Another failed Darwinian prediction III

The DNA code is not unique:
Shortly after the discovery of the DNA code, which is used in cells to construct proteins, evolutionists began theorizing how it evolved. The same code was found in very different species which means that the same code was present in their distant, common ancestor. So the DNA code arose early in evolutionary history and remained essentially unchanged thereafter. And since it arose so early in evolutionary history, in the first primitive cell, the code must not be unique or special. For how could such a code have evolved so early in the history of life? As Nobel Laureate Francis Crick wrote in 1968, “There is no reason to believe, however, that the present code is the best possible, and it could have easily reached its present form by a sequence of happy accidents.” (Crick) Or as one widely used undergraduate molecular biology text later put it, “The code seems to have been selected arbitrarily (subject to some constraints, perhaps).” (Alberts et. al., 9) And an evolution textbook further explained, “The code is then what Crick called a ‘frozen accident.’ The original choice of a code was an accident; but once it had evolved, it would be strongly maintained.” (Ridley, 48)

In other words, somehow the DNA code evolved into place but it has little or no special or particular properties. But we now know that the code’s arrangement uniquely reduces the effects of mutations and reading errors. As one research study concluded, the DNA code is “one in a million” in terms of efficiency in minimizing these effects. (Freeland) Several other studies have confirmed these findings and have discovered more unique and special properties of the code. One found that the DNA code is a very rare code, even when compared to other codes which already have the error correcting capability. (Itzkovitz) Another found that the code does not optimize merely one function, but rather optimizes “a combination of several different functions simultaneously.” (Bollenbach) As one paper concluded, the code’s properties were “unexpected and still cry out for explanation.” (Vetsigian)

References

Alberts, Bruce., D. Bray, J. Lewis, M. Raff, K. Roberts, J. Watson. 1994. Molecular Biology of the Cell. 3d ed. New York: Garland Publishing.

Bollenbach, T., K. Vetsigian, R. Kishony. 2007. “Evolution and multilevel optimization of the genetic code.” Genome Research 17:401-404.

Crick, Francis. 1968. “The origin of the genetic code.” J. Molecular Biology 38:367-379.

Freeland, S., L. Hurst. 1998. “The genetic code is one in a million.” J. Molecular Evolution 47:238-248.

Itzkovitz, S., U. Alon. 2007. “The genetic code is nearly optimal for allowing additional information within protein-coding sequences.” Genome Research 17:405-412.

Ridley, Mark. 1993. Evolution. Boston: Blackwell Scientific.

Vetsigian, K., C. Woese, N. Goldenfeld. 2006. “Collective evolution and the genetic code.” Proceedings of the National Academy of Sciences 103:10696-10701.

Why the real world continues to be the elephant in the room re:darwinism.

Common Sense Design Principles and the Real World:
Ann Gauger January 11, 2016 3:00 AM

A recent paper in PLOS Genetics considers the origins of new "genes" in humans and chimps. By comparing RNA sequences, researchers identified over 600 transcriptionally active "genes" that appear to be present only in humans and not in chimps or the other mammal species tested. They claimed that these "genes" were the product of evolution from previously non-coding, untranscribed DNA. They argued that some of the "genes" are made into proteins and perhaps may be subject to selection, meaning that they are evolving.

I put genes in quote because this is not what the term gene typically means. It used to be that a gene was a stretch of DNA that coded for a protein, meaning it was a stretch of DNA that was copied into RNA (transcribed), and then translated into protein.

These researchers are using "gene" to signify any stretch of DNA that is copied (transcribed) into RNA and that meets certain criteria (size, the frequency with which they found it, etc.). They do not require that the RNA be turned into protein. In fact most of the time it probably isn't. But still they call them genes. Only in some cases do they find evidence that these genes actually make protein, protein that may be evolving new functions, they say.

Something to bear in mind -- all these conclusions are based only on the comparison of DNA sequences among species. They are conclusions based on the assumption that the differences reflect some sort of genetic history based on common descent -- the conclusions are not based on any experiments or observations of real events happening in real time.

As to their claims: I believe them when they say there are more than 600 regions of the genome that are transcribed in a manner unique to humans. After all, humans are different from chimps and can reasonably be expected to have genetic differences. Second, they may even be genes, if they produce a functional RNA, which is possible. I suspect they will be functional as RNAs. Third, these genes are in parts of the genome that used to be thought of as junk. Well, that's no surprise either. ID proponents have always expected most DNA to have a function and not be junk.

What I doubt is the claim that these genes evolved from untranscribed random sequences that somehow acquired promoter sequences, became transcribed, and even further, sometimes became translated and then became functional. The reason I doubt this? Douglas Axe's and my work on the evolution of enzymes, and a dose of common sense.

First of all, it is no trivial thing to "acquire" the promoter sequences that turn on a gene's transcription, and the signals that say when to stop. That one little undemonstrated word hides a multitude of requirements, and probably signifies a designer's action. Second, the words "became translated" hide all sorts of complex signals and activities, and likely require a designer as well. But the biggest problem of all is the business of taking non-functional protein and turning it into functional protein.

This scenario is what we tested in our most recent paper in BIO-Complexity. First, how hard is it to take a piece of junk protein and turn it into a brand new functional enzyme -- without a designer -- even if the junk protein already has a small amount of the new function to start? The answer -- it's not possible. We tested it in silico (using a computer program called Stylus, available online), and in the lab with a real protein. We were unable to improve the "junk" protein's function much at all, even after multiple rounds of mutation and selection.

Second, it's not possible to take a weakly functional, but already structured enzyme and change it to a new function at wild-type levels, even when the protein's not junk to start, and already has a small amount of the new function. If it has the wrong shape, the function can't be improved much at all -- nowhere near the levels normal wild-type enzymes have.

Third, if you are only a few selectable mutations away from a new function, it is possible to get there -- as long as each step is an improvement. That means in order for evolution to be able to make a wild-type enzyme, it has to begin with something that is most of the way there -- it's already pretty much the enzyme that's needed. New proteins have to be essentially of the right design in order to be improved to wild-type function.

Why bother with these experiments on proteins in the first place, you may ask. The answer is this -- what is true in the microscopic world about evolution is also true in the macroscopic world. What works (or doesn't work) with enzyme evolution demonstrates what evolution can or can't accomplish on a large scale.

If it's not possible to evolve new proteins from any starting point, evolving buttercups or cows won't work either. That is, unless the buttercups and cows pretty much already are buttercups and cows.

Evolution can't build something new from scratch. And it can't reconfigure something that already exists into something different. That's why I doubt the story of evolving new human genes from random non-coding sequences. I don't doubt that the genes are there -- they are. It's just that I think they were designed, not evolved.

Now for the dose of common sense. Let's turn the microscopic to macroscopic analogy on its head and use what we already know of design in the macroscopic world.

We all know you can't take a pile of scrap metal and turn it into a washing machine. You'd have to start from scratch, even though they are both made mostly of metal. What about turning a washing machine into a dishwasher? There's more similarity there -- after all, they both wash things. Still, neither process will happen without a designer or without considerable refashioning. Now what if a washing machine was merely broken? What if it had a few loose bolts and a torn gasket on the door? A blindfolded repairman might be able to fix that. That would be harder but not impossible. But even this analogy breaks down because the repairman is intelligent.

These are not perfect comparisons to biological processes -- the examples used all require intelligence and are man-made. But these things are simpler than enzymes, so perhaps our design intuitions do transfer to the biological realm.


Don't just take my word for it, though. For the real experimental data, read the paper and see for yourself. Check out the experiments that demonstrate in real time what really can and can't be accomplished.

Biology and Maths make a second try at a closer relationship

Biology and Mathematics
Evolution News & Views May 24, 2011 6:00 AM

Perhaps mathematics can explain certain biological phenomenon.

While the chemistry and physics students suffered through semester after semester of mathematics, the biology students finished their calculus sequence and moved on. The idea was that biology does not lend itself to mathematical application in the same way chemistry and physics does, so students didn't need very much math. However, that may be old news. According to an article in New Statesman by Ian Stewart, biology may be undergoing another revolution and the result will be "biomathematics":
Maths has played a leading role in the physical sciences for centuries, but in the life sciences it was little more than a bit player, a routine tool for analysing data. However, it is moving towards centre stage, providing new understanding of the complex processes of life.
Stewart mentions at the beginning of the article that biology has undergone five great revolutions:
• Invention of the microscope
• Classification
• Evolution
• Discovery of the Gene
• Discovery of the structure of DNA
He contends that mathematics may be the new, sixth revolution in biology. If we are talking about scientific revolutions in the sense that Thomas Kuhn describes them in The Structure of Scientific Revolutions, then the important point here is while the prior revolutions may have provided a greater understanding of biology they did not account for certain other observations. The next revolution provides a different framework by which that field of science operates, and opens the door for asking different kinds of questions.

What drives the research questions is the framework through which you are asking the questions. Stewart indicates that mathematics provides an apt framework for looking at the complexity of biological systems and for bringing up new research questions. He provides three interesting examples of research that was guided by questions that came out of mathematical theory. This post will look at one of them, animal markings. This particular theory had to do with work based on Alan Turing's equations and Mendelbrot's fractals.

Two scientists from Japan wanted to study the striking stripe pattern on a particular type of tropical angelfish (Pomacanthus imperator). They applied Turing's mathematical models to the patterns on the angelfish, but came up with odd results. The Turing model predicted that the angelfish's stripes move along its body. So the scientists decided to test this theory. From the article:

It seemed wildly unlikely, but when Kondo and Asai photographed specimens of the angelfish over periods of several months, they found that the stripes slowly migrated across its surface. Moreover, defects in the pattern of otherwise regular stripes, known as dislocations, broke up and re-formed exactly as Turing's equations predicted. They did this because the pigment proteins leaked from cell to cell, drifting from the fish's tail towards its head. (In animals whose stripes are fixed, this does not happen; but once the size of the animal and other factors are known, the maths can predict whether its markings will move.)
Most likely these scientists would not have considered the possibly of the angelfish's markings migrating across its body had they not used the mathematical models which pointed towards this research.

As scientists delve deeper into biological systems, they find more and more layers of complexity. Mathematics can help scientists understand the mechanisms behind the function.

Stewart mentions how DNA had changed the way we do biology. DNA, and genetics in general, turned biology into a micro-scale endeavor. Biochemistry emerged as a prominent discipline. Stewart points out that while we are able to identify the DNA sequence, we still do not understand how the genes work together:
A creature's genome is fundamental to its form and behaviour, but the information in the genome no more tells us everything about the creature than a list of components tells us how to build furniture from a flat-pack. What matters is how those components are used, the processes that they undergo in a living creature. And the best tool we possess for finding out what processes do is mathematics.
Stephen Meyer discusses how mathematics, particularly information theory, can help our understanding of DNA in chapter 4 of his book, Signature in the Cell. One of the important features to applying information theory to DNA is that DNA is mathematically similar to text (he compares it to English text) because it is not only non-compressible information, but is capable of carrying information. But it doesn't just carry information, it also conveys functional information. This leads to new research questions, particularly in origin of life research.


From a philosophical standpoint, what does it mean that these biological systems can be explained by mathematical theories (DNA and information theory, animal markings and fractals, viruses and geometry, plankton and chaos theory)? The mathematical predictability certainly implies non-randomness. It also seems to imply layers of complexity and layers of information. These layers of complexity seem to indicate something more than unguided or random processes. It seems to indicate either a front-loading of information or at least some kind of mechanism that has the end goal in mind.

Chimera: coming soon to a lab near you.

Scientists Make Part-Human Animals -- Good Idea?
Wesley J. Smith January 8, 2016 12:13 PM

Public money is being used to pay for research that create animals that are part human. From the MIT Technology Review story:

Braving a funding ban put in place by America's top health agency, some U.S. research centers are moving ahead with attempts to grow human tissue inside pigs and sheep with the goal of creating hearts, livers, or other organs needed for transplants.

The effort to incubate organs in farm animals is ethically charged because it involves adding human cells to animal embryos in ways that could blur the line between species.

This begins to cross into Dr. Moreau territory. Even the often compliant NIH is alarmed:

The agency, in a statement, said it was worried about the chance that animals' "cognitive state" could be altered if they ended up with human brain cells. The NIH action was triggered after it learned that scientists had begun such experiments with support from other funding sources, including from California's state stem-cell agency.

The human-animal mixtures are being created by injecting human stem cells into days-old animal embryos, then gestating these in female livestock. Based on interviews with three teams, two in California and one in Minnesota, MIT Technology Review estimates that about 20 pregnancies of pig-human or sheep-human chimeras have been established during the last 12 months in the U.S., though so far no scientific paper describing the work has been published, and none of the animals were brought to term.

Birthing these animals will be the next step. And who knows what health problems they could have? This is an animal welfare issue as well as bearing obviously on human exceptionalism.

Creating such chimeric beings isn't the same thing as, say, genetically altering an animal so their organs can be used for transplant, or inserting a human gene to make transgenic animals that produce a specific hormone in their milk for medicinal uses.

Hard regulatory lines need to be drawn -- which won't be easy -- and all public money limited to research that is both ethical and respectful of proper boundaries between humans and all other species.


Scientists clearly cannot be trusted to govern themselves on this matter. It is time to set well-defined limits.

Ps. Of course it's far too late to put this genie back in the bottle the lure of potential profits and fear of losing out to the competition is going to trump any appeal to virtue.

A clash of titans IV

On the uniting of the United Kingdom

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.