Search This Blog

Sunday, 14 February 2016

Peer reviewed findings re:probability and evolution

Microbes Vs.Darwin II

More on How Microbes Make Earth Habitable:

Evolution News & Views February 14, 2016 12:03 AM

Last week we discussed how microbes maintain the viability of life on our planet ("How Microbes Make Earth Habitable"). In the same vein, more news just arrived about the carbon and nitrogen cycles.

Following up on MIT's findings about plankton taking carbon to the ocean bottom, Ohio State has just concluded from the three-year Tara Oceans oceanography expedition that plankton -- and some viruses -- are "key to carrying carbon" from the atmosphere down to the seafloor sediments. They took pictures of microbes at different depths to learn which ones are carrying carbon downward as they sink to the bottom. The research has helped scientists understand "the interplay of organisms in the ocean and of their role in the health of the planet."

As for nitrogen, Current Biology posted a Primer on "The Nitrogen Cycle," confirming that it "is entirely controlled by microbial activities." Before man started producing chemical fertilizers, "nearly all of the reactive nitrogen in the biosphere was generated and recycled by microorganisms."

Microbes Follow Icebergs

Another interesting interaction between geology and life was reported by the BBC News. Mark Kinver writes that "Giant icebergs play [a] 'major role' in [the] ocean carbon cycle." An aerial image shows a brilliant bloom of phytoplankton following one such giant iceberg in its wake. What's happening? The bloom is "triggered by the distribution of nutrients -- such as iron -- from an iceberg's meltwater." What this signifies is important:

"We estimate that giant icebergs account for between 10% and 20% of the actual vertical rate of carbon going from the surface to the deep (Southern) Ocean," he suggested....

Plankton scientist Dr Richard Kirby, who was not involved in this study, observed: "The phytoplankton at the sunlit surface of the sea has played a central role in the sequestration of carbon over millennia to affect the atmospheric concentration of this greenhouse gas, and so the Earth's climate.

"This interesting paper shows how much we still have to learn about these microscopic organisms, and how a changing climate may affect them, and also the food web they support." [Emphasis added.]

Bacteria Attack Lignin

Readers of Evolution News may remember Ann Gauger and Matt Leisola's design inference about lignin, the complex molecule that gives wood its strength. They argued that no organism has exploited this energy-rich substance -- which is good news for us, because "the indigestibility of lignin may be an essential requirement for the balance of life," Gauger wrote. "Lignin slows the degradation of wood, thus allowing the buildup of humus in the soil, which in turn permits plant growth and all resulting life that depends on plants."

Now, news from Rice University says that bacteria use a "tag team" approach to break apart this complex substance that locks up more than half a plant's sugar and holds a third of the carbon in biomass. This finding does not impact the conclusions of Gauger and Leisola, because the bacteria "chew through" the lignin to get to the cellulose they can digest. But "it's a very slow process, which is why it can take years for dead trees to decompose." The rate of decomposition of this energy-rich substance is what's interesting for considerations of planetary carbon cycling and habitability.

Bacteria Prepare the Land for Habitation

Another interesting interaction of microbes with geology happens on land. Biocrusts are accumulations of cryptic bacteria that inhabit the surfaces of arid soils. A paper in Nature Communications notes the ecological impact of these microbial habitats:

Much of the arid soil surfaces can be populated by cryptic photosynthetic assemblages known as biological soil crusts (or biocrusts), which are known to impart stability against erosion, to modify the hydrological properties of soils, and to contribute significantly to arid land fertility.

Researchers from Arizona and California found that the bacteria, mostly the nitrogen-fixing variety, produce a secondary metabolite called scytonemin that acts as a "sunscreen". It strongly absorbs solar radiation and dissipates it as heat, raising soil temperatures as much as 10°C, an effect that is "not without consequences" for soil microbial communities. While potentially making deserts more arid, this effect is good for temperate and arctic zones: "biocrusts in cold climates, that is, in polar settings or during winter months when activity is limited by temperature, the warming can be expected to be largely beneficial to biological entities."

About 41 percent of the earth's surface is arid, and this is where biocrusts figure prominently. By producing this sunscreen molecule, bacteria protect the soil from harmful radiation while simultaneously raising the temperature in cold arid lands to promote the growth of complex plants in ecological succession -- all this while stabilizing the soil, reducing erosion and fixing nitrogen that higher plants need. It's another case that has just come to light of global benefit from the world's smallest organisms.

For these reasons, microbial effects on land surface albedo may have global scale repercussions historically and in the present, and should be evaluated in models of planetary radiation budgets as a new twist of biosphere-climate feedback interactions. This may shed some light into the apparent inconsistency in temperature changes recorded in arid lands. Contrary to model predictions, temperature has been shown to increase when removing vegetation there, an apparent paradox that could potentially be explained by biocrust colonization. Based on estimates of the global biomass of cyanobacteria in soil biocrusts, one can easily calculate that there must currently exist about 15 million metric tons of scytonemin at work, warming soil surfaces worldwide.

Big Animals Help Earth's Habitability, Too

From orbit, a bear would appear as small as a microbe. Current Biology published another indication that all living things, even the big ones, have a stake in keeping the earth habitable. In "Megafauna move nutrients uphill," Michael Gross points to research about whales, salmon, birds and bears that reveal large animals' roles in moving phosphorus and nitrogenous compounds from the deep ocean to the mountains. These "ecosystem engineers" perform an "important ecosystem service" by distributing nutrients to higher elevations.

Given the laws of gravity and the hydrological cycle, there is a strong likelihood that nutrients available on land, even though they may go through many cycles around the food web, will eventually be washed out to the sea. In the oceans, there is the risk that they will drop out of the photic zone and reach the sea floor, where they will be buried in sediment that may only be returned to circulation on geological timescales, some tens or hundreds of millions of years later.

Animals can make important contributions to stem this flow, as was first reported for whales back in 2010 (Curr. Biol. (2010) 20, R541). Researchers studying the ecology of sperm whales found that they harvest nutrients such as iron from great depths (often more than 1,000 metres), where they hunt cephalopods, but release them when they defecate near the surface.

The nutrients are incorporated into microbes, plankton, and fish that become prey for birds and mammals. These larger animals, in turn, transport the nutrients up rivers and mountains. Although Michael Gross focuses on how humans are disrupting this natural system, one can only stand in awe of how the living web distributes the very atoms and molecules needed for complex life around the globe.

Tiny Creatures, Major Roles

It takes more than a rocky planet in a habitable zone to sustain life. Some twenty factors are listed in the film The Privileged Planet relating to geology, the atmosphere, the magnetic field, and other abiotic phenomena. We've seen that that life itself maintains the habitability of the earth in surprising ways. By means of coded instructions in their genomes, the tiniest of creatures play major roles in maintaining the essential cycles of the planet: the hydrologic cycle, nitrogen cycle, oxygen cycle, carbon cycle, and more.


Evolutionists may weave stories about how these remarkable interactions arose gradually as life emerged and progressed. The instances above, though, should call into question whether any life could have subsisted on a bare earth without at least some of these processes already in operation. When these observations are combined with the other evidences of fine-tuning in the earth, the laws of physics, and the universe, the inference to design seems irresistible.

Is it time to give Darwin the pink slip.

On Darwin Day, Darwinism Is Well Past Its "Sell By" Date:
Michael Denton February 12, 2016 2:04 AM 



Today is Darwin Day, marking the birthday of Charles Darwin, who is celebrated around the world as a secular saint. Everywhere there will be eulogies to neo-Darwinism as a philosophy, touting the support it provides to the mechanistic worldview and the notion that life is an artifact of time and chance. Darwinism in that sense, almost akin to a faith, is indeed going strong.

Yet Darwinism as a scientific theory remains, as it always has been, a highly speculative evolutionary model. My new book,  Evolution: Still a Theory in Crisis, makes that clear. I document in detail old ideas and new research that come together to severely undermine classic Darwinism and point to a new non-Darwinian paradigm for biology in the 21st century.


As the book shows, key features of the biological realm flatly contradict the Darwinian mechanism of natural selection and the notion that all features of living things are or were in some ancestral form adaptive. My new book is a sequel to my 1985 work, Evolution: A Theory in Crisis , and it shows how the crisis has deepened over the past three decades.To understand the core weakness of the Darwinian worldview, it is important to understand what Darwinian natural selection requires. The process will work its magic, building up functional structures in organisms, only when two very strict conditions are met: First, the structure must be adaptive -- that is, helpful to the organism in flourishing in its environment -- and second, there must be a continuum of structures, functional all along the way, leading from an ancestor species to the descendent.

That is, the thing we are trying to explain must in some way help the creature survive, and between the creature and the creature's ancestor there must be a gradual change, each step of which is stable and enhances fitness, or success in reproduction.

Problem number one is that there are a great number of complex structures in nature that are not led up to by known functional pathways, and imagining what these pathways might have been is in most cases very hard. But this challenge is greatly compounded by an additional problem: that in many cases complex structures convey not the slightest evidence that they ever performed an adaptive function in putative ancestral forms. This may come as a surprise to the student of evolution. The trade language of biology has focused on the concepts of adaptation, fitness, and utility for so long that it has in a sense blinded us to the universe of apparently non-adaptive order that permeates the entire organic realm.

For example, what is the adaptive fitness of the shape of a maple leaf? Or the shape of any leaf, for that matter? Nor are examples of seemingly non-adaptive order limited to the shapes of leaves. Some of the best examples are embedded deep within the biological world -- among the characteristics that define and separate the basic kinds or types of plants and animals from each other.

Consider the pentadactyl (five-finger) design of the tetrapod limb, witnessed in the human arm and leg: one bone (the humerus in the upper arm, the femur in the upper leg), two bones (the radius and ulna in your lower arm, the tibia and fibula in the lower leg ), five fingers and five toes. This unique design occurs in the fore and hind limbs of all tetrapod (four-limbed) vertebrates, including human beings.

It is clear that in all tetrapod limbs the same basic design has been adapted to very different uses. However, given that the adaptive forms of the fore and hind limbs differ to some degree in every known tetrapod, it is very difficult to explain how the underlying pattern could have been arrived at so as to serve some adaptive end in a hypothetical fore and hind limb of an ancestral tetrapod. The Darwinian explanation, attributing the underlying structure to previous rounds of natural selection, is self-evidently ad hoc.

If we can't explain what specific adaptive function the pentadactyl design serves in any known extant or extinct species of tetrapod, there are no grounds for the Darwinian claim that there was some hypothetical species in some hypothetical environment where this unique design did serve some mysteriously obscure adaptive function in both limbs. In this case, even "just so stories" can't legitimate the Darwinian account.

The challenge to the Darwinian framework is not restricted to the tetrapod limb, but applies almost universally to a veritable universe of other novel structures -- the insect body plan, the concentric whorl pattern underlying all flowers, and the enucleated red blood cell found in all mammals, which was the subject of my own doctoral work at King's College in London.

Contributing further to the challenge inherent in so much non-adaptive order are revelations from the new field of evolutionary developmental biology (evo-devo). We now know that the paths of evolution have been highly constrained by a set of universally conserved developmental genetic mechanisms that transcend any immediate adaptive utility. Moreover, evo-devo implies that in the case of many novelties, internal constraints have played a decisive role in evolutionary origins.

In my new book, I detail vast quantities of evidence from the most up-to-date scientific literature, all supporting the radical idea that Darwinism played a very minor role in the history of life, and that evolutionary biology in the 21st century will have to seek an entirely new causal framework.

Darwinists will of course continue to insist that classic Darwinism can provide a completely plausible explanation of all evolutionary phenomena. But the reality is that Darwin's theory is well past its "sell by" date. By Darwin Day next year, we can confidently predict the situation will appear no less dire, and likely even more so.

Editor's note: Get your copy of Evolution: Still a Theory in Crisis now. For a limited time, you'll enjoy a 30 percent discount at CreateSpace   by using the discount code QBDHMYJH. 

Another failed Darwinian prediction VII

The pentadactyl pattern and common descent:

The pentadactyl structure—five digits (four fingers and a thumb for humans) at the end of the limb structure—is one of the most celebrated proof texts for evolution. The pentadactyl structure is found throughout the tetrapods and its uses include flying, grasping, climbing and crawling. Such diverse activities, evolutionists reason, should require diverse limbs. There seems to be no reason why all should need a five digit limb. Why not three digits for some, eight for others, 13 for some others, and so forth? And yet they all are endowed with five digits. As Darwin explained, “What can be more curious than that the hand of a man, formed for grasping, that of a mole for digging, the leg of the horse, the paddle of the porpoise, and the wing of the bat, should all be constructed on the same pattern, and should include similar bones, in the same relative positions?” (Darwin, 382)

Such a suboptimal design must be an artefact of common descent—a suboptimal design that was handed down from a common ancestor rather than specifically designed for each species. And the common descent pattern formed by this structure is often claimed as strong evidence for evolution. (Berra, 21; Campbell et. al., 509; Futuyma, 47; Johnson and Losos, 298;  Johnson and Raven, 286; Mayr, 26) One text calls it a “classic example” of evolutionary evidence. (Ridley, 45)

But this prediction is now known to be false as the digit structure in the tetrapods does not conform to the common descent pattern. In fact, appendages have various digit structures and they are distributed across the species in various ways. This is found both in extant species and in the fossil record. As evolutionist Stephen Jay Gould explained, “The conclusion seems inescapable, and an old ‘certainty’ must be starkly reversed.” (Gould)

This means that evolutionists cannot model the observed structures and pattern of distribution merely as a consequence of common descent. Instead, a complicated evolutionary history is required (Brown) where the pentadactyl structure re-evolves in different lineages, and appendages evolve, are lost, and then evolve again. And as one recent study concluded, “Our phylogenetic results support independent instances of complete limb loss as well as multiple instances of digit and external ear opening loss and re-acquisition. Even more striking, we find strong statistical support for the re-acquisition of a pentadactyl body form from a digit-reduced ancestor. … The results of our study join a nascent body of literature showing strong statistical support for character loss, followed by evolutionary re-acquisition of complex structures associated with a generalized pentadactyl body form.” (Siler and Brown)

References

Berra, Tim. 1990. Evolution and the Myth of Creationism. Stanford: Stanford University Press.

Brown, R., et. al. 2012. “Species delimitation and digit number in a North African skink.” Ecology and Evolution 2:2962-73.

Campbell, Neil, et. al. 2011. Biology. 5th ed. San Francisco: Pearson.

Darwin, Charles. 1872. The Origin of Species. 6th ed. London: John Murray.
http://darwin-online.org.uk/content/frameset?itemID=F391&viewtype=text&pageseq=1

Futuyma, Douglas. 1982. Science on Trial: The Case for Evolution. New York: Pantheon Books.

Gould, Steven Jay. 1991. “Eight (or Fewer) Little Piggies.” Natural History 100:22-29.

Johnson, G., J. Losos. 2008. The Living World. 5th ed. New York: McGraw-Hill.

Johnson, G., P. Raven. 2004. Biology. New York: Holt, Rinehart and Winston.

Mayr, Ernst. 2001. What Evolution Is. New York: Basic Books.

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

Siler C., R. Brown. 2011. “Evidence for repeated acquisition and loss of complex body-form characters in an insular clade of Southeast Asian semi-fossorial skinks.” Evolution 65:2641-2663.