Primeval nanotech v. Darwinism.

Irreducible Complexity in Molecular Machine Assembly
Evolution News | @DiscoveryCSC

We know that many molecular machines are irreducibly complex (IC) in their operation. Even more IC is the process of assembling them in the cell. A good example of this is the process of building our good old standby machine, ATP synthase (review our  animation to Proceedings of the National Academy of Sciences recognize the F0 rotating part and the F1 synthesis part).

A new “tour de force” paper by He et al. in the Proceedings of the National Academy of Sciences (PNAS), co-authored by Nobel laureate John E. Walker (who at age 77 is still researching these tiny rotary engines), describes new insights into how these multi-part machines are assembled. In a companion Commentary on PNAS, three scientists (Song, Pfanner and Becker) put it bluntly: “The assembly of the mitochondrial ATP synthase is a complicated process that involves the coordinated association of mitochondrially and nuclear encoded subunits.” Here’s a taste of what they mean (don’t worry; this won’t be on the test):

Based on their findings [He et al.], they propose an elegant model of how the membrane domain of human ATP synthase is built (Fig. 1, Upper). In one branch, an F1–c-ring intermediate associates with the peripheral stalk and the supernumerary subunits e and g. In the other branch, the F1 domain first assembles with the peripheral stalk and supernumerary subunits e, g, and f. Both pathways merge in a key assembly intermediate that contains the F1 domain, the c-ring, the peripheral stalk, and the supernumerary subunits e, g, and f. In all these vestigial [i.e., incomplete] ATP synthase complexes, the inhibitory protein IF1 is enriched to prevent ATP hydrolysis by the uncoupled ATP synthase. The presence of the supernumerary subunits e, g, and f is crucial for the subsequent integration of the mitochondrially encoded subunits ATP6 and ATP8 that are stabilized by addition of 6.8PL. Thus, the proton-conducting channel between ATP6 and the c-ring is formed. At this stage, ATP synthesis is coupled to the proton-motive force and the inhibitory protein IF1 is released. Finally, DAPIT is added to the assembly line to promote dimerization and oligomerization of the ATP synthase.

Whether or not you can follow the jargon is not as important as what they witnessed:  an “elegant” process that requires precise timing and coordination. Different machine parts must arrive on schedule, and assemble into intermediate (vestigial) forms that are nonfunctional alone. An inhibitor protein makes sure the machine doesn’t switch on ahead of schedule. The proton-conducting channel has to form just right so that it doesn’t “leak” protons. Only when all the parts are ready does the machine begin to rotate, but even then, the work isn’t complete. Another player is “added to the assembly line” to position the machines on the folds of the mitochondrial membrane (called cristae) at precise angles and spacings for optimum productivity.

The parts must arrive at the construction site on time. Some of them come from the nucleus, which must seem like many miles away at the scale of the machine. Some are built locally by genes within the mitochondrial genome. Interestingly, there are differences between yeast and humans regarding which genes are encoded where, and in what order they are assembled. But the proof of the pudding is in the respiration after eating: both versions of the machine work efficiently for their respective organisms.

The intermediate structure, somewhat like a scaffold on which the machine will be built, is also irreducibly complex:

We have shown that the assembly of human ATP synthase in the inner organellar membrane involves the formation of a monomeric intermediate made from 25 nuclear-encoded proteins into which the two mitochondrially encoded subunits are inserted and then sealed by association of another nuclear-encoded protein, thereby dimerizing the complex. Association of a final nuclear protein oligomerizes the dimers back-to-face along the cristae edges.

Notice that parts from the different genomes have to work tightly together. It’s like a manufacturing plant receiving parts locally and from India that have to meet agreed-on specifications to match. There are also rules for import, just like for parts arriving from a far country. The nuclear-encoded parts have to pass through two distinct checkpoints (the inner and outer membranes of the mitochondrion), which each have their robotic security personnel to validate them and facilitate their transport to the inside.

Previous work has shown how the completed “factory” of machines is organized within the mitochondrion. A specific nuclear protein seals them in two’s (dimers) at an angle, such that the rotating F0 proton pumps can maximize the intake of proton fuel, while the F1 parts, where ATP synthesis occurs, are farther apart to not crowd the output molecules. A “final nuclear protein” joins the dimers together (oligomerizes them) along the membrane edges. The longitudinal spacing is also tightly controlled, so that they don’t crowd each other. Every point of the assembly is programmatically directed. When everything is completed, rows of ATP synthase motors are arranged like turbines in a hydroelectric plant, feeding off a flow of protons produced by upstream machines in the respiration transport chain.

Ribosome Assembly

Viewers of cellular animations like those in Unlocking the Mystery of Life could never forget the assembly-line process inside the ribosome, where precisely-sequenced messenger RNAs are matched with transfer RNAs carrying amino acids to form proteins. The entrance tunnels for the ingredients and the exit tunnels for the polypeptides, and everything in between, must be positioned exactly for correct operation. The ribosome is certainly one of the most stunning examples of information translation in all of nature. But how is the ribosome itself built?

Nature  has provided an early version of an unedited manuscript by Sanghai et al. about ribosome assembly. Although it has been accepted for publication, it will be subject to editorial revisions. The subject matter, though, appears to show another stunning case of irreducible complexity in the construction of this important molecular machine. Here’s the Abstract:

Early co-transcriptional events of eukaryotic ribosome assembly result in the formation of precursors of the small (40S) and large (60S) ribosomal subunits. A multitude of transient assembly factors regulate and chaperone the systematic folding of pre-ribosomal RNA subdomains. However, due to limited structural information, the role of these factors during early nucleolar 60S assembly is not fully understood. Here we have determined cryo-EM reconstructions of the nucleolar pre-60S ribosomal subunit in different conformational states at resolutions up to 3.4 Å. These reconstructions reveal how steric hindrance and molecular mimicry are used to prevent both premature folding states and binding of later factors. This is accomplished by the concerted activity of 21 ribosome assembly factors that stabilize and remodel pre-ribosomal RNA and ribosomal proteins. Among these factors, three Brix-domain proteins and their binding partners form a ring-like structure at rRNA domain boundaries to support the architecture of the maturing particle. Mutually exclusive conformations of these pre-60S particles suggest that the formation of the polypeptide exit tunnel is achieved through different folding pathways during subsequent stages of ribosome assembly. These structures rationalize previous genetic and biochemical data and highlight the mechanisms driving eukaryotic ribosome assembly in a unidirectional manner.

The requirements of IC are met in this description: “a multitude of transient assembly factors” regulate and systematically fold the proteins that will be used to construct the machine. The authors mention “21 ribosome assembly factors that stabilize and remodel” the RNA and proteins before the machine is even operational. Inside the growing ribosome, a scaffold holds factors for the exit tunnel in place. Everything is choreographed in time and space with “mechanisms driving… assembly in a unidirectional manner.”

Here we see numerous parts working together on a timeline. The parts alone do not work individually. You can have all the proteins delivered to the construction site, and nothing will happen without the programmed mechanisms to put them together in order. Some parts hold others in place, others guide the folding of protein parts, and some even prevent premature assembly. All the pathways for assembly of the subdomains are regulated by a master program, so that each group of steps follows a “unidirectional” plan toward the finished product. It’s a marvelous IC assembly process that produces an IC machine. If five parts of a mousetrap are sufficient to indicate IC, how about dozens of parts, all following a programmatic sequence of assembly?

In Unlocking, concerning the assembly of the bacterial flagellum, Paul Nelson described how the hierarchical IC of machine assembly in the cell challenges Darwinian theory. “In order to construct that flagellar mechanism, or tens of thousands of other such mechanisms in the cell, you require other machines to regulate the assembly of these structures. And those machines themselves require other machines for their assembly.” Jonathan Wells nailed the point by saying, “If even one of these pieces is missing, or put in the wrong place, your motor isn’t going to work. So this apparatus to assemble the flagellar motor is itself irreducibly complex. In fact, what we have here is irreducible complexity all the way down.”

Ancient whale returns for second helping of Darwinists' homework.

Of Whales and Timescales
Andrew Jones

Joshua Swamidass, assistant professor in the Department of Pathology and Immunology at Washington University, has responded to an Evolution News article about whale evolution. The original article concluded:

We don’t find the “pattern” that evolution predicts “should be found in the fossil record at certain times.” Rather, we find that truly aquatic whales appear abruptly. And even if we accept some of the fossils as “intermediates” between whale and land mammals, there is not enough time for the complex adaptations needed for whales’ fully aquatic lifestyle to evolve. Whatever the correct explanation is for the origin of whales, unguided evolutionary mechanisms are not the answer.

Swamidass writes:

Looking at this progression [of skulls] we uncover an amazing fact. Surprisingly, whales have the same body plan as a terrestrial mammal! It’s the same body plan, with several intermediate forms. Looking at several features (e.g. ears, bone density, teach), we can see this transition beautifully. Look how we can see the nostrils slowly move back to the top of the head…

Yes, it is beautiful. One adapted for land, another for water, and one is intermediate. But take care; nothing is actually moving in those pictures. Any transition is in the interpretive imagination of the beholder.

Getting back to the claim that millions of years is “not enough time.” There is no genetic or mathematical analysis to back up this conjecture. What types of genetic changes are required for whale evolution? How unlikely or likely are they?

Consider a paper published in PLOS Computational Biology,  “The Time Scale of Evolutionary Innovation.” The authors explore how long it should take for evolution to make a complex coordinated change to a sequence. They find that mutation alone would be little different from creating a completely fresh sequence each time using random letters, but that if natural selection is acting to “regenerate” the original sequence, and if the original sequence happens to be near the target, then evolution is much more likely to make the transition. This should be common sense, I think. Note the core result: a sequence of length L requiring only k specific coordinated changes will require Lk+1 trials. They describe this as “polynomial” because it is polynomial in L but it is exponential in k.

What this means is, if it takes 100 generations for a specific mutation to occur, it will take (at least) 10 thousand generations for a specific set of 2 mutations to occur, and 100 million generations for a specific set of 4 mutations to occur. At human generation lengths that would be 2 billion years. Two billion years, for a 4-letter “innovation.” That puts a hard limit on what kind of magic we can expect from evolution. This basic problem is then greatly exacerbated by population genetic effects; each mutation must not only occur, it must become fixed or at least well established in the population, and there is no selection to help until you get the last mutation in the set.

Now consider the mutations that actually have occurred in humans in recent human history. Some have been interesting, including significant tweaks to melanism, and milk digestion, but none of them are spectacular (no X-Men) and certainly none have constructed new biochemical systems or new healthy morphology. The waiting times problem informs us that all the mutations in the history of the human species must have been similarly banal. Think about that for a moment. Are you surprised? You should be if you believe we evolved from something like an ape. Evolution has to work one step at a time. It cannot do the kind of complex coordinated magic that a human designer or engineer can. If you believe humans evolved, you have to believe it can happen without any complex coordinated changes at all (in this context complex means just 4 or more specific letters at the same time — not 4 new proteins). In fact, the exponential character of the waiting times problem tells us that all of evolution must have been similarly limited, right back to the Cambrian explosion. In turn, that raises the question of how the radical innovations of the Cambrian explosion could have occurred

From a Batmobile to a Yellow Submarine

The Evolution News article argued that for a land mammal to become a whale, or a Batmobile to become a Yellow Submarine, it would require multiple coordinated changes. To many people this would be a trivial and common sense assumption, even without the detail given in the article. However, citing another paper, “Molecular evolution tracks macroevolutionary transitions in Cetacea,” Swamidass pushes back:

It is remarkable how many of the changes required for whale evolution are caused by loss of function mutations (which end causing “pseudogenes”), or small tweaks to proteins. This is one of the big surprises of mammalian evolution. Large changes can take place with tweaks to the genetic code. Eyes adapt to underwater vision by losing a rhodopsin gene. Hind Limbs are lost with the loss of a homeobox gene. Taste buds are lost when two genes are lost. Smell receptors are almost entirely lost in most species too. In all these cases, we see remnants of the broken genes, and in many cases the details of how these losses increase function are well understood.

This is all true. It is true that overall efficiency can be increased by losing unused functional components. On a design view, it makes sense to deactivate things that are not being used. Often this needs no more than a flip of a switch, and this no great challenge for evolution either. On the other hand, why would the random loss of information make a functional body plan? Researchers have created legless mice by knocking out a Hox gene, in an effort to understand snakes, but the resulting mice were simply paralyzed and could not mate. Also, note that at some point evolution has to explain the origin of all the proteins, Hox genes, as well as the rhodopsins and receptors that have been lost, and that is rather more difficult. An evolutionary process that creates nothing new is soon going to run out of other organisms’ proteins to borrow.

Remarkably, it does not appear any new enzymes or de novo genes are required in whale evolution. It appears that small tweaks to existing proteins, or loss or alteration of the function of existing genes, account for the changes we see at this point.

True, that is not where the challenge to whale evolution lies. But why is it remarkable to see no new genes? It turns out that a large number of genes are taxonomically restricted or ORFan genes. That means they seem to appear without evolutionary history in the twigs and leaves of the tree of life. Moreover, some even  turn out to be essential, which would be very odd if they have been added last by evolution. The existence of these genes is a common problem elsewhere in the evolutionary story, even though it appears not to be relevant to whales. Protein coding genes are hard to explain when they appear de novo — see  Doug Axe’s work as well as this recent EN article .

Also, there does not appear to be any reason that a large number of these changes must happen at the same time. They appear gradually in the tree, and it’s not clear at all why they would need to be “coordinated”. They do not appear to need to occur at the same place and time to be useful. So this does not make these transitions unlikely.

This is where we have to disagree. Some of the changes listed might be independent, small, and easy, but there are also some pretty massive, complex ones that would seem to need coordination. For one example, losing tooth enamel does not make baleen plates. For another, whale testes are inside the body. In itself this appears to be a trivial change, and it makes good design sense in terms of streamlining. That is, until you try to implement it, and find that mammalian testes become infertile if kept too warm, so now you need a cooling system, or else a redesign of the reproductive system. It is not so trivial any more. And the changes do need to be coordinated. What selective advantage is there in a cooling system? None unless you have testes there. What selective advantage is there in internal testes? None, unless a cooling system is there. It turns out that dolphins and whales have mysteriously acquired an elaborate counter-current cooling system that keeps the testes the same cool temperature as its fins! That system is not trivial, and it is not going to evolve with just one or two mutations.

A Design Perspective

Considering this from a design perspective, and speaking as one experienced in doing design, it’s going to be tough to convince me that one could “evolve” a program with a series of single-letter changes, deletions, and random copy-pasting, all while it continues to compile and function. The notion is in conflict with our experience of how complex functional systems actually work.

We have also argued that homoplasies constitute evidence of common design. Swamidass argues these can be explained by convergent evolution

Also, we also see convergent mutations between whales, bats (echolocation), and beavers (diving adaptations to blood). These “homoplasies” are the rare exceptions to the nested clade pattern of common descent, and are exactly what we expect in evolutionary process, just like we see recurrent mutations in cancer, and convergent evolution in human HLA variation. Everyone agrees that human variation arises by natural processes, and that cancer arises by natural processes, yet we see homeoplasies here too; this is what we expect from common descent.

But another way of looking at it is that evolutionists have adapted their expectations in response to the evidence that homoplasies exist. They have long known about character traits that don’t fit the canonical Darwinian explanation of a branching tree, and convergent evolution has long been proposed as an explanation, but the truth is the authors of the original paper on bats and whales found this particular result “surprising” and “remarkable.”  From my own experience, I remember trying to persuade an evolution-evangelist that molecular homoplasies exist between extremely distant species, and he wouldn’t believe me! I will try to explain why.

Now, convergent evolution can happen, but it really depends on the particular circumstances. Convergence in cancer and HLA are different from convergence between bats and dolphins because they both involve very high mutation rates, coupled with strong selection effects acting on very small changes. In HLA the changes are concentrated in a tiny region of the genome. In cancer, strong positive selection acts on mutations that each help the cancer, but destroy some normal function.

It is one thing to find weak points where cars tend to break independently in the same place, or even how one breakage leads to another (e.g., brakes first then everything else as it careens of the road). It would be quite strange if cars independently acquired sonar capabilities, and even more so if the software upgrades were identical.

Imagine you assign a coding exercise to computer-science students. It is quite possible that two students would come to roughly the same solution, since there are likely only a few good solutions. That is how convergent evolution is supposed to work. However, what if they had not only the same general solution, but identical code too? Or imagine two history students write an essay about the causes of World War I. It is possible they come to the same conclusion. But if you see identical prose, you have to suspect plagiarism: it strongly suggests that the text or code was designed once and then used multiple times.

And that is why my friend did not believe me; because he did not believe the coding sequences would converge. It is easy to imagine, if evolution could find complex solutions at all, that it could find something similar again, but it is much harder to imagine that evolution would converge on the same code, since the mutations that write it are supposed to be random, especially if the code has been diverging for some time. However, now that we have found that there are molecular homoplasies at great taxonomic distance, the committed evolution-believers are surprisingly unfazed: all it means, they argue, is that there must be only one solution that works and natural selection finds it every time (while listening to Wagner). That’s an interesting theory, but can you prove it? If the evolution of complex traits is so predictable and reliable, it seems we should be able to set it up and see it happening.

Meanwhile, can you hear the students accused of plagiarism? But sir, it’s the only solution! And we are both geniuses! Hmm. If you are both geniuses, I look forward to your next assignment.

There is a much more parsimonious solution: common design.

Either way, the larger problem is that the changes involved in adapting a generic mammalian template into a whale are certainly not all simple, independent, single-letter changes. It seems obvious that multiple coordinated changes would be needed, and it turns out that would require a lot longer than mere millions of years.

Internet porn and diminishing returns.

After human exceptionalism:Ascent of the law of the jungle?

Now It's "Posthumanist Ethical Pluralism"
Wesley J. Smith 

The New York Times continually publishes  opinion pieces and news articles aimed at undermining human exceptionalism and the understanding that we have the highest moral value.

This is exceedingly dangerous. If human life doesn't have the highest ultimate objective value simply and merely because it is human -- an equal value to be distinguished from all other life forms on the planet -- there is no way to philosophically defend universal human rights.

Moreover, if we can't distinguish between our inherent value and that of animals, we will not elevate their status to our level but diminish our own to theirs.

Now, the Times has an extended interview with anti-humanist scholar Cary Wolfe, conducted by Natasha Lennard. Wolfe, who directs Rice University's Center for Critical and Cultural Theory, advocates a "posthumanist ethical pluralism" among us and with the rest of life on the planet.

Of course, Wolfe makes the usual claim among such believers that what is done to an animal or other life form should be judged as morally equivalent to the same thing being done to a human. From the interview:

N.L.: How might a posthumanist approach to undoing interspecies hierarchies intervene with structures of violence among humans themselves? Trump's election reflects and emboldens white supremacy and misogyny to a frightening degree. Could a posthumanist intervention risk moving focus away from a direct and much needed struggle against these things, or could it help?

What a moronic question. Can we all roll our eyes and hoot in unison?

And catch the big-brained vapid answer:

C.W. Oh, I think it can help enormously, by drawing out more clearly the broader base that these struggles share in what I've called a posthumanist ethical pluralism. My position has always been that all of these racist and sexist hierarchies have always been tacitly grounded in the deepest -- and often most invisible -- hierarchy of all: the ontological divide between human and animal life, which in turn grounds a pernicious ethical hierarchy. As long as you take it for granted that it's O.K. to commit violence against animals simply because of their biological designation, then that same logic will be available to you to commit violence against any other being, of whatever species, human or not, that you can characterize as a "lower" or more "primitive" form of life. This is obvious in the history of slavery, imperialism and violence against indigenous peoples. And that's exactly what racism and misogyny do: use a racial or sexual taxonomy to countenance a violence that doesn't count as violence because it's practiced on people who are assumed to be lower or lesser, and who in that sense somehow "deserve it."

But we don't believe any of that. Indeed, we have instituted increasingly stringent animal welfare laws precisely because we understand that as humans we have duties of humane care toward animals.

Moreover, raising chickens for eggs and inseminating cows does not lead to "rape culture."

What the hell would instituting a society based on "posthuman ethical pluralism" mean in actual practice? Unsurprisingly such practical questions are left unanswered in the interview:

C.W. The first imperative of posthumanism is to insist that when we are talking about who can and can't be treated in a particular way, the first thing we have to do is throw out the distinction between "human" and "animal" -- and indeed throw out the desire to think that we can index our treatment of various beings, human or not, to some biological, taxonomic designation. Does this mean that all forms of life are somehow "the same"? No, it means exactly the opposite: that the question of "human" versus "animal" is a woefully inadequate philosophical tool to make sense of the amazing diversity of different forms of life on the planet, how they experience the world, and how they should be treated.

If we reject the moral hierarchy of life with us at the apex, does it mean we can't eat meat? Does it mean we must fundamentally harm ourselves by ceasing animal experimentation?

In the real world -- yes, I know that is not where professors tend to live -- all of this is simply unworkable. And the potential adverse impact of trying to impose policies based on such thinking would do unquantifiable harm to human thriving.

But do note that the entire discussion rests on the extent and depth of human moral duties that we assign to ourselves. And indeed, the entire question proves the moral hierarchy that Wolfe is at such pains to deny. No other species in the known universe could even engage the question, much less decide that altruism requires elevating morally lesser life forms into equal -- or higher -- consideration with our own.

Among the ranks of the insane.

Yet more from the ranks of the insane.

Nature's Engineers v. Darwin.

Masters of Physics in the Living World
Evolution News | @DiscoveryCSC

Throughout the living world, cells, plants and animals display proficiency in dynamics — the physics of movement. Pulling off these successful moves often involves precise coordination of different physical laws.

Damselfly Elasticity

We all know about dragonflies (Günter Bechly’s specialty), those brilliant hovering insects that delight children and adults. Damselflies are similar, except slightly smaller and more slender. We could spend time talking about these amazing insects’ use of optical flow navigation, predictive hunting techniques, or other capabilities that inspire human engineers. Today, let’s learn about another trait requiring mastery of physics: the flexibility of the joints in their wings. A new paper in  PLOS ONE revealed an amazing protein that makes the wings springy and flexible. In “Morphological and mechanical properties of flexible resilin joints on damselfly wings,” they introduce the protein resilin:

The main focus of this study is on the flexible element that has been found on the wings of damselflies, called resilin. Resilin is the rubber-like protein found in specialized regions of the cuticle of most insects that gives low stiffness, high strain and efficient energy storage that functions in insect flight. Weis-Fogh first described resilin from the flight systems of locusts and dragonflies, it was described to be similar to swollen isotropic rubber, but its elastic behaviour is unlike any other natural or synthetic polymer. Additionally, resilin was shown to have remarkable mechanical properties where it is two decades [i.e., orders of magnitude] higher than for elastin, suggesting that resilin is a more mobile bio-polymer. 

An insect wing needs to achieve the optimum tradeoff of elasticity and durability. It cannot tear too easily in the wind, but it cannot be too stiff, either. The resilin protein has the ideal properties for flexibility and energy storage. It can deform and then pop back into position with a spring-like response. “Resilin functions as an elastic spring that demonstrates extraordinary extensibility and elasticity,” the four authors say. The springiness comes from the precise placement of the correct amino acids in the sequence.

Using atomic force microscopy and other techniques, the researchers measured the physical properties of resilin that give it such ideal properties, allowing wings to flex and get the most lift for amount of energy consumed. There’s more than just the availability of resilin to the insect. The researchers also found that the distribution of resilin varies throughout the wing, putting the flexibility where it is most needed. That’s a separate design principle from the material alone:

The structural analysis revealed that the flexibility of the wings varied from one area to another, and the resilin distribution pattern was the mechanism that controlled the characteristics of the wing…. Additionally, the AFM images revealed resilin nanostructures of varied sizes and enabled the calculation of elasticity values at each section of the wing; membrane, mobile and immobile joints in Rhinocypha spp…. While studies on silks and elastin received a lot of attention in the past decade, this has now change [sic] to focus on recombinant resilin; structure-mechanical properties of the resilin with potentially greater application in a variety of fields.

As is common in papers dealing with natural designs, biomimetics has overtaken evolution as the focus of interest. The authors are excited to think about how their discovery could help engineers use this “remarkable” springy protein for “greater application in a variety of fields.” Flubber, perhaps? Nature had it first!

High Jump Champs

Who could forget the remarkable gears of the planthopper we wrote about five years ago that store elastic energy for its rapid jumps? Well, Current Biology published an interesting “Quick Guide” to “Insect Jumping Springs” that shows there’s more than one way to leap. Although Sutton and Burrows don’t mention the gears, they do share some “Wow!” facts about planthoppers:

A planthopper can accelerate in less than 1 millisecond to a take-off velocity of 5 [meters per second], requiring a power output (energy per given time) of tens of thousands of Watts per kilogram of muscle.

How can they get such superpowers, when muscle can only generate 300 Watts per kilogram? There’s another physical limitation, too: the faster a muscle contracts, the less power it can generate, “exacerbating the problem.” Furthermore, for a jumping insect, the power can only operate when it’s in contact with the ground. A poor planthopper seems to have three strikes against it.

How do these insects do it? They jump by using springs; devices that allow energy to be stored gradually in mechanical deformations and then released abruptly.

In insects that use springs to jump, the legs are first moved into the same cocked position and the joints locked. The power-producing muscles then contract slowly over periods of 100 milliseconds to a few seconds without moving the legs; instead, the force generated distorts parts of the skeleton, which store mechanical energy. The sudden release of these loaded skeletal springs then powers the rapid propulsive movements of the legs. The elastic recoil of the spring returns the stored energy very quickly. The power is amplified because almost all the energy produced by the slow contraction of muscle is returned to the leg in a much shorter time, delivering the thousands of W kg–1 of mechanical power required for jumping.

The authors compare this to stretching an archery bow and releasing the stored energy rapidly. “Compare how far you can throw an arrow with how far you can fire it with a bow,” they comment. Known insects that use springs for jumping include fleas, grasshoppers, froghoppers, planthoppers, flea beetles, and “even in a cockroach,” but many more are likely to be discovered. If you see an insect achieving more than 300 Watts per kilogram of muscle, it’s probably using a spring mechanism. And now, once again, we find that protein resilin we just learned about:

These springs are a composite of hard, highly-sclerotized cuticle and the highly-elastic protein resilin. A hard material such as sclerotized cuticle can store considerable energy even if deformed by only a small amount, but is susceptible to fracture. Resilin, on the other hand, is much softer, stores much less energy when deformed a similar amount, but is resilient and able to strain large amounts if necessary. It returns quickly and reliably to its original shape upon repeated deformations.

What a remarkable thing: the same protein is used for completely different functions in the damselfly wing and in the froghopper leg. Notice, too, that resilin has to cooperate with the structures around it. By itself, it could neither fly nor jump. As with the previous article, the authors end with biomimetics — a design focus. Imitating the jumps of insects will require detailed research, showing that design is not a science stopper, but an inspiration for scientific understanding and application:

The shape and material composition of these biological springs are very different from man-made springs. If we wish to apply biological lessons to modern spring design we need to address three outstanding questions. First, how does the geometry of the biological springs affect their ability to bend, store and release energy? How are the different springs adapted to meet the specific needs of different insects? Finally, what contributions do the hard and soft component materials make to the properties of the springs that enable such reliable storage and release of energy?

That’s another example of what we said at the beginning: achieving these feats of dynamics “involves precise coordination of different physical laws.” In this case materials science, energetics, elasticity, acceleration, and more were involved. Even then, nothing would work without the brain programming to use it.

Plant Gyroscopes

Plants seem so passive, just blowing in the wind, with nowhere to go. We know, however, that certain plants can move rapidly by storing turgor pressure, such as the sensitive plant and the Venus flytrap. There’s one area in botany that really puts the dynamite in dynamics: seed dispersal. A fascinating new study from Pomona College and the Rancho Santa Ana Botanic Garden, reported by  Phys.org,  reveals a highly unusual example: a plant that has mastered the Frisbee toss! And it’s a most unlikely contender: the wild petunia Ruellia ciliatiflora — “not actually very closely related to petunias, though it does produce pretty flowers.” (Hey, it’s time to plant your garden annuals for spring color.) So how does this humble little flower disperse its seeds over large distances? Get ready for some more “Wow!” expressions, because we have another world record to share:

What is most striking about the plant is the way it disperses its seeds — by flinging them great distances when its fruit is exposed to water. But until now, little research has been done to find out how the flower flings them so far. To learn more, the researchers brought some of the plants into their lab and filmed seed dispersal using a high-speed camera.

The researchers discovered that there are multiple factors at play. One is the glue-like material that holds the seeds in place, another is the disc shape of the seeds. Little hooks behind the seeds also assist in launching them. Perhaps most importantly, spin develops due to the way the seed is flung. In slowing down the action, the researchers observed that the seeds spin up to 1,660 times per second, making them the fastest spinners known in nature.

Faster than a spinning Frisbee, this plant accelerates its seeds’ angular momentum to this incredible speed, faster than any animal can (including a human Frisbee champ), giving the seed more lift and farther distance. How does it do it? The authors did not say. They did find that the rapid spinning has a purpose: a surprising gyroscopic effect:

The videos offered evidence of the assist the seeds get from spinning — some of those ejected did not spin, and only traveled half as far as those that did. And those that did were able to travel as far as seven meters and were launched at speeds up to 22 miles per hour. Oddly, they spin vertically and counterclockwise, like a Frisbee on its side. The spin, the researchers found, resulted in a gyroscopic effect, keeping the seeds stabilized while the backspin produced less drag, keeping the seeds aloft longer and thus allowing them to fly farther.

That’s amazing. Who would have thought a plant could launch seeds at 22 mph with a spin of 1,660 rotations per second? Those seeds must have seemed like a blurry bullet passing by before the high-speed camera revealed the secret. Once again, we see that this plant had to utilize multiple laws of physics to succeed: properties of materials, gyroscopic effects, aerodynamics and hydrodynamics (since water is involved). How many mutations did that take?

These three examples show that there’s a world of design out there needing to be revealed. If you earn a degree in biomimetics or physics, never lose your inspiration at the ingenuity of living designs. They are the real PhDs. Scientists are their students.

The assault on Adam and Eve continues.

Adam and the Genome and the Mysterious Origin of De Novo Genes
Evolution News | @DiscoveryCSC

In his book in  Adam and the Genome, which we’ve been reviewing, a final case where biologist Dennis Venema deals with evidence that is irrelevant to the existence of Adam and Eve is his claim about ORFan genes. These are genes that don’t resemble genes in other organisms. They are “orphans.”

According to Venema, a theistic evolutionist associated with BioLogos, these genes are no problem for unguided evolution to explain. That is because they spontaneously arise “de novo” from non-gene-coding sequences in DNA.

Once again, as will not come as a surprise if you have followed the present review series, Venema’s target is intelligent design theorist Stephen Meyer. (Possible alternative title for this book: Adam and Steve.) Venema writes:


Though Meyer claims that “evolutionary biologists typically use the term ‘de novo origination’ to describe unexplained increases in genetic information” and that the term “does not refer to any known mutational process,” this is simply not the case.  De novo genes come from DNA sequences that are only a few mutational steps away from becoming a transcribed and translated gene.

(Adam and the Genome, p. 86)

Venema doesn’t provide enough context to show what Meyer actually wrote about de novo gene origination. Here’s what Meyer said in  Darwin’s Doubt on the subject:

Many other papers invoke de novo origination of genes. Long mentions, for example, a study seeking to explain the origin of an antifreeze protein in an Antarctic fish that cites “de novo amplification of a short DNA sequence to spawn a novel protein with a new function.” Likewise, Long cites an article in Science to explain the origin of two human genes involved in neurodevelopment that appealed to “de novo generation of building blocks — single genes or gene segments coding for protein domains,” where an exon spontaneously “originated from a unique noncoding sequence.” …

Another 2009 paper in the journal Genome Research was appropriately titled “Darwinian Alchemy: Human Genes from Noncoding RNA.” It investigated the de novo origin of genes and acknowledged, “The emergence of complete, functional genes — with promoters, open reading frames (ORFs), and functional proteins — from ‘junk’ DNA would seem highly improbable, almost like the elusive transmutation of lead into gold that was sought by medieval alchemists.” Nonetheless, the article asserted without saying how that: “evolution by natural selection can forge completely new functional elements from apparently nonfunctional DNA — the process by which molecular evolution turns lead into gold.”


(Darwin’s Doubt, p. 220)

What do we see? Meyer discusses sources that explain how de novo genes are thought to come from noncoding DNA sequences — “from ‘junk’ DNA” — just as Venema says they do. Venema suggests Meyer doesn’t acknowledge this possibility, yet, plainly, Meyer cites from papers on de novo gene origin that discuss this very idea. Meyer doesn’t miss the point that Venema accuses him of missing.


Meyer is correct to explain that the processes underlying de novo gene origination are mysterious and unestablished. Geneticist Michael Lynch, for one, writes:

[A] remarkable one-third of the predicted genes in the human genome have no identifiable homologue in any other well-characterized non-primate species, even other mammals (Dehal et al. 200L). This poorly understood genomic feature is not unique to humans (or primates), as it has been repeatedly found in the sequenced genomes of other metazoans. The source and functionality of these orphan genes remains unresolved. Many might simply be derivatives of ancestral coding sequences subject to unusually rapid rates of substitution and/or rearrangement, and relatively short proteins may fortuitously arise de novo from chance open reading frames in noncoding DNA that happen to be located near spurious transcription factor binding sites (Begun et al. 2006).


(Michael Lynch, The Origins of Genome Architecture, 2007, p. 49

Thus, Lynch admits that many mysteries surround the origin of de novo genes. No wonder the paper Meyer points to calls this process “Darwinian Alchemy.”


Of course, Meyer and many other ID proponents would be highly skeptical of claims that non-coding DNA could spontaneously transform into a functional gene. Indeed, one paper he cites notes that such an event is “highly improbable.” The problem is that proponents of de novo gene origins never address the likelihood of a patch of functionless “junk” DNA spontaneously mutating into a functional, useful gene. Again, here’s what Meyer writes, rebutting Long et al. 2003 who also invoke de novo gene origin:

Thus, ultimately, the scenarios featured in Long’s review essay do not explain the origin of the specified information in either genes or sections of genes. That would require a cause capable of solving the combinatorial inflation problem discussed in the previous chapters. But none of the scenarios discussed in Long’s article even addresses this problem, let alone demonstrates the mathematical plausibility of the mechanisms they cite.


(Darwin’s Doubt, p. 221)

This is the same problem we saw with Venema’s discussions of other evolutionary explanations for the origin of genes via gene duplication: no discussion is ever given to the likelihood of a noncoding region suddenly transforming into a functional gene. Venema might infer common ancestry between a gene and some noncoding region via sequence homology, but that does not demonstrate that an unguided evolutionary mechanism was likely to cause the conversion.


Unless Venema specifically addresses the likelihood of converting some non-coding “junk” sequence of DNA into a fully functional, useful orphan gene, he has not responded to Meyer’s argument.

Why we should all be grateful that the vertebrate eye was not designed by Darwinists.

Mystery of the reverse-wired eyeball solved
To be presented at the 2015 APS March Meeting in San Antonio, Texas, March 5

AMERICAN PHYSICAL SOCIETY


From a practical standpoint, the wiring of the human eye - a product of our evolutionary baggage - doesn't make a lot of sense. In vertebrates, photoreceptors are located behind the neurons in the back of the eye - resulting in light scattering by the nervous fibers and blurring of our vision. Recently, researchers at the Technion - Israel Institute of Technology have confirmed the biological purpose for this seemingly counterintuitive setup.

"The retina is not just the simple detector and neural image processor, as believed until today," said Erez Ribak, a professor at the Technion - Israel Institute of Technology. "Its optical structure is optimized for our vision purposes." Ribak and his co-authors will describe their work during the 2015 American Physical Society March Meeting, on Thursday, March 5 in San Antonio, Texas.

Ribak's interest in the optical structure of the retina stems from his previous work applying astrophysics and astronomy techniques to improve the ability of scientists and ophthalmologists to view the retina at high detail.

Previous experiments with mice had suggested that Müller glia cells, a type of metabolic cell that crosses the retina, play an essential role in guiding and focusing light scattered throughout the retina. To test this, Ribak and his colleagues ran computer simulations and in-vitro experiments in a mouse model to determine whether colors would be concentrated in these metabolic cells. They then used confocal microscopy to produce three-dimensional views of the retinal tissue, and found that the cells were indeed concentrating light into the photoreceptors.

"For the first time, we've explained why the retina is built backwards, with the neurons in front of the photoreceptors, rather than behind them," Ribak said.

Future research for Ribak and his colleagues includes using water-filled goggles to reduce corneal aberrations, allowing observers to gain a finer view of the retina at depth.

Patristic writings re;the immortality of the soul.

The skilled trades :still the smart choice IV

The design debate through the looking glass

Design through the Looking Glass

Evolution News & Views 

You don't have to hold an amino acid up to a mirror to see its mirror image. Amino acids (except for one, glycine) come in pairs, like gloves, on the real-world side of the looking glass. So do the sugars used in DNA and RNA; they are assigned a "handedness" based on conventional rules of describing their orientation in 3-D space. In all other physical respects, chemical and thermodynamic, they are identical in their activity. This makes them difficult to separate.

The phenomenon is known as chirality. The chiral "isoforms" are called enantiomers of each other. Left-handed enantiomers are preceded byL- (from Latin levo) as in L-alanine, while right-handed enantiomers are preceded by D- (fromdextro) as in D-ribose. A mixture of both hands is said to be racemic, or heterochiral. A pure mixture of one hand is called homochiral.

With only rare exceptions, all living things use just one "hand" of these molecular gloves: left-handed amino acids in proteins, and right-handed sugars in nucleic acids. How this came about has long been a mystery, as four Chinese scientists from Tsinghua University in Beijing explain in Nature Chemistry:

Despite biology's seemingly limitless diversity and the vastness of its territories that permeate into virtually every corner of the Earth, at the fundamental level of biochemistry, all known forms of life are narrowly defined by a single version of molecular machinery based on L-amino acids and D-ribose nucleic acids. Although rare examples of the use of D-amino acids, such as D-aspartic acid in animal brains, and L-sugars, such as L-arabinose in plants, do exist, the central dogma and most of the biological macromolecules have followed the homochirality established by life's earliest ancestors. Processes that led biology onto this particular chiral path have remained largely elusive, even though experimental evidence for breaking the mirror symmetry has been reported and many theoretical models have been proposed.[Emphasis added.]

As it stands, no experimental or theoretical model explains the origin of life's homochirality by natural processes. Some experimenters have produced a slight enantiomeric excess of one hand or the other, but usually with non-biological chemicals, and nothing approaching the purity of life's chiral molecules. Proteins and nucleic acids cannot work with mixed handedness. A single wrong-handed building block is enough to destroy DNA, RNA, and proteins. As we saw last year, checkpoints ensure that life's building blocks remain homochiral.

This purity of handedness baffles materialists, because their causal toolkit only includes natural law and chance. The probability of getting a single-handed polymer from racemic ingredients is comparable to getting a string of coin tosses coming up all heads. The longer the sequence, the more improbable it becomes -- quickly swamping the chance hypothesis. Yet as Wang et al. state, our knowledge of natural laws isn't helping solve the problem.

Recently, an in vitro selected catalytic RNA capable of incorporating nucleotides in a cross-chiral fashion without enantiomeric cross-inhibition was reported. The fact that no known laws of physics and chemistry preclude biology's use of either of the two chiral systems, mirror-image twins of one another, has led to an intriguing question as to whether a parallel mirror-image world of biology running on a chirally inverted version of molecular machinery could be found in the universe or be created in the laboratory.

Turning from origins to application, they describe their initial attempts to create mirror-image life:

We reasoned that towards synthesizing a mirror-image biological system, an imperative step would be to reconstitute a chirally inverted version of the central dogma of molecular biology with D-amino acid enzymes and L-ribose nucleic acids--although reconstituting a mirror-image, ribosome-based translation systemthrough the total synthesis of all the ribosomal RNA (rRNA) and protein building blocks is still beyond the current technology, the totalchemical synthesis of (small enough) mirror-image polymerases might be feasible. Here we set out to synthesize such a mirror-image polymerase and to test if two steps in the central dogma, the template-directed polymerization of DNA and the transcription into RNA, can be carried out in a synthetic mirror-image molecular system (Fig. 1a).

(For present purposes, we won't dispute the central dogma, although biologist Jonathan Wells has written extensively on its problems.)

These scientists did, in fact, succeed in getting some template-driven polymerization and transcription of opposite-handed amino acids. It was very slow, but it demonstrates that, in principle, life could exist in a mirror image of itself. Alice through the looking glass would appear identical to her mirror image, but would not be able to eat opposite-handed food!

Commenting on this work for Nature, Mark Peplow explains why synthetic mirror-image biomolecules have desirable properties:

In principle, looking-glass versions of these molecules should work together in the same way as normal ones -- but they might be resistant to attack by conventional viruses or enzymes that have not evolved in a looking-glass world.

That makes mirror-image biochemistry a potentially lucrative business. One company that hopes so is Noxxon Pharma in Berlin. It uses laborious chemical synthesis to make mirror-image forms of short strands of DNA or RNA called aptamers, which bind to therapeutic targets such as proteins in the body to block their activity. The firm has several mirror-aptamer candidates in human trials for diseases including cancer; the idea is that their efficacy might be improved because theyaren't degraded by the body's enzymes. A process to replicate mirror-image DNA could offer a much easier route to making the aptamers, says Sven Klussmann, Noxxon Pharma's chief scientific officer.

Wang et al. took the smallest known polymerase enzyme, just 174 amino acids long, and laboriously constructed a right-handed counterpart. They succeeded in getting it to extend a primer from 12 nucleotides to 18 nucleotides in 4 hours. Getting it to 52 nucleotides took 36 hours -- a "glacial pace," Peplow remarks. Nevertheless, it was an important discovery. Both the normal and mirror-image enzymes worked independently, without interference, when mixed in the same test tube.

The Design Inference

The researchers admit it would be a "daunting task" to build a mirror-image version of a ribosome where translation could take the left-handed RNA and translate it into a right-handed protein. Building a "looking glass cell" is a far-off dream. At this stage, though, we can draw some conclusions about chance and design.

Peplow confirms that homochirality remains a vexing problem. He surely would have said otherwise if a likely non-random cause were known.

In their research paper, the Tsinghua researchers also present their work as an effort to investigate why life's chirality is the way it is. This remains mysterious: it may simply be down to chance, or it could have been triggered by a fundamental asymmetry in nature.

But Steven Benner, at the Foundation for Applied Molecular Evolution in Alachua, Florida, says it's unlikely that creating a mirror form of biochemical life could shed any light on this question. Almost every physical process behaves identically when viewed in a mirror. The only known exceptions -- called 'parity violations' -- lie in the realm ofsubatomic physics. Such tiny differences would never show up in these biochemical experiments, says Benner.

Benner and Peplow just conceded that natural law cannot explain homochirality. To a materialist, that leaves chance. For a short polypeptide of 100 amino acids to have formed by chance would be ½ x ½ x ½ ... 100 times: 1 chance in 2100, which is approximately 1 in 1030. There aren't enough probabilistic resources to make this likely to happen in a primordial soup of racemic amino acids. But then, even if it did, homochiral DNA or RNA would have to form independently out of its own racemic building blocks. There's just no realistic chance of success in a materialistic world. Intelligence, by contrast, can easily select one hand over the other; consider how quickly an eight-year-old could sort a pile of coins into heads and tails.

Another conclusion from this paper is that homochirality as observed in life is contingent: i.e., it could exist in the opposite mirror-image form. There is no chemical or thermodynamic reason why proteins must be left-handed as opposed to right-handed, or why nucleic acids must be right-handed as opposed to left-handed. The experiments show that chemical reactions can proceed just as well in a mirror-image world. When a choice has been made one way to the exclusion of other possibilities, and it is beyond the reach of chance, it gives indication that intelligence has embedded information into the system.

Finally, these researchers demonstrate empirically how intelligence can embed information into a system. They purposefully selected building blocks of one hand to construct their polymerase. They had a goal, and a means of reaching it. If we rightly judge their work as a product of intelligent design -- as glacially slow as it was -- how much more the products of a cell that work rapidly and accurately, using machinery at a level of sophistication beyond our ability to imitate?

It's logical. If a system on the far side of the looking glass is intelligently designed, then the system on the near side is also intelligently designed. Only a fun-house mirror could distort that conclusion.