From the ark?

New Paper in Evolution Journal: Humans and Animals Are (Mostly) the Same Age?
Andrew Jones

Could it be that animals were designed together with humans and instantiated at the same time too? Or did they get off the same spaceship? Or off the same boat?
An exciting new paper in the journal Human Evolution has been published which you can read here. Popular science reports such as this have incautiously claimed, “They found out that 9 out of 10 animal species on the planet came to being at the same time as humans did some 100,000 to 200,000 years ago.”

But to be more precise, what they actually found is that the most recent common ancestor of those species seems to have lived during that time period. 

This could indicate intelligent design, an event where species came into existence for the first time. But it could also indicate something else, such as a population crash (or crashes) that affected almost all life on Earth. Either way, if the paper is right, it would be a shock to established scientific expectations.

“This conclusion is very surprising,” co-author David Thaler of the University of Basel is quoted as saying, “and I fought against it as hard as I could.” His co-author is fellow geneticist Mark Stoeckle of Rockefeller University in New York.


Here is how the scientific reasoning works:

Nucleotide diversity π is the average number of differences per site between two aligned nucleotide sequences. The differences are assumed to be due to mutations accumulated on both sequences since they diverged. Therefore the nucleotide diversity π should be twice the mutation rate multiplied by the time to common ancestor of those sequences:  π = 2 μ T, where μ is the mutation rate per generation and T is the time since the common ancestor in generations.

If ordinary steady neutral evolution has been happening, then the time to common ancestor is expected to be about N, the effective population size. Therefore the nucleotide diversity is expected to be about 2 μ N. 

The mutation rate μ shows some variation, but N is believed to vary widely across the animal kingdom. Therefore the nucleotide diversity that we observe should vary widely too. 


But, according to these authors using data from the BOLD database, the nucleotide diversity does not vary greatly. Instead, these authors find that for 90% of all species, the observed levels of π suggest that T falls within the last 100-200kYr.

I am intrigued, but to be honest, I don’t quite know what to make of it just yet, and don’t want to jump to any conclusions. This kind of inference is complicated; the paper does not explain where they sourced estimates of mutation rate and effective population size. 


Moreover, studies of different kinds of sequences can seem to tell widely different stories. In an earlier paper from 2014,the authors point out that the idea of a single global population crash is, “almost a Noah’s Ark hypothesis,” though “This appears unlikely.” They speculate instead that “perhaps long-term climate cycles might cause widespread periodic bottlenecks.” 

In any case, one thing is clear: reconstructing the past is a complicated business and it is still full of surprises. There may be even bigger surprises in store.

Scientism's attempted shotgun wedding?

In Defense of Theistic Evolution, Denis Lamoureux Rewrites History
Jonathan Witt | @JonathanRWitt

Writing in the Journal of the American Scientific Affiliation, Denis O. Lamoureux has published a dismissive review of Theistic Evolution: A Scientific, Philosophical, and Theological Critique.

The review article’s title, “Intelligent Design Theory: The God of the Gaps Rooted in Concordism,” deftly signals Lamoureux’s two-pronged strategy: First, paint intelligent design as a fallacious God-of-the-gaps argument (when in fact it’s an argument to the best explanation  based on what we know).

And second: Motive monger — in this case, by attributing the anthology’s conclusions to a religious motivation while giving short shrift to the book’s hundreds of pages of scientific evidence and argument.

Those criticisms of ID are low-hanging fruit for the writers at Evolution News, but here I want to focus on another problem with the review.

Scientism’s Grand Progress Narrative

At one point early on, Lamoureux confidently asserts the following:

First, according to a God-of-the-gaps approach to divine action, there are “gaps” in the continuum of natural processes, and these “discontinuities” in nature indicate places where God has miraculously intervened  in the world. …

If there are gaps in the continuum of natural processes, then science will identify them, and over time these gaps will “widen” with further research. That is, as scientists explore a true gap in nature where God has intervened, evidence will increase and demonstrate that there are no natural mechanisms to account for the origin or operation of a physical feature.

There is an indisputable pattern in the history of science. The God-of-the-gaps understanding of divine action has repeatedly failed. Instead of the gaps in nature getting wider with the advance of science, they have always been closed or filled by the ever-growing body of scientific information. In other words, history reveals that these purported gaps have always been gaps in knowledge  and not actual gaps in nature  indicative of the intervening hand of the Lord.

The lesser problem here is his tendentious use of the word “gaps.” The language suggests that it’s somehow a failure of God for the universe to be something less than a deist’s fantasy — a grand pool shot from the Big Bang without any need for subsequent creative involvement. That’s an aesthetic presupposition, and a manifestly suspect aesthetic presupposition.

That’s the lesser problem with the quote above, a problem  to delve into more fully at another time. Here I want to highlight the more glaring problem: Lamoureux’s assertion of “an indisputable pattern in the history of science.” The alleged historical pattern is manifestly untrue.

It was given formal structure by the 19th-century French philosopher August Comte, but in common parlance the claim runs something like this:

Humans used to attribute practically every mysterious force in nature to the doings of the gods. They stuffed a god into any and every gap in their knowledge of the natural world, shrugged, and moved on. Since then, the number of gaps has been shrinking without pause, filled with purely material explanations for everything from lightning bolts to romantic attraction. The moral of this grand story: always hold out for the purely material explanation, even when the evidence seems to point in the other direction. Materialism, in other words, is our manifest destiny; get used to it colonizing every cause in the cosmos.

This grand progress narrative is regularly employed with great confidence, but it’s contradicted by key developments in the physical and life sciences.

For example, through much of the 19th century, the scientific consensus was that microscopic life was relatively simple, little more than microscopic sacks of Jell-O. The scientific community also accepted the idea of spontaneous generation — that creatures sprang to life spontaneously out of things like dew and rotting meat. Taken together, these pieces of conventional scientific wisdom suggested that the origin of the first living cell deep in the past was hardly worthy of the term “mystery” — a material explanation seemed obvious.

But in 1861 Louis Pasteur conducted a series of experiments that discredited the notion of spontaneous generation. And in the next century, scientists began amassing evidence of just how complex even the simplest cell is. Today we know that cells are micro-miniaturized factories of astonishing sophistication and that, even more to the point, such sophistication is essential for them to be able to survive and reproduce.Origin-of-life researchers concede  that no adequate material explanation has been found for the origin of the cell.

So, we have come to learn that spontaneous generation was a fantasy. We have discovered that even the simplest cells are highly sophisticated and information-rich organisms. And the only cause we have ever witnessed actually producing novel information is intelligent design. Thus, modern scientific observations have collapsed a long-standing material explanation for the origin of life and simultaneously strengthened the competing design explanation. This development runs directly counter to scientism’s grand narrative.

A common rebuttal is that inferring design in such cases amounts to “giving up on science,” and that science should always hold out for a purely material explanation. But this is mere question begging. What if the first living cell really was the work of intelligent design? Being open to that possibility and following the evidence isn’t giving up on science but on scientism, a dogma resting on a progress narrative flatly contradicted by the historical record.

Evidence from Cosmology

Cosmology and physics provide another counter-example to the grand narrative Lamoureux asserts. In Darwin’s time, conventional scientific wisdom held that the universe was eternal. Given this, it was broadly assumed that there could hardly be any mystery about its origin: it simply had always existed. But developments in physics and astronomy have overturned the easy embrace of an eternal cosmos, and scientists are now in broad agreement that our universe had a beginning. What many thought had never happened and so required no explanation — the origin of the universe — suddenly cried out for an explanation.

Near the same time that scientists were realizing this, there was a growing awareness of what is now widely known in cosmology as the fine-tuning problem. This is the curious fact that the various laws and constants of nature appear finely calibrated to allow for life in the universe — calibrated to such a precise degree that even committed materialists have abandoned blunt appeals to chance.

To explain away this problem, the disciples of scientism have now resorted to saying there must be countless other universes, with our universe simply being one of the lucky ones with the right configuration to allow intelligent life to evolve.

Not every physicist has played along. Several, including some Nobel laureates, have assessed the growing body of evidence for fine-tuning and pointed to intelligent design as the most reasonable explanation. Physicist and Nobel laureate Charles Townes put it this way:

Intelligent design, as one sees it from a scientific point of view, seems to be quite real. This is a very special universe: it’s remarkable that it came out just this way. If the laws of physics weren’t just the way they are, we couldn’t be here at all. The sun couldn’t be there, the laws of gravity and nuclear laws and magnetic theory, quantum mechanics, and so on have to be just the way they are for us to be here.

Scientism’s grand progress narrative holds that as we learn more and more about the world, purely natural or material explanations inevitably will arise and grow stronger, while design arguments will inevitably collapse under the weight of new discoveries. But the opposite has happened in cosmology and origin-of-life studies.

Despite this, Lamoureux and other critics of intelligent design go right on recycling their grand narrative as if it were the whole truth and nothing but the truth. It is not. It ignores truths both historical and scientific.

The human body irreducibly complex and undeniably designed.

The Designed Body: Irreducible Complexity on Steroids = Exquisite Engineering - 
Steve Laufmann

Life thrives. It flourishes almost everywhere we look, even in remarkably inhospitable places. Perhaps because life is so common, it’s easy to lose sight of how tenuous it is. Life depends on a delicate balance of forces. Tip that balance and death is inevitable.

Howard Glicksman’s profound 81-part series, The Designed Body, concluded last September here at Evolution News. Dr. Glicksman offers uncommon insights into the inner workings of the human body (i.e., this thing I’m trapped inside of). As a hospice physician, he understands what it takes for a human body to survive, and how various dysfunctions can foul up the works and cause death. He makes these easy to understand, and offers important lessons for readers willing to work their way through the medical bits. I would like to add here my own reflections on the subject.

The series by Dr. Glicksman discusses 40 interrelated chemical and physiological parameters that the human body must carefully balance to sustain life. The body deploys amazing, interconnected solutions to manage them.

The parameters are: (1) oxygen, (2) carbon dioxide, (3) hydrogen ion, (4) water, (5) sodium, (6) potassium, (7) glucose, (8) calcium, (9) iron, (10) ammonia, (11) albumin transport, (12) proteins, (13) insulin, (14) glucagon, (15) thyroid hormone, (16) cortisol, (17) testosterone, (18) estrogen, (19) aldosterone, (20) parathormone, (21) digestive enzymes, (22) bile, (23) red blood cells, (24) white blood cells, (25) platelets, (26) clotting factors, (27) anti-clotting factors, (28) complement, (29) antibodies, (30) temperature, (31) heart rate, (32) respiratory rate, (33) blood pressure, (34) lung volume, (35) airway velocity, (36) cardiac output, (37) liver function, (38) kidney function, (39) hypothalamic function, (40) nerve impulse velocity.

I drew seven insights from the series.

Life can only exist when swimming upstream against uncharitable natural forces.

To survive, a human body must constantly struggle against powerful and unrelenting natural forces. When the body succumbs to any one of these forces, it reaches equilibrium with the environment — a condition commonly known as “death.”

A complex body plan places enormous demands on survival.

Single-celled organisms can only survive in a suitable substrate — where the organism (cell) is in direct contact with the environment, from which it must draw all the raw materials it needs to survive, and into which it can shunt its waste products without being poisoned by them.

In contrast, the vast majority of the cells in the human body are physically isolated from the environment, so survival depends on other means to deliver the needed raw materials and slough off any toxic waste materials for each one of its trillions of cells. Controlling so many factors is complicated work, and takes a lot of systems.

Goldilocks or death.

For each of these 40 chemical and physiological factors, the body must maintain its function within a narrow range of possible values. In effect, the body must do just the right things in just the right places at just the right times, in just the right quantities and at just the right speeds. Survival depends on maintaining balance within these tight tolerances.

This is an example of the Goldilocks Principle — everything must be just right for life to be possible. As Glicksman says, “Real numbers have real consequences.” When the numbers cannot be maintained at the right levels, the body dies.

As an example, let’s look at what’s needed for cellular respiration:

The cell is the basic building block of the human body. Each cell must successfully fight diffusion and osmosis in order to maintain its internal volume and required chemical content. This takes energy, which must come from somewhere.

To meet its energy needs, the cell breaks down glucose according to a simple chemical formula: C6H12O6 + 6O2 = 6CO2 + 6H2O. The glucose molecule and six oxygen molecules are converted into six molecules of carbon dioxide and six molecules of water. These are all stable molecules, so it takes some doing to make this work. In a complex 3-stage process, the cell uses 20+ specialized enzymes and carrier molecules (each made up of 300+ specifically-ordered amino acids), to break down the chemical bonds of the glucose molecule, thereby releasing energy which the cell uses to operate its machinery, including the critical sodium-potassium pumps that control the cell’s content and volume.

Obviously, a supply of oxygen is essential. But this presents a few problems for the body. While glucose can be stored in the body for later use, oxygen can’t, so it must be supplied continuously, and in the right quantities to meet current demand.

Without enough oxygen, the cell runs out of energy, its sodium-potassium pumps fail, the cell’s internal volume and chemical content can’t be maintained, and the cell dies. When sufficient cells within an organ die, the functions provided by that organ cease, causing downstream functions to fail, and so on. Without corrective action, this leads to a chain reaction of failure. In just a few minutes a lack of oxygen will kill the entire body.

On the other hand, when the body gets enough oxygen, the process generates carbon dioxide, which, if not removed, elevates the cell’s hydrogen ion level, which leads to cell death.

So the cell must efficiently “gate” oxygen into the cell and carbon dioxide out of the cell through the cell membrane. Given that the cell is surrounded by a few trillion other cells, each of which is independently maintaining the same cell content and volume functions, the body must manage overall substantive flows of oxygen (in) and carbon dioxide (out).

This requires an efficient transport subsystem (e.g., a circulatory system), complete with a pump (heart), transport medium (blood), and means to exchange oxygen and carbon dioxide with the air in the environment (lungs).

But this is not so easy. Blood’s fluid component is mainly water, and oxygen doesn’t dissolve well in water. So the body adds a complex iron-based protein called hemoglobin to the blood, which binds to the oxygen so it can be transported efficiently throughout the body. To make this work, though, the body needs still other (sub)systems to acquire, store, and process just enough iron (too much is toxic), and then process it into hemoglobin.

And there’s a separate process and subsystems to deliver glucose to the cells. Glicksman gives a lot more detail, but you get the idea: a lot of moving parts are required.

Survival depends on specialization, integration, and coordination.

Solving these problems in practice gets tricky.

To achieve the large variety of functions needed for survival, the body uses around 200 different, specialized types of cells. To achieve the requisite functions for each body subsystem, these cells must be arrayed in just the right locations with respect to their relevant subsystem(s).

Only when each subsystem is properly arrayed and functioning can the body survive. But solutions at the subsystem level tend to present new problems to overcome, and these typically rely on other autonomous subsystems, which are comprised of other specialized cells that are arranged in just the right ways to achieve their function. All of these must coordinate with each other.

In the example above, the circulatory subsystem transports raw materials to those trillions of individual cells. But inertia, friction, and gravity present challenges to circulation, so the system needs additional control mechanisms, involving cardiac output, blood pressure, and blood flow, to ensure that circulation is effective throughout the body.

A human body must operate effectively in at least three different levels: (1) the cells, (2) the subsystems, and (3) the whole body. The challenge to craft effective mechanisms across all three levels to address all 40 survival parameters is mind-boggling, and the body has somehow acquired ingenious solutions.

Every one of the body’s control systems is irreducibly complex.

For each of the 40 survival factors, the human body requires at least one control system. Every control system, whether in a biological or a human-engineered system, must include some means to perform each of the following functions:

Sensors, to measure that which is being controlled. There must be enough sensors, in the right locations (to sense that which is being controlled), and with suitable sensitivity to the needed tolerances.
Data integrators, to combine data from many sensors.
Control logic, to determine what adjustments are needed to achieve the desired effects. In some cases the logic may drive changes across multiple subsystems. In all cases, the logic must be correct to achieve proper function.
Effectors, to modify that which is being controlled.
Signaling infrastructure, to carry signals from the sensors to the data integrator(s) and/or controller, and from the controller to the effectors. Signals must carry the correct information, be directed to the right components, and arrive in a timely fashion.
Effectors must be capable of some or all of the following functions (depending on the factor being controlled):

Receptors, to receive signals regarding adjustments that must be made.
An organ, tissue, or other body subsystem capable of affecting the factor being controlled.
Harvesters, to obtain any needed chemicals from the environment — in the right amounts, at the right times — and convert them as needed for a particular use (eg, iron into hemoglobin).
Garbage collection, to expel unneeded chemical byproducts, which may be toxic in sufficient quantities.
Each control system must be dynamic enough to maintain the tight tolerances required in the timeframes needed. For example, it just wouldn’t do for the oxygen control system to take ten minutes to increase oxygen levels, if the body will die in four minutes without more oxygen.

Every one of the body’s control systems uses hundreds to millions of individual parts. This is irreducible complexity on steroids.

The body is a coherent mesh of interdependent systems.

None of the control systems Glicksman describes can achieve its functions alone — each relies on other body subsystems for help. To achieve this, the control mechanisms must work together toward an outcome that none can “see” or control end to end. Together, they form a mesh of interlocking control systems.

The human body is a coherent assembly of interdependent subsystems. Each subsystem is a coherent system in its own right, made up of an assembly of lower level components. Each lower level component is itself an assembly of even lower level components. We can follow this composition pattern of assembled components all the way down to proteins, amino acids, and the DNA code.

And, lest this be too easy, functional coherence requires process coherence across the body’s lifecycle, from fertilization to maturity and reproduction. Process coherence further constrains the body’s systems, and makes survival even more difficult.

Coherence requires all the right parts in all the right places doing all the rights things at all the right times in all the right quantities at all the right speeds — together, as a whole. This means the correct relative locations, sizes, shapes, orientations, capacities, and dynamics, with the correct fabrication specifications, assembly instructions, and operating processes. To coordinate its internal activities, the body integrates its parts and communicates using multiple types of signaling (eg, point-to-point, multi-point, broadcast). To maintain function, it uses still other mechanisms for error correction, failure prevention, threat detection, and defense, throughout its many levels of systems and subsystems.

The body’s parts are functionally interdependent, yet operationally autonomous. Aside from being extraordinarily hard to achieve with so many moving parts, this is what an engineer would call elegant design. The architecture of the human body is exquisite.

The whole is greater than the sum of the parts.

For the human body, though, the whole is much more than the sum of its parts. This is exactly what we see with all complex engineered systems. In fact, this is a defining characteristic of engineered systems.

With humans, the whole is also quite remarkable in its own right. It’s almost as if the body was designed specifically to enable the mind: thought, language, love, nobility, self-sacrifice, art, creativity, industry, and my favorite enigma (for Darwinists): music.

The human body enables these things, but does not determine them. As near as we can tell, no combination of the body’s substrate — information, machinery, or operations — alone can achieve these things.

Yet it’s exactly these things that make human life worth living. These are essential to our human experience. Human life involves so much more than merely being alive.

This simple observation flies in the face of Darwinian expectations. How can bottom-up, random processes possibly achieve such exquisitely engineered outcomes — outcomes that deliver a life experience well beyond the chemistry and physics of the body?

Such questions have enormous implications for worldviews, and for the ways that humans live their lives. I’ll look at some of those in a further post tomorrow.

RNA v. Darwinism's simple beginning

No Mere Bike Messenger, RNA Code Surpassing DNA in Complexity - 
Evolution News

The concept of a “DNA Code” has a long pedigree in genetics. But what about the other nucleic acids — the RNAs that use ribose instead of deoxyribose? Are they just simple conveyors of the library of genetic information in DNA, a humble bicycle messenger of the cell? Or do they have their own code? Last month, Nature published a Technology Feature by Kelly Rae Chi with an intriguing title, “The RNA code comes into focus.”

Chi begins with the m6am RNA modification we first mentioned in January, but doesn’t end there. Modifications to RNA bases are turning up all over, and their functions are just beginning to be understood. A feel for the importance of these new findings can be had by following the money:

In the past few years, He’s group has discovered evidence suggesting that RNA modifications provide a way to regulate transcripts involved in broad cellular roles, such as switching on cell-differentiation programs. Researchers need better technologies to explore these links; and, in October 2016, the US National Institutes of Health awarded He and Pan a 5-year, US$10.6-million grant to establish a centre to develop methods for identifying and mapping RNA modifications. [Emphasis added.]

On March 2, Japan’s RIKEN lab issued a news item stating, “Improved gene expression atlas shows that many human long non-coding RNAs may actually be functional.” RIKEN’s FANTOM Consortium is constructing a map of human non-coding RNAs. The latest findings calls to mind the surprises with DNA under ENCODE, but this time with RNA under FANTOM:

The atlas, which contains 27,919 long non-coding RNAs, summarizes for the first time their expression patterns across the major human cell types and tissues. By intersecting this atlas with genomic and genetic data, their results suggest that 19,175 of these RNAs may be functional, hinting that there could be as many — or even more — functional non-coding RNAs than the approximately 20,000 protein-coding genes in the human genome.

The atlas, published by Nature on March 9, expands into the RNA sphere from findings in the ENCODE and GENCODE databases. As with ENCODE, scientists so far are cataloging expression profiles without necessarily understanding actual functions. Presumably, though, cells have reasons for expressing these long non-coding RNAs (lncRNAs). The search for the actual functions is poised to bear fruit, as it did with ENCODE.

On the same day (March 9), Nature published another article finding “More uses for genomic junk.” Karen Adelman and Emily Egan point out that previous studies may have missed the functions of “junk DNA” by overlooking the key:

In addition to protein-coding messenger RNAs, our cells produce a plethora of diverse non-coding RNA molecules. Many of these are generated from sequences that are distant from genes, and include regulatory DNA sequences called enhancers. Transcription factors bound at enhancers are thought to regulate gene expression by looping towards genes in 3D space. The potential functions of non-coding enhancer RNAs (eRNAs) in this process have been avidly debated, but there has been a tendency to write them off as accidentally transcribed by-products of enhancer–gene interactions. After all, how could short, unstable, heterogeneous RNAs have a role in gene regulation? Writing in Cell, Bose et al. reveal that these eRNAs can indeed be functional, when produced in proximity to the enzyme CBP.

And what does the enzyme CBP do?

One transcriptional co-activator is the acetyltransferase enzyme CBP, which, along with its close relative p300, associates with DNA in enhancer regions, where it adds acetyl groups to histones and transcription factors. This acetylation promotes the recruitment of numerous transcriptional co-activators and chromatin-remodelling proteins that have acetyl-binding regions, along with the RNA-synthesizing enzyme polymerase II (Pol II).

In other words, CBP (a protein enzyme) and enhancer RNAs need to be together to work. The implication is clear; far from being accidental by-products, eRNAs are functional. They are involved in making genes accessible to the translation machinery, and regulating their expression. Transcription, long thought to be the engine, is just part of a much more complex factory.

A model is emerging in which transcription is itself an early step in enhancer activation. Pol II is recruited by transcription factors and maintains opens chromatin. Once the enzyme begins to transcribe, the nascent eRNA it produces stimulates co-activator proteins such as CBP in the region in a sequence- and stability-independent manner. The activities of these proteins promote the recruitment of more transcription factors, Pol II and chromatin-remodelling proteins, enabling full enhancer activation. In addition, Pol II itself can serve as a vehicle for attracting chromatin-modifying enzymes that spread more molecular marks associated with chromatin activation across the transcribed region. In this manner, transcription of enhancers can generate a positive-feedback loop that stabilizes both enhancer activity and gene-expression profiles.

Overall, the current study fundamentally changes the discourse around eRNA functions, by demonstrating that these RNAs can have major, locus-specific roles in enhancer activity that do not require a particular RNA-sequence context or abundance. Furthermore, by providing strong evidence that CBP interacts with eRNAs as they are being transcribed, this study highlights the value of investigating nascent RNAs for understanding enhancer activity.

Speaking of 3D space, researchers at the Max Delbrück Center for Molecular Medicine (MDC) have been producing a 3D map of the genome, underscoring the complex dance of DNA, RNA, and proteins:

Cells face a daunting task. They have to neatly pack a several meter-long thread of genetic material into a nucleus that measures only five micrometers across. This origami creates spatial interactions between genes and their switches, which can affect human health and disease. Now, an international team of scientists has devised a powerful new technique that ‘maps’ this three-dimensional geography of the entire genome. Their paper is published in Nature.

The paper explains the Genome Architecture Mapping (GAM) technique they created and how it elucidates the interactions between genes and their enhancers.

GAM also reveals an abundance of three-way contacts across the genome, especially between regions that are highly transcribed or contain super-enhancers, providing a level of insight into genome architecture that, owing to the technical limitations of current technologies, has previously remained unattainable. Furthermore, GAM highlights a role for gene-expression-specific contacts in organizing the genome in mammalian nuclei.

Isn’t that a worthy function? Keeping the genome organized is not a role that ‘genetic junk’ is likely to succeed at.

Another clue to function in RNA comes from a finding announced by Science Daily, “Start codons in DNA may be more numerous than previously thought.” When DNA needs to be translated into messenger RNA (mRNA), it was thought that a ‘start codon’ identified the start of the gene, and that there were only seven of these in the genetic code. But nobody had ever checked, this article says. Scientists from the National Institute of Standards and Technology found, to their surprise, that there are “at least 47 possible start codons, each of which can instruct a cell to begin protein synthesis.” Indeed, “It could be that all codons could be start codons.” The possibilities this opens up for expanding the complexity of RNA transcripts can only be imagined at this point.

We’ll end with one more example of the revolution in RNA functions. Scientists at Indiana University and colleagues found an example of “Hybrid incompatibility caused by an epiallele.” The open-access study, published in PNAS, “demonstrates a case of epigenetic gene silencing rather than pseudogene creation by mutation” in the lab plant Arabidopsis. Here’s a case where the RNA tail seems to wag the DNA dog:

Multicopy transgenes frequently become methylated and silenced, particularly when inserted into the genome as inverted repeats that can give rise to double-stranded RNAs. Such double-stranded RNAs can be diced into small interfering RNAs (siRNAs) that guide the cytosine methylation of homologous DNA sequences, a process known as RNA-directed DNA methylation (RdDM)…. This interesting case study has shown that naturally occurring RdDM, involving a new paralog that inactivates the ancestral paralog in trans, can be a cause of hybrid incompatibility.

Bypassing genetic mutations and natural selection, this “previously unrecognized epigenetic phenomenon” might help explain cases of apparently rapid speciation by a non-Darwinian process. We’ll leave that possibility for others to investigate.

In short, RNA has graduated from servant to master. The numerous RNA transcripts floating around in the nucleus, once thought to be genetic “noise,” may actually be the performance, like virtuosos in an orchestra bringing static notes written in DNA to life. This huge shift in thinking appears to be deeply problematic for neo-Darwinism. It sounds like a symphony of intelligent design.

- See more at: https://www.evolutionnews.org/2017/03/no-mere-bike-messenger-rna-code-surpassing-dna-in-complexity/#sthash.HkYGU29R.dpuf

Information v. Darwin.

Groundbreaking Paper Shows Thousands of New Genes Needed for the Origin of Animals

Evolution News | @DiscoveryCSC

Someday we may get tired of being vindicated. But not yet! Günter Bechly recently  discussed a new paper that confirmed Stephen Meyer’s claims in Darwin’s Doubt that arthropods appeared abruptly in the Cambrian explosion, without evolutionary precursors in the Precambrian. Another recent groundbreaking paper in Nature Communications has also provided massive confirmation of Meyer’s arguments in the book that new genes were required at the origin of animals.

An Uncontroversial Idea?

Whether you’re an evolutionary biologist or a proponent of intelligent design, the notion that the origin of animals required new genes — even numerous new genes — might strike you as uncontroversial. But this claim was strongly challenged by UC Berkeley evolutionary paleontologist Charles Marshall who reviewed Darwin’s Doubt in the journal Science. It actually became a centerpiece of the debate between Marshall and Meyer about the Cambrian explosion. (For replies to Marshall, here, here, here, here, here, and here.) Here’s the substance of Marshall’s counter-argument, as it was published in Science:

His [Meyer’s] case against current scientific explanations of the relatively rapid appearance of the animal phyla rests on the claim that the origin of new animal body plans requires vast amounts of novel genetic information coupled with the unsubstantiated assertion that this new genetic information must include many new protein folds. In fact, our present understanding of morphogenesis indicates that new phyla were not made by new genes but largely emerged through the rewiring of the gene regulatory networks (GRNs) of already existing genes (1).

Marshall didn’t stop there. He went further, saying that Meyer has an “idiosyncratic fixation with new protein folds” and “an outdated understanding of morphogenesis” — all due to Meyer’s supposedly inaccurate claims that the Cambrian explosion would have required the origin of many new genes. Now this new paper, “Reconstruction of the ancestral metazoan genome reveals an increase in genomic novelty,” provides a direct refutation of Marshall’s insistence that the origin of animals didn’t require lots of new genes.

From the paper:

Recent studies show that many genes typically associated with metazoan functions actually pre-date animals themselves, supporting functional co-option of ‘unicellular genes’ during the genesis of metazoans. 

However, the role of genome novelty in animal origins has not been fully evaluated. We hypothesize that genomic novelty had a major impact in this transition, particularly involving biological functions which are hallmarks of animal multicellularity (gene regulation, signalling, cell adhesion, and cell cycle). Here we apply a comparative genomics approach using sophisticated methods, newly developed programs, and a comprehensive taxon sampling. The reconstruction of the ancestral genome of the last common ancestor of animals shows a set of biological functions similar to other eukaryote ancestors, while revealing an unexpected expansion of gene diversity. These analyses also highlight 25 groups of genes only found in animals that are highly retained in all their genomes, with essential functions linked to animal multicellularity.

They conclude that “many new” genes were necessary during the origin of animals: 

Thus, the first animal genome was not only showing a higher proportion of Novel HG [homology groups], but these also perform major multicellular functions in the modern fruit fly genome. The implication is that the transition was accompanied by an increase of genomic innovation, including many new, divergent, and subsequently ubiquitous genes encoding regulatory functions associated with animal multicellularity.

These “homology groups” (HGs) are exactly what they sound like — groups of genes that are similar. A “novel HG” is a group of genes that is found in animals, or particular groups of animals, that do not exist elsewhere. This indicates that these groups of genes were necessary for these animals to exist.

An Open-Access Paper; Check It Out 

Just how many novel HGs (and genes) are we talking about? The paper is open access, and readers can easily see that  Figure 1 shows that while 1189 HGs are necessary for the origin of Metazoa (multicellular organisms with differentiated tissues), as one moves farther up the animal tree, hundreds if not thousands of additional novel HGs are required:

For the origin of Eumetazoa (sponges + Planulozoa + Bilateria), 494 novel HGs are required.

For the origin of Planulozoa (ctenophores, placozoans, cnidarians + bilaterians), 1201 novel HGs are needed.

For the origin of Bilateria (animals with two-sided symmetry — a left and a right side), an additional 1580 HGs are required! According to Figure 2, about 16 percent of the bilaterian genome entails novel HGs!

No wonder  a commentary by the paper’s lead author at The Conversation cites “a burst of new genes” associated with the origin of animals:

We discovered the first animal had an exceptional number of novel genes, four times more than other ancestors. This means the evolution of animals was driven by a burst of new genes not seen in the evolution of their unicellular ancestors.

Straightforward Methodology

The methodology used by the paper is relatively straightforward. It compared the genomes of modern-day animals to determine what genes they share in common. This was then used to determine which genes were present in the genomes of the putative common ancestors of various animal groups. By comparing the common genes shared at different levels of the animal taxonomic hierarchy, they were able to determine how many new genes would have to appear at various stages of animal evolution. 

Of course the paper’s authors assume that these organisms share common ancestors and evolved by Darwinian natural selection — ideas that are challenged by the abrupt appearance of animals in the Cambrian period and by experimental work showing the difficulty of evolving new genes by standard Darwinian mechanisms of random mutation and blind natural selection. However, regarding the paper’s claims that many new genes were required during the origin of animals, the reasoning is sound, and it demonstrates conclusively that thousands of new genes would have been necessary for the origin of animals. Marshall was wrong. 

It wasn’t only in the journal Science that Marshall attacked Meyer on this subject. He said much the same in a radio debate against Meyer. In our “Listener’s Guide to the Meyer-Marshall Radio Debate” we explained what happened:

During the debate, Marshall amplified this argument by claiming that Meyer’s argument presupposed an outdated “1980s model of the way genes operate” and that his book “confronted a different set of problems that hark back to an older age.” According to Marshall, biologists no longer believe that building the diverse forms of Cambrian animals would require evolving new genes (or, at least, many new genes). Instead, Marshall argued, again, that new body plans could be generated by rewiring networks of already-existing genes, especially those which are part of the developmental gene regulatory networks (dGRNs) that control the timing and expression of pre-existing genes during animal development. Marshall pointed out that animals have far fewer genes than we once expected, and that today it is thought that “animals use essentially the same genes, just deployed slightly differently.” By changing the deployment of those genes — by rewiring their dGRNs — Marshall thinks new body plans can arise. 

It’s worth noting that throughout the debate, Meyer didn’t concede on Marshall’s claims that new genes aren’t necessary. Instead, he argued that even if we assume for the sake of the argument that Marshall is right that new genes aren’t necessary to build animals, that doesn’t solve the problem because rewiring the dGRNs still requires a huge input of information.

Dual Information Problems

In that regard, the new Nature Communications paper shows that Marshall’s evolutionary viewpoint faces information problems on two fronts. Figure 2c indicates that by far the largest classes of novel genes in the metazoa are related to generating nucleic acid binding proteins, and transcription factors. This suggests that not only were many new genes needed in the origin of Metazoa, but those new genes had profound influences on gene regulation — i.e., they were involved with rewiring of GRNs. 

Thus both Meyer and Marshall were right that dGRNs needed to be wired to build animals — but they were right in the most devastating manner for Darwinism, namely that the rewiring of the dGRNS was mediated by entirely new genes. The paper’s demonstration that thousands of new genes would have been required during the origin of animals is nothing short of a spectacular vindication of Meyer’s perspective on this question, and a strong falsification of Marshall’s viewpoint.

On Christian neutrality:The Watchtower Society's commentary.

Neutrality

Definition: The position of those who do not take sides with or give support to either of two or more contending parties. It is a fact of ancient and modern-day history that in every nation and under all circumstances true Christians have endeavored to maintain complete neutrality as to conflicts between factions of the world. They do not interfere with what others do about sharing in patriotic ceremonies, serving in the armed forces, joining a political party, running for a political office, or voting. But they themselves worship only Jehovah, the God of the Bible; they have dedicated their lives unreservedly to him and give their full support to his Kingdom.

What scriptures have had a bearing on the attitude of Christians toward the authority of secular governments?

Rom. 13:1, 5-7: “Let every soul be in subjection to the superior authorities [governmental rulers], for there is no authority except by God . . . There is therefore compelling reason for you people to be in subjection, not only on account of that wrath but also on account of your conscience. . . . Render to all their dues, to him who calls for the tax, the tax; to him who calls for the tribute, the tribute; to him who calls for fear, such fear; to him who calls for honor, such honor.” (No government could exist without God’s permission. Regardless of the conduct of individual officials, true Christians have shown them respect because of the office they occupied. For example, regardless of the use that governments have made of tax money, worshipers of Jehovah have made honest payment of their taxes in return for those services from which everyone could benefit.)

Mark 12:17: “Jesus then said: ‘Pay back Caesar’s things to Caesar, but God’s things to God.’” (So Christians have always recognized that they must not only “pay back” money in the form of taxes to the secular government but also fulfill the superior obligations they have toward God.)

Acts 5:28, 29: “[A spokesman for the Jewish high court] said: ‘We positively ordered you [the apostles] not to keep teaching upon the basis of this name [of Jesus Christ], and yet, look! you have filled Jerusalem with your teaching, and you are determined to bring the blood of this man upon us.’ In answer Peter and the other apostles said: ‘We must obey God as ruler rather than men.’” (When there has been a direct conflict between the commands of human rulers and the requirements of God, true Christians have imitated the example of the apostles by putting obedience to God first.)

What scriptures have always had a bearing on the attitude of true Christians toward participation in carnal warfare?

Matt. 26:52: “Jesus said to him: ‘Return your sword to its place, for all those who take the sword will perish by the sword.’” (Could there have been any higher cause for which to fight than to safeguard the Son of God? Yet, Jesus here indicated that those disciples were not to resort to weapons of physical warfare.)

Isa. 2:2-4: “It must occur in the final part of the days that the mountain of the house of Jehovah will become firmly established above the top of the mountains . . . And he will certainly render judgment among the nations and set matters straight respecting many peoples. And they will have to beat their swords into plowshares and their spears into pruning shears. Nation will not lift up sword against nation, neither will they learn war anymore.” (Individuals out of all nations must personally decide what course they will pursue. Those who have heeded Jehovah’s judgment give evidence that he is their God.)

2 Cor. 10:3, 4: “Though we walk in the flesh, we do not wage warfare according to what we are in the flesh. For the weapons of our warfare are not fleshly, but powerful by God for overturning strongly entrenched things.” (Paul here states that he never resorted to fleshly weapons, such as trickery, high-sounding language, or carnal weapons, to protect the congregation against false teachings.)

Luke 6:27, 28: “I [Jesus Christ] say to you who are listening, Continue to love your enemies, to do good to those hating you, to bless those cursing you, to pray for those who are insulting you.”

Is it not true that Jehovah allowed ancient Israel to engage in warfare?

Jehovah directed ancient Israel to use warfare to take possession of the land that he himself designated as their inheritance and to execute people whose depraved practices and defiance of the true God caused Jehovah to view them as being no longer fit to live. (Deut. 7:1, 2, 5; 9:5; Lev. 18:24, 25) Nevertheless, mercy was shown to Rahab and to the Gibeonites because they demonstrated faith in Jehovah. (Josh. 2:9-13; 9:24-27) In the Law covenant God laid down rules for warfare that he would approve, stipulating exemptions and the manner in which this warfare was to be carried out. Such were truly holy wars of Jehovah. That is not true of the carnal warfare of any nation today.

With the establishing of the Christian congregation, a new situation came into existence. Christians are not under the Mosaic Law. Christ’s followers were to make disciples of people of all nations; so worshipers of the true God would in time be found in all those nations. However, what is the motive of those nations when they go to war? Is it to carry out the will of the Creator of all the earth or is it to further some nationalistic interest? If true Christians in one nation were to go to war against another nation, they would be fighting against fellow believers, against people who prayed for help to the same God that they did. Appropriately, Christ directed his followers to lay down the sword. (Matt. 26:52) He himself, glorified in the heavens, would henceforth carry out the execution of those who showed defiance of the true God and His will.—2 Thess. 1:6-8; Rev. 19:11-21.

As to serving in the armed forces, what does secular history disclose about the attitude of early Christians?

“A careful review of all the information available goes to show that, until the time of Marcus Aurelius [Roman emperor from 161 to 180 C.E.], no Christian became a soldier; and no soldier, after becoming a Christian, remained in military service.”—The Rise of Christianity (London, 1947), E. W. Barnes, p. 333.

“We who were filled with war, and mutual slaughter, and every wickedness, have each through the whole earth changed our warlike weapons,—our swords into ploughshares, and our spears into implements of tillage,—and we cultivate piety, righteousness, philanthropy, faith, and hope, which we have from the Father Himself through Him who was crucified.”—Justin Martyr in “Dialogue With Trypho, a Jew” (2nd century C.E.), The Ante-Nicene Fathers (Grand Rapids, Mich.; reprint of 1885 Edinburgh edition), edited by A. Roberts and J. Donaldson, Vol. I, p. 254.

“They refused to take any active part in the civil administration or the military defence of the empire. . . . it was impossible that the Christians, without renouncing a more sacred duty, could assume the character of soldiers, of magistrates, or of princes.”—History of Christianity (New York, 1891), Edward Gibbon, pp. 162, 163.

What scriptures have always had a bearing on the attitude of true Christians toward involvement in political issues and activities?

John 17:16: “They are no part of the world, just as I [Jesus] am no part of the world.”

John 6:15: “Jesus, knowing they [the Jews] were about to come and seize him to make him king, withdrew again into the mountain all alone.” Later, he told the Roman governor: “My kingdom is no part of this world. If my kingdom were part of this world, my attendants would have fought that I should not be delivered up to the Jews. But, as it is, my kingdom is not from this source.”—John 18:36.

Jas. 4:4: “Adulteresses, do you not know that the friendship with the world is enmity with God? Whoever, therefore, wants to be a friend of the world is constituting himself an enemy of God.” (Why is the matter so serious? Because, as 1 John 5:19 says, “the whole world is lying in the power of the wicked one.” At John 14:30, Jesus referred to Satan as being “the ruler of the world.” So, no matter what worldly faction a person might support, under whose control would he really come?)

Regarding political involvement, what do secular historians report as being the attitude of those known as early Christians?

“Early Christianity was little understood and was regarded with little favor by those who ruled the pagan world. . . . Christians refused to share certain duties of Roman citizens. . . . They would not hold political office.”—On the Road to Civilization, A World History (Philadelphia, 1937), A. Heckel and J. Sigman, pp. 237, 238.

“The Christians stood aloof and distinct from the state, as a priestly and spiritual race, and Christianity seemed able to influence civil life only in that manner which, it must be confessed, is the purest, by practically endeavouring to instil more and more of holy feeling into the citizens of the state.”—The History of the Christian Religion and Church, During the Three First Centuries (New York, 1848), Augustus Neander, translated from German by H. J. Rose, p. 168.

What scriptures have always had a bearing on the attitude of true Christians toward ceremonies involving flags and national anthems?

1 Cor. 10:14: “Flee from idolatry.” (Also Exodus 20:4, 5)

1 John 5:21: “Little children, guard yourselves from idols.”

Luke 4:8: “In reply Jesus said to him: ‘It is written, “It is Jehovah your God you must worship, and it is to him alone you must render sacred service.”’”

See also Daniel 3:1-28.

Do such patriotic symbols and ceremonies really have religious significance?

“[Historian] Carlton Hayes pointed out long ago that the ritual of flag-worship and oath-taking in an American school is a religious observance. . . . And that these daily rituals are religious has been at last affirmed by the Supreme Court in a series of cases.”—The American Character (New York, 1956), D. W. Brogan, pp. 163, 164.

“Early flags were almost purely of a religious character. . . . The national banner of England for centuries—the red cross of St. George—was a religious one; in fact the aid of religion seems ever to have been sought to give sanctity to national flags, and the origin of many can be traced to a sacred banner.”—Encyclopædia Britannica (1946), Vol. 9, p. 343.

“In a public ceremony presided over by the vice president of the [Military Supreme] Court, on the 19th of November, honors were shown to the Brazilian flag. . . . After the flag was hoisted, Minister General of the Army Tristao de Alencar Araripe expressed himself concerning the commemoration in this manner: ‘ . . . flags have become a divinity of patriotic religion which imposes worship . . . The flag is venerated and worshiped . . . The flag is worshiped, just as the Fatherland is worshiped.’”—Diario da Justiça (Federal Capital, Brazil), February 16, 1956, p. 1906.

With reference to patriotic ceremonies, what does secular history say about the attitude of those known as early Christians?

“Christians refused to . . . sacrifice to the emperor’s genius—roughly equivalent today to refusing to salute the flag or repeat the oath of allegiance. . . . Very few of the Christians recanted, although an altar with a fire burning on it was generally kept in the arena for their convenience. All a prisoner had to do was scatter a pinch of incense on the flame and he was given a Certificate of Sacrifice and turned free. It was also carefully explained to him that he was not worshiping the emperor; merely acknowledging the divine character of the emperor as head of the Roman state. Still, almost no Christians availed themselves of the chance to escape.”—Those About to Die (New York, 1958), D. P. Mannix, pp. 135, 137.

“The act of emperor worship consisted in sprinkling a few grains of incense or a few drops of wine on an altar which stood before an image of the emperor. Perhaps at our long remove from the situation we see in the act nothing different from . . . lifting the hand in salute to the flag or to some distinguished ruler of state, an expression of courtesy, respect, and patriotism. Possibly a good many people in the first century felt just that way about it but not so the Christians. They viewed the whole matter as one of religious worship, acknowledging the emperor as a deity and therefore being disloyal to God and Christ, and they refused to do it.”—The Beginnings of the Christian Religion (New Haven, Conn.; 1958), M. F. Eller, pp. 208, 209.

Has the neutrality of Christians meant that they are not interested in the welfare of their neighbors?

Certainly not. They know well and conscientiously endeavor to apply the command repeated by Jesus: “You must love your neighbor as yourself.” (Matt. 22:39) Also the counsel recorded by the apostle Paul: “Let us work what is good toward all, but especially toward those related to us in the faith.” (Gal. 6:10) They have been convinced that the greatest good that they can do for their neighbors is to share with them the good news of God’s Kingdom, which will lastingly solve the problems facing mankind and which opens up to those who embrace it the marvelous prospect of eternal life.