Another failed Darwinian prediction XI

             MicroRNA:


Genes hold information that is used to construct protein and RNA molecules which do various tasks in the cell. A gene is copied in a process known as transcription. In the case of a protein-coding gene the transcript is edited and converted into a protein in a process known as translation. All of this is guided by elaborate regulatory processes that occur before, during and after this sequence of transcription, editing and translation.

For instance, some of our DNA which was thought to be of little use actually has a key regulatory role. This DNA is transcribed into strands of about 20 nucleotides, known as microRNA. These short snippets bind and interfere with RNA transcripts—copies of DNA genes—when the production of the gene needs to be slowed.

MicroRNAs can also help to modify the translation process by stimulating programmed ribosomal frameshifting. Two microRNAs attach to the RNA transcript resulting in a pseudoknot, or triplex, RNA structure form which causes the reading frameshift to occur. (Belew)

MicroRNAs do not only come from a cell’s DNA. MicroRNAs can also be imported from nearby cells, thus allowing cells to communicate and influence each other. This helps to explain how cells can differentiate in a growing embryo according to their position within the embryo. (Carlsbecker)

MicroRNAs can also come from the food we eat. In other words, food not only contains carbohydrates, proteins, fat, minerals, vitamins and so forth, it also contains information—in the form of these regulatory snippets of microRNA—which regulate our gene production. (Zhang)

While microRNAs regulate the production of proteins, the microRNAs themselves also need to be regulated. So there is a network of proteins that tightly control microRNA production as well as their removal. “Just the sheer existence of these exotic regulators,” explained one scientist, “suggests that our understanding about the most basic things—such as how a cell turns on and off—is incredibly naïve.” (Hayden)

Two basic predictions that evolutionary theory makes regarding microRNAs are that (i) like all of biology, they arose gradually via randomly occurring biological variation (such as mutations) and (ii) as a consequence of this evolutionary origin, microRNAs should approximately form evolution’s common descent pattern. Today’s science has falsified both of these predictions.

MicroRNAs are unlikely to have gradually evolved via random mutations, for too many mutations are required. Without the prior existence of genes and the protein synthesis process microRNAs would be useless. And without the prior existence of their regulatory processes, microRNAs would wreak havoc.

Given the failure of the first prediction, it is not surprising that the second prediction has also failed. The microRNA genetic sequences do not fall into the expected common descent pattern. That is, when compared across different species, microRNAs do not align with the evolutionary tree. As one scientist explained, “I've looked at thousands of microRNA genes and I can't find a single example that would support the traditional [evolutionary] tree.” (Dolgin)

While there remain questions about these new phylogenetic data, “What we know at this stage,” explained another evolutionist, “is that we do have a very serious incongruence.” In other words, different types of data report very different evolutionary trees. The conflict is much greater than normal statistical variations.

“There have to be,” added another evolutionist, “other explanations.” One explanation is that microRNAs evolve in some unexpected way. Another is that the traditional evolutionary tree is all wrong. Or evolutionists may consider other explanations. But in any case, microRNAs are yet another example of evidence that does not fit evolutionary expectations. Once again, the theory will need to be modified in complex ways to fit the new findings.

In the meantime, scientists are finding that imposing the common descent pattern, where microRNAs must be conserved across species, is hampering scientific research:

These results highlight the limitations that can result from imposing the requirement that miRNAs be conserved across organisms. Such requirements will in turn result in our missing bona fide organism-specific miRNAs and could perhaps explain why many of these novel miRNAs have not been previously identified. (Londin)

Evolutionary theory has been limiting the science. While the common descent pattern has been the guide since the initial microRNA studies, these researchers “liberated” themselves from that constraint, and this is leading to good scientific progress:

In the early days of the miRNA field, there was an emphasis on identifying miRNAs that are conserved across organisms … Nonetheless, species-specific miRNAs have also been described and characterized as have been miRNAs that are present only in one or a few species of the same genus. Therefore, enforcing an organism-conservation requirement during miRNA searches is bound to limit the number of potential miRNAs that can be discovered, leaving organism- and lineage-specific miRNAs undiscovered. In our effort to further characterize the human miRNA repertoire, we liberated ourselves from the conservation requirement … These findings strongly suggest the possibility of a wide-ranging species-specific miRNA-ome that has yet to be characterized. (Londin)

The two microRNA predictions have been falsified and, not surprisingly, the evolutionary assumption has hampered the scientific research of how microRNAs work.

References

Belew, Ashton T., et. al. 2014. “Ribosomal frameshifting in the CCR5 mRNA is regulated by miRNAs and the NMD pathway.” Nature 512:265-9.

Carlsbecker, Annelie, et. al. 2010. “Cell signalling by microRNA165/6 directs gene dose-dependent root cell fate.” Nature 465:316-21.

Dolgin, Elie. 2012. “Phylogeny: Rewriting evolution.” Nature 486:460-2.

Hayden, Erika Check. 2010. “Human genome at ten: Life is complicated.” Nature 464:664-7.

Londin, Eric, et. al. 2015. “Analysis of 13 cell types reveals evidence for the expression of numerous novel primate- and tissue-specific microRNAs.” Proc Natl Acad Sci USA 112:E1106-15.

Zhang, L., et. al. 2012. “Exogenous plant MIR168a specifically targets mammalian LDLRAP1: evidence of cross-kingdom regulation by microRNA.” Cell Research 22:107-26.

The brand of the beast.

If Patients Were Pets
Wesley J. Smith February 29, 2016 2:44 PM

A Canadian government panel -- charged with recommending terms for the Supreme Court-imposed right to euthanasia -- wants MDs (and nurses) to have lower conscience rights than veterinarians. What do I mean? If someone presents a pet to be euthanized, the veterinarian can say no if she thinks the condition of the animal does not warrant that extreme action.

But if the panel gets its way, not so with doctors. It wants all MDs required by law to either kill the legally qualified patient or -- if they have a religious or other predicated conscience objection to committing homicide -- to provide an "effective referral" to a colleague to perform the lethal injection.

"Effective referral" will likely mean procuring a death doctor they know will be willing to do the deed, which is the law in Victoria, Australia, around abortion. From the report:

RECOMMENDATION 10 That the Government of Canada work with the provinces and territories and their medical regulatory bodies to establish a process that respects a health care practitioner's freedom of conscience while at the same time respecting the needs of a patient who seeks medical assistance in dying. At a minimum, the objecting practitioner must provide an effective referral for the patient.

Some objecting doctors might try to get around the effective referral requirement by claiming they didn't find the patient legally qualified medically. But conscientiously, religiously, or morally objecting nurses would have no such wiggle room.

The panel wants nurses to be allowed to kill. But since they wouldn't be the ones determining whether a patient was qualified legally for euthanasia, nurses would face the stark choice of administering the lethal injection when directed by a doctor, or being insubordinate and losing their livelihood. The same would no doubt apply to pharmacists who would concoct the death brew.

Not only that, but religious medical institutions will be required to permit euthanasia in their facilities if the panel has its way. This includes Catholic nursing homes if they receive government funding, which, I am told, is how Canada's system works. Again, from the report:

RECOMMENDATION 11 That the Government of Canada work with the provinces and territories to ensure that all publicly funded health care institutions provide medical assistance in dying.

Here's the bottom line: If the panel's recommendations are enacted, to practice medicine, nursing, pharmacy, or run a nursing home or hospice in Canada will require participation or complicity in the killing of sick, disabled, and mentally ill patients.


There's a word for that. Hint: It is the antithesis of liberty.

The case for design is as plain as nose on your face.

The Physics and Biology of Olfaction
Evolution News & Views March 1, 2016 3:26 AM 

If you've seen Living Waters, you were undoubtedly amazed at the complexity of operations going on inside a salmon's nose. Yet that animation vastly oversimplifies the olfactory sense. New findings continue to bring scientists closer to understanding how it works, adding to what we previously reported in September.

Last time we focused on the olfactory epithelium, the tissue that receives the odor molecules. We saw how it is organized into a hierarchical pattern that provides the best possible reception for different kinds of odorants. Each nostril's epithelium contains half a million olfactory sensory neurons (OSNs), long cells with cilia at one end and an axon at the other end. The cilia are where the odor molecules make contact with olfactory receptors (ORs). When a molecule "fits" just right, the receptor responds, triggering a cascade of activity. But what makes a good fit?

Vibrating Locks and Keys

There's been a lively debate about that. The leading view was that the molecule's shape fits the shape of the receptor like a "lock and key." In the 1990s, however, Luca Turin and others proposed a "vibrational" theory to account for shortcomings in the shape model. Why, for instance, do different shapes produce similar smell sensations in some cases, and similar shapes produce different sensations in others? Because the debate between the "shapists" and "vibrationists" has remained unsettled, the animators at Illustra alluded to both possibilities, showing the molecule fitting like a glove but also vibrating. (It's possible, too, that both theories are partly right.)

The vibration theory was thought to be down for the count last year when a team failed to find evidence for it in an experiment with mouse olfactory receptors in a petri dish. The receptors didn't react differently to two molecules with the same shape but different vibration frequencies. Now, though, the vibration theorists are back with a vengeance. John Hewitt tells about this at PhysOrg. A team from Italy, publishing in Scientific Reports, found evidence for discrimination between molecules with identical shapes but different vibrations. Four pairs of odorant molecules were carefully designed to be identical except that some hydrogen atoms were replaced with deuterium (heavy hydrogen, containing an extra neutron). The slight mass difference in these "isotopomers" ("same topology") alters the vibration frequency of the molecule. These same-shaped odorants were wafted into the noses of honeybees while the scientists monitored their brains in real time.

Sure enough, the bees appeared able to discriminate them, showing very different responses to the same-shaped pairs. "Considering the close structural correspondence between isotopomers," Hewitt writes, "the experimental truths observed here would be difficult for even the most ardent adherent to the shapist receptor philosophy to sweep under the rug." The implications are interesting for design theorists. Hewitt continues:

The authors observe that the shape-independent discrimination capabilities they found can not be dismissed as idiosyncratic to a few peculiar olfactory receptors, rather, they are a more general feature of ligand-receptor interaction. Much of the palpable in-house derision that members of the larger olfactory and neuroscience communities routine reserve for the vibrational theory might be traced to a deeper, more insidious fear: despite exhaustively focused efforts, they have no idea how receptors actually work. [Emphasis added.]

Hewitt sees a possible overarching principle at work in biological sensing. How did living things apply themselves to the task of "quickly (in evolutionary time) coming up with and artfully deploying 'universal detectors'" that are applied for diverse inputs, in everything from olfaction to vision to touch? Even the suntan response to UV light deploys this strategy. "Nature has unleashed her unbridled imagination," he quips -- and artfully so.

Score one for the vibrationists. The debate will continue, undoubtedly, but more to our interest, it illustrates the complexity of the olfactory sense and its extreme precision that has baffled scientists for decades. Imagine a honeybee, fruit fly, or salmon being able to discriminate twin molecules that differ only by one or two atomic mass units. Design doesn't get better than that.

Dynamic Switchboard

Meanwhile, a recent paper in Nature Communications takes us down the other end of the olfactory neuron to the tip of the axon. As shown in the Illustra animation, the nerve endings of a million OSNs converge on a remarkable organ, the olfactory bulb (OB), which is studded with connection points called glomeruli. In an amazing example of preprogrammed networking, these axons "know" during development somehow which glomerulus to attach to, depending on the type of odorant receptor they express (and there are hundreds of those). Axons for one receptor might grow toward a glomerulus on top of the bulb; axons for another to the backside. Between top-bottom, front-back, and left-right, the OB has three axes by which to discriminate connections coming from different classes of receptors. This is the first stage of sorting and classifying odorant types. (Note: it gets even more complicated from there.)

These scientists from the NIH and Carnegie Mellon University wanted to find out how malleable the olfactory inputs are. Once set up, is the olfactory tissue set for life? Can the olfactory bulb be rewired as conditions change or the fish grows older? When a new neuron replaces an old one, does it wire up the same way? The short answer is that rewiring is not only possible, but it occurs throughout adult life. Why might that be?

Incorporation of new neurons enables plasticity and repair of circuits in the adult brain. Adult neurogenesis is a key feature of the mammalian olfactory system, with new olfactory sensory neurons (OSNs) wiring into highly organized olfactory bulb (OB) circuits throughout life. However, neither when new postnatally generated OSNs first form synapses nor whether OSNs retain the capacity for synaptogenesis once mature, is known. Therefore, how integration of adult-born OSNs may contribute to lifelong OB plasticity is unclear. Here, we use a combination of electron microscopy, optogenetic activation and in vivo time-lapse imaging to show that newly generated OSNs form highly dynamic synapses and are capable of eliciting robust stimulus-locked firing of neurons in the mouse OB. Furthermore, we demonstrate that mature OSN axons undergo continuous activity-dependent synaptic remodelling that persists into adulthood. OSN synaptogenesis, therefore, provides a sustained potential for OB plasticity and repair that is much faster than OSN replacement alone.

Notice that reference to the "highly organized olfactory bulb circuits." Unlike Hewitt, who verged off into evolutionary speculations in his article after describing those "artfully deployed" sensors, these scientists didn't go the storytelling route. Their approach was to observe a phenomenon and find a purpose for it.

So what is the purpose of rapid structural remodelling of OSN synapses? Synapse turnover clearly plays an essential role during circuit formation (and in the case of the OB, incorporation of newborn neurons into existing circuits) by enabling selection, refinement and error correction. Hence, transient pre- or post-synaptic structures may represent those that fail to locate a synaptic partner, or form inappropriate connections that are rapidly eliminated. This may explain why immature OSN presynaptic terminals are formed and eliminated more rapidly than their mature counterparts (Figs 4, 5). Alternatively, these transient synaptic structures may represent short-lived synaptic contacts that temporarily contribute to network function, or play other roles such as promoting axon branch stabilization. Whatever the role of transient synaptic structures, ongoing synapse formation and elimination endows OB circuits with a plasticity potential that can be harnessed when needed, such as during learning or in response to altered experience.

That's the spirit. There must be a role, a purpose, a potential. At first, it would appear startling that so much rewiring takes place. What chip manufacturer would alter integrated circuits while they are in use? Maybe manufacturers could learn something from the way life does things.

Clearly a salmon is undergoing a lot of "learning" and "altered experience" as it grows from fingerling to adult, swimming downstream through a welter of new sensory experiences, memorizing hundreds of new odors and mapping them into its memory. It's possible that the brain and the olfactory bulb are triggering some of that rewiring in elaborate feedback loops, strengthening the connections to weak signals or reducing the connections to overpowering signals. It brings to mind a skilled technician on a sound board turning knobs and moving sliders to get the ideal overall experience in auditory space. In olfactory space, though, the salmon's sliders are automated. "Whatever the role" of these transient connections, we can infer from the results -- such as that a salmon can detect odorants at parts per trillion -- that they contribute to the spectacular performance of the olfactory system.

We've discussed "plasticity" before as a challenge to Darwinism. Why would a blind evolutionary process create "plasticity potential" that can be "harnessed when needed" in case of an altered experience? Darwinian evolution has no foresight. Plasticity makes perfect sense, though, from a design-based perspective on biology. There's no better example than right there in a salmon's nose, where the olfactory system will be encountering numerous new environments over a period of years. The scientists' expectations of roles for synaptic plasticity were confirmed in their conclusions (readers can find the details in the open-access paper).

One more thing. The scientists found that rewiring is "much faster" than replacement. While OSNs are replaced throughout life, the rewiring "plasticity potential" provides a more rapid response, giving the animal both high-speed (transient) and low-speed (permanent) fine tuning of its olfactory system. Since this is true of mice, it's undoubtedly true for us as well.


Now go out and smell the roses.

Homology vs. Darwin

The Types: Why Shared Characteristics Are Bad News for Darwinism
Michael Denton February 29, 2016 3:28 AM 

Editor's note: In his new book Evolution: Still a Theory in Crisis, Michael Denton not only updates the argument from his groundbreaking Evolution: A Theory in Crisis (1985) but also presents a powerful new critique of Darwinian evolution. This article is one in a series in which Dr. Denton summarizes some of the most important points of the new book. For the full story, get your copy of Evolution: Still a Theory in Crisis. For a limited time, you'll enjoy a 30 percent discount at  CreateSpace by using the discount code QBDHMYJH.

One of the major achievements of pre-Darwinian biology was the discovery that the living world is organized into a hierarchy of ever more inclusive classes or Types, each clearly defined by a unique homolog or suite of homologs possessed by all the members of the Type and which in many cases have remained invariant in divergent phylogenetic lines for tens or hundreds of millions of years.

Seeking an explanation for the distinctness of the Types and determining their ontological status was seen to be one of the major tasks of 19th-century biology. Virtually all pre-Darwinian biologists, and many after Darwin, saw the Types as immanent and invariant parts of the world-order, no less than crystals or atoms.

There is currently a widespread impression that pre-Darwinian biologists derived their discontinuous-typological conception of nature from all sorts of discredited metaphysical beliefs. This view has been severely criticized by recent researchers and shown to be largely a myth created by twentieth-century advocates of the neo-Darwinian evolutionary synthesis1 -- what Ron Amundson calls "Synthesis Historiography."2 As Amundson shows, whatever their metaphysical leaning, pre-Darwinian biologists did not derive their view of the Types as changeless components of the world order from any a priori metaphysics but from solid empirical observations.

The 19th-century structuralist conception of the Type, and of an ascending hierarchy of taxa or Types of ever-widening comprehensiveness as immanent features of nature, was close to the classic Aristotelian worldview. But it was based on the facts of biology, not on a philosophical a priori assumption -- Aristotelian, Platonic, or otherwise.

Today, 150 years after Darwin, Owen's "biological atoms" are as distinct as ever. The vast majority of all organisms can be assigned to unique classes based on their possession of particular defining homologs or novelties that are not led up to via Darwin's "innumerable transitional forms."

For readers subjected to popular and pervasive claims by evolutionary biologists that there are innumerable transitional forms of organisms, it might come as something of a surprise that there are unique taxon-defining novelties not led up to gradually from some antecedent form, and that remain invariant after their actualization for vast periods of time.

There is indeed something incongruous about the very notion of distinct taxa and genuine immutable "taxon-defining novelties" in the context of the functionalist Darwinian framework, which implies that all taxa-defining traits should be led up to via long series of adaptive transitional forms! On such a Darwinian model, taxa-defining novelties should not exist; neither should distinct Types in which all members possess unique defining novelties not shared by the members of any other taxa.

Let me reiterate: If evolution has occurred as conceived of by Darwin, invariant taxa-defining novelties, not led up to via long sequences of transitional forms from some antecedent structure, should not exist.

Ironically, it is only because organisms can be classified into distinct groups on the basis of their possession of invariant unique homologs that descent with modification can be inferred in the first place. If it was not for the invariance of the homologs and the Types they define, the common descent of all the members of a particular clade from a common ancestor would be in serious doubt. The living realm would conform to a chaotic network rather than an orderly branching tree.

Types are still as distinct today as they were for Richard Owen, Agassiz, and the other typologists and structuralists in the pre-Darwinian era and even for Darwin himself.3 They are still clearly defined by homologs or synapomorphies that are true evolutionary novelties without antecedent in earlier putative ancestral forms.

References:

(1) Mary Winsor, "The Creation of the Essentialism Story: An Exercise in Metahistory," History and Philosophy of the Life Sciences 28 (2006): 149-174.

(2) Amundson, The Changing Role of the Embryo in Evolutionary Thought, 11.


(3) Charles Darwin, Origin of Species, 6th ed. (London: John Murray 1872), 264 (Chapter 10): "The distinctness of specific forms, and their not being blended together by innumerable transitional links, is a very obvious difficulty."