Ragnarok for the RNA world?

As a Solution to the Origin of Life, RNA World Model Comes Under Attack

According to a recent article at New Scientist, "Why 'RNA world' theory on origin of life may be wrong after all," the RNA world model of the origin of life is under attack:

Life has a chicken-and-egg problem: enzymes are needed to make nucleic acids -- the genetic material -- but to build them you need the genetic information contained in nucleic acids. So most researchers assume that the earliest life, long before the evolution of cells, consisted of RNA molecules. These contain genetic information but can also fold into complex shapes, so could serve as enzymes to help make more RNA in their own image -- enabling Darwinian evolution on a molecular level.

At some point, the idea goes, this RNA world ended when life outsourced enzymatic functions to proteins, which are more versatile. The key step in this switch was the evolution of the ribosome, a structure that builds protein molecules from genetic blueprints held in RNA.

But such a transition would require abandoning the enzymatic functions of RNA and reinventing them in proteins. "That is not a simple model," says Loren Williams, a biochemist at the Georgia Institute of Technology in Atlanta.

That's a reasonable point at the end of the quote: If a self-replicating system has all of the enzymatic functions it needs from RNAs (something that hasn't been demonstrated), then rebuilding that system using an entirely different type of molecule (proteins) would be an extremely difficult task and highly unlikely. Yet this is essentially precisely what the classical RNA world model requires.

But there are many other criticisms of the RNA world model. A 2012 paper inBiology Direct by biochemist Harold S Bernhardt keenly titled, "The RNA world hypothesis: the worst theory of the early evolution of life (except for all the others)," notes that "the following objections have been raised to the RNA world hypothesis":

(i) RNA is too complex a molecule to have arisen prebiotically; (ii) RNA is inherently unstable; (iii) catalysis is a relatively rare property of long RNA sequences only; and (iv) the catalytic repertoire of RNA is too limited.

Now the author himself accepts the view that the RNA world is the best materialistic model for the origin of life. But he's very frank about its problems. For example, regarding the objection that "RNA is too complex a molecule to have arisen prebiotically," he writes:

RNA is an extremely complex molecule, with four different nitrogen-containing heterocycles hanging off a back-bone of alternating phosphate and D-ribose groups joined by 3',5' linkages. Although there are a number of problems with its prebiotic synthesis, there are a few indications that these may not be insurmountable. Following on from the earlier work of Sanchez and Orgel, Powner, Sutherland and colleagues have published a pathway for the synthesis of pyrimidine nucleotides utilizing plausibly prebiotic precursor molecules, albeit with the necessity of their timed delivery (this requirement for timed delivery has been criticized by Benner and colleagues, although most origin of life models invoke a succession of changing conditions, dealing as they do with the evolution of chemical systems over time; what is critical is the plausibility of the changes).

We covered the research of Powner and Sutherland here and here, pointing out that it was carefully designed to yield the desired results and noting how the goal-directed nature of the experiment undermines claims of the model's plausibility under unguided natural conditions. Hence the criticism that it has an unlikely "requirement for timed delivery."

Bernhardt then moves on to another criticism:

RNA is often considered too unstable to have accumulated in the prebiotic environment. RNA is particularly labile at moderate to high temperatures, and thus a number of groups have proposed the RNA world may have evolved on ice, possibly in the eutectic phase (a liquid phase within the ice solid).

But there's a major problem with the "cold" origin of life hypothesis: at low temperatures, reactions become so slow that nothing interesting ever happens. That's going to be a problem for many types of organic chemistry necessary for the origin of life. This is an especially significant problem when one considers that life appeared on earth very rapidly after conditions became favorable:

"...we have now what we believe is strong evidence for life on Earth 3,800 thousand million years [ago]. This brings the theory for the Origin of Life on Earth down to a very narrow range ... we are now thinking, in geochemical terms, of instant life..." (C. Ponnamperuma,Evolution from Space 1981.)

"[W]e are left with very little time between the development of suitable conditions for life on the earth's surface and the origin of life. Life is not a complex accident that required immense time to convert the vastly improbable into the nearly certain. Instead, life, for all its intricacy, probably arose rapidly about as soon as it could." (Stephen Jay Gould, "An Early Start," Natural History, February, 1978.)

A cold origin of life makes it much more difficult for life to arise under such a short timescale. Moreover, the notion that the early earth was cold rather than hot flies in the face of everything geologists have ever said about the conditions on the early earth.

Next, Bernhardt notes that "Catalysis is a relatively rare property of long RNA sequences only," and he offers a nice discussion of the gross improbability of randomly producing a long, self-replicating RNA molecule:

The RNA world hypothesis has been criticized because of the belief that long RNA sequences are needed for catalytic activity, and for the enormous numbers of andomized sequences required to isolate catalytic and binding functions using in vitro selection. For example, the best ribozyme replicase created so far -- able to replicate an impressive 95-nucleotide stretch of RNA -- is ~190 nucleotides in length, far too long a sequence to have arisen through any conceivable process of random assembly. And typically 10,000,000,000,000-1,000,000,000,000,000 randomized RNA molecules are required as a starting point for the isolation of ribozymic and/or binding activity in in vitro selection experiments, completely divorced from the probable prebiotic situation. As Charles Carter, in a published review of our recent paper inBiology Direct, puts it:

"I, for one, have never subscribed to this view of the origin of life, and I am by no means alone. The RNA world hypothesis is driven almost entirely by the flow of data from very high technology combinatorial libraries, whose relationship to the prebiotic world is anything but worthy of "unanimous support". There are several serious problems associated with it, and I view it as little more than a popular fantasy" (reviewer's report in [5]).

1014 - 1016 is an awful lot of RNA molecules.

Don't miss what's being said here: the argument directly parallels ID proponents who observe that it's extremely unlikely for an RNA molecule with just the right nucleotide sequence needed for self-replication to arise by chance. In other words, he's making the information sequence challenge to the origin of life.

Now Bernhardt proposes that perhaps the first self-replicating RNA was much shorter, reducing the probabilistic obstacles to randomly generating the right nucleotide sequence. But the evidence that this is actually possible is non-existent. Indeed, one of the reviewers, Eugene Koonin, points out that such a self-replicating RNA -- whether long or short -- has yet to be demonstrated:

I basically agree with Bernhardt. The RNA World scenario is bad as a scientific hypothesis: it is hardly falsifiable and is extremely difficult to verify due to a great number of holes in the most important parts. To wit, no one has achieved bona fide self-replication of RNA which is the cornerstone of the RNA World.

Finally, Bernhardt explains a fourth problem with the RNA world model, namely "The catalytic repertoire of RNA is too limited":

It has been suggested that the probable metabolic requirements of an RNA world would have exceeded the catalytic capacity of RNA. The majority of naturally occurring ribozymes catalyze phosphoryl transfer reactions -- the making and breaking of RNA phosphodiester bonds. Although the most efficient of these ribozymes catalyze the reaction at a comparable rate to protein enzymes -- and in vitro selection has isolated ribozymes with a far wider range of catalytic abilities -- the estimate of proteins being one million times fitter than RNA as catalysts seems reasonable, presumably due to proteins being composed of 22 chemically rather different amino acids as opposed to the 4 very similar nucleotides of RNA.

While Bernhardt discusses the various kinds of reactions that RNA can catalyze, he admits "RNAs are, in most cases, worse catalysts than proteins." That sounds like Bernhardt just conceded the validity of the criticism that he described against the RNA world. Somehow, however, he manages to spin the inferiority of RNA catalysis, turning it into not a knock against the RNA world, but an argument for it: "This [the inferior catalytic abilities of RNA] implies that their [RNA's] presence in modern biological systems can best be explained by their being remnants of an earlier stage of evolution, which were too embedded in biological systems to allow replacement easily."

So RNA is used by living organisms -- despite its inferior catalytic abilities -- only because evolution wasn't able to replace it? But aren't we constantly told how proteins can evolve to accommodate virtually any need of an organism? Doesn't this suggest severe limits to the evolvability of proteins? Now it seems that limits to evolution have become an argument forevolution.

This tortured logic brings us back to the criticism raised in the recent New Scientist article: the RNA world model is unlikely to be correct because it requires that proteins (with superior chemistry-catalyzing abilities) somehow swooped in and replaced what RNA was doing. That seems very unlikely. But Bernhardt again tries to spin this dilemma into an argument for the RNA world -- that difficulties replacing RNA with protein point to the fact that RNA was once a precursor of life. However, if it's so hard to replace RNA with proteins, how do we know that it happened in all the other cases required by the RNA world model?

It seems that whether proteins did or did not replace RNA, we're being told that in either case that's evidence for the RNA world. No wonder Eugene Koonin called the model "unfalsifiable."

So why does anyone prefer the RNA world model, given all its problems? Koonin provides the answer in his reviewer's comments at the end of Bernhardt's article -- it's because he requires some materialistic model, and other materialistic models clearly won't explain the origin of replication:

[T]he RNA World appears to be an outright logical inevitability. 'Something' had to start efficiently replicating to kick off evolution, and proteins do not have this ability.

Koonin's argument thus goes like this: We know that unguided evolution is true, so some evolutionary model must be correct. If other unguided models of life's origins won't work, then the RNA world must be correct, because "something" had to happen to get life started.

But what if the RNA world itself has many problems and so it isn't a viable solution? That's not an option Koonin seems willing to consider. He's right that "something" has to get life started. But there is a third way that Koonin hasn't considered. That third way -- the "something" he won't consider -- is the only known cause that can generate the kind of highly complex and specified digital sequences required at the origin of life: intelligent design.

Tree of the undead ?

Zombie Science: Jonathan Wells on Overselling Darwin’s Tree of Life
David Klinghoffer | @d_klinghoffer

There’s no denying the sly brilliance of the evolutionary Tree of Life, memorialized in Darwin’s Origin by the only illustration in that famous book. In its own origin, of course, the Tree of Life is a sacred and mysterious image from the Book of Genesis. Evolutionary theory takes it and twists into the symbol of an idea, universal common ancestry, that collides heads on with the simplest reading of the Genesis creation account. Take that, creationists!

All of life may be related as Darwin hypothesized, or it may not. Certainly, though, the science behind the evolutionary tree of life has been vastly oversold. Author of  Zombie Science: More Icons of Evolution,  biologist Jonathan Wells explains in a new video conversation why that is so.

With his own sly humor, Dr. Wells points out some scientific problems with regarding Darwin’s Tree as unassailable fact. There can be only one “true tree,” yet fossil, molecular, and other data fail to resolve into any such thing. At the time of the publication of Dr. Wells’s 2000 book, Icons of Evolution, many scientists still hoped that this situation would resolve itself. It hasn’t. Seventeen years later, inferences from available data are even more confusing. There is still no realistic prospect of a “true tree” emerging.

Meanwhile, increasing awareness of orphan genes, genes without parallels from one taxon to another, collide head on with evolutionary expectations. Researchers proposing their own “trees” are compelled to cherry-pick, simply ignoring the inconvenient yet widespread orphans.

It looks more and more like the true tree is an illusion. “The reason we get a tree,” in the first place, says Dr. Wells, “is only because we assume at the outset that it’s there.” Meanwhile, year after year, Darwin’s apologists persuade the public, including school kids, that all is well and scientists are homing in on the one and only tree. This is zombie science in its purest, most staggering, shuffling form.

Ancient nanotech v. Darwin

Cell Machines Maintain the Planet for Life
Evolution News | @DiscoveryCSC

Count the mentions of the word “machines” in this news from the University of Liverpool:

“Nanotechnology reveals hidden depths of bacterial ‘machines’…”

“New research from the University of Liverpool, published in the journal  Nanoscale has probed the structure and material properties of protein machines in bacteria, which have the capacity to convert carbon dioxide into sugar through photosynthesis.”

“Unique internal ‘machines’ in cyanobacteria, called carboxysomes, allow the organisms to convert carbon dioxide to sugar and provide impacts on global biomass production and our environment.”

“So far, little is known about how these ‘machines’ are constructed and maintain their organisation to perform carbon fixation activity.”

“They then used electron microscopy and atomic force microscopy to visualise the morphology and internal protein organization of these bacterial machines.”

“‘We’re now just starting to understand how these bacterial machines are built and work in nature. Our long-term vision is to harness the knowledge to make further steps towards better design and engineering of bio-inspired machines,’ added Dr Liu. ‘The knowledge and techniques can be extended to other biological machines.’” [Emphasis added.]

That’s a lot of machine language for one short article! And it doesn’t even include related words like mechanical, nanotechnology, and structure. They’re talking about an amazing little organelle in cyanobacteria (once considered among the most primitive of cells) called the carboxysome — one of those tiny wonders most people don’t know about but depend on for life.

Cyanobacteria are a phylum of bacteria that produce oxygen and energy during photosynthesis, similar to green plants. They are among the most abundant organisms in oceans and fresh water.

As the article states, the machines in carboxysomes “provide impacts on global biomass production and our environment” by using sunlight to turn carbon dioxide into sugar, releasing oxygen for us to breathe.

Carboxysomes are polyhedral structures resembling a viral capsid, except that these living machine factories are “much softer and structurally flexible, which is correlated to their formation dynamics and regulation in bacteria.” Zooming in, we find higher levels of organization. The paper in Nanoscale says:

The protein shell serves as a physical barrier to protect enzymes from the cytosol and a selectively permeable membrane to mediate transport of enzyme substrates and products.

There’s more. The team found three structural domains inside, “a single-layered icosahedral shell, an inner layer and paracrystalline arrays of interior Rubisco.” Rubisco? Is that some kind of cracker? No — it’s another one of the most important things in nature you may have never heard of, and here it is, laid out in nice orderly rows in a geometric nanofactory.

Short for “Ribulose 1,5-bisphosphate carboxylase/oxygenase” (thank goodness), Rubisco is the most abundant protein on earth. According to PNAS, this machine solves an “abominably perplexing puzzle” of distinguishing between “featureless” molecules of carbon dioxide and oxygen, and it “may be nearly perfectly optimized” to do so. Once it was thought to be a slow, sluggish enzyme that leaks, but the authors find otherwise:

We assert that all Rubiscos may be nearly perfectly adapted to the differing CO2, O2, and thermal conditions in their subcellular environments, optimizing this compromise between CO2/O2 specificity and the maximum rate of catalytic turnover.

Commenting in Nature on that 2006 paper, Howard Griffiths added some amazing facts about Rubisco:

Rubisco has the reputation of being slow and inefficient, but it is one of life’s big successes: globally there is an estimated 5–10 kg Rubisco for every person on Earth, and each year it reacts with 15% of the total pool of atmospheric CO2.

Working alongside Rubisco in those neatly arranged layers inside the carboxysome is another amazing enzyme, carbonic anhydrase. Last year, we learned about how this “fine-tuned” enzyme (one of the few that employs zinc in its active site) helps salmon get an energy boost for their muscles when they leap waterfalls. Here it is again in cyanobacteria, working with Rubisco to regulate the levels of carbon dioxide by converting it to bicarbonate or back again as needed. The Protein Data Bank says, “Carbonic anhydrase is an enzyme that assists rapid inter-conversion of carbon dioxide and water into carbonic acid, protons and bicarbonate ions.” This ubiquitous enzyme is found in mammals, plants, algae, and bacteria.

The current study in Nanoscale explains why compartmentalization of these machines is important:

Within the cytosol which is a crowded and changing environment, it is important that carboxysomes are sufficiently robust to ensure the proper protein assembly, encapsulation of Rubisco enzymes and functional architecture. On the other hand, they are also flexible and dynamic to allow metabolite passage, turnover of building modules and interactions with other cellular components.

It’s not a prison, in other words, but a lively factory with windows and doors, yet it sequesters the machines safely for their protection. Carboxysomes are examples of bacterial microcompartments (BMCs) we’ve discussed before. These sure look designed: “The protein shell, structurally resembling virus capsids, is made of multiple protein paralogs forming hexagons and pentagons, and acts as a physical barrier that controls the passage of substrates and products of enzymatic reactions.” One can find spontaneous hexagons in nature, but some of them are clearly designed: those that exhibit “functional coherence” to use Doug Axe’s term (Undeniable, p. 160, pp. 178-181).

The authors don’t seem to have much use for evolutionary theory; anyway, they never mention it in the paper. But they did have design on their minds:

The study provides novel insights into the inherent structure and physical elasticity of native β-carboxysomes. It will empower our toolbox for the design and construction of functional metabolic machinery with applications in bioengineering and nanotechnology.

The report from the University of Liverpool amplifies the design theme:

“We’re now just starting to understand how these bacterial machines are built and work in nature. Our long-term vision is to harness the knowledge to make further steps towards better design and engineering of bio-inspired machines,” added Dr Liu, “The knowledge and techniques can be extended to other biological machines.”

Let’s end with some “wow” facts about a tiny cyanobacterium you may not have heard of. It contains these molecular factories (carboxysomes) loaded with Rubisco and carbonic anhydrase, working day and night to cleanse our atmosphere and regulate global carbon. Its name is Prochlorococcus. Sallie W. Chisholm says this about it in her Quick Guide in  Current Biology:

“We now know that there are about 100 million of these tiny powerhouses in each liter of seawater over vast oceanic regions,” and yet “they are 100 body lengths away” from each other.

Prochlorococcus “is the smallest and most abundant photosynthetic cell on Earth.”

“There is an estimated 3 x 10(exp)27 of them in the oceans, collectively weighing twice as much as all humans, and sporting a surface area 100 times that of the Earth.”

“They constitute half of the chlorophyll over vast ocean ecosystems, single-handedly supplying significant amounts of organic carbon to the rest of the microbial food web.”

“…they are extremely efficient photosynthetic machines.”

“…their genomes represent one of the most streamlined blueprints for life.”

“With a lower bound of 1,800 genes, they synthesize biomass using only solar energy, CO2 and inorganic compounds. That’s minimal life. That’s impressive!”

Carboxysomes rule the world. What if there had not been enough magnesium (for the chlorophyll) and zinc (for the carbonic anhydrase) close to the surface to supply the layers of enzymes in the factories of all those trillion quintillion cells? The Earth seems to have set the stage for complex life, a point Michael Denton would no doubt appreciate.

Your survival guide to Darwinism's zombie apocalypse.

For the Public School Biology Teacher, Zombie Science Makes an Outstanding Resource
David Klinghoffer | @d_klinghoffer

Imagine you’re a public high school biology teacher in a state where you are permitted to share objective scientific critiques of evolutionary theory in the classroom – the strengths and weaknesses of Darwinism. Where do you turn for a reliable, responsible resource to help you clarify the issues for your students?

Here’s a great idea: check out biologist Jonathan Wells’s new book,  Zombie Science: More Icons of Evolution. Dr. Wells and fellow biologist Ray Bohlin talk about that in a new ID the Future podcast.

Listen to it here now, or download it here.

Dr. Bohlin was closely involved with recent revisions to science standards in Texas, and he describes what happened in his state. So let’s say you’re a 9th grade biology teacher there. You want to talk with students about the consistent pattern of abrupt appearance of species in the fossil record – an observation inconsistent with Darwinian predictions; about the mystery of where biological information in DNA comes from, or the puzzle of whale evolution.

Zombie Science covers all of these subjects. The idea, obviously, isn’t to use it as textbook. It’s written (very accessibly) with the thoughtful adult in mind, not for a 9th grader. But teachers will find the book very useful for the background it provides.

Wells and Bohlin do note that in a public high school setting, it would be very ill advised to take the discussion some steps further to the question of design in life’s origins. If Darwinism is hobbled as an explanation for biology’s grandeur, however, what then? Dr. Bohlin admits that as a teacher, he’s uncomfortable saying “I don’t know.” But this is the wisest response.

Letting the stones speak.

Letting the stones speak II

Phillip Johnson tells why he will not buy the wares of a blind watchmaker.

Discarded on the battlefield?

Evolutionary Biologist Backs Off from Computer Simulations
David Klinghoffer | @d_klinghoffer

PZ Myers is an atheist activist and evolutionary biologist whose blog is more about promoting his left-wing politics than it is about evolution. But this caught my eye. In denouncing me for a  brief post here recommending a podcast interview with Introduction to Evolutionary Informatics   co-author Winston Ewert, Professor Myers tellingly backs off from the idea of computer simulations of evolution,at least where the Cambrian explosion is concerned.

He doesn’t like our use of the term “falsify,” or that I call the geologically sudden Cambrian event an “event.” But these are minor points. This I find very interesting. Dr. Myers writes:

I also take exception to creationist’s [sic] constant focus on “computer models”. Computer models are useful tools for assessing some ideas, but they’re no substitute for real data…especially when the events you’re pursuing are not simple, and have a million different equally valid ways of producing a result. Again with the binary thinking: Cambrian evolution will not be described with a “yes” or a “no”.

I’m also going to call shenanigans on his assumptions. The Cambrian was not an “event”. It was a long, multi-million year series of events, and it was driven by multiple phenomena. There was the pre-Cambrian bioturbation revolution, in which the evolution of worms with hydraulic skeletons drove massive turnover of nutrients in sediments; there was the gradual increase in atmospheric oxygen, which made more energetic organisms possible; there was a long history of evolution of animal lineages before the Cambrian that set the stage with breadth and depth of diversity. How do you “simulate” all that on a computer? And why bother, because you know creationists like Klinghoffer will simply reject any result that shows an increase in complexity without an infusion of biological information (whatever that means) as cheating?

Most importantly, no one with any sense or competence would carry out such a simulation to falsify creationism, an endeavor with no reward, since they’ll just move the goalposts as they always have.

Now, Dr. Ewert’s point was that computer evolution simulations, as a rule, fail. I would expect this. If they succeeded, that would be a problem for alternatives to unguided evolution.

Ewert was simply reiterating the conclusion that he and co-authors Robert Marks and William Dembski reach, after meticulous investigation, in their book. As Marks puts it,“There exists no model successfully describing undirected Darwinian evolution. Period. By ‘model,’ we mean definitive simulations or foundational mathematics required of a hard science.” In turn, Marks, Dembski, and Ewert were responding to the challenge of a distinguished mathematician, Gregory Chaitin, in his book,Proving Darwin: Making Biology Mathematical

Dr. Chaitin wrote:

The honor of mathematics requires us to come up with a mathematical theory of evolution and either prove that Darwin was wrong or right!

Giving some mathematical rigor to evolutionary theory is not the “focus” of “creationists,” as Myers thinks. Gregory Chaitin is not a “creationist,” or a proponent of the theory of intelligent design. But he is a candid and gracious interlocutor. In a comment about the Marks-Dembski-Ewert book, he said that it was “An honest attempt to discuss what few people seem to realize is an important problem.” Well, well.

Others feel similarly. Here are a couple of further comments gathered by the publisher. Bijan Nemati of the Jet Propulsion Laboratory:

With penetrating brilliance, and with a masterful exercise of pedagogy and wit, the authors take on Chaitin’s challenge, that Darwin’s theory should be subjectable to a mathematical assessment and either pass or fail. Surveying over seven decades of development in algorithmics and information theory, they make a compelling case that it fails.

Professor Donald Wunsch, who directs the Applied Computational Intelligence Lab at Missouri University of Science & Technology:

Introduction to Evolutionary Informatics is a lucid, entertaining, even witty discussion of important themes in evolutionary computation, relating them to information theory. It’s far more than that, however. It is an assessment of how things might have come to be the way they are, applying an appropriate scientific skepticism to the hypothesis that random processes can explain many observed phenomena.

That – whether “random processes can explain many observed phenomena” in life – is exactly the question to consider. Another atheist evolutionary biologist, Richard Dawkins, used to think that simulations held out great promise for settling the issue. (See, for example, Jonathan Witt’s post,Richard Dawkins’s Weasel Program Is Bad in Ways You Never Dreamed ) This is not an issue that “creationists” invented.

And now, just as a major work of ID research arrives, at the cutting edge of thinking on the subject, PZ Myers whines about how simulations are hopeless anyway: “How do you ‘simulate’ all that on a computer? And why bother, because you know creationists like Klinghoffer will simply reject any result that shows an increase in complexity…”

It’s just what Robert Marks wrote here the other day.. He responded to ten common objections to the evidence in Introduction to Evolutionary Informatics. This one is Myers in a nutshell:

2. But Darwinian evolution is so complicated, it can’t be modeled!

If this objection is true, we have reached the same conclusion by different paths: There exists no model successfully describing undirected Darwinian evolution.

Which means that on anyone’s honest analysis, Darwinism fails to deliver on an expectation of what Marks calls “hard science.”

Myers is saying that simulations can’t work, and even if they could, “no one with any sense or competence” would “bother” going through with the exercise for fear of being shown the door by…who? Me? What?? Sorry, that is just a pathetic excuse, among the lamest from evolutionary advocates that I’ve heard in a while, which is saying something.

Incidentally, for more on the Cambrian explosion from the perspective of biological information and the challenge of making evolution mathematically rigorous, see our brief video, The Information Enigma, highlighting the work of Doug Axe and Stephen Meyer. Click on the image – a scene from the video – at the top of this post.

Giving"on time" a whole new meaning.

Hyper-precise atomic clocks face off to redefine time:
Next-generation timekeepers can only be tested against each other.

Elizabeth Gibney

02 June 2015


Happy birthday, caesium clock. Now move over. As the atomic clock used to define time itself turns 60, tests are set to begin on a new generation of clocks that are designed to give the caesium version a run for its money.

Such timekeepers would enable a variety of experiments, including testing whether the fundamental constants of nature really are constant over time, and, eventually, a more precise official definition of the second.

Atomic clocks track the frequency of electromagnetic waves emitted by atoms as they change energy states. First demonstrated by British physicist Louis Essen in June 1955, the caesium clock became the world’s official timekeeper in 1967 — defining the second as the time it takes for the microwaves that are absorbed or emitted when caesium atoms switch between states to cycle through 9,192,631,770 oscillations.

Over the past decade, various laboratories have created prototype optical atomic clocks, which use different elements such as strontium and ytterbium that emit and absorb higher-frequency photons in the visible spectrum. This finer slicing of time should, in principle, make them more accurate: it is claimed that the best of these clocks gain or lose no more than one second every 15 billion years (1018 seconds) — longer than the current age of the Universe — making them 100 times more precise than their caesium counterparts. Optical clocks are claimed to be the best timekeepers in existence, but the only way to verify this in practice is to compare different models against each other and see whether they agree.

Starting on 4 June, four European laboratories will kick off this testing process — the National Physical Laboratory (NPL) in Teddington, UK; the department of Time-Space Reference Systems at the Paris Observatory; the German National Metrology Institute (PTB) in Braunschweig, Germany; and Italy’s National Institute of Metrology Research in Turin. Between them, the labs host a variety of optical clocks that harness different elements in different experimental set-ups.

For the first test, each institute will transmit a signal related to the optical frequency of its clocks to a satellite, which will beam the frequencies back down to the other labs. This will allow the labs to compare the frequencies of light emitted by their clocks and thus measure whether they all keep time to the same beat.

“We all think our clocks have a very good potential for achieving the highest accuracy.”
“It’s really exciting,” says Andrew Ludlow, a physicist at an optical-clock powerhouse run by the US National Institute of Standards and Technology (NIST) in Boulder, Colorado, who is not involved in the project. “A couple of comparisons of optical clocks have been made before, but on nothing like this scale.” With more clocks, it should be easier to root out the source of any discrepancies, adds Helen Margolis, a physicist at the NPL.

She notes that a higher frequency does not necessarily mean a more accurate clock, because varying sensitivities to environmental factors can affect the ability of different clocks to keep time in practice. The hope is that all the clocks will agree, suggesting that they are as precise as claimed. If some clocks do not, it will indicate that improvements are needed.

The initial test is only a prelude to a more accurate test, however, because it has one big limitation: to beam light to a satellite, it must be converted to a microwave frequency — which means that much of the potential extra accuracy gained by using visible light is lost. By increasing the rate of data transfer, the European labs hope to improve the accuracy of current state-of-the-art satellite comparisons by ten, but it will still be limited to one part in 1016. So the main function of the satellite test is to build confidence in optical clocks and show that they perform at least as well as existing caesium clocks, say researchers.

The more accurate test will transmit signals in the visible spectrum through fibre-optic cables to the labs. This will allow the clocks to be compared with an accuracy similar to the expected accuracies of the clocks themselves. Some of the labs have already established such links, and tests have begun on sections between Paris and Teddington, and Paris and Braunschweig. “Eventually, this would allow a four-way comparison. That’s the vision,” says Margolis.

“There is friendly competition,” she adds. “We all think our clocks have a very good potential for achieving the highest accuracy or we wouldn’t be working on them.”

Fibre-optic links between optical atomic clocks already exist elsewhere, such as between the NIST lab and its partner lab JILA, also in Boulder. But these span shorter distances than the European network and are mostly between just two labs. “Europe is in a unique position as it has a high density of the best clocks in the world,” says Fritz Riehle, a physicist at PTB.

Even if the clocks pass this later test, usurping the caesium clock to create a more precise definition of the second will not be easy. International atomic time — on which coordinated universal time, or UTC, is based — is currently calculated by averaging measurements from hundreds of atomic clocks. Doing the same with optical atomic clocks would require a way to aggregate time at this precise level; using the fibre-optic method across oceans is not currently feasible.

In the meantime, ever more precise time is important for improving global positioning systems, high-resolution radio astronomy and the time-stamping of financial transactions, as well as spotting tiny variations in fundamental constants. “Most attempts to unify gravity with other forces would lead to variations of fundamental constants in the expanding Universe,” says Marianna Safronova, a theorist at the University of Delaware in Newark.

On evidence lite cosmogony.

What Becomes of Science When the Evidence Does Not Matter?

Denyse O'Leary

Fine-tuning of the universe is so unpleasant a subject for materialists that it cannot really become a controversy. The desired evidence favors a random universe, accidentally spilled. Differing points of view on the findings would, of course, be funded by the government. But the randomness would be agreed upon up front.

On the other hand, if evidence matters, our universe appears fine-tuned.

In the end it is not really an issue about the evidence. Help! we are drowning in evidence! The universe’s expansion speed is said to be just right for life, the Higgs boson seems to be fine-tuned,  and Earth has a “unique” iron signature, just as a few examples.

This from Natalie Wolchover at  Quanta Magazine: “As things stand, the known elementary particles, codified in a 40-year-old set of equations called the ‘Standard Model,’ lack a sensible pattern and seem astonishingly fine-tuned for life.” Why does being fine-tuned for life “lack a sensible pattern”? What if that is the pattern?

The alternative sounds like saying that the letters STOP on a sign do not form a sensible pattern.

Cocktail napkin objections are always on offer, to be sure. For example, we are informed that evidence no longer counts the way it used to: We evolved to see patterns where there are none (the “staggering genius” of Charles Darwin). Indeed, the Principle of Mediocrity is now a  guiding assertion. The  Birthday Problem  is often used in pop science to claim that we underestimate what sheer randomness can do: “In a room of just 23 people there’s a 50-50 chance of two people having the same birthday. In a room of 75 there’s a 99.9% chance of two people matching.” Yes, but that embarrasingly familiar social icebreaker speaks only to what we might randomly guess, not to facts about our universe.

We are also told that the universe, apart from our planet, is  hostile to life. But if ours is a dedicated environment, could it not be like the human womb during a pregnancy: Life outside is hostile? How does that come to mean that there is no design? Would the circumstances not suggest the opposite?

Some ask, how could a designer know  know what to do, in order to create a universe and intelligent life? Well, it is hard to say, as we have never come close to that ourselves. Perhaps we should try it before offering criticism. Others ask, “Who designed the designer?” which feels somewhat like asking, “How did my old math teacher, who explained why one cannot divide by zero, come to exist?” Is there no point at which a given trail of enquiry legitimately ends?

Some questions do require a more thoughtful response: Astrophysicist Ethan Siegel informs us at Forbes that the odds of our existence are  not infinitely small, as we might have supposed, because our existence “already disproves that possibility!” But wait. We are not talking about the odds of an incidental unusual event but those of a long pattern of statistically abnormal events. Similarly, design is held in some quarters to be an argument from ignorance: “We also cannot rule out hitherto unknown naturalistic causation.” No, but we cannot rule out fairies at the bottom of the garden either. What’s realistic?

Canadian teacher Tim Barnett offers, by way of illustration of the problem of what to rule out: A lucky poker player has been dealt five royal flushes, noting that the probability of getting a single royal flush is one in 649,739… “After the fifth royal flush, you insist that I’m cheating. That is, I’m designing the outcome. But what if I responded, “Yes, five consecutive royal flushes is highly unlikely, but unlikely things happen all the time. In fact, for you to exist your mom and dad had to meet, fall in love, and have sex…” Does anyone ever use such a standard in real life?

Lawyer Barry Arrington plaintively asks, Why won’t these “improbable things happen all the time” people play poker with me?

Barnett notes, “It’s not merely the high improbability of an event that leads to a design inference. It’s the high improbability combined with an independently specified outcome that leads to the conclusion of design.” Presumably, that is why the cocktail set won’t play poker with Arrington.

And then religion looms: Christian evolutionists have begun to quarrel with fine-tuning, a development predicted by Wayne University biologist Wayne Rossiter in his  Shadow of Oz: Theistic Evolution and the Absent God, (pp. 106, 153) At BioLogos, Casper Hesp argues, “I believe it is unwise to turn fine-tuning into an argument based on the gaps in our understanding, because the properties of the universe could become more amenable to scientific explanation in the future.” That is a curious approach: Has Hesp any reason to expect that more discoveries will lead to fewer perceptions of fine-tuning? The trend has been very much the opposite.

Recently, atheist cosmologist Andreas Albrecht has also warned “deeply religious” people not to put their faith in “apparent” fine-tuning: “And when people do engage in these debates, they seem to find a reason to believe what they want to believe, regardless of how the science unfolds.”

But in this case, the evidence favors the “deeply religious.” Why should they not put their faith in it? And the future of science may depend in part on how the tension between evidence and naturalism plays out in a basic issue like this.

Instant animals.Just add hype.

Researchers Proclaim: Instant Animals by Chance

Evolution News & Views February 16, 2016 12:06 AM 

An old preacher wrote in his sermon notes, "Point weak; pound pulpit harder." That seems to happen, too, whenever a major new success for evolution is announced. A recent headline from the University of Oregon proclaimed, "A mutation, a protein combo, and life went multicellular." Sarah Kaplan at the Washington Post rose to the pulpit and began with a stirring invocation. "Startling new finding: 600 million years ago, a biological mishap changed everything."

How? Well, in the high-stakes game of evolution, mutations in DNA that get passed on can be like bad photocopies, but...

But if the flaw is wrong in exactly the right way, the incredible can happen: disease resistance, sharper eyesight, swifter feet, big brains, better beaks for Darwin's finches. [Emphasis added.]

Before we can catch our breath, Kaplan pounds the pulpit harder:

In a paper published in the open-access journal eLife this week, researchers say they have pinpointed what may well be one of evolution's greatest copy mess-ups yet: the mutation that allowed our ancient protozoa predecessors to evolve into complex, multi-cellular organisms....

Incredibly, in the world of evolutionary biology, all it took was one tiny tweak, one gene, and complex life as we know it was born.

Kaplan has not even reached the climax of her rhetoric, but before getting swept away by the performance, let's pause to look at the evidence. It comes from a paper in eLife by principal author Kenneth Prehoda at the University of Oregon who, with eight others, reported on the "Evolution of an ancient protein function involved in organized multicellularity in animals."

Basically, they claim that a single mutation "repurposed" an enzyme that made multicellularity possible. A common guanylate kinase enzyme (gk), used by all living things to regulate the supply of nucleotides for the genetic code, underwent a mutation that enabled it to learn a new function. The new GKPID enzyme, found primarily in animals and choanoflagellates, is important for cell adhesion and spindle orientation. The mutation gave it a new shape that enabled it to bind to a different ligand. Sometime later, GKPID found a new partner in Pins, a protein on the inner membrane that (with some helper enzymes) connects to both the spindle microtubule and the complex that receives signals from neighboring cells. Astrobiology Magazine explains why this appears significant:

In cells from a broad range of animal species, the spindle is rotated relative to surrounding cells by a protein scaffold known as the guanylate kinase protein interaction domain (GK-PID). It acts as a kind of molecular carabiner by binding to two different partner molecules: an 'anchor' protein on the inside of the cell membrane that indicates the position of adjacent cells and a motor protein that pulls on mitotic spindle filaments. Once hooked together by GK-PID, the motors pull the chromosomes toward the anchors, orienting new daughter cells in line with neighboring cells.

Prehoda gives the gist of the idea himself in a video clip:

It's a neat story; a random mutation at a critical juncture in the history of life opens up a world of possibilities for cells to work together. It's just what Darwin dreamed of: an unguided process, co-option, innovation, at the right place and the right time to create endless forms most beautiful. No wonder this story reverberated around the world in hyped headlines like Kaplan's. Pound the pulpit harder!

In the wild world of pre-complex life, this development was orders of magnitude better than Twitter for getting organisms organized. Every example of cells collaborating that has arisen since -- from the trilobites of 500 million years ago to the dinosaurs, woolly mammoths and you -- probably relied on it or some other similar mutation.

We'll have to add this one to the explanations for the Cambrian explosion. Mutation -- trilobites!

You can't blame Kaplan and other reporters for taking this supposition and running up the whole evolutionary tree with it. In Astrobiology Magazine's coverage, co-author Joe Thornton said, "That one ancient mutation yielded a wholly new molecular function, which helped set the stage for multicellular animals to eventually evolve." Indeed, Prehoda told the Oregon Register-Guard newspaper:

From a microbiology standpoint, Prehoda said, there's no argument about evolution. "You can make evolution happen on a rapid time scale in the lab," he said. "We've witnessed evolution. Evolution is just a fact, hands down."

Prehoda said this, incidentally, in response to "the ire of anti-evolutionists" when the story went viral. Reporter Diane Dietz says in her article, "University of Oregon researcher's paper on evolution stirs debate; he says the transformation of single-celled organisms to multi-celled creatures occurred more easily than many scientists believed." She continues:

A paper on evolutionary biology he and co-authors published this month on eLifeSciences, an electronic scholarly journal, was ground-breaking enough that scientists nationally took notice -- and so provocative that it became clickbait for opponents of evolutionary theory.

Those anti-evolutionists. All they've got is religion.

By contrast, the so-called intelligent design theory put forth by believers who say a divine entity created humans is based on the idea that organisms are so complex that they couldn't arise from the random, step-by-step process of evolution. As a result, Prehoda now finds his email box stuffed with missives from unhappy anti-evolutionists.

The writers' general message is: "You say we come from cells and monkeys, but we come from God," Prehoda said.

Obviously, that is not how ID advocates argue. Prehoda's story is so beset by scientific and logical flaws it doesn't need divine assistance to point it out. Ann Gauger gave a calm, scholarly critique of a similar claim about the origin of multicellularity last year, without any appeals to God, religion, or personal belief. Following her example:

The claim relies on circumstantial evidence.

It's a little hard to do "molecular time travel" when working with living cells, without presupposing evolutionary common ancestry.

If the guanylate kinase was co-opted to become GKPID, what about all the other things it connects to? Was everything co-opted from something else, including the Pins complex on the membrane, and the microtubules in the spindle complex? You can't push co-option too far, or else you end up borrowing from nothing.

It's nice that cells with GKPID can orient their spindles to neighboring cells, but that's a far cry from multicellularity. If one cell gets the mutation, it still doesn't have any goal to line up with its neighbor. Nothing interesting will happen (unless one presupposes that "evolution" will latch onto this new capability). Indeed, if all the choanoflagellates get the mutation, the best they could do is blindly point to neighboring cells in an unguided, chaotic manner.

The signal from the neighboring cell has to be interpreted. Nothing interesting will happen if the mutant hollers, "I've got my carabiner ready!" and the neighbor is deaf, or responds, "No comprendo."

Ann Gauger's critique of the previous such claim bears repeating: much, much more is involved. One of the "simplest" colonies of all, Volvox, has sexual reproduction, alternation of generations, inversion, digestive enzymes, gene regulation, specialized roles, and more.

The authors use loaded words like ancient and primitive copiously. These terms presuppose what they need to prove about evolution. There's nothing primitive about a choanoflagellate, with its genetic code, ribosomes, flagellum and all the complexities of a living cell.

Even if a guanylate kinase differs from GKPID by one mutation, they are both functional within complex systems and regulatory networks. Many other proteins are structurally similar but have different functions. Similarity does not prove ancestry.

If GKPID appeared by mutation, how did the rest of the cell know what to do with it? There has to be genetic coding and gene regulation. Unless the new function is encoded in harmony with the systems that regulate it, it will be treated as a defect and eliminated. To think it will immediately be useful smacks of Lamarckism.

10. The authors admit a "long time" gap between the mutation and the ability to link up to the Pins complex and the spindle orientation complex. Was this a "latent capacity" sitting around waiting to be utilized? "We agree that this is puzzling," they admit. "Because whatever we say here would be very speculative, we did not go into much detail on this point." Even more puzzling, the GKPID does not bind to the Pins complex in the same organism, but only to one from a fruit fly!

In a moment of epistemic modesty, the authors admit that their supposition doesn't really amount to much. It's a case of glittering generalities at best, sweetened with high hopes.

Our analyses do not establish a complete history of the spindle orientation complex. Many key steps remain to be reconstructed, including how and when the interaction between GKPID and KHC-73 evolved, the mechanisms by which Pins' acquired its linker and GoLoco sequences, and the relationship of these components to other molecular complexes and pathways involved in animal spindle orientation. Despite these knowledge gaps, our observations establish a broad overview of the history of the GKPID complex, provide a detailed mechanistic reconstruction of a key event, and point to the importance of reusing molecules -- and specific surfaces within them -- for fortuitous new purposes that have the potential to become biologically essential.

Unusual for a journal paper, this one includes the dialogue between the reviewers and the authors. The criticisms and responses are well worth reading. Despite the editors' interest in publishing this paper, they were clearly concerned about the authors' tendency to overstate their case.

Our major critique is that the broader interpretation is overstated in terms of the centrality of KHC73-DLG-PINS to spindle orientation in all animals and multicellularity in general, and in terms of external orientation being a unique novelty of animals. We also think that some clarification / caveats are needed regarding the experiments on positioning in Choanoflagellates. Finally, we think the manuscript would benefit from more discussion of some puzzling aspects of the co-evolution of GKPID and PINS (or lack thereof).

The editors charged "overstated" multiple times. Embarrassed, the authors confessed and repented somewhat:

We have modified the text in numerous ways to be more cautious on this point and to base our claims more solidly on what is known in the literature....

More generally, we have gone through the text and have changed our wording to dispel the impression that GKPID complex is the sole driver of spindle orientation in all animals and all cell types and to avoid the implication that the evolution of the GKPID complex explains all instances of spindle orientation in all animals.

Unfortunately, this confession didn't make it into Kaplan's sermon or into Prehoda's bombast, "We've witnessed evolution. Evolution is just a fact, hands down." Overstated? That's an understatement.