Yet more on reality's AntiDarwinian bias.II

Peer-Reviewed Article on Transposable Elements Cites "Irreducible Complexity" and Other "Teleologic" Factors
Casey Luskin December 24, 2015 1:07 PM

A new peer-reviewed article in Wiley's eLS, "Transposons in Eukaryotes (Part B): Genomic Consequences of Transposition," reviews the role of transposable elements (TEs). Plant geneticist Wolf-Ekkehard Lönnig argues that "irreducibly complex" structures may defy explanation by TEs or other Darwinian factors:

A general difficulty to be mentioned in this context (but not inherent in the selfish DNA hypothesis) is that mutation and selection may not be the full explanation for the origin of species; that is, the factors of the neo-Darwinian scenario may find their limits, for example, in the generation of 'irreducibly complex structures' (Behe, 2006, 2007). This is a term used to describe structures that, according to Behe, cannot be explained by a piecemeal production via intermediate steps. Among the examples discussed by Behe are the origins of (1) the cilium, (2) the bacterial flagellum with filament, hook and motor embedded in the membranes and cell wall and (3) the biochemistry of blood clotting in humans. Moreover, the traps of Utricularia (Lönnig, 2012) and some other carnivorous plant genera as well as several further apparatus in the animal and plant world appear to pose similar problems for the modern synthesis (joints, echo location, deceptive flowers, the reproductive system of the Australian gastric brooding frog Rheobatrachus silus, the mechanical gears of the nymph stage of the leaf hopper Issus coleoptratus etc.). Up to now, none of these systems has been satisfactorily explained by neo-Darwinism. Whether accelerated TE activities with all the above named mutagenic consequences can solve the questions posed remains doubtful in the eyes of the critical observer. Moreover, natural selection itself may not have the stringency usually ascribed to it (for details, see ReMine, 1993; Lönnig, 2001, 2012, 2014).
(Wolf-Ekkehard Lönnig, "Transposons in Eukaryotes (Part B): Genomic Consequences of Transposition," In: eLS. John Wiley & Sons, Ltd: Chichester. DOI: 10.1002/9780470015902.a0026265 (August 2015).)

While unguided mutational processes involving TEs seem incapable of producing irreducibly complex structures, the article notes that some believe there may be "teleologic benefits" from TE activities:
Concerning the totally unexpected and extraordinarily high level of current DNA transposition activities in bats in clear contrast to near extinction or absence of such elements in all other mammals, Huang et al. (2012) give sympathetic consideration to 'teleologic benefits' (among others) promoting active DNA transposons in the order Chiroptera (perhaps via HT; Tang et al., 2015). A 'pacemaker proponent' sensu lato may perhaps ask whether teleologic benefits could also be involved in an independent origin of the Transip TEs and the immune system of jawed vertebrates (not to mention teleology in the sense of Behe, 2006, 2007).
The article cites ID scientists including Jonathan Wells and Richard Sternberg while noting that they and other researchers think that non-coding DNA is largely functional:
In the wake of the ENCODE (encyclopedia of DNA elements) project, several authors are even favouring positions that almost approach the assumption of 100% functional DNA in all genomes, that is, there is no junk DNA in the genomes of plants and animals at all (Shapiro and von Sternberg, 2005;Wells, 2011).
The article concludes by observing that "several lines of evidence" including "irreducibly complex systems" challenge current evolutionary models and should spur us to follow the evidence unswervingly:
[S]everal lines of evidence concerning the origin of life forms, possibly from irreducibly complex systems such as the bacterial flagellum to Darwin's 'abominable mystery' of the origin of angiosperms as well as the Cambrian explosion (for the latter cf. Erwin and Valentine, 2013) may surpass our present knowledge of the causes and factors involved in variation so far known (including TEs) -- this, as well as the strongly divergent opinions on TEs and evolution -- should be a powerful incentive for further efficient empirical and theoretical research wherever it may lead.

"Wherever it may lead..." That sounds like good advice.

File under "well said" XVII

"Well done is better than well said."
Benjamin Franklin

The Fourth horseman is getting deadlier.

Tinkerer V. Artist

Why Would Evolution Produce Non-Essential Genes?
Evolution News & Views December 22, 2015 2:09 PM

Recent papers have tried to identify the subset of all genes in a genome that are essential for viability. In "The Indispensable Genome," Science Magazine considers this capability a turning point in biology:

Game-changing moments in functional genomics often reflect the development and application of powerful new reagents and methods to provide new phenotypic insight on a global scale. Three independent studies describe systematic, genome-scale approaches to defining human genes that are indispensable for viability, which collectively form the essential gene set. On pages 1092 and 1096 of this issue, Blomen et al. (1) and Wang et al. (2), respectively, report a consistent set of ~2000 genes that are indispensable for viability in human cells. Moreover, very similar results were obtained by Hart et al. (3). For the first time, we now have a firm handle on the core set of essential genes that are required for human cell division. This opens the door to studying the roles of essential genes, how gene essentiality depends on genetic and tissue contexts, and how essential genes evolve. [Emphasis added.]

This achievement follows on the heels of yeast studies where researchers found only 1/6 of its 6,000 genes to be essential. That's an astonishingly low fraction. What functions do essential genes perform?

The yeast essential genes encode proteins that drive basic cellular functions such as transcription, translation, DNA replication, cell division cycle control, and fundamental metabolism. Moreover, the yeast essential genes share several attributes that reflect their critical role in cellular life. For example, they are often conserved and evolutionarily constrained, are highly expressed, and encode abundant proteins that tend to form stable complexes and thus are rich in protein-protein interactions.

The landscape of essential genes in human cells can now be explored using the conceptual framework established in yeast.

All three studies on human cells found only 10 percent of the 20,000 genes in the human genome are essential. What is the other 90 percent doing?

Boone and Andrews, authors of the review, indicate that patterns in the human essential genome are similar to those in the yeast essential genome:

All three groups found that human essential genes are highly conserved, and much like yeast, they encode abundant proteins that engage in protein-protein interactions. The core set of human cell essential genes also tend not to be duplicated and appear to have increased evolutionary constraints, as they evolve slowly and are associated with fewer deleterious single-nucleotide polymorphisms. Although many essential genes are involved in fundamental biological processes including transcription, translation, and DNA replication, a substantial fraction remains functionally uncharacterized. Indeed, each analysis prioritized a wealth of uncharacterized genes whose essential roles are waiting to be explored.

That leaves about 18,000 "non-essential" genes to explore. One possibility is that they really are essential, too, when partnered with other genes. Yeast cells, for instance, can survive two non-lethal single mutations, but die when both occur together. This is called "synthetic lethality." Researchers have identified hundreds of thousands of these synthetic lethal interactions in yeast, they say. Initial studies in humans show the following pattern (notice the use of the phrase "functional information"):

Blomen et al. begin to address the extent of synthetic lethal interactions in human cells by screening a set of five nonessential genes with roles in secretion for synthetic lethal negative genetic interactions. They discovered an average of ∼20 synthetic lethal double-mutant interactions for a given nonessential gene, and these interactions tend to occur with functionally related genes. Even this relatively small genetic network suggests that the properties of the extensive genetic networks mapped for yeast are conserved and can now be mapped efficiently in human cells. The genetic network described by Blomen et al. ought to catalyze large-scale, collaborative efforts to map genetic interactions in human cells. Such an effort promises to enable functional annotation of the human genome, because genetic interaction profiles are rich in functional information and provide a quantitative measure of gene function.

These discoveries have the effect of raising the number of essential genes. If a cell can't survive a double hit on two interacting genes (a "synthetic lethal" condition), this indicates functionality even if each gene can take a hit on its own.

The studies of Blomen et al., Wang et al., and Hart et al. reveal the core essential gene set for human cells, setting the stage for the next wave of new genetic and chemical-genetic science that will take place directly in human cells. A future challenge will be to develop genetic tools, such as conditional alleles of essential genes, for exploring the terminal phenotypes and the various molecular mechanisms underlying the lethality associated with perturbation of different essential functions.

How often do double mutants occur in non-essential genes? If infrequent, synthetic lethals will be invisible to purifying selection. A non-essential gene can mutate and life will go on. Wang et al. say as much:

Essential genes should be under strong purifying selection and should thus show greater evolutionary constraint than that of nonessential genes. Consistent with this expectation, the essential genes found in our screens were more broadly retained across species, showed higher levels of conservation between closely related species, and contain fewer inactivating polymorphisms within the human species, as compared with their dispensable counterparts (Fig. 2, E to G). Essential genes also tend to have higher expression and encode proteins that engage in more protein-protein interactions.

Blomen et al. claim similar findings: essential genes show more conservation. They claim that "old" essential genes "emerged in premetazoans." But then, to their surprise, they found new essential genes incorporated into old existing functional genes:

Remarkably, the products of "new" essential genes are more often connected with old rather than other new essential gene products, suggesting that they largely function within ancient molecular machineries (fig. S9, B and C).

In PNAS, Rubin et al. looked for "The essential gene set of a photosynthetic organism." They identified "718 putative essential genes" for the photosynthetic lifestyle of a cyanobacterium.

There are certain limitations to the essentiality information determined here. Although we identified genes that are essential to the organism when individually mutated, they do not represent a minimal gene set. Essential processes for which there are redundant genes will not be discovered using an approach based on single mutants. In S. elongates, however, this complication is of lesser concern than in most other cyanobacteria because of its small genome size, which at a streamlined 2.7 Mbp, harbors little redundancy. In addition, the findings of essentiality reported here apply only to the specific laboratory conditions used and are likely to be different for a subset of genes under other growth conditions. Finally, because ncRNAs, regulatory regions, and other intergenic regions are much smaller, on average, than protein-coding genes, the essentiality calls for these regions are inherently of lower confidence than those made for protein-coding genes. Therefore, conclusions of essentiality for non-coding loci and to a lesser extent, protein-coding genes must be validated by targeted mutation before definitive statements can be made about their essentiality.

In short, the count of essential genes will vary by lab and researcher. This is definitely a work in progress, so measures of essential genes will need refinement with more study.

Contrasting Predictions

Let's integrate this information by contrasting the predictions of design and Darwinism about essentiality. The distinctions are not clear cut. On the one hand, Darwinians would like to see purifying selection acting to eliminate non-essential genes because, for large populations like yeast, they incur a metabolic cost. On the other hand, Darwinians have historically appealed to "junk DNA" and "vestigial organs" to explain things that do not appear essential, pointing to the weakness of purifying selection to eliminate mutations.

Design advocates, too, maintain competing expectations in tension. They would like to find functions for all gene activity to falsify the junk-DNA myth. But they would like to allow for functions beyond mere survival: functions that a designer with an artistic taste would create for beauty and pleasure.

So who's winning this debate on essentiality? It's too early to tell. Not enough is known yet. Based on experience with ENCODE and modENCODE, it seems likely that more functions will be found for everything in the genome (barring neutral or near-neutral mutations), but they will not always be essential for survival. There is a wealth of phenotypic evidence to support this: the beautiful spirals of a conch shell, elaborate patterns in fur and feathers, and other cases of elegant design that seem to go beyond the requirements for reproduction. Animals could satisfy Darwin's criteria by being all gray and just getting by till they have offspring, but life is incredibly vibrant with "useless" beauty. One suspects that genotypic evidence will follow suit.


Boone and Andrews point to "a wealth of uncharacterized genes whose essential roles are waiting to be explored." Who is better prepared to explain what the "substantial fraction" of genes that remain "functionally uncharacterized" do -- those who start with the assumption that "if it works, it's not happening by accident" or those who expect cobbled-together bits of junk?

On our neighbours' minds.

Furry, Feathery, and Finny Animals Speak Their Minds 
Denyse O'Leary December 22, 2015 3:27 AM 

Much research on animal minds is rooted in Darwinian naturalist assumptions -- a long slow continuum of intelligence from somewhere just north of cytoplasm to humans. These assumptions may have set us back. First, just being a life form includes a drive to survive and an ability to adapt for that purpose, which we do not find in rocks. Many life forms can also communicate for those purposes. But, so far as we know, they lack consciousness or sentience, the ability to feel things. There is no slow ascent; there is a steep cliff.
At the other end of the spectrum are apes, who belong to the same order of life as ourselves. Discussions of their intelligence often assume that they are entering a "Stone Age" (such as the Lascaux cave artists lived in, 20 000 years ago). However, while apes tend to be more intelligent than most mammals, they are not becoming like humans. And smart birds give apes serious competition, when tested.

So what can we learn from other vertebrate life forms, forms that show intelligence but are not closely related to us, do not seem much like us, and are not apparently heading in our direction?

Can Animal Mind Be Explained by "Instinct"?

At one time, it was supposed that most animals were simply born with instincts about what to do. The term is not used much now because it mainly meant that we do not know the source of the animal's information. We are now learning many of these sources.

We have recently discovered, for example, that migrating birds can use the mineral magnetite, embedded above their beaks, to use Earth's magnetic fields for direction.

We learned in recent decades how young birds "know" that they should follow their mother: As Spark Notes explains, following the work of animal behaviorist Konrad Lorenz (1903-1989):

Johnson and Bolhuis identified two independent neural systems that control filial imprinting in precocial birds. Newly hatched chicks will follow almost anything that has eyes and moves. After the chick follows something, another part of the brain, analogous to the frontal cortex, recognizes and imprints on the individual being followed. These mechanisms are independent. There is an instinct for chicks to follow, and then they learn what they are following.
But the "follow her" system is not strictly genetic:

It might seem odd that being able to identify and follow a mother does not have a genetic mechanism. Yet with a neural rather than genetic mechanism, the chick gains flexibility that might help in survival. If a chick's mother dies, the chick can then be adopted by another family member or conspecific.
Yes indeed. Famously, the young bird may follow a psychology student, a stick, or a cat, with varying results. Bird rescuers use hand puppets of bird faces when caring for nestlings, to return them later to a natural setting. Clearly, not all we need to know about an organism is in its genes.

How then does the male weaverbird know how to build a nest? That's apparently not simply a genetic program either; the birds must learn some of the techniques by experience.

Genetics, neural networks, and experience all make animal learning much more complex and information-rich than the concept of "instinct" implied. But we are not yet in the realm of "intelligence." The migrating and nest-building birds access existing solutions to longstanding problems; they do not come up with new ones.

Both birds and mammals can learn to solve new problems presented to them. Let's look at some recent finds in mammals first, bearing in mind that we have only really begun to look at their intelligence seriously. It is early days yet, so some sketchiness is inevitable.

Mammals' Unexpected Intelligence

We find intelligence where we did not expect it. Pigs, for example (despite their reputation), are "socially complex as other intelligent mammals, including primates" (Natural History Magazine). That is surprising because pigs don't usually form close relationships with humans, as dogs do. And hog farming operations don't encourage intelligence.

We know more about the intelligent animal we are close to. In terms of communication, horses' surprisingly varied facial expressions are more similar to those of humans on one measurement than those of chimps are:

The Equine Facial Action Coding System (EquiFACS), as devised by the Sussex team in collaboration with researchers at the University of Portsmouth and Duquesne University, identified 17 "action units" (discrete facial movements) in horses. This compares with 27 in humans, 13 in chimps and 16 in dogs.
That might account for the human-horse bond (there seems no similar chimp-horse bond).

Horses', dogs', and cats' tail communications are also easy to read (they are intended to be). So just as dogs can understand finger pointing even though they don't have fingers, humans can understand some dog messages even though we don't have tails. The habit of co-operative communication can overcome physical barriers.

Thus, one understudied question is whether and when mammal intelligence changes on account of association with humans. Let us say that an indoor domestic dog or cat is freed from the need to hunt, protect herself, or raise offspring. Consequently, she enjoys a vastly increased life expectancy. Some such animals focus on status issues with respect to people and other dogs/cats, etc., generating layers of social complexity that are unlikely in a wilderness environment. She shows no progress toward human intelligence, but her human environment may determine how much canine or feline intelligence she lives to display.

"Feathered Primates" without Primate Brains?

Ravens can match or beat chimpanzees on some accepted tests of animal intelligence. Some researchers call crows "feathered primates." New Zealand crows' causal understanding (within limits) is said to rival that of 5-7 year old children. Or 7- to 10-year old children.

Some New Caledonian crows can use three tools in succession to reach food, and can also enact Aesop's fable by dropping stones into a jar of water till floating food rises.

It's not just crows. Pigeons' ability with numbers up to nine is "indistinguishable from that displayed by monkeys." Even the intelligence of the chicken "startles," according to Scientific American ("communication skills on par with those of some primates").

But how do we understand bird intelligence, given that bird brains show significant differences from mammal brains? And we can hardly fall back on common ancestry.

Language ability is an uncertain guide. Some birds are popularly held to be intelligent because they can imitate the human voice. This ability may be related to structural features of those bird species' brains:

In addition to having defined centers in the brain that control vocal learning called "cores," parrots have what the scientists call "shells," or outer rings, which are also involved in vocal learning.
That "shell" structure may be related to some parrots' ability to dance to music as well. But these birds probably don't know what they are saying or doing apart from the fact that, like the bicycling cockatoo, they are typically rewarded for doing it.

Alex the parrot (1976-2007), possibly the most famous "intelligent bird" personality, could use human language to communicate needs. However, he had only typical parrot needs. Alex was not achieving more human-like intelligence--as his researcher and patron Irene Pepperberg acknowledged:

"I avoid the language issue," she said. "I'm not making claims. His behavior gets more and more advanced, but I don't believe years from now you could interview him." She continued: "What little syntax he has is very simplistic. Language is what you and I are doing, an incredibly complex form of communication."
Put another way, if an intelligent dog had "vocal cords" (a syrinx) like a parrot, he could tell a human in words that he needs to go outside or have his water dish refilled. But he does not go on to express interest in things that do not naturally concern a dog.

One interesting thing we learned recently about smart crows is that they don't depend much on learning from each other (social learning):

Logan and colleagues found that the crows don't imitate or copy actions at all. "So there goes that theory," she said. ...
Even if one crow is at an apparatus and tries unsuccessfully to open the door, if he or she sees another crow on the second apparatus actually solving the problem correctly, the first crow doesn't use that information. "The social learning attracts them to a particular object and then they solve it through trial and error learning after that," Logan said.

The crows' pattern of learning seems different from human learning, and may be related to an inability to grasp or convey abstract information. Which brings us to the recent claim that crows fear death because many crows purposefully avoid places where other crows have died:

And this fear of a potential deadly situation stays with them. Even six weeks later more than a third of 65 pairs of crows continued to respond this way.
But, like the claim that chimpanzees mourn their dead, this one is founded on a misunderstanding: "Death" -- unlike danger or loss, which are experienced viscerally -- is a pure abstraction, like the number 23. An intelligent life form must understand not merely nature but the nature of nature to know what "death" means.

So we come to a culturally unexpected conclusion: Bird intelligence is a respectable competitor on a continuum with primate intelligence. But, like theirs, it is on a different track from that of humans.

Then There Are Those Cold-Blooded Reptiles and Fish...

A number of recent marketing strategies promise sales through appealing to a customer's "self-centered" reptilian brain. But that piece of business folk wisdom is based on a myth:

It is the idea that we have three brains: a reptilian one, the paleomammalian one and the mammalian one. The story goes that these were acquired one after another during evolution. The details differ with the writer. But it is all a myth based on an idea from the '70s of Paul MacLean which he republished in 1990. Over the years in has been popularized by Sagan and Koestler among others.
The brain is hardly so simple. Reptiles lack certain brain structures found in mammals, but like birds they sometimes use the ones they have for purposes that apparently display intelligence: Crocodilians (alligators and crocodiles) are reported to use sticks as decoys, play, and work in teams. Tortoises may well be smarter than once believed, though here we rely mainly on anecdotes, not formal studies, for now.

Even fish have shown signs of what seems like intelligence. We are told that pairs of rabbitfishes "cooperate and support each other while feeding":

While such behaviour has been documented for highly social birds and mammals, it has previously been believed to be impossible for fishes. ... "We found that rabbitfish pairs coordinate their vigilance activity quite strictly, thereby providing safety for their foraging partner," says Dr Simon Brandl from the ARC Centre of Excellence for Coral Reef Studies.
Why don't reptiles and fish appear intelligent? Here is a possible clue: Anole lizards were found as capable as tits (birds) in a problem-solving test for a food reward. But the anoles, being exothermic, don't need much food -- which hinders research. When reptiles and fish need to solve problems, they often use the brain structures available to them quite effectively. The rest of the time they may be comfortably inert. If so, the relationship between brain structure and intelligence is more complex than we have supposed.

Factors That May Promote Intelligence in Vertebrates

We have seen that, while brain structure is not the absolute limitation once supposed, cold-bloodedness (exothermic metabolism) may reduce the need for intelligence without actually preventing it. Conversely, living with humans may promote intelligence by creating systematic rewards for achievement. Nature, it is true, rewards intelligence, but not systematically, like a dedicated trainer seeking a response. So there are rough general trends in intelligence, as in evolution, but they appear to be patterns, not laws.

Do the patterns relate in some way to anatomy? Can we say, for example, that intelligence requires a multicellular life form that has a spinal column and a brain? What can the vast world of invertebrates tell us about that?

Who is hearer of prayer?:The Watchtower Society's commentary.

Should We Pray to Jesus?:

A RESEARCHER recently polled over 800 youths from more than a dozen religious denominations, asking whether they believed that Jesus answers prayers. Over 60 percent said that they firmly believe that he does. However, one youth crossed out the name Jesus on the survey and wrote “God” instead.

What do you think? Should we address our prayers to Jesus or to God?* To find the answer, first let us consider how Jesus taught his disciples to pray.

TO WHOM DID JESUS TEACH US TO PRAY?:
Jesus praying to his Father[Picture on pages 14, 15]
In praying to his heavenly Father, Jesus set an example for us to follow
HIS TEACHING: When one of his disciples asked Jesus, “Lord, teach us how to pray,” Jesus replied: “Whenever you pray, say: ‘Father.’” (Luke 11:1, 2) Further, in his famous Sermon on the Mount, Jesus urged his listeners to pray. He said: “Pray to your Father.” He also reassured them by saying: “Your Father knows what you need even before you ask him.” (Matthew 6:6, 8) On his final night as a human, Jesus told his disciples: “If you ask the Father for anything, he will give it to you in my name.” (John 16:23) Jesus thus taught us to pray to the one who is both his Father and our Father, Jehovah God.—John 20:17.

HIS EXAMPLE: In line with the way he taught others to pray, Jesus personally prayed: “I publicly praise you, Father, Lord of heaven and earth.” (Luke 10:21) On another occasion, “Jesus raised his eyes heavenward and said: ‘Father, I thank you that you have heard me.’” (John 11:41) And as he was dying, Jesus prayed: “Father, into your hands I entrust my spirit.” (Luke 23:46) In praying to his heavenly Father—the “Lord of heaven and earth”—Jesus set a clear example for all to follow. (Matthew 11:25; 26:41, 42; 1 John 2:6) Is that how Jesus’ early disciples understood his instructions?

TO WHOM DID THE EARLY CHRISTIANS PRAY?


Within weeks of Jesus’ return to heaven, his disciples were being harassed and threatened by their opposers. (Acts 4:18) Of course, they reached out in prayer—but to whom did they turn? “They raised their voices with one accord to God,” praying that he would continue helping them “through the name of [his] holy servant Jesus.” (Acts 4:24, 30) So the disciples followed Jesus’ guidelines on prayer. They prayed to God, not to Jesus.

Years later, the apostle Paul described the manner in which he and his associates prayed. Writing to fellow Christians, he said: “We always thank God, the Father of our Lord Jesus Christ, when we pray for you.” (Colossians 1:3) Paul also wrote to his fellow believers about “always giving thanks to our God and Father for everything in the name of our Lord Jesus Christ.” (Ephesians 5:20) From these words, we see that Paul encouraged others to pray to his “God and Father for everything”—but, of course, in Jesus’ name.—Colossians 3:17.

Like the early Christians, we can show our love for Jesus by heeding his advice on prayer. (John 14:15) As we pray to our heavenly Father—and to him alone—the words of Psalm 116:1, 2 will become ever more meaningful to us: “I love Jehovah because he hears my voice . . . I will call on him as long as I live.”*

According to the Scriptures, God and Jesus are not equal. For more information, see chapter 4 of the book What Does the Bible Really Teach? published by Jehovah’s Witnesses.

In order for our prayers to be acceptable to God, we must sincerely endeavor to live up to his requirements. For more information, see chapter 17 of the book What Does the Bible Really Teach?

Did They Pray to Jesus?:

The Bible records a few occasions when faithful humans spoke to the heavenly Jesus—and sometimes to angels. (Acts 9:4, 5, 10-16; 10:3, 4; Revelation 10:8, 9; 22:20) But were those men praying to these heavenly creatures? No. In all such instances, the heavenly creatures initiated the communication. Faithful men and women reserved prayer for God alone.—Philippians 4:6.

The Biblical deluge global or local?:The Bible's answer

We can begin our examination of this issue with God's proclamation to the prophet Noah.Genesis6:13 ASV "And God said unto Noah, The end of all flesh is come before me; for the earth is filled with violence through them; and, behold, I will destroy them with the earth." Genesis6:17ASV"And I, behold, I do bring the flood of waters upon this earth, to destroy all flesh, wherein is the breath of life, from under heaven; everything that is in the earth shall die." Points to note here: the wickedness of man has become,in the eyes of the creator,a global problem requiring a global response. Later the apostle Peter invokes the historical account as a warning to those who doubt Jehovah God's ability/willingness to act decisively to bring an end to the present corruption of our global civilisation 2Peter3:5,7.As you read Peter's words recorded at the cited passage do you get the impression that he thought of the flood as a local event?
Another consideration would be the preparations that Noah were instructed to make.Genesis6:14-16ASV"Make thee an ark of gopher wood; rooms shalt thou make in the ark, and shalt pitch it within and without with pitch. 15And this is how thou shalt make it: the length of the ark three hundred cubits, the breadth of it fifty cubits, and the height of it thirty cubits. 16A light shalt thou make to the ark, and to a cubit shalt thou finish it upward; and the door of the ark shalt thou set in the side thereof; with lower, second, and third stories shalt thou make it." Thus the creator outlined decades of work for his servants.Much of which seems superfluous if we understand the deluge as a local event.Why not simply have Noah and his family migrate from the targeted locale?The local fauna esp.the birds could likewise evacuate the area.
Finally we can examine the Bible's description of the event itself:
Genesis7:17NASB"Then the flood came upon the earth for forty days, and the water increased and lifted up the ark, so that it rose above the earth. 18The water prevailed and increased greatly upon the earth, and the ark floated on the surface of the water. 19The water prevailed more and more upon the earth, so that all the high mountains everywhere under the heavens were covered. 20The water prevailed fifteen cubits higher, and the mountains were covered. 21All flesh that moved on the earth perished, birds and cattle and beasts and every swarming thing that swarms upon the earth, and all mankind; 22of all that was on the dry land, all in whose nostrils was the breath of the spirit of life, died. 23Thus He blotted out every living thing that was upon the face of the land, from man to animals to creeping things and to birds of the sky, and they were blotted out from the earth; and only Noah was left, together with those that were with him in the ark. 24The water prevailed upon the earth one hundred and fifty days." Points to note:The flood is described as covering all of earth's tallest mountains by at least twenty two feet.The flood brings and end to all terrestrial life outside of the ark.The waters of this flood kept rising for one hundred and fifty days,very unlike any local flood in recorded history.Genesis8:5NASB"The water decreased steadily until the tenth month; in the tenth month, on the first day of the month, the tops of the mountains became visible." This is after eight months.
Interestingly there are flood legends native to cultures globally many of which bear such uncanny parallels to the Bible's account that in would be unreasonable to postulate an independent origin to them,rather it seems more likely that in these we have echoes of a spectacular event etched in humankind's collective memory.This too seems to point to a global event.

On the "logic" of the abyss.

Assessing the "Logic" of Legalized Euthanasia

Wesley J. Smith December 17, 2015 1:59 PM 

ournalist Andrew Coyne has written some of the best critiques of legalized euthanasia of which I am aware. He has another A+ effort out in Canada's National Post, reacting to the recommendations of an ethics panel for implementing that country's Supreme Court order to allow euthanasia. From "The Absurd Logic of Assisted Suicide":

When dispatching a patient by lethal injection, would a doctor be obliged to sterilize the needle?

I think they almost certainly would. Old habits die hard, you should pardon the expression, and the unconscious need to shroud an act that at time of writing remains illegal under the Criminal Code as a routine medical procedure would make it unthinkable to do otherwise, however nonsensical it may be.

That's the thing about normalizing suicide. It requires us to set aside all prior assumptions except the most absurd ones. It rushes past all sorts of distinctions that might once have seemed important -- between killing yourself and killing someone else, for example -- yet clutches wildly at others, as if they were any more likely to withstand the momentum of its logic.

Exactly. Once you accept euthanasia's premise, your mindset turns 180 degrees: Up becomes down, in becomes out, compassion becomes killing. Coyne's conclusion shows exactly where Canada -- and the U.S., if we keep following the same path (albeit, more slowly) -- are heading:

Advocates see suicide...as a release from suffering; not as an evil to be prevented, but as a service to be provided (indeed, the panel recommends it be done at public expense).

This presents the right to die, not as a limited one, such as the right to drive, but as an unlimited one, inhering in all persons -- rather like the right to life. And, it has to be said, it is by far the more coherent of the two arguments.

For if assisted suicide is a right to be released from suffering, how can that be restricted to adults? Are we to condemn children to endless torment, where we would not an adult?

Likewise for the mentally incompetent: Are we really so indifferent to their pain as to allow their disability to stand in the way of its alleviation? If they are unable to consent to their own death, should they not be assisted, intellectually, in the same way as those physically unable to kill themselves are to be assisted?

This is not some dire prophecy. It is, as the panel reminds us, the logic of assisted suicide. By making it lawful to euthanize children, we would only be following where Belgium and the Netherlands have led; by applying it to the mentally ill, we would be doing no more than Switzerland has already done.

If that is where we want to go, so be it. But let us at least be clear that that is what is really at stake.

Indeed. The lure of death is becoming like a black hole from which little light escapes. Or as Coyne put it so well several years ago in the wake of widespread public support for a father who murdered his 12-year-old daughter because she had cerebral palsy:

A society that believes in nothing can offer no argument even against death. A culture that has lost its faith in life cannot comprehend why it should be endured.

I fear we are devolving into that nihilistic society. It is still not too late to stop the slide. But we had better do that quickly, or we will soon be over the cliff.

One more reason to doubt.

Fossil Discovery Adds Another Phylum to the Cambrian Explosion

Casey Luskin December 15, 2015 2:04 PM 

The Cambrian explosion just got a bit more explosive with the discovery of a likely member of phylum Kinorhyncha from rocks in South China that are about 530 million years old. If you've never heard of kinorhynch worms, also called "mud dragons," that's probably because they are very tiny, seldom discussed, and found living only in certain marine environments around the world. As the Encyclopedia of Life explains:

Around 150 species of kinorhynchs have been described since this group was first discovered on the northern coast of France in 1841, nearly all of them less than 1 mm long. They have been collected as far north as Greenland and as far south as Antarctica, as well as in the Black Sea. Most live in marine sand or mud from the intertidal zone to a depth of 5000 to 8,000 meters, but some are known from algal mats or holdfasts, sandy beaches, and brackish estuaries and others have been found living on hydrozoans, bryozoans, or sponges.

Science Daily reports on the fossil, noting that "[a]n historic find --- made in South China -- fills a huge gap in the known fossil record of kinorhynchs," since the new fossil species, Eokinorhynchus rarus, is very similar to living kinorhynchs:

Similarities between the fossils of E. rarus and living, modern kinorhynchs include their hollow spines arranged in a five-fold symmetry and their body segments each consisting of articulated plates. However, E. rarus differs from modern species with more numerous segments. Hence the belief of an ancestorship.

The technical paper, "Armored kinorhynch-like scalidophoran animals from the early Cambrian," puts it this way:

Here we describe several early Cambrian (~535 million years old) kinorhynch-like fossils, including the new speciesEokinorhynchus rarus and two unnamed but related forms. E. rarus has characteristic scalidophoran features, including an introvert with pentaradially arranged hollow scalids. Its trunk bears at least 20 annuli each consisting of numerous small rectangular plates, and is armored with five pairs of large and bilaterally placed sclerites. Its trunk annuli are reminiscent of the epidermis segments of kinorhynchs.... Eokinorhynchus rarus also shows intriguing similarities with extant kinorhynchs, suggesting a close phylogenetic relationship.

In Figure 2.5 of Darwin's Doubt, Steve Meyer reports that about 20 of 27 animal phyla with known fossil records appear in the Cambrian period. Prior to this find, phylum Kinorhyncha was not known to have a fossil record. Now we can update Meyer's tabulation to report that 21 of the 28 phyla with known fossil records apparently first appear -- abruptly no less -- in the Cambrian explosion of animal body plans.

Despite this non-Darwinian pattern of origin, the papers' authors speculate that these ancient (and extant) kinorhynchs might shed light on the origin of arthropods, but that's largely only because they are segmented -- as various other living phyla are as well. Given that kinorhynchs entirely lack limbs and also lack arthropod-like eyes, it seems that they aren't going to help us much towards understanding the unique defining characteristics of arthropods.

The paper also explains that these fossils come from about 535 million years ago in a section of strata bearing the "small shelly fossils," in the early Cambrian period. As Meyer and I have discussed, some mistakenly cite the "small shelly fossils" (SSFs) as possible evidence of a gradual evolution of the Cambrian animals. But in this case, studies of the SSFs are showing the Cambrian explosion to be more explosive.

The paper even suggests that studying these enigmatic SSFs may reveal that known phyla are represented in species not previously assigned to living groups:

Nonetheless, the paleontological data and phylogenetic interpretation presented here invite further exploration of the phosphatization taphonomic window and careful re-examination of small shelly fossils (e.g., Paracarinachites spinus and Kaiyangites novoli) in search of Cambrian kinorhynchs.

If they're right, then correctly classifying SSFs might be key to understanding the abrupt appearance, not gradual evolution, of the Cambrian phyla. This reminds me of a comment by Douglas Erwin and James Valentine in The Cambrian Explosion where they predicted that even some small and soft-bodied phyla without fossil records likely first appeared in the early Cambrian:

[A] great variety and abundance of animal fossils appear in deposits dating from a geologically brief interval between about 530 to 520 Ma, early in the Cambrian period. During this time, nearly all the major living animal groups (phyla) that have skeletons first appeared as fossils (at least one appeared earlier). Surprisingly, a number of those localities have yielded fossils that preserve details of complex organs at the tissue level, such as eyes, guts, and appendages. In addition, several groups that were entirely soft-bodied and thus could be preserved only under unusual circumstances also first appear in those faunas. Because many of those fossils represent complex groups such as vertebrates (the subgroup of the phylum Chordata to which humans belong) and arthropods, it seems likely that all or nearly all the major phylum-level groups of living animals, including many small soft-bodied groups that we do not actually find as fossils, had appeared by the end of the early Cambrian. This geologically abrupt and spectacular record of early animal life is called the Cambrian explosion. (The Cambrian Explosion, p. 5, emphases added)

It would seem that this new small, soft-bodied fossil find confirms that Erwin and Valentine are probably correct.

A clash of titans II

On countering criminal recidivism:The Norwegian experience.

another failed Darwinian prediction.

Competition is greatest between neighbors:

Darwin’s basic theory of evolution, by itself, did not account for the tree-like, hierarchical pattern the species were thought to form. Darwin was keenly aware of this shortcoming and wrestled with it for years. He finally conceived of a solution for why modified offspring would continue to evolve away and diverge from their parents. The principle of divergence, the last major theoretical addition before Darwin published his book, held that competition tends to be strongest between the more closely related organisms. This would cause a splitting and divergence, resulting in the traditional evolutionary tree pattern. (Desmond and Moore 1991, 419-420; Ridley, 378-379)

But no such trend has been observed. In a major study of competition between freshwater green algae species, the level of competition between pairs of species was found to be uncorrelated with the evolutionary distance between the pair of species. As the researchers explained, Darwin “argued that closely related species should compete more strongly and be less likely to coexist. For much of the last century, Darwin’s hypothesis has been taken at face value […] Our results add to a growing body of literature that fails to support Darwin’s original competition-relatedness hypothesis.” (Venail, et. al., 2, 9) The team spent months trying to resolve the problem, but to no avail. As one of the researchers explained:

It was completely unexpected. When we saw the results, we said “this can’t be.” We sat there banging our heads against the wall. Darwin’s hypothesis has been with us for so long, how can it not be right? … When we started coming up with numbers that showed he [Darwin] wasn’t right, we were completely baffled. … We should be able to look at the Tree of Life, and evolution should make it clear who will win in competition and who will lose. But the traits that regulate competition can’t be predicted from the Tree of Life. (Cimons)

Why this long-standing prediction was not confirmed remains unknown. Apparently there are more complicating factors that influence competition in addition to evolutionary relatedness.

References

Cimons, Marlene. 2014. “Old Idea About Ecology Questioned by New Findings.” National Science Foundation.

Desmond, Adrian, James Moore. 1991. Darwin: The Life of a Tormented Evolutionist. New York: W. W. Norton.

Ridley, Mark. 1993. Evolution. Boston: Blackwell Scientific.

Venail , P.A., A. Narwani , K. Fritschie, M. A. Alexandrou, T. H. Oakley, B. J. Cardinale. 2014. “The influence of phylogenetic relatedness on competition and facilitation among freshwater algae in a mesocosm experiment.” Journal of Ecology, DOI: 10.1111/1365-2745.12271.

A line in the sand XXVII

A line in the sand. XXVI

Yet more Darwinian Hagiography

Darwin's Origin Is Voted Most "Influential," but Here's the Rest of the Story
Sarah Chaffee December 9, 2015 11:13 AM 


Recently to mark Academic Book Week, Charles Darwin's On the Origin of Species was named history's most influential academic book. Out of twenty titles (including works by Plato, Shakespeare, and Marx) assembled by librarians, publishers, and booksellers in the UK, the public voted Darwin's as the most significant.

But in terms of actual scientific value and influence, the Origin may not be number one. Writing in The Guardian, Rebekah Higgitt recommends a different title -- Newton's Principia. She notes:

Along with Opticks it was widely and internationally revered for centuries, setting the model for what successful scientific results and programmes of research should look like. It was not just central to mathematical physics and astronomy, for the aim of developing predictive mathematical theories became the ultimate goal across nearly all sciences and beyond...

...Principia's mathematics may have been improved and developed, but it set the agenda and the theory remained triumphant until the early 20th century and, even after Einstein, has not been overthrown -- after all, it was what was required to land a rocket on the moon.

Asking whether a book has enabled further scientific discoveries seems like a reasonable criterion. Measured that way, contrary to what some have asserted, On the Origin of Species falls short. Judged for its heuristic value, evolutionary theory has had little impact on biology research or medical advancement. Even Jerry Coyne admits as much, writing in Nature:

[I]f truth be told, evolution hasn't yielded many practical or commercial benefits. Yes, bacteria evolve drug resistance, and yes, we must take countermeasures, but beyond that there is not much to say. Evolution cannot help us predict what new vaccines to manufacture because microbes evolve unpredictably. But hasn't evolution helped guide animal and plant breeding? Not very much. Most improvement in crop plants and animals occurred long before we knew anything about evolution, and came about by people following the genetic principle of "like begets like."

But while Darwin's work hasn't done a lot for science or medicine, it has had a great influence on culture.

University of Glasgow's Professor Andrew Prescott told The Guardian:

Darwin used meticulous observation of the world around us, combined with protracted and profound reflection, to create a book which has changed the way we think about everything -- not only the natural world, but religion, history and society. Every researcher, no matter whether they are writing books, creating digital products or producing artworks, aspires to produce something as significant in the history of thought as Origin of Species.

While Prescott praises Darwin's book, the work's influence over the past 150 years, its popularity and acclaim, could rightly be called tragic. Discovery Institute's John G. West summarizes in the Preface to Darwin Day in America: How Our Politics and Culture Have Been Dehumanized in the Name of Science:

At the dawn of the last century, leading scientists and politicians giddily predicted that modern science -- especially Darwinian biology -- would supply solutions to all the intractable problems of American society, from crime to poverty to sexual maladjustment.

Instead, politics and culture were dehumanized as a new generation of "scientific" experts began treating human beings as little more than animals or machines:

In criminal justice, these experts denied the existence of free will and proposed replacing punishment with invasive "cures" such as the lobotomy.

In welfare, they proposed eliminating the poor by sterilizing those deemed biologically unfit.

In business, they urged the selection of workers based on racist theories of human evolution and the development of advertising methods to more effectively manipulate consumer behavior.

In sex education, they advocated creating a new sexual morality based on "normal mammalian behavior," without regard to longstanding ethical or religious imperatives.

See the trailer for Dr. West's book here.

Since the Origin won its latest accolade in the context of Academic Book Week, it's fair to ask what defines an academic book. A fairly coherent standard would be to evaluate a book's contribution to its specific field - be that mathematics, politics, English, philosophy, or natural sciences. Experts could evaluate the scope of its contribution or its importance to further developments in the field. Otherwise, the quest for "most influential academic book" devolves into a popularity contest. In that case, why limit it to academic books at all?

So is On the Origin of Species the most influential academic book? Probably not. Unfortunately, as we know too well, it has been and remains one of the most influential and popular works in the world for reasons that are not necessarily academic at all.

But there is something very positive about the book, a quality that I wish were more influential. Darwin was a great writer, and a candid one. In the Origin, he was very open about possible challenges to his theory. He understood that it had significant potential weaknesses. As Darwin famously noted, "A fair result can be obtained only by fully stating and balancing the facts and arguments on both sides of each question..." He knew that his work must be treated as open to scrutiny.


Yet today, schools present evolution to students as scientific fact. What we need in education is more candor and objectivity -- to look at "the facts and arguments on both sides" of the debate, just as Darwin urged. Students could learn from his humility. So could we all.

The enigma that fuels the doubt

Is the real planet of the apes coming soon?

Stand by for apes entering the Stone Age
December 11, 2015 Posted by News under Animal minds, Intelligent Design




As we saw with tool use, many claims [about ape behaviour] are phrased essentially as predictions that the primates are in the process of developing a culture like that of humans, rather than behaving as they have, largely unnoticed, for tens of millennia. For example, we were told earlier this year that “Apes may be closer to speaking than many scientists think. Koko, the gorilla who has lived with humans for forty years can “control her larynx enough to produce a controlled grunting sound.” While Koko is a very accomplished gorilla, she doesn’t seem to be progressing toward human speech, and it is unclear why she would need to.

Similarly, we are told that bonobo infant noise points to the origin of human language and can challenge “how we think about the evolution of communication and potentially move the dividing line between humans and other apes.” Really? Despite having done nothing similar for bonobos in all this time? We also hear that monkeys recognize the basic structure of language, but they do not go on to but develop a language either.

In any event, when primate researchers say that bonobo infant noise challenges “how we think about the evolution of communication and potentially move the dividing line between humans and other apes,” who are the “we” who are challenged? They themselves seem quite convinced that there is no significant dividing line, no matter what the state of the evidence.

And their position cannot easily be assailed. They can go on looking for evidence indefinitely, and the developments in ape consciousness that would prove them right would, if they ever occur, be millennia in the future.

Meanwhile, subsequent research did not support one claim that chimps learn other troupes’ “languages.”More.

Lots of people have to want to believe this stuff. Otherwise, it would be challenged more.

Question: Couldn’t we care about apes, humane treatment of apes, and their conservation without all the “just like us” nonsense? Do current stats show that the nonsense is really helping numbers?:

Gorilla and chimpanzee populations in Central Africa continue to decline due to poaching, habitat loss and disease. National parks and reserves in six range countries protect only 21 percent of western lowland gorillas and central chimpanzees, according to a new report.


See also: What can we hope to learn about animal minds?

The lion and the lamb may be able to get along after all.

Converting carnivores to herbivores
December 12, 2015 Posted by News under Evolution, Genetics, News


By knocking out plants’ don’t-eat-my-seeds chemicals

From The Scientist:

Researchers are converting carnivores into herbivores in a bid to make raising animals such as alligators, trout, and salmon more sustainable.

It’s no mean feat turning a meat-hungry predator into a plant eater. The American alligator is an apex predator of southern waterways from Texas to the Carolinas. In the wild, adult alligators eat fish, frogs, turtles, snakes, birds, and just about any small mammal they can catch. On alligator farms, the animals chow down on fishmeal and oil processed from wild stocks of sardines, anchovies, and other forage fish harvested from the open ocean. While populations of these fish species have plummeted over the past two decades due to intense fishing pressure, global demand for fishmeal and fish oil has continued to climb, and prices have quadrupled in recent decades. Now, researchers are searching for alternative feed ingredients for alligators and other carnivores farmed for human consumption.

Talk about the lion lying down with the lamb … the alligators were switched from fishmeal to vegan with only a slight reduction in growth.

Scientists have learned that fishmeal and fish oil contain a balance of about 40 nutrients, including vitamins A and D, amino acids (such as methionine and lysine), minerals (such as iron, zinc, selenium, and iodine), and long-chain fatty acids. More.

The trick is to balance the nutrients so that the ‘gator version of Boost is equivalent to the nutrients from whatever the ‘gator can catch.

Get this:

The most common ingredient today in aquaculture feed is soybeans. Soybean meal is widely available, nutritious, and relatively inexpensive, usually costing about one-quarter of fishmeal’s price. But soybeans, like many other plants, have evolved chemicals called “antinutrients” to discourage predators from consuming their seeds. Soybean’s antinutrients include lectins, oligosaccharides, and trypsin inhibitors. Each anti-nutrient might be harmless alone, but together they can cause an inflammatory condition in some fish called intestinal enteritis, which can reduce growth and produce additional waste that must be cleaned up.

They just happened to have evolved “antinutrients” and a chemical ecology balance was somehow struck.

A clash of titans.

I.D continues to run up the score.

Less Junk, More ID Predictions Confirmed
December 7, 2015 Posted by PaV under Intelligent Design

It is simply a matter of time before the Darwinists (I know they prefer “evolutionary biologists,” but evolution is not evolution without “Origin of Species”) will have to give up.

Every day in labs around the world, more and more function is being found for “junk” DNA. This is a two-fold problem for the Darwinists.

The first problem is that this is NOT what they predicted, even though, quite cavalierly, they say then never said any such thing. But, of course, we know better.

Second, there’s the problem of “de novo” genes, and the solution for this is to look to so-called “junk” DNA as a potential template for these ‘new’ genes. If “junk” DNA is ‘neutral,’ then no problem; but if it has a function, then the nursery from which they can harvest “de novo” genes from within the genome lessens. As I say, it’s a matter of time.

From Phys.Org we have a snippet from a news summary:

In the first study to run a genome-wide analysis of Short Tandem Repeats (STRs) in gene expression, a large team of computational geneticists led by investigators from Columbia Engineering and the New York Genome Center have shown that STRs, thought to be just neutral, or “junk,” actually play an important role in regulating gene expression. The work, which uncovers a new class of genetic variants that modulate gene expression, is published on Nature Genetics’s Advance Online Publication website on December 7.

Erlich’s study looked at Short Tandem Repeats (STRs), variants that create what look like typos: stutter vs. stututututututter. Most researchers, assuming that STRs were neutral, dismissed them as not important. In addition, these variants are extremely hard to study. “They look so different to analysis algorithms,” Erlich notes, “that they just usually classify them as noise and skip these positions.”

And, revealing a mechanism I have long suspected could be the true purpose, or function, of these repeated elements, they say:


Erlich used a multitude of statistical genetic and integrative genomics analyses to reveal that STRs have a function: they act like springs or knobs that can expand and contract, and fine-tune the nearby gene expression. Different lengths correspond to different tensions of the spring and can control gene expression and disease traits.

File under 'well said' XVI

Whatever is begun in anger ends in shame.
Benjamin Franklin