Some assembly required?

Can You Build WALL-E from Repeating Legos?
Evolution News & Views January 8, 2016 3:31 AM

"A central question in protein evolution is the extent to which naturally occurring proteins sample the space of folded structures accessible to the polypeptide chain." Thus begins a new paper on sequence space for proteins, a concept that has been key to work by leading ID theorists Douglas Axe, Stephen Meyer, and William Dembski. This is the question: Out of the vast space of possible amino acid sequences, how many can fold into functional proteins? ID argues that functional space is such a small subset of sequence space, the probability that a blind search will find any is vanishingly small.

Nine researchers led by some of our Seattle neighbors over at the University of Washington, publishing in Nature, decided to investigate how much of the sequence space nature has sampled. It's obviously far too big a space to search, so they limited it to just "repeat proteins" -- those that use certain structural motifs over and over.

To our knowledge, all designed repeat protein structures to date have been based on naturally occurring families. These families may cover all stable repeat protein structures that can be built from the 20 amino acids or, alternatively, natural evolution may only have sampled a subset of what is possible.

By applying experimental protein design, they show that you can get many more potential proteins by simply repeating certain "building blocks" over and over, something like assembling Lego pieces blindly. They manufactured some Lego-like protein kits by generating scads of "a simple helix-loop-helix-loop building block" and putting them together using an automated process. Out of 83 they built, 44 showed a stable fold. But is this experiment about evolution or intelligent design?

We have shown that a wide range of novel repeat proteins can be generated by tandem repeating a simple helix-loop-helix-loop building block. As illustrated by the comparison of 15 design models to the corresponding crystal structures (Fig. 4), our approach allows precise control over structural details throughout a broad range of geometries and curvatures. The design models and sequences are very different from each other and from naturally occurring repeat proteins, without any significant sequence or structural homology to known proteins (Extended Data Fig. 8). This work achieves key milestones in computational protein design: the design protocol is completely automatic, the folds are unlike those in nature, more than half of the experimentally tested designs have the correct overall structure as assessed by SAXS, and the crystal structures demonstrate precise control over backbone conformation for proteins over 200 amino acids. The observed level of control over the repeating helix-loop-helix-loop architecture shows that computational protein design has matured to the point of providing alternatives to naturally occurring scaffolds, including graded and tunable variation difficult to achieve starting from existing proteins. We anticipate that the 44 successful designs described in this work (Extended Data Fig. 9), and sets generated using similar protocols for other repeat units, will be widely useful starting points for the design of new protein functions and assemblies.

Note that word "function" at the end. A search of the paper shows nothing about whether any one of the design models actually does anything. Yet they seem to have one ear open to the possible whisper of Darwin speaking in the background:

Naturally occurring repeat protein families, such as ankyrins, leucine-rich repeats, TAL effectors and many others, have central roles in biological systems and in current molecular engineering efforts. Our results suggest that these families are only the tip of the iceberg of what is possible for polypeptide chains: there are clearly large regions of repeat protein space that are not sampled by currently known repeat protein structures. Repeat protein structures similar to our designs may not have been characterized yet, or perhaps may simply not exist in nature.

The authors only mention evolution twice. It's not really a focus in this paper. The word "design," however, appears a whopping 74 times, even before the Methods section. They did interesting and important work. But lest anyone think their conclusion weakens the arguments of Axe, Meyer, and Dembski by expanding the potential functional space accessible to random search within sequence space, let's apply a heavy dose of realism.

They sampled only part of the "repeat protein" portion of sequence space.

They began with "building block" motifs that already fold (helices and loops).

They used only left-handed (homochiral) amino acids.

They did not test to see if any of the stable structures perform a function.

They did not test to see if any of their structures could interact with other proteins or structures (for this problem, see this earlier article on this subject).

Their work was highly dependent on intelligent design (i.e., their own).

You could liken their results to a robot programmed to assemble Legos according to a rule: "fasten, twist, repeat." If the Lego pieces are already designed, the algorithm can say nothing about where the pieces came from. As all kids know, the holes in Lego pieces have to be spaced properly to fit together. Similarly, amino acids need to be properly sequenced to fold into a helix or loop. If that's a given, it's not surprising that you could generate quite a few unique structures by the algorithm "fasten, twist, repeat." Even WALL-E the robot could do that without thinking. Whether anything worthwhile would result is dubious.

Actually, you can assemble a WALL-E robot using Lego pieces now. The Lego company offers that and many other elaborate, complex kits that go well beyond the simple building-block sets from decades ago. A kid could put the WALL-E pieces together and show off his pride and joy in a matter of hours or maybe even minutes. But could nature pull that off by blind search? Think of the programming that would be required to get WALL-E to assemble his likeness out of Lego pieces! It's intelligent design all the way down.


Here's the take-home: Despite a hint of "protein evolution" in this paper, the experimental evidence has again vindicated ID. Without a mind directing assembly of amino acids according to a design goal, nothing interesting will happen by chance or repetition by an aimless process. Sequence space is too vast and functional space too vanishingly small to expect success by blind search.

Darwinism Vs. the real world XXIII

Defending the City: The Immune System's Irreducibly Complex System:
Howard Glicksman January 9, 2016 4:08 AM

Editor's note: Physicians have a special place among the thinkers who have elaborated the argument for intelligent design. Perhaps that's because, more than evolutionary biologists, they are familiar with the challenges of maintaining a functioning complex system, the human body. With that in mind, Evolution News & Views is delighted to present this series, "The Designed Body." For the complete series, see here. Dr. Glicksman practices palliative medicine for a hospice organization.

Let's review a few things that this series has shown are needed for human survival. The body is made up of trillions of cells, each of which must control its volume and chemical content while receiving what it needs from the blood to live, grow, and work properly. Since it is made up of matter, the body is subject to the laws of nature, which demand that it constantly take in oxygen to provide itself with the energy it needs to live. Unlike with glucose, the body can't store oxygen for future use.

These laws also demand that the body have the right amounts and distributions of water, sodium, and potassium for blood volume, and the proper resting membrane potential for adequate nerve, muscle, and heart function. Additionally, since blood has mass, it needs the heart to pump it through the circulatory system to the tissues with enough pressure against natural forces like inertia, vascular resistance, and gravity..

If the body doesn't have the right levels of oxygen, water, sodium, potassium, blood pressure, or blood flow, then cell death takes place. When the cells in the brainstem die -- the ones that tell the body to breathe in air, control its cardiovascular system, and make it conscious of its surroundings -- the body is considered dead. The most common pathway to death is by cardiopulmonary arrest. Without respiration, the body can't bring in new supplies of oxygen and get rid of toxic carbon dioxide. Without the heart pumping, there is no blood flow to the brain. So, together, cardiopulmonary arrest causes death very soon after.

Life does not exist in a vacuum or merely in the imagination of evolutionary biologists. As we saw in the most recent articles in this series, small blood vessels of the body constantly undergo injury from the everyday activities of life. For our earliest ancestors to survive long enough to reproduce, they needed a well-controlled clotting mechanism (hemostasis) in place that would turn on only when it was needed and turn off and stay off when it wasn't.

Bleeding disorders -- where the clotting mechanism won't turn on -- can cause a brain hemorrhage from even minimal trauma, or hypovolemic shock from spontaneous gastrointestinal bleeding. Hypercoagulable states -- where the clotting mechanism turns on at the wrong time -- can easily cause death from a heart attack, stroke, or pulmonary embolism. Either way, unless hemostasis is properly controlled, the body is as good as dead. But well-controlled hemostasis is dependent on having a finely tuned system of pro- and anti-clotting factors that must be produced in adequate quantities by the endothelium that lines the blood vessels and liver.

Hemostasis is a type of defense system the body uses to prevent itself from bleeding to death from injuries and accidents. But that's not the only one it has. The bones, muscles, and nerves work together to allow the body to detect danger and avoid or defend against it. However, survival also requires us to defend ourselves from enemies that we can't detect with the senses. We are perpetually exposed to germs: microorganisms that are too small to be seen with the naked eye. These consist mostly of bacteria, viruses, and fungi. If such microbes invade the body and become widespread, then serious disease, debility, and even death can result.

Against microbial attack, the body has a two-pronged defense strategy. The first line of defense is the epithelium.This tissue separates and protects the interior cells of the body from the effects of the outside world. The skin is an epithelial tissue consisting of many different types of cells that provides passive resistance to invasion by microbes. Skin also protects the body from mechanical and chemical injury, ultraviolet radiation, extreme heat and cold, excessive fluid loss, and helps to control body temperature. The respiratory, gastrointestinal, and genitourinary systems also have an epithelial lining that separates their underlying tissue from the effects of the environment. Microbes that are inhaled, or swallowed, or are able to enter the urinary tract, come up against these barriers.

If the invading microorganisms breach the first line and enter into the tissues, then the second line of defense, the immune system, swings into action. The immune system consists of many different cells and proteins. In ancient times, when invaders breached the walls of a town, they usually met armed resistance. By using their weapons and shields for protection, the intruders would kill and loot their way through the town, thus conquering it. Similarly, after breaching a passive barrier like the skin, usually through a cut or scrape, invading microbes attempt to loot the body by using the nutrients in its fluids to live, grow, and multiply.

As with a town stormed by a finite number of attackers, a microbial infection usually involves a relatively small invading force. But once inside the body, the infection is able to multiply rapidly by using the resources of its host. It's the job of the immune system to limit this activity as much as possible to preserve organ function.

Although there are many different types of bacteria, viruses, and fungi, the few that have developed the ability to breach the first line of defense and do battle with the immune system are called pathogens (Gk. pathos = disease + gennan = to produce). Some of these pathogenic organisms enter the cells, take over their metabolism, rapidly reproduce and then send out the next generation of microbes into the body after the cell dies. Many others can live within the tissue fluid between the cells and multiply and spread locally.

Infections are possible in almost every organ of the body. Progression of infection within a given organ system can lead to severe body malfunction. If the lungs develop pneumonia, this can significantly diminish their ability to bring in oxygen and release carbon dioxide and, particularly in people with emphysema, can lead to respiratory failure and cardiopulmonary arrest. If the gastrointestinal tract develops gastroenteritis, the associated vomiting and diarrhea, particularly in the very young and old, can lead to dehydration, chemical imbalance, hypovolemic shock, and cardiopulmonary arrest. If the brain develops encephalitis or meningitis, the nerve malfunction aggravated by the increased pressure can lead to brain death.

If the pathogens are not stopped within the tissues they initially infect, they can migrate into the lymphatics. The lymphatic system consists of very thin walled tiny channels that carry lymph (L. lympha = water), a liquid that comes from the fluid not reabsorbed at the venous end of the capillary. Every tissue and organ in the body is drained by lymphatic vessels, which eventually come together to drain into the venous system.

It is through the lymphatic system that microbes gain access to the bloodstream and all of the tissues and organs of the body. By working their way through the lymphatics and into the bloodstream, these organisms can cause septicemia and irreversible shock, resulting in death for about 250,000 people in this country every year.


Without the epithelial tissue of the body protecting it from microbial invasion, life would have been impossible for our earliest ancestors. But the experience of death-dealing infections throughout the world also tells us that without a properly working immune system, the same applies. How the immune system works and what it takes to control it so we can live within the world of microbes will be the subject of my next few articles.

Conflict in the making?

The watchtower Society's commentary on self-control.

SELF-CONTROL:

Keeping in check, restraining, or controlling one’s person, actions, speech, or thoughts. (Ge 43:31; Es 5:10; Ps 119:101; Pr 10:19; Jer 14:10; Ac 24:25) The Hebrew and Greek terms involving self-control literally denote having power or control over oneself. Self-control is a ‘fruit of God’s spirit’ (Ga 5:22, 23); and Jehovah, though possessing unlimited powers, has exercised it at all times. Instead of taking immediate action against wrongdoers, he has allowed time to pass so that they might have the opportunity to turn from their bad ways and thereby gain his favor.—Jer 18:7-10; 2Pe 3:9.

However, once it was firmly established that those to whom time for repentance had been extended would not avail themselves of his mercy, Jehovah rightly ceased to refrain from executing his judgment. A case in point involves the desolaters of Jerusalem. Failing to recognize that Jehovah allowed them to gain control of Israel to discipline the Israelites for unfaithfulness, these desolaters treated them without mercy and carried the discipline farther than God’s judgment had required. (Compare Isa 47:6, 7; Zec 1:15.) Jehovah had foreknown this and, through the prophet Isaiah, indicated that the time would come when he would no longer hold back from punishing the desolaters: “I have kept quiet for a long time. I continued silent. I kept exercising self-control. Like a woman giving birth I am going to groan, pant, and gasp at the same time. I shall devastate mountains and hills, and all their vegetation I shall dry up.”—Isa 42:14, 15.

Christ Jesus also exercised self-control. The apostle Peter, when calling to the attention of house servants the need to be in subjection to their owners, wrote: “In fact, to this course you were called, because even Christ suffered for you, leaving you a model for you to follow his steps closely. . . . When he was being reviled, he did not go reviling in return. When he was suffering, he did not go threatening, but kept on committing himself to the one who judges righteously.”—1Pe 2:21-23.

In “the last days” lack of self-control was to be one of the characteristics marking those who would not be practicing true Christianity. (2Ti 3:1-7) However, since Christians are to be imitators of God and of his Son (1Co 11:1; Eph 5:1), they should strive to cultivate self-control in all things. (1Co 9:25) The apostle Peter stated: “Supply to your faith virtue, to your virtue knowledge, to your knowledge self-control, to your self-control endurance, to your endurance godly devotion, to your godly devotion brotherly affection, to your brotherly affection love. For if these things exist in you and overflow, they will prevent you from being either inactive or unfruitful regarding the accurate knowledge of our Lord Jesus Christ.”—2Pe 1:5-8.

The quality of self-control should especially be in evidence among those serving as overseers in Christian congregations. (Tit 1:8) If overseers are to deal effectively with problems inside the congregation, they must maintain self-control in word and deed. The apostle Paul counseled Timothy: “Further, turn down foolish and ignorant questionings, knowing they produce fights. But a slave of the Lord does not need to fight, but needs to be gentle toward all, qualified to teach, keeping himself restrained under evil, instructing with mildness those not favorably disposed.”—2Ti 2:23-25.

Failure to exercise self-control in a given situation can tarnish a long record of faithful service and plunge one into all kinds of difficulties. An illustration of this is what happened to King David. Though loyal to true worship and having love for the righteous principles of God’s law (compare Ps 101), David committed adultery with Bath-sheba, and this led to his having her husband Uriah placed in a battle position where death was a near certainty. As a consequence, for years afterward, David was plagued with severe difficulties within his family. (2Sa 12:8-12) His case also demonstrates the wisdom of avoiding situations that can lead to a loss of self-control. Whereas he could have left the rooftop of his palace, David evidently kept on looking at Bath-sheba as she bathed herself and so came to have a passion for her.—2Sa 11:2-4.


Similarly, it would not be good for a person lacking self-control to remain single when he could enter into an honorable marriage and thereby protect himself against committing fornication. In this regard, the apostle Paul wrote: “If they do not have self-control, let them marry, for it is better to marry than to be inflamed with passion.”—1Co 7:9, 32-38.

On our neighbours' minds II

Does Intelligence Depend on a Specific Type of Brain?
Denyse O'Leary January 7, 2016 1:03 PM

All life forms participate in some kind of intelligence and intentionality, in the sense that for billions of years they have sought to live and have adapted for that purpose. Nonetheless, animals that also demonstrate individual intelligence are orders of magnitude less intelligent than humans -- whether they are closely related to us physically (apes) or not (bird species).

We know their intelligence by its effects, in the same way we know gravity by its effects -- without being quite sure what it is. But we have some signposts.

Anatomy Probably Matters, But It Is Not Clear How

Even though shellfish, like octopuses, strive to stay alive, they could not open a jar to do so. Anatomy prevents it. Appendages may reward attempts at reasoning by expanding the search space for solutions. But they do not directly cause that search, any more than hands "caused" the Lascaux cave paintings. If they did, chimps would be painting caves too.

Painting? Domesticated elephants can be taught to "paint" identifiable figures with their trunks. But they are following a series of motions guided and rewarded by by their trainers. They don't know that they are painting, or how it looks to humans.

Chimpanzees have been taught to "paint" as well, but their problem is the opposite: They work readily with the materials, of their own volition, but don't attempt to represent anything, probably because their brains do not work that way.

Anatomy, it seems, can only expand search space for a purpose already envisioned by the mind. It does not expand the mind, so far as we can tell.

Tool Use May Be a Product of Definition

Use of tools is often used as a measure of intelligence, but the examples we have raises questions about what qualifies as tool use, and what it means. This becomes especially tricky when dealing with tool-use by invertebrates, or other creatures vastly different from humans in their complexity and anatomy.

Octopuses, which have very different brains from vertebrates, have been filmed carrying away halved coconut shells to use as shelters. Recently, crows were also filmed (via hidden close-up cameras) twisting sticks to make hooks to root insects out of tree bark:

Humans have previously seen the crows making the tools in artificial situations, in which scientists baited feeding sites and provided the raw tools; but researchers say the New Caledonian crows have never been filmed doing this in a completely natural setting

Also:

"Crows really hate losing their tools, and will use all sorts of tricks to keep them safe," Rutz said in a statement. "We even observed them storing tools temporarily in tree holes, the same way a human would put a treasured pen into a pen holder."

These findings are fascinating, but they also highlight the limits of assessing intelligence through tool use. First, confirming the crows' natural behavior is important, but it should not come as a surprise. Had the crows never behaved this way in nature and never been coached by humans either, it would be remarkable indeed if they tumbled to it all by themselves in captivity. Life forms of widely varying (apparent) intelligence store and hide things for later use, so that is not hard evidence of remarkable intelligence.

Brain imaging tests show that animals "treat sticks, hooks, and other tools as extensions of their bodies." If so, they probably do not abstract the concept of "tool" (that is, not-self), which limits their ability to envision other possible uses for a tool.

In any event, how we define tool use is complex, and somewhat muddled. As noted earlier, apes using stones are claimed to be entering the Stone Age. But no similar claim is made for great antshrikes, who apparently only recently started smashing snail shells using stones (the snails were a new arrival in their habitat).

Then what about birds that drop shellfish onto stones from the air, to break them? Does it make a difference if the presence or absence of suitable natural media influences choices of method?

Greater vasa parrots of Madagascar use pebbles for grinding minerals from seashells, though it is worth noting that many birds, including wild parrots, may eat little bits of insoluble minerals anyway, to aid in digestion. If the pebbles are tools, is the grit a tool? Are false teeth a tool? At any rate, the bird may not see any difference, and is probably not heading in any direction in particular in the use of tools.

The ability to modify tools -- often cited as evidence of additional intelligence -- prompts the same question: Does modifying a tool -- regarded as an extension of the appendage -- involve more intellectual effort than finding and marking a suitable scratching tree, as a sort of stationary comb? As you can see, even the seemingly simple task of identifying tool-use is difficult. We need much more observation of life forms in their natural habitats in order to spot larger patterns in (one hopes) a growing body of data on animal intelligence.

Sometimes, interpreting tool-use through the lens of naturalism leads to lapses in common sense. Take, for example, this section from an otherwise informative article by Annalee Newitz at I09, "The Mysterious Tool-Making Culture Shared by Crows and Humans" We are advised, "The fact that humans use tools doesn't make us unique among animals."

True, but we then hear:

Riskier environments seem to spur tool use, perhaps because food sources are more difficult to come by. And in addition, animals with large toolkits -- like humans -- seem to invent more tools as their populations grow. This could help explain why humanity's population explosion over the past century has been accompanied by an explosion in tool diversity, including radical new technologies.

Animals with large toolkits -- like humans?

If Newitz thought anything remotely similar had happened among non-human life forms, she did not mention it.

No matter how it is spun, the difference between the bent stick and the New Horizons satellite mapping Pluto is not merely one of degree. The crow is interested in rooting for grubs, and even if it develops other uses for the stick, it will never be interested in mapping Pluto. That isn't a "shared culture" at all, and we are back with the same conundrum of animal vs. human minds.

Are There Patterns in Invertebrate Brains and Intelligence?

Reptiles and fish sometimes show signs of intelligence despite having quite different brains from mammals. But, being exothermic, they don't do much of anything very often. For example, turtles may rescue each other, but can also spend months in a state of icy torpor with little adverse effect. At one time, it was assumed that the intelligence to rescue would not co-exist with lengthy inertia (the reptilian or triune brain hypothesis). Actually, the two qualities can co-exist, though they wouldn't be simultaneous.

Invertebrate just means "not a vertebrate," so there is no single type of invertebrate brain:

Invertebrates have immensely diverse nervous structures and body plans, revealing the variety of solutions evolved by animals living successfully in all kinds of niches.

And that is where things get a bit complicated. Starfish, essentially, do not have a brain or even ganglia, just a nerve ring. Their behavior has accordingly been attributed to "self-organized behavioral patterns" not strictly determined by external stimuli. It would be good to unpack what that implies.

Crayfish seem somewhere in the middle, that is, smarter than we used to think, even though the crustacean brain (a "microbrain" of three fused ganglia) is often studied on account of its comparative simplicity.

We keep learning new complexities of other invertebrate behavior too. For example, mantis shrimp use a polarizing light display to warn their fellows that a hiding place from predators is already taken.

Commentator Eric Metaxas recently drew public attention to the "genius" invertebrate, the octopus. Octopuses, we are told, are practically aliens. But how unusual are they and why?

U.S. researcher Dr. Clifton Ragsdale, from the University of Chicago, said: "The octopus appears to be utterly different from all other animals, even other molluscs, with its eight prehensile arms, its large brain and its clever problem-solving abilities."

It also has an unusually large genome, with more protein-coding genes than humans have (33,000 vs., 25, 000):

This excess results mostly from the expansion of a few specific gene families, Ragsdale says. One of the most remarkable gene groups is the protocadherins, which regulate the development of neurons and the short-range interactions between them. The octopus has 168 of these genes -- more than twice as many as mammals. This resonates with the creature's unusually large brain and the organ's even-stranger anatomy. Of the octopus's half a billion neurons -- six times the number in a mouse -- two-thirds spill out from its head through its arms, without the involvement of long-range fibres such as those in vertebrate spinal cords. The independent computing power of the arms, which can execute cognitive tasks even when dismembered, have made octopuses an object of study for neurobiologists such as Hochner and for roboticists who are collaborating on the development of soft, flexible robots.

It seems that a relatively big brain benefits even an invertebrate -- but we are now left to wonder how the octopus acquired one. Researchers consider it a striking example of convergent evolution -- with vertebrates.

What Do We Know About Insect Intelligence?

We don't know very much about insect intelligence. The envisioned long, slow continuum of intelligence from mite to man has meant that many explicitly non-human types of intelligence have been written off or explained away. Brain researcher Antoine Wystrach helps us understand how ants perceive the world:

Counter-intuitively, years of bottom-up research has revealed that ants do not integrate all this information into a unified representation of the world, a so-called cognitive map. Instead they possess different and distinct modules dedicated to different navigational tasks. ... These results demonstrate that the navigational intelligence of ants is not in an ability to build a unified representation of the world, but in the way different strategies cleverly interact to produce robust navigation.

He adds, "We need to keep in mind that this is only our current level of understanding. Even insect brains are far too complex to be fully understood in the near future. "

If the current description proves accurate, the ant may show considerable intelligence, but not have a unified sense of self, in the same way that a dog or raven probably does (all these sensations are happening to me). Other researchers are less cautious, claiming that insects may have consciousness and "could even be able to count."

But consciousness is the central conundrum in philosophy even for humans. And, as Clever Hans and similar co-operative animals have shown, the ability to count, like tool use, is not necessarily reliable evidence of intelligence. The count may be driven by metabolism, prompting, or simply the fact that a given number of efforts succeeds (without the number being abstracted in any way).

The way insect intelligence develops may be different as well. Bees, like many insects, exhibit "an incredibly wide variety of intelligent behaviors." But, according to some researchers, insect intelligence tends to increase when individuality is suppressed (the hive mind):

Compared to social species, they found solitary species had significantly larger brain parts known as the mushroom bodies, which are used for multisensory integration, associative learning and spatial memory -- the best available measure of complex cognition in these insects. The finding supports the idea that, as insect social behavior evolved, the need for such complex cognition in individuals actually decreased.

Some have described this "hive" model of intelligence as a "superorganism":

We will see that the 1.5 kilograms (3 pounds) of bees in a honeybee swarm, just like the 1.5 kilograms (3 pounds) of neurons in a human brain, achieve their collective wisdom by organizing themselves in such a way that even though each individual has limited information and limited intelligence, the group as a whole makes a first-rate collective.

If so, animal intelligences can be highly developed and yet quite different from each other. No specific type of brain is required and humans remain outliers.


But intelligence is not all we wonder about. There is also the question of subjectivity -- a sense of self. If jellyfish were conscious of their apparent intention to catch fish, would they have a mind without a brain? When starved amoebas form a slime mold, and act temporarily as a colony, do they have a hive mind, which simply dissipates when they find food and break up? Intelligence is today's unknown country. But some animal intelligences do encourage a sense of self, as anyone who has lived with a group of domestic animals will attest. Can there be a sort of minimal self?

In search of high quality ignorance II

In Science Education, "Confusion" Can Be a Synonym for Stimulation
Sarah Chaffee January 7, 2016 2:25 PM 

Writing at NPR's Cosmos and Culture blog, psychology professor Tania Lombrozo highlights the role that confusion can play in learning -- especially in science ("Sometimes Confusion Is a Good Thing"). This may seem paradoxical. Isn't dispelling confusion an aim of education?

In fact, Lombrozo argues, it may be helpful in some contexts. She refers to a study by Sidney D'Mello, Blair Lehman, Reinhard Pekrun, and Art Graesser in the journal Learning and Instruction. The researchers induced confusion by exposing learners to contradictory opinions and then asking them to decide which opinion had the most scientific merit. Student confusion was correlated with enhanced learning. Although correct answers were later provided to the students in the study, this may not be possible in areas of ongoing scientific debate.

The authors note:

The most obvious implication of this research is that there might be some practical benefits for designing educational interventions that intentionally perplex learners. Learners complacently experience a state of low arousal when they are in comfortable learning environments involving passive reading and accumulating shallow facts without challenges...

As I have observed here before, allowing students to grapple with scientific questions engages them in the act of inquiry. Note that there is a difference between uncertainty that is irrelevant to the question at hand (due to a teacher's lack of clarity, for example, or the inability to find the right page in the textbook) and experiencing the dynamic tension between alternate viewpoints.

Lombrozo reflects:

One possibility is that confusion is not itself beneficial, but rather a marker that an important cognitive process has taken place: The learner has appreciated some inconsistency or deficit in her prior beliefs. But another possibility is that confusion is itself a step toward learning -- an experience that motivates the learner to reconcile an inconsistency or remedy some deficit. In this view, confusion isn't just a side effect of beneficial cognitive processes, but a beneficial process itself. Supporting this stronger view, there's evidence that experiencing difficulties in learning can sometimes be desirable, leading to deeper processing and better long-term memory.

In science, it is uncertainty, and the urge to explore the unknown, that leads to discovery. Research aims to extend the current body of knowledge, not merely to regurgitate what has already been found. In the Journal of Cell Science, Martin Schwartz writes about working on his PhD:

I remember the day when Henry Taube (who won the Nobel Prize two years later) told me he didn't know how to solve the problem I was having in his area. I was a third-year graduate student and I figured that Taube knew about 1000 times more than I did (conservative estimate). If he didn't have the answer, nobody did.

That's when it hit me: nobody did. That's why it was a research problem. And being my research problem, it was up to me to solve. Once I faced that fact, I solved the problem in a couple of days. (It wasn't really very hard; I just had to try a few things.) The crucial lesson was that the scope of things I didn't know wasn't merely vast; it was, for all practical purposes, infinite. That realization, instead of being discouraging, was liberating. If our ignorance is infinite, the only possible course of action is to muddle through as best we can.

Unanswered questions are central to ongoing scientific inquiry. They spur further investigation. Exposing students to the interplay between questions and answers prepares them to engage in research.

In the study of life's origins, for example, many fundamental questions are unresolved. Priestley Medalist George M. Whitesides wrote, "Most chemists believe, as do I, that life emerged spontaneously from mixtures of molecules in the prebiotic Earth. How? I have no idea." Similarly, leading molecular biologist Eugene Koonin noted:

Despite many interesting results to its credit, when judged by the straightforward criterion of reaching (or even approaching) the ultimate goal, the origin-of-life field is a failure -- we still do not have even a plausible coherent model, let alone a validated scenario, for the emergence of life on Earth.... A succession of exceedingly unlikely steps is essential for the origin of life, from the synthesis and accumulation of nucleotides to the origin of translation; through the multiplication of probabilities, these make the final outcome seem almost like a miracle.

Koonin acknowledges that some progress has been made, but falls back on the controversial multiverse theory to explain how life sprang into existence against all odds. The enigma of biological origins offers an ideal opportunity for students to learn about a field of persistent scientific uncertainty. Isn't this better than insisting that students accept evolution as "fact," then work backward to explain all that they see in that dogmatic light?

Another mystery is the Cambrian explosion. As many of our readers will know, nearly two-thirds of known animal body plans appeared in a roughly 5 to 10 million-year period -- a brief span in geological terms. Some scientists question the ability of natural selection and random mutation to produce so many diverse animals in such a short period. In their book The Cambrian Explosion, Douglas Erwin and James Valentine wrote:

One important concern has been whether the microevolutionary patterns commonly studied in modern organisms by evolutionary biologists are sufficient to understand and explain the events of the Cambrian or whether evolutionary theory needs to be expanded to include a more diverse set of macroevolutionary processes. We strongly hold to the latter position.

Similarly, in reviewing Erwin and Valentine's book, the journal Science noted:

The Ediacaran and Cambrian periods witnessed a phase of morphological innovation in animal evolution unrivaled in metazoan history, yet the proximate causes of this body plan revolution remain decidedly murky. The grand puzzle of the Cambrian explosion surely must rank as one of the most important outstanding mysteries in evolutionary biology.

Yet textbooks generally avoid acknowledging this mystery. In Icons of Evolution, Jonathan Wells writes:

Since booklets published by the National Academy of Sciences ignore the fossil and molecular evidence and call evolution a "fact," perhaps it is not surprising to find biology textbooks doing the same. "Descent with modification from common ancestors is a scientific fact, that is, a hypothesis so well supported by evidence that we take it to be true," according to Douglas Futuyma's 1998 college textbook Evolutionary Biology....Although Futuyma's book subsequently discusses the Cambrian explosion, its emphasis is on explaining it away rather than dealing candidly with its challenge to Darwinian theory.

It does not matter what you call it; uncertainty, grappling with puzzling questions, acknowledging areas of scientific ignorance -- it is pedagogically sound and a real and integral part of science. This is one reason that Discovery Institute recommends teaching both the scientific strengths and weaknesses of evolutionary theory. Our science education policy states:

[Discovery Institute] believes that evolution should be fully and completely presented to students, and they should learn more about evolutionary theory, including its unresolved issues. In other words, evolution should be taught as a scientific theory that is open to critical scrutiny, not as a sacred dogma that can't be questioned.


John Scopes himself put it well: "If you limit a teacher to only one side of anything, the whole country will eventually have only one thought... I believe in teaching every aspect of every problem or theory." Our position is simply that, in science education, admitting areas of honest uncertainty should extend to evolution as much as to any other subject. By withholding such stimulation, educators do students no favor.

Off the deep end II

From Animal Rights Activists, a Crazy Proposed Constitutional Amendment
Wesley J. Smith January 6, 2016 11:46 AM

The Humane Party, animal rights advocates, have published a proposed constitutional amendment. I quote it here not because I think it will be enacted, but because it illustrates the subversive belief system -- the absolutist ideology -- that drives "animal rights." From the press release:

Full Text of the Abolition Amendment to the U.S. Constitution

Section 1. Neither slavery nor involuntary servitude of any sentient being shall exist within the United States or any place subject to their jurisdiction.

Section 2. Congress may, from time to time, refine the definition of 'sentient being' for the purposes of this article in accord with advances in science, except that in no event shall this definition be altered so as to exclude from this definition any species or individual organism that is, or would have been if existent, classified in the kingdom animalia as of the date of ratification of this article.

Section 3. Congress shall have the power to enforce this article by appropriate legislation.

Realize that flies are sentient. Fish are sentient. Even oysters are sentient, which is why they make a pearl out of an irritating grain of sand.

If enacted, this would mean no cattle ranching, fish farms, animal research, zoos, or pets. After all, our dogs and cats are owned by us.

Animal rights isn't about being nicer to animals. As the "Vegan Fox" explains above, it is about elevating all fauna to equal legal and moral status with humans. It's a frightening illustration of our dissipated times that millions of people support this nihilism.

Ps. Surely the fact that we humans can choose to cease being omnivores for whatever reasons we fancy puts us in a different moral/mental category from say dragonflies that routinely prey on weaker members of their own species.

Can anyone conceive of similar protest movements occurring among the carnivores of the animal kingdom.And let's not forget that in many poorer parts of the world man eating predators continue to be responsible for thousands of human deaths yet I've heard no reports of progressive crocodiles,for instance, picketing for an end to this slaughter in the Asian and African countryside by their fellow crocodilians.Just for the record I am fully aware that humanity as a specie is a far greater danger to our fellow travelers on spaceship earth than the converse but I am also convinced that given our technological superiority things would have been far worse if we had not sought to morally/mentally distinguish ourselves from the subhuman species with which we share our planet.There is of course considerable room for improvement but for this we must take our cue from above from not below from the angels not the apes. 

Out of thin air?

As an Explanation of the Cambrian Explosion, the Oxygen Theory Takes a Lethal Blow
David Klinghoffer January 6, 2016 1:43 PM 

The oxygen idea had already taken blows, including from us, but this would seem to be the end of it. The notion was that rising oxygen levels permitted and therefore somehow spurred the Cambrian explosion, the geologically abrupt emergence of complex animal life less than 600 million years ago. It is as if the possibility of breathing deep was so enticing as to coax a vast infusion of biological information, needed to generate most known animal body plans, from nonexistence into existence. "Oh, whistle, and I'll come to you, my lad."

Now a team reports in Proceedings of National Academy of Sciences that there was adequate oxygen long before, so long as to decisively blunt the oxygen theory. This seems definitive. From Science Daily:

Animals evolved by about 600 million years ago, which was late in Earth's history. The late evolution of animals, and the fact that oxygen is central for animal respiration, has led to the widely promoted idea that animal evolution corresponded with a late a rise in atmospheric oxygen concentrations.
"But sufficient oxygen in itself does not seem to be enough for animals to rise. This is indicated by our studies," say postdoc Emma Hammarlund and Professor Don Canfield, Nordic Center for Earth Evolution, University of Southern Denmark.

Together with colleagues from the China National Petroleum Corporation and the University of Copenhagen, Hammarlund and Canfield have analyzed sediment samples from the Xiamaling Formation in China. Their analyses reveal that a deep ocean 1.4 billion years ago contained at least 4% of modern oxygen concentrations.

How did they make the determination? The Abstract summarizes ("Sufficient oxygen for animal respiration 1,400 million years ago"):
The Mesoproterozoic Eon [1,600-1,000 million years ago (Ma)] is emerging as a key interval in Earth history, with a unique geochemical history that might have influenced the course of biological evolution on Earth. Indeed, although this time interval is rather poorly understood, recent chromium isotope results suggest that atmospheric oxygen levels were <0 .1="" 1="" 3="" a="" an="" ancient="" and="" animal="" approach="" are="" atmospheric="" bacteria="" biomarker="" block.="" bottom="" carbon="" china="" column.="" comprehensive="" consistent="" contrast="" cycle="" demonstrate="" deposition="" develop="" different="" distribution="" document="" during="" dynamics="" enrichments="" evolution="" explore="" formation="" geochemical="" green="" have="" in="" inhibited="" levels="" life.="" low="" ma="" marine="" metal="" metals="" minimum="" model="" north="" of="" our="" oxygen="" oxygenated="" patterns="" presence="" present="" redox-sensitive="" results="" reveal="" sediments="" show="" simple="" sufficiently="" sulfur="" that="" the="" thus="" to="" trace="" unit="" using="" water="" waters="" we="" with="" xiamaling="" yet="" zone.="">4% of present-day levels. Therefore, in contrast to previous suggestions, we show that there was sufficient oxygen to fuel animal respiration long before the evolution of animals themselves.
Emma Hammarlund encapsulates the bad news:

The sudden diversification of animals probably was a result of many factors. Maybe the oxygen rise had less to do with the animal revolution than we previously assumed.

But you know what, failed scientific theories that seem to lend support to materialism have a way of defying death. They stick around even well after the evidence has turned against them. I'd bet you that popular and even professional science sources will still be touting the oxygen theory years from now, as if nothing had happened.

Namibia to the defence of religious liberty

Namibia Supreme Court Upholds Patients’ Rights and Religious Freedom:


The Supreme Court of Namibia has ruled to protect a patient’s right to bodily self-determination and personal autonomy in making treatment decisions. The Court also recognized the validity of a written advance directive informing health-care providers of the patient’s treatment wishes.

Childbirth and a Medical Emergency
The legal case before the Court concerned the health of Efigenia Semente, one of Jehovah’s Witnesses. In preparation for the birth of her third child, Mrs. Semente informed her physician that she would not accept blood transfusions because of her religious convictions. She also gave him an advance medical directive in the form of a durable power of attorney. In this document, Mrs. Semente expressed her unequivocal refusal of blood and designated her husband as her health-care agent to make decisions for her if she became incapacitated.

The physician safely delivered her daughter on September 8, 2012, but Mrs. Semente required postdelivery surgery. Her husband, as her health-care agent, consented. However, complications arose during the surgery, and the physician wished to administer a blood transfusion. Mr. Semente refused on his wife’s behalf, consistent with her advance medical directive. The doctor successfully operated without a blood transfusion, but Mrs. Semente came out of surgery with low hemoglobin levels.

High Court Intervention
On September 13, 2012, while Mrs. Semente was recovering from surgery, her eldest brother applied to the High Court of Namibia to be appointed as her legal curator so that he—instead of her husband—could direct her medical treatment. Although neither Mrs. Semente nor her husband received notice of her brother’s application, the court conducted a hearing in their absence and ordered her brother appointed as curator. Her brother thereafter directed the medical staff to transfuse Mrs. Semente against her will, but she repeated her refusal and resisted their efforts, thus preventing the transfusion.

When Mrs. Semente learned that the court had appointed her brother as her curator, she made an urgent application to the High Court to rescind the order. She argued that she was of sound mind when her brother applied for curatorship and that her brother’s authorization of a blood transfusion violated both her religious beliefs and her right to bodily self-determination. The court dismissed her application and allowed her brother to continue as her curator.

Although Mrs. Semente’s doctor testified that she would die without a transfusion, her condition improved with nonblood medical management, and she was discharged from the hospital on September 26, 2012, without being transfused. However, the High Court had appointed her brother as her curator indefinitely. Viewing the curatorship as a violation of her personal autonomy and basic human rights, Mrs. Semente appealed to the Supreme Court of Namibia.

“The facts of this matter concern some of [the] most essential human rights issues likely to arise in litigation. They relate to the right to bodily autonomy, the right to freely practice one’s religion, and the freedom from discrimination.”—Supreme Court of Namibia.
Supreme Court Judgment
On June 24, 2015, the Supreme Court of Namibia upheld Mrs. Semente’s fundamental rights and rescinded her brother’s curatorship. The Supreme Court condemned as “entirely inappropriate” the lack of notice to Mrs. Semente and her husband and the High Court’s one-sided hearing that appointed Mrs. Semente’s brother as her curator.

The Supreme Court highlighted that the Namibia Constitution guarantees personal liberty and human dignity as the basis of patient autonomy. The Court stated: “The principle of patient autonomy reflects that it is a basic human right for an individual to be able to assert control over his or her own body. . . . Medical practitioners must inform their patients about the material risks and benefits of the recommended treatment but it is up to the patient to decide whether to proceed with a particular course of treatment.”

“It is a basic human right for an individual to be able to assert control over his or her own body.”—Supreme Court of Namibia.
Ultimately, in reviewing Mrs. Semente’s competency to refuse blood transfusions, the Supreme Court concluded that the High Court gave insufficient weight to her durable power of attorney. The Supreme Court further stated: “Written advanced directives which are specific, not compromised by undue influence, and signed at a time when the patient has decisional capacity constitute clear evidence of a patient’s intentions regarding their medical treatment.”

The Supreme Court also addressed the question of whether a child’s right to be raised by her parents restricts her parents’ right to choose their medical treatment. After reviewing international case law, the Court concluded that “the right to choose what can and cannot be done to one’s body, whether one is a parent or not, is an inalienable human right.”


The Supreme Court of Namibia has strengthened the right to bodily self-determination and has recognized advance medical directives as evidence of a patient’s values and treatment choices. By upholding the rights to bodily integrity and religious freedom, the Supreme Court has protected basic human dignity and liberty for all Namibians.

The Watchtower Society's commentary on "patience"

LONG-SUFFERING:
The patient endurance of wrong or provocation, combined with a refusal to give up hope for improvement in the disturbed relationship. Long-suffering therefore has a purpose, looking particularly to the welfare of the one causing the disagreeable situation. It does not mean the condoning of wrong, however. When the purpose for long-suffering is accomplished, or when there is no point in further putting up with the situation, long-suffering ends. It ends either with good to those giving provocation or with action against the wrongdoers. In any case the one exercising long-suffering is not harmed in spirit.

The literal meaning of the Hebrew expression translated “slow to anger” (“long-suffering” in some translations) is “length of nostrils [where anger flares up].” (Ex 34:6; Nu 14:18; see ANGER.) The Greek word ma·kro·thy·miʹa (long-suffering) literally means “longness of spirit.” (Ro 2:4, Int) Both the Hebrew and Greek expressions denote patience, forbearance, slowness to anger. The English word “suffering” in the word “long-suffering” has the sense of “putting up with, permitting, tolerating, holding up, or delaying.” “Long-suffering” means more than merely enduring pain or trouble. It does not mean merely “suffering long” but involves deliberate restraint.

The Scriptures reveal God’s evaluation of long-suffering and point out the foolishness and bad results of not maintaining “longness of spirit.” The long-suffering person may seem weak, but he actually is using discernment. “He that is slow to anger is abundant in discernment, but one that is impatient is exalting foolishness.” (Pr 14:29) Long-suffering is better than physical mightiness, and it will accomplish more. “He that is slow to anger is better than a mighty man, and he that is controlling his spirit than the one capturing a city.”—Pr 16:32.

The man who is not ‘long in spirit,’ but who bursts forth without restraint, is open to the invasion of any and all improper thoughts and actions, for: “As a city broken through, without a wall, is the man that has no restraint for his spirit.” (Pr 25:28) “All his spirit is what a stupid one lets out, but he that is wise keeps it calm to the last.” (Pr 29:11) For these reasons, the wise man counsels not to be ‘short in spirit’: “Do not hurry yourself in your spirit to become offended, for the taking of offense is what rests in the bosom of the stupid ones.”—Ec 7:9.

Jehovah’s Long-Suffering. When Jehovah took Moses up into Mount Horeb and showed him some of his glory, he declared before Moses: “Jehovah, Jehovah, a God merciful and gracious, slow to anger and abundant in loving-kindness and truth, preserving loving-kindness for thousands, pardoning error and transgression and sin, but by no means will he give exemption from punishment.” (Ex 34:5-7) This truth about Jehovah’s slowness to anger was repeated by Moses, David, Nahum, and others.—Nu 14:18; Ne 9:17; Ps 86:15; 103:8; Joe 2:13; Jon 4:2; Na 1:3.

While long-suffering is an attribute of Jehovah, it is always expressed in harmony with his primary attributes of love, justice, wisdom, and power. (1Jo 4:8; De 32:4; Pr 2:6; Ps 62:11; Isa 40:26, 29) Justice is due, first of all, to God’s own name. That name must be exalted above all others in the universe; and this is essential for the well-being of all his creatures. The magnifying of his name is one of his chief reasons for long-suffering, as the apostle Paul explains: “If, now, God, although having the will to demonstrate his wrath and to make his power known, tolerated with much long-suffering vessels of wrath made fit for destruction, in order that he might make known the riches of his glory upon vessels of mercy, which he prepared beforehand for glory, namely, us, whom he called not only from among Jews but also from among nations, what of it?” (Ro 9:22-24) God, in exercising long-suffering, is taking out a people for his name. And by means of them he is magnifying himself in all the earth.—Ac 15:14; 1Co 3:9, 16, 17; 2Co 6:16.

God exhibited his long-suffering in the very early part of man’s history. Rebellion of the first human couple had brought violation of his law. But instead of executing them immediately, as God could have justly done, in love he displayed long-suffering. This was for their as-yet-unborn descendants, to whom such long-suffering meant everything (his patience means salvation for many [2Pe 3:15]). More important, God also had in view the magnifying of his glory by means of the Seed of promise. (Ge 3:15; Joh 3:16; Ga 3:16) And God not only was long-suffering at that time but he knew that he would have to put up with imperfect mankind for several thousand years of history, delaying punishment against a world at enmity with him. (Jas 4:4) Some have misunderstood and misused God’s long-suffering toward them, missing its purpose by viewing it as slowness rather than as loving patience.—Ro 2:4; 2Pe 3:9.

Nowhere is the long-suffering of God more evident than in his dealings with the ancient nation of Israel. (Ro 10:21) Time and again he received them back after they had fallen away, were punished, and repented. They killed his prophets and finally his own Son. They fought the preaching of the good news by Jesus and his apostles. But God’s long-suffering was not wasted. There was a remnant that proved faithful. (Isa 6:8-13; Ro 9:27-29; 11:5) He used some of such faithful ones to write his Word under inspiration. (Ro 3:1, 2) The Law he gave showed that all mankind are sinners and need a redeemer, and it pointed to that One who would give his life as a ransom price and who would be exalted to the high position of King. (Ga 3:19, 24) Patterns of that Kingdom and of Christ’s priesthood were provided (Col 2:16, 17; Heb 10:1), and examples for us to follow or avoid were set forth. (1Co 10:11; Heb 6:12; Jas 5:10) All these things are essential to mankind for the gaining of everlasting life.—Ro 15:4; 2Ti 3:16, 17.

Jehovah not long-suffering forever. On the other hand, God is long-suffering only as long as it is in harmony with justice, righteousness, and wisdom. The fact that long-suffering is exercised when a bad or provocative situation exists shows that it is meant to give opportunity for those involved in the bad situation to change, to straighten up. When matters come to a point where it is seen that there is no hope of such change, justice and righteousness would be violated if long-suffering should continue. Then God acts in wisdom to remove the bad situation. His patience comes to an end.

An example of this forbearance on God’s part and of its coming to an end is found in God’s dealing with men before the Flood. A deplorable condition existed, and God said: “My spirit shall not act toward man indefinitely in that he is also flesh. Accordingly his days shall amount to a hundred and twenty years.” (Ge 6:3) Later, regarding Israel’s misuse of Jehovah’s long-suffering, Isaiah said: “But they themselves rebelled and made his holy spirit feel hurt. He now was changed into an enemy of theirs; he himself warred against them.”—Isa 63:10; compare Ac 7:51.

For these reasons Christians are entreated not to “accept the undeserved kindness of God and miss its purpose.” (2Co 6:1) They are counseled: “Do not be grieving [saddening] God’s holy spirit.” (Eph 4:30, Int) Also, “Do not put out the fire of the spirit.” (1Th 5:19) Otherwise they may continue to the point of sin and blasphemy against God’s spirit, in effect outraging it, in which case there is no repentance or forgiveness, only destruction.—Mt 12:31, 32; Heb 6:4-6; 10:26-31.

Jesus Christ. Jesus Christ exemplified long-suffering among humans. Of him, the prophet Isaiah wrote: “He was hard pressed, and he was letting himself be afflicted; yet he would not open his mouth. He was being brought just like a sheep to the slaughtering; and like a ewe that before her shearers has become mute, he also would not open his mouth.” (Isa 53:7) He put up with the weaknesses of his apostles and the insults and discourtesies heaped upon him by bitter, vicious enemies. Yet he did not retaliate in kind, by word or action. (Ro 15:3) When the apostle Peter acted injudiciously in cutting off the ear of Malchus, Jesus reproved him with the words: “Return your sword to its place, . . . do you think that I cannot appeal to my Father to supply me at this moment more than twelve legions of angels? In that case, how would the Scriptures be fulfilled that it must take place this way?”—Mt 26:51-54; Joh 18:10, 11.

Why is it important for Christians to cultivate long-suffering?

From the foregoing it is evident that long-suffering originates with Jehovah God. It is a fruit of his spirit. (Ga 5:22) Man, made in the image and likeness of God, has a measure of this quality and can develop it by following God’s Word and the direction of his holy spirit. (Ge 1:26, 27) Christians are therefore commanded to cultivate and display this quality. (Col 3:12) It is an identifying mark of a minister of God. (2Co 6:4-6) The apostle Paul says: “Be long-suffering toward all.” (1Th 5:14) He indicates that it is essential to exercise this quality in order to be pleasing to God. But one’s long-suffering is not genuine if it is accompanied by grumbling and complaining. Paul shows that the commendable thing is to “be long-suffering with joy.”—Col 1:9-12.

Aside from the joy that one gets through the practice of long-suffering, the rewards are great. Jehovah is rewarded by having his name glorified. The challenge against the righteousness and rightfulness of God’s sovereignty is proved wrong, and he is vindicated. (Ge 3:1-5; Job 1:7-11; 2:3-5) What if he had put Adam, Eve, and Satan to death at the time of the rebellion? Some might have concluded that Satan had a point in his challenge. But by long-suffering, Jehovah gave men the opportunity to prove under test that they prefer his sovereignty over them and that they want to serve him because of his fine qualities, yes, to demonstrate that they prefer Jehovah’s sovereignty to complete independence, knowing that it is far better.—Ps 84:10.

Jesus Christ, because of long-suffering in obedience to God, received a most marvelous reward, being exalted to the superior position of kingship and being given “the name that is above every other name,” by his Father. (Php 2:5-11) Besides this, he receives a “bride” made up of his spiritual brothers, the New Jerusalem, which is represented as a city, the foundation stones of which have on them the names of the 12 apostles of the Lamb.—2Co 11:2; Re 21:2, 9, 10, 14.


Likewise, the reward is rich for all persons cultivating long-suffering and maintaining it in harmony with God’s purpose. (Heb 6:11-15) They have the satisfaction of copying God’s quality, of doing God’s will, and of having God’s approval. Additionally, their long-suffering will bring accomplishment in helping others to know God and to gain everlasting life.—1Ti 4:16.

Lamarck's revenge III

Epigenetics, a Revolution with a Long Onramp, Poised to Accelerate Design Thinking
Some revolutions have long onramps. Modern epigenetics has been around for well over a decade, but its impact has yet to be fully explored. Which interpretation of biology -- evolution or intelligent design -- stands the best chance of advancing scientific understanding of genomics through epigenetics research?

Well, it is indeed a revolution; that's what senior reporter Heidi Ledford calls it in her Nature Outlook piece, "Epigenetics: the genome unwrapped." She ends with remarks by Tomasz Jurkowski, a biochemist and epigeneticist at the University of Stuttgart in Germany who is racing against other researchers to untangle DNA's secrets:

He takes the competition in stride -- it is the price of entry into the fast lane. Epigenetics is on the verge of a revolution, he says. "This is just the beginning," he says. With just a little more time, "It will develop into a completely new field." [Emphasis added.]

As with any field in such a revolutionary condition, the ultimate outcome is unpredictable. That's why Ledford's subtitle reads, "Epigeneticists are harnessing genome-editing technologies to tackle a central question hanging over the community -- does their field matter?"

There's reason to think it will matter -- a lot. Of the many epigenetic markers already identified, many have shown to affect an organism's phenotype. Some of them have been shown to be heritable, opening up new vistas of epigenetic inheritance. Now, with the updated CRISPR-Cas9 gene editing tool, despite its potential for ethical quandaries (see discoverer Jennifer Doudna in Nature worrying about the Pandora's box she opened), epigenetics researchers are pushing the accelerator pedal.

Ledford describes how CRISPR-Cas9 -- Science Magazine's 2015 "Breakthrough of the Year" -- has already allowed one research team to speed around another team that did things the old-fashioned way.

René Maehr, an immunologist at the University of Massachusetts Medical School in Worcester and his colleagues fused an enzyme called histone demethylase, which removes methyl groups from histones, to a deactivated Cas9 enzyme, and then programmed it to target regions of DNA believed to enhance the expression of certain genes. The result was a functional map of genetic 'enhancer' sequences that allows researchers to determine what these enhancers do, how strongly, and -- most importantly -- where they are located in the genome.

Question: Why were they seeking "to determine what these enhancers do"? Answer: They didn't believe they were junk. They watched the target gene increase its expression significantly. "That result started to convince me that the acetylation of histones may be a direct cause of gene activation." This suggests a new layer of specified complexity that supersedes the old Central Dogma that viewed DNA as the master controller. Functional mapping now steps up from genes to the epigenetic markers that regulate them.

Researchers don't know if all epigenetic marks have such dramatic effects. "For all we know, they might have very minor effects on gene expression except in a few special cases," a researcher at the Fred Hutchinson Cancer Center in Seattle opines. We may not have long to find out.

Now, however, researchers have a tool to pick apart the detail. Because of its simplicity and versatility, CRISPR-Cas9 opens up an opportunity to launch the kind of large-scale projects needed to reach that level of understanding. "If we want to target a region in the genome, we can have that targeting molecule here tomorrow for five dollars," says Reddy. "We're going to get to march through every single one of these modifications and figure out what they actually do."

You don't try to figure out what pieces of junk do. Whatever the outcome of the "ambitious projects" ahead, "the rapid pace of the field is already defying expectations," Ledford writes. Let's look at some other recent articles for clues.

Epigenetic markers may shed light on the long-standing mystery of the molecular basis for caste-specific behavior in ant colonies. (Science Magazine):

These findings reveal the epigenome as a likely substrate underlying caste-based division of labor in eusocial insects. Furthermore, in light of the conserved role of CBP in learning and memory in both invertebrates and mammals, these data suggest that CBP-mediated histone acetylation may similarly facilitate the complex social interactions found in vertebrate species.

Epigenetic markers affecting the immune system change with habitat, researchers found when comparing methylation marks on forest-dwelling African tribes with sedentary farmers. (Pasteur Institute):

These results partly explain why some people are predisposed to certain diseases. "Our research shows that changing lifestyles and habitats have a major influence on our epigenome and that urbanization significantly affects the epigenetic profiles of the immune system. This demonstrates how important it is, alongside more traditional genetic research, to investigate how epigenetic changes could result in an immune system that is more prone to the development of autoimmune diseases, allergies, inflammation and so on," explains Lluis Quintana-Murci. [Italics in original.]

"Epigenetic discovery suggests DNA modifications more diverse than previously thought" (University of Cambridge):

The world of epigenetics -- where molecular 'switches' attached to DNA turn genes on and off -- has just got bigger with the discovery by a team of scientists from the University of Cambridge of a new type of epigenetic modification.... It's possible that we struck lucky with this modifier, but we believe it is more likely that there are many more modifications that directly regulate our DNA."

This is just a taste of the kind of high-level research that is attracting grant money. The project at Cambridge, for instance, was funded by the Biotechnology and Biological Sciences Research Council, Human Frontier Science Program, Isaac Newton Trust, Wellcome Trust, Cancer Research UK, and the Medical Research Council.

Four years ago, we discussed whether the epigenome is "Evolution's Newest Nightmare." Current Biology put up a brave front, claiming that epigenetics might promise "interesting new angles in the study of evolution." That's hard to support now. None of the articles quoted above had any use for evolutionary theory. Indeed, how could they? If epigenetic markers regulate genes; if they act like molecular switches; if they can be placed into functional maps -- then they represent a higher level of complex specified information that defies the neo-Darwinian mutation/selection story.


Stated explicitly or not, it's design-based thinking that leads scientists to build functional maps of epigenetic markers and motivates them to "figure out what they actually do." Who would waste time or money on junk? The downfall of the junk-DNA concept gives scientists encouragement to seek new levels of specified complexity in epigenetic regulation. The future of epigenomics looks bright -- for intelligent design.