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.

On faith in Jah and his Christ:The Watchtower Society's commentary.

BELIEF IN JESUS ESSENTIAL

Anthony: Hi, Tim. It’s good to see you again.

Tim: It is good to see you too.

Anthony: I brought the latest issues of The Watchtower and Awake! for you. I think you will really enjoy the articles in these magazines.

Tim: Thank you. Actually, I’m glad you came by today because there is something I want to ask you.

Anthony: Sure, what is it?

Tim: The other day, I was speaking with a coworker. I told him about the pamphlets you gave me and how interesting they are. But he said that I shouldn’t read them because Jehovah’s Witnesses do not believe in Jesus. Is that true? I told my coworker that I would ask the next time you visited.

Anthony: Well, I’m glad you asked me. It’s good that you are going straight to the source. After all, what better way is there to find out what a person believes than to ask the person himself?

Tim: That’s what I figured.

Anthony: The truth is, Jehovah’s Witnesses most certainly believe in Jesus. In fact, we feel that exercising faith in Jesus is vital to salvation.

Tim: I thought you did, but when my coworker said that you don’t believe in Jesus, it made me curious. I guess you and I never really discussed it before.

Anthony: May I show you some Bible verses that highlight the importance of exercising faith in Jesus? These are verses that Jehovah’s Witnesses often use in their ministry.

Tim: OK.

Anthony: A good place to start is with Jesus’ own words recorded at John 14:6. These words are part of a conversation that Jesus had with one of his apostles. We read: “Jesus said to him: ‘I am the way and the truth and the life. No one comes to the Father except through me.’” According to that verse, what is the only way to approach the Father?

Tim: Through Jesus.

Anthony: Correct. And Jehovah’s Witnesses firmly believe that. Let me ask you this: From what you know about God’s requirements, when a person prays, in whose name should he offer the prayer?

Tim: In the name of Jesus.

Anthony: I agree. And that’s why every prayer I offer is said in Jesus’ name. The same is true of all the prayers of Jehovah’s Witnesses.

Tim: That’s good to know.

Anthony: Another scripture we might consider is John 3:16. That verse is so important that it has been called the Gospel in miniature. The idea is that if you could take everything that was written about Jesus’ earthly life and ministry and boil it down to one verse, this would be it. Maybe you would like to read this scripture.

 Tim: OK. It says: “For God loved the world so much that he gave his only-begotten Son, so that everyone exercising faith in him might not be destroyed but have everlasting life.”

Anthony: Thank you. Are you familiar with this verse?

Tim: Yes, I’ve heard it a lot, and I often see it quoted on signs and billboards.

Anthony: It is a famous verse. Looking at it carefully, notice what Jesus said. He said that God’s love makes it possible for humans to enjoy everlasting life—but only if we do what?

Tim: Exercise faith.

Anthony: Yes. Specifically, faith in the only-begotten Son, Jesus Christ. And this point—that faith in Jesus opens the way to everlasting life—is made right here on page 2 of the magazine I brought you. Regarding the purpose of The Watchtower, it says that among other things, this magazine “promotes faith in Jesus Christ, who died so that we might gain everlasting life and who is now ruling as King of God’s Kingdom.”

Tim: Well, there you go. Right in your own magazine is proof that Jehovah’s Witnesses believe in Jesus.

Anthony: Precisely.

Tim: So, then, why do people say that you don’t believe in Jesus?

Anthony: There are probably a number of reasons why people say that. In some cases, people say it simply because they have heard other people say it. Or they may have been taught this misconception by their minister.

Tim: I’m just thinking here—maybe some people say that you don’t believe in Jesus because you call yourselves Jehovah’s Witnesses, notJesus’ Witnesses.

Anthony: That could be a reason too.

Tim: Why do you talk about Jehovah so much?

“I HAVE MADE YOUR NAME KNOWN”

Anthony: For one thing, we believe that it is important to use God’s personal name, Jehovah—just as his Son, Jesus, did. Consider what Jesus said in prayer to his Father. It’s recorded at John 17:26. Would you please read that verse?

Tim: Sure. “I have made your name known to them and will make it known, so that the love with which you loved me may be in them and I in union with them.”

Anthony: Thank you. Notice that Jesus said he had made God’s name known. Why do you suppose he did that?

Tim: Hmm. I’m not sure.

Exercising faith in Jesus is vital to salvation

Anthony: Well, maybe we could look at another scripture that sheds light on the matter. I am thinking of Acts 2:21. There we read: “Everyone who calls on the name of Jehovah will be saved.” Now, I’m sure you would agree that if calling on the name of Jehovah is a requirement for salvation, Jesus was no doubt aware of this requirement.

Tim: Yes, of course.

Anthony: So the salvation of his followers is one reason why it was important to Jesus that they know and use God’s name. And it’s one of the main reasons why we talk about Jehovah so much. We feel that it is important to make known God’s personal name and help others call on that name.

Tim: But even if people don’t know God’s name or use it directly, they still know who they’re talking about when they refer to God.

Anthony: That may be true. Even so, by telling us his personal name, God has made it easier for us to draw close to him.

Tim: What do you mean?

 Anthony: Think of it this way: We didn’t need to know Moses’ personal name. We could have known him simply as the man who parted the Red Sea or the man who received the Ten Commandments. Likewise with Noah—why know his name? He could have just been referred to as the man who built an ark and saved his family and the animals. For that matter, even Jesus Christ could have been known simply as the one who came from heaven and died for our sins. Right?

Tim: I suppose so.

Anthony: But God made sure that we knew the personal names of those individuals. There’s nothing that adds that special touch like a personal name. Even though we have never met Moses, Noah, or Jesus, just knowing their name makes these men more real to us.

Tim: I never thought of it that way before, but that makes sense!

Anthony: And that’s another reason why Jehovah’s Witnesses use God’s personal name so much. We want to help people build faith in Jehovah God as a real Person whom they can draw close to. At the same time, we place great emphasis on the role that Jesus plays in our salvation. Perhaps we could read one more scripture that drives home this point.

Tim: Sure.

Anthony: Earlier we read John 14:6. Remember, Jesus said that he is “the way and the truth and the life.” Let’s go back a few verses and notice his words found at John 14:1. Would you please read what Jesus said in the last part of that verse?

Tim: OK. It says: “Exercise faith in God; exercise faith also in me.”

Anthony: Thank you. Would you say, then, that true faith is an either-or matter? Is it a question of belief in Jesus versus belief in Jehovah?

Tim: No. Jesus said we need both.

Anthony: That’s right. And I am sure you would agree that it’s not enough just to say that we have faith in God and in Jesus. Really, we need to live our lives in a way that backs up that claim.

Tim: Definitely.

Anthony: But just how does a person demonstrate that he truly has faith in God and in Jesus? Maybe we can discuss that question another time. *

Tim: I would like that.

Do you have a particular Bible subject that you have wondered about? Are you curious about any of the beliefs or religious practices of Jehovah’s Witnesses? If so, do not hesitate to ask one of Jehovah’s Witnesses. He or she will be pleased to discuss such matters with you.