Next to the witness stand for design;whales

More "Design of Life" Evidence: Whales

Evolution News & Views November 4, 2015 7:32 AM

Living Waters: Intelligent Design in the Oceans of the Earth shares amazing information about humpback whales: their enigmatic songs, their multiple adaptations for aquatic life that defy the evolutionary mechanism, and the "miraculous web" of blood vessels that refrigerates the male reproductive organs to safe levels for sperm production. All of it defies explanations based on natural selection. But that's just the beginning when it comes to the largest animals that have ever lived -- larger even than the largest dinosaurs (see Brian Switek's discussion onSlate). Want to see humpback songs as sheet music? The Smithsonianhas printouts and recordings.

More About the Male Refrigeration System

The system actually works better when the whale swims hard. How can that be, when the testes are located right between the abdominal swimming muscles? It's like trying to keep a refrigerator cold between two furnaces.

It works because the blood pumps harder during exercise, allowing more heat to escape into the water through the dorsal fin and tail. The higher volume of cool venous blood then enters the "miraculous web" (Latin rete mirabile, read more here) between the abdominal muscles, where the heat from the arteries is transferred to the cooler veins before entering the testes. It's a marvelous solution: a "counter-current heat exchanger" (CCHE) mechanism.

As Richard Sternberg and Paul Nelson explain in the film, without both internal testes and the refrigeration mechanism existing simultaneously, natural selection would halt, and whales would have gone extinct. Females, too, have a CCHE to protect the young during pregnancy. Similar CCHE systems are found in other marine mammals such as manatees and seals, providing more unlikely examples of "convergent evolution."

Conserving Energy

Blue whales are the largest whales, making them the largest animals on earth. How do they sustain their massive weight? An article from NOAA Fisheries says that they target the highest-quality prey in order to maximize energy gain.

These huge animals can span a basketball court and weigh as much as 25 large elephants combined, the article says. But they feed on tiny fish called krill that are less than an inch long. When prey is scarce, blue whales conserve oxygen for deep dives. When the fish are plentiful, they ram through the schools at high speed, a strategy called lunge-feeding. They have their ROI (return on investment) all figured out. By watching tagged blue whales off the California coast, Elliott Hazen and a NOAA research team were able to figure out their optimization strategy.

"The magic number for krill seems to be about 100 to 200 individuals in a cubic meter of water," Hazen said. "If it's below that range, blue whales use a strategy to conserve oxygen and feed less frequently. If it's above that, they'll feed at very high rates and invest more effort."

Long-Distance Travelers

Whales have an incredible capacity for long-distance migration. A pygmy blue whale set a new record. Science reports that a female named Isabela that had been photographed at the Galapagos Islands was seen eight years later off the coast of Chile, having traveled 5,200 kilometers, "the longest recorded latitudinal migration made by any Southern Hemisphere blue whale on record." Most likely this is an annual trip the whales make, over 3,200 miles one-way.

Humpback whales are long-distance migrators too. The Australians have "a cause for celebration" now that conservation efforts have led to a remarkable rebound in their numbers down under, Science Daily said.

Captain Dave Anderson, featured in the Illustra film, often sees humpbacks off Dana Point, California, that have traveled south from Alaska, where they had delighted viewers on cruise ships. PhysOrgreports the first sighting of a humpback near Hawaii on September 29, over a month earlier than normal. About 10,000 humpbacks winter in the oceans around Hawaii, usually November through May. That's where Anderson got that beautiful drone shot of a humpback with her calf.

Lucky Shot

You may recall the dramatic slow-motion scene in Living Waters of a humpback breaching the surface, rising high above the water and landing on its back with a mighty splash. Lad Allen and Jerry Harned got lucky on that shot. They were filming off the coast of Monterey with their Red Epic high-speed camera, looking for whales. But where are you going to point the camera, when they could be anywhere around the 360-degree horizon?arned pointed it out over the featureless water, turned on the pre-roll (a kind of camera memory) hopefully. As if on cue, the whale shot up right in the center of the field. Jerry hurriedly switched on the record button and got the whole sequence in high-definition slow motion -- a shot that still gives him chills when he thinks about it. As Paul Nelson said, "the language fails" when you see such wonders.

The Planet Needs Whales

Whales play a vital role in the global nutrient cycle. The Proceedings of the National Academy of Sciences published a special issue in October about large mammals. One of the papers discussed "Global nutrient transport in a world of giants," describing the oversized role that whales play in spreading nitrogen around for other ecological communities:

Despite their vastly decreased numbers, the important role of whales in distributing nutrients is just now coming to light.Whales transport nutrients laterally, in moving between feeding and breeding areas, and vertically, by transporting nutrients from nutrient-rich deep waters to surface waters via fecal plumes and urine. Studies in the Gulf of Maine show that cetaceans and other marine mammals deliver large amounts of N to the photic zone by feeding at or below the thermocline and then excreting urea and metabolic fecal N near the surface. [Emphasis added.]

The scientists estimate that whales transport almost four times as much nitrogen as terrestrial animals do. They also transport phosphorus and iron.

"Because of their enormous size and high mobility (and despite having many fewer species), great whales might have once transported nutrients away from concentration gradients more efficiently than terrestrial mammals," the writers say. These nutrients are also "assimilated more rapidly, and contribute to system productivity more directly than on land."

One of the diagrams in the paper, reproduced by Science Daily, shows the dependency of land animals on this nutrient cycle. Seabirds and "anadromous fish" like salmon carry these nutrients up rivers, where land animals like bears feed on the fish, profiting from the nutrients that whales had brought up from the deep ocean.

The authors even think that whales play a role in carbon dioxide levels that can affect the planet's climate. They estimate that whale populations have been reduced by 90 percent from levels before the Moby Dick whaling days -- raising alarms about ecological damage to planetary ecosystems. This interconnectedness of life raises fresh impetus to preserve these magnificent creatures.

A paper in Nature Communications reports something interesting about whale guts. Baleen whales have microbiomes with similarities to land animals, including humans. This is likely because, although they feed exclusively on marine animals, they have to digest chitin -- a polysaccharide from arthropod exoskeletons that is somewhat similar to the cellulose in plants that cows eat.

Like land herbivores, whales also have a foregut that helps pre-digest the polysaccharides. Since there are similarities and differences in the gut microbiomes, though, it's not clear they successfully tied the findings to the old tale of whale evolution from a four-footed land animal.

"Mammals host gut microbiomes of immense physiological consequence, but the determinants of diversity in these communities remain poorly understood," the paper begins sheepishly. "Diet appearsto be the dominant factor, but host phylogeny also seems to be an important, if unpredictable, correlate."

Sternberg explains in the film how the whale-evolution Captain Dave Anderson has taken an active role in rescuing whales. A thousand whales and dolphins a day, he says, die from being trapped in fishing nets. His Dolphin Safari website tells the story of Lily the gray whale, whose rescue made TV news and inspired an award-winning book Anderson wrote to raise awareness of the plight of marine mammals caught in nets.

Recently, he has been developing a low-cost floating beacon that whale watchers can fasten to nets that whales are dragging along with them. This allows rescuers to find the whale again and cut it free, using a special pole with V-shaped knife that allows the rescuer to cut off the net off without harming the animal.

Sadly, whales and dolphins are also threatened by a growing problem: plastic trash. PhysOrg show a picture of a dead sperm whale on a beach on Taiwan that was found to have plastic bags and fishing nets in its stomach. This may be one cause of the mysterious beachings of whales you hear about from time to time.

Anderson tells about how mylar balloons, let loose by thoughtless partygoers, often wind up in the ocean. Deflated and floating on the surface, they are mistaken for jellyfish, part of the whale's diet, and can lead to death when ingested. We all need to realize that trash washed down our storm drains can threaten the most magnificent animals on earth.

But let's end on a happy note. The drones that gave the Illustra team such spectacular aerial photographs of whales and dolphins are proving useful for science. NOAA Fisheries reports that hubcap-sized hexacopter drones are now being used to study gray whales from above. Like humpbacks, gray whales have made a remarkable comeback since 1994 when restrictions on whaling were imposed. With these new aerial monitoring tools, scientists hope to spread this success story to other species that are still endangered.

"Hopefully in the not-too-distant future," a NOAA marine biologist says, "there will be many healthy populations of large whales to study." With that, the beauty of their intelligent design will also be preserved for posterity.sequence is more "artistic license" than demonstrable fact.Captain Dave Anderson has taken an active role in rescuing whales. A thousand whales and dolphins a day, he says, die from being trapped in fishing nets. His Dolphin Safari website tells the story of Lily the gray whale, whose rescue made TV news and inspired an award-winning book Anderson wrote to raise awareness of the plight of marine mammals caught in nets.

Recently, he has been developing a low-cost floating beacon that whale watchers can fasten to nets that whales are dragging along with them. This allows rescuers to find the whale again and cut it free, using a special pole with V-shaped knife that allows the rescuer to cut off the net off without harming the animal.

Sadly, whales and dolphins are also threatened by a growing problem: plastic trash. PhysOrg show a picture of a dead sperm whale on a beach on Taiwan that was found to have plastic bags and fishing nets in its stomach. This may be one cause of the mysterious beachings of whales you hear about from time to time.

Anderson tells about how mylar balloons, let loose by thoughtless partygoers, often wind up in the ocean. Deflated and floating on the surface, they are mistaken for jellyfish, part of the whale's diet, and can lead to death when ingested. We all need to realize that trash washed down our storm drains can threaten the most magnificent animals on earth.

But let's end on a happy note. The drones that gave the Illustra team such spectacular aerial photographs of whales and dolphins are proving useful for science. NOAA Fisheries reports that hubcap-sized hexacopter drones are now being used to study gray whales from above. Like humpbacks, gray whales have made a remarkable comeback since 1994 when restrictions on whaling were imposed. With these new aerial monitoring tools, scientists hope to spread this success story to other species that are still endangered.

"Hopefully in the not-too-distant future," a NOAA marine biologist says, "there will be many healthy populations of large whales to study." With that, the beauty of their intelligent design will also be preserved for posterity.

Is democracy past its prime?:Pros and cons.

The revolution rolls on

Michael Behe's Challenge -- Past, Present, and Future
Evolution News & Views

Twenty years after Darwin's Black Box, the irreducibly complex outboard motors showcased by Michael Behe still confound Darwinism. That's one theme of our upcoming documentary Revolutionary:  Revolutionary: Michael Behe & The Mystery of Molecular Machines, which heads to Texas next month for previews. Behe's challenge is the past, the present, and the future.

Look at this quote from a paper in the  Proceedings of the National Academy of Sciences:

The bacterial flagellar system has been an object of intense study for many years. It has helped to elucidate issues of assembly, motility, and chemotaxis at a molecular level in a relatively simple system, typically containing ∼40 different proteins. It has also been the icon for creationists in the United States who deny evolution. [Emphasis added.]
Ah, the bacterial flagellar system. The paper by scientists from Germany, the Netherlands, Israel, and the U.S. (University of Virginia) purports to show how a simpler flagellum in a species of archaea provides evidence for evolution of the more complex flagellum in bacteria. It's satisfying to reflect that the authors remain irritated by the "creationist" icon. They can't let it rest.

As expected, they refuse to cite Behe directly (or any other ID source), so their only references supporting the "creationist" charge are to 6-to-12-year-old writings by Kenneth Miller, Barbara Forrest, and E.H. Egelmann. Have it your way. What matters is the substance of Behe's argument and evidence, which attracted the attention of researchers in four nations.

Meanwhile, farther east -- particularly in Japan -- scientists don't seem quite so motivated to defend Darwin. Two new papers dealing with molecular motors show their openness to design thinking.

Cilium Mimicry

The first deals with designing a mimic of cilia, another one of Behe's examples of irreducibly complex (IC) systems. Five biomedical engineers from Tokyo, writing in Science Advances, succeeded in making "Artificial cilia as autonomous nanoactuators." They call this "Design of a gradient self-oscillating polymer brush with controlled unidirectional motion."

Here, we have prepared a polymer brush surface similar to a living cilium, exhibiting self-oscillating and unidirectional wave motion of the grafted polymer at the nanometer scale.... This study provides a new concept to design autonomous polymer brush surfaces effective in the nanometer scale as bioinspired dynamic soft materials.
They pay tribute to the design in cilia and other cellular machines that inspired their own work:

Spatiotemporally well-ordered mechanical actuation of biomacromolecules in the nanometer-order scale driven by chemical reactions, such as enzymatic reactions, plays an important role in living organisms. For example, motor proteins bind to a polarized cytoskeletal filaments and use the energy derived from repeated cycles of adenosine 5′-triphosphate hydrolysis to move steadily along them. In addition, many motor proteins carry membrane-enclosed organelles to their appropriate locations in the cell. Cytoskeletal motor proteins move unidirectionally along an oriented polymer track. In this process, they use chemical energy to propel themselves along a linear path, and the direction of sliding is dependent on the structural polarity of the track. Recently, the construction and design of these biomolecular motor systems with well-controlled unidirectional motion have become an area of great focus in advanced sciences.
The word "design" appears ten times in the paper. References to evolution are completely absent.

Another team worked on imitating the cilia in hair cells of the inner ear. Publishing in Nature's journal Scientific Reports, they proudly announce, "Here we present a novel, completely biomimetic flow sensor which attempts to replicate the intricate morphological organization and function of the hair bundles of the hair cells" found in zebrafish. Neither of the cheap imitations, however, contain anything like intraflagellar transport in biological cilia (see our report). As for the origin of these intricate structures, the team treated evolution as magic: "Nature's evolutionary path led to sensors of high functionality and robustness, in terms of material properties, anatomical architecture and energy expenditure." That's all the press Darwin got. They used the word design, though, 15 times.

Flagellum Focus

Back in the 1990s, Behe relied on relatively crude electron micrographs of flagella. Imagine twenty years ago if he had been able to see in detail one protein in the stator of the flagellum. That's what Japanese scientists from Nagoya University revealed with advanced imaging techniques. So has the case for design grown stronger or weaker since Darwin's Black Box was published? A paper in Nature's open-access journal Scientific Reports reveals the answer. You can see their composite image of the stator protein MotA here:



It looks more like a well-designed outboard motor than ever!

Many bacterial species use spiral propellers (flagella) attached to motors to move through a liquid environment. An interaction between the rotor and stator components of the motor generates the rotational force required for movement. The stator converts electrochemical energy into mechanical force after undergoing a structural change caused by a movement of charged particles (ions) through an internal channel. Previous studies investigated the stator and its interaction with the rotor by constructing mutant proteins and analyzing their functions. However, little was known about stator structure.
A team of Japanese researchers led by Homma's laboratory of Nagoya University have now purified the stator protein MotA from a bacterium found in hot springs (Aquifex aeolicus) and analyzed its three-dimensional structure using electron microscopy mainly in cooperation with Namba's laboratory of Osaka University.

The stator protein MotA shows an elegantly crafted channel for ions. These are arranged in groups of four at the base of the stator on the cytoplasmic side. Two slender molecules of MotB extend into the periplasm. Identifying the structure is an important step on the way to figuring out how the flagellum works.

The stator is one of the most important parts for the proper functioning of the bacterial flagellar motor, and is believed to work as an energy-converting unit that transduces electrochemical potential gradient across the cytoplasmic membrane into mechanical force. The interaction surfaces of the stator and the rotor have been well studied by mutational analyses. However, the mechanism governing energy conversion remains unknown because of the lack of structural information on the stator.
How is chemical energy converted into rotational energy (torque)? "It is believed that the ion influx through the channel induces a conformational change in the stator, allowing its interaction with the rotor to generate torque," they say.

A little reflection suggests that the components must be well matched. Imagine for a moment a flow of ping-pong balls trying to turn a large metal turbine. It wouldn't work. Somehow, in ways still to be determined two decades after Behe's book was published, tiny hydrogen ions or sodium ions are able to make particular parts of the stator undergo conformational changes that can get the rotor to turn. How that works is bound to be interesting. We know from the discussion in Unlocking the Mystery of Life that not only must the parts be well matched, they must be assembled in the right order, in the right amounts, at the right place and time -- all directed by instructions in the genetic code.

While these Japanese researchers do not mention Behe or his conclusions, their work underscores the case for irreducible complex molecular machines as prima facie evidence for intelligent design. Nowhere do they credit evolution for the motors of the cell:

Various motor proteins are essential for different biological activities such as cell locomotion, cell morphogenesis, metabolism, and material transport. Motor proteins convert various types of energy, such as ATP hydrolysis or electrochemical potential, into mechanical force for directional motion. Motor proteins are divided into two types: linear motors, such as myosin-actin and kinesin/dynein microtubule motors; and rotary motors, such as ATP synthase and bacterial flagellar motor.
Behe's intuitive first impression of the flagellum, "That's an outboard motor!" has stood the test of time. That's what the Japanese teams still call the cilium and the flagellum in 2016.

Scratching the Itch

Now back to the PNAS paper. Did the Western nations solve Michael Behe's challenge? If so, they have a strange way of claiming success:

The proteins that form the bacterial flagellar system have no known homologs in eukaryotic cells. The eukaryotic flagellar [sic], based on a microtubule-containing axoneme, is vastly more complicated. In fact, the current estimate for the number of different proteins in the axoneme is ∼425. In contrast, the archaeal flagellar system appears simpler than the bacterial one and can contain as few as 13 different proteins. As with the eukaryotic flagellar system, the archaeal one does not have homology with the bacterial one and must have arisen by means of convergent evolution.
Ah yes, convergent evolution again. But think about what they say here. The "vastly more complicated" eukaryotic flagellum has no known commonalities with the bacterial flagellum, and the bacterial flagellum has no homolog in the archaeal flagellum: "In archaeal flagellins, however, no homology has yet been found outside of the N-terminal domain with any bacterial or eukaryotic proteins." Do they show any common ancestry between these motors? None. Are we to believe, then, that blind processes happened upon three naturalistic miracles independently?

Notice that the archaeal flagellar system that "appears simpler" contains as few as 13 different proteins. How many different parts were required for the mousetrap? Behe's pithy illustration of an IC system had only five parts. How much more is an IC system with 13 parts, or with 40 parts, each unrelated to machines with similar functions in other types of cells?

If the best that evolutionists can come up with in response to Behe is "convergent evolution," then his 1996 statement can be seen as prescient: "An irreducibly complex biological system, if there is such a thing, would be a powerful challenge to Darwinian evolution" (p. 39). Only he could reword it now with much more confidence: Irreducibly complex biological systems continue to pose a powerful challenge to Darwinian evolution and are best explained by intelligent design.

Will the real macroevolution please stand up

“Macroevolution” and Its Discontents
Evolution News

The term “macroevolution” has problems. Why? Among other things, because it’s a term that means different things to different people. Case in point: an email correspondent points out a random usage on a BioLogos Forum thread, “Is evolution continuing? Is God still creating?” It’s a comment from a Forum participant, Socratic.Fanatic, about rabbits:

Northern and southern populations of a common species of North American rabbit is quickly becoming TWO distinct species and populations which can no longer cross-reproduce. It is a great example of macroevolution directly observable right in front of our eyes.

Without wishing to jump down Fanatic’s throat, we took a moment to Google that one and could not find anything that resembles it — nothing about speciation in a North American rabbits. It’s possible we didn’t look hard enough. In any case, the phrase “quickly becoming” suggests the populations have achieved reproductive isolation, which implies they aren’t truly distinct species.

We asked for a reference, and no doubt Fanatic will supply one in good time. It’s possible that he’s thinking of two squirrel populations on opposite sides of the Grand Canyon, which are almost identical.

In any event, let’s review two different classes of definitions of “macroevolution” found in a couple of college biology textbooks that we just grabbed off the shelf. They give two different definitions of the word.

(1) One, represented by Douglas Futuyma textbook Evolutionary Biology (1998),defines “macroevolution” in terms of the taxonomic hierarchy: “the origin and diversification of higher taxa.”

And what are “higher taxa”? Higher taxa are generally considered any taxa above “species.” That would include genera and above. That point will become important in just a moment.

(2) Others, represented by Campbell’s Biology (1999), define “macroevolution” in terms of the origin of biological novelty: “Evolutionary change on a grand scale, encompassing the origin of novel designs, evolutionary trends, adaptive radiation, and mass extinction.”

Regarding Definition (1), Michael Behe takes a similar approach in The Edge of Evolution  where he says evolution at the species level is feasible.

He allows that evolution at the genera, family, or order level could be possible. But as he argues in the book, evolution at the class level or above is “beyond the edge of evolution.” So if macroevolution includes evolution at the genera, family, or order level, Behe concludes that what some consider “macroevolution” might be possible.

As for Definition (2), the theory of intelligent design has no problems with macroevolution when defined as “mass extinction.” However, many ID proponents are skeptical that material mechanisms can produce novel traits. So here it might be fair to say ID poses its biggest challenge to “macroevolution.”

But the formation of a new species isn’t necessarily a big deal for ID. In fact, pending clarification on the rabbit issue, we’re skeptical that this rabbit example entails the evolution of any kind of biological novelty. At best it’s probably just two species that are partially reproductively separated.

In short, what’s at stake are somewhat semantic questions about how we define “macroevolution.” The key point is that we know there are limits to what Darwinian evolution can accomplish. We see these limits in experiments on features that require multiple mutations before giving any advantage. Darwinian evolution gets stuck.

For example, Douglas Axe has found that in prokaryotes the limit is more than six mutations to get an advantage. Behe suggests that in multicellular organisms, any feature that requires more than two mutations to give an advantage is beyond the limit of what unguided evolution can do.

Anything below these limits is microevolution. Anything above it cannot happen by Darwinian mechanisms, mathematically speaking. Perhaps one could say that is “macroevolution.”


- See more at: http://evolutionnews.org/2017/03/macroevolution-and-its-complaints/#sthash.tofHv6XE.dpuf

For a change,something we can all agree on.

The science of intelligent design typically focuses on details, “steel-hard facts,” as as Douglas Axe puts it.Sometimes, if carried to an extreme, that can be a fault. Now and again, therefore, it’s good to take a step back and ponder the biggest picture of life and its wonder, beauty, and charm.

In this from BBC One, David Attenborough offers the voiceover — a reading of the lyrics of Louis Armstrong’s “What a Wonderful World.” Perfect. All this from dumb natural forces and blind shuffling? Also nice to report that we came across on this over at Why Evolution Is True,where there would more typically be cause for clash than concord. Cheers, Dr. Coyne!

A discovery is turning OOL Science's circus into a full fledged carnival

Life in the Fast Lane — Microfossils, 3.77 Billion Years Old, Pose Challenge to Materialist Presuppositions - 
Evolution News

A paper in Nature reports the discovery of fossil microbes possibly older, even much older, than any found previously. The lead author is biogeochemist Matthew Dodd, a PhD student at University College London. If the paper is right, these Canadian fossils could be 3.77 billion years old, or even as old as — hold onto your hat, in case you’re wearing one — 4.28 billion years.

From the Abstract:

Although it is not known when or where life on Earth began, some of the earliest habitable environments may have been submarine-hydrothermal vents. Here we describe putative fossilized microorganisms that are at least 3,770 million and possibly 4,280 million years old in ferruginous sedimentary rocks, interpreted as seafloor-hydrothermal vent-related precipitates, from the Nuvvuagittuq belt in Quebec, Canada. These structures occur as micrometre-scale haematite tubes and filaments with morphologies and mineral assemblages similar to those of filamentous microorganisms from modern hydrothermal vent precipitates and analogous microfossils in younger rocks. The Nuvvuagittuq rocks contain isotopically light carbon in carbonate and carbonaceous material, which occurs as graphitic inclusions in diagenetic carbonate rosettes, apatite blades intergrown among carbonate rosettes and magnetite–haematite granules, and is associated with carbonate in direct contact with the putative microfossils.

This new paper is interesting to compare with a paper from last year, Nutman et al.,“Rapid emergence of life shown by discovery of 3,700-million-year-old microbial structures,”  -   also in Nature, which found microbial structures that are a bit younger.

But the “microbial structures” from Nutman et al. 2016 are different from these new “microfossils” presented by Dodd et al. 2017. In Nutman et al., they only found stromatolite-type structures rather than actual microfossils. Some stromatolite experts were a bit skeptical that what they found were really stromatolites.

But the new paper by Dodd and his colleagues, “Evidence for early life in Earth’s oldest hydrothermal vent precipitates,”  seems to offer potential bacteria-like microfossils. They are tiny black carbonaceous spheres and “hematite tubes” which the authors think are biogenically created. We’ve seen more convincing ancient microfossils, but these aren’t bad.

According to Dodd et al., these new finds would be the oldest known microfossils, if that is in fact what they are. Very interesting. If so, that just keeps pushing unquestionable evidence of life’s existence on Earth further and further back, which leaves less and less time for the origin of life to have occurred by unguided chemical evolution after Earth became habitable.

If they are in fact 4.28 billion years old, then that would mean there was life very, very early in Earth’s history — as Cyril Ponnamperuma said, it’s like “instant life.”

In zeroing in on this point, theWashington Post  quotes Dodd:

If their results are confirmed, they will boost a belief that organisms arose very early in the history of Earth — and may find it just as easy to evolve on worlds beyond our own.

“The process to kick-start life may not need a significant length of time or special chemistry, but could actually be a relatively simple process to get started,” said Matthew Dodd, , a biogeochemist at University College London and the lead author of the paper. “It has big implications for whether life is abundant or not in the universe.”

A “relatively simple process”? He’s right about the discovery having “big implications,” but maybe not in the way he intends.

It seems there are three observations to make: 1) The more we know, the more it seems that life arose rapidly on the early Earth, even more quickly that we previously realized. 2) How even the simplest life could arise, given materialist presuppositions, remains a profound mystery. This is the subject of Stephen Meyer’s book Signature in the Cell. 3) If life arises so easily, as Coyne’s friend Dr. Dodd suggests, then it’s strange we’ve seen no signs of it, at least not in an intelligent form, across the cosmos.

Taken together, these call into question materialist presuppositions, in the light of which 1, 2, and 3 present a tangle of contradictions. On the other hand, as a source of purposeful agency able to bring life into existence 1) quickly, 2) despite obstacles in the path of purely material processes, 3) uniquely, as it appears for now, on one planet, intelligent design fits the bill.


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A victory for academic freedom?

In Indiana, State Senate Affirms Teaching Evidence For and Against Evolution
Sarah Chaffee

This week, the Indiana State Senate passed, by a 40-9 vote, a resolution recognizing the need for academic freedom for teachers when approaching controversial scientific issues.

The resolution,  SR 17, notes in part:

Whereas, The Indiana General Assembly understands that an important purpose of science education is to inform students about scientific evidence and to help students develop the critical thinking skills they need in order to become intelligent, productive, and scientifically informed citizens;

Whereas, The Indiana General Assembly further understands the recommendation by the U.S. Congress, as stated in the report language of the 2001 No Child Left Behind Act, namely, "Where topics are taught that may generate controversy (such as biological evolution), that the curriculum should help students to understand the full range of scientific views that exist, why such topics can generate controversy, and how scientific discoveries can profoundly affect society";

...

Whereas, The Indiana General Assembly understands that neither recommendations, nor endorsements, nor implications by the courts have the force of law, but to avoid legal or other conflicts, teachers should not be intimidated, fired, or restricted from following the recommendation named herein or students penalized for holding differing positions based on the evidence objectively presented, as long as they meet specified curriculum requirements otherwise;

...

Be it resolved by the Senate of the General Assembly of the State of Indiana:

SECTION 1. That the Indiana Senate urges the Department of Education to reinforce support of teachers who choose to teach a diverse curriculum.

"I am encouraged by the strong stand the Senate has taken in favor of open discussion and examination of evidence in science education," said Senator Jeff Raatz, a sponsor of the resolution. He continued:

To be clear, this resolution only concerns subjects already allowed in the curriculum. It does not introduce new or additional topics. Indiana students benefit from practicing scientific inquiry skills in the classroom; SR 17 sends a signal to teachers that the Senate supports them in fostering an environment of critical thinking on scientific issues.

Indeed, so that there is no misunderstanding, let's remind ourselves of what kind of teaching this legislation encourages . On evolution, that could include discussing, for example, whether the Galápagos finches provide evidence of macroevolution, or just microevolution. It could mean understanding the strengths and weaknesses of theories of universal common ancestry, by considering the fossil record and studying the Cambrian explosion.

Acknowledging the importance of examining the evidence for and against scientific ideas such as evolution is a step forward. Teachers face pressure to teach evolution and other subjects dogmatically. In this resolution, the Indiana Senate calls for freedom for teachers to present evidence objectively. Students will benefit from learning more about evolution and similar subjects, from practicing critical thinking, and engaging in scientific inquiry.

The alternative would be to insist that teachers be vulnerable to retribution for sharing this evidence with students. SR 17 is thus not "antiscience" nor does it "target evolution," as the  National Center for Science Education claims. Treating a theory as worthy of fair questioning based on mainstream scientific sources, just like any other scientific theory, is pro-science and demonstrates concern for scientific objectivity and academic freedom.

We commend the Indiana Senate for this action.

Lamarck's gold?

Epigenomics "Gold Rush" Is Underway
Evolution News & Views 

More than a century ago, hardy individuals dropped everything to search for Klondike gold. Today, a new breed of adventurers is changing course to search for a different kind of gold: information at a scale so tiny, it couldn't be read until recently. It's called "non-genetic information."

Biochemists are as excited as prospectors without having to haul packs up remote snowbanks. More secrets of the cell are coming to light, revealing new levels of regulation in the burgeoning field of epigenetics. In Nature, Cassandra Willyard expresses the fervor that is growing in labs around the world: "An epigenetics gold rush: new controls for gene expression." As she reports on "How rediscovered chemical tags on DNA and RNA are shaking up the field," she uses the word excited or exciting five times. It began in 2008, she explains:

At the time, biologists were getting excited about the epigenome -- the broad array of chemical marks that decorate DNA and its protein scaffold. These marks act like a chemical notation, telling the cell which genes to express and which to keep silent. As such, the epigenome helps to explain how cells with identical DNA can develop into the multitude of specialized types that make up different tissues. The marks help cells in the heart, for example, maintain their identity and not turn into neurons or fat cells. Misplaced epigenetic marks are often found in cancerous cells. [Emphasis added.]
What's new is the assignment of RNA tags to the glossary of non-genetic information. Geneticists were familiar with methyl tags on DNA and histone proteins (the "histone code"), but only recently were these tags recognized as functional elements on the bases of RNA as well.In January, we shared one  of those discoveries: a tag named m6a that affects the stability of messenger RNA (mRNA). The number and position of tags on the mRNA affect its lifetime, and consequently its activity. Jaffrey's team considered this "dynamic and reversible epitranscriptomic mark" an instance of "epitranscriptomic information that determines the fate of mRNA."

Willyard now has more examples to share. Dr. Chuan He, a chemist at the National Institutes of Health, and his colleague Chao Pan at the University of Chicago set out to look for "chemical notation" on RNA molecules. When they started working together in 2009, He and Pan knew of about 100 chemical tags on RNA, but "nobody knew what they did." How often are major discoveries made by expecting function? Look what has happened with that focus:

Nine years later, such research has given birth to an 'ome of its own, the epitranscriptome. He and others have shown that a methyl group attached to adenine, one of the four bases in RNA, has crucial roles in cell differentiation, and may contribute to cancer, obesity and more. In 2015, He's lab and two other teams uncovered the same chemical mark on adenine bases in DNA (methyl marks had previously been found only on cytosine), suggesting that the epigenome may be even richer than previously imagined. Research has taken off. "I think we're approaching a golden age of epigenomics and epitranscriptomics," says Christopher Mason, a geneticist at Weill Cornell Medical College in New York City. "We can actually start to see all these modifications that we knew have been there for decades."
Their experience mirrors the downfall of the junk DNA myth. Non-coding DNA had been known for many years, but only when researchers intentionally looked for function did the golden age come. Now a new vein of gold is being found in long-ignored RNA tags (some of them known since 1974), but it required breaking out of old dogmas.

The governing rule of molecular biology -- the central dogma -- holds that information flows from DNA to messenger RNA to protein. Many scientists therefore viewed mRNA as little more than a courier, carrying the genetic information encoded in a cell's nucleus to the protein factories in the cytoplasm. That's one reason why few researchers paid much attention to the modifications made to mRNA.
Some of the delay is excusable. Scientists didn't have the tools we have now for "powerful mass spectrometry and high-throughput sequencing techniques," Willyard explains. Even with those tools, the work remains difficult. We can only wonder, though, if 'gold fever' might have accelerated the development of the tools.

In about 2010, the reversible m6a mark was discovered. "To He, it seemed like proof of an RNA-based system of gene regulation." The hidden gold veins started to shine under the flashlights. Further studies "revealed more than 12,000 methylated sites on mRNAs, originating from 7,000 genes."

The maps showed that the distribution of m6A is not random. Its location suggested that the mark might have a role in alternative splicing of RNA transcripts, a mechanism that allows cells to produce multiple versions of a protein from a single gene.
Since then, researchers have uncovered the molecular machines controlling the tags. "Each requires a writer to place it, an eraser to remove it and a reader to interpret it," Willyard says; "As the identities of these proteins emerged, scientists have come to understand that m6A affects not only RNA splicing, but also translation and RNA stability." They started finding function all over the place.

This change in mRNA content, which He calls a transcriptome switch, requires precision and careful timing. He thinks that the methyl marks might be a way for cells to synchronize the activity of thousands of transcripts.
By now, labs from Tel Aviv to Boston to Pasadena had gold fever. Researchers wanted to learn how different tissues tag their RNAs, and how the marks differ between organisms from algae to humans. Why, for instance, were some of these marks easier to find in bacteria than mammals? Earlier researchers had walked right past the gold veins.

In 2013, He's postdoc Fu had found an intriguing paper from the 1970s, which showed that algal DNA contains methylated adenine. "Nobody ever knew the function, and nobody ever followed up," Fu says.
Fu and a colleague started looking for these marks in algae, and found it in more than 14,000 genes. "And the distribution wasn't random," Willyard points out. It clustered near start sites for transcription. The postdocs reasoned that the mark "might be promoting gene activation." And so it was. Then they discovered that the marks are present in higher animals, too, but at low levels. Catch the fever:

Greer's lab head, Yang Shi, knew that He had uncovered 6mA in algae, and asked him for help. When He heard what Shi had found, he was excited. "We decided we're going to do this together," He says. A couple of months later, He met a researcher in China who had found 6mA in the fruit fly Drosophila. "I almost fell to the floor," He says. In April 2015, the three papers came out simultaneously in Cell.
Andrew Xiao, who studies epigenetics at Yale University in New Haven, Connecticut, read the articles with interest. Xiao and his colleagues had identified 6mA in mammalian cells, but they hadn't published their results. "Literally we thought nobody will take interest in this field," Xiao says. The Cell articles proved him wrong. "We realized we should hurry up."

And thus it goes. Marks are found to appear, surge, then disappear, indicating they act like a "molecular switch" during development. "His paper was absolutely a bombshell," one researcher exclaimed, reacting to clear evidence that a certain tag is functional. Another calls the work "incredibly exciting." Willyard continues the gold rush metaphor in a section, "Mining for more marks." They're talking like excited miners looking into their gold pans.

"We are only in the beginning of the story," Rechavi says. And as the techniques improve, scientists will be able to see these marks more clearly. The wealth of research possibilities makes Mason feel "euphoric", he says. "It's like the most exciting time to be working in the field."
Sound familiar? Vestigial organs must be leftovers of evolution; wait: they have a function! Noncoding DNA strands must be leftovers of evolution: wait, they have a function! These useless tags on RNA, "nobody knew the function, and nobody ever followed up." Wait! There's gold in them thar hills!

For an encore, look at this article from the National Institute of Standards and Technology (NIST) , "Start codons in DNA and RNA may be more numerous than previously thought." It's a bad-news, good-news story about the fall of another dogma. This one is about so-called "start codons" at the beginnings of genes. "It was previously thought that only seven of the 64 possible triplet codons trigger protein synthesis." But then, to their surprise, Stanford and NIST researchers found that some genes were being expressed without start codons.

To the best of their knowledge, no one had ever systematically explored whether translation could be initiated from all 64 codons. No one had ever proved that you cannot start translation from any codon.
"We kind of all collectively asked ourselves: had anyone ever looked?" said Hecht. A further review of available literature on the topic indicated that the answer was no....

The implications of the work could be quite profound for our understanding of biology.

"We want to know everything going on inside cells so that we can fully understand life at a molecular scale and have a better chance of partnering with biology to flourish together," said Stanford professor and JIMB colleague and advisor, Drew Endy. "We thought we knew the rules, but it turns out there's a whole other level we need to learn about. The grammar of DNA might be even more sophisticated than we imagined."

Needless to say, this discovery opens up additional vistas of information and control in the genome. Also, needless to say, these articles are strangely silent about Darwinian evolution.

Advocates of intelligent design should be pleased but unsurprised by these discoveries. And not to push the gold rush analogy too far, but we note that back in the day, many prospectors who set out for their journey to Alaska and the Klondike did so by way of Seattle. They equipped themselves and embarked just blocks away from what are today Discovery Institute's offices.


We're not saying, "We told you so" (although we did). Instead, let's all capitalize on the excitement of this gold rush. Isn't the search for function more rewarding than tossing unknown phenomena to the junk pile? ID is delightedly to point the way for the gold rushers to likely veins, with the modest reminder, Knowing how minds create hierarchical levels of information, you can expect to find functions similar to those in computer networks -- only even more sophisticated.

Long dead,human exceptionalism is gradually being buried unlamented.

Peter Singer Thinks Intellectually Disabled Less Valuable than Pigs

Wesley J. Smith

In his apologetics for infanticide, Princeton bioethicist Peter Singer has used a baby with Down syndrome as an example of a killable infant based on utilitarian measurements. (He actually supports infanticide because babies -- whether disabled or not -- are, in his view, not "persons.")

To Singer, moral value primarily comes from intellectual capacities, and that means developmentally and cognitively disabled human beings (also, the unborn and infants) have less value than other human beings, and indeed, a lower worth than some animals.

Were society ever to adopt Singer's bigoted anti-human exceptionalism views, it would mark the end of universal human rights, opening the door to tyrannical campaigns against the most weak and vulnerable -- you know, the kind of people that the Singers of the world deem resource wasters.

It would also break the spine of unconditional love, as our children would have to earn their place by possessing requisite capacities.

Consider the recent statements by Singer, published in the Journal of Practical Ethics, in which he explains why he would adopt out a child with Down syndrome. He then expresses a profound bigotry against people with cognitive and developmental disabilities (emphasis added):

For me, the knowledge that my [hypothetical Down] child would not be likely to develop into a person whom I could treat as an equal, in every sense of the word, who would never be able to have children of his or her own, who I could not expect to grow up to be a fully independent adult, and with whom I could expect to have conversations about only a limited range of topics would greatly reduce my joy in raising my child and watching him or her develop.

"Disability" is a very broad term, and I would not say that, in general, "a life with disability" is of less value than one without disability. Much will depend on the nature of the disability.

But let's turn the question around, and ask why someone would deny that the life of a profoundly intellectually disabled human being is of less value than the life of a normal human being. Most people think that the life of a dog or a pig is of less value than the life of a normal human being.

On what basis, then, could they hold that the life of a profoundly intellectually disabled human being with intellectual capacities inferior to those of a dog or a pig is of equal value to the life of a normal human being? This sounds like speciesism to me, and as I said earlier, I have yet to see a plausible defence of speciesism. After looking for more than forty years, I doubt that there is one.

Invidious discrimination exists when equals -- e.g., all human beings -- are denigrated as unequal based on some category that the bigot believes reduces the status of the discriminated against human, e.g., racism, sexism, and Singer-style discrimination against people with cognitive or developmental disabilities.

But human beings and animals do not inhabit the same moral realm. It is not wrong or discrimination to view and treat us differently than we do them.

Moreover, the very concept of "speciesism" -- used liberally in animal rights activism and bioethics -- is inherently and invidiously anti-human because it reduces us to so many carbon molecules with no inherent value beyond our cognitive capabilities at the moment of measurement. To repeat myself, the idea of speciesism, like utilitarianism, makes universal human rights impossible to sustain intellectually.

Assuming such utilitarian values would destroy the principles of Western civilization. And never mind the real capacities of many people with Down, whom Singer mischaracterizes, or their extraordinary loving natures -- which I have yet to see Singer opine much about. To Singer, intellect trumps all.

That's bigotry any way you look at it, no different from racism, except that his victims are less able to defend themselves.

I have always found it odd that Singer faces little of the opprobrium society metes out to other bigots. Indeed, he was brought to Princeton from Australia and given one of the world's most prestigious chairs in bioethics precisely because of these attitudes.

Despite supporting the propriety of killing babies, I have no doubt that Singer will continue to be the New York Times' favorite philosopher.