Back to the Drawing board re:planet formation?

Weirdly tilted exoplanet knocks formation theory out of line
November 27, 2015 Posted by News under Exoplanets, Intelligent Design


From New Scientist: Recent theory:

The idea is that smaller, colder stars have thicker atmospheres. “That provides handles with which the star can grab onto the planet and vice versa,” Winn says. Over time, those gravitational handles exert a tidal force on the planet, pulling it and its star into alignment.

But then:

But one Jupiter-mass planet discovered earlier this year, HATS-14b, seems to threaten that idea. Because it tightly circles a small star, its orbit should have flattened out quickly – but the orbit is instead tilted a whopping 76 degrees from the plane in which its star spins.

“It should have aligned with the spin of the host star, and what we’re finding is that it has not,” says study leader George Zhou, who conducted the research at the Australian National University in Canberra. “It was quite obvious from some of the very first measurements that it was an outlier.” … Understanding why, or finding other planets like HATS-14b, could knock down the tidal theory – which even Winn is starting to doubt.

In another new paper, Winn and Gongjie Li of Harvard University address another flaw in the traditional idea… More.

Hmmmm. The first exoplanets began to be discovered in the early 1990s. It’s probably too early for strong theories.

Here’s the abstract:

The obliquities of planet-hosting stars are clues about the formation of planetary systems. Previous observations led to the hypothesis that for close-in giant planets, spin-orbit alignment is enforced by tidal interactions. Here, we examine two problems with this hypothesis. First, Mazeh and coworkers recently used a new technique — based on the amplitude of starspot-induced photometric variability — to conclude that spin-orbit alignment is common even for relatively long-period planets, which would not be expected if tides were responsible. We re-examine the data and find a statistically significant correlation between photometric variability and planetary orbital period that is qualitatively consistent with tidal interactions. However it is still difficult to explain quantitatively, as it would require tides to be effective for periods as long as tens of days. Second, Rogers and Lin argued against a particular theory for tidal re-alignment by showing that initially retrograde systems would fail to be re-aligned, in contradiction with the observed prevalence of prograde systems. We investigate a simple model that overcomes this problem by taking into account the dissipation of inertial waves and the equilibrium tide, as well as magnetic braking. We identify a region of parameter space where re-alignment can be achieved, but it only works for close-in giant planets, and requires some fine tuning. Thus, while we find both problems to be more nuanced than they first appeared, the tidal model still has serious shortcomings. Open access – Gongjie Li, Joshua N. Winn

From president to emperor?Pros and cons.

The spoon rather than the knife?Pros and cons.

Long live big brother?Pros and cons.

A clash of Titans XL

A clash of Titans XXXIX

Playing with fire?

On Darwinism's zombie stories.

Daddy and Baby: Evolutionary Legends Die Hard

David Klinghoffer 

A colleague shares this gem from a get-together with friends:

I was hanging out with some friends last night and one of them is pregnant. Another gal in the group told her that her baby will look like the dad at first because this is a product of evolution -- a way to confirm paternity. Of course I knew it was a just-so story and here's an article in Scientific American actually admitting that. I just think it's interesting because they rarely admit stuff like that. This article is old, but obviously people still talk about the issue.

The referenced article is from 2011:

Fact or Fiction: Do Babies Resemble Their Fathers More Than Their Mothers?

Recent studies do not support the claim of an enhanced resemblance between fathers and their young offspring

Does junior really have his father's nose?

A common bit of parenting folklore holds that babies tend to look more like their fathers than their mothers, a claim with a reasonable evolutionary explanation. Fathers, after all, do not share a mother's certainty that a baby is theirs, and are more likely to invest whatever resources they have in their own offspring. Human evolution, then, could have favored children that resemble their fathers, at least early on, as a way of confirming paternity.

The paternal-resemblance hypothesis got some scientific backing in 1995, when a study in Nature by Nicholas Christenfeld and Emily Hill of the University of California, San Diego, showed that people were much better at matching photos of one-year-old children with pictures of their fathers than with photos of their mothers....

Case closed? Hardly. "It's a very sexy result, it's seductive, it's what evolutionary psychology would predict -- and I think it's wrong," says psychologist Robert French of the National Center for Scientific Research in France. A subsequent body of research, building over the years in the journal Evolution & Human Behavior, has delivered results in conflict with the 1995 paper, indicating that young children resemble both parents equally. Some studies have even found that newborns tend to resemble their mothers more than their fathers.

It goes on from there. Read the rest.

The other day Doug Axe referred to the "legend" of natural selection with its creative prowess in generating biological novelties. But of course the legend has many sub-legends and derivatives. They die hard.

How many years, how many decades from now do you think consumers of science media will be getting together and sharing this particular tall tale, after even professional evolutionists have ceased to believe in it?

When cheer leading supersedes fact-checking.

Feathers on a Bird or Dinosaur Tail? The Media Are Certain; the Scientific Evidence Less So
Evolution News & Views 

A section of a 99-million-year-old feathered tail discovered in a chunk of amber in Myanmar belongs to a juvenile dinosaur, a coelurosaur, not a bird. The media are certain of it. The actual evidence is more ambiguous. National Geographic pounds the pulpit for a feathered dino:

First Dinosaur Tail Found Preserved in Amber
The tail of a 99-million-year-old dinosaur, including bones, soft tissue, and even feathers, has been found preserved in amber, according to a report published today in the journal Current Biology.

While individual dinosaur-era feathers have been found in amber, and evidence for feathered dinosaurs is captured in fossil impressions, this is the first time that scientists are able to clearly associate well-preserved feathers with a dinosaur, and in turn gain a better understanding of the evolution and structure of dinosaur feathers.

...

The semitranslucent mid-Cretaceous amber sample, roughly the size and shape of a dried apricot, captures one of the earliest moments of differentiation between the feathers of birds of flight and the feathers of dinosaurs.

...

The presence of articulated tail vertebrae in the sample enabled researchers to rule out the possibility that the feathers belonged to a prehistoric bird. Modern birds and their closest Cretaceous ancestors feature a set of fused tail vertebrae called a pygostyle that enables tail feathers to move as a single unit.

The reason that they claim it is a dinosaur and not a bird is because this is supposedly from a "long-tailed" individual. Most birds with bony tails are short-tailed, meaning they have fewer vertebrae in their tail compared to dinosaurs. Under ten vertebrae, perhaps only six or seven, would be the norm for a bony-tailed bird.

So what do they think about the number of vertebrae in this amber fossil? They say the living individual "likely" had more than 25 vertebrae.

But this is a matter of inference, because, as the paper admits, the soft tissue in the fossil is so undifferentiated from the bone that it is very difficult to tell what is tissue and what are vertebrae. As the paper puts it in technical language:

SR X-ray μCT scanning of DIP-V-15103 revealed that soft tissues have a density insufficiently different from the partially replaced skeletal elements to permit X-ray imaging and virtual dissection of osteology alone. Consequently, many diagnostic and comparative osteological details remain obscured.
At most, they can see clear evidence of only two vertebrae in this tail. From that they extrapolate that it had more than 25:

However, two vertebrae are clearly delineated ventrally (Figures 1F-1H). Extrapolating lengths of these vertebrae, the preserved tail section contains at least eight full vertebrae and part of a ninth.
So when they extrapolate from the two visible vertebrae, they get nine. That would certainly not preclude the creature from being a bird. In fact, some fossil birds had up to 20 to 23 vertebrae. As another paper states:

Archaeopteryx retained an ancestral caudal vertebral count of between 20 and 23. The next most basal bird, Jeholornis, from the Jiufotang Formation of China and dated at approximately 120 million years old, was also long-tailed, and had 22 caudal vertebrae that are nearly identical to those of Archaeopteryx.
If it did have up to 20 to 23 vertebrae, it could still be a bird. Yet again it's not clear exactly how many vertebrae this tail had because too much of it is missing.

The paper goes on:

Even with the skin adpressed to the bony surface, no features other than the grooved ventral sulci of two centra are clearly visible. This lack of topography suggests that the vertebrae lack prominent neural arches, transverse processes, or hemal arches. Therefore, the preserved segment is only a small mid to distal portion of what was likely a relatively long tail, with the total caudal vertebral count not reasonably less than 15, and likely greater than 25.
So they claim that the shape of the vertebrae suggests that what they are seeing is from the middle of the tail, and the actual tail was much longer. They admit that most features are not "clearly visible." Given that you can barely distinguish soft tissue from bone in this fossil, their inferences go too far.

Indeed while researcher Ryan McKellar tells Science Daily that "the feathers definitely are those of a dinosaur not a prehistoric bird," the paper itself is more circumspect, saying "it can likely be excluded from the long-tailed birds" (emphasis added). The Supplemental Information that goes with the paper includes the notable statement:

[T]here is a distinctive ventral groove on the caudal centra of the specimen, which is widely distributed among non-avialan theropods but which has yet to be reported in avialans (though the possibility of its presence in the two known long-tailed birds Archaeopteryx and Jeholornis cannot be excluded).
As a final note, one could argue that the age of the fossil (about 99 Ma) suggests that this individual lived long after known long-tailed bony-tailed birds. According to this paper, the most recent long-tailed bony-tailed bird lived about 122 million years ago.

That would be a very weak argument, however, since evolutionists regularly tolerate chronological gaps in the fossil record much greater than 20 million years. In fact they do this in their dinosaur-to-bird hypothesis.

After all, the dinosaurs that they claim supposedly gave rise to birds lived about 125 million years ago, but true birds like Archaeopteryx lived as far as about 150 million years ago. That's a major time gap. So if one were to propose that perhaps the long-tailed birds known from ~122 million years ago survived until ~99 million years ago, you would not be extrapolating fossil lineages any more than they already do.

In any case, all praise is due to the researchers for discovering and presenting this beautiful fossil with its unmistakable feathers. Probably no known feathers this old have ever been preserved in such gorgeous detail.


But unfortunately we have so little material, and the bone is so difficult to distinguish from the soft tissue, that any strong claims about this tail should be greeted with skepticism. This paper will not be the last word on the nature of the animal that sported this wonderful tail.

Optimal and then some.

Respect for Kinesin Grows
Evolution News & and Views December 10, 2015 5:39 PM 



The Discovery Institute video "Workhorse of the Cell: Kinesin" premiered last year on YouTube. Since then, additional facts about these molecular motors have come to light. Some highlights:

Relay Handoff

Kinesin-II, one of the extended family of kinesin motors, is involved in a "relay race" on a micro-miniature scale. It demonstrates how different families of molecular motors cooperate. This one works in synergy with other cargo-carrying motors in the important complex function known as "intra-flagellar transport" (IFT) that builds and maintains cilia and flagella. An important example occurs in the neurons of the eye.

O'Hagan and Barr, writing for Nature Cell Reports, describe "A motor relay on ciliary tracks" between kinesin-II and another motor. It turns out that kinesin-II is the marathoner running up the neuron into the crowded transition zone (TZ), where it "hands off" its cargo a sprinter named OSM-3 that runs it up to the cilium tip.

Peterman, Scholey and colleagues have now discovered a previously unappreciated complexity in the cooperation of anterograde motors using advanced techniques ....

They find that kinesin-II acts as an import motor that transports cargos from the distal dendrite into the ciliary TZ (Fig. 1). Because the TZ is cluttered with obstacles such as Y-link attachments, kinesin-II (with its tendency to frequently detach from microtubules) may easily sidestep obstructions, switching to an adjacent microtubule protofilament to continue on its path to deliver cargo to the PS [proximal segment]. A similar model of obstacle avoidance was proposed to function in axons, in which kinesin-2 binds the same cargo as kinesin-1 to allow the complex to sidestep around Tau protein obstacles.

The authors then observed gradual acceleration of IFT in the PS, accompanied by a gradual decrease in abundance of kinesin-II and concurrent increase in OSM-3 (KIF17) (Fig. 1). The acceleration resulting from changing the ratio of kinesin-II to OSM-3 did not match previous predictions from in vitro data. Instead, a biased contribution model, in which OSM-3 outcompetes kinesin-II ten-fold, fitted the acceleration observed in vivo. These results suggested a 'handover zone' in the PS, in which kinesin-II gradually hands over its transport duties to the faster and more processive OSM-3, which then acts as an efficient long-range motor to bring IFT complexes to the ciliary tip. [Emphasis added.]

Noting that different kinds of cilia in various species have different families of motors acting together, the authors describe "an emerging theme" in IFT research. They sugest that "kinesin-II plays an essential role in ciliogenesis, whereas accessory motors are associated with specializations in ciliary form and function." Many debilitating diseases are known to occur from mutations in IFT.

It's amusing how they used the word "evolution" only one time. "Why did evolution add another anterograde motor when heterotrimeric kinesin-II seems capable of doing the job alone in algae?" As it turns out, this relay race is an efficient way to get the job done. Kinesin-II and OSM-3 each have their strengths, and each one is matched for its environment. Then, at the ciliary tip, another molecular motor -- dynein -- takes cargo back down.

The paper by Scholey and Peterman and colleagues in Nature Cell Biology doesn't have anything to say about evolution. Instead, the scientists explain why "functional differentiation" provides the best way to get cargo delivered on time:

Dissociated kinesin-II motors undergo rapid turnaround and recycling to the ciliary base, whereas OSM-3 is recycled mainly to the handover zone. This reveals a functional differentiation in which the slower, less processive kinesin-II imports IFT trains into the cilium and OSM-3 drives their long-range transport, thereby optimizing cargo delivery.

Kinesin-II is no slouch as a runner. In our video, it appears to walk slowly and deliberately, but remember: the narrator says it can take a hundred steps a second. The researchers seem to like the word "optimize," using it four times in all, such as:

We propose that the functional differentiation of kinesin-II and OSM-3 into an import motor and transport motor, respectively, optimizes sequential steps of anterograde IFT to build the cilium. The system thus exploits each kinesin-2's specific motor properties and requires that the number of motors on the cargo, that is, the IFT train, is well orchestrated, resulting in a gradual exchange of the different motors to ensure reliable handover of cargo (Fig. 7). In a broader context, the deployment of similar, same-polarity yet functionally differentiated motors may represent a common strategy for optimizing intracellular transport.

"Optimize" is a design term. Evolutionists, by contrast, are fond of "tinkering," wherein natural selection supposedly cobbles together parts just to get by. Which word is a better match to the observations?

Myosin Mimicry

Another walking motor is myosin, which walks along actin filaments instead of microtubules. Bioengineers at Emory University weren't quite able to imitate its motion, but they did improve on previous attempts by inventing a DNA-based motor that rolls like a wheel. At first, the news from Emory makes it sound like they bested nature:

"Unlike other synthetic DNA-based motors, which use legs to 'walk' like tiny robots, ours is the first rolling DNA motor, making it far faster and more robust," says Khalid Salaita, the Emory University chemist who led the research. "It's like the biological equivalent of the invention of the wheel for the field of DNA machines."

But then they have nothing but praise for natural myosin:

The field of synthetic DNA-based motors, also known as nano-walkers, is about 15 years old. Researchers are striving to duplicate the action of nature's nano-walkers. Myosin, for example, are tiny biological mechanisms that "walk" on filaments to carry nutrients throughout the human body.

"It's the ultimate in science fiction," Salaita says of the quest to create tiny robots, or nano-bots, that could be programmed to do your bidding. "People have dreamed of sending in nano-bots to deliver drugs or to repair problems in the human body."

So far, however, mankind's efforts have fallen far short of nature's myosin, which speeds effortlessly about its biological errands. "The ability of myosin to convert chemical energy into mechanical energy is astounding," Salaita says. "They are the most efficient motors we know of today."

The engineer makes this blunder in his reasoning, though:

"Our DNA-based motor can travel one centimeter in seven days, instead of 20 years, making it 1,000 times faster than the older versions," Salaita says. "In fact, nature's myosin motors are only 10 times faster than ours, and it took them billions of years to evolve."

For one thing, myosins are present in the earliest cells we know of, so it didn't take them "billions of years to evolve." For another, if he applied intelligence to build a cheap mimic, wouldn't that be evidence that the superior product required an intelligent cause?

Molecular Ruler

We see myosin at work in another role described in a paper in Nature Communications: helping maintain the cytoskeleton. There's an "evolutionarily conserved" group of "Rho-associated coiled-coil kinases" (ROCK) that "are essential regulators of the actin cytoskeleton" on which myosins travel. The authors give us a glimpse into the precarious balance of motors that keep a cell's membrane intact:

The ability of cells to change shape underpins physiological processes from embryonic development through pathogen clearance in the immune system. The plasma membrane of cells exhibits high mechanical resistance yet permits enormous changes in cell shape. This apparent paradox is resolved by a dynamic network of actin and myosin filaments beneath the plasma membrane that forms the cortical cytoskeleton. Stress fibres, bundles of actin fibres and myosin II motors traverse the cell between focal adhesions that anchor the cell in the extracellular matrix. Actomyosin contraction against these anchors generates the force required for shape change and cell motility. Phosphorylation of regulatory myosin light chain (RMLC) stimulates myosin activity, leading to contractile force generation. The Rho-associated coiled-coil kinases (ROCK) are essential for the maintenance and integrity of stress fibres in the cell by directly and/or indirectly phosphorylating RMLC. A null mutant of the Drosophila Rok gene or deletion of ROCK1 or ROCK2 in mice results in prenatal lethality.

Their diagrams show that ROCK acts as a "molecular ruler" due to the length of its coiled coil. "This represents a new type of spatial control, and hence a new paradigm for kinase regulation."

They try to make a case for ROCK evolving at the origin of multicellularity, but it's little more than speculation. "Given the role of ROCK in regulating actin dynamics at focal adhesions, it is tempting to speculate that the emergence of ROCK together with the integrin-mediated signalling machinery was a crucial event in metazoan evolution." Exactly how machinery "emerges" by blind processes is not clear. One thing is clear: it is "evolutionarily conserved throughout the animal kingdom." In fact, it is "remarkably well conserved across more than 600 million years of evolution." That's hardly something to make an evolutionist cheer. We'll take their concluding automotive analogy instead. It sounds more like design.

Our findings indicate that the activity of the Rho kinases is regulated by the spatial positioning of kinase and substrate in the cell, much like the clutch in a car engine determines whether the car is in gear or not. The engine, or kinase, is always running, but the car, or cell, doesn't move unless the clutch, or substrate, is engaged. This represents a new paradigm in kinase-substrate regulation, whereby substrate specificity and corresponding activity are simply governed by the precise spatial positioning of enzyme and substrate.

So there you have it. Cells are inhabited by molecular motors and engines with precision parts operating under tight regulations. Now you can watch our video animation with a little more appreciation for what these amazing molecular machines do for all life, including you.

Jehovah's Justice prevails

Why accepting I.D may not necessitate an embrace of the supernatural.

ID for Materialists:
January 25, 2016 Posted by Barry Arrington under Intelligent Design

Teleology in biology is unavoidable.  Dawkins was surely correct when he wrote that “Biology is the study of complicated things that give the appearance of having been designed for a purpose.”  He even characterized that appearance as “overwhelming.”  Of course, Dawkins does not believe living things were designed, and his entire project has been to convince his readers that the overwhelming appearance of design is an illusion.

The problem with the “it is all a grand illusion” position is that as science has progressed – even in the relatively short time since Dawkins wrote those words in 1987 – it has become increasingly more difficult to believe.  Advances in our understanding of genetics have revealed a semiotic code of staggering elegance and complexity, the replication of which is far beyond the ability of our best computer programmers.  The more we know about the cell, the more it becomes apparent that it is a marvel of nano-technology.  Origin of life researchers, when they are honest, admit that even the most simple life is miraculously complex, and the likelihood of living things having arose spontaneously through chance interactions of matter is vanishingly small.  I could go on, but you get the picture.

What is an honest materialist to do?  One approach is to jettison materialism altogether, as famous former arch-atheist Antony Flew did.  Flew insisted that while he did not believe in a personal God, he was nevertheless driven to deism by advances in origins of life science.  He wrote that “[t]he philosophical question that has not been answered in origin-of-life studies is this: How can a universe of mindless matter produce beings with intrinsic ends, self-replication capabilities, and ‘coded chemistry’?”  That question remains unanswered.

Another approach is to retain one’s materialism while positing the existence of yet-undiscovered natural telic laws.  This is the approach Thomas Nagel took in his Mind and Cosmos: Why the Materialist Neo-Darwinian Conception of Nature is Almost Certainly False.  It occurred to me recently that this approach may well be the most likely way for honest, curious and courageous materialists to accept the evidence on its own terms and at the same time find common ground with ID proponents.

RDFish is one of the most voracious proponents of materialism (which he prefers to call monist physicalism) ever to appear in these pages.  In one of his comments he argued that biological ID is committed to dualism.  I responded by arguing that while biological ID is certainly consistent with metaphysical dualism, it is not necessarily tied to it, and it can be accepted even by physicalist monists.  See here.

In the linked post I argued that a physicalist monist can accept a version of ID through the following reasoning:

Design, meaning the capacity to arrange matter for a purpose, exists as a category of causation.
The capacity to arrange matter for a purpose can be reduced to any force that is capable of arranging matter in the present so that it will have an effect in the future.
There are at least two candidates for causal forces that have the capacity to arrange matter for a purpose. (a)  intelligent agents who have an immaterial mental capacity; (b) an impersonal non-conscious yet-to-be-discovered natural telic force.
The monist rejects the existence of intelligent agents with immaterial mental capacities, because the existence of such agents obviously entails dualism.
Instead, the monist can resort to the natural telic force.
If such a natural telic force exists, the existence of design as a category of causation is no obstacle to accepting the truth of monist physicalism.
This get us to:

If monist physicalism is true and a natural telic force exists, it is nevertheless possible objectively to infer design.
Therefore, design may be inferred under monist physicalism using the explanatory filter.
Therefore, ID does not depend on dualist metaphysical assumptions and can be accepted by a monist.
Which brings us back to Nagel.  In his book Nagel argued that Neo-Darwinism has failed to account for the data and is therefore almost certainly false.  But Nagel is an inveterate atheist and he is unwilling to give up on atheistic monism.  For Nagel, rejecting Neo-Darwinism does not entail embracing a dualist conception of ID.  Instead, he has posited what can be called a monist conception of ID by proposing the existence of natural telic laws.

In his book Being as Communion Bill Dembski writes that Nagel’s conception of teleology is completely consistent with ID writ large:

Nagel proposes to understand teleology in terms of natural teleological laws.  These laws would be radically different from the laws of physics and chemistry that currently are paradigmatic of the laws of nature.  And yet, as we shall see, such teleological laws fit quite naturally within an information-theoretic framework . . . his proposal, given in Mind and Cosmos . . . connects point for point with the account of information given in this book.  Indeed, Nagel’s teleological laws are none other than the directed searches (or alternative searches) that are the basis of Conservation of Information . . . of this book.

When orthodox Christian theist Bill Dembski says that he and vigorously atheistic materialist Thomas Nagel hold views that can – at a fundamental level – be reconciled, the rest of us should sit up and take notice.  And Dembski is not alone among theists in noting how Nagel’s views are compatible with their tradition broadly construed.  Christian philosopher Edward Feser writes:

[Nagel] rightly suggests that theists ought to be open to the idea of immanent teleology of the Aristotelian sort.  He may not be aware that medieval theologians like Aquinas were committed to precisely that.

Of course, Aquinas believed in the immanent teleology inherent in all things.  The only difference between Aquinas and Nagel is that Aquinas believed that God infused those things with immanent teleology; whereas Nagel believes the teleology results from a natural telic law.  But for our purposes isn’t the obvious teleology – that even Dawkins recognizes while denying – the important thing, at least as an initial question about the objective nature of things?

If theists and materialists can agree about the objective existence of teleology in nature, can we not also agree that – at least while we are doing science – questions about the ultimate provenance of that teleology can be held in abeyance?

I see a number of advantages of this approach for both sides.  For the materialists, the advantages are obvious.  They will be able to accept on face value the common sense conclusion their materialism has until now forced them to deny.  Teleology exists.  And at the same time they will not be forced to allow Lewontin’s dreaded “divine foot” in the door, because a “natural telic law” is not even an agent, far less a divine (or even conscious) agent.  For theists, as I have argued all along, ID can be adopted to both a monist and a dualist metaphysics.  And I, when I am not doing science, will continue to argue that God is the best candidate for the provenance of the teleology.  At the same time, by allowing for the possibility of a natural telic law, we ID proponents will not have the doors of science slammed in our face on account of the “creationism in a cheap tuxedo” argument.

The better choice.