the symbolic lake of fire

The lake of fire represents a different, or second, kind of death. Although it too represents a state of total inactivity, it is different in that the Bible says nothing about a resurrection from the second death. For example, the Bible says that Jesus has “the keys of hell and of death,” showing that he has the authority to release people from the death brought by Adam’s sin. (Revelation 1:18; 20:13,King James Version) However, neither Jesus nor anyone else has a key to the lake of fire. That symbolic lake represents eternal punishment in the form of permanent destruction.—2 Thessalonians 1:9.

Identical to Gehenna, the Valley of Hinnom

Gehenna (Greek ge′en·na) is mentioned 12 times in the Bible. Like the lake of fire, it is a symbol of eternal destruction. Although some translations render this word as “hell,” Gehenna is different from hell (Hebrew sheʼohl′, Greek hai′des).

The Valley of Hinnom

The word “Gehenna” literally means “Valley of Hinnom,” referring to a valley just outside Jerusalem. In Bible times, the city residents used this valley as a garbage dump. They kept a fire constantly burning there to destroy refuse; maggots consumed anything that the fire did not reach.

Jesus used Gehenna as a symbol of everlasting destruction. (Matthew 23:33) He said that in Gehenna “the maggot does not die and the fire is not put out.” (Mark 9:47, 48) He thus alluded to the conditions in the Valley of Hinnom and also to the prophecy atIsaiah 66:24, which says: “They will go out and look on the carcasses of the men who rebelled against me; for the worms on them will not die, and their fire will not be extinguished.” Jesus’ illustration describes, not torture, but complete annihilation. The worms and fire consume carcasses, or dead bodies, not living people.

The Bible gives no indication of any return from Gehenna. “The lake of fire” and “the fiery Gehenna” both represent permanent, everlasting destruction.—Revelation 20:14, 15; 21:8; Matthew 18:9.

How “tormented day and night forever and ever”?

If the lake of fire is a symbol of destruction, why does the Bible say that in it the Devil, the wild beast, and the false prophet “will be tormented day and night forever and ever”? (Revelation 20:10) Consider four reasons why this torment does not refer to literal torture:

1. For the Devil to be tortured eternally, he would have to be kept alive forever. However, the Bible says that he will be brought to nothing, or put out of existence.—Hebrews 2:14.
2. Everlasting life is a gift from God, not a punishment.—Romans 6:23.
3. The wild beast and the false prophet are symbols and cannot experience literal torture.
4. The context of the Bible indicates that the torment of the Devil is everlasting restraint or destruction.

The word used for “torment” in the Bible can also mean “a condition of restraint.” For example, the Greek word for “tormentors” used at Matthew 18:34is rendered as “jailers” in many translations, showing the connection between the words “torment” and “restraint.” Likewise, the parallel accounts at Matthew 8:29 and Luke 8:30, 31 equate “torment” with “the abyss,” a figurative place of complete inactivity or death. (Romans 10:7; Revelation 20:1, 3) In fact, several times the book of Revelation uses the word “torment” in a symbolic sense.—Revelation 9:5; 11:10; 18:7, 10.

Yet more on life's anti-Darwinian bias.

Octopus Genome Defies Evolutionary Expectations

Evolution News & Views August 21, 2015 3:20 AM

Cephalopods, from the Latin for "head-foot," are among the strangest creatures in the ocean. Though classified in phylum Mollusca, they seem vastly different from snails or clams. Colorful octopus and cuttlefish swim by in the introduction to Living Waters: Intelligent Design in the Oceans of the Earth, but it would require whole separate films to do them justice -- for they are among the smartest and most functionally diverse animals on the planet: flexible, adaptable, and well-equipped for rapid motion, effective hunting, and quick camouflage.

Their numbers include the giant squid, cuttlefish, and the beautifully coiled shelled nautilus. Now that the first octopus genome has been sequenced, scientists are beginning to learn about the complex genetic information behind their capabilities.

Nature published the first genome of a cephalopod, the California two-spot octopus, Octopus bimaculoides. It was a massive undertaking. The octopus genome is comparable to the human genome in size and complexity. In fact, it has "a greater number of protein-coding genes -- some 33,000, compared with fewer than 25,000 in Homo sapiens," says Alison Abbott in the same issue of Nature.

This excess results mostly from the expansion of a few specific gene families, Ragsdale says. One of the most remarkable gene groups is the protocadherins, which regulate the development of neurons and the short-range interactions between them. The octopus has 168 of these genes -- more than twice as many as mammals. This resonates with the creature's unusually large brain and the organ's even-stranger anatomy. Of the octopus'shalf a billion neurons -- six times the number in a mouse -- two-thirds spill out from its head through its arms, without the involvement of long-range fibres such as those in vertebrate spinal cords. The independent computing power of the arms, which can execute cognitive tasks even when dismembered, have made octopuses an object of study for neurobiologists such as Hochner and for roboticists who are collaborating on the development of soft, flexible robots.

A gene family that is involved in development, the zinc-finger transcription factors, is also highly expanded in octopuses. At around 1,800 genes, it is the second-largest gene family to be discovered in an animal, after the elephant's 2,000 olfactory-receptor genes. [Emphasis added.]

Is this an example of the power of Darwinian evolution to progressively expand existing traits? Don't ask the geneticists; they're too busy trying to figure out where all the unique genes came from.

The analysis also turned up hundreds of other genes that are specific to the octopus and highly expressed in particular tissues. The suckers, for example, express a curious set of genes that are similar to those that encode receptors for the neurotransmitter acetylcholine. The genes seem to enable the octopus'sremarkable ability to taste with its suckers.

Scientists identified six genes for proteins called reflectins, which are expressed in an octopus's skin. These alter the way light reflects from the octopus, giving the appearance of a different colour -- one of several ways that an octopus can disguise itself, along with changing its texture, pattern or brightness.

Another discovery hinted at the basis of an octopus'sintelligence. The genome contains systems that can allow tissues to rapidly modify proteins to change their function. Electrophysiologists had predicted that this could explain how octopuses adapt their neural-network properties to enable such extraordinary learning and memory capabilities.

How could so many unique genes arise by blind neo-Darwinian processes? It's unsatisfying to hear scientists assume they "developed" somehow.

The octopus's position in the Mollusca phylum illustrates evolution at its most spectacular, Hochner says. "Very simple molluscs like the clam -- they just sit in the mud, filtering food. And then we have the magnificent octopus, which left its shell and developed the most-elaborate behaviours in water."

The paper is no help. It just speaks of "cephalopod morphologicalinnovations, including their large and complex nervous systems." And then, the authors find they cannot appeal to a favorite explanatory tool, gene duplication:

Based primarily on chromosome number, several researchersproposed that whole-genome duplications were important in theevolution of the cephalopod body plan, paralleling the role ascribed to the independent whole-genome duplication events that occurred early in vertebrate evolution. Although this is an attractive framework for both gene family expansion and increased regulatory complexity across multiple genes, we found no evidence for it. The gene family expansions present in octopus are predominantly organized in clusters along the genome, rather than distributed in doubly conserved synteny as expected for a paleopolyploid.... Although genes that regulate development are often retained in multiple copies after paleopolyploidy in other lineages, they are not generally expanded in octopus relative to limpet, oyster and other invertebrate bilaterians.

With whole-genome duplication out, what's left? Essentially, magic:

Mechanisms other than whole-genome duplications can drive genomic novelty, including expansion of existing gene families,evolution of novel genes, modification of gene regulatory networks, and reorganization of the genome through transposon activity. Within the O. bimaculoides genome, we found evidence for all of these mechanisms, including expansions in several gene families, a suite of octopus- and cephalopod-specific genes, and extensive genome shuffling.

"Evolution of novel genes" --? Isn't that the question at hand? Where do novel genes come from? They found "a suite of octopus- and cephalopod-specific genes" that seem to have appeared out of nowhere. As for mechanisms that "can drive genomic novelty," their list does little more than assume that making more of existing things and shuffling them around will create novel things that do something useful. Try that with a copy machine, a book, and scissors. "Modification of gene regulatory networks" is no help, either. Stephen Meyer documented in Darwin's Doubt how modifications to GRNs are almost always lethal, and never innovative.

Running out of options, the authors turn to a perennial cop-out: convergence.

A search of available transcriptome data from the longfin inshoresquid Doryteuthis (formerly, Loligo) pealei also demonstrated an expanded number of protocadherin genes... Surprisingly, our phylogenetic analyses suggest that the squid and octopus protocadherin arrays arose independently. Unlinked octopus protocadherins appear to have expanded ~135 Mya, after octopuses diverged from squid. In contrast, clustered octopus protocadherins are much more similar in sequence, either due to more recent duplications or gene conversion as found in clustered protocadherins in zebrafish and mammals....

Finally, the independent expansions and nervous system enrichment of protocadherins in coleoid cephalopods and vertebrates offers a striking example of convergent evolution between these clades at the molecular level.

Maybe octopus evolved from fish into mammals. We jest, of course, but the genomic data are not proving helpful to Darwin. After comparing the genome to other creatures near and far, finding more examples of unique genes and convergences, the authors close by trying to put the octopus in context with the family tree of lophotrochozoans ("crest-wheel" animals, a controversial supergroup of phyla that includes animals as diverse as worms, clams, and brachiopods). Watch again for the magical appearance of innovations:

Using a relaxed molecular clock, we estimate that the octopus and squid lineages diverged ~270 Mya, emphasizing the deep evolutionary history of coleoid cephalopods... Our analyses found hundreds of coleoid- and octopus-specific genes, many of which were expressed in tissues containing novel structures, including the chromatophore-laden skin, the suckers and the nervous system.... Taken together, these novel genes, the expansion of C2H2 ZNFs, genome rearrangements, and extensive transposable element activity yield a new landscape for both trans- and cis-regulatory elements in the octopus genome, resulting in changes in an otherwise 'typical' lophotrochozoan gene complement thatcontributed to the evolution of cephalopod neural complexity and morphological innovations.

Maybe this is why Alison Abbott jokes about the octopus having the genome of an alien. "With its eight prehensile arms lined with suckers, camera-like eyes, elaborate repertoire of camouflage tricks and spooky intelligence, the octopus is like no other creature on Earth."

Over at Science, Dennis Normile has nothing new to offer. The octopus genome "surprises and teases," he says. He quotes a team member from the University of Chicago who speaks for the team: "We were really pretty surprised by a bunch of things we found." Another researcher offers this unhelpful comment on the implications for evolution: "there is more than one way to grow a genome."

The popular media took all these surprises in stride, never doubting Darwin, but having little to say about him, either. Most pointed out that the genome-duplication trick doesn't work for the octopus. Discussion of evolution is remarkably scarce in the articles. One exception is Science Daily. Its write-up not only credits blind nature for all the octopus's innovations, but launches into a victory speech for cosmic Darwinism:

As humans, we like to think we are unique in evolutionary terms, but the octopus could reveal that this is not the case. One reason the octopus fascinates scientists is that its brain became organized to be able to carry out such incredible, complex taskswithout adopting the principles of the vertebrate brain. Further examination will tell if the building blocks of its nervous system are as radically different from those of vertebrate landlubbers like us, as the octopus's abilities suggest.

This is not as unlikely as it sounds. Even if the octopus evolvedin a completely different ecosystem, evolution can have only so many solutions to a given problem. If similarities are in fact found, this would significantly alter our perspective on the emergence of life elsewhere in the universe.

David Klinghoffer has pointed out how off-putting triumphalism like this can be. Can't reporters just be honest about the problems with traditional evolutionary explanations? In Living Waters, Discovery Institute's Richard Sternberg and Paul Nelson discuss how improbable it is to get two coordinated mutations for a new function. For the case of whale evolution, the time required for just two mutations for some adaptation vastly exceeds the time available for the transition. A similar problem is evident with octopus evolution from a "simple" mollusk.

Science can observe and enjoy wonders of nature without a Darwinian narrative gloss. Though Live Science's coverage of the Nature paper was heavy on the gloss, a different Live Science article described another species, the large Pacific striped octopus (LPSO), with whimsical delight and very little talk about evolution. This species (despite its name, able to compact itself the size of a tennis ball), tricks its prey the way a human jokester taps on a friend's opposite shoulder, making him turn the wrong way.

"One of the things that impresses me most about this species is 

its great diversity of predatory behavior," Caldwell told Live Science. Not only does this striped octopus trick unsuspecting shrimp, but it also eats snails by first boring small holes into their shells with the end of its arm and then injecting its prey with a deadly, digestive fluid, he said. And despite their diminutive size, LPSOs are strong enough to break apart a clam shell and spritely enough to pounce on a quick-footed crab.

But the extraordinary eating habits of this critter don't end there. Once an LPSO catches its supper, it isn't above sharing the meal with others, said Caldwell, who notes that the animal's ability to peacefully share food with other octopuses is both unusual andvery exciting to biologists.

Scientific investigation can still be "very exciting" without the Darwinian angle. There are many more species of cephalopods worth investigating. Some live deep at hydrothermal vents. Some live in shallow tide pools. They come in all sizes. The mimic octopus amazes scientists. There is much to occupy biologists' time learning about these wonderful animals, without having to fit them into an evolutionary tree.

"There are over 300 known species of octopus, and more are described every year. But the fact is that while we think we knowa lot about octopus behavior and physiology, everything we knowcomes from a handful of species," Caldwell said. "So when I tell you the LPSO is an unusual species with very unique behavior, I really don't know that."

Meanwhile, several of the articles mention that engineers are studying octopuses in search of ideas for soft robots, distributed networks, and propulsion techniques. "Humans invented flying machines by mimicking birds," Science Daily says. "We can look forward to octopuses inspiring robots that give us easy access to the ocean floor."

It's unlikely to be productive trying to trace an assumed evolutionary ancestry that requires heavy doses of "innovation" or "convergence" to accept. Why not tackle the questions amenable to observation and understanding? Biomimetics is showing the usefulness of a design approach. Let's follow that evidence where it leads.

On Dawkins' 'own goal'

Richard Dawkins Opens Mouth; Inserts Foot

Jonathan M. June 21, 2010 9:51 AM

In 2003, the BBC launched a documentary series known as Atheism: A Rough History of Disbelief, presented by the atheist Jonathan Miller. The interviews that were conducted, being too lengthy for inclusion in the 2003 series, were later archived in a 2004 documentary series, entitled The Atheism Tapes, a supplementary series of six programs, consisting of the uncut interviews with a single contributing atheist.

One such film featured Jonathan Miller interviewing our old friend, Richard Dawkins

Three minutes into the embedded interview, in speaking of the purported instances of irreducible complexity in nature, Richard Dawkins succeeds in decimating any pretense to neo-Darwinism's status as a falsifiable proposition. He states, "There cannot have been intermediate stages that were not beneficial. There's no room in natural selection for the sort of foresight argument...It doesn't happen like that. There's got to be a series of advantages all the way...If you can't think of one, then that's your problem, not natural selection's problem."

Is Richard Dawkins suggesting that the purported explanatory adequacy of neo-Darwinism is not a testable proposition? If there are no biochemical systems which cannot, in principle, be accounted for by natural selection, then how is one to evaluate Darwinism's explanatory adequacies? At what point is one justified in saying, "Natural selection is an inadequate explanation and we must hence search for an alternative explanation"?

One might have thought that Richard Dawkins would have stopped digging at this point. But Dawkins had not finished: "Well, I suppose that it is a sort of matter of faith on my part since the theory is so coherent and so powerful."

What is so coherent and so powerful? If defined simply as common ancestry, critics of Darwinism may be inclined to agree. If he means the efficacy of the mechanism, then that is what he is intent on demonstrating. Thus, simple appeals to 'matters of faith' is not what one might regard as a sound argument.

Exjunk:A prequel.

"Junk" RNA Found to Encode Peptides That Regulate Fruit Fly Development

Jonathan M. July 27, 2010 9:21 AM |

Advocates of intelligent design have long been skeptical of the claim that the majority of our genome is nonfunctional gibberish, a mere relic of our evolutionary past. Many of the key arguments for common ancestry are based around the supposition that certain loci of our genome are functionless. But the gaps in our knowledge of the genome (in which such supposition resides) are continually shrinking.

A recent paper published in Science by Kondo et al. reported on the discovery that some of the supposed "non-coding" regions of the RNA transcript actually actively encode for short peptides that regulate genes involved inDrosophila development.

According to the Abstract,

A substantial proportion of eukaryotic transcripts are considered to be noncoding RNAs because they contain only short open reading frames (sORFs). Recent findings suggest, however, that some sORFs encode small bioactive peptides. Here, we show that peptides of 11 to 32 amino acids encoded by the polished rice (pri) sORF gene control epidermal differentiation in Drosophila by modifying the transcription factor Shavenbaby (Svb). Pri peptides trigger the amino-terminal truncation of the Svb protein, which converts Svb from a repressor to an activator. Our results demonstrate that during Drosophila embryogenesis, Pri sORF peptides provide a strict temporal control to the transcriptional program of epidermal morphogenesis.

The paper states that,

We and others recently identified an evolutionarily conserved sORF gene, referred to as polished rice ( pri) or tarsal-less (tal) in Drosophila, and mille-pattes (mlpt) in Tribolium (9-11). primRNA is a polycistronic transcript that encodes four similar peptides, 1 to 32 amino acids in length, that play a redundant role in Drosophila embryogenesis (9, 10). Embryos that lack pri display prominent defects, including the absence of trichomes and aberrant tracheal architecture (9, 10). Reduced pri activity in imaginal development results in abnormal leg morphogenesis (10, 12). Similarly, mlpt knockdown in Tribolium leads to appendage defects and the transformation of segmental identity (11).

The gene containing the Short Open Reading Frame (sORF) is a polycistronic transcript (meaning it carries the information of several genes, which are translated into multiple proteins) from a gene called polished rice, so named because the flies that have a mutation in the gene lack characteristic hairs in the fly embryo which resemble grains of rice. The researchers found that this RNA transcript encodes for four short peptides, ranging from 1 to 32 amino acids long.

The researchers report their finding "that the polished rice peptides trigger the truncation of a protein called Shavenbaby, which regulates the development of the hairs."

A related report by Nature News makes the following comment:

Short peptides could be lurking virtually anywhere in the genome, says Desplan. Sequence analysis suggests that DNA regions capable of encoding tiny peptides exist in front of many protein-coding genes, but few researchers believe that these regions are doing anything useful, he adds.

The article further comments,

Meanwhile, Gerstein notes that the polished rice peptides could also have implications for how we view pseudogenes, which have long been thought to be defunct relics of protein-coding genes. Pseudogenes often contain many signals that would stop protein synthesis and, as a result, could only encode short amino-acid chains. "Maybe this would provide a new way for pseudogenes to have some sort of function," he says.

The researchers conclude, 

Besides the mechanisms of epidermal differentiation, our studies suggest broader functions for Pri peptides. Although pri is also required for tracheal morphogenesis (9), we observed normaltrachea in svb mutant embryos (fig. S9), indicating that Pri peptides probably regulate additional developmental factors. Recent large-scale analyses indicate that thousands of unexplored transcripts are also probably encoding polypeptides of less than 100 amino acids in mice and humans (1, 21, 7). Future functional analyses should elucidate how small peptides encoded by transcripts improperly termed ncRNAs contribute to various biological processes including development and differentiation. [Emphasis mine]