Here we go.
Here we go.
When we think about volcanoes, the images that typically come to mind are violent eruptions that devastate the surrounding landscapes and bring death or serious injury to anyone so unfortunate as to be in the vicinity. Figure 1, for example, shows the lava flows from the 1985 eruption of the Nevado del Ruiz volcano, which killed more than 23,000 people and destroyed the town of Armero, Colombia.
Figure 1: Town of Armero, Colombia, wiped out by the 1985 eruption of Nevada del Ruiz
People are quick, however, to return to the regions near recent volcanic eruptions. The reason why is that the volcanic rocks and ash from eruptions contain stores of rich nutrients that yield bumper harvests of food crops.
This curse and blessing of volcanic eruptions raises an interesting question: wouldn’t it be great if volcanic eruptions were especially frequent when nobody lived near the volcanoes and especially infrequent when people were exploiting their rich soils for food? A recently published paper by five geologists shows that such a marvelous timing has indeed occurred, and it ranks as yet another fine-tuned feature of our planet that allows humans to enjoy sustained global high-technology civilization.
The paper published in Quaternary Science Reviews updates a hypothesis, based on evidence that volcanic activity in Iceland increased after the last glacial maximum, that deglaciation produces enhanced volcanic activity.1 The five geologists reanalyzed the four longest and most reliable tephra records.
Tephra is fragmented material ejected by a volcanic eruption regardless of fragment size, composition, or how the fragmented material got to its location. Where the tephra is hot enough, it will fuse together into pyroclastic rock or tuff (volcanic ash compacted to form solid rock). Figure 2 shows tephra layers from multiple eruptions of the Hekla volcano.
Figure 2: Tephra Layers in South Central Iceland from the Hekla Volcano
The geological team investigated four tephra records that covered multiple glacial cycles. These four records were all linked with oxygen-18 measurements that accurately revealed both the recent historical records of sea level variations and variations in the global mean (average) temperature. Scientists obtained the four tephra records from different latitudes and different geotectonic settings.
All the tephra records exhibited the Milankovitch periodicities of precession (23,000 years), rotation axis tilt (41,000 years), and orbital eccentricity (approximately 100,000 years). I have written previously about Earth’s Milankovitch cycles here,2 here,3 and here,4 and how they in large part explain the repeated episodes of glaciations and deglaciations that characterize the ice age cycle of the past 2.588 million years.
All the tephra records show that periods of increased volcanic eruption frequencies coincide with the dramatic deglaciations that occur at the glacial-interglacial transitions. Evidently, the release of the load of ice and snow on the continental landmasses ignites volcanic eruptions.
The long duration tephra records in this study, however, add up to just four. Thus, the five geologists call for “more precise tephra time series (preservation and age optimized) from different regions (glaciated versus non-glaciated) and geological settings (island arcs, continental arcs, intraplate)”5 … “to decipher the impact of these factors on a global perspective of how climate may control volcanism.”6
Enhanced volcanic eruptions at the beginning of an interglacial period imply that much of Earth’s continental landmasses and its lakes, rivers, and oceans receive a delivery of nutrients that allows microbes, vegetation, and animals to flourish. This fertilization event coincides with another fertilization event that I wrote about in Improbable Planet. I stated there that at the beginning of an interglacial “fine loess (wind-blown dust) from dried-out parts of the floodplains of glacial braided rivers carried layers of crucial nutrients onto the lowland plains below, making them richly fertile.”7
As I have explained in another blog,8 the interglacial we are experiencing right now is unique. It is the longest lasting interglacial and the only one where there has been an extended duration (9,500 years) of extreme climate stability. The current warm period has followed the most severe glacial period in the entire ice age cycle.
The severity and rapidity of the deglaciation from that glacial period resulted—at the time of the beginning of our interglacial period—in the greatest delivery of fine loess and other nutrients from volcanic eruptions. These especially intense and simultaneous fertilization events, to a large degree, explain why humans today are able to grow so much food on Earth’s plains and valleys and why we are able to harvest so much shellfish and other fish from Earth’s oceans, seas, lakes, and rivers.
These especially intense and simultaneous fertilization events give us more reasons to thank God for his supernatural blessings poured out on humanity. They also demonstrate that God planned in advance that billions of us would experience sufficiently high-technology civilization that makes possible the rapid spread of his message of redemption from human sin.
Original article: How Cyclical Volcanic Activity Benefits Humanity
I don’t like to think of myself as technology-challenged, but I am beginning to wonder if I just might be. As a case in point, I have no clue about all the things my iPhone can do. It isn’t uncommon for someone (usually much younger than me) to point out features of my iPhone that I didn’t even know existed. (And, of course, there is the TV remote—but that will have to serve as material for another lead.)
The human genome is a lot like my iPhone. The more the scientific community learns about it, the more complex it becomes and the more functionality it displays—functionality about which no one in the scientific community had a clue. It has become commonplace for scientists to discover that features of the human genome—long thought to be useless vestiges of an evolutionary history—actually serve a critical role in the structure and function of the genome.
Long noncoding RNAs (lncRNAs) illustrate this point nicely. This broad category of RNA molecules consists of transcripts (where genetic information is transferred from DNA to messenger RNA) that are over 200 nucleotides in length but are not translated into proteins.
Though numbers vary from source to source, estimates indicate that somewhere between 60 to 90 percent of the human genome is transcribed. Yet only 2 percent of the genome consists of transcripts that are directly used to produce proteins. Of the transcripts that are untranslated, researchers estimate that somewhere between 60,000 to 120,000 of the transcripts are noncoding RNAs. Researchers categorize these transcripts as microRNAs(miRNAs), piwi-interacting RNAs (piwiRNAs), small interfering RNAs (siRNAs) and lncRNAs. The first three types of RNAs are relatively small in size and play a role in regulating gene expression.
Figure 1: Transcription and Translation
Initially, researchers thought for the most part that lncRNAs were transcriptional noise—junk. But this view has changed in recent years. Evidence continues to accrue demonstrating that lncRNAs play a wide range of roles in the cell.1 And as evidence for the utility of lncRNAs mounts, the case for the design of the human genome expands.
The Functional Utility of Long Noncoding RNAs
As it turns out, lncRNAs are extremely versatile molecules that can interact with: (1) other RNA molecules, (2) DNA, (3) proteins, and (4) cell membranes. This versatility opens up the possibility that these molecules play a diverse role in cellular metabolism.
Recently, Harry Krause, a molecular geneticist from the University of Toronto, published two review articles summarizing the latest insights into lncRNA function. These insights, including the four to follow, demonstrate the functional pervasiveness of the transcripts.
lncRNAs regulate gene expression. lncRNAs influence gene expression by a variety of mechanisms. One is through interactions with other transcripts forming RNA-RNA duplexes that typically interfere with translation of protein-coding messenger RNAs.
Researchers have recently learned that lncRNAs can also influence gene expression by interacting with DNA. These interactions result in either: (1) a triple helix, made up of two DNA strands intertwined with one RNA strand, or (2) a double helix with the lncRNA intertwined with one of the DNA strands, leaving the other exposed as a single strand. When these duplexes form, the lncRNA forms a hairpin loop that can either indiscriminately or selectively attract transcription factors.
Figure 2: A Hairpin Loop
Though researchers are still learning about the role lncRNAs play in gene regulation, these varied interactions with DNA and proteins suggest that lncRNAs may influence gene expression through a variety of mechanisms.
lncRNAs form microbodies within the nucleus and cytoplasm. A second function recognizes that lncRNAs interact with proteins to form hydrogel-like structures in the nucleus and cytoplasm. These structures are dense and heavily cross-linked subcellular structures that serve as functionally specific regions without a surrounding membrane. (In a sense, the microbodies could be viewed as somewhat analogous to ribosomes, the protein-RNA complexes that synthesize proteins.) In the nucleus, microbodies play a role in transcriptional processing, storage, and stress response. In the cytoplasm, microbodies play a role in storage, processing, and trafficking.
lncRNAs interact with cell membranes. A third role stems from laboratory studies where lncRNAs have been shown to interact with model cell membranes. Such interactions suggest that lncRNAs may play a role in mediating biochemical processes that take place at cell membranes. Toward this end, researchers have recently observed certain lncRNA species interacting with phosphatidylinositol 3,4,5-triphosphate. This cell membrane component plays a central role in signal transduction inside cells.
lncRNAs are associated with exosomes. Finally, lncRNAs have been found inside membrane-bound vesicles that are secreted by cells (called exosomes). These vesicles mediate cell-cell communication.
In short, the eyes of the scientific community have been opened. And they now see the functional importance and functional diversity of lncRNAs. Given the trend line, it seems reasonable to think that the functional range of lncRNAs will only expand as researchers continue to study the human genome (and genomes of other organisms).
The growing recognition of the functional versatility of lncRNAs aligns with studies demonstrating that other regions of the genome—long thought to be nonfunctional—do, in fact, play key roles in gene expression and other facets of cellular metabolism. Most significantly, toward this end, the functional versatility of lncRNAs supports the conclusions of the ENCODE Project—conclusions that have been challenged by some people in the scientific community.
The ENCODE Project
A program carried out by a consortium of scientists with the goal of identifying the functional DNA sequence elements in the human genome, the ENCODE Project, reported phase II results in the fall of 2012. (Currently, ENCODE is in phase IV.) To the surprise of many, the ENCODE Project reported that around 80 percent of the human genome displays biochemical activity—hence, function—with the expectation that this percentage should increase as results from phases III and IV of the project are reported.
The ENCODE results have generated quite a bit of controversy. One of the most prominent complaints about the ENCODE conclusions relates to the way the consortium determined biochemical function. Critics argue that ENCODE scientists conflated biochemical activity with function. As a case in point, the critics argue that most of the transcripts produced by the human genome (which include lncRNAs) must be biochemical noise. This challenge flows out of predictions of the evolutionary paradigm. Yet, it is clear that the transcripts produced by the human genome are functional, as numerous studies on the functional significance of lncRNAs attest. In other words, the biochemical activity detected by ENCODE equates to biochemical function—at least with respect to transcription.
A New View of Genomes
These types of insights are radically changing scientists’ view of the human genome. Rather than a wasteland of junk DNA sequences stemming from the vestiges of an evolutionary history, genomes appear to be incredibly complex, sophisticated biochemical systems, with most of the genome serving useful and necessary functions.
We have come a long way from the early days of the human genome project. When completed in 2003, many scientists at that time estimated that around 95 percent of the human genome consists of junk DNA. That acknowledgment seemingly provided compelling evidence that humans must be the product of an evolutionary history.
Nearly 15 years later the evidence suggests that the more we learn about the structure and function of genomes, the more elegant and sophisticated they appear to be. It is quite possible that most of the human genome is functional.
For creationists and intelligent design proponents, this changing view of the human genome—similar to discovering exciting new features of an iPhone—provides reasons to think that it is the handiwork of our Creator. A skeptic might ask, Why would a Creator make genomes littered with so much junk? But if a vast proportion of genomes consists of functional sequences, this challenge no longer carries weight and it becomes more and more reasonable to interpret genomes from within a creation model/intelligent design framework.
Original article: Long Noncoding RNAs Extend the Case for Creation
“‘It’s wonderful how you can turn words,’ as Polonius says in Hamlet,” laughed Ivan. “You turn my words against me. Well, I am glad. Yours must be a fine God, if man created Him in his image and likeness. You asked just now what I was driving at. You see, I am fond of collecting certain facts, and, would you believe, I even copy anecdotes of a certain sort from newspapers and books, and I’ve already got a fine collection. The Turks, of course, have gone into it, but they are foreigners. I have specimens from home that are even better than the Turks. You know we prefer beating—rods and scourges—that’s our national institution. Nailing ears is unthinkable for us, for we are, after all, Europeans. But the rod and the scourge we have always with us and they cannot be taken from us. Abroad now they scarcely do any beating. Manners are more humane, or laws have been passed, so that they don’t dare to flog men now. But they make up for it in another way just as national as ours. And so national that it would be practically impossible among us, though I believe we are being inoculated with it, since the religious movement began in our aristocracy. I have a charming pamphlet, translated from the French, describing how, quite recently, five years ago, a murderer, Richard, was executed—a young man, I believe, of three and twenty, who repented and was converted to the Christian faith at the very scaffold. This Richard was an illegitimate child who was given as a child of six by his parents to some shepherds on the Swiss mountains. They brought him up to work for them. He grew up like a little wild beast among them. The shepherds taught him nothing, and scarcely fed or clothed him, but sent him out at seven to herd the flock in cold and wet, and no one hesitated or scrupled to treat him so. Quite the contrary, they thought they had every right, for Richard had been given to them as a chattel, and they did not even see the necessity of feeding him. Richard himself describes how in those years, like the Prodigal Son in the Gospel, he longed to eat of the mash given to the pigs, which were fattened for sale. But they wouldn’t even give him that, and beat him when he stole from the pigs. And that was how he spent all his childhood and his youth, till he grew up and was strong enough to go away and be a thief. The savage began to earn his living as a day laborer in Geneva. He drank what he earned, he lived like a brute, and finished by killing and robbing an old man. He was caught, tried, and condemned to death. They are not sentimentalists there. And in prison he was immediately surrounded by pastors, members of Christian brotherhoods, philanthropic ladies, and the like. They taught him to read and write in prison, and expounded the Gospel to him. They exhorted him, worked upon him, drummed at him incessantly, till at last he solemnly confessed his crime. He was converted. He wrote to the court himself that he was a monster, but that in the end God had vouchsafed him light and shown grace. All Geneva was in excitement about him—all philanthropic and religious Geneva. All the aristocratic and well-bred society of the town rushed to the prison, kissed Richard and embraced him; ‘You are our brother, you have found grace.’ And Richard does nothing but weep with emotion, ‘Yes, I’ve found grace! All my youth and childhood I was glad of pigs’ food, but now even I have found grace. I am dying in the Lord.’ ‘Yes, Richard, die in the Lord; you have shed blood and must die. Though it’s not your fault that you knew not the Lord, when you coveted the pigs’ food and were beaten for stealing it (which was very wrong of you, for stealing is forbidden); but you’ve shed blood and you must die.’ And on the last day, Richard, perfectly limp, did nothing but cry and repeat every minute: ‘This is my happiest day. I am going to the Lord.’ ‘Yes,’ cry the pastors and the judges and philanthropic ladies. ‘This is the happiest day of your life, for you are going to the Lord!’ They all walk or drive to the scaffold in procession behind the prison van. At the scaffold they call to Richard: ‘Die, brother, die in the Lord, for even thou hast found grace!’ And so, covered with his brothers’ kisses, Richard is dragged on to the scaffold, and led to the guillotine. And they chopped off his head in brotherly fashion, because he had found grace. Yes, that’s characteristic. That pamphlet is translated into Russian by some Russian philanthropists of aristocratic rank and evangelical aspirations, and has been distributed gratis for the enlightenment of the people. The case of Richard is interesting because it’s national. Though to us it’s absurd to cut off a man’s head, because he has become our brother and has found grace, yet we have our own speciality, which is all but worse. Our historical pastime is the direct satisfaction of inflicting pain. There are lines in Nekrassov describing how a peasant lashes a horse on the eyes, ‘on its meek eyes,’ everyone must have seen it. It’s peculiarly Russian. He describes how a feeble little nag has foundered under too heavy a load and cannot move. The peasant beats it, beats it savagely, beats it at last not knowing what he is doing in the intoxication of cruelty, thrashes it mercilessly over and over again. ‘However weak you are, you must pull, if you die for it.’ The nag strains, and then he begins lashing the poor defenseless creature on its weeping, on its ‘meek eyes.’ The frantic beast tugs and draws the load, trembling all over, gasping for breath, moving sideways, with a sort of unnatural spasmodic action—it’s awful in Nekrassov. But that’s only a horse, and God has given horses to be beaten. So the Tatars have taught us, and they left us the knout as a remembrance of it. But men, too, can be beaten. A well-educated, cultured gentleman and his wife beat their own child with a birch-rod, a girl of seven. I have an exact account of it. The papa was glad that the birch was covered with twigs. ‘It stings more,’ said he, and so he began stinging his daughter. I know for a fact there are people who at every blow are worked up to sensuality, to literal sensuality, which increases progressively at every blow they inflict. They beat for a minute, for five minutes, for ten minutes, more often and more savagely. The child screams. At last the child cannot scream, it gasps, ‘Daddy! daddy!’ By some diabolical unseemly chance the case was brought into court. A counsel is engaged. The Russian people have long called a barrister ‘a conscience for hire.’ The counsel protests in his client’s defense. ‘It’s such a simple thing,’ he says, ‘an everyday domestic event. A father corrects his child. To our shame be it said, it is brought into court.’ The jury, convinced by him, give a favorable verdict. The public roars with delight that the torturer is acquitted. Ah, pity I wasn’t there! I would have proposed to raise a subscription in his honor! Charming pictures.”
An Excerpt from Chapter IV – Rebellion, The Brothers Karamazov – Fyodor Dostoyevsky
Fishing for hexagons.