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

Follow UD News at Twitter!

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!