Yet more damage control re:the Cambrian explosion.

Cambrian Explosion Blues
Evolution News | @DiscoveryCSC

What else is new in the campaign to explain the Cambrian explosion in Darwinian terms, despite the evidence? An article in The Australian says, “Fossils found in Gabon rewrite timeline of life on Earth,” as if finding earlier complexity is going to help the evolutionary story.

Fossils discovered in west Africa have pushed back the dawn of multicellular life on Earth by at least 1.5 billion years, scientists believe.

Just how complex the newly discovered organisms are is sure to be hotly debated.

But there can be no doubt that the creatures unearthed from the hills of Gabon, visible to the naked eye, have upended standard evolutionary timelines.

“The cursor on the origin of complex multicellular life is no longer 600 million years ago, as has long been maintained, but more like 2.1 billion years,” said Abderrazak El Albani, a researcher at the University of Poitiers and lead author of the study. 

The fossils, appearing to represent colonial organisms, vary from 12 centimeters to five inches. What are they? Ediacarans? The cookie-shaped fossils certainly don’t represent anything familiar, and the authors don’t draw any connections with what came later.

Up to now, conventional scientific wisdom held that the planet was populated only by single-celled microbes until the so-called Cambrian explosion, a major surge of biodiversity that began some 600 million years ago [actually, more like 530 million or 540 at most].

Ever-more complex life forms emerged rapidly from there, eventually creating an evolutionary tree with homo sapiens atop one of its branches.

“Multicellularity represents one of the principle thresholds in evolutionary history,” Philip Donoghue and Jonathan Antcliffe from the University of Bristol said in a commentary, also in Nature.

But the new organism, which appears to have lived in colonies, shows that the drive toward complexity began much sooner.

The article also claims that these organisms had a membrane-bound nucleus protecting its chromosomes! This announcement cannot help the Darwinian story. Earlier complexity, with no affinity to what followed, does not fit what Darwin had in mind. Perhaps the dating of the strata is wrong. If not, it looks like a proverbial Precambrian Rabbit that will have “upended standard evolutionary timelines” until the Darwin damage control committee can come up with a new story.

Fast-forwarding to the Ediacaran era, NASA put out another positivist spin at  Astrobiology Magazine about the enigmatic animals that flourished before the Cambrian explosion:

Microbial mats that existed on sea floors prior to the “Cambrian explosion” provided the foundation for early animal life to arise, new research looking at trace fossils of that early life has found.

When Charles Darwin wrote On the Origin of Species and for decades thereafter, scientists ascribed the beginning of animal life to the Cambrian, eventually pinned to about 540 million years ago when trilobites and other multicellular organisms emerged in a relatively short timeframe.

In recent years, however, astonishing complexity has been discovered in the period right before the advent of the Cambrian explosion, revising the scientific view of the origins of the most complex, multicellular life on Earth.

“By the time we get to the Cambrian — which has much more familiar organisms — a lot of the evolution had already happened on Earth,” says paleobiologist Mary Droser at the NASA Astrobiology Institute at the University of California, Riverside.

Droser presents a queer idea that microbial mats caused animals to appear.

The range and diversity of microbial mats that served as the foothold for Ediacara biota would prove even more pivotal to the ecology of these ancient habitats. The mats offered an alternative path from the free-floating lifestyle of microscopic algae and bacteria as something for the new and enterprising species to attach to or feed from on a shifting seafloor. The stability and environmental complexity provided by the sticky mats made the extensive seafloor habitable.

In this magical world, microbial mats made animals evolve, and the animals returned the favor:

The appearance, diversification, and evolution of Ediacara biota are inextricably linked to these mats. Researchers have found that with the rise of complex animals comes advancements in the microbial mats themselves, revealing the ecological interplay between the species, Droser says.

And so, the story goes, the evolving life could ride out the storms and exploit the shared benefits they provided each other. “Earth’s first vertebrates, mobility, early mollusks, skeletons, plant-like reproduction and population struggles such as competition over resources and space, which are all vital components of modern animal ecosystems today” were just a matter of time.

What is her evidence for this tale? Droser only presents Dickinsonia, Spriggina, and various “evolutionary dead ends” with no clear connection to the twenty new phyla appearing in the Cambrian explosion.

“We would argue that the beginning of animal life as we know it begins in the Precambrian,” says Droser. “By the time that you get to the Cambrian, all of the major groups are established.”

What? There’s a blatant falsehood for you Where are her arthropods? Where are the ctenophores? echinoderms? brachiopods? Where are bilaterian animals with eyes, guts, and articulated limbs? Her only empirical evidence for this claim is an inference from patterns in microbial mats that might indicate mobility of some Ediacarans like Dickinsonia and Spriggina. “Sprigginia [sic] fossils are some of the most complex fossils found in the Ediacaran period,” she says enthusiastically. “Vaguely resembling soft-bodied trilobites, Sprigginia has a head-like region and repeating segments running the length of its body.”

This greatly overstates the evidence. They are not true segments, and a head-like region is not a head. Meyer dealt with Spriggina in detail in his book (pp. 82-85), quoting numerous authorities such as Conway Morris, Valentine, and Erwin who do not believe a connection exists with any Ediacaran animal to the Cambrian biota. In fact, as Meyer explains on page 86 and following, the Ediacarans themselves exploded onto the scene. Most paleontologists believe the Ediacarans went extinct before the sudden appearance of twenty new animal phyla in the Cambrian. The NASA astrobiologists make a fake bridge across the divide that cannot hold the weight of all the new body plans needing to get across.

Ironically, another entry in  Astrobiology Magazine undermines the “oxygen theory” for the rise of Cambrian animals.

A study by University of California, Berkeley geochemists presents new evidence that high levels of oxygen were not critical to the origin of animals.

The researchers found that the transition to a world with an oxygenated deep ocean occurred between 540 and 420 million years ago. They attribute this to an increase in atmospheric O2 to levels comparable to the 21 percent oxygen in the atmosphere today.

This inferred rise comes hundreds of millions of years after the origination of animals, which occurred between 700 and 800 million years ago.

Basically, animals already had arrived before dissolved oxygen was sufficient to contribute to the “emergence” of animals. So much for that explanation.

On beating higher Ed.

The Watchtower Society's commentary on "the Word".

WORD, THE:

The term “word” in the Scriptures most frequently translates the Hebrew and Greek words da·varʹ and loʹgos. These words in the majority of cases refer to an entire thought, saying, or statement rather than simply to an individual term or unit of speech. (In Greek a ‘single word’ is expressed by rheʹma [Mt 27:14], though it, too, can mean a saying or spoken matter.) Any message from the Creator, such as one uttered through a prophet, is “the word of God.” In a few places Loʹgos (meaning “Word”) is a title given to Jesus Christ.

The Word of God. “The word of Jehovah” is an expression that, with slight variations, occurs hundreds of times in the Scriptures. By “the word of Jehovah” the heavens were created. God said the word and it was accomplished. “God proceeded to say: ‘Let light come to be.’ Then there came to be light.” (Ps 33:6; Ge 1:3) It should not be understood from this that Jehovah himself does no work. (Joh 5:17) But he does have myriads of angels that respond to his word and carry out his will.—Ps 103:20.

Creation, animate and inanimate, is subject to God’s word, and can be used by him to accomplish his purposes. (Ps 103:20; 148:8) His word is dependable; what God promises he also remembers to do. (De 9:5; Ps 105:42-45) As he himself has said, his word “will last to time indefinite”; it will never return without accomplishing its purpose.—Isa 40:8; 55:10, 11; 1Pe 1:25.

Jehovah is a communicative God, in that he reveals to his creatures in a variety of ways what his will and purposes are. God’s words were spoken, doubtless through an angel, to such men as Adam, Noah, and Abraham. (Ge 3:9-19; 6:13; 12:1) At times he used holy men like Moses and Aaron to make known his purposes. (Ex 5:1) “Every word” that Moses commanded Israel was in effect the word of God to them. (De 12:32) God also spoke through the mouth of prophets such as Elisha and Jeremiah, and prophetesses such as Deborah.—2Ki 7:1; Jer 2:1, 2; Jg 4:4-7.

Many of the divine commandments were committed to writing from the time of Moses forward. The Decalogue, commonly called the Ten Commandments and known in the Hebrew Scriptures as “the Ten Words,” was first delivered orally and later ‘written by the finger of God’ on stone tablets. (Ex 31:18; 34:28; De 4:13) These commandments were called the “Words” at Deuteronomy 5:22.—See TEN WORDS.

Joshua wrote additional “words in the book of God’s law” under divine inspiration, and this was true with other faithful Bible writers. (Jos 24:26; Jer 36:32) Eventually all such writings were collected together and made up what is called the Sacred Scriptures or Holy Bible. “All Scripture . . . inspired of God” would include, today, all the canonical Biblical books. (2Ti 3:16; 2Pe 1:20, 21) In the Christian Greek Scriptures, God’s inspired word is often spoken of as simply “the word.”—Jas 1:22; 1Pe 2:2.

There are many synonyms for God’s word. For example, in Psalm 119, where references to Jehovah’s “word(s)” occur more than 20 times, synonyms are found in poetic parallelisms—such terms as law, reminders, orders, regulations, commandments, judicial decisions, statutes, and sayings of Jehovah. This also shows that the expression “word” means a complete thought or message.

The word of God is also described in a number of other ways that give it breadth and meaning. It is “the ‘word’ [or “saying” (rheʹma)] of faith” (Ro 10:8, Int), “the word [or message (form of loʹgos)] of righteousness” (Heb 5:13), and “the word of the reconciliation” (2Co 5:19). God’s word or message is like “seed,” which, if planted in good soil, brings forth much fruitage (Lu 8:11-15); his sayings are also said to ‘run with speed.’—Ps 147:15.

Preachers and Teachers of the Word. The greatest exponent and supporter of Jehovah’s inspired word of truth was the Lord Jesus Christ. He astounded people by his methods of teaching (Mt 7:28, 29; Joh 7:46), yet he took no credit to himself, saying, “the word that you are hearing is not mine, but belongs to the Father who sent me.” (Joh 14:24; 17:14; Lu 5:1) Faithful disciples of Christ were those who remained in his word, and this, in turn, set them free from ignorance, superstition, and fear, also from slavery to sin and death. (Joh 8:31, 32) Often it was necessary for Jesus to take issue with the Pharisees, whose traditions and teachings made void “the word [or declaration] of God.”—Mt 15:6; Mr 7:13.

It is not just a matter of hearing the word of God preached. Rather, acting upon and showing obedience to that message is also essential. (Lu 8:21; 11:28; Jas 1:22, 23) After being well trained for the ministry, the apostles and disciples, in turn, obeyed the word and took up the preaching and teaching themselves. (Ac 4:31; 8:4, 14; 13:7, 44; 15:36; 18:11; 19:10) As a result, “the word of God went on growing, and the number of the disciples kept multiplying.”—Ac 6:7; 11:1; 12:24; 13:5, 49; 19:20.

The apostles and their associates were no peddlers of the Scriptures, as the false shepherds were. What they preached was the straight, unadulterated message of God. (2Co 2:17; 4:2) The apostle Paul told Timothy: “Do your utmost to present yourself approved to God, a workman with nothing to be ashamed of, handling the word of the truth aright.” Furthermore, Timothy was commanded: “Preach the word, be at it urgently in favorable season, in troublesome season.” (2Ti 2:15; 4:2) Paul also counseled Christian wives to watch their conduct, “so that the word of God may not be spoken of abusively.”—Tit 2:5.

Ever since the Devil contradicted what God had said in the garden of Eden, there have been many satanic opponents of God’s word. Many persons who have upheld God’s word have lost their lives for doing so, as both Bible prophecy and history testify. (Re 6:9) It is also a fact of history that persecution has failed to stop the proclamation of God’s word.—Php 1:12-14, 18; 2Ti 2:9.

The Power of God’s Word and Spirit. God’s word exerts tremendous power upon its hearers. It means life. God demonstrated to Israel in the wilderness that “not by bread alone does man live but by every expression of Jehovah’s mouth does man live.” (De 8:3; Mt 4:4) It is “the word of life.” (Php 2:16) Jesus spoke the words of God, and he said: “The sayings [rheʹma·ta] that I have spoken to you are spirit and are life.”—Joh 6:63.

The apostle Paul wrote: “The word [or message (loʹgos)] of God is alive and exerts power and is sharper than any two-edged sword and pierces even to the dividing of soul and spirit, and of joints and their marrow, and is able to discern thoughts and intentions of the heart.” (Heb 4:12) It reaches the heart and reveals whether one is actually living according to right principles.—1Co 14:23-25.

The word of God is the truth and can sanctify one for God’s use. (Joh 17:17) It can make a person wise and happy; it can accomplish whatever work God purposes for it. (Ps 19:7-9; Isa 55:10, 11) It can equip a person completely for every good work and can enable him to conquer the wicked one.—2Ti 3:16, 17; compare 1Jo 2:14.

Of Jesus’ preaching it is said: “God anointed him with holy spirit and power, and he went through the land doing good and healing all those oppressed by the Devil; because God was with him.” (Ac 10:38) The apostle Paul accomplished conversions of persons, even pagans, “not with persuasive words of [men’s] wisdom but with a demonstration of spirit and power.” (1Co 2:4) The words that he spoke by God’s holy spirit, based on the Scriptures, the Word of God, worked powerfully to make the conversions. He told the congregation at Thessalonica: “The good news we preach did not turn up among you with speech alone but also with power and with holy spirit and strong conviction.”—1Th 1:5.

John the Baptizer came “with Elijah’s spirit and power.” He had Elijah’s “spirit,” his drive and force. Jehovah’s spirit also directed John, so that he spoke the words of God, words that exerted strong power; he was able very successfully to “turn back the hearts of fathers to children and the disobedient ones to the practical wisdom of righteous ones, to get ready for Jehovah a prepared people.”—Lu 1:17.

The message of the good news from God’s Word the Bible should therefore not be underrated. These words are more powerful than any words men can devise or speak. The ancient Beroeans were commended for “carefully examining the Scriptures” to see whether what an apostle taught was correct. (Ac 17:11) God’s ministers, speaking God’s powerful Word, are energized and backed up by “power of holy spirit.”—Ro 15:13, 19.

“The Word” as a Title. In the Christian Greek Scriptures “the Word” (Gr., ho Loʹgos) also appears as a title. (Joh 1:1, 14; Re 19:13) The apostle John identified the one to whom this title belongs, namely, Jesus, he being so designated not only during his ministry on earth as a perfect man but also during his prehuman spirit existence as well as after his exaltation to heaven.

“The Word was a god.” Regarding the Son’s prehuman existence, John says: “In the beginning the Word was, and the Word was with God, and the Word was a god.” (Joh 1:1, NW) The King James Version and the Douay Version read: “In the beginning was the Word, and the Word was with God, and the Word was God.” This would make it appear that the Word was identical with Almighty God, while the former reading, in the New World Translation, indicates that the Word is not the God, Almighty God, but is a mighty one, a god. (Even the judges of ancient Israel, who wielded great power in the nation, were called “gods.” [Ps 82:6; Joh 10:34, 35]) Actually, in the Greek text, the definite article ho, “the,” appears before the first “God,” but there is no article before the second.

Other translations aid in getting the proper view. The interlinear word-for-word reading of the Greek translation in the Emphatic Diaglott reads: “In a beginning was the Word, and the Word was with the God, and a god was the Word.” The accompanying text of the Diaglott uses capital and small capital letters for the God, and initial capital and lowercase letters for the second appearance of “God” in the sentence: “In the Beginning was the LOGOS, and the LOGOS was with GOD, and the LOGOS was God.”

These renderings would support the fact that Jesus, being the Son of God and the one used by God in creating all other things (Col 1:15-20), is indeed a “god,” a mighty one, and has the quality of mightiness, but is not the Almighty God. Other translations reflect this view. The New English Bible says: “And what God was, the Word was.” The Greek word translated “Word” is Loʹgos; and so Moffatt’s translation reads: “The Logos was divine.” The American Translation reads: “The Word was divine.” Other readings, by German translators, follow. By Böhmer: “It was tightly bound up with God, yes, itself of divine being.” By Stage: “The Word was itself of divine being.” By Menge: “And God (= of divine being) the Word was.” And by Thimme: “And God of a sort the Word was.” All these renderings highlight the quality of the Word, not his identity with his Father, the Almighty God. Being the Son of Jehovah God, he would have the divine quality, for divine means “godlike.”—Col 2:9; compare 2Pe 1:4, where “divine nature” is promised to Christ’s joint heirs.

The Four Gospels—A New Translation, by Professor Charles Cutler Torrey (2nd ed., 1947), says: “In the beginning was the Word, and the Word was with God, and the Word was god. When he was in the beginning with God all things were created through him; without him came no created thing into being.” (Joh 1:1-3) Note that what the Word is said to be is spelled without a capital initial letter, namely, “god.”

This Word, or Loʹgos, was God’s only direct creation, the only-begotten son of God, and evidently the close associate of God to whom God was speaking when he said: “Let us make man in our image, according to our likeness.” (Ge 1:26) Hence John continued, saying: “This one was in the beginning with God. All things came into existence through him, and apart from him not even one thing came into existence.”—Joh 1:2, 3.

Other scriptures plainly show that the Word was God’s agent through whom all other things came into existence. There is “one God the Father, out of whom all things are, . . . and there is one Lord, Jesus Christ, through whom all things are.” (1Co 8:6) The Word, God’s Son, was “the beginning of the creation by God,” otherwise described as “the firstborn of all creation; because by means of him all other things were created in the heavens and upon the earth.”—Re 3:14; Col 1:15, 16.

Earthly ministry and heavenly glorification. In due time a change came about. John explains: “So the Word became flesh and resided among us [as the Lord Jesus Christ], and we had a view of his glory, a glory such as belongs to an only-begotten son from a father.” (Joh 1:14) By becoming flesh, the Word became visible, hearable, feelable to eyewitnesses on earth. In this way men of flesh could have direct contact and association with “the word of life,” which, John says, “was from the beginning, which we have heard, which we have seen with our eyes, which we have viewed attentively and our hands felt.”—1Jo 1:1-3.

The glorified Lord Jesus Christ continues to carry the title “the Word,” as noted in Revelation 19:11-16. There in a vision of heaven John says he saw a white horse whose rider was called “Faithful and True,” “The Word of God”; and “upon his outer garment, even upon his thigh, he has a name written, King of kings and Lord of lords.”

Why God’s Son is called “the Word.” A title often describes the function served or the duty performed by the bearer. So it was with the title Kal-Hatzé, meaning “the voice or word of the king,” that was given an Abyssinian officer. Based on his travels from 1768 to 1773, James Bruce describes the duties of the Kal-Hatzé as follows. He stood by a window covered with a curtain through which, unseen inside, the king spoke to this officer. He then conveyed the message to the persons or party concerned. Thus the Kal-Hatzé acted as the word or voice of the Abyssinian king.—Travels to Discover the Source of the Nile, London, 1790, Vol. III, p. 265; Vol. IV, p. 76.

Recall, too, that God made Aaron the word or “mouth” of Moses, saying: “He must speak for you to the people; and it must occur that he will serve as a mouth to you, and you will serve as God to him.”—Ex 4:16.

In a similar way God’s firstborn Son doubtless served as the Mouth, or Spokesman, for his Father, the great King of Eternity. He was God’s Word of communication for conveying information and instructions to the Creator’s other spirit and human sons. It is reasonable to think that prior to Jesus’ coming to earth, on many of the occasions when God communicated with humans he used the Word as his angelic mouthpiece. (Ge 16:7-11; 22:11; 31:11; Ex 3:2-5; Jg 2:1-4; 6:11, 12; 13:3) Since the angel that guided the Israelites through the wilderness had ‘Jehovah’s name within him,’ he may have been God’s Son, the Word.—Ex 23:20-23; see JESUS CHRIST (Prehuman Existence).

Showing that Jesus continued to serve as his Father’s Spokesman, or Word, during his earthly ministry, he told his listeners: “I have not spoken out of my own impulse, but the Father himself who sent me has given me a commandment as to what to tell and what to speak. . . . Therefore the things I speak, just as the Father has told me them, so I speak them.”—Joh 12:49, 50; 14:10; 7:16, 17.

Is the sun setting on scientific objectivity?

Science and the "Darkness of the West"

David Klinghoffer

Writing in the London Times, Melanie Phillips is on fire with a righteous indignation at the "dark ages," the eclipse of wisdom and integrity, into which science has fallen. She starts with climate change but is only warming up:

The problem of scientific integrity, however, goes far wider. Psychology, neuroscience, physics and other scientific areas have been convulsed by revelations of dodgy research.

Richard Horton, editor-in-chief of The Lancet, has written bleakly: "The case against science is straightforward: much of the scientific literature, perhaps half, may simply be untrue."

One reason is that cash-strapped universities, competing for money and talent, exert huge pressure on academics to publish more and more to meet the box-ticking criteria set by grant-funding bodies. Corners are being cut and mistakes being made.

But whatever happened to peer-review, the supposed kitemark of scientific integrity produced by the collective judgment of other researchers? Well, that seems to have gone south too. In 1998 Fiona Godlee, editor of the British Medical Journal, sent an article containing eight deliberate mistakes to more than 200 of the BMJ's regular reviewers. Not one picked out all the mistakes. On average, they reported fewer than two; some did not spot any.

This reminds me of the PLOS ONE "Creator" censorship story. I was shocked by this statement from a spokesman for the journal:

This past year PLOS ONE published more than 28,000 articles that were handled by a community of more than 6,000 editors and 76,000 reviewers.

Twenty eight thousand articles? Six thousand editors? Seventy six thousand reviewers? Just one journal? That is absurd. The spokesman's point was that despite "quality control checks" the occasional error, like attributing the human hand to the "design" of a "Creator," should not be unexpected. But with such a volume of material being published, it's obvious that some interest beyond the enlightenment of the scientific community is being served. There's an industrial quality to the enterprise. Is anyone reading all this stuff? Reviewing it? Editing it? Seems not. Or is it more about satisfying metric expectations, "box-ticking criteria set by grant-funding bodies"?

Phillips:

The problem lies with research itself. The cornerstone of scientific authority rests on the notion that replicating an experiment will produce the same result. If replication fails, the research is deemed flawed. But failure to replicate is widespread. ...
A 2005 study by John Ioannidis, an epidemiologist at Stanford University, said the majority of published research findings were probably false.
At most, no more than about one in four findings from early-phase clinical trials would be true; epidemiological studies might have only a one in five chance of being true. "Empirical evidence on expert opinion", he wrote, "shows that it is extremely unreliable".

What lies behind it all? Simply the pressure facing scholars from the scientific-industrial-publishing complex? Not just that:

Underlying much of this disarray is surely the pressure to conform to an idea, whether political, commercial or ideological. Ideological fads produce financial and professional incentives to conform and punishment for dissent, whether loss of grant-funding or lack of advancement. As Professor Ioannidis observed: "For many current scientific fields, claimed research findings may often be simply accurate measures of the prevailing bias."

Deeper still:

Underlying this loss of scientific bearings is a closed intellectual circle. Scientists pose as secular priests. They alone, they claim, hold the keys to the universe. ...The resulting absence of openness and transparency is proving the scientists' undoing. In the words of Richard Horton, "science has taken a turn towards darkness". But science defines modernity. It is our gold standard of truth and reason. This is the darkness of the West too.


"Scientists pose as secular priests." True. Now go back and watch that excruciatingly stupid video from Bill Nye where the celebrity science educator dismisses philosophy in the most shallow, ignorant terms.

You can track what James Burnham called the "suicide of the West" in a number of areas of public life. The general culture is rife with barbarism. That's nothing you don't already know. But Philips is picking up on a little acknowledged truth. Confined by ideology and a "closed intellectual circle," science, far from being an exception to the trend of decline as some might say, is fully part of it.

On atheism's smugness; A rogue's view.

On empiricism and the fine-tuning argument for I.D.

It's design all the way down.

Intelligent Design in Dog Spit and in Rotten Wood
Evolution News | @DiscoveryCSC

It’s not often you get a scientific paper about dog spit, but let’s see what we find in one that appeared in PLOS ONE this month:“Salivary proteomics of healthy dogs: An in-depth catalog” by Torres et al. Thank goodness scientists are willing to boldly go where few have gone before, like inside the dark cavern of a dog’s mouth. Their objective:

To provide an in-depth catalog of the salivary proteome and endogenous peptidome of healthy dogs, evaluate proteins and peptides with antimicrobial properties, and compare the most common salivary proteins and peptides between different breed phylogeny groups. [Emphasis added.]

Seven scientists decided to check the saliva from 36 dogs of 19 breeds. Using cotton swabs and collection kits, they carefully collected saliva from the gums of the dogs, including some of their own pets, after making sure the dogs were free of periodontal disease. They classified the breeds into four groups. Then they examined the saliva with state-of-the-art mass spectrometers. What they found was really quite astounding:

2,491 proteins and endogenous peptides were found in the saliva of healthy dogs with no periodontal disease. All dog phylogeny groups’ saliva was rich in proteins and peptides with antimicrobial functions. The ancient breeds group was distinct in that it contained unique proteins and was missing many proteins and peptides present in the other groups.

Thousands of proteins in dog spit! This is an order of magnitude more protein types than previous research estimated. Would you have expected so much complex specified information in a clear, sticky, unappetizing liquid? If we estimate an average of 250 amino acids per protein or peptide, three bases per amino acid codon, and four bits per DNA letter, that amounts to 7.5 megabits of CSI in dog spit! A friendly lick from your pet paints your face with intelligent design.

Each protein, you recall, is made of precise sequences of amino acids, all left-handed, representing translations of the DNA code. And as Jonathan Wells has made clear, the DNA code is only one code out of several cellular codes that guide the protein product from its initial transcription into the final translation and fold, and guide it to its place of function: in this case, the dog’s mouth. So 7.5 megabits is on the low side of the true CSI in dog saliva.

Furthermore, these proteins are there for a reason:

One of the most important functions of saliva is to protect the oral cavity and indirectly other organs against infections. In this study, 7 of the top 10 most abundant proteins have immune functions. Additionally, we identified 26 peptides and proteins (as well as some isoforms) that have been reported to have antimicrobial functions in human saliva; 4 of these were also in the top 10 most abundant in canine saliva. Six of the 26 proteins and peptides were not present in all four breed groups indicating the variability among individual dogs or dog breeds. There are likely many additional proteins and peptides with antimicrobial functions in the 2,491 identified in the study.

Needless to say, many of the proteins in saliva are also important for digestion, although dogs seem to wolf down their food without giving saliva much time to act. But as pet owners know, dogs salivate heavily. Those proteins guard the hatch with megabits of CSI. It’s a good thing they have all those antimicrobials and immune proteins handy, the way they pick up food off the floor and drink out of the toilet.

Saliva may also have behavioral functions involved in canine communication. Lest you think all that drooling shows friendship,  Live Science cautions, “Your dog may be licking its mouth because it thinks you’re a jerk.” But that’s a question for another time.

CSI in Rotten Wood

Turn over a rotting log, and you are likely to see some unlovable critters scampering away from the light, and find moist mushrooms sprouting from every crevice. It’s not the kind of thing you would want to drag into the house or choose for firewood. We can be thankful that organisms love this habitat, though, because they perform a vital function, breaking down wood for the next generation of plants.

Most of us are aware of the role of fungi in decomposing wood. What surprised researchers at the Helmholtz Centre for Environmental Research was how much of it there is in a rotting log. Once again, actual counts jumped by an order of magnitude over previous estimates:

So far, little research has been conducted on fungi that live on dead trees, although they are vital to the forest ecology by breaking down dead wood and completing the element cycle between plants and soil. Soil biologists from the Helmholtz Centre for Environmental Research (UFZ) have now discovered that the number of fungus species inhabiting dead trees is 12 times higher than previously thought.

You may recall Ann Gauger’s lignin challenge to evolution based on a BIO-Complexity  paper by Leisola, Pastinen, and Axe. Lignin is a tough molecule to digest, even though it is rich with energy. One would think many organisms would have evolved ways to exploit this food source, but only fungi have that ability. It’s striking that their function works for the good of the whole ecosystem. The Helmholtz Centre agrees:

Fungi that live on trees perform an important function in the forest ecosystem by breaking down dead wood. This is no easy feat, because wood is very resilient. It is held together by a biopolymer known as lignin, which together with cellulose and hemicellulose form the cell wall of woody plants and give the wood its stability. Fungi are able to break down the robust lignin and the flexible cellulose fibres by releasing enzymes that cause the polymers to degrade and become mineralised. As part of the ecosystem’s cycle, the leftover material becomes part of the humus layer, which gives the soil its stability and forms the substrate for a new generation of trees.

A photo shows how researchers measured fungi abundances. They observed 300 fallen trees from 11 species, including deciduous trees and conifers.

The trees included seven deciduous species such as beech, oak, poplar and ash and four coniferous species: spruce, Scots pine, Douglas fir and larch. Three years later they returned to see what kind of fungal communities had established themselves in the trunks. The results were astonishing: “The diversity of fungi living in the trees was an order of magnitude greater than previously thought,” says Dr Witoon Purahong, a soil ecologist based at UFZ in Halle and the first author of the study.

They couldn’t identify all the fungi, but estimated a total of 1,254 “operational taxonomic units” (unnamed species) per trunk. Surprisingly, the conifers, which in the evolutionary scheme are earlier and more primitive than deciduous trees, had the most fungal diversity. Another unexpected finding was that fungi are picky about their trees: “For example, oak and ash each harbour very specific communities [of] fungal species whose composition is very different from those found on other deciduous trees.” Even trees that have similar wood composition have distinct fungal communities.

They point to “millions of years of co-evolution between trees and wood-inhabiting fungi,” but then admit another conundrum. “What is fascinating, however, as Buscot adds, is that in some cases the specialisation of fungi on dead wood is greater than the one of symbiotic fungi on living plants.” Complexity seems to have arisen earlier.

Conclusion

These two research projects, unusual as they are, give valuable insights into working ecosystems (a dog’s mouth and a forest floor), that may lead to applications for human health and biodiversity conservation. Beyond that, though, you may sense the astonishment at finding more complexity than expected. Within each habitat investigated, science keeps finding vastly more complexity than simple mutation and selection could ever hope to produce. Furthermore, each protein, and each fungus, has a vital role to play in systems larger than themselves. Isn’t that what intelligent design science would have predicted?

Psam 33 American Standard Version.

1Rejoice in Jehovah, O ye righteous: Praise is comely for the upright.

2Give thanks unto Jehovah with the harp: Sing praises unto him with the psaltery of ten strings.

3Sing unto him a new song; Play skilfully with a loud noise.

4For the word of Jehovah is right; And all his work is done in faithfulness.

5He loveth righteousness and justice: The earth is full of the lovingkindness of Jehovah.

6By the word of Jehovah were the heavens made, And all the host of them by the breath of his mouth.

7He gathereth the waters of the sea together as a heap: He layeth up the deeps in store-houses.

8Let all the earth fear Jehovah: Let all the inhabitants of the world stand in awe of him.

9For he spake, and it was done; He commanded, and it stood fast.

10Jehovah bringeth the counsel of the nations to nought; He maketh the thoughts of the peoples to be of no effect.

11The counsel of Jehovah standeth fast for ever, The thoughts of his heart to all generations.

12Blessed is the nation whose God is Jehovah, The people whom he hath chosen for his own inheritance.

13Jehovah looketh from heaven; He beholdeth all the sons of men;

14From the place of his habitation he looketh forth Upon all the inhabitants of the earth,

15He that fashioneth the hearts of them all, That considereth all their works.

16There is no king saved by the multitude of a host: A mighty man is not delivered by great strength.

17A horse is a vain thing for safety; Neither doth he deliver any by his great power.

18Behold, the eye of Jehovah is upon them that fear him, Upon them that hope in his lovingkindness;

19To deliver their soul from death, And to keep them alive in famine.

20Our soul hath waited for Jehovah: He is our help and our shield.

21For our heart shall rejoice in him, Because we have trusted in his holy name.

22Let thy lovingkindness, O Jehovah, be upon us, According as we have hoped in thee.

On the empty tomb.

Primeval tech v. Darwinism again.

Driverless autos will be the death of civilisation?:Pros and cons.

Will the real definition of a 'species' please stand up?

The common Asian toad is actually three “species”
February 17, 2016 Posted by News under Genomics, speciation, News

A research project has tested the hypothesis that Asian common toad populations across Southeast Asia are genetically similar owing to their commensal nature and high dispersive ability. To the researchers’ surprise, three genetically divergent groups of toads were found, each in a different geographic area (mainland Southeast Asia, coastal Myanmar and the islands of Java and Sumatra).

The ranges of these three groups of toads were also found to have statistically different climates. This suggests that the toads may be adapting to local climatic conditions and evolving into separate species. Thus, toads of one group may not be able to disperse and persist within the range of another group because of climatic differences. More.

Of course, we would only know if they were evolving into separate species, as opposed to just well-adapted local variants, if they could no longer produce fertile offspring together .See, for example, the deflated tale of Darwin’s finches?

But every time one brings up the fact that the concept of speciation is groaning under the weight of sheer meaninglessness, Darwin’s followers write in to remind us that everyone knows that, but so what?

Funny, the old Brit toff called his book On the Origin of Species, but his follower say it doesn’t matter if the concept of species has more holes than a cheese grater.

See also: Rethink evolution for progress in science

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Here’s the abstract:

The Asian common toad (Duttaphrynus melanostictus) is a human commensal species that occupies a wide variety of habitats across tropical Southeast Asia. We test the hypothesis that genetic variation in D. melanostictus is weakly associated with geography owing to natural and human-mediated dispersal facilitated by its commensal nature. Phylogenetic and population genetic analyses of mitochondrial and nuclear DNA sequence variation, and predictive species distribution modelling, unexpectedly recovered three distinct evolutionary lineages that differ genetically and ecologically, corresponding to the Asian mainland, coastal Myanmar and the Sundaic islands. The persistence of these three divergent lineages, despite ample opportunities for recent human-mediated and geological dispersal, suggests that D. melanostictus actually consists of multiple species, each having narrower geographical ranges and ecological niches, and higher conservation value, than is currently recognized. These findings also have implications for the invasion potential of this human commensal elsewhere, such as in its recently introduced ranges on the islands of Borneo, Sulawesi, Seram and Madagascar. (paywall) – Guinevere O. U. Wogan, Bryan L. Stuart, Djoko T. Iskandar, Jimmy A. McGuire. Deep genetic structure and ecological divergence in a widespread human commensal toad. Biology Letters, 2016; 12 (1): 20150807 DOI: 10.1098/rsbl.2015.0807

Vox populi is rarely vox dei?

The 1% have pulled up the ladder?:Pros and Cons

As 'just so' as it gets.

The Curious Incident of the Non-Rafting Foxes

David Klinghoffer 

Blink and you might miss this unexpected bit of common sense, embedded in a NY Times article on adorable dwarf foxes native to California's Channel Islands  ("Foxes That Endure Despite a Lack of Genetic Diversity")

. How did they get there? They were evidently ferried thousands of years ago by Native Americans, who seemed to regard them as totem animals. 

It's unlikely the foxes made the trip on their own; the islands are separated from the mainland by 12 to 70 miles of open ocean. Another clue pointing to human help: Native Americans painted foxes on rocks and gave them ceremonial burials. Foxes may have had a spiritual importance to them.

However the animals arrived on the Channel Islands, they adapted quickly. The oldest island fox fossils date back 7,000 years and show that they were small even then. [Emphasis added.]

Fine. Because otherwise how else could a fox make the passage? Just imagine: foxes rafting across 12 miles of ocean on their own, never mind 70 miles -- perhaps hitching a ride on a tree trunk or other matted vegetation torn from the ground in a violent storm. It's like something out of a kids' cartoon. That indeed sounds pretty "unlikely." Actually, "absurd" is more like it.

Now would you believe unaided animals journeying across oceans waters not for 12 or 70 but hundred of miles? Because the journal Nature tells us monkeys did it.  From the Washington Post:

Ancient primates may have traveled from South America to North America about 21 million years ago -- back when the continents were separated by 100 miles of water. The swashbuckling monkeys are reported in a study published Wednesday in Nature

"We never would've predicted they would've been here," lead author Jonathan Bloch of the Florida Museum of Natural History  told Nature.

Bloch and his colleagues identified seven monkey teeth encased in 21-million-year-old rocks in the Panama Canal Basin. The teeth, which belong to a previously undiscovered  capuchin-like  species they have dubbed Panamacebus transitus, represent the oldest evidence of monkeys on the North American continent -- and the first evidence of a mammal crossing the ocean that once separated it from South America.

They "never would've predicted" it because it sounds too unlikely. Yet "the idea of monkeys rafting around unintentionally on beds of vegetation isn't as crazy as it sounds."

No? It's not allowed to be "crazy" because after all, how did the monkeys get to South America to begin with? Against our will, because it's against common sense, we're once again forced to say by rafting:

[M]onkeys had to cross over from Africa. Most scientists believe that happened about 40 million years ago. The Atlantic Ocean would have been a bit narrower than it is now, because of the way the continents have shifted, but it still would have been quite the trip. The monkeys in question were probably carried off to sea on uprooted trees after some kind of storm or other natural disaster.

Ah yes, the theory of animal rafting by uprooted tree and violent storm. The distribution of animals across the globe is often brandished by Darwinists as evidence for common descent. But as  Casey Luskin has pointed here,  biogeography -- the study of that distribution -- in fact poses one of the toughest challenges for evolutionary theory. Monkeys are a case in point:

[O]ne of the most severe biogeographical puzzles for Darwinian theory is the origin of South American monkeys, called "platyrrhines." Based upon molecular and morphological evidence, New World platyrrhine monkeys are thought to be descended from African "Old World" or "catarrhine" monkeys. The fossil record shows that monkeys have lived in South America for about the past 30 million years. But plate tectonic history shows that Africa and South America split off from one another between 100 and 120 million years ago (mya), and that South America was an isolated island continent from about 80 - 3.5 mya. If South American monkeys split off from African monkeys around 30 mya, proponents of neo-Darwinism must somehow account for how they crossed hundreds, if not thousands, of kilometers of open ocean to end up in South America.

This problem for evolutionary biologists has been recognized by numerous experts. A Harper Collins textbook on human evolution states: "The origin of platyrrhine monkeys puzzled paleontologists for decades. ... When and how did the monkeys get to South America?" Primatologists John G. Fleagle and Christopher C. Gilbert put it this way in a scientific volume on primate origins:

The most biogeographically challenging aspect of platyrrhine evolution concerns the origin of the entire clade. South America was an island continent throughout most of the Tertiary...and paleontologists have debated for much of this century how and where primates reached South America.

Primate specialist Walter Carl Hartwig is similarly blunt: "The platyrrhine origins issue incorporates several different questions. How did platyrrhines get to South America?" Such basic, vexing questions certainly don't lend credence to the NCSE's claims of "consistency between biogeographic and evolutionary patterns."

For those unfamiliar with the sort of arguments made by neo-Darwinian biogeographers, responses to these puzzles can be almost too incredible to believe. A Harper Collins textbook explains: "The 'rafting hypothesis' argues that monkeys evolved from prosimians once and only once in Africa, and ... made the water-logged trip to South America." And of course, there can't be just one seafaring monkey, or the monkey will soon die leaving no offspring. Thus, at least two monkeys (or perhaps a single pregnant monkey) must have made the rafting voyage.

Fleagle and Gilbert observe that the rafting hypothesis "raises a difficult biogeographical issue" because "South America is separated from Africa by a distance of at least 2600 km, making a phylogenetic and biogeographic link between the primate faunas of the two continents seem very unlikely." But they are wedded to an evolutionary paradigm, meaning that they are obligated to find such a "link" whether it is likely or not. They argue that in light of "[t]he absence of any anthropoids from North America, combined with the considerable morphological evidence of a South American-African connection with the rodent and primate faunas" that therefore "the rafting hypothesis is the most likely scenario for the biogeographic origin of platyrrines."

In other words, the "unlikely" rafting hypothesis is made "likely" only because we know common descent must be true.

To borrow a famous image from Sherlock Holmes, the instance with the Channel Island foxes is a case of the dog that didn't bark in the night. From  "The Adventure of the Silver Blaze,"centered on a race horse gone missing:

Gregory (Scotland Yard detective): "Is there any other point to which you would wish to draw my attention?"

Holmes: "To the curious incident of the dog in the night-time."

Gregory: "The dog did nothing in the night-time."

Holmes: "That was the curious incident."

The dog didn't bark because it knew its owner. The foxes didn't raft because, under evolutionary theory, they didn't need to. Monkeys did raft, even across a whole wide ocean, because evolution required it. On other hand, if the theory needed foxes to do so, you can be sure they would obediently hop aboard. It should be the facts that drive startling conclusions, not the theory that's supposed to explain the facts. But with evolution the roles of fact and theory are often reversed. 

Animals do the most striking things, like sailing across oceans on their own, on demand. These are theory-driven "facts," not a fact-driven theory. The non-rafting foxes are the thing that gives the game away. They are, as Holmes says, the curious incident.

Dogs, by the way, like horses and foxes, are not thought to raft. Not yet!

A walk through the mind of a Titan.

On the price of beating swords into ploughshares

South Korean Jehovah’s Witnesses Face Stigma of Not Serving in Army:
By CHOE SANG-HUN

OCTOBER 3, 2015

SEOUL, South Korea — Since he was a teenager, Kim Min-hwan knew he would have to make a choice: abandon his religious convictions or go to prison.

Mr. Kim is a member of the Jehovah’s Witnesses, who for decades have faced jail terms as conscientious objectors under South Korea’s Military Service Act. Since his release from prison in 2013, Mr. Kim has found the stigma too great to find a meaningful job, though he was a chemical engineering major. He spends his days volunteering at the Jehovah’s Witnesses headquarters south of Seoul.

“I was predestined to become a convict because I believed in the creator,” Mr. Kim, 31, said in an interview. “I want South Korea to recognize that there are other, nonmilitary ways for us to serve the community.”

Over the years, Jehovah’s Witnesses have filed a series of appeals asking the Constitutional Court to rule that the Military Service Act violates the constitutional right to freedom of conscience and religion. Hopes for an end to their travails rose in July, when the court held a public hearing on multiple appeals only four years after it had rejected similar petitions. The court is likely to rule on the matter before the end of the year.

Jehovah’s Witnesses were once dragged into military boot camps and stockades, where they were vilified as “commies” and “traitors” and even tortured and killed. Few spoke out for them in South Korea, where mainstream churches viewed them as a cult and people obsessed over threats from the North.In democratic South Korea today, young male Jehovah’s Witnesses no longer suffer brutal beatings. But 600 to 700 conscientious objectors are still sent to prison on average each year — nearly all of them Jehovah’s Witnesses. They account for more than 90 percent of all imprisoned conscientious objectors in the world, according to Jehovah’s Witnesses, the United Nations Human Rights Council and rights groups.

The two Koreas are technically still at war after a truce ended the Korean War in 1953, and tensions have increased under the new North Korean leader, Kim Jong-un. Many here argue that not punishing conscientious objectors would compromise South Korea’s ability to deter North Korea’s 1.1 million-strong military.

“North Korea remains a direct and present military threat,” Seo Kyu-young, a Defense Ministry legal counsel, said at a recent hearing at the Constitutional Court. “If we introduce alternative services, we would see a sharp rise in the number of people evading the draft under the pretext of conscience,” he said.

Acting on suggestions from both the Constitutional Court and the country’s National Human Rights Commission, the government announced plans in 2007 to introduce alternative service for conscientious objectors. But the conservative government of President Lee Myung-bak, who took office the following year, rejected them, citing a lack of national consensus.

For decades, the idea of alternatives to military training — serving as firefighters or in homeless shelters, for example — has been unspeakable in South Korea. The typical 21-month stint in the 650,000-member military has been billed as a “sacred duty” for all able-bodied men — and the price of freedom. When cabinet appointees face confirmation hearings, the first thing lawmakers investigate is whether they or their sons avoided military service.

Yet maintaining a conscript army has become more of a challenge. Postwar generations considered universal conscription an irritating interruption in their careers. They also grew disenchanted with recurring corruption, abuse and disciplinary problems in the military.

“South Korean men don’t want to serve in the military if they have a choice, so they get angry if others don’t while they have to,” said Park Yu-ho, 27, who refused to join the military partly as a protest against recent beating deaths in military camps and shooting rampages by abused soldiers.

Today, conscientious objectors are tried in civilian court and are usually given 18 months in prison. This year, they began to get some support from lower courts, where six of them were found not guilty even though their acquittals were appealed by prosecutors.The abuse of conscientious objectors was one of the worst and most ignored human rights violations under the military dictatorship of the 1970s. Conscript officials raided Jehovah’s Witness churches to haul away draft-age men. When they refused to take up arms, they were beaten “like punching bags,” according to the presidential commission on suspicious deaths in the military.

In its reports in 2008, the commission attributed the deaths of five Jehovah’s Witnesses between 1975 and 1985 to beatings and torture that were “routine” among boot camp instructors and military policemen handling conscientious objectors.

The reports, the first of their kind, described “barbarian acts that should never have happened in a civilized society” — including starvation, water torture, and solitary cells smaller than a telephone booth where Jehovah’s Witnesses were forced to stand for days without sleep.

An officer threatened to tie a Jehovah’s Witness to a pole and force him to have a blood infusion, the commission said. One Jehovah’s Witness, Jung Chun-guk, was drafted two more times after his release from prison and each time chose a prison term, serving a total of seven years and 10 months beginning in 1969.Hong Young-il, 49, who served two years in prison from 1990 to 1992, said a military interrogator once put a pistol to his forehead and pretended to execute him.

Much of the abuse took place in full view of other trainees at boot camps, a scene familiar to many who passed through them in the 1970s and ’80s. Even though corporal punishment was a common disciplinary tool in the army then, widespread bias against Jehovah’s Witnesses bolstered society’s silence about their persecution.

“A cellmate convicted of sexually molesting a 5-year-old child liked hectoring me over the importance of defending the country,” said Ryu Yong-beom, 60, a Jehovah’s Witness who served three years in prison in the 1970s.

The denigration of objectors as “commies” or “jongbuk” — North Korea followers — continues today. In a letter sent to a local newspaper in January, Kim Kyung-muk, a filmmaker and imprisoned conscientious objector, said that other convicts chastised him for “not being qualified to be a South Korean citizen.”

After prison, conscientious objectors see their job opportunities seriously limited, as the government and big companies discriminate against ex-convicts, especially those who avoided the draft.

The United Nations Human Rights Committee and Amnesty International have repeatedly urged South Korea to allow alternative service for conscientious objectors. The committee called their imprisonment a violation of the International Covenant on Civil and Political Rights, to which South Korea is a signatory.

South Korea interprets the covenant differently. Its Parliament has never acted on calls for alternative service from its National Human Rights Commission, citing, as President Lee’s government had, a lack of national consensus.

“This debate is a luxury we can’t afford as long as North Korea is there,” said Cho Myung-sik, 36, a veteran. “Besides, how are you going to tell genuine conscientious objectors from fakers if we introduce alternative services? How are you going to ensure fairness between them and those serving in the military?”

Some Jehovah’s Witnesses have emigrated to the United States to save their sons from imprisonment. Several South Korean conscientious objectors have recently won refugee status in Canada, France and Australia.

For Mr. Ryu and his wife, Jung Seon-hee, change has been too slow. She said her two brothers were beaten “half dead” in military jail in the 1980s. Her son was released last year after serving 15 months. In July, another son, Ryu Heung-sun, was sentenced to one and a half years.

“I had hoped that our suffering would end by my sons’ generation,” Ms. Jung said. “I am sad that this country remains so primitive, unable to show lenience to a minority like us.”

A clash of Titans. LXVII

Minors have no right to privacy?:Pros and cons.

Pakistan,frenemy of the west?:Pros and cons.