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Sunday, August 21, 2011

Is the concept of abiogenesis actually scientific? Is there any substance to it? Plus, more bad news for Darwinism...

As usual, Creation-Evolution headlines keep their fingers on the pulse of the scientific community and does a good job of separating the wheat of evidence from the chaff of propaganda:

Origin of Life Made Easy

Posted on August 13, 2011 in Origins, Origin of Life, Darwin and Evolution, Issues, Philosophy of Science, Awards, Dumb Ideas

As anyone knows who has been given directions and told “you can’t miss it,” sounding easy and being easy can be entirely different things.  Reporters sometimes make the most difficult step in evolution – the origin of life – look like a cinch through the use of suggestive metaphors, like the commonly-invoked phrase, “building blocks of life.”  The directions in their articles usually lead to dead ends at worst, or, at best, baby steps on a long march, most of the route TBD, a TLA (three letter acronym) meaning “to be determined.”

Tool kit:  This metaphor was presented by PhysOrg in an article entitled, “Meteorites: Tool kits for creating life on Earth.”  The main idea was that nucleobases could have been formed in meteorites and come to earth special delivery.  (Science Daily and New Scientist identified these nucleobases as adenine and guanine.)  “The earliest forms of life on Earth may have been assembled from materials delivered to Earth by meteorites,” PhysOrg said.  Jim Cleaves (Carnegie Geophysical Laboratory) added, “This shows us that meteorites may have been molecular tool kits, which provided the essential building blocks for life on Earth.”

Plausible precursor:  This metaphor was offered by Science Daily, “Study Builds On Plausible Scenario for Origin of Life On Earth.”  The study, conducted at Scripps, attempted to find precursors to RNA.  The article repeatedly spoke of RNA precursors, not RNA itself, which depends on the difficult-to-synthesize sugar ribose (“Did borax evolve into 20-mule teams?”, 01/09/2004).  What these precursors are was not identified, but the very word precursor uses the power of suggestion to invoke images of progress.

Evolutionary force driving simple to complex:  “Is this how simple life got complicated?” an article PhysOrg teased.  Within the article, Andrew Murray invoked the image of an “evolutionary force” that led single cells to leap to multicellular life forms.  But what he studied was how living yeast cells seem to do better in clumps than individually.  Yeast cells already have the cellular machinery that challenges theories of the origin of life.

These analogies vastly oversimplify what goes on in living cells.  For instance, this article on Science Daily used the word machine and machinery 16 times, describing how DNA is acted on by protein machines that provide quality control during cell division.  Without cell division, evolution cannot act, because it needs to naturally select copies, or offspring.

Dr. Robert Shapiro knows that a living cell is anything but simple.  He has said that the leap from simple molecules to a cell is greater than the distance between a bacterium and an elephant (cited on  In Nature last week (August 4),1 he reviewed David Deamer’s new book First Life: Discovering the Connections between Stars, Cells, and How Life Began (University of California Press, 2011).  Shapiro criticized Deamer’s hypothesis that life began in droplets surrounded by fatty acids.  In fact, all simplistic scenarios overlook the complexity of life as we know it:

Today, the simplest living cells depend on molecules that are far more intricate than those that have been isolated from sources unrelated to life (abiotic), such as meteorites. The most noteworthy chemical substances in life are functioning polymers — large molecules made of smaller units called monomers, connected in a specific order. The nucleic acids RNA and DNA, carriers of genetic information and heredity, are made of connected nucleotide monomers. Similarly, proteins are vital polymer catalysts that are made by combining monomer amino acids. Such modern biological constructions were unlikely to have been present on the early Earth.

As an example, Shapiro noted that the RNA World hypothesis, while elegantly simple, is “staggeringly improbable.”  It is doubtful he would be impressed by the presence of nucleobases in a meteorite:

Nucleotides, for example, are not encountered in nature beyond organisms or laboratory synthesis. To construct RNA, high concentrations of four select nucleotides would be needed in the same location, with others being excluded. If this is the prerequisite for life, then it is an unusual phenomenon, rare in the Universe.

Deamer’s dream of a fatty vesicle as a container for the RNA world, Shapiro continued, fails for the same reason: “Unfortunately, his theory retains the improbable generation of self-replicating polymers such as RNA.”  In fact, Shapiro added, “Deamer’s insight deflates the synthetic proofs put forward in numerous papers supporting the RNA world.”  Using that unfortunate word Unfortunately once again, though, he undermined Deamer’s “insight” into spontaneous vesicle formation as essentially useless:

Unfortunately, the chemicals that he suggests for inclusion are drawn from modern biology, not from ancient geochemistry. We should let nature inform us, rather than pasting our ideas onto her.

Incidentally, Nature News said that the scientific community has largely dismissed last year’s claim that arsenic-based life was possible (see “Arsenic and Old Lake,” 12/02/2010).  Rosie Redfield (U of British Columbia) is trying to replicate the experiment by Felisa Wolfe-Simon, even though it is almost “guaranteed to fail,” according to Erika Check Hayden.  Her article, though, focused more on how blog reporting of attempts to replicate controversial experiments is changing the face of peer review.  Said Jonathan Eisen (U of California), “This is a great case study for open science, because it raises issues about peer review, it raises issues about sharing data and materials, and it raises issues about engaging the public and press more actively in science.”  The Facebook-Twitter age is opening doors of science labs, where both good and bad can be seen in near real time.

1. Robert Shapiro, “Astrobiology: Life’s beginnings,” Nature 476 (04 August 2011), pages 30–31, doi:10.1038/476030a.

David Klinghoffer has a better metaphor for these origin-of-life stories.  Saying that molecular “building blocks of life” can form naturally is like explaining Bach’s music by saying natural sources for the ink are readily available (see Evolution News). 

One of the best recent collections of quotes on how “staggeringly improbable” the origin of life is, as understood by workers in the field, can be found in Rabbi Moshe Averick’s book Nonsense of a High Order: The Confused and Illusory World of the Atheist (Tradition and Reason Press, 2010).  In Part II, Averick quotes Shapiro and many other leaders in origin-of-life studies, making it abundantly clear from their own writings that evolutionists are completely clueless about how life started.  For instance, on pages 94-95, he quotes five leading astrobiologists admitting that the origin of life seems like a miracle.

Those quotes should be kept at hand when reading science news articles with their glittering generalities making it sound like the origin of life is easy as apple pie.  Evolutionists need to make apple pie without first assuming apples.  In fact, as Carl Sagan said in Cosmos, to really make an apple pie from scratch, you must begin by inventing the universe.  Good luck—when all you have to start with is nothing (08/09/2011).
If you never read the post; "A Review: Chemical barriers to life, no natural sources for life and information and powerful evidence for design." then you might want to go catch up?

The remarkably bad news for Darwinists just keeps on coming.  Further research within the cell reveals more usual.

Your Rotary Engines Are Arranged in Factories

Posted on August 17, 2011 in Microbiology, Cell Biology, Origins, Darwin and Evolution, Intelligent Design, Awards, Amazing Facts

As if ATP synthase was not amazing enough, a team of scientists in Germany now tells us they are arranged in rows with other equipment to optimize performance.  From electron micrographs of intact mitochondria, they were able to detect the rotary engines of ATP synthase and other parts of the respiratory chain.  Their diagram in an open-source paper in PNAS looks for all the world like a factory.

CEH has reported on ATP synthase many times (for concise explanation with animation, see CMI).  Your body, and every other living thing on earth, depends on a steady supply of the ATP “energy pellets” they synthesize.  The two-part rotary engines rely on a constant flow of protons (proton motive force, or pmf).  These protons are produced by other engines, Complex I (NADH dehydrogenase; for structure of this piston engine, see 07/06/2010), Complex III (cytochrome c reductase), and Complex IV (cytochrome c oxidase), through a series of mechanical and chemical reactions.  The protons enter ATP synthase through its bottom structure, called F0, which is embedded in the mitochondrial membrane, causing it to rotate (the authors said it “works like a proton-driven turbine”).  A stator and central stalk transfer the energy to the top part, F1, where three catalytic centers, arranged like orange slices, take in ADP and phosphate to create ATP – molecules with stored energy that travel throughout the cell to power almost everything.

Each of these molecular machines are wonders of design efficiency in themselves. The new paper by Davies et al. augments that wonder by showing how they are all arranged for maximum performance.1  In order to save words, we are attaching their diagram (Figure 5) from the open-source paper; readers are encouraged to go to the source provided for caption and details.1  The proton-pumping machines (green) are arranged along folds of the cristae (blue) so that the protons don’t wander away from the ATP synthase machines (yellow).  Since Complexes I, III, and IV act as proton “sources” and ATP synthase as proton “sinks”, a flow is set up toward the tight folds where the ATP synthase (yellow) are located.

Davies et al, PNAS doi: 10.1073/pnas.1103621108

In addition, the ATP synthase engines are so arranged in pairs (dimers), their F0 parts almost touching, their F1 parts separated, by angles ranging from 40° to 70° depending on the species.  These dimers are then arranged in long rows like one might see in a hydroelectric plant.  In this way, the flow of protons is channeled exactly where it is needed for optimal performance of the turbines.  Concerning this “striking arrangement,” the authors said, “We propose that the supramolecular organization of respiratory chain complexes as proton sources and ATP synthase rows as proton sinks in the mitochondrial cristae ensures optimal conditions for efficient ATP synthesis.

The authors had virtually nothing to say about how this might have evolved, noting only that the structure is “conserved during evolution” in every sample they examined (3 species of fungi including yeast, potato, and mammal).  What this means is a lack of evolution over nearly two billion years, in the standard evolutionary timeline.  Furthermore, it is apparent that evolutionary theory contributed little or nothing to their investigation.  It was really a study of how these structures are optimized for function: “The mutual arrangement of electron transfer complexes as proton sources and ATP synthase complexes as proton sinks in the membrane is therefore of fundamental interest and importance for understanding mitochondrial energy conversion.”  They used the word optimal three times in the paper.

1. Davies et al., “Macromolecular organization of ATP synthase and complex I in whole mitochondria,” Proceedings of the National Academy of Sciences, published online before print August 11, 2011, doi: 10.1073/pnas.1103621108.

We have to just keep piling it on till people get it and vote Darwin out of office as Science Czar.  In terms of understanding designs in nature like this, are you better off than you were 150 years ago?

Oh, and one more thing. That sequential fossil record? Funny how a lot of creatures who disappeared from the fossil record suddenly show up now. If the fosssil record was a record of long ages and continual extinctions and evoloutionary steps, how do you explain Lazarus Taxa?

Frilled Shark

Living Fossils Rise from the Dead

Posted on August 20, 2011 in Biology, Terrestrial Zoology, Marine Biology, Fossils, Origins, Darwin and Evolution, Awards, Dumb Ideas

The oxymoron “living fossil” is suggestive.  Seeing a plant or animal come to life, when it was only known from fossils, might seem miraculous.  Perhaps, though, the phrase was invented to rescue Darwinian theory from the vast ages it requires.  Is it credible to believe the time gaps?  Here are two recent stories about creatures long thought dead, only to be found doing “Quite well, thank you.”

Tick talk.  Researchers in South Africa were sure that the living fossil they found represented an “evolutionary missing link” that might help explain relationships between several lineages of arthropods that “evolved” the blood feeding trait independently.  This led to queer sentences like this in their PLoS One paper.1  “Thus, even though blood-feeding evolved in the ancestral tick lineage, the adaptation to the mammalian and avian blood-feeding interfaces occurred independently in the soft and hard tick families.”  It also seems weird for the ancestor of diverse lineages of ticks to be doing just fine in a living form, with no evolutionary change for many millions of years:

In conclusion, phylogenetic analysis indicates that N. namaqua groups basal to both tick families and is the closest extant lineage to the last common ancestral tick lineage. Its argasid-like feeding behaviour and biology provides compelling evidence for the evolution of a blood-feeding lifestyle within the last common ancestral tick lineage. The semi-arid nature of the Northern Cape as found in Namaqualand and the Karoo has been maintained since Permian times. The partiality of N. namaqua for xeric environments and small reptiles could therefore be an indication of a lifestyle maintained for more than 250 million years. This would truly make this tick species a living fossil.

Real eel:  Another living fossil announced recently is a “primitive” looking eel found swimming in a cave on Palau that PhysOrg said is squirming into the record books.  Why?  “A new species of eel found in the gloom of an undersea cave is a ‘living fossil’ astonishingly similar to the first eels that swam some 200 million years ago, biologists reported on Wednesday.” 

The BBC News included a short video clip of the slick-looking swimmer.  Going on about how “primitive” it looked (at first glance, it looks rather stylish), the article quoted the scientists giving their evaluation:  “In some features it is more primitive than recent eels, and in others, even more primitive than the oldest known fossil eels, suggesting that it represents a ‘living fossil’ without a known fossil record.”  This begs the question of why it survives intact to this day, unevolved.  Even worse, the article put forth an apparent contradiction:  “Their results suggest this new family has been evolving independently for the last 200m years, placing their origins in the early Mesozoic era, when dinosaurs were beginning their domination of the planet.”  If it has been evolving for 200 million years, why does it look primitive?  Why is it a living fossil?

“The term "living fossil" was coined by Charles Darwin in his book On the Origin of Species,” the article on PhysOrg informed its readers.  “It is used to describe species that have survived for millions of years, exploiting niches that are so stable that there is little pressure on them to evolve.”  Of course, to evolve is an active verb infinitive that cannot be applied to dumb eels, as if they had any choice in the matter, environmental pressure or not.  And if stable niches reduce the pressure on evolution, it would be surprising that anything in the ocean, one of the first stable habitats on earth, ever evolved as Darwinians claim they did.

1. Mans, de Klerk, Pienaar, and Latif, “Nuttalliella namaqua: A Living Fossil and Closest Relative to the Ancestral Tick Lineage: Implications for the Evolution of Blood-Feeding in Ticks,” Public Library of Science One, 6(8): e23675. doi:10.1371/journal.pone.0023675.

Stop letting Darwinists get away with these word games.  If their theory explains extreme diversification alongside extreme stasis, then it is explaining opposite things with equal ease.  Therefore, “living fossil” explains nothing.  As an oxymoron, it is all moron and no oxy.

The evidence only makes sense without the millions of years.  The living creatures resemble the fossil creatures because they are not separated by vast swaths of mythical time, but came from a created world with much more diversity than our impoverished remnant.  Close the time gap.  (This gives “Darwin-of-the-gaps” a new twist.)


Below is a partial list of Lazarus Taxa discovered up to about 2008:

Coelacanth (1938)
Takahe (1948)
Bermuda petrel (1951)
Monoplacophora (1952)
Mountain pygmy possum (1966)
New Holland mouse (1967)
Long-legged warbler (1974)
Chacoan peccary (1975)
Gray's monitor (1975)
Prionomyrmex macrops ant (1977)
Gold-fronted bowerbird (1981)
Berlepsch's Parotia (1985)
Jerdon's courser (1986)
Mahogany glider (1989)
Night parrot (1990)
Woolly flying squirrel (1990)
São Tomé Grosbeak (1991)
Cebu flowerpecker (1992)
Madagascar serpent-eagle (1993)
Arakan forest turtle (1994)
Gilbert's poteroo (1994)
Laotian rock rat (1996)
New Zealand longhorn beetle (1996)
Forest owlet (1997)
Edward's pheasant (1998)
Tammar wallaby (1998)
Fernandina rice rat (1999)
La Gomera giant lizard (1999)
Madeiran land snail (1999)
Telmatobufo venustus frog (1999)
Bavarian pine vole (2000)
Philippine bare-backed fruit bat (2000)
Lord Howe Island stick bug (2001)
Cone-billed tanager (2003)
Cuban solenodon (2003)
New Zealand storm petrel (2003)
Terror skink (2003)
Burchell's zebra (2004)
Canterbury knobbed weevil (2004)
Gracilidris dolichoderine ant (2006)
Giant palouse earthworm (2006)

Above: The okapi, officially recognized as a species in 1901 after being considered for years to be an imaginary animal, known as the "African unicorn."

Kaempfer's woodpecker (2006)
Large-billed reed warbler (2006)
Madagascar pochard (2006)
Painted frog (2006)
Isthmohyla rivularis frog (2007)
La Palma giant lizard (2007)
frog (2008)
Banggai crow (2008)

Here is a list of organisms that may never have been "lost" but rather remain structurally unchanged from their fossil forms:


Living fossils

A potential problem for those who think that the Earth is millions of years old! If you assume that evolution is operating and natural selection is at work then it must be a difficulty that quite a few creatures and plants are exactly the same now as their fossils.


Araucaria araucana the Monkey Puzzle tree
Ginkgo tree (Nasikabatrachus sahyadrensis)
Horsetails Equisetum (Equisetaceae)
Metasequoia Dawn Redwood (Cupressaceae)
Sciadopitys tree (Sciadopityaceae)
Whisk ferns Psilotum (Psilotaceae)
Welwitschia (Welwitschiaceae)
Wollemia tree (Araucariaceae)


Aardvark (Orycteropus afer)
Cypriot mouse (Mus cypriacus)
Red Panda (Ailurus fulgens)
Okapi (Okapia johnstoni)
Koala (Phascolarctos cinereus)
Laotian Rock Rat (Laonastes aenigmamus)
Volcano rabbit (Romerolagus diazi)
Amami rabbit (Pentalagus furnessi)
Iriomote cat (Prionailurus iriomotensis)
Monito del Monte (Dromiciops gliroides)
monotremes (the platypus and echidna)
Mountain Beaver (Aplodontia rufa)
Acanthisittidae (New Zealand "wrens")
Hoatzin(Ophisthocomus hoazin)
Broad-billed Sapayoa (Sapayoa aenigma)
Bearded Reedling (Panurus biarmicus)
Coliiformes (mousebirds, 6 living species in 2 genera)
Magpie-goose (Anseranas semipalmata)


Pig-nosed turtle
Crocodilia (crocodiles, gavials and alligators)
Tuatara (Sphenodon punctatus and Sphenodon guntheri)


Purple frog (Nasikabatrachus sahyadrensis)
Bony fish
Bowfin (Amia calva)
Coelacanth (the lobed-finned Latimeria menadoensis and Latimeria chalumnae)
Queensland lungfish (Neoceratodus fosteri)
Sturgeons and paddlefish (Acipenseriformes)


Frilled shark (Chlamydoselachus anguineus)


Mantophasmatodea (gladiators; a few living species)
Mymarommatid wasps (10 living species in genus Palaeomymar)
Nevrorthidae (3 species-poor genera)
Notiothauma reedi (a scorpionfly relative)
Orussidae (parasitic wood wasps; about 70 living species in 16 genera)
Peloridiidae (peloridiid bugs; fewer than 30 living species in 13 genera)
Sikhotealinia zhiltzovae (a jurodid beetle)
Syntexis libocedrii (Anaxyelidae cedar wood wasp)


glypheoid lobsters (3 living species: Neoglyphea inopinata, N. neocaledonica, and Laurentaeglyphea neocaledonica)
Stomatopods (Mantis shrimp)
Triops cancriformis (also known as Tadpole shrimp) (a notostracid crustacean)
Nautilina (e.g. Nautilus pompilius)
Neopilina galateae, a monoplacophorid mollusc
Ennucula superba (Nut clam)

Other invertebrates

Horseshoe crab (only 4 living species of the class Xiphosura, family Limulidae: Limulus polyphemus,Tachypleus gigas, Tachypleus tridentatus and Carcinoscorpius rotundicauda)
Lingula anatina (an inarticulate brachiopod)
Valdiviathyris quenstedti (a craniforman brachiopod)

Excerpt from CreationRevolution:

Cyanobacteria or Blue-green Algae
One of my favorite examples of living fossils is blue-green algae also known as cyanobacteria. According to evolutionists cyanobacteria are one of the oldest living organisms on the earth. If they are as old as evolutionists believe them to be (some as old as 3.5 billion years), you would expect that they would have evolved and changed so much that there wouldn’t be any living today that would anything like those living today. Take a close look at the photos below of cyanobacteria fossils compared to the same ones living today.

Pictures labeled A, C and E are from rocks in the former Soviet Union, showing micro fossils of bacteria. Picture A is approximately 950 million years old, picture C has been dated to approximately 850 million years ago and picture F is the oldest specimen dating to approximately 1550 million years ago (1.55 billion years ago). The pictures labeled B, D and F are from cyanobacteria colonies found today in Mexico (stromatolites).

Evidence, evidence and more evidence.   Evidence that supports a Universe designed by a Creator God rather than a random series of miraculous mistakes.  Evidence that the fossil record is the result of one massive flood event and not millions and millions of gradual evolution.

Completely unrelated postscipt:  You may have noticed that Borepatch is often linked to posts that I make.   Borepatch is kind of a brain candy holiday for the brain in terms of random and interesting posting patterns.   From Borepatch I discovered Slow Wave and so here is one cartoon from that site: